Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, 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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:702131 original size:28 final size:28
Alignment explanation
Indices: 702091--702151 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
702081 TTCTCTTTAT
702091 TATTCATCCATTCTT-AGTGGGTTAAAAG
1 TATTCATCCATTCTTGA-TGGGTTAAAAG
702119 TATTCATCCATTCTTGATGGGTTAAAAG
1 TATTCATCCATTCTTGATGGGTTAAAAG
*
702147 CATTC
1 TATTC
702152 TTATTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (28 bp):
TATTCATCCATTCTTGATGGGTTAAAAG
Found at i:702409 original size:17 final size:17
Alignment explanation
Indices: 702387--702421 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
702377 GTTGTAAAAT
702387 AGATATCAAACAAAGTC
1 AGATATCAAACAAAGTC
**
702404 AGATATCATTCAAAGTC
1 AGATATCAAACAAAGTC
702421 A
1 A
702422 ATTTCATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (17 bp):
AGATATCAAACAAAGTC
Found at i:711269 original size:21 final size:20
Alignment explanation
Indices: 711245--711292 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
711235 TTATATCTGT
711245 TATTTATGTTAAATT-TTATTA
1 TATTTATGTT--ATTATTATTA
711266 TATTTAATGTTATTATTATTA
1 TATTT-ATGTTATTATTATTA
711287 T-TTTAT
1 TATTTAT
711293 TATAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 12 0.48
22 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTTATGTTATTATTATTA
Found at i:711278 original size:15 final size:17
Alignment explanation
Indices: 711242--711281 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
711232 ATTTTATATC
711242 TGTTATT-TATGTTAAA
1 TGTTATTATATGTTAAA
*
711258 TTTTATTATAT-TT-AA
1 TGTTATTATATGTTAAA
711273 TGTTATTAT
1 TGTTATTAT
711282 TATTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 10 0.48
16 8 0.38
17 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (17 bp):
TGTTATTATATGTTAAA
Found at i:711300 original size:17 final size:18
Alignment explanation
Indices: 711275--711309 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
711265 ATATTTAATG
*
711275 TTATTATTATT-ATTTTA
1 TTATAATTATTAATTTTA
711292 TTATAATTATTAATTTTA
1 TTATAATTATTAATTTTA
711310 AATTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATAATTATTAATTTTA
Found at i:711422 original size:13 final size:13
Alignment explanation
Indices: 711350--711425 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
711340 AACTCGTATC
* *
711350 ATATTTTAAATCT
1 ATATATTAAATAT
* * *
711363 ATTTATTTAATAA
1 ATATATTAAATAT
711376 ATATATT-AATCAT
1 ATATATTAAAT-AT
*
711389 ATCATATTACAT-T
1 AT-ATATTAAATAT
711402 AT-TATTAAATAT
1 ATATATTAAATAT
711414 ATATATTAAATA
1 ATATATTAAATA
711426 ACAATACAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
11 7 0.14
12 6 0.12
13 29 0.59
14 5 0.10
15 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATTAAATAT
Found at i:716783 original size:11 final size:11
Alignment explanation
Indices: 716760--716823 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
716750 ACATATGAGT
716760 AAATAGAAT-AA
1 AAATA-AATAAA
716771 AAATAAATAAA
1 AAATAAATAAA
716782 AAATAAA-ACAA
1 AAATAAATA-AA
716793 AAAT-AAT--A
1 AAATAAATAAA
*
716801 ATATAAATTAAA
1 AAATAAA-TAAA
716813 AAATAAA-AAA
1 AAATAAATAAA
716823 A
1 A
716824 TTAAAATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
8 4 0.09
9 2 0.05
10 11 0.25
11 20 0.45
12 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:716788 original size:17 final size:17
Alignment explanation
Indices: 716766--716822 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
716756 GAGTAAATAG
*
716766 AATAAAAATAAATAAAA
1 AATAAAAAAAAATAAAA
716783 AATAAAACAAAAATAATAA
1 AATAAAA-AAAAATAA-AA
*
716802 TATAAATTAAAAAATAAAA
1 AATAAA--AAAAAATAAAA
716821 AA
1 AA
716823 ATTAAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 10 0.30
20 8 0.24
21 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAAAAAAAAATAAAA
Found at i:721332 original size:25 final size:26
Alignment explanation
Indices: 721304--721373 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
721294 TTATAGGGGT
* * * *
721304 AAAATGGT-CATTTGACTGAAAGGGC
1 AAAATGGTAAATTTGACTAAAAAGGA
*
721329 AAAATGGTAAATTTGACAAAAAAGGA
1 AAAATGGTAAATTTGACTAAAAAGGA
721355 AAAATGGTAAATTTGACTA
1 AAAATGGTAAATTTGACTA
721374 TATTTAAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
25 8 0.21
26 30 0.79
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (26 bp):
AAAATGGTAAATTTGACTAAAAAGGA
Found at i:721831 original size:21 final size:22
Alignment explanation
Indices: 721789--721831 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
721779 TTTGGTTATT
*
721789 CTTCATTGTTTTTCTCCTTATC
1 CTTCATTGTTTTTCTCCATATC
* *
721811 CTTCCTTG-TTTTCTTCATATC
1 CTTCATTGTTTTTCTCCATATC
721832 TCTCACTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.09, C:0.28, G:0.05, T:0.58
Consensus pattern (22 bp):
CTTCATTGTTTTTCTCCATATC
Found at i:726681 original size:12 final size:12
Alignment explanation
Indices: 726664--726689 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
726654 ATAAAAGGAC
726664 AAAAGAGAGAGA
1 AAAAGAGAGAGA
726676 AAAAGAGAGAGA
1 AAAAGAGAGAGA
726688 AA
1 AA
726690 GAGGTGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAAAGAGAGAGA
Found at i:729241 original size:19 final size:19
Alignment explanation
Indices: 729217--729254 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
729207 ATTATTTGAT
729217 ATTGTTCGGTGACATTAAA
1 ATTGTTCGGTGACATTAAA
729236 ATTGTTCGGTGACATTAAA
1 ATTGTTCGGTGACATTAAA
729255 GCTAGGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
ATTGTTCGGTGACATTAAA
Found at i:734198 original size:17 final size:18
Alignment explanation
Indices: 734176--734216 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
734166 AAGTCTAAAA
*
734176 TATATTATT-TTTATATT
1 TATATTATTATTTATAAT
734193 TATATT-TTATTTATAAT
1 TATATTATTATTTATAAT
734210 TA-ATTAT
1 TATATTAT
734217 GAGGACACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATTATTATTTATAAT
Found at i:736801 original size:12 final size:12
Alignment explanation
Indices: 736784--736814 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
736774 CAAACCACAA
736784 ACAAGACTCTAC
1 ACAAGACTCTAC
736796 ACAAGACTCTAC
1 ACAAGACTCTAC
736808 ACAAGAC
1 ACAAGAC
736815 CCCAACTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.32, G:0.10, T:0.13
Consensus pattern (12 bp):
ACAAGACTCTAC
Found at i:747754 original size:11 final size:11
Alignment explanation
Indices: 747734--747763 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
747724 TCTCTCTTTC
747734 TATCATATATA
1 TATCATATATA
*
747745 TATGATATATA
1 TATCATATATA
747756 TATCATAT
1 TATCATAT
747764 GTATCTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (11 bp):
TATCATATATA
Found at i:750461 original size:15 final size:15
Alignment explanation
Indices: 750428--750465 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
750418 TAAAAGCATC
*
750428 ATTAT-TTTTTATTT
1 ATTATCTTTCTATTT
*
750442 TTTATCTTTCTATTT
1 ATTATCTTTCTATTT
750457 ATTATCTTT
1 ATTATCTTT
750466 TTGCTCAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATCTTTCTATTT
Found at i:750658 original size:14 final size:15
Alignment explanation
Indices: 750641--750669 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
750631 ATTTTTTCTT
750641 TTTTCAATTT-TCAA
1 TTTTCAATTTATCAA
750655 TTTTCAATTTATCAA
1 TTTTCAATTTATCAA
750670 CTTAACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTCAATTTATCAA
Found at i:755110 original size:2 final size:2
Alignment explanation
Indices: 755103--755127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
755093 TGTAAGTGGA
755103 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
755128 ACATTTTCAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:758273 original size:2 final size:2
Alignment explanation
Indices: 758266--758295 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
758256 TGGAAGAGAC
758266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
758296 AGTTACCCTA
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):
TA
Found at i:759617 original size:23 final size:23
Alignment explanation
Indices: 759583--759652 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
759573 AAATTAATTA
759583 TTAATAAT-AAATTTTTATTTAAT
1 TTAA-AATAAAATTTTTATTTAAT
*
759606 TTAAAATAAAATTTTTA-TTAAA
1 TTAAAATAAAATTTTTATTTAAT
* * **
759628 ATAAATTAAAAAATTTATTTAAT
1 TTAAAATAAAATTTTTATTTAAT
759651 TT
1 TT
759653 TTTTAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 20 0.53
23 18 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAAATAAAATTTTTATTTAAT
Found at i:763409 original size:6 final size:7
Alignment explanation
Indices: 763389--763413 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
763379 TATTAAAATA
763389 TTATTTT
1 TTATTTT
763396 TTATTTT
1 TTATTTT
763403 TTATTTT
1 TTATTTT
763410 TTAT
1 TTAT
763414 AAAAAATAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTATTTT
Found at i:763605 original size:29 final size:28
Alignment explanation
Indices: 763554--763630 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
763544 CGTTAATTAT
*
763554 AAAAAAAAATTTAATT-CA-A-AACAAA
1 AAAAAAAAATTTAATTAAATATAACAAA
763579 AATAAAAAAATTTAATTAAATATAACAAA
1 AA-AAAAAAATTTAATTAAATATAACAAA
* *
763608 AAAATAAATATTTATTTAAATAT
1 AAAA-AAAAATTTAATTAAATAT
763631 TACATCGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.05
26 14 0.32
27 1 0.02
28 3 0.07
29 24 0.55
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAAAAAATTTAATTAAATATAACAAA
Found at i:770228 original size:33 final size:35
Alignment explanation
Indices: 770186--770269 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 35
770176 ATTTTTAATG
* *
770186 TTATATATTTTCTTTTTTTATTATAATCTTATATA
1 TTATGTATTTTCTTTTTTTAATATAATCTTATATA
* * *
770221 TT-T-TATTTTCATTTTTTAATATAATTTTCTATA
1 TTATGTATTTTCTTTTTTTAATATAATCTTATATA
*
770254 TTATGTATTTTATTTT
1 TTATGTATTTTCTTTT
770270 AATTTGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 28 0.68
34 2 0.05
35 11 0.27
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (35 bp):
TTATGTATTTTCTTTTTTTAATATAATCTTATATA
Found at i:770240 original size:28 final size:26
Alignment explanation
Indices: 770177--770240 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
770167 CTTAAATATA
* *
770177 TTTTTAATGTTATATATTTTCTTTTT
1 TTTTTAATCTTATATATTTTATTTTT
770203 TTATTATAATCTTATATATTTTATTTTCAT
1 TT-TT-TAATCTTATATATTTTATTTT--T
770233 TTTTTAAT
1 TTTTTAAT
770241 ATAATTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 23 0.72
29 2 0.06
30 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTTAATCTTATATATTTTATTTTT
Found at i:773264 original size:3 final size:3
Alignment explanation
Indices: 773256--773281 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
773246 CAAATCCTAC
773256 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
773282 CACCGCCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:778037 original size:108 final size:111
Alignment explanation
Indices: 777918--778167 Score: 330
Period size: 108 Copynumber: 2.3 Consensus size: 111
777908 CTTTTTTAGA
* * *
777918 GACGAGCAAATACAAATTTTAACTCATTCTTTCTCC-AATTTCATTTAAAAATTTGTTTTTGTT-
1 GACGAGCAAATACAAATTTTAACTAATTCTTTCCCCTAATTTCATTTAAAAATTTGCTTTTGTTA
* *
777981 TCTTTAAATCTAACACCCCTTGGA-TT-ACTTTGCATTTTGTAAAGT
66 T-TTTAAATCTAACACCCCTTGCATTTAACTTTGCATTTTATAAAGT
* *
778026 GATGAGCAAATACAAATTTTAACTAATT-TTTCCCCTGATTTCATTTAAAAATTTGCTTTTGTTA
1 GACGAGCAAATACAAATTTTAACTAATTCTTTCCCCTAATTTCATTTAAAAATTTGCTTTTGTTA
* * **
778090 TTTTAAATCTAATACCTCTTGCATTTAAAACTTTGTTTTTTATAAAGT
66 TTTTAAATCTAACACCCCTTGCATTT--AACTTTGCATTTTATAAAGT
*
778138 GACAAGCAAATACAAATTTTAACTAATTCT
1 GACGAGCAAATACAAATTTTAACTAATTCT
778168 CTCCTTTTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
107 6 0.05
108 70 0.57
109 3 0.02
112 42 0.34
113 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (111 bp):
GACGAGCAAATACAAATTTTAACTAATTCTTTCCCCTAATTTCATTTAAAAATTTGCTTTTGTTA
TTTTAAATCTAACACCCCTTGCATTTAACTTTGCATTTTATAAAGT
Found at i:781563 original size:3 final size:3
Alignment explanation
Indices: 781555--781583 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
781545 ACCATGAGAA
781555 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
781584 GGTTTGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:790519 original size:10 final size:10
Alignment explanation
Indices: 790498--790530 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
790488 TTTACTCAAA
790498 TTTTTAAA-T
1 TTTTTAAAGT
790507 TTTTTAAAGT
1 TTTTTAAAGT
790517 TTTTT-AAGT
1 TTTTTAAAGT
790526 TTTTT
1 TTTTT
790531 CACTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (10 bp):
TTTTTAAAGT
Found at i:790627 original size:16 final size:18
Alignment explanation
Indices: 790591--790634 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
790581 TTTTTATTCA
*
790591 ATTTTTTTTTATATTATT
1 ATTTTATTTTATATTATT
790609 ATTTTATTTTA-ATTA-T
1 ATTTTATTTTATATTATT
*
790625 ATTCTATTTT
1 ATTTTATTTT
790635 GCTCATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 4 0.17
18 10 0.42
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTATTTTATATTATT
Found at i:790774 original size:15 final size:16
Alignment explanation
Indices: 790756--790790 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
790746 TTGTTATGTG
*
790756 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
790771 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
790787 AATT
1 AATT
790791 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:792815 original size:6 final size:6
Alignment explanation
Indices: 792806--792837 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
792796 GATGGGGACT
*
792806 TCCCTA TCCCCA TCCCCA TCCCCA TCCCCA TC
1 TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TC
792838 GCCTTTCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.62, G:0.00, T:0.22
Consensus pattern (6 bp):
TCCCCA
Found at i:795163 original size:60 final size:60
Alignment explanation
Indices: 795056--795173 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
795046 AATTAATTTT
* * * *
795056 AATGTGAATTTGCTATTATGTAGTATGTATTATGTTTAGTCTATTAATTTCTTAAATCAG
1 AATGTGAATTTACTATTATGTAGCATGTATCATGTTTAGTCTATTAATTTATTAAATCAG
* * *
795116 AATGTGAATTTACTATTATGTAGCATGTATCATTTTTTATTC-CTTAATTTATTAAATC
1 AATGTGAATTTACTATTATGTAGCATGTATCA-TGTTTAGTCTATTAATTTATTAAATC
795174 GGATTGAGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 43 0.86
61 7 0.14
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (60 bp):
AATGTGAATTTACTATTATGTAGCATGTATCATGTTTAGTCTATTAATTTATTAAATCAG
Found at i:795594 original size:3 final size:3
Alignment explanation
Indices: 795588--795632 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
795578 TATTATGGTT
795588 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
795633 CATATAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:801288 original size:18 final size:21
Alignment explanation
Indices: 801265--801305 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
801255 CTTGTGAGGA
801265 TGATGAAG-AAC-T-TCTTAG
1 TGATGAAGTAACATATCTTAG
801283 TGATGAAGTAACATATCTTAG
1 TGATGAAGTAACATATCTTAG
801304 TG
1 TG
801306 TCATTTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 1 0.05
21 8 0.40
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (21 bp):
TGATGAAGTAACATATCTTAG
Found at i:804701 original size:2 final size:2
Alignment explanation
Indices: 804694--804718 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
804684 AAAAATGCCA
804694 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
804719 AAATTAGGAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:805080 original size:16 final size:16
Alignment explanation
Indices: 805060--805095 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
805050 CTTCATTCGA
*
805060 GTTTTTTC-TCATAAG
1 GTTTTTTCTTAATAAG
805075 GTTTTTTCTTAATAAG
1 GTTTTTTCTTAATAAG
805091 GTTTT
1 GTTTT
805096 AATGAGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.58
Consensus pattern (16 bp):
GTTTTTTCTTAATAAG
Found at i:806290 original size:542 final size:539
Alignment explanation
Indices: 805416--806897 Score: 1610
Period size: 543 Copynumber: 2.7 Consensus size: 539
805406 AAGATCTTCT
* * ** * * *
805416 TACTCTATTAATAC-TTTTTTCTTCTAGTTGGTT-TTTCAAGTTATTTTTCACAATAGATATCAA
1 TACTTTATTAATACTTTTTTTCTTATAGTT-GTTCTTTCAAGTTAGATTTCATAACAAATATCAA
* *
805479 TTAATAAAAAATTATTAATTATTTTTTAAATAAATTGTTAATATATTGTAGAAAATAATGTACTC
65 TTAATAAAAAATTATTAATTATTTTTTAAATAAATTGTTAATATCTTGTATAAAATAATGT-CTC
* * ** * * *
805544 TTG-AAAGAATTATGTACTCATTTTCCTTCACTCAATTTTTTTCTTCTGAGGTTTTTTCCTAGTA
129 TTGAAAAGAATTATATACT-ATTTTCTTTCACTCAGGTTTTTTCTTATGAGATTTTTTCCTAATA
** * *
805608 TTGTTTTAACAAAGCATATTCTTAATGCAATAGACATTTAATATGAAGTATTATGAATATATGAG
193 AGGTTTTAAC-AAGCATATTCTTAATGCAATAGACATTTAAAATGAAGTGTTATGAATATATGAG
* * * * * * * * *
805673 TAAATTTTCATTATGTCATGGTCCAATATTTTAGACTAGGCTTGGCAGCCTAAATAAGCCAAACA
257 TGAATTTCCATTATGTCACGGACCCAGATTTTAAACTAGGCTAGGCAGCCTAAATAGGCCAAACA
* * * * *
805738 ACTTAACAGGCCAAATACAAAAGTGTAATCTAATTTAAATTCTTATATTTCATTATGTATATCTA
322 AC-TAACAGGCCAAACACAAGAGTGTAATATGATTTAAATTCTTATATTTGATTATGTATATCTA
* * *
805803 GATTTAGATTATATTGGATT-A-A-GATTTAATACATCCAAAGCAAAT-ATCTTAGCATTATTTT
386 GATTTAGATTATATTGGATTAAGATGATTTAATACATCCAAAGCAAATCCT-TTAACATTATCTT
*
805864 TATCTTATAAATTCTATCTAGATAAGGGTTTATTAG-TCTATAAATAAAT-TCCTCACTTCATTT
450 TATCTTATAAATTCTATCTAGATAAGGGTTTATTAGCT-TATAAATAAGTCT-CTCACTTCATTT
*
805927 ATAAATATACACTCTCGAA-AAATATTTTC
513 ATAAATACACACTCTCGAATAAA-A--TTC
*
805956 TAACTTTATTAATACTTTTTTTCTTATAGTTGTTCTTTCAATTTAGATTTCATAACAAATATCAA
1 T-ACTTTATTAATACTTTTTTTCTTATAGTTGTTCTTTCAAGTTAGATTTCATAACAAATATCAA
* ***
806021 TTAATAAAAAAATTATTAATTAGTTTTTAAATAAACACTTAATATCTTGTATAAAATAATGTGCT
65 TTAAT-AAAAAATTATTAATTATTTTTTAAATAAATTGTTAATATCTTGTATAAAATAATGT-CT
* *
806086 AC-TGAAAAGAATTATATACTATTTTCTTTCACTCGGGTTTTTTCTTATGAGATTTTTTTCTAAT
128 -CTTGAAAAGAATTATATACTATTTTCTTTCACTCAGGTTTTTTCTTATGAGATTTTTTCCTAAT
** * * *
806150 AAGGTTTTAACAAGGTTTATTCTTAATACAATAGATA-TTAAAATGGAGTGTTATGAATATATGA
192 AAGGTTTTAACAA-GCATATTCTTAATGCAATAGACATTTAAAATGAAGTGTTATGAATATATGA
* * * *
806214 ATGAATTTCCATTATGTCACGGGCCCAGATTTTAAACTAGGCTAAGCTA-CCTAAATTGGCCAAA
256 GTGAATTTCCATTATGTCACGGACCCAGATTTTAAACTAGGCTAGGC-AGCCTAAATAGGCCAAA
* * * * *
806278 CAGTCTAACAGGCTAGACACAAGAGTGTAGTTTGATTTAAATTCTTATATTTGATTATGTATATC
320 CA-ACTAACAGGCCAAACACAAGAGTGTAATATGATTTAAATTCTTATATTTGATTATGTATATC
* * * **
806343 TAAATATAGATGTAGATTATATTGGATTAAGGTTATGATTTAATGCATTCAAATTAAATCCTTTA
384 ------TAGATTTAGATTATATTGGATTAA-G--ATGATTTAATACATCCAAAGCAAATCCTTTA
* * *
806408 ATATTATCTTTATCTTATAAATTCTATCTATATAAGGGTTTATTAGCTTATAAATAGGTCTCTCA
440 ACATTATCTTTATCTTATAAATTCTATCTAGATAAGGGTTTATTAGCTTATAAATAAGTCTCTCA
* * *
806473 TTTTATTTGTAAATACACACTCTCGAATAAAA---
505 CTTCATTTATAAATACACACTCTCGAATAAAATTC
*
806505 T-C-TT-TT--TACTTGTTTTTCTTATAATTGTTCTTTCAAGTTAGATTTCATAACAAATATCAA
1 TACTTTATTAATACTT-TTTTTCTTATAGTTGTTCTTTCAAGTTAGATTTCATAACAAATATCAA
* * *
806565 CTAATAAAAAATTATTAATTATTTTTTAAATAAATTGTTATTATCTTGTATAAAATAATGTATTC
65 TTAATAAAAAATTATTAATTATTTTTTAAATAAATTGTTAATATCTTGTATAAAATAATGT-CTC
* * * ** *
806630 TTGAAAAGAATTATATACTCTTTTCCTTTCATTCAGGTTTTTTCTTATTA-A-GGTTTCCTACTA
129 TTGAAAAGAATTATATACTATTTT-CTTTCACTCAGGTTTTTTCTTATGAGATTTTTTCCTAATA
** * *
806693 AGGTTTTAACATAGCATATTCTTAATGCAATAGACATTTAAGGTTAAGTGTTATGAATATACGAG
193 AGGTTTTAACA-AGCATATTCTTAATGCAATAGACATTTAAAATGAAGTGTTATGAATATATGAG
* * * * * *
806758 TGAATTTCCATTATATCAC-GACCCAAGGTTATATA-TCAAGTTAGGCAGCCTAAATAGGCCAAA
257 TGAATTTCCATTATGTCACGGACCC-AGATTTTAAACT-AGGCTAGGCAGCCTAAATAGGCCAAA
* * * * *
806821 CAACCTAATAGGCCTAACATAAGAGTGTAATATGAGTTAAATTCTTATATTTGATTTTGTATATC
320 CAA-CTAACAGGCCAAACACAAGAGTGTAATATGATTTAAATTCTTATATTTGATTATGTATATC
*
806886 TGGATTTAGATT
384 TAGATTTAGATT
806898 TAGATTTAGA
Statistics
Matches: 789, Mismatches: 119, Indels: 71
0.81 0.12 0.07
Matches are distributed among these distances:
537 10 0.01
540 1 0.00
541 15 0.02
542 218 0.28
543 322 0.41
544 87 0.11
545 2 0.00
546 2 0.00
547 1 0.00
548 21 0.03
549 2 0.00
553 1 0.00
554 101 0.13
555 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (539 bp):
TACTTTATTAATACTTTTTTTCTTATAGTTGTTCTTTCAAGTTAGATTTCATAACAAATATCAAT
TAATAAAAAATTATTAATTATTTTTTAAATAAATTGTTAATATCTTGTATAAAATAATGTCTCTT
GAAAAGAATTATATACTATTTTCTTTCACTCAGGTTTTTTCTTATGAGATTTTTTCCTAATAAGG
TTTTAACAAGCATATTCTTAATGCAATAGACATTTAAAATGAAGTGTTATGAATATATGAGTGAA
TTTCCATTATGTCACGGACCCAGATTTTAAACTAGGCTAGGCAGCCTAAATAGGCCAAACAACTA
ACAGGCCAAACACAAGAGTGTAATATGATTTAAATTCTTATATTTGATTATGTATATCTAGATTT
AGATTATATTGGATTAAGATGATTTAATACATCCAAAGCAAATCCTTTAACATTATCTTTATCTT
ATAAATTCTATCTAGATAAGGGTTTATTAGCTTATAAATAAGTCTCTCACTTCATTTATAAATAC
ACACTCTCGAATAAAATTC
Found at i:808816 original size:545 final size:544
Alignment explanation
Indices: 807236--809545 Score: 2509
Period size: 545 Copynumber: 4.3 Consensus size: 544
807226 TTGTAGATAT
* * * * *
807236 ACACTCTCGAATAAGATCTTTTTATTCTATTAATACGTTTTTCATATAATTGTTCTTTTAAGTTA
1 ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
* **
807301 TATTGT-AGAACAAATATCAATTAATAAAAGGTTATTAATT-TTTTTAAATAAATTGTTAATATC
66 TATT-TCATAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTGTTAATATC
* * * * * * * * *
807364 TTGTATCAAATAATGTATTCTTGAAAAGAATTGTGTATTATTTTCCCTTCAATTAGG-TT-TTGT
130 TTGTATAAAATAATGTACTCTTAAAAAAAATTATGTACTCTTTTTCCTTC-ATTTGGATTGTT-T
* * * *
807427 TTTAGGAGGTTTTTTTCTTAGTAAGCTTTTAATGAGGCATATTCTTAATATAATGGACATTTAAG
193 CTTATGAGGTTTTTTTC-TAGTAAGGTTTTAATGAGACATATTCTTAATATAATGGACATTTAAG
* * * * *
807492 GTGGACTGTTATGAATATATGAGTGAGTTTTCATTATGTCATGGCCCAAGATTTTAGATCAGGCT
257 GTAGAGTGTTATGAATAAATAAGTGAATTTTCATTATGTCAT-GCCCAAGATTTTAGATCAGGCT
* * * *
807557 AGGCAGCCTAAATAGGCGAAATAGCCTAACAGGCTTGACACAAAAGTGTAATCTGAGTTAAATTC
321 AGGCAGCCTAAATAGGCCAAATAGCCTAACAAGCCTGACACAAGAGTGTAATCTGAGTTAAATTC
*
807622 TTATATTTGATTA--TATATCTAGATTTAGATGTAGATTAGATTGGATTAAGATTAAGATTCAAT
386 TTATATTTGATTATGTATATCTAGATTTAGATGTAGATTAGATT-G--TAAGATTAAGATTTAAT
* * *
807685 GCATCCAAATCAACCCCTTAGCATTATCTTTATCTTATAAATTCTATCTAGATAAGAGTTTATTA
448 GCATCCAAATCAA-CCC--A-TATTAGCATTATCTTATAAATTCTATCTAGATAAGAGTTTATTA
* * * *
807750 G-CTTATAAATA-AGCTTTTAACTTTATTTGTAAATAC
509 GTC-TATAAATAGATC-TCTAACTTCATTTGTAAATGC
* * * *
807786 ACACTCTCGAATAAGATTTTTTTACTCTATTAATA-TTTTTTATTATATTTGTTCTTTCAAGTTA
1 ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
**
807850 TATTTCATAACAAATATCAATTAATAAAAGGTTATTAATTATTTTTTAAATAAATTGTTAATATC
66 TATTTCATAACAAATATCAATTAATAAAAAATTATTAATTA-TTTTTAAATAAATTGTTAATATC
* * * * * * * *
807915 TTGTGTAAAATAATGTACTTTTAAAAAGAATTATGTACTTTTTTTCCTTGA-ATCGATTTTTTTC
130 TTGTATAAAATAATGTACTCTTAAAAAAAATTATGTACTCTTTTTCCTTCATTTGGA-TTGTTTC
* * *
807979 TTATGAGGTTTTTTTCCTAGTAAGATTTTAATGAGATATATTTTTAATATAATGGACATTTAAGG
194 TTATGAGGTTTTTTT-CTAGTAAGGTTTTAATGAGACATATTCTTAATATAATGGACATTTAAGG
* * * * * *
808044 TACAGTGTTATGAATATATGAGTGAATTTCCATTATGTCAATGCCTAAGATTTTAGATCCGGCTA
258 TAGAGTGTTATGAATAAATAAGTGAATTTTCATTATGTC-ATGCCCAAGATTTTAGATCAGGCTA
* * * * * *
808109 GGTAGCTTAAATAAGCCAAACAGGCTAACAAGCCTGCCACAAGAGTGTAATCTGAGTTAAATTCT
322 GGCAGCCTAAATAGGCCAAATAGCCTAACAAGCCTGACACAAGAGTGTAATCTGAGTTAAATTCT
* * * *
808174 TATATTTGATTATGTATATCGAGATTTAGATGCAGATTATATTG---GATTAAGATTTAATGTAT
387 TATATTTGATTATGTATATCTAGATTTAGATGTAGATTAGATTGTAAGATTAAGATTTAATGCAT
* * *
808236 CCAAATCAACCCCTTAGTATTATCTTTATCTTATAAATTTTAT-TAAGATAAGAGTTTATTAGTC
452 CCAAATCAA-CCC--A-TATTAGCATTATCTTATAAATTCTATCT-AGATAAGAGTTTATTAGTC
* * *
808300 TATAAATAGATCCCTCACTTCATTTATAAATGC
512 TATAAATAGATCTCTAACTTCATTTGTAAATGC
* * * *
808333 ATACTCTCGAATAAAATCTTCTTACTCTATTAATACTTTTTTCTTATATTTGTTCTTTAAAGTTA
1 ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
* *
808398 TATTTCATAACAAATATCAATTAATAAAAAAATATTAATTATTTTTAAATAAATTGTTAATACCT
66 TATTTCATAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTGTTAATATCT
* *
808463 TGTATAAAATAATGTACTCTTAAAAAAAATT-TATACTCTTTTTCCTTCATTTGGATTGTTTCTG
131 TGTATAAAATAATGTACTCTTAAAAAAAATTATGTACTCTTTTTCCTTCATTTGGATTGTTTCTT
* * * * * * *
808527 ATGAAGTTTTTTTCTAGTAAGGTTTTAATAAGACATACTCTTAATACAGTGAACATTAAAGGTAG
196 ATGAGGTTTTTTTCTAGTAAGGTTTTAATGAGACATATTCTTAATATAATGGACATTTAAGGTAG
* * * *
808592 AGTGTAATGAATAAATAAGTGAATTTTCATTATATCACGACCCAAGATTTTAGA-CTAGGCTAGC
261 AGTGTTATGAATAAATAAGTGAATTTTCATTATGTCATG-CCCAAGATTTTAGATC-AGGCTAGG
* * * * *
808656 CATCCTAAATAGGCCAAATAGCCTAACAAACCAGACACGAGAGTGTAATTTGAGTTAAATTCTTA
324 CAGCCTAAATAGGCCAAATAGCCTAACAAGCCTGACACAAGAGTGTAATCTGAGTTAAATTCTTA
**
808721 TATTTGATTATACATATCTAGATTTAGATGTAGATTAGATTGGATCAAGATTAAGATTTAATGCA
389 TATTTGATTATGTATATCTAGATTTAGATGTAGATTAGATT-G-T-AAGATTAAGATTTAATGCA
* *
808786 TCCAAATCAA-CCAT-TTAGCATTATCTTATAAATTCTATCTAGATAAG-GATTTAGTAGCCTAT
451 TCCAAATCAACCCATATTAGCATTATCTTATAAATTCTATCTAGATAAGAG-TTTATTAGTCTAT
*
808848 AAATAGATCTCTCACTTCATTTGTAAATGC
515 AAATAGATCTCTAACTTCATTTGTAAATGC
* * *
808878 ACACTCTCAAATAAGATTTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTCAAGTTA
1 ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
* * * *
808943 TATTTCATAA-AAAAATCAATTAATACAAAATTACTAATTATTTTTTAATAAATTGTTAATATCT
66 TATTTCATAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTGTTAATATCT
* ** ** * * *
809007 TGTATAAAATAATATACTCTCGAAAAAAATTATGTACTCTTTTTTTTTCACTCGTG-TTTTTTCT
131 TGTATAAAATAATGTACTCTTAAAAAAAATTATGTACTCTTTTTCCTTCATTTG-GATTGTTTCT
* * * * * *
809071 TATGAGGTTTTTTTTCTAGTAAGGTTTCAACGAGGCATATTTTTAATAAAATGGACATTTAAGAT
195 TATGAGG-TTTTTTTCTAGTAAGGTTTTAATGAGACATATTCTTAATATAATGGACATTTAAGGT
* * *
809136 -GAAGTGTTTTGAATATAACAA-TGAA-TTTCTATTATGTCATGCCTCAAGATTTTAGATTAGGC
259 AG-AGTGTTATGAATA-AATAAGTGAATTTTC-ATTATGTCATGCC-CAAGATTTTAGATCAGGC
* * * *
809198 TAGTCAACCT-AAT--G-------G--------GCCTGACACAAGAGTGTAATCTAATTTAAATT
320 TAGGCAGCCTAAATAGGCCAAATAGCCTAACAAGCCTGACACAAGAGTGTAATCTGAGTTAAATT
* * * *
809245 CTTGTATTTGATTATGTACATCTAGATTTAGATATAGATTAGA-T-TAAGATTAAAATTTAAT-C
385 CTTATATTTGATTATGTATATCTAGATTTAGATGTAGATTAGATTGTAAGATTAAGATTTAATGC
* * * * * *
809307 TATCCAAATCAAATCCCATAGCGCTATCTTTATCTTATGAATTCTAT-TTGAATAAGGGTTTATT
450 -ATCCAAATC-AA-CCCATA---TTAGCATTATCTTATAAATTCTATCTAG-ATAAGAGTTTATT
* * * **
809371 AGTCTA-AAATAGGTCTTTAATTTCATTTGTAAATAT
508 AGTCTATAAATAGATCTCTAACTTCATTTGTAAATGC
* * * * *
809407 ACATTTTTGAATAAGATCTTCTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAATTA
1 ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
* *
809472 TATTTCAAAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTATTAATATCT
66 TATTTCATAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTGTTAATATCT
809537 TGTATAAAA
131 TGTATAAAA
809546 AATTTTAAAT
Statistics
Matches: 1512, Mismatches: 204, Indels: 108
0.83 0.11 0.06
Matches are distributed among these distances:
522 1 0.00
523 24 0.02
524 3 0.00
526 4 0.00
527 1 0.00
528 64 0.04
529 92 0.06
530 93 0.06
531 1 0.00
536 1 0.00
543 1 0.00
544 80 0.05
545 356 0.24
546 133 0.09
547 187 0.12
548 69 0.05
549 64 0.04
550 34 0.02
551 272 0.18
552 6 0.00
553 26 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (544 bp):
ACACTCTCGAATAAGATCTTTTTACTCTATTAATACTTTTTTCTTATAGTTGTTCTTTAAAGTTA
TATTTCATAACAAATATCAATTAATAAAAAATTATTAATTATTTTTAAATAAATTGTTAATATCT
TGTATAAAATAATGTACTCTTAAAAAAAATTATGTACTCTTTTTCCTTCATTTGGATTGTTTCTT
ATGAGGTTTTTTTCTAGTAAGGTTTTAATGAGACATATTCTTAATATAATGGACATTTAAGGTAG
AGTGTTATGAATAAATAAGTGAATTTTCATTATGTCATGCCCAAGATTTTAGATCAGGCTAGGCA
GCCTAAATAGGCCAAATAGCCTAACAAGCCTGACACAAGAGTGTAATCTGAGTTAAATTCTTATA
TTTGATTATGTATATCTAGATTTAGATGTAGATTAGATTGTAAGATTAAGATTTAATGCATCCAA
ATCAACCCATATTAGCATTATCTTATAAATTCTATCTAGATAAGAGTTTATTAGTCTATAAATAG
ATCTCTAACTTCATTTGTAAATGC
Found at i:809553 original size:22 final size:22
Alignment explanation
Indices: 809495--809553 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
809485 ATATCAATTA
809495 ATAAAAAATTATTAATTATTTT
1 ATAAAAAATTATTAATTATTTT
809517 -TAAATAAATTATTAA-TATCTTGT
1 ATAAA-AAATTATTAATTAT-TT-T
809540 ATAAAAAATT-TTAA
1 ATAAAAAATTATTAA
809554 ATTAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 7 0.21
22 16 0.48
23 6 0.18
24 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAAAAAATTATTAATTATTTT
Found at i:811634 original size:27 final size:28
Alignment explanation
Indices: 811582--811633 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
811572 CGAATTTTAT
*
811582 TTTTTAAAGATTTTGAAATGAGAAAATA
1 TTTTTAAAGATTTTGAAATCAGAAAATA
*
811610 TTTTTAAA-ATTTT-ATATCAGAAAA
1 TTTTTAAAGATTTTGAAATCAGAAAA
811634 AATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 5 0.23
28 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (28 bp):
TTTTTAAAGATTTTGAAATCAGAAAATA
Found at i:820481 original size:29 final size:29
Alignment explanation
Indices: 820407--820485 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
820397 ATGAGCTAAT
* *
820407 AAAGAAAAA-CTGTACGTGAACAGGTACA
1 AAAGAAAAAGTTGTACATGAACAGGTACA
* * *
820435 AGAG-AGAAGTTGTACATGAATAGGTACA
1 AAAGAAAAAGTTGTACATGAACAGGTACA
820463 AAAGAAAAAGTTGTACATGAACA
1 AAAGAAAAAGTTGTACATGAACA
820486 AGTATAGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 3 0.07
28 22 0.54
29 16 0.39
ACGTcount: A:0.49, C:0.10, G:0.23, T:0.18
Consensus pattern (29 bp):
AAAGAAAAAGTTGTACATGAACAGGTACA
Found at i:821817 original size:17 final size:17
Alignment explanation
Indices: 821795--821828 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
821785 AAATCCAATT
*
821795 TGAAATTTAATTAATAA
1 TGAAATTTAAGTAATAA
821812 TGAAATTTAAGTAATAA
1 TGAAATTTAAGTAATAA
821829 AGCTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
TGAAATTTAAGTAATAA
Found at i:822500 original size:22 final size:22
Alignment explanation
Indices: 822447--822500 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
822437 TCAACCACAA
* *
822447 TCTTCCTTTTTTTATCCTTCTT
1 TCTTCCTTTGTTTATCATTCTT
* *
822469 TCTTCTTTTGTTTATGATT-TT
1 TCTTCCTTTGTTTATCATTCTT
822490 TCTTTCCTTTG
1 TC-TTCCTTTG
822501 AAAGCTGCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (22 bp):
TCTTCCTTTGTTTATCATTCTT
Found at i:822552 original size:20 final size:20
Alignment explanation
Indices: 822527--822566 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
822517 CCCCTTTTTA
822527 GCCTAAAAAAGCCATTTCAT
1 GCCTAAAAAAGCCATTTCAT
*
822547 GCCTAAAAAAGCCCTTTCAT
1 GCCTAAAAAAGCCATTTCAT
822567 AAACACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.25
Consensus pattern (20 bp):
GCCTAAAAAAGCCATTTCAT
Found at i:826313 original size:35 final size:34
Alignment explanation
Indices: 826264--826329 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
826254 CTGATCCTGC
*
826264 AAAAAGCATATTGTAAAGGTTACGCCTGATCTTA
1 AAAAAGCATATTGTAAAGGTTAAGCCTGATCTTA
* *
826298 AAAAAGGCATGTTGTAAAGGTTAAGCTTGATC
1 AAAAA-GCATATTGTAAAGGTTAAGCCTGATC
826330 CTATTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (34 bp):
AAAAAGCATATTGTAAAGGTTAAGCCTGATCTTA
Found at i:830490 original size:13 final size:13
Alignment explanation
Indices: 830472--830516 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
830462 AGATGGTGAC
*
830472 ATGATATGTTAAT
1 ATGATATGATAAT
830485 ATGATATGATAAT
1 ATGATATGATAAT
*
830498 GTGATTATGATAAT
1 ATGA-TATGATAAT
830512 ATGAT
1 ATGAT
830517 TATGCGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
ATGATATGATAAT
Found at i:830508 original size:14 final size:14
Alignment explanation
Indices: 830472--830520 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
830462 AGATGGTGAC
*
830472 ATGA-TATGTTAAT
1 ATGATTATGATAAT
830485 ATGA-TATGATAAT
1 ATGATTATGATAAT
*
830498 GTGATTATGATAAT
1 ATGATTATGATAAT
830512 ATGATTATG
1 ATGATTATG
830521 CGGTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 15 0.47
14 17 0.53
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (14 bp):
ATGATTATGATAAT
Found at i:833603 original size:19 final size:19
Alignment explanation
Indices: 833579--833619 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
833569 TTTTGAAATT
833579 TTTTAATATTAATTAGATA
1 TTTTAATATTAATTAGATA
* * *
833598 TTTTAATTTTTATTTGATA
1 TTTTAATATTAATTAGATA
833617 TTT
1 TTT
833620 CAATGTTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTAATATTAATTAGATA
Found at i:834833 original size:247 final size:249
Alignment explanation
Indices: 834374--834868 Score: 619
Period size: 247 Copynumber: 2.0 Consensus size: 249
834364 TTTTTGTCAG
834374 CCGTAAAACACTTTAAACTCAAGAATAAAAAGTTAAATATTCAATTTTCAGAAAATTATATTTGC
1 CCGTAAAACACTTTAAACTCAAGAATAAAAAGTTAAATATTCAATTTTCAGAAAATTATATTTGC
* * ** *
834439 TTGACATAATTGACTTGTTACATTAAATCTCACACATTTACATCAATATTTTGATAATATTTGTT
66 TTGACATAATTAACTTGTTACAGTAAATCTCACACATGCACATCAATATTTTGATAATACTTGTT
* * *
834504 CCACCTTTATAATGTTTTATGTTAATTCTTACTACTGTACGTCAAGGCTTTTTAACTACTAATTT
131 -CACATTTATAATGTTTTA-GTTAATTCTTACCACTGTACGTCAAGGCTTTTCAACTACTAATTT
** *
834569 TCATTATAATTCTTTTTATCTTTACTATTATTCATGTATAGATTAAAATTTGTAAA
194 TCACCATAATTCTTTTTATCCTTACTATTATTCATGTATAGATTAAAATTTGTAAA
* * * *
834625 CCGTAAAACACTTTAAACTTGAA-AAT-AACAGTTTAAATATTTAATTTTGTC-GAAAATTATGT
1 CCGTAAAACACTTTAAAC-TCAAGAATAAAAAG-TTAAATATTCAA-TTT-TCAGAAAATTATAT
* * * *
834687 TTGTTTGATATAATTAACTTTTTA-AGGTAAATCTCACACATGCACATCAATATTTTGATAATGC
62 TTGCTTGACATAATTAACTTGTTACA-GTAAATCTCACACATGCACATCAATATTTTGATAATAC
* ** * * *
834751 TTGTT-ACATTT-TTAT-TTTTCA-TTAATTCTTACCGTTTTACGTTAAGGCTTTTCAACTATTA
126 TTGTTCACATTTATAATGTTTT-AGTTAATTCTTACCACTGTACGTCAAGGCTTTTCAACTACTA
* *
834812 ATTTTCACCATAATTCTTTTTATCCTTACTATTGTTTATGTATAGATTAAAATTTGT
190 ATTTTCACCATAATTCTTTTTATCCTTACTATTATTCATGTATAGATTAAAATTTGT
834869 CAGTTGTAAA
Statistics
Matches: 211, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
247 85 0.40
248 4 0.02
249 4 0.02
250 9 0.04
251 33 0.16
252 74 0.35
253 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (249 bp):
CCGTAAAACACTTTAAACTCAAGAATAAAAAGTTAAATATTCAATTTTCAGAAAATTATATTTGC
TTGACATAATTAACTTGTTACAGTAAATCTCACACATGCACATCAATATTTTGATAATACTTGTT
CACATTTATAATGTTTTAGTTAATTCTTACCACTGTACGTCAAGGCTTTTCAACTACTAATTTTC
ACCATAATTCTTTTTATCCTTACTATTATTCATGTATAGATTAAAATTTGTAAA
Found at i:839635 original size:21 final size:21
Alignment explanation
Indices: 839584--839638 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
839574 TGCTTAAAGT
* * *
839584 TCGACTATGGCTCTTATAGGG
1 TCGACTATGTCTTTTATAGAG
*
839605 TCAACTATGTCTTTTATAGAG
1 TCGACTATGTCTTTTATAGAG
839626 TCGACTATGTCTT
1 TCGACTATGTCTT
839639 CTCTATTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGACTATGTCTTTTATAGAG
Found at i:847086 original size:77 final size:77
Alignment explanation
Indices: 846995--847158 Score: 204
Period size: 77 Copynumber: 2.1 Consensus size: 77
846985 GAATTTCTCC
* *
846995 AATTAAAATGCTATCTTTAATTTTAAGAATTTCTTTTAAAATAAAAAATAATTTCCTATTCTTT-
1 AATTAAAATGCTATCCTTAATTTTAAGAATTTCTTTTAAAATAAAAAACAATTTCCTATT-TTTG
**
847059 ATGAATCACCCAA
65 ATGAATCAAACAA
* * * * *** *
847072 AATTAAAATTCTATCCTTACTTTTAGGAATTTCTTTTAAAGTTGGAAACAATTTTCTATTTTTGA
1 AATTAAAATGCTATCCTTAATTTTAAGAATTTCTTTTAAAATAAAAAACAATTTCCTATTTTTGA
847137 TGAATCAAACAA
66 TGAATCAAACAA
847149 AATTAAAATG
1 AATTAAAATG
847159 GATGGCATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
76 3 0.04
77 70 0.96
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (77 bp):
AATTAAAATGCTATCCTTAATTTTAAGAATTTCTTTTAAAATAAAAAACAATTTCCTATTTTTGA
TGAATCAAACAA
Found at i:863129 original size:21 final size:21
Alignment explanation
Indices: 863095--863170 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
863085 AATGTTACCG
863095 ATTTGTATTT-TAAATATTAAT
1 ATTT-TATTTATAAATATTAAT
863116 ATTTTATTTATAAAT-TTAATT
1 ATTTTATTTATAAATATTAA-T
* * *
863137 ATTAGTATTTA-AAATACTATT
1 ATT-TTATTTATAAATATTAAT
*
863158 ATTTTATTCATAA
1 ATTTTATTTATAA
863171 TTTAAGCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 14 0.31
21 23 0.51
22 8 0.18
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTTATTTATAAATATTAAT
Found at i:863203 original size:44 final size:42
Alignment explanation
Indices: 863099--863212 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
863089 TTACCGATTT
* * * **
863099 GTATTTTAAATATTAATATTTTATTTATAAATTTAATTATTA
1 GTATTTAAAATATTATTATTTTATTCATAAATTTAAGCATTA
*
863141 GTATTTAAAATACTATTATTTTATTCAT-AATTTAAGCATTA
1 GTATTTAAAATATTATTATTTTATTCATAAATTTAAGCATTA
* *
863182 TTATGATTAAAATATTCATTATTTTAATCAT
1 GTAT--TTAAAATATT-ATTATTTTATTCAT
863213 TTTTAAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 14 0.23
42 24 0.40
43 9 0.15
44 13 0.22
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (42 bp):
GTATTTAAAATATTATTATTTTATTCATAAATTTAAGCATTA
Found at i:863958 original size:66 final size:66
Alignment explanation
Indices: 863852--863984 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
863842 GAATGGCTAT
863852 TCATTAAAATCTTGTAAAATGTTGGATTATATATTACCCTCCCCTTTTGGTATGTTTGGTTCATA
1 TCATTAAAATCTTGTAAAATGTTGGATTATATATTACCCTCCCCTTTTGGTATGTTTGGTTCATA
863917 A
66 A
863918 TCATTAAAATCTTGTAAAATGTTGGATTATATATTACCCTCCCCTTTTGGTATGTTTGGTTCATA
1 TCATTAAAATCTTGTAAAATGTTGGATTATATATTACCCTCCCCTTTTGGTATGTTTGGTTCATA
863983 A
66 A
863984 T
1 T
863985 AAGGAATAGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (66 bp):
TCATTAAAATCTTGTAAAATGTTGGATTATATATTACCCTCCCCTTTTGGTATGTTTGGTTCATA
A
Found at i:864938 original size:30 final size:28
Alignment explanation
Indices: 864873--864938 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
864863 TTACAACGGC
* *
864873 TTTTTCACATGTTCACCACAAACCCATG
1 TTTTTAACAGGTTCACCACAAACCCATG
* *
864901 ATTTTAACAGGTTCACCACAAAACTCATGG
1 TTTTTAACAGGTTCACCAC-AAACCCAT-G
864931 TTTTTAAC
1 TTTTTAAC
864939 TAATTCACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.52
29 7 0.23
30 8 0.26
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (28 bp):
TTTTTAACAGGTTCACCACAAACCCATG
Found at i:865061 original size:22 final size:21
Alignment explanation
Indices: 865036--865103 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
865026 TACAAAATAA
865036 CTTTTCAAAGCTAAGTTAAAAC
1 CTTTTCAAAGCTAAG-TAAAAC
* *
865058 CTTTAC-AAG-AATAGTAATAA-
1 CTTTTCAAAGCTA-AGTAA-AAC
*
865078 CTTTTCAAAGCTAAGCTAGAAC
1 CTTTTCAAAGCTAAG-TAAAAC
865100 CTTT
1 CTTT
865104 ACAAGAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
20 9 0.26
21 14 0.40
22 12 0.34
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (21 bp):
CTTTTCAAAGCTAAGTAAAAC
Found at i:865090 original size:42 final size:42
Alignment explanation
Indices: 865031--865112 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
865021 ACCTTTACAA
*
865031 AATAACTTTTCAAAGCTAAGTTAAAACCTTTACAAGAATAGT
1 AATAACTTTTCAAAGCTAAGCTAAAACCTTTACAAGAATAGT
*
865073 AATAACTTTTCAAAGCTAAGCTAGAACCTTTACAAGAATA
1 AATAACTTTTCAAAGCTAAGCTAAAACCTTTACAAGAATA
865113 ACAAGAGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (42 bp):
AATAACTTTTCAAAGCTAAGCTAAAACCTTTACAAGAATAGT
Found at i:866326 original size:22 final size:23
Alignment explanation
Indices: 866284--866326 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
866274 TAAAAGCTAA
*
866284 ATCATTTCAAAAATTTATCAAAT
1 ATCATTTCAAAAATGTATCAAAT
866307 ATCA-TTCAAATAATGT-TCAA
1 ATCATTTCAAA-AATGTATCAA
866327 GCAAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (23 bp):
ATCATTTCAAAAATGTATCAAAT
Found at i:866474 original size:14 final size:14
Alignment explanation
Indices: 866455--866507 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
866445 ACAAAAAAAA
866455 TTAATAATATTTGT
1 TTAATAATATTTGT
*
866469 TTAATAATACTTGCT
1 TTAATAATATTTG-T
** *
866484 TTAATTTTGTTTTGT
1 TTAATAAT-ATTTGT
866499 TTAATAATA
1 TTAATAATA
866508 CCTTTGATAC
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 12 0.41
15 14 0.48
16 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (14 bp):
TTAATAATATTTGT
Found at i:866488 original size:15 final size:14
Alignment explanation
Indices: 866455--866488 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
866445 ACAAAAAAAA
*
866455 TTAATAATATTTGT
1 TTAATAATACTTGT
866469 TTAATAATACTTGCT
1 TTAATAATACTTG-T
866484 TTAAT
1 TTAAT
866489 TTTGTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (14 bp):
TTAATAATACTTGT
Found at i:870394 original size:8 final size:8
Alignment explanation
Indices: 870381--870409 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
870371 TCTCTCTCAA
870381 ACTTTCTT
1 ACTTTCTT
870389 ACTTTCTT
1 ACTTTCTT
870397 ACTTTCTT
1 ACTTTCTT
870405 ACTTT
1 ACTTT
870410 GTTTTTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (8 bp):
ACTTTCTT
Found at i:872812 original size:4 final size:4
Alignment explanation
Indices: 872789--872844 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
872779 ATGAATTAAT
* * * * *
872789 ATTA ATTG ATTA ACTA ATTA ATTA ATTA TTTAA ATTA TTTA ATTA AATA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT-A ATTA ATTA ATTA ATTA
872838 ATTA ATT
1 ATTA ATT
872845 TATAAAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:872852 original size:29 final size:29
Alignment explanation
Indices: 872798--872881 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
872788 TATTAATTGA
* * *
872798 TTAACTAATTAATTAA-TTATTTAAATTAT
1 TTAATTAAATAATTAATTTATTAAAATT-T
872827 TTAATTAAATAATTAATTTA-TAAAATTT
1 TTAATTAAATAATTAATTTATTAAAATTT
*
872855 TAAATTAAATAATTTAA-TTATTTAAAA
1 TTAATTAAATAA-TTAATTTA-TTAAAA
872882 GTTAACTAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 15 0.32
29 24 0.51
30 8 0.17
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAATTAAATAATTAATTTATTAAAATTT
Found at i:872873 original size:13 final size:13
Alignment explanation
Indices: 872803--872874 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
872793 ATTGATTAAC
*
872803 TAATTAATTAA-T
1 TAATTAAATAATT
* *
872815 TATTTAAATTATT
1 TAATTAAATAATT
872828 TAATTAAATAA-T
1 TAATTAAATAATT
872840 TAATTTATAA-AATTT
1 TAA-TTA-AATAA-TT
872855 TAAATTAAATAATT
1 T-AATTAAATAATT
872869 TAATTA
1 TAATTA
872875 TTTAAAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
12 12 0.25
13 20 0.42
14 7 0.15
15 7 0.15
16 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTAAATAATT
Found at i:873234 original size:59 final size:59
Alignment explanation
Indices: 873171--873287 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
873161 GTCCTTGTTT
* * *
873171 GCCACAAGAAGATGCTTTCTGCTAAAAGAAGCCAAAAGTAGCCGAAAGTAACCTTGTCC
1 GCCACAAGAAGATGCTTTCTGCCAAAAGAAGACAAAAGTAGCCGAAAGCAACCTTGTCC
*
873230 GCCACAAGAAGATGCTTTCTGCCAAGAGAAGACAAAAGTAGCCGAAAGCAACCTTGTC
1 GCCACAAGAAGATGCTTTCTGCCAAAAGAAGACAAAAGTAGCCGAAAGCAACCTTGTC
873288 TGATCAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (59 bp):
GCCACAAGAAGATGCTTTCTGCCAAAAGAAGACAAAAGTAGCCGAAAGCAACCTTGTCC
Found at i:876981 original size:13 final size:13
Alignment explanation
Indices: 876963--876989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
876953 AATAAACCTT
876963 TTACTCTATTCCA
1 TTACTCTATTCCA
876976 TTACTCTATTCCA
1 TTACTCTATTCCA
876989 T
1 T
876990 CAGTCATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (13 bp):
TTACTCTATTCCA
Found at i:879428 original size:68 final size:70
Alignment explanation
Indices: 879344--879479 Score: 231
Period size: 68 Copynumber: 2.0 Consensus size: 70
879334 GATGGCATTA
* *
879344 GTATATTATAAAGGTGTAATGTCCAG-TTCTTTGTTCTCTATC-TTGGAATATGAAATCAGAAAT
1 GTATATTATAAAGGTGTAATATCCAGCTTCATTGTTCTCTATCATTGGAATATGAAATCAGAAAT
879407 TTAAT
66 TTAAT
879412 GTATATTATAAAGGTGTAATATCCAGCTTTCATTGTTCTCTATCATTGGAATATGAAATCAGAAA
1 GTATATTATAAAGGTGTAATATCCAGC-TTCATTGTTCTCTATCATTGGAATATGAAATCAGAAA
879477 TTT
65 TTT
879480 TCTGTTCTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 25 0.40
70 15 0.24
71 23 0.37
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (70 bp):
GTATATTATAAAGGTGTAATATCCAGCTTCATTGTTCTCTATCATTGGAATATGAAATCAGAAAT
TTAAT
Found at i:881571 original size:25 final size:25
Alignment explanation
Indices: 881538--881590 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
881528 ATGTTATTTA
* * *
881538 ATATTTAATATTATATAACATAT-TG
1 ATATATAATAATAAATAACA-ATGTG
881563 ATATATAATAATAAATAACAATGTG
1 ATATATAATAATAAATAACAATGTG
881588 ATA
1 ATA
881591 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (25 bp):
ATATATAATAATAAATAACAATGTG
Found at i:881813 original size:30 final size:28
Alignment explanation
Indices: 881772--881843 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 28
881762 AATAATTAAT
881772 TATAAAAATTTATTAAATTAAAAATAAAAA
1 TATAAAAATTTATTAAA-T-AAAATAAAAA
* *
881802 TATATAAATTTACTTAAATATAATAAAAA
1 TATAAAAATTTA-TTAAATAAAATAAAAA
881831 -ATAAAAATTTATT
1 TATAAAAATTTATT
881844 TAAAACTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 2 0.05
28 10 0.26
29 9 0.24
30 12 0.32
31 5 0.13
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAAAAATTTATTAAATAAAATAAAAA
Found at i:882223 original size:7 final size:7
Alignment explanation
Indices: 882208--882241 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
882198 TCAACTCAAT
882208 AATAAAA
1 AATAAAA
*
882215 AAGAAAA
1 AATAAAA
882222 AATAAAA
1 AATAAAA
882229 AATAAAA
1 AATAAAA
882236 AA-AAAA
1 AATAAAA
882242 TACAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (7 bp):
AATAAAA
Found at i:891936 original size:67 final size:67
Alignment explanation
Indices: 891857--891990 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
891847 GTCAAATATT
891857 AGGTAAAATGTTCATGGTGTGAAAGCAGTTTCCTTGCATTAGATATTGAAATAGTATTTTGTGAA
1 AGGTAAAATGTTCATGGTGTGAAAGCAGTTTCCTTGCATTAGATATTGAAATAGTATTTTGTGAA
891922 AA
66 AA
891924 AGGTAAAATGTTCATGGTGTGAAAGCAGTTTCCTTGCATTAGATATTGAAATAGTATTTTGTGAA
1 AGGTAAAATGTTCATGGTGTGAAAGCAGTTTCCTTGCATTAGATATTGAAATAGTATTTTGTGAA
891989 AA
66 AA
891991 TGTTATATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (67 bp):
AGGTAAAATGTTCATGGTGTGAAAGCAGTTTCCTTGCATTAGATATTGAAATAGTATTTTGTGAA
AA
Found at i:898183 original size:366 final size:364
Alignment explanation
Indices: 897512--898232 Score: 1289
Period size: 366 Copynumber: 2.0 Consensus size: 364
897502 TTGATTTCGC
* * *
897512 TAAGTTCACCCTTCGTTGTGGGCAAGCAAAAGAATTGTGCCTCTTCATCTACAAGTAAACCATGG
1 TAAGTTCACCCTACATTGTGGGCAAGCAAAAGAAGTGTGCCTCTTCATCTACAAGTAAACCATGG
* * *
897577 AATCTGGGAATTGTTGGCCCCTTTATTTGTAGAAGAACCACAACTGTTTTGTCCAGCATAAGGCA
66 AATCTGGGAATTGTTGCCCCCTTTATTTGTAAAAGAACCACAACTGTTTTGTCCACCATAAGGCA
897642 TTATACCCTTGCCTTTATTGTGCTTTTCAACATTGGTTGCACCCCAATTAGTTTTATTGGTTGTG
131 TTATACCCTTGCCTTTATTGTGCTTTTCAACATTGGTTGCACCCCAATTAGTTTTATTGGTTGTG
* *
897707 GTAGCCGTCGATATTTTTGTTGGGATGTTTGATAACCTCGCCTTGCTTCAAAATTTCTGGCCACT
196 ATAGCCCTCGATATTTTTGTTGGGATGTTTGATAACCTCGCCTTGCTTCAAAATTTCTGGCCACT
*
897772 GGGTGCCATATAAGGGCTTTCTAGCACCATAGCGTAAAACTTATTTTTTCTGCTGCTAAAGCATA
261 GGGTGCCATATAAGGGCTTTCTAGCACCATAGCGTAAAACTTA-TTTTTCTGCTACTAAAGCATA
897837 TTGACAAGCATCCTAAATGTTGTACAAATGACAAGCATCT
325 TTGACAAGCATCCTAAATGTTGTACAAATGACAAGCATCT
*
897877 TAAGTTCACCCTACATTGTGGGCAAGCAAAAGAAGTGTGCCTCTTCATCTCACAAGTAAACCATT
1 TAAGTTCACCCTACATTGTGGGCAAGCAAAAGAAGTGTGCCTCTTCATCT-ACAAGTAAACCATG
897942 GAATCTGGGAATTGTTGCCCCCTTTATTTGTAAAAGAACCACAACTGTTTTGTCCACCATAAGGC
65 GAATCTGGGAATTGTTGCCCCCTTTATTTGTAAAAGAACCACAACTGTTTTGTCCACCATAAGGC
*
898007 ATTATACCCTTGCCTTTATTGTTCTTTTCAACATTGGTTGCACCCCAATTAGTTTTATTGGTTGT
130 ATTATACCCTTGCCTTTATTGTGCTTTTCAACATTGGTTGCACCCCAATTAGTTTTATTGGTTGT
*
898072 GATAGCCCTCGATATTTTTGTTGGGATGTTTGATAACCTCGCCTTGCTTCAAAATTTCTTGCCAC
195 GATAGCCCTCGATATTTTTGTTGGGATGTTTGATAACCTCGCCTTGCTTCAAAATTTCTGGCCAC
* * *
898137 TGGTTGCCTTATAAGGGCTTTCTAGCACCATAGCGTAAGACTTATTTTTCTGCTACTAAAGCATA
260 TGGGTGCCATATAAGGGCTTTCTAGCACCATAGCGTAAAACTTATTTTTCTGCTACTAAAGCATA
898202 TTGACAAGCATCCTAAATGTTGTACAAATGA
325 TTGACAAGCATCCTAAATGTTGTACAAATGA
898233 AATACTCCCA
Statistics
Matches: 340, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
365 98 0.29
366 242 0.71
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (364 bp):
TAAGTTCACCCTACATTGTGGGCAAGCAAAAGAAGTGTGCCTCTTCATCTACAAGTAAACCATGG
AATCTGGGAATTGTTGCCCCCTTTATTTGTAAAAGAACCACAACTGTTTTGTCCACCATAAGGCA
TTATACCCTTGCCTTTATTGTGCTTTTCAACATTGGTTGCACCCCAATTAGTTTTATTGGTTGTG
ATAGCCCTCGATATTTTTGTTGGGATGTTTGATAACCTCGCCTTGCTTCAAAATTTCTGGCCACT
GGGTGCCATATAAGGGCTTTCTAGCACCATAGCGTAAAACTTATTTTTCTGCTACTAAAGCATAT
TGACAAGCATCCTAAATGTTGTACAAATGACAAGCATCT
Found at i:905587 original size:31 final size:32
Alignment explanation
Indices: 905549--905611 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
905539 TTAAATTTGA
905549 ATTATAATAA-A-TAAAAAATAAAATATATGAG
1 ATTATAATAAGACT-AAAAATAAAATATATGAG
*
905580 ATTATAATAAGAGCTGAAAATAAAATATATGA
1 ATTATAATAAGA-CTAAAAATAAAATATATGA
905612 CACTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 16 0.57
34 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (32 bp):
ATTATAATAAGACTAAAAATAAAATATATGAG
Found at i:914659 original size:15 final size:15
Alignment explanation
Indices: 914641--914673 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
914631 AAAGCTGAGA
914641 AAAGAAAGAAGG-AAG
1 AAAGAAA-AAGGAAAG
914656 AAAGAAAAAGGAAAG
1 AAAGAAAAAGGAAAG
914671 AAA
1 AAA
914674 AGGGACAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGGAAAG
Found at i:914685 original size:12 final size:11
Alignment explanation
Indices: 914655--914697 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
914645 AAAGAAGGAA
*
914655 GAAAGAAAAAG
1 GAAAGAAAAGG
914666 GAAAGAAAAGG
1 GAAAGAAAAGG
*
914677 GACAAGAAAAGA
1 GA-AAGAAAAGG
914689 GAGAAGAAA
1 GA-AAGAAA
914698 CGAGCAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAAGAAAAGG
Found at i:914736 original size:20 final size:20
Alignment explanation
Indices: 914711--914763 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
914701 GCAATAGGAG
914711 AAGAGAAAGAGAGAA-AAAGA
1 AAGAGAAAGAGAGAAGAAA-A
*
914731 AAGAGAAAGTGAGAAGAAAA
1 AAGAGAAAGAGAGAAGAAAA
914751 AAGAGAAAGAGAG
1 AAGAGAAAGAGAG
914764 GGAAAAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (20 bp):
AAGAGAAAGAGAGAAGAAAA
Found at i:914756 original size:32 final size:31
Alignment explanation
Indices: 914658--914758 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 31
914648 GAAGGAAGAA
*
914658 AGAAAAAGGAAAGA-AAAGG-GACA-AGAAAAG
1 AGAAAAA-GAAAGAGAAAGGAGA-AGAAAAAAG
* *
914688 AG-AGAAGAAACGAGCAATAGGAGAAGAGAAAGAG
1 AGAAAAAGAAA-GAG-AA-AGGAGAAGA-AAAAAG
914722 AGAAAAAGAAAGAGAAAGTGAGAAGAAAAAAG
1 AGAAAAAGAAAGAGAAAG-GAGAAGAAAAAAG
914754 AGAAA
1 AGAAA
914759 GAGAGGGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
28 4 0.07
29 5 0.09
30 2 0.04
31 2 0.04
32 16 0.28
33 12 0.21
34 9 0.16
35 7 0.12
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.02
Consensus pattern (31 bp):
AGAAAAAGAAAGAGAAAGGAGAAGAAAAAAG
Found at i:914917 original size:18 final size:18
Alignment explanation
Indices: 914877--914933 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
914867 AAAGGAGAGG
914877 AAAAGAAATAAAAGGAAGAA
1 AAAAGAAA-AAAA-GAAGAA
*
914897 AAAAGGAAAACAAGAAGAA
1 AAAA-GAAAAAAAGAAGAA
914916 AAAAGAAAAAAAGAAGAA
1 AAAAGAAAAAAAGAAGAA
914934 CAGTTCACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.38
19 10 0.29
20 7 0.21
21 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAGAAGAA
Found at i:915129 original size:22 final size:20
Alignment explanation
Indices: 915086--915139 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
915076 ATGATGTTTT
* *
915086 AAAATAGAGAAATAAAAGAA
1 AAAATAGATAAATAAAAAAA
915106 AAAATAGATAAAGTTAAAAAAA
1 AAAATAGATAAA--TAAAAAAA
* *
915128 AAGATGGATAAA
1 AAAATAGATAAA
915140 CATCTAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATAGATAAATAAAAAAA
Found at i:915291 original size:20 final size:21
Alignment explanation
Indices: 915259--915302 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
915249 TGAGAAAAAT
915259 AAAATAAATATTAAGT-AGTA
1 AAAATAAATATTAAGTAAGTA
915279 AAAAGTAAA-ATTAAGTAAGTA
1 AAAA-TAAATATTAAGTAAGTA
915300 AAA
1 AAA
915303 TGGTAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (21 bp):
AAAATAAATATTAAGTAAGTA
Found at i:915358 original size:2 final size:2
Alignment explanation
Indices: 915351--915377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
915341 AAGAAAATAC
915351 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
915378 AAAGATACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:921323 original size:41 final size:41
Alignment explanation
Indices: 921276--921359 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
921266 ATTTAAAGAA
* *
921276 AGATAATACCCTATATAAAGTGGTGAATGCAAAAGAATTCG
1 AGATAATACCCTATATAAAGAGGTGAACGCAAAAGAATTCG
921317 AGATAATACCCTATATAAAGAGGTGAACGCAAAAGAATTCG
1 AGATAATACCCTATATAAAGAGGTGAACGCAAAAGAATTCG
921358 AG
1 AG
921360 TTTTAACCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.21
Consensus pattern (41 bp):
AGATAATACCCTATATAAAGAGGTGAACGCAAAAGAATTCG
Found at i:921378 original size:41 final size:41
Alignment explanation
Indices: 921276--921378 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
921266 ATTTAAAGAA
* * * *
921276 AGATAATACCCTATATAAAGTGGTGAATGCAAAAGAATTCG
1 AGATAATAACCTATAAAAAGAGGTGAACGCAAAAGAATTCG
* *
921317 AGATAATACCCTATATAAAGAGGTGAACGCAAAAGAATTCG
1 AGATAATAACCTATAAAAAGAGGTGAACGCAAAAGAATTCG
**
921358 AG-TTTTAACCTATCAAAAAGA
1 AGATAATAACCTAT-AAAAAGA
921379 AAAAAAAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 8 0.15
41 47 0.85
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (41 bp):
AGATAATAACCTATAAAAAGAGGTGAACGCAAAAGAATTCG
Found at i:923176 original size:31 final size:30
Alignment explanation
Indices: 923078--923180 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
923068 GTTGGTGTGA
**
923078 AAGA-GTTTAAGCCCAATCAAACTAGCATCC
1 AAGATGTTTAAGCCCAAT-TTACTAGCATCC
* * * * * *
923108 AAAATGTTTAAGTCCAGTTATATTGGCA-CA
1 AAGATGTTTAAGCCCAATT-TACTAGCATCC
*
923138 AAGATGTTTAAGCCCAATTTAGGTAGCATCC
1 AAGATGTTTAAGCCCAATTTA-CTAGCATCC
923169 AAGATGTTTAAG
1 AAGATGTTTAAG
923181 TCTAGCTATG
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
29 2 0.04
30 24 0.44
31 29 0.53
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (30 bp):
AAGATGTTTAAGCCCAATTTACTAGCATCC
Found at i:923236 original size:63 final size:62
Alignment explanation
Indices: 923021--923407 Score: 306
Period size: 61 Copynumber: 6.3 Consensus size: 62
923011 ACAAAAAAGA
* * * * * * ****
923021 GTTTAAGCCCAATTTAATTGGCATCCAAGATGTATAAGTCCAGTTATGTTGGTGTGAA-AGA-
1 GTTTAAGCCCAATTT-ACTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGAGAT
** * * *
923082 GTTTAAGCCCAATCAAACTAGCATCCAAAATGTTTAAGTCCAGTTATATTGGCAC-AA-AGAT
1 GTTTAAGCCCAAT-TTACTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGAGAT
* * *
923143 GTTTAAGCCCAATTTAGGTAGCATCCAAGATGTTTAAGTCTAGCTATGTTAGCACAAAGAGAT
1 GTTTAAGCCCAATTTA-CTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGAGAT
* * * * * *
923206 GTTTAAGCCTAGTTATACTAGCATCTAAGATGTTTAAGGCTAGTTATATTGGCATAAAGACGA-
1 GTTTAAGCCCAATT-TACTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGA-GAT
* ** *
923269 --TTAAGCTCAATTTAGCTAGCATTTAAGATGTTTAAGTCTAGCTATGTTGGCACAAAGAGAT
1 GTTTAAGCCCAATTTA-CTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGAGAT
* * * ** * * *
923330 GTTTAAGCCCAGTTATACTGGCATCCCAGACATTTAAGCCTAGTTATACTGGCATCAAA-A-AT
1 GTTTAAGCCCAATT-TACTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCA-CAAAGAGAT
*
923392 GTTTAAGCTCAATTTA
1 GTTTAAGCCCAATTTA
923408 GCTGGCATTA
Statistics
Matches: 264, Mismatches: 49, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
60 10 0.04
61 138 0.52
62 16 0.06
63 90 0.34
64 10 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (62 bp):
GTTTAAGCCCAATTTACTAGCATCCAAGATGTTTAAGTCTAGCTATATTGGCACAAAGAGAT
Found at i:923254 original size:124 final size:124
Alignment explanation
Indices: 923016--923415 Score: 457
Period size: 124 Copynumber: 3.2 Consensus size: 124
923006 TGCACACAAA
** * * * * ****
923016 AAAGA-GTTTAAGCCCAATTTAATTGGCATCCAAGATGTATAAGTCCAGTTATGTTGGTGTGAA-
1 AAAGATGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTTGGCACAAAG
* * * *
923079 AGA-GTTTAAGCCCAATCAAACTAGCATCCAAAATGTTTAAGTCC-AGTTATATTGGCAC
66 AGATGTTTAAGCCCAGTTATACTAGCATCCAAGATGTTTAAG-CCTAGTTATATTGGCAC
* *
923137 AAAGATGTTTAAGCCCAATTTAGGTAGCATCCAAGATGTTTAAGTCTAGCTATGTTAGCACAAAG
1 AAAGATGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTTGGCACAAAG
* * * *
923202 AGATGTTTAAGCCTAGTTATACTAGCATCTAAGATGTTTAAGGCTAGTTATATTGGCAT
66 AGATGTTTAAGCCCAGTTATACTAGCATCCAAGATGTTTAAGCCTAGTTATATTGGCAC
* * * **
923261 AAAGACGATTAAGCTCAATTTAGCTAGCATTTAAGATGTTTAAGTCTAGCTATGTTGGCACAAAG
1 AAAGATGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTTGGCACAAAG
* * ** *
923326 AGATGTTTAAGCCCAGTTATACTGGCATCCCAGACATTTAAGCCTAGTTATACTGGCATC
66 AGATGTTTAAGCCCAGTTATACTAGCATCCAAGATGTTTAAGCCTAGTTATATTGGCA-C
* * *
923386 AAAAATGTTTAAGCTCAATTTAGCTGGCAT
1 AAAGATGTTTAAGCCCAATTTAGCTAGCAT
923416 TAGGCTTAGA
Statistics
Matches: 235, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
121 5 0.02
122 47 0.20
123 4 0.02
124 153 0.65
125 26 0.11
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (124 bp):
AAAGATGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTTGGCACAAAG
AGATGTTTAAGCCCAGTTATACTAGCATCCAAGATGTTTAAGCCTAGTTATATTGGCAC
Found at i:923397 original size:31 final size:31
Alignment explanation
Indices: 923102--923399 Score: 173
Period size: 31 Copynumber: 9.6 Consensus size: 31
923092 AATCAAACTA
*
923102 GCATCCAAA-ATGTTTAAGTCC-AGTTATATTG
1 GCAT-CAAAGATGTTTAAG-CCTAGTTATACTG
* * * *
923133 GCA-CAAAGATGTTTAAGCCCAATT-TAGGTA
1 GCATCAAAGATGTTTAAGCCTAGTTATA-CTG
* * * ** *
923163 GCATCCAAGATGTTTAAGTCTAGCTATGTTA
1 GCATCAAAGATGTTTAAGCCTAGTTATACTG
*
923194 GCA-CAAAGAGATGTTTAAGCCTAGTTATACTA
1 GCATC-AA-AGATGTTTAAGCCTAGTTATACTG
* * *
923226 GCATCTAAGATGTTTAAGGCTAGTTATATTG
1 GCATCAAAGATGTTTAAGCCTAGTTATACTG
* * * *
923257 GCAT-AAAGACGATTAAG-CTCAATT-TAGCTA
1 GCATCAAAGATGTTTAAGCCT-AGTTATA-CTG
** * * **
923287 GCATTTAAGATGTTTAAGTCTAGCTATGTTG
1 GCATCAAAGATGTTTAAGCCTAGTTATACTG
*
923318 GCA-CAAAGAGATGTTTAAGCCCAGTTATACTG
1 GCATC-AA-AGATGTTTAAGCCTAGTTATACTG
** **
923350 GCATCCCAGACATTTAAGCCTAGTTATACTG
1 GCATCAAAGATGTTTAAGCCTAGTTATACTG
*
923381 GCATCAAAAATGTTTAAGC
1 GCATCAAAGATGTTTAAGC
923400 TCAATTTAGC
Statistics
Matches: 201, Mismatches: 50, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
29 12 0.06
30 35 0.17
31 102 0.51
32 50 0.25
33 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (31 bp):
GCATCAAAGATGTTTAAGCCTAGTTATACTG
Found at i:925728 original size:21 final size:20
Alignment explanation
Indices: 925703--925751 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
925693 GAGTTGTGAA
925703 GAAAAAAAGACAAAAAAAAAT
1 GAAAAAAAGA-AAAAAAAAAT
*
925724 GAAAAAAAGAAGAAAAAAAT
1 GAAAAAAAGAAAAAAAAAAT
925744 -AAAAAAAG
1 GAAAAAAAG
925752 TGTGAGAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.30
20 9 0.33
21 10 0.37
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (20 bp):
GAAAAAAAGAAAAAAAAAAT
Found at i:925750 original size:11 final size:11
Alignment explanation
Indices: 925704--925742 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
925694 AGTTGTGAAG
925704 AAAAAAAGACAA
1 AAAAAAAGA-AA
925716 AAAAAAATGAAA
1 AAAAAAA-GAAA
*
925728 AAAAGAAGAAA
1 AAAAAAAGAAA
925739 AAAA
1 AAAA
925743 TAAAAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 15 0.60
13 2 0.08
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:926198 original size:19 final size:19
Alignment explanation
Indices: 926176--926218 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
926166 AAAATATTCA
926176 AAAAAAAAAACAAATGATG
1 AAAAAAAAAACAAATGATG
** *
926195 AAAATGAAAATAAATGATG
1 AAAAAAAAAACAAATGATG
*
926214 GAAAA
1 AAAAA
926219 CAGGAGACAG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAAAAAAAACAAATGATG
Found at i:926204 original size:20 final size:20
Alignment explanation
Indices: 926182--926218 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
926172 TTCAAAAAAA
926182 AAAACAAATGAT-GAAAATG
1 AAAACAAATGATGGAAAATG
*
926201 AAAATAAATGATGGAAAA
1 AAAACAAATGATGGAAAA
926219 CAGGAGACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAACAAATGATGGAAAATG
Found at i:927910 original size:22 final size:22
Alignment explanation
Indices: 927860--927918 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
927850 GAGCAACCTT
*
927860 TTCTTTAAAACCTCCGGGTTCA
1 TTCTTCAAAACCTCCGGGTTCA
*
927882 -TCTTCAAAACCTTCGGGTAT-A
1 TTCTTCAAAACCTCCGGGT-TCA
927903 TTCTTCAAAACCTCCG
1 TTCTTCAAAACCTCCG
927919 AGTAATTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (22 bp):
TTCTTCAAAACCTCCGGGTTCA
Found at i:928017 original size:123 final size:123
Alignment explanation
Indices: 927798--928238 Score: 684
Period size: 123 Copynumber: 3.6 Consensus size: 123
927788 AAATTTCAAA
*
927798 TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAGGAGCAACCTTTTC
1 TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAAGAGCAACCTTTTC
*
927863 TTTAAAACCTCCGGGTTCATCTTCAAAACCTTCGGGTATATTCTTCAAAACCTCCGAG
66 TTTAAAACCTCCGGGTACATCTTCAAAACCTTCGGGTATATTCTTCAAAACCTCCGAG
* * *
927921 TAATTAGTTTTTAGATTTCATTAAAAGTTATGTATCCTCATTTGGAGATGAAGAGCAACCTTTTC
1 TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAAGAGCAACCTTTTC
* * *
927986 TTTAAAACCTCCAGGTACATCTTCAAAACCTTCAGGTATATTCTTCAAAACCTCCGAA
66 TTTAAAACCTCCGGGTACATCTTCAAAACCTTCGGGTATATTCTTCAAAACCTCCGAG
* * * * *
928044 TTATTAGTTTTTAGATTTTATAAAAAGTTACATAGCCTCATTTAGAGATGAAGAGCAGCCTTTTC
1 TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAAGAGCAACCTTTTC
* * * *
928109 TTTAAAACCTCTGGGTACATCTTCAAAACCTTTGGGTATATCCTTCAAAACCTCCAAG
66 TTTAAAACCTCCGGGTACATCTTCAAAACCTTCGGGTATATTCTTCAAAACCTCCGAG
** * * *
928167 TAATTAGTTTCCAGATTTCATTAAAAGTTACGTAGCCTCATTTGGAGATGAGGAGCAACATTTTC
1 TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAAGAGCAACCTTTTC
928232 TTTAAAA
66 TTTAAAA
928239 ACCTTTGGGT
Statistics
Matches: 285, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 285 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (123 bp):
TAATTAGTTTTTAGATTTCATTAAAAGTTACGTAGCCTCATTTAGAGATGAAGAGCAACCTTTTC
TTTAAAACCTCCGGGTACATCTTCAAAACCTTCGGGTATATTCTTCAAAACCTCCGAG
Found at i:928033 original size:22 final size:22
Alignment explanation
Indices: 927983--928040 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
927973 GAGCAACCTT
*
927983 TTCTTTAAAACCTCCAGGTACA
1 TTCTTCAAAACCTCCAGGTACA
* *
928005 -TCTTCAAAACCTTCAGGTATA
1 TTCTTCAAAACCTCCAGGTACA
928026 TTCTTCAAAACCTCC
1 TTCTTCAAAACCTCC
928041 GAATTATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (22 bp):
TTCTTCAAAACCTCCAGGTACA
Found at i:928157 original size:22 final size:21
Alignment explanation
Indices: 928107--928162 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
928097 AGCAGCCTTT
*
928107 TCTTTAAAACCTCTGGGTACA
1 TCTTCAAAACCTCTGGGTACA
* *
928128 TCTTCAAAACCTTTGGGTATA
1 TCTTCAAAACCTCTGGGTACA
928149 TCCTTCAAAACCTC
1 T-CTTCAAAACCTC
928163 CAAGTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (21 bp):
TCTTCAAAACCTCTGGGTACA
Found at i:928336 original size:9 final size:9
Alignment explanation
Indices: 928318--928359 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
928308 CTGTTTATAT
928318 AAAAAA-AA
1 AAAAAACAA
928326 AAAAAACAA
1 AAAAAACAA
928335 AAAAAACAA
1 AAAAAACAA
*
928344 AAAAAATTAA
1 AAAAAA-CAA
928354 AAAAAA
1 AAAAAA
928360 TGTCAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 6 0.19
9 17 0.55
10 8 0.26
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (9 bp):
AAAAAACAA
Found at i:928336 original size:10 final size:10
Alignment explanation
Indices: 928318--928359 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
928308 CTGTTTATAT
928318 AAAAA-AAAA
1 AAAAACAAAA
928327 AAAAAC-AAA
1 AAAAACAAAA
928336 AAAAACAAAA
1 AAAAACAAAA
**
928346 AAAATTAAAA
1 AAAAACAAAA
928356 AAAA
1 AAAA
928360 TGTCAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:929078 original size:40 final size:41
Alignment explanation
Indices: 929027--929116 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 41
929017 ACCGAAGTAA
*
929027 AGAAGAGGAAAG-AAGGCTGCCGGCACGTG-GAAAGAAAGAGAG
1 AGAAG-GGAAAGAAAGGCTGCCAGC-C-TGAGAAAGAAAGAGAG
* *
929069 AG-AGGGAAAGAAAGGTTGCCAGCCTGAGAAAGAGAGAGAG
1 AGAAGGGAAAGAAAGGCTGCCAGCCTGAGAAAGAAAGAGAG
929109 AGAAGGGA
1 AGAAGGGA
929117 GACGTCGGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 2 0.05
40 21 0.50
41 17 0.40
42 2 0.05
ACGTcount: A:0.43, C:0.10, G:0.41, T:0.06
Consensus pattern (41 bp):
AGAAGGGAAAGAAAGGCTGCCAGCCTGAGAAAGAAAGAGAG
Found at i:929757 original size:3 final size:3
Alignment explanation
Indices: 929749--929786 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
929739 AATATATAAG
929749 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
929787 GTACGATACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:939485 original size:28 final size:28
Alignment explanation
Indices: 939445--939508 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
939435 GAACATATAA
939445 TATGATTGGTGAACAGGTTGCTTGGATT
1 TATGATTGGTGAACAGGTTGCTTGGATT
*
939473 TATGATTGGTGAATAGGTTGCTTGGATT
1 TATGATTGGTGAACAGGTTGCTTGGATT
*
939501 TGTGATTG
1 TATGATTG
939509 ATTCGACTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (28 bp):
TATGATTGGTGAACAGGTTGCTTGGATT
Found at i:942181 original size:21 final size:20
Alignment explanation
Indices: 942155--942198 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
942145 TTAAATTAAA
942155 TTATTTTAATTTAATTTTACT
1 TTATTTTAATTTAA-TTTACT
**
942176 TTATTTTGGTTTAATTTACT
1 TTATTTTAATTTAATTTACT
942196 TTA
1 TTA
942199 AGAAGAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (20 bp):
TTATTTTAATTTAATTTACT
Found at i:951716 original size:22 final size:22
Alignment explanation
Indices: 951691--951732 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
951681 TAAAAATTAC
951691 TATTATATAAATTATATTTTTT
1 TATTATATAAATTATATTTTTT
* * *
951713 TATTTTTTAAATTTTATTTT
1 TATTATATAAATTATATTTT
951733 ATTTTTGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTATATAAATTATATTTTTT
Found at i:957449 original size:343 final size:344
Alignment explanation
Indices: 956814--957500 Score: 1074
Period size: 343 Copynumber: 2.0 Consensus size: 344
956804 GATCTTAGTC
* * *
956814 GCTACTGATATTTACCAAATTAATGATCGCAGTTTGGGATTTTTGTAAGAATTCAACTTACAAAA
1 GCTACTGATATTTACCAAATTAATGATAGCAGTTTGGAATTTTTATAAGAATTCAACTTACAAAA
*
956879 CCTAATTTAGAGAGTTTAGTCTTTGTATAGTGCTAACACTCTCAACAAAGTATAAAACATATGAT
66 CCTAATTTAGAGAGTTTAGTCTTTGTATAGTGCTAACAC-CTCAACAAAGTACAAAACATATGAT
** *
956944 GCTAGCTCCTAGTTTGTTATATCTCATCCTAAGTGATAAATCATAAACAAGGACTAAATATATGA
130 GCTAGCTCCTAGTTCATTATATCTCATCCTAAGTGATAAATCATAAACAAGGACTAAATATATCA
* * * *
957009 CAATCACACGAAGATGGGAAAAATCTAATTAAATAGAGATGAACACATAACATTGCCCACTCCTT
195 CAATCACACAAACATGAGAAAAATCTAATTAAATAGAGATGAACACATAACATCGCCCACTCCTT
* *
957074 AGAACAACTTTGTCCTCAACATTGGAATAAGGGAGCCTTCTATTGAAATCTTCCTTGGCATCTCA
260 AGAACAACCTTGTCCTCAACATTGGAATAAGGGAGCCTTCTATTGAAATCTTACTTGGCATCTCA
*
957139 AACCCCATTCATTCAATGTT
325 AACCCCATTCATACAATGTT
*
957159 GCTACCTGATATTTACCAAATTAATGATAGCGGTTTGGAATTTTTATAAGAATTCAACTTACAAA
1 GCTA-CTGATATTTACCAAATTAATGATAGCAGTTTGGAATTTTTATAAGAATTCAACTTACAAA
* * * * * *
957224 ACTTAA-TTGGAGAGTTTATTCTTTGTATAGTGCTAACA-CTCAAGAAAGTACGAAACATGTGAT
65 ACCTAATTTAGAGAGTTTAGTCTTTGTATAGTGCTAACACCTCAACAAAGTACAAAACATATGAT
*
957287 GCTAGCTCCTAGTTCATTATATCTCATCCTAAGTGATAAATCATAAACAAGGAGTAAATATATCA
130 GCTAGCTCCTAGTTCATTATATCTCATCCTAAGTGATAAATCATAAACAAGGACTAAATATATCA
* *
957352 TAATCACACAAACATGAGAAATATCTAATTAAATAGAGATGAACACATAACATCGCCCACTCCTT
195 CAATCACACAAACATGAGAAAAATCTAATTAAATAGAGATGAACACATAACATCGCCCACTCCTT
* * * *
957417 AGAACAACCTTGTCGTCAACATT-GATATAAGGGATCCTTCTCTTGAAATCTTACTTGGCATTTC
260 AGAACAACCTTGTCCTCAACATTGGA-ATAAGGGAGCCTTCTATTGAAATCTTACTTGGCATCTC
957481 AAACCCCATTCATACAATGT
324 AAACCCCATTCATACAATGT
957501 CGCCATGCAT
Statistics
Matches: 312, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
342 2 0.01
343 215 0.69
345 34 0.11
346 61 0.20
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (344 bp):
GCTACTGATATTTACCAAATTAATGATAGCAGTTTGGAATTTTTATAAGAATTCAACTTACAAAA
CCTAATTTAGAGAGTTTAGTCTTTGTATAGTGCTAACACCTCAACAAAGTACAAAACATATGATG
CTAGCTCCTAGTTCATTATATCTCATCCTAAGTGATAAATCATAAACAAGGACTAAATATATCAC
AATCACACAAACATGAGAAAAATCTAATTAAATAGAGATGAACACATAACATCGCCCACTCCTTA
GAACAACCTTGTCCTCAACATTGGAATAAGGGAGCCTTCTATTGAAATCTTACTTGGCATCTCAA
ACCCCATTCATACAATGTT
Found at i:959817 original size:37 final size:39
Alignment explanation
Indices: 959752--959825 Score: 125
Period size: 37 Copynumber: 1.9 Consensus size: 39
959742 TTTAACTTAT
959752 TTAAGTAATGCTTGTAAAAAATTGTTCTATATTTTTTAAC
1 TTAAGTAATGCTTGT-AAAAATTGTTCTATATTTTTTAAC
959792 TTAAGT-ATGCTTGT-AAAATTGTTCTATATTTTTT
1 TTAAGTAATGCTTGTAAAAATTGTTCTATATTTTTT
959826 CAAGAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 20 0.59
39 8 0.24
40 6 0.18
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (39 bp):
TTAAGTAATGCTTGTAAAAATTGTTCTATATTTTTTAAC
Found at i:962234 original size:122 final size:123
Alignment explanation
Indices: 962016--962243 Score: 334
Period size: 122 Copynumber: 1.9 Consensus size: 123
962006 GGTTGAAATT
* ** * * *
962016 AAACAAGATGCATAGCAGTATGCTATGTTTCTTTATTGCTGGGATTAATAATGTTTCAAGAATAG
1 AAACAAGATGCATAGCAGTATGCCATGTTTCCGTATTGATGGGATTAAGAATGTTGCAAGAATAG
*
962081 TCTTGGTGTTTTACCACAACTTACCAAAGGTCTT-CTTTTAAACAAGATGTGTACCAA
66 TCTTGGTATTTTACCACAACTTACCAAAGGTCTTCCTTTTAAACAAGATGTGTACCAA
* *
962138 AAACAAGATGCTTAGCAGTATGCCATGTTTCCGTATTGATGGGATTAAGAATGTTGCAAGAATGG
1 AAACAAGATGCATAGCAGTATGCCATGTTTCCGTATTGATGGGATTAAGAATGTTGCAAGAATAG
* *
962203 TCTTGGTATTTTACCTCAGA-TTACCAGAGGTCTTCCTTTTA
66 TCTTGGTATTTTACCACA-ACTTACCAAAGGTCTTCCTTTTA
962244 CTTCAGTGCA
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
122 86 0.92
123 7 0.08
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (123 bp):
AAACAAGATGCATAGCAGTATGCCATGTTTCCGTATTGATGGGATTAAGAATGTTGCAAGAATAG
TCTTGGTATTTTACCACAACTTACCAAAGGTCTTCCTTTTAAACAAGATGTGTACCAA
Found at i:966251 original size:2 final size:2
Alignment explanation
Indices: 966244--966270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
966234 GCATCTGTAT
966244 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
966271 TGTATCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:969885 original size:44 final size:43
Alignment explanation
Indices: 969810--969920 Score: 150
Period size: 44 Copynumber: 2.6 Consensus size: 43
969800 TTAGTGTGTA
* * * *
969810 AGGAAAATGGGAATGAGTGATGAAATGGGGAAAGGATTAGCAG
1 AGGAAAATGGGAATGAGTGAAGAAATAGGGAAAGGAGTAGAAG
* *
969853 AGGAGAAACGGGAATGGGTGAAGAAATAGGGAAAGGAGTAGAAG
1 AGGA-AAATGGGAATGAGTGAAGAAATAGGGAAAGGAGTAGAAG
*
969897 AGGAAAATGGGAATGAGCGAAGAA
1 AGGAAAATGGGAATGAGTGAAGAA
969921 TTCGATCGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 21 0.36
44 37 0.64
ACGTcount: A:0.45, C:0.03, G:0.41, T:0.12
Consensus pattern (43 bp):
AGGAAAATGGGAATGAGTGAAGAAATAGGGAAAGGAGTAGAAG
Found at i:976378 original size:16 final size:18
Alignment explanation
Indices: 976343--976396 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
976333 AGGAGAAAAG
*
976343 AGAAAGGAGAGGAGAGAA
1 AGAAAGGAGAGGAAAGAA
976361 AGAAAGG-G-GGAAAGAA
1 AGAAAGGAGAGGAAAGAA
*
976377 AGAAAGGA-A-GAAAGGA
1 AGAAAGGAGAGGAAAGAA
976393 AGAA
1 AGAA
976397 GAAGAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 24 0.75
17 1 0.03
18 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (18 bp):
AGAAAGGAGAGGAAAGAA
Found at i:984108 original size:42 final size:42
Alignment explanation
Indices: 984029--984109 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
984019 TTGACCATAT
* *
984029 ATCAAAGGTGGCAAGATTGTATCAACTACCAAATAAAACCTA
1 ATCAAAGGTGGCAAGACTCTATCAACTACCAAATAAAACCTA
* * *
984071 ATCAAAGG-GGTAAGACTCTATCAATTACCCAATTAAAAC
1 ATCAAAGGTGGCAAGACTCTATCAACTA-CCAAATAAAAC
984110 TAAGCATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 15 0.45
42 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (42 bp):
ATCAAAGGTGGCAAGACTCTATCAACTACCAAATAAAACCTA
Found at i:988844 original size:21 final size:21
Alignment explanation
Indices: 988818--988870 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
988808 AGAGGGAAAA
988818 GTATCCATACATTTCCCCAAT
1 GTATCCATACATTTCCCCAAT
*
988839 GTATCCATACATTTCCCTAAT
1 GTATCCATACATTTCCCCAAT
*
988860 GTATCGATACA
1 GTATCCATACA
988871 CTCCTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (21 bp):
GTATCCATACATTTCCCCAAT
Found at i:989848 original size:24 final size:24
Alignment explanation
Indices: 989821--989880 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
989811 TAATTTTATC
989821 CAAATAATTAAACTAAAA-AAAATT
1 CAAATAA-TAAACTAAAACAAAATT
989845 CAAACTAATAAACTAAAACCAAAATT
1 CAAA-TAATAAACTAAAA-CAAAATT
*
989871 -AAATAGTAAA
1 CAAATAATAAA
989881 AACTCACTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 20 0.62
25 6 0.19
26 6 0.19
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (24 bp):
CAAATAATAAACTAAAACAAAATT
Found at i:990150 original size:52 final size:52
Alignment explanation
Indices: 990065--990165 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
990055 AGTATATGTT
* *
990065 TATGGAAATTATATTGAAGAAAGATTAAGTAAGTTTGTGCTCTAATTTTGGC
1 TATGAAAATTATATTGAAGAAAGATGAAGTAAGTTTGTGCTCTAATTTTGGC
* *
990117 TATGAAAATTATATTGTAGAAAGATGAATTAAGTTTGTGCTCTAATTTT
1 TATGAAAATTATATTGAAGAAAGATGAAGTAAGTTTGTGCTCTAATTTT
990166 TGTTATGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (52 bp):
TATGAAAATTATATTGAAGAAAGATGAAGTAAGTTTGTGCTCTAATTTTGGC
Found at i:996567 original size:29 final size:29
Alignment explanation
Indices: 996525--996644 Score: 143
Period size: 29 Copynumber: 4.1 Consensus size: 29
996515 CTTTAACACT
* *
996525 TTTTGTCTTAATTTAGAGAAGAAAATATA
1 TTTTATCTTAATTTAGACAAGAAAATATA
* *
996554 TTTTATCTTAATTTAAACAAGAAATTATA
1 TTTTATCTTAATTTAGACAAGAAAATATA
* *
996583 -TTTGTCTTAATTTAAGACAAGAAATATATG
1 TTTTATCTTAATTT-AGACAAGAAA-ATATA
* *
996613 TTTTATCTTAATCTAGACAAGAAAACATA
1 TTTTATCTTAATTTAGACAAGAAAATATA
996642 TTT
1 TTT
996645 AATTTAGACA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.16
29 40 0.53
30 13 0.17
31 11 0.14
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTATCTTAATTTAGACAAGAAAATATA
Found at i:996643 original size:59 final size:57
Alignment explanation
Indices: 996526--996644 Score: 166
Period size: 59 Copynumber: 2.1 Consensus size: 57
996516 TTTAACACTT
* * **
996526 TTTGTCTTAATTTAGAGAAGAAAATATATTTTATCTTAATTTAAACAAGAAATTATA
1 TTTGTCTTAATTTAGACAAGAAAATATATTTTATCTTAATCTAAACAAGAAAACATA
* *
996583 TTTGTCTTAATTTAAGACAAGAAATATATGTTTTATCTTAATCTAGACAAGAAAACATA
1 TTTGTCTTAATTT-AGACAAGAAA-ATATATTTTATCTTAATCTAAACAAGAAAACATA
996642 TTT
1 TTT
996645 AATTTAGACA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 13 0.24
58 9 0.17
59 32 0.59
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (57 bp):
TTTGTCTTAATTTAGACAAGAAAATATATTTTATCTTAATCTAAACAAGAAAACATA
Found at i:996646 original size:23 final size:23
Alignment explanation
Indices: 996620--996667 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
996610 ATGTTTTATC
*
996620 TTAATCTAGACAAGAAAACATAT
1 TTAATCTAGACAACAAAACATAT
* *
996643 TTAATTTAGACAACATAACATAT
1 TTAATCTAGACAACAAAACATAT
996666 TT
1 TT
996668 GTCTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAATCTAGACAACAAAACATAT
Found at i:997907 original size:21 final size:21
Alignment explanation
Indices: 997883--997931 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
997873 AGGAAAACTA
*
997883 CTAAAATACTTAATTGTAAAC
1 CTAAAATACTTAATTCTAAAC
997904 CTAAAATACTTAATTCTAAAC
1 CTAAAATACTTAATTCTAAAC
997925 CTAAAAT
1 CTAAAAT
997932 CTCAAAGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (21 bp):
CTAAAATACTTAATTCTAAAC
Found at i:1006155 original size:71 final size:71
Alignment explanation
Indices: 1005996--1006180 Score: 169
Period size: 71 Copynumber: 2.6 Consensus size: 71
1005986 AGAAGGGGTT
* * *
1005996 GATCTTGGACCAAAAGGTTTGTATTTCATCCATTTCTCCTTCACAAGATTGACTATTAAAGCTCT
1 GATCTTGGACCAAAATGTCTGTATTTCATCCATTTCTCCTTCACAAGATCGACTATTAAAGCTCT
*
1006061 ATAGTT
66 ATAGTA
* * * * * * * * *
1006067 GATCTTAGATCAGAATGTCTGCT-TTTGATTCATTTTTCCTTCACCAGATCGACTA-TAGAGGGT
1 GATCTTGGACCAAAATGTCTG-TATTTCATCCATTTCTCCTTCACAAGATCGACTATTA-AAGCT
*
1006130 CTGTAGTA
64 CTATAGTA
* * *
1006138 GATCTTGGACCAAAATGTTTGCATTTCCTCCATTT-TCCCTTCA
1 GATCTTGGACCAAAATGTCTGTATTTCATCCATTTCT-CCTTCA
1006181 TAAGGCTGAC
Statistics
Matches: 88, Mismatches: 22, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
70 3 0.03
71 84 0.95
72 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (71 bp):
GATCTTGGACCAAAATGTCTGTATTTCATCCATTTCTCCTTCACAAGATCGACTATTAAAGCTCT
ATAGTA
Found at i:1007952 original size:12 final size:12
Alignment explanation
Indices: 1007933--1007979 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
1007923 CAGAATAGTT
1007933 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1007945 -CTTTGCTG-CTC
1 TC-TTGCTGCCTC
1007956 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1007968 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1007980 CAAAATCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.43
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:1007959 original size:23 final size:23
Alignment explanation
Indices: 1007933--1007976 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1007923 CAGAATAGTT
1007933 TCTTGCTGCCTC-CTTTGCTGCTC
1 TCTTGCTGCCTCTC-TTGCTGCTC
1007956 TCTTGCTGCCTCTCTTGCTGC
1 TCTTGCTGCCTCTCTTGCTGC
1007977 CTCCAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.00, C:0.39, G:0.18, T:0.43
Consensus pattern (23 bp):
TCTTGCTGCCTCTCTTGCTGCTC
Found at i:1016493 original size:12 final size:12
Alignment explanation
Indices: 1016464--1016511 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
1016454 CAGAATAGTT
1016464 TCTTGCTG-CTCC
1 TCTTGCTGCCT-C
*
1016476 TTTTGCTGCCTC
1 TCTTGCTGCCTC
1016488 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1016500 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1016512 CAAAATCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 31 0.94
13 2 0.06
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.44
Consensus pattern (12 bp):
TCTTGCTGCCTC
Done.