Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 51
Found at i:9863384 original size:18 final size:18
Alignment explanation
Indices: 9863361--9863399 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9863351 GTTCTGAAGT
* *
9863361 ACCAACTTCTGGTCAAAC
1 ACCAACATCTGATCAAAC
9863379 ACCAACATCTGATCAAAC
1 ACCAACATCTGATCAAAC
9863397 ACC
1 ACC
9863400 CGGGAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.36, G:0.08, T:0.18
Consensus pattern (18 bp):
ACCAACATCTGATCAAAC
Found at i:9875606 original size:18 final size:17
Alignment explanation
Indices: 9875575--9875608 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9875565 AGTCCATCCT
9875575 TAAAATTTAAATTAGTG
1 TAAAATTTAAATTAGTG
*
9875592 TAAAGATTTAGATTAGT
1 TAAA-ATTTAAATTAGT
9875609 ATAAGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAAATTTAAATTAGTG
Found at i:9878608 original size:26 final size:26
Alignment explanation
Indices: 9878577--9878672 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 26
9878567 AAATCAACAG
9878577 ATATTAAAAACAAGGGTTAAATGCAA
1 ATATTAAAAACAAGGGTTAAATGCAA
*
9878603 ATATTAAAAACAA--ATTCAAA-GCACA
1 ATATTAAAAACAAGGGTT-AAATGCA-A
*
9878628 GATATTAAAAACAAGAAAGGGTTAAATGCAG
1 -ATATTAAAAAC----AAGGGTTAAATGCAA
9878659 ATATTAAAAACAAG
1 ATATTAAAAACAAG
9878673 TTCAAAGCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
24 5 0.09
25 4 0.07
26 27 0.47
30 13 0.23
31 3 0.05
32 5 0.09
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (26 bp):
ATATTAAAAACAAGGGTTAAATGCAA
Found at i:9878702 original size:56 final size:56
Alignment explanation
Indices: 9878573--9878681 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
9878563 CATTAAATCA
9878573 ACAGATATTAAAAAC----AAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
1 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
* *
9878625 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAGATATTAAAAACAAGTTCAAAGC
1 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
9878681 A
1 A
9878682 TAGTTCATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
52 15 0.29
56 36 0.71
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (56 bp):
ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
Found at i:9883713 original size:23 final size:23
Alignment explanation
Indices: 9883687--9883763 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
9883677 AATTGATTTA
9883687 TAAAATATTAAATTATAAATTAT
1 TAAAATATTAAATTATAAATTAT
* *
9883710 T-AAAT-GTATAATTAGAAATTAGT
1 TAAAATATTA-AATTATAAATTA-T
*
9883733 TAAAA-ATTTAAA-TATAATTTAAT
1 TAAAATA-TTAAATTATAAATT-AT
9883756 TAAAATAT
1 TAAAATAT
9883764 AATATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.05
22 15 0.36
23 16 0.38
24 7 0.17
25 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAAATATTAAATTATAAATTAT
Found at i:9883714 original size:22 final size:22
Alignment explanation
Indices: 9883684--9883759 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 22
9883674 TTAAATTGAT
*
9883684 TTATAAAATATTAAATTATAAA
1 TTATTAAATATTAAATTATAAA
* *
9883706 TTATTAAAT-GTATAATTAGAAA
1 TTATTAAATATTA-AATTATAAA
* *
9883728 TTAGTTAAAAATTTAAA-TATAAT
1 TTA-TTAAATA-TTAAATTATAAA
9883751 TTAATTAAA
1 TT-ATTAAA
9883760 ATATAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 2 0.05
22 19 0.45
23 16 0.38
24 3 0.07
25 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TTATTAAATATTAAATTATAAA
Found at i:9883723 original size:15 final size:15
Alignment explanation
Indices: 9883684--9883720 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
9883674 TTAAATTGAT
*
9883684 TTATAAAATATTAAA
1 TTATAAATTATTAAA
9883699 TTATAAATTATTAAA
1 TTATAAATTATTAAA
9883714 TGTATAA
1 T-TATAA
9883721 TTAGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TTATAAATTATTAAA
Found at i:9886849 original size:2 final size:2
Alignment explanation
Indices: 9886842--9886871 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9886832 TTCATCTTTC
9886842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9886872 CATCTCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9887264 original size:16 final size:17
Alignment explanation
Indices: 9887243--9887277 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9887233 TTGTATATGC
9887243 AAAAAATCAAC-ACTAA
1 AAAAAATCAACTACTAA
*
9887259 AAAAAATCATCTACTAA
1 AAAAAATCAACTACTAA
9887276 AA
1 AA
9887278 CTAGGTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAATCAACTACTAA
Found at i:9890268 original size:22 final size:23
Alignment explanation
Indices: 9890242--9890303 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
9890232 TGTATAAATA
9890242 TTAT-ATTTAAATTTTAATTAAT
1 TTATAATTTAAATTTTAATTAAT
*
9890264 TTATAATTATACA-TTT-ATTAAT
1 TTATAATT-TAAATTTTAATTAAT
9890286 TTATAATTTAACATTTTA
1 TTATAATTTAA-ATTTTA
9890304 TAAATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 2 0.06
22 19 0.58
23 9 0.27
24 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATAATTTAAATTTTAATTAAT
Found at i:9890309 original size:23 final size:23
Alignment explanation
Indices: 9890229--9890309 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
9890219 ATAAAAACTA
9890229 ATTTGTATAAATATTAT-ATTTAA-
1 ATTT-TATAAAT-TTATAATTTAAC
*
9890252 ATTTTAATTAATTTATAA-TTATAC
1 ATTTT-ATAAATTTATAATTTA-AC
*
9890276 A-TTTATTAATTTATAATTTAAC
1 ATTTTATAAATTTATAATTTAAC
9890298 ATTTTATAAATT
1 ATTTTATAAATT
9890310 AATTTAATGG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
22 23 0.46
23 26 0.52
24 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (23 bp):
ATTTTATAAATTTATAATTTAAC
Found at i:9899326 original size:48 final size:48
Alignment explanation
Indices: 9899270--9899369 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
9899260 ACTTGTCATC
9899270 CCTGCACAGTCCTTTTGAAATTGCAGCTGAGGATTGGGAAGAGAGATT
1 CCTGCACAGTCCTTTTGAAATTGCAGCTGAGGATTGGGAAGAGAGATT
9899318 CCTGCACAGTCCTTTTGAAATTGCAGCTGAGGATTGGGAAGAGAGATT
1 CCTGCACAGTCCTTTTGAAATTGCAGCTGAGGATTGGGAAGAGAGATT
9899366 CCTG
1 CCTG
9899370 ACATGGTTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (48 bp):
CCTGCACAGTCCTTTTGAAATTGCAGCTGAGGATTGGGAAGAGAGATT
Found at i:9902639 original size:13 final size:13
Alignment explanation
Indices: 9902621--9902647 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9902611 CCAAGAAAGC
9902621 TTCAAGATACTAG
1 TTCAAGATACTAG
9902634 TTCAAGATACTAG
1 TTCAAGATACTAG
9902647 T
1 T
9902648 AAGCAATGAT
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:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TTCAAGATACTAG
Found at i:9905423 original size:20 final size:20
Alignment explanation
Indices: 9905398--9905435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9905388 GAATGCTAGT
*
9905398 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
9905418 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
9905436 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:9906185 original size:149 final size:149
Alignment explanation
Indices: 9905915--9906218 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
9905905 GGGTAGAGGG
9905915 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
9905980 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
9906045 TATGGCACTACGGTGCAAT
131 TATGGCACTACGATGCAAT
9906064 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
9906129 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
9906194 TATGGCACTACGATGCAAT
131 TATGGCACTACGATGCAAT
9906213 TCTACG
1 TCTACG
9906219 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGATGCAAT
Found at i:9906241 original size:23 final size:23
Alignment explanation
Indices: 9906197--9906241 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9906187 ATCATTATAT
*
9906197 GGCACTACGATGCAATTCTACGG
1 GGCACTACGATGCAATTATACGG
* * *
9906220 GGCACTTCGGTGCATTTATACG
1 GGCACTACGATGCAATTATACG
9906242 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGG
Found at i:9908265 original size:2 final size:2
Alignment explanation
Indices: 9908258--9908293 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9908248 CAAGCCAATA
9908258 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9908294 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9908419 original size:2 final size:2
Alignment explanation
Indices: 9908412--9908450 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9908402 AACACCGGAA
9908412 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9908451 TATGCCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9933731 original size:20 final size:20
Alignment explanation
Indices: 9933674--9933724 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
9933664 ATCCTATTCT
9933674 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
9933694 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
9933714 CTGGTAATCTT
1 CTGGTAATCTT
9933725 ACATTCCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:9934494 original size:2 final size:2
Alignment explanation
Indices: 9934393--9934483 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
9934383 TTTTATCTTT
9934393 TA TA 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 TA TA
9934435 TA TA 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 TA TA
9934477 TA TA TA T
1 TA TA TA T
9934484 GCATTATATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9943500 original size:23 final size:24
Alignment explanation
Indices: 9943460--9943509 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
9943450 GGGTGTGATG
9943460 AAAATAATATCTTAAGAAAATAAT
1 AAAATAATATCTTAAGAAAATAAT
* * *
9943484 AAAAT-ATCTCTTTAGAAAATAGT
1 AAAATAATATCTTAAGAAAATAAT
9943507 AAA
1 AAA
9943510 TTTTGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
AAAATAATATCTTAAGAAAATAAT
Found at i:9957042 original size:32 final size:31
Alignment explanation
Indices: 9956998--9957057 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
9956988 CAGTTGATAG
* *
9956998 AAATATATAATTT-AATCTTAGTTTTAAATTT
1 AAATAAATAATTTGAAT-TTAATTTTAAATTT
9957029 AAATAAATAAATTTGAATTTAATTTTAAA
1 AAATAAAT-AATTTGAATTTAATTTTAAA
9957058 AAATACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.28
32 15 0.60
33 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
AAATAAATAATTTGAATTTAATTTTAAATTT
Found at i:9957070 original size:26 final size:26
Alignment explanation
Indices: 9957020--9957070 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
9957010 TAATCTTAGT
*
9957020 TTTAAATTTAAATAAATAAATTTGAA
1 TTTAAATTTAAATAAATAAAATTGAA
*
9957046 TTTAATTTTAAA-AAATACAAATTGA
1 TTTAAATTTAAATAAATA-AAATTGA
9957071 TACCCCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (26 bp):
TTTAAATTTAAATAAATAAAATTGAA
Found at i:9959226 original size:2 final size:2
Alignment explanation
Indices: 9959219--9959243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9959209 TTATCTTTAA
9959219 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
9959244 ATTTTCCTTT
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:9979119 original size:18 final size:18
Alignment explanation
Indices: 9979060--9979111 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
9979050 AACATTCCCA
*
9979060 GTAATCTTATTCCCGCCG
1 GTAATCCTATTCCCGCCG
*
9979078 GTAATCCTATTCCTGCCG
1 GTAATCCTATTCCCGCCG
9979096 GTAATCCTATTCCCGC
1 GTAATCCTATTCCCGC
9979112 TGATAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.35, G:0.15, T:0.33
Consensus pattern (18 bp):
GTAATCCTATTCCCGCCG
Found at i:9983512 original size:23 final size:20
Alignment explanation
Indices: 9983474--9983514 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
9983464 GATTTACATG
9983474 AAAATAATAAATCAGAAAAT
1 AAAATAATAAATCAGAAAAT
9983494 AAAATATATATAATCCAGAAA
1 AAAATA-ATA-AAT-CAGAAA
9983515 GAACATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 3 0.17
23 6 0.33
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAATAATAAATCAGAAAAT
Found at i:9991970 original size:23 final size:23
Alignment explanation
Indices: 9991943--9991998 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
9991933 TTGTTTCATC
9991943 TTCTTTCTTTTGAAACTATATCT
1 TTCTTTCTTTTGAAACTATATCT
9991966 TTCTTTCTTTTGAAACTATATCT
1 TTCTTTCTTTTGAAACTATATCT
9991989 TTGC-TTCTTT
1 TT-CTTTCTTT
9991999 GTTGTCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (23 bp):
TTCTTTCTTTTGAAACTATATCT
Found at i:9993311 original size:3 final size:3
Alignment explanation
Indices: 9993303--9993329 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9993293 ACTAAAACAC
9993303 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
9993330 TTTTTCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9997638 original size:39 final size:39
Alignment explanation
Indices: 9997587--9997664 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
9997577 TTATTAATAA
9997587 AAAATAAATCAAGGTCTATATCATTTAATTCTTTTAAAT
1 AAAATAAATCAAGGTCTATATCATTTAATTCTTTTAAAT
9997626 AAAATAAATCAAGGTCTATATCATTTAATTCTTTTAAAT
1 AAAATAAATCAAGGTCTATATCATTTAATTCTTTTAAAT
9997665 TTTATGGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (39 bp):
AAAATAAATCAAGGTCTATATCATTTAATTCTTTTAAAT
Found at i:10000191 original size:21 final size:21
Alignment explanation
Indices: 10000162--10000261 Score: 139
Period size: 21 Copynumber: 4.8 Consensus size: 21
10000152 AATTCGACGA
10000162 GAGAGATCCCCATATGC-CTGT
1 GAGAGATCCCCATATGCTC-GT
*
10000183 GAGAAATCCCCATATGCTCGT
1 GAGAGATCCCCATATGCTCGT
*
10000204 GAGAAATCCCCATATGCTCGT
1 GAGAGATCCCCATATGCTCGT
** *
10000225 GAGAGATCCCTGTATGCACGT
1 GAGAGATCCCCATATGCTCGT
10000246 GAGAGATCCCCATATG
1 GAGAGATCCCCATATG
10000262 ATCGGAGCCA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
21 70 0.99
22 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
GAGAGATCCCCATATGCTCGT
Found at i:10020106 original size:29 final size:29
Alignment explanation
Indices: 10020073--10020135 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
10020063 CTAAATAAGT
*
10020073 TTACACCTAAATTA-ATTTGATGTTATTGC
1 TTACACC-AAATTAGATTTGATGTCATTGC
* * *
10020102 TTACATCAATTTAGTTTTGATGTCATTGC
1 TTACACCAAATTAGATTTGATGTCATTGC
10020131 TTACA
1 TTACA
10020136 TTAATTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (29 bp):
TTACACCAAATTAGATTTGATGTCATTGC
Found at i:10031627 original size:21 final size:21
Alignment explanation
Indices: 10031602--10031649 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
10031592 AACATATTTT
* *
10031602 AAAATATTATTTTTTCTATTG
1 AAAATATTAATTTTACTATTG
*
10031623 AAAATATTAATTTTACTATTT
1 AAAATATTAATTTTACTATTG
10031644 AAAATA
1 AAAATA
10031650 AATATTTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
AAAATATTAATTTTACTATTG
Found at i:10033144 original size:60 final size:60
Alignment explanation
Indices: 10033014--10033197 Score: 167
Period size: 60 Copynumber: 3.1 Consensus size: 60
10033004 GCATCATATG
*** * *
10033014 TCCCCAAACTATGATAATCATTTTAAATTGGTCCTTAAACTTTTGAATATT-TCAA-TTCTA
1 TCCCCAAACTATGACCCTCATTATAAATTGGTCCTTAAACTTTTGAACATTCT-AATTTC-A
** * * ** * *
10033074 TCTTCTAACTATTACTTTTATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCA
1 TCCCCAAACTATGACCCTCATTATAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCA
* ** *
10033134 TCCCCAAACTATGACCCTCATTCTAAATTGGTCCCCAAACTTTTGAATCTTTC-AATTTCA
1 TCCCCAAACTATGACCCTCATTATAAATTGGTCCTTAAACTTTTGAA-CATTCTAATTTCA
10033194 TCCC
1 TCCC
10033198 AAAATATCCA
Statistics
Matches: 98, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
60 90 0.92
61 8 0.08
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.41
Consensus pattern (60 bp):
TCCCCAAACTATGACCCTCATTATAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCA
Found at i:10034007 original size:50 final size:50
Alignment explanation
Indices: 10033915--10034183 Score: 200
Period size: 50 Copynumber: 5.6 Consensus size: 50
10033905 GTAGCAGTAA
* ** * *
10033915 AGCGCGCCCCCTGAACCGCGCTATACGCTGATTTGACGCCACGTGGGTAT
1 AGCGCGCCCTCTGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
* * * *
10033965 AGTGCGCCCTCTGCCCCGCGATATACGGTGATCTGGCACCACGTGGGTAT
1 AGCGCGCCCTCTGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
* ** **
10034015 AGCGCGCCCCCTGATCCGCGCTATACGC----C--AC-GTA-G-GGGTAT
1 AGCGCGCCCTCTGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
** * * *
10034056 AGCGCG-GATCAATG-GCCGCGCTATACGCTGATTTGACGCCACGTGGGTAT
1 AGCGCGCCCTC--TGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
* * * *
10034106 AGCGCGCCCTCTGCCCCGCGATATACGGTGATCTGGCACCACATGGGTAT
1 AGCGCGCCCTCTGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
* ** *
10034156 AGCGCGCCCCCTGATCTGCGCTATACGC
1 AGCGCGCCCTCTGCCCCGCGCTATACGC
10034184 CACGTAGGGG
Statistics
Matches: 166, Mismatches: 40, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
40 1 0.01
41 25 0.15
42 3 0.02
43 1 0.01
44 1 0.01
46 1 0.01
47 2 0.01
48 1 0.01
49 3 0.02
50 126 0.76
51 2 0.01
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCTCTGCCCCGCGCTATACGCTGATCTGACACCACGTGGGTAT
Found at i:10034158 original size:141 final size:141
Alignment explanation
Indices: 10033930--10034224 Score: 545
Period size: 141 Copynumber: 2.1 Consensus size: 141
10033920 GCCCCCTGAA
*
10033930 CCGCGCTATACGCTGATTTGACGCCACGTGGGTATAGTGCGCCCTCTGCCCCGCGATATACGGTG
1 CCGCGCTATACGCTGATTTGACGCCACGTGGGTATAGCGCGCCCTCTGCCCCGCGATATACGGTG
*
10033995 ATCTGGCACCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATACGCCACGTAGGGGTATAGCG
66 ATCTGGCACCACATGGGTATAGCGCGCCCCCTGATCCGCGCTATACGCCACGTAGGGGTATAGCG
*
10034060 CGGATCAATGG
131 CGGATCAAGGG
10034071 CCGCGCTATACGCTGATTTGACGCCACGTGGGTATAGCGCGCCCTCTGCCCCGCGATATACGGTG
1 CCGCGCTATACGCTGATTTGACGCCACGTGGGTATAGCGCGCCCTCTGCCCCGCGATATACGGTG
*
10034136 ATCTGGCACCACATGGGTATAGCGCGCCCCCTGATCTGCGCTATACGCCACGTAGGGGTATAGCG
66 ATCTGGCACCACATGGGTATAGCGCGCCCCCTGATCCGCGCTATACGCCACGTAGGGGTATAGCG
*
10034201 CGGATCAGGGG
131 CGGATCAAGGG
10034212 CCGCGCTATACGC
1 CCGCGCTATACGC
10034225 CGTACCAAAA
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 149 1.00
ACGTcount: A:0.18, C:0.32, G:0.31, T:0.20
Consensus pattern (141 bp):
CCGCGCTATACGCTGATTTGACGCCACGTGGGTATAGCGCGCCCTCTGCCCCGCGATATACGGTG
ATCTGGCACCACATGGGTATAGCGCGCCCCCTGATCCGCGCTATACGCCACGTAGGGGTATAGCG
CGGATCAAGGG
Found at i:10038841 original size:111 final size:111
Alignment explanation
Indices: 10038643--10038975 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
10038633 ATTACAAAAA
* *
10038643 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
10038708 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
10038754 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
10038819 AATTAAAACGTTAAAATATTACCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
*
10038865 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
10038930 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
10038976 ATGATTTCCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
Found at i:10039125 original size:10 final size:11
Alignment explanation
Indices: 10039107--10039142 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
10039097 AAGATAGAGT
10039107 ATTTGAGAGAA
1 ATTTGAGAGAA
10039118 ATTT-AGAG-A
1 ATTTGAGAGAA
10039127 ATTTGAGAG-A
1 ATTTGAGAGAA
10039137 ATTTGA
1 ATTTGA
10039143 TGTGATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 15 0.62
11 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:10045843 original size:81 final size:81
Alignment explanation
Indices: 10045733--10045903 Score: 220
Period size: 81 Copynumber: 2.1 Consensus size: 81
10045723 TTACTCAAAC
* * *
10045733 CGGGAGAAGCCGAATCACTGTCGTCTCTCTTCTTTCTTTTCAAAGTCTGAACTGATTCTTTCGAG
1 CGGGAGAAGCAGAATCACTGTCGTCTCTCTTCTTTCTTTTCAAAGTCTGAACTAATTCTTTCGAA
* *
10045798 TTTCTCAA-ATGAACAT
66 CTTC-CAAGAGGAACAT
* * * **
10045814 CGGGAGAAGCATAAT-AGCTGTTGTCTCTCTTCTTTCTTTTCAAAGTTTGTGCTAATTCTTTCGA
1 CGGGAGAAGCAGAATCA-CTGTCGTCTCTCTTCTTTCTTTTCAAAGTCTGAACTAATTCTTTCGA
10045878 ACTTCCAAGAGGAACAT
65 ACTTCCAAGAGGAACAT
10045895 CGGGAGAAG
1 CGGGAGAAG
10045904 AAGATTCTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 4 0.05
81 74 0.95
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (81 bp):
CGGGAGAAGCAGAATCACTGTCGTCTCTCTTCTTTCTTTTCAAAGTCTGAACTAATTCTTTCGAA
CTTCCAAGAGGAACAT
Found at i:10050612 original size:16 final size:17
Alignment explanation
Indices: 10050581--10050613 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10050571 TTGTAGTGTA
*
10050581 TATTATGGTTTAATTCT
1 TATTATGGTGTAATTCT
10050598 TATTAT-GTGTAATTCT
1 TATTATGGTGTAATTCT
10050614 GTGGATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (17 bp):
TATTATGGTGTAATTCT
Found at i:10051235 original size:12 final size:12
Alignment explanation
Indices: 10051218--10051242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10051208 TAAAAAACCA
10051218 AAAATTAATATC
1 AAAATTAATATC
10051230 AAAATTAATATC
1 AAAATTAATATC
10051242 A
1 A
10051243 CTTATCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATATC
Found at i:10059458 original size:2 final size:2
Alignment explanation
Indices: 10059451--10059486 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10059441 TTATTACTAG
10059451 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
10059487 AAGAGGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10060511 original size:2 final size:2
Alignment explanation
Indices: 10060504--10060532 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10060494 CCAGATTTCT
10060504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
10060533 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10064668 original size:21 final size:21
Alignment explanation
Indices: 10064614--10064687 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
10064604 AGAATTTAAA
** * *
10064614 GTTTATATAATAGGATTTAAG
1 GTTTATATGTTAGGGTTTAGG
10064635 GTTTATA-GTTTAGAGG-TTAGG
1 GTTTATATG-TTAG-GGTTTAGG
*
10064656 TTTTATATGTTAGGGTTTAGG
1 GTTTATATGTTAGGGTTTAGG
*
10064677 GTTTATGTGTT
1 GTTTATATGTT
10064688 CGAGTTTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (21 bp):
GTTTATATGTTAGGGTTTAGG
Found at i:10064694 original size:21 final size:21
Alignment explanation
Indices: 10064629--10064695 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
10064619 TATAATAGGA
*
10064629 TTTAAGGTTTATAGT-TTAGAG
1 TTTAGGGTTTAT-GTGTTAGAG
* * * *
10064650 GTTAGGTTTTATATGTTAGGG
1 TTTAGGGTTTATGTGTTAGAG
*
10064671 TTTAGGGTTTATGTGTTCGAG
1 TTTAGGGTTTATGTGTTAGAG
10064692 TTTA
1 TTTA
10064696 AGTTATGCCA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTATGTGTTAGAG
Found at i:10064996 original size:17 final size:17
Alignment explanation
Indices: 10064974--10065010 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10064964 ATTCGAGTTT
*
10064974 GAGTTCGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
10064991 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
10065008 GAG
1 GAG
10065011 CTCAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:10065009 original size:11 final size:11
Alignment explanation
Indices: 10064995--10065059 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
10064985 TTAATCGAGT
*
10064995 TCGAGCTTGAA
1 TCGAGCTTCAA
10065006 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
10065018 TCGAGCTTCAA
1 TCGAGCTTCAA
*
10065029 TCGAGC-TCGAGTC
1 TCGAGCTTC-A--A
10065042 TCGAGCTTCAA
1 TCGAGCTTCAA
10065053 TCGAGCT
1 TCGAGCT
10065060 CTTGAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.07
11 22 0.50
12 8 0.18
13 9 0.20
14 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:10065050 original size:24 final size:23
Alignment explanation
Indices: 10064989--10065060 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
10064979 CGAGCTTTAA
*
10064989 TCGAGTTCGAGCTTGAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
* **
10065012 TCAAAATCGAGCTTCAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
10065035 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCTTCAATCGAGC
10065059 TC
1 TC
10065061 TTGAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (23 bp):
TCGAGTTCGAGCTTCAATCGAGC
Found at i:10066812 original size:2 final size:2
Alignment explanation
Indices: 10066805--10066869 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
10066795 GAATCAAAGT
10066805 TA TA 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 TA TA
10066847 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
10066870 GTGAACACGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10068303 original size:34 final size:34
Alignment explanation
Indices: 10068264--10068344 Score: 153
Period size: 34 Copynumber: 2.4 Consensus size: 34
10068254 TTCTTGAGAG
*
10068264 TTGTTTTTTCCTTTTTATCAAGAGAGAATTATCA
1 TTGTTTTCTCCTTTTTATCAAGAGAGAATTATCA
10068298 TTGTTTTCTCCTTTTTATCAAGAGAGAATTATCA
1 TTGTTTTCTCCTTTTTATCAAGAGAGAATTATCA
10068332 TTGTTTTCTCCTT
1 TTGTTTTCTCCTT
10068345 GGTAGATCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAAGAGAGAATTATCA
Found at i:10068358 original size:36 final size:34
Alignment explanation
Indices: 10068264--10068359 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
10068254 TTCTTGAGAG
* **
10068264 TTGTTTTTTCCTTTTTATCAAGAGAGAATTATCA
1 TTGTTTTCTCCTTTAGATCAAGAGAGAATTATCA
**
10068298 TTGTTTTCTCCTTTTTATCAAGAGAGAATTATCA
1 TTGTTTTCTCCTTTAGATCAAGAGAGAATTATCA
*
10068332 TTGTTTTCTCCTTGGTAGATCGAGAGAG
1 TTGTTTTCTCCTT--TAGATCAAGAGAG
10068360 GTTGTAATTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
34 46 0.82
36 10 0.18
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTAGATCAAGAGAGAATTATCA
Found at i:10073899 original size:31 final size:31
Alignment explanation
Indices: 10073858--10073930 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
10073848 TCATAATCAT
* * *
10073858 TAAACATTTAAGGTATTTTCACTTTAGTCAC
1 TAAACATTTAAAGCATTTTCAATTTAGTCAC
*
10073889 TAAACTTTTAAAGCATTTTCAATTTAGTCTA-
1 TAAACATTTAAAGCATTTTCAATTTAGTC-AC
10073920 TAAA-ATTTAAA
1 TAAACATTTAAA
10073931 ATTTTACATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 6 0.17
31 29 0.81
32 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (31 bp):
TAAACATTTAAAGCATTTTCAATTTAGTCAC
Found at i:10082859 original size:21 final size:21
Alignment explanation
Indices: 10082830--10082882 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
10082820 ATTCTGACTA
10082830 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
10082851 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
10082872 TCGCAATGCGA
1 TCGCATTGCGA
10082883 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:10082897 original size:20 final size:20
Alignment explanation
Indices: 10082872--10082944 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
10082862 TTTTCCTAAT
10082872 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
10082892 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
10082912 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
10082932 TCGCAACGCGAAT
1 TCGCAATGCGAAT
10082945 CTGACTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:10082954 original size:20 final size:20
Alignment explanation
Indices: 10082931--10083017 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
10082921 GAATATGTAA
*
10082931 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
10082951 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
10082971 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
10082991 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
10083011 ATCGCAA
1 ATCGCAA
10083018 TACTGAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:10082955 original size:40 final size:40
Alignment explanation
Indices: 10082872--10083002 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
10082862 TTTTCCTAAT
* * * *
10082872 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTA-AA
1 TCGCAACGCGAATATGTAAATCGCAACGCGAAT-CTG-ACTA
*
10082912 TCGCAATGCGAATATGTAAATCGCAACGCGAATCTGACTA
1 TCGCAACGCGAATATGTAAATCGCAACGCGAATCTGACTA
* * * *
10082952 TCGCAACGCGATTATG-ACTATCGCAACGAGATTCTGACTA
1 TCGCAACGCGAATATGTA-AATCGCAACGCGAATCTGACTA
10082992 TCGCAACGCGA
1 TCGCAACGCGA
10083003 TTCTGACTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.04
40 77 0.96
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGAATATGTAAATCGCAACGCGAATCTGACTA
Found at i:10083910 original size:24 final size:24
Alignment explanation
Indices: 10083853--10083912 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
10083843 TAGTCAGTAT
10083853 TCAAAATTTGATCTTGGTCAATAC
1 TCAAAATTTGATCTTGGTCAATAC
* ** *
10083877 CCGGACTTTGATCTTGGTCAATAC
1 TCAAAATTTGATCTTGGTCAATAC
*
10083901 TCAAATTTTGAT
1 TCAAAATTTGAT
10083913 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (24 bp):
TCAAAATTTGATCTTGGTCAATAC
Found at i:10086357 original size:14 final size:14
Alignment explanation
Indices: 10086338--10086391 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
10086328 GGAAATGACT
10086338 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
10086352 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
10086371 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
10086385 ATCGCAA
1 ATCGCAA
10086392 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:10086406 original size:34 final size:33
Alignment explanation
Indices: 10086318--10086413 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
10086308 TCATTTGACT
* **
10086318 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
10086352 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
10086385 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
10086414 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:10086409 original size:20 final size:19
Alignment explanation
Indices: 10086351--10086417 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
10086341 GCAACGAGAG
10086351 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
10086370 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
10086384 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
10086404 AATCGCAACGCGAA
1 AATCGCAATGCGAA
10086418 TTTAGTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:10088695 original size:20 final size:20
Alignment explanation
Indices: 10088607--10088693 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
10088597 GAAACTTAAA
10088607 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
10088627 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
10088647 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
10088667 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
10088687 ATCGCAA
1 ATCGCAA
10088694 TGTGATTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:10088763 original size:20 final size:20
Alignment explanation
Indices: 10088726--10088772 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
10088716 GATTCTTTTG
*
10088726 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGACAAATTCGCA
** *
10088746 TTGCGATAGACATTTTCGCG
1 TTGCGATAGACAAATTCGCA
10088766 TTGCGAT
1 TTGCGAT
10088773 TTTGTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
TTGCGATAGACAAATTCGCA
Found at i:10090710 original size:20 final size:19
Alignment explanation
Indices: 10090686--10090806 Score: 81
Period size: 20 Copynumber: 6.5 Consensus size: 19
10090676 TGAAACTTAA
10090686 AATCGCAACACGAAAATGAC
1 AATCGCAACACG-AAATGAC
* *
10090706 TATCGC-A-ACGCAA-G--
1 AATCGCAACACGAAATGAC
* *
10090720 AATCGCAACGCGAAATGAA
1 AATCGCAACACGAAATGAC
10090739 AATCGCAACACGAAAATGAC
1 AATCGCAACACG-AAATGAC
* * * *
10090759 AATCGTAACGCGAATTTAAC
1 AATCGCAACACGAA-ATGAC
* * *
10090779 TATCGCAACGCGAAATGAA
1 AATCGCAACACGAAATGAC
10090798 AATCGCAAC
1 AATCGCAAC
10090807 GACAGAATCG
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 5 0.06
17 3 0.04
18 3 0.04
19 24 0.31
20 36 0.47
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (19 bp):
AATCGCAACACGAAATGAC
Found at i:10090744 original size:53 final size:56
Alignment explanation
Indices: 10090684--10090806 Score: 171
Period size: 53 Copynumber: 2.2 Consensus size: 56
10090674 TCTGAAACTT
* *
10090684 AAAATCGCAACACGAAAATGACTATCGCAACGC-AA-GA-ATCGCAACGCGAAATG
1 AAAATCGCAACACGAAAATGACAATCGCAACGCGAATAACATCGCAACGCGAAATG
*
10090737 AAAATCGCAACACGAAAATGACAATCGTAACGCGAATTTAACTATCGCAACGCGAAATG
1 AAAATCGCAACACGAAAATGACAATCGCAACGCGAA--TAAC-ATCGCAACGCGAAATG
10090796 AAAATCGCAAC
1 AAAATCGCAAC
10090807 GACAGAATCG
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
53 31 0.51
54 2 0.03
57 1 0.02
59 27 0.44
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.14
Consensus pattern (56 bp):
AAAATCGCAACACGAAAATGACAATCGCAACGCGAATAACATCGCAACGCGAAATG
Found at i:10090763 original size:39 final size:39
Alignment explanation
Indices: 10090720--10090807 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
10090710 GCAACGCAAG
*
10090720 AATCGCAACGCGAAATGAA-AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAATGAACAATCGCAACACG-AAATGAA
* * * * *
10090759 AATCGTAACGCGAATTTAACTATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAACAATCGCAACACGAAATGAA
10090798 AATCGCAACG
1 AATCGCAACG
10090808 ACAGAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 31 0.76
40 10 0.24
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (39 bp):
AATCGCAACGCGAAATGAACAATCGCAACACGAAATGAA
Found at i:10091207 original size:22 final size:22
Alignment explanation
Indices: 10091143--10091207 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
10091133 TGACCGTGAA
* * *
10091143 TGATTTCG-CCGAGATGGAGAT
1 TGATTTCGTCGGAGATGGGGAC
* *
10091164 TGATATCGTCGGAGATGTGGAC
1 TGATTTCGTCGGAGATGGGGAC
10091186 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
10091208 GGATGTCGCC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.22, C:0.14, G:0.37, T:0.28
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:10091427 original size:20 final size:20
Alignment explanation
Indices: 10091404--10091476 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
10091394 CGATAGTCAG
* *
10091404 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
10091424 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
10091444 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
10091464 ATTCGCATTGCGA
1 ATTCGCATTGCGA
10091477 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:10091497 original size:21 final size:21
Alignment explanation
Indices: 10091473--10091518 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10091463 TATTCGCATT
10091473 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
10091494 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
10091515 GCGA
1 GCGA
10091519 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:10093047 original size:20 final size:20
Alignment explanation
Indices: 10093022--10093065 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
10093012 TAACTTGCTA
* * *
10093022 CACCTTTAAAAATGATCTAG
1 CACCTTGAAAAATAATATAG
10093042 CACCTTGAAAAATAATATAG
1 CACCTTGAAAAATAATATAG
10093062 CACC
1 CACC
10093066 GTCAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (20 bp):
CACCTTGAAAAATAATATAG
Found at i:10093072 original size:20 final size:20
Alignment explanation
Indices: 10093029--10093077 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
10093019 CTACACCTTT
* * * *
10093029 AAAAATGATCTAGCACCTTG
1 AAAAATAATATAGCACCGTC
10093049 AAAAATAATATAGCACCGTC
1 AAAAATAATATAGCACCGTC
10093069 -AAAATAATA
1 AAAAATAATA
10093078 AATAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAAATAATATAGCACCGTC
Found at i:10093600 original size:21 final size:21
Alignment explanation
Indices: 10093576--10093619 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
10093566 TCTTTAAAAG
10093576 TTGAAAAATATATTTTCAATT
1 TTGAAAAATATATTTTCAATT
*
10093597 TTGAAAAGTATATTTTCAATT
1 TTGAAAAATATATTTTCAATT
10093618 TT
1 TT
10093620 TTCTTTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
TTGAAAAATATATTTTCAATT
Found at i:10097332 original size:5 final size:5
Alignment explanation
Indices: 10097322--10097349 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10097312 CATAGAGAAG
10097322 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
10097350 ATAGAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:10108946 original size:131 final size:131
Alignment explanation
Indices: 10108712--10108974 Score: 499
Period size: 131 Copynumber: 2.0 Consensus size: 131
10108702 GTAAATGAAG
*
10108712 AAATGATACTATTATACTGTTACCTTATTTCCATTTCTTGATGTGTTGTGTTTCAACTTTAGTTT
1 AAATGATACTATTATACTGTTACCTTATTTCCATTTCTTGATGTGTTGTGTTTCAAATTTAGTTT
*
10108777 CTTTTGATTATTTTTTTAGGTTAATAGGATTATTCATGTGGTAAGTTGTAAATATGTAACAGGCG
66 CTTTTGATTAGTTTTTTAGGTTAATAGGATTATTCATGTGGTAAGTTGTAAATATGTAACAGGCG
10108842 A
131 A
10108843 AAATGATACTATTATACTGTTACCTTATTTCCATTTCTTGATGTGTTGTGTTTCAAATTTAGTTT
1 AAATGATACTATTATACTGTTACCTTATTTCCATTTCTTGATGTGTTGTGTTTCAAATTTAGTTT
*
10108908 CTTTTGATTAGTTTTTTAGGTTAATAGGATTATTCATGTGGTAAGTTGTAAATATGTAACGGGCG
66 CTTTTGATTAGTTTTTTAGGTTAATAGGATTATTCATGTGGTAAGTTGTAAATATGTAACAGGCG
10108973 A
131 A
10108974 A
1 A
10108975 CTCATAGCAT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (131 bp):
AAATGATACTATTATACTGTTACCTTATTTCCATTTCTTGATGTGTTGTGTTTCAAATTTAGTTT
CTTTTGATTAGTTTTTTAGGTTAATAGGATTATTCATGTGGTAAGTTGTAAATATGTAACAGGCG
A
Found at i:10111373 original size:2 final size:2
Alignment explanation
Indices: 10111368--10111418 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
10111358 TGTGTGTGTG
10111368 TA TA TA TA TA TA TA TA TA TA T- 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 TA TA
10111409 TA TA TA TA TA
1 TA TA TA TA TA
10111419 GACCTGAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10123375 original size:54 final size:55
Alignment explanation
Indices: 10123301--10123410 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
10123291 ATAGGCCATA
10123301 AAATCATCTGGATAAATTTTTGATGATTTGAATGTTAGGTTGCCGAGCCA-TAAG
1 AAATCATCTGGATAAATTTTTGATGATTTGAATGTTAGGTTGCCGAGCCACTAAG
10123355 AAATCATCTGGATAAATTTTTGATGATTTGAATGTTAGGTTGCCGAGCCACTAAG
1 AAATCATCTGGATAAATTTTTGATGATTTGAATGTTAGGTTGCCGAGCCACTAAG
10123410 A
1 A
10123411 GCAATGGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 50 0.91
55 5 0.09
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (55 bp):
AAATCATCTGGATAAATTTTTGATGATTTGAATGTTAGGTTGCCGAGCCACTAAG
Found at i:10126279 original size:39 final size:39
Alignment explanation
Indices: 10126236--10126311 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
10126226 AGCATCAATA
* *
10126236 AAAAATATAAATAAAATATCTAAATTATATGAAAATTTT
1 AAAAATATAAAGAAAATATCTAAACTATATGAAAATTTT
*
10126275 AAAAATATAAAGAAAATATCTGAACTATATGAAAATT
1 AAAAATATAAAGAAAATATCTAAACTATATGAAAATT
10126312 AAAAAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (39 bp):
AAAAATATAAAGAAAATATCTAAACTATATGAAAATTTT
Found at i:10126289 original size:20 final size:21
Alignment explanation
Indices: 10126236--10126295 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
10126226 AGCATCAATA
*
10126236 AAAAATATAAATAAAATATCT
1 AAAAATATAAAGAAAATATCT
* * *
10126257 -AAATTAT-ATGAAAAT-TTT
1 AAAAATATAAAGAAAATATCT
10126275 AAAAATATAAAGAAAATATCT
1 AAAAATATAAAGAAAATATCT
10126296 GAACTATATG
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.07
19 12 0.41
20 13 0.45
21 2 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAAATATAAAGAAAATATCT
Found at i:10129949 original size:11 final size:11
Alignment explanation
Indices: 10129926--10129958 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
10129916 ATTTTAAATT
10129926 TATAATTTAAA
1 TATAATTTAAA
10129937 TATAATTTAAA
1 TATAATTTAAA
*
10129948 TATGATTTAAA
1 TATAATTTAAA
10129959 AATATACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
TATAATTTAAA
Found at i:10130746 original size:31 final size:31
Alignment explanation
Indices: 10130711--10130774 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
10130701 GACTTTAACT
**
10130711 AAATTCAAGTGTTAAATTAATAATTCATCTA
1 AAATTCAAGAATTAAATTAATAATTCATCTA
* * *
10130742 AAATTTAAGAATTAAATTAATATTTTATCTA
1 AAATTCAAGAATTAAATTAATAATTCATCTA
10130773 AA
1 AA
10130775 TATTAGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTCAAGAATTAAATTAATAATTCATCTA
Found at i:10131498 original size:2 final size:2
Alignment explanation
Indices: 10131485--10131514 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
10131475 AGCATATAAT
10131485 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
10131515 TTACACGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10133280 original size:13 final size:13
Alignment explanation
Indices: 10133262--10133288 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10133252 ACCTACTTTC
10133262 TCCACCCTTCCTT
1 TCCACCCTTCCTT
10133275 TCCACCCTTCCTT
1 TCCACCCTTCCTT
10133288 T
1 T
10133289 TTATTTTCTT
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:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (13 bp):
TCCACCCTTCCTT
Found at i:10138689 original size:20 final size:22
Alignment explanation
Indices: 10138663--10138717 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
10138653 TATCATTTAA
10138663 ATAAAATTATTATA-TTTAAT-
1 ATAAAATTATTATATTTTAATC
* *
10138683 TTAAAA-TATTACATTTTAATC
1 ATAAAATTATTATATTTTAATC
10138704 GATAAAATTATTAT
1 -ATAAAATTATTAT
10138718 TACTCCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.22
20 11 0.41
22 5 0.19
23 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAAATTATTATATTTTAATC
Found at i:10145108 original size:2 final size:2
Alignment explanation
Indices: 10145101--10145139 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
10145091 TTTAACTAGA
10145101 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10145140 TATTAAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10146004 original size:100 final size:98
Alignment explanation
Indices: 10145817--10146014 Score: 362
Period size: 100 Copynumber: 2.0 Consensus size: 98
10145807 GAATAAAATT
10145817 GGGAGTAAACAAAAGTTTGTGTTGGGCACAGCAAAATGACCGTACAATTTGCACATATTTTTGGC
1 GGGAGTAAACAAAAGTTTGTGTTGGGCACAGCAAAATGACCGTACAATTTGCACATATTTTTGGC
10145882 AAATTTTGATTCATCGTTTCCAAA-ATCAGCTC
66 AAATTTTGATTCATCGTTTCCAAACATCAGCTC
10145914 GGGAGTAAACAAAAGTTTGTGTTGGGCACAGCAAAATTGACCGTACAATTTGCCCACATATTTTT
1 GGGAGTAAACAAAAGTTTGTGTTGGGCACAGCAAAA-TGACCGTACAATTTG--CACATATTTTT
10145979 GGCAAATTTTGATTCATCGTTTCCAAACATCAGCTC
63 GGCAAATTTTGATTCATCGTTTCCAAACATCAGCTC
10146015 TCACAGATCG
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
97 36 0.37
98 15 0.15
100 38 0.39
101 8 0.08
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (98 bp):
GGGAGTAAACAAAAGTTTGTGTTGGGCACAGCAAAATGACCGTACAATTTGCACATATTTTTGGC
AAATTTTGATTCATCGTTTCCAAACATCAGCTC
Found at i:10148842 original size:23 final size:23
Alignment explanation
Indices: 10148808--10148852 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
10148798 CTTTCATGCA
10148808 TTATTTTTTA-TTTATCAAAATT
1 TTATTTTTTATTTTATCAAAATT
*
10148830 TTATTTTTGTATTTTATGAAAAT
1 TTATTTTT-TATTTTATCAAAAT
10148853 AATAGATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATTTTTTATTTTATCAAAATT
Found at i:10149460 original size:16 final size:16
Alignment explanation
Indices: 10149439--10149471 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10149429 TATGATCCAT
10149439 TTACATAGTGTAAAAC
1 TTACATAGTGTAAAAC
10149455 TTACATAGTGTAAAAC
1 TTACATAGTGTAAAAC
10149471 T
1 T
10149472 CTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (16 bp):
TTACATAGTGTAAAAC
Found at i:10150364 original size:2 final size:2
Alignment explanation
Indices: 10150359--10150386 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10150349 GAGAGAAAAA
10150359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10150387 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10155690 original size:55 final size:55
Alignment explanation
Indices: 10155610--10155719 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
10155600 ATACTCAACC
10155610 TGAAAATAATCGTATAATTGATCTTTATTTATTAAGCATGATTATAATACTTCTCT
1 TGAAAATAATCGTATAATTGATCTTTATTTATTAAGCATGATTATAAT-CTTCTCT
10155666 TGAAAATAAT-GTATAATTGATCTTTATTTATTAAGCATGATTATAATCTTCTCT
1 TGAAAATAATCGTATAATTGATCTTTATTTATTAAGCATGATTATAATCTTCTCT
10155720 ATGTCTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 7 0.13
55 37 0.69
56 10 0.19
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (55 bp):
TGAAAATAATCGTATAATTGATCTTTATTTATTAAGCATGATTATAATCTTCTCT
Found at i:10156785 original size:36 final size:36
Alignment explanation
Indices: 10156738--10156808 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
10156728 TTATATGTAT
10156738 ATACATATCACGAGTGCATTAGAAATCTTAATTGTC
1 ATACATATCACGAGTGCATTAGAAATCTTAATTGTC
10156774 ATACATATCACGAGTGCATTAGAAATCTTAATTGT
1 ATACATATCACGAGTGCATTAGAAATCTTAATTGT
10156809 GTAACCTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (36 bp):
ATACATATCACGAGTGCATTAGAAATCTTAATTGTC
Found at i:10157210 original size:2 final size:2
Alignment explanation
Indices: 10157203--10157231 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10157193 CAAATTTTTA
10157203 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10157232 TATTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10157691 original size:6 final size:6
Alignment explanation
Indices: 10157680--10157705 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10157670 GGGCGTCAAG
10157680 TGTGAT TGTGAT TGTGAT TGTGAT TG
1 TGTGAT TGTGAT TGTGAT TGTGAT TG
10157706 CAAGCGATCG
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:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGTGAT
Found at i:10159476 original size:3 final size:3
Alignment explanation
Indices: 10159468--10159506 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
10159458 ATGAGTTTCC
10159468 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10159507 TTTGTATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10160128 original size:222 final size:221
Alignment explanation
Indices: 10159742--10160189 Score: 835
Period size: 222 Copynumber: 2.0 Consensus size: 221
10159732 TAAAATTTTA
* *
10159742 AAAATGTAAAATATGTAGTTGAGATATTTTAAATATAAATTTTGAACATTTTGAAAATTATTAAA
1 AAAATGTAAAATATGTAGTTAAAATATTTTAAATATAAATTTTGAACATTTTGAAAATTATTAAA
10159807 CTAATATTAAATAAATAAAATTTGAATTAATCAATTGATTTTAAACATTAGACCTATATATTTTA
66 CTAATATTAAATAAATAAAATTTGAATTAATCAATTGATTTTAAACATTAGACCTATATATTTTA
*
10159872 TTTTTAACTAACAAAATGATGACATATCAAATATTTGTTGCGGAAGACGGCTATCGGATAGAGTA
131 TTTTTAACTAACAAAATGATGACATATCAAATATTTGTTGCGGAAGACGGCTATCGGATAGAGCA
10159937 AAATCGCAACTGATAATTTGAGAAAAT
196 AAATCGCAACTGATAA-TTGAGAAAAT
10159964 AAAATGTAAAATATGTAGTTAAAA-ATTTTTAAATATAAATTTTGAACATTTTGAAAATTATTAA
1 AAAATGTAAAATATGTAGTTAAAATA-TTTTAAATATAAATTTTGAACATTTTGAAAATTATTAA
*
10160028 ACTAATATTAAATAAATCAAATTTGAATTAATCAATTGATTTTAAACATTAGACCTATATATTTT
65 ACTAATATTAAATAAATAAAATTTGAATTAATCAATTGATTTTAAACATTAGACCTATATATTTT
10160093 ATTTTTAACTAACAAAATGATGACATATCAAATATTTGTTGCGGAAGACGGCTATCGGATAGAGC
130 ATTTTTAACTAACAAAATGATGACATATCAAATATTTGTTGCGGAAGACGGCTATCGGATAGAGC
10160158 AAAATCGCAACTGATAATTGAGAAAAT
195 AAAATCGCAACTGATAATTGAGAAAAT
10160185 AAAAT
1 AAAAT
10160190 AAGATAAAAG
Statistics
Matches: 221, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
221 16 0.07
222 205 0.93
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (221 bp):
AAAATGTAAAATATGTAGTTAAAATATTTTAAATATAAATTTTGAACATTTTGAAAATTATTAAA
CTAATATTAAATAAATAAAATTTGAATTAATCAATTGATTTTAAACATTAGACCTATATATTTTA
TTTTTAACTAACAAAATGATGACATATCAAATATTTGTTGCGGAAGACGGCTATCGGATAGAGCA
AAATCGCAACTGATAATTGAGAAAAT
Found at i:10161253 original size:15 final size:15
Alignment explanation
Indices: 10161233--10161262 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10161223 GCCTGGATTC
10161233 GCCATGTACCGACTA
1 GCCATGTACCGACTA
10161248 GCCATGTACCGACTA
1 GCCATGTACCGACTA
10161263 AACACTCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
GCCATGTACCGACTA
Found at i:10174331 original size:4 final size:4
Alignment explanation
Indices: 10174324--10174401 Score: 75
Period size: 4 Copynumber: 19.5 Consensus size: 4
10174314 TAAAATGTTG
* * * *
10174324 ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATAC ACAC ACAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
10174372 ATAG ATAC ACAC ACAT ATAC ATAC ACAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
10174402 GCATGGATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (4 bp):
ATAC
Found at i:10174369 original size:16 final size:16
Alignment explanation
Indices: 10174324--10174401 Score: 84
Period size: 16 Copynumber: 4.9 Consensus size: 16
10174314 TAAAATGTTG
*
10174324 ATACATACATACATAC
1 ATACATACACACATAC
* * *
10174340 ATGCATGCATACATAC
1 ATACATACACACATAC
*
10174356 ATACACACACACATAC
1 ATACATACACACATAC
* * *
10174372 ATAGATACACACACAT
1 ATACATACACACATAC
10174388 ATACATACACACAT
1 ATACATACACACAT
10174402 GCATGGATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (16 bp):
ATACATACACACATAC
Found at i:10174370 original size:20 final size:20
Alignment explanation
Indices: 10174326--10174396 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
10174316 AAATGTTGAT
** *
10174326 ACATACATACATACATGCAT
1 ACATACATACATACACACAC
*
10174346 GCATACATACATACACACAC
1 ACATACATACATACACACAC
*
10174366 ACATACATAGATACACACAC
1 ACATACATACATACACACAC
*
10174386 ATATACATACA
1 ACATACATACA
10174397 CACATGCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.48, C:0.28, G:0.04, T:0.20
Consensus pattern (20 bp):
ACATACATACATACACACAC
Found at i:10184509 original size:15 final size:15
Alignment explanation
Indices: 10184474--10184510 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
10184464 TCTCTATTTT
10184474 TTAAAATTTTAAATC
1 TTAAAATTTTAAATC
10184489 TT-AAATTTTAAA-C
1 TTAAAATTTTAAATC
10184502 TTCAAAATT
1 TT-AAAATT
10184511 ATAAGTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 10 0.50
15 7 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAAATTTTAAATC
Found at i:10185203 original size:37 final size:36
Alignment explanation
Indices: 10185128--10185203 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
10185118 TTTTTATATT
*
10185128 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
10185164 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
10185201 TTT
1 TTT
10185204 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:10198439 original size:2 final size:2
Alignment explanation
Indices: 10198375--10198425 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
10198365 ATTTTGGTTA
10198375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10198417 AT AT AT AT A
1 AT AT AT AT A
10198426 ATTATTTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10201951 original size:30 final size:32
Alignment explanation
Indices: 10201916--10201981 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
10201906 ATCGAATCGG
*
10201916 TTTTTAAAA-TCATGTTCGGGTCGGGTCA-AT
1 TTTTTAAAAGTCATATTCGGGTCGGGTCAGAT
* *
10201946 TTTTTAAAAGGTGATATTCTGGTCGGGTCAGAT
1 TTTTTAAAA-GTCATATTCGGGTCGGGTCAGAT
10201979 TTT
1 TTT
10201982 GGTTTAGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
32 16 0.53
33 5 0.17
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (32 bp):
TTTTTAAAAGTCATATTCGGGTCGGGTCAGAT
Found at i:10205223 original size:12 final size:12
Alignment explanation
Indices: 10205206--10205230 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10205196 ATTTACATCT
10205206 ATAGGACTTTAC
1 ATAGGACTTTAC
10205218 ATAGGACTTTAC
1 ATAGGACTTTAC
10205230 A
1 A
10205231 GATTGTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATAGGACTTTAC
Found at i:10206535 original size:27 final size:27
Alignment explanation
Indices: 10206483--10206535 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
10206473 TAAAATGTAT
*
10206483 ATAAATTAATATAAAATAGAAATAAAC
1 ATAAATTAATATAAAATAAAAATAAAC
10206510 ATAAATT-ATA-AAAATATAAAAGTAAA
1 ATAAATTAATATAAAATA-AAAA-TAAA
10206536 TATTTAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 11 0.48
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (27 bp):
ATAAATTAATATAAAATAAAAATAAAC
Found at i:10215577 original size:17 final size:18
Alignment explanation
Indices: 10215555--10215591 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
10215545 GAGAACCAAG
10215555 CCTCGTT-TTCCTCT-CAT
1 CCTCGTTGTT-CTCTACAT
10215572 CCTCGTTGTTCTCTACAT
1 CCTCGTTGTTCTCTACAT
10215590 CC
1 CC
10215592 GGTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.08, C:0.41, G:0.08, T:0.43
Consensus pattern (18 bp):
CCTCGTTGTTCTCTACAT
Found at i:10217358 original size:34 final size:33
Alignment explanation
Indices: 10217299--10217415 Score: 142
Period size: 34 Copynumber: 3.7 Consensus size: 33
10217289 TATATATATA
10217299 TATATATTATTA-ATT-A-TATATATATAATATTT
1 TATATATT-TTATATTAATTATA-ATATAATATTT
10217331 TATATATTTTATATTAATTATACATAT-ATAATTT
1 TATATATTTTATATTAATTATA-ATATAAT-ATTT
10217365 TATATATTTTATATTAATTAT-ATATAATA-TT
1 TATATATTTTATATTAATTATAATATAATATTT
10217396 T-TATATTTT-TATTAATTATA
1 TATATATTTTATATTAATTATA
10217416 TAATACAAAC
Statistics
Matches: 78, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
29 10 0.13
30 8 0.10
31 6 0.08
32 16 0.21
33 5 0.06
34 33 0.42
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATATTTTATATTAATTATAATATAATATTT
Found at i:10217572 original size:15 final size:14
Alignment explanation
Indices: 10217508--10217585 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
10217498 TTCTCAAAAT
*
10217508 AACCCTAAACCTTA
1 AACCCTAAACTTTA
* * *
10217522 AATCATAAAC-CTA
1 AACCCTAAACTTTA
*
10217535 AACCCCAAACTTTA
1 AACCCTAAACTTTA
10217549 AACCCTAAACATTTA
1 AACCCTAAAC-TTTA
* *
10217564 AATCTTAAA-TCTTA
1 AACCCTAAACT-TTA
10217578 AACCCTAA
1 AACCCTAA
10217586 TTTTTTTTCT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
13 10 0.20
14 28 0.57
15 11 0.22
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTAAACTTTA
Found at i:10222180 original size:27 final size:28
Alignment explanation
Indices: 10222135--10222188 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
10222125 TAAACAAATT
10222135 ATTTGTCTTTTTAAAGTTTACAACAAAA
1 ATTTGTCTTTTTAAAGTTTACAACAAAA
10222163 ATTTGTC-TTTTAAAGTTTACAACAAA
1 ATTTGTCTTTTTAAAGTTTACAACAAA
10222189 TTATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (28 bp):
ATTTGTCTTTTTAAAGTTTACAACAAAA
Found at i:10222304 original size:12 final size:12
Alignment explanation
Indices: 10222283--10222323 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
10222273 TTTAAAAATT
10222283 TTAT-ATTTAATA
1 TTATAATTTAA-A
10222295 TTA-AATTTAAA
1 TTATAATTTAAA
10222306 TTATAATTTAAA
1 TTATAATTTAAA
*
10222318 ATATAA
1 TTATAA
10222324 AATATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATTTAAA
Found at i:10222347 original size:14 final size:16
Alignment explanation
Indices: 10222326--10222363 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
10222316 AAATATAAAA
*
10222326 TATAAAAA-AATGAAT
1 TATAAAAATATTGAAT
10222341 TATAAAAATATTGAAT
1 TATAAAAATATTGAAT
10222357 TATAAAA
1 TATAAAA
10222364 GTAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TATAAAAATATTGAAT
Found at i:10222409 original size:21 final size:20
Alignment explanation
Indices: 10222357--10222417 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
10222347 AATATTGAAT
*
10222357 TATAAAAGTAAATATAAAAA
1 TATAAAAGTAAATTTAAAAA
* **
10222377 TACAATTTGTAAATCTTAAAAA
1 TATAA-AAGTAAAT-TTAAAAA
10222399 TATAAAAGTAAATATTAAA
1 TATAAAAGTAAAT-TTAAA
10222418 TTAAACTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.13
21 17 0.55
22 10 0.32
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
TATAAAAGTAAATTTAAAAA
Found at i:10222476 original size:20 final size:22
Alignment explanation
Indices: 10222431--10222477 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
10222421 AACTTTTATA
*
10222431 ATTTAATATTTTTATAATTCAT
1 ATTTTATATTTTTATAATTCAT
10222453 -TTTTATATTTTTA-AA-TCAT
1 ATTTTATATTTTTATAATTCAT
10222472 ATTTTA
1 ATTTTA
10222478 AACTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 7 0.30
21 12 0.52
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATATTTTTATAATTCAT
Found at i:10222500 original size:7 final size:7
Alignment explanation
Indices: 10222488--10222513 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10222478 AACTTAATTT
10222488 TAAAATA
1 TAAAATA
10222495 TAAAATA
1 TAAAATA
10222502 TAAAATA
1 TAAAATA
10222509 TAAAA
1 TAAAA
10222514 AGTTTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:10227855 original size:34 final size:34
Alignment explanation
Indices: 10227817--10227887 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
10227807 ATTTTTATGT
10227817 TTAATTTAGTAAGAATTAGTTTAAATTATGAAAA
1 TTAATTTAGTAAGAATTAGTTTAAATTATGAAAA
10227851 TTAATTTAGTAAGAATTAGTTTAAATTATGAAAA
1 TTAATTTAGTAAGAATTAGTTTAAATTATGAAAA
10227885 TTA
1 TTA
10227888 TTTGAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.42
Consensus pattern (34 bp):
TTAATTTAGTAAGAATTAGTTTAAATTATGAAAA
Found at i:10227858 original size:19 final size:19
Alignment explanation
Indices: 10227830--10227896 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
10227820 ATTTAGTAAG
*
10227830 AATTAGTTTAAATTATGAA
1 AATTAATTTAAATTATGAA
* *
10227849 AATTAATTT--AGTA--AG
1 AATTAATTTAAATTATGAA
*
10227864 AATTAGTTTAAATTATGAA
1 AATTAATTTAAATTATGAA
10227883 AATT-ATTTGAAATT
1 AATTAATTT-AAATT
10227897 TACTAACTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
15 9 0.25
17 6 0.17
18 3 0.08
19 18 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.43
Consensus pattern (19 bp):
AATTAATTTAAATTATGAA
Found at i:10228175 original size:3 final size:3
Alignment explanation
Indices: 10228167--10228199 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10228157 CCATGCTTTT
10228167 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10228200 GGGTAAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10229094 original size:17 final size:17
Alignment explanation
Indices: 10229072--10229118 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
10229062 TGAGGAGAGA
10229072 AGAAAAAGAAAAATGAG
1 AGAAAAAGAAAAATGAG
*
10229089 AGAAAAAGGAAAATGAG
1 AGAAAAAGAAAAATGAG
*
10229106 AAAAAAAGAAAAA
1 AGAAAAAGAAAAA
10229119 GGGGATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (17 bp):
AGAAAAAGAAAAATGAG
Found at i:10229490 original size:59 final size:57
Alignment explanation
Indices: 10229367--10229523 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 57
10229357 CTATAACTTT
* * * * *
10229367 TATTTTAAATTGGCCTCTAAACTTTTAAACATTCAATTTCATCCCCAAATTAGGACTC
1 TATTCTAAATTGTCCTC-AAACTTTTGAACATTCAATTTCATCCCCAAAGTAGAACTC
* * *
10229425 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTATAATTTCATTCCCAAAGTATGAAC-C
1 T-ATTCTAAATT-GTCCTCAAACTTTTGAACATT-CAATTTCATCCCCAAAGTA-GAACTC
* *
10229485 TATTCTAAATTGGTCCCCATACTTTTGAACATTTCAATT
1 TATTCTAAATT-GTCCTCAAACTTTTGAACA-TTCAATT
10229524 CTTTCCCAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
58 1 0.01
59 52 0.64
60 25 0.31
61 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (57 bp):
TATTCTAAATTGTCCTCAAACTTTTGAACATTCAATTTCATCCCCAAAGTAGAACTC
Found at i:10233008 original size:78 final size:77
Alignment explanation
Indices: 10232914--10233057 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 77
10232904 ATTTATATAC
* *
10232914 TTTTAAATATTTCAAATTAAAAGATATTTATTATTT-TTTAGTTTAAATATTAAAAAGATATTAA
1 TTTTAAATATTTCAAATTAAAAAATATTTATTATTTCTTAAGTTTAAATATT-AAAA-ATATTAA
10232978 AAACATCTATATCT
64 AAACATCTATATCT
* * * *
10232992 TTTTTAATATTTCAAATTAAAAAATATTTTTTATTTCTTAATTTTGAATATTAAAAATATTAAAA
1 TTTTAAATATTTCAAATTAAAAAATATTTATTATTTCTTAAGTTTAAATATTAAAAATATTAAAA
10233057 A
66 A
10233058 TATATCAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
77 10 0.17
78 37 0.63
79 12 0.20
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (77 bp):
TTTTAAATATTTCAAATTAAAAAATATTTATTATTTCTTAAGTTTAAATATTAAAAATATTAAAA
ACATCTATATCT
Found at i:10242794 original size:36 final size:35
Alignment explanation
Indices: 10242750--10242822 Score: 137
Period size: 36 Copynumber: 2.1 Consensus size: 35
10242740 TTCTGGTCCT
10242750 GAGTTTTTAATGCATTTTCTTGGTTTACAAACCATA
1 GAGTTTTTAATGCATTTTCTTGGTTTAC-AACCATA
10242786 GAGTTTTTAATGCATTTTCTTGGTTTACAACCATA
1 GAGTTTTTAATGCATTTTCTTGGTTTACAACCATA
10242821 GA
1 GA
10242823 ATTAGGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 9 0.24
36 28 0.76
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (35 bp):
GAGTTTTTAATGCATTTTCTTGGTTTACAACCATA
Found at i:10243757 original size:35 final size:35
Alignment explanation
Indices: 10243711--10243778 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
10243701 AATTTAGGTC
10243711 TTAGTTATCTTTGTTGCTGTTTATCTTTTTGAAAT
1 TTAGTTATCTTTGTTGCTGTTTATCTTTTTGAAAT
* *
10243746 TTAGTTCTCTTTGTTGTTGTTTATCTTTTTGAA
1 TTAGTTATCTTTGTTGCTGTTTATCTTTTTGAA
10243779 TCTCATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (35 bp):
TTAGTTATCTTTGTTGCTGTTTATCTTTTTGAAAT
Found at i:10245149 original size:10 final size:10
Alignment explanation
Indices: 10245136--10245169 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
10245126 ATTTAATTTA
10245136 TTTTTATTAT
1 TTTTTATTAT
10245146 TTTTTATTAT
1 TTTTTATTAT
10245156 TTTTTATTAT
1 TTTTTATTAT
10245166 TTTT
1 TTTT
10245170 GAGGATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTATTAT
Done.