Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, 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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 51
Found at i:2539038 original size:41 final size:41
Alignment explanation
Indices: 2538901--2539036 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
2538891 CGCTTTGAAA
* *
2538901 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTACGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
2538942 ATCGCGTTACGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTACGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * * *
2538982 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTACGATTATGTATTATCGCGTTGCGAAAGTCAGT
2539023 ATCGCATTACGATT
1 ATCGCATTACGATT
2539037 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.40
41 40 0.53
42 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTACGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2539049 original size:41 final size:41
Alignment explanation
Indices: 2539004--2539112 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 41
2538994 TTTTGTATTA
2539004 TCGCATTGCGATAGTCA-GTA-TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGAT--TCACGTATTCGCATTACGATTTTCCCAAT
* * * *
2539045 TCGCATTTCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
* * * *
2539086 TCGCGTTGCGATTTACTTATTCACATT
1 TCGCATTGCGATTCACGTATTCGCATT
2539113 GCGAATTGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 55 0.93
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
Found at i:2539050 original size:21 final size:21
Alignment explanation
Indices: 2539024--2539099 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2539014 ATAGTCAGTA
*
2539024 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2539045 TCGCATTTCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2539065 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
2539086 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
2539100 ACTTATTCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2539068 original size:20 final size:20
Alignment explanation
Indices: 2539043--2539116 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
2539033 GATTTTCCCA
*
2539043 ATTCGCATTTCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
2539063 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
2539084 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
*
2539104 ATTCACATTGCGA
1 ATTCGCATTGCGA
2539117 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:2539113 original size:41 final size:41
Alignment explanation
Indices: 2539027--2539116 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
2539017 GTCAGTATCG
* * *
2539027 CATTACGATTTTCCCAATTCGCATTTCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
*
2539068 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1 CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
2539109 CATTGCGA
1 CATTGCGA
2539117 ATTGGGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
Found at i:2540038 original size:121 final size:121
Alignment explanation
Indices: 2539824--2540057 Score: 378
Period size: 121 Copynumber: 1.9 Consensus size: 121
2539814 ATATTTGCGA
* * *
2539824 AAATCCATCGAACAATATCACCAATTATTGGACTCCGAGGTAATATGTCAATATGTGAAGGTGTT
1 AAATCCATCGAACAATATCACCAACTATTGAACTCCGAGGTAATATGCCAATATGTGAAGGTGTT
*
2539889 GGTGAACAACAGTCAAAGATCCTTTGTTCAGTGATAGTTACATTTATTTGGCATAG
66 GGTGAACAAAAGTCAAAGATCCTTTGTTCAGTGATAGTTACATTTATTTGGCATAG
* ** *
2539945 AAATCCGTCGAACAATATCACTGACTATTGAACTCTGAGGTAATATGCCAATATGTGAAGGTGTT
1 AAATCCATCGAACAATATCACCAACTATTGAACTCCGAGGTAATATGCCAATATGTGAAGGTGTT
* *
2540010 GGTGAACAAAATTCAAAGATCCTTTGTTCAGTGTTAGTTACATTTATT
66 GGTGAACAAAAGTCAAAGATCCTTTGTTCAGTGATAGTTACATTTATT
2540058 CGAGACCAGT
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 103 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (121 bp):
AAATCCATCGAACAATATCACCAACTATTGAACTCCGAGGTAATATGCCAATATGTGAAGGTGTT
GGTGAACAAAAGTCAAAGATCCTTTGTTCAGTGATAGTTACATTTATTTGGCATAG
Found at i:2543022 original size:24 final size:20
Alignment explanation
Indices: 2542968--2543007 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2542958 AATATTTGGG
2542968 GTTTATTGGCCTAATGGATC
1 GTTTATTGGCCTAATGGATC
2542988 GTTTATTGGCCTAATGGATC
1 GTTTATTGGCCTAATGGATC
2543008 ATGTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTTATTGGCCTAATGGATC
Found at i:2546184 original size:62 final size:62
Alignment explanation
Indices: 2546087--2546211 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
2546077 ATTTAAAGGA
2546087 TCGACATAAGTCCACTCGTATTCATACCATTATGAATATCTATATTAAAGAGAAAAGTCAAC
1 TCGACATAAGTCCACTCGTATTCATACCATTATGAATATCTATATTAAAGAGAAAAGTCAAC
2546149 TCGACATAAGTCCACTCGTATTCATACCATTATGAATATCTATATTAAAGAGAAAAGTCAAC
1 TCGACATAAGTCCACTCGTATTCATACCATTATGAATATCTATATTAAAGAGAAAAGTCAAC
2546211 T
1 T
2546212 GAAGTGGACA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (62 bp):
TCGACATAAGTCCACTCGTATTCATACCATTATGAATATCTATATTAAAGAGAAAAGTCAAC
Found at i:2548784 original size:43 final size:41
Alignment explanation
Indices: 2548725--2548808 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 41
2548715 ACTAATTTAC
* *
2548725 TAATAGATAATAAAAAATAATAAATTACTAATATATTAATTTT
1 TAATAAATAATAAAAAATAATAAATTAATAAT-TATT-ATTTT
* *
2548768 TAATAAATAATTAAAAATATTAAATTAATAATTATTATTTT
1 TAATAAATAATAAAAAATAATAAATTAATAATTATTATTTT
2548809 ACTACACCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 5 0.14
42 4 0.11
43 28 0.76
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (41 bp):
TAATAAATAATAAAAAATAATAAATTAATAATTATTATTTT
Found at i:2555074 original size:32 final size:32
Alignment explanation
Indices: 2555006--2555093 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
2554996 ATAGTGACTT
* * *
2555006 CACTTCGTCGGTCGATCTT-CCTTTCCCTCGC
1 CACTTCGTCGGCCGATCTTCCCCTTCCCTAGC
* *
2555037 CACTTCGTCGGCCTATCTTCCCCTTCCCTAGT
1 CACTTCGTCGGCCGATCTTCCCCTTCCCTAGC
*
2555069 GACTTC-TACGGCCGATCTTCCCCTT
1 CACTTCGT-CGGCCGATCTTCCCCTT
2555094 TCGAGTTCTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 18 0.38
32 30 0.62
ACGTcount: A:0.09, C:0.42, G:0.15, T:0.34
Consensus pattern (32 bp):
CACTTCGTCGGCCGATCTTCCCCTTCCCTAGC
Found at i:2555696 original size:15 final size:15
Alignment explanation
Indices: 2555676--2555706 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2555666 TTTTTAGGAA
2555676 AAATAGTTACTAATT
1 AAATAGTTACTAATT
2555691 AAATAGTTACTAATT
1 AAATAGTTACTAATT
2555706 A
1 A
2555707 TGGATTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AAATAGTTACTAATT
Found at i:2556601 original size:29 final size:29
Alignment explanation
Indices: 2556569--2556626 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2556559 TTGTTTAATC
2556569 GGTTTCTAATTTGAATCTTGTATTTATTT
1 GGTTTCTAATTTGAATCTTGTATTTATTT
* *
2556598 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGAATCTTGTATTTATTT
2556627 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (29 bp):
GGTTTCTAATTTGAATCTTGTATTTATTT
Found at i:2563618 original size:18 final size:18
Alignment explanation
Indices: 2563595--2563630 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2563585 CGATGATAAA
2563595 GCACCCAGGAGAGTCCGG
1 GCACCCAGGAGAGTCCGG
2563613 GCACCCAGGAGAGTCCGG
1 GCACCCAGGAGAGTCCGG
2563631 TCAGTAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.39, T:0.06
Consensus pattern (18 bp):
GCACCCAGGAGAGTCCGG
Found at i:2567294 original size:25 final size:25
Alignment explanation
Indices: 2567250--2567299 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2567240 AATTTTAAAA
*
2567250 TAAAAATAAAAATATATATTTAGAT
1 TAAAAATAAAAATATATATTAAGAT
*
2567275 TAAAAATACAAATA-ATTATTAAGAT
1 TAAAAATAAAAATATA-TATTAAGAT
2567300 ATTCAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (25 bp):
TAAAAATAAAAATATATATTAAGAT
Found at i:2568591 original size:26 final size:28
Alignment explanation
Indices: 2568527--2568591 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 28
2568517 TATATTTTTT
*
2568527 ATTAATAATA-T-ATTTTCAATTTTAAA
1 ATTAATAATATTCATTTTCAATTCTAAA
*
2568553 ATTTTATAA-ATTCATTTT-AA-TCTAAA
1 A-TTAATAATATTCATTTTCAATTCTAAA
2568579 ATTAATAATATTC
1 ATTAATAATATTC
2568592 GTAATTTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 6 0.19
26 12 0.38
27 9 0.28
28 5 0.16
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTAATAATATTCATTTTCAATTCTAAA
Found at i:2569169 original size:42 final size:45
Alignment explanation
Indices: 2569123--2569208 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 45
2569113 CAGAGATAAA
*
2569123 AATATATGATTAATAGAAAATA-T-AAAAA-ATATATGAAATTTC
1 AATATATGATTAACAGAAAATATTAAAAAATATATATGAAATTTC
**
2569165 AATATATTCTTAACAGAAAATATTAAAAAATATATATGAAATTT
1 AATATATGATTAACAGAAAATATTAAAAAATATATATGAAATTT
2569209 TAAAATTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 19 0.50
43 1 0.03
44 5 0.13
45 13 0.34
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (45 bp):
AATATATGATTAACAGAAAATATTAAAAAATATATATGAAATTTC
Found at i:2572797 original size:19 final size:21
Alignment explanation
Indices: 2572768--2572839 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 21
2572758 AAGGATAGAT
2572768 TTACA-ATATAAGCATA-CTA
1 TTACATATATAAGCATACCTA
* *
2572787 -TACATATATAAACGTACCTA
1 TTACATATATAAGCATACCTA
*
2572807 TTACATTATATAAGCGTACCTA
1 TTACA-TATATAAGCATACCTA
2572829 TTACATCATAT
1 TTACAT-ATAT
2572840 TTACCTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.09
19 9 0.20
20 3 0.07
21 5 0.11
22 24 0.53
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.35
Consensus pattern (21 bp):
TTACATATATAAGCATACCTA
Found at i:2572819 original size:22 final size:22
Alignment explanation
Indices: 2572787--2572839 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2572777 AAGCATACTA
2572787 TACA-TATATAAACGTACCTAT
1 TACATTATATAAACGTACCTAT
*
2572808 TACATTATATAAGCGTACCTAT
1 TACATTATATAAACGTACCTAT
*
2572830 TACATCATAT
1 TACATTATAT
2572840 TTACCTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
TACATTATATAAACGTACCTAT
Found at i:2573202 original size:20 final size:20
Alignment explanation
Indices: 2573174--2573221 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2573164 ATAGATACTT
* *
2573174 TACAATATAAGCACTACCTA
1 TACATTATAAACACTACCTA
*
2573194 TACATTATAAACGCTACCTA
1 TACATTATAAACACTACCTA
2573214 -ACATTATA
1 TACATTATA
2573222 TAAGCGCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (20 bp):
TACATTATAAACACTACCTA
Found at i:2573229 original size:21 final size:21
Alignment explanation
Indices: 2573178--2573244 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
2573168 ATACTTTACA
*
2573178 ATATAAGCACTACCTATACATT
1 ATATAAGCGCTACCTA-ACATT
2573200 ATA-AA-CGCTACCTAACATT
1 ATATAAGCGCTACCTAACATT
*
2573219 ATATAAGCGCTACCTAAACATC
1 ATATAAGCGCTACCT-AACATT
2573241 ATAT
1 ATAT
2573245 TTACCTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.20
20 10 0.25
21 10 0.25
22 12 0.30
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (21 bp):
ATATAAGCGCTACCTAACATT
Found at i:2573508 original size:410 final size:417
Alignment explanation
Indices: 2572633--2574266 Score: 2540
Period size: 410 Copynumber: 4.0 Consensus size: 417
2572623 TTAATAATAT
*
2572633 ATATATTGT-ACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT-AAACT
1 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
2572696 CACTCAAAAGATAACCTTAAATT-ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTAT-AAA
66 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
2572759 AGGATAG--A-TTTACAATATAAGCA-TA-CTATACATATATAAACG-TACCTATTACATTATAT
131 AGGATAGATACTTTACAATATAAGCACTACCTATACATATATAAACGATACCTA-TACATTATAT
*
2572818 AAGCG-TACCTATTACATCATA-TTTACC--TATATTAAAAGTGTCCATACTTTTTATAAAAAGG
195 AAGCGCTACCTATTACATCATATTTTACCTATATATTGAAAGTGTCCATACTTTTTATAAAAAGG
*
2572879 ATCGATACTT-TTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGTGTTTCATATTTTCC
260 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGTGTTTCATGTTTTCC
2572943 A-CTACAATATTAATTTAATAATT--TTTACACAAAAAA-TA-TTGATTG-TTTGATATTTTATA
325 ACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATA
* * *
2573002 AATATA-TTAGAATTTTTAATTTAATAATA
390 AAAATATTTAGAA-TTTAAATTTAACAA-A
**
2573031 TATATATCGTAACGTAAAAAATAAATCATTAGACGGGTATAATTACTAAATTAATATCTTAAAAC
1 -ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
2573096 TCACTCAAAAGATAACCTTAAATTAATG-TTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
65 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
*
2573160 AAGGATAGATACTTTACAATATAAGCACTACCTATACAT-TATAAACGCTACCTA-ACATTATAT
130 AAGGATAGATACTTTACAATATAAGCACTACCTATACATATATAAACGATACCTATACATTATAT
* *
2573223 AAGCGCTACCTA-AACATCATA-TTTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAAAA
195 AAGCGCTACCTATTACATCATATTTTACCTA-TATATTGAAAGTGTCCATACTTTTTATAAAAAG
2573285 GATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
259 GATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTT
* *
2573350 CCACTTACAATATTAATTTAATAATTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTA
323 CCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
*
2573414 TAAAAATATTTAGAATTTTAATTTAACAAA
388 TAAAAATATTTAGAATTTAAATTTAACAAA
*
2573444 ATATATCGTAACGT-AAAAA-AAATCATTAGACGCGTATAATTACTAAATTAATATCTTAAAACT
1 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
* *
2573507 CACTCAAAAGAT-ACCTTAAATTAATGTTTTCCACAGTGAAAACAGTATAGACAC-TTTATAAAA
66 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
*
2573570 AGGATAGATACTTTACAATATAAGCACTACCTAT-TAT-TATAAACGATACCTATTACATTATAT
131 AGGATAGATACTTTACAATATAAGCACTACCTATACATATATAAACGATACCTA-TACATTATAT
2573633 AAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA-TGTCCATACTTTTTATAAAAA
195 AAGCGCTACCTATTACATCATA-TTTTACCTA-TATATTGAAAGTGTCCATACTTTTTATAAAAA
*
2573697 TGATCGATACTTC-TTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTT
258 GGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTT
*
2573761 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTT
322 TCCACCTACAATATTAATTTAATAA-TTCATTTACACAAAAAATTATTTGATTGTTTTGATATTT
2573826 TATAAAATATTATTTAGAATTTAAATTTAAC-AA
386 TATAAAA-A-TATTTAGAATTTAAATTTAACAAA
*
2573859 A-ATATCGTAACGTAAAAAATAAATCATTAG-TGCCTATAATTACTAAATTAATATCTTAAAACT
1 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
*
2573922 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT--AGACTTTTATAAAA
66 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
* *
2573985 AGGATAGATACTTTACAATA-AACCACTACCTATTACATTATATAAACGATACCTATTACTTTAT
131 AGGATAGATACTTTACAATATAAGCACTACCTA-TACA-TATATAAACGATACCTA-TACATTAT
2574049 ATAAGCGCTACC---TACATCATATTTTACCTAT-TATTGAAAGTGTCCATACTTTTTATAAAAA
193 ATAAGCGCTACCTATTACATCATATTTTACCTATATATTGAAAGTGTCCATACTTTTTATAAAAA
*
2574110 GGATCGATAC-TCTTTTAAAGTTATGTAA-TTATGTTTCAATTTTTTAACAGTGTTTCATG-TTT
258 GGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGTGTTTCATGTTTT
2574172 CCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
323 CCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
2574237 TAAATAATATTTAGAATTTAAATTTAACAA
388 TAAA-AATATTTAGAATTTAAATTTAACAA
2574267 CATTAACCAA
Statistics
Matches: 1159, Mismatches: 30, Indels: 82
0.91 0.02 0.06
Matches are distributed among these distances:
399 8 0.01
400 47 0.04
401 61 0.05
402 13 0.01
404 1 0.00
405 43 0.04
406 16 0.01
407 36 0.03
408 84 0.07
409 129 0.11
410 150 0.13
411 37 0.03
412 127 0.11
413 107 0.09
414 101 0.09
415 97 0.08
416 66 0.06
417 1 0.00
418 35 0.03
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (417 bp):
ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
AGGATAGATACTTTACAATATAAGCACTACCTATACATATATAAACGATACCTATACATTATATA
AGCGCTACCTATTACATCATATTTTACCTATATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGTGTTTCATGTTTTCCA
CCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAA
AAATATTTAGAATTTAAATTTAACAAA
Found at i:2573619 original size:19 final size:21
Alignment explanation
Indices: 2573587--2573647 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
2573577 ATACTTTACA
2573587 ATATAAGC-ACTACCTATTATT
1 ATATAAGCGA-TACCTATTATT
2573608 ATA-AA-CGATACCTATTACATT
1 ATATAAGCGATACCTATT--ATT
*
2573629 ATATAAGCGCTACCTATTA
1 ATATAAGCGATACCTATTA
2573648 CATCATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 10 0.29
22 2 0.06
23 10 0.29
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (21 bp):
ATATAAGCGATACCTATTATT
Found at i:2573642 original size:23 final size:23
Alignment explanation
Indices: 2573587--2573655 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
2573577 ATACTTTACA
*
2573587 ATATAAGCACTACCTATT--ATT
1 ATATAAGCGCTACCTATTACATT
*
2573608 ATA-AA-CGATACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2573629 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2573652 ATAT
1 ATAT
2573656 TTTTACCTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.22
20 2 0.05
21 9 0.22
22 2 0.05
23 18 0.45
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2573715 original size:21 final size:21
Alignment explanation
Indices: 2573673--2573715 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2573663 TATTATATTG
*
2573673 AAATGTCCATACTTTTTATAA
1 AAATGTCCATACTTCTTATAA
*
2573694 AAATGATCGATACTTCTT-TAA
1 AAATG-TCCATACTTCTTATAA
2573715 A
1 A
2573716 GTTATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATGTCCATACTTCTTATAA
Found at i:2574039 original size:23 final size:23
Alignment explanation
Indices: 2574002--2574062 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
2573992 ATACTTTACA
*
2574002 ATAAACCACTACCTATTACATTAT
1 ATAAACGA-TACCTATTACATTAT
*
2574026 ATAAACGATACCTATTACTTTAT
1 ATAAACGATACCTATTACATTAT
* *
2574049 ATAAGCGCTACCTA
1 ATAAACGATACCTA
2574063 CATCATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 26 0.79
24 7 0.21
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (23 bp):
ATAAACGATACCTATTACATTAT
Found at i:2574431 original size:25 final size:25
Alignment explanation
Indices: 2574403--2574467 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
2574393 ACTCAAAAGA
*
2574403 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2574428 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2574453 TGTACATACCTAAAT
1 TGTACATACCTAAAT
2574468 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:2576106 original size:19 final size:19
Alignment explanation
Indices: 2576060--2576108 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2576050 TTATATTCAC
*
2576060 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
2576079 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
2576098 ATACAAAATTA
1 ATACAAAATTA
2576109 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2577934 original size:33 final size:33
Alignment explanation
Indices: 2577897--2577962 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2577887 CATCTTAATA
*
2577897 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
2577930 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2577963 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2578021 original size:21 final size:21
Alignment explanation
Indices: 2577996--2578039 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2577986 CCCCTTATGC
2577996 CTCTCAAGTGTT-TCTTCGACT
1 CTCTCAAGT-TTCTCTTCGACT
2578017 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2578038 CT
1 CT
2578040 TGATTGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.14, C:0.32, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2580268 original size:17 final size:18
Alignment explanation
Indices: 2580246--2580288 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2580236 ATATATCCGG
2580246 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2580263 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2580283 TATCAT
1 TATCAT
2580289 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2580306 original size:20 final size:19
Alignment explanation
Indices: 2580251--2580297 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2580241 TCCGGTATCA
2580251 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2580270 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2580291 TTTTACC
1 TTTTACC
2580298 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2580459 original size:20 final size:20
Alignment explanation
Indices: 2580432--2580478 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2580422 TCCGGTAACG
2580432 TTTTACCGATTTTATCAT-T
1 TTTTACCGATTTTATCATAT
*
2580451 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCATAT
2580472 TTTTACC
1 TTTTACC
2580479 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGATTTTATCATAT
Found at i:2580522 original size:181 final size:182
Alignment explanation
Indices: 2580218--2580690 Score: 734
Period size: 181 Copynumber: 2.6 Consensus size: 182
2580208 CGTACTTACG
* *
2580218 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2580283 TATCATATTTTTACCTGTTATATCGTTATGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
2580348 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
2580399 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGATTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2580464 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
2580529 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * *
2580581 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
2580645 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2580691 AATTTGGATC
Statistics
Matches: 266, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 167 0.63
182 98 0.37
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2581221 original size:228 final size:229
Alignment explanation
Indices: 2580757--2581243 Score: 879
Period size: 229 Copynumber: 2.1 Consensus size: 229
2580747 ACCTACTTTT
2580757 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
2580822 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
* *
2580887 GAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAT
131 AAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
2580952 CAAATATAATAATAAATATGTTTTCCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCCACAGTGAA
2580986 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
*
2581051 A-TTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
* *
2581115 AAAATTATTTGATTGTTTTGATATTTTATAAATTATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
2581180 CCAAAGATAATAATAAATATATTTT-CACAGTGAA
195 CCAAAGATAATAATAAATATATTTTCCACAGTGAA
*
2581214 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
2581244 GATGCTTTAC
Statistics
Matches: 249, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
228 113 0.45
229 136 0.55
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (229 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
AAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCCACAGTGAA
Found at i:2584573 original size:29 final size:30
Alignment explanation
Indices: 2584540--2584613 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
2584530 TATGGTCAAA
** *
2584540 AATCAATTTGACCACCGAACT-TTCAATTG
1 AATCAATCAGACCACCCAACTATTCAATTG
*
2584569 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATCAGACCACCCAACTATTCAATTG
** *
2584599 GTTCAATCAAACCAC
1 AATCAATCAGACCAC
2584614 TGGCCGTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (30 bp):
AATCAATCAGACCACCCAACTATTCAATTG
Found at i:2585411 original size:15 final size:16
Alignment explanation
Indices: 2585383--2585416 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2585373 AATTGAACCA
2585383 AAATTTATTGTCTTTT
1 AAATTTATTGTCTTTT
*
2585399 AAATTT-TTTTCTTTT
1 AAATTTATTGTCTTTT
2585414 AAA
1 AAA
2585417 GAATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (16 bp):
AAATTTATTGTCTTTT
Found at i:2585840 original size:20 final size:20
Alignment explanation
Indices: 2585798--2585840 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2585788 ATTAGTCGTG
* * *
2585798 AATAATTTATTTAATCTATT
1 AATAATTTATTTAAACAAAT
*
2585818 AATAGTTTATTTAAACAAAT
1 AATAATTTATTTAAACAAAT
2585838 AAT
1 AAT
2585841 TTGTTTACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAATTTATTTAAACAAAT
Found at i:2590841 original size:21 final size:21
Alignment explanation
Indices: 2590817--2590879 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2590807 GCTTAGAATT
*
2590817 TGTCTCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
2590838 TGTCCCGAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
2590859 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
2590880 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:2594942 original size:21 final size:21
Alignment explanation
Indices: 2594918--2594980 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
2594908 GCTTAGAATT
2594918 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
* *
2594939 TGTCTCAAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
2594960 TGTCCCGAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
2594981 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:2595841 original size:24 final size:20
Alignment explanation
Indices: 2595788--2595845 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2595778 TTCCCATTGA
*
2595788 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
2595808 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
2595831 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2595846 CTACCACGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:2599627 original size:247 final size:248
Alignment explanation
Indices: 2599078--2599723 Score: 880
Period size: 247 Copynumber: 2.5 Consensus size: 248
2599068 CTTATTCATA
* * *
2599078 TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGA--GTC-GAGTTTCTAATTCATTTATTCG
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGAGGGTCGGA-TTTCTAATTCATATATTCG
* *
2599140 GGTCGGGTTGGGTGAAACTTTATTTTGGTAGGGTCAGGTCGGGTTTTTTTAAGTGTGATATTCGG
65 GGTCGGGTCGGGTGAAACTTTATTTT--TA--GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGG
*
2599205 GTCGGGTCAGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTTAC
125 GTC--G---GG-TCGGGTTTAGGGTGAAAAAAACCGAACCGACCCGAAAATATATATAATTTTAC
2599270 CTTATATATTTAGGAATAATTACAATAATACCCCTATATATATTTTTTTTTCAATTAAGTCACTG
184 CTTATATATTTAGGAATAATTACAATAATACCCC---ATATA-TTTTTTTTCAATTAAGTCACTG
2599335 TTTT
245 TTTT
2599339 TATTAAATAAAAATATTTTTTTATTATTTCGGGTC--GGGTCGGATTTCTAATTCATATATT-GG
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGAGGGTCGGATTTCTAATTCATATATTCGG
* * *
2599401 GTCGGGTCGGGTGAAACTTTA-TTTTATTCGGGTCAGGTTTTTTAAGTGTGATATTAGGGTCGGG
66 GTCGGGTCGGGTGAAACTTTATTTTTAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGG
*
2599465 TCGGGTTTAGGGTG-AAAAAACTGAACCGACCCGAAAATATATATAATTTTACCTTATATATTTA
131 TCGGGTTTAGGGTGAAAAAAACCGAACCGACCCGAAAATATATATAATTTTACCTTATATATTTA
*
2599529 GGAATAATTACAATAATACCCC-TCTA-TTTTTTTCAATTAAGTCACTGTTTT
196 GGAATAATTACAATAATACCCCATATATTTTTTTTCAATTAAGTCACTGTTTT
2599580 TATTAAATAAAAATATTTTTTTTATTATTTCGGGTCAAGTAGGGTCGGATTTCTAATTCATATAT
1 TATTAAATAAAAATA-TTTTTTTATTATTTCGGGTC--G-AGGGTCGGATTTCTAATTCATATAT
* *
2599645 TCGGGTTGGGTCGGGTGAAACTTTATTTTGTTCGAGTCGGGTTGGGTTTTTTAAGTGTGATATTC
62 TCGGGTCGGGTCGGGTGAAACTTTA-TTT-TT--AGTCGGGTCGGGTTTTTTAAGTGTGATATTC
*
2599710 GGGTCGAGTCGGGT
123 GGGTCGGGTCGGGT
2599724 CGGGTTTTTT
Statistics
Matches: 353, Mismatches: 17, Indels: 38
0.87 0.04 0.09
Matches are distributed among these distances:
241 40 0.11
242 20 0.06
243 3 0.01
247 95 0.27
248 36 0.10
249 2 0.01
250 2 0.01
251 2 0.01
252 1 0.00
253 40 0.11
254 23 0.07
255 8 0.02
257 2 0.01
259 3 0.01
260 22 0.06
261 52 0.15
262 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (248 bp):
TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGAGGGTCGGATTTCTAATTCATATATTCGG
GTCGGGTCGGGTGAAACTTTATTTTTAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGG
TCGGGTTTAGGGTGAAAAAAACCGAACCGACCCGAAAATATATATAATTTTACCTTATATATTTA
GGAATAATTACAATAATACCCCATATATTTTTTTTCAATTAAGTCACTGTTTT
Found at i:2599723 original size:37 final size:38
Alignment explanation
Indices: 2599676--2599763 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
2599666 TTTATTTTGT
2599676 TCGAGTCGGGTTGGG-TTTTTTAAGTGTGATATTCGGG
1 TCGAGTCGGGTTGGGTTTTTTTAAGTGTGATATTCGGG
*
2599713 TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGAGTCGGGTTGGGTTTTTTTAAGTGTGATATTCGGG
*
2599751 TCGGGTTCGGGTT
1 TCGAG-TCGGGTT
2599764 TAGGGTGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 14 0.30
38 26 0.57
39 6 0.13
ACGTcount: A:0.11, C:0.10, G:0.39, T:0.40
Consensus pattern (38 bp):
TCGAGTCGGGTTGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:2600336 original size:16 final size:18
Alignment explanation
Indices: 2600315--2600360 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2600305 TATGGAATTG
2600315 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
2600331 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
2600349 GATTCCAATTCC
1 GATTCCAATTCC
2600361 CTCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2601318 original size:16 final size:15
Alignment explanation
Indices: 2601292--2601330 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2601282 TGATATAAAA
*
2601292 AATTATTTTTTATTT
1 AATTTTTTTTTATTT
2601307 AATATTTTTTTTATTT
1 AAT-TTTTTTTTATTT
2601323 AATTTTTT
1 AATTTTTT
2601331 AAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
AATTTTTTTTTATTT
Found at i:2605495 original size:8 final size:8
Alignment explanation
Indices: 2605482--2605522 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2605472 CTCATTTTCA
2605482 GAGAATTT
1 GAGAATTT
2605490 GAGAATTT
1 GAGAATTT
*
2605498 -AGAGTTT
1 GAGAATTT
*
2605505 GGGAATTT
1 GAGAATTT
2605513 GAGAATTT
1 GAGAATTT
2605521 GA
1 GA
2605523 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2605828 original size:128 final size:128
Alignment explanation
Indices: 2605593--2606221 Score: 1152
Period size: 128 Copynumber: 4.9 Consensus size: 128
2605583 TAATCGGAGT
2605593 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2605658 CATTGCCCTATTATGTCACTCACGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
2605721 TC-AGGGGACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
2605785 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2605849 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2605914 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2605977 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2606042 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2606105 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2606170 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2606222 AATCAGGTAA
Statistics
Matches: 481, Mismatches: 18, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 479 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2606690 original size:33 final size:34
Alignment explanation
Indices: 2606620--2606719 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
2606610 AAATTTAATG
*
2606620 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * * *
2606654 TTAAATTT-AAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
2606687 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
2606720 AACATTTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 27 0.50
34 27 0.50
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:2606707 original size:39 final size:39
Alignment explanation
Indices: 2606639--2606716 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
2606629 GAATACTATA
2606639 ATTTATATTTTAAATTTAAATTTAAATAATAT-TATTTTT
1 ATTTATATTTTAAATTTAAA-TTAAATAATATGTATTTTT
* * *
2606678 ATTTTTATTTTAAATTTCGAA-TAATATAATTTGTATTTT
1 ATTTATATTTTAAATTT-AAATTAA-ATAATATGTATTTT
2606717 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 3 0.09
39 22 0.67
40 8 0.24
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (39 bp):
ATTTATATTTTAAATTTAAATTAAATAATATGTATTTTT
Found at i:2607269 original size:21 final size:21
Alignment explanation
Indices: 2607239--2607311 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
2607229 TATGGTATAA
*
2607239 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
2607260 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
2607281 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
2607302 AACCCTGCGG
1 AACCCTGCGG
2607312 AGATGGCATA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
20 3 0.06
21 41 0.85
22 4 0.08
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2607341 original size:21 final size:21
Alignment explanation
Indices: 2607315--2607362 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2607305 CCTGCGGAGA
*
2607315 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2607336 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2607357 GGGCAT
1 TGGCAT
2607363 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2609099 original size:17 final size:16
Alignment explanation
Indices: 2609077--2609163 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 16
2609067 GCAAAAAAAT
2609077 TAATAATTCTAAATAAA
1 TAATAATT-TAAATAAA
*
2609094 TAATAA-TTATATAAA
1 TAATAATTTAAATAAA
* *
2609109 T-ATTATTTTAATAAA
1 TAATAATTTAAATAAA
*
2609124 AAATAATATTTAAATAAA
1 TAAT-A-ATTTAAATAAA
* *
2609142 TATTTAATATAAA-AAA
1 TA-ATAATTTAAATAAA
2609158 TAATAA
1 TAATAA
2609164 CTATTTAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 3 0.06
15 18 0.33
16 8 0.15
17 12 0.22
18 12 0.22
19 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:2609133 original size:18 final size:18
Alignment explanation
Indices: 2609106--2609141 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2609096 ATAATTATAT
* *
2609106 AAATATTATTTTAATAAA
1 AAATAATATTTAAATAAA
2609124 AAATAATATTTAAATAAA
1 AAATAATATTTAAATAAA
2609142 TATTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAATATTTAAATAAA
Found at i:2609138 original size:29 final size:30
Alignment explanation
Indices: 2609086--2609162 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
2609076 TTAATAATTC
* *
2609086 TAAATAAATAATAATTATATAAAT-ATTATT
1 TAAATAAAAAATAA-TATATAAATAAATATT
* *
2609116 TTAATAAAAAATAATATTTAAATAAATATT
1 TAAATAAAAAATAATATATAAATAAATATT
2609146 TAATATAAAAAATAATA
1 TAA-ATAAAAAATAATA
2609163 ACTATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 8 0.20
30 19 0.47
31 13 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATAAAAAATAATATATAAATAAATATT
Found at i:2609157 original size:31 final size:33
Alignment explanation
Indices: 2609086--2609163 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
2609076 TTAATAATTC
* **
2609086 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTAAATAAATATTATAATAA
*
2609120 TAAAAAATAATATTTAAATAAATATT-TAAT-A
1 TAAAAAATAATAATTAAATAAATATTATAATAA
2609151 TAAAAAATAATAA
1 TAAAAAATAATAA
2609164 CTATTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 13 0.33
32 2 0.05
33 20 0.51
34 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAATAATAATTAAATAAATATTATAATAA
Found at i:2609188 original size:34 final size:33
Alignment explanation
Indices: 2609121--2609195 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
2609111 TTATTTTAAT
* * *
2609121 AAAAAATAATATTTAAATAAATATTTAATATAA
1 AAAAAATAATATTTAAAAAAATATCTAACATAA
2609154 AAAATAATAACTATTTAAAAAAATA-CTAACATAA
1 AAAA-AATAA-TATTTAAAAAAATATCTAACATAA
2609188 AAATAAAT
1 AAA-AAAT
2609196 TTCTTACCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 4 0.11
34 18 0.50
35 14 0.39
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAAAATAATATTTAAAAAAATATCTAACATAA
Found at i:2609392 original size:16 final size:16
Alignment explanation
Indices: 2609371--2609406 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2609361 TTAATGGAAG
2609371 GCGCGTCCCCGGGGAT
1 GCGCGTCCCCGGGGAT
2609387 GCGCGTCCCCGGGGAT
1 GCGCGTCCCCGGGGAT
2609403 GCGC
1 GCGC
2609407 TTTCCACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.39, G:0.44, T:0.11
Consensus pattern (16 bp):
GCGCGTCCCCGGGGAT
Found at i:2618073 original size:30 final size:30
Alignment explanation
Indices: 2618036--2618101 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
2618026 TAGTTTAACC
*
2618036 AAATACTAAACTAAGGTTATTGGCTAAATT
1 AAATACTAAACTAAGGTTAGTGGCTAAATT
*
2618066 GAATACTAAACTAAGGTTAGTGGCTAAATT
1 AAATACTAAACTAAGGTTAGTGGCTAAATT
2618096 AAATAC
1 AAATAC
2618102 AAAATAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (30 bp):
AAATACTAAACTAAGGTTAGTGGCTAAATT
Found at i:2623990 original size:21 final size:23
Alignment explanation
Indices: 2623965--2624015 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
2623955 ATAAGGGAAA
2623965 ATATATACACATA-TTACTATAT
1 ATATATACACATACTTACTATAT
** *
2623987 -TATATATTCATACTTATTATAT
1 ATATATACACATACTTACTATAT
2624009 ATATATA
1 ATATATA
2624016 TAGGGTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 8 0.33
23 6 0.25
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATACACATACTTACTATAT
Found at i:2627426 original size:19 final size:18
Alignment explanation
Indices: 2627393--2627433 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
2627383 TTTTCATTTG
*
2627393 ATTATTATTTATATTATT
1 ATTATTATATATATTATT
2627411 ATTATTATGATATATTATT
1 ATTATTAT-ATATATTATT
2627430 ATTA
1 ATTA
2627434 AATAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTATTATATATATTATT
Found at i:2628822 original size:3 final size:3
Alignment explanation
Indices: 2628809--2628867 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
2628799 TTATTTGCAA
* *
2628809 TAT TAT T-T TAT TAT TAT TAT T-T TTT TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
2628852 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
2628868 TATATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
2 5 0.11
3 40 0.85
4 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:2628841 original size:18 final size:17
Alignment explanation
Indices: 2628809--2628868 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
2628799 TTATTTGCAA
2628809 TATTATTTTATTATTAT
1 TATTATTTTATTATTAT
*
2628826 TATTTTTTTAATTATTAT
1 TATTATTTT-ATTATTAT
* *
2628844 T-TCATTATTATTATTTT
1 TATTATT-TTATTATTAT
2628861 TATTATTT
1 TATTATTT
2628869 ATATAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTTATTATTAT
Found at i:2628841 original size:29 final size:30
Alignment explanation
Indices: 2628809--2628870 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
2628799 TTATTTGCAA
*
2628809 TATTATTTTATTATTATTATTTTT-TTAAT
1 TATTATTTCATTATTATTATTTTTATTAAT
*
2628838 TATTATTTCATTATTATTATTTTTATTATT
1 TATTATTTCATTATTATTATTTTTATTAAT
2628868 TAT
1 TAT
2628871 ATAAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (30 bp):
TATTATTTCATTATTATTATTTTTATTAAT
Found at i:2628880 original size:2 final size:2
Alignment explanation
Indices: 2628868--2628913 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2628858 TTTTATTATT
*
2628868 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2628910 TA TA
1 TA TA
2628914 ATAAATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2631220 original size:8 final size:7
Alignment explanation
Indices: 2631196--2631237 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2631186 TTTTCATACA
2631196 TGCA-TT
1 TGCATTT
2631202 TGCATTT
1 TGCATTT
2631209 TGCATCTT
1 TGCAT-TT
2631217 TGCATTT
1 TGCATTT
* *
2631224 TTCATTG
1 TGCATTT
2631231 TGCATTT
1 TGCATTT
2631238 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2631220 original size:15 final size:14
Alignment explanation
Indices: 2631196--2631237 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2631186 TTTTCATACA
2631196 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2631209 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2631224 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2631238 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2637908 original size:22 final size:22
Alignment explanation
Indices: 2637879--2637933 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2637869 ATCTACACTC
2637879 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2637901 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2637923 TTCAAAGATGA
1 TTCAAAGATGA
2637934 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2638823 original size:187 final size:184
Alignment explanation
Indices: 2638483--2638854 Score: 663
Period size: 187 Copynumber: 2.0 Consensus size: 184
2638473 CCAATCAACA
* **
2638483 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGA
1 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGA
2638548 AATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCT
66 AATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCT
*
2638613 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
131 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
2638667 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATG
*
2638732 AAATTGTTGAAAAGTAAGAAAATGATTTCCTTAGTTTTTTTTTACTTAGTAAACTATTTCCCACA
65 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAG--TTTTTTTACTTAGTAAACTATTTCCCACA
*
2638797 TCTGTAAGTCCTACAGTGCGTGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
128 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
2638854 T
1 T
2638855 TTCAAAGCCT
Statistics
Matches: 179, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
184 55 0.31
185 39 0.22
187 85 0.47
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (184 bp):
TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGA
AATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCT
GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
Found at i:2639119 original size:113 final size:115
Alignment explanation
Indices: 2638909--2639787 Score: 707
Period size: 113 Copynumber: 7.6 Consensus size: 115
2638899 TTTTTCTTAA
* *
2638909 AACATTTCCA-GAAGAGTTCAAAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
2638973 GAGAAGAACTTGTTTAACTTTTTGCTTGAATTC-ATCACTCGAT-GGATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCACTCGATAGGATC
*
2639021 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
2639086 GAGAAGAACTTGTTTAACTTTTTGCTTGAATTC-ATCACTCGAT-GGATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCACTCGATAGGATC
* *
2639134 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* ** * *
2639199 GAGAAGAACTTGTTCGA-C---T--TT--AGT-T-TGA-TCGAT-GGATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCACTCGATAGGATC
* * *
2639237 AACATTTCCA-G-AAAGTTCATAATGAGAAGAACTTATCTAAAG-AGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
2639299 GAGAAGAGCTTGTTCAACCTTTTGCATG-ACTCTATCACAGAAGGAGATAGATCAGCATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCAC---------TCGAT-AGGATC
* * * *
2639358 AACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-ATGAAGAAGAAGTTCATAA
1 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * *
2639421 TGAGAAGAGCTTATTTAACCTTTTG-TTTAACTCTATCACAGAAGCAGATAGATCAACATC
65 TGAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCAC----TC-GATAG-----GATC
* *
2639481 AACATTTCCA-GAAGTGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
2639541 GAGAAGAGCTTGTTCAACCTTTTGCATG-ACTCTATCACACAAGGAGATAGATCAGCATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCACTC-----GATAG----G-ATC
* * * *
2639600 AACTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
2639664 GAGAAGAGCTTATTTAACCTTTTG-TTTAACTCTATCACAGAAGCAGATAGATCAACATC
66 GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCAC----TC-GATAG-----GATC
* * *
2639723 AACATTTCCA-GAAGTGTTCATAATGAGAAGAACTCATCCG-A-AA--AAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
2639783 GAGAA
66 GAGAA
2639788 AGATTTGTTC
Statistics
Matches: 647, Mismatches: 68, Indels: 97
0.80 0.08 0.12
Matches are distributed among these distances:
100 34 0.05
101 29 0.04
102 1 0.00
103 19 0.03
104 3 0.00
105 2 0.00
106 1 0.00
107 4 0.01
108 1 0.00
109 3 0.00
112 9 0.01
113 179 0.28
115 1 0.00
118 4 0.01
119 96 0.15
120 26 0.04
121 20 0.03
122 51 0.08
123 162 0.25
124 1 0.00
127 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (115 bp):
AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTTAACCTTTTGCTTGAACTCTATCACTCGATAGGATC
Found at i:2639303 original size:100 final size:103
Alignment explanation
Indices: 2639124--2639313 Score: 305
Period size: 100 Copynumber: 1.9 Consensus size: 103
2639114 AATTCATCAC
* *
2639124 TCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 TCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAAGAAGA
2639189 AGTTCATAATGAGAAGAACTTGTTCGACTTTAGTTTGA
66 AGTTCATAATGAGAAGAACTTGTTCGACTTTAGTTTGA
* * *
2639227 TCGATGGATCAACATTTCCA-G-AAAGTTCATAATGAGAAGAACTTATCTAAAG-AGGAAGAAGA
1 TCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAAGAAGA
*
2639289 AGTTCATAATGAGAAGAGCTTGTTC
66 AGTTCATAATGAGAAGAACTTGTTC
2639314 AACCTTTTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 33 0.41
101 28 0.35
102 1 0.01
103 19 0.23
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (103 bp):
TCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACTTTAGTTTGA
Found at i:2639549 original size:242 final size:242
Alignment explanation
Indices: 2639234--2639807 Score: 1017
Period size: 242 Copynumber: 2.4 Consensus size: 242
2639224 TGATCGATGG
* * *
2639234 ATCAACATTTCCAGAA-AGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA-A--AAGAAGAAGTTCATAA
*
2639298 TGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTT
63 TGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACACAAGGAGATAGATCAGCATCAACTT
*
2639363 TTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAGTTCATAATGAGAAG
128 TTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAG
2639428 AGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
193 AGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
2639478 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGTTCATAATGA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGTTCATAATGA
2639543 GAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACACAAGGAGATAGATCAGCATCAACTTTTC
66 GAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACACAAGGAGATAGATCAGCATCAACTTTTC
*
2639608 CAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGC
131 CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGC
2639673 TTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
196 TTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
*
2639720 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCCGAAAAAGAAGAAGTTCATAATGA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGTTCATAATGA
* *
2639785 GAA-AGATTTGTTCAACTTTTTGC
66 GAAGAG-CTTGTTCAACCTTTTGC
2639808 TAGATTACAT
Statistics
Matches: 319, Mismatches: 9, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
241 2 0.01
242 275 0.86
244 17 0.05
245 25 0.08
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (242 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACACAAGGAGATAGATCAGCATCAACTTTTC
CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGC
TTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
Found at i:2639573 original size:119 final size:121
Alignment explanation
Indices: 2639234--2639807 Score: 809
Period size: 123 Copynumber: 4.7 Consensus size: 121
2639224 TGATCGATGG
*
2639234 ATCAACATTTCCAG-AAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGA-GAAGAAGAAGTTCATAA
* * *
2639298 TGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
65 TGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAAC
*
2639355 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTTATCTGAAGA-GAAGAAGAAGTTCATA
* * **
2639420 ATGAGAAGAGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
64 ATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAAC
** *
2639478 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA-A-AAGAAGAAGTTCATAAT
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAGAAGAAGTTCATAAT
* * * *
2639541 GAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACACAAGGAGATAGATCAGC
66 GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAAC
*
2639597 ATCAACTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTTATCTGAAGA-GAAGAAGAAGTTCATA
* * **
2639662 ATGAGAAGAGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGATCAAC
64 ATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAAC
** * *
2639720 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCCGAA-A-AAGAAGAAGTTCATAAT
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAGAAGAAGTTCATAAT
* *
2639783 GAGAA-AGATTTGTTCAACTTTTTGC
66 GAGAAGAG-CTTGTTCAACCTTTTGC
2639808 TAGATTACAT
Statistics
Matches: 402, Mismatches: 44, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
118 2 0.00
119 113 0.28
120 27 0.07
121 16 0.04
122 53 0.13
123 191 0.48
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (121 bp):
ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAAC
Found at i:2640020 original size:3 final size:3
Alignment explanation
Indices: 2640014--2640066 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
2640004 TTTTCATTTG
*
2640014 ATT ATT ATT -TAT ATT ATT ATT ATT ATT ATT ATT ATT ATG ATAT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
2640060 ATT ATT A
1 ATT ATT A
2640067 AATAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 41 0.91
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2641446 original size:3 final size:3
Alignment explanation
Indices: 2641433--2641490 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
2641423 TTATTTGCAA
*
2641433 TAT TAT T-T TAT TAT TAT TAT T-T T-T TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
2641475 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
2641491 TATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 38 0.81
4 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:2641452 original size:14 final size:14
Alignment explanation
Indices: 2641433--2641490 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
2641423 TTATTTGCAA
2641433 TATTATTTTATTAT
1 TATTATTTTATTAT
2641447 TATTATTTT-TTAAT
1 TATTATTTTATT-AT
*
2641461 TATTATTTCATTAT
1 TATTATTTTATTAT
2641475 TATTATTTTTATTAT
1 TATTA-TTTTATTAT
2641490 T
1 T
2641491 TATATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.05
14 26 0.67
15 11 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:2641503 original size:2 final size:2
Alignment explanation
Indices: 2641491--2641520 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2641481 TTTTATTATT
*
2641491 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2641521 ATAAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2646486 original size:20 final size:20
Alignment explanation
Indices: 2646463--2646514 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2646453 AACGCGATCC
2646463 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2646483 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2646503 CCAAAATCGCAA
1 CCAGAATCGCAA
2646515 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2646664 original size:20 final size:20
Alignment explanation
Indices: 2646570--2646958 Score: 480
Period size: 20 Copynumber: 19.4 Consensus size: 20
2646560 GATTTTCCAT
* ** *
2646570 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2646590 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2646610 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2646630 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2646650 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2646670 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2646690 TATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2646710 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2646730 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2646750 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2646770 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2646790 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2646810 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2646830 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2646850 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2646870 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2646890 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2646910 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2646930 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2646950 AATCACAAC
1 AATCGCAAC
2646959 ACTGAAATTT
Statistics
Matches: 325, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 319 0.98
21 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2647878 original size:12 final size:12
Alignment explanation
Indices: 2647861--2647885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2647851 ATATAATCCT
2647861 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2647873 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2647885 G
1 G
2647886 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2650256 original size:33 final size:34
Alignment explanation
Indices: 2650169--2650454 Score: 255
Period size: 33 Copynumber: 8.5 Consensus size: 34
2650159 CGGAAAATAC
* *
2650169 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
2650202 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
2650236 AATCGCAATGCGAAATGAAAAAT-GCGAA--ATGAA
1 AATCGCAATGCGAAATG-AAAATCGC-AACGATGAA
* *
2650269 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
2650302 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
2650340 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
2650373 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
2650406 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
2650439 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2650455 TATAAACGCA
Statistics
Matches: 224, Mismatches: 11, Indels: 36
0.83 0.04 0.13
Matches are distributed among these distances:
32 8 0.04
33 144 0.64
34 38 0.17
35 8 0.04
36 8 0.04
37 1 0.00
38 17 0.08
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:2650259 original size:14 final size:14
Alignment explanation
Indices: 2650242--2650270 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2650232 AGAGAATCGC
2650242 AATGCGAAATGAAA
1 AATGCGAAATGAAA
2650256 AATGCGAAATGAAA
1 AATGCGAAATGAAA
2650270 A
1 A
2650271 TCGCAATGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AATGCGAAATGAAA
Found at i:2650315 original size:52 final size:51
Alignment explanation
Indices: 2650169--2650432 Score: 266
Period size: 52 Copynumber: 5.2 Consensus size: 51
2650159 CGGAAAATAC
*
2650169 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAACGA--AAGAATCGCAATGC-GAAATGAA
* *
2650222 AATCGCAA-CG--A-GAGAATCGCAATGCGAAATGAA---AAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA--CGAAA-GAATCGCAATGCGAAATGAA
* *
2650269 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAA
1 AATCGCAA-GCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
2650321 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
2650373 AATCGCAA-CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
2650425 AATCGCAA
1 AATCGCAA
2650433 CGAGATAATC
Statistics
Matches: 184, Mismatches: 9, Indels: 37
0.80 0.04 0.16
Matches are distributed among these distances:
47 24 0.13
48 14 0.08
49 14 0.08
50 11 0.06
51 6 0.03
52 107 0.58
53 8 0.04
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (51 bp):
AATCGCAAGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:2650334 original size:85 final size:84
Alignment explanation
Indices: 2650236--2650454 Score: 350
Period size: 85 Copynumber: 2.6 Consensus size: 84
2650226 GCAACGAGAG
* * *
2650236 AATCGCAATGCGAAATGAAAAATGCGAAATGAA-AATCGCAATGCGAAATGAAAATCGCAACGAC
1 AATCGCAATGCGAAATG-AAAAT-CGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAACGAA
*
2650300 AGAATCGCAATGCGAAATTAA
64 AGAATCGCAATGCGAAATGAA
2650321 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGAAA
1 AATCGCAATGCGAAATGAAAATCGCAACG-AAGAATCGCAATGCGAAATGAAAATCGCAACGAAA
2650386 GAATCGCAATGCGAAATGAA
65 GAATCGCAATGCGAAATGAA
*
2650406 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGA-AGAATCGCAATGCGAAAT
2650455 TATAAACGCA
Statistics
Matches: 126, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
83 5 0.04
84 8 0.06
85 113 0.90
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (84 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAACGAAAG
AATCGCAATGCGAAATGAA
Found at i:2650359 original size:14 final size:14
Alignment explanation
Indices: 2650340--2650394 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
2650330 GCGAAATGAA
2650340 AATCGCAACGAAAG
1 AATCGCAACGAAAG
2650354 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2650371 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2650387 AATCGCAA
1 AATCGCAA
2650395 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2650433 original size:52 final size:51
Alignment explanation
Indices: 2650201--2650454 Score: 271
Period size: 52 Copynumber: 5.0 Consensus size: 51
2650191 CCCAACATGA
*
2650201 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
*
2650253 AAA----AATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G
1 AAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATG
*
2650302 -AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
1 AAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATG
2650354 -AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
* *
2650404 AAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
2650455 TATAAACGCA
Statistics
Matches: 181, Mismatches: 7, Indels: 28
0.84 0.03 0.13
Matches are distributed among these distances:
47 24 0.13
48 7 0.04
49 11 0.06
50 11 0.06
52 128 0.71
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (51 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
Found at i:2650570 original size:19 final size:19
Alignment explanation
Indices: 2650461--2650562 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2650451 AAATTATAAA
2650461 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2650480 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2650500 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2650516 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2650533 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2650552 CGCATTGCGAT
1 CGCATTGCGAT
2650563 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2650688 original size:14 final size:14
Alignment explanation
Indices: 2650669--2650705 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2650659 CATCAATTAC
2650669 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2650683 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2650697 ACAAATCAA
1 ACAAATCAA
2650706 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2652704 original size:14 final size:14
Alignment explanation
Indices: 2652685--2652741 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2652675 GCGAAATGAA
*
2652685 AATCGCAACGACAG
1 AATCGCAACGAAAG
2652699 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2652716 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2652732 AATCGCAACG
1 AATCGCAACG
2652742 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2652712 original size:33 final size:33
Alignment explanation
Indices: 2652666--2652758 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2652656 GCGAAACCAA
*
2652666 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2652699 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2652732 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2652759 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2652723 original size:19 final size:19
Alignment explanation
Indices: 2652629--2652763 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2652619 TAGTTTACTT
* *
2652629 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2652649 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2652668 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2652687 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2652701 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2652720 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2652734 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2652753 TCGCAATGCGA
1 TCGCAACGCGA
2652764 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2652781 original size:19 final size:19
Alignment explanation
Indices: 2652759--2652887 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2652749 AAAATCGCAA
2652759 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2652778 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2652792 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2652811 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2652825 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2652844 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2652863 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2652883 TGCGA
1 TGCGA
2652888 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2652801 original size:33 final size:33
Alignment explanation
Indices: 2652759--2652850 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2652749 AAAATCGCAA
2652759 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2652792 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2652825 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2652851 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2653078 original size:93 final size:93
Alignment explanation
Indices: 2652919--2653385 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
2652909 GCAAATTGAA
2652919 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2652984 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2653012 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2653077 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2653105 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2653170 GCAGAATTGGCATCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2653198 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2653262 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2653290 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2653355 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2653383 ACT
1 ACT
2653386 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.25
93 279 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:2653355 original size:185 final size:186
Alignment explanation
Indices: 2652919--2653385 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
2652909 GCAAATTGAA
2652919 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2652984 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
2653049 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
2653105 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2653170 GCAGAATTGGCATCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
2653234 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
2653290 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2653355 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
2653386 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 125 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:2655108 original size:14 final size:14
Alignment explanation
Indices: 2655089--2655179 Score: 74
Period size: 14 Copynumber: 5.7 Consensus size: 14
2655079 TTGAAATGAA
2655089 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2655103 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2655117 AATGACTGTCGCAACGAGAG
1 -A--A---TCGCAACGAGAG
*
2655137 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2655156 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2655170 AATCGCAACG
1 AATCGCAACG
2655180 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
14 32 0.50
15 2 0.03
16 2 0.03
17 4 0.06
18 1 0.02
19 11 0.17
20 12 0.19
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2655161 original size:19 final size:19
Alignment explanation
Indices: 2655137--2655201 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2655127 GCAACGAGAG
2655137 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2655156 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2655170 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2655189 AATCGCAATGCGA
1 AATCGCAACGCGA
2655202 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2655162 original size:33 final size:33
Alignment explanation
Indices: 2655081--2655196 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
2655071 TCTTTTGGTT
*
2655081 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
***
2655114 GAGAATGACTGTCGCAACGAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGAGAGAATCGCAACGC
2655148 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2655181 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2655197 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
33 46 0.61
34 29 0.39
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2655232 original size:14 final size:14
Alignment explanation
Indices: 2655213--2655267 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2655203 TTTGGTTTCG
2655213 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2655227 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2655246 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2655260 CGTTGCGA
1 CGTTGCGA
2655268 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2655245 original size:33 final size:33
Alignment explanation
Indices: 2655197--2655267 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2655187 AAAATCGCAA
**
2655197 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2655230 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2655263 TGCGA
1 TGCGA
2655268 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2655275 original size:33 final size:33
Alignment explanation
Indices: 2655208--2655289 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2655198 GCGATTTTGG
***
2655208 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2655241 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2655274 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2655290 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2655294 original size:20 final size:20
Alignment explanation
Indices: 2655220--2655308 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2655210 TCGCGTTGCG
2655220 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2655240 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2655253 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2655273 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2655293 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2655309 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2655430 original size:33 final size:33
Alignment explanation
Indices: 2655388--2655458 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2655378 AATACTAACT
*
2655388 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2655421 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2655454 TGAAA
1 TGAAA
2655459 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2655692 original size:22 final size:22
Alignment explanation
Indices: 2655640--2655694 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2655630 TGGTTGTGAG
**
2655640 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2655662 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2655684 GGATTTCTTCG
1 GGATTTCTTCG
2655695 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2655865 original size:20 final size:20
Alignment explanation
Indices: 2655840--2656032 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
2655830 CTTTAAATAT
2655840 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2655860 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
2655882 -TCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
2655901 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2655921 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2655941 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2655961 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2655981 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2656001 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2656021 CGCGTTGCGATT
1 CGCGTTGCGATT
2656033 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2656005 original size:60 final size:60
Alignment explanation
Indices: 2655842--2656013 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
2655832 TTAAATATCG
** * *
2655842 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTATGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
2655903 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
2655963 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
2656014 TCATATTCGC
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 68 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:2656113 original size:20 final size:20
Alignment explanation
Indices: 2656088--2656139 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2656078 AAGAATCGCG
*
2656088 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2656108 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2656128 TTGCGATTCTGG
1 TTGCGATTCTGG
2656140 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:2656698 original size:17 final size:17
Alignment explanation
Indices: 2656676--2656738 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
2656666 TTCAGCAATT
*
2656676 GCTTATATATGTCTTCA
1 GCTTATACATGTCTTCA
2656693 GCTTATACATG-CTTCA
1 GCTTATACATGTCTTCA
* *
2656709 --TAAAATC-TGTCTTCA
1 GCTTATA-CATGTCTTCA
2656724 GCTTATACATGTCTT
1 GCTTATACATGTCTT
2656739 GAGGTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 5 0.14
15 6 0.17
16 6 0.17
17 19 0.53
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (17 bp):
GCTTATACATGTCTTCA
Found at i:2663487 original size:13 final size:13
Alignment explanation
Indices: 2663469--2663496 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2663459 TGTACCGATA
2663469 CACATTGCCTATG
1 CACATTGCCTATG
2663482 CACATTGCCTATG
1 CACATTGCCTATG
2663495 CA
1 CA
2663497 TCGATGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (13 bp):
CACATTGCCTATG
Found at i:2668830 original size:21 final size:21
Alignment explanation
Indices: 2668786--2668865 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
2668776 ACACTAGTTA
*
2668786 GTGCATCGATGCATACCTTGAAT
1 GTGCATCGATGC--ACCATGAAT
*
2668809 GTGCATCGATTCACCATGAAT
1 GTGCATCGATGCACCATGAAT
*
2668830 GTGCATCGATGCACTC-TG-TT
1 GTGCATCGATGCAC-CATGAAT
*
2668850 GTGCATCGATACACCA
1 GTGCATCGATGCACCA
2668866 GTCGGGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.02
20 14 0.28
21 23 0.46
22 1 0.02
23 11 0.22
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCACCATGAAT
Found at i:2672339 original size:20 final size:21
Alignment explanation
Indices: 2672314--2672361 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2672304 ATTTATCTTT
2672314 TAAATTTTA-TAAAAAATATA
1 TAAATTTTATTAAAAAATATA
*
2672334 TAAATTTTATTAAAAAGTATA
1 TAAATTTTATTAAAAAATATA
*
2672355 TGAATTT
1 TAAATTT
2672362 AAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TAAATTTTATTAAAAAATATA
Found at i:2675034 original size:15 final size:15
Alignment explanation
Indices: 2675014--2675043 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2675004 CTTGGTGATG
2675014 TTTGTTATACAATTA
1 TTTGTTATACAATTA
2675029 TTTGTTATACAATTA
1 TTTGTTATACAATTA
2675044 ATTCGAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTGTTATACAATTA
Found at i:2679802 original size:20 final size:20
Alignment explanation
Indices: 2679773--2679811 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2679763 TTTCCACCAC
*
2679773 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2679793 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2679812 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2686033 original size:13 final size:13
Alignment explanation
Indices: 2686015--2686053 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2686005 GTCATAAATC
2686015 TATGACGCGCATT
1 TATGACGCGCATT
*
2686028 TATGACACGCATT
1 TATGACGCGCATT
2686041 TATGACGCGCATT
1 TATGACGCGCATT
2686054 GCGCGTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:2686175 original size:85 final size:85
Alignment explanation
Indices: 2686025--2686189 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 85
2686015 TATGACGCGC
* * * * *
2686025 ATTTATGACACGCATTTATGACGCGCATTGCGCGTCATTGAAGCCCCCGTCATAAAAGAATATGA
1 ATTTATGACACGCATTTATGACGCACATTGCACGTCATTGAAGCACACGTCATAAAAGAAGATGA
* *
2686090 CACGCATTTGTGTGTTATAA
66 CACACATTCGTGTGTTATAA
*
2686110 ATTTATGACACGCATTTATGAC-CTACATTGCATGTCATTGAAGCACACGTCATTAAAA-AAGAT
1 ATTTATGACACGCATTTATGACGC-ACATTGCACGTCATTGAAGCACACGTCA-TAAAAGAAGAT
2686173 GACACACATTCGTGTGT
64 GACACACATTCGTGTGT
2686190 CGTGATTGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 64 0.91
86 5 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACGCACATTGCACGTCATTGAAGCACACGTCATAAAAGAAGATGA
CACACATTCGTGTGTTATAA
Found at i:2686607 original size:21 final size:19
Alignment explanation
Indices: 2686569--2686614 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2686559 AATTAATCCT
2686569 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
2686589 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
2686610 A-TAAT
1 ACTAAT
2686615 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:2693887 original size:2 final size:2
Alignment explanation
Indices: 2693880--2693934 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2693870 TGTATGGTGC
2693880 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2693922 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2693935 ACGAAATTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2694135 original size:20 final size:20
Alignment explanation
Indices: 2694097--2694135 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2694087 CGATGAGGTA
* * *
2694097 GTATTGATACCATGGAACAG
1 GTATCGATACCAAGCAACAG
2694117 GTATCGATACCAAGCAACA
1 GTATCGATACCAAGCAACA
2694136 TCGAACCAAA
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:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
GTATCGATACCAAGCAACAG
Found at i:2694214 original size:20 final size:20
Alignment explanation
Indices: 2694165--2694222 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
2694155 CACCGGAAGG
* * *
2694165 GGGTATCGATACCATAGTAT
1 GGGTATCGATACCATGGCAA
2694185 GGTAGTATCGATACCATGGCAA
1 GG--GTATCGATACCATGGCAA
2694207 GGGTATCGATACCATG
1 GGGTATCGATACCATG
2694223 TAACATCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
22 17 0.52
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATGGCAA
Found at i:2694295 original size:94 final size:91
Alignment explanation
Indices: 2694094--2694312 Score: 255
Period size: 94 Copynumber: 2.4 Consensus size: 91
2694084 TACCGATGAG
*
2694094 GTAGTAT-TGATACCATGGAACAGGTATCGATACCAAGCAACATCGAACCAAATTTTGGTATCAC
1 GTAGTATCT-ATACCATGGAA-GGGTATCGATACCAAGCAACATCGAACCAAATTTTGGTATCAC
*
2694158 CGGAAGGGGGTATCGATACCATAGTATG
64 CGGAAGGGGGTATCGATACCATAGTATA
* * * *
2694186 GTAGTATCGATACCATGGCAAGGGTATCGATACCATGTAACATCGAATCTAAA-TTTGGTATCGA
1 GTAGTATCTATACCATGG-AAGGGTATCGATACCAAGCAACATCGAA-CCAAATTTTGGTATC--
* * *
2694250 TACTGG-AGGGGGTATCGGTATCATAGTATA
62 -ACCGGAAGGGGGTATCGATACCATAGTATA
*
2694280 GTAGTATCTATACCATTGTAAGGGTATCGATAC
1 GTAGTATCTATACCA-TGGAAGGGTATCGATAC
2694313 TGAAGAACAA
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
92 48 0.44
93 6 0.06
94 49 0.45
95 6 0.06
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (91 bp):
GTAGTATCTATACCATGGAAGGGTATCGATACCAAGCAACATCGAACCAAATTTTGGTATCACCG
GAAGGGGGTATCGATACCATAGTATA
Found at i:2694957 original size:79 final size:79
Alignment explanation
Indices: 2694756--2694977 Score: 322
Period size: 79 Copynumber: 2.8 Consensus size: 79
2694746 GGCATTGTGT
* *
2694756 GTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATAGGTGCATTATCAGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGCCATACTTGAAATGCATATGGGTGCATTATCAGCATAAAAG
2694821 AATAATGCATATGG
66 AATAATGCATATGG
* *
2694835 GTGCATTATTGGCATGAAAGGATGTCATAGC-TGAAATGCATATGGGTGCATTATTAGCATAAAA
1 GTGCATTATTGGCATGAAAGGATGCCATA-CTTGAAATGCATATGGGTGCATTATCAGCATAAAA
2694899 GAATAATGCATATGG
65 GAATAATGCATATGG
** * * * *
2694914 GTGCATTATTGGCATGACTGGATGCCA-ACATTGATATGTATATGGGTGCATTGTCAACATAAAA
1 GTGCATTATTGGCATGAAAGGATGCCATAC-TTGAAATGCATATGGGTGCATTATCAGCATAAAA
2694978 AATGTTATAA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
77 1 0.01
78 1 0.01
79 126 0.98
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
GTGCATTATTGGCATGAAAGGATGCCATACTTGAAATGCATATGGGTGCATTATCAGCATAAAAG
AATAATGCATATGG
Found at i:2695320 original size:29 final size:29
Alignment explanation
Indices: 2695270--2695330 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2695260 TATGCCAGTT
* * *
2695270 AGATGAACGGTTAAATAATGTTGAGTAAA
1 AGATGAAAGGTCAAACAATGTTGAGTAAA
*
2695299 AGATGAAAGGTCAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACAATGTTGAGTAAA
2695328 AGA
1 AGA
2695331 ATAATGGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (29 bp):
AGATGAAAGGTCAAACAATGTTGAGTAAA
Done.