Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:578214 original size:27 final size:24
Alignment explanation
Indices: 578159--578219 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 24
578149 AAAATATTTG
578159 AAAATATAT-TTTTTGAAAATTAT
1 AAAATATATATTTTTGAAAATTAT
* *
578182 ATAATATATAGTTTTTGAAAACGTTTT
1 AAAATATATA-TTTTTGAAAA--TTAT
578209 AAAATATATAT
1 AAAATATATAT
578220 AATATATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 8 0.26
25 10 0.32
26 1 0.03
27 12 0.39
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
AAAATATATATTTTTGAAAATTAT
Found at i:578222 original size:36 final size:37
Alignment explanation
Indices: 578169--578358 Score: 176
Period size: 36 Copynumber: 5.1 Consensus size: 37
578159 AAAATATATT
578169 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
*
578205 TTTT-AAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
* * * *
578240 TTATGAAAACATTTATATAATATA-A-TTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAA-CG
* *
578278 TTTTGAAAATATATATAATATATAGTTTTTAAAAAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTT-----GAAAACG
* * *
578320 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
578356 TTT
1 TTT
578359 ATATATATAT
Statistics
Matches: 129, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
35 19 0.15
36 38 0.29
37 16 0.12
38 23 0.18
41 6 0.05
42 22 0.17
43 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
Found at i:578258 original size:122 final size:119
Alignment explanation
Indices: 578051--578291 Score: 389
Period size: 117 Copynumber: 2.0 Consensus size: 119
578041 TTTTAAAATA
*
578051 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATAATATACTTTTGAAAA
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAAATATAATATACTTTTGAAAA
578116 CGTTATGAAAACATTTATAT-ATATAA-TTTTAAAAA-AATATTTGAAAATATAT
66 CGTTATGAAAACATTTATATAATATAATTTTTAAAAACAAT-TTTGAAAATATAT
578168 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATATAATATATACTTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTT-AAA-A-ATAT-A-ATATACTTTT
*
578233 GAAAACGTTATGAAAACATTTATATAATATAATTTTTAAAAACCATTTTGAAAATATAT
61 GAAAACGTTATGAAAACATTTATATAATATAATTTTTAAAAACAATTTTGAAAATATAT
578292 ATAATATATA
Statistics
Matches: 114, Mismatches: 2, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
117 41 0.36
118 2 0.02
119 1 0.01
120 4 0.04
121 1 0.01
122 35 0.31
123 6 0.05
124 22 0.19
125 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (119 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAAATATAATATACTTTTGAAAA
CGTTATGAAAACATTTATATAATATAATTTTTAAAAACAATTTTGAAAATATAT
Found at i:578329 original size:42 final size:41
Alignment explanation
Indices: 578270--578353 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
578260 TATAATTTTT
* *
578270 AAAAACCATTTTGAAAATATATATAATATATAGTTTTTAAAA
1 AAAAAACATTTTAAAAATATATATAATATAT-GTTTTTAAAA
* * *
578312 AAAAAACATTTTAAAAATTTATATATTATATGTTTTTGAAA
1 AAAAAACATTTTAAAAATATATATAATATATGTTTTTAAAA
578353 A
1 A
578354 CGTTTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (41 bp):
AAAAAACATTTTAAAAATATATATAATATATGTTTTTAAAA
Found at i:581525 original size:19 final size:19
Alignment explanation
Indices: 581503--581548 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
581493 ATTTAGACAT
*
581503 TTTGCATTTTTTTATTTTC
1 TTTGCATTTTATTATTTTC
581522 TTTGCATTTTATTATTTTC
1 TTTGCATTTTATTATTTTC
*
581541 TCTGCATT
1 TTTGCATT
581549 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTATTATTTTC
Found at i:585148 original size:164 final size:164
Alignment explanation
Indices: 584878--585745 Score: 885
Period size: 165 Copynumber: 5.3 Consensus size: 164
584868 TGCAGCTTAG
* * * * *
584878 CTCAAGGCCAGAAGGGCTACCTGCCA-CTAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
584942 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
585007 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* * * *
585041 CTCAAGGCTAGAAGGGTTATCTGTCGCCAAAGACCTTTGGGTTCGACTACGCTCAGCTCCTAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
585106 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
585171 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* *
585205 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTCCGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * **
585270 CACATCATTTGCAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
** * * *
585335 CACTCAGCTTCGGGGGCACATCATTTGCAGCATAA
130 CACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* * * * * *
585370 CTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * * * * * *
585435 CACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTC
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTT-AAGTTC
* * * * * * * *
585499 GACTCCGCTCAGCTCCAA-GGCACATCATTTGCAGCATAG
125 GATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* * * * ** * * * *
585538 CTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGG
* * * * * * * *
585600 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTC
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTT-AAGTTC
* * * * * * * *
585664 GACTCCGCTCAGCTCCAA-GGCACATCATTTGCAGCATAG
125 GATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* * * * *
585703 CTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCTTCGAGTTCGA
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGA
585746 TTATATTCAA
Statistics
Matches: 633, Mismatches: 63, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
163 21 0.03
164 186 0.29
165 354 0.56
166 2 0.00
167 2 0.00
168 46 0.07
169 22 0.03
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
Found at i:585474 original size:249 final size:246
Alignment explanation
Indices: 584906--585745 Score: 973
Period size: 249 Copynumber: 3.4 Consensus size: 246
584896 ACCTGCCACT
* * * * *
584906 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAG
* * * * * * *
584971 AAGGGCTATCTG--CC-AAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTT
66 AAGGGCTATCTGTACCAAAAGA-CCTTCGAGTTCGACTCCGCTCAGCTCCAA-GGCACATCATTT
* * * * * * *** * * *
585032 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCGCCAAAGACCTTTGGGTTCGACTACGCTCAG
129 GCAGCATAGCTTAAGTCGAGAAGGGCTATC--T-GCCAAAGACCCCCGAGTTCGATTACACTCAG
* * * * *
585097 CTCCTA-GGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGC-C-A
191 CTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAA
* * * * * * * *
585150 AAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGGCG
* *
585214 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTCCGCTCAGCTCCAAGGCACATCATT
64 AGAAGGGCTATCTGT-ACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATT
* * *
585279 TGCAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCT
128 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
*
585344 TCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
193 TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACAA
* *
585400 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGTAGCATAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAG
*
585465 AAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTG
66 AAGGGCTATCTGT-ACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTG
585530 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
130 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
* * * * *
585595 GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
195 GAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CA-CAA
* * * * *
585649 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAG
*
585714 AAGGGCTATCTG---CTAAAGACCTTCGAGTTCGA
66 AAGGGCTATCTGTACCAAAAGACCTTCGAGTTCGA
585746 TTATATTCAA
Statistics
Matches: 510, Mismatches: 72, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
244 20 0.04
245 88 0.17
246 42 0.08
247 1 0.00
248 39 0.08
249 299 0.59
250 21 0.04
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (246 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAG
AAGGGCTATCTGTACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGC
AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCG
AGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAA
Found at i:586474 original size:36 final size:36
Alignment explanation
Indices: 586362--586536 Score: 134
Period size: 36 Copynumber: 5.0 Consensus size: 36
586352 TTTGCAAATT
* *
586362 GTTTTT-AAAAATACATAATAATATAG-TTT-AAAAC
1 GTTTTTGAAAATTATATAAT-ATATAGTTTTGAAAAC
* * * * *
586396 ATTTTTGAAAATATGTATATTATATAGTTTTTAAAAT
1 GTTTTTGAAAAT-TATATAATATATAGTTTTGAAAAC
*
586433 ATTTTTGAAAATTATATAATATATAGTTTTGAAAAC
1 GTTTTTGAAAATTATATAATATATAGTTTTGAAAAC
*
586469 GTTTTT--AAA-TATAT-ATAATATACTTTTGAAAAC
1 GTTTTTGAAAATTATATAAT-ATATAGTTTTGAAAAC
* * *
586502 G-TTATGAAAACATT-TATAATATATAATTTTAAAAA
1 GTTTTTG-AAA-ATTATATAATATATAGTTTTGAAAA
586537 AACCATTTTG
Statistics
Matches: 115, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
32 5 0.04
33 21 0.18
34 8 0.07
35 12 0.10
36 50 0.43
37 19 0.17
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (36 bp):
GTTTTTGAAAATTATATAATATATAGTTTTGAAAAC
Found at i:586479 original size:71 final size:72
Alignment explanation
Indices: 586336--586491 Score: 169
Period size: 72 Copynumber: 2.2 Consensus size: 72
586326 ACATATACAC
* *
586336 ATAT-TATTATACAGTTTTTGCAAATTGTTTTTAAAAATACATAATAATATAGTTTAAAACATTT
1 ATATATATTATACAGTTTTTGAAAATTGTTTTGAAAAATACATAATAATATAGTTTAAAACATTT
586400 TTGAAAAT
66 TT-AAAAT
* * * * *
586408 ATGTATATTATATAGTTTTT-AAAATAT-TTTTGAAAATTATATAAT-ATATAGTTTTGAAAACG
1 ATATATATTATACAGTTTTTGAAAAT-TGTTTTGAAAAATACATAATAATATAG-TTT-AAAACA
586470 TTTTT-AAAT
63 TTTTTAAAAT
*
586479 ATATATAATATAC
1 ATATATATTATAC
586492 TTTTGAAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
71 20 0.29
72 25 0.36
73 25 0.36
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (72 bp):
ATATATATTATACAGTTTTTGAAAATTGTTTTGAAAAATACATAATAATATAGTTTAAAACATTT
TTAAAAT
Found at i:586559 original size:14 final size:15
Alignment explanation
Indices: 586542--586570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
586532 AAAAAAACCA
586542 TTTTGAAAA-TATAT
1 TTTTGAAAATTATAT
586556 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
586571 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTTGAAAATTATAT
Found at i:586602 original size:25 final size:22
Alignment explanation
Indices: 586541--586604 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 22
586531 TAAAAAAACC
586541 ATTTTGAAAATATATTTTTGAAA
1 ATTTT-AAAATATATTTTTGAAA
*
586564 ATTATATAATATATAGTTTTTGAAA
1 ATT-T-TAAAATATA-TTTTTGAAA
586589 ACGTTTTAAAATATAT
1 A--TTTTAAAATATAT
586605 AATATATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 3 0.09
24 9 0.26
25 19 0.56
26 1 0.03
27 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTTTAAAATATATTTTTGAAA
Found at i:586605 original size:34 final size:35
Alignment explanation
Indices: 586556--586734 Score: 145
Period size: 34 Copynumber: 5.1 Consensus size: 35
586546 GAAAATATAT
586556 TTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAA-TATATAATATATAGTTTTTGAAAACG
*
586592 TTTT-AAAATATATAATATATA-CTTTTGAAAACG
1 TTTTGAAAATATATAATATATAGTTTTTGAAAACG
* * * * *
586625 TTATGAAAACAT-TTATAATATA-TTTTTAAAAACCA
1 TTTTGAAAATATATAAT-ATATAGTTTTTGAAAA-CG
** *
586660 TTTTGAAAATATAT-ATAATATATGTTTTAAAAAAAACA
1 TTTTGAAAATATATAAT-ATATA-GTTTT--TGAAAACG
* * *
586698 TTTTAAAAATTTATATTATAT-GTTTTTGAAAACG
1 TTTTGAAAATATATAATATATAGTTTTTGAAAACG
586732 TTT
1 TTT
586735 ATATATATAT
Statistics
Matches: 118, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
33 17 0.14
34 40 0.34
35 23 0.19
36 10 0.08
37 4 0.03
38 18 0.15
39 6 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATATATAATATATAGTTTTTGAAAACG
Found at i:586676 original size:122 final size:119
Alignment explanation
Indices: 586431--586673 Score: 420
Period size: 122 Copynumber: 2.0 Consensus size: 119
586421 AGTTTTTAAA
*
586431 ATATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTTAAATATATATAATATACTTTT
1 ATATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTAAAATATATATAATATACTTTT
586496 GAAAACGTTATGAAAACATTTATAATATATAATTTTAAAAAAACCATTTTGAAAAT
66 GAAAACGTTATGAAAACATTTATAATATAT-ATTTT-AAAAAACCATTTTGAAAAT
586552 ATATTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATA-ATATATACTT
1 ATATTTTTGAAAATTATATAATATATAG-TTTTGAAAACGTTTTAAAATATATATA-ATATACTT
586616 TTGAAAACGTTATGAAAACATTTATAATATAT-TTTT-AAAAACCATTTTGAAAAT
64 TTGAAAACGTTATGAAAACATTTATAATATATATTTTAAAAAACCATTTTGAAAAT
586670 ATAT
1 ATAT
586674 ATAATATATG
Statistics
Matches: 119, Mismatches: 1, Indels: 7
0.94 0.01 0.06
Matches are distributed among these distances:
118 22 0.18
120 4 0.03
121 29 0.24
122 64 0.54
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (119 bp):
ATATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTAAAATATATATAATATACTTTT
GAAAACGTTATGAAAACATTTATAATATATATTTTAAAAAACCATTTTGAAAAT
Found at i:586707 original size:38 final size:34
Alignment explanation
Indices: 586556--586723 Score: 126
Period size: 36 Copynumber: 4.8 Consensus size: 34
586546 GAAAATATAT
* ** *
586556 TTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTAAAAATT-TATAATATAT-GTTTTAAAAAACA
* * * *
586592 TTTT-AAAATATATAATATATACTTTT-GAAAACG
1 TTTTAAAAATTTATAATATAT-GTTTTAAAAAACA
* *
586625 TTATGAAAACATTTATAATATAT-TTTTAAAAACCA
1 TT-TTAAAA-ATTTATAATATATGTTTTAAAAAACA
*
586660 TTTTGAAAATATATATAATATATGTTTTAAAAAAAACA
1 TTTT-AAAA-ATTTATAATATATGTTTT--AAAAAACA
*
586698 TTTTAAAAATTTATATTATATGTTTT
1 TTTTAAAAATTTATAATATATGTTTT
586724 TGAAAACGTT
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
33 9 0.08
34 21 0.19
35 30 0.27
36 36 0.32
37 4 0.04
38 11 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
TTTTAAAAATTTATAATATATGTTTTAAAAAACA
Found at i:586765 original size:16 final size:17
Alignment explanation
Indices: 586746--586778 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
586736 TATATATATA
586746 TTATTATT-ATTTATTT
1 TTATTATTAATTTATTT
*
586762 TTATTTTTAATTTATTT
1 TTATTATTAATTTATTT
586779 ATTTCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTAATTTATTT
Found at i:588877 original size:29 final size:28
Alignment explanation
Indices: 588834--588888 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
588824 GTTGGGTCAA
*
588834 CATTTTGTAACTTTTAACAGTCGAATGAT
1 CATTTTATAACTTTTAACAGTC-AATGAT
* *
588863 CATTTTATAATTTTTAATAGTCAATG
1 CATTTTATAACTTTTAACAGTCAATG
588889 GACTTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (28 bp):
CATTTTATAACTTTTAACAGTCAATGAT
Found at i:589834 original size:18 final size:18
Alignment explanation
Indices: 589811--589848 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
589801 ATAAACGGGG
589811 ACTCGATCTACAAAATAC
1 ACTCGATCTACAAAATAC
589829 ACTCGATCTACAAAATAC
1 ACTCGATCTACAAAATAC
589847 AC
1 AC
589849 CTCAAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (18 bp):
ACTCGATCTACAAAATAC
Found at i:590346 original size:22 final size:21
Alignment explanation
Indices: 590321--590368 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
590311 TCTTAAATAC
*
590321 ATATATTATTTATAAGTATT-AT
1 ATATATTATATATAA-T-TTAAT
590343 ATATA-TATATATAATTTAAT
1 ATATATTATATATAATTTAAT
590363 ATATAT
1 ATATAT
590369 GTGTGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 8 0.35
21 8 0.35
22 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATATTATATATAATTTAAT
Found at i:590571 original size:28 final size:25
Alignment explanation
Indices: 590535--590588 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
590525 GCGACAATAA
*
590535 TTTTAAAATTGTATTTTTGTAATTATTT
1 TTTTAAAATT-TA-ATTT-TAATTATTT
*
590563 TTTTCAAATTTAATTTTAATTATTT
1 TTTTAAAATTTAATTTTAATTATTT
590588 T
1 T
590589 AATTACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 2 0.08
28 9 0.38
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTAAAATTTAATTTTAATTATTT
Found at i:590845 original size:40 final size:40
Alignment explanation
Indices: 590801--590884 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
590791 TAATTAATAT
* ** *
590801 AATAAAAATTTAAGTTTTAGAAAAAATCATTAAAAGTTAA
1 AATAAAAATGTAAACTTTACAAAAAATCATTAAAAGTTAA
** *
590841 AATAAAAATGTAAACTTTACAAATTATCATTAAAAGTTGA
1 AATAAAAATGTAAACTTTACAAAAAATCATTAAAAGTTAA
590881 AATA
1 AATA
590885 TGATAAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (40 bp):
AATAAAAATGTAAACTTTACAAAAAATCATTAAAAGTTAA
Found at i:592404 original size:2 final size:2
Alignment explanation
Indices: 592397--592490 Score: 84
Period size: 2 Copynumber: 48.0 Consensus size: 2
592387 TTTCCAACCC
* * *
592397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
592439 GA CA CA GA TA AA T- TA T- TT TA TT 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
592479 TA TA TA TA TA TA
1 TA TA TA TA TA TA
592491 GATTGTCAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:592501 original size:54 final size:52
Alignment explanation
Indices: 592409--592517 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
592399 TATATATATA
* *
592409 TATATATATATATATATATATAGATTTTTAGACACAGATAAATTATTTTATT
1 TATATATATATATATATATATAGATATATAGACACAGATAAATTATTTTATT
* **
592461 TATATATATATATATATATATATATATATAGATTGTCAGATAAATTATTTTATT
1 TATATATATATATATATATATAGATATATAGA--CACAGATAAATTATTTTATT
592515 TAT
1 TAT
592518 GAAAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
52 29 0.58
54 21 0.42
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (52 bp):
TATATATATATATATATATATAGATATATAGACACAGATAAATTATTTTATT
Found at i:594064 original size:29 final size:29
Alignment explanation
Indices: 594022--594081 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
594012 ATACAGTGGT
594022 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
594051 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
594080 CT
1 CT
594082 GTGTGTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.32, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:594142 original size:17 final size:16
Alignment explanation
Indices: 594120--594190 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
594110 ATGCAATCAA
594120 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
* * *
594137 CATGGGGGAGGGGATG
1 CATGGGCGTGGGAATG
594153 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
594170 CATGGG-GTGGGAATG
1 CATGGGCGTGGGAATG
594185 CATGGG
1 CATGGG
594191 GGAGGGGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (16 bp):
CATGGGCGTGGGAATG
Found at i:594155 original size:16 final size:16
Alignment explanation
Indices: 594130--594196 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
594120 CATGGGACGT
594130 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
* * *
594146 GGGGATGCATGGGACGT
1 GGGAATGCATGGG-GGA
*
594163 GGGAATGCAT-GGGGT
1 GGGAATGCATGGGGGA
594178 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
594194 GGG
1 GGG
594197 GATGGTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 21 0.49
17 10 0.23
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.15
Consensus pattern (16 bp):
GGGAATGCATGGGGGA
Found at i:594157 original size:33 final size:32
Alignment explanation
Indices: 594120--594190 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
594110 ATGCAATCAA
*
594120 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGAATG
*
594153 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
594185 CATGGG
1 CATGGG
594191 GGAGGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:594181 original size:15 final size:15
Alignment explanation
Indices: 594128--594191 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
594118 AACATGGGAC
594128 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
594144 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
594159 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
594176 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
594191 G
1 G
594192 GAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.45
16 10 0.24
17 13 0.31
ACGTcount: A:0.20, C:0.08, G:0.55, T:0.17
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:594781 original size:21 final size:21
Alignment explanation
Indices: 594756--594799 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
594746 AATCTAGTTA
594756 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
594777 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
594798 AT
1 AT
594800 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:594809 original size:28 final size:29
Alignment explanation
Indices: 594776--594837 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
594766 TAGTATAAAT
*
594776 TATTAGTTTGTTAGTTTAAGTTA-TATTA
1 TATTAGTTTATTAGTTTAAGTTATTATTA
594804 TATTAGTTTATTAGTTTAAGTTATTATTA
1 TATTAGTTTATTAGTTTAAGTTATTATTA
594833 TATTA
1 TATTA
594838 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (29 bp):
TATTAGTTTATTAGTTTAAGTTATTATTA
Found at i:594908 original size:49 final size:48
Alignment explanation
Indices: 594800--594901 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 48
594790 TTTAAGTTAT
*
594800 ATTATATTAGTTTATTAGTTTAAGTTATTATTATATTATATAAAAAATTA
1 ATTA-ATTAGTTTCTTAGTTTAAGTTATTA-TATATTATATAAAAAATTA
*
594850 GTTAATTAGTTTCTTAGTTTAAGTTATTA-A-A-TATA-AAAAATATTA
1 ATTAATTAGTTTCTTAGTTTAAGTTATTATATATTATATAAAAA-ATTA
594895 ATTAATT
1 ATTAATT
594902 TGTTAGTGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 5 0.10
45 14 0.29
46 1 0.02
47 1 0.02
49 24 0.50
50 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (48 bp):
ATTAATTAGTTTCTTAGTTTAAGTTATTATATATTATATAAAAAATTA
Found at i:595384 original size:20 final size:21
Alignment explanation
Indices: 595340--595384 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
595330 AAATATTGTG
**
595340 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
595361 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
595381 TTTA
1 TTTA
595385 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:595667 original size:26 final size:25
Alignment explanation
Indices: 595638--595696 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
595628 ACTAAATCAT
*
595638 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
595664 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
595690 ATTATTA
1 ATTATTA
595697 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:596823 original size:26 final size:26
Alignment explanation
Indices: 596789--597120 Score: 297
Period size: 26 Copynumber: 13.3 Consensus size: 26
596779 AGGCACGATG
* *
596789 TTTGGTAATAATCATTATAGTAATGA
1 TTTGATAATAATCATTATAATAATGA
596815 TTTGATAATAATCATTATAATAATGA
1 TTTGATAATAATCATTATAATAATGA
*
596841 TTT-AGTAATAATCATTATAAAAATGA
1 TTTGA-TAATAATCATTATAATAATGA
*
596867 -TT--TAATAATGATT-T-A-AAT-A
1 TTTGATAATAATCATTATAATAATGA
* * * *
596886 TTTAATAATTTGATGATT-TAGTAATGA
1 TTTGATAA--TAATCATTATAATAATGA
*
596913 TTTGATAATAATCATTATAGTAATGA
1 TTTGATAATAATCATTATAATAATGA
596939 TTTGATAATAATCATTATAAT-ATGA
1 TTTGATAATAATCATTATAATAATGA
596964 TTT-AGTAATAATCATTATAA-AATGA
1 TTTGA-TAATAATCATTATAATAATGA
* * * *
596989 TTTAATAATGAT--TTA-AAT-TTTA
1 TTTGATAATAATCATTATAATAATGA
* * * * *
597011 -ATGAT-TTGATGATT-TAGTAATGA
1 TTTGATAATAATCATTATAATAATGA
*
597034 TTTGATAATAATCATTATAGTAATGA
1 TTTGATAATAATCATTATAATAATGA
597060 TTTGATAATAATCATTATAATAATGA
1 TTTGATAATAATCATTATAATAATGA
* *
597086 TTTAATAATAATCATTATAAAAATGA
1 TTTGATAATAATCATTATAATAATGA
*
597112 TTTAATAAT
1 TTTGATAAT
597121 GATTTAAATA
Statistics
Matches: 259, Mismatches: 26, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.00
20 9 0.03
21 4 0.02
22 12 0.05
23 15 0.06
24 13 0.05
25 50 0.19
26 147 0.57
27 8 0.03
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TTTGATAATAATCATTATAATAATGA
Found at i:597035 original size:121 final size:124
Alignment explanation
Indices: 596789--597177 Score: 696
Period size: 124 Copynumber: 3.2 Consensus size: 124
596779 AGGCACGATG
*
596789 TTTGGTAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
1 TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
*
596854 ATTATAAAAATGATTTAATAATGATTTAAATATTTAATAATTTGATGATTTAGTAATGA
66 ATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA
596913 TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAT-ATGATTTAGTAATAATC
1 TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
596977 ATTAT-AAAATGATTTAATAATGATTTAAAT-TTTAATGATTTGATGATTTAGTAATGA
66 ATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA
*
597034 TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATC
1 TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
*
597099 ATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAATAATGA
66 ATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA
* *
597158 TTTTATAATAATTATT-TAGT
1 TTTGATAATAATCATTATAGT
597178 TATTATTTAG
Statistics
Matches: 256, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
121 73 0.29
122 46 0.18
123 51 0.20
124 86 0.34
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
ATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA
Found at i:597135 original size:19 final size:20
Alignment explanation
Indices: 597106--597160 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 20
597096 ATCATTATAA
597106 AAATGATTTAATAATGATTT
1 AAATGATTTAATAATGATTT
597126 AAAT-A-TT--TAATGATTT
1 AAATGATTTAATAATGATTT
*
597142 -GATGATTTAATAATGATTT
1 AAATGATTTAATAATGATTT
597161 TATAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 2 0.07
18 2 0.07
19 10 0.33
20 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (20 bp):
AAATGATTTAATAATGATTT
Found at i:597401 original size:17 final size:17
Alignment explanation
Indices: 597376--597408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
597366 ACTAAATATT
*
597376 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
597393 TAATGATTTGATACTA
1 TAATGATTTGATACTA
597409 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:597401 original size:25 final size:23
Alignment explanation
Indices: 597322--597401 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
597312 GATTTATTGT
597322 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
597343 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
597370 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
597392 GTAATGATTT
1 -TAAT-ATTT
597402 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:599580 original size:15 final size:14
Alignment explanation
Indices: 599557--599587 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
599547 TACAACACTA
599557 AACTTTAATATAAT
1 AACTTTAATATAAT
599571 AACTTATAATATAAT
1 AACTT-TAATATAAT
599586 AA
1 AA
599588 ACTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:600084 original size:21 final size:21
Alignment explanation
Indices: 600054--600106 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
600044 CCCTTTCTTC
*
600054 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
600075 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
600096 TTCTTTCTTTC
1 TTCTTTCTTTC
600107 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:600097 original size:17 final size:16
Alignment explanation
Indices: 600077--600108 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
600067 TTCTCCCTTT
600077 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
600094 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
600109 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:600141 original size:23 final size:23
Alignment explanation
Indices: 600111--600156 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
600101 TCTTTCTCGG
600111 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
600134 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
600157 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:600197 original size:25 final size:25
Alignment explanation
Indices: 600169--600220 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
600159 TTTCTTTTAT
600169 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
600194 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
600219 AA
1 AA
600221 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:600410 original size:13 final size:13
Alignment explanation
Indices: 600392--600423 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
600382 GGCTGCATGT
600392 GAATGGATGATGG
1 GAATGGATGATGG
600405 GAATGGATGATGG
1 GAATGGATGATGG
600418 GAATGG
1 GAATGG
600424 CGCCGGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (13 bp):
GAATGGATGATGG
Found at i:600522 original size:17 final size:17
Alignment explanation
Indices: 600522--600581 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
600512 CGCTCGTATG
600522 GCTCGCATGGGGAGAAC
1 GCTCGCATGGGGAGAAC
* *****
600539 GCTCGTATGGCTCCTAC
1 GCTCGCATGGGGAGAAC
600556 -CTCGCATGGGGAGAAC
1 GCTCGCATGGGGAGAAC
*
600572 GCTCGTATGG
1 GCTCGCATGG
600582 CTCGCATGGG
Statistics
Matches: 29, Mismatches: 13, Indels: 2
0.66 0.30 0.05
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (17 bp):
GCTCGCATGGGGAGAAC
Found at i:600533 original size:26 final size:26
Alignment explanation
Indices: 600497--600610 Score: 165
Period size: 26 Copynumber: 4.1 Consensus size: 26
600487 GCATGCACAC
600497 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
600523 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
600549 CTCCTACCTCGCATGGGGAGAACGCTCGTATGG
1 -------CTCGCATGGGGAGAACGCTCGTATGG
600582 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
600608 CTC
1 CTC
600611 CTATGCATGG
Statistics
Matches: 81, Mismatches: 0, Indels: 14
0.85 0.00 0.15
Matches are distributed among these distances:
26 55 0.68
33 26 0.32
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCGTATGG
Found at i:600565 original size:33 final size:32
Alignment explanation
Indices: 600497--600662 Score: 157
Period size: 26 Copynumber: 5.5 Consensus size: 32
600487 GCATGCACAC
600497 CTCGCATGGGGAGAACGCTCGTATGG------
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
600523 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
600555 CCTCGCATGGGGAGAACGCTCGTATGG------
1 -CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
600582 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
*
600614 -T-GCATGGGGAGAACCATTGGCTCGTATGGCTCGTA
1 CTCGCATGGGGAGAA-C----GCTCGTATGGCTCCTA
600649 -T-GCATGGGGAGAAC
1 CTCGCATGGGGAGAAC
600663 CATTGGCTCG
Statistics
Matches: 121, Mismatches: 1, Indels: 28
0.81 0.01 0.19
Matches are distributed among these distances:
26 52 0.43
30 12 0.10
31 2 0.02
33 26 0.21
34 1 0.01
35 28 0.23
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.21
Consensus pattern (32 bp):
CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
Found at i:600566 original size:59 final size:59
Alignment explanation
Indices: 600495--600627 Score: 245
Period size: 59 Copynumber: 2.3 Consensus size: 59
600485 CTGCATGCAC
600495 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
1 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
600554 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
1 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
600613 A--T-GCATGGGGAGAAC
1 ACCTCGCATGGGGAGAAC
600628 CATTGGCTCG
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
56 13 0.18
57 1 0.01
59 60 0.81
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.20
Consensus pattern (59 bp):
ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
Found at i:600644 original size:35 final size:35
Alignment explanation
Indices: 600598--600685 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
600588 TGGGGAGAAC
*
600598 GCTCGTATGGCTCCTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
600633 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
600668 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
600686 TCACCCCGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:600697 original size:12 final size:12
Alignment explanation
Indices: 600680--600709 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
600670 TCGTATGGCT
600680 CGTATGTCACCC
1 CGTATGTCACCC
600692 CGTATGTCACCC
1 CGTATGTCACCC
600704 CGTATG
1 CGTATG
600710 GCCACCTCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.20, T:0.27
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:602645 original size:23 final size:23
Alignment explanation
Indices: 602612--602659 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
602602 CCTTTCGGGC
602612 AAAGAGAAGACCCCACCGACCTG
1 AAAGAGAAGACCCCACCGACCTG
*
602635 AAAGAGCAGACCCCACCGACCTG
1 AAAGAGAAGACCCCACCGACCTG
602658 AA
1 AA
602660 GATTACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.35, G:0.21, T:0.04
Consensus pattern (23 bp):
AAAGAGAAGACCCCACCGACCTG
Found at i:603388 original size:20 final size:20
Alignment explanation
Indices: 603363--603402 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
603353 TTTGGTTCAC
*
603363 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAGTG
603383 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
603403 AATAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:608439 original size:29 final size:30
Alignment explanation
Indices: 608407--608470 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
608397 CAATTCTTCC
608407 CTTTTATTTTTATATA-AAAAATCAT-TATT
1 CTTTTATTTTTATATATAAAAAT-ATCTATT
*
608436 CTTTTATTTTTATATATGAAAATATCTATT
1 CTTTTATTTTTATATATAAAAATATCTATT
608466 CTTTT
1 CTTTT
608471 TGTATACCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (30 bp):
CTTTTATTTTTATATATAAAAATATCTATT
Found at i:608685 original size:28 final size:29
Alignment explanation
Indices: 608610--608686 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 29
608600 ACAAAACGAC
*
608610 GTTTAATTAT-TAAATAAAATTAATGACAT
1 GTTTAATTATATATAT-AAATTAATGACAT
* * *
608639 GTTTTTTAAATAAAAATATAAA-TAATGACAT
1 G---TTTAATTATATATATAAATTAATGACAT
608670 GTTTAATTATATATATA
1 GTTTAATTATATATATA
608687 TATATATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
28 13 0.35
29 1 0.03
31 10 0.27
32 10 0.27
33 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
GTTTAATTATATATATAAATTAATGACAT
Found at i:612371 original size:4 final size:4
Alignment explanation
Indices: 612362--612405 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
612352 CAATGCATGT
*
612362 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
612406 TTGAACATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:613281 original size:21 final size:23
Alignment explanation
Indices: 613247--613288 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
613237 ATAGTCTTTT
613247 TTTTTACCACTTTTT-ATAATTC
1 TTTTTACCACTTTTTAATAATTC
*
613269 TTTTTA-CATTTTTTAATAAT
1 TTTTTACCACTTTTTAATAAT
613289 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTACCACTTTTTAATAATTC
Found at i:629871 original size:41 final size:40
Alignment explanation
Indices: 629826--629905 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
629816 TGTAAAAAAA
*
629826 AATAATA-ATGAAAATAAAATAA-GAAAATATATATATATAAC
1 AATAATAGA-GAAAA-AAAATAATGAAAATAAATATA-ATAAC
*
629867 AATAATAGAGAAAAAAAATAATGTAAATAAATATAATAA
1 AATAATAGAGAAAAAAAATAATGAAAATAAATATAATAA
629906 TAAAGAAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 11 0.31
41 23 0.66
42 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (40 bp):
AATAATAGAGAAAAAAAATAATGAAAATAAATATAATAAC
Found at i:629960 original size:100 final size:101
Alignment explanation
Indices: 629854--630181 Score: 251
Period size: 109 Copynumber: 3.1 Consensus size: 101
629844 ATAAGAAAAT
629854 ATATATATATAACAATA-ATAGAGA-AAAAAAATAATGTAAATAAATATAATAATAAAGAAGTAA
1 ATATATATATAA-AATACATAGAGATAAAAAAATAATGTAAATAAATATAATAATAAAGAAGTAA
629917 AGAAATAGGGTAAAATACAAAATGTGTACATATATAC
65 AGAAATAGGGTAAAATACAAAATGTGTACATATATAC
* * * *
629954 ATATATATATATATATACATATGTA-ATATAACATATAAATG-AAATAATACTATACTAATAATA
1 ATATATATATA-AAATACATA-G-AGATA-AAAAAAT-AATGTAAATAA-A-TATAATAATAA-A
* * * * * *
630017 -AATGTATACG-AAT-GTAG-AAAAAACTAATAATAGTATA-AAATATAT
58 GAA-GTA-AAGAAATAG-GGTAAAATAC-AA-AAT-GTGTACATATATAC
* * * * *
630062 ATAAATATTATAATGTAATATAAAAAGATAATTAAAACTAATGTAAATAAATATAATAATAAAGA
1 ATATATA-TATAA---AATACATAGAGATAA--AAAAATAATGTAAATAAATATAATAATAAAGA
630127 AGTAAAGAAATAGGGTAAAATACAAAATGTGTACATATATATAC
60 AGTAAAGAAATAGGGTAAAATACAAAATGTGTAC--ATATATAC
630171 ATATATATATA
1 ATATATATATA
630182 TATATAATAT
Statistics
Matches: 171, Mismatches: 26, Indels: 54
0.68 0.10 0.22
Matches are distributed among these distances:
100 14 0.08
101 4 0.02
102 2 0.01
103 2 0.01
104 11 0.06
105 5 0.03
106 23 0.13
107 15 0.09
108 32 0.19
109 41 0.24
110 8 0.05
111 14 0.08
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (101 bp):
ATATATATATAAAATACATAGAGATAAAAAAATAATGTAAATAAATATAATAATAAAGAAGTAAA
GAAATAGGGTAAAATACAAAATGTGTACATATATAC
Found at i:629965 original size:14 final size:13
Alignment explanation
Indices: 629943--629990 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
629933 ACAAAATGTG
629943 TACATATATACATA
1 TACATATATA-ATA
*
629957 TATATATAT-ATA
1 TACATATATAATA
*
629969 TACATATGTAATA
1 TACATATATAATA
629982 TAACATATA
1 T-ACATATA
629991 AATGAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.36
13 4 0.14
14 14 0.50
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (13 bp):
TACATATATAATA
Found at i:630106 original size:215 final size:210
Alignment explanation
Indices: 629880--630313 Score: 735
Period size: 211 Copynumber: 2.0 Consensus size: 210
629870 AATAGAGAAA
*
629880 AAAAATAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
1 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
*
629945 CATATATACATATATATATATATATACATATGTAATATAACATATAAATGAAATAATACTATACT
66 CATATAT--ATACATATATATATAT--ATA--TAATATAACATATAAATGAAATAATACTATACT
* * * *
630010 AATAATAAATGTATACGAATG-TAGAAAAAACTAATAATAGTATAAAATATATATAAATATTATA
125 AATAATAAATATATACGAATGATAAAAAAAACTAATAATAATATAAAACATATATAAATATTATA
630074 ATGTAATATAAAAAGATAATT
190 ATGTAATATAAAAAGATAATT
630095 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
1 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
*
630160 CATATATATACATATATATATATATATAATATAACATATAAGTGAAATAATACTATACTAATAAT
66 CATATATATACATATATATATATATATAATATAACATATAAATGAAATAATACTATACTAATAAT
630225 AAATATATACGAATGTATAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTA
131 AAATATATACGAATG-ATAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTA
630290 ATATAAAAAGATAATT
195 ATATAAAAAGATAATT
630306 AAAACTAA
1 AAAACTAA
630314 AATCCAGAGA
Statistics
Matches: 210, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
209 52 0.25
211 72 0.34
213 15 0.07
215 71 0.34
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.30
Consensus pattern (210 bp):
AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
CATATATATACATATATATATATATATAATATAACATATAAATGAAATAATACTATACTAATAAT
AAATATATACGAATGATAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTAA
TATAAAAAGATAATT
Found at i:630173 original size:10 final size:10
Alignment explanation
Indices: 630158--630187 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
630148 ACAAAATGTG
630158 TACATATATA
1 TACATATATA
630168 TACATATATA
1 TACATATATA
*
630178 TATATATATA
1 TACATATATA
630188 ATATAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TACATATATA
Found at i:630178 original size:12 final size:12
Alignment explanation
Indices: 630161--630199 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
630151 AAATGTGTAC
630161 ATATATATACAT
1 ATATATATACAT
*
630173 ATATATATATAT
1 ATATATATACAT
630185 ATA-ATATAACAT
1 ATATATAT-ACAT
630197 ATA
1 ATA
630200 AGTGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATACAT
Found at i:631819 original size:105 final size:105
Alignment explanation
Indices: 631637--632306 Score: 1259
Period size: 105 Copynumber: 6.4 Consensus size: 105
631627 GCATCGTTTC
*
631637 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
631702 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* **
631742 GAGTCCAATATCCCTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
631807 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTGTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
631847 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
631912 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
631952 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
632017 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
632057 GAGTCCAATATCCTTCGTTGTGAGGTTGGAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
632122 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
632162 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
632227 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTATGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
632267 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
632307 GGTAAAACCT
Statistics
Matches: 550, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 550 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:633109 original size:53 final size:53
Alignment explanation
Indices: 633052--633152 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
633042 TTCTTTTTTC
* * *
633052 TTTTTCTTTTTTTT-AATTTCAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTT
1 TTTTTCTTTTTTTTCAACTT-AGGACGCCCTCTCGGGTTTTCACCCTAAACGTT
* *
633105 TTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
633153 GCGAAGTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 38 0.90
54 4 0.10
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.50
Consensus pattern (53 bp):
TTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTT
Found at i:642575 original size:20 final size:20
Alignment explanation
Indices: 642536--642579 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
642526 ATGGTTAGTA
*
642536 AAATAAAAATAAATGAAAAT
1 AAATAAAAATAAAAGAAAAT
642556 AAATAAAAATAACAAG-AAAT
1 AAATAAAAATAA-AAGAAAAT
642576 AAAT
1 AAAT
642580 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAAAGAAAAT
Found at i:643728 original size:41 final size:40
Alignment explanation
Indices: 643683--643762 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
643673 TGTAAAAAAA
*
643683 AATAATA-ATGAAAATAAAATAA-GAAAATATATATATATAAC
1 AATAATAGA-GAAAA-AAAATAATGAAAATAAATATA-ATAAC
*
643724 AATAATAGAGAAAAAAAATAATGTAAATAAATATAATAA
1 AATAATAGAGAAAAAAAATAATGAAAATAAATATAATAA
643763 TAAAGAAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 11 0.31
41 23 0.66
42 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (40 bp):
AATAATAGAGAAAAAAAATAATGAAAATAAATATAATAAC
Found at i:643813 original size:8 final size:8
Alignment explanation
Indices: 643800--643845 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
643790 ACAAAATGTG
643800 TACATATA
1 TACATATA
643808 TACATATA
1 TACATATA
*
643816 TATATATA
1 TACATATA
*
643824 TACATATG
1 TACATATA
643832 TA-ATATA
1 TACATATA
643839 -ACATATA
1 TACATATA
643846 AATGAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 1 0.03
7 9 0.27
8 23 0.70
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:644028 original size:10 final size:10
Alignment explanation
Indices: 644013--644050 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
644003 ACAAAATGTG
644013 TACATATATA
1 TACATATATA
644023 TACATATATA
1 TACATATATA
*
644033 TATATA-ATA
1 TACATATATA
644042 TAACATATA
1 T-ACATATA
644051 AGTGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 4 0.17
10 19 0.79
11 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (10 bp):
TACATATATA
Found at i:644164 original size:207 final size:209
Alignment explanation
Indices: 643737--644164 Score: 711
Period size: 207 Copynumber: 2.0 Consensus size: 209
643727 AATAGAGAAA
*
643737 AAAAATAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
1 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
*
643802 CATATATACATATATATATATATACATATGTAATATAACATATAAATGAAATAATACTATACTAA
66 CA-ATATA-ATATACATATATATA-ATA-GTAATATAACATATAAATGAAATAATACTATACTAA
* * * *
643867 TAATAAATGTATACGAATGTAGAAAAAACTAATAATAGTATAAAATATATATAAATATTATAATG
127 TAATAAATATATACGAATGTAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATG
643932 TAATATAAAAAGATAATT
192 TAATATAAAAAGATAATT
643950 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
1 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
*
644015 C-ATAT-ATATACATATATAT-ATA-TAATATAACATATAAGTGAAATAATACTATACTAATAAT
66 CAATATAATATACATATATATAATAGTAATATAACATATAAATGAAATAATACTATACTAATAAT
644076 AAATATATACGAATGTATAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTA
131 AAATATATACGAATG--TAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTA
644141 ATATAAAAAGATAATT
194 ATATAAAAAGATAATT
644157 AAAACTAA
1 AAAACTAA
644165 AATCCAGAGA
Statistics
Matches: 206, Mismatches: 7, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
205 52 0.25
207 72 0.35
209 13 0.06
211 4 0.02
213 65 0.32
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.30
Consensus pattern (209 bp):
AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAAGAAATAGGGTAAAATACAAAATGTGTA
CAATATAATATACATATATATAATAGTAATATAACATATAAATGAAATAATACTATACTAATAAT
AAATATATACGAATGTAAAAAAAACTAATAATAATATAAAACATATATAAATATTATAATGTAAT
ATAAAAAGATAATT
Found at i:647866 original size:2 final size:2
Alignment explanation
Indices: 647859--647894 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
647849 TTAAATTTGA
647859 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
647895 TTTTATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:652628 original size:40 final size:40
Alignment explanation
Indices: 652573--652661 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
652563 CATCACACGG
652573 CCACTACCCGCTACATGTACCTTTCTAAATCTACACCCGC
1 CCACTACCCGCTACATGTACCTTTCTAAATCTACACCCGC
*
652613 CCACTACCCGCTACATGTACCTTTCTAAATCTACACCTGC
1 CCACTACCCGCTACATGTACCTTTCTAAATCTACACCCGC
652653 CCACTACCC
1 CCACTACCC
652662 TCTAAAATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.25, C:0.44, G:0.07, T:0.25
Consensus pattern (40 bp):
CCACTACCCGCTACATGTACCTTTCTAAATCTACACCCGC
Found at i:653519 original size:283 final size:290
Alignment explanation
Indices: 652967--653539 Score: 1097
Period size: 283 Copynumber: 2.0 Consensus size: 290
652957 TTAAGTTATA
652967 CAACTGTAATTATATTTATTAATTTTCCATTTATTACTCTAAAAGATTTATAATGATCGTTTTTA
1 CAACTGTAATTATATTTATTAATTTTCCATTTATTACTCTAAAAGATTTATAATGATCGTTTTTA
653032 TGTATAAGATTTACTTTTAAATTTTGGAAAACAATGGAGAGGGTCAATGGTTTATAAAAATTCGT
66 TGTATAAGATTTACTTTTAAATTTTGGAAAACAATGGAGAGGGTCAATGGTTTATAAAAATTCGT
653097 AAGTCCTAGCAAATGGAAAAGCAGCAATCCTTGTAAATAAGCAAAGCACCATACTTTAGCATGTC
131 AAGTCCTAGCAAATGGAAAAGCAGCAATCCTTGTAAATAAGCAAAGCACCATACTTTAGCATGTC
653162 AATAGTTTGTTTTTATCTTGGATATGCCTTACTTACATTTCCTTGTTTGTAATGCAAATAAAAGA
196 AATAGTTTGTTTTTATCTTGGATATGCCTTACTTACATTTCCTTGTTTGTAATGCAAATAAAAGA
653227 GAAGAAGAATACTTCAATAAAGAGATAAAT
261 GAAGAAGAATACTTCAATAAAGAGATAAAT
653257 CAACTGT-A-TATA-TTATTAA-TTTCCATTTATTACTCTAAAAGA-TTATAATGATCGTTTTTA
1 CAACTGTAATTATATTTATTAATTTTCCATTTATTACTCTAAAAGATTTATAATGATCGTTTTTA
653317 TGTATAAGATTTACTTTTAAATTTTGGAAAACAAT-G-GAGGGTCAATGGTTTATAAAAATTCGT
66 TGTATAAGATTTACTTTTAAATTTTGGAAAACAATGGAGAGGGTCAATGGTTTATAAAAATTCGT
653380 AAGTCCTAGCAAATGGAAAAGCAGCAATCCTTGTAAATAAGCAAAGCACCATACTTTAGCATGTC
131 AAGTCCTAGCAAATGGAAAAGCAGCAATCCTTGTAAATAAGCAAAGCACCATACTTTAGCATGTC
653445 AATAGTTTGTTTTTATCTTGGATATGCCTTACTTACATTTCCTTGTTTGTAATGCAAATAAAAGA
196 AATAGTTTGTTTTTATCTTGGATATGCCTTACTTACATTTCCTTGTTTGTAATGCAAATAAAAGA
653510 GAAGAAGAATACTTCAATAAAGAGATAAAT
261 GAAGAAGAATACTTCAATAAAGAGATAAAT
653540 TTGTCTTGTG
Statistics
Matches: 283, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
283 187 0.66
284 1 0.00
285 53 0.19
286 23 0.08
287 7 0.02
288 4 0.01
289 1 0.00
290 7 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (290 bp):
CAACTGTAATTATATTTATTAATTTTCCATTTATTACTCTAAAAGATTTATAATGATCGTTTTTA
TGTATAAGATTTACTTTTAAATTTTGGAAAACAATGGAGAGGGTCAATGGTTTATAAAAATTCGT
AAGTCCTAGCAAATGGAAAAGCAGCAATCCTTGTAAATAAGCAAAGCACCATACTTTAGCATGTC
AATAGTTTGTTTTTATCTTGGATATGCCTTACTTACATTTCCTTGTTTGTAATGCAAATAAAAGA
GAAGAAGAATACTTCAATAAAGAGATAAAT
Found at i:657926 original size:22 final size:20
Alignment explanation
Indices: 657877--657927 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
657867 CACTTTGGGA
657877 TTTATTTGA-GTTTGTATGG
1 TTTATTTGAGGTTTGTATGG
*
657896 TTGGA-TTGAGGTTTGTGTATGG
1 TT-TATTTGAGG-TT-TGTATGG
657918 TTTATTTGAG
1 TTTATTTGAG
657928 TATGTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 3 0.12
22 14 0.56
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (20 bp):
TTTATTTGAGGTTTGTATGG
Found at i:658242 original size:31 final size:31
Alignment explanation
Indices: 658204--658282 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
658194 AAAATTAAAC
*
658204 ATATTTTT-AATTGAAGATAAGAATAAAATAT
1 ATATTTTTAAATT-AAAATAAGAATAAAATAT
658235 ATATTTTTAAATTAAAATAAGAATAAAATAT
1 ATATTTTTAAATTAAAATAAGAATAAAATAT
*
658266 AT-TTTTAAAAGTTAAAA
1 ATATTTTTAAA-TTAAAA
658283 CATATAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 7 0.16
31 33 0.75
32 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.39
Consensus pattern (31 bp):
ATATTTTTAAATTAAAATAAGAATAAAATAT
Found at i:660250 original size:49 final size:49
Alignment explanation
Indices: 660193--660291 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
660183 AACTAAAGTA
660193 CTTACTTTCGCAATGCAGTTTCAATGAGAGACTCGGGAGCACAATTCCT
1 CTTACTTTCGCAATGCAGTTTCAATGAGAGACTCGGGAGCACAATTCCT
660242 CTTACTTTCGCAATGCAGTTTCAATGAGAGACTCGGGAGCACAATTCCT
1 CTTACTTTCGCAATGCAGTTTCAATGAGAGACTCGGGAGCACAATTCCT
660291 C
1 C
660292 ATGACGGGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (49 bp):
CTTACTTTCGCAATGCAGTTTCAATGAGAGACTCGGGAGCACAATTCCT
Found at i:663503 original size:15 final size:15
Alignment explanation
Indices: 663485--663518 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
663475 ACACACACGA
*
663485 ATCAGTACAACTTAT
1 ATCAGTACAACTAAT
663500 ATCAGTACAACTAAT
1 ATCAGTACAACTAAT
663515 ATCA
1 ATCA
663519 ATATAGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (15 bp):
ATCAGTACAACTAAT
Found at i:667173 original size:31 final size:31
Alignment explanation
Indices: 667135--667196 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
667125 AAGTGTTCTA
*
667135 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
667166 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
667197 ATGTGCCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:667229 original size:22 final size:22
Alignment explanation
Indices: 667201--667251 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
667191 CTTTGCATGT
667201 GCCATGCACGTCGGAAGAGGTC
1 GCCATGCACGTCGGAAGAGGTC
667223 GCCATGCACGTCGGAAGAGGTC
1 GCCATGCACGTCGGAAGAGGTC
667245 GCC-TGCA
1 GCCATGCA
667252 TGCAGTGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.14
Consensus pattern (22 bp):
GCCATGCACGTCGGAAGAGGTC
Found at i:667276 original size:22 final size:23
Alignment explanation
Indices: 667249--667292 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
667239 GAGGTCGCCT
**
667249 GCATGCAGTGGGGAGC-AGGCGA
1 GCATGCAACGGGGAGCAAGGCGA
667271 GCATGCAACGGGGAGCAAGGCG
1 GCATGCAACGGGGAGCAAGGCG
667293 CAGGACAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.25, C:0.20, G:0.48, T:0.07
Consensus pattern (23 bp):
GCATGCAACGGGGAGCAAGGCGA
Found at i:667344 original size:29 final size:29
Alignment explanation
Indices: 667297--667384 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
667287 AAGGCGCAGG
*
667297 ACAAGGTCGCCCAGCGTGCATGACGACCT
1 ACAAGGTCGCCCGGCGTGCATGACGACCT
* * * *
667326 ACCATGTCGCCTGGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGACGACCT
* *
667355 ACAAGGTCGCCCGGAGGGCATGACGACCT
1 ACAAGGTCGCCCGGCGTGCATGACGACCT
667384 A
1 A
667385 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.15
Consensus pattern (29 bp):
ACAAGGTCGCCCGGCGTGCATGACGACCT
Found at i:687495 original size:24 final size:25
Alignment explanation
Indices: 687468--687520 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
687458 GTTCATTTAT
687468 GTTCGTG-AACGTTCGGTTATGTTC
1 GTTCGTGTAACGTTCGGTTATGTTC
* * *
687492 GTTC-TGTTATGTTCGTTTATGTTC
1 GTTCGTGTAACGTTCGGTTATGTTC
687516 GTTCG
1 GTTCG
687521 GTTATGTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.49
Consensus pattern (25 bp):
GTTCGTGTAACGTTCGGTTATGTTC
Found at i:687500 original size:14 final size:14
Alignment explanation
Indices: 687477--687532 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
687467 TGTTCGTGAA
687477 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
687491 CGTTCTGTTATGTT
1 CGTTCGGTTATGTT
687505 CG-T---TTATGTT
1 CGTTCGGTTATGTT
687515 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
687529 CGTT
1 CGTT
687533 TGTGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.07, C:0.14, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:687524 original size:24 final size:24
Alignment explanation
Indices: 687478--687539 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
687468 GTTCGTGAAC
* *
687478 GTTCGGTTATGTTCGTTCTGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
687502 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
687526 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
687540 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:687549 original size:24 final size:24
Alignment explanation
Indices: 687478--687552 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
687468 GTTCGTGAAC
* * *
687478 GTTCGGTTATGTTCGTTCTGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
* *
687502 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
* *
687526 GTTCGTTTGTGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
687550 GTT
1 GTT
687553 TAACCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCAGTTAT
Found at i:687549 original size:38 final size:38
Alignment explanation
Indices: 687477--687552 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
687467 TGTTCGTGAA
* *
687477 CGTTCGGTTATGTTCGTTCTGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTCTGTTATATTCATTTATGTT
687515 CGTTCGGTTATGTTCGTT-TGTGT-TCATTCATTTATGTT
1 CGTTCGGTTATGTTCGTTCTGT-TAT-ATTCATTTATGTT
687553 TAACCCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.55
Consensus pattern (38 bp):
CGTTCGGTTATGTTCGTTCTGTTATATTCATTTATGTT
Found at i:688641 original size:16 final size:16
Alignment explanation
Indices: 688622--688688 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
688612 TTTATGTTTG
688622 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
688638 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
** *
688654 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
688670 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
688684 TTTAT
1 TTTAT
688689 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
16 40 0.89
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:688657 original size:32 final size:32
Alignment explanation
Indices: 688616--688680 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
688606 CCAACGTTTA
* **
688616 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
*
688648 TGTTCGTTTATGTTCGTGCGCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
688680 T
1 T
688681 TTATTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
Found at i:688770 original size:16 final size:16
Alignment explanation
Indices: 688749--688779 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
688739 AAAAAAAATT
688749 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
688765 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
688780 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:695513 original size:59 final size:59
Alignment explanation
Indices: 695385--695497 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 59
695375 AATTGTCGGT
*
695385 GACTATTTTGTAACTTTTAATAGTTAGAGACTCAACAAAATAATGTCATATAGGCAAGG
1 GACTATTTTGTAACTTTTAATAGTGAGAGACTCAACAAAATAATGTCATATAGGCAAGG
* * *
695444 GACTATTTTGTAACTTTTAATGGTCGATG-GACTCAACAAAGTAATGTCCTATAG
1 GACTATTTTGTAACTTTTAATAGT-GA-GAGACTCAACAAAATAATGTCATATAG
695498 TTAGGGGATC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 23 0.48
60 24 0.50
61 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (59 bp):
GACTATTTTGTAACTTTTAATAGTGAGAGACTCAACAAAATAATGTCATATAGGCAAGG
Found at i:699624 original size:44 final size:44
Alignment explanation
Indices: 699575--699706 Score: 165
Period size: 44 Copynumber: 3.0 Consensus size: 44
699565 ATTAATTGTC
* ** **
699575 TTTCTTCTCAAGAAATTCTTTACTTGTTTTAACGATTAGTTTTA
1 TTTCTTCTCAAGAAATTCTTTACTTGTTTGAACGACCAACTTTA
* * *
699619 TTTCTTTTCAAGAAATTCTTTACTTGTTTGAACTACCAACTTTC
1 TTTCTTCTCAAGAAATTCTTTACTTGTTTGAACGACCAACTTTA
* *
699663 TTTCTTCTCAAGAAATTCTTTATTTCGTTTGAACTACCAACTTT
1 TTTCTTCTCAAGAAATTCTTTACTT-GTTTGAACGACCAACTTT
699707 GTCCTTTTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 59 0.77
45 18 0.23
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (44 bp):
TTTCTTCTCAAGAAATTCTTTACTTGTTTGAACGACCAACTTTA
Found at i:699640 original size:22 final size:22
Alignment explanation
Indices: 699575--699640 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
699565 ATTAATTGTC
*
699575 TTTCTTCTCAAGAAATTCTTTA
1 TTTCTTTTCAAGAAATTCTTTA
* * * *
699597 CTTGTTTT-AACGATTAGT-TTTA
1 TTTCTTTTCAA-GA-AATTCTTTA
699619 TTTCTTTTCAAGAAATTCTTTA
1 TTTCTTTTCAAGAAATTCTTTA
699641 CTTGTTTGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 8
0.65 0.19 0.17
Matches are distributed among these distances:
21 4 0.13
22 23 0.74
23 4 0.13
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.53
Consensus pattern (22 bp):
TTTCTTTTCAAGAAATTCTTTA
Found at i:702047 original size:2 final size:2
Alignment explanation
Indices: 702040--702076 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
702030 AGAAGTCTTA
702040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
702077 GATTGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:702991 original size:2 final size:2
Alignment explanation
Indices: 702984--703023 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
702974 ATATAGATTG
702984 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
703024 TGAAAGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:704185 original size:25 final size:24
Alignment explanation
Indices: 704152--704208 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
704142 TTAGAATGTT
* * *
704152 AATGGTTATAAAATAATTTAAATTA
1 AATGATTATAAAAAAAATTAAA-TA
704177 AATGATTATAAAAAAAATTAAATA
1 AATGATTATAAAAAAAATTAAATA
704201 AAT-ATTAT
1 AATGATTAT
704209 TTTATAGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 19 0.66
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (24 bp):
AATGATTATAAAAAAAATTAAATA
Found at i:715563 original size:14 final size:14
Alignment explanation
Indices: 715544--715571 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
715534 TCCCCTTAAT
715544 TTTTAAATTGGTGA
1 TTTTAAATTGGTGA
715558 TTTTAAATTGGTGA
1 TTTTAAATTGGTGA
715572 CCAAAGTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTTAAATTGGTGA
Found at i:717793 original size:3 final size:3
Alignment explanation
Indices: 717785--717811 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
717775 AAAGAGAATA
717785 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
717812 CACTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:717945 original size:19 final size:20
Alignment explanation
Indices: 717901--717946 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
717891 CTTATTTATT
*
717901 TTATTTTTTTAGTTATTCAA
1 TTATTTTTTTAATTATTCAA
*
717921 TAATTTTTTTAAATTA-T-AA
1 TTATTTTTTT-AATTATTCAA
717940 TTATTTT
1 TTATTTT
717947 GATACATGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 8 0.36
20 10 0.45
21 4 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTTTTTTAATTATTCAA
Found at i:721943 original size:3 final size:3
Alignment explanation
Indices: 721935--721959 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
721925 ATTAATTCTC
721935 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
721960 GTTCAAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:726397 original size:22 final size:20
Alignment explanation
Indices: 726348--726398 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
726338 CACTTTGGGA
726348 TTTATTTGA-GTTTGTATGG
1 TTTATTTGAGGTTTGTATGG
*
726367 TTGGA-TTGAGGTTTGTGTATGG
1 TT-TATTTGAGG-TT-TGTATGG
726389 TTTATTTGAG
1 TTTATTTGAG
726399 TATGTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 3 0.12
22 14 0.56
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (20 bp):
TTTATTTGAGGTTTGTATGG
Found at i:727421 original size:19 final size:20
Alignment explanation
Indices: 727384--727421 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
727374 TTTTTCATTA
*
727384 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
727404 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
727422 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:727473 original size:21 final size:21
Alignment explanation
Indices: 727449--727491 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
727439 TCATATTCGT
* *
727449 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
727470 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
727491 T
1 T
727492 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:733772 original size:103 final size:103
Alignment explanation
Indices: 733594--733914 Score: 608
Period size: 103 Copynumber: 3.1 Consensus size: 103
733584 TAATGTCCAT
733594 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
733659 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
733697 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
733762 GACCTT-ACACATGTTCCAAAGAATACATATATGTCCCG
66 GA-CTTCACACATGTTCCAAAGAATACATATATGTCCCG
733800 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
733865 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
733903 AAGGACCACATA
1 AAGGACCACATA
733915 GACCCTCTAC
Statistics
Matches: 213, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
102 3 0.01
103 207 0.97
104 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:734483 original size:21 final size:21
Alignment explanation
Indices: 734459--734501 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
734449 TCATATTCGT
* *
734459 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
734480 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
734501 T
1 T
734502 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:734958 original size:3 final size:3
Alignment explanation
Indices: 734950--734993 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
734940 TCTCACGTAT
*
734950 GAA GAA GAA GAGG GAA GAA GAA GGAA GAA GAA GAAA GAA GAA GA
1 GAA GAA GAA GA-A GAA GAA GAA -GAA GAA GAA G-AA GAA GAA GA
734994 TGACTCTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 28 0.78
4 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:734968 original size:10 final size:10
Alignment explanation
Indices: 734953--734992 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
734943 CACGTATGAA
*
734953 GAAGAAGAGG
1 GAAGAAGAAG
734963 GAAGAAGAAG
1 GAAGAAGAAG
734973 GAAGAAGAAG
1 GAAGAAGAAG
*
734983 AAAGAAGAAG
1 GAAGAAGAAG
734993 ATGACTCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:740699 original size:35 final size:35
Alignment explanation
Indices: 740653--740719 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
740643 CACTTGAACA
*
740653 AGTACACTAAATGAAATGCAGTTATTAAACCAACC
1 AGTACACTAAATGAAATACAGTTATTAAACCAACC
740688 AGTACACTAAATGAAATACAGTTATTAAACCA
1 AGTACACTAAATGAAATACAGTTATTAAACCA
740720 GTCTACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (35 bp):
AGTACACTAAATGAAATACAGTTATTAAACCAACC
Found at i:744750 original size:21 final size:21
Alignment explanation
Indices: 744726--744766 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
744716 AGTTTATTTT
744726 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
744747 TAAACTTTGTTTCAATTATC
1 TAAACTTTATTTCAATTATC
744767 AAACTTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:744815 original size:33 final size:33
Alignment explanation
Indices: 744762--744860 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
744752 TTTGTTTCAA
744762 TTATCAAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTGAAT
*
744794 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
744827 TTATCAAATTTGGAAGTATTTAAGTATTTCAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTGAAT
744860 T
1 T
744861 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 10 0.16
33 51 0.84
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (33 bp):
TTATCAAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:744889 original size:13 final size:13
Alignment explanation
Indices: 744846--744900 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
744836 TTGGAAGTAT
744846 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
744859 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
744873 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
744886 TTAAGTATTTGAA
1 TTAAGTATTTCAA
744899 TT
1 TT
744901 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:745122 original size:21 final size:21
Alignment explanation
Indices: 745096--745152 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
745086 TGGAGCGTGG
*
745096 GGGAATCGGTACCCTCTAATA
1 GGGAATCGGTTCCCTCTAATA
* *
745117 GGGAATCGGTTCCATCTCATA
1 GGGAATCGGTTCCCTCTAATA
745138 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
745153 AAGTGTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTAATA
Found at i:745768 original size:15 final size:17
Alignment explanation
Indices: 745742--745773 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
745732 TTCTATGGGA
745742 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
745758 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
745774 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:750358 original size:18 final size:20
Alignment explanation
Indices: 750313--750357 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
750303 TCCCAGTTTA
*
750313 CTCCTCTTCTCCCCTCTCTC
1 CTCCTCTCCTCCCCTCTCTC
*
750333 CTCACTCTCCTCCCTCTCTTTC
1 CTC-CTCTCCTCCC-CTCTCTC
750355 CTC
1 CTC
750358 TTCTTCCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 9 0.43
22 9 0.43
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (20 bp):
CTCCTCTCCTCCCCTCTCTC
Found at i:750981 original size:2 final size:2
Alignment explanation
Indices: 750936--750967 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
750926 ATTATGCACG
750936 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
750968 GATGTGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:756180 original size:20 final size:20
Alignment explanation
Indices: 756157--756204 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
756147 TATCGCATTG
*
756157 CGATTTACAAGTTCGCGTTA
1 CGATTTACAAATTCGCGTTA
* *
756177 CGATTTTTCAAATTCGCGTTG
1 CGA-TTTACAAATTCGCGTTA
756198 CGATTTA
1 CGATTTA
756205 TTCTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTA
Found at i:756194 original size:21 final size:23
Alignment explanation
Indices: 756168--756213 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
756158 GATTTACAAG
756168 TTCGCGTTACGATTT-TTC-AAA
1 TTCGCGTTACGATTTATTCTAAA
*
756189 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTACGATTTATTCTAAA
756212 TT
1 TT
756214 TGTTGCGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 3 0.14
23 5 0.23
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (23 bp):
TTCGCGTTACGATTTATTCTAAA
Found at i:756239 original size:21 final size:19
Alignment explanation
Indices: 756209--756272 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
756199 GATTTATTCT
*
756209 AAATTTGTTGCGATAGTCC
1 AAATTCGTTGCGATAGTCC
* *
756228 AAATTCACGTTGAGATTTATTCC
1 AAATT--CGTTGCGA--TAGTCC
*
756251 AAATTCGTTGCGATAGTTC
1 AAATTCGTTGCGATAGTCC
756270 AAA
1 AAA
756273 ATCGCAACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 12 0.34
21 13 0.37
23 10 0.29
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (19 bp):
AAATTCGTTGCGATAGTCC
Found at i:756239 original size:42 final size:42
Alignment explanation
Indices: 756185--756272 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
756175 TACGATTTTT
* * * *
756185 CAAATTCGCGTTGCGATTTATTCTAAATTTGTTGCGATAGTC
1 CAAATTCACGTTGAGATTTATTCCAAATTCGTTGCGATAGTC
*
756227 CAAATTCACGTTGAGATTTATTCCAAATTCGTTGCGATAGTT
1 CAAATTCACGTTGAGATTTATTCCAAATTCGTTGCGATAGTC
756269 CAAA
1 CAAA
756273 ATCGCAACGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (42 bp):
CAAATTCACGTTGAGATTTATTCCAAATTCGTTGCGATAGTC
Found at i:757109 original size:19 final size:19
Alignment explanation
Indices: 757085--757151 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
757075 TCGTTGCGAT
757085 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
757104 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* * *
757127 CTTGAACTGTCGCAACGAA
1 TTTGGACTATCGCAACGAA
757146 TTTGGA
1 TTTGGA
757152 AAATCGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 15 0.41
21 13 0.35
23 9 0.24
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:757158 original size:19 final size:19
Alignment explanation
Indices: 757093--757159 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 19
757083 ATTTTGGACT
757093 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* *
757114 ATCGCAACGCGAACTT-GAACT
1 ATCGCAA--CGAATTTGGAA-A
*
757135 GTCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
757154 ATCGCA
1 ATCGCA
757160 TTGCGATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 11 0.31
20 4 0.11
21 14 0.39
22 1 0.03
23 6 0.17
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:757184 original size:21 final size:21
Alignment explanation
Indices: 757155--757207 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
757145 ATTTGGAAAA
757155 TCGCATTGCGATAGTCGA-AGT
1 TCGCATTGCGATAGTCGATA-T
*
757176 TCGCGTTGCGATAGTCGATAT
1 TCGCATTGCGATAGTCGATAT
757197 TCGCATTGCGA
1 TCGCATTGCGA
757208 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGATAT
Found at i:761048 original size:60 final size:60
Alignment explanation
Indices: 760975--761099 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
760965 ATGGTCCTTA
* * *** * * *
760975 ACTATAGAGCGTTGTTTTATTGAGT-TTTTTGACTATTAAAAGTTACAAAATGATCTTTTG
1 ACTATAGAGCGTTGCTTTATTAAGTCCACTT-ACTATTAAAAGCTACAAAATGATCATCTG
*
761035 ACTATA-AGACGTTGCTTTGTTAAGTCCACTTACTATTAAAAGCTACAAAATGATCATCTG
1 ACTATAGAG-CGTTGCTTTATTAAGTCCACTTACTATTAAAAGCTACAAAATGATCATCTG
761095 ACTAT
1 ACTAT
761100 TTATATATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.04
60 50 0.93
61 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (60 bp):
ACTATAGAGCGTTGCTTTATTAAGTCCACTTACTATTAAAAGCTACAAAATGATCATCTG
Done.