Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, 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: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:797973 original size:20 final size:21
Alignment explanation
Indices: 797948--797999 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
797938 AGTGGAGAGA
*
797948 AAAGAAAAAGAAAAA-GAAAG
1 AAAGAAAAAGAAAAATAAAAG
797968 AAAG-AAAAGAAAAATAAAAG
1 AAAGAAAAAGAAAAATAAAAG
*
797988 AAA-ATAAAGAAA
1 AAAGAAAAAGAAA
798000 GAAAGACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (21 bp):
AAAGAAAAAGAAAAATAAAAG
Found at i:797973 original size:25 final size:25
Alignment explanation
Indices: 797945--798035 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
797935 AGAAGTGGAG
797945 AGAAAAGAAAAAGAAAAAG-AAAGAA
1 AGAAAAGAAAAA-AAAAAGAAAAGAA
* *
797970 AGAAAAGAAAAATAAAAGAAAATAA
1 AGAAAAGAAAAAAAAAAGAAAAGAA
* *
797995 AG-AAAGAAAGACAAAAAAGGACAACAA
1 AGAAAAGAAA-A-AAAAAA-GAAAAGAA
*
798022 ATAAAAGAAAAAAA
1 AGAAAAGAAAAAAA
798036 GAGTTGCAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
24 12 0.22
25 20 0.36
26 8 0.15
27 8 0.15
28 7 0.13
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (25 bp):
AGAAAAGAAAAAAAAAAGAAAAGAA
Found at i:798005 original size:41 final size:40
Alignment explanation
Indices: 797945--798037 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
797935 AGAAGTGGAG
* * *
797945 AGAAAAGAA-AAAGAAAAAGAAAGAAAGAAAAGAAAAATAAA
1 AGAAAAAAAGAAAGAAAGACAAA-AAAGAAAA-AAAAATAAA
* * *
797986 AGAAAATAAAGAAAGAAAGACAAAAAAGGACAACAAATAAA
1 AGAAAA-AAAGAAAGAAAGACAAAAAAGAAAAAAAAATAAA
798027 AGAAAAAAAGA
1 AGAAAAAAAGA
798038 GTTGCAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 5 0.11
41 20 0.45
42 8 0.18
43 11 0.25
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (40 bp):
AGAAAAAAAGAAAGAAAGACAAAAAAGAAAAAAAAATAAA
Found at i:798010 original size:24 final size:23
Alignment explanation
Indices: 797945--798010 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
797935 AGAAGTGGAG
797945 AGAAAAGAAAAAGAAAAAGAAAGAA
1 AGAAAAG--AAAGAAAAAGAAAGAA
* *
797970 AGAAAAGAAAAATAAAAGAAAATAA
1 AGAAAAGAAAGA-AAAAG-AAAGAA
797995 AG-AAAGAAAGACAAAA
1 AGAAAAGAAAGA-AAAA
798011 AAGGACAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 17 0.49
25 14 0.40
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (23 bp):
AGAAAAGAAAGAAAAAGAAAGAA
Found at i:798010 original size:29 final size:30
Alignment explanation
Indices: 797945--798003 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
797935 AGAAGTGGAG
797945 AGAAAAGA-AAAAGAAAAAGAAAGAAAGAAA
1 AGAAAA-ATAAAAGAAAAAGAAAGAAAGAAA
*
797975 AGAAAAATAAAAG-AAAATAAAGAAAGAAA
1 AGAAAAATAAAAGAAAAAGAAAGAAAGAAA
798004 GACAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (30 bp):
AGAAAAATAAAAGAAAAAGAAAGAAAGAAA
Found at i:798336 original size:19 final size:18
Alignment explanation
Indices: 798302--798342 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
798292 GTGGAAAGAG
798302 TATTTTTTAATAAAATAA
1 TATTTTTTAATAAAATAA
*
798320 TATTTTATTAATGAAATAA
1 TATTTT-TTAATAAAATAA
798339 TATT
1 TATT
798343 AAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTTTTTAATAAAATAA
Found at i:803822 original size:30 final size:30
Alignment explanation
Indices: 803786--803847 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
803776 GATTGAGGAT
*
803786 GAAGATGACATACAAAGAGATGAAGATGAA
1 GAAGATGACATACAAAGAGATGAAAATGAA
** *
803816 GAAGATGACATGGAAGGAGATGAAAATGAA
1 GAAGATGACATACAAAGAGATGAAAATGAA
803846 GA
1 GA
803848 TGAAGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.31, T:0.13
Consensus pattern (30 bp):
GAAGATGACATACAAAGAGATGAAAATGAA
Found at i:804228 original size:23 final size:23
Alignment explanation
Indices: 804183--804253 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
804173 ATGAAACAAA
* *
804183 TTAAAAATTT-TATATATAATTTT
1 TTAAAAATTTAT-TATTTACTTTT
804206 TTAAAAATTTATTATTTACTTTTTT
1 TTAAAAATTTATTATTTAC--TTTT
* *
804231 TTAGAAATTTACTATTTACTTTT
1 TTAAAAATTTATTATTTACTTTT
804254 GTATCTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
25 21 0.51
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
TTAAAAATTTATTATTTACTTTT
Found at i:804230 original size:25 final size:25
Alignment explanation
Indices: 804202--804253 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
804192 TTATATATAA
*
804202 TTTTTTAAAAATTTATTATTTACTT
1 TTTTTTAAAAATTTACTATTTACTT
*
804227 TTTTTTAGAAATTTACTATTTACTT
1 TTTTTTAAAAATTTACTATTTACTT
804252 TT
1 TT
804254 GTATCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTTTAAAAATTTACTATTTACTT
Found at i:810427 original size:28 final size:29
Alignment explanation
Indices: 810387--810442 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
810377 TCCATTGGAA
810387 ATTTCCAATGG-AATTCCATTGAAAATTC
1 ATTTCCAATGGAAATTCCATTGAAAATTC
**
810415 ATTTCCAATGGAAATTCTGTTGAAAATT
1 ATTTCCAATGGAAATTCCATTGAAAATT
810443 TCCAACAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (29 bp):
ATTTCCAATGGAAATTCCATTGAAAATTC
Found at i:815383 original size:16 final size:16
Alignment explanation
Indices: 815364--815421 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
815354 ACCAACAAAC
*
815364 AAACATATAATAACAT
1 AAACACATAATAACAT
* * *
815380 AAACACACCAACAA-AC
1 AAACACA-TAATAACAT
*
815396 AAACATATAATAACAT
1 AAACACATAATAACAT
815412 AAACACATAA
1 AAACACATAA
815422 CAATGCAAGC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 4 0.13
16 23 0.74
17 4 0.13
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.16
Consensus pattern (16 bp):
AAACACATAATAACAT
Found at i:815386 original size:32 final size:32
Alignment explanation
Indices: 815345--815418 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
815335 AGAAATTGTT
815345 CATAAACACACCAACAAACAAACATATAATAA
1 CATAAACACACCAACAAACAAACATATAATAA
815377 CATAAACACACCAACAAACAAACATATAATAA
1 CATAAACACACCAACAAACAAACATATAATAA
815409 CATAAACACA
1 CATAAACACA
815419 TAACAATGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.62, C:0.26, G:0.00, T:0.12
Consensus pattern (32 bp):
CATAAACACACCAACAAACAAACATATAATAA
Found at i:826056 original size:27 final size:26
Alignment explanation
Indices: 826004--826102 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 26
825994 ATGTTTGGTC
826004 TTAATTTAGACAAAAAAATATGTTTTT
1 TTAATTTAGACAAAAAAATA-GTTTTT
*
826031 TTAATTTAAGACAAGAAAAATATTTTTTAT
1 TTAATTT-AGACAA-AAAAATA-GTTTT-T
* * *
826061 CTTAATCTAGACAAGAAAATATAGTTATC
1 -TTAATTTAGACAA-AAAA-ATAGTTTTT
*
826090 TCAATTTAGACAA
1 TTAATTTAGACAA
826103 GATAAAATNN
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 7 0.12
28 17 0.28
29 12 0.20
30 15 0.25
31 9 0.15
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (26 bp):
TTAATTTAGACAAAAAAATAGTTTTT
Found at i:826073 original size:30 final size:30
Alignment explanation
Indices: 825969--826110 Score: 127
Period size: 29 Copynumber: 4.9 Consensus size: 30
825959 CTTTAACATG
* *
825969 TTTATCTTAATTTAGAC-A-ATAAATCATGT
1 TTTATCTTAATTTAGACAAGAAAAAT-ATTT
** *
825998 TTGGTCTTAATTTAGACAA-AAAAATATGT
1 TTTATCTTAATTTAGACAAGAAAAATATTT
826027 TTT-T-TTAATTTAAGACAAGAAAAATATTT
1 TTTATCTTAATTT-AGACAAGAAAAATATTT
* *
826056 TTTATCTTAATCTAGACAAG-AAAATA-TA
1 TTTATCTTAATTTAGACAAGAAAAATATTT
* *
826084 GTTATCTCAATTTAGACAAGATAAAAT
1 TTTATCTTAATTTAGACAAGA-AAAAT
826111 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
27 7 0.07
28 25 0.26
29 39 0.41
30 19 0.20
31 6 0.06
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTATCTTAATTTAGACAAGAAAAATATTT
Found at i:826332 original size:27 final size:28
Alignment explanation
Indices: 826294--826413 Score: 127
Period size: 28 Copynumber: 4.2 Consensus size: 28
826284 TCATGTTTGG
826294 TCTTAATTTAAACAAGAAAATATGTTTT-
1 TCTTAATTTAAACAAGAAAATAT-TTTTA
826322 T-TTAATTTAAACAAGAAAAATATTTTTA
1 TCTTAATTTAAACAAG-AAAATATTTTTA
* * * *
826350 TCTTCATCTAGACAAGAAAATATATTTA
1 TCTTAATTTAAACAAGAAAATATTTTTA
* * *
826378 TCTCAATTTAGACAAGATAAAATATTTTTG
1 TCTTAATTTAAACAAG--AAAATATTTTTA
826408 TCTTAA
1 TCTTAA
826414 GTAAAGACAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
27 18 0.23
28 33 0.43
29 11 0.14
30 15 0.19
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (28 bp):
TCTTAATTTAAACAAGAAAATATTTTTA
Found at i:837862 original size:68 final size:68
Alignment explanation
Indices: 837602--837863 Score: 215
Period size: 68 Copynumber: 3.9 Consensus size: 68
837592 CACCATTTAC
* * * *
837602 TCATCTCATA-AGATATATGGAAA-ATACATCAGATACATAACCTCATGGCATTCATCATGCTTT
1 TCATCTCATATA-ATATAT-GAAATATACATCATATACATAATCTCATGGCATTCATCATGCATA
*
837665 CTCAA
64 CTTAA
* * * * * *
837670 TCATCTCATGTAGTATAT-AGAATATACATCATATACATTATCTCATGGCATTAAACATGCATAT
1 TCATCTCATATAATATATGA-AATATACATCATATACATAATCTCATGGCATTCATCATGCATAC
837734 TTAA
65 TTAA
* ** * * * * * * * * *
837738 TCACCTCATATGGTATATGGAATTTATATCATATATACAATCTTATAGTATACATCATGCATACT
1 TCATCTCATATAATATATGAAATATACATCATATACATAATCTCATGGCATTCATCATGCATACT
837803 TAA
66 TAA
* * * ** *
837806 TCATCTCATACAATATATGAAATTTACATCACATTTATAATCTTATGGCATTCATCAT
1 TCATCTCATATAATATATGAAATATACATCATATACATAATCTCATGGCATTCATCAT
837864 AGCAAACATG
Statistics
Matches: 151, Mismatches: 39, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
66 1 0.01
67 2 0.01
68 147 0.97
69 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (68 bp):
TCATCTCATATAATATATGAAATATACATCATATACATAATCTCATGGCATTCATCATGCATACT
TAA
Found at i:851921 original size:185 final size:191
Alignment explanation
Indices: 851591--851964 Score: 548
Period size: 185 Copynumber: 2.0 Consensus size: 191
851581 ATGACATGGT
*
851591 ATGTAGAAATGCAGAATCACACTGACTTAAATCAGAAAATGAATATGGAAAGGTAGAAAATAAAA
1 ATGTAGAAATGCAGAATCACACTGACTTAAATCAGAAAATGAATATGGAAAGCTAGAAAATAAAA
* * *
851656 GAAAAACAAAAAGAAAATTAATAAAGAAATGTTGTCAGCTAAACTTGGAAGCCAAAAGTAAATGA
66 GAAAAACAAAAAG--AA-TAATAAAGAAATGCTGTCAGCTAAACTTGGAAGCCAAAACTAAACGA
* *
851721 TCACGTCAGTCCTAGCAACACAGAACAGAACAAGAATAAAGCTATATTTGGTTAATTAATTGCC
128 TCACATCACTCCTAGCAACACAGAACAGAACAAGAATAAAGCTATATTTGGTTAATTAATTGCC
*
851785 ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAAT-TCGGAAAGACT-G-AAA-AA
1 ATGTAGAAATGCAGAATCACACTGACTTAAATCAGAAAATGAATAT-GGAAAG-CTAGAAAATAA
* *
851846 AA-AAAAA-GAAAAG-A-AATAAAGAAATGCTGTCAGCTGAACTTGGAAGCCAAAACTAAACGAT
64 AAGAAAAACAAAAAGAATAATAAAGAAATGCTGTCAGCTAAACTTGGAAGCCAAAACTAAACGAT
* *
851907 CACATCACTCCTAGCAACACAGAATAGAACAAGAATAAGGCTATATTTGGTTAATTAA
129 CACATCACTCCTAGCAACACAGAACAGAACAAGAATAAAGCTATATTTGGTTAATTAA
851965 GTCCCTGTCA
Statistics
Matches: 167, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
185 97 0.58
187 1 0.01
190 5 0.03
191 5 0.03
192 4 0.02
193 4 0.02
194 50 0.30
195 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (191 bp):
ATGTAGAAATGCAGAATCACACTGACTTAAATCAGAAAATGAATATGGAAAGCTAGAAAATAAAA
GAAAAACAAAAAGAATAATAAAGAAATGCTGTCAGCTAAACTTGGAAGCCAAAACTAAACGATCA
CATCACTCCTAGCAACACAGAACAGAACAAGAATAAAGCTATATTTGGTTAATTAATTGCC
Found at i:856020 original size:3 final size:3
Alignment explanation
Indices: 856012--856036 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
856002 ATTTTAAATC
856012 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
856037 GTATTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:856532 original size:2 final size:2
Alignment explanation
Indices: 856527--856552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
856517 TTTCTCAATT
856527 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
856553 AAGATAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:859685 original size:3 final size:3
Alignment explanation
Indices: 859677--859701 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
859667 CTTTGGTTGG
859677 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
859702 AGTGCCTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:860359 original size:22 final size:22
Alignment explanation
Indices: 860308--860359 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
860298 CTAACATGGC
860308 ATAATATT-TTATTTTTAATTA
1 ATAATATTATTATTTTTAATTA
* * *
860329 AAAAAATTATT-TTTTATAATTT
1 ATAATATTATTATTTT-TAATTA
860351 ATAATATTA
1 ATAATATTA
860360 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATAATATTATTATTTTTAATTA
Found at i:860384 original size:29 final size:31
Alignment explanation
Indices: 860325--860386 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
860315 TTTATTTTTA
* *
860325 ATTAAAAAAATTATTTTTTATAATTTATAAT
1 ATTAAAAAAATTATTATTTATAACTTATAAT
*
860356 ATTAAAAAAATT-TTATTTGTAACTT-TAAT
1 ATTAAAAAAATTATTATTTATAACTTATAAT
860385 AT
1 AT
860387 GATTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 10 0.36
31 12 0.43
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTAAAAAAATTATTATTTATAACTTATAAT
Found at i:860448 original size:27 final size:27
Alignment explanation
Indices: 860411--860468 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
860401 ATTTCATTTT
*
860411 ATTT-TTTAAAATATTAATAATTTATA
1 ATTTATTTAAAAGATTAATAATTTATA
*
860437 GTTTATTTAAAAGATTAATAATTTATA
1 ATTTATTTAAAAGATTAATAATTTATA
860464 ATTTA
1 ATTTA
860469 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTATTTAAAAGATTAATAATTTATA
Found at i:860545 original size:14 final size:15
Alignment explanation
Indices: 860528--860556 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
860518 TATAATTAGA
860528 ATTTTAAATT-TTTT
1 ATTTTAAATTCTTTT
860542 ATTTTAAATTCTTTT
1 ATTTTAAATTCTTTT
860557 TTGGTTCTCT
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:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTAAATTCTTTT
Found at i:876581 original size:75 final size:74
Alignment explanation
Indices: 876496--876653 Score: 208
Period size: 75 Copynumber: 2.1 Consensus size: 74
876486 TTCCATTGGA
* * * * * *
876496 AATTTCCAACGGAATTTTTCGTTGGTAAAGCATTTTCCATGAAAAATTCCGTTGGAAATAATTCT
1 AATTTTCAACGGAATTTTTCGTTGGAAAAGCATTTCCCATGAAAAATTCCG-TGAAAAAAATTAT
*
876561 GTAGGAAAGG
65 GTAAGAAAGG
* *
876571 AATTTTCAACGGATTTTTTCGTTGGAAAAGCATTTCCCATGAAAAATTTCGTGAAAAAAATTATG
1 AATTTTCAACGGAATTTTTCGTTGGAAAAGCATTTCCCATGAAAAATTCCGTGAAAAAAATTATG
**
876636 TAAGAAATT
66 TAAGAAAGG
876645 AATTTTCAA
1 AATTTTCAA
876654 TAGAAATTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 26 0.36
75 46 0.64
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (74 bp):
AATTTTCAACGGAATTTTTCGTTGGAAAAGCATTTCCCATGAAAAATTCCGTGAAAAAAATTATG
TAAGAAAGG
Found at i:877297 original size:12 final size:12
Alignment explanation
Indices: 877279--877321 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
877269 TTAATTTCTT
877279 CACGTATTTCCC
1 CACGTATTTCCC
*
877291 CATGTATTTCCC
1 CACGTATTTCCC
*
877303 CACGTATTTCCT
1 CACGTATTTCCC
877315 CACGTAT
1 CACGTAT
877322 CTTACCCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (12 bp):
CACGTATTTCCC
Found at i:879281 original size:6 final size:6
Alignment explanation
Indices: 879265--879303 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
879255 TTTGTCTTTG
* * *
879265 TCTTCG TCTTCA ACTTCA TCTTCA TCTTCA TTTTCA TCT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCT
879304 CCTTCCATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.31, G:0.03, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:884402 original size:21 final size:22
Alignment explanation
Indices: 884373--884416 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
884363 AAGTGATTAA
884373 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
884394 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
884416 T
1 T
884417 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:885074 original size:12 final size:13
Alignment explanation
Indices: 885059--885094 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
885049 AGAGATTTTT
885059 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
885071 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
885083 GAGGCAGCAAGA
1 GAGGCAGCAAGA
885095 AACTATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:892052 original size:9 final size:9
Alignment explanation
Indices: 892038--892062 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
892028 GCTCTTAGGA
892038 GAAGAATGG
1 GAAGAATGG
892047 GAAGAATGG
1 GAAGAATGG
892056 GAAGAAT
1 GAAGAAT
892063 TGGGGAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (9 bp):
GAAGAATGG
Found at i:898063 original size:32 final size:32
Alignment explanation
Indices: 897999--898063 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
897989 AAAGGTGTTA
* * *
897999 AATTTTTACAAAAAAGACAATAGCATCTTTAT
1 AATTTTGACAAAAAAGACAATAGAAACTTTAT
*
898031 AATTTTGACTAAAAAGACAAT-GAAACTCTTAT
1 AATTTTGACAAAAAAGACAATAGAAACT-TTAT
898063 A
1 A
898064 TTTAAAGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (32 bp):
AATTTTGACAAAAAAGACAATAGAAACTTTAT
Found at i:898720 original size:18 final size:18
Alignment explanation
Indices: 898697--898741 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
898687 TTTAAATATA
898697 AAAATAATAAAAAAAATT
1 AAAATAATAAAAAAAATT
*
898715 AAAAT-AT-AAAGAAATT
1 AAAATAATAAAAAAAATT
898731 AAAA-AATAAAA
1 AAAATAATAAAA
898742 TAAGTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.58
17 5 0.21
18 5 0.21
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAATAAAAAAAATT
Found at i:903802 original size:2 final size:2
Alignment explanation
Indices: 903797--903827 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
903787 TATATATATA
903797 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
903828 TATTTATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:911836 original size:19 final size:19
Alignment explanation
Indices: 911782--911838 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
911772 AGGAATTATC
* *
911782 TAGACCTTTTAGGCTTATT
1 TAGACCTTTTGGGCTTGTT
* *
911801 TAAACCTTTTGGACTTGTT
1 TAGACCTTTTGGGCTTGTT
911820 TAGACCTTTTGGGCTTGTT
1 TAGACCTTTTGGGCTTGTT
911839 GGAGTTTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (19 bp):
TAGACCTTTTGGGCTTGTT
Found at i:915163 original size:19 final size:20
Alignment explanation
Indices: 915131--915170 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
915121 CTTTTTGGTC
915131 TCTTATAGACCTTCAAACCT
1 TCTTATAGACCTTCAAACCT
* *
915151 TCTT-TAGATCTTCCAACCT
1 TCTTATAGACCTTCAAACCT
915170 T
1 T
915171 TTCCAGACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (20 bp):
TCTTATAGACCTTCAAACCT
Found at i:915301 original size:38 final size:38
Alignment explanation
Indices: 915259--915338 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
915249 GCAAAGAGGA
915259 AGAAGGTATATAAGAATTTTCAAGGTTGTGTTGAAATG
1 AGAAGGTATATAAGAATTTTCAAGGTTGTGTTGAAATG
* *
915297 AGAAGGTATATAAGAATTTTCGAGGTTGTGTTGCAATG
1 AGAAGGTATATAAGAATTTTCAAGGTTGTGTTGAAATG
915335 AGAA
1 AGAA
915339 ATGAAGCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (38 bp):
AGAAGGTATATAAGAATTTTCAAGGTTGTGTTGAAATG
Found at i:916848 original size:28 final size:26
Alignment explanation
Indices: 916812--916865 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
916802 AATATGTTAC
*
916812 AAATAAATAAATTATACTAAATATAAAT
1 AAATAAATAAATTACA-TAAATA-AAAT
916840 AAATAAATAAATTACATAAATAAAAT
1 AAATAAATAAATTACATAAATAAAAT
916866 TCTAATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 6 0.24
28 15 0.60
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATAAATAAATTACATAAATAAAAT
Found at i:916860 original size:9 final size:9
Alignment explanation
Indices: 916815--916865 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
916805 ATGTTACAAA
916815 TAAATAAAT
1 TAAATAAAT
*
916824 TATACTAAAT
1 TA-AATAAAT
916834 ATAAATAAA-
1 -TAAATAAAT
916843 TAAATAAAT
1 TAAATAAAT
*
916852 TACATAAAT
1 TAAATAAAT
*
916861 AAAAT
1 TAAAT
916866 TCTAATCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.24
9 13 0.38
10 11 0.32
11 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAATAAAT
Found at i:916866 original size:14 final size:13
Alignment explanation
Indices: 916812--916863 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
916802 AATATGTTAC
916812 AAATAAATAAATT
1 AAATAAATAAATT
* *
916825 ATACTAAATATAAAT
1 A-AATAAATA-AATT
916840 AAATAAATAAATT
1 AAATAAATAAATT
*
916853 ACATAAATAAA
1 AAATAAATAAA
916864 ATTCTAATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 14 0.44
14 14 0.44
15 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAATAAATT
Found at i:917497 original size:30 final size:30
Alignment explanation
Indices: 917429--917523 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
917419 TAATAAAGGG
**
917429 TTATTT-AATTTAAAATAAAAATA-CCAAAT
1 TTATTTGAA-TTAAAATAAAAATATAAAAAT
917458 CTTATTTGAATTAAAATAAAAATATAAAAAT
1 -TTATTTGAATTAAAATAAAAATATAAAAAT
* *
917489 TTGA-TTGAA-CATAATAAAAATATAAAAAT
1 TT-ATTTGAATTAAAATAAAAATATAAAAAT
917518 TTATTT
1 TTATTT
917524 TAAGTTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 22 0.39
30 27 0.47
31 7 0.12
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (30 bp):
TTATTTGAATTAAAATAAAAATATAAAAAT
Found at i:923140 original size:16 final size:16
Alignment explanation
Indices: 923119--923149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
923109 GTTCCTTTAT
923119 ATACATATACATATAC
1 ATACATATACATATAC
*
923135 ATACATATATATATA
1 ATACATATACATATA
923150 TGTAGTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATATACATATAC
Found at i:923404 original size:2 final size:2
Alignment explanation
Indices: 923397--923428 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
923387 AGTAAGTTCT
923397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
923429 GTTTAGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:923631 original size:131 final size:133
Alignment explanation
Indices: 923275--923650 Score: 519
Period size: 131 Copynumber: 2.8 Consensus size: 133
923265 ATACATAGAC
*
923275 ATATATATATATATATATGTGGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGA
1 ATATATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGA
* *
923340 ATCAATATCTTTGCAAATTGCAGGAAAA-TTGCCTAATATTAGA-TCGAAGTAAGTTCTTATATA
66 ATCAATATCTTTGCAAATTGCAGGAAAATTTACCTAATTTTAGATTCGAAGTAAG-T-TTATATA
923403 TATAT
129 TATAT
* *
923408 ATATATATATATATATATATAGTTTAGTT-GTATGCATGTATTCAATGTGCATGTTTAAAATAAG
1 ATATATATATATATATATGTAGTTTA-TTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAG
* * *
923472 AATCAATATCTTTGCAAATTGTAGGAAAATTTACCTAATTTTAGATTGGAAGTAAG-TTGT-TAT
65 AATCAATATCTTTGCAAATTGCAGGAAAATTTACCTAATTTTAGATTCGAAGTAAGTTTATATAT
923535 ATAT
130 ATAT
* * * * * * *
923539 GTATATATATGTATGTATGTACTTTATTCTTATGCATGTGTTCTATGTGCATGTTCAAAATAAGA
1 ATATATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGA
* * * *
923604 ATCAATATCTTTTCAAATTGGAAGAAAATTTTCCTAATTTTAGATTC
66 ATCAATATCTTTGCAAATTGCAGGAAAATTTACCTAATTTTAGATTC
923651 TAATATGACT
Statistics
Matches: 217, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
130 2 0.01
131 102 0.47
132 3 0.01
133 86 0.40
134 15 0.07
135 9 0.04
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (133 bp):
ATATATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGA
ATCAATATCTTTGCAAATTGCAGGAAAATTTACCTAATTTTAGATTCGAAGTAAGTTTATATATA
TAT
Found at i:930509 original size:2 final size:2
Alignment explanation
Indices: 930502--930531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
930492 AATGTATATG
930502 CA CA 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 CA CA
930532 TGTATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:938045 original size:2 final size:2
Alignment explanation
Indices: 938038--938083 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
938028 GAAGATAACA
938038 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
938080 TC TC
1 TC TC
938084 GATCTTCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:939584 original size:164 final size:164
Alignment explanation
Indices: 939406--939722 Score: 449
Period size: 164 Copynumber: 1.9 Consensus size: 164
939396 TACGTCTAAT
*
939406 TAAGTTTTTATATTTTTATTTTAAGTCAAATA-AGCTTTCATATCTAATGATTGA-CTAATTGTC
1 TAAGTTTTTATATTTTTATTTTAAGTCAAATAGA-CTTTCATATCTAATGA-TGAGCTAATTATC
* * * * *
939469 ATTAGTCAAAATATTACTTGTTATTTTATATTTATGTGACAGCGATATAGCGTTAATATGATGTT
64 ATTAGTCAAAATATTACTTGTAATTTTATATTCACGTGACAGCGATATAACGTTAATATGATATT
* * * *
939534 GATGTGGAAAGTGAAAAATATTATATGACTATGTTA
129 AACGTGAAAAGTAAAAAATATTATATGACTATGTTA
* * *
939570 TAAGTTTTTATATTTTTATTTTAAGTCAAATAGACTTTTATGTCTAATGATGAGCTACTTATCAT
1 TAAGTTTTTATATTTTTATTTTAAGTCAAATAGACTTTCATATCTAATGATGAGCTAATTATCAT
* ** *
939635 TAGTTAAAATATTACTTGTAATTTTATATTCACGTGACATTGATATAACGTTGATATGATATTAA
66 TAGTCAAAATATTACTTGTAATTTTATATTCACGTGACAGCGATATAACGTTAATATGATATTAA
939700 CGTGAAAAGTAAAAAATATTATA
131 CGTGAAAAGTAAAAAATATTATA
939723 CGATCATGTT
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
163 3 0.02
164 130 0.97
165 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (164 bp):
TAAGTTTTTATATTTTTATTTTAAGTCAAATAGACTTTCATATCTAATGATGAGCTAATTATCAT
TAGTCAAAATATTACTTGTAATTTTATATTCACGTGACAGCGATATAACGTTAATATGATATTAA
CGTGAAAAGTAAAAAATATTATATGACTATGTTA
Found at i:951385 original size:20 final size:20
Alignment explanation
Indices: 951360--951410 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
951350 GTTCTTCATG
951360 TATCGATACATTTAGACAA-A
1 TATCGATACATTTAGA-AATA
* * *
951380 TATCGATAGATTTTGAAATC
1 TATCGATACATTTAGAAATA
951400 TATCGATACAT
1 TATCGATACAT
951411 GTTTTTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTTAGAAATA
Found at i:963828 original size:3 final size:3
Alignment explanation
Indices: 963820--963851 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
963810 AGAGAGAGAT
963820 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
963852 TGCAAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:984546 original size:35 final size:35
Alignment explanation
Indices: 984471--984547 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
984461 TGGGATTAGC
*
984471 CGAAACCCTCACAATAGCCTTTTCACAGAATTAAG
1 CGAAACCCTCACAATAGCCTTTTCACAGAATCAAG
* *
984506 CGAAACCCTTACAATAGGCTTTTCAC-GAGATCAAG
1 CGAAACCCTCACAATAGCCTTTTCACAGA-ATCAAG
*
984541 TGAAACC
1 CGAAACC
984548 TTTCAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.22
Consensus pattern (35 bp):
CGAAACCCTCACAATAGCCTTTTCACAGAATCAAG
Found at i:988971 original size:29 final size:29
Alignment explanation
Indices: 988930--988987 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
988920 GATATTGAAA
*
988930 ATATCTTGCTTAGTTACTGT-GAATATTGT
1 ATATCTTGCTTAGCTACTGTAG-ATATTGT
*
988959 ATATCTTGTTTAGCTACTGTAGATATTGT
1 ATATCTTGCTTAGCTACTGTAGATATTGT
988988 GAATGTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (29 bp):
ATATCTTGCTTAGCTACTGTAGATATTGT
Found at i:990992 original size:20 final size:20
Alignment explanation
Indices: 990967--991004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
990957 TAAAGAAAAA
990967 TTTTGGA-ATAAAATAATAAT
1 TTTTGGATA-AAAATAATAAT
990987 TTTTGGATAAAAATAATA
1 TTTTGGATAAAAATAATA
991005 TTAAGATAAT
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:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTGGATAAAAATAATAAT
Found at i:992021 original size:7 final size:7
Alignment explanation
Indices: 991997--992034 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
991987 TAACAAAGCA
991997 AAAG-AG
1 AAAGAAG
992003 AAAGAAAG
1 AAAG-AAG
*
992011 AAAGGAG
1 AAAGAAG
992018 AAAGAAG
1 AAAGAAG
992025 AAAGAAG
1 AAAGAAG
992032 AAA
1 AAA
992035 AAGTTGACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 4 0.14
7 18 0.64
8 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:995734 original size:76 final size:75
Alignment explanation
Indices: 995618--995787 Score: 199
Period size: 76 Copynumber: 2.3 Consensus size: 75
995608 GTAGGTTTTT
* **
995618 TATTTTGTCATTTTT-AAAATTTTTAATTTTTAATTCAAAAA-TAAAAA-TTTAAGTAAAAGTA-
1 TATTTTTTCATTTTTCAAAATTAATAATTTTTAATTCAAAAATTAAAAATTTTAAGTAAAA--AC
995679 ATTTTTTATCGTC
64 A-TTTTTATCGTC
*
995692 TATCTTTTTCATTTTTCAAAATTAAT-ATTTCTTAATTTAAAAATTAAAAATTTTAAGTAAAAAC
1 TAT-TTTTTCATTTTTCAAAATTAATAATTT-TTAATTCAAAAATTAAAAATTTTAAGTAAAAAC
*
995756 ATTTTTATCTTC
64 ATTTTTATCGTC
*
995768 TATTTTTTC-TTTTTCCAAAT
1 TATTTTTTCATTTTTCAAAAT
995788 CTTTGATTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
74 13 0.15
75 21 0.25
76 32 0.38
77 7 0.08
78 11 0.13
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (75 bp):
TATTTTTTCATTTTTCAAAATTAATAATTTTTAATTCAAAAATTAAAAATTTTAAGTAAAAACAT
TTTTATCGTC
Found at i:1000848 original size:20 final size:19
Alignment explanation
Indices: 1000825--1000874 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1000815 ATATTATGTA
1000825 TGAGTATTTATGTAAAGATT
1 TGAGTATTTATG-AAAGATT
* *
1000845 TGAGTTATATATGAATGATT
1 TGAG-TATTTATGAAAGATT
1000865 TGAGGTATTT
1 TGA-GTATTT
1000875 TGATAAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (19 bp):
TGAGTATTTATGAAAGATT
Found at i:1001129 original size:20 final size:20
Alignment explanation
Indices: 1001092--1001131 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1001082 AGTAAGGACA
*
1001092 CTTGGAAACCATCGATAGAT
1 CTTGGAAACCATCAATAGAT
* *
1001112 CTTGGAATCTATCAATAGAT
1 CTTGGAAACCATCAATAGAT
1001132 GGCCAAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CTTGGAAACCATCAATAGAT
Found at i:1001863 original size:10 final size:10
Alignment explanation
Indices: 1001848--1001881 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1001838 TTAGAATAAA
1001848 ATGTGTGTGT
1 ATGTGTGTGT
1001858 ATGTGTGTGT
1 ATGTGTGTGT
*
1001868 GTGTGTGTGT
1 ATGTGTGTGT
1001878 ATGT
1 ATGT
1001882 TTGCTCGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (10 bp):
ATGTGTGTGT
Found at i:1013718 original size:45 final size:47
Alignment explanation
Indices: 1013580--1013797 Score: 237
Period size: 47 Copynumber: 4.7 Consensus size: 47
1013570 GACAGGGCTG
* *
1013580 TGACACGACAGGGTTCAGAGTTTGATGACACGGCATGGAGGGAATCTG
1 TGACACGACAGAGTTCAGAGTTTG-TGACACGGCATGGAGGGAATCTA
** * * *
1013628 TGACACTCCAAAGTTCAGAGTTTGTGACACGACATAGAGGGAATCTA
1 TGACACGACAGAGTTCAGAGTTTGTGACACGGCATGGAGGGAATCTA
* * *
1013675 TGACACGCCAGAGTTCAGAG-TT-TGACATGGCATGGATGGAATCTA
1 TGACACGACAGAGTTCAGAGTTTGTGACACGGCATGGAGGGAATCTA
* * *
1013720 TGACACGATAGTA-TTTAGAGTTTGTGACACGCCATGGAGGGAATCTA
1 TGACACGACAG-AGTTCAGAGTTTGTGACACGGCATGGAGGGAATCTA
* * *
1013767 TGACAAGGCA-AGGTTCAGGGTTTGTGACACG
1 TGACACGACAGA-GTTCAGAGTTTGTGACACG
1013798 CCGGTGTTCA
Statistics
Matches: 141, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
45 35 0.25
46 5 0.04
47 81 0.57
48 20 0.14
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (47 bp):
TGACACGACAGAGTTCAGAGTTTGTGACACGGCATGGAGGGAATCTA
Found at i:1013905 original size:163 final size:163
Alignment explanation
Indices: 1013640--1013958 Score: 415
Period size: 163 Copynumber: 2.0 Consensus size: 163
1013630 ACACTCCAAA
* * * *
1013640 GTTCAGAGTTTGTGACACGACATAGAGGGAATCTATGACACGCCAGAGTTCAGAGTTTGACATGG
1 GTTCAAAGTTTGTGACACGACATAGAGGGAATCTATAACACGCCAGAGTTCAGAGTATGACACGG
* * * * *
1013705 CATGGATGGAATCTATGACACGATAGTATTTAGAGTTTGTGACACGCCATGGAGGGAATCTATGA
66 CATGGATGAAATCTATGACACGACAGTATTCAGAGTTTGTGACACGCCATAGAAGGAATCTATGA
*
1013770 CAAGGCAAGGTTCAGGGTTTGTGACACGCCGGT
131 CAAGACAAGGTTCAGGGTTTGTGACACGCCGGT
* * * * * *
1013803 GTTCAAAGTTTGTGACATGGCTTGGAGGGAATCTGA-AACATGCTAGAGTTCAGAGTATGACACG
1 GTTCAAAGTTTGTGACACGACATAGAGGGAATCT-ATAACACGCCAGAGTTCAGAGTATGACACG
* * * *
1013867 GCATGGATGAAATCTGTGACACTACAGTATTCAGAGTTTGTGACACGCCATAGAAGGAATCTGTT
65 GCATGGATGAAATCTATGACACGACAGTATTCAGAGTTTGTGACACGCCATAGAAGGAATCTATG
* * *
1013932 ACACGACAGGGTTTAGGGTTTGTGACA
130 ACAAGACAAGGTTCAGGGTTTGTGACA
1013959 TGCCATGGAG
Statistics
Matches: 132, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
163 131 0.99
164 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (163 bp):
GTTCAAAGTTTGTGACACGACATAGAGGGAATCTATAACACGCCAGAGTTCAGAGTATGACACGG
CATGGATGAAATCTATGACACGACAGTATTCAGAGTTTGTGACACGCCATAGAAGGAATCTATGA
CAAGACAAGGTTCAGGGTTTGTGACACGCCGGT
Found at i:1013928 original size:47 final size:47
Alignment explanation
Indices: 1013804--1014231 Score: 355
Period size: 47 Copynumber: 9.2 Consensus size: 47
1013794 CACGCCGGTG
* * * ** *
1013804 TTCAAAGTTTGTGACATGGCTTGGAGGGAATCTGAAACA-TGCTAG-A
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTAC-AGTA
* * *
1013850 GTTCAGAG--TATGACACGGCATGGATGAAATCTGTGACACTACAGTA
1 -TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTACAGTA
* * * * * **
1013896 TTCAGAGTTTGTGACACGCCATAGAAGGAATCTGTTACACGACAGGG
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTACAGTA
* * * * *
1013943 TTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGGCAC-ACCAGTA
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTA-CAGTA
*
1013990 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGT-CA-AA
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACAC-TACAGTA
* * *
1014036 GTTCAGAG-TT-TGACACGGTATGGATGGAATCTGTGACACGACAGTA
1 -TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTACAGTA
* *
1014082 TTTAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACA-TGCCAG-A
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACT-ACAGTA
* * * *
1014128 GTTCAGAG-TT-TGACATGGCATGGATGGAATCTGTGACACAACAATA
1 -TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTACAGTA
* * * *
1014174 TTCAGATTTTGTGACACGCCATGGAGGGAATTTGTGATAC-ACTAG-A
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTAC-AGTA
1014220 GTTCAGAGTTTG
1 -TTCAGAGTTTG
1014232 ACATGACAAC
Statistics
Matches: 305, Mismatches: 56, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
45 101 0.33
46 19 0.06
47 185 0.61
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (47 bp):
TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACTACAGTA
Found at i:1014099 original size:92 final size:91
Alignment explanation
Indices: 1013804--1014234 Score: 490
Period size: 92 Copynumber: 4.7 Consensus size: 91
1013794 CACGCCGGTG
* * * ** * *
1013804 TTCAAAGTTTGTGACATGGCTTGGAGGGAATCTGAAACATG-CTAGAGTTCAGAGTATGACACGG
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTC-AGAGTTCAGAGTTTGACACGG
*
1013868 CATGGATGAAATCTGTGACACTACAGTA
65 CATGGATGGAATCTGTGACAC-ACAGTA
* * * * * * * * *
1013896 TTCAGAGTTTGTGACACGCCATAGAAGGAATCTGTTACACGACAGGGTTTAGGGTTTGTGACATG
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAG-TT-TGACACG
* * *
1013961 CCATGGAGGGAATCTGTGGCACACCAGTA
64 GCATGGATGGAATCTGTGACACA-CAGTA
* *
1013990 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAAAGTTCAGAGTTTGACACGGT
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTGACACGGC
1014055 ATGGATGGAATCTGTGACACGACAGTA
66 ATGGATGGAATCTGTGACAC-ACAGTA
* * * *
1014082 TTTAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACATGCCAGAGTTCAGAGTTTGACATGGC
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTGACACGGC
*
1014147 ATGGATGGAATCTGTGACACAACAATA
66 ATGGATGGAATCTGTGACAC-ACAGTA
* * *
1014174 TTCAGATTTTGTGACACGCCATGGAGGGAATTTGTGATACAC-T-AGAGTTCAGAGTTTGACA
1 TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTG--ACACGTCAGAGTTCAGAGTTTGACA
1014235 TGACAACATT
Statistics
Matches: 286, Mismatches: 46, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
92 203 0.71
93 6 0.02
94 77 0.27
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (91 bp):
TTCAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTGACACGGC
ATGGATGGAATCTGTGACACACAGTA
Found at i:1014228 original size:139 final size:138
Alignment explanation
Indices: 1013789--1014231 Score: 473
Period size: 139 Copynumber: 3.2 Consensus size: 138
1013779 GTTCAGGGTT
* * * * * ** *
1013789 TGTGACACGCCGGTGTTCAAAGTTTGTGACATGGCTTGGAGGGAATCTGAAACATGCTAGAGTTC
1 TGTGACACGACAGAGTTCAGAGTTTGTGACATGGCATGGAGGGAATCTGTGACATGCCAGAGTTC
* * * * *
1013854 AGAGTATGACACGGCATGGATGAAATCTGTGACACTACAGTATTCAGAGTTTGTGACACGCCATA
66 AGAGTTTGACACGGCATGGATGGAATCTGTGACACAACAATATTCAGA-TTTGTGACACGCCATG
1013919 GAAGGAATC
130 GAAGGAATC
* * * * * * **
1013928 TGTTACACGACAGGGTTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGGCACACCAGTA-TT
1 TGTGACACGACAGAGTTCAGAGTTTGTGACATGGCATGGAGGGAATCTGTGACATGCCAG-AGTT
* ** * **
1013992 CAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACACGTCAA-AGTTCAGAGTT-TGACACGGT
65 CAGAG-TT-TGACACGGCATGGATGGAATCTGTGACACAACAATA-TTCAGATTTGTGACACGCC
*
1014055 ATGGATGGAATC
127 ATGGAAGGAATC
* *
1014067 TGTGACACGACAGTA-TTTAGAGTTTGTGACACGGCATGGAGGGAATCTGTGACATGCCAGAGTT
1 TGTGACACGACAG-AGTTCAGAGTTTGTGACATGGCATGGAGGGAATCTGTGACATGCCAGAGTT
*
1014131 CAGAGTTTGACATGGCATGGATGGAATCTGTGACACAACAATATTCAGATTTTGTGACACGCCAT
65 CAGAGTTTGACACGGCATGGATGGAATCTGTGACACAACAATATTCAGA-TTTGTGACACGCCAT
* *
1014196 GGAGGGAATT
129 GGAAGGAATC
*
1014206 TGTGATAC-ACTAGAGTTCAGAGTTTG
1 TGTGACACGAC-AGAGTTCAGAGTTTG
1014232 ACATGACAAC
Statistics
Matches: 248, Mismatches: 45, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
137 36 0.15
138 9 0.04
139 163 0.66
140 5 0.02
141 35 0.14
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (138 bp):
TGTGACACGACAGAGTTCAGAGTTTGTGACATGGCATGGAGGGAATCTGTGACATGCCAGAGTTC
AGAGTTTGACACGGCATGGATGGAATCTGTGACACAACAATATTCAGATTTGTGACACGCCATGG
AAGGAATC
Found at i:1014281 original size:23 final size:23
Alignment explanation
Indices: 1014220--1014282 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1014210 ATACACTAGA
* *
1014220 GTTCAGAGTT-TGACATGACAAC
1 GTTCAGGGTTGTGACACGACAAC
* * *
1014242 ATTCAAGGTTTGTGACACGGCAAC
1 GTTC-AGGGTTGTGACACGACAAC
1014266 GTTCAGGGTTGTGACAC
1 GTTCAGGGTTGTGACAC
1014283 TCCACTGAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.09
23 16 0.50
24 13 0.41
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (23 bp):
GTTCAGGGTTGTGACACGACAAC
Found at i:1014916 original size:62 final size:62
Alignment explanation
Indices: 1014840--1015020 Score: 254
Period size: 62 Copynumber: 2.9 Consensus size: 62
1014830 ATATCGTGTC
* * * * * *
1014840 ACGACATTTGACTTGATATGCATAGCGTGTCACCACATTTTACTTGTTTTGCATGGCATGTG
1 ACGACCTTTTACTTGTTATGCATGGCGTGTGACCACATTTTACTTGTTATGCATGGCATGTG
* * * **
1014902 ACGACCTTTTACTTGTTGTGCATGGCATGTGACCACATTTTACATGTTATGCATGGTGTGTG
1 ACGACCTTTTACTTGTTATGCATGGCGTGTGACCACATTTTACTTGTTATGCATGGCATGTG
*
1014964 ACAACCTTTTACTTGTTATGCATGGCGTGTGACCACATTTTACTTGTTATGCATGGC
1 ACGACCTTTTACTTGTTATGCATGGCGTGTGACCACATTTTACTTGTTATGCATGGC
1015021 NNNNNNNNNN
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 103 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
ACGACCTTTTACTTGTTATGCATGGCGTGTGACCACATTTTACTTGTTATGCATGGCATGTG
Found at i:1015018 original size:31 final size:31
Alignment explanation
Indices: 1014834--1015020 Score: 230
Period size: 31 Copynumber: 6.0 Consensus size: 31
1014824 ATCTGCATAT
* * * * *
1014834 CGTGTCACGACATTTGACTTGATATGCATAG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
* *
1014865 CGTGTCACCACATTTTACTTGTTTTGCATGG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
* * * *
1014896 CATGTGACGACCTTTTACTTGTTGTGCATGG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
* *
1014927 CATGTGACCACATTTTACATGTTATGCATGG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
* * *
1014958 TGTGTGACAACCTTTTACTTGTTATGCATGG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
1014989 CGTGTGACCACATTTTACTTGTTATGCATGG
1 CGTGTGACCACATTTTACTTGTTATGCATGG
1015020 C
1 C
1015021 NNNNNNNNNN
Statistics
Matches: 134, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
CGTGTGACCACATTTTACTTGTTATGCATGG
Found at i:1017547 original size:23 final size:23
Alignment explanation
Indices: 1017519--1017619 Score: 166
Period size: 23 Copynumber: 4.4 Consensus size: 23
1017509 TGCAACCATG
*
1017519 TGGCGTGTCACCGCACTAGGGCA
1 TGGCGTGTCACCCCACTAGGGCA
*
1017542 TGGCGTGTCACCGCACTAGGGCA
1 TGGCGTGTCACCCCACTAGGGCA
1017565 TGGCGTGTCACCCCACTAGGGCA
1 TGGCGTGTCACCCCACTAGGGCA
* *
1017588 TGGCGTGTCACCCCATTGGGGCA
1 TGGCGTGTCACCCCACTAGGGCA
1017611 TGGCGTGTC
1 TGGCGTGTC
1017620 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.20
Consensus pattern (23 bp):
TGGCGTGTCACCCCACTAGGGCA
Found at i:1023883 original size:40 final size:40
Alignment explanation
Indices: 1023850--1023970 Score: 156
Period size: 40 Copynumber: 3.0 Consensus size: 40
1023840 GAAAAAGCAT
1023850 TGACATTGTAAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
1 TGACATTGTAAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
* * *
1023890 TGACGTTG-AGAGGTTGTGCTTGCTCCTTTTCAAAAGGTAG
1 TGACATTGTA-AGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
* * **
1023930 TGACATTGTGAGGTTGTGTTTGCT-CTCTCAAAAAGGTAG
1 TGACATTGTAAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
1023969 TG
1 TG
1023971 CTTGTGAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 15 0.21
40 55 0.79
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (40 bp):
TGACATTGTAAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
Found at i:1023983 original size:39 final size:40
Alignment explanation
Indices: 1023859--1023983 Score: 134
Period size: 40 Copynumber: 3.1 Consensus size: 40
1023849 TTGACATTGT
* *
1023859 AAGGTTGTGCTTGCTCCTCTTGAAAAGGTAGTGACGT-TGA
1 AAGGTTGTGCTTGCTCCTC-TCAAAAGGTAGTGACTTGTGA
* *
1023899 GAGGTTGTGCTTGCTCCTTTTCAAAAGGTAGTGACATTGTG-
1 AAGGTTGTGCTTGCTCC-TCTCAAAAGGTAGTGAC-TTGTGA
*
1023940 -AGGTTGTGTTTGCT-CTCTCAAAAAGGTAGTG-CTTGTGA
1 AAGGTTGTGCTTGCTCCTCTC-AAAAGGTAGTGACTTGTGA
1023978 AAGGTT
1 AAGGTT
1023984 ATGCCTACTC
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
37 5 0.07
38 4 0.05
39 17 0.23
40 43 0.59
41 2 0.03
42 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (40 bp):
AAGGTTGTGCTTGCTCCTCTCAAAAGGTAGTGACTTGTGA
Found at i:1023995 original size:79 final size:80
Alignment explanation
Indices: 1023850--1023996 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 80
1023840 GAAAAAGCAT
** * * * *
1023850 TGACATTGTAAGGTTGTGCTTGCTCCTCTTGAAAAGGTAGTGACGTTGAGAGGTTGTGCTTGCTC
1 TGACATTGTAAGGTTGTGCTTGCTCCTCTCAAAAAGGTAGTGACGTTGAAAGGTTATGCCTACTC
1023915 CTTTTCAAAAGGTAG
66 CTTTTCAAAAGGTAG
* * *
1023930 TGACATTGTGAGGTTGTGTTTGCT-CTCTCAAAAAGGTAGTG-CTTGTGAAAGGTTATGCCTACT
1 TGACATTGTAAGGTTGTGCTTGCTCCTCTCAAAAAGGTAGTGACGT-TGAAAGGTTATGCCTACT
1023993 CCTT
65 CCTT
1023997 GAAAGGCAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 2 0.04
79 33 0.58
80 22 0.39
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (80 bp):
TGACATTGTAAGGTTGTGCTTGCTCCTCTCAAAAAGGTAGTGACGTTGAAAGGTTATGCCTACTC
CTTTTCAAAAGGTAG
Found at i:1030478 original size:18 final size:18
Alignment explanation
Indices: 1030444--1030504 Score: 95
Period size: 18 Copynumber: 3.3 Consensus size: 18
1030434 AAAATATTAA
1030444 TATTTTATTTATAAAATAT
1 TATTTTATTT-TAAAATAT
1030463 TATTTTATTTTAAAATAT
1 TATTTTATTTTAAAATAT
*
1030481 TATTTTAATTTAAAATAT
1 TATTTTATTTTAAAATAT
*
1030499 TCTTTT
1 TATTTT
1030505 TACATGTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 30 0.75
19 10 0.25
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTATTTTAAAATAT
Found at i:1043004 original size:19 final size:19
Alignment explanation
Indices: 1042976--1043017 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1042966 ATCTCCCGTT
*
1042976 AGTTTGAAATTCACCAGTA
1 AGTTTAAAATTCACCAGTA
1042995 AGTTTAAAATTCACCAGTA
1 AGTTTAAAATTCACCAGTA
1043014 AGTT
1 AGTT
1043018 CTTGTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
AGTTTAAAATTCACCAGTA
Found at i:1048235 original size:377 final size:376
Alignment explanation
Indices: 1047424--1048481 Score: 1792
Period size: 377 Copynumber: 2.8 Consensus size: 376
1047414 TCCTTTAGTG
* * * * * *
1047424 AAGGCAATAGCATCAACGCTGCAGTGCCACACTCCCAGCGTTGCAGCATTGATGCTACTGCCTTC
1 AAGGCAGTGGCATCAACGCCGCAGCGCCACACTCCCAACGTTGCAGCGTTGATGCTACTGCCTTC
1047489 ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCT-TAATAAAGAAAAA
66 ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
1047553 TCCAAACCATA-TTATTATAACCCTGCTATAATAAAGAAC-ACAATCATCCTGATTGTAAAAAGA
131 TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAACTACAATCATCCTGATTGTAAAAAGA
* *
1047616 AAGTTTATGCCCCATCAGACCTTAGTAGATGACATTGACCATATTTATAAGCTCAATCTGATGAT
196 AAG-TTGTGCCCCATCAGACCTTAGTATATGACATTGACCATATTTATAAGCTCAATCTGATGAT
** *
1047681 ATTGTCATAGACTGCTGTTTGGTGAAGGCAGTAGCATCAACGCTGCAGCG-TTGGAGTGTGGCGC
260 ATTGTCATAGACTGCTGTTTGGTGAAGGCAGTAGCATCAACGCTGCAGCGCTAAGAGTGTGGAGC
* * *
1047745 TGCAGCGTTGATGCTATTGCCTTCACCAAGGGGACAGCGCTGGGACATGCAC
325 TACAACGTTGATGCTATTGCCTTCACCAAGGGGACAACGCTGGGACATGCAC
* *
1047797 AAGGCAGTGGCATCAACGCTGCAGCGCCACACTCCCAACGTTTCAGCGTTGATGCTACTGCCTTC
1 AAGGCAGTGGCATCAACGCCGCAGCGCCACACTCCCAACGTTGCAGCGTTGATGCTACTGCCTTC
1047862 ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
66 ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
1047927 TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAACTACAATCATCCTGTATTGTAAAAAG
131 TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAACTACAATCATCCTG-ATTGTAAAAAG
1047992 AAAGTTGTGCCCCATCAGACCTTAGTATATGACATTGACCATATTTATAAGCTCAATCTGATGAT
195 AAAGTTGTGCCCCATCAGACCTTAGTATATGACATTGACCATATTTATAAGCTCAATCTGATGAT
* *
1048057 ATTGTCATAGACTGCTATTTGGTGAAGGCAGTAGCATCAATGCTGCAGCGCTAAGAGTGTGGAGC
260 ATTGTCATAGACTGCTGTTTGGTGAAGGCAGTAGCATCAACGCTGCAGCGCTAAGAGTGTGGAGC
*
1048122 TACAACGTTGATGCTATTGCCTTCACCAAGGGGACAACGTTGGGACATGCACC
325 TACAACGTTGATGCTATTGCCTTCACCAAGGGGACAACGCTGGGACATGCA-C
* * *
1048175 AA-GCAGTGGCATTAATGCCGCAGCGCCACACTCCCAACGCTGCAGCGTTGATGCTACTGCCTTC
1 AAGGCAGTGGCATCAACGCCGCAGCGCCACACTCCCAACGTTGCAGCGTTGATGCTACTGCCTTC
*
1048239 ACCAAACAGCAGTATATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
66 ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
*
1048304 TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAAATACAATCATCCTGGATTGT-AAAAG
131 TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAACTACAATCATCCT-GATTGTAAAAAG
1048368 AAAGTTGTGCCCCATCAGACCTTAGTATATGACA-TGACCATATTTATAAGCTCAATCTGATGAT
195 AAAGTTGTGCCCCATCAGACCTTAGTATATGACATTGACCATATTTATAAGCTCAATCTGATGAT
*
1048432 ATTGTCATA-A-TGCTGTTTGGTGAAGGCAATAGCATCAACGCTGCAGCGCT
260 ATTGTCATAGACTGCTGTTTGGTGAAGGCAGTAGCATCAACGCTGCAGCGCT
1048482 GGGCAAACAG
Statistics
Matches: 651, Mismatches: 27, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
373 147 0.23
374 25 0.04
375 67 0.10
376 158 0.24
377 250 0.38
378 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (376 bp):
AAGGCAGTGGCATCAACGCCGCAGCGCCACACTCCCAACGTTGCAGCGTTGATGCTACTGCCTTC
ACCAAACAGCAGTCTATGACATTGGTGAAGGCATGCCAAAATAACCATGCTATAATAAAGAAAAA
TCCAAACCATATTTATTATAACCCTGCTATAATAAAGAACTACAATCATCCTGATTGTAAAAAGA
AAGTTGTGCCCCATCAGACCTTAGTATATGACATTGACCATATTTATAAGCTCAATCTGATGATA
TTGTCATAGACTGCTGTTTGGTGAAGGCAGTAGCATCAACGCTGCAGCGCTAAGAGTGTGGAGCT
ACAACGTTGATGCTATTGCCTTCACCAAGGGGACAACGCTGGGACATGCAC
Found at i:1052776 original size:25 final size:24
Alignment explanation
Indices: 1052748--1052795 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1052738 GTTGGAGCAA
*
1052748 TTAAGACTGTAAATTCAGTGGAAAG
1 TTAAGACTATAAATTCA-TGGAAAG
*
1052773 TTAAGAGTATAAATTCATGGAAA
1 TTAAGACTATAAATTCATGGAAA
1052796 CTCTGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (24 bp):
TTAAGACTATAAATTCATGGAAAG
Found at i:1053253 original size:35 final size:35
Alignment explanation
Indices: 1053213--1053279 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1053203 TATTGTATAA
1053213 AGAATAATAAAAACAAGTGAAGCACTACTTCATAT
1 AGAATAATAAAAACAAGTGAAGCACTACTTCATAT
* * *
1053248 AGAATAATTAAAACAAGTGAAGTACTATTTCA
1 AGAATAATAAAAACAAGTGAAGCACTACTTCA
1053280 CACACAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (35 bp):
AGAATAATAAAAACAAGTGAAGCACTACTTCATAT
Found at i:1059967 original size:2 final size:2
Alignment explanation
Indices: 1059960--1059994 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1059950 AAACCTCTTT
1059960 TA TA TA TA 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 TA TA TA TA T
1059995 GCACACACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1062347 original size:2 final size:2
Alignment explanation
Indices: 1062340--1062377 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1062330 TATGAACGGT
1062340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1062378 GTTTCATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1066332 original size:12 final size:13
Alignment explanation
Indices: 1066305--1066333 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1066295 CCAAAATTTC
1066305 AAAGCTTTGTTCT
1 AAAGCTTTGTTCT
1066318 AAAGCTTTG-TCT
1 AAAGCTTTGTTCT
1066330 AAAG
1 AAAG
1066334 TCACCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (13 bp):
AAAGCTTTGTTCT
Found at i:1066701 original size:7 final size:7
Alignment explanation
Indices: 1066689--1066723 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1066679 GTCCAATAAT
1066689 AGTGGCA
1 AGTGGCA
1066696 AGTGGCA
1 AGTGGCA
1066703 AGTGGCA
1 AGTGGCA
1066710 AGTGGCA
1 AGTGGCA
1066717 AGTGGCA
1 AGTGGCA
1066724 TGCATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (7 bp):
AGTGGCA
Found at i:1074762 original size:15 final size:16
Alignment explanation
Indices: 1074734--1074771 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1074724 TATTTTACAT
1074734 TAACGTTATAAAAATTA
1 TAAC-TTATAAAAATTA
1074751 TAACTTAT-AAAATTA
1 TAACTTATAAAAATTA
*
1074766 TTACTT
1 TAACTT
1074772 GTAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 4 0.20
17 4 0.20
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (16 bp):
TAACTTATAAAAATTA
Found at i:1075549 original size:32 final size:32
Alignment explanation
Indices: 1075462--1075542 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
1075452 TTAAAACAAA
*
1075462 GTTATTATACGTCATGTTGAAAAAAAAATATC
1 GTTATTACACGTCATGTTGAAAAAAAAATATC
* ** *
1075494 GTTGTTACACACCATGTTGAAAAAAAAATATT
1 GTTATTACACGTCATGTTGAAAAAAAAATATC
1075526 GTTATTACACGTCATGT
1 GTTATTACACGTCATGT
1075543 ATAAAAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (32 bp):
GTTATTACACGTCATGTTGAAAAAAAAATATC
Found at i:1075596 original size:114 final size:114
Alignment explanation
Indices: 1075393--1075602 Score: 287
Period size: 115 Copynumber: 1.8 Consensus size: 114
1075383 GTTGTACATT
* * ** * *
1075393 ATGTTGAAAACAAATATTATTATTACATGTTTTATATAAAAATATGTTATACGTCATGATTAAAA
1 ATGTTGAAAAAAAATATTATTATTACACGTCATATATAAAAACATGCTATACGTCATGATTAAAA
*
1075458 CAAAGTTATTATACGTCATGTTGAAAAAAAAATATCGTTGTTACACACC
66 CAAAGTTATTATACATCATGTTGAAAAAAAAATATCGTTGTTACACACC
* * * *
1075507 ATGTTGAAAAAAAAATATTGTTATTACACGTCATGTATAAAAACATGCTATACGTTATGGTTAAA
1 ATGTTG-AAAAAAAATATTATTATTACACGTCATATATAAAAACATGCTATACGTCATGATTAAA
* *
1075572 A-AAAGTTGTTATACATTATGTTGAAAAAAAA
65 ACAAAGTTATTATACATCATGTTGAAAAAAAA
1075603 TATTAGTGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 33 0.40
115 49 0.60
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (114 bp):
ATGTTGAAAAAAAATATTATTATTACACGTCATATATAAAAACATGCTATACGTCATGATTAAAA
CAAAGTTATTATACATCATGTTGAAAAAAAAATATCGTTGTTACACACC
Found at i:1075680 original size:29 final size:29
Alignment explanation
Indices: 1075647--1075711 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1075637 ACACGTCATA
*
1075647 TTAAAAAAA-AGTTATTATTATACACCATG
1 TTAAAAAAATA-TTATTATTACACACCATG
* **
1075676 TTAAAAAAATATTATTGTTACACGTCATG
1 TTAAAAAAATATTATTATTACACACCATG
1075705 TTAAAAA
1 TTAAAAA
1075712 CAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (29 bp):
TTAAAAAAATATTATTATTACACACCATG
Found at i:1075681 original size:27 final size:28
Alignment explanation
Indices: 1075636--1075711 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
1075626 AAAAATTTGT
*
1075636 TACACGTCATATTAAAAAAAAGTTATTATT-A
1 TACACG-CATGTT-AAAAAAA--TATTATTGA
*
1075667 TACAC-CATGTTAAAAAAATATTATTGT
1 TACACGCATGTTAAAAAAATATTATTGA
1075694 TACACGTCATGTTAAAAA
1 TACACG-CATGTTAAAAA
1075712 CAATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 7 0.17
27 5 0.12
28 7 0.17
29 16 0.40
31 5 0.12
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (28 bp):
TACACGCATGTTAAAAAAATATTATTGA
Found at i:1076729 original size:26 final size:26
Alignment explanation
Indices: 1076700--1076778 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
1076690 ATTCATATTT
1076700 TAAAATATTAAAAATTAAATTATAAA
1 TAAAATATTAAAAATTAAATTATAAA
* * * *
1076726 TAAAATATTAATATTTAAATGATCAAT
1 TAAAATATTAAAAATTAAATTAT-AAA
*
1076753 TACAAATATTTAAAA-TAAATTATAAA
1 TA-AAATATTAAAAATTAAATTATAAA
1076779 GTATTACTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 22 0.52
27 11 0.26
28 9 0.21
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (26 bp):
TAAAATATTAAAAATTAAATTATAAA
Found at i:1076744 original size:19 final size:18
Alignment explanation
Indices: 1076708--1076745 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1076698 TTTAAAATAT
1076708 TAAAAATTAAATTATAAA
1 TAAAAATTAAATTATAAA
1076726 TAAAATATTAATATT-TAAA
1 TAAAA-ATTAA-ATTATAAA
1076745 T
1 T
1076746 GATCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 10 0.56
20 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAATTAAATTATAAA
Found at i:1076886 original size:117 final size:104
Alignment explanation
Indices: 1076757--1076969 Score: 203
Period size: 117 Copynumber: 1.9 Consensus size: 104
1076747 ATCAATTACA
* * *
1076757 AATATTTAAAATAAATTATAAAGTATTACTATTT-AAAAATAAAATAAAATAAAAATAAATAAGC
1 AATATTTAAAATAAATTACAAAGTATTAATATTTAAAAAATAAAATAAAAT-AAAA-AAATAAAC
*
1076821 ATAATAACATTTAAATTACATATAAAATATTAATAATTAAATT
64 ATAATAACATTTAAATTA-A-ATAAAATAGTAATAATTAAATT
* * * *
1076864 NNNNNNNNNNAATATTTTAAATAAATTACCAATTCTTAATATTTAAAAAATAAAATAAAATAAAA
1 ----------AATATTTAAAATAAATTACAAAGTATTAATATTTAAAAAATAAAATAAAATAAAA
* *
1076929 AATTAAACATAATAATATTTAAATTAAATAAAATAGTAATA
56 AAATAAACATAATAACATTTAAATTAAATAAAATAGTAATA
1076970 CTTTAAAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
114 13 0.15
115 1 0.01
116 23 0.27
117 32 0.38
118 16 0.19
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.33
Consensus pattern (104 bp):
AATATTTAAAATAAATTACAAAGTATTAATATTTAAAAAATAAAATAAAATAAAAAAATAAACAT
AATAACATTTAAATTAAATAAAATAGTAATAATTAAATT
Found at i:1076929 original size:17 final size:20
Alignment explanation
Indices: 1076907--1076945 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
1076897 TCTTAATATT
1076907 TAAAAAA-TAAA-ATAA-AA
1 TAAAAAATTAAACATAATAA
1076924 TAAAAAATTAAACATAATAA
1 TAAAAAATTAAACATAATAA
1076944 TA
1 TA
1076946 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 4 0.21
20 4 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAAAATTAAACATAATAA
Found at i:1076951 original size:24 final size:24
Alignment explanation
Indices: 1076924--1076983 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
1076914 TAAAATAAAA
1076924 TAAAAAATTAAACATAATAATA-TT
1 TAAAAAATTAAA-ATAATAATACTT
*
1076948 TAAATTAAA-TAAAATAGTAATACTT
1 TAAA--AAATTAAAATAATAATACTT
*
1076973 TAAAATATTAA
1 TAAAAAATTAA
1076984 TGATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 10 0.33
26 3 0.10
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAAATTAAAATAATAATACTT
Found at i:1077009 original size:26 final size:26
Alignment explanation
Indices: 1076975--1077027 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1076965 TAATACTTTA
*
1076975 AAATATTAATGA-TTAAATTATAAATT
1 AAATATTAAT-ATTTAAATAATAAATT
* *
1077001 AAATGTTAATATTTAAATAATCAATT
1 AAATATTAATATTTAAATAATAAATT
1077027 A
1 A
1077028 TTAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
AAATATTAATATTTAAATAATAAATT
Found at i:1077183 original size:41 final size:42
Alignment explanation
Indices: 1077105--1077183 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
1077095 CTATTTAAAA
* *
1077105 TAAATAAATTATTAATATTTTAAAATATTAATGATTAAAATC
1 TAAATAAATTATTAATATTTTAAAACATCAATGATTAAAATC
* *
1077147 TAAATCAAATT-TTTATA-TTTAAAACATCAATTATTAA
1 TAAAT-AAATTATTAATATTTTAAAACATCAATGATTAA
1077184 TACTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 17 0.53
42 10 0.31
43 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (42 bp):
TAAATAAATTATTAATATTTTAAAACATCAATGATTAAAATC
Found at i:1077240 original size:21 final size:21
Alignment explanation
Indices: 1077216--1077285 Score: 54
Period size: 24 Copynumber: 3.2 Consensus size: 21
1077206 GATTGATCAC
1077216 AATAATATTTAAATAAAATAAA
1 AATAATATTTAAATAAAAT-AA
* *
1077238 ATATTAATATTTAAATACTAAT-G
1 A-A-TAATATTTAAATA-AAATAA
**
1077261 GTTAATATTTAAA-AAAATAA
1 AATAATATTTAAATAAAATAA
1077281 AATAA
1 AATAA
1077286 AATAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
19 3 0.08
20 4 0.11
21 11 0.31
22 1 0.03
23 1 0.03
24 13 0.36
25 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (21 bp):
AATAATATTTAAATAAAATAA
Found at i:1077326 original size:84 final size:83
Alignment explanation
Indices: 1077180--1077356 Score: 232
Period size: 84 Copynumber: 2.1 Consensus size: 83
1077170 ACATCAATTA
* * * * *
1077180 TTAATACTTAAAAAAATGAAATAAAAGATTGATCACAATAATATTTAAATAAAATAAAATATTAA
1 TTAATATTTAAAAAAATAAAATAAAAAATTGATCACAATAATACTCAAATAAAATAAAATATTAA
1077245 TAT-TTAAATACTAATGG
66 TATCTTAAATACTAATGG
* * *
1077262 TTAATATTTAAAAAAATAAAATAAAATAAATTTATCATAATAATACTCAAATTAAATAAAATATT
1 TTAATATTTAAAAAAATAAAAT-AAA-AAATTGATCACAATAATACTCAAATAAAATAAAATATT
* *
1077327 AATATCTTAAATATTAATGT
64 AATATCTTAAATACTAATGG
1077347 TTAA-ATTTAA
1 TTAATATTTAA
1077357 TATTTAAATG
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
82 20 0.24
83 3 0.04
84 43 0.52
85 16 0.20
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (83 bp):
TTAATATTTAAAAAAATAAAATAAAAAATTGATCACAATAATACTCAAATAAAATAAAATATTAA
TATCTTAAATACTAATGG
Found at i:1077362 original size:13 final size:14
Alignment explanation
Indices: 1077320--1077524 Score: 70
Period size: 15 Copynumber: 14.2 Consensus size: 14
1077310 AAATTAAATA
1077320 AAATATTAATATCTT
1 AAATATTAATAT-TT
*
1077335 AAATATTAATGTTT
1 AAATATTAATATTT
1077349 AAAT-TTAATATTT
1 AAATATTAATATTT
*
1077362 AAATGATCAAT-TATT
1 AAAT-ATTAATAT-TT
*
1077377 AATATTTTAAATAAATTGT
1 AA-ATATT-AAT--ATT-T
* *
1077396 CAATTATTAATATGT
1 -AAATATTAATATTT
* ** * *
1077411 AAAAAAGAA-AATG
1 AAATATTAATATTT
*
1077424 AAAGATTAATATTAT
1 AAATATTAATATT-T
1077439 AAAATATTAATGA-TT
1 -AAATATTAAT-ATTT
*
1077454 AAAT-TGTAA-A-TA
1 AAATAT-TAATATTT
*
1077466 AAATATTAATACTT
1 AAATATTAATATTT
1077480 AAATTATTAAT-TCTT
1 AAA-TATTAATAT-TT
*
1077495 -AATATT-ATAATT
1 AAATATTAATATTT
1077507 AAATTATTAATATTT
1 AAA-TATTAATATTT
1077522 AAA
1 AAA
1077525 AAATCGAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 48
0.65 0.12 0.22
Matches are distributed among these distances:
12 13 0.09
13 28 0.20
14 31 0.22
15 39 0.28
16 17 0.12
17 1 0.01
18 4 0.03
19 5 0.04
20 2 0.01
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:1077476 original size:42 final size:42
Alignment explanation
Indices: 1077419--1077525 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
1077409 GTAAAAAAGA
* * *
1077419 AAATGAAAGATTAATATTATAAAATATTAATGATTAA-ATTGT
1 AAATAAAATATTAATATT-TAAAATATTAATGATTAATATTAT
* * **
1077461 AAATAAAATATTAATACTTAAATTATTAATTCTTAATATTAT
1 AAATAAAATATTAATATTTAAAATATTAATGATTAATATTAT
* *
1077503 AATTAAATTATTAATATTTAAAA
1 AAATAAAATATTAATATTTAAAA
1077526 AATCGAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 15 0.28
42 38 0.72
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (42 bp):
AAATAAAATATTAATATTTAAAATATTAATGATTAATATTAT
Found at i:1082812 original size:14 final size:14
Alignment explanation
Indices: 1082793--1082820 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1082783 ATTCGAGAGG
1082793 GGCTTCTGCAGGCC
1 GGCTTCTGCAGGCC
1082807 GGCTTCTGCAGGCC
1 GGCTTCTGCAGGCC
1082821 CATGCTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.36, G:0.36, T:0.21
Consensus pattern (14 bp):
GGCTTCTGCAGGCC
Found at i:1083670 original size:2 final size:2
Alignment explanation
Indices: 1083663--1083688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1083653 GGTGGTATGT
1083663 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1083689 GGTGGTTCAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1087412 original size:39 final size:41
Alignment explanation
Indices: 1087358--1087440 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 41
1087348 GATGTCAAAA
1087358 GTACATAATGCTCCTC-T-GTATTCTATATAATTTTATCAG
1 GTACATAATGCTCCTCATGGTATTCTATATAATTTTATCAG
1087397 GTACATAATGCTCCTCAAATATGGTATTCTATATAATTTTATCA
1 GTACATAATGCTCCTC----ATGGTATTCTATATAATTTTATCA
1087441 AGCACCTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
39 16 0.42
44 1 0.03
45 21 0.55
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (41 bp):
GTACATAATGCTCCTCATGGTATTCTATATAATTTTATCAG
Found at i:1090383 original size:20 final size:21
Alignment explanation
Indices: 1090358--1090413 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1090348 AGGGGAAGGT
1090358 AAAGAAAGAAAAAGAAGAAA-
1 AAAGAAAGAAAAAGAAGAAAG
*
1090378 AAAGAAAAAGGAAAAAGAGGAAAG
1 AAAG--AAA-GAAAAAGAAGAAAG
*
1090402 AAAGGAAGAAAA
1 AAAGAAAGAAAA
1090414 GAAACAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.13
21 5 0.17
22 5 0.17
23 12 0.40
24 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAAGAAAG
Found at i:1093388 original size:21 final size:21
Alignment explanation
Indices: 1093360--1093409 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1093350 AAATTTAACT
1093360 GAAAAAGAAAACATAAA-AAAA
1 GAAAAAGAAAACA-AAAGAAAA
* *
1093381 GGAAAAGAAAAGAAAAGAAAA
1 GAAAAAGAAAACAAAAGAAAA
1093402 GAAAAAGA
1 GAAAAAGA
1093410 GAGATGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
GAAAAAGAAAACAAAAGAAAA
Found at i:1093409 original size:6 final size:5
Alignment explanation
Indices: 1093362--1093406 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
1093352 ATTTAACTGA
*
1093362 AAAAG AAAAC ATAAA- AAAAGG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG A-AAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAA
1093407 AGAGAGATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
4 3 0.08
5 26 0.72
6 7 0.19
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:1096017 original size:6 final size:6
Alignment explanation
Indices: 1096008--1096033 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1095998 TATTATTATA
1096008 CAAACT CAAACT CAAACT CAAACT CA
1 CAAACT CAAACT CAAACT CAAACT CA
1096034 CACGATATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
CAAACT
Found at i:1111255 original size:24 final size:26
Alignment explanation
Indices: 1111228--1111283 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1111218 ACATATAACA
1111228 GTAATATT-TTTTTCAA-CAT-GACAT
1 GTAATATTCTTTTTCAACCATAG-CAT
* *
1111252 GTAACATTCTTTTTTAACCATAGCAT
1 GTAATATTCTTTTTCAACCATAGCAT
1111278 GTAATA
1 GTAATA
1111284 ATAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.27
25 7 0.27
26 11 0.42
27 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (26 bp):
GTAATATTCTTTTTCAACCATAGCAT
Found at i:1114007 original size:126 final size:120
Alignment explanation
Indices: 1113758--1114007 Score: 356
Period size: 121 Copynumber: 2.0 Consensus size: 120
1113748 AAAAGATATA
* *
1113758 AAAACAGCTATAGTCCATTTCCTTCTATCAAACATAAGCATCTATGAGGTAGATAAAAAAAACAA
1 AAAACAGCTATAGTCCATTTCCTTCTACCAAACATAAGCATCTATGAGGCAGATAAAAAAAACAA
* * * *
1113823 AGTCATTAGAAAAATTAAAAATTAGGGTTTTCAGAGATGAAGAAACCCTAGCGAT
66 AATCATTAGAAAAACTAAAAATTAGGGTTTTCAGAAATGAAGAAACCCTAGAGAT
* *
1113878 AAAACAAGCTATAGTTCATTTCCTTCTACCAAACATAAGCATCTATTAGGCAGATATAGAAAAAA
1 AAAAC-AGCTATAGTCCATTTCCTTCTACCAAACATAAGCATCTATGAGGCAGATA-A-AAAAAA
* *
1113943 CAAAAATCATTAAGAAATAGCTAACAATTAGGGTTTTCAGAAATGAAGAAACCCTAGAGAT
63 C-AAAATCATT-AGAAA-AACTAAAAATTAGGGTTTTCAGAAATGAAGAAACCCTAGAGAT
1114004 AAAA
1 AAAA
1114008 ACTAATAAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
120 5 0.04
121 46 0.40
122 1 0.01
123 7 0.06
124 8 0.07
125 5 0.04
126 42 0.37
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24
Consensus pattern (120 bp):
AAAACAGCTATAGTCCATTTCCTTCTACCAAACATAAGCATCTATGAGGCAGATAAAAAAAACAA
AATCATTAGAAAAACTAAAAATTAGGGTTTTCAGAAATGAAGAAACCCTAGAGAT
Found at i:1123390 original size:21 final size:21
Alignment explanation
Indices: 1123361--1123401 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1123351 TCACCCGCCA
1123361 CCATCATTTTCCATTCTTTTG
1 CCATCATTTTCCATTCTTTTG
* **
1123382 CCATTATTTTCTTTTCTTTT
1 CCATCATTTTCCATTCTTTT
1123402 CTCTTTACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.61
Consensus pattern (21 bp):
CCATCATTTTCCATTCTTTTG
Found at i:1124230 original size:19 final size:19
Alignment explanation
Indices: 1124190--1124228 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1124180 TTAATATTTT
*
1124190 AATATTATTTTATTAATAA
1 AATATTATTTTATTAAAAA
1124209 AATATTATTTT-TTAAAAA
1 AATATTATTTTATTAAAAA
1124227 AA
1 AA
1124229 ATTTTCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTATTTTATTAAAAA
Found at i:1132397 original size:118 final size:116
Alignment explanation
Indices: 1132228--1132514 Score: 400
Period size: 113 Copynumber: 2.5 Consensus size: 116
1132218 TGACCCCTTC
* * * *
1132228 TAATATTGGCCTAAGACTTAATAAAACTATTTTAATTAAGTCATTGCAAATTAAAATTAAATTAA
1 TAATGTTGGCCTTATACTTAATAAAACTATTTTAATTAAGTCATTACAAATTAAAA--AAATTAA
* *
1132293 ATTAAATTTACTTTATTTGTTTGCAATTAAGGCTTTAATATTATAACTAATTA
64 ATTAAATTTACTTTATTTGTTTACAATTAAGACTTTAATATTATAACTAATTA
* * *
1132346 TAATGTTGGCCTTCTACTTAATAAAACTATTTCAATTAAGTCATTATAAATT---AAAATTAAAT
1 TAATGTTGGCCTTATACTTAATAAAACTATTTTAATTAAGTCATTACAAATTAAAAAAATTAAAT
*
1132408 TAAATTTACTTTATTTGTTTACAATTATGACTTTAATATTATAACTAATTA
66 TAAATTTACTTTATTTGTTTACAATTAAGACTTTAATATTATAACTAATTA
* * * * *
1132459 TAATGTTGGCTTTATACTTAATTAAACTATTTTAATTAAGTCTTTAGAAGTTAAAA
1 TAATGTTGGCCTTATACTTAATAAAACTATTTTAATTAAGTCATTACAAATTAAAA
1132515 CCTAGTGTAT
Statistics
Matches: 149, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
113 102 0.68
115 1 0.01
116 1 0.01
118 45 0.30
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (116 bp):
TAATGTTGGCCTTATACTTAATAAAACTATTTTAATTAAGTCATTACAAATTAAAAAAATTAAAT
TAAATTTACTTTATTTGTTTACAATTAAGACTTTAATATTATAACTAATTA
Found at i:1135091 original size:26 final size:26
Alignment explanation
Indices: 1135055--1135114 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1135045 ACCATCCAAG
* *
1135055 TATAAACATTGTTCAGCAACACAAAA
1 TATAACCATTGTTCAACAACACAAAA
*
1135081 TATAACCATTGTTCAACATCACAAAA
1 TATAACCATTGTTCAACAACACAAAA
1135107 TATAACCA
1 TATAACCA
1135115 AATATAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (26 bp):
TATAACCATTGTTCAACAACACAAAA
Found at i:1138780 original size:20 final size:20
Alignment explanation
Indices: 1138755--1138792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1138745 CATCTAAGGT
1138755 GCTTTAATCAATTAAAGTAG
1 GCTTTAATCAATTAAAGTAG
*
1138775 GCTTTAATCGATTAAAGT
1 GCTTTAATCAATTAAAGT
1138793 GTTATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
GCTTTAATCAATTAAAGTAG
Found at i:1144695 original size:25 final size:25
Alignment explanation
Indices: 1144663--1144722 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1144653 AGTTTGTGAT
*
1144663 ATATATGTGGCAAGGCCACGGGTTG
1 ATATATGTGGCAAGGCCACGAGTTG
** **
1144688 ATATATGTGGCTTGGCCTTGAGTTG
1 ATATATGTGGCAAGGCCACGAGTTG
1144713 ATATATGTGG
1 ATATATGTGG
1144723 TTGCGACCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.33
Consensus pattern (25 bp):
ATATATGTGGCAAGGCCACGAGTTG
Found at i:1146036 original size:37 final size:37
Alignment explanation
Indices: 1145989--1146063 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1145979 TTTAAATTAG
1145989 TTATTTTGGTGAGTCAATCTAATCTTAGTTAATTTTA
1 TTATTTTGGTGAGTCAATCTAATCTTAGTTAATTTTA
1146026 TTATTTTGGTGAGTCAATCTAATCTTAGTTAATTTTA
1 TTATTTTGGTGAGTCAATCTAATCTTAGTTAATTTTA
1146063 T
1 T
1146064 ACTTAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (37 bp):
TTATTTTGGTGAGTCAATCTAATCTTAGTTAATTTTA
Found at i:1147173 original size:2 final size:2
Alignment explanation
Indices: 1147166--1147208 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1147156 AACTGAGTTA
*
1147166 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1147208 A
1 A
1147209 TAATAATCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1148030 original size:21 final size:21
Alignment explanation
Indices: 1148006--1148067 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
1147996 GTTCATGCAA
*
1148006 TTCATGACAAAGATAGATGCT
1 TTCATGACAAAGACAGATGCT
1148027 TTCATGACAAAGACAGATGCT
1 TTCATGACAAAGACAGATGCT
*
1148048 TTCATGACAAAGACTGATGC
1 TTCATGACAAAGACAGATGC
1148068 CATCATGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (21 bp):
TTCATGACAAAGACAGATGCT
Found at i:1148576 original size:4 final size:4
Alignment explanation
Indices: 1148553--1148597 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
1148543 TTCAAAACTC
* *
1148553 TTAT TTTT TTAG TT-T TTAT TTAT TTAT TTAT TTA- TT-T TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1148598 CTTTTTAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:1148593 original size:22 final size:23
Alignment explanation
Indices: 1148553--1148597 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1148543 TTCAAAACTC
*
1148553 TTATTTTTTTAGTTTTTATTTAT
1 TTATTTATTTAGTTTTTATTTAT
1148576 TTATTTATTTA-TTTTTATTTAT
1 TTATTTATTTAGTTTTTATTTAT
1148598 CTTTTTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (23 bp):
TTATTTATTTAGTTTTTATTTAT
Found at i:1148604 original size:22 final size:22
Alignment explanation
Indices: 1148556--1148604 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
1148546 AAAACTCTTA
1148556 TTTT-TTTAGTTTTTATTTATT
1 TTTTATTTAGTTTTTATTTATT
1148577 TATTTATTTA-TTTTTATTTATCT
1 T-TTTATTTAGTTTTTATTTAT-T
1148600 TTTTA
1 TTTTA
1148605 GTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTAGTTTTTATTTATT
Found at i:1155090 original size:67 final size:67
Alignment explanation
Indices: 1154961--1155091 Score: 163
Period size: 67 Copynumber: 2.0 Consensus size: 67
1154951 GAAGATTACT
* * *** * * *
1154961 TTGGATGATGATTGTGATGCCACCTATGGAGAATACTTTGGGTGATGTCGTATATTGTGATATTG
1 TTGGATGATGATTATGATGCCACCTATGAAGAATACTCCAGGTGATGCCGTACATTGGGATATTG
1155026 CC
66 CC
* * *
1155028 TTGGATGATTATTATGATGCCACCTATGAAGAATGCTCCAGGTGATGCCGTCCATTGGGATATT
1 TTGGATGATGATTATGATGCCACCTATGAAGAATACTCCAGGTGATGCCGTACATTGGGATATT
1155092 ACCCCAAACA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (67 bp):
TTGGATGATGATTATGATGCCACCTATGAAGAATACTCCAGGTGATGCCGTACATTGGGATATTG
CC
Found at i:1159554 original size:20 final size:19
Alignment explanation
Indices: 1159529--1159582 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1159519 TATTTCGTGG
*
1159529 CTTTGAAACTAAAACAACAT
1 CTTTGAAATTAAAA-AACAT
*
1159549 CTTTGAAATTGAAAAAATAT
1 CTTTGAAATT-AAAAAACAT
1159569 CTTTGAAATTAAAA
1 CTTTGAAATTAAAA
1159583 TTCATGACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (19 bp):
CTTTGAAATTAAAAAACAT
Found at i:1162853 original size:94 final size:92
Alignment explanation
Indices: 1162750--1163152 Score: 325
Period size: 90 Copynumber: 4.5 Consensus size: 92
1162740 ATCCATAATT
*
1162750 TTTTATTGATTTACAA-AACAAAAATTATATGAAAATTATATATATAATATACTAAATATATAAT
1 TTTTATTGATTTACAATAACAAAAATTATATGAAAA-TATATATATAATACA-TAAATATATAAT
1162814 GATGTACAATAAGGAAAATTGTATACATAA
64 GATGTACAATAAGGAAAA-TGTATACATAA
* * * *
1162844 TTTTATTGATTTACAATAAC-AAAAGTA-AT--ATATATGTATATAATACATACA-AT-TAATGA
1 TTTTATTGATTTACAATAACAAAAATTATATGAAAATATATATATAATACATAAATATATAATGA
**
1162903 --TA-AAT-TTGATGAAATGTATATTCATAA
66 TGTACAATAAGGA--AAATGTATA--CATAA
*
1162930 TTTTTATTGATTTACAA-AA-AAAAATTATATGAAAACTATATATATAATACATATAATATATAT
1 -TTTTATTGATTTACAATAACAAAAATTATATGAAAA-TATATATATAATACATA-AATATATAA
*
1162993 TGATGTACAATAAGGAAAAGTATATACATAA
63 TGATGTACAATAAGGAAAA-TGTATACATAA
* * * *
1163024 TTGTATTGATTTATAATAAC-AAAAGTA-AT--ATATATA-ATATAATACAT--ATA-ACTAATG
1 TTTTATTGATTTACAATAACAAAAATTATATGAAAATATATATATAATACATAAATATA-TAATG
** * *
1163081 A--TA-AAT-TTGATGAAATATATACCATTA
65 ATGTACAATAAGGA--AAATGTATA-CATAA
*
1163108 TTTTATTGATTTACAAAAACAAAAATTATATGAAAACTATATATA
1 TTTTATTGATTTACAATAACAAAAATTATATGAAAA-TATATATA
1163153 ACATATATAT
Statistics
Matches: 250, Mismatches: 28, Indels: 66
0.73 0.08 0.19
Matches are distributed among these distances:
82 2 0.01
83 11 0.04
84 35 0.14
85 12 0.05
86 23 0.09
87 24 0.10
88 4 0.02
89 20 0.08
90 36 0.14
91 5 0.02
92 2 0.01
93 23 0.09
94 35 0.14
95 8 0.03
96 8 0.03
97 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (92 bp):
TTTTATTGATTTACAATAACAAAAATTATATGAAAATATATATATAATACATAAATATATAATGA
TGTACAATAAGGAAAATGTATACATAA
Found at i:1162990 original size:180 final size:180
Alignment explanation
Indices: 1162660--1163165 Score: 701
Period size: 180 Copynumber: 2.8 Consensus size: 180
1162650 CGACTATATG
* * * * *
1162660 TACATAATTTTTATTTATTTACAATAACAAAAATTATATAGATGTAT-TAA-AC--ACAA-AATA
1 TACATAA-TTTTATTGATTTACAATAACAAAAGTAATATATATGTATATAATACATACAATAATG
* *
1162720 ATAAAGTTGATGTAATATATATCCATAATTTTTTATTGATTTACAAAACAAAAATTATATGAAAA
65 ATAAATTTGATGAAATATATATCCATAA-TTTTTATTGATTTACAAAACAAAAATTATATGAAAA
* * *
1162785 TTATATATATAATATACTA-AATATATAATGATGTACAATAAGGAAAATTGTA
129 CTATATATATAATATA-TATAATATATAATGATGTACAATAAGGAAAAGTATA
1162837 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATATGTATATAATACATACAATTAATG
1 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATATGTATATAATACATACAA-TAATG
* *
1162902 ATAAATTTGATGAAATGTATATTCATAATTTTTATTGATTTACAAAA-AAAAATTATATGAAAAC
65 ATAAATTTGATGAAATATATATCCATAATTTTTATTGATTTACAAAACAAAAATTATATGAAAAC
* *
1162966 TATATATATAATACATATAATATATATTGATGTACAATAAGGAAAAGTATA
130 TATATATATAATATATATAATATATAATGATGTACAATAAGGAAAAGTATA
* * * *
1163017 TACATAATTGTATTGATTTATAATAACAAAAGTAATATATAT-AATATAATACATATAACTAATG
1 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATATGTATATAATACATACAA-TAATG
*
1163081 ATAAATTTGATGAAATATATA-CCATTA-TTTTATTGATTTACAAAAACAAAAATTATATGAAAA
65 ATAAATTTGATGAAATATATATCCATAATTTTTATTGATTTAC-AAAACAAAAATTATATGAAAA
1163144 CTATATATA-ACATATATATAAT
129 CTATATATATA-ATATATATAAT
1163166 TTTTATTGAT
Statistics
Matches: 296, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
176 35 0.12
177 24 0.08
178 11 0.04
179 76 0.26
180 104 0.35
181 19 0.06
182 27 0.09
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (180 bp):
TACATAATTTTATTGATTTACAATAACAAAAGTAATATATATGTATATAATACATACAATAATGA
TAAATTTGATGAAATATATATCCATAATTTTTATTGATTTACAAAACAAAAATTATATGAAAACT
ATATATATAATATATATAATATATAATGATGTACAATAAGGAAAAGTATA
Found at i:1163033 original size:37 final size:37
Alignment explanation
Indices: 1162990--1163061 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1162980 ATATAATATA
*
1162990 TATTGATGTACAATAAGGAAAAGT-ATATACATAATTG
1 TATTGATGTACAATAA-CAAAAGTAATATACATAATTG
* * *
1163027 TATTGATTTATAATAACAAAAGTAATATATATAAT
1 TATTGATGTACAATAACAAAAGTAATATACATAAT
1163062 ATAATACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 6 0.20
37 24 0.80
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (37 bp):
TATTGATGTACAATAACAAAAGTAATATACATAATTG
Found at i:1182997 original size:20 final size:19
Alignment explanation
Indices: 1182959--1182997 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1182949 TTTCACCAAC
* *
1182959 AACAAAAACATCCACACAA
1 AACAAAAACATCAAAACAA
1182978 AACAAAAACTATCAAAACAA
1 AACAAAAAC-ATCAAAACAA
1182998 GACTGAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.08
Consensus pattern (19 bp):
AACAAAAACATCAAAACAA
Done.