Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 81 of 199
Found at i:28992745 original size:16 final size:18
Alignment explanation
Indices: 28992706--28992739 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28992696 AAAGTTTATA
28992706 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28992723 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28992740 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28992853 original size:25 final size:23
Alignment explanation
Indices: 28992825--28992877 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
28992815 AAGATGACTG
28992825 TATAAAAAATTTCATCAAATAAAAA
1 TATAAAAAA-TT-ATCAAATAAAAA
* * *
28992850 TATATAAAATTATTAAATAATAA
1 TATAAAAAATTATCAAATAAAAA
28992873 TATAA
1 TATAA
28992878 TATAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 14 0.58
24 2 0.08
25 8 0.33
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
TATAAAAAATTATCAAATAAAAA
Found at i:28993643 original size:9 final size:9
Alignment explanation
Indices: 28993629--28993695 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
28993619 GTAGTGATTC
*
28993629 AATTTGGTT
1 AATTCGGTT
*
28993638 AATTTGGTT
1 AATTCGGTT
28993647 AATTCAGG-T
1 AATTC-GGTT
*
28993656 AATTCGGGT
1 AATTCGGTT
28993665 AATTCGGTT
1 AATTCGGTT
*
28993674 AATTCGGGT
1 AATTCGGTT
28993683 AATTCGGTT
1 AATTCGGTT
28993692 AATT
1 AATT
28993696 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
8 2 0.04
9 48 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28993658 original size:18 final size:18
Alignment explanation
Indices: 28993629--28993695 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 18
28993619 GTAGTGATTC
* * *
28993629 AATTTGGTTAATTTGGTT
1 AATTCGGTTAATTCGGGT
28993647 AATTCAGG-TAATTCGGGT
1 AATTC-GGTTAATTCGGGT
28993665 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
28993683 AATTCGGTTAATT
1 AATTCGGTTAATT
28993696 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.05
18 40 0.91
19 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:28993667 original size:27 final size:27
Alignment explanation
Indices: 28993637--28993696 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
28993627 TCAATTTGGT
28993637 TAATTTGGTTAATTCAGGTAATTCGGG
1 TAATTTGGTTAATTCAGGTAATTCGGG
* * *
28993664 TAATTCGGTTAATTCGGGTAATTCGGT
1 TAATTTGGTTAATTCAGGTAATTCGGG
28993691 TAATTT
1 TAATTT
28993697 TTAACCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.43
Consensus pattern (27 bp):
TAATTTGGTTAATTCAGGTAATTCGGG
Found at i:28995361 original size:15 final size:17
Alignment explanation
Indices: 28995330--28995361 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28995320 GTCCTGTTTG
28995330 TTCTTAATTTCATAAAT
1 TTCTTAATTTCATAAAT
28995347 TTCTT-ATTT-ATAAAT
1 TTCTTAATTTCATAAAT
28995362 CTTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCTTAATTTCATAAAT
Found at i:28995890 original size:29 final size:30
Alignment explanation
Indices: 28995817--28995893 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
28995807 TCAAAATTGA
* *
28995817 AAAGTATAGAGATTGAAATTGAGCAATGTG
1 AAAGTATAGAGACTAAAATTGAGCAATGTG
* *
28995847 AGAAGTATAGGGACTAAAATTGATCAAAT-T-
1 A-AAGTATAGAGACTAAAATTGAGC-AATGTG
28995877 AAAGTATAGAGACTAAA
1 AAAGTATAGAGACTAAA
28995894 TTCATAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 15 0.38
30 2 0.05
31 20 0.50
32 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (30 bp):
AAAGTATAGAGACTAAAATTGAGCAATGTG
Found at i:28996220 original size:28 final size:28
Alignment explanation
Indices: 28996189--28996249 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
28996179 CTCGAAGTTC
**
28996189 AAAACCTCAAATCCGCAATTTGAAATTT
1 AAAACCTCAAATCCAAAATTTGAAATTT
* *
28996217 AAAACTTCAAATCTAAAATTTGAAATTT
1 AAAACCTCAAATCCAAAATTTGAAATTT
28996245 AAAAC
1 AAAAC
28996250 TTAAAACCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAACCTCAAATCCAAAATTTGAAATTT
Found at i:28996228 original size:14 final size:14
Alignment explanation
Indices: 28996211--28996251 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28996201 CCGCAATTTG
28996211 AAATTTAAAACTTC
1 AAATTTAAAACTTC
* * *
28996225 AAATCTAAAATTTG
1 AAATTTAAAACTTC
28996239 AAATTTAAAACTT
1 AAATTTAAAACTT
28996252 AAAACCCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATTTAAAACTTC
Found at i:28996262 original size:28 final size:28
Alignment explanation
Indices: 28996205--28996262 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
28996195 TCAAATCCGC
* * *
28996205 AATTTGAAATTTAAAACTTCAAATCTAA
1 AATTTGAAATTTAAAACTTAAAACCCAA
28996233 AATTTGAAATTTAAAACTTAAAACCCAA
1 AATTTGAAATTTAAAACTTAAAACCCAA
28996261 AA
1 AA
28996263 AAAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (28 bp):
AATTTGAAATTTAAAACTTAAAACCCAA
Found at i:28996535 original size:30 final size:29
Alignment explanation
Indices: 28996502--28996557 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
28996492 AAAAAGCCCT
28996502 TTTTTTCAA-TATTTATCGAAATGGGCCGG
1 TTTTTT-AATTATTTATCGAAATGGGCCGG
*
28996531 TTTTTTAATTATTTATCGGAATGGGCC
1 TTTTTTAATTATTTATCGAAATGGGCC
28996558 ATTTTCAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (29 bp):
TTTTTTAATTATTTATCGAAATGGGCCGG
Found at i:28997804 original size:17 final size:17
Alignment explanation
Indices: 28997761--28997802 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
28997751 AAGTTGATAT
28997761 GTTAGTTTTAGATGGTA
1 GTTAGTTTTAGATGGTA
28997778 GTTAGTTTTAGATGGTA
1 GTTAGTTTTAGATGGTA
28997795 GTT-GTTTT
1 GTTAGTTTT
28997803 TATTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (17 bp):
GTTAGTTTTAGATGGTA
Found at i:28999421 original size:105 final size:105
Alignment explanation
Indices: 28999239--28999435 Score: 385
Period size: 105 Copynumber: 1.9 Consensus size: 105
28999229 GATGCGTGCT
28999239 TTTGGTAGAGGTATTATTTTTGACACATGTTTTAGTATATGAGTTAACTATAAACTAATTTGATT
1 TTTGGTAGAGGTATTATTTTTGACACATGTTTTAGTATATGAGTTAACTATAAACTAATTTGATT
*
28999304 GATAATATTTAGCCACTCTCATGAGTTCGCTAATGCTACA
66 GATAATATTTAGCCACTCTCAAGAGTTCGCTAATGCTACA
28999344 TTTGGTAGAGGTATTATTTTTGACACATGTTTTAGTATATGAGTTAACTATAAACTAATTTGATT
1 TTTGGTAGAGGTATTATTTTTGACACATGTTTTAGTATATGAGTTAACTATAAACTAATTTGATT
28999409 GATAATATTTAGCCACTCTCAAGAGTT
66 GATAATATTTAGCCACTCTCAAGAGTT
28999436 ATTTTTAGCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 91 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (105 bp):
TTTGGTAGAGGTATTATTTTTGACACATGTTTTAGTATATGAGTTAACTATAAACTAATTTGATT
GATAATATTTAGCCACTCTCAAGAGTTCGCTAATGCTACA
Found at i:29003747 original size:22 final size:22
Alignment explanation
Indices: 29003719--29003763 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29003709 CTACAAGGGG
29003719 TATGCTTTACTTTATTTATCTA
1 TATGCTTTACTTTATTTATCTA
29003741 TATGCTTTACTTTATTTATCTA
1 TATGCTTTACTTTATTTATCTA
29003763 T
1 T
29003764 CTTTCGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.60
Consensus pattern (22 bp):
TATGCTTTACTTTATTTATCTA
Found at i:29026774 original size:1 final size:1
Alignment explanation
Indices: 29026768--29026795 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
29026758 TTTGCTTCCT
29026768 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
29026796 GGACTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29028034 original size:46 final size:44
Alignment explanation
Indices: 29027967--29028296 Score: 240
Period size: 44 Copynumber: 7.6 Consensus size: 44
29027957 ATTATACAGG
* * *
29027967 TCTTATCTCCCTAAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGA
* *
29028013 TCTTATCTCCCTGAGATTACAGCGGAGCGGATCAAAG-AT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAG--A
* * * * *
29028057 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGA
* * * * *
29028096 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC--A-CATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATCAGA
* *
29028137 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGA
* ** * *
29028183 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-AATCAGA
* *
29028227 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-A-CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCA-GA
*
29028270 TCCTATCTCCCTGA-AGTTACAGTGGAG
1 TCTTATCTCCCTGAGA-TTACAGTGGAG
29028297 TGGATTAAAA
Statistics
Matches: 226, Mismatches: 41, Indels: 37
0.74 0.13 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 24 0.11
41 28 0.12
42 6 0.03
43 26 0.12
44 70 0.31
45 1 0.00
46 68 0.30
47 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGA
Found at i:29028247 original size:44 final size:43
Alignment explanation
Indices: 29027967--29028335 Score: 200
Period size: 44 Copynumber: 8.5 Consensus size: 43
29027957 ATTATACAGG
* * ** * *
29027967 TCTTATCTCCCTAAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* * * *
29028013 TCTTATCTCCCTGAGATTACAGCGGAGCGGATCAAAG-ATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAG--A
* * * *
29028057 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
* * * * * *
29028096 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGAGA
* ** * *
29028137 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* *
29028183 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* * **
29028227 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* ** ** *
29028270 TCCTATCTCCCTGA-AGTTACAGTGGAGTGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGA-GA
* *
29028314 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
29028336 CAGAGTAGGT
Statistics
Matches: 250, Mismatches: 56, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.10
40 1 0.00
41 30 0.12
42 9 0.04
43 32 0.13
44 86 0.34
45 2 0.01
46 64 0.26
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
Found at i:29028316 original size:87 final size:88
Alignment explanation
Indices: 29028137--29028336 Score: 217
Period size: 87 Copynumber: 2.3 Consensus size: 88
29028127 TCACATCAGG
* * *
29028137 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* **
29028202 CAGTGGAGCAGATTGAAGCCAGAGA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* * *
29028227 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC
** *
29028290 AGTGGAGTGGATTAAAATAAAG-GA
65 AGTGGAGCAGATT-AAAGAAAGAGA
* *
29028314 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCCCTGAGATTACAGC
29028337 AGAGTAGGTC
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
86 2 0.02
87 53 0.56
88 4 0.04
89 1 0.01
90 34 0.36
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAGAAAGAGA
Found at i:29029354 original size:1 final size:1
Alignment explanation
Indices: 29029348--29029372 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29029338 AGCATTTCGG
29029348 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
29029373 AAAAGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29031913 original size:23 final size:23
Alignment explanation
Indices: 29031874--29031918 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29031864 TTAAAATCTA
*
29031874 AAAAATAGAAAGATTAATTTTCT
1 AAAAATAGAAAGATTAAATTTCT
*
29031897 AAAAATA-AAAGGGTTAAATTTC
1 AAAAATAGAAA-GATTAAATTTC
29031919 AAATGCACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (23 bp):
AAAAATAGAAAGATTAAATTTCT
Found at i:29038545 original size:14 final size:14
Alignment explanation
Indices: 29038526--29038557 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29038516 TGAAAATACA
29038526 TATAAAAAAGTCTT
1 TATAAAAAAGTCTT
29038540 TATAAAAAAGTCTT
1 TATAAAAAAGTCTT
29038554 TATA
1 TATA
29038558 CTTAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (14 bp):
TATAAAAAAGTCTT
Found at i:29040033 original size:24 final size:24
Alignment explanation
Indices: 29040006--29040057 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29039996 TTCATAGATC
*
29040006 AAATAAATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATACT
*
29040030 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
29040054 AAAT
1 AAAT
29040058 CTTCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:29040316 original size:22 final size:22
Alignment explanation
Indices: 29040288--29040349 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
29040278 GCCCGGCCCG
*
29040288 TTTTTTAATAAAATTAAAATTA
1 TTTTTTAATAAAATTAAAACTA
29040310 TTTTTTAAATAAAATTAAAACTA
1 TTTTTT-AATAAAATTAAAACTA
* * *
29040333 ATTGTTATTAAAATTAA
1 TTTTTTAATAAAATTAA
29040350 TTGTTAGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTTTAATAAAATTAAAACTA
Found at i:29040362 original size:16 final size:16
Alignment explanation
Indices: 29040325--29040364 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29040315 TAAATAAAAT
* *
29040325 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29040341 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29040357 TAAAATTA
1 TAAAATTA
29040365 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:29040443 original size:59 final size:59
Alignment explanation
Indices: 29040375--29040632 Score: 507
Period size: 59 Copynumber: 4.4 Consensus size: 59
29040365 TCAAATTATT
*
29040375 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29040434 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29040493 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29040552 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29040611 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
29040633 ATTAATTGTT
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 198 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:29040626 original size:9 final size:9
Alignment explanation
Indices: 29040614--29040641 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29040604 TTTATCAAAT
29040614 TATTAATTG
1 TATTAATTG
29040623 TATTAATTG
1 TATTAATTG
29040632 TATTAATTG
1 TATTAATTG
29040641 T
1 T
29040642 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:29047654 original size:40 final size:41
Alignment explanation
Indices: 29047593--29047817 Score: 384
Period size: 41 Copynumber: 5.5 Consensus size: 41
29047583 GACTTTATGT
29047593 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
29047634 CTAGCAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
29047674 CTAGCAAGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
29047714 CTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
29047755 CTAGTAGGCTAAGTGCCGGTGATCTGAATCA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
29047796 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
29047818 ATATGTTAAA
Statistics
Matches: 175, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
40 80 0.46
41 95 0.54
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:29054942 original size:44 final size:44
Alignment explanation
Indices: 29054894--29054978 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
29054884 TTAATGGATT
*
29054894 ACATATATGTTAGTCAAATATATGTATTGAATTTGACAGGTGGA
1 ACATATATGTTAGCCAAATATATGTATTGAATTTGACAGGTGGA
*
29054938 ACATATATGTTAGCCGAATATATGTATTGAATTTGACAGGT
1 ACATATATGTTAGCCAAATATATGTATTGAATTTGACAGGT
29054979 TGAAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (44 bp):
ACATATATGTTAGCCAAATATATGTATTGAATTTGACAGGTGGA
Found at i:29055380 original size:41 final size:41
Alignment explanation
Indices: 29055335--29055600 Score: 430
Period size: 41 Copynumber: 6.5 Consensus size: 41
29055325 GACTTTATGT
29055335 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
29055376 CTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
29055417 CTAGTAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
29055457 CTAGAAAGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
29055497 CTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
29055538 CTAGTAGGCTAAGTGCCGGTGATCTGAATCA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
*
29055579 CTAGCAGGCAAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
29055601 ATATGTTAAA
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
40 77 0.37
41 133 0.63
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:29057965 original size:32 final size:32
Alignment explanation
Indices: 29057924--29057986 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
29057914 AAATGCGGTT
29057924 CATCCTTGGTACGCAGATATAGTAAACTATCC
1 CATCCTTGGTACGCAGATATAGTAAACTATCC
29057956 CATCCTTGGTACGCAGATATAGTAAACTATC
1 CATCCTTGGTACGCAGATATAGTAAACTATC
29057987 TCGTCACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (32 bp):
CATCCTTGGTACGCAGATATAGTAAACTATCC
Found at i:29059582 original size:22 final size:21
Alignment explanation
Indices: 29059547--29059598 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
29059537 TTGAAAAGAA
*
29059547 ATTATT-TTTTTAATTTTCCT
1 ATTATTATTTTTAATTTTACT
29059567 ATTATTATTATTTAATTTTACT
1 ATTATTATT-TTTAATTTTACT
29059589 ATT-TTATTTT
1 ATTATTATTTT
29059599 ACTTTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 7 0.24
22 14 0.48
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTATTTTTAATTTTACT
Found at i:29062959 original size:36 final size:36
Alignment explanation
Indices: 29062915--29062984 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
29062905 GTCCAGGCTC
*
29062915 GCCCGAGGGAAAATTCCTAAGCCCGGGCCCGGCCCG
1 GCCCGAGGGAAAATTCCTAAGCCCGAGCCCGGCCCG
*
29062951 GCCCGAGGGAAAATTCCTAAGCCCGAGCCTGGCC
1 GCCCGAGGGAAAATTCCTAAGCCCGAGCCCGGCC
29062985 TAGCCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.37, G:0.31, T:0.10
Consensus pattern (36 bp):
GCCCGAGGGAAAATTCCTAAGCCCGAGCCCGGCCCG
Found at i:29063033 original size:20 final size:20
Alignment explanation
Indices: 29063008--29063051 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29062998 AATAAACACC
*
29063008 AAAAAAAT-TTTTGAAAATTA
1 AAAAAAATATTTT-AAAAATA
*
29063028 AAAAAAGTATTTTAAAAATA
1 AAAAAAATATTTTAAAAATA
29063048 AAAA
1 AAAA
29063052 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAAAATATTTTAAAAATA
Found at i:29064481 original size:92 final size:88
Alignment explanation
Indices: 29064376--29064581 Score: 274
Period size: 91 Copynumber: 2.3 Consensus size: 88
29064366 GCACTCAAGT
* * *
29064376 TTTTCAAAAAAAGCAATTAAGTCTCTG-TCTTTTTTTTTGCACTCATTTGGGTACTTGAACTTTC
1 TTTTCAAAAAAAGCAATTAAGCCTCTGCTC-TTTTTTTT-CAATCAATTGGGTACTTGAACTTTC
*
29064440 AAAAT-ATATCAAAAAAGCCCTTAAACC
64 AAAATGAT-TCAAAAAA-CCCTCAAA-C
*
29064467 TTTTCAAGAAAAAGCAATTAAGCCCCTGCTCTTTTTTTTCAATCAATTGGGTACTTGAACTTTCA
1 TTTTCAA-AAAAAGCAATTAAGCCTCTGCTCTTTTTTTTCAATCAATTGGGTACTTGAACTTTCA
* *
29064532 AAATGCTTCAAAAGACCCTCAAAC
65 AAATGATTCAAAAAACCCTCAAAC
29064556 TTTTC-AAAAAAGCAATTAAGCCTCTG
1 TTTTCAAAAAAAGCAATTAAGCCTCTG
29064582 ATTTTATTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
87 19 0.18
88 1 0.01
89 6 0.06
90 7 0.07
91 42 0.40
92 27 0.26
93 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (88 bp):
TTTTCAAAAAAAGCAATTAAGCCTCTGCTCTTTTTTTTCAATCAATTGGGTACTTGAACTTTCAA
AATGATTCAAAAAACCCTCAAAC
Found at i:29064714 original size:9 final size:9
Alignment explanation
Indices: 29064702--29064813 Score: 52
Period size: 9 Copynumber: 12.0 Consensus size: 9
29064692 AAAAATAGTA
29064702 AAAAATTAT
1 AAAAATTAT
29064711 -AAAATATAT
1 AAAAAT-TAT
*
29064720 AGAAA-TAT
1 AAAAATTAT
29064728 AAAAATTAT
1 AAAAATTAT
*
29064737 -AAAATTTT
1 AAAAATTAT
* *
29064745 ATAAAGTCAT
1 A-AAAATTAT
29064755 AAGAAAATTAT
1 -A-AAAATTAT
*
29064766 ACAGAA-TAT
1 A-AAAATTAT
*
29064775 AAAGAAATAT
1 AAA-AATTAT
**
29064785 AAATTTTAT
1 AAAAATTAT
29064794 AAAAAAATTAT
1 --AAAAATTAT
29064805 AAAAATTAT
1 AAAAATTAT
29064814 CGTACCAAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
8 20 0.26
9 24 0.32
10 18 0.24
11 14 0.18
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29064987 original size:36 final size:38
Alignment explanation
Indices: 29064947--29065029 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
29064937 GGTCATTAAT
* * *
29064947 TTTTTTATGATTTT-TATAAAAAA-TTAAAATTTTTTA
1 TTTTTTATGATTTTACAAAAAAAATTTAAAATTTATTA
*
29064983 TTTTTTATGATTTTACAAAAAAAATTTATAATTTATTA
1 TTTTTTATGATTTTACAAAAAAAATTTAAAATTTATTA
29065021 TATTTTTAT
1 T-TTTTTAT
29065030 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 14 0.35
37 7 0.17
38 12 0.30
39 7 0.17
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (38 bp):
TTTTTTATGATTTTACAAAAAAAATTTAAAATTTATTA
Found at i:29065215 original size:88 final size:89
Alignment explanation
Indices: 29065081--29065287 Score: 242
Period size: 88 Copynumber: 2.3 Consensus size: 89
29065071 AAGAGCAGGG
* * * *
29065081 GCTTAATTGC-TTTTTTAAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAATTCAATTACCC
1 GCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTAATACATTTTGAAAATTCAAGTACCC
*
29065145 AATTGAGTG-AAAAAAAAGTAAGA
66 AATTGAGTGAAAAAAAAAGGAAGA
* * * *
29065168 GCTTAATTGCTTTTTTTGAAGAAGTTTGAGGG-CATTTTTAATACATTTTGAAAATTCAAGTGCT
1 GCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGTC-TTTTTAATACATTTTGAAAATTCAAGTACC
* *
29065232 TAATTGAGTGAAAAAAAAAGGAAGG
65 CAATTGAGTGAAAAAAAAAGGAAGA
* *
29065257 GCTTAATTACTTTTCTTTTTAAAAA-TTTGAG
1 GCTTAATTGC-TTT-TTTTAAAAAAGTTTGAG
29065288 AACTTTTTAC
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
87 11 0.11
88 52 0.51
89 21 0.21
90 9 0.09
91 8 0.08
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (89 bp):
GCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTAATACATTTTGAAAATTCAAGTACCC
AATTGAGTGAAAAAAAAAGGAAGA
Found at i:29065514 original size:2 final size:2
Alignment explanation
Indices: 29065507--29065536 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29065497 ACGCACACGC
29065507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29065537 TACAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29066091 original size:22 final size:23
Alignment explanation
Indices: 29066063--29066113 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
29066053 CTATTTTTTA
29066063 AAAAATATTT-AAAATTTAAAAT
1 AAAAATATTTGAAAATTTAAAAT
*
29066085 AAAAATATTTGAAATTTTAAAAT
1 AAAAATATTTGAAAATTTAAAAT
29066108 ATAAAA
1 A-AAAA
29066114 GAAATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.38
23 12 0.46
24 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAATATTTGAAAATTTAAAAT
Found at i:29066804 original size:31 final size:31
Alignment explanation
Indices: 29066769--29066849 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
29066759 AGTTAGAAAT
* *
29066769 GATCTAAAACGTAAGTAATCAAAATAAAAAC
1 GATCTAAAACGTAAGTAACCAAAATAAAAAA
* *
29066800 GATCTAAAATGTAAGTGACCAAAATAAAAAA
1 GATCTAAAACGTAAGTAACCAAAATAAAAAA
* *
29066831 GATCTAAAACATTAGTAAC
1 GATCTAAAACGTAAGTAAC
29066850 TGAATTGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.56, C:0.12, G:0.11, T:0.21
Consensus pattern (31 bp):
GATCTAAAACGTAAGTAACCAAAATAAAAAA
Found at i:29071178 original size:28 final size:29
Alignment explanation
Indices: 29071110--29071178 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
29071100 TGATAATCAT
*
29071110 ATTAATTTTATTACTTGAAAATATAATTA
1 ATTAATTTTATCACTTGAAAATATAATTA
*
29071139 A-TAACTACTTATCACTTGAAAA-AT-ATTA
1 ATTAA-T-TTTATCACTTGAAAATATAATTA
29071167 AGTTAATTTTAT
1 A-TTAATTTTAT
29071179 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
28 12 0.36
29 5 0.15
30 16 0.48
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (29 bp):
ATTAATTTTATCACTTGAAAATATAATTA
Found at i:29072007 original size:21 final size:21
Alignment explanation
Indices: 29071959--29072011 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
29071949 AGCAGTGGCG
29071959 GTGAGATTA-ATTACTGTAGC
1 GTGAGATTAGATTACTGTAGC
*
29071979 GATAAGATTAGA-TACTGTAGC
1 G-TGAGATTAGATTACTGTAGC
29072000 AGTGAGATTAGA
1 -GTGAGATTAGA
29072012 AACAGCGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATTACTGTAGC
Found at i:29078902 original size:16 final size:15
Alignment explanation
Indices: 29078881--29078940 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
29078871 CTTAAAAGTT
29078881 TTTTATATAATATAAA
1 TTTTATATAATA-AAA
*
29078897 TTTTATAAAATAAAA
1 TTTTATATAATAAAA
*
29078912 ATTTATA-AA-AAAA
1 TTTTATATAATAAAA
*
29078925 -GTTATATAATATAAA
1 TTTTATATAATA-AAA
29078940 T
1 T
29078941 ATTTCAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.14
13 6 0.16
14 3 0.08
15 12 0.32
16 11 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TTTTATATAATAAAA
Found at i:29078918 original size:15 final size:16
Alignment explanation
Indices: 29078882--29078921 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29078872 TTAAAAGTTT
* *
29078882 TTTATATAATATAAAT
1 TTTATAAAATATAAAA
29078898 TTTATAAAATA-AAAA
1 TTTATAAAATATAAAA
29078913 TTTATAAAA
1 TTTATAAAA
29078922 AAAGTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTATAAAATATAAAA
Found at i:29078918 original size:29 final size:30
Alignment explanation
Indices: 29078886--29078953 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
29078876 AAGTTTTTTA
*
29078886 TATAATATAAA-TTTTATAAAATAAAAATT
1 TATAATATAAAGTTATATAAAATAAAAATT
* * *
29078915 TATAA-AAAAAGTTATATAATATAAATATT
1 TATAATATAAAGTTATATAAAATAAAAATT
29078944 TCA-AATATAA
1 T-ATAATATAA
29078954 CAAAAAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.13
29 23 0.74
30 4 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
TATAATATAAAGTTATATAAAATAAAAATT
Found at i:29088566 original size:41 final size:41
Alignment explanation
Indices: 29088487--29088669 Score: 286
Period size: 39 Copynumber: 4.5 Consensus size: 41
29088477 GGCCCATTTT
29088487 TATTTTAAAAATTTT-AAAAATTAAAAAAA-TATTTTAAAAA
1 TATTTT-AAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
29088527 TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
29088568 TATTTTAAAA--TTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
* *
29088607 TATTTTAAAATTTTAAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTAAAATTTT--AAAAAATTAAAAAAAGTATTTTAAAAA
29088649 TATTTTAAAATTTTAAAAAAT
1 TATTTTAAAATTTTAAAAAAT
29088670 AAATATATTT
Statistics
Matches: 135, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
39 47 0.35
40 27 0.20
41 23 0.17
42 30 0.22
43 8 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:29088578 original size:31 final size:29
Alignment explanation
Indices: 29088522--29088585 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 29
29088512 AAAATATTTT
29088522 AAAAATATTTTAAAATTTTAAAAAATTAA
1 AAAAATATTTTAAAATTTTAAAAAATTAA
*
29088551 AAAAAGTATTTTAAAAATATTT-TAAAATTAA
1 AAAAA-TATTTT-AAAAT-TTTAAAAAATTAA
29088582 AAAA
1 AAAA
29088586 TTAAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.16
30 6 0.19
31 17 0.55
32 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAATATTTTAAAATTTTAAAAAATTAA
Found at i:29089129 original size:13 final size:13
Alignment explanation
Indices: 29089111--29089135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29089101 AGTTCTTCAT
29089111 TACTTTTGAGAAG
1 TACTTTTGAGAAG
29089124 TACTTTTGAGAA
1 TACTTTTGAGAA
29089136 ATTTGATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TACTTTTGAGAAG
Found at i:29091176 original size:14 final size:13
Alignment explanation
Indices: 29091146--29091172 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29091136 AAATATAATT
29091146 ATAATCCCATTAA
1 ATAATCCCATTAA
29091159 ATAATCCCATTAA
1 ATAATCCCATTAA
29091172 A
1 A
29091173 ATAAGTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATCCCATTAA
Found at i:29101960 original size:30 final size:30
Alignment explanation
Indices: 29101926--29101987 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
29101916 ACTTATTTTA
* *
29101926 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAAGCAT
29101956 TTGTTAATTTTATTATTATTTTAAAAGCAT
1 TTGTTAATTTTATTATTATTTTAAAAGCAT
29101986 TT
1 TT
29101988 ACTTATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAAGCAT
Found at i:29104573 original size:18 final size:19
Alignment explanation
Indices: 29104546--29104584 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29104536 GGTATTTTAC
*
29104546 TAAAATAATACAAAAA-AA
1 TAAAAAAATACAAAAATAA
29104564 TAAAAAAATACAAAAATAA
1 TAAAAAAATACAAAAATAA
29104583 TA
1 TA
29104585 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAAAAAATACAAAAATAA
Found at i:29105836 original size:155 final size:154
Alignment explanation
Indices: 29105187--29106064 Score: 1115
Period size: 155 Copynumber: 5.7 Consensus size: 154
29105177 ATAAAATCTG
* * **
29105187 AAAA-AATATAAAATAATAAAA-TACATAAATAATATATTTTTATTGAAAGTAATAAAATTTGGG
1 AAAATAATGTAAAATAATAAAATTAGA-AAATAATATATTTTTATTGAAAGTAATAAAATCAGGG
* * * * *
29105250 AAAAAATATGAATAAA-GGTTCGAAATAAAGGTTATTTTTTGAAATTTATTTAAAAAACACACTA
65 AAAAAATACGAACAAAGGGCT-GAAATAAGGGTT-TTTTTT-AAATTTAATTAAAAAACACACTA
*
29105314 AATTAATAAATTTCAAACATAATGTACT
127 AATTAATACATTTCAAACATAATGTACT
**
29105342 AAAATAATGTAAAATAATAAAATTAGAAAATAATATA-TTTT-TT-AAAGTAATAAAATCCTGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCAGGGA
* * * *
29105404 AAAAATACAAACAAAGGG-TCGAAATAAGGGTTTTTTACTAAA-TTAA--AAAAAACAGAAGT-A
66 AAAAATACGAACAAAGGGCT-GAAATAAGGGTTTTTT-TTAAATTTAATTAAAAAACA-CACTAA
*
29105464 ATTAATACATTTCAAACACAATGTACT
128 ATTAATACATTTCAAACATAATGTACT
* * * * *
29105491 AAAATAATGCAAAATGATAAAA-TACAAAAATAATATATTTTTATTGGAAGTAATAAAATCCGAG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAATCAG-G
* * * * * *
29105555 AAAAAAATACGAACAAAGGGCTGAAATAA--GTTTTTTTTTACTTT-ATTTAAAAATACAGTAAA
64 GAAAAAATACGAACAAAGGGCTGAAATAAGGGTTTTTTTTAAATTTAATTAAAAAACACACTAAA
*
29105617 TTAATATATTTCAAACATAATGTACT
129 TTAATACATTTCAAACATAATGTACT
*
29105643 AAACTAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCAGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCAGGG-
*
29105708 AAAAAATACGAACAAATGGCTGAAATAAGGGTTTTTTTTAAATTTAATTAAAAAACACACTAAAT
65 AAAAAATACGAACAAAGGGCTGAAATAAGGGTTTTTTTTAAATTTAATTAAAAAACACACTAAAT
29105773 TAATACATTTCAAACATAATGTACT
130 TAATACATTTCAAACATAATGTACT
* * * *
29105798 AAAATAATGTAAAATAATAAAATTATAAAATAAAATATTTTTATTGAAAGAAATAAAATCCAGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAAT-CAGGG
* *
29105863 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTGTAAATTTATTTAAAAAACACACTAAA
65 AAAAAATACGAACAAAGGGCTGAAATAAGGGTTTTTTT-TAAATTTAATTAAAAAACACACTAAA
29105928 TTAATACATTTCAAACATAATGGT-CT
129 TTAATACATTTCAAACATAAT-GTACT
* *
29105954 AAACTAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATAGAAAGTAATAAAATTC-GGG
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCAGGG
* **
29106018 AAAAAATACGAATAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTT
65 AAAAAATACGAACAAAGGGCTGAAATAAGGGTTTTTTT--TAAATTT
29106065 GTTTTGAAGT
Statistics
Matches: 637, Mismatches: 61, Indels: 49
0.85 0.08 0.07
Matches are distributed among these distances:
148 2 0.00
149 65 0.10
150 9 0.01
151 18 0.03
152 133 0.21
153 70 0.11
154 18 0.03
155 177 0.28
156 139 0.22
157 6 0.01
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (154 bp):
AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCAGGGA
AAAAATACGAACAAAGGGCTGAAATAAGGGTTTTTTTTAAATTTAATTAAAAAACACACTAAATT
AATACATTTCAAACATAATGTACT
Found at i:29111349 original size:23 final size:23
Alignment explanation
Indices: 29111304--29111350 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29111294 TAAAAATAAT
*
29111304 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
29111327 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
29111350 A
1 A
29111351 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:29113756 original size:251 final size:251
Alignment explanation
Indices: 29113313--29113786 Score: 876
Period size: 251 Copynumber: 1.9 Consensus size: 251
29113303 GCAGTGTTAT
*
29113313 ACATGAGGGCAACCGGCCTACCACCTGGCCTACCACATGAGTAGACCACCACTCATATTGTTGGT
1 ACATGAGGGCAACCGGCCTACCACCTGGCCCACCACATGAGTAGACCACCACTCATATTGTTGGT
29113378 GACAAGGCATTACCAGGCATGGGACCTCCCACTATAAATACCTTCCATCACGATGAAGAGAGGAT
66 GACAAGGCATTACCAGGCATGGGACCTCCCACTATAAATACCTTCCATCACGATGAAGAGAGGAT
*
29113443 CTTTTGACCCTTTCAGCAACCCTAAGCATTTGCCTATTACGCTTACCTTCCCTTGCCTTTAGACC
131 CTTTTGACCCTTTCAGCAACCCTAAGCATTTGCCTACTACGCTTACCTTCCCTTGCCTTTAGACC
*
29113508 TTCCTCACTCCTTTCCTTCTCTCGTCCTCCAAGCCACCCGCTTTTAGAGGGAATGC
196 TTCCTCACTCATTTCCTTCTCTCGTCCTCCAAGCCACCCGCTTTTAGAGGGAATGC
* *
29113564 ACATGAGGGCAACCGGCCTACCACCTGGCCCACCACATGGGTAGACCACCACTCGTATTGTTGGT
1 ACATGAGGGCAACCGGCCTACCACCTGGCCCACCACATGAGTAGACCACCACTCATATTGTTGGT
*
29113629 GACAAGGCATTACCAGGCATGGGACCTCCCCCTATAAATACCTTCCATCACGATGAAGAGAGGAT
66 GACAAGGCATTACCAGGCATGGGACCTCCCACTATAAATACCTTCCATCACGATGAAGAGAGGAT
29113694 CTTTTGACCCTTTCAGCAACCCTAAGCATTTGCCTACTACGCTTACCTTCCCTTGCCTTTAGACC
131 CTTTTGACCCTTTCAGCAACCCTAAGCATTTGCCTACTACGCTTACCTTCCCTTGCCTTTAGACC
* *
29113759 TTCTTCACTCATTTCCTTCTTTCGTCCT
196 TTCCTCACTCATTTCCTTCTCTCGTCCT
29113787 TTTCAACTTT
Statistics
Matches: 215, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
251 215 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (251 bp):
ACATGAGGGCAACCGGCCTACCACCTGGCCCACCACATGAGTAGACCACCACTCATATTGTTGGT
GACAAGGCATTACCAGGCATGGGACCTCCCACTATAAATACCTTCCATCACGATGAAGAGAGGAT
CTTTTGACCCTTTCAGCAACCCTAAGCATTTGCCTACTACGCTTACCTTCCCTTGCCTTTAGACC
TTCCTCACTCATTTCCTTCTCTCGTCCTCCAAGCCACCCGCTTTTAGAGGGAATGC
Found at i:29119936 original size:23 final size:23
Alignment explanation
Indices: 29119905--29119952 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29119895 TTTTGTACAA
29119905 TTCTAATTTGAACTTAGATTATT
1 TTCTAATTTGAACTTAGATTATT
* *
29119928 TTCTGATTTGAATTTAGATTATT
1 TTCTAATTTGAACTTAGATTATT
29119951 TT
1 TT
29119953 TAAAGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (23 bp):
TTCTAATTTGAACTTAGATTATT
Found at i:29121659 original size:42 final size:42
Alignment explanation
Indices: 29121606--29121804 Score: 195
Period size: 42 Copynumber: 4.7 Consensus size: 42
29121596 GCTCAAAAAC
* *
29121606 TGAACAGAAGCTTGTAAGAGCTAAACAGAAAC-CTATAAGGGT
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTC-ATAAGAGT
* * * * *
29121648 TGAACAAAAGCTCGTAACAGCTGAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGT
* * * ** *
29121690 TAAACAAAAGCTCATAAGAGCCGAACAGAAACTCCTAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGT
* * *
29121732 TGAACAGAAGCTCGAAAAAGCTAAAC-GAAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAACAG-AAACTCATAAGAGT
* * *
29121774 TAAACAGAAGCTCGAAAGAGCTAAACGGAAA
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAA
29121805 GTAAAACACA
Statistics
Matches: 129, Mismatches: 25, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 126 0.98
43 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGT
Found at i:29121705 original size:21 final size:21
Alignment explanation
Indices: 29121620--29121799 Score: 75
Period size: 21 Copynumber: 8.6 Consensus size: 21
29121610 CAGAAGCTTG
* *
29121620 TAAGAGCTAAACAGAAACCT-A
1 TAAGAGTTAAACA-AAAGCTCA
* * *
29121641 TAAGGGTTGAACAAAAGCTCG
1 TAAGAGTTAAACAAAAGCTCA
* * * *
29121662 TAACAGCTGAACGGAAA-CTCA
1 TAAGAGTTAAAC-AAAAGCTCA
*
29121683 TATGAGTTAAACAAAAGCTCA
1 TAAGAGTTAAACAAAAGCTCA
*** *
29121704 TAAGAGCCGAACAGAAA-CTCC
1 TAAGAGTTAAACA-AAAGCTCA
* *
29121725 TAAGAGTTGAACAGAAGCTCGA
1 TAAGAGTTAAACAAAAGCTC-A
* *
29121747 -AAAAGCTAAACGAAAA-CTCA
1 TAAGAGTTAAAC-AAAAGCTCA
* *
29121767 TATGAGTTAAACAGAAGCTCGA
1 TAAGAGTTAAACAAAAGCTC-A
*
29121789 -AAGAGCTAAAC
1 TAAGAGTTAAAC
29121800 GGAAAGTAAA
Statistics
Matches: 115, Mismatches: 34, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
20 14 0.12
21 91 0.79
22 10 0.09
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.16
Consensus pattern (21 bp):
TAAGAGTTAAACAAAAGCTCA
Found at i:29121764 original size:84 final size:84
Alignment explanation
Indices: 29121641--29121794 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
29121631 CAGAAACCTA
* * * * *
29121641 TAAGGGTTGAACAAAAGCTCGTAACAGCTGAACGGAAACTCATATGAGTTAAACAAAAGCTC-AT
1 TAAGAGTTGAACAAAAGCTCGAAAAAGCTAAACGAAAACTCATATGAGTTAAACAAAAGCTCGA-
29121705 AAGAGCCGAACAGAAACTCC
65 AAGAGCCGAACAGAAACTCC
* *
29121725 TAAGAGTTGAACAGAAGCTCGAAAAAGCTAAACGAAAACTCATATGAGTTAAACAGAAGCTCGAA
1 TAAGAGTTGAACAAAAGCTCGAAAAAGCTAAACGAAAACTCATATGAGTTAAACAAAAGCTCGAA
29121790 AGAGC
66 AGAGC
29121795 TAAACGGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
84 61 0.98
85 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (84 bp):
TAAGAGTTGAACAAAAGCTCGAAAAAGCTAAACGAAAACTCATATGAGTTAAACAAAAGCTCGAA
AGAGCCGAACAGAAACTCC
Found at i:29122367 original size:31 final size:31
Alignment explanation
Indices: 29122332--29122390 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
29122322 TACAACCCAT
*
29122332 TTTTTCAATAATTTCACAAA-AAATCCTTGTA
1 TTTTT-AATAATTTAACAAATAAATCCTTGTA
* *
29122363 TTTTTACTAATTTAACAAATTAATCCTT
1 TTTTTAATAATTTAACAAATAAATCCTT
29122391 AATCGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTTTAATAATTTAACAAATAAATCCTTGTA
Found at i:29122459 original size:169 final size:169
Alignment explanation
Indices: 29122257--29122595 Score: 597
Period size: 169 Copynumber: 2.0 Consensus size: 169
29122247 AGTCCCTGAG
* *
29122257 CCCAAAATATACAAATTAACCATTTTAATGCAAACCCATGCTAGATGAATATTCATGGCATTCAA
1 CCCAAAACATACAAATTAACCATTTTAATGCAAACCCATACTAGATGAATATTCATGGCATTCAA
* *
29122322 TACAACCCATTTTTTCAATAATTTCACAAAAAATCCTTGTATTTTTACTAATTTAACAAATTAAT
66 TACAACCCATTTTTGCAATAATTTAACAAAAAATCCTTGTATTTTTACTAATTTAACAAATTAAT
**
29122387 CCTTAATCGAAAAATTCATCAAAATCACTTAACAAAATA
131 CCTTAATAAAAAAATTCATCAAAATCACTTAACAAAATA
* * *
29122426 CCCAAAACATGCAAATTAACCATTTTAATGCAAACCCATACTAGCTGAATATTCATGTCATTCAA
1 CCCAAAACATACAAATTAACCATTTTAATGCAAACCCATACTAGATGAATATTCATGGCATTCAA
29122491 TACAACCCATTTTTGCAATAATTTAACAAAAAATCCTTGTATTTTTACTAATTTAACAAATTAAT
66 TACAACCCATTTTTGCAATAATTTAACAAAAAATCCTTGTATTTTTACTAATTTAACAAATTAAT
29122556 CCTTAATAAAAAAATTCATCAAAATCACTTAACAAAATA
131 CCTTAATAAAAAAATTCATCAAAATCACTTAACAAAATA
29122595 C
1 C
29122596 TTTTAAATAA
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
169 161 1.00
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (169 bp):
CCCAAAACATACAAATTAACCATTTTAATGCAAACCCATACTAGATGAATATTCATGGCATTCAA
TACAACCCATTTTTGCAATAATTTAACAAAAAATCCTTGTATTTTTACTAATTTAACAAATTAAT
CCTTAATAAAAAAATTCATCAAAATCACTTAACAAAATA
Found at i:29122700 original size:33 final size:33
Alignment explanation
Indices: 29122663--29122728 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
29122653 TCATTAAGGG
29122663 CAATATCCAAAATCTTTAACAAAATAAAAAACT
1 CAATATCCAAAATCTTTAACAAAATAAAAAACT
*
29122696 CAATATCCAAAATCTTTAACAAAATCAAAAACT
1 CAATATCCAAAATCTTTAACAAAATAAAAAACT
29122729 AAGGTAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (33 bp):
CAATATCCAAAATCTTTAACAAAATAAAAAACT
Found at i:29127719 original size:6 final size:6
Alignment explanation
Indices: 29127708--29127732 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29127698 TAAATCAATG
29127708 AACACC AACACC AACACC AACACC A
1 AACACC AACACC AACACC AACACC A
29127733 TGGAAGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
AACACC
Found at i:29132405 original size:39 final size:38
Alignment explanation
Indices: 29132337--29132419 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 38
29132327 ACCTCATCCT
** * *
29132337 TGCGAGGTTTACGCGAGCTCCCTCTTGCGACCTTGTCTC
1 TGCGAGGCCTACGCGAGCTCCCTCATGCGACC-TATCTC
*
29132376 TGCGAGGCCTACGCGAGCT-CCTCCATGCGAGCTATCTC
1 TGCGAGGCCTACGCGAGCTCCCT-CATGCGACCTATCTC
29132414 TGCGAG
1 TGCGAG
29132420 CATCTTGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 14 0.37
39 24 0.63
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.25
Consensus pattern (38 bp):
TGCGAGGCCTACGCGAGCTCCCTCATGCGACCTATCTC
Found at i:29133455 original size:21 final size:21
Alignment explanation
Indices: 29133431--29133490 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
29133421 AGGAAAATGC
29133431 TTTTAAAAGTAGGGTTTTGT-
1 TTTTAAAAGTAGGGTTTTGTG
* *
29133451 TTTTTAGAGTTAGGG-TTTGTG
1 TTTTAAAAG-TAGGGTTTTGTG
* *
29133472 ATTTATAAAGCAGGGTTTT
1 TTTTA-AAAGTAGGGTTTT
29133491 TAGATTTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
20 12 0.40
21 12 0.40
22 6 0.20
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTTAAAAGTAGGGTTTTGTG
Found at i:29135448 original size:19 final size:19
Alignment explanation
Indices: 29135426--29135470 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
29135416 AAAAATTTAT
*
29135426 TAAAAATTAGAAAAAAATA
1 TAAAAATCAGAAAAAAATA
*
29135445 TAAAAATCATAAAAAAATA
1 TAAAAATCAGAAAAAAATA
29135464 TATAAAA
1 TA-AAAA
29135471 AATTGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
TAAAAATCAGAAAAAAATA
Found at i:29135480 original size:10 final size:11
Alignment explanation
Indices: 29135416--29135473 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
29135406 TTTAATTATT
* *
29135416 AAAAATTTATT
1 AAAAATATATA
*
29135427 AAAAAT-TAGA
1 AAAAATATATA
29135437 AAAAA-ATAT-
1 AAAAATATATA
29135446 AAAAATCATA-A
1 AAAAAT-ATATA
29135457 AAAAATATATA
1 AAAAATATATA
29135468 AAAAAT
1 AAAAAT
29135474 TGTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 5 0.13
10 12 0.31
11 22 0.56
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AAAAATATATA
Found at i:29135503 original size:21 final size:21
Alignment explanation
Indices: 29135477--29135521 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29135467 AAAAAATTGT
* *
29135477 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
29135498 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
29135519 AAA
1 AAA
29135522 TATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:29135778 original size:27 final size:30
Alignment explanation
Indices: 29135748--29135810 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
29135738 AAAAAGTTCT
29135748 AATTTTTAAT-AAATTT-TAATTTTTTT-A
1 AATTTTTAATAAAATTTATAATTTTTTTGA
*
29135775 AATTTTTATTAAAATTTAATAATTTTTTTGA
1 AATTTTTAATAAAATTT-ATAATTTTTTTGA
29135806 AATTT
1 AATTT
29135811 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.29
28 6 0.19
30 10 0.32
31 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
AATTTTTAATAAAATTTATAATTTTTTTGA
Found at i:29135782 original size:17 final size:17
Alignment explanation
Indices: 29135747--29135780 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29135737 TAAAAAGTTC
29135747 TAATTTTTAATAAATTT
1 TAATTTTTAATAAATTT
*
29135764 TAATTTTT-TTAAATTT
1 TAATTTTTAATAAATTT
29135780 T
1 T
29135781 TATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTTAATAAATTT
Found at i:29135782 original size:47 final size:49
Alignment explanation
Indices: 29135714--29135831 Score: 122
Period size: 47 Copynumber: 2.5 Consensus size: 49
29135704 ATTTACACTT
* *
29135714 TTTTATTTTTTTTACGA-TTTTAATAAAAAGTT-CTAATTTTTAAT-AAA
1 TTTTATTTTTTTTACAATTTTTAATAAAAAGTTAATAATTTTT-ATGAAA
* * * *
29135761 TTTTAATTTTTTTA-AATTTTT-ATTAAAATTTAATAATTTTTTTGAAA
1 TTTTATTTTTTTTACAATTTTTAATAAAAAGTTAATAATTTTTATGAAA
*
29135808 -TTTATTTTTTTTATAATTTTTAAT
1 TTTTATTTTTTTTACAATTTTTAAT
29135832 GAGAGCAAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
46 22 0.37
47 35 0.59
48 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (49 bp):
TTTTATTTTTTTTACAATTTTTAATAAAAAGTTAATAATTTTTATGAAA
Found at i:29136009 original size:42 final size:41
Alignment explanation
Indices: 29135926--29136007 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
29135916 GGAAAAAGTA
29135926 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
1 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
29135967 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
1 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
29136008 TGATGCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.44
Consensus pattern (41 bp):
GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
Found at i:29136074 original size:129 final size:127
Alignment explanation
Indices: 29135840--29136075 Score: 312
Period size: 129 Copynumber: 1.8 Consensus size: 127
29135830 ATGAGAGCAA
* *
29135840 GGGCTTAATTGCTTTTTTGAAAATTTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
1 GGGCCTAATTGCTTTTTTGAAAAGTTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
*** * * *
29135905 CAATTGAGTGGGGAAAAAGTAGGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTTG
66 CAATTGAGTGAAAAAAAAGGAGGGACCTAATTAC-TTTTTTGAAGAAGTTTGAGGGTCTTTTG
*
29135968 GGGCCTAATTGCTTTTTTTGAAGAAGTTT-GAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTG
1 GGGCCTAATTGC-TTTTTTGAA-AAGTTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
** *
29136032 CTTAATTGAGTGCAAAAAAAAAGGAGGGACTTAATTACTTTTTT
64 CCCAATTGAGTG--AAAAAAAAGGAGGGACCTAATTACTTTTTT
29136076 TATTTTTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
128 11 0.12
129 53 0.58
130 11 0.12
131 17 0.18
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.39
Consensus pattern (127 bp):
GGGCCTAATTGCTTTTTTGAAAAGTTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
CAATTGAGTGAAAAAAAAGGAGGGACCTAATTACTTTTTTGAAGAAGTTTGAGGGTCTTTTG
Found at i:29137644 original size:26 final size:26
Alignment explanation
Indices: 29137622--29137672 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
29137612 TTCATATATT
29137622 TGAAAACTTATTTTAAAAAATATTTA
1 TGAAAACTTATTTTAAAAAATATTTA
*
29137648 TGAAAACTTATTTTAAAGAATATTT
1 TGAAAACTTATTTTAAAAAATATTT
29137673 TTTAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TGAAAACTTATTTTAAAAAATATTTA
Found at i:29137659 original size:14 final size:13
Alignment explanation
Indices: 29137620--29137661 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
29137610 TCTTCATATA
29137620 TTTGAAAACTTAT
1 TTTGAAAACTTAT
**
29137633 TTT-AAAAAATAT
1 TTTGAAAACTTAT
29137645 TTATGAAAACTTAT
1 TT-TGAAAACTTAT
29137659 TTT
1 TTT
29137662 AAAGAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.39
13 5 0.22
14 9 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTGAAAACTTAT
Found at i:29142369 original size:64 final size:64
Alignment explanation
Indices: 29142290--29142427 Score: 240
Period size: 64 Copynumber: 2.2 Consensus size: 64
29142280 ACAAAGCAAA
* *
29142290 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTACATTGGGCATTAGTTTATAAGGAAC
1 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
29142354 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
1 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
**
29142418 ACCAATAACA
1 GGCAATAACA
29142428 GTATTTTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (64 bp):
GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
Found at i:29146566 original size:18 final size:19
Alignment explanation
Indices: 29146543--29146582 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
29146533 ATTGTAAAAA
29146543 TATTTTATA-AAAATAAAT
1 TATTTTATAGAAAATAAAT
29146561 TATTTTATAGGAAAATAAAT
1 TATTTTATA-GAAAATAAAT
29146581 TA
1 TA
29146583 ATCTTTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TATTTTATAGAAAATAAAT
Found at i:29148555 original size:16 final size:16
Alignment explanation
Indices: 29148534--29148603 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
29148524 TTTGGTTCGC
* *
29148534 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
29148550 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
29148566 TATAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29148582 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29148598 TGTAAT
1 TGTAAT
29148604 AGCATAATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29148912 original size:17 final size:17
Alignment explanation
Indices: 29148752--29148905 Score: 72
Period size: 17 Copynumber: 9.0 Consensus size: 17
29148742 TTATTATTAA
29148752 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
29148770 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
* ***
29148787 -TCTTAATATTAAATATTCTT
1 AT-ATAAT-TT-AATA-AAAT
29148807 ATATGAATTTAATAAAAT
1 ATAT-AATTTAATAAAAT
* * *
29148825 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
29148841 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
29148860 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
29148872 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29148889 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29148906 TCTTAATATT
Statistics
Matches: 100, Mismatches: 20, Indels: 33
0.65 0.13 0.22
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 3 0.03
15 6 0.06
16 10 0.10
17 35 0.35
18 18 0.18
19 11 0.11
20 7 0.07
21 4 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29149166 original size:122 final size:120
Alignment explanation
Indices: 29148732--29149347 Score: 1108
Period size: 120 Copynumber: 5.1 Consensus size: 120
29148722 TTAATCATAT
*
29148732 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
29148797 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
29148852 TTTAAAATAATTATTATTAAATATAATTTAAT-AAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
29148916 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
29148972 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
29149037 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
29149092 TTTAAAATAATTATTATTAAAAATGTAATTTAGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
29149157 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
29149214 TTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTTAAT
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TTAAT
*
29149279 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
63 ATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
29149337 TTTAAAATAAT
1 TTTAAAATAAT
29149348 AAAATTTGAA
Statistics
Matches: 484, Mismatches: 7, Indels: 7
0.97 0.01 0.01
Matches are distributed among these distances:
119 30 0.06
120 193 0.40
121 30 0.06
122 158 0.33
123 73 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:29149251 original size:15 final size:16
Alignment explanation
Indices: 29149205--29149269 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 16
29149195 ATAATACTAT
29149205 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
29149220 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
29149233 AAAATATAATTTAGTAA
1 AAAATATAATTTAAT-A
29149250 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
29149267 AAA
1 AAA
29149270 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 4 0.10
17 8 0.21
18 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:29149257 original size:18 final size:17
Alignment explanation
Indices: 29149232--29149269 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
29149222 AATTATTATT
*
29149232 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
29149249 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
29149267 AAA
1 AAA
29149270 TTCTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:29149392 original size:20 final size:20
Alignment explanation
Indices: 29149345--29149383 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29149335 AATTTAAAAT
*
29149345 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
29149365 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
29149384 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:29149659 original size:17 final size:17
Alignment explanation
Indices: 29149637--29149704 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
29149627 CTTATATGCT
29149637 TTAATTTATTGCATGTA
1 TTAATTTATTGCATGTA
*
29149654 TTAATTTATTTTTCA--TA
1 TTAATTTA--TTGCATGTA
*
29149671 TTATTTTTATAT-CATGTA
1 TTA-ATTTAT-TGCATGTA
29149689 TTAATTTATTGCATGT
1 TTAATTTATTGCATGT
29149705 TTGTATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
16 4 0.10
17 24 0.59
18 9 0.22
19 4 0.10
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (17 bp):
TTAATTTATTGCATGTA
Found at i:29154236 original size:15 final size:14
Alignment explanation
Indices: 29154216--29154246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
29154206 AAATCAACTC
29154216 CACATATTCTTATAT
1 CACATATTCTTA-AT
29154231 CACATATTCTTAAT
1 CACATATTCTTAAT
29154245 CA
1 CA
29154247 ACAGAGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (14 bp):
CACATATTCTTAAT
Found at i:29154612 original size:29 final size:29
Alignment explanation
Indices: 29154573--29154635 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
29154563 GTCTGGCCCA
29154573 TGTGGCCCACACGGCCTAGCACATAGTCG
1 TGTGGCCCACACGGCCTAGCACATAGTCG
* * * *
29154602 TGTGGCTCACACGGCCTCGCATATGGTCG
1 TGTGGCCCACACGGCCTAGCACATAGTCG
29154631 TGTGG
1 TGTGG
29154636 TCGTAAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (29 bp):
TGTGGCCCACACGGCCTAGCACATAGTCG
Found at i:29154945 original size:24 final size:24
Alignment explanation
Indices: 29154918--29154966 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
29154908 AAAACTTTCG
*
29154918 AAACAAACCCAAAATTGAATTTAA
1 AAACAAACCCAAAATCGAATTTAA
29154942 AAACAAACCCAAAATCGAATTTAA
1 AAACAAACCCAAAATCGAATTTAA
29154966 A
1 A
29154967 CTTTTACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.18
Consensus pattern (24 bp):
AAACAAACCCAAAATCGAATTTAA
Found at i:29155642 original size:15 final size:15
Alignment explanation
Indices: 29155622--29155654 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29155612 TTTGGTTAGA
*
29155622 TAAATTTGCATGGAT
1 TAAATTTGCATGAAT
29155637 TAAATTTGCATGAAT
1 TAAATTTGCATGAAT
29155652 TAA
1 TAA
29155655 GAGTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (15 bp):
TAAATTTGCATGAAT
Found at i:29156929 original size:40 final size:39
Alignment explanation
Indices: 29156808--29156948 Score: 126
Period size: 40 Copynumber: 3.6 Consensus size: 39
29156798 ACTTCGAGTT
* ** *
29156808 GATGAGACACTGGGTGTCAATTTACTACTTCGAATTAATTC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATT-A-TC
* **
29156849 GATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGTC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTA-TC
*
29156886 GATGAGGCACTGGGTGTCAAACTATTACTTTGAATTATCC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTAT-C
* * *
29156926 GATGAGGTATTGGGTGCCAAACT
1 GATGAGGCACTGGGTGTCAAACT
29156949 GGTGTGTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 19 0.23
38 12 0.15
39 3 0.04
40 33 0.40
41 15 0.18
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTATC
Found at i:29165628 original size:27 final size:30
Alignment explanation
Indices: 29165594--29165655 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
29165584 TATTATTGAT
29165594 TTTTTATTCAT-AAA-A-TTATTTTTATAA
1 TTTTTATTCATAAAACATTTATTTTTATAA
** *
29165621 TTTTTATTTTTAAAACATTTTTTTTTATAA
1 TTTTTATTCATAAAACATTTATTTTTATAA
29165651 TTTTT
1 TTTTT
29165656 GGATATGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 3 0.10
29 1 0.03
30 16 0.55
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTTATTCATAAAACATTTATTTTTATAA
Found at i:29165629 original size:15 final size:15
Alignment explanation
Indices: 29165609--29165655 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
29165599 ATTCATAAAA
29165609 TTATTTTTATAATTT
1 TTATTTTTATAATTT
* *
29165624 TTATTTTTAAAACATT
1 TTATTTTTATAA-TTT
29165640 TT-TTTTTATAATTT
1 TTATTTTTATAATTT
29165654 TT
1 TT
29165656 GGATATGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTTATAATTT
Found at i:29170638 original size:5 final size:5
Alignment explanation
Indices: 29170628--29170653 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29170618 AATATTTATA
29170628 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
29170654 TGAAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:29172110 original size:21 final size:21
Alignment explanation
Indices: 29172086--29172133 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29172076 CATCTTCAGT
*
29172086 AACTTCTTATTCTTCAGCAAC
1 AACTTCTTATTCTGCAGCAAC
* *
29172107 AACTTCTTCTTCTGCAGCAGC
1 AACTTCTTATTCTGCAGCAAC
29172128 AACTTC
1 AACTTC
29172134 CTTCTCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (21 bp):
AACTTCTTATTCTGCAGCAAC
Found at i:29182217 original size:80 final size:80
Alignment explanation
Indices: 29182084--29182371 Score: 380
Period size: 80 Copynumber: 3.6 Consensus size: 80
29182074 TATTGGATTA
* *
29182084 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTATTCCC-GATTGCACTTACGTGCCCCTATTTGT
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTA-CCCCTGATTACACTTACGTGCCCCTATTTGT
* *
29182148 ACTTTGGTACTCATGG
65 ACTTCGGTACTCCTGG
* * *
29182164 TTGCAGTTGCGTGCCCCTGTTTGTACTTTGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
* **
29182229 CTTCGGTATTCCTAA
66 CTTCGGTACTCCTGG
* * * * *
29182244 TTGCACTTATGTGCCCCTGTTTGTACTTCAGTACCCCTGATTGCACTTATGTGCCCATATTTGTA
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
*
29182309 CTTCGGTACCCCTGG
66 CTTCGGTACTCCTGG
* * * *
29182324 TTACACTTACGTGCCCTTGTTTGCACTTCGGTACCCCTGATCACACTT
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTT
29182372 TGGTTCCCCT
Statistics
Matches: 178, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
79 3 0.02
80 175 0.98
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (80 bp):
TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
CTTCGGTACTCCTGG
Found at i:29182350 original size:20 final size:20
Alignment explanation
Indices: 29182084--29182351 Score: 105
Period size: 20 Copynumber: 13.4 Consensus size: 20
29182074 TATTGGATTA
29182084 TTGCACTTACGTGCCCCTGT
1 TTGCACTTACGTGCCCCTGT
* ** *
29182104 TTGTACTT-CGGTATTCCC-GA
1 TTGCACTTAC-GT-GCCCCTGT
*
29182124 TTGCACTTACGTGCCCCTAT
1 TTGCACTTACGTGCCCCTGT
* ** * * * *
29182144 TTGTACTTTGGTACTCATGG
1 TTGCACTTACGTGCCCCTGT
* *
29182164 TTGCAGTTGCGTGCCCCTGT
1 TTGCACTTACGTGCCCCTGT
* ** * *
29182184 TTGTACTTTGGTACCCCTGA
1 TTGCACTTACGTGCCCCTGT
* *
29182204 TTACACTTACGTGCCCCTAT
1 TTGCACTTACGTGCCCCTGT
* *** **
29182224 TTGTACTT-CGGTATTCCTAA
1 TTGCACTTAC-GTGCCCCTGT
*
29182244 TTGCACTTATGTGCCCCTGT
1 TTGCACTTACGTGCCCCTGT
* * *
29182264 TTGTACTT-CAGTACCCCTGA
1 TTGCACTTAC-GTGCCCCTGT
* * *
29182284 TTGCACTTATGTGCCCATAT
1 TTGCACTTACGTGCCCCTGT
* * *
29182304 TTGTACTT-CGGTACCCCTGG
1 TTGCACTTAC-GTGCCCCTGT
* *
29182324 TTACACTTACGTGCCCTTGT
1 TTGCACTTACGTGCCCCTGT
29182344 TTGCACTT
1 TTGCACTT
29182352 CGGTACCCCT
Statistics
Matches: 165, Mismatches: 73, Indels: 20
0.64 0.28 0.08
Matches are distributed among these distances:
19 5 0.03
20 155 0.94
21 5 0.03
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCACTTACGTGCCCCTGT
Found at i:29182371 original size:40 final size:40
Alignment explanation
Indices: 29182083--29182364 Score: 341
Period size: 40 Copynumber: 7.0 Consensus size: 40
29182073 TTATTGGATT
*
29182083 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTATTCCC-G
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTA-CCCCTG
* * * *
29182123 ATTGCACTTACGTGCCCCTATTTGTACTTTGGTACTCATG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
29182163 GTTGCAGTTGCGTGCCCCTGTTTGTACTTTGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * ** *
29182203 ATTACACTTACGTGCCCCTATTTGTACTTCGGTATTCCTA
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* *
29182243 ATTGCACTTATGTGCCCCTGTTTGTACTTCAGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * *
29182283 ATTGCACTTATGTGCCCATATTTGTACTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
29182323 GTTACACTTACGTGCCCTTGTTTGCACTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
29182363 AT
1 AT
29182365 CACACTTTGG
Statistics
Matches: 204, Mismatches: 37, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.00
40 203 1.00
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:29187462 original size:18 final size:17
Alignment explanation
Indices: 29187429--29187467 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
29187419 TTTTATAAAT
29187429 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
29187447 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
29187464 TGTG
1 TGTG
29187468 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:29187720 original size:23 final size:23
Alignment explanation
Indices: 29187694--29187814 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
29187684 TTGTTATTGA
29187694 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
29187717 TCAGTGGTAGCTACGGCTACATAT
1 TCAGTGGTAGCTTCGGCTACAT-T
*
29187741 T-AGTGGTAGCTTCAGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
29187763 TCAGTGGTAGCTACGGCTACGTA
1 TCAGTGGTAGCTTCGGCTACATT
*
29187786 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
29187809 TCAGTG
1 TCAGTG
29187815 TGGCACTTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.02
23 83 0.95
24 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:29187749 original size:46 final size:46
Alignment explanation
Indices: 29187693--29187814 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
29187683 ATTGTTATTG
29187693 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* * *
29187739 ATTAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
29187785 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
29187815 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:29194496 original size:18 final size:18
Alignment explanation
Indices: 29194473--29194507 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29194463 TGCTTCGGCG
29194473 ACGTAATGTAATATCATT
1 ACGTAATGTAATATCATT
29194491 ACGTAATGTAATATCAT
1 ACGTAATGTAATATCAT
29194508 ACACTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
ACGTAATGTAATATCATT
Found at i:29199145 original size:6 final size:6
Alignment explanation
Indices: 29199134--29199191 Score: 80
Period size: 6 Copynumber: 9.3 Consensus size: 6
29199124 AGAGGAGACG
* *
29199134 GATTTA GATTTA GATCTTT GGATTTT GATTTT GATTTT GATTTT GATTTT
1 GATTTT GATTTT GAT-TTT -GATTTT GATTTT GATTTT GATTTT GATTTT
29199184 GATTTT GA
1 GATTTT GA
29199192 AATTGGAGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
6 41 0.84
7 5 0.10
8 3 0.06
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:29200190 original size:22 final size:22
Alignment explanation
Indices: 29200147--29200190 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29200137 TTTTAATAAT
*
29200147 AAAAATATTTTTACTTTCATTCC
1 AAAAATATTTTTA-TTTAATTCC
29200170 AAAAAGTATTTTT-TTTAATTC
1 AAAAA-TATTTTTATTTAATTC
29200191 AATTTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAAATATTTTTATTTAATTCC
Found at i:29207571 original size:31 final size:31
Alignment explanation
Indices: 29207530--29207590 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
29207520 TGTATTTTTT
29207530 TAATTAAGTGACTAA-AATGAAAATTTACCCA
1 TAATTAAGTGACTAATAATG-AAATTTACCCA
* *
29207561 TAATTTAGTGACTAATAATGTAATTTACCC
1 TAATTAAGTGACTAATAATGAAATTTACCC
29207591 TCACATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
TAATTAAGTGACTAATAATGAAATTTACCCA
Found at i:29208181 original size:18 final size:19
Alignment explanation
Indices: 29208134--29208186 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
29208124 AAAAAGAGCT
*
29208134 AAAACAAAACACGAAGTTCA
1 AAAACAAAACAC-AACTTCA
* *
29208154 AAACCCAAACA-AACTTCA
1 AAAACAAAACACAACTTCA
*
29208172 AAAACAAAACCCAAC
1 AAAACAAAACACAAC
29208187 CTATAACACT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 14 0.54
19 3 0.12
20 9 0.35
ACGTcount: A:0.60, C:0.28, G:0.04, T:0.08
Consensus pattern (19 bp):
AAAACAAAACACAACTTCA
Found at i:29209519 original size:34 final size:34
Alignment explanation
Indices: 29209471--29209537 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
29209461 TGATTATACT
29209471 GGTAACAAGCCACGAAGCAATCAAGAATCAAACC
1 GGTAACAAGCCACGAAGCAATCAAGAATCAAACC
* *
29209505 GGTAACAAGGCACGAGGCAATCAAGAATCAAAC
1 GGTAACAAGCCACGAAGCAATCAAGAATCAAAC
29209538 TCTTCCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (34 bp):
GGTAACAAGCCACGAAGCAATCAAGAATCAAACC
Found at i:29221297 original size:16 final size:16
Alignment explanation
Indices: 29221273--29221303 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29221263 TGTTTAGTTT
29221273 ACTGGAATGAAATAAG
1 ACTGGAATGAAATAAG
*
29221289 ACTGTAATGAAATAA
1 ACTGGAATGAAATAA
29221304 CTATTTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (16 bp):
ACTGGAATGAAATAAG
Found at i:29222594 original size:69 final size:69
Alignment explanation
Indices: 29222446--29222635 Score: 253
Period size: 67 Copynumber: 2.8 Consensus size: 69
29222436 CATAAATAAA
* * * *
29222446 AAAAAGTTATATTACTCCACCACCGCACCCAATTATACATACAAAAAGTG--AACCTACAATGAC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
29222509 ATAC
66 ATAC
* * * *
29222513 AAAAAGTGATATTAGTCCACTACCACACCTATTTACACATACAAAAAGTGACAACCTACAATTAC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
*
29222578 ATAT
66 ATAC
* *
29222582 GAAAAGTTATATTAGTTCACCACCACACCCATTTACAC--ACAAAAAGTGACAACC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACC
29222636 CTCTATGGTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
67 59 0.55
69 48 0.45
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (69 bp):
AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
ATAC
Found at i:29223162 original size:17 final size:16
Alignment explanation
Indices: 29223121--29223162 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
29223111 AATTCAATTT
*
29223121 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
29223137 T-ATACTAAACAATTCAA
1 TAATA-TAAA-AATTCAA
29223154 TAATATAAA
1 TAATATAAA
29223163 TAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 11 0.50
18 3 0.14
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:29223798 original size:9 final size:9
Alignment explanation
Indices: 29223781--29223811 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29223771 TCGAGTTGAT
29223781 TCGAATAAC
1 TCGAATAAC
*
29223790 TCGATTAAC
1 TCGAATAAC
29223799 TCGAATAAC
1 TCGAATAAC
29223808 TCGA
1 TCGA
29223812 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:29225430 original size:27 final size:27
Alignment explanation
Indices: 29225400--29225458 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
29225390 GGATTTTTTT
* *
29225400 ATTTTTTTAT-TTTTTATTCTTTTCAAA
1 ATTTTTTTATCTTTCT-TTCTTTCCAAA
* *
29225427 ATTTGTTTCTCTTTCTTTCTTTCCAAA
1 ATTTTTTTATCTTTCTTTCTTTCCAAA
29225454 ATTTT
1 ATTTT
29225459 GACGTTGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTTTTTTATCTTTCTTTCTTTCCAAA
Found at i:29230328 original size:18 final size:17
Alignment explanation
Indices: 29230307--29230354 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
29230297 TAAATAAATA
*
29230307 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAA-TGAAC
*
29230325 AATGATTTGTAAATGAAC
1 AATGTTTTG-AAATGAAC
*
29230343 AATATTTTGAAA
1 AATGTTTTGAAA
29230355 ACGAACGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.40
Consensus pattern (17 bp):
AATGTTTTGAAATGAAC
Found at i:29230733 original size:25 final size:25
Alignment explanation
Indices: 29230670--29230751 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
29230660 TTAAACTGAA
* *
29230670 ACTGAAACTATCT-TTGATAGTATAT
1 ACTGAAACTA-CTATAGGTAGTATAT
* *
29230695 CCTGAAACTGCTATAGGTAGTATAT
1 ACTGAAACTACTATAGGTAGTATAT
* * *
29230720 ATTGAGACTACTATAGATA-TACTAT
1 ACTGAAACTACTATAGGTAGTA-TAT
29230745 ACTGAAA
1 ACTGAAA
29230752 ACACTTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
24 4 0.09
25 40 0.91
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (25 bp):
ACTGAAACTACTATAGGTAGTATAT
Found at i:29238260 original size:9 final size:9
Alignment explanation
Indices: 29238248--29238315 Score: 75
Period size: 9 Copynumber: 7.4 Consensus size: 9
29238238 AAAAATAAAA
29238248 AATTCGGGT
1 AATTCGGGT
29238257 AATTTTC-GGT
1 AA--TTCGGGT
*
29238267 AATTCGGTT
1 AATTCGGGT
* *
29238276 AATTTGGTT
1 AATTCGGGT
29238285 AATTCGGGT
1 AATTCGGGT
29238294 AATTCGGGT
1 AATTCGGGT
*
29238303 AATTCGAGT
1 AATTCGGGT
29238312 AATT
1 AATT
29238316 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.06
9 40 0.78
10 5 0.10
11 3 0.06
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:29240568 original size:24 final size:24
Alignment explanation
Indices: 29240525--29240706 Score: 109
Period size: 24 Copynumber: 7.6 Consensus size: 24
29240515 CATACACATA
* * *
29240525 ACACCCGCGAACCCCTATCACTAG
1 ACACCTGCAAACCCCTATCACCAG
*
29240549 -CTACCTGCAAACCCCAATCACCAG
1 AC-ACCTGCAAACCCCTATCACCAG
** * *
29240573 ACATTTGCGAACCCCTATCACTAG
1 ACACCTGCAAACCCCTATCACCAG
* * *
29240597 ACACATGCGAACCCCTATCGCCAG
1 ACACCTGCAAACCCCTATCACCAG
* **
29240621 -CTACCTACAAACCCCTATCATTAG
1 AC-ACCTGCAAACCCCTATCACCAG
* **
29240645 ACACATGTGAACCCCTATCACCAG
1 ACACCTGCAAACCCCTATCACCAG
* * * *
29240669 -CTACTTGCGAACCCTTATCACCAA
1 AC-ACCTGCAAACCCCTATCACCAG
* *
29240693 ACACATGCGAACCC
1 ACACCTGCAAACCC
29240707 TTTAATGTAT
Statistics
Matches: 122, Mismatches: 30, Indels: 12
0.74 0.18 0.07
Matches are distributed among these distances:
23 3 0.02
24 116 0.95
25 3 0.02
ACGTcount: A:0.31, C:0.40, G:0.11, T:0.18
Consensus pattern (24 bp):
ACACCTGCAAACCCCTATCACCAG
Found at i:29240610 original size:48 final size:48
Alignment explanation
Indices: 29240531--29240706 Score: 203
Period size: 48 Copynumber: 3.7 Consensus size: 48
29240521 CATAACACCC
* * * *
29240531 GCGAACCCCTATCACTAG-CTACCTGCAAACCCCAATCACCAGAC-ATTT
1 GCGAACCCCTATCACTAGAC-ACATGCGAACCCCTATCACCAG-CTACTT
* *
29240579 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCGCCAGCTACCT
1 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
* * * *
29240627 ACAAACCCCTATCATTAGACACATGTGAACCCCTATCACCAGCTACTT
1 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
* * *
29240675 GCGAACCCTTATCACCAAACACATGCGAACCC
1 GCGAACCCCTATCACTAGACACATGCGAACCC
29240707 TTTAATGTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.01
48 105 0.98
49 1 0.01
ACGTcount: A:0.31, C:0.39, G:0.11, T:0.18
Consensus pattern (48 bp):
GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
Found at i:29240657 original size:72 final size:72
Alignment explanation
Indices: 29240531--29240691 Score: 198
Period size: 72 Copynumber: 2.2 Consensus size: 72
29240521 CATAACACCC
* * ** *
29240531 GCGAACCCCTATCACTAGCTACCTGCAAACCCCAATCACCAGACATTTGCGAACCCCTATCACTA
1 GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
29240596 GAC-ACAT
66 G-CTACAT
* * ** *
29240603 GCGAACCCCTATCGCCAGCTACCTACAAACCCCTATCATTAGACACATGTGAACCCCTATCACCA
1 GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
*
29240668 GCTACTT
66 GCTACAT
*
29240675 GCGAACCCTTATCACCA
1 GCGAACCCCTATCACCA
29240692 AACACATGCG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
71 1 0.01
72 74 0.99
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.19
Consensus pattern (72 bp):
GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
GCTACAT
Found at i:29241929 original size:14 final size:15
Alignment explanation
Indices: 29241910--29241939 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29241900 TCTTTCCTTT
29241910 TTATTTTT-TTTTTC
1 TTATTTTTCTTTTTC
29241924 TTATTTTTCTTTTTC
1 TTATTTTTCTTTTTC
29241939 T
1 T
29241940 GGGCATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (15 bp):
TTATTTTTCTTTTTC
Found at i:29242140 original size:39 final size:39
Alignment explanation
Indices: 29242057--29242140 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
29242047 TTCTTCTGTC
*
29242057 AAATTCTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
1 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
29242096 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
1 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
29242135 AAATTT
1 AAATTT
29242141 GTCCTCACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (39 bp):
AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
Found at i:29242843 original size:13 final size:12
Alignment explanation
Indices: 29242817--29242853 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
29242807 GTAGCAGCCC
29242817 AGAAAAAAGAAAA
1 AGAAAAAAG-AAA
29242830 AGAACAAAAGAAA
1 AGAA-AAAAGAAA
29242843 AGAAAAAAGAA
1 AGAAAAAAGAA
29242854 GAGGAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 11 0.48
14 5 0.22
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:29244677 original size:18 final size:18
Alignment explanation
Indices: 29244653--29244698 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
29244643 TTTTTTATTT
29244653 TTCATATTCGTTTTACGA
1 TTCATATTCGTTTTACGA
* **
29244671 TTTATATTTATTTTACGA
1 TTCATATTCGTTTTACGA
29244689 TTCATATTCG
1 TTCATATTCG
29244699 AGGTTCAGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (18 bp):
TTCATATTCGTTTTACGA
Found at i:29244892 original size:15 final size:15
Alignment explanation
Indices: 29244860--29244892 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29244850 CGATTAAGGT
29244860 CATAATTCATAACGC
1 CATAATTCATAACGC
29244875 CATAAGTTCATAAC-C
1 CATAA-TTCATAACGC
29244890 CAT
1 CAT
29244893 TTACACACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (15 bp):
CATAATTCATAACGC
Done.