Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold285
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: 951911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 24374 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:402127 original size:11 final size:11
Alignment explanation
Indices: 402099--402142 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
402089 TTGATGTTTC
*
402099 ACTATTGTTTT
1 ACTATTATTTT
*
402110 CCTATTATTTT
1 ACTATTATTTT
*
402121 ACTATTATATT
1 ACTATTATTTT
*
402132 ACTACTATTTT
1 ACTATTATTTT
402143 GTTGTTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (11 bp):
ACTATTATTTT
Found at i:406767 original size:15 final size:15
Alignment explanation
Indices: 406747--406777 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
406737 TAGCTTTGAA
*
406747 CTTCAGGTCGCAGTG
1 CTTCAGGTCACAGTG
406762 CTTCAGGTCACAGTG
1 CTTCAGGTCACAGTG
406777 C
1 C
406778 GATGGTGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (15 bp):
CTTCAGGTCACAGTG
Found at i:407463 original size:8 final size:8
Alignment explanation
Indices: 407450--407507 Score: 53
Period size: 8 Copynumber: 6.5 Consensus size: 8
407440 TTATAAATTT
407450 TTTTATAG
1 TTTTATAG
407458 TTTTATAG
1 TTTTATAG
407466 TTTTATAG
1 TTTTATAG
*
407474 ATTTTTAATAT
1 --TTTT-ATAG
407485 TTTTATAATG
1 TTTTAT-A-G
407495 TTTTATAAG
1 TTTTAT-AG
407504 TTTT
1 TTTT
407508 TTTATAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 18 0.42
9 10 0.23
10 12 0.28
11 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (8 bp):
TTTTATAG
Found at i:407518 original size:9 final size:9
Alignment explanation
Indices: 407438--407523 Score: 59
Period size: 10 Copynumber: 8.9 Consensus size: 9
407428 GTTTAATTAA
407438 TTTTATAAAT
1 TTTTAT-AAT
* *
407448 TTTTTTATAG
1 TTTTATA-AT
*
407458 TTTTAT-AG
1 TTTTATAAT
407466 TTTTATAGAT
1 TTTTATA-AT
407476 TTTTA-ATAT
1 TTTTATA-AT
407485 TTTTATAAT
1 TTTTATAAT
407494 GTTTTATAAGTTT
1 -TTTTATAA---T
407507 TTTTATAAT
1 TTTTATAAT
407516 TTTTATAA
1 TTTTATAA
407524 GTTTATGTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
8 8 0.13
9 20 0.32
10 26 0.41
12 8 0.13
13 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:412234 original size:10 final size:10
Alignment explanation
Indices: 412219--412248 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
412209 GCGTTCTTTC
412219 TGTTGTTCTT
1 TGTTGTTCTT
412229 TGTTGTTCTT
1 TGTTGTTCTT
412239 TGTTGTTCTT
1 TGTTGTTCTT
412249 CTTTTCGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.20, T:0.70
Consensus pattern (10 bp):
TGTTGTTCTT
Found at i:415234 original size:86 final size:86
Alignment explanation
Indices: 414986--415241 Score: 316
Period size: 86 Copynumber: 3.0 Consensus size: 86
414976 CATACAAGTG
* * * *
414986 GTGGCTTGTCCATAAAA-TCTAGTGGCAGATTATTTAATCTGCAAATATGTTGTGCACTCACCAC
1 GTGGCTTGTCCACAAAACTC-AGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAAC
* * *
415050 AAGTGGCATTAACTGTAAATAC
65 AAGTGGCAGTAATTGCAAATAC
* * * * * * * *
415072 GTGGCTTGCCCACAAAACCCAGTGACAATTTGTTTAATTTGAAAATATGTTGTGAACTTACAACA
1 GTGGCTTGTCCACAAAACTCAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACA
**
415137 AGTGATAGTAATTGCAAATAC
66 AGTGGCAGTAATTGCAAATAC
**
415158 GTGGCTTGTCCACAAAACTCAGTGGCAGTTTGTTTAATCTGCAACCATGTTGTGCACTCACAACA
1 GTGGCTTGTCCACAAAACTCAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACA
*
415223 AGTGGCAGTAATTACAAAT
66 AGTGGCAGTAATTGCAAAT
415242 GTTTTTATCT
Statistics
Matches: 139, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
86 138 0.99
87 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (86 bp):
GTGGCTTGTCCACAAAACTCAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACA
AGTGGCAGTAATTGCAAATAC
Found at i:415646 original size:21 final size:22
Alignment explanation
Indices: 415615--415655 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
415605 TTTGTTTTTT
415615 TTAAAGTT-AAAAGTCAAAACCA
1 TTAAAGTTAAAAAGT-AAAACCA
415637 TTAAA-TTAAAAAGTAAAAC
1 TTAAAGTTAAAAAGTAAAAC
415656 TACGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (22 bp):
TTAAAGTTAAAAAGTAAAACCA
Found at i:417090 original size:13 final size:12
Alignment explanation
Indices: 417068--417104 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
417058 TTAAATTTTA
417068 ATTAAACTTAAT
1 ATTAAACTTAAT
*
417080 ATTAGAACTTACT
1 ATTA-AACTTAAT
417093 ATTAAACTTAAT
1 ATTAAACTTAAT
417105 TAAAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (12 bp):
ATTAAACTTAAT
Found at i:417643 original size:27 final size:27
Alignment explanation
Indices: 417584--417644 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
417574 GTCCCTATAT
417584 TCTTTTTATATTTAAAATTTAATCTTCC
1 TCTTTTTATATTTAAAATTTAATC-TCC
*
417612 -ATTTTTAT-TTCTAGAAATTTAATC-CC
1 TCTTTTTATATT-TA-AAATTTAATCTCC
417638 TCTTTTT
1 TCTTTTT
417645 GTTGGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 4 0.14
27 14 0.50
28 10 0.36
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (27 bp):
TCTTTTTATATTTAAAATTTAATCTCC
Found at i:418090 original size:35 final size:35
Alignment explanation
Indices: 417994--418093 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 35
417984 ATAAAATATA
417994 AAATATGTAATTATAATTAACACAATAAAATTTGAT
1 AAATAT-TAATTATAATTAACACAATAAAATTTGAT
* * *
418030 ACATATTAA--ATATTTAA-A-AATTAAAATAATT-TT
1 AAATATTAATTATAATTAACACAA-TAAAAT--TTGAT
418063 AAATA-TAATTATAATTAACACAATAAAATTT
1 AAATATTAATTATAATTAACACAATAAAATTT
418094 ACAAATACGA
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
31 2 0.04
32 10 0.19
33 14 0.27
34 9 0.17
35 10 0.19
36 7 0.13
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (35 bp):
AAATATTAATTATAATTAACACAATAAAATTTGAT
Found at i:427332 original size:27 final size:29
Alignment explanation
Indices: 427301--427356 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
427291 TGCTTAGAGT
*
427301 TCTATTAAA-TAA-TAACTTTATTTTACA
1 TCTATAAAATTAACTAACTTTATTTTACA
*
427328 TCTATAAAATTAACGTAACTTTTTTTTAC
1 TCTATAAAATTAAC-TAACTTTATTTTAC
427357 TTCAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 3 0.12
30 13 0.54
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (29 bp):
TCTATAAAATTAACTAACTTTATTTTACA
Found at i:427805 original size:211 final size:212
Alignment explanation
Indices: 427428--427857 Score: 844
Period size: 211 Copynumber: 2.0 Consensus size: 212
427418 ATTTTATTTT
427428 TAAAATTGACACAAAATTTTAACTATAATTATTTTTAAAGTTAATTTATTAATATAATAGAAAAT
1 TAAAATTGACACAAAATTTTAACTATAATTATTTTTAAAGTTAATTTATTAATATAATAGAAAAT
427493 AAAGGGTATTCTCATCAGTTCAAAAGCTTTTCCAAACCCGTGCTTCTATATATATTATAGATAAT
66 AAAGGGTATTCTCATCAGTTCAAAAGCTTTTCCAAACCCGTGCTTCTATATATATTATAGATAAT
427558 ATTTGATGCATTATCAGTGTATGAGATCATCAATGAGTAAAACAAAAAATAGTGTAATACTTATT
131 ATTTGATGCATTATCAGTGTATGAGATCATCAATGAGTAAAACAAAAAATAGTGTAATACTTATT
427623 AAAAAATAATAAAATAG
196 AAAAAATAATAAAATAG
427640 TAAAATTGACAC-AAATTTTAACTATAATTATTTTTAAAGTTAATTTATTAATATAATAGAAAAT
1 TAAAATTGACACAAAATTTTAACTATAATTATTTTTAAAGTTAATTTATTAATATAATAGAAAAT
427704 AAAGGGTATTCTCATCAGTTCAAAAGCTTTTCCAAACCCGTGCTTCTATATATATTATAGATAAT
66 AAAGGGTATTCTCATCAGTTCAAAAGCTTTTCCAAACCCGTGCTTCTATATATATTATAGATAAT
427769 ATTTGATGCATTATCAGTGTATGAGATCATCAATGAGTAAAACAAAAAATAGTGTAATACTTATT
131 ATTTGATGCATTATCAGTGTATGAGATCATCAATGAGTAAAACAAAAAATAGTGTAATACTTATT
427834 AAAAAATAATAAAATAG
196 AAAAAATAATAAAATAG
*
427851 TATAATT
1 TAAAATT
427858 CATTTCATAT
Statistics
Matches: 217, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
211 205 0.94
212 12 0.06
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (212 bp):
TAAAATTGACACAAAATTTTAACTATAATTATTTTTAAAGTTAATTTATTAATATAATAGAAAAT
AAAGGGTATTCTCATCAGTTCAAAAGCTTTTCCAAACCCGTGCTTCTATATATATTATAGATAAT
ATTTGATGCATTATCAGTGTATGAGATCATCAATGAGTAAAACAAAAAATAGTGTAATACTTATT
AAAAAATAATAAAATAG
Found at i:434595 original size:18 final size:17
Alignment explanation
Indices: 434570--434610 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
434560 AAAAAGTAAT
434570 ATATTTAAATATATGATTA
1 ATATTTAAAT-TAT-ATTA
434589 A-ATTTAAATTATATTA
1 ATATTTAAATTATATTA
434605 ATATTT
1 ATATTT
434611 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 8 0.38
19 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATTTAAATTATATTA
Found at i:434613 original size:19 final size:20
Alignment explanation
Indices: 434566--434611 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
434556 TTAGAAAAAG
434566 TAATATATTTAAATATATGAT
1 TAATAT-TTTAAATATATGAT
434587 TAA-A-TTTAAAT-TAT-AT
1 TAATATTTTAAATATATGAT
434603 TAATATTTT
1 TAATATTTT
434612 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 10 0.43
20 1 0.04
21 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATTTTAAATATATGAT
Found at i:434642 original size:21 final size:21
Alignment explanation
Indices: 434603--434652 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
434593 TAAATTATAT
* * *
434603 TAATATTTTTATTTTAAAAAG
1 TAATATATTTATCTCAAAAAG
**
434624 TAATATATTTATCTCAAAATT
1 TAATATATTTATCTCAAAAAG
434645 TAATATAT
1 TAATATAT
434653 GATTAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
TAATATATTTATCTCAAAAAG
Found at i:434662 original size:17 final size:17
Alignment explanation
Indices: 434640--434718 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
434630 ATTTATCTCA
434640 AAATTTAATATATGATT
1 AAATTTAATATATGATT
* *
434657 AAATTTAAAATAAGATTT
1 AAATTTAATATATGA-TT
*
434675 AAATATTTA-ATATGCCATT
1 AAAT-TTAATATATG--ATT
* *
434694 AAATTAGAATATA-AATT
1 AAATT-TAATATATGATT
434711 AAATTTAA
1 AAATTTAA
434719 AACTAATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.04
17 21 0.44
18 11 0.23
19 10 0.21
20 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATTTAATATATGATT
Found at i:434756 original size:17 final size:17
Alignment explanation
Indices: 434734--434766 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
434724 ATTCAACAAT
434734 AATTAAAATAA-ATTTAA
1 AATT-AAATAATATTTAA
434751 AATTAAATAATATTTA
1 AATTAAATAATATTTA
434767 TGAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAAATAATATTTAA
Found at i:434970 original size:16 final size:16
Alignment explanation
Indices: 434951--435000 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
434941 TTTGAGTATG
*
434951 AGAAAATTGGAGCCCA
1 AGAAAATTTGAGCCCA
* * *
434967 AGAAAGTTTGAGCTCG
1 AGAAAATTTGAGCCCA
*
434983 AGCAAATTTGAGCCCA
1 AGAAAATTTGAGCCCA
434999 AG
1 AG
435001 CCCAAAATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (16 bp):
AGAAAATTTGAGCCCA
Found at i:434977 original size:32 final size:32
Alignment explanation
Indices: 434935--435000 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
434925 TTTGAATCCG
*
434935 AGAAAATTTGAG-TATGAGAAAATTGGAGCCCA
1 AGAAAATTTGAGCT-CGAGAAAATTGGAGCCCA
* * *
434967 AGAAAGTTTGAGCTCGAGCAAATTTGAGCCCA
1 AGAAAATTTGAGCTCGAGAAAATTGGAGCCCA
434999 AG
1 AG
435001 CCCAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (32 bp):
AGAAAATTTGAGCTCGAGAAAATTGGAGCCCA
Found at i:435253 original size:21 final size:19
Alignment explanation
Indices: 435232--435282 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
435222 AATTTGGATA
435232 AATGTTTTGTTATATTTTAT
1 AATGTTTTGTTATA-TTTAT
* *
435252 AATATTTTATTCATATTT-T
1 AATGTTTTGTT-ATATTTAT
435271 AATGTTTTGTTA
1 AATGTTTTGTTA
435283 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 10 0.38
20 12 0.46
21 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (19 bp):
AATGTTTTGTTATATTTAT
Found at i:435318 original size:9 final size:9
Alignment explanation
Indices: 435304--435367 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
435294 TTAATTATCG
435304 ATAATTTTT
1 ATAATTTTT
435313 ATAA-TTTT
1 ATAATTTTT
435321 ATAATTTTT
1 ATAATTTTT
* * *
435330 ACAACATGTT
1 ATAA-TTTTT
* *
435340 AAAAGTTTT
1 ATAATTTTT
435349 ATAATTTTT
1 ATAATTTTT
435358 ATAATATTTT
1 ATAAT-TTTT
435368 GAACTACATT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
8 8 0.18
9 26 0.59
10 10 0.23
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
ATAATTTTT
Found at i:437597 original size:32 final size:32
Alignment explanation
Indices: 437552--437629 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
437542 TGTGACAGGC
* * *
437552 CGTGTGAGCCACACGATCTGGGCCAATTGGGT
1 CGTGTGGGCCACACGATCTGAGCCAATTAGGT
* *
437584 TGTGTGGGTCACACGATCTGAGCCAATTAGGT
1 CGTGTGGGCCACACGATCTGAGCCAATTAGGT
437616 CGTGTGGGCCACAC
1 CGTGTGGGCCACAC
437630 AAGCGTGTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.23
Consensus pattern (32 bp):
CGTGTGGGCCACACGATCTGAGCCAATTAGGT
Found at i:446467 original size:6 final size:7
Alignment explanation
Indices: 446451--446475 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
446441 TACAAATTGC
446451 TTTTCAT
1 TTTTCAT
446458 TTTTCAT
1 TTTTCAT
446465 TTTTCAT
1 TTTTCAT
446472 TTTT
1 TTTT
446476 GACCCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCAT
Found at i:447702 original size:2 final size:2
Alignment explanation
Indices: 447695--447725 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
447685 ATGAAATCCA
*
447695 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
447726 CCAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:452444 original size:129 final size:128
Alignment explanation
Indices: 452215--452467 Score: 472
Period size: 129 Copynumber: 2.0 Consensus size: 128
452205 TAACCCTTAC
*
452215 CTAGTGTCACATTAAAATCTATATTCAAGTTAGACCAATTTATTTTCTAGACATCTACGAGACAA
1 CTAGTGTCACATTAAAATCTATATTCAAGTTAGACAAATTTATTTTCTAGACATCTACGAGACAA
452280 GTGCATTACACTTAAGCATACACATAACTCCTAAGCTTTGCTGGGTATGAAGGATGGAATTAT
66 GTGCATTACACTTAAGCATACACATAACTCCTAAGCTTTGCTGGGTATGAAGGATGGAATTAT
452343 CTAGTGTCACATTAAAATCTATATTTCAAGTTAGACAAATTTATTTTCTAGACATCTACGAGACA
1 CTAGTGTCACATTAAAATCTATA-TTCAAGTTAGACAAATTTATTTTCTAGACATCTACGAGACA
452408 AGTGCATTACACTTAAGCATACACGA-AACTCCTAAGCTTTGCTGGGTATGAAGGATGGAA
65 AGTGCATTACACTTAAGCATACAC-ATAACTCCTAAGCTTTGCTGGGTATGAAGGATGGAA
452468 AGGAGCGAGG
Statistics
Matches: 122, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
128 23 0.19
129 98 0.80
130 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (128 bp):
CTAGTGTCACATTAAAATCTATATTCAAGTTAGACAAATTTATTTTCTAGACATCTACGAGACAA
GTGCATTACACTTAAGCATACACATAACTCCTAAGCTTTGCTGGGTATGAAGGATGGAATTAT
Found at i:456808 original size:29 final size:30
Alignment explanation
Indices: 456775--456836 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
456765 TCGATTTAAT
456775 ATGCAATTGGATA-CATG-AACTTTGATT-TG
1 ATGCAATT--ATAGCATGAAACTTTGATTGTG
456804 ATGCAATTATAGGCATGAAACTTTGATTGTG
1 ATGCAATTATA-GCATGAAACTTTGATTGTG
456835 AT
1 AT
456837 TAAAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
29 12 0.41
30 10 0.34
31 4 0.14
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (30 bp):
ATGCAATTATAGCATGAAACTTTGATTGTG
Found at i:458563 original size:21 final size:21
Alignment explanation
Indices: 458539--458608 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
458529 CTGAACCTCG
*
458539 AACCTAAAACACTGAACTCTA
1 AACCTAAAATACTGAACTCTA
* ** *
458560 AACCT-GAATTTTGAACTCTG
1 AACCTAAAATACTGAACTCTA
*
458580 AACCTAAAATGCTGAACTCTA
1 AACCTAAAATACTGAACTCTA
458601 AACCTAAA
1 AACCTAAA
458609 TCTTGACCGC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (21 bp):
AACCTAAAATACTGAACTCTA
Found at i:458575 original size:41 final size:41
Alignment explanation
Indices: 458530--458614 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
458520 TTTTTTTACC
* *
458530 TGAAC-CTCGAACCTAAAACACTGAACTCTAAACCTGAATTT
1 TGAACTCT-GAACCTAAAACACTGAACTCTAAACCTAAATCT
**
458571 TGAACTCTGAACCTAAAATGCTGAACTCTAAACCTAAATCT
1 TGAACTCTGAACCTAAAACACTGAACTCTAAACCTAAATCT
458612 TGA
1 TGA
458615 CCGCAGACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (41 bp):
TGAACTCTGAACCTAAAACACTGAACTCTAAACCTAAATCT
Found at i:459024 original size:21 final size:21
Alignment explanation
Indices: 458998--459047 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
458988 CAATTTACGA
* *
458998 TTCAAGGTTCAAAGTTCAGGG
1 TTCAAGGTTCAAAGGTCAAGG
* *
459019 TTCAAGATTCAGAGGTCAAGG
1 TTCAAGGTTCAAAGGTCAAGG
*
459040 TTTAAGGT
1 TTCAAGGT
459048 CGGAGTTTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
TTCAAGGTTCAAAGGTCAAGG
Found at i:462870 original size:36 final size:37
Alignment explanation
Indices: 462826--462901 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
462816 CCTGTATTTC
462826 TTTCCTAAA-GGTTTCCACGTAAAATCTGTGTTTTAT
1 TTTCCTAAAGGGTTTCCACGTAAAATCTGTGTTTTAT
462862 TTTCCTAAAGGGTTTCCACGTAAAATCTGTGTTTTAT
1 TTTCCTAAAGGGTTTCCACGTAAAATCTGTGTTTTAT
462899 TTT
1 TTT
462902 TCTTTCTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
36 9 0.23
37 30 0.77
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (37 bp):
TTTCCTAAAGGGTTTCCACGTAAAATCTGTGTTTTAT
Found at i:466176 original size:72 final size:73
Alignment explanation
Indices: 466058--466202 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 73
466048 ATCCATTTTG
* * *
466058 AATTACTGGTTAATTAATAAATCTATTTTTATTTAAATTTAATTATAAAAATATTAATATTAATA
1 AATTACTGGTTAATTAAAAAAACCATTTTTATTTAAATTTAATTATAAAAATATTAATATTAATA
466123 AAAAAATA
66 AAAAAATA
466131 AATTACTGG-TAATTAAAAAAACCATTTTTATTTAAATTTAATTATAAAAATATTAATATTAATA
1 AATTACTGGTTAATTAAAAAAACCATTTTTATTTAAATTTAATTATAAAAATATTAATATTAATA
466195 AAAAAATA
66 AAAAAATA
466203 GATTTTTACA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 60 0.87
73 9 0.13
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (73 bp):
AATTACTGGTTAATTAAAAAAACCATTTTTATTTAAATTTAATTATAAAAATATTAATATTAATA
AAAAAATA
Found at i:467821 original size:21 final size:19
Alignment explanation
Indices: 467797--467838 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
467787 AATTCGTTGG
467797 TTAAGCTCAGAATATATATAA
1 TTAAGCTCA-AATATAT-TAA
*
467818 TTAAGTTCAAATATATTAA
1 TTAAGCTCAAATATATTAA
467837 TT
1 TT
467839 TATATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAAGCTCAAATATATTAA
Found at i:467900 original size:2 final size:2
Alignment explanation
Indices: 467893--467929 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
467883 GACCCCTTAA
467893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
467930 TGTTGCCCAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:482139 original size:14 final size:14
Alignment explanation
Indices: 482120--482149 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
482110 CATTGTTTTC
482120 CCTGTACCAGGAGG
1 CCTGTACCAGGAGG
482134 CCTGTACCAGGAGG
1 CCTGTACCAGGAGG
482148 CC
1 CC
482150 CAAAGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.13
Consensus pattern (14 bp):
CCTGTACCAGGAGG
Found at i:499668 original size:38 final size:38
Alignment explanation
Indices: 499617--499693 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
499607 CATCCTTGGA
499617 AAAATTACCACATAAGGACTTATTTAGTTCAAAATCAT
1 AAAATTACCACATAAGGACTTATTTAGTTCAAAATCAT
499655 AAAATTACCACATAAGGACTTATTTAGTTCAAAATCAT
1 AAAATTACCACATAAGGACTTATTTAGTTCAAAATCAT
499693 A
1 A
499694 TTTTCTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (38 bp):
AAAATTACCACATAAGGACTTATTTAGTTCAAAATCAT
Found at i:505358 original size:13 final size:13
Alignment explanation
Indices: 505323--505361 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
505313 ATTAAGATTA
505323 TTATTTTTTAATAT
1 TTATTTTTT-ATAT
*
505337 TT-TTATTTATAT
1 TTATTTTTTATAT
505349 TTATTTTTTATAT
1 TTATTTTTTATAT
505362 AATTTCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 14 0.64
14 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTTTATAT
Found at i:508849 original size:31 final size:30
Alignment explanation
Indices: 508765--508849 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
508755 CTCTAAAAAA
* *
508765 TTTTAACTT-AGTTTTTAAATT-TTAAAATT
1 TTTTAA-TTGAGTTTTTAAATTATAAAAATG
* *
508794 TTTTAATTGAGTTTTTGAACTATAAATAATG
1 TTTTAATTGAGTTTTTAAATTATAAA-AATG
*
508825 TTTTAATTGAGTTCTTAAATTATAA
1 TTTTAATTGAGTTTTTAAATTATAA
508850 GTATTTGTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 16 0.35
30 3 0.07
31 25 0.54
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTAATTGAGTTTTTAAATTATAAAAATG
Found at i:511387 original size:22 final size:24
Alignment explanation
Indices: 511347--511390 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
511337 TGATAATATG
511347 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
511371 TTTTGA-ATAA-AAATTAAAGT
1 TTTTGATATAACAAATTAAAGT
511391 TGAACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:511443 original size:20 final size:20
Alignment explanation
Indices: 511420--511457 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
511410 GATAAAATCA
511420 AGTTAAAAC-TGTTTCAATTG
1 AGTTAAAACAT-TTTCAATTG
511440 AGTTAAAACATTTTCAAT
1 AGTTAAAACATTTTCAAT
511458 CATGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTTAAAACATTTTCAATTG
Found at i:511464 original size:20 final size:19
Alignment explanation
Indices: 511415--511473 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
511405 AAAATGATAA
511415 AATCAAGTTAAAACTGTTTC
1 AATC-AGTTAAAACTGTTTC
*
511435 AATTGAGTTAAAACAT-TTTC
1 AA-TCAGTTAAAAC-TGTTTC
*
511455 AATCATGTTAAAATTGTTT
1 AATCA-GTTAAAACTGTTT
511474 TTAAACAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.09
20 27 0.84
21 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
AATCAGTTAAAACTGTTTC
Found at i:513195 original size:3 final size:3
Alignment explanation
Indices: 513165--513237 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
513155 CACAAAGCGG
* * * *
513165 TAA TAG TAA TAA TAG TAA CAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
513213 -AA T-T TAA TTA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
513238 CAGTAACAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:514145 original size:18 final size:17
Alignment explanation
Indices: 514100--514148 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
514090 AAAATCCCTC
* *
514100 CTTTTCTATTTTTCTTT
1 CTTTTCAATTTTTCATT
514117 CTTGTTACAATTTTTCATT
1 CTT-TT-CAATTTTTCATT
514136 CTCTTTCAATTTT
1 CT-TTTCAATTTT
514149 GTTGTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 9 0.33
19 14 0.52
20 1 0.04
ACGTcount: A:0.14, C:0.18, G:0.02, T:0.65
Consensus pattern (17 bp):
CTTTTCAATTTTTCATT
Found at i:521456 original size:196 final size:196
Alignment explanation
Indices: 521122--521707 Score: 987
Period size: 196 Copynumber: 3.0 Consensus size: 196
521112 TTAAAAAGTG
* * *
521122 CAAGCACATTCCATTTTCATT-TCAAGTGGTTTCAATCCAACGCAATTTGACCTATAATAATTAG
1 CAAGCACATTCCATTTTC-TTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAG
521186 TAATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCC
65 TAATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCC
521251 CTTGAGCACAAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
130 CTTGAGCACAAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
521316 CA
195 CA
521318 CAAGCACATTCCATTTTCTTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
1 CAAGCACATTCCATTTTCTTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
521383 AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
521448 TTGAGCACAAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAGC
131 TTGAGCACAAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAGC
521513 A
196 A
521514 CAAGCACATTCCATTTTCTTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
1 CAAGCACATTCCATTTTCTTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
* * * * **
521579 AATATAAGATATCCTTCCAAGAAATTACGTCATGGTGCATTTAGTATGTGTTCCCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
* * * * * * * *
521644 TAGAGCACAAAG-AAGTTTTAAGTGAATCAAACTCAACCACAAGAGTGTCTTTTTATACAGAAAG
131 TTGAGCAC-AAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
521708 TCCTACAAGG
Statistics
Matches: 371, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
195 2 0.01
196 366 0.99
197 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (196 bp):
CAAGCACATTCCATTTTCTTCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
TTGAGCACAAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAGC
A
Found at i:531611 original size:4 final size:4
Alignment explanation
Indices: 531604--531635 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
531594 GGATGGATGG
*
531604 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
531636 TGTGAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:538363 original size:11 final size:11
Alignment explanation
Indices: 538347--538386 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
538337 CTTTAAGAAT
538347 GAAGGCAATGC
1 GAAGGCAATGC
538358 GAAGGCAATGC
1 GAAGGCAATGC
538369 GAAGGCAATGC
1 GAAGGCAATGC
*
538380 AAAGGCA
1 GAAGGCA
538387 GCCTTGTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.35, T:0.07
Consensus pattern (11 bp):
GAAGGCAATGC
Found at i:539140 original size:33 final size:33
Alignment explanation
Indices: 539049--539142 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
539039 CTTCATAAGT
* * * *
539049 TTGTACGCCTTCTACATCACCCTACCCATCAGC
1 TTGTACCCCTTCTACATCACCTTCCCCAGCAGC
* * * *
539082 TTCTACCCTTTC-AGCATCGCATTCCCCAGCAGC
1 TTGTACCCCTTCTA-CATCACCTTCCCCAGCAGC
*
539115 TTGTACCCCTTCTACAACACCTTCCCCA
1 TTGTACCCCTTCTACATCACCTTCCCCA
539143 TCTAAACCTA
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 1 0.02
33 44 0.96
34 1 0.02
ACGTcount: A:0.20, C:0.44, G:0.09, T:0.28
Consensus pattern (33 bp):
TTGTACCCCTTCTACATCACCTTCCCCAGCAGC
Found at i:539177 original size:18 final size:18
Alignment explanation
Indices: 539153--539198 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
539143 TCTAAACCTA
*
539153 CCCCATCAACATTACCCT
1 CCCCATCAACATCACCCT
*
539171 TCCCATCAACATCACCCT
1 CCCCATCAACATCACCCT
539189 CCCCATCAAC
1 CCCCATCAAC
539199 TTTTACCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.52, G:0.00, T:0.20
Consensus pattern (18 bp):
CCCCATCAACATCACCCT
Found at i:540274 original size:84 final size:84
Alignment explanation
Indices: 540133--540294 Score: 288
Period size: 84 Copynumber: 1.9 Consensus size: 84
540123 TTCGAACGGC
* *
540133 AAGTGATTTTTGGAATACTACCACTCCCCTCTTTGCAGCAGTAACCGGTGCGAAGTTGTCCCGTA
1 AAGTGATTTTTGGAATACTACCACTCCCCTCTTTGCAGCAGTAACCGATACGAAGTTGTCCCGTA
540198 TTCGTCATAAACTAATGGT
66 TTCGTCATAAACTAATGGT
*
540217 AAGTGATTTTTGGAATACTGCCACTCCCCTCTTTGCAGCAGTAACCGATACGAAGTTGTCCCGTA
1 AAGTGATTTTTGGAATACTACCACTCCCCTCTTTGCAGCAGTAACCGATACGAAGTTGTCCCGTA
*
540282 TTCGTCATGAACT
66 TTCGTCATAAACT
540295 GTATTCCCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (84 bp):
AAGTGATTTTTGGAATACTACCACTCCCCTCTTTGCAGCAGTAACCGATACGAAGTTGTCCCGTA
TTCGTCATAAACTAATGGT
Found at i:542148 original size:992 final size:992
Alignment explanation
Indices: 540207--542191 Score: 3594
Period size: 992 Copynumber: 2.0 Consensus size: 992
540197 ATTCGTCATA
* *
540207 AACTAATGGTAAGTGATTTTTGGAATACTGCCACTCCCCTCTTTGCAGCAGTAACCGATACGAAG
1 AACTAACGGCAAGTGATTTTTGGAATACTGCCACTCCCCTCTTTGCAGCAGTAACCGATACGAAG
540272 TTGTCCCGTATTCGTCATGAACTGTATTCCCTTAAAAAAGGTACTCTAACTATCATTGAATATGT
66 TTGTCCCGTATTCGTCATGAACTGTATTCCCTTAAAAAAGGTACTCTAACTATCATTGAATATGT
*
540337 AGCAAAAATACAAAATACATGTGCCTTGATCGAGGCCTCTGGTTCTCGGATTTCGGAGGCGAAAA
131 AGCAAAAATACAAAATACATGTGCCTTGATCGAGGCCTCTGGTTCTCGGATCTCGGAGGCGAAAA
540402 AGGTTGAAATTGTTCTTGTAGGTCTACCTCTAAAATTTGATGCCGTGATTACGTTAGCATCGTTC
196 AGGTTGAAATTGTTCTTGTAGGTCTACCTCTAAAATTTGATGCCGTGATTACGTTAGCATCGTTC
*
540467 TCGTCAGAACCGTTACCGTTTCACCATCTCGTTGATGTGCTTCCCGAATATGATAATTGGCAGAT
261 TCGTCAAAACCGTTACCGTTTCACCATCTCGTTGATGTGCTTCCCGAATATGATAATTGGCAGAT
* *
540532 GCGTGTGATTCCAGAGGAGGTGTTGATTCATGCCAATTTTGTTGAATCTGTTCCATTGTCATTGA
326 GCGTGTGATTCCAGAGGAGGTGTTGATTCATGCCAATTTTGTTGAATCTGTTCCATTGCCACTGA
540597 TGGTGGCATCTGTCCGTTGTGGCCGTCCTCCGTCTGGTGGTCGAGACAGAGGGTTTCGTTCTCAA
391 TGGTGGCATCTGTCCGTTGTGGCCGTCCTCCGTCTGGTGGTCGAGACAGAGGGTTTCGTTCTCAA
* * *
540662 ATACAATGCTAGATCTGTAGTAGATTTGGGCATTTAGCCTAGCGATGCTATTATCGTTATAACCG
456 ATACAATGCCAAATCTGTAGTAGATTTGGGCATTTAGCCTAGCGATGCTATTATCATTATAACCG
* *
540727 TGATTATGTCGTCTAGTCATCGGTGGCTCGGGCTTCAACCCTGGTCGGTTGTGTGGCTCAAGGTT
521 TGATTATGTCGTCTAGTCATCGGTGGCTCGGGCTTCAAACCTGGTCAGTTGTGTGGCTCAAGGTT
*
540792 CGACTGCTGGAATATCATTTTTGACGCAGGTTTCTGGTGGGTTTGATGGCCCATCAACAATGCCA
586 CGACTGCTGGAATATCATTTTCGACGCAGGTTTCTGGTGGGTTTGATGGCCCATCAACAATGCCA
* *
540857 AATGCTCTCGTTTCTGGCGATGAATTTTGCGCCGTGCCTCACTTGCCTAGGTGGTCCACTAGGCC
651 AATGCTCTCGTTTCTGGCGATGAATTTTGCACCGTGCCTCACTTGCCTAGGTGGTCCACTAGGCA
*
540922 TTCTAACCCATTTGTTGGTCTTGGTGATTGGTTTAGGCACACGGCTGGGTCAGGATTGAATGTTG
716 TCCTAACCCATTTGTTGGTCTTGGTGATTGGTTTAGGCACACGGCTGGGTCAGGATTGAATGTTG
*
540987 GGCTGGGCAGTATCCTTCTCATTTAGTGCCTGAGTAGGATTCCTATTTTAGACCGCATACTGCTG
781 GGCTGGGCAGTATCCTTCTCATTTAGTGCCTGAGTAGGATTCCTATTTTAAACCGCATACTGCTG
* *
541052 GGTTTGGGCCTACTACTGTGAGGCCAAATGTTTATGGCACTTTTTCTGGGCTGCCCGTGCGTGAC
846 GGTTTGGGCCTACTACTGTGAGGCCAAATGTTTATGGCACTTTTTCTGGGCTGCACGTGCGTGAA
* *
541117 AGGCCTTCTGGTCTAAACCATGACTGTGGGCCGTAGGCAAATAAATTTTCATATAGGCCAACATC
911 AGGCCTTCTGGTCCAAACCATGACTGTGGGCCATAGGCAAATAAATTTTCATATAGGCCAACATC
*
541182 TAATTGTGTGGAGTTTG
976 CAATTGTGTGGAGTTTG
* **
541199 AACTAACGGCAAGTGATTTTTGGAATACTGTCACTCCCCTCTTTGCAGCAGTAACC-AGTGTGAA
1 AACTAACGGCAAGTGATTTTTGGAATACTGCCACTCCCCTCTTTGCAGCAGTAACCGA-TACGAA
*
541263 GTTGTCCCGTATTCGTCATGAACTGTATTCCCTTAAAAAAGGTACTCTAACTATTATTGAATATG
65 GTTGTCCCGTATTCGTCATGAACTGTATTCCCTTAAAAAAGGTACTCTAACTATCATTGAATATG
541328 TAGCAAAAATACAAAATACATGTGCCTTGATCGAGGCCTCTGGTTCTCGGATCTCGGAGGCGAAA
130 TAGCAAAAATACAAAATACATGTGCCTTGATCGAGGCCTCTGGTTCTCGGATCTCGGAGGCGAAA
541393 AAGGTTGAAATTGTTCTTGTAGGTCTACCTCTAAAATTTGATGCCGTGATTACGTTAGCATCGTT
195 AAGGTTGAAATTGTTCTTGTAGGTCTACCTCTAAAATTTGATGCCGTGATTACGTTAGCATCGTT
*
541458 CTCGTCAAAACTGTTACCGTTTCACCATCTCGTTGATGTGCTTCCCGAATATGATAATTGGCAGA
260 CTCGTCAAAACCGTTACCGTTTCACCATCTCGTTGATGTGCTTCCCGAATATGATAATTGGCAGA
*
541523 TGCGTGTGATTCTAGAGGAGGTGTTGATTCATGCCAATTTTGTTGAATCTGTTCCATTGCCACTG
325 TGCGTGTGATTCCAGAGGAGGTGTTGATTCATGCCAATTTTGTTGAATCTGTTCCATTGCCACTG
* *
541588 ATGGTGGCATCTGTCCGTTGTGGCCGTCCTCCGTCTGGTGGTCGAGACAGAGGGTTTTGTTCTCG
390 ATGGTGGCATCTGTCCGTTGTGGCCGTCCTCCGTCTGGTGGTCGAGACAGAGGGTTTCGTTCTCA
*
541653 AATACAATGCCAAATTTGTAGTAGATTTGGGCATTTAGCCTAGCGATGCTATTATCATTATAACC
455 AATACAATGCCAAATCTGTAGTAGATTTGGGCATTTAGCCTAGCGATGCTATTATCATTATAACC
*
541718 GTGATTATGTCGTCTAGTCATCGGTGGCTCGGGCTTCAAATCTGGTCAGTTGTGTGGCTCAAGGT
520 GTGATTATGTCGTCTAGTCATCGGTGGCTCGGGCTTCAAACCTGGTCAGTTGTGTGGCTCAAGGT
* * * *
541783 TCGGCTGCTGGAATATCATTTTCGACGTAGGTTTCTGGTGGGTTTGATGGCCCCTCAATAATGCC
585 TCGACTGCTGGAATATCATTTTCGACGCAGGTTTCTGGTGGGTTTGATGGCCCATCAACAATGCC
* *
541848 AAATGCTCTCGTTTCTGGCGATGAGTTTTGCACTGTGCCTCACTTGCCTAGGTGGTCCACTAGGC
650 AAATGCTCTCGTTTCTGGCGATGAATTTTGCACCGTGCCTCACTTGCCTAGGTGGTCCACTAGGC
541913 ATCCTAACCCATTTGTTGGTCTTGGTGATTGGTTTAGGCACACGGCTGGGTCAGGATTGAATGTT
715 ATCCTAACCCATTTGTTGGTCTTGGTGATTGGTTTAGGCACACGGCTGGGTCAGGATTGAATGTT
*
541978 GGGCTGGGCAGTATCCTTCTCATTTAGTGCCTGAGTAGGATTCCTATTTTAAACTGCATACTGCT
780 GGGCTGGGCAGTATCCTTCTCATTTAGTGCCTGAGTAGGATTCCTATTTTAAACCGCATACTGCT
* *
542043 GGGTTTGGGCCTACTGCTGTGAGGCCAAATGTTTATGGTACTTTTTCTGGGCTGCACGTGCGTGA
845 GGGTTTGGGCCTACTACTGTGAGGCCAAATGTTTATGGCACTTTTTCTGGGCTGCACGTGCGTGA
542108 AAGGCCTTCTGGTCCAAACCATGACTGTGGGCCATAGGCAAATAAATTTTCATATAGGCCAACAT
910 AAGGCCTTCTGGTCCAAACCATGACTGTGGGCCATAGGCAAATAAATTTTCATATAGGCCAACAT
542173 CCAATTGTGTGGAGTTTG
975 CCAATTGTGTGGAGTTTG
542191 A
1 A
542192 TAATTCTCTT
Statistics
Matches: 952, Mismatches: 40, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
991 1 0.00
992 951 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (992 bp):
AACTAACGGCAAGTGATTTTTGGAATACTGCCACTCCCCTCTTTGCAGCAGTAACCGATACGAAG
TTGTCCCGTATTCGTCATGAACTGTATTCCCTTAAAAAAGGTACTCTAACTATCATTGAATATGT
AGCAAAAATACAAAATACATGTGCCTTGATCGAGGCCTCTGGTTCTCGGATCTCGGAGGCGAAAA
AGGTTGAAATTGTTCTTGTAGGTCTACCTCTAAAATTTGATGCCGTGATTACGTTAGCATCGTTC
TCGTCAAAACCGTTACCGTTTCACCATCTCGTTGATGTGCTTCCCGAATATGATAATTGGCAGAT
GCGTGTGATTCCAGAGGAGGTGTTGATTCATGCCAATTTTGTTGAATCTGTTCCATTGCCACTGA
TGGTGGCATCTGTCCGTTGTGGCCGTCCTCCGTCTGGTGGTCGAGACAGAGGGTTTCGTTCTCAA
ATACAATGCCAAATCTGTAGTAGATTTGGGCATTTAGCCTAGCGATGCTATTATCATTATAACCG
TGATTATGTCGTCTAGTCATCGGTGGCTCGGGCTTCAAACCTGGTCAGTTGTGTGGCTCAAGGTT
CGACTGCTGGAATATCATTTTCGACGCAGGTTTCTGGTGGGTTTGATGGCCCATCAACAATGCCA
AATGCTCTCGTTTCTGGCGATGAATTTTGCACCGTGCCTCACTTGCCTAGGTGGTCCACTAGGCA
TCCTAACCCATTTGTTGGTCTTGGTGATTGGTTTAGGCACACGGCTGGGTCAGGATTGAATGTTG
GGCTGGGCAGTATCCTTCTCATTTAGTGCCTGAGTAGGATTCCTATTTTAAACCGCATACTGCTG
GGTTTGGGCCTACTACTGTGAGGCCAAATGTTTATGGCACTTTTTCTGGGCTGCACGTGCGTGAA
AGGCCTTCTGGTCCAAACCATGACTGTGGGCCATAGGCAAATAAATTTTCATATAGGCCAACATC
CAATTGTGTGGAGTTTG
Found at i:549713 original size:38 final size:38
Alignment explanation
Indices: 549650--549726 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
549640 TAAAGGTTGT
** * *
549650 GATCGTAAATTAGCGAATTGCGAGATTCATTAAATCTC
1 GATCGTAAATTAGCGAACCGCGAGATTAATAAAATCTC
* *
549688 GATCGTAAATTAGCGGACCGTGAGATTAATAAAATCTC
1 GATCGTAAATTAGCGAACCGCGAGATTAATAAAATCTC
549726 G
1 G
549727 TAAGTAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (38 bp):
GATCGTAAATTAGCGAACCGCGAGATTAATAAAATCTC
Found at i:557002 original size:42 final size:42
Alignment explanation
Indices: 556921--557115 Score: 171
Period size: 44 Copynumber: 4.5 Consensus size: 42
556911 ACATACAATT
* * * * *
556921 CCATATCCCACATATGGTCTTACATGTTAT-CACATATCGATG
1 CCATAGCCCAGATATGGTCTTACACG-AATCCATATATCGATG
* *
556963 CCAATAGCCCAGCTATGATCTTACACGAAT-CATATATCGATG
1 CC-ATAGCCCAGATATGGTCTTACACGAATCCATATATCGATG
*
557005 CCA-ATGTCCCATATATGGTCTTACACGTAATCACATATATCGATG
1 CCATA-G-CCCAGATATGGTCTTACACG-AATC-CATATATCGATG
* * *
557050 CCATATCCTAGATATGGTCTTACACAAAGTCCCATATATCGATG
1 CCATAGCCCAGATATGGTCTTACACGAA-T-CCATATATCGATG
* * *
557094 TCATACCCCAGCTATGGTCTTA
1 CCATAGCCCAGATATGGTCTTA
557116 TATGAAATCA
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 34 0.27
43 24 0.19
44 48 0.38
45 16 0.13
46 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (42 bp):
CCATAGCCCAGATATGGTCTTACACGAATCCATATATCGATG
Found at i:567954 original size:26 final size:26
Alignment explanation
Indices: 567918--567969 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
567908 ATGAGTTCAT
567918 TTTTCAATTTCCATATAATAGAAAGG
1 TTTTCAATTTCCATATAATAGAAAGG
*
567944 TTTTCAATTTCCATATAATCGAAAGG
1 TTTTCAATTTCCATATAATAGAAAGG
567970 GTGTAGACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTTCAATTTCCATATAATAGAAAGG
Found at i:575828 original size:5 final size:6
Alignment explanation
Indices: 575802--575826 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
575792 AAGTGCTTAG
575802 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
575827 GAGATTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:589412 original size:3 final size:3
Alignment explanation
Indices: 589404--589434 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
589394 ACTGTTTCTA
*
589404 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
589435 CTACATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:611480 original size:3 final size:3
Alignment explanation
Indices: 611472--611539 Score: 91
Period size: 3 Copynumber: 21.3 Consensus size: 3
611462 ATTTAGTCCC
*
611472 TTA TTA TTA TTA TTA TGTAA CTAA TTA GTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-T-A -TTA TTA -TTA TTA TTA TTA TTA TTA TTA
611521 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
611540 CATTTACTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
3 52 0.88
4 5 0.08
5 1 0.02
6 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:614588 original size:28 final size:28
Alignment explanation
Indices: 614548--614678 Score: 111
Period size: 28 Copynumber: 4.7 Consensus size: 28
614538 TTCGAAATCT
*
614548 AATCCATACAAACTCTTACTTGGAAGAA
1 AATCCATACAAACTCTTACTTGAAAGAA
*
614576 AATCCATACAAACTCGTT-CTTGAAAGAT
1 AATCCATACAAACTC-TTACTTGAAAGAA
** ** * * * *
614604 AATTTATGTAGACTCTTACCTGGATGAA
1 AATCCATACAAACTCTTACTTGAAAGAA
* * *
614632 AATCCATACAAACTCGTGCTTGAAAGAT
1 AATCCATACAAACTCTTACTTGAAAGAA
* *
614660 AATTCATACAAACTTTTAC
1 AATCCATACAAACTCTTAC
614679 ATGCGAATTC
Statistics
Matches: 75, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
27 2 0.03
28 71 0.95
29 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
AATCCATACAAACTCTTACTTGAAAGAA
Found at i:624417 original size:20 final size:20
Alignment explanation
Indices: 624380--624418 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
624370 TTAATAATGA
* *
624380 TAAAATTATACTTAAATTTT
1 TAAAATAATAATTAAATTTT
*
624400 TAAAATAATAATTTAATTT
1 TAAAATAATAATTAAATTT
624419 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATAATAATTAAATTTT
Found at i:637044 original size:371 final size:371
Alignment explanation
Indices: 636346--637465 Score: 1875
Period size: 371 Copynumber: 3.0 Consensus size: 371
636336 AATTGAGCAT
* * * * * *
636346 TACTATCGGTTTTATATATTCATTGTTGGTATCGATTCATTGCTAACAGAAATGAATTCTCGCTT
1 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
* * * * * * *
636411 TAATGATGAAGCAGTTG-AGTGACTTGTTCTTAACTCCAATTTGGATCTACACGATAATTACAAA
66 TAATGATGAGGCAG-TGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAA
* * * * * * *
636475 GCTTTTTTGTGTGGAAGATATTTGCAAGCCTATGAATGATTTTTATCTAAACAATTTTACGGAGC
130 ACTTTTTT-TGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGC
* * * * *
636540 AAAAAAAGCTACACATGAAGATTCGATTGGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAG
194 -AAGAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAG
636605 TTGCAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTAT
258 TTGCAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTAT
636670 TTATCCTCTTCTTGATAGAATTATTTGTCTTGTGGACTCTTCTCGTGTC
323 TTATCCTCTTCTTGATAGAATTATTTGTCTTGTGGACTCTTCTCGTGTC
636719 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
1 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
636784 TAATGATGAGGCAGTGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAAA
66 TAATGATGAGGCAGTGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAAA
636849 CTTTTTTTGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGCAA
131 CTTTTTTTGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGCAA
636914 GAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAGTTG
196 GAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAGTTG
636979 CAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTATTTA
261 CAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTATTTA
637044 TCCTCTTCTTGATAGAATTATTTGTCTTGTGGACTCTTCTCGTGTC
326 TCCTCTTCTTGATAGAATTATTTGTCTTGTGGACTCTTCTCGTGTC
637090 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
1 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
637155 TAATGATGAGGCAGTGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAAA
66 TAATGATGAGGCAGTGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAAA
637220 CTTTTTTTGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGCAA
131 CTTTTTTTGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGCAA
637285 GAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAGTTG
196 GAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAGTTG
* * * * * *
637350 CAGAAAGCTTCTACAGTTGTTGAGTTGTGTCAGGTGCTAACTAAGATAAATAACTTAAGTATTTA
261 CAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTATTTA
* * * *
637415 TCATCTTCTTGATAGAATT-TTTCATCTCGTGCACTCTTCTCGTGTC
326 TCCTCTTCTTGATAGAATTATTT-GTCTTGTGGACTCTTCTCGTGTC
637461 TACTA
1 TACTA
637466 CAACAACCAA
Statistics
Matches: 710, Mismatches: 35, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
370 3 0.00
371 535 0.75
372 52 0.07
373 120 0.17
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (371 bp):
TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
TAATGATGAGGCAGTGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAAA
CTTTTTTTGTGGAATATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGCAA
GAAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATACTCATGAAAGCACAGAGTTG
CAGAAAGCTTCTACAGTTGCTGAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTATTTA
TCCTCTTCTTGATAGAATTATTTGTCTTGTGGACTCTTCTCGTGTC
Found at i:641390 original size:12 final size:13
Alignment explanation
Indices: 641361--641406 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
641351 AAATTTATAA
641361 TTTATAATTTTT-
1 TTTATAATTTTTG
*
641373 TATA-AATTTTTG
1 TTTATAATTTTTG
*
641385 TTTA-AATTTATG
1 TTTATAATTTTTG
641397 TTTATAATTT
1 TTTATAATTT
641407 GTATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 7 0.24
12 17 0.59
13 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (13 bp):
TTTATAATTTTTG
Found at i:641913 original size:17 final size:17
Alignment explanation
Indices: 641891--641924 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
641881 AATAAGGAAA
*
641891 GTAATCTTAGAAGATTT
1 GTAATCCTAGAAGATTT
*
641908 GTAATCCTATAAGATTT
1 GTAATCCTAGAAGATTT
641925 AATTTTGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (17 bp):
GTAATCCTAGAAGATTT
Found at i:657583 original size:162 final size:159
Alignment explanation
Indices: 657233--657554 Score: 403
Period size: 160 Copynumber: 2.0 Consensus size: 159
657223 TTAGTAAGCA
* * * * * * *
657233 AATTATCACAGTTATAATGGTAAAACCAAAGAAAAAGTGCTAGCAATGGTACATAATGTTAAGCA
1 AATTACCACAATTATAAAGATAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGCA
* * * *
657298 CCCAAGCAAGAACCAATATACTAGGCAAGAAACCTAATTTGAATATCGAGCCACAGAGAACTAAA
66 CCCAAGCAAGAACCAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAGAACTAAA
***
657363 GACTTAACTAATGAACAGTGGGACCAGTT
131 GACTTAACTAATGAACAGAAAGACCAGTT
* * * * *
657392 AAATTATCACAGTTATAATGATAAAACCAAAGTAAAAGTGATAGCTACGGTACAAAATGTTAAGC
1 -AATTACCACAATTATAAAGATAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGC
* *
657457 ATCCAAGCAAGAACCAATAGACTATAGGCAAGAAGCCTAATTCGAACATCAAGCCACAGAGAACT
65 ACCCAAGCAAGAACCAATAGAC--TAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAGAACT
*
657522 AATGACTTAACTAATGAAC-GAAAAGACCAGTT
128 AAAGACTTAACTAATGAACAG-AAAGACCAGTT
657554 A
1 A
657555 TTCCCCGTAA
Statistics
Matches: 143, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
160 78 0.55
161 2 0.01
162 63 0.44
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (159 bp):
AATTACCACAATTATAAAGATAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGCA
CCCAAGCAAGAACCAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAGAACTAAA
GACTTAACTAATGAACAGAAAGACCAGTT
Found at i:665016 original size:1 final size:1
Alignment explanation
Indices: 665012--665045 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
665002 ACCCCCCCCC
*
665012 AAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
665046 TCATTAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:677983 original size:19 final size:19
Alignment explanation
Indices: 677955--678012 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
677945 ACTAAACTTT
*
677955 GTTAAGTATAATTAAGTT-A
1 GTTAATTATAATTAA-TTAA
*
677974 GTTAATTATAGTTAATTAA
1 GTTAATTATAATTAATTAA
* *
677993 GCTAATTATTGATTAATTAA
1 GTTAATTA-TAATTAATTAA
678013 TGATTAATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.06
19 21 0.66
20 9 0.28
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (19 bp):
GTTAATTATAATTAATTAA
Found at i:679755 original size:25 final size:25
Alignment explanation
Indices: 679721--679772 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
679711 TCAAGCTAGT
679721 AGCTTATCATATTAAATTGTTATTG
1 AGCTTATCATATTAAATTGTTATTG
679746 AGCTTATCATATTAAATTGTTATTG
1 AGCTTATCATATTAAATTGTTATTG
679771 AG
1 AG
679773 GTAAGTTATG
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:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (25 bp):
AGCTTATCATATTAAATTGTTATTG
Found at i:681081 original size:12 final size:12
Alignment explanation
Indices: 681045--681083 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
681035 TAGAAAACCT
*
681045 TAACTTTAACTT
1 TAACTTTAACTC
*
681057 TAACTTTATCTC
1 TAACTTTAACTC
*
681069 TAACTCTAACTC
1 TAACTTTAACTC
681081 TAA
1 TAA
681084 TGGTCATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACTTTAACTC
Found at i:682782 original size:8 final size:8
Alignment explanation
Indices: 682766--682796 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
682756 GACTTATATG
682766 AAAAA-AA
1 AAAAAGAA
682773 AAAAAGAA
1 AAAAAGAA
682781 AAAAAGAA
1 AAAAAGAA
682789 AAAAAGAA
1 AAAAAGAA
682797 GGGGGGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:684995 original size:2 final size:2
Alignment explanation
Indices: 684980--685011 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
684970 GTTGTTGTAA
684980 AT AT -T AT A- 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
685012 GTATTCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:719889 original size:11 final size:11
Alignment explanation
Indices: 719875--719909 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
719865 AAAATATCAT
*
719875 AAAATTTATAA
1 AAAAATTATAA
719886 AAAAATTATAA
1 AAAAATTATAA
*
719897 AAAAGTTATAA
1 AAAAATTATAA
719908 AA
1 AA
719910 TGTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:721039 original size:21 final size:22
Alignment explanation
Indices: 721015--721062 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
721005 CCCTATCTTA
*
721015 GTATTTTTAGGCCTAACAATT-
1 GTATTTTTAAGCCTAACAATTG
721036 GTATTTTTAAGCCTAACAATTG
1 GTATTTTTAAGCCTAACAATTG
721058 GTATT
1 GTATT
721063 AGAGCTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (22 bp):
GTATTTTTAAGCCTAACAATTG
Found at i:729596 original size:92 final size:93
Alignment explanation
Indices: 729482--729667 Score: 365
Period size: 92 Copynumber: 2.0 Consensus size: 93
729472 AAATAAAAAA
729482 TATATATTTAATATATAATTCGGGTCGGGCCGAGCCCGTGCAAAAAAAATTTTACCTGAGGCCCG
1 TATATATTTAATATATAATTCGGGTCGGGCCGAGCCCGTGCAAAAAAAATTTTACCTGAGGCCCG
729547 GCCTATTTTCTAAACGGGTCTCGTTTTT
66 GCCTATTTTCTAAACGGGTCTCGTTTTT
729575 TATATATTTAA-ATATAATTCGGGTCGGGCCGAGCCCGTGCAAAAAAAATTTTACCTGAGGCCCG
1 TATATATTTAATATATAATTCGGGTCGGGCCGAGCCCGTGCAAAAAAAATTTTACCTGAGGCCCG
729639 GCCTATTTTCTAAACGGGTCTCGTTTTT
66 GCCTATTTTCTAAACGGGTCTCGTTTTT
729667 T
1 T
729668 TGCCCAAACT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 82 0.88
93 11 0.12
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (93 bp):
TATATATTTAATATATAATTCGGGTCGGGCCGAGCCCGTGCAAAAAAAATTTTACCTGAGGCCCG
GCCTATTTTCTAAACGGGTCTCGTTTTT
Found at i:730221 original size:19 final size:19
Alignment explanation
Indices: 730197--730247 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
730187 TTTTAACAAT
730197 AATTCTAAAAAGA-ATAAAA
1 AATTCTAAAAA-ATATAAAA
*
730216 AATTCTAAAAAATATTAAA
1 AATTCTAAAAAATATAAAA
*
730235 AATTCTGAAAAAT
1 AATTCTAAAAAAT
730248 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (19 bp):
AATTCTAAAAAATATAAAA
Found at i:731630 original size:19 final size:19
Alignment explanation
Indices: 731606--731656 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
731596 TTTTAACAAT
731606 AATTCTAAAAAGA-ATAAAA
1 AATTCTAAAAA-ATATAAAA
*
731625 AATTCTAAAAAATATTAAA
1 AATTCTAAAAAATATAAAA
*
731644 AATTCTGAAAAAT
1 AATTCTAAAAAAT
731657 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (19 bp):
AATTCTAAAAAATATAAAA
Found at i:737480 original size:40 final size:40
Alignment explanation
Indices: 737420--737557 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
737410 AACACACCAG
* *
737420 TTTGGCACCCAGTGCCTCATCGGTTAATTTGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGTTAATCTGAAGTAATAA
* * * *
737460 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGTTAATCTGAAGTAATAA
* *
737498 -TTGACACCCAATGCCTCATCGAATTAATCCT-AAGTAATAA
1 TTTGACACCCAGTGCCTCATCG-GTTAAT-CTGAAGTAATAA
* *
737538 ATTGACACCCAGTGTCTCAT
1 TTTGACACCCAGTGCCTCAT
737558 TGACTCAAAG
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 19 0.24
38 9 0.11
39 3 0.04
40 31 0.39
41 17 0.22
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGTTAATCTGAAGTAATAA
Found at i:738454 original size:19 final size:20
Alignment explanation
Indices: 738411--738449 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
738401 ATTAATAAGC
738411 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
738430 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
738450 TTACACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:743921 original size:21 final size:21
Alignment explanation
Indices: 743895--743936 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
743885 AGGGAGGTAG
*
743895 CGGTTCATGGTGGTGATGCGT
1 CGGTTCACGGTGGTGATGCGT
743916 CGGTTCACGGTGGTGATGCGT
1 CGGTTCACGGTGGTGATGCGT
743937 TGATGGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.43, T:0.31
Consensus pattern (21 bp):
CGGTTCACGGTGGTGATGCGT
Found at i:759452 original size:9 final size:9
Alignment explanation
Indices: 759435--759471 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
759425 TGAATTTTCG
759435 AATTCGAAT
1 AATTCGAAT
*
759444 AACTCGAAT
1 AATTCGAAT
759453 AATTCGAAT
1 AATTCGAAT
759462 AATTCGAAT
1 AATTCGAAT
759471 A
1 A
759472 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:765189 original size:15 final size:16
Alignment explanation
Indices: 765151--765191 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
765141 ATAATTTTTT
765151 TAAT-TTTAAAAATAC
1 TAATATTTAAAAATAC
765166 TAATA--TAAAAAT-C
1 TAATATTTAAAAATAC
765179 TAATATTTAAAAA
1 TAATATTTAAAAA
765192 AAAATCCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATATTTAAAAATAC
Found at i:781654 original size:8 final size:8
Alignment explanation
Indices: 781641--781673 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
781631 AAACAAAACT
781641 TAAATACA
1 TAAATACA
781649 TAAATACA
1 TAAATACA
781657 TAAATACA
1 TAAATACA
781665 TAAATACA
1 TAAATACA
781673 T
1 T
781674 CAGATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAATACA
Found at i:785532 original size:91 final size:92
Alignment explanation
Indices: 785376--785559 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 92
785366 ATTATATGAT
785376 AAAATTATATTTTAATCTCTCAAAAATTTATAATTCAATTCTTCTCTTTAAAAAAGGTTTGGATT
1 AAAATTATATTTTAATCTCTCAAAAATTTATAATTCAATTCTTCTCTTTAAAAAAGGTTTGGATT
785441 CTCAAAATTTAACATGATTTCGGAAAA
66 CTCAAAATTTAACATGATTTCGGAAAA
785468 AAAATTATA-TTTAATCTCTCAAAAATTTATAATTCAATTCTTCTCTTTAAAAAAGGTTTGGATT
1 AAAATTATATTTTAATCTCTCAAAAATTTATAATTCAATTCTTCTCTTTAAAAAAGGTTTGGATT
785532 CTCAAAATTTAACATGATTTCGGAAAA
66 CTCAAAATTTAACATGATTTCGGAAAA
785559 A
1 A
785560 TTAAATCATA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 83 0.90
92 9 0.10
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (92 bp):
AAAATTATATTTTAATCTCTCAAAAATTTATAATTCAATTCTTCTCTTTAAAAAAGGTTTGGATT
CTCAAAATTTAACATGATTTCGGAAAA
Found at i:789776 original size:2 final size:2
Alignment explanation
Indices: 789769--789794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
789759 GCAGACTTAT
789769 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
789795 TAATGCTAAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:806185 original size:31 final size:31
Alignment explanation
Indices: 806150--806218 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
806140 ATACAAAATG
*
806150 GTTACTGAACTATTTGAAAGTTTTCATTTAA
1 GTTACTGAACTATTTAAAAGTTTTCATTTAA
* *
806181 GTTACTGAATTATTTAAAAGTTTTTATTTAA
1 GTTACTGAACTATTTAAAAGTTTTCATTTAA
806212 GTTACTG
1 GTTACTG
806219 GGTTGTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (31 bp):
GTTACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:807862 original size:15 final size:16
Alignment explanation
Indices: 807835--807865 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
807825 AGAAATCGAC
807835 AGAAAATAAAGAAAAG
1 AGAAAATAAAGAAAAG
807851 AGAAAA-AAAGAAAAG
1 AGAAAATAAAGAAAAG
807866 GAAGCGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AGAAAATAAAGAAAAG
Found at i:814384 original size:20 final size:20
Alignment explanation
Indices: 814351--814390 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
814341 CCCTTGCAGT
* *
814351 CTAAATTTTTCAAATTTTTC
1 CTAAAATTTCCAAATTTTTC
814371 CTAAAATTTCCAAATTTTTC
1 CTAAAATTTCCAAATTTTTC
814391 TGATATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
CTAAAATTTCCAAATTTTTC
Found at i:818819 original size:43 final size:42
Alignment explanation
Indices: 818771--818857 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
818761 TATTCCCCTT
818771 TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCCTGTCAATTC
1 TGACTTGATTTGTGGAATCAGTTTTAGTTAAG-CTGTCAATTC
*
818814 TGACTTGATTTGTGGAATCAGTTTTAGTTTAGCTGTCAATTC
1 TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCTGTCAATTC
818856 TG
1 TG
818858 CCATTACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (42 bp):
TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCTGTCAATTC
Found at i:821004 original size:27 final size:27
Alignment explanation
Indices: 820966--821022 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
820956 AATGGCGTGT
820966 CAATAGGAGTTTTCAGAGACTCATTTG
1 CAATAGGAGTTTTCAGAGACTCATTTG
820993 CAATAGGAGTTTTCAGAGACTCATTTG
1 CAATAGGAGTTTTCAGAGACTCATTTG
821020 CAA
1 CAA
821023 ACTGGTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
CAATAGGAGTTTTCAGAGACTCATTTG
Found at i:821800 original size:7 final size:6
Alignment explanation
Indices: 821779--821808 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
821769 ATATCTCTCT
821779 CCCTCTC CCCTCC CCCTCC CCCTCC CCCTC
1 CCCTC-C CCCTCC CCCTCC CCCTCC CCCTC
821809 TCTCTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (6 bp):
CCCTCC
Found at i:821802 original size:12 final size:13
Alignment explanation
Indices: 821779--821810 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
821769 ATATCTCTCT
821779 CCCTCTCCCCTCC
1 CCCTCTCCCCTCC
821792 CCCTC-CCCCTCC
1 CCCTCTCCCCTCC
821804 CCCTCTC
1 CCCTCTC
821811 TCTCTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCTCTCCCCTCC
Found at i:822627 original size:17 final size:16
Alignment explanation
Indices: 822605--822651 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
822595 GTTATGCCAA
*
822605 TTGGCGAACTCTTTGCT
1 TTGGCGAACTCTTTG-G
*
822622 TTGGCGAGA-TCTATGG
1 TTGGCGA-ACTCTTTGG
822638 TTGGCGAACTCTTT
1 TTGGCGAACTCTTT
822652 TGTTAAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 12 0.48
18 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (16 bp):
TTGGCGAACTCTTTGG
Found at i:823425 original size:58 final size:58
Alignment explanation
Indices: 823355--823473 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
823345 TTTTTATTTT
823355 ATATTTGTATAAGGTAAGTATTCTTTCTTTGTAAATGATGAAAAATGTATGTGTATGA
1 ATATTTGTATAAGGTAAGTATTCTTTCTTTGTAAATGATGAAAAATGTATGTGTATGA
823413 ATATTTGTATAAGGTAAGTATTCTTTCTTTGTAAATGATGAAAAATGTATGTGTATGA
1 ATATTTGTATAAGGTAAGTATTCTTTCTTTGTAAATGATGAAAAATGTATGTGTATGA
823471 ATA
1 ATA
823474 ACGGTTATTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.43
Consensus pattern (58 bp):
ATATTTGTATAAGGTAAGTATTCTTTCTTTGTAAATGATGAAAAATGTATGTGTATGA
Found at i:833008 original size:16 final size:16
Alignment explanation
Indices: 832987--833026 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
832977 TTGGGATGAC
* *
832987 AATATTTATTTAGATA
1 AATATTTAATTAAATA
833003 AATATTTAATTAAATA
1 AATATTTAATTAAATA
833019 AA-ATTTAA
1 AATATTTAA
833027 ATAGATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATATTTAATTAAATA
Found at i:833024 original size:27 final size:28
Alignment explanation
Indices: 832994--833047 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
832984 GACAATATTT
* *
832994 ATTTAGATAAATATTTAATTA-AATAAA
1 ATTTAAATAAATAATTAATTATAATAAA
*
833021 ATTTAAATAGATAATTAATTATAATAA
1 ATTTAAATAAATAATTAATTATAATAA
833048 TAGGTACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
ATTTAAATAAATAATTAATTATAATAAA
Found at i:833034 original size:15 final size:16
Alignment explanation
Indices: 832987--833034 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
832977 TTGGGATGAC
**
832987 AATATTTATTTAGATA
1 AATATTTAAATAGATA
* *
833003 AATATTTAATTAAATA
1 AATATTTAAATAGATA
833019 AA-ATTTAAATAGATA
1 AATATTTAAATAGATA
833034 A
1 A
833035 TTAATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATATTTAAATAGATA
Found at i:838762 original size:13 final size:13
Alignment explanation
Indices: 838744--838768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
838734 AAAAATTCAA
838744 AACACGAAAAATC
1 AACACGAAAAATC
838757 AACACGAAAAAT
1 AACACGAAAAAT
838769 TAAAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
AACACGAAAAATC
Found at i:843895 original size:3 final size:3
Alignment explanation
Indices: 843887--843914 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
843877 AACACCCAGG
843887 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
843915 CTCCTCCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:848587 original size:31 final size:32
Alignment explanation
Indices: 848528--848592 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
848518 GGCAAATTAC
848528 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
848560 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
848591 AA
1 AA
848593 ATTATTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:855425 original size:32 final size:32
Alignment explanation
Indices: 855384--855621 Score: 401
Period size: 32 Copynumber: 7.5 Consensus size: 32
855374 AAATTACAAC
855384 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855416 AGTAATTGAATCCTAAT-AAAACTCTTTCAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855447 AATAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855479 AGTAATTGAATCCTAAT-AAAACTCTTTCAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855510 AATAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855542 AGTAATTGAATCCTAAT-AAAACTCTTTCAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
*
855573 AATAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
855605 AGTAATTGAATCCTAAT
1 AGTAATTGAATCCTAAT
855622 GAATTAAATT
Statistics
Matches: 191, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
31 87 0.46
32 104 0.54
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (32 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAAG
Found at i:855485 original size:63 final size:63
Alignment explanation
Indices: 855386--855621 Score: 472
Period size: 63 Copynumber: 3.7 Consensus size: 63
855376 ATTACAACAG
855386 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
1 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
855449 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
1 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
855512 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
1 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
855575 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAAT
1 TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAAT
855622 GAATTAAATT
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 173 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (63 bp):
TAATTGAATCCTAATAAAAACTCTTTAAAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAA
Found at i:862201 original size:31 final size:31
Alignment explanation
Indices: 862130--862213 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
862120 TACTAAAAGA
* *
862130 ATAGCTTAGGTACCACTTGTGACAAAAAAAAT
1 ATAGTTTAGGTACCAATT-TGACAAAAAAAAT
* * **
862162 AAAGGTTTAGGTACCAATTTGAGAAAAATGAT
1 ATA-GTTTAGGTACCAATTTGACAAAAAAAAT
*
862194 ATAGTTTAGGTACTAATTTG
1 ATAGTTTAGGTACCAATTTG
862214 TGGCTTTAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
31 16 0.37
32 14 0.33
33 13 0.30
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (31 bp):
ATAGTTTAGGTACCAATTTGACAAAAAAAAT
Found at i:863120 original size:135 final size:135
Alignment explanation
Indices: 862870--863138 Score: 434
Period size: 135 Copynumber: 2.0 Consensus size: 135
862860 TTTTTGTTTC
862870 TTCCTATTCTCGAAAAAGTTCAATAGTTAAAAATCTTATACTAAACTCAACACCCATGAGTGCCG
1 TTCCTATTCTCGAAAAAGTTCAATAGTTAAAAATCTTATACTAAACTCAACACCCATGAGTGCCG
* *
862935 AGATACTCCTTCGAAAAACATATTTTAATAAATAAGTTTTCCATTGTCAGAAATTAAAAAAATTC
66 AGATACTCCTTCAAAAAACATATTTTAATAAATAAGTTTTCCATTGTCAGAAATTAAAAAAAATC
863000 TAATA
131 TAATA
* * *
863005 TTCCTATTCTCGAAAAAGTTCAATAGTTAAAAA-CTCTATATTAAACTCGACACCCATGAGTGTC
1 TTCCTATTCTCGAAAAAGTTCAATAGTTAAAAATCT-TATACTAAACTCAACACCCATGAGTGCC
* * *
863069 GAGATACTCCTT-AAAAAATATATATTTAATAAATAAGTTTTTCATTTTCAGAAATTAAAAAAAA
65 GAGATACTCCTTCAAAAAACATAT-TTTAATAAATAAGTTTTCCATTGTCAGAAATTAAAAAAAA
863133 TCTAAT
129 TCTAAT
863139 GTTTCTGTAA
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
134 11 0.09
135 113 0.91
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (135 bp):
TTCCTATTCTCGAAAAAGTTCAATAGTTAAAAATCTTATACTAAACTCAACACCCATGAGTGCCG
AGATACTCCTTCAAAAAACATATTTTAATAAATAAGTTTTCCATTGTCAGAAATTAAAAAAAATC
TAATA
Found at i:867963 original size:111 final size:111
Alignment explanation
Indices: 867769--867990 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
867759 GTAGAAATTC
867769 GAGAGCACCCTTTTATCATTTTGTGGGAAGCATTCGGCGTCTATGAATTGGAGCATATGAATCAA
1 GAGAGCACCCTTTTATCATTTTGTGGGAAGCATTCGGCGTCTATGAATTGGAGCATATGAATCAA
867834 AACATTTTATCTGGGGTTAATCCTTTTTTTTTCTTGCCTGAATGGA
66 AACATTTTATCTGGGGTTAATCCTTTTTTTTTCTTGCCTGAATGGA
867880 GAGAGCACCCTTTTATCATTTTGTGGGAAGCATTCGGCGTCTATGAATTGGAGCATATGAATCAA
1 GAGAGCACCCTTTTATCATTTTGTGGGAAGCATTCGGCGTCTATGAATTGGAGCATATGAATCAA
*
867945 AACATTTTATCTGGGGTTAATCGTTTTTTTTTCTTGCCTGAATGGA
66 AACATTTTATCTGGGGTTAATCCTTTTTTTTTCTTGCCTGAATGGA
867991 TTTCGGATAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (111 bp):
GAGAGCACCCTTTTATCATTTTGTGGGAAGCATTCGGCGTCTATGAATTGGAGCATATGAATCAA
AACATTTTATCTGGGGTTAATCCTTTTTTTTTCTTGCCTGAATGGA
Found at i:872715 original size:21 final size:22
Alignment explanation
Indices: 872673--872717 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
872663 GAAGAAAACT
**
872673 ATCGTTTTTCATATCATTATTA
1 ATCGTTTTTCATATCAGGATTA
*
872695 ATCGTTTTTCATGT-AGGATTA
1 ATCGTTTTTCATATCAGGATTA
872716 AT
1 AT
872718 AGTTGGTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (22 bp):
ATCGTTTTTCATATCAGGATTA
Found at i:879920 original size:51 final size:51
Alignment explanation
Indices: 879865--880111 Score: 393
Period size: 51 Copynumber: 5.0 Consensus size: 51
879855 GATCACATTT
*
879865 ATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTA-CACCTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCA-CTC
879916 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
879967 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAG------CT-
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
880011 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
880062 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
880112 TATTCGGTTT
Statistics
Matches: 182, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
44 40 0.22
45 2 0.01
50 2 0.01
51 136 0.75
52 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:880038 original size:95 final size:95
Alignment explanation
Indices: 879865--880114 Score: 401
Period size: 95 Copynumber: 2.6 Consensus size: 95
879855 GATCACATTT
* * *
879865 ATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACACCTCATCACTTGTCACTT
1 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAG------CT-ATCACTTATCACTT
879930 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
59 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
879967 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGTCACTG
1 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGTCACTG
880032 ATCAGATAAGTGTAGCTAAAGCTACCACTC
66 ATCAGATAAGTGTAGCTAAAGCTACCACTC
*
880062 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
880115 TCGGTTTTCG
Statistics
Matches: 144, Mismatches: 4, Indels: 7
0.93 0.03 0.05
Matches are distributed among these distances:
95 102 0.71
96 2 0.01
102 40 0.28
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (95 bp):
ATCACTTGTCTCTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGTCACTG
ATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:890968 original size:50 final size:50
Alignment explanation
Indices: 890844--891140 Score: 245
Period size: 50 Copynumber: 5.8 Consensus size: 50
890834 GAATATAACA
* * * ** ** * * *
890844 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTAGG
* * * * * ** *
890893 TGCCAATGTCATATCCCAGATATGGTATTACATGGGAATTCACATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTAGG
* * ** * *
890943 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTAGG
* *
890993 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTAGG
* * *
891043 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-C-CTCA-CATCT--A-GG
* * *
891099 TGCCAATGCCATGTCCCAGACATGGTTTTACATGGGATCTCA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCA
891141 TCCTCTTAAT
Statistics
Matches: 202, Mismatches: 39, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
49 35 0.17
50 120 0.59
51 1 0.00
52 3 0.01
53 4 0.02
54 4 0.02
56 35 0.17
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTAGG
Found at i:891018 original size:100 final size:102
Alignment explanation
Indices: 890906--891140 Score: 276
Period size: 100 Copynumber: 2.3 Consensus size: 102
890896 CAATGTCATA
* * * *
890906 TCCCAGATATGGTATTACATGGGAATTCACATATAGGTGCCCATGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTATTACATGGGAACTCACATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
* *
890971 TACGGGGGACCTCTC-ATCTC-GGTGCCAACGCCATG
66 TACAGGGGACCTCTCAATCTCAGATGCCAACGCCATG
* * * * * *
891006 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCTCAGACATGGTCT
1 TCCCAGACATGGTATTACATGGGAACTCACATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
* *
891071 TACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATG
66 TACAGGGGACCTCTC--AATCTC-A-GATGCCAACGCCATG
* *
891112 TCCCAGACATGGTTTTACATGGGATCTCA
1 TCCCAGACATGGTATTACATGGGAACTCA
891141 TCCTCTTAAT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 68 0.61
103 5 0.04
106 39 0.35
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (102 bp):
TCCCAGACATGGTATTACATGGGAACTCACATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
TACAGGGGACCTCTCAATCTCAGATGCCAACGCCATG
Found at i:893016 original size:25 final size:25
Alignment explanation
Indices: 892978--893066 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
892968 GGACACACCA
* * * *
892978 TAGCTCGTAAGAGCGTCCCGCTATT
1 TAGCTCTTATGAGCATCCCGATATT
* * *
893003 TAGCTCTTATGAGCACCCCGTTATA
1 TAGCTCTTATGAGCATCCCGATATT
* *
893028 T-GACTCTTTTGAGCTTCCCGATATT
1 TAG-CTCTTATGAGCATCCCGATATT
*
893053 TGGCTCTTATGAGC
1 TAGCTCTTATGAGC
893067 TTCCTGATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.02
25 48 0.96
26 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (25 bp):
TAGCTCTTATGAGCATCCCGATATT
Found at i:893067 original size:25 final size:25
Alignment explanation
Indices: 892988--893131 Score: 98
Period size: 25 Copynumber: 5.8 Consensus size: 25
892978 TAGCTCGTAA
* * *
892988 GAGCGTCCCGCTATTTAGCTCTTAT
1 GAGCTTCCCGATATTTGGCTCTTAT
** * * * *
893013 GAGCACCCCGTTATATGACTCTTTT
1 GAGCTTCCCGATATTTGGCTCTTAT
893038 GAGCTTCCCGATATTTGGCTCTTAT
1 GAGCTTCCCGATATTTGGCTCTTAT
* * *
893063 GAGCTTCCTGAT-TAATGGCT-TTCTT
1 GAGCTTCCCGATAT-TTGGCTCTT-AT
*
893088 GAGCTTCCC-AT-TTATGGCTCGTAT
1 GAGCTTCCCGATATT-TGGCTCTTAT
**
893112 GAGCTTTTCGATATTTGGCT
1 GAGCTTCCCGATATTTGGCT
893132 TGCAAGAGCT
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
24 19 0.21
25 70 0.77
26 2 0.02
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGATATTTGGCTCTTAT
Found at i:893090 original size:50 final size:50
Alignment explanation
Indices: 892988--893117 Score: 133
Period size: 50 Copynumber: 2.6 Consensus size: 50
892978 TAGCTCGTAA
* * * **
892988 GAGCGTCCCGCTATTTAGCTCTTATGAGCACCCCGTTATATGACTCTTTT
1 GAGCTTCCCGATATTTGGCTCTTATGAGCTTCCCGTTATATGACTCTTTT
* *
893038 GAGCTTCCCGATATTTGGCTCTTATGAGCTTCCTGATTA-ATGGCT-TTCTT
1 GAGCTTCCCGATATTTGGCTCTTATGAGCTTCCCG-TTATATGACTCTT-TT
*
893088 GAGCTTCCC-AT-TTATGGCTCGTATGAGCTT
1 GAGCTTCCCGATATT-TGGCTCTTATGAGCTT
893118 TTCGATATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.03
49 19 0.28
50 45 0.65
51 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (50 bp):
GAGCTTCCCGATATTTGGCTCTTATGAGCTTCCCGTTATATGACTCTTTT
Found at i:900608 original size:19 final size:20
Alignment explanation
Indices: 900577--900614 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
900567 CATGCAAACT
900577 AAGAAAGGAAATGAAAGAAA
1 AAGAAAGGAAATGAAAGAAA
*
900597 AAGAAA-GAAATGAGAGAA
1 AAGAAAGGAAATGAAAGAA
900615 CGCATGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.05
Consensus pattern (20 bp):
AAGAAAGGAAATGAAAGAAA
Found at i:901256 original size:20 final size:20
Alignment explanation
Indices: 901213--901256 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
901203 TTGTGAAAAT
* * *
901213 TTTGAAATTTAGGAGTTTAA
1 TTTGAAAATAAGGAGTTAAA
901233 -TTGAAAATAAGGAGTTAAA
1 TTTGAAAATAAGGAGTTAAA
901252 TTTGA
1 TTTGA
901257 TTTAAAGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (20 bp):
TTTGAAAATAAGGAGTTAAA
Found at i:907412 original size:15 final size:15
Alignment explanation
Indices: 907394--907423 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
907384 GCAACCCACG
907394 TGAAATTGTTAATGA
1 TGAAATTGTTAATGA
907409 TGAAATTGTTAATGA
1 TGAAATTGTTAATGA
907424 ATACATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
TGAAATTGTTAATGA
Found at i:911574 original size:178 final size:178
Alignment explanation
Indices: 911271--911622 Score: 614
Period size: 178 Copynumber: 2.0 Consensus size: 178
911261 AATTTATATG
*
911271 GGGTAGGCTTGAAAGGCTCAAATGATCCAAATAAAATGTGCCTAAATCATGTTTAGGTTCTTATG
1 GGGTAGGCTTGAAAGGCTCAAATGATCCAAATAAAATGTGCCTAAATCATGTTTAGATTCTTATG
* ** * *
911336 CCTCCTAAGATTTCGCCTCAAGAAAGTTACTAAGTTGATTCTAAGAACTTAAATCTTCATGCATG
66 CCTCCTAAGATTTCGCCTCAAAAAAGTTACTAAGTCAAATCTAAGAACTTAAACCTTCATGCATG
* * *
911401 TTTATAAAAAGAAGTTTAATTTTCATGGTAAAAGGCTAAATAAGCTTA
131 TTTATAAAAAGAAGTTTAATTCTCACGATAAAAGGCTAAATAAGCTTA
*
911449 GGGTAGGCTTGAAAGGCTCAAATGGTCCAAATAAAATGTGCCTAAATCATGTTTAGATTCTTATG
1 GGGTAGGCTTGAAAGGCTCAAATGATCCAAATAAAATGTGCCTAAATCATGTTTAGATTCTTATG
911514 CCTCCTAAGATTTCGCCTCAAAAAAGTTACTAAGTCAAATCTAAGAACTTAAACCTTCATGCATG
66 CCTCCTAAGATTTCGCCTCAAAAAAGTTACTAAGTCAAATCTAAGAACTTAAACCTTCATGCATG
911579 TTTATAAAAAGAAGTTTAATTCTCACGATAAAAGGCTAAATAAG
131 TTTATAAAAAGAAGTTTAATTCTCACGATAAAAGGCTAAATAAG
911623 ACCTAAGAAT
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 164 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (178 bp):
GGGTAGGCTTGAAAGGCTCAAATGATCCAAATAAAATGTGCCTAAATCATGTTTAGATTCTTATG
CCTCCTAAGATTTCGCCTCAAAAAAGTTACTAAGTCAAATCTAAGAACTTAAACCTTCATGCATG
TTTATAAAAAGAAGTTTAATTCTCACGATAAAAGGCTAAATAAGCTTA
Found at i:913229 original size:30 final size:30
Alignment explanation
Indices: 913195--913378 Score: 167
Period size: 30 Copynumber: 6.1 Consensus size: 30
913185 CAATGGAAAG
913195 GGATAGCTTCGGCTATCAAATTATGAAAAA
1 GGATAGCTTCGGCTATCAAATTATGAAAAA
913225 GGATAGCTTCGGCTATCAAATTAT-AAAAA
1 GGATAGCTTCGGCTATCAAATTATGAAAAA
* * * *
913254 GGGATAGCTTCAGCTGTCAACTTGT-AAAAA
1 -GGATAGCTTCGGCTATCAAATTATGAAAAA
* * *
913284 GAGATAGCTTGGGATATCAAATTATGAAAAT
1 G-GATAGCTTCGGCTATCAAATTATGAAAAA
* * * * * * *
913315 GGAT-GGTGACGACCATCGAACTATGAAAAG
1 GGATAGCT-TCGGCTATCAAATTATGAAAAA
* * *
913345 GGATAGTTTCGGCTATCAAATCATGAAAAG
1 GGATAGCTTCGGCTATCAAATTATGAAAAA
913375 GGAT
1 GGAT
913379 GGTGACGACT
Statistics
Matches: 122, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
29 8 0.07
30 107 0.88
31 7 0.06
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (30 bp):
GGATAGCTTCGGCTATCAAATTATGAAAAA
Found at i:913264 original size:60 final size:60
Alignment explanation
Indices: 913191--913458 Score: 197
Period size: 60 Copynumber: 4.5 Consensus size: 60
913181 CGACCAATGG
*
913191 AAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATAGCTTCGGCTATCAAATTATAA
1 AAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATAGCTTCGGCTATCAAATTATGA
* * * * * *
913251 AAAGGGATAGCTTCAGCTGTCAACTTGT-AAAAAGAGATAGCTTGGGATATCAAATTATGA
1 AAAGGGATAGCTTCGGCTATCAAATTATGAAAAAG-GATAGCTTCGGCTATCAAATTATGA
* * * * * * * * * *
913311 AAATGGAT-GGTGACGACCATCGAACTATGAAAAGGGATAGTTTCGGCTATCAAATCATGA
1 AAAGGGATAGCT-TCGGCTATCAAATTATGAAAAAGGATAGCTTCGGCTATCAAATTATGA
* * * * * * ** * * *
913371 AAAGGGAT-GGTGACGACTATC-AACTATGAAAAGGGAT-G-TGACAACCATTAAAATATGA
1 AAAGGGATAGCT-TCGGCTATCAAATTATGAAAAAGGATAGCT-TCGGCTATCAAATTATGA
*
913429 AAAGGGATAGCTTCGGCTATCGAATTATGA
1 AAAGGGATAGCTTCGGCTATCAAATTATGA
913459 GAAGGAATGG
Statistics
Matches: 166, Mismatches: 36, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
57 1 0.01
58 27 0.16
59 33 0.20
60 100 0.60
61 5 0.03
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.25
Consensus pattern (60 bp):
AAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATAGCTTCGGCTATCAAATTATGA
Found at i:913374 original size:90 final size:90
Alignment explanation
Indices: 913191--913463 Score: 241
Period size: 90 Copynumber: 3.1 Consensus size: 90
913181 CGACCAATGG
* * * * * * * *
913191 AAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATAGCT-TCGGCTATCAAATTATAAAAAG
1 AAAGGGATAGCTTGGGATATCAAATTATGAAAAAGGAT-GGTGACGACCATCAAAATATGAAAAG
* * * * *
913255 GGATAGCTTCAGCTGTCAACTTGTAA
65 GGATAGCTTCGGCTATCAAATTATGA
* * * *
913281 AAAGAGATAGCTTGGGATATCAAATTATGAAAATGGATGGTGACGACCATCGAACTATGAAAAGG
1 AAAGGGATAGCTTGGGATATCAAATTATGAAAAAGGATGGTGACGACCATCAAAATATGAAAAGG
* *
913346 GATAGTTTCGGCTATCAAATCATGA
66 GATAGCTTCGGCTATCAAATTATGA
* * * * * *
913371 AAAGGGAT-G-GTGACGACTATC-AACTATGAAAAGGGAT-GTGACAACCATTAAAATATGAAAA
1 AAAGGGATAGCTTG-GGA-TATCAAATTATGAAAAAGGATGGTGACGACCATCAAAATATGAAAA
*
913432 GGGATAGCTTCGGCTATCGAATTATGA
64 GGGATAGCTTCGGCTATCAAATTATGA
*
913459 GAAGG
1 AAAGG
913464 AATGGTGACA
Statistics
Matches: 149, Mismatches: 31, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
88 50 0.34
89 19 0.13
90 80 0.54
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (90 bp):
AAAGGGATAGCTTGGGATATCAAATTATGAAAAAGGATGGTGACGACCATCAAAATATGAAAAGG
GATAGCTTCGGCTATCAAATTATGA
Found at i:913391 original size:30 final size:29
Alignment explanation
Indices: 913298--913436 Score: 136
Period size: 30 Copynumber: 4.7 Consensus size: 29
913288 TAGCTTGGGA
*
913298 TATCAAATTATGAAAATGGATGGTGACGAC
1 TATCAAA-TATGAAAAGGGATGGTGACGAC
* * * ** *
913328 CATCGAACTATGAAAAGGGATAGTTTCGGC
1 TATC-AAATATGAAAAGGGATGGTGACGAC
913358 TATCAAATCATGAAAAGGGATGGTGACGAC
1 TATCAAAT-ATGAAAAGGGATGGTGACGAC
* *
913388 TATCAACTATGAAAAGGGAT-GTGACAAC
1 TATCAAATATGAAAAGGGATGGTGACGAC
* *
913416 CATTAAAATATGAAAAGGGAT
1 TA-TCAAATATGAAAAGGGAT
913437 AGCTTCGGCT
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
28 8 0.09
29 31 0.35
30 47 0.53
31 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (29 bp):
TATCAAATATGAAAAGGGATGGTGACGAC
Found at i:913435 original size:88 final size:89
Alignment explanation
Indices: 913306--913472 Score: 237
Period size: 88 Copynumber: 1.9 Consensus size: 89
913296 GATATCAAAT
* * * * *
913306 TATGAAAATGGATGGTGACGACCATCGAACTATGAAAAGGGATAGTTTCGGCTATCAAATCATGA
1 TATGAAAAGGGATGGTGACAACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATCATGA
*
913371 AAAGGGATGGTGACGACTATCAAC
66 AAAGGAATGGTGACGACTATCAAC
* * *
913395 TATGAAAAGGGAT-GTGACAACCATTAAAATATGAAAAGGGATAGCTTCGGCTATCGAATTATGA
1 TATGAAAAGGGATGGTGACAACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATCATGA
*
913459 GAAGGAATGGTGAC
66 AAAGGAATGGTGAC
913473 AACCATCGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 56 0.82
89 12 0.18
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (89 bp):
TATGAAAAGGGATGGTGACAACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATCATGA
AAAGGAATGGTGACGACTATCAAC
Found at i:934698 original size:40 final size:40
Alignment explanation
Indices: 934653--934728 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
934643 ATGCTTGAAA
*
934653 ATTATATTTTATTTTTGGGATAGCTATAAAATTATTAATT
1 ATTATATTTTATTTTTGGGATAGCTATAAAAATATTAATT
934693 ATTATATTTTATTTTTGGGATAGCTATAAAAATATT
1 ATTATATTTTATTTTTGGGATAGCTATAAAAATATT
934729 TATAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.51
Consensus pattern (40 bp):
ATTATATTTTATTTTTGGGATAGCTATAAAAATATTAATT
Found at i:940109 original size:26 final size:26
Alignment explanation
Indices: 940080--940131 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
940070 TTATTTGAAT
* *
940080 TTATAAAAAAAATTTTAAAATTATAA
1 TTATAAAAAAAATTTAAAAATCATAA
**
940106 TTATGTAAAAAATTTAAAAATCATAA
1 TTATAAAAAAAATTTAAAAATCATAA
940132 AAAATTTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
TTATAAAAAAAATTTAAAAATCATAA
Found at i:943862 original size:31 final size:31
Alignment explanation
Indices: 943804--943862 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
943794 ATCCCATTCC
* * *
943804 AGGGATAGCCCGGTTCGGTGGTGTCCCACAA
1 AGGGATAACCCGGTTCGGTGATATCCCACAA
943835 AGGGATAACCCGGCTTCGGT-ATATCCCA
1 AGGGATAACCCGG-TTCGGTGATATCCCA
943863 TCCTCGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (31 bp):
AGGGATAACCCGGTTCGGTGATATCCCACAA
Done.