Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 8 of 12
Found at i:4876874 original size:21 final size:21
Alignment explanation
Indices: 4876850--4876896 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4876840 AAAATTTATT
4876850 AAATTTAAAATAAAAAT-ATAA
1 AAATTT-AAATAAAAATAATAA
* *
4876871 AAATTTAATTAAATATAATAA
1 AAATTTAAATAAAAATAATAA
4876892 AAATT
1 AAATT
4876897 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTTAAATAAAAATAATAA
Found at i:4901473 original size:16 final size:16
Alignment explanation
Indices: 4901452--4901483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4901442 AACTAAAATG
*
4901452 TCATTTATTTTTTCTC
1 TCATTTATTTTCTCTC
4901468 TCATTTATTTTCTCTC
1 TCATTTATTTTCTCTC
4901484 AAATAATGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (16 bp):
TCATTTATTTTCTCTC
Found at i:4903392 original size:12 final size:11
Alignment explanation
Indices: 4903353--4903400 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
4903343 TTTTTGACTA
4903353 ATTATTATATC
1 ATTATTATATC
* *
4903364 ATTTTTATATT
1 ATTATTATATC
4903375 ATTATTATCATC
1 ATTATTAT-ATC
4903387 ATTATTATTATC
1 ATTATTA-TATC
4903399 AT
1 AT
4903401 AACTCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 16 0.52
12 14 0.45
13 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTATATC
Found at i:4903392 original size:15 final size:15
Alignment explanation
Indices: 4903372--4903400 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4903362 TCATTTTTAT
4903372 ATTATTATTATCATC
1 ATTATTATTATCATC
4903387 ATTATTATTATCAT
1 ATTATTATTATCAT
4903401 AACTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATTATCATC
Found at i:4906119 original size:17 final size:19
Alignment explanation
Indices: 4906083--4906122 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
4906073 ATTAACAAGT
4906083 ATATTTATCATCTATTTAA
1 ATATTTATCATCTATTTAA
*
4906102 ATATTTAT-AT-TTTTTAA
1 ATATTTATCATCTATTTAA
4906119 ATAT
1 ATAT
4906123 ATTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 2 0.10
19 8 0.40
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTATCATCTATTTAA
Found at i:4916778 original size:15 final size:16
Alignment explanation
Indices: 4916747--4916780 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4916737 ACCAATTTTT
*
4916747 TAAAACTACTGAAAAC
1 TAAAACAACTGAAAAC
4916763 TAAAACAACT-AAAAC
1 TAAAACAACTGAAAAC
4916778 TAA
1 TAA
4916781 TGATGTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (16 bp):
TAAAACAACTGAAAAC
Found at i:4919951 original size:17 final size:17
Alignment explanation
Indices: 4919925--4919965 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4919915 TAAAATATAC
*
4919925 AAAT-TATGTATAAATT
1 AAATATATGTATAAATA
*
4919941 AAATATATGTATATATA
1 AAATATATGTATAAATA
4919958 AAATATAT
1 AAATATAT
4919966 ATTACTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATATATGTATAAATA
Found at i:4920368 original size:212 final size:217
Alignment explanation
Indices: 4919928--4920398 Score: 614
Period size: 212 Copynumber: 2.2 Consensus size: 217
4919918 AATATACAAA
*
4919928 TTATGTATAAATTAAATATATGTATATATAAAATATATATTACTTTATTATATATATGAAATTAA
1 TTATGTATAAATTAAATATA--TATATATAATA-ATATATTACTTTATTATATATATGAAATTAA
* * ** *
4919993 CGATACAACTTATATATTATAATATTTTAATTTTTATATCAAAGTTTGTTTAAATAATAATTAAT
63 CGACACAACTTATATATTATAATA--TT-AGTTTTATATCAAAGTTTGAATAAATAATAACTAAT
* * *
4920058 TATAAATAATATGTTACAAAAATTAAGATGATAACTAATAAAATTATTAAGTGTAATCATATAAA
125 TATAAACAATATATTACAAAAATTAAGATGATAACTAATAAAACTATTAAGTGTAATCATATAAA
*
4920123 TAGAGTCTATTAGAAGTTACAGTAATGT
190 TAGAGTCTATTAGAAGTTACAGTAATAT
* * *
4920151 TTATGTATAAATTAAATATATATACATACATAATATATTAC-TTA-TGTATATATGAAATTAATG
1 TTATGTATAAATTAAATATATATATATA-ATAATATATTACTTTATTATATATATGAAATTAACG
* *
4920214 ACACAACTTATATGTTAT-A-A-T-GTTTTATATCAAAGTTTGAATAAATAATAACTAGTTATAA
65 ACACAACTTATATATTATAATATTAGTTTTATATCAAAGTTTGAATAAATAATAACTAATTATAA
* * *
4920275 ACAATATATTATAAAAATTAAGATGATAATTAATAAAGCTATTAAGTGTAATCATATAAATCA-A
130 ACAATATATTACAAAAATTAAGATGATAACTAATAAAACTATTAAGTGTAATCATATAAAT-AGA
* * *
4920339 GTTTATTATAAGTTATAGTAATAT
194 GTCTATTAGAAGTTACAGTAATAT
*
4920363 TTATGTATAAATTAAATATATGTATATATATAATAT
1 TTATGTATAAATTAAATATATATATATA-ATAATAT
4920399 TTATGCAATT
Statistics
Matches: 222, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
212 144 0.65
213 1 0.00
214 1 0.00
217 1 0.00
218 1 0.00
219 33 0.15
220 3 0.01
221 16 0.07
222 2 0.01
223 20 0.09
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (217 bp):
TTATGTATAAATTAAATATATATATATAATAATATATTACTTTATTATATATATGAAATTAACGA
CACAACTTATATATTATAATATTAGTTTTATATCAAAGTTTGAATAAATAATAACTAATTATAAA
CAATATATTACAAAAATTAAGATGATAACTAATAAAACTATTAAGTGTAATCATATAAATAGAGT
CTATTAGAAGTTACAGTAATAT
Found at i:4920668 original size:16 final size:16
Alignment explanation
Indices: 4920647--4920680 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4920637 CTAATATATT
4920647 TTAAGTATATTATTAA
1 TTAAGTATATTATTAA
*
4920663 TTAAGTTTATTATTAA
1 TTAAGTATATTATTAA
4920679 TT
1 TT
4920681 CTTCTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAAGTATATTATTAA
Found at i:4920718 original size:23 final size:23
Alignment explanation
Indices: 4920690--4920735 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
4920680 TCTTCTTAAT
4920690 ATATATAAAAAAATTATATACATTA
1 ATATAT-AAAAAA-TATATACATTA
*
4920715 ATATATATAAAATATATACAT
1 ATATATAAAAAATATATACAT
4920736 AAAAAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATATAAAAAATATATACATTA
Found at i:4923559 original size:34 final size:35
Alignment explanation
Indices: 4923483--4923559 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
4923473 ATAAAATTGA
* *
4923483 AATTTAAATAATCAAAAACAAATATCTCAAATATC
1 AATTTAAATAATCAAAAACAAATATCTCAAACAAC
* *
4923518 AACTTAAATAATTAAAAACAAATAT-TCAAACAAC
1 AATTTAAATAATCAAAAACAAATATCTCAAACAAC
4923552 AATTTAAA
1 AATTTAAA
4923560 CATTACAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (35 bp):
AATTTAAATAATCAAAAACAAATATCTCAAACAAC
Found at i:4925627 original size:2 final size:2
Alignment explanation
Indices: 4925620--4925646 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4925610 CACTAAGTTC
4925620 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4925647 AAGCCGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4925915 original size:2 final size:2
Alignment explanation
Indices: 4925903--4925943 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
4925893 GGCTAGGCAT
* *
4925903 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4925944 TGGGTTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4928235 original size:25 final size:25
Alignment explanation
Indices: 4928202--4928249 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4928192 AGAAAATAAG
4928202 AAAAGGAAAAAGGAAAAAAGGAAGA
1 AAAAGGAAAAAGGAAAAAAGGAAGA
* *
4928227 AAAATGAAAATGGAAAAAAGGAA
1 AAAAGGAAAAAGGAAAAAAGGAA
4928250 TGAGAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (25 bp):
AAAAGGAAAAAGGAAAAAAGGAAGA
Found at i:4928552 original size:15 final size:15
Alignment explanation
Indices: 4928524--4928572 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
4928514 TGGAAAATTG
*
4928524 AAAAGTAAAA-AAGA
1 AAAAGAAAAAGAAGA
*
4928538 AAAGGAAAAAGAAGA
1 AAAAGAAAAAGAAGA
4928553 AAAAGAAAAAGAAAGA
1 AAAAGAAAAAG-AAGA
4928569 AAAA
1 AAAA
4928573 AGAAGAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 8 0.27
15 14 0.47
16 8 0.27
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAGAAGA
Found at i:4928583 original size:17 final size:19
Alignment explanation
Indices: 4928530--4928597 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 19
4928520 ATTGAAAAGT
*
4928530 AAAAAAGAA-AAGGAAAAAG
1 AAAAAAGAAGAA-GAAAACG
*
4928549 AAGAAAAAGAAAAAG-AAA-G
1 -A-AAAAAGAAGAAGAAAACG
*
4928568 AAAAAAGAAGAGGAAAACG
1 AAAAAAGAAGAAGAAAACG
4928587 AAGAAAAGAAG
1 AA-AAAAGAAG
4928598 GATGTAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 4 0.10
20 12 0.29
21 9 0.22
22 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAGAAGAAAACG
Found at i:4929762 original size:24 final size:25
Alignment explanation
Indices: 4929720--4929776 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
4929710 AAAATATATT
*
4929720 ATAAAATTTTAAAATTTTTATAAAA
1 ATAAAATTATAAAATTTTTATAAAA
* *
4929745 ATGAAATTATAAAATTTTTTTAAAA
1 ATAAAATTATAAAATTTTTATAAAA
4929770 ATAAAAT
1 ATAAAAT
4929777 AATTTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATAAAATTATAAAATTTTTATAAAA
Found at i:4932597 original size:24 final size:24
Alignment explanation
Indices: 4932562--4932621 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
4932552 TTTACCTAAT
*
4932562 AACCTAGTTTGTACAAAAAGAAAC
1 AACCTAGCTTGTACAAAAAGAAAC
*
4932586 AACCTAGCTTGTACAAGAAGAAAC
1 AACCTAGCTTGTACAAAAAGAAAC
* *
4932610 AGCCTAACTTGT
1 AACCTAGCTTGT
4932622 TTCTTAGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
AACCTAGCTTGTACAAAAAGAAAC
Found at i:4933060 original size:15 final size:15
Alignment explanation
Indices: 4933040--4933088 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
4933030 CTTTATAATA
*
4933040 TAATATGATTACAGG
1 TAATATGATTACAAG
* * *
4933055 TAATATTAATATAAG
1 TAATATGATTACAAG
*
4933070 TAATATGATTATAAG
1 TAATATGATTACAAG
4933085 TAAT
1 TAAT
4933089 GTAATTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (15 bp):
TAATATGATTACAAG
Found at i:4933095 original size:15 final size:15
Alignment explanation
Indices: 4933064--4933110 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4933054 GTAATATTAA
* *
4933064 TATAAGTAATATGAT
1 TATAAGTAATGTAAT
4933079 TATAAGTAATGTAAT
1 TATAAGTAATGTAAT
* *
4933094 TATAAATAATGTTAT
1 TATAAGTAATGTAAT
4933109 TA
1 TA
4933111 CAGAGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (15 bp):
TATAAGTAATGTAAT
Found at i:4933098 original size:30 final size:30
Alignment explanation
Indices: 4933033--4933112 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
4933023 TTTGTTACTT
* *
4933033 TATAATATAATATGATTACAGGTAATATTAA
1 TATAA-ATAATATGATTACAAGTAATAGTAA
* *
4933064 TATAAGTAATATGATTATAAGTAAT-GTAA
1 TATAAATAATATGATTACAAGTAATAGTAA
* *
4933093 TTATAAATAATGTTATTACA
1 -TATAAATAATATGATTACA
4933113 GAGAAAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 3 0.08
30 32 0.80
31 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (30 bp):
TATAAATAATATGATTACAAGTAATAGTAA
Found at i:4933344 original size:6 final size:6
Alignment explanation
Indices: 4933333--4933380 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
4933323 ATGTCATATA
* * *
4933333 TTTTAT TTTTAT TTATTAT TATAAT TTATAT ATTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTT
4933381 TAATATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:4933372 original size:13 final size:13
Alignment explanation
Indices: 4933331--4933410 Score: 73
Period size: 13 Copynumber: 6.4 Consensus size: 13
4933321 TAATGTCATA
4933331 TATTT-TAT-TTT
1 TATTTATATATTT
4933342 TATTTAT-TATTAT
1 TATTTATATATT-T
*
4933355 AATTTATATATTT
1 TATTTATATATTT
4933368 TATTT-T-TATTT
1 TATTTATATATTT
*
4933379 T-TTAATATAATTT
1 TATTTATAT-ATTT
4933392 TATATTATATATTT
1 TAT-TTATATATTT
4933406 TATTT
1 TATTT
4933411 TAATTTATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.04
11 13 0.23
12 5 0.09
13 19 0.34
14 12 0.21
15 5 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:4933406 original size:25 final size:28
Alignment explanation
Indices: 4933328--4933422 Score: 63
Period size: 27 Copynumber: 3.4 Consensus size: 28
4933318 TTTTAATGTC
* *
4933328 ATATATTTTATTTTTATTTATTATTATAATTT
1 ATATATTTTA-TATTATATATT-TTAT-A-TT
* *
4933360 ATATATTTTAT-TT-T-TATTTTTTAAT
1 ATATATTTTATATTATATATTTTATATT
*
4933385 ATA-ATTTTATATTATATATTTTATTTT
1 ATATATTTTATATTATATATTTTATATT
*
4933412 AATTTATTTTA
1 -ATATATTTTA
4933423 CNNNNNNNNN
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
24 7 0.13
25 6 0.12
26 2 0.04
27 11 0.21
28 6 0.12
29 7 0.13
30 2 0.04
31 1 0.02
32 10 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
ATATATTTTATATTATATATTTTATATT
Found at i:4933411 original size:32 final size:32
Alignment explanation
Indices: 4933328--4933411 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
4933318 TTTTAATGTC
* *
4933328 ATATATTTTATTTTTATTTATTATTATAATTT
1 ATATATTTTATTTTTATTTTTTAATATAATTT
4933360 ATATATTTTATTTTTATTTTTTAATATAATTT
1 ATATATTTTATTTTTATTTTTTAATATAATTT
*
4933392 -TATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
4933412 AATTTATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 9 0.19
32 39 0.81
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTTTTAATATAATTT
Found at i:4938171 original size:17 final size:18
Alignment explanation
Indices: 4938135--4938178 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4938125 ATTTAGTTTT
* *
4938135 ATAAGTTTTTTTTTATAA
1 ATAAGTTATTTTGTATAA
4938153 ATAAGTTATTTTGTA-AA
1 ATAAGTTATTTTGTATAA
*
4938170 ATAATTTAT
1 ATAAGTTAT
4938179 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
ATAAGTTATTTTGTATAA
Found at i:4938476 original size:19 final size:20
Alignment explanation
Indices: 4938441--4938479 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4938431 ATAAATAAAG
4938441 GTATATTTTCTTTAAAAAAA
1 GTATATTTTCTTTAAAAAAA
*
4938461 GTATGTTTTC-TTAAAAAAA
1 GTATATTTTCTTTAAAAAAA
4938480 ATTTCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
GTATATTTTCTTTAAAAAAA
Found at i:4938480 original size:20 final size:20
Alignment explanation
Indices: 4938441--4938480 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4938431 ATAAATAAAG
*
4938441 GTATATTTTCTTTAAAAAAA
1 GTATATTTTCTTAAAAAAAA
*
4938461 GTATGTTTTCTTAAAAAAAA
1 GTATATTTTCTTAAAAAAAA
4938481 TTTCGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
GTATATTTTCTTAAAAAAAA
Found at i:4938545 original size:18 final size:17
Alignment explanation
Indices: 4938509--4938547 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
4938499 TCTGAAATTC
* *
4938509 TTTTTTTAAAAATTTTA
1 TTTTTTTAAAAAATCTA
4938526 TTTTTTATAAAAAATCTA
1 TTTTTT-TAAAAAATCTA
4938544 TTTT
1 TTTT
4938548 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTAAAAAATCTA
Found at i:4940139 original size:26 final size:26
Alignment explanation
Indices: 4940101--4940150 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4940091 CAAGTTGATC
*
4940101 AAAAAAAACCATGATATTCATAATGA
1 AAAAAAAAACATGATATTCATAATGA
4940127 AAAAAAAAACATGATATTCATAAT
1 AAAAAAAAACATGATATTCATAAT
4940151 TCATTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAAAAAAACATGATATTCATAATGA
Found at i:4947588 original size:3 final size:3
Alignment explanation
Indices: 4947576--4947608 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4947566 AACCCAGCAG
*
4947576 CAC CAT CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
4947609 TGGGAGCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.64, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:4957625 original size:15 final size:16
Alignment explanation
Indices: 4957605--4957639 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4957595 GAGGATGTAG
*
4957605 AGAAAC-AGTTGATGC
1 AGAAACTAGGTGATGC
4957620 AGAAACTAGGTGATGC
1 AGAAACTAGGTGATGC
4957636 AGAA
1 AGAA
4957640 GCCAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (16 bp):
AGAAACTAGGTGATGC
Found at i:4961940 original size:2 final size:2
Alignment explanation
Indices: 4961933--4961969 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4961923 CGAACTCGAT
4961933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4961970 TGTGAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4981340 original size:22 final size:22
Alignment explanation
Indices: 4981315--4981371 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
4981305 AGTTTTTAAA
*
4981315 CATTGCATAATTAATTTTTAGG
1 CATTGCATGATTAATTTTTAGG
** *
4981337 CATTGTGTGATTCATTTTTAGG
1 CATTGCATGATTAATTTTTAGG
*
4981359 TATTGCATGATTA
1 CATTGCATGATTA
4981372 GTTGATACGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (22 bp):
CATTGCATGATTAATTTTTAGG
Found at i:4981364 original size:44 final size:44
Alignment explanation
Indices: 4981261--4981371 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
4981251 TAGTTTTTAT
* *
4981261 AGTTTTTAAGTATTTCATAATTGATTTTTAAGAATTACGTGATC
1 AGTTTTTAAGTATTGCATAATTAATTTTTAAGAATTACGTGATC
** * * **
4981305 AGTTTTTAAACATTGCATAATTAATTTTTAGGCATTGTGTGATTC
1 AGTTTTTAAGTATTGCATAATTAATTTTTAAGAATTACGTGA-TC
* *
4981350 A-TTTTTAGGTATTGCATGATTA
1 AGTTTTTAAGTATTGCATAATTA
4981372 GTTGATACGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 51 0.94
45 3 0.06
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (44 bp):
AGTTTTTAAGTATTGCATAATTAATTTTTAAGAATTACGTGATC
Found at i:4982087 original size:20 final size:20
Alignment explanation
Indices: 4982059--4982098 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4982049 AAAATTTTAA
* *
4982059 AAAATAAAAAAATTTAAAAT
1 AAAACAAAAAAATATAAAAT
4982079 AAAACAAAAAAATATAAAAT
1 AAAACAAAAAAATATAAAAT
4982099 TTTTTGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAACAAAAAAATATAAAAT
Found at i:4988692 original size:29 final size:29
Alignment explanation
Indices: 4988650--4988737 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
4988640 TTCCTTGTTC
* *
4988650 TCTTATACTTGTTCACGTACAGCTTTTTT
1 TCTTGTACCTGTTCACGTACAGCTTTTTT
* ** *
4988679 TCTTGTACCTGTTCATGTACAGCTTACTC
1 TCTTGTACCTGTTCACGTACAGCTTTTTT
*
4988708 TCTTGTACCTGTTCACGTACAGTTTTTTT
1 TCTTGTACCTGTTCACGTACAGCTTTTTT
4988737 T
1 T
4988738 TATTAACTCC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.49
Consensus pattern (29 bp):
TCTTGTACCTGTTCACGTACAGCTTTTTT
Found at i:4996389 original size:67 final size:67
Alignment explanation
Indices: 4996296--4996428 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 67
4996286 CTGGGTCTTA
* * * *
4996296 TTTTTAAGTTCTGTCAGAGTCGCTGTTTAGAACTCAATCACTCAAACTAGTGATGTGATTCATTT
1 TTTTTAAGTTCTGTCAGAGCCACTGTTTAGAACTCAATCACTCAAACTAGTCATATGATTCATTT
4996361 TT
66 TT
* * *
4996363 TTTTTAAGTTCTGTCAGAGCCACTGTTTTGAACTCAATCACTCTAACTTGTCATATGATTCATTT
1 TTTTTAAGTTCTGTCAGAGCCACTGTTTAGAACTCAATCACTCAAACTAGTCATATGATTCATTT
4996428 T
66 T
4996429 ATTGATTGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (67 bp):
TTTTTAAGTTCTGTCAGAGCCACTGTTTAGAACTCAATCACTCAAACTAGTCATATGATTCATTT
TT
Found at i:5000039 original size:2 final size:2
Alignment explanation
Indices: 5000032--5000064 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5000022 NNNNNNNNNN
*
5000032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5000065 TTTCATCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5011511 original size:4 final size:4
Alignment explanation
Indices: 5011502--5011527 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5011492 AGATCAACAA
5011502 CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT
5011528 CTCTCAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:5012672 original size:28 final size:28
Alignment explanation
Indices: 5012606--5012734 Score: 147
Period size: 27 Copynumber: 4.7 Consensus size: 28
5012596 ATAAAAAAAA
* *
5012606 TTTTAACATGATATGTAATAATTATA-T
1 TTTTAACATAATATATAATAATTATATT
*
5012633 TTTTAATATAATATATAATAATTATATT
1 TTTTAACATAATATATAATAATTATATT
*
5012661 TTTTAATATAATATATAATAAATT-TATT
1 TTTTAACATAATATATAAT-AATTATATT
* * *
5012689 TTTTAACATGACATATATTAATTATA-T
1 TTTTAACATAATATATAATAATTATATT
* *
5012716 TTTTAACGTAATTTATAAT
1 TTTTAACATAATATATAAT
5012735 TAAAAAAGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
27 42 0.48
28 41 0.47
29 4 0.05
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (28 bp):
TTTTAACATAATATATAATAATTATATT
Found at i:5012736 original size:28 final size:29
Alignment explanation
Indices: 5012606--5012737 Score: 141
Period size: 28 Copynumber: 4.8 Consensus size: 29
5012596 ATAAAAAAAA
* *
5012606 TTTTAACATGATATGTAA-TAATTATA-T
1 TTTTAACATAATATATAATTAATTATATT
*
5012633 TTTTAATATAATATATAA-TAATTATATT
1 TTTTAACATAATATATAATTAATTATATT
* *
5012661 TTTTAATATAATATATAATAAATT-TATT
1 TTTTAACATAATATATAATTAATTATATT
* *
5012689 TTTTAACATGACATAT-ATTAATTATA-T
1 TTTTAACATAATATATAATTAATTATATT
* *
5012716 TTTTAACGTAATTTATAATTAA
1 TTTTAACATAATATATAATTAA
5012738 AAAAGTATCA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
27 42 0.47
28 43 0.48
29 4 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTAACATAATATATAATTAATTATATT
Found at i:5020618 original size:19 final size:21
Alignment explanation
Indices: 5020577--5020626 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
5020567 TCTTTTTTTT
5020577 TAAATTATAATATTAAAATTTA
1 TAAATTAT-ATATTAAAATTTA
*
5020599 TAAATTATATA-TATAA-TTA
1 TAAATTATATATTAAAATTTA
*
5020618 TAAAATATA
1 TAAATTATA
5020627 CAAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 4 0.15
21 3 0.12
22 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTATATATTAAAATTTA
Found at i:5020621 original size:28 final size:27
Alignment explanation
Indices: 5020582--5020636 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5020572 TTTTTTAAAT
* *
5020582 TATAATATTAAAATTTATAAATTATATA
1 TATAATATTAAAATATACAAA-TATATA
5020610 TATAAT-TATAAAATATACAAATATATA
1 TATAATAT-TAAAATATACAAATATATA
5020637 AACATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TATAATATTAAAATATACAAATATATA
Found at i:5022236 original size:23 final size:23
Alignment explanation
Indices: 5022210--5022257 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5022200 AGTGTAATCA
5022210 TATAAATAAAATCTAT-TATAAAT
1 TATAAA-AAAATCTATATATAAAT
* *
5022233 TATAAAAATATTTATATATAAAT
1 TATAAAAAAATCTATATATAAAT
5022256 TA
1 TA
5022258 AATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAAAAAAATCTATATATAAAT
Found at i:5023571 original size:2 final size:2
Alignment explanation
Indices: 5023555--5023595 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
5023545 TTTCTTTCAA
*
5023555 AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5023595 A
1 A
5023596 GAACGTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5024289 original size:2 final size:2
Alignment explanation
Indices: 5024282--5024306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5024272 CTGATTATTT
5024282 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 T
5024307 TCAAATTAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5028955 original size:3 final size:3
Alignment explanation
Indices: 5028947--5028988 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
5028937 CAAAGAACAT
*
5028947 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5028989 GAAAAACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5033103 original size:3 final size:3
Alignment explanation
Indices: 5033095--5033127 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5033085 ATAGCGATTC
*
5033095 GGA GGA GGA AGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
5033128 AGCGGATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:5033482 original size:12 final size:12
Alignment explanation
Indices: 5033467--5033502 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5033457 ACAGTAACAT
5033467 TAACAATAATAA
1 TAACAATAATAA
5033479 TAACAATAATAA
1 TAACAATAATAA
* *
5033491 TAGCAACAATAA
1 TAACAATAATAA
5033503 CCATAGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.64, C:0.11, G:0.03, T:0.22
Consensus pattern (12 bp):
TAACAATAATAA
Found at i:5038095 original size:19 final size:20
Alignment explanation
Indices: 5038053--5038095 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5038043 CATTAATCAA
*
5038053 TAAAT-TAAATACTTAAATG
1 TAAATATAAATAATTAAATG
5038072 T-AATATAAATAATTAAAT-
1 TAAATATAAATAATTAAATG
5038090 TAAATA
1 TAAATA
5038096 ATTGAGCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAATATAAATAATTAAATG
Found at i:5043359 original size:11 final size:11
Alignment explanation
Indices: 5043343--5043367 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5043333 CTTCAAACTT
5043343 AAAAAAATAAA
1 AAAAAAATAAA
5043354 AAAAAAATAAA
1 AAAAAAATAAA
5043365 AAA
1 AAA
5043368 TACAAACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:5045991 original size:49 final size:49
Alignment explanation
Indices: 5045932--5046030 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
5045922 TTGACTAATC
5045932 ATGTCTGATGTTTGATGTGATTGGTTGCTTACTTCAAATTGAGGAACTA
1 ATGTCTGATGTTTGATGTGATTGGTTGCTTACTTCAAATTGAGGAACTA
*
5045981 ATGTTTGATGTTTGATGTGATTGGTTGCTTACTTCAAATTGAGGAACTA
1 ATGTCTGATGTTTGATGTGATTGGTTGCTTACTTCAAATTGAGGAACTA
5046030 A
1 A
5046031 AATATAGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.41
Consensus pattern (49 bp):
ATGTCTGATGTTTGATGTGATTGGTTGCTTACTTCAAATTGAGGAACTA
Found at i:5053109 original size:3 final size:3
Alignment explanation
Indices: 5053052--5053093 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5053042 CCTCGCACCA
5053052 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
5053094 TTCCGCGCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:5056691 original size:19 final size:19
Alignment explanation
Indices: 5056667--5056724 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
5056657 TCTTTGGAAC
*
5056667 AATTATGTTTATTCAAAAA
1 AATTATATTTATTCAAAAA
* *
5056686 AATTATATTTTATT-TAAAT
1 AATTATA-TTTATTCAAAAA
5056705 AATTATATTTATTTCAAAAA
1 AATTATATTTA-TTCAAAAA
5056725 GTTTGTGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.13
19 18 0.58
20 9 0.29
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTATATTTATTCAAAAA
Found at i:5072671 original size:29 final size:28
Alignment explanation
Indices: 5072626--5072689 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
5072616 AATTATTAAT
* *
5072626 TATAAAAATTTATTTAATTTAAAATAAAA
1 TATAAAAATTTAATTAA-ATAAAATAAAA
*
5072655 TATAAAAATTTAATTAAATATAATAAAA
1 TATAAAAATTTAATTAAATAAAATAAAA
5072683 -ATAAAAA
1 TATAAAAA
5072690 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 7 0.22
28 9 0.28
29 16 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TATAAAAATTTAATTAAATAAAATAAAA
Found at i:5074059 original size:4 final size:5
Alignment explanation
Indices: 5074024--5074065 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
5074014 TCGTAGCTCA
* *
5074024 AAAAA AAAAA AAAAG AAAAG AAAAG AAAAG -AAAG -AAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
5074066 CCAAAATCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5076793 original size:116 final size:117
Alignment explanation
Indices: 5076610--5076844 Score: 312
Period size: 116 Copynumber: 2.0 Consensus size: 117
5076600 TAGTATTTAC
*
5076610 TTCTCCACTTGCAATTGGCACGTTTACAAGCGCAAAGTTGATTATGGTTGCACATTGTTGCCACC
1 TTCTCCACTTGCAATTGGCACGTTTACAAGCGCAAAGTTGATTATGGTTACACATTGTTGCCACC
* * *
5076675 TTAGTGTGCTTCTAAGTTTTGCCCTTAAATTGAACTCACCAAATCATGT-TT
66 TTAGTGTACTTCTAAGCTTTGCCCTTAAATCGAACTCACCAAATCATGTATT
* ** * * **
5076726 TTCTCCACTTGCAATTGGCATGTTTACAA-CTGTGAAGTTGATTGTGGTTACACCTTGTTGCTGC
1 TTCTCCACTTGCAATTGGCACGTTTACAAGC-GCAAAGTTGATTATGGTTACACATTGTTGCCAC
* * * *
5076790 CTTAGTTTACTTTTAAGCTTTGCCCTTAAATCGTACTCACCTAATCATGTATT
65 CTTAGTGTACTTCTAAGCTTTGCCCTTAAATCGAACTCACCAAATCATGTATT
5076843 TT
1 TT
5076845 TCTTTCCTGA
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
115 1 0.01
116 97 0.95
117 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.39
Consensus pattern (117 bp):
TTCTCCACTTGCAATTGGCACGTTTACAAGCGCAAAGTTGATTATGGTTACACATTGTTGCCACC
TTAGTGTACTTCTAAGCTTTGCCCTTAAATCGAACTCACCAAATCATGTATT
Found at i:5095122 original size:144 final size:144
Alignment explanation
Indices: 5094857--5095141 Score: 437
Period size: 144 Copynumber: 2.0 Consensus size: 144
5094847 AGCTGAACCC
* *
5094857 CAGCAGCTTGCAAATCAACCTAAGCAGTCAGGTTTATCAGTTACTCCCAGAGAAAAAAGGACTCA
1 CAGCAGCTTGCAAATAAACCTAAGCAATCAGGTTTATCAGTTACTCCCAGAGAAAAAAGGACTCA
*
5094922 ACTCACCGAACAGTTAGCCTTTTCTCCTAATTTCAAGGCTAAAAGTTTTCAATCAGAGTATAAAA
66 ACTCACCGAACAGTCAGCCTTTTCTCCTAATTTCAAGGCTAAAAGTTTTCAATCAGAGTATAAAA
5094987 ATGTTCATGTACCT
131 ATGTTCATGTACCT
* * * * * * *
5095001 CAGCGGCTTGCAAATAAACCTAAGCAATCTGGTTTTTCAGTTGCTGCTAGAGAAAAAAGGATTCA
1 CAGCAGCTTGCAAATAAACCTAAGCAATCAGGTTTATCAGTTACTCCCAGAGAAAAAAGGACTCA
** *
5095066 ACTC-CCTGAACAGTCAGGTTTTTCTCCTAATTTCAAGGCTAGAAGTTTTCAATCAGAGTATAAA
66 ACTCACC-GAACAGTCAGCCTTTTCTCCTAATTTCAAGGCTAAAAGTTTTCAATCAGAGTATAAA
5095130 AATGTTCATGTA
130 AATGTTCATGTA
5095142 TGGGAAGGTT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
143 2 0.02
144 125 0.98
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (144 bp):
CAGCAGCTTGCAAATAAACCTAAGCAATCAGGTTTATCAGTTACTCCCAGAGAAAAAAGGACTCA
ACTCACCGAACAGTCAGCCTTTTCTCCTAATTTCAAGGCTAAAAGTTTTCAATCAGAGTATAAAA
ATGTTCATGTACCT
Found at i:5112154 original size:6 final size:6
Alignment explanation
Indices: 5112143--5112291 Score: 72
Period size: 6 Copynumber: 24.8 Consensus size: 6
5112133 TGTTTCTTGT
* * ** *
5112143 TGCTGC TGCTGC TG-TAGC TGTTGC TGCTGC TGTTGC TG-TAAT TGCTGA
1 TGCTGC TGCTGC TGCT-GC TGCTGC TGCTGC TGCTGC TGCT-GC TGCTGC
* * * * *
5112191 TGCTGC AGCTGC TG-TAAG- TGTTGC TGTTGT TGCTGG TGCTGC TGCTGC
1 TGCTGC TGCTGC TGCT--GC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
*** ** ** *
5112239 TGCTGC AATTGC TGCTGC TGCTGC TGCAAC TGCAAC TGTTGC TGCTGC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
5112287 TGCTG
1 TGCTG
5112292 GTTCATGTAA
Statistics
Matches: 110, Mismatches: 25, Indels: 16
0.73 0.17 0.11
Matches are distributed among these distances:
5 4 0.04
6 102 0.93
7 4 0.04
ACGTcount: A:0.09, C:0.23, G:0.32, T:0.36
Consensus pattern (6 bp):
TGCTGC
Found at i:5112166 original size:21 final size:21
Alignment explanation
Indices: 5112140--5112291 Score: 92
Period size: 21 Copynumber: 6.8 Consensus size: 21
5112130 GGTTGTTTCT
5112140 TGTTGCTGCTGCTGCTGTAGC
1 TGTTGCTGCTGCTGCTGTAGC
5112161 TGTTGCTGCTGCTGTTGCTGTAATTGC
1 TGTTGCTGCTGC---TGCTGT-A--GC
* *
5112188 TGATGCTGCAGCTGCTGTAAG-
1 TGTTGCTGCTGCTGCTGT-AGC
* *
5112209 TGTTGCTGTTGTTGCTGGT-GC
1 TGTTGCTGCTGCTGCT-GTAGC
* ** *
5112230 TGCTGCTGCTGCTGCAATTGC
1 TGTTGCTGCTGCTGCTGTAGC
* * *
5112251 TGCTGCTGCTGCTGCAACTGCAAC
1 TGTTGCTGCTGCTG---CTGTAGC
5112275 TGTTGCTGCTGCTGCTG
1 TGTTGCTGCTGCTGCTG
5112292 GTTCATGTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.02
21 55 0.54
22 3 0.03
24 29 0.28
25 1 0.01
27 12 0.12
ACGTcount: A:0.09, C:0.23, G:0.32, T:0.37
Consensus pattern (21 bp):
TGTTGCTGCTGCTGCTGTAGC
Found at i:5112233 original size:9 final size:9
Alignment explanation
Indices: 5112221--5112291 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 9
5112211 TTGCTGTTGT
*
5112221 TGCTGGTGC
1 TGCTGCTGC
5112230 TGCTGCTGC
1 TGCTGCTGC
***
5112239 TGCTGCAAT
1 TGCTGCTGC
5112248 TGCTGCTGC
1 TGCTGCTGC
5112257 TGCTGCTGC
1 TGCTGCTGC
** **
5112266 AACTGCAAC
1 TGCTGCTGC
*
5112275 TGTTGCTGC
1 TGCTGCTGC
5112284 TGCTGCTG
1 TGCTGCTG
5112292 GTTCATGTAA
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.08, C:0.28, G:0.31, T:0.32
Consensus pattern (9 bp):
TGCTGCTGC
Found at i:5112271 original size:27 final size:27
Alignment explanation
Indices: 5112220--5112291 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
5112210 GTTGCTGTTG
* **
5112220 TTGCTGGTGCTGCTGCTGCTGCTGCAA
1 TTGCTGCTGCTGCTGCTGCAACTGCAA
5112247 TTGCTGCTGCTGCTGCTGCAACTGCAA
1 TTGCTGCTGCTGCTGCTGCAACTGCAA
* *
5112274 CTGTTGCTGCTGCTGCTG
1 TTGCTGCTGCTGCTGCTG
5112292 GTTCATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.08, C:0.28, G:0.31, T:0.33
Consensus pattern (27 bp):
TTGCTGCTGCTGCTGCTGCAACTGCAA
Found at i:5112796 original size:3 final size:3
Alignment explanation
Indices: 5112790--5112849 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
5112780 TCAATTTCCT
* * * * * * *
5112790 CTG CTG CTG CGG CTG CTG CTG TTG TTG CTG CTG TTG TTG CTG TTG TTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
5112838 CTG CTG CTG CTG
1 CTG CTG CTG CTG
5112850 TAACATCTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (3 bp):
CTG
Found at i:5112818 original size:12 final size:12
Alignment explanation
Indices: 5112803--5112846 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
5112793 CTGCTGCGGC
5112803 TGCTGCTGTTGT
1 TGCTGCTGTTGT
5112815 TGCTGCTGTTGT
1 TGCTGCTGTTGT
* *
5112827 TGCTGTTGTTGC
1 TGCTGCTGTTGT
5112839 TGCTGCTG
1 TGCTGCTG
5112847 CTGTAACATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.34, T:0.48
Consensus pattern (12 bp):
TGCTGCTGTTGT
Found at i:5120298 original size:2 final size:2
Alignment explanation
Indices: 5120291--5120341 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5120281 CTATTACAGA
5120291 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
5120333 AT AT AT AT A
1 AT AT AT AT A
5120342 GATCCCAACC
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:5132202 original size:25 final size:25
Alignment explanation
Indices: 5132168--5132218 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5132158 CGTCACTCTT
5132168 CGTACCACTAATGACTCCCCTTGTG
1 CGTACCACTAATGACTCCCCTTGTG
*
5132193 CGTACCACTAATGACTCTCCTTGTG
1 CGTACCACTAATGACTCCCCTTGTG
5132218 C
1 C
5132219 AGGATACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (25 bp):
CGTACCACTAATGACTCCCCTTGTG
Found at i:5138440 original size:27 final size:26
Alignment explanation
Indices: 5138406--5138471 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
5138396 ATAAAAACTT
*
5138406 ATTTAATTCAA-AATAAAAAATATAATA
1 ATTTAATTAAAGAATAAAAAATA-AA-A
5138433 ATTTAATTAAAGGTAATAAAAAATAAAA
1 ATTTAATTAAA-G-AATAAAAAATAAAA
*
5138461 ATTTATTTAAA
1 ATTTAATTAAA
5138472 TCTTATTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 10 0.29
28 11 0.32
29 2 0.06
30 11 0.32
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (26 bp):
ATTTAATTAAAGAATAAAAAATAAAA
Found at i:5143773 original size:14 final size:14
Alignment explanation
Indices: 5143754--5143783 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5143744 GCTCTTGAAT
5143754 GTGAGCCATGGAAG
1 GTGAGCCATGGAAG
*
5143768 GTGAGCCGTGGAAG
1 GTGAGCCATGGAAG
5143782 GT
1 GT
5143784 TCACTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.47, T:0.17
Consensus pattern (14 bp):
GTGAGCCATGGAAG
Found at i:5144355 original size:8 final size:8
Alignment explanation
Indices: 5144342--5144366 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5144332 ATGGGCAATA
5144342 GTATCACT
1 GTATCACT
5144350 GTATCACT
1 GTATCACT
5144358 GTATCACT
1 GTATCACT
5144366 G
1 G
5144367 ATAGGGGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (8 bp):
GTATCACT
Found at i:5158548 original size:36 final size:36
Alignment explanation
Indices: 5158508--5158580 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
5158498 ATCACGCCCG
*
5158508 TCAACATTCTCATGCTCCTGCACCAACCAGCATCCA
1 TCAACATTCTCATACTCCTGCACCAACCAGCATCCA
* * * *
5158544 TCAACATTCTTATACTCCTGTAGCAATCAGCATCCA
1 TCAACATTCTCATACTCCTGCACCAACCAGCATCCA
5158580 T
1 T
5158581 ATCTGAGGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.36, G:0.08, T:0.27
Consensus pattern (36 bp):
TCAACATTCTCATACTCCTGCACCAACCAGCATCCA
Found at i:5164054 original size:20 final size:21
Alignment explanation
Indices: 5164016--5164054 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5164006 ATTCAAAGAG
* *
5164016 TTAAATTTAAATTATTATTTT
1 TTAAATTTAAAATAATATTTT
5164037 TTAAA-TTAAAATAATATT
1 TTAAATTTAAAATAATATT
5164055 ATATGTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAATTTAAAATAATATTTT
Found at i:5164068 original size:24 final size:21
Alignment explanation
Indices: 5164016--5164071 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 21
5164006 ATTCAAAGAG
* *
5164016 TTAAATTTAAATTATTATTTT
1 TTAAATTAAAATTATTATTGT
5164037 TTAAATTAAAATAATATTATATGT
1 TTAAATTAAAAT--TATTAT-TGT
5164061 TTAAATTAAAA
1 TTAAATTAAAA
5164072 AAATTAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 11 0.37
23 6 0.20
24 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAATTAAAATTATTATTGT
Found at i:5170205 original size:31 final size:30
Alignment explanation
Indices: 5170161--5170223 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5170151 AATTATAAAT
* * *
5170161 TATAAAGACTTATTTTGACTTAAAATAGAAA
1 TATAAAAACTTA-TTTGACTCAAAATAAAAA
*
5170192 TATAAAAATTTATTTGACTCAAAATAAAAA
1 TATAAAAACTTATTTGACTCAAAATAAAAA
5170222 TA
1 TA
5170224 CAAACGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (30 bp):
TATAAAAACTTATTTGACTCAAAATAAAAA
Found at i:5171079 original size:3 final size:3
Alignment explanation
Indices: 5171071--5171100 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5171061 ATCTTAAATG
5171071 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5171101 TGCCATAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5175807 original size:131 final size:131
Alignment explanation
Indices: 5175415--5175800 Score: 673
Period size: 131 Copynumber: 2.9 Consensus size: 131
5175405 TAGCCTTTAA
* * * * *
5175415 TTGAATCATTCTTTTAGACTTAGTCTTTCAGAACATTTTATAATGTTATAGAAGTGGGCTAGGCT
1 TTGAATCATTCTTTCAAACTTAGTCTTTCAGAATATTTTATAATGTTATAGAAGTAGGCTAGGCC
*
5175480 CAAGTGATATTTTGTACCTTAGTGGTTTATTTTTTATCTTACTTGACTCGATCTTTTTACTATGG
66 CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTCGATCTTTTTACTATGG
5175545 T
131 T
* * *
5175546 TTGAATCATTCTTTCAAACTTAGTCTTTTAAAATATTTTATAATGTTATAGAAGTAGGCTAAGCC
1 TTGAATCATTCTTTCAAACTTAGTCTTTCAGAATATTTTATAATGTTATAGAAGTAGGCTAGGCC
*
5175611 CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTTGATCTTTTTACTATGG
66 CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTCGATCTTTTTACTATGG
5175676 T
131 T
5175677 TTGAATCATTCTTTCAAACTTAGTCTTTCAGAATATTTTATAATGTTATAGAAGTAGGCTAGGCC
1 TTGAATCATTCTTTCAAACTTAGTCTTTCAGAATATTTTATAATGTTATAGAAGTAGGCTAGGCC
*
5175742 CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTCGATTTTTTTA
66 CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTCGATCTTTTTA
5175801 TAATGGTAAA
Statistics
Matches: 240, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 240 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (131 bp):
TTGAATCATTCTTTCAAACTTAGTCTTTCAGAATATTTTATAATGTTATAGAAGTAGGCTAGGCC
CAAGTGATATTTTGTACCTTGGTGGTTTATTTTTTATCTTACTTGACTCGATCTTTTTACTATGG
T
Found at i:5196577 original size:2 final size:2
Alignment explanation
Indices: 5196570--5196594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5196560 GAGTATCCAG
5196570 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 T
5196595 TACAAAGCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5198861 original size:14 final size:14
Alignment explanation
Indices: 5198842--5198886 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
5198832 GATCTACATA
5198842 AAAACAAGAAGAAG
1 AAAACAAGAAGAAG
5198856 AAAACAAGAAGAAG
1 AAAACAAGAAGAAG
*
5198870 AAAACAAGAACAAG
1 AAAACAAGAAGAAG
5198884 AAA
1 AAA
5198887 CGAGATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAACAAGAAGAAG
Found at i:5205060 original size:39 final size:38
Alignment explanation
Indices: 5205017--5205090 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
5205007 TTTTTATAAA
* *
5205017 AATCATTCAATGCAATTAAAATTTTTATTTACAAATAGT
1 AATCATTCAATGCAATT-AAATTCTAATTTACAAATAGT
* *
5205056 AATCATTTAATGCAATTAGATTCTAATTTACAAAT
1 AATCATTCAATGCAATTAAATTCTAATTTACAAAT
5205091 TGGGTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.48
39 16 0.52
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (38 bp):
AATCATTCAATGCAATTAAATTCTAATTTACAAATAGT
Found at i:5206128 original size:18 final size:18
Alignment explanation
Indices: 5206105--5206139 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5206095 TTATTTATTT
5206105 AATTTTTTAT-TATTTTAA
1 AATTTTTT-TGTATTTTAA
5206123 AATTTTTTTGTATTTTA
1 AATTTTTTTGTATTTTA
5206140 CATACGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
AATTTTTTTGTATTTTAA
Found at i:5211980 original size:15 final size:15
Alignment explanation
Indices: 5211957--5211998 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5211947 AATTTATAAT
*
5211957 GTAATGTGATTACAG
1 GTAATGTGATTACAA
* *
5211972 GTAACGTGATTGCAA
1 GTAATGTGATTACAA
5211987 GTAATGTGATTA
1 GTAATGTGATTA
5211999 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (15 bp):
GTAATGTGATTACAA
Found at i:5212204 original size:33 final size:34
Alignment explanation
Indices: 5212167--5212240 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
5212157 TTTTAATGTC
* *
5212167 ATATATTTTATTTTTATTTC-TTATTATAATCTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
*
5212200 ATATATTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
*
5212234 TTATATT
1 ATATATT
5212241 AATCATTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (34 bp):
ATATATTTTATTTTCATTTCTTTAATATAATCTT
Found at i:5214123 original size:18 final size:18
Alignment explanation
Indices: 5214096--5214142 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5214086 CCTTTGAATT
*
5214096 ATTATTTTTATTCAAATA
1 ATTATATTTATTCAAATA
5214114 ATTATATTTATTCAAATA
1 ATTATATTTATTCAAATA
*
5214132 ATTGTATTTAT
1 ATTATATTTAT
5214143 ACAACAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTATATTTATTCAAATA
Found at i:5218396 original size:14 final size:15
Alignment explanation
Indices: 5218372--5218419 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 15
5218362 NNNNNNNCAT
5218372 TAAAAATATATT-TA
1 TAAAAATATATTATA
5218386 -AAAAATGATATTATA
1 TAAAAAT-ATATTATA
*
5218401 TAAAAAT-TAATA-A
1 TAAAAATATATTATA
5218414 TAAAAA
1 TAAAAA
5218420 ATACAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.43
14 9 0.30
15 2 0.07
16 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAAATATATTATA
Found at i:5218460 original size:19 final size:19
Alignment explanation
Indices: 5218424--5218495 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
5218414 TAAAAAATAC
5218424 AAATATACTTATATTTTAA
1 AAATATACTTATATTTTAA
*
5218443 TAAATATAGTTA-ATTTTAA
1 -AAATATACTTATATTTTAA
5218462 AAATTGATA-TTATATTTTTAA
1 AAA-T-ATACTTATA-TTTTAA
5218483 AAA-AGTACTTATA
1 AAATA-TACTTATA
5218496 AATCAAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
18 4 0.09
19 13 0.29
20 19 0.42
21 9 0.20
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (19 bp):
AAATATACTTATATTTTAA
Found at i:5219886 original size:4 final size:4
Alignment explanation
Indices: 5219879--5219903 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5219869 CAATCATGAG
5219879 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5219904 AGAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5223018 original size:13 final size:14
Alignment explanation
Indices: 5222995--5223040 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
5222985 CAAATAACTT
5222995 ATTTAATAAAAAT-A
1 ATTT-ATAAAAATAA
*
5223009 ATTTATAAAAGTAA
1 ATTTATAAAAATAA
*
5223023 ATTTAT-CAAATAA
1 ATTTATAAAAATAA
5223036 ATTTA
1 ATTTA
5223041 AATTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (14 bp):
ATTTATAAAAATAA
Found at i:5223025 original size:14 final size:13
Alignment explanation
Indices: 5223003--5223040 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
5222993 TTATTTAATA
5223003 AAAAT-AATTTAT
1 AAAATAAATTTAT
5223015 AAAAGTAAATTTAT
1 AAAA-TAAATTTAT
*
5223029 CAAATAAATTTA
1 AAAATAAATTTA
5223041 AATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 10 0.43
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (13 bp):
AAAATAAATTTAT
Found at i:5232865 original size:31 final size:30
Alignment explanation
Indices: 5232827--5232896 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
5232817 GGTTTTTTCA
5232827 AATTGAATAGAATCAG-TTTTAGAGTTTGTTG
1 AATTGAATA-AAT-AGATTTTAGAGTTTGTTG
* *
5232858 AATTGAATTAAATTGATTTTAGGGTTTGTTG
1 AATTGAA-TAAATAGATTTTAGAGTTTGTTG
5232889 AATTGAAT
1 AATTGAAT
5232897 TGATTTCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 31 0.89
32 2 0.06
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.44
Consensus pattern (30 bp):
AATTGAATAAATAGATTTTAGAGTTTGTTG
Found at i:5232889 original size:26 final size:26
Alignment explanation
Indices: 5232860--5232917 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5232850 GTTTGTTGAA
* * *
5232860 TTGAATTAAATTGATTTTAGGGTTTG
1 TTGAATTAAATTGATTTCAAGATTTG
*
5232886 TTGAATTGAATTGATTTCAAGATTTG
1 TTGAATTAAATTGATTTCAAGATTTG
5232912 TTGAAT
1 TTGAAT
5232918 CGGTTTTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (26 bp):
TTGAATTAAATTGATTTCAAGATTTG
Found at i:5233063 original size:21 final size:23
Alignment explanation
Indices: 5233039--5233087 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 23
5233029 AAAAAAAAAA
5233039 AATTTTAAAATATTT-TTAAA-T
1 AATTTTAAAATATTTGTTAAAGT
*
5233060 AA-TTTAAAATTTTTGTTAAAGT
1 AATTTTAAAATATTTGTTAAAGT
5233082 -ATTTTA
1 AATTTTA
5233088 CCTTGATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 11 0.46
21 8 0.33
22 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
AATTTTAAAATATTTGTTAAAGT
Found at i:5234787 original size:2 final size:2
Alignment explanation
Indices: 5234780--5234807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5234770 GTTGAAAAGT
5234780 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
5234808 GATTAGTTAC
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):
TA
Found at i:5236344 original size:42 final size:42
Alignment explanation
Indices: 5236285--5236364 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
5236275 GCTGACAGTG
*
5236285 TATAACTTCCATACACTGTCAGTGCATTAAATATAAATTTTA
1 TATAACTTCCATACACTGTCAGTACATTAAATATAAATTTTA
* *
5236327 TATAATTTTCATACACTGTCAGTACATTAAATATAAAT
1 TATAACTTCCATACACTGTCAGTACATTAAATATAAAT
5236365 CGTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (42 bp):
TATAACTTCCATACACTGTCAGTACATTAAATATAAATTTTA
Found at i:5238036 original size:17 final size:17
Alignment explanation
Indices: 5237973--5238041 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
5237963 TATAAAAAAA
5237973 ATTAAATAAACTT-T-T
1 ATTAAATAAACTTATAT
* *
5237988 ATTATAT-TA-TTATAT
1 ATTAAATAAACTTATAT
* *
5238003 -TTAAATAAATTTTTAT
1 ATTAAATAAACTTATAT
5238019 ATTAAATAAACTTATAT
1 ATTAAATAAACTTATAT
5238036 AATTAA
1 -ATTAA
5238042 TAATTGATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.05
14 7 0.17
15 8 0.20
16 5 0.12
17 14 0.34
18 5 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAATAAACTTATAT
Found at i:5247003 original size:13 final size:14
Alignment explanation
Indices: 5246963--5247007 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
5246953 AATATAATTG
*
5246963 AAAAACATAAATAA
1 AAAAATATAAATAA
*
5246977 TAATAATATAAATAA
1 -AAAAATATAAATAA
5246992 AAAAAT-TAAATAA
1 AAAAATATAAATAA
5247005 AAA
1 AAA
5247008 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 10 0.37
14 5 0.19
15 12 0.44
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATATAAATAA
Found at i:5261123 original size:24 final size:25
Alignment explanation
Indices: 5261076--5261123 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5261066 TATGTTAAAA
* *
5261076 TTTAAAATTTTTTATAATATAAATG
1 TTTAAAATTTTTAATAAGATAAATG
*
5261101 TTTAATATTTTTAATAAGA-AAAT
1 TTTAAAATTTTTAATAAGATAAAT
5261124 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTAAAATTTTTAATAAGATAAATG
Found at i:5263148 original size:2 final size:2
Alignment explanation
Indices: 5263141--5263168 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5263131 CTCCCTCCCC
5263141 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
5263169 ATGTGCGTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5270011 original size:441 final size:438
Alignment explanation
Indices: 5269206--5270360 Score: 1293
Period size: 441 Copynumber: 2.6 Consensus size: 438
5269196 TATTTTTTAG
* * *
5269206 AATTTAACAAACCC-TTCTTCATAGTTTGCATAAACTACTAAGGGATAACAAGAATAACAGAAA-
1 AATTCAACAAACCCTTTCTT-ATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAGAAAG
* * *
5269269 ACATTTTTAAAGAAAAAGAAGAACCTAACAGGGAAGGAAAGAAAACAAAGAAAATATGCAGAAAA
65 A-TTTTTTAAAGAAAAAGAAGAACCCAGCA-GGAAGGAAAG-AAACAAAG-AAATATGCAGAAAA
* * * ** * *
5269334 CAGAGAGAGTAGATGAGAGGCTTAGTGTGTGTTACGAATGAGGTAGGGAGACTGTATTTATAGGC
126 TAGAGAGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGT
* * * * * *
5269399 AAGAAATGAAGTAAACATTGCACCAAATCAGGAGAATGAGTTAAACATTGCACCAAATCAGGGGC
191 AAGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGT-GACGTTGCACCAAATCAGGGG-
* * * *
5269464 TTGAGAAAAACCTGGTCAACATGTATATTCAGTCACGTAAACATTGTAGCAAATTAAGATAAACT
254 TTGAGAAAAA-CTGGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACT
* * * * *
5269529 CAGTCAGCATGGTAGAGTTTGAGTTTGATTCAATCAATGGTATCATTGT-TTTAAGGATAATTTT
318 CAGTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCCTTAAGGATAATTTT
** * * * *
5269593 T-ATCTCTTTATAATAC-AAACTAGGTGC-AAAAGGACTATAGCGGTTATCCTTCAA
383 TGCCCT-TTTAGAATACAAAACTAGATGCAAAAAGAACTATAGCGATTATCCTTCAA
* * * * * *
5269647 GATTCAATAAACCCTTTCTTATAGTTTGTATAAATTATTAAAGGATAACAAAAACAACAGAAAGA
1 AATTCAACAAACCCTTTCTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAGAAAGA
* * * * *
5269712 TTTTTTAGAGAAAAAGAAGAACCCAGTGAGGAAGGAAAGAAAGTAGAGAACATATGCAAAAAATA
66 TTTTTTAAAGAAAAAGAAGAACCCAG-CAGGAAGGAAAGAAA-CAAAGAA-ATATGCAGAAAATA
* * * *
5269777 AAGAGGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGGGGTAAGGAGACTGTATTTATAAGTA
128 GAGA-GAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGTA
* * *
5269842 AGGAATAAAGTGAACATTGTACCAAATTTGGAGAATGAGGTGACGTTGCACCAAATCATGGGGTT
192 AGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGTGACGTTGCACCAAATCA-GGGGTT
** * * * * * *
5269907 GAGAAAAACTAGGTTTACATGTATACTCAGTTAGGTAGACGTTGCAGCAAATCAAGAAAAATTTA
256 GAGAAAAACT-GGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACTCA
5269972 GTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCCTTAAGGATAATTTTTG
320 GTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCCTTAAGGATAATTTTTG
* * *
5270037 CCCTTTTAGAATACAAAACTTGATGCAAAAAGAACTGTAGTGATTATCCTTCAA
385 CCCTTTTAGAATACAAAACTAGATGCAAAAAGAACTATAGCGATTATCCTTCAA
* * * * * * *
5270091 AATTTAACAAA-CTTTTCTTTATAGTTGGCACAAGCTACTAAGGGATAACAAAAACAGCAAAAAG
1 AATTCAACAAACCCTTTC-TTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAGAAAG
* * *
5270155 TTTTTTTAAAGAAAAAGAAGAACCCAGCAGAGAAAGAAAGAATACAAAGCAAATATGTAGAAAAT
65 ATTTTTTAAAGAAAAAGAAGAACCCAGCAG-GAAGGAAAGAA-ACAAAG-AAATATGCAGAAAAT
* ** * **
5270220 AGAGAAGAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGGGAGGCAATATTTATAGGT
127 AGAG-AGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGT
* * *
5270285 AAAGAATGAAGTGAACGTTGCACCCAATTAGGAGAAT-ATGGTGAACGTTGCACCAAATCAGGAG
191 AAGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGA-GGTG-ACGTTGCACCAAATCAGG-G
5270349 GTT-AGGAAAAAC
253 GTTGA-GAAAAAC
5270361 CTAAGGAAAG
Statistics
Matches: 593, Mismatches: 100, Indels: 38
0.81 0.14 0.05
Matches are distributed among these distances:
440 7 0.01
441 208 0.35
442 120 0.20
443 19 0.03
444 208 0.35
445 31 0.05
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (438 bp):
AATTCAACAAACCCTTTCTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAGAAAGA
TTTTTTAAAGAAAAAGAAGAACCCAGCAGGAAGGAAAGAAACAAAGAAATATGCAGAAAATAGAG
AGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGTAAGGA
ATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGTGACGTTGCACCAAATCAGGGGTTGAGAA
AAACTGGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACTCAGTCAGC
ATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCCTTAAGGATAATTTTTGCCCTTT
TAGAATACAAAACTAGATGCAAAAAGAACTATAGCGATTATCCTTCAA
Found at i:5270246 original size:444 final size:437
Alignment explanation
Indices: 5269206--5270360 Score: 1298
Period size: 444 Copynumber: 2.6 Consensus size: 437
5269196 TATTTTTTAG
* * * * *
5269206 AATTTAACAAACCCTTCTTCATAGTTTGCATAAACTACTAAGGGATAACAAGAATAACAGAAAAC
1 AATTTAACAAACCTTTCTTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACA-AAAAG
* * * *
5269271 A-TTTTTAAAGAAAAAGAAGAACCTAACAGGGAAGGAAAGAAAACAAAGAAAATATGCAGAAAAC
65 ATTTTTTAAAGAAAAAGAAGAACCCAGCAGAGAAGGAAAG-AAACAAAG-AAATATGCAGAAAAT
* * ** * *
5269335 AGAG-AGAGTAGATGAGAGGCTTAGTGTGTGTTACGAATGAGGTAGGGAGACTGTATTTATAGGC
128 AGAGAAGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGT
* * * * * *
5269399 AAGAAATGAAGTAAACATTGCACCAAATCAGGAGAATGAGTTAAACATTGCACCAAATCAGGGGC
193 AAGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGT-GACGTTGCACCAAATCAGGGG-
* * * *
5269464 TTGAGAAAAACCTGGTCAACATGTATATTCAGTCACGTAAACATTGTAGCAAATTAAGATAAACT
256 TTGAGAAAAA-CTGGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACT
* * * * *
5269529 CAGTCAGCATGGTAGAGTTTGAGTTTGATTCAATCAATGGTATCATTGTTTTAAGGATAATTTTT
320 CAGTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCTTAAGGATAATTTTT
* * * * *
5269594 ATCTCTTTATAATACAAACTAGGTGCAAAAGGACTATAGCGGTTATCCTTCAA
385 ACCTCTTTAGAATACAAACTAGATGCAAAAGAACTATAGCGATTATCCTTCAA
* * * * * * * *
5269647 GATTCAATAAACCCTTTC-TTATAGTTTGTATAAATTATTAAAGGATAACAAAAACAACAGAAAG
1 AATTTAACAAA-CCTTTCTTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAAAAAG
* * * * *
5269711 ATTTTTTAGAGAAAAAGAAGAACCCAG-TGAGGAAGGAAAGAAAGTAGAGAACATATGCAAAAAA
65 ATTTTTTAAAGAAAAAGAAGAACCCAGCAGA-GAAGGAAAGAAA-CAAAGAA-ATATGCAGAAAA
* * * * *
5269775 TAAAGAGGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGGGGTAAGGAGACTGTATTTATAAG
127 TAGAGAAGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGG
* * *
5269840 TAAGGAATAAAGTGAACATTGTACCAAATTTGGAGAATGAGGTGACGTTGCACCAAATCATGGGG
192 TAAGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGTGACGTTGCACCAAATCA-GGGG
** * * * * *
5269905 TTGAGAAAAACTAGGTTTACATGTATACTCAGTTAGGTAGACGTTGCAGCAAATCAAGAAAAATT
256 TTGAGAAAAACT-GGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACT
*
5269970 TAGTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCCTTAAGGATAATTTT
320 CAGTCAGCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTAT-CTTAAGGATAATTTT
* * * *
5270035 TGCC-CTTTTAGAATACAAAACTTGATGCAAAAAGAACTGTAGTGATTATCCTTCAA
384 TACCTC-TTTAGAATAC-AAACTAGATGC-AAAAGAACTATAGCGATTATCCTTCAA
* * * * * *
5270091 AATTTAACAAACTTTTCTTTATAGTTGGCACAAGCTACTAAGGGATAACAAAAACAGCAAAAAGT
1 AATTTAACAAACCTTTCTTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAAAAAGA
* *
5270156 TTTTTTAAAGAAAAAGAAGAACCCAGCAGAGAAAGAAAGAATACAAAGCAAATATGTAGAAAATA
66 TTTTTTAAAGAAAAAGAAGAACCCAGCAGAGAAGGAAAGAA-ACAAAG-AAATATGCAGAAAATA
* ** * **
5270221 GAGAAGAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGGGAGGCAATATTTATAGGTA
129 GAGAAGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGTA
* * *
5270286 AAGAATGAAGTGAACGTTGCACCCAATTAGGAGAAT-ATGGTGAACGTTGCACCAAATCAGGAGG
194 AGGAATGAAGTGAACATTGCACCAAATTAGGAGAATGA-GGTG-ACGTTGCACCAAATCAGG-GG
5270350 TT-AGGAAAAAC
256 TTGA-GAAAAAC
5270361 CTAAGGAAAG
Statistics
Matches: 588, Mismatches: 106, Indels: 36
0.81 0.15 0.05
Matches are distributed among these distances:
440 12 0.02
441 201 0.34
442 119 0.20
443 15 0.03
444 209 0.36
445 32 0.05
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (437 bp):
AATTTAACAAACCTTTCTTTATAGTTTGCATAAACTACTAAGGGATAACAAAAACAACAAAAAGA
TTTTTTAAAGAAAAAGAAGAACCCAGCAGAGAAGGAAAGAAACAAAGAAATATGCAGAAAATAGA
GAAGAGAAGATAAGAGGCTTAGTGTGTGTTGTGACTGAGGTAGGGAGACTGTATTTATAGGTAAG
GAATGAAGTGAACATTGCACCAAATTAGGAGAATGAGGTGACGTTGCACCAAATCAGGGGTTGAG
AAAAACTGGTCAACATGTATACTCAGTCACGTAAACATTGCAGCAAATCAAGAAAAACTCAGTCA
GCATGGTAAAGTTTGAGTTTGATGCAATCAATGGTATCACTATCTTAAGGATAATTTTTACCTCT
TTAGAATACAAACTAGATGCAAAAGAACTATAGCGATTATCCTTCAA
Found at i:5270442 original size:40 final size:41
Alignment explanation
Indices: 5270390--5270473 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 41
5270380 AAAAAAGAAA
5270390 AGGAGATAAGAGGCTTAATGTGTGTTGTGACTGAAGTAG-G
1 AGGAGATAAGAGGCTTAATGTGTGTTGTGACTGAAGTAGAG
* * *
5270430 AGGAGATAAGAGGTTTAGTGTGTGTTGTGACTGAGGTAGAG
1 AGGAGATAAGAGGCTTAATGTGTGTTGTGACTGAAGTAGAG
5270471 AGG
1 AGG
5270474 CAGTATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.29, C:0.04, G:0.40, T:0.27
Consensus pattern (41 bp):
AGGAGATAAGAGGCTTAATGTGTGTTGTGACTGAAGTAGAG
Found at i:5270585 original size:203 final size:203
Alignment explanation
Indices: 5270226--5270632 Score: 568
Period size: 203 Copynumber: 2.0 Consensus size: 203
5270216 AAATAGAGAA
* *
5270226 GAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGGGAGGCAATATTTATAGGTAAAGAA
1 GAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGAGAGGCAATATTTATAGGCAAAGAA
* * * * * * *
5270291 TGAAGTGAACGTTGCACCCAATTAGGAGAATATGGTGAACGTTGCACCAAATCAGGAGGTTAGGA
66 TGAAATGAACGTTGCACCAAATCAGAAAAATATGGTGAAAGTTACACCAAATCAGGAGGTTAGGA
* *
5270356 AAAACCTAAGGAAAGAATATAGAGAAAA-AAGAAAAGGAGATAAGAGGCTTAATGTGTGTTGTGA
131 AAAACCTAAGGAAAAAATACAGAGAAAAGAAG-AAAGGAGATAAGAGGCTTAATGTGTGTTGTGA
5270420 CTGAAGTAG
195 CTGAAGTAG
* ** *
5270429 GAGGAGATAAGAGGTTTAGTGTGTGTTGTGACTGAGGTAGAGAGGCAGTATTTATAGGCAAAGAA
1 GAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGAGAGGCAATATTTATAGGCAAAGAA
* *
5270494 TGAAATGGACGTTGCACCAAATCAGAAAAATGAT-TTGAAAGTTACACCAAATCAAGG-GGTTAG
66 TGAAATGAACGTTGCACCAAATCAGAAAAAT-ATGGTGAAAGTTACACCAAATC-AGGAGGTTAG
* ** *
5270557 GAAAAACCTAGGGAAAAAATACAGAGAAAAGAAGGGAGGAGATAAGAGGCTTAGTGTGTGTTGTG
129 GAAAAACCTAAGGAAAAAATACAGAGAAAAGAAGAAAGGAGATAAGAGGCTTAATGTGTGTTGTG
*
5270622 ACTGAGGTAG
194 ACTGAAGTAG
5270632 G
1 G
5270633 GAGACAGTAT
Statistics
Matches: 179, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
203 171 0.96
204 8 0.04
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.22
Consensus pattern (203 bp):
GAGGAGATAAGAGGCTTAGTGTGCATTGTGACTGAGGTAGAGAGGCAATATTTATAGGCAAAGAA
TGAAATGAACGTTGCACCAAATCAGAAAAATATGGTGAAAGTTACACCAAATCAGGAGGTTAGGA
AAAACCTAAGGAAAAAATACAGAGAAAAGAAGAAAGGAGATAAGAGGCTTAATGTGTGTTGTGAC
TGAAGTAG
Found at i:5273324 original size:20 final size:20
Alignment explanation
Indices: 5273284--5273335 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
5273274 AATTGTATTA
5273284 TAATCAAGAACATTACTTTT
1 TAATCAAGAACATTACTTTT
5273304 TAATACAAGAACATTACTTTT
1 TAAT-CAAGAACATTACTTTT
5273325 TAATTCAAGAA
1 TAA-TCAAGAA
5273336 ATCTATATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.13
21 25 0.83
22 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (20 bp):
TAATCAAGAACATTACTTTT
Found at i:5276354 original size:52 final size:52
Alignment explanation
Indices: 5276276--5276380 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
5276266 GACCCACCCA
5276276 AACATCACCAACTGAGCCCCGAACCTTCCTTCTCTCAGCAAAAACCAATAGT
1 AACATCACCAACTGAGCCCCGAACCTTCCTTCTCTCAGCAAAAACCAATAGT
5276328 AACATCACCAACTGAGCCCCGAACCTTCCTTCTCTCAGCAAAAACCAATAGT
1 AACATCACCAACTGAGCCCCGAACCTTCCTTCTCTCAGCAAAAACCAATAGT
5276380 A
1 A
5276381 GCTTAGCTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.35, C:0.36, G:0.10, T:0.19
Consensus pattern (52 bp):
AACATCACCAACTGAGCCCCGAACCTTCCTTCTCTCAGCAAAAACCAATAGT
Found at i:5280729 original size:31 final size:28
Alignment explanation
Indices: 5280656--5280732 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
5280646 TTTGTCCATT
5280656 TTTTAATTTAATTATTTTATAAAAAATTA
1 TTTTAATTTAATT-TTTTATAAAAAATTA
*** * *
5280685 TAACAATTAAATTTTTTAATTTTAAAAATTA
1 TTTTAATTTAATTTTTT-A--TAAAAAATTA
5280716 TTTTAATTTAATTTTTT
1 TTTTAATTTAATTTTTT
5280733 TAATATTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
28 4 0.11
29 10 0.28
31 22 0.61
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAATTTAATTTTTTATAAAAAATTA
Found at i:5280925 original size:20 final size:19
Alignment explanation
Indices: 5280891--5280930 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5280881 TTCTTTCTTA
5280891 TTTTTTCTTTCTTTCCCTC
1 TTTTTTCTTTCTTTCCCTC
* *
5280910 TTTTTTCATTTTTTTCTCTC
1 TTTTTTC-TTTCTTTCCCTC
5280930 T
1 T
5280931 CTTCGGACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTCTTTCTTTCCCTC
Found at i:5287872 original size:19 final size:19
Alignment explanation
Indices: 5287848--5287884 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5287838 ATTAAATTAA
5287848 TTAATTTAATTT-TTAAAAT
1 TTAA-TTAATTTATTAAAAT
5287867 TTAATTAATTTATTAAAA
1 TTAATTAATTTATTAAAA
5287885 ATAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTAATTTATTAAAAT
Found at i:5289081 original size:14 final size:14
Alignment explanation
Indices: 5289062--5289107 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5289052 AATCCACCAT
5289062 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
5289076 TTTCTTTCATTTTT-
1 TTTCTTTC-TTTTTC
5289090 TTTC--TCTTATTTC
1 TTTCTTTCTT-TTTC
5289103 TTTCT
1 TTTCT
5289108 GCGCCTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.07
12 5 0.18
13 4 0.14
14 12 0.43
15 5 0.18
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:5296568 original size:14 final size:15
Alignment explanation
Indices: 5296538--5296573 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5296528 AGAAAGAAAT
*
5296538 AAGAAAAAAAAATGA
1 AAGAAAGAAAAATGA
5296553 AAGAAAGAAAAA-GA
1 AAGAAAGAAAAATGA
5296567 AAGAAAG
1 AAGAAAG
5296574 TGGTGGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAGAAAGAAAAATGA
Found at i:5298853 original size:14 final size:14
Alignment explanation
Indices: 5298843--5298869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5298833 AAGAGAAAAT
5298843 AAATGAAAGAAAGA
1 AAATGAAAGAAAGA
5298857 AAATGAAAGAAAG
1 AAATGAAAGAAAG
5298870 TGGTGAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.07
Consensus pattern (14 bp):
AAATGAAAGAAAGA
Found at i:5300414 original size:18 final size:20
Alignment explanation
Indices: 5300384--5300420 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5300374 AAATATTTAT
5300384 TTTTAATAAATT-AATTAAA
1 TTTTAATAAATTAAATTAAA
5300403 TTTTAA-AAATTAAATTAA
1 TTTTAATAAATTAAATTAA
5300421 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAATAAATTAAATTAAA
Found at i:5300421 original size:31 final size:33
Alignment explanation
Indices: 5300386--5300454 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
5300376 ATATTTATTT
5300386 TTAATAAATT-AATTAAATTT-TAAAAAT-TAAA
1 TTAATAAATTAAATT-AATTTATAAAAATATAAA
* * *
5300417 TTAATAATTTAAATTATTTTATAAAAATATTAA
1 TTAATAAATTAAATTAATTTATAAAAATATAAA
5300450 TTAAT
1 TTAAT
5300455 TATCAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 13 0.41
32 11 0.34
33 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAATAAATTAAATTAATTTATAAAAATATAAA
Found at i:5300499 original size:14 final size:14
Alignment explanation
Indices: 5300480--5300506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5300470 CAATTCACCA
5300480 CTTTCTTTCATTTT
1 CTTTCTTTCATTTT
5300494 CTTTCTTTCATTT
1 CTTTCTTTCATTT
5300507 CTCTCCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCTTTCATTTT
Found at i:5302642 original size:83 final size:83
Alignment explanation
Indices: 5302550--5302717 Score: 293
Period size: 83 Copynumber: 2.0 Consensus size: 83
5302540 AGTCATTGGA
5302550 GAGGAGGCAGGGCTTATTGCCAACTCTACAATGTCTCGAC-GCGACAGCGATTGGGTAGCATGTA
1 GAGGAGGCAGGGCTTATTGCCAACTCTACAATGTCTCGACAG-GACAGCGATTGGGTAGCATGTA
5302614 AAGTTCATTGATGGAAATG
65 AAGTTCATTGATGGAAATG
* * *
5302633 GAGGAGGCAGGGCTTGTTGCCAACTCTACAGTGTCTCGACAGGACCGCGATTGGGTAGCATGTAA
1 GAGGAGGCAGGGCTTATTGCCAACTCTACAATGTCTCGACAGGACAGCGATTGGGTAGCATGTAA
5302698 AGTTCATTGATGGAAATG
66 AGTTCATTGATGGAAATG
5302716 GA
1 GA
5302718 ATTGCTAATT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
83 80 0.99
84 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (83 bp):
GAGGAGGCAGGGCTTATTGCCAACTCTACAATGTCTCGACAGGACAGCGATTGGGTAGCATGTAA
AGTTCATTGATGGAAATG
Found at i:5313998 original size:18 final size:18
Alignment explanation
Indices: 5313971--5314005 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5313961 TTTATAACAT
*
5313971 ATTAACTAAAATAAAAAA
1 ATTAAATAAAATAAAAAA
*
5313989 ATTAAATAAATTAAAAA
1 ATTAAATAAAATAAAAA
5314006 GGAATTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTAAATAAAATAAAAAA
Found at i:5314192 original size:24 final size:22
Alignment explanation
Indices: 5314148--5314197 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
5314138 AACAACAAAA
5314148 AAAATTTCAATTTCAAAAAACAC
1 AAAATTTCAATTTCAAAAAAC-C
*
5314171 AAAATTCTCAAGTTTC-GAAAACC
1 AAAATT-TCAA-TTTCAAAAAACC
5314194 AAAA
1 AAAA
5314198 CCCTAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 11 0.46
24 9 0.38
25 4 0.17
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAATTTCAATTTCAAAAAACC
Found at i:5314808 original size:35 final size:36
Alignment explanation
Indices: 5314769--5314840 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
5314759 TTTTTTTTAC
**
5314769 CTTTTCTTTTAAACGTAT-TAAGATAAAACTGATTA
1 CTTTTCTTTTAAAAATATATAAGATAAAACTGATTA
*
5314804 CTTTTCTTTTAAAAATATGATAAGGTAAAACTGATTA
1 CTTTTCTTTTAAAAATAT-ATAAGATAAAACTGATTA
5314841 ATTTAGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 16 0.50
37 16 0.50
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (36 bp):
CTTTTCTTTTAAAAATATATAAGATAAAACTGATTA
Found at i:5320139 original size:63 final size:61
Alignment explanation
Indices: 5320016--5320143 Score: 154
Period size: 63 Copynumber: 2.0 Consensus size: 61
5320006 ACGAGGAAAG
* **
5320016 AAAGAGAAAAAGGAAGAAAAAATGAAAAGCCCATCACCAAAGTGCAAGGATGGAAGAGAGAA
1 AAAGAGAAAAA-GAAGAAAAAATGAAAAGCCCATCACCAAAGAGCAACAATGGAAGAGAGAA
5320078 AAAGAGAAAGAA-AAGAAAAAA-GAAGAAGAACCCATCACCAAAGAGCAACAAT-GAAGCAGAGA
1 AAAGAGAAA-AAGAAGAAAAAATGAA-AAG--CCCATCACCAAAGAGCAACAATGGAAG-AGAGA
5320140 A
61 A
5320141 AAA
1 AAA
5320144 AAAAAGAGCC
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
60 3 0.05
61 12 0.21
62 13 0.22
63 30 0.52
ACGTcount: A:0.60, C:0.12, G:0.23, T:0.05
Consensus pattern (61 bp):
AAAGAGAAAAAGAAGAAAAAATGAAAAGCCCATCACCAAAGAGCAACAATGGAAGAGAGAA
Found at i:5320221 original size:18 final size:19
Alignment explanation
Indices: 5320179--5320222 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5320169 TATGCGCAGC
* *
5320179 AAGAAATAAGAGAAAAATA
1 AAGAAAGAAGAGAAAAAGA
*
5320198 ATGAAAGAA-AGAAAAAGA
1 AAGAAAGAAGAGAAAAAGA
5320216 AAGAAAG
1 AAGAAAG
5320223 TGGTGGACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAGAAAGAAGAGAAAAAGA
Found at i:5320297 original size:34 final size:34
Alignment explanation
Indices: 5320239--5320319 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
5320229 ACTGCGTAGC
5320239 AATTT-AA-TAATTAATTAATATTTTTATAAA-AT
1 AATTTAAATTAATTAATTAATATTTTTA-AAATAT
*
5320271 AATTTAAATTAATTAATTTAAT-TTTTTAAAATTT
1 AATTTAAATTAATTAA-TTAATATTTTTAAAATAT
*
5320305 AA-TTAAATTTATTAA
1 AATTTAAATTAATTAA
5320320 AAATAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 5 0.12
33 17 0.40
34 16 0.37
35 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
AATTTAAATTAATTAATTAATATTTTTAAAATAT
Found at i:5320308 original size:20 final size:20
Alignment explanation
Indices: 5320283--5320321 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5320273 TTTAAATTAA
* *
5320283 TTAATTTAATTTTTTAAAAT
1 TTAATTAAATTTATTAAAAT
5320303 TTAATTAAATTTATTAAAA
1 TTAATTAAATTTATTAAAA
5320322 ATAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTAAATTTATTAAAAT
Done.