Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006071.1 Hibiscus syriacus cultivar Beakdansim tig00014370_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: 851632
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 4
Found at i:472700 original size:2 final size:2
Alignment explanation
Indices: 472695--472720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
472685 GTGTGTGTGA
472695 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
472721 GCTCGAGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473120 original size:2 final size:2
Alignment explanation
Indices: 473113--473154 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
473103 GAAGTTTTTA
473113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
473155 TTAAATAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:477225 original size:22 final size:22
Alignment explanation
Indices: 477181--477225 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
477171 AAATTGTTTA
* **
477181 TAAAAAATTAAAATATTTTAAT
1 TAAAAAATCAAAATATTAAAAT
*
477203 TAAAATATCAAAATATTAAAAT
1 TAAAAAATCAAAATATTAAAAT
477225 T
1 T
477226 GTATAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAATCAAAATATTAAAAT
Found at i:477995 original size:24 final size:23
Alignment explanation
Indices: 477951--477996 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
477941 TATTTTATTT
477951 TATTTTATTTATTATTAAAAATG
1 TATTTTATTTATTATTAAAAATG
477974 TATTTTAATTTATGTATTAAAAA
1 TATTTT-ATTTAT-TATTAAAAA
477997 ATAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTTATTTATTATTAAAAATG
Found at i:478005 original size:28 final size:24
Alignment explanation
Indices: 477951--478010 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 24
477941 TATTTTATTT
*
477951 TATTTT-ATTTATTATTAAAAATG
1 TATTTTAATTTATTATTAAAAATA
477974 TATTTTAATTTATGTATTAAAAAATAAA
1 TATTTTAATTTAT-TATT-AAAAAT--A
478002 TATTTTAAT
1 TATTTTAAT
478011 ATAACCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 6 0.19
24 6 0.19
25 4 0.13
26 6 0.19
28 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TATTTTAATTTATTATTAAAAATA
Found at i:479236 original size:20 final size:20
Alignment explanation
Indices: 479187--479224 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
479177 TGTTTGTTTG
479187 GCTCTGAATGAAACCATTCA
1 GCTCTGAATGAAACCATTCA
*
479207 GCTCTGAATGGAACCATT
1 GCTCTGAATGAAACCATT
479225 TAGCATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
GCTCTGAATGAAACCATTCA
Found at i:484668 original size:84 final size:84
Alignment explanation
Indices: 484330--484838 Score: 396
Period size: 84 Copynumber: 6.0 Consensus size: 84
484320 ACCATGCAGT
* * * * * * * *** *
484330 TGATATGCCTCTGAGATGAATAAAATCGAACTCAAAAGTCTTGATGTTGGTGGATAATCCTTCTA
1 TGATGTGCCTTTGAGCTGAGTATAATCGAACTCAAAGGTCTT-TTGTTGACAGATAACCCTTCTA
* *
484395 GCCTTGAGTTATGCTTCAAA
65 GCCTTGAGCTATGCTGCAAA
* * * * *
484415 AGATGTGTCTTTAAGCTGAGTGTAATCGAACTCAAAAGGTTTTTTGTTGACAGATAACCCTTCTA
1 TGATGTGCCTTTGAGCTGAGTATAATCGAACTC-AAAGGTCTTTTGTTGACAGATAACCCTTCTA
*
484480 GCCTTGAGTTATGCTGCAAA
65 GCCTTGAGCTATGCTGCAAA
* * * * * * * * * *
484500 TGACGTGCCTTGGAACTGAATGA-AATCGAATCTTAAAGGT-ATTTGATGACATATAGCTCTTCT
1 TGATGTGCCTTTGAGCTGAGT-ATAATCGAA-CTCAAAGGTCTTTTGTTGACAGATAACCCTTCT
* * * *
484563 CA-ACTTAAGCTATACTACAAA
64 -AGCCTTGAGCTATGCTGCAAA
* * * * * *
484584 TGATATTCCTTTGAGCTGAATATAATTGAACTCGAAGGTCTTTTATTGACAGATAACCCTTCTAG
1 TGATGTGCCTTTGAGCTGAGTATAATCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAG
*
484649 CCTTGAGTTATGCTGCAAA
66 CCTTGAGCTATGCTGCAAA
* * ** * * * * * * *
484668 TGACGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAGCCCATCTTG
1 TGATGTGCCTTTGAGCTGAGTATAATCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAG
* * * *
484733 ACTTAAGCTATACTACAAA
66 CCTTGAGCTATGCTGCAAA
* * * *
484752 TGATGTGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTTTGTT-AGCAAATAACCCTTCTT
1 TGATGTGCCTTTGAGCTGAGTATAATCGAACTCAAAGGTCTTTTGTTGA-CAGATAACCCTTCTA
*
484816 GCCTTGAGCTAAGCTGCAAA
65 GCCTTGAGCTATGCTGCAAA
484836 TGA
1 TGA
484839 GCACGATATC
Statistics
Matches: 323, Mismatches: 93, Indels: 17
0.75 0.21 0.04
Matches are distributed among these distances:
83 9 0.03
84 217 0.67
85 88 0.27
86 9 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (84 bp):
TGATGTGCCTTTGAGCTGAGTATAATCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAG
CCTTGAGCTATGCTGCAAA
Found at i:484739 original size:168 final size:168
Alignment explanation
Indices: 484423--484838 Score: 530
Period size: 168 Copynumber: 2.5 Consensus size: 168
484413 AAAGATGTGT
* * * *
484423 CTTTAAGCTGAGTGTAATCGAACTCAAAAGGTTTTTTGTTGACAGATAACCCTTCTAGCCTTGAG
1 CTTTGAGCTGAGTATAATCGAACTC-GAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAG
* * * *
484488 TTATGCTGCAAATGACGTGCCTTGGAACTGAATGAAATCGAATCTTAAAGGTATTTGATGACATA
65 TTATGCTGCAAATGACGTGCCTTGGAACTGAACGAAATCGAAACTCAAAGGTATTTGATGACAGA
* * *
484553 TAGCTCTTCTCAACTTAAGCTATACTACAAATGATATTC
130 TAGCCCATCTCAACTTAAGCTATACTACAAATGATATGC
* * *
484592 CTTTGAGCTGAATATAATTGAACTCGAAGGTCTTTTATTGACAGATAACCCTTCTAGCCTTGAGT
1 CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGT
* * * * * * *
484657 TATGCTGCAAATGACGTGCCTTGGAGCTGAGCGTAGTC-AAACTCAAAGGTCTTTGGTTGGCAGA
66 TATGCTGCAAATGACGTGCCTTGGAACTGAACGAAATCGAAACTCAAAGGTATTT-GATGACAGA
** *
484721 TAGCCCATCTTGACTTAAGCTATACTACAAATGATGTGC
130 TAGCCCATCTCAACTTAAGCTATACTACAAATGATATGC
* * *
484760 CTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTTTGTT-AGCAAATAACCCTTCTTGCCTTGAG
1 CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGA-CAGATAACCCTTCTAGCCTTGAG
* *
484824 CTAAGCTGCAAATGA
65 TTATGCTGCAAATGA
484839 GCACGATATC
Statistics
Matches: 213, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
167 14 0.07
168 178 0.84
169 21 0.10
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (168 bp):
CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGT
TATGCTGCAAATGACGTGCCTTGGAACTGAACGAAATCGAAACTCAAAGGTATTTGATGACAGAT
AGCCCATCTCAACTTAAGCTATACTACAAATGATATGC
Found at i:485201 original size:43 final size:44
Alignment explanation
Indices: 485153--485255 Score: 147
Period size: 43 Copynumber: 2.4 Consensus size: 44
485143 TTCGTCATGA
* *
485153 AGTTGAAACCGTGGATGT-GTGGGCATGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCCGTCGTGG
* *
485196 AGTTGAAATCATGGAT-TCGTGGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCCGTCGTGG
*
485239 AGTTGAAATTGTGGATG
1 AGTTGAAATCGTGGATG
485256 GCCCATTCGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 51 0.98
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (44 bp):
AGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCCGTCGTGG
Found at i:485630 original size:43 final size:43
Alignment explanation
Indices: 485485--485630 Score: 202
Period size: 43 Copynumber: 3.4 Consensus size: 43
485475 TTTGTTGTGA
* * * * *
485485 AGTTGAAATCGTGAATGTATGGGCACGATATCCTCCGTTGTGG
1 AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
* * * *
485528 AGTTGAAATTGTGGATATGTTGGTACGATATCCTCCGTCGTGG
1 AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
485571 AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
1 AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
*
485614 AGTTAAAATCGCGGATG
1 AGTTAAAATCGTGGATG
485631 ACCCCTTCAT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (43 bp):
AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
Found at i:486256 original size:32 final size:32
Alignment explanation
Indices: 486182--486256 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
486172 TTGCATCAGG
* *
486182 ATGTTGAATCCCCAAATATGCCACAATATTCA
1 ATGTTGAATCTCCAAATATGCCACAACATTCA
* *
486214 ATGTTGAATCTCCAAATATGCCCCAACATTTA
1 ATGTTGAATCTCCAAATATGCCACAACATTCA
*
486246 CTGTTGAATCT
1 ATGTTGAATCT
486257 TTAAAGATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCACAACATTCA
Found at i:486423 original size:23 final size:23
Alignment explanation
Indices: 486397--486464 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
486387 CTTCTTCTTT
486397 TATTTTCAAAAGTTTTGAAAATG
1 TATTTTCAAAAGTTTTGAAAATG
** *
486420 TA-TTAGAAGAGTTTTGAAAAATG
1 TATTTTCAAAAGTTTTG-AAAATG
*
486443 T-TTAATCAAAAGTTTTGAAAAT
1 TATT-TTCAAAAGTTTTGAAAAT
486465 ATTGCCCCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 11 0.31
23 15 0.43
24 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (23 bp):
TATTTTCAAAAGTTTTGAAAATG
Found at i:487320 original size:16 final size:16
Alignment explanation
Indices: 487301--487340 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
487291 TTTCTTTGCT
*
487301 TTTTCTTTTTTGCTTC
1 TTTTCTTTTTTGATTC
487317 TTTTC-TTTTTGATTC
1 TTTTCTTTTTTGATTC
487332 TTGTTCTTT
1 TT-TTCTTT
487341 GCTTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.52
16 8 0.38
17 2 0.10
ACGTcount: A:0.03, C:0.15, G:0.07, T:0.75
Consensus pattern (16 bp):
TTTTCTTTTTTGATTC
Found at i:487741 original size:20 final size:20
Alignment explanation
Indices: 487716--487757 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
487706 TTTCTGCTTC
487716 TTGCTCCCGGCATGCCTCAA
1 TTGCTCCCGGCATGCCTCAA
*
487736 TTGCTCCCGGTATGCCTCAA
1 TTGCTCCCGGCATGCCTCAA
487756 TT
1 TT
487758 ACTCAGGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.36, G:0.19, T:0.31
Consensus pattern (20 bp):
TTGCTCCCGGCATGCCTCAA
Found at i:490808 original size:22 final size:20
Alignment explanation
Indices: 490767--490816 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
490757 TAAATTCAAA
490767 AAATTAAAATAACAGTGACT
1 AAATTAAAATAACAGTGACT
*
490787 AAATTAAAAGTTAATAGTGACT
1 AAATTAAAA--TAACAGTGACT
*
490809 AAAATAAA
1 AAATTAAA
490817 GGAAATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (20 bp):
AAATTAAAATAACAGTGACT
Found at i:494052 original size:5 final size:5
Alignment explanation
Indices: 494037--494067 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
494027 AATAACAATA
*
494037 TTAAT TGAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
494068 GATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:494171 original size:14 final size:14
Alignment explanation
Indices: 494152--494178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
494142 TATTAGTTCT
494152 AATTATGAAGATAA
1 AATTATGAAGATAA
494166 AATTATGAAGATA
1 AATTATGAAGATA
494179 TACAACCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
AATTATGAAGATAA
Found at i:496919 original size:18 final size:18
Alignment explanation
Indices: 496896--496932 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
496886 CTTAAAAAAG
*
496896 TGGAACTTGTTATAAGGT
1 TGGAACTAGTTATAAGGT
*
496914 TGGAACTAGTTCTAAGGT
1 TGGAACTAGTTATAAGGT
496932 T
1 T
496933 TTGCCCGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (18 bp):
TGGAACTAGTTATAAGGT
Found at i:497445 original size:27 final size:28
Alignment explanation
Indices: 497402--497462 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
497392 TCTGATTGCT
* *
497402 TATTTTGCTGTATTAT-ACAATTTGCAA-
1 TATTTTGCTGTAATATAACAACTTG-AAG
497429 TATTTTGTCTG-AATATAACAACTTGAAG
1 TATTTTG-CTGTAATATAACAACTTGAAG
497457 TATTTT
1 TATTTT
497463 TTTATCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48
Consensus pattern (28 bp):
TATTTTGCTGTAATATAACAACTTGAAG
Found at i:502546 original size:36 final size:36
Alignment explanation
Indices: 502506--502577 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
502496 ATCAAACAAC
*
502506 TGAAAACTTGTCAAAACACAGAGAAAAACATATTAT
1 TGAAAACTTGCCAAAACACAGAGAAAAACATATTAT
502542 TGAAAACTTGCCAAAACACAGAGAAAAACATATTAT
1 TGAAAACTTGCCAAAACACAGAGAAAAACATATTAT
502578 GAAGGCAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (36 bp):
TGAAAACTTGCCAAAACACAGAGAAAAACATATTAT
Found at i:502659 original size:20 final size:19
Alignment explanation
Indices: 502634--502675 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
502624 AAAATAAGAG
502634 AAAAATAAAAATACAATATA
1 AAAAATAAAAATACAATA-A
*
502654 AAAAATAAAAATATAATAA
1 AAAAATAAAAATACAATAA
502673 AAA
1 AAA
502676 TATACAGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATAAAAATACAATAA
Found at i:502678 original size:11 final size:11
Alignment explanation
Indices: 502637--502679 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
502627 ATAAGAGAAA
*
502637 AATAAAAATAC
1 AATAAAAATAT
*
502648 AATATAAA-A-
1 AATAAAAATAT
502657 AATAAAAATAT
1 AATAAAAATAT
502668 AATAAAAATAT
1 AATAAAAATAT
502679 A
1 A
502680 CAGACGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 19 0.68
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAAAAATAT
Found at i:505491 original size:22 final size:22
Alignment explanation
Indices: 505463--505506 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
505453 AAAAGGCCAT
505463 AAATATTCAAAGAGATGAACTG
1 AAATATTCAAAGAGATGAACTG
505485 AAATATTCAAAGAGATGAACTG
1 AAATATTCAAAGAGATGAACTG
505507 GAATCGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (22 bp):
AAATATTCAAAGAGATGAACTG
Found at i:507649 original size:29 final size:29
Alignment explanation
Indices: 507617--507709 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
507607 ATAGTCGGGT
507617 GACTATTTTGTAACTTTTAATAGTTAAGA
1 GACTATTTTGTAACTTTTAATAGTTAAGA
*** * *
507646 GACTTAATAAAGCAAC-ATTATATAGTT-AGAA
1 GAC-T-ATTTTGTAACTTTTA-ATAGTTAAG-A
*
507677 GACTATTTTGTAACTTTTAATAGTTAAGG
1 GACTATTTTGTAACTTTTAATAGTTAAGA
507706 GACT
1 GACT
507710 TATTAAATCA
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
29 19 0.40
30 12 0.26
31 16 0.34
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (29 bp):
GACTATTTTGTAACTTTTAATAGTTAAGA
Found at i:516244 original size:160 final size:160
Alignment explanation
Indices: 515980--516300 Score: 642
Period size: 160 Copynumber: 2.0 Consensus size: 160
515970 CCACATACAA
515980 CTTCCAAGAAGTGAGCCGCAGATCTCTAATAGGATTTCCTATTGATATGTAAAAATGATAATGCC
1 CTTCCAAGAAGTGAGCCGCAGATCTCTAATAGGATTTCCTATTGATATGTAAAAATGATAATGCC
516045 TCCTAAATTTGGTGAAAACGTTGCACTTCAGGTAAACTCTTTTCGACAAACAATAAATATGGTGA
66 TCCTAAATTTGGTGAAAACGTTGCACTTCAGGTAAACTCTTTTCGACAAACAATAAATATGGTGA
516110 AGAACGAGATCATACCAATGGTCGGTGCTC
131 AGAACGAGATCATACCAATGGTCGGTGCTC
516140 CTTCCAAGAAGTGAGCCGCAGATCTCTAATAGGATTTCCTATTGATATGTAAAAATGATAATGCC
1 CTTCCAAGAAGTGAGCCGCAGATCTCTAATAGGATTTCCTATTGATATGTAAAAATGATAATGCC
516205 TCCTAAATTTGGTGAAAACGTTGCACTTCAGGTAAACTCTTTTCGACAAACAATAAATATGGTGA
66 TCCTAAATTTGGTGAAAACGTTGCACTTCAGGTAAACTCTTTTCGACAAACAATAAATATGGTGA
516270 AGAACGAGATCATACCAATGGTCGGTGCTC
131 AGAACGAGATCATACCAATGGTCGGTGCTC
516300 C
1 C
516301 CTCTCTGCTT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (160 bp):
CTTCCAAGAAGTGAGCCGCAGATCTCTAATAGGATTTCCTATTGATATGTAAAAATGATAATGCC
TCCTAAATTTGGTGAAAACGTTGCACTTCAGGTAAACTCTTTTCGACAAACAATAAATATGGTGA
AGAACGAGATCATACCAATGGTCGGTGCTC
Found at i:516633 original size:39 final size:39
Alignment explanation
Indices: 516579--516653 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
516569 AACTGGCAAA
516579 AGTTCACTTGGTCATGCAGTATCATACAAATAGGTCACT
1 AGTTCACTTGGTCATGCAGTATCATACAAATAGGTCACT
516618 AGTTCACTTGGTCATGCAGTATCATACAAATAGGTC
1 AGTTCACTTGGTCATGCAGTATCATACAAATAGGTC
516654 GCTAAGGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (39 bp):
AGTTCACTTGGTCATGCAGTATCATACAAATAGGTCACT
Found at i:517249 original size:5 final size:5
Alignment explanation
Indices: 517239--517280 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
517229 TAGTTATATT
517239 GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GG
1 GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GGTAA GG
517281 AATCCAGGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.19
Consensus pattern (5 bp):
GGTAA
Found at i:520149 original size:5 final size:6
Alignment explanation
Indices: 520110--520146 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
520100 GACACGTATT
520110 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
520147 CGAGACGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:523728 original size:20 final size:20
Alignment explanation
Indices: 523703--523750 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
523693 AACAGTACTA
* *
523703 TCGCAACGTGATTTTTAAAT
1 TCGCAACGAGATTTTCAAAT
523723 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
523743 TCGCAACG
1 TCGCAACG
523751 CTAATTACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAAAT
Found at i:523787 original size:37 final size:37
Alignment explanation
Indices: 523743--523872 Score: 93
Period size: 37 Copynumber: 3.4 Consensus size: 37
523733 ATTTTCAAAT
*
523743 TCGCAACGCTAATTACCGATATAGGTAAAAAGTACTA
1 TCGCAACGCGAATTACCGATATAGGTAAAAAGTACTA
* * ** * * * *
523780 TCGCAACGCGATTTA-C-AAATTCGCAACGAAATTTTCAAA
1 TCGCAACGCGAATTACCGATATAGGTAA--AAA-GTAC-TA
* * *
523819 TTTGCAACACTAATTACCGATATAGGTAAAAAGTACTA
1 -TCGCAACGCGAATTACCGATATAGGTAAAAAGTACTA
523857 TCGCAACGCGAATTAC
1 TCGCAACGCGAATTAC
523873 AAATTCGCAA
Statistics
Matches: 63, Mismatches: 23, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
35 6 0.10
36 1 0.02
37 29 0.46
38 3 0.05
39 3 0.05
40 14 0.22
41 1 0.02
42 6 0.10
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (37 bp):
TCGCAACGCGAATTACCGATATAGGTAAAAAGTACTA
Found at i:523793 original size:77 final size:77
Alignment explanation
Indices: 523655--523904 Score: 365
Period size: 77 Copynumber: 3.2 Consensus size: 77
523645 CAAAATCGCA
* * * * ** * * **
523655 ATTTTCCAAATTCACAACGTTGATTACCGATGTAAATAAACAGTACTATCGCAACGTGATTTTTA
1 ATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGATTTACA
523720 AATTCGCAACGAG
65 AATTCGCAACGAG
523733 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGATTTACAA
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGATTTACAA
*
523798 ATTCGCAACGAA
66 ATTCGCAACGAG
* * *
523810 ATTTTCAAATTTGCAACACTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGAATTACAA
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGATTTACAA
523875 ATTCGCAACGAG
66 ATTCGCAACGAG
523887 ATTTTCAAATTCGCAACG
1 ATTTTCAAATTCGCAACG
523905 TGGTTTTCAA
Statistics
Matches: 155, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
77 150 0.97
78 5 0.03
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (77 bp):
ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAAAAGTACTATCGCAACGCGATTTACAA
ATTCGCAACGAG
Found at i:523805 original size:20 final size:20
Alignment explanation
Indices: 523780--523826 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
523770 AAAAGTACTA
**
523780 TCGCAACGCGATTTACAAAT
1 TCGCAACGAAATTTACAAAT
*
523800 TCGCAACGAAATTTTCAAAT
1 TCGCAACGAAATTTACAAAT
*
523820 TTGCAAC
1 TCGCAAC
523827 ACTAATTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (20 bp):
TCGCAACGAAATTTACAAAT
Found at i:523882 original size:20 final size:20
Alignment explanation
Indices: 523857--523945 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
523847 AAAAGTACTA
* *
523857 TCGCAACGCGAATTACAAAT
1 TCGCAACGCGATTTTCAAAT
*
523877 TCGCAACGAGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
* *
523897 TCGCAACGTGGTTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
* *
523917 TCGTAACGCGGTTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
523937 TCGCAACGC
1 TCGCAACGC
523946 TAATTACCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:524031 original size:20 final size:20
Alignment explanation
Indices: 524003--524154 Score: 114
Period size: 20 Copynumber: 7.5 Consensus size: 20
523993 TAAACGCGCT
*
524003 TTGCAAATTTGACTATCGTG
1 TTGCGAATTTGACTATCGTG
* *
524023 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGTG
* *
524043 TTGTGAATTTGA-AATTCAGTG
1 TTGCGAATTTGACTA-TC-GTG
*
524064 TTGCAAATTTGACTTAT-GTG
1 TTGCGAATTTGAC-TATCGTG
* *
524084 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TA-TCGTG
** * *
524104 TTGTAAATTTGACTTTAGTG
1 TTGCGAATTTGACTATCGTG
*
524124 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGTG
524144 TTGCGAATTTG
1 TTGCGAATTTG
524155 GAAATTGGAT
Statistics
Matches: 99, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
18 3 0.03
19 5 0.05
20 70 0.71
21 17 0.17
22 3 0.03
23 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGTG
Found at i:524073 original size:41 final size:42
Alignment explanation
Indices: 524018--524136 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 42
524008 AATTTGACTA
* *
524018 TCGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGA-A-AT
1 TCGTGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACAGAT
*
524058 TCAGTGTTGCAAATTTGACTTATGTGTTGCG-ATTT-ACAGAT
1 TC-GTGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACAGAT
* * *
524099 TCGCGTTGTAAATTTGACTTTAGTGTTGCGAATTTGAC
1 TCGTGTTGCAAATTTGACTTTTGTGTTGCGAATTTGAC
524137 TATCGCGTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
39 1 0.01
40 31 0.46
41 33 0.49
42 2 0.03
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.44
Consensus pattern (42 bp):
TCGTGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACAGAT
Found at i:524143 original size:40 final size:41
Alignment explanation
Indices: 524003--524154 Score: 145
Period size: 40 Copynumber: 3.8 Consensus size: 41
523993 TAAACGCGCT
* * * *
524003 TTGCAAATTTGACTA-TCGTGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTCGCGTTGCAAATTTGACTTTAGTG
* * *
524043 TTGTGAATTTGA-AATTCAGTGTTGCAAATTTGAC-TTATGTG
1 TTGCGAATTTGACTATTC-GCGTTGCAAATTTGACTTTA-GTG
* *
524084 TTGCG-ATTT-ACAGATTCGCGTTGTAAATTTGACTTTAGTG
1 TTGCGAATTTGAC-TATTCGCGTTGCAAATTTGACTTTAGTG
*
524124 TTGCGAATTTGACTA-TCGCGTTGCGAATTTG
1 TTGCGAATTTGACTATTCGCGTTGCAAATTTG
524155 GAAATTGGAT
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.02
40 54 0.59
41 34 0.37
42 2 0.02
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (41 bp):
TTGCGAATTTGACTATTCGCGTTGCAAATTTGACTTTAGTG
Found at i:524194 original size:101 final size:100
Alignment explanation
Indices: 524007--524194 Score: 220
Period size: 101 Copynumber: 1.9 Consensus size: 100
523997 CGCGCTTTGC
* * * * *
524007 AAATTTGACTATCGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGAAATTCAGTGTTGCAAAT
1 AAATTTGACTATAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAAATT-AGTGTTGCAAAT
* * *
524072 TTGACTTATGTGTTGCGATTTACAGATTCGCGTTGT
65 TGGACTTACGCGTTGCGATTTACAGATTCGCGTTGT
*
524108 AAATTTGACTTTAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGGAAATT-G-GATTGCGAA
1 AAATTTGACTATAGTGTTGCGAATTTGACTATCGCGTTGCGAATTT-GAAATTAGTG-TTGC-AA
*
524171 ATTGGAGTT-CGCGTTGCGAATTTA
63 ATTGGACTTACGCGTTGCG-ATTTA
524195 TTGGTCATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
99 1 0.01
100 12 0.16
101 54 0.74
102 6 0.08
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (100 bp):
AAATTTGACTATAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAAATTAGTGTTGCAAATT
GGACTTACGCGTTGCGATTTACAGATTCGCGTTGT
Found at i:528849 original size:34 final size:34
Alignment explanation
Indices: 528811--528879 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
528801 GATCCGAATT
528811 CAATCGATCTCTCATTACAACCCCTGAACCTAAA
1 CAATCGATCTCTCATTACAACCCCTGAACCTAAA
528845 CAATCGATCTCTCATTACAACCCCTGAACCTAAA
1 CAATCGATCTCTCATTACAACCCCTGAACCTAAA
528879 C
1 C
528880 CCTCTCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.36, G:0.06, T:0.23
Consensus pattern (34 bp):
CAATCGATCTCTCATTACAACCCCTGAACCTAAA
Found at i:530221 original size:26 final size:26
Alignment explanation
Indices: 530185--530241 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
530175 TGCAATCCAA
*
530185 GCATCAGGATGTAATTCATGATGCCT
1 GCATCAGGATGTAATCCATGATGCCT
530211 GCATCAGGATGTAATCCATGATGCCT
1 GCATCAGGATGTAATCCATGATGCCT
530237 GCATC
1 GCATC
530242 CTACAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (26 bp):
GCATCAGGATGTAATCCATGATGCCT
Found at i:535899 original size:69 final size:69
Alignment explanation
Indices: 535817--535954 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
535807 CATCAAATCT
535817 GATCGATTTCGATTTGATTTTATTGAAATAAAATATTTGGTAAAATTTAAATAAATCTTATTGAA
1 GATCGATTTCGATTTGATTTTATTGAAATAAAATATTTGGTAAAATTTAAATAAATCTTATTGAA
535882 ATTA
66 ATTA
535886 GATCGATTTCGATTTGATTTTATTGAAATAAAATATTTGGTAAAATTTAAATAAATCTTATTGAA
1 GATCGATTTCGATTTGATTTTATTGAAATAAAATATTTGGTAAAATTTAAATAAATCTTATTGAA
535951 ATTA
66 ATTA
535955 TTAAAATTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (69 bp):
GATCGATTTCGATTTGATTTTATTGAAATAAAATATTTGGTAAAATTTAAATAAATCTTATTGAA
ATTA
Found at i:538282 original size:2 final size:2
Alignment explanation
Indices: 538275--538300 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
538265 AATCCGATTA
538275 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
538301 TTATGGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549099 original size:2 final size:2
Alignment explanation
Indices: 549086--549125 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
549076 CATGGGTTTC
*
549086 AT AT AA 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
549126 GCACAATCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:553082 original size:25 final size:22
Alignment explanation
Indices: 553037--553092 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
553027 GTAAATTTTA
* *
553037 TTTTATTTTTTAAAAAATAAAG
1 TTTTATTTATTAAAAAATAAAC
553059 TTTTATTGTATTAAAAAACCTAAAC
1 TTTTATT-TATTAAAAAA--TAAAC
553084 TTTTTATTT
1 -TTTTATTT
553093 TATACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.25
23 9 0.32
25 5 0.18
26 7 0.25
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTATTTATTAAAAAATAAAC
Found at i:561999 original size:2 final size:2
Alignment explanation
Indices: 561992--562016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
561982 AACTCTGATA
561992 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
562017 ACAGAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:562614 original size:51 final size:50
Alignment explanation
Indices: 562544--562689 Score: 134
Period size: 51 Copynumber: 2.9 Consensus size: 50
562534 TTCTTCTCCT
* *
562544 CTTCTTTCTTCCCTTCTTCTTCCTTCTTGCCTTCTTCCTTCTTTTCTCCC-C
1 CTTCTTTCTTCTCTCCTTCTTCCTTCTT-CCTTCTTCCTTCTTTTC-CCCTC
* * ** * *
562595 CTTCTTTCTTTTCTCCTTCTTCTTTCTTCTCCCCCTCTTTCTTTTCCCCTC
1 CTTCTTTCTTCTCTCCTTCTTCCTTCTTC-CTTCTTCCTTCTTTTCCCCTC
* * *
562646 CTTCCTTCTTCTCTCCCTCTTTCTT-TTCACCTTCTTCCTTCTTT
1 CTTCTTTCTTCTCTCCTTCTTCCTTCTT--CCTTCTTCCTTCTTT
562690 GGCTCCTCTT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
50 6 0.08
51 67 0.91
52 1 0.01
ACGTcount: A:0.01, C:0.42, G:0.01, T:0.56
Consensus pattern (50 bp):
CTTCTTTCTTCTCTCCTTCTTCCTTCTTCCTTCTTCCTTCTTTTCCCCTC
Found at i:562634 original size:33 final size:33
Alignment explanation
Indices: 562573--562688 Score: 160
Period size: 33 Copynumber: 3.4 Consensus size: 33
562563 TTCCTTCTTG
*
562573 CCTTCTTCCTTCTTTTCTCCCCCTTCTTTCTTTTCT
1 CCTTCTTCCTTC--TTCTCCCCC-TCTTTCTTTTCA
* *
562609 CCTTCTTCTTTCTTCTCCCCCTCTTTCTTTTCC
1 CCTTCTTCCTTCTTCTCCCCCTCTTTCTTTTCA
* *
562642 CCTCCTTCCTTCTTCTCTCCCTCTTTCTTTTCA
1 CCTTCTTCCTTCTTCTCCCCCTCTTTCTTTTCA
562675 CCTTCTTCCTTCTT
1 CCTTCTTCCTTCTT
562689 TGGCTCCTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
33 53 0.73
34 9 0.12
36 11 0.15
ACGTcount: A:0.01, C:0.44, G:0.00, T:0.55
Consensus pattern (33 bp):
CCTTCTTCCTTCTTCTCCCCCTCTTTCTTTTCA
Found at i:562681 original size:15 final size:15
Alignment explanation
Indices: 562592--562681 Score: 72
Period size: 15 Copynumber: 5.6 Consensus size: 15
562582 TTCTTTTCTC
562592 CCCCTTCTTTCTTTT
1 CCCCTTCTTTCTTTT
*
562607 CTCCTTCTTCTTTCTTCT
1 C-CC--CTTCTTTCTTTT
*
562625 CCCCCTCTTTCTTTT
1 CCCCTTCTTTCTTTT
* *
562640 CCCCTCCTTCCTTCTT
1 CCCCTTCTTTCTT-TT
*
562656 CTCTCCCTCTTTCTTTT
1 C-C-CCTTCTTTCTTTT
*
562673 CACCTTCTT
1 CCCCTTCTT
562682 CCTTCTTTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
15 27 0.47
16 5 0.09
17 6 0.10
18 20 0.34
ACGTcount: A:0.01, C:0.44, G:0.00, T:0.54
Consensus pattern (15 bp):
CCCCTTCTTTCTTTT
Found at i:562689 original size:18 final size:18
Alignment explanation
Indices: 562537--562689 Score: 103
Period size: 18 Copynumber: 9.1 Consensus size: 18
562527 CTGTGGCTTC
562537 TTCTCC-TCTTCTTTC--
1 TTCTCCTTCTTCTTTCTT
*
562552 TTC-CCTTCTTCTTCCTT
1 TTCTCCTTCTTCTTTCTT
* *
562569 CTT-GCCTTCTTCCTTCTT
1 -TTCTCCTTCTTCTTTCTT
**
562587 TTCTCCCCCTTCTTTCTT
1 TTCTCCTTCTTCTTTCTT
562605 TTCTCCTTCTTCTTTC--
1 TTCTCCTTCTTCTTTCTT
* *
562621 TTCTCC-CCCTCTTTCTT
1 TTCTCCTTCTTCTTTCTT
* * *
562638 TTCCCCTCCTTCCTTCTT
1 TTCTCCTTCTTCTTTCTT
*
562656 CTCTCC--C-TCTTTCTT
1 TTCTCCTTCTTCTTTCTT
* *
562671 TTCACCTTCTTCCTTCTT
1 TTCTCCTTCTTCTTTCTT
562689 T
1 T
562690 GGCTCCTCTT
Statistics
Matches: 106, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
14 2 0.02
15 29 0.27
16 7 0.07
17 8 0.08
18 60 0.57
ACGTcount: A:0.01, C:0.42, G:0.01, T:0.56
Consensus pattern (18 bp):
TTCTCCTTCTTCTTTCTT
Found at i:562698 original size:33 final size:32
Alignment explanation
Indices: 562573--562703 Score: 129
Period size: 33 Copynumber: 3.9 Consensus size: 32
562563 TTCCTTCTTG
* *
562573 CCTTCTTCCTTCTTTTCTCCCCCTTCTTTCTTTTCT
1 CCTTCTTCCTTC--TTCT-CTCC-TCTTTCTTTTCA
* * *
562609 CCTTCTTCTTTCTTCTCCCCCTCTTTCTTTTCC
1 CCTTCTTCCTTCTTCT-CTCCTCTTTCTTTTCA
*
562642 CCTCCTTCCTTCTTCTCTCCCTCTTTCTTTTCA
1 CCTTCTTCCTTCTTCTCT-CCTCTTTCTTTTCA
562675 CCTTCTTCCTTCTT-TGGCTCCTCTTTCTT
1 CCTTCTTCCTTCTTCT--CTCCTCTTTCTT
562704 CTCCGGTTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
32 2 0.02
33 61 0.72
34 11 0.13
36 11 0.13
ACGTcount: A:0.01, C:0.43, G:0.02, T:0.55
Consensus pattern (32 bp):
CCTTCTTCCTTCTTCTCTCCTCTTTCTTTTCA
Found at i:579736 original size:41 final size:41
Alignment explanation
Indices: 579685--579901 Score: 142
Period size: 41 Copynumber: 5.3 Consensus size: 41
579675 TTTTCCCAAT
* *
579685 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTCATAAA
* * * *
579726 TCGCAATGCG-AT-ACTGACTATCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAA-TTTCATAAA
* * * * * * *
579767 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCATAAT
1 TCGCAATGCGA-ATAAGTAAATCGCAATGCGAATTTCATAAA
* * * *
579808 TCGCAATGCGAATACGTAAATCGCAACGCG-A-TTAAGCAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTCA-TAAA
* * * *
579848 TCGCAATGCGAATTAGGAAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAA-TAAGTAAATCGCAATGCGAATTTCATAAA
579889 TCGCAATGCGAAT
1 TCGCAATGCGAAT
579902 CTTACTATCG
Statistics
Matches: 134, Mismatches: 31, Indels: 23
0.71 0.16 0.12
Matches are distributed among these distances:
39 5 0.04
40 25 0.19
41 99 0.74
42 3 0.02
43 1 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTCATAAA
Found at i:579780 original size:21 final size:21
Alignment explanation
Indices: 579621--579818 Score: 86
Period size: 21 Copynumber: 9.6 Consensus size: 21
579611 CAGTTTCCAT
* * * *
579621 ATTCGCAACGCGATTATGACA
1 ATTCGCAATGCGATTTTCATA
579642 A-TCGCAATGCGATTTTCCA-A
1 ATTCGCAATGCGATTTT-CATA
* ** * **
579662 TTTCGCGTTACGATTTTCCCA
1 ATTCGCAATGCGATTTTCATA
* *
579683 ATTCGCAATGCGA--ATAAGTA
1 ATTCGCAATGCGATTTTCA-TA
* * * *
579703 AATCGCAATGCGAATTTGAAA
1 ATTCGCAATGCGATTTTCATA
* ** *
579724 AATCGCAATGCGATACTGACT-
1 ATTCGCAATGCGATTTTCA-TA
* *
579745 A-TCGCAATGCAATTTTCCTA
1 ATTCGCAATGCGATTTTCATA
* * *
579765 ATTCGCATTGCGATTTACGT-
1 ATTCGCAATGCGATTTTCATA
*
579785 ATTCGCATTGCGATTTTCATA
1 ATTCGCAATGCGATTTTCATA
579806 ATTCGCAATGCGA
1 ATTCGCAATGCGA
579819 ATACGTAAAT
Statistics
Matches: 131, Mismatches: 36, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.02
20 59 0.45
21 68 0.52
22 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCATA
Found at i:579833 original size:20 final size:20
Alignment explanation
Indices: 579685--579919 Score: 138
Period size: 20 Copynumber: 11.6 Consensus size: 20
579675 TTTTCCCAAT
*
579685 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
** *
579705 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATACG-TAAA
*
579726 TCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
* * *
579746 TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAA--TACGTAAA
* * *
579767 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
* * * * *
579787 TCGCATTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
579808 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
579828 TCGCAACGCGATTAAGCAAA
1 TCGCAATGCGAATACGTAAA
* *
579848 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
579869 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
579889 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
579909 TCGCAATGCGA
1 TCGCAATGCGA
579920 TTTACATAGC
Statistics
Matches: 170, Mismatches: 33, Indels: 24
0.75 0.15 0.11
Matches are distributed among these distances:
19 4 0.02
20 107 0.63
21 54 0.32
22 4 0.02
23 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:579839 original size:61 final size:60
Alignment explanation
Indices: 579774--579927 Score: 168
Period size: 61 Copynumber: 2.5 Consensus size: 60
579764 AATTCGCATT
* * *
579774 GCGATTTACGTATTCGCATTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAAC
1 GCGATTTACGTA-TCGCAATGCGATTTACATAAATCGCAATGCGAATACGTAAATCGCAAC
* ** * * *
579835 GCGATTAAGCAAATCGCAATGCGAATTAGGA-AAATCGCAATGCGAATACGTAAATCGCAAT
1 GCGATTTA-CGTATCGCAATGCGATTTA-CATAAATCGCAATGCGAATACGTAAATCGCAAC
579896 GCGAATCTTAC-TATCGCAATGCGATTTACATA
1 GCG-AT-TTACGTATCGCAATGCGATTTACATA
579928 GCGCCATTCG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
60 1 0.01
61 66 0.88
62 6 0.08
63 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
GCGATTTACGTATCGCAATGCGATTTACATAAATCGCAATGCGAATACGTAAATCGCAAC
Found at i:580491 original size:19 final size:18
Alignment explanation
Indices: 580478--580569 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
580468 ATCGCATTGT
*
580478 GATTTTCATTTCGCGTTGT
1 GATTTTCATTTCGC-TTGC
*
580497 GA--TTC-TCTCG-TTGC
1 GATTTTCATTTCGCTTGC
580511 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGC-TTGC
580530 GATTTTC---TCG-TTGC
1 GATTTTCATTTCGCTTGC
580544 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGC-TTGC
580563 GATTTTC
1 GATTTTC
580570 TCGTTGCGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 16 0.27
16 10 0.17
17 10 0.17
19 24 0.40
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.49
Consensus pattern (18 bp):
GATTTTCATTTCGCTTGC
Found at i:580520 original size:33 final size:33
Alignment explanation
Indices: 580478--580579 Score: 177
Period size: 33 Copynumber: 3.1 Consensus size: 33
580468 ATCGCATTGT
* *
580478 GATTTTCATTTCGCGTTGTGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTTTCTCGTTGC
580511 GATTTTCATTTCGCGTTGCGATTTTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTTTCTCGTTGC
*
580544 GATTTTCATTTCGCATTGCGATTTTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTTTCTCGTTGC
580577 GAT
1 GAT
580580 AGTCAGTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTTTCTCGTTGC
Found at i:580597 original size:20 final size:20
Alignment explanation
Indices: 580572--580610 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
580562 CGATTTTCTC
580572 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
580592 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
580611 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:580725 original size:14 final size:14
Alignment explanation
Indices: 580706--580743 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
580696 CACCAATTAA
580706 ACAAATCAATATTT
1 ACAAATCAATATTT
* *
580720 ACAAATCATTTTTT
1 ACAAATCAATATTT
580734 ACAAATCAAT
1 ACAAATCAAT
580744 TAAACAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
ACAAATCAATATTT
Found at i:582200 original size:42 final size:42
Alignment explanation
Indices: 582154--582246 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
582144 CCTCTTCAAC
* *
582154 GATGACAGTGGCCTCTTGAACGGA-GGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAAC-GATGGGAGGGGACTCTTGAGG
* *
582196 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
582238 GATGACAGG
1 GATGACAGG
582247 TGAGTCGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.22, C:0.15, G:0.43, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:582206 original size:21 final size:21
Alignment explanation
Indices: 582182--582242 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
582172 AACGGAGGGG
*
582182 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
582203 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
582224 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
582243 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:582629 original size:20 final size:20
Alignment explanation
Indices: 582606--582673 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
582596 AAACTTACTT
582606 TCGCAACGCGGAAATAACTA
1 TCGCAACGCGGAAATAACTA
*
582626 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATAACTA
* *
582646 TCGAAACGCGGAAATGAA-AA
1 TCGCAACGCGGAAAT-AACTA
582666 TCGCAACG
1 TCGCAACG
582674 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 41 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGGAAATAACTA
Found at i:582681 original size:14 final size:14
Alignment explanation
Indices: 582662--582720 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
582652 CGCGGAAATG
582662 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
582676 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
582695 AAAATCGCAACGAC
1 AAAATCGCAACGAC
582709 AAAATCGCAACG
1 AAAATCGCAACG
582721 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:582698 original size:33 final size:33
Alignment explanation
Indices: 582645--582725 Score: 135
Period size: 33 Copynumber: 2.4 Consensus size: 33
582635 GGAAATGACT
*
582645 ATCGAAACGCGGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGACAAA
*
582679 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
582712 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
582726 CACAAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 36 0.82
34 8 0.18
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:582733 original size:33 final size:33
Alignment explanation
Indices: 582645--582736 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
582635 GGAAATGACT
* *
582645 ATCGAAACGCGGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGC-GAAATCAAAATCGCAACGACAAA
* *
582679 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAAATCGCAACGACAAA
582712 ATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAACGCGAAATCA-AAATCGCA
582737 TTACGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.02
33 44 0.83
34 8 0.15
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATCAAAATCGCAACGACAAA
Found at i:582754 original size:19 final size:19
Alignment explanation
Indices: 582732--582795 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
582722 GAAACACAAA
582732 TCGCATTACGATTTTCATT
1 TCGCATTACGATTTTCATT
* *
582751 TCGCGTTGCGATTTT-A--
1 TCGCATTACGATTTTCATT
582767 TCG--TTACGATTTTCATT
1 TCGCATTACGATTTTCATT
*
582784 TCGCATTGCGAT
1 TCGCATTACGAT
582796 AGCCATTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
19 19 0.53
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTACGATTTTCATT
Found at i:582832 original size:20 final size:20
Alignment explanation
Indices: 582780--582823 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
582770 TTACGATTTT
*
582780 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
582799 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
582819 CATTT
1 CATTT
582824 TCGTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:583391 original size:17 final size:18
Alignment explanation
Indices: 583369--583415 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
583359 CGGGTCGATC
583369 AGGTGATGGCTCT-GGTG
1 AGGTGATGGCTCTGGGTG
*
583386 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
583404 AGGTGATGGCTC
1 AGGTGATGGCTC
583416 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.15, C:0.13, G:0.45, T:0.28
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:584642 original size:20 final size:20
Alignment explanation
Indices: 584594--584652 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
584584 AATAGTTTCT
* *
584594 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
584614 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
584634 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
584653 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:584923 original size:22 final size:22
Alignment explanation
Indices: 584896--584939 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
584886 GATGGAGATA
584896 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
584918 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
584940 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:585225 original size:41 final size:41
Alignment explanation
Indices: 585106--585243 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
585096 CGCTTTGAAA
* * *
585106 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
585147 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
585187 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
585228 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
585244 CCAAATTCGC
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 32 0.41
41 46 0.59
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:585240 original size:20 final size:20
Alignment explanation
Indices: 585126--585239 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
585116 GATTATGTAT
*
585126 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
585146 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
585166 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
585186 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
585207 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
585227 TATCGCGTTGCGA
1 TATCGCGTTGCGA
585240 TTTTCCAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:585258 original size:21 final size:20
Alignment explanation
Indices: 585229--585280 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
585219 ATAGTCAGTA
* *
585229 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
585250 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
585270 TCGCATTGCGA
1 TCGCATTGCGA
585281 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:585259 original size:41 final size:41
Alignment explanation
Indices: 585133--585261 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 41
585123 TATTATCTCG
* * * ** *
585133 TTGCGAAAGTCAGTATTGAGTTGCGAAATT-AAGTATCG-A
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
* ** * *
585172 GTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 -TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
585214 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCA
585255 TTGCGAT
1 TTGCGAT
585262 TTACTTATTC
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 26 0.35
41 46 0.62
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
Found at i:585322 original size:21 final size:22
Alignment explanation
Indices: 585270--585322 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
585260 ATTTACTTAT
585270 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
585291 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
585312 TCGCATTGCGA
1 TCGCATTGCGA
585323 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:589673 original size:16 final size:18
Alignment explanation
Indices: 589638--589674 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
589628 GTAAGTTTTT
*
589638 TTTGTGTTTACTTCTGTA
1 TTTGTGTTTACTTCTATA
589656 TTTGT-TTTACTT-TATA
1 TTTGTGTTTACTTCTATA
589672 TTT
1 TTT
589675 CTGGATGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.68
Consensus pattern (18 bp):
TTTGTGTTTACTTCTATA
Found at i:600262 original size:31 final size:30
Alignment explanation
Indices: 600224--600362 Score: 90
Period size: 29 Copynumber: 4.7 Consensus size: 30
600214 TTGAATATGC
*
600224 AAAAGTTTAGGGATTAATTTAGAATGATATT
1 AAAAGTTTAGGGATTAATTTAGAATGAT-TA
* * * * *
600255 CATAGTTT-GGAGATGAAATTGGAATG-TTA
1 AAAAGTTTAGG-GATTAATTTAGAATGATTA
* *
600284 AAAAGTTTAAGGATTAATTTAGAATGA-GA
1 AAAAGTTTAGGGATTAATTTAGAATGATTA
* * * * *
600313 GATAA-TTTTGGGATAAAATTAGAAT-ATTT
1 -AAAAGTTTAGGGATTAATTTAGAATGATTA
*
600342 AAAAGTTTAAGGATTAATTTA
1 AAAAGTTTAGGGATTAATTTA
600363 AATTGAGAGT
Statistics
Matches: 77, Mismatches: 25, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
28 4 0.05
29 48 0.62
30 7 0.09
31 18 0.23
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (30 bp):
AAAAGTTTAGGGATTAATTTAGAATGATTA
Found at i:600353 original size:58 final size:60
Alignment explanation
Indices: 600207--600380 Score: 189
Period size: 58 Copynumber: 3.0 Consensus size: 60
600197 TGACTATGGT
** * * *
600207 GATAAAATTGAATATGCAAAAGTTTAGGGATTAATTTAGAATGATA-TTCATAGTTTGGA
1 GATAAAATTGAATATTAAAAAGTTTAAGGATTAATTTAGAATGAGAGATCATAGTTTGGA
* * *
600266 GATGAAATTGGAATGTTAAAAAGTTTAAGGATTAATTTAGAATGAGAGAT-A-ATTTTGG-
1 GATAAAATT-GAATATTAAAAAGTTTAAGGATTAATTTAGAATGAGAGATCATAGTTTGGA
* *
600324 GATAAAATTAGAATATTTAAAAGTTTAAGGATTAATTTA-AATTGAGAG-TTATAGTTT
1 GATAAAATT-GAATATTAAAAAGTTTAAGGATTAATTTAGAA-TGAGAGATCATAGTTT
600381 TAAAACTGAC
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 3 0.03
58 42 0.43
59 18 0.19
60 33 0.34
61 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (60 bp):
GATAAAATTGAATATTAAAAAGTTTAAGGATTAATTTAGAATGAGAGATCATAGTTTGGA
Found at i:603091 original size:28 final size:29
Alignment explanation
Indices: 603051--603156 Score: 117
Period size: 28 Copynumber: 3.7 Consensus size: 29
603041 TCCAGAACAT
603051 GTAATTCATTTTACGTAAACAAATTT-AG
1 GTAATTCATTTTACGTAAACAAATTTCAG
* ** *
603079 GTAATTCATTTTACGTAAATAGTTTTCAT
1 GTAATTCATTTTACGTAAACAAATTTCAG
*
603108 GTAATTCATTTTACGTAAA-ATAATTTTCAA
1 GTAATTCATTTTACGTAAACA-AA-TTTCAG
* *
603138 GTAATCCATTTTACATAAA
1 GTAATTCATTTTACGTAAA
603157 TTATTTTCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.36
29 20 0.30
30 22 0.33
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTACGTAAACAAATTTCAG
Found at i:603117 original size:57 final size:59
Alignment explanation
Indices: 603048--603157 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 59
603038 TTTTCCAGAA
* * *
603048 CATGTAATTCATTTTACGTAAACA-AA-TTT-AGGTAATTCATTTTACGTAAATAGTTTT
1 CATGTAATTCATTTTACGTAAA-ATAATTTTCAAGTAATCCATTTTACATAAATAGTTTT
603105 CATGTAATTCATTTTACGTAAAATAATTTTCAAGTAATCCATTTTACATAAAT
1 CATGTAATTCATTTTACGTAAAATAATTTTCAAGTAATCCATTTTACATAAAT
603158 TATTTTCCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
56 1 0.02
57 24 0.51
58 3 0.06
59 19 0.40
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (59 bp):
CATGTAATTCATTTTACGTAAAATAATTTTCAAGTAATCCATTTTACATAAATAGTTTT
Found at i:603119 original size:15 final size:14
Alignment explanation
Indices: 603051--603125 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
603041 TCCAGAACAT
603051 GTAATTCATTTTAC
1 GTAATTCATTTTAC
* * *
603065 GTAA-ACAAATTTAG
1 GTAATTC-ATTTTAC
603079 GTAATTCATTTTAC
1 GTAATTCATTTTAC
* *
603093 GTAAAT-AGTTTTCAT
1 GTAATTCA-TTTT-AC
603108 GTAATTCATTTTAC
1 GTAATTCATTTTAC
603122 GTAA
1 GTAA
603126 AATAATTTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
13 2 0.04
14 32 0.70
15 11 0.24
16 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (14 bp):
GTAATTCATTTTAC
Found at i:603121 original size:29 final size:29
Alignment explanation
Indices: 603048--603164 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
603038 TTTTCCAGAA
* *
603048 CATGTAATTCATTTTACGTAAACAAATTT
1 CATGTAATTCATTTTACGTAAATAATTTT
* *
603077 -AGGTAATTCATTTTACGTAAATAGTTTT
1 CATGTAATTCATTTTACGTAAATAATTTT
603105 CATGTAATTCATTTTACGTAAAATAATTTT
1 CATGTAATTCATTTTACGT-AAATAATTTT
* * * *
603135 CAAGTAATCCATTTTACATAAATTATTTT
1 CATGTAATTCATTTTACGTAAATAATTTT
603164 C
1 C
603165 CAAAAAAATC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
28 24 0.32
29 27 0.36
30 25 0.33
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (29 bp):
CATGTAATTCATTTTACGTAAATAATTTT
Found at i:613714 original size:21 final size:20
Alignment explanation
Indices: 613688--613744 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
613678 ATATTATCAT
*
613688 AATAATAATATATTTCGATAA
1 AATAATTATA-ATTTCGATAA
* *
613709 AATAATTTTACATTTCGGTAA
1 AATAATTATA-ATTTCGATAA
613730 AATAATTATAATTTC
1 AATAATTATAATTTC
613745 TATGAACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
AATAATTATAATTTCGATAA
Found at i:617576 original size:17 final size:18
Alignment explanation
Indices: 617548--617581 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
617538 TAATTAAATA
617548 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
617566 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
617582 ACTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:625872 original size:22 final size:22
Alignment explanation
Indices: 625847--625913 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
625837 CTTGTATAAA
625847 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
625869 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
625891 TGCACCGAAGTCCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
625913 T
1 T
625914 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:626698 original size:67 final size:67
Alignment explanation
Indices: 626551--626701 Score: 214
Period size: 68 Copynumber: 2.2 Consensus size: 67
626541 TTTTCTCATG
* * *
626551 GGGGAATCGGTTCCCCCCCTTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
626616 GA
66 GA
* * * *
626618 GGAGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GG-GGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
626682 TGAA
65 TG-A
626686 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
626702 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 26 0.35
68 49 0.65
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
GA
Found at i:626711 original size:21 final size:21
Alignment explanation
Indices: 626681--626723 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
626671 ATCATATTCG
* *
626681 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
626702 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
626723 T
1 T
626724 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:626718 original size:67 final size:68
Alignment explanation
Indices: 626556--626723 Score: 189
Period size: 68 Copynumber: 2.5 Consensus size: 68
626546 TCATGGGGGA
** *
626556 ATCGGTTCCCCCCCTTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGA
1 ATCGGTTCCCCCCAATGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAGGA
626621 GGT
66 GGT
** * * * *
626624 ATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGAAGG
1 ATCGGTTCCCCCCAATGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG-AGG
626688 -GGT
65 AGGT
** *
626691 ATCGGTTCCCCTTGAAT-GGGTACCGATTCCCCT
1 ATCGGTTCCCC-CCAATGGGGTATCGATTCCCCT
626724 AACCCAGAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
67 39 0.45
68 48 0.55
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (68 bp):
ATCGGTTCCCCCCAATGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAGGA
GGT
Found at i:632741 original size:22 final size:22
Alignment explanation
Indices: 632724--632790 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
632714 CTCGTATAAA
632724 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
632746 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
632768 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
632790 T
1 T
632791 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:633569 original size:67 final size:68
Alignment explanation
Indices: 633424--633574 Score: 223
Period size: 68 Copynumber: 2.2 Consensus size: 68
633414 TTTTCTCATG
* * *
633424 GGGGAATCGGTTCCCCCCCTTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
633489 GAG
66 GAA
* * * *
633492 GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
633556 GAA
66 GAA
633559 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
633575 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 27 0.36
68 48 0.64
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
GAA
Found at i:633596 original size:21 final size:21
Alignment explanation
Indices: 633554--633596 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
633544 ATCATATTCG
* * *
633554 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTACCC
*
633575 TTGAATGGGTACCGATTACCC
1 TTGAAGGGGTACCGATTACCC
633596 T
1 T
633597 AACCCAGAAA
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:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTACCC
Found at i:637660 original size:21 final size:20
Alignment explanation
Indices: 637636--637794 Score: 135
Period size: 21 Copynumber: 7.7 Consensus size: 20
637626 CATATTCGCA
637636 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCG-G
*
637657 TTGCGATAGTCGAAGTTCGTG
1 TTGCGATAGTCCAAGTTCG-G
** * *
637678 TTGCGATTTTTCAAATTC-G
1 TTGCGATAGTCCAAGTTCGG
637697 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
* * *
637718 TTACGATTTATTCCAAATTC-G
1 TTGCGA--TAGTCCAAGTTCGG
637739 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
* *
637760 TTGCGATTTATTCCAAATTC-G
1 TTGCGA--TAGTCCAAGTTCGG
637781 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
637795 AATCGCAACG
Statistics
Matches: 111, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
19 32 0.29
21 59 0.53
23 20 0.18
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCGG
Found at i:637684 original size:42 final size:41
Alignment explanation
Indices: 637630--637794 Score: 217
Period size: 42 Copynumber: 4.0 Consensus size: 41
637620 GATTTACATA
* * * *
637630 TTCGCATTGCGA-TAGTCCAAGTTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAATTC--GTTGCGATAGTCCAAG
* *
637672 TTCGTGTTGCGATT-TTTCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATTATTCCAAATTCGTTGCGATAGTCCAAG
*
637712 TTCGCGTTACGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCCAAG
637754 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCCAA
637795 AATCGCAACG
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
40 25 0.23
41 2 0.02
42 82 0.75
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:638651 original size:19 final size:19
Alignment explanation
Indices: 638627--638693 Score: 89
Period size: 19 Copynumber: 3.3 Consensus size: 19
638617 TCGTTGCGAT
638627 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
638646 TTTGGAATAAATCGCAATGCGAA
1 TTTGGACT--ATCGCAA--CGAA
638669 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
638688 TTTGGA
1 TTTGGA
638694 AAATCGCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 17 0.40
21 14 0.33
23 11 0.26
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:638680 original size:42 final size:40
Alignment explanation
Indices: 638621--638707 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 40
638611 CACCCGTCGT
*
638621 TGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGCAA
1 TGCGAATTTGGACTATCGCAACGAATTTGG-A-AAATCGCAA
*
638663 TGCGAATTTGGACTATCGCAACGAATTTGGAAAATCGCAT
1 TGCGAATTTGGACTATCGCAACGAATTTGGAAAATCGCAA
638703 TGCGA
1 TGCGA
638708 TAGTCAAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 13 0.30
41 1 0.02
42 29 0.67
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (40 bp):
TGCGAATTTGGACTATCGCAACGAATTTGGAAAATCGCAA
Found at i:638699 original size:19 final size:19
Alignment explanation
Indices: 638635--638701 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 19
638625 ATTTTGGACT
638635 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
**
638656 ATCGCAATGCGAATTTGGACT
1 ATCGCAA--CGAATTTGGAAA
638677 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
638696 ATCGCA
1 ATCGCA
638702 TTGCGATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 16 0.40
21 14 0.35
22 1 0.03
23 9 0.22
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:638745 original size:57 final size:57
Alignment explanation
Indices: 638672--638785 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
638662 ATGCGAATTT
638672 GGACTATCGCAACGAATTTGGAAAATCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
1 GGACTATCGCAACGAATTTGGAAAATCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
* * *
638729 GGACTATCGCAACGAATTTGGAAAATCGCATTGCGATAGTCGATGTTTGCGTTGCGA
1 GGACTATCGCAACGAATTTGGAAAATCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
638786 ATCTGGAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (57 bp):
GGACTATCGCAACGAATTTGGAAAATCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
Found at i:639539 original size:230 final size:226
Alignment explanation
Indices: 639104--639568 Score: 610
Period size: 229 Copynumber: 2.0 Consensus size: 226
639094 ACATAACCGA
** * *
639104 TTAATTACTGAAAACATTATCAACCATAATAACATAACGTGTATTGCTTATGTAATGTAATAGGT
1 TTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAATGCTTATGTAATGTAATAAGT
* * * *
639169 AGCGTCTTTTTAAAGCTAATAGAACCTCAAAAATCCGACGATAACAAAATATGTTAATTAATTGA
66 AGCGACTTTTTAAAGATAATAGAACCTCAAAAATCCGACGATAACAAAACATGTTAATTAATTAA
*
639234 TTTGTTATCAATATTATCAACATATTAGATAGCGCCTAAAATATTTCCAAAGTTTAAGCTGATGG
131 TTTGTTATCAATATTATCAACATATTAGATAGCGCCTAAAATATTTCCAAAGTTTAAGCTGAAGG
* * *
639299 AGCTTTAGAAATATGACGATAACAAAATAGG
196 AGCCTTAGAAATACGACGATAACAAAATAAG
* * * * *
639330 TTAATTACTAGAAACATTATTATCAATCATAATAACATTACAAGTAATGTTTATTTAATGTAATA
1 TTAATTACT-GAAA-A-CATTATCAACCATAATAACATAACAAGTAATGCTTATGTAATGTAATA
* * * * * * *
639395 AGTAGCGACTTTTTAAAGATGATGGAGCCTTAGAAATCTGACGATAACAAAACATGTTAATTACT
63 AGTAGCGACTTTTTAAAGATAATAGAACCTCAAAAATCCGACGATAACAAAACATGTTAATTAAT
639460 TAATTTTGTTATCAATATTATCAACATATTA-AGTAGCGCCTAAAATATTAT-CAAAGTTTAAGC
128 TAA-TTTGTTATCAATATTATCAACATATTAGA-TAGCGCCTAAAATATT-TCCAAAGTTTAAGC
* * * *
639523 TGAAGGGGCCTTAGAAATCCGATGATAACAAATTAAG
190 TGAAGGAGCCTTAGAAATACGACGATAACAAAATAAG
639560 TTAATTACT
1 TTAATTACT
639569 TATTTTTGTT
Statistics
Matches: 205, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
226 9 0.04
227 4 0.02
228 1 0.00
229 97 0.47
230 93 0.45
231 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (226 bp):
TTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAATGCTTATGTAATGTAATAAGT
AGCGACTTTTTAAAGATAATAGAACCTCAAAAATCCGACGATAACAAAACATGTTAATTAATTAA
TTTGTTATCAATATTATCAACATATTAGATAGCGCCTAAAATATTTCCAAAGTTTAAGCTGAAGG
AGCCTTAGAAATACGACGATAACAAAATAAG
Found at i:639704 original size:108 final size:107
Alignment explanation
Indices: 639421--639692 Score: 312
Period size: 109 Copynumber: 2.5 Consensus size: 107
639411 AGATGATGGA
* * * *
639421 GCCTTAGAAATCTGACGATAACAAAACATGTTAATTACTTAATTTTGTTATCAATATTATCAACA
1 GCCTTAGAAATCCGACGATAACAAAATAAGTTAATTACTT-ATTTTGTTATAAATATTATCAACA
* ** * *
639486 TATTAAGTAGCGCCTAAAATATTATCAAAGTTTAAGCTGAAGGG
65 TATTAAGTAGAGCAAAAAATATTACCAAAATTTAAGCTGAA-GG
* * * *
639530 GCCTTAGAAATCCGATGATAACAAATTAAGTTAATTACTTATTTTTGTTATTAATTTTATCAACA
1 GCCTTAGAAATCCGACGATAACAAAATAAGTTAATTACTTA-TTTTGTTATAAATATTATCAACA
* * *
639595 TATTAGGTAGAGCAAAAAATGTTACCAAAATTTAAGCTGATA-T
65 TATTAAGTAGAGCAAAAAATATTACCAAAATTTAAGCTGA-AGG
* * * * *
639638 GCCTTTGAAATCCCACGACAACAAAATAGGTTAATTTCTTATTTTGTTATAAATA
1 GCCTTAGAAATCCGACGATAACAAAATAAGTTAATTACTTATTTTGTTATAAATA
639693 AATATTAACA
Statistics
Matches: 137, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
107 12 0.09
108 35 0.26
109 89 0.65
110 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (107 bp):
GCCTTAGAAATCCGACGATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACAT
ATTAAGTAGAGCAAAAAATATTACCAAAATTTAAGCTGAAGG
Found at i:639922 original size:17 final size:17
Alignment explanation
Indices: 639897--639932 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
639887 AGTTATAGAG
*
639897 TATGGATACATTATTAT
1 TATGAATACATTATTAT
639914 TATGAATACATTATTAT
1 TATGAATACATTATTAT
639931 TA
1 TA
639933 ACATTTAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (17 bp):
TATGAATACATTATTAT
Found at i:640326 original size:75 final size:75
Alignment explanation
Indices: 640240--640399 Score: 171
Period size: 75 Copynumber: 2.1 Consensus size: 75
640230 GTAACACATA
* *
640240 TTTAACATAATAAGTAACACATGTTTTA-TTTTATCCTTTACATTATTAGTAA-CATTTAAACAA
1 TTTAACGTAATAAGTAACACATATTTTATTTTTATCC-TTACATTATTAGTAATC-TTTAAACAA
*
640303 ACTAGTAGGTAT
64 ACTAGTAGATAT
** *** * * **
640315 TTTAACGTAATAAGTCTCGTTTATTTTATTTTTTTGCTTACATTATTCTTAATCTTTAAACAAAC
1 TTTAACGTAATAAGTAACACATATTTTATTTTTATCCTTACATTATTAGTAATCTTTAAACAAAC
*
640380 TGGTAGATAT
66 TAGTAGATAT
640390 TTTAACGTAA
1 TTTAACGTAA
640400 CAGATGGTGC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
75 63 0.90
76 7 0.10
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (75 bp):
TTTAACGTAATAAGTAACACATATTTTATTTTTATCCTTACATTATTAGTAATCTTTAAACAAAC
TAGTAGATAT
Found at i:640435 original size:17 final size:19
Alignment explanation
Indices: 640410--640446 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
640400 CAGATGGTGC
*
640410 TTATTTTATT-TT-ACCTT
1 TTATATTATTATTAACCTT
640427 TTATATTATTATTAACCTT
1 TTATATTATTATTAACCTT
640446 T
1 T
640447 AAACAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTATTATTAACCTT
Found at i:640435 original size:75 final size:74
Alignment explanation
Indices: 640263--640453 Score: 194
Period size: 75 Copynumber: 2.5 Consensus size: 74
640253 GTAACACATG
* * *
640263 TTTTATTTTATCC-TTTACATTATTAGTAACATTTAAACAAACTAGTAGGTATTTTAACGTAATA
1 TTTTATTTTA-CCTTTTACATTATTATTAAC-TTTAAACAAACTAGTAGATATTTTAACGTAACA
*
640327 AGTCTCGTTTA
64 AGTCTCGCTTA
* * *
640338 TTTTATTTT--TTTGCTTACATTATTCTTAATCTTTAAACAAACTGGTAGATATTTTAACGTAAC
1 TTTTATTTTACCTT--TTACATTATTATTAA-CTTTAAACAAACTAGTAGATATTTTAACGTAAC
*
640401 -AGATGGT-GCTTA
63 AAG-T-CTCGCTTA
*
640413 TTTTATTTTACCTTTTATATTATTATTAACCTTTAAACAAA
1 TTTTATTTTACCTTTTACATTATTATTAA-CTTTAAACAAA
640454 TCAATAACTA
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
73 1 0.01
74 2 0.02
75 89 0.93
76 2 0.02
77 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (74 bp):
TTTTATTTTACCTTTTACATTATTATTAACTTTAAACAAACTAGTAGATATTTTAACGTAACAAG
TCTCGCTTA
Found at i:640490 original size:23 final size:23
Alignment explanation
Indices: 640464--640536 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
640454 TCAATAACTA
* *
640464 ATTTAATGTAATAGGTAACGTTT
1 ATTTAACGTAATAGGTAACGTCT
* *
640487 ATTTAACGTAATAGGTAGCATCT
1 ATTTAACGTAATAGGTAACGTCT
* *
640510 ATTTAACATAATAGGTATCGTCT
1 ATTTAACGTAATAGGTAACGTCT
640533 ATTT
1 ATTT
640537 TATTTTACTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (23 bp):
ATTTAACGTAATAGGTAACGTCT
Found at i:640610 original size:75 final size:75
Alignment explanation
Indices: 640511--640693 Score: 267
Period size: 75 Copynumber: 2.4 Consensus size: 75
640501 GTAGCATCTA
* * * *
640511 TTTAACATAATAGGTATCGTCTATTTTATTTTACTGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTATCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
*
640576 CGGTAGGTAT
66 CGGTAGGTAG
* * * * *
640586 TTTAACGTAATAGGTAACACCTATTTTATTTTACCGTTTACATTTTTAATAGCCTTCAAACAAAC
1 TTTAACATAATAGGTATCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
640651 CGGTAGGTAG
66 CGGTAGGTAG
*
640661 TTTAACATAATATGTATCGCCTATTTTATTTTA
1 TTTAACATAATAGGTATCGCCTATTTTATTTTA
640694 ACCGGTTAAG
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (75 bp):
TTTAACATAATAGGTATCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
CGGTAGGTAG
Found at i:641493 original size:23 final size:23
Alignment explanation
Indices: 641463--641522 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
641453 CAGTAGCTAG
*
641463 TTTAACGTAATAGGTAACACTTA
1 TTTAACGTAATAGGTAACACCTA
* *
641486 TTTAACGTAATAGATATCACCTA
1 TTTAACGTAATAGGTAACACCTA
*
641509 TTTAACATAATAGG
1 TTTAACGTAATAGG
641523 CAACGTCTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (23 bp):
TTTAACGTAATAGGTAACACCTA
Found at i:641681 original size:74 final size:75
Alignment explanation
Indices: 641509--641691 Score: 235
Period size: 75 Copynumber: 2.5 Consensus size: 75
641499 ATATCACCTA
* ** * * *
641509 TTTAACATAATAGGCAACGTCTGTTTTATTTTAATGTTCACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAACACCTATTTTATTTTAACGTTCACATTATTAGTAACCTTCAAACAAAC
*
641574 CGGTAGATAT
66 CGGTAGATAG
* * * * *
641584 TTTAACGTAATATGTAACACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAA-AAAG
1 TTTAACATAATAGGTAACACCTATTTTATTTTAACGTTCACATTATTAGTAACCTTCAAACAAAC
641648 CGGTATG-TAG
66 CGGTA-GATAG
641658 TTTAACATAATAGGTAACACCTATTTTATTTTAA
1 TTTAACATAATAGGTAACACCTATTTTATTTTAA
641692 TCGGTTAAGT
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
74 41 0.45
75 51 0.55
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (75 bp):
TTTAACATAATAGGTAACACCTATTTTATTTTAACGTTCACATTATTAGTAACCTTCAAACAAAC
CGGTAGATAG
Found at i:642308 original size:30 final size:30
Alignment explanation
Indices: 642272--642331 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
642262 CCAAGTTGCT
642272 GGCCGCCCCACTAATTATGTATCATGGATA
1 GGCCGCCCCACTAATTATGTATCATGGATA
642302 GGCCGCCCCACTAATTATGTATCATGGATA
1 GGCCGCCCCACTAATTATGTATCATGGATA
642332 AAAAGCACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (30 bp):
GGCCGCCCCACTAATTATGTATCATGGATA
Found at i:648414 original size:17 final size:17
Alignment explanation
Indices: 648392--648427 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
648382 AACTTATAAA
648392 ATTTTAAAAATAAAAAT
1 ATTTTAAAAATAAAAAT
*
648409 ATTTTAACAATAAAAAT
1 ATTTTAAAAATAAAAAT
648426 AT
1 AT
648428 AAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTTAAAAATAAAAAT
Found at i:668312 original size:2 final size:2
Alignment explanation
Indices: 668305--668340 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
668295 AGCAATATTA
668305 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
668341 CACTCTTTTT
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:672912 original size:23 final size:23
Alignment explanation
Indices: 672879--672941 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
672869 CATCTTATAT
*
672879 GGCACTTCGGTGCATTTTTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
672902 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
672925 GGTACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
672942 ATATGAGATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:687811 original size:60 final size:60
Alignment explanation
Indices: 687664--687811 Score: 140
Period size: 60 Copynumber: 2.5 Consensus size: 60
687654 GAACATAATA
* * * * *
687664 AATAGTTGAGTGACCCTTT-TGTAACTTTTAATAGTCGAGAGACTTAACAAAGTAACACTC
1 AATAGTTGGGGGACCATTTGTGT-ACTTTTAATAGTCGAGAGACTTAACAAAATAACACCC
* * * * * * *
687724 TATATTTGGAGGATCAGTTTGT-AACTTTTAATAGTCGA-AGAACTTAATAAAATAATACCC
1 AATAGTTGGGGGACCA-TTTGTGTACTTTTAATAGTCGAGAG-ACTTAACAAAATAACACCC
687784 AATAGTTGGGGGACCATTTGTGTACTTT
1 AATAGTTGGGGGACCATTTGTGTACTTT
687812 ACCCCAAAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
59 7 0.10
60 56 0.84
61 3 0.04
62 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (60 bp):
AATAGTTGGGGGACCATTTGTGTACTTTTAATAGTCGAGAGACTTAACAAAATAACACCC
Found at i:691788 original size:28 final size:28
Alignment explanation
Indices: 691756--691830 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
691746 ATAATATTCA
* * * *
691756 TCTTGATTCTACATGAGATTTGTTCCCT
1 TCTTGATTCTGCATGAGATTAGTCCCCG
* *
691784 TCTTGATTCTGCATGGGCTTAGTCCCCG
1 TCTTGATTCTGCATGAGATTAGTCCCCG
*
691812 TCTTGGTTCTGCATGAGAT
1 TCTTGATTCTGCATGAGAT
691831 CTCTTTCCCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (28 bp):
TCTTGATTCTGCATGAGATTAGTCCCCG
Found at i:698978 original size:36 final size:35
Alignment explanation
Indices: 698938--699008 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
698928 TCTACTACCT
* *
698938 TTGAAAACCCTAACTTCCAAAAAAATCAAAAACCCA
1 TTGAAAACCATAACCTCC-AAAAAATCAAAAACCCA
* *
698974 TTGAAAATCATAACCTCCACAAAATCAAAAACCCA
1 TTGAAAACCATAACCTCCAAAAAATCAAAAACCCA
699009 AAAATCGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.52, C:0.28, G:0.03, T:0.17
Consensus pattern (35 bp):
TTGAAAACCATAACCTCCAAAAAATCAAAAACCCA
Found at i:702995 original size:23 final size:24
Alignment explanation
Indices: 702959--703018 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
702949 AATTTTGAGA
702959 ATTTATTTAAAAAATTAAAAATATT
1 ATTTA-TTAAAAAATTAAAAATATT
*
702984 -TTTATTAAAAAA-TAAATATATT
1 ATTTATTAAAAAATTAAAAATATT
703006 ATTT-TTAAAAAAT
1 ATTTATTAAAAAAT
703019 AGTCCCCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 17 0.53
23 11 0.34
24 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTATTAAAAAATTAAAAATATT
Found at i:704782 original size:14 final size:14
Alignment explanation
Indices: 704763--704801 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
704753 TAATGGGGAG
704763 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
704777 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
704791 GAATCTCTGCA
1 TAATCCCTGCA
704802 TATAGATAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:709496 original size:141 final size:145
Alignment explanation
Indices: 709238--709511 Score: 520
Period size: 141 Copynumber: 1.9 Consensus size: 145
709228 ACCCTGTTTG
709238 TCTTGGATAATCCAAGCTTAATTCAAATTTAAAACGAAATGGTGACTGGATTTGGAGTTGATTAA
1 TCTTGGATAATCCAAGCTTAATTCAAATTTAAAACGAAATGGTGACTGGATTTGGAGTTGATTAA
709303 ACAATATGGTAACTCATGAAAAGAGCTGTTGGGGTTGGATAATGACTGATGCCCTGTGACAGAGT
66 ACAATATGGTAACTCATGAAAAGAGCTGTTGGGGTTGGATAATGACTGATGCCCTGTGACAGAGT
709368 GCCCTGTTTTTATGT
131 GCCCTGTTTTTATGT
709383 TCTTGGATAATCCAAGCTTAA-TCAAATTTAAAA-GAAATGGTGACTGGATTTGGA-TTGATT-A
1 TCTTGGATAATCCAAGCTTAATTCAAATTTAAAACGAAATGGTGACTGGATTTGGAGTTGATTAA
709444 ACAATATGGTAACTCATGAAAAGAGCTGTTGGGGTTGGATAATGACTGATGCCCTGTGACAGAGT
66 ACAATATGGTAACTCATGAAAAGAGCTGTTGGGGTTGGATAATGACTGATGCCCTGTGACAGAGT
709509 GCC
131 GCC
709512 ATGATCCACA
Statistics
Matches: 129, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
141 69 0.53
142 6 0.05
143 21 0.16
144 12 0.09
145 21 0.16
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (145 bp):
TCTTGGATAATCCAAGCTTAATTCAAATTTAAAACGAAATGGTGACTGGATTTGGAGTTGATTAA
ACAATATGGTAACTCATGAAAAGAGCTGTTGGGGTTGGATAATGACTGATGCCCTGTGACAGAGT
GCCCTGTTTTTATGT
Found at i:711731 original size:136 final size:135
Alignment explanation
Indices: 711491--711762 Score: 478
Period size: 136 Copynumber: 2.0 Consensus size: 135
711481 GGATCGAGCA
711491 ACTGTACCAGATTCGGCACGATTTTATCCTTTTTGACTTCTCTGCAATTTTGAGAGATGGTACTA
1 ACTGTACCAGATTCGGCACGATTTTATCCTTTTTGACTTCTCTGCAATTTTGAGAGATGGTACTA
711556 AGCTTGATAGGGCTTGAGCAGCTACCTCTCTCGCACTG-TTGA-TTAGCTTCGAGAA-TCTGATG
66 AGCTTGATAGGGCTTGAGCAGCTACCTCTCTCGCACTGTTTGATTTAGCTTCGAGAATTCTGATG
711618 AGAAG
131 AGAAG
*
711623 ACTGTACCAGATTCGGCACGCTTTTATCATCCTTTTTGACTTCTCTGCAATTTTGAGAGATGGTT
1 ACTGTACCAGATTCGGCACG-ATTT-T-ATCCTTTTTGACTTCTCTGCAATTTTGAGAGATGG-T
711688 ACTAAGCTTGATAGGGCTTGAGCAGCTACCTCTCTCGCACTGTTTGATTTAGCTTCGAGAATTCT
62 ACTAAGCTTGATAGGGCTTGAGCAGCTACCTCTCTCGCACTGTTTGATTTAGCTTCGAGAATTCT
711753 GATGAGAAG
127 GATGAGAAG
711762 A
1 A
711763 GTGATGCAGC
Statistics
Matches: 132, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
132 20 0.15
133 3 0.02
134 1 0.01
135 35 0.27
136 43 0.33
137 4 0.03
138 13 0.10
139 13 0.10
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (135 bp):
ACTGTACCAGATTCGGCACGATTTTATCCTTTTTGACTTCTCTGCAATTTTGAGAGATGGTACTA
AGCTTGATAGGGCTTGAGCAGCTACCTCTCTCGCACTGTTTGATTTAGCTTCGAGAATTCTGATG
AGAAG
Found at i:725044 original size:18 final size:18
Alignment explanation
Indices: 725021--725055 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
725011 ACAGAGAGGG
725021 AAGCTTTGTTTAACACAT
1 AAGCTTTGTTTAACACAT
725039 AAGCTTTGTTTAACACA
1 AAGCTTTGTTTAACACA
725056 GAACTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (18 bp):
AAGCTTTGTTTAACACAT
Found at i:754450 original size:14 final size:14
Alignment explanation
Indices: 754413--754451 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
754403 TAGTCTTTTG
754413 TTTTCACAAATTTA
1 TTTTCACAAATTTA
*
754427 -TTTCAAAAATTTA
1 TTTTCACAAATTTA
754440 TTTTCACAAATT
1 TTTTCACAAATT
754452 ATCATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTCACAAATTTA
Found at i:756770 original size:2 final size:2
Alignment explanation
Indices: 756765--756794 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
756755 ATATAAATGA
756765 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
756795 TTGTAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:757052 original size:2 final size:2
Alignment explanation
Indices: 757045--757086 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
757035 GATCTCGTCC
757045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
757087 CGAAACCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.