Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2349680 original size:103 final size:104
Alignment explanation
Indices: 2349502--2349754 Score: 391
Period size: 103 Copynumber: 2.4 Consensus size: 104
2349492 TATCCCAACC
* * *
2349502 TTTTCATGTTGGTGTGAGCCTTCAAGATACCCCACATGGATAATATCTATCTTTTTCATACTGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATCTATCTTTTTCATACTGAT
* *
2349567 GTGAACCTTCAAGATGCCTCACATGGATTACTTTTGTCT
66 GTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
* * * * * *
2349606 TTTT-ATGCTGATGTGAACCTTCAAGATGCCTCATATGGATTATTTCTATCTTTTTCATGCTGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATCTATCTTTTTCATACTGAT
2349670 GTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
66 GTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
*
2349709 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATAGATAATAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATAT
2349755 AGACCTCCAA
Statistics
Matches: 131, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
103 92 0.70
104 39 0.30
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (104 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATCTATCTTTTTCATACTGAT
GTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
Found at i:2351051 original size:6 final size:6
Alignment explanation
Indices: 2351036--2351094 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
2351026 CTTGTTTCAA
2351036 TTTCTT TTT-TT CTTT-TT TTTCTT TTTCTT TTTC-- TTTCTT TTTCCTT
1 TTTCTT TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT-CTT
*
2351082 TTTCTT TCTCTT T
1 TTTCTT TTTCTT T
2351095 CTTTTTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 32 0.68
7 6 0.13
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:2351062 original size:23 final size:24
Alignment explanation
Indices: 2351037--2351103 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 24
2351027 TTGTTTCAAT
2351037 TTCTTTTTTTCTTTTTTTT-CTTT
1 TTCTTTTTTTCTTTTTTTTCCTTT
2351060 TTC--TTTTTCTTTCTTTTTCCTTT
1 TTCTTTTTTTCTTT-TTTTTCCTTT
2351083 TTCTTTCTCTTTCTTTTTTTT
1 TTCTTT-T-TTTCTTTTTTTT
2351104 TCTGATGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.24
22 5 0.13
23 10 0.26
25 1 0.03
26 6 0.16
27 7 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTCTTTTTTTCTTTTTTTTCCTTT
Found at i:2351090 original size:33 final size:32
Alignment explanation
Indices: 2351036--2351106 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
2351026 CTTGTTTCAA
* *
2351036 TTTCTTTTTTTCTTTTTTTTCTTTTTCTTTTTC
1 TTTC-TTTTTCCTTTTTTTTCTCTTTCTTTTTC
*
2351069 TTTCTTTTTCCTTTTTCTTTCTCTTTCTTTTTT
1 TTTCTTTTTCCTTTTT-TTTCTCTTTCTTTTTC
2351102 TTTCT
1 TTTCT
2351107 GATGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (32 bp):
TTTCTTTTTCCTTTTTTTTCTCTTTCTTTTTC
Found at i:2357851 original size:28 final size:28
Alignment explanation
Indices: 2357808--2357867 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
2357798 ACATAACACC
* *
2357808 TAAAATCAATGACTAAATA-GAAATTAA
1 TAAAATCAATGACTAAAAATGAAATAAA
2357835 TAAAATCATAGTG-CTAAAAATGAAATAAA
1 TAAAATCA-A-TGACTAAAAATGAAATAAA
2357864 TAAA
1 TAAA
2357868 CATAGGGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.29
28 7 0.25
29 13 0.46
ACGTcount: A:0.60, C:0.07, G:0.08, T:0.25
Consensus pattern (28 bp):
TAAAATCAATGACTAAAAATGAAATAAA
Found at i:2359073 original size:3 final size:3
Alignment explanation
Indices: 2359058--2359117 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
2359048 AATTAATTAG
* *
2359058 TAA TAA TAT TAA TAA TAA TAA TAA TAA T-A TAGA TAA TAA -AA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
2359102 TAA T-A TAA TTAA TAA T
1 TAA TAA TAA -TAA TAA T
2359118 GTTTTTTCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 6 0.12
3 36 0.75
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2362811 original size:181 final size:182
Alignment explanation
Indices: 2362507--2362870 Score: 721
Period size: 181 Copynumber: 2.0 Consensus size: 182
2362497 ATTCTAAATT
2362507 AGATTTACTGCTAGTGATTCCATTACCCAAACAATCAGGGGTATTCAGGAATATACTTTGAATTC
1 AGATTTACTGCTAGTGATTCCATTACCCAAACAATCAGGGGTATTCAGGAATATACTTTGAATTC
2362572 ATAGGATTTCAGTCCAATTGAACCAAATGAGGTATTCAGAATCTTTTCATTCCGCGTTACTTGTG
66 ATAGGATTTCAGTCCAATTGAACCAAATGAGGTATTCAGAATCTTTTCATTCCGCGTTACTTGTG
2362637 TTTTCAAACATGAACGAAGTGATTTTAGATG-AAATATAGAATCGAAGATTC
131 TTTTCAAACATGAACGAAGTGATTTTAGATGAAAATATAGAATCGAAGATTC
2362688 AGATTTACTGCTAGTGATTCCATTACCCAAACAATCAGGGGTATTCAGGAATATACTTTGAATTC
1 AGATTTACTGCTAGTGATTCCATTACCCAAACAATCAGGGGTATTCAGGAATATACTTTGAATTC
2362753 ATAGGATTTCAGTCCAATTGAACCAAATGAGGTATTCAGAATCTTTTCATTCCGCGTTACTTGTG
66 ATAGGATTTCAGTCCAATTGAACCAAATGAGGTATTCAGAATCTTTTCATTCCGCGTTACTTGTG
2362818 TTTTCAAACATGAACGAAGTGATTTTAGATGAAAATATAGAATCGAAGATTC
131 TTTTCAAACATGAACGAAGTGATTTTAGATGAAAATATAGAATCGAAGATTC
2362870 A
1 A
2362871 AGTCATTTAT
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 161 0.88
182 21 0.12
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (182 bp):
AGATTTACTGCTAGTGATTCCATTACCCAAACAATCAGGGGTATTCAGGAATATACTTTGAATTC
ATAGGATTTCAGTCCAATTGAACCAAATGAGGTATTCAGAATCTTTTCATTCCGCGTTACTTGTG
TTTTCAAACATGAACGAAGTGATTTTAGATGAAAATATAGAATCGAAGATTC
Found at i:2397600 original size:101 final size:100
Alignment explanation
Indices: 2397412--2397612 Score: 235
Period size: 101 Copynumber: 2.0 Consensus size: 100
2397402 TATCTAACCT
* * *
2397412 TTTTATTAATTTGTTTGAAATATTATACGACCTTGCAGTGACCTGATCCGGGGTATGATCCACAT
1 TTTTATTAATTTGTTTGAAATATTATACGACATTACAGTGACCTGATCCGGGGTACGA-CCACAT
* * * ** * **
2397477 TATTATGGTTCGGGTTCTATTAACTCCTAACTTTTG
65 TATTACGATTCAGACTCCATTAACAACTAACTTTTG
* *
2397513 TTTTATTAATTTGTTTGAATTATTATACGACATTACGGTGA-CTCGATCCGGGGTACGA-CATGC
1 TTTTATTAATTTGTTTGAAATATTATACGACATTACAGTGACCT-GATCCGGGGTACGACCA--C
2397576 ATTATTACGATTCAGACTCCATTAACAACTAACTTTT
63 ATTATTACGATTCAGACTCCATTAACAACTAACTTTT
2397613 CTAACTTCCA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
99 2 0.02
100 2 0.02
101 80 0.95
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (100 bp):
TTTTATTAATTTGTTTGAAATATTATACGACATTACAGTGACCTGATCCGGGGTACGACCACATT
ATTACGATTCAGACTCCATTAACAACTAACTTTTG
Found at i:2397656 original size:4 final size:4
Alignment explanation
Indices: 2397647--2397684 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
2397637 ACAACTAATT
*
2397647 TTTA TTTA TTTA TTTA TTTA CTTA TTTA TTTA TCTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA T
2397685 GTTCTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:2397880 original size:13 final size:14
Alignment explanation
Indices: 2397849--2397883 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2397839 CTTTTACTTA
2397849 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
*
2397863 TTTAATTTCA-TTC
1 TTTAATTTCAGTCC
2397876 TTTAATTT
1 TTTAATTT
2397884 ACTTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.23, C:0.14, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:2403328 original size:99 final size:99
Alignment explanation
Indices: 2403052--2403382 Score: 413
Period size: 99 Copynumber: 3.4 Consensus size: 99
2403042 AGCAAAGATA
* * *
2403052 AAAAATGTTCTCACTTGAGATGGTTTTTCTTAAAACCAATTTCATTTTCTTTTGAAATATTTCCC
1 AAAAAT-TTATCACTTGAGATGGTTTTTCTTAAAATC-ATTTCA-TTTCTTTTGAAATAGTTCCC
* **
2403117 TTTGGAACACAAATTTTGAATTTTTTTCACTCGAAAC
63 ATTGGAACACAAATTTTGAAAATTTTTCACTCGAAAC
* * * * * *
2403154 AAAAATTTATCACTAGAAATGTTTTTTCCTTAAAATCAATT--TTGC--TTGAAATAGTTCCCCT
1 AAAAATTTATCACTTGAGATGGTTTTT-CTTAAAATCATTTCATTTCTTTTGAAATAGTTCCCAT
* * *
2403215 TGGAACACAGATTTTGAAAATTTTCCACTCAAAAC
65 TGGAACACAAATTTTGAAAATTTTTCACTCGAAAC
*
2403250 -AAAATTTATCACTTGAGATGTTTTTTCTTAAAATCTATTTCATTTCTTTTGAAATAGTTCCCAT
1 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATC-ATTTCATTTCTTTTGAAATAGTTCCCAT
* *
2403314 TGGAACACATATTTT-TAAATTTTTCACTCGAAAC
65 TGGAACACAAATTTTGAAAATTTTTCACTCGAAAC
2403348 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAAT
1 AAAAATTTATCACTTGAGATGGTTTTTCTTAAAAT
2403383 TAATTTTGCT
Statistics
Matches: 198, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
94 9 0.05
95 27 0.14
96 44 0.22
97 3 0.02
98 19 0.10
99 62 0.31
101 20 0.10
102 14 0.07
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (99 bp):
AAAAATTTATCACTTGAGATGGTTTTTCTTAAAATCATTTCATTTCTTTTGAAATAGTTCCCATT
GGAACACAAATTTTGAAAATTTTTCACTCGAAAC
Found at i:2404203 original size:138 final size:139
Alignment explanation
Indices: 2403802--2404334 Score: 735
Period size: 139 Copynumber: 3.8 Consensus size: 139
2403792 CAACCTTGGC
** *
2403802 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
** * * * *
2403867 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATAGAGTTGGATTAGCAACACATTA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGCAACACCTCA
2403932 CTAGAGGGA
131 CTAGAGGGA
* * *
2403941 TTATCATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
*
2404006 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAACAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGCAACACCTCA
* *
2404071 ATTGAGGGA
131 CTAGAGGGA
* * * *
2404080 TCAACATTTCCAGTGGAGATTTCATAATGAGAAGATCTCATCCTATGAGGGA-AAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
* *
2404144 ATGAGAAGAACTTGTTTAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGCAACACCTCA
* *
2404209 CTCGAGGAA
131 CTAGAGGGA
* * * * * * *
2404218 TCAAAATTTTCAGTGAAGAATTCATAACGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
** * * *
2404283 ATGAGAAGAACTTGTTCAAGTTTAGCTCGTTTCTATCACAAAAGGAGTTGGA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTC-ATCACATATGGAGTTGGA
2404335 ACGACACTAA
Statistics
Matches: 348, Mismatches: 44, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
138 124 0.36
139 209 0.60
140 15 0.04
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGCAACACCTCA
CTAGAGGGA
Found at i:2404297 original size:277 final size:279
Alignment explanation
Indices: 2403802--2404334 Score: 784
Period size: 277 Copynumber: 1.9 Consensus size: 279
2403792 CAACCTTGGC
*
2403802 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAAAGTTCATA
* * * *
2403867 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATAGAGTTGGATTAGCAACACATTA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATAGAGTTGAATCAGCAACACATCA
* * ** * * * *
2403932 CTAGAGGGATTATCATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAA
131 CTAGAGGAATCAAAATTTCTAGTGAAGAATTCATAACGAGAAGAACTCATCCAACGAGGGAGAAA
* *
2403997 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTC-ATCACATATGGAGTTGGATCAA
196 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGTTGGATCAA
2404061 CAACACCTCAATTGAGGGA
261 CAACACCTCAATTGAGGGA
* * * *
2404080 TCAACATTTCCAGTGGAGATTTCATAATGAGAAGATCTCATCCTATGAGGGA-AAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAAAGTTCATA
* * * *
2404144 ATGAGAAGAACTTGTTTAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATAGAGTTGAATCAGCAACACATCA
*
2404209 CTCGAGGAATCAAAATTT-TCAGTGAAGAATTCATAACGAGAAGAACTCATCCAACGAGGGAGAA
131 CTAGAGGAATCAAAATTTCT-AGTGAAGAATTCATAACGAGAAGAACTCATCCAACGAGGGAGAA
* ** *
2404273 GAAGTTCATAATGAGAAGAACTTGTTCAAGTTTAGCTCGTTTCTATCACAAAAGGAGTTGGA
195 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGTTGGA
2404335 ACGACACTAA
Statistics
Matches: 225, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
276 1 0.00
277 160 0.71
278 64 0.28
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (279 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATAGAGTTGAATCAGCAACACATCA
CTAGAGGAATCAAAATTTCTAGTGAAGAATTCATAACGAGAAGAACTCATCCAACGAGGGAGAAA
AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGTTGGATCAA
CAACACCTCAATTGAGGGA
Found at i:2404618 original size:3 final size:3
Alignment explanation
Indices: 2404608--2404670 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
2404598 TATTTTTATT
2404608 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2404655 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
2404671 CAAAATATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2405639 original size:16 final size:17
Alignment explanation
Indices: 2405603--2405639 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2405593 ATGTGTTGTT
2405603 TTTTAATTTTATGTTTA
1 TTTTAATTTTATGTTTA
*
2405620 -TTTAGTTTTAT-TTTA
1 TTTTAATTTTATGTTTA
2405635 TTTTA
1 TTTTA
2405640 TTATTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTATGTTTA
Found at i:2405841 original size:104 final size:104
Alignment explanation
Indices: 2405673--2405921 Score: 410
Period size: 104 Copynumber: 2.4 Consensus size: 104
2405663 TATCGCTCCT
* * * *
2405673 AATTATTA-ACCGACCTTGCGATAACCTGATCTGGGATATGACCCGCATTATTACGATCTAGACT
1 AATTATTATA-CGACCTTGTGGTGACCTGATCTGGGGTATGACCCGCATTATTACGATCTAGACT
2405737 TTACTAATTTATAACACTAACATTTTTATTTATTTGTTTG
65 TTACTAATTTATAACACTAACATTTTTATTTATTTGTTTG
2405777 AATTATTATACGACCTTGTGGTGACCTGATCTGGGGTATGACCCGCATTATTACGATCTAGACTT
1 AATTATTATACGACCTTGTGGTGACCTGATCTGGGGTATGACCCGCATTATTACGATCTAGACTT
* *
2405842 TACTAATTTCTAACTCTAACATTTTTATTTATTTGTTTG
66 TACTAATTTATAACACTAACATTTTTATTTATTTGTTTG
* *
2405881 AATTATTATACTACCTTGTGGTGACGTGATCTGGGGTATGA
1 AATTATTATACGACCTTGTGGTGACCTGATCTGGGGTATGA
2405922 TCTGTAACAT
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
104 135 0.99
105 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (104 bp):
AATTATTATACGACCTTGTGGTGACCTGATCTGGGGTATGACCCGCATTATTACGATCTAGACTT
TACTAATTTATAACACTAACATTTTTATTTATTTGTTTG
Found at i:2406844 original size:65 final size:65
Alignment explanation
Indices: 2406684--2406844 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
2406674 TTGTTTAAGG
* * * **
2406684 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCAAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCAAATAGGATTT
2406747 A
65 A
* *
2406748 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCAAATAGGATTTA
*
2406812 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
2406845 ACCTTTATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCAAATAGGATTTA
Found at i:2407359 original size:18 final size:18
Alignment explanation
Indices: 2407336--2407370 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2407326 CTAGGAGATT
2407336 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2407354 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2407371 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2408443 original size:149 final size:150
Alignment explanation
Indices: 2408270--2408586 Score: 523
Period size: 151 Copynumber: 2.1 Consensus size: 150
2408260 GAGTCGAGGG
* ** *
2408270 TCTACGCGGTCCTTCGGG-ATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACA
1 TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAAACACA
2408334 TA-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATATGGTCCTTATGGACATCAT
66 TACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATATGGTCCTTATGGACATCAT
2408398 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
*
2408419 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAAACAC
1 TCTACGCGGTCCTTCGGGA-ATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAAACAC
* *
2408484 ATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTAT
65 ATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATATGGTCCTTATGGACATCAT
2408549 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
2408570 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2408587 TGCAATTATA
Statistics
Matches: 157, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
149 18 0.11
150 1 0.01
151 137 0.87
152 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAAACACA
TACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATATGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:2408587 original size:23 final size:23
Alignment explanation
Indices: 2408554--2408598 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2408544 ATTATTATAT
*
2408554 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2408577 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2408599 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2411894 original size:65 final size:65
Alignment explanation
Indices: 2411734--2411894 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
2411724 TTGTTTAAGG
* * * **
2411734 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
2411797 A
65 A
*
2411798 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
2411862 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
2411895 ACCTTTATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:2412409 original size:18 final size:18
Alignment explanation
Indices: 2412386--2412420 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2412376 CTAGGAGATT
2412386 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2412404 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2412421 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2413713 original size:148 final size:149
Alignment explanation
Indices: 2413305--2413765 Score: 797
Period size: 149 Copynumber: 3.1 Consensus size: 149
2413295 GAGTCGAGGG
2413305 TCTACGCGGTCCTTCGGG--ATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
2413368 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2413433 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2413452 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
*
2413517 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATATGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2413582 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * **
2413601 TCTACGCGGTCCTT-GGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
* * *
2413665 ACT-TTATCCCTAGCATATGTATATGATTCTTAAGAAATTCTATGTGGTCCTTATGGACATTATT
66 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
2413729 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
2413749 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2413766 TGCAATTATA
Statistics
Matches: 300, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
147 19 0.06
148 136 0.45
149 145 0.48
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2413766 original size:23 final size:23
Alignment explanation
Indices: 2413733--2413777 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2413723 ATTATTATAT
*
2413733 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2413756 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2413778 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2414621 original size:4 final size:4
Alignment explanation
Indices: 2414612--2414642 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2414602 ACTGTTAATT
*
2414612 TTTA TTTA TTTA TTTA CTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2414643 TATGTTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2414849 original size:28 final size:29
Alignment explanation
Indices: 2414791--2414852 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2414781 TTCGCATTCA
* * *
2414791 AATTTTTGTCCTTTACTTTTTATTTATTT
1 AATTTTAGTCCTTTACATTTCATTTATTT
2414820 AATTTTAGTCCTTTA-ATTTCA-TTACTTT
1 AATTTTAGTCCTTTACATTTCATTTA-TTT
2414848 AATTT
1 AATTT
2414853 ACTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 14 0.48
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (29 bp):
AATTTTAGTCCTTTACATTTCATTTATTT
Found at i:2418516 original size:3 final size:3
Alignment explanation
Indices: 2418502--2418532 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2418492 TTTTACTTAT
2418502 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
2418533 ACAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2425083 original size:69 final size:70
Alignment explanation
Indices: 2424927--2425113 Score: 172
Period size: 69 Copynumber: 2.7 Consensus size: 70
2424917 TATATATATA
* * * * *
2424927 ATATTTATT-TCAGGTGTCTAGTATAGGAGCCCCGAAGGATTAAAGTGA-TTCACATGGGAGTAC
1 ATATTTATTCT-AGGTGTCTAGCACAGGAGCCCCGAAGGATTAGAGTGACTTCACATGAGAGCAC
*
2424990 CTAATC
65 ATAATC
* * *
2424996 ATATTTATAC-ACGATGTCTCGCACAGGAGCCCCGAAGGATTAGAGTGACTTGCAC-T-AGAGCA
1 ATATTTATTCTA-GGTGTCTAGCACAGGAGCCCCGAAGGATTAGAGTGACTT-CACATGAGAGCA
*
2425058 CATATTC
64 CATAATC
* * *
2425065 ATATTTATTCTAGGTGTCTTGCAC-GAGAACACC-AAGGATTAGAGTGACT
1 ATATTTATTCTAGGTGTCTAGCACAG-GAGCCCCGAAGGATTAGAGTGACT
2425114 CATAAATTGT
Statistics
Matches: 97, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
68 18 0.19
69 72 0.74
70 4 0.04
71 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (70 bp):
ATATTTATTCTAGGTGTCTAGCACAGGAGCCCCGAAGGATTAGAGTGACTTCACATGAGAGCACA
TAATC
Found at i:2433389 original size:2 final size:2
Alignment explanation
Indices: 2433382--2433427 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2433372 GGATTTAATG
2433382 TA TA TA TA 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
2433424 TA TA
1 TA TA
2433428 GACACTAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2433462 original size:3 final size:3
Alignment explanation
Indices: 2433456--2433483 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2433446 CGTTTTTTTA
2433456 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2433484 AATAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2435616 original size:15 final size:16
Alignment explanation
Indices: 2435596--2435633 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2435586 AGGCTAAATA
2435596 ATAATAATATTATA-T
1 ATAATAATATTATATT
*
2435611 ATAATATTATTATATT
1 ATAATAATATTATATT
2435627 ATAATAA
1 ATAATAA
2435634 CGTTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATAATATTATATT
Found at i:2436402 original size:20 final size:20
Alignment explanation
Indices: 2436340--2436645 Score: 382
Period size: 20 Copynumber: 15.2 Consensus size: 20
2436330 AGACTAACAG
* * *
2436340 ATGACCCAAAGGATTTACAT
1 ATGACCCGAAGGCTTTACAA
*
2436360 ATTACCCGAAGGCTTTTACAA
1 ATGACCCGAAGGC-TTTACAA
* * *
2436381 ATGACCTGGAGGCTTTATAA
1 ATGACCCGAAGGCTTTACAA
*
2436401 ATGGCCC-AGAGGCTTTAC-A
1 ATGACCCGA-AGGCTTTACAA
* *
2436420 ATAGACTCGGAGGCTTTACAA
1 AT-GACCCGAAGGCTTTACAA
*
2436441 ATGACCCGAAGGTTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
2436461 ATGACCCGAAGTCTTTACAA
1 ATGACCCGAAGGCTTTACAA
2436481 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
2436501 ATGACCTGGAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* * *
2436521 ATGACCCTAATGTTTTACAA
1 ATGACCCGAAGGCTTTACAA
2436541 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
2436561 AAGACCTGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
2436581 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
2436601 ATGACCTGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
2436621 ATGACCCAAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
2436641 ATGAC
1 ATGAC
2436646 TGTGTTGGTT
Statistics
Matches: 243, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.01
20 221 0.91
21 19 0.08
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:2443290 original size:27 final size:30
Alignment explanation
Indices: 2443239--2443296 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
2443229 AAATATACGC
* *
2443239 ATATATATATATATAATAACTAAAA-TAAA
1 ATATATATAAATATAAAAACTAAAATTAAA
2443268 ATATATA-AAATATAAAAAC-AAAATTAAA
1 ATATATATAAATATAAAAACTAAAATTAAA
2443296 A
1 A
2443297 CACGCAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 15 0.58
29 7 0.27
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
ATATATATAAATATAAAAACTAAAATTAAA
Found at i:2447686 original size:21 final size:21
Alignment explanation
Indices: 2447660--2447699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2447650 CAGAACCCCA
*
2447660 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2447681 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2447700 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2451547 original size:22 final size:21
Alignment explanation
Indices: 2451505--2451544 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2451495 GAGTTTGTTT
*
2451505 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2451526 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2451545 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2453930 original size:16 final size:15
Alignment explanation
Indices: 2453909--2453949 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
2453899 TTCGGGCTAA
2453909 ATATAATAATATTAAT
1 ATATAATAATATT-AT
*
2453925 ATATAATATTATTAT
1 ATATAATAATATTAT
2453940 ATTATAATAA
1 A-TATAATAA
2453950 CGTATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATAATAATATTAT
Found at i:2453932 original size:13 final size:13
Alignment explanation
Indices: 2453908--2453941 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2453898 CTTCGGGCTA
2453908 AATATAATAATATT
1 AATAT-ATAATATT
2453922 AATATATAATATT
1 AATATATAATATT
*
2453935 ATTATAT
1 AATATAT
2453942 TATAATAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATAATATT
Found at i:2458087 original size:35 final size:35
Alignment explanation
Indices: 2458047--2458119 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
2458037 GAGGCTGTGG
2458047 GGGTAGGGTGGGGTGGGATGTGGGAGAGGAGGGTA
1 GGGTAGGGTGGGGTGGGATGTGGGAGAGGAGGGTA
2458082 GGGTAGGGTGGGGTGGGATGTGGGAGAGGAGGGTA
1 GGGTAGGGTGGGGTGGGATGTGGGAGAGGAGGGTA
2458117 GGG
1 GGG
2458120 GTGTGCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.67, T:0.16
Consensus pattern (35 bp):
GGGTAGGGTGGGGTGGGATGTGGGAGAGGAGGGTA
Found at i:2458163 original size:13 final size:13
Alignment explanation
Indices: 2458145--2458170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2458135 CGATCCGACC
2458145 GATCCGATCCGTT
1 GATCCGATCCGTT
2458158 GATCCGATCCGTT
1 GATCCGATCCGTT
2458171 TTTCAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
GATCCGATCCGTT
Found at i:2458868 original size:21 final size:21
Alignment explanation
Indices: 2458824--2458869 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2458814 AATTTACGTG
*
2458824 TTTAGTATCTAAATTTTCAGT
1 TTTAGTATCTAAATTTTCAAT
*
2458845 TTTAGTATTTAAACTTTT-AAT
1 TTTAGTATCTAAA-TTTTCAAT
2458866 TTTA
1 TTTA
2458870 TGTTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAGTATCTAAATTTTCAAT
Found at i:2459827 original size:37 final size:36
Alignment explanation
Indices: 2459751--2459823 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
2459741 TTTTTATATT
2459751 TTTAATTTTGTAAAAAAATTTATATAAATATTATAAA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATAAA
* *
2459788 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTAAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATAAA
2459824 ATTTGTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 16 0.48
37 13 0.39
38 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
Found at i:2459850 original size:18 final size:17
Alignment explanation
Indices: 2459803--2459851 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
2459793 TTTTTTAAAG
*
2459803 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
2459821 AAAATTTGTAATATTAT
1 AAAATATATAATATTAT
2459838 ACAAATATATAATA
1 A-AAATATATAATA
2459852 AGGACAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:2461331 original size:9 final size:9
Alignment explanation
Indices: 2461271--2461333 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
2461261 TTGTTCTTTT
2461271 TTTTTA-TA
1 TTTTTATTA
*
2461279 TTTTTTTTA
1 TTTTTATTA
**
2461288 TTTTTAACA
1 TTTTTATTA
2461297 TCTTTTA-TA
1 T-TTTTATTA
2461306 TTTTCTTATTA
1 -TTT-TTATTA
2461317 TTTTTATTA
1 TTTTTATTA
2461326 TTTTTATT
1 TTTTTATT
2461334 TTTCCTTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
8 5 0.11
9 26 0.58
10 12 0.27
11 2 0.04
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2461337 original size:27 final size:27
Alignment explanation
Indices: 2461271--2461342 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 27
2461261 TTGTTCTTTT
2461271 TTTTTATATTTT-TTTTATTTTTAACA
1 TTTTTATATTTTCTTTTATTTTTAACA
**
2461297 TCTTTTATATTTTCTTATTATTTTTATTA
1 T-TTTTATATTTTCTT-TTATTTTTAACA
2461326 TTTTTAT-TTTTCCTTTT
1 TTTTTATATTTT-CTTTT
2461343 CTCTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.03
27 17 0.43
28 11 0.28
29 11 0.28
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTTATATTTTCTTTTATTTTTAACA
Found at i:2461566 original size:30 final size:32
Alignment explanation
Indices: 2461497--2461567 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 32
2461487 ATTGTTTATT
* * *
2461497 TATTTATTGTTTTTTCTTTTGATTTATTATCAT
1 TATTTATT-TTTCTTCTTTTGATTTATTATAAA
*
2461530 TA-TTATTTTTCTTC-TTTGGTTTATT-TAAA
1 TATTTATTTTTCTTCTTTTGATTTATTATAAA
2461559 TATTTATTT
1 TATTTATTT
2461568 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 4 0.12
30 16 0.48
31 6 0.18
32 5 0.15
33 2 0.06
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (32 bp):
TATTTATTTTTCTTCTTTTGATTTATTATAAA
Found at i:2461584 original size:14 final size:14
Alignment explanation
Indices: 2461561--2461593 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2461551 TATTTAAATA
*
2461561 TTTATTTATTATTT
1 TTTATCTATTATTT
2461575 TTTATCTATTATTT
1 TTTATCTATTATTT
2461589 TTTAT
1 TTTAT
2461594 TTTTTTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATCTATTATTT
Found at i:2465229 original size:64 final size:64
Alignment explanation
Indices: 2465128--2465358 Score: 444
Period size: 64 Copynumber: 3.6 Consensus size: 64
2465118 TGCAATTTTT
*
2465128 AGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
2465192 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACGACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
2465256 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
2465320 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
2465359 GAAACAACAC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 164 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:2465517 original size:121 final size:121
Alignment explanation
Indices: 2465366--2466097 Score: 1052
Period size: 121 Copynumber: 6.0 Consensus size: 121
2465356 CTCGAAACAA
* * * *
2465366 CACAAGCAGCAATACAACCCTTGGATTTCAACTTCATGACGAAGGATATCCGATTAAAAGCTCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
*
2465431 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATACC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
* * * * *
2465487 CACAAGTAGCAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGTTATCCAATTTAAGGCTCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
* * *
2465552 CTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
** *
2465608 CACAAGCATTAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
* * * * *
2465673 CTTCACAAAGAAGGAGCCATCCATGATTTCAACTTCACGACCAATGATATCATGCC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
* ** * * *
2465729 CATAAGCAATAATGCAACCCTTGGATTTCAACTTCACGATGAAGGATATTCGATTCAAAGCTCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
2465794 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGA-GCC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATC-ATGCC
* * * * * * *
2465850 CATAAGCATCAATACGACCCTTGGATTTCAATTTCACAACGAAGGATATCCAATTCAAAGATCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
* * * *
2465915 CTTCACAACTAATGAGCCATCCACGATTTTAACTTCACGACAAAGGATATCGTGCC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
* *
2465971 CACAAGTAGCAATGCAACCCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAA
1 CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
* * * *
2466036 CTTCACACCGAATGAGCCATCCACGATTTCAACTTCACGAGGAAGGTTATCGTGCC
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
2466092 CACAAG
1 CACAAG
2466098 AATGAGCCAT
Statistics
Matches: 546, Mismatches: 63, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
121 545 1.00
122 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (121 bp):
CACAAGCAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAA
CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCC
Found at i:2465794 original size:242 final size:242
Alignment explanation
Indices: 2465366--2466222 Score: 1101
Period size: 242 Copynumber: 3.5 Consensus size: 242
2465356 CTCGAAACAA
* * * * *
2465366 CACAAGCAGCAATACAACCCTTGGATTTCAACTTCATGACGAAGGATATCCGATTAAAAGCTCAA
1 CACAAGCATCAATACAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAA
* *
2465431 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATACCCACAAGTAG
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACAAAGGATATCATGCCCACAAGTAG
* * *
2465496 CAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGTTATCCAATTTAAGGCTCAACTTCACAAC
131 CAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAC
* *
2465561 GAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
196 GAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* *
2465608 CACAAGCATTAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAA
1 CACAAGCATCAATACAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAA
* * * * * * * *
2465673 CTTCACAAAGAAGGAGCCATCCATGATTTCAACTTCACGACCAATGATATCATGCCCATAAGCAA
66 CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACAAAGGATATCATGCCCACAAGTAG
* * * *
2465738 TAATGCAACCCTTGGATTTCAACTTCACGATGAAGGATATTCGATTCAAAGCTCAACTTCACAAC
131 CAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAC
*
2465803 GAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGAGCC
196 GAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* * * *
2465850 CATAAGCATCAATACGACCCTTGGATTTCAATTTCAC-AACGAAGGATATCCAATTCAAAGATCA
1 CACAAGCATCAATACAACCCTTGGATTTCAACTTCACGAA-GAAGGATATCCAATTCAAAGCTCA
* * *
2465914 ACTTCACAACTAATGAGCCATCCACGATTTTAACTTCACGACAAAGGATATCGTGCCCACAAGTA
65 ACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACAAAGGATATCATGCCCACAAGTA
2465979 GCAATGCAACCCTTGGATTTCAACTTCACGACA-AAGGATATCCAATTCAAAGCTCAACTTCACA
130 GCAATGCAACCCTTGGATTTCAACTTCACGA-AGAAGGATATCCAATTCAAAGCTCAACTTCACA
* * *
2466043 CCGAATGAGCCATCCACGATTTCAACTTCACGAGGAAGGTTATCGTGCC
194 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* * *
2466092 CACAAGAATGAGCCATCCCGATTTCAACTGCAACTCTTGGATTTCAACTTCACGACGAAGGATAT
1 CAC----A--AG------C-A--TCAA-TACAACCCTTGGATTTCAACTTCACGAAGAAGGATAT
* * * * * *
2466157 ACAATTCAAGGCTCAAATTCACGAA-GAATGAGCCATCC-CGATTTCGACTTCACAACGAAGGAT
50 CCAATTCAAAGCTCAACTTCAC-AACGAATGAGCCATCCACGATTTCAACTTCACGACAAAGGAT
2466220 ATC
114 ATC
2466223 GTACCTAAAA
Statistics
Matches: 529, Mismatches: 66, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
241 2 0.00
242 431 0.81
246 1 0.00
248 2 0.00
254 1 0.00
255 1 0.00
257 28 0.05
258 60 0.11
259 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (242 bp):
CACAAGCATCAATACAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAA
CTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACAAAGGATATCATGCCCACAAGTAG
CAATGCAACCCTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAC
GAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
Found at i:2466055 original size:363 final size:372
Alignment explanation
Indices: 2465380--2466227 Score: 1132
Period size: 363 Copynumber: 2.3 Consensus size: 372
2465370 AGCAGCAATA
* * *
2465380 CAACCCTTGGATTTCAACTTCATGACGAAGGATATCCGATTAAAAGCTCAACTTCACAACGAATG
1 CAACCCTTGGATTTCAACTTCACGACGAAGGATATACGATTCAAAGCTCAACTTCACAACGAATG
* *
2465445 AGCCATCCACGATTTCAACTTCACGACGAAGGATATC-ATACCCACAAGTAGCAATGCAACCCTT
66 AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGATACCCACAAGCAGCAATACAACCCTT
* * * * *
2465509 GGATTTCAACTTCACGAAGAAGGTTATCCAATTTAAGGCTCAACTTCACAACGAAGGGGCCATCC
131 GGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGATCAACTTCACAACGAAGGAGCCATCC
* **
2465574 ACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCATTAATGCAACCCTTGGATTTCAA
196 ACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAA
*
2465639 CTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAAGAAGGAGCCATCCATGATTTCA
261 CTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAAGAAGGAGCCATCCACGATTTCA
*
2465704 ACTTCACGACCAATGATATCATG-CC-C-ATAAG-CA-A-T-AA-TG
326 ACTTCACGACCAAGGATATCATGCCCACAATAAGCCACATTCAACTG
* *
2465743 CAACCCTTGGATTTCAACTTCACGATGAAGGATATTCGATTCAAAGCTCAACTTCACAACGAATG
1 CAACCCTTGGATTTCAACTTCACGACGAAGGATATACGATTCAAAGCTCAACTTCACAACGAATG
* * * *
2465808 AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGA-GCCCATAAGCATCAATACGACCCTT
66 AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGATACCCACAAGCAGCAATACAACCCTT
* * *
2465872 GGATTTCAATTTCAC-AACGAAGGATATCCAATTCAAAGATCAACTTCACAACTAATGAGCCATC
131 GGATTTCAACTTCACGAA-GAAGGATATCCAATTCAAAGATCAACTTCACAACGAAGGAGCCATC
* *
2465936 CACGATTTTAACTTCACGACAAAGGATATCGTGCCCACAAGTAGCAATGCAACCCTTGGATTTCA
195 CACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCA
** *
2466001 ACTTCACGACA-AAGGATATCCAATTCAAAGCTCAACTTCACACCGAATGAGCCATCCACGATTT
260 ACTTCACGA-AGAAGGATATCCAATTCAAAGCTCAACTTCACAAAGAAGGAGCCATCCACGATTT
** * * *
2466065 CAACTTCACGAGGAAGGTTATCGTGCCCACAAGAATGAGCCATCCCGATTTCAACTG
324 CAACTTCACGACCAAGGATATCATGCCCAC---AATAAGCCA---C-A-TTCAACTG
* * * *
2466122 CAACTCTTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGCTCAAATTCACGAA-GAAT
1 CAACCCTTGGATTTCAACTTCACGACGAAGGATATACGATTCAAAGCTCAACTTCAC-AACGAAT
* *
2466186 GAGCCATCC-CGATTTCGACTTCACAACGAAGGATATCG-TACC
65 GAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGATACC
2466228 TAAAAGATTG
Statistics
Matches: 422, Mismatches: 42, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
362 2 0.00
363 308 0.73
364 4 0.01
365 1 0.00
369 4 0.01
370 2 0.00
375 1 0.00
377 1 0.00
378 31 0.07
379 66 0.16
380 2 0.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (372 bp):
CAACCCTTGGATTTCAACTTCACGACGAAGGATATACGATTCAAAGCTCAACTTCACAACGAATG
AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGATACCCACAAGCAGCAATACAACCCTT
GGATTTCAACTTCACGAAGAAGGATATCCAATTCAAAGATCAACTTCACAACGAAGGAGCCATCC
ACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAA
CTTCACGAAGAAGGATATCCAATTCAAAGCTCAACTTCACAAAGAAGGAGCCATCCACGATTTCA
ACTTCACGACCAAGGATATCATGCCCACAATAAGCCACATTCAACTG
Found at i:2466661 original size:3 final size:3
Alignment explanation
Indices: 2466655--2466704 Score: 73
Period size: 3 Copynumber: 15.7 Consensus size: 3
2466645 TTTAAAAAAA
2466655 TAT TATT TATT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2466703 TA
1 TA
2466705 ACATAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 35 0.76
4 11 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2468338 original size:29 final size:30
Alignment explanation
Indices: 2468312--2468369 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2468302 TTATTATTTT
2468312 TACATTTTCTCTTTATTTTA-ATTTATTTAA
1 TACATTTTCTC-TTATTTTATATTTATTTAA
* *
2468342 TATATTTTTTCTTATTTTATATTT-TTTA
1 TACATTTTCTCTTATTTTATATTTATTTA
2468370 TTCCTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (30 bp):
TACATTTTCTCTTATTTTATATTTATTTAA
Found at i:2468400 original size:4 final size:4
Alignment explanation
Indices: 2468379--2468495 Score: 52
Period size: 4 Copynumber: 29.5 Consensus size: 4
2468369 ATTCCTTTTG
* * *
2468379 ATTT ATTT TTATT GTTT ATTT ATTT ATTT A-TT ATTT -TTT CTTTT GATTT
1 ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT -ATTT
* *
2468428 A-TC ATCATT ATTT ATTT A-TT ATTT -TTT -TCTT CTTT GATTT ATTT
1 ATTT AT--TT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT -ATTT ATTT
**
2468472 AAAT ATTT ATTT A-TT ATTT -TTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
2468496 CTAATATTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
3 21 0.24
4 51 0.58
5 13 0.15
6 3 0.03
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2468423 original size:45 final size:41
Alignment explanation
Indices: 2468399--2468493 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 41
2468389 ATTGTTTATT
* **
2468399 TATTTATTTATTATTTT-TTCTTTTGATTTATCATCATTATT
1 TATTTA-TTATTTTTTTCTTCTTTTGATTTATTTTCATTATT
* *
2468440 TATTTATTATTTTTTTCTTC-TTTGATTTA-TTTAAATATT
1 TATTTATTATTTTTTTCTTCTTTTGATTTATTTTCATTATT
2468479 TATTTATTATTTTTT
1 TATTTATTATTTTTT
2468494 ATCTAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 21 0.44
40 18 0.38
41 9 0.19
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (41 bp):
TATTTATTATTTTTTTCTTCTTTTGATTTATTTTCATTATT
Done.