Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:383320 original size:14 final size:15
Alignment explanation
Indices: 383277--383322 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
383267 GCAAAGCAAA
**
383277 AAAAAAAGAGCAAA-
1 AAAAAAAGAAAAAAG
383291 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
383306 AAAAAAA-AAATAAG
1 AAAAAAAGAAAAAAG
383320 AAA
1 AAA
383323 CGAATCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:384221 original size:12 final size:11
Alignment explanation
Indices: 384179--384243 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 11
384169 AAGGGGCAAT
384179 ATTTTTTCAAA
1 ATTTTTTCAAA
384190 ATTTTTT-ATTAA
1 ATTTTTTCA--AA
384202 ACTTTTTTCAAA
1 A-TTTTTTCAAA
384214 ATTCTTTT-AATTA
1 ATT-TTTTCAA--A
384227 ATATTTTTCAAA
1 AT-TTTTTCAAA
384239 ATTTT
1 ATTTT
384244 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
10 1 0.02
11 14 0.31
12 13 0.29
13 13 0.29
14 4 0.09
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTTTCAAA
Found at i:384221 original size:25 final size:23
Alignment explanation
Indices: 384179--384243 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 23
384169 AAGGGGCAAT
384179 ATTTTTTCAAAATTTTTT-ATTAA
1 ATTTTTTCAAAATTTTTTAATT-A
384202 ACTTTTTTCAAAATTCTTTTAATTA
1 A-TTTTTTCAAAATT-TTTTAATTA
384227 ATATTTTTCAAAATTTT
1 AT-TTTTTCAAAATTTT
384244 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.03
24 16 0.42
25 18 0.47
26 3 0.08
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTTCAAAATTTTTTAATTA
Found at i:387337 original size:20 final size:20
Alignment explanation
Indices: 387292--387341 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
387282 GTATGAACAA
*
387292 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
387313 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
387333 TATCGATAC
1 TATCGATAC
387342 CAAGCATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:387987 original size:30 final size:30
Alignment explanation
Indices: 387953--388010 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
387943 TATGCAAAGA
*
387953 TGTTCTATGTGAATA-AATGCTATGTGAAAT
1 TGTTCTACGTGAATATAAT-CTATGTGAAAT
*
387983 TGTTCTACGTGAATATGATCTATGTGAA
1 TGTTCTACGTGAATATAATCTATGTGAA
388011 TAAAAGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (30 bp):
TGTTCTACGTGAATATAATCTATGTGAAAT
Found at i:388170 original size:24 final size:24
Alignment explanation
Indices: 388123--388258 Score: 179
Period size: 24 Copynumber: 5.7 Consensus size: 24
388113 GTTGTACGCA
*
388123 GTCCTTCGGGAC-AATTCTATGTG
1 GTCCTTCGGGACAAATTCTACGTG
388146 GTCCTTCGGGACAAATTCTACGTG
1 GTCCTTCGGGACAAATTCTACGTG
*
388170 GTCCTTCGGGACAAATTCTAGGTG
1 GTCCTTCGGGACAAATTCTACGTG
* *
388194 GTCCTTCAGGACAAATTATACGTG
1 GTCCTTCGGGACAAATTCTACGTG
**
388218 GTCCTTTAGGACAAATTCTACGTG
1 GTCCTTCGGGACAAATTCTACGTG
388242 G-CACTTCGGTG-CAAATT
1 GTC-CTTCGG-GACAAATT
388259 ATATGAGTAG
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.13
24 87 0.86
25 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (24 bp):
GTCCTTCGGGACAAATTCTACGTG
Found at i:388382 original size:2 final size:2
Alignment explanation
Indices: 388370--388414 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
388360 ATTGAAAGAG
*
388370 TA TA AA 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
388412 TA T
1 TA T
388415 GTAGTCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:388678 original size:27 final size:27
Alignment explanation
Indices: 388633--388684 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
388623 TTCGAATAAT
* *
388633 AAGACGAGTAAGCACGGGTAGGATGAC
1 AAGACGAGTAAACAAGGGTAGGATGAC
388660 AAGACGAGTAAACAAGGGTAGGATG
1 AAGACGAGTAAACAAGGGTAGGATG
388685 GCATATTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.37, T:0.12
Consensus pattern (27 bp):
AAGACGAGTAAACAAGGGTAGGATGAC
Found at i:389665 original size:18 final size:19
Alignment explanation
Indices: 389630--389665 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
389620 TATCTGAAAG
*
389630 CCAATGATAATTGTATTTT
1 CCAATGATAATTGGATTTT
389649 CCAATGAT-ATTGGATTT
1 CCAATGATAATTGGATTT
389666 GATAAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (19 bp):
CCAATGATAATTGGATTTT
Found at i:416390 original size:2 final size:2
Alignment explanation
Indices: 416383--416442 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
416373 GGACAAAAAG
416383 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
416425 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
416443 GGTATCAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:417787 original size:58 final size:57
Alignment explanation
Indices: 417697--417805 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
417687 CTAATTAGCC
417697 AAAAAAAATCATAAGTACCAAAATTGAATAAAAAGCCAAGTATG-TACCTAATCGGATA
1 AAAAAAAATCATAAGTACCAAAATTGAAT-AAAAGCCAAGT-TGTTACCTAATCGGATA
* * *
417755 AAAAAAAATTATAAGTATC-AAATTGAACTAAAAGTCAAGTTGTTACCTAAT
1 AAAAAAAATCATAAGTACCAAAATTGAA-TAAAAGCCAAGTTGTTACCTAAT
417806 AACATAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
56 2 0.04
57 26 0.57
58 18 0.39
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (57 bp):
AAAAAAAATCATAAGTACCAAAATTGAATAAAAGCCAAGTTGTTACCTAATCGGATA
Found at i:418831 original size:31 final size:31
Alignment explanation
Indices: 418795--418854 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
418785 AACTTAAAAG
* * *
418795 AGTTTTCCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
418826 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
418855 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:419382 original size:21 final size:19
Alignment explanation
Indices: 419320--419384 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
419310 TTAAATCAAA
419320 ATAAT-TAAAATAAATA-T
1 ATAATATAAAATAAATATT
419337 AT-ATATAAAAT-AAT-TT
1 ATAATATAAAATAAATATT
419353 ATATGATATAAAATTAAATATCT
1 ATA--ATATAAAA-TAAATAT-T
419376 ATAATATAA
1 ATAATATAA
419385 TATTAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
16 8 0.21
17 8 0.21
19 8 0.21
20 1 0.03
21 9 0.23
22 1 0.03
23 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAATATAAAATAAATATT
Found at i:419400 original size:28 final size:28
Alignment explanation
Indices: 419362--419486 Score: 96
Period size: 28 Copynumber: 4.4 Consensus size: 28
419352 TATATGATAT
419362 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
* * * * * * *
419391 AAAAATAATATTTAATTTATTTTAAAAAATATT
1 AAAATTAATATCT-A--TAATAT-AATATTA-A
419424 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
419452 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
419476 AAAATTAATAT
1 AAAATTAATAT
419487 TAAAATTAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
24 15 0.20
25 3 0.04
26 4 0.05
27 1 0.01
28 17 0.22
29 11 0.14
30 4 0.05
31 4 0.05
32 6 0.08
33 11 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:419438 original size:61 final size:63
Alignment explanation
Indices: 419361--419514 Score: 228
Period size: 61 Copynumber: 2.5 Consensus size: 63
419351 TTATATGATA
*
419361 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTT-TAAAA-AATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATAATAT
*
419423 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAA-TAATAT
*
419487 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
419515 TTAAATATAA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
61 48 0.56
62 20 0.23
63 1 0.01
64 17 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATAATAT
Found at i:419460 original size:14 final size:14
Alignment explanation
Indices: 419424--419491 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
419414 AAAAAATATT
*
419424 AAAATTAATATCTAT
1 AAAATTAATAT-TAA
*
419439 AATA-TAATATTAA
1 AAAATTAATATTAA
419452 AAAATTAATATT--
1 AAAATTAATATTAA
* *
419464 -TAATTTAT-TTAA
1 AAAATTAATATTAA
419476 AAAATTAATATTAA
1 AAAATTAATATTAA
419490 AA
1 AA
419492 TTAAAATCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.05
11 6 0.15
13 11 0.27
14 19 0.46
15 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTAATATTAA
Found at i:419480 original size:24 final size:27
Alignment explanation
Indices: 419424--419488 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 27
419414 AAAAAATATT
419424 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATAT-TATAATATAATATTAA
*
419452 AAAATTAATATT-TAAT-TTAT-TTAA
1 AAAATTAATATTATAATATAATATTAA
419476 AAAATTAATATTA
1 AAAATTAATATTA
419489 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 11 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATTAATATTATAATATAATATTAA
Found at i:419521 original size:12 final size:12
Alignment explanation
Indices: 419476--419526 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
419466 ATTTATTTAA
419476 AAAATT-AATATT
1 AAAATTAAATA-T
419488 AAAATTAAA-AT
1 AAAATTAAATAT
*
419499 CAAA-TATAATAT
1 AAAATTA-AATAT
419511 AAAATTAAATAT
1 AAAATTAAATAT
419523 AAAA
1 AAAA
419527 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:434561 original size:43 final size:43
Alignment explanation
Indices: 434514--434595 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
434504 ACGTCTAAAT
*
434514 TCAAAATAACAATCCA-AGCATACACCCAACTAACATATTACAA
1 TCAAAATAACAATCCACA-CATACACCAAACTAACATATTACAA
* * * *
434557 TCAAATTAACAATTCACATATACATCAAACTAACATATT
1 TCAAAATAACAATCCACACATACACCAAACTAACATATT
434596 GAGTCGAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 32 0.97
44 1 0.03
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.24
Consensus pattern (43 bp):
TCAAAATAACAATCCACACATACACCAAACTAACATATTACAA
Found at i:439414 original size:21 final size:23
Alignment explanation
Indices: 439372--439414 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
439362 TGTTGTAATT
* *
439372 AAATCAATATTTTTATTGAATAA
1 AAATCAATATTTTTAGTAAATAA
439395 AAAT-AAT-TTTTTAGTAAATA
1 AAATCAATATTTTTAGTAAATA
439415 TATTATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 3 0.17
23 4 0.22
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
AAATCAATATTTTTAGTAAATAA
Found at i:440880 original size:42 final size:41
Alignment explanation
Indices: 440790--440956 Score: 126
Period size: 42 Copynumber: 3.9 Consensus size: 41
440780 ATTAATTTTA
* * * *
440790 TTTTTATTTTTATAATTAAAGCTCTTAATTTTTAT-AATCTCACA
1 TTTTTACTTTTATAATTAGAGC-CCTAATTTTT-TCAATCT-A-T
*
440834 TTTTTA-TATTTATAATTA-AGCCCATATTTTTTTCAATCCTAT
1 TTTTTACT-TTTATAATTAGAGCCC-TAATTTTTTCAAT-CTAT
* *
440876 TTTTTACTTTTATAATTAGGATCCCTAATTTTTTCAATCTCT
1 TTTTTACTTTTATAATTA-GAGCCCTAATTTTTTCAATCTAT
* *
440918 TTTTTACTGTTATTAATTAGA-CTCTTAATTTTCTTCAAT
1 TTTTTACTTTTA-TAATTAGAGC-CCTAATTTT-TTCAAT
440957 ACCACTTTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
41 1 0.01
42 42 0.40
43 40 0.38
44 22 0.21
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.55
Consensus pattern (41 bp):
TTTTTACTTTTATAATTAGAGCCCTAATTTTTTCAATCTAT
Found at i:441021 original size:42 final size:41
Alignment explanation
Indices: 440972--441070 Score: 180
Period size: 41 Copynumber: 2.4 Consensus size: 41
440962 TTTTTACCGC
440972 TATAATTGAGGTCTTTAGTTTTTTCAATCTCACTTTTATATT
1 TATAATTGAGGTCTTTAGTTTTTT-AATCTCACTTTTATATT
*
441014 TATAATTGAGGTCCTTAGTTTTTTAATCTCACTTTTATATT
1 TATAATTGAGGTCTTTAGTTTTTTAATCTCACTTTTATATT
441055 TATAATTGAGGTCTTT
1 TATAATTGAGGTCTTT
441071 TGTAATACCC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 32 0.58
42 23 0.42
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (41 bp):
TATAATTGAGGTCTTTAGTTTTTTAATCTCACTTTTATATT
Found at i:442615 original size:15 final size:15
Alignment explanation
Indices: 442575--442629 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
442565 TTGGATAATG
*
442575 CTACGTGAAATTTGTT
1 CTACGTGAAA-TTGTC
* *
442591 CTAAGTGAAAATGTC
1 CTACGTGAAATTGTC
*
442606 CTACGTGAAATTATC
1 CTACGTGAAATTGTC
*
442621 CTATGTGAA
1 CTACGTGAA
442630 TAAGATACAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 23 0.72
16 9 0.28
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (15 bp):
CTACGTGAAATTGTC
Found at i:442800 original size:24 final size:23
Alignment explanation
Indices: 442742--442809 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
442732 GGGTTCTACA
*
442742 CGGTCATTCGGGACAAATCTATG
1 CGGTCCTTCGGGACAAATCTATG
* *
442765 TGATCCTTCGGGACAAAT-TATACG
1 CGGTCCTTCGGGACAAATCTAT--G
442789 CGGTCCTTCGGGACAAATCTA
1 CGGTCCTTCGGGACAAATCTA
442810 CTTGACACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.08
23 15 0.41
24 17 0.46
25 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
CGGTCCTTCGGGACAAATCTATG
Found at i:442821 original size:47 final size:47
Alignment explanation
Indices: 442742--442881 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
442732 GGGTTCTACA
*
442742 CGGTCATTCGGGACAAATCTA-TGTGATC-CTTCGG-GACAAATTATACG
1 CGGTCCTTCGGGACAAATCTACT-TGA-CACTTCGGTG-CAAATTATACG
* *
442789 CGGTCCTTCGGGACAAATCTACTTGACACTTCGGTGCAAATTCTACT
1 CGGTCCTTCGGGACAAATCTACTTGACACTTCGGTGCAAATTATACG
* * *
442836 TGG-CACTTCGGTG-CAAATTCTACTTGGCACTTCGGTGCAATTTATA
1 CGGTC-CTTCGG-GACAAA-TCTACTTGACACTTCGGTGCAAATTATA
442882 TGAGTAGTGG
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
46 2 0.03
47 50 0.62
48 28 0.35
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (47 bp):
CGGTCCTTCGGGACAAATCTACTTGACACTTCGGTGCAAATTATACG
Found at i:442842 original size:24 final size:24
Alignment explanation
Indices: 442794--442875 Score: 132
Period size: 24 Copynumber: 3.5 Consensus size: 24
442784 ATACGCGGTC
*
442794 CTTCGG-GACAAA-TCTACTTGACA
1 CTTCGGTG-CAAATTCTACTTGGCA
442817 CTTCGGTGCAAATTCTACTTGGCA
1 CTTCGGTGCAAATTCTACTTGGCA
442841 CTTCGGTGCAAATTCTACTTGGCA
1 CTTCGGTGCAAATTCTACTTGGCA
442865 CTTCGGTGCAA
1 CTTCGGTGCAA
442876 TTTATATGAG
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
23 10 0.18
24 46 0.82
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTACTTGGCA
Found at i:442951 original size:29 final size:29
Alignment explanation
Indices: 442919--442979 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
442909 AACCTCAATG
* *
442919 TACTTGCATACCTTGAGTTCTCAGCTGTA
1 TACTCGCATACCTTGAGTTCTCAGCGGTA
442948 TACTCGCATACCTTGAGTTCTCAGCGGTA
1 TACTCGCATACCTTGAGTTCTCAGCGGTA
442977 TAC
1 TAC
442980 GTTGGGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (29 bp):
TACTCGCATACCTTGAGTTCTCAGCGGTA
Found at i:446888 original size:21 final size:21
Alignment explanation
Indices: 446864--446908 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
446854 AATGGGTTTG
446864 GATTTGATTTAATTTGTG-ACT
1 GATTTGATTTAATTTG-GAACT
* *
446885 GATTTGGTTTGATTTGGAACT
1 GATTTGATTTAATTTGGAACT
446906 GAT
1 GAT
446909 GGGGTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.49
Consensus pattern (21 bp):
GATTTGATTTAATTTGGAACT
Found at i:447651 original size:134 final size:133
Alignment explanation
Indices: 447377--447731 Score: 548
Period size: 134 Copynumber: 2.6 Consensus size: 133
447367 GTTCGGGTCG
* * * * * * * *
447377 TCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACTGCTCATACGT
1 TCTAGGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTC-GGGAATGACACGGCTCATACGT
*
447442 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTTCGCGATGAGGACGACT
65 GATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACT
447507 GATTA
129 GATTA
*
447512 TCTAGGGGTGACATAGCTCATACGTGATGAAGAGATCTGGTCGGGAAATGACACGGCTCATACGT
1 TCTAGGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGGG-AATGACACGGCTCATACGT
* *
447577 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTG
65 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTG
*
447642 GTTA
130 ATTA
*
447646 TCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGT
1 TCTAGGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTC-GGGAATGACACGGCTCATACGT
447711 GATGAAGAGTTCTGGCCATCT
65 GATGAAGAGTTCTGGCCATCT
447732 ATAAGGATAA
Statistics
Matches: 202, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
134 135 0.67
135 67 0.33
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (133 bp):
TCTAGGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGGGAATGACACGGCTCATACGTG
ATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTGA
TTA
Found at i:447792 original size:29 final size:29
Alignment explanation
Indices: 447760--447865 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
447750 AAAGCAACTG
447760 ACTCAAAGATGATGTTTCAAAAGAAATAA
1 ACTCAAAGATGATGTTTCAAAAGAAATAA
* * *
447789 ACTCAAAGATGATGTTTCAAAACCAACT-G
1 ACTCAAAGATGATGTTTCAAAA-GAAATAA
* *
447818 ACTCAAAGATGATGTTTCAAAAGAAACAT
1 ACTCAAAGATGATGTTTCAAAAGAAATAA
*
447847 ACTCAAAGATGATTTTTCA
1 ACTCAAAGATGATGTTTCA
447866 TTAAAAATTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 2 0.03
29 62 0.93
30 3 0.04
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (29 bp):
ACTCAAAGATGATGTTTCAAAAGAAATAA
Found at i:447810 original size:58 final size:58
Alignment explanation
Indices: 447745--447865 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 58
447735 AGGATAATAA
* *
447745 TTTCAAAAGCAACTGACTCAAAGATGATGTTTCAAAAGAAATAAACTCAAAGATGATG
1 TTTCAAAACCAACTGACTCAAAGATGATGTTTCAAAAGAAACAAACTCAAAGATGATG
* *
447803 TTTCAAAACCAACTGACTCAAAGATGATGTTTCAAAAGAAACATACTCAAAGATGATT
1 TTTCAAAACCAACTGACTCAAAGATGATGTTTCAAAAGAAACAAACTCAAAGATGATG
447861 TTTCA
1 TTTCA
447866 TTAAAAATTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (58 bp):
TTTCAAAACCAACTGACTCAAAGATGATGTTTCAAAAGAAACAAACTCAAAGATGATG
Found at i:448103 original size:91 final size:90
Alignment explanation
Indices: 447937--448162 Score: 271
Period size: 91 Copynumber: 2.5 Consensus size: 90
447927 GTTAAGAGAC
* *
447937 ACAATCTCAAAG-ATTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAA
1 ACAAACTCAAAGAATTTTTCAAAAGAAAC-GACTCAAAGATTTTTCTCAAG-AAAACTGTCTCAA
*
448001 GAGAGAAAAAACTTTATTTCAAAAGAA
64 GAGAGAAAAAACTTTAGTTCAAAAGAA
* * * * *
448028 ACAAACTCAAATATTTTGGTTTCAAAAGAAACGACTCAAAGATTTTT-TCATG-AAATTGTCTTA
1 ACAAACTCAAAGA-ATT--TTTCAAAAGAAACGACTCAAAGATTTTTCTCAAGAAAACTGTCTCA
*
448091 AGAGA-AACAAAACTTTGGTTCAAAAGAA
63 AGAGAGAA-AAAACTTTAGTTCAAAAGAA
* *
448119 ACAAACTCAAAGAATTTTTCAAAAGAAACAACTCAAAGAATTTT
1 ACAAACTCAAAGAATTTTTCAAAAGAAACGACTCAAAGATTTTT
448163 ATTTCAAAAG
Statistics
Matches: 117, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
88 26 0.22
90 4 0.03
91 54 0.46
93 6 0.05
94 15 0.13
95 12 0.10
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (90 bp):
ACAAACTCAAAGAATTTTTCAAAAGAAACGACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGA
GAGAAAAAACTTTAGTTCAAAAGAA
Found at i:448230 original size:33 final size:30
Alignment explanation
Indices: 448104--448267 Score: 169
Period size: 29 Copynumber: 5.5 Consensus size: 30
448094 GAAACAAAAC
*
448104 TTTGGTTCAAAAGAAACAAACTCAAAGAA-
1 TTTGTTTCAAAAGAAACAAACTCAAAGAAT
448133 -TT-TTTCAAAAGAAAC-AACTCAAAGAAT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAAT
* * *
448160 TTTATTTCAAAAGAAAC-AACTCACAGACT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAAT
448189 TTTGTTTCAAAAGAAACAAACTCAAAGATAGGT
1 TTTGTTTCAAAAGAAACAAACTCAAAGA-A--T
** *
448222 TTTGTTTCAAGGGAAACAATCTCAAAG-AT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAAT
* *
448251 GTTTGTTTTAAGAGAAA
1 -TTTGTTTCAAAAGAAA
448268 ATGTCTTAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 15
0.82 0.08 0.11
Matches are distributed among these distances:
26 11 0.09
27 12 0.10
28 4 0.03
29 40 0.34
30 23 0.20
31 1 0.01
33 25 0.22
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (30 bp):
TTTGTTTCAAAAGAAACAAACTCAAAGAAT
Found at i:448254 original size:59 final size:54
Alignment explanation
Indices: 448109--448254 Score: 148
Period size: 62 Copynumber: 2.5 Consensus size: 54
448099 AAAACTTTGG
*
448109 TTCAAAAGAAACAAACTCAAAGAATTTTTCAAAAGAAACAACTCAAAGAATTTTAT
1 TTCAAAAGAAAC-AACTCAAAG-ATGTTTCAAAAGAAACAACTCAAAGAATTTTAT
* *
448165 TTCAAAAGAAACAACTCACAGACTTTTGTTTCAAAAGAAACAAACTCAAAGATAGGTTTTGT
1 TTCAAAAGAAACAACTCAAAGA----TGTTTCAAAAGAAAC-AACTCAAAGA-A--TTTTAT
**
448227 TTCAAGGGAAACAATCTCAAAGATGTTT
1 TTCAAAAGAAACAA-CTCAAAGATGTTT
448255 GTTTTAAGAG
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
54 1 0.01
55 8 0.11
56 12 0.16
58 14 0.19
59 15 0.20
60 1 0.01
62 17 0.23
63 7 0.09
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (54 bp):
TTCAAAAGAAACAACTCAAAGATGTTTCAAAAGAAACAACTCAAAGAATTTTAT
Found at i:448306 original size:67 final size:66
Alignment explanation
Indices: 448234--448382 Score: 144
Period size: 66 Copynumber: 2.2 Consensus size: 66
448224 TGTTTCAAGG
* * * * *
448234 GAAACAATCTCAAAGATGTTTGT-TTTAAGAGAAAATGTCTTAAAAGAGACAAACCTTTGTTTTC
1 GAAACAATCTCAAAGAT-TTT-TCTTCAAAAGAAAATATCTCAAAAGAGACAAAACTTTGTTTTC
448298 ATAA
64 A-AA
* * * *
448302 -AAACAGA-CTTAAAGATTTTTCTTCAAAAGGAACTATCTCAAAAGAGACAAAATTTTGTTTTCA
1 GAAACA-ATCTCAAAGATTTTTCTTCAAAAGAAAATATCTCAAAAGAGACAAAACTTTGTTTTCA
448365 AA
65 AA
448367 GAAAC-ATACTCAAAGA
1 GAAACAAT-CTCAAAGA
448383 CTATCTCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
64 1 0.02
65 3 0.05
66 48 0.73
67 13 0.20
68 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (66 bp):
GAAACAATCTCAAAGATTTTTCTTCAAAAGAAAATATCTCAAAAGAGACAAAACTTTGTTTTCAA
A
Found at i:448391 original size:49 final size:49
Alignment explanation
Indices: 448333--448431 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
448323 TTCAAAAGGA
*
448333 ACTATCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAG
1 ACTATCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAG
448382 ACTATCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAG
1 ACTATCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAG
448431 A
1 A
448432 TTTTTTTCAT
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:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (49 bp):
ACTATCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAG
Found at i:448446 original size:38 final size:38
Alignment explanation
Indices: 448402--448474 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
448392 AAGAGACAAA
*
448402 ATTTTGTTATCA-AAGAAACATACTCAAAGATTTTTTTC
1 ATTTTGTT-TCAGAAGAAACAGACTCAAAGATTTTTTTC
* **
448440 ATTTTGTTTTAGGTGAAACAGACTCAAAGATTTTT
1 ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTT
448475 CAATAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.07
38 28 0.93
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (38 bp):
ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTTTTC
Found at i:451434 original size:31 final size:31
Alignment explanation
Indices: 451367--451426 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
451357 CAATTTAAGG
*
451367 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
451398 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
451427 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:451513 original size:19 final size:19
Alignment explanation
Indices: 451491--451538 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
451481 AATGTTTTTA
*
451491 TGAACAGTAAATTACTATT
1 TGAACAGTAAATCACTATT
* *
451510 TGAACAGTAAATCATTGTT
1 TGAACAGTAAATCACTATT
451529 TGAACAGTAA
1 TGAACAGTAA
451539 CCCGAGGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (19 bp):
TGAACAGTAAATCACTATT
Found at i:451671 original size:21 final size:21
Alignment explanation
Indices: 451645--451686 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
451635 ATTTGCATAT
*
451645 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
451666 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
451687 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:451748 original size:21 final size:21
Alignment explanation
Indices: 451715--451754 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
451705 TTTTTACAGA
*
451715 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
451737 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
451755 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:452008 original size:34 final size:32
Alignment explanation
Indices: 451969--452038 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
451959 TTTTGTAAAG
*
451969 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
452003 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
452035 GGGA
1 GGGA
452039 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:452922 original size:19 final size:20
Alignment explanation
Indices: 452898--452945 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
452888 AACAATTTTC
*
452898 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
452917 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
452937 TTTTGAAAA
1 TTTTGAAAA
452946 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:454283 original size:31 final size:31
Alignment explanation
Indices: 454216--454275 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
454206 CAATTTAAGG
*
454216 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
454247 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
454276 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:454367 original size:19 final size:19
Alignment explanation
Indices: 454340--454387 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
454330 AATGTTTTTA
* * *
454340 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTAATATT
454359 TGAACAGTAAATTAATATT
1 TGAACAGTAAATTAATATT
454378 TGAACAGTAA
1 TGAACAGTAA
454388 CCCGAGGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTAATATT
Found at i:454519 original size:21 final size:21
Alignment explanation
Indices: 454493--454534 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
454483 ATTTGAATAT
*
454493 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
454514 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
454535 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:454596 original size:21 final size:21
Alignment explanation
Indices: 454563--454602 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
454553 TTTTTGCAGA
*
454563 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
454585 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
454603 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:454857 original size:34 final size:32
Alignment explanation
Indices: 454818--454887 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
454808 TTTTGTAAAG
*
454818 GGGAAAGGTTCTAGCTTAGACCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGACCG-G-AAAAACTA
* * *
454852 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGACCGGAAAAACTA
454884 GGGA
1 GGGA
454888 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGACCGGAAAAACTA
Found at i:458602 original size:28 final size:29
Alignment explanation
Indices: 458551--458626 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 29
458541 TAAACAGCAT
* ** *
458551 AAACAGGAATTTAAAATACTAAAAT-CAA
1 AAACAGAAATTTAAAGGACCAAAATCCAA
*
458579 TAACAGAAATTTAAAGGACCAAAATGCCAA
1 AAACAGAAATTTAAAGGACCAAAAT-CCAA
*
458609 AAACAGAAA-CTAAAGGAC
1 AAACAGAAATTTAAAGGAC
458627 TAAACAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 20 0.51
29 8 0.21
30 11 0.28
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (29 bp):
AAACAGAAATTTAAAGGACCAAAATCCAA
Found at i:469529 original size:9 final size:9
Alignment explanation
Indices: 469515--469632 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
469505 GCTGCTGGAA
469515 ACCGGTTTG
1 ACCGGTTTG
*
469524 ACCGGTTTTCA
1 ACCGG-TTT-G
469535 ACCGGTTCTG
1 ACCGGTT-TG
469545 ACCGGTTTG
1 ACCGGTTTG
*
469554 ACCGGTTTCA
1 ACCGGTTT-G
*
469564 ACCGGTTCG
1 ACCGGTTTG
469573 AACCGGTTTG
1 -ACCGGTTTG
*
469583 ACCGGTCTG
1 ACCGGTTTG
*
469592 AATCGGTTTG
1 -ACCGGTTTG
*
469602 ACCGGTCTG
1 ACCGGTTTG
*
469611 AATCGGTTTG
1 -ACCGGTTTG
469621 ACCGGTTTG
1 ACCGGTTTG
469630 ACC
1 ACC
469633 CGACCCGACC
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
9 41 0.47
10 41 0.47
11 6 0.07
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:469559 original size:19 final size:20
Alignment explanation
Indices: 469514--469627 Score: 130
Period size: 19 Copynumber: 5.8 Consensus size: 20
469504 GGCTGCTGGA
* *
469514 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
469534 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
*
469554 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
469573 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
469592 AATCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
469611 AATCGGTTTGACCGGTT
1 AACCGGTTTGACCGGTT
469628 TGACCCGACC
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.04
19 54 0.64
20 18 0.21
21 9 0.11
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.31
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:469577 original size:29 final size:30
Alignment explanation
Indices: 469514--469588 Score: 127
Period size: 29 Copynumber: 2.5 Consensus size: 30
469504 GGCTGCTGGA
469514 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
469545 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
469573 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
469589 CTGAATCGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.65
30 14 0.33
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:469598 original size:29 final size:28
Alignment explanation
Indices: 469515--469607 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
469505 GCTGCTGGAA
469515 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
469545 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
469573 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
469602 ACCGGT
1 ACCGGT
469608 CTGAATCGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 37 0.64
30 14 0.24
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:469639 original size:5 final size:5
Alignment explanation
Indices: 469629--469669 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
469619 TGACCGGTTT
*
469629 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
469670 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:469653 original size:22 final size:22
Alignment explanation
Indices: 469627--469676 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
469617 TTTGACCGGT
469627 TTGACCCGACCCGACCCGACCG
1 TTGACCCGACCCGACCCGACCG
469649 TTGACCCGACCCGACCCGACCG
1 TTGACCCGACCCGACCCGACCG
469671 TTGACC
1 TTGACC
469677 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (22 bp):
TTGACCCGACCCGACCCGACCG
Found at i:469678 original size:7 final size:7
Alignment explanation
Indices: 469666--469696 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
469656 GACCCGACCC
469666 GACCGTT
1 GACCGTT
469673 GACCGTT
1 GACCGTT
469680 GACCGTT
1 GACCGTT
469687 GACCGTT
1 GACCGTT
469694 GAC
1 GAC
469697 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:470614 original size:32 final size:32
Alignment explanation
Indices: 470578--470654 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
470568 GTAGGCCCTG
*
470578 CGGCCCTAAGATGTGTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGGCTCTCA
* * *
470610 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 CGG-CCCTAAGATGTATCTTAGGTAGGCTCTCA
470642 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
470655 TCCCTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
30 5 0.14
31 16 0.44
32 10 0.28
33 5 0.14
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
Found at i:476814 original size:9 final size:9
Alignment explanation
Indices: 476800--476887 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
476790 GCTGCTGGAA
476800 ACCGGTTTG
1 ACCGGTTTG
*
476809 ACCGGTTTCA
1 ACCGGTTT-G
*
476819 ACCGGTTCG
1 ACCGGTTTG
476828 AACCGGTTTG
1 -ACCGGTTTG
*
476838 ACCGGTCTG
1 ACCGGTTTG
*
476847 AATCGGTTTG
1 -ACCGGTTTG
*
476857 ACCGGTCTG
1 ACCGGTTTG
*
476866 AATCGGTTTG
1 -ACCGGTTTG
*
476876 ACCGGTCTG
1 ACCGGTTTG
476885 ACC
1 ACC
476888 CGACCCGACC
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
9 33 0.53
10 29 0.47
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:476823 original size:19 final size:19
Alignment explanation
Indices: 476800--476885 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
476790 GCTGCTGGAA
* *
476800 ACCGGTTTG-ACCGGTTTCA
1 ACCGGTCTGAACCGGTTT-G
476819 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
*
476838 ACCGGTCTGAATCGGTTTG
1 ACCGGTCTGAACCGGTTTG
*
476857 ACCGGTCTGAATCGGTTTG
1 ACCGGTCTGAACCGGTTTG
476876 ACCGGTCTGA
1 ACCGGTCTGA
476886 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
18 1 0.02
19 52 0.84
20 9 0.15
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.29
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:476853 original size:29 final size:29
Alignment explanation
Indices: 476799--476862 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
476789 GGCTGCTGGA
*
476799 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
476828 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
476857 -ACCGGT
1 AACCGGT
476863 CTGAATCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:476930 original size:7 final size:7
Alignment explanation
Indices: 476916--476946 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
476906 GACCCAACCC
476916 GACCGTT
1 GACCGTT
*
476923 GTCCGTT
1 GACCGTT
476930 GACCGTT
1 GACCGTT
476937 GACCGTT
1 GACCGTT
476944 GAC
1 GAC
476947 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:481127 original size:45 final size:45
Alignment explanation
Indices: 481078--481313 Score: 312
Period size: 45 Copynumber: 5.2 Consensus size: 45
481068 TATTCATTAT
* * * *
481078 TTTCATTAATGACATTCTTTCAAGACTTTAATGCACAGTTGTGCA
1 TTTCATTTATGACATCCTTTCATGACTTTAATGCACAGTTATGCA
* *
481123 TTTCATTTATGTCATCCTTTCATGACTTTAATGCACTGTTATGCA
1 TTTCATTTATGACATCCTTTCATGACTTTAATGCACAGTTATGCA
* * * *
481168 TTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGACTTTAATGCACAGTTATGCA
* ** *
481213 TTTCATTTATGTCATCCTTTCATCTCTTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGACTTTAATGCACAGTTATGCA
* *
481258 TTTCATTTATGACATCTTTTCATGCCTTTAATGCACCA-TTATGCA
1 TTTCATTTATGACATCCTTTCATGACTTTAATGCA-CAGTTATGCA
481303 TTTCATTTATG
1 TTTCATTTATG
481314 TAATGAAAAC
Statistics
Matches: 171, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 170 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGACATCCTTTCATGACTTTAATGCACAGTTATGCA
Found at i:481213 original size:90 final size:90
Alignment explanation
Indices: 481086--481314 Score: 350
Period size: 90 Copynumber: 2.5 Consensus size: 90
481076 ATTTTCATTA
* * * * * *
481086 ATGACATTCTTTCAAGACTTTAATGCACAGTTGTGCATTTCATTTATGTCATCCTTTCATGACTT
1 ATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATCACTT
*
481151 TAATGCACTGTTATGCATTTAATTT
66 TAATGCACCGTTATGCATTTAATTT
* *
481176 ATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATCTCTT
1 ATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATCACTT
*
481241 TAATGCACCGTTATGCATTTCATTT
66 TAATGCACCGTTATGCATTTAATTT
* *
481266 ATGACATCTTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGT
1 ATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGT
481315 AATGAAAACA
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 126 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (90 bp):
ATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATCACTT
TAATGCACCGTTATGCATTTAATTT
Found at i:485258 original size:20 final size:20
Alignment explanation
Indices: 485235--485309 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
485225 GGATTATCAA
*
485235 TGGTCCTTCGGGATAAACAG
1 TGGTCCTTCGGGACAAACAG
* *
485255 TGGTCCTTCGAGAC--ATAG
1 TGGTCCTTCGGGACAAACAG
* * *
485273 TGGTTCTTCGGAACAATCAG
1 TGGTCCTTCGGGACAAACAG
485293 TGGTCCTTCGGGACAAA
1 TGGTCCTTCGGGACAAA
485310 TATTCAGTGC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
18 14 0.33
20 28 0.67
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (20 bp):
TGGTCCTTCGGGACAAACAG
Found at i:485276 original size:18 final size:18
Alignment explanation
Indices: 485252--485303 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
485242 TCGGGATAAA
485252 CAGTGGTCCTTCGAGACAT
1 CAGTGGTCCTTCG-GACAT
*
485271 -AGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGG-AC-AT
485290 CAGTGGTCCTTCGG
1 CAGTGGTCCTTCGG
485304 GACAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 13 0.46
19 2 0.07
20 12 0.43
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
CAGTGGTCCTTCGGACAT
Found at i:485282 original size:38 final size:38
Alignment explanation
Indices: 485235--485307 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
485225 GGATTATCAA
* *
485235 TGGTCCTTCGGGATAAACAGTGGTCCTTCGAGACATAG
1 TGGTCCTTCGGAACAAACAGTGGTCCTTCGAGACATAG
* * *
485273 TGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACA
1 TGGTCCTTCGGAACAAACAGTGGTCCTTCGAGACA
485308 AATATTCAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (38 bp):
TGGTCCTTCGGAACAAACAGTGGTCCTTCGAGACATAG
Found at i:488752 original size:15 final size:15
Alignment explanation
Indices: 488732--488769 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
488722 GAATTTAGTC
488732 GGAGCCATCTGATAT
1 GGAGCCATCTGATAT
488747 GGAGCCATCTGATAT
1 GGAGCCATCTGATAT
488762 GGAGCCAT
1 GGAGCCAT
488770 AGAAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (15 bp):
GGAGCCATCTGATAT
Found at i:491029 original size:45 final size:46
Alignment explanation
Indices: 490974--491168 Score: 211
Period size: 45 Copynumber: 4.3 Consensus size: 46
490964 ATTATTCATT
* * *
490974 ATTTTCATTTATGGCATCCTTTCATGCCTTTAATACA-TAGTTGTGC
1 ATTTT-ATTTATGGCATCCTTTCATGCCTTTAATGCACCAGTTATGC
** * *
491020 ATTTTATTTA-CACTATTCTTTCATGACTTTAATGCACC-GTTATGC
1 ATTTTATTTATGGC-ATCCTTTCATGCCTTTAATGCACCAGTTATGC
* *
491065 ATTTTTCATTTATGGCATCATTTCATGCCTTTAATGCACCA-TTATAC
1 A-TTTT-ATTTATGGCATCCTTTCATGCCTTTAATGCACCAGTTATGC
* *
491112 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA-CTGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCAGTTATGC
*
491157 ATTTCATTTATG
1 ATTTTATTTATG
491169 TAATGAAAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 15
0.80 0.11 0.10
Matches are distributed among these distances:
44 2 0.02
45 78 0.62
46 12 0.10
47 32 0.26
48 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCAGTTATGC
Found at i:491107 original size:21 final size:21
Alignment explanation
Indices: 491083--491148 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
491073 TTTATGGCAT
491083 CATTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
* *
491104 CATTATACATTTCATTT-ATGGCATC
1 CATT-T-CA-TGCCTTTAAT-GCA-C
491129 C-TTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
491149 TGTTATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 5 0.14
23 5 0.14
24 10 0.29
25 2 0.06
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (21 bp):
CATTTCATGCCTTTAATGCAC
Found at i:491133 original size:92 final size:91
Alignment explanation
Indices: 490974--491168 Score: 243
Period size: 92 Copynumber: 2.1 Consensus size: 91
490964 ATTATTCATT
* * * * * *
490974 ATTTTCATTTATGGCATCCTTTCATGCCTTTAATACATAGTTGTGCATTTTATTTACACTATTCT
1 ATTTTCATTTATGGCATCATTTCATGCCTTTAATACACAGTTATACATTTCATTTACACTATCCT
491039 TTCATGACTTTAATGCACCGTTATGC
66 TTCATGACTTTAATGCACCGTTATGC
* **
491065 ATTTTTCATTTATGGCATCATTTCATGCCTTTAATGCACCA-TTATACATTTCATTTATGGC-AT
1 A-TTTTCATTTATGGCATCATTTCATGCCTTTAATACA-CAGTTATACATTTCATTTA-CACTAT
* *
491128 CCTTTCATGCCTTTAATGCACTGTTATGC
63 CCTTTCATGACTTTAATGCACCGTTATGC
491157 A-TTTCATTTATG
1 ATTTTCATTTATG
491169 TAATGAAAAC
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
90 11 0.12
91 1 0.01
92 76 0.84
93 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (91 bp):
ATTTTCATTTATGGCATCATTTCATGCCTTTAATACACAGTTATACATTTCATTTACACTATCCT
TTCATGACTTTAATGCACCGTTATGC
Found at i:491724 original size:95 final size:94
Alignment explanation
Indices: 491532--491730 Score: 242
Period size: 95 Copynumber: 2.1 Consensus size: 94
491522 ACCTTCCATG
*
491532 GTATCGATACTTGTATACTATGGTACTGATACCCTTTTTAGTATCGATACCATTTCTACATTCTG
1 GTATCGATACTTGTATACTATGGTACCGATACCCTTTTTAGTATCGATACCATTTCTACATTCTG
* * * *
491597 TAATTCATGGTATCAATACTTTTCTTTCA
66 TAATCCATAGTATCAATAATTTCCTTTCA
* * *
491626 GTATCGATACTAT-TATATTATGGTACCGATACTCTTTTTTAGTATCGATACCATTT-TGGCATT
1 GTATCGATACT-TGTATACTATGGTACCGATAC-CCTTTTTAGTATCGATACCATTTCT-ACATT
** *
491689 CTAG-AATCCATAGTATTGATAATTTCCTTTTA
63 CT-GTAATCCATAGTATCAATAATTTCCTTTCA
491721 GTATCGATAC
1 GTATCGATAC
491731 CCCATCAGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
94 29 0.32
95 60 0.67
96 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (94 bp):
GTATCGATACTTGTATACTATGGTACCGATACCCTTTTTAGTATCGATACCATTTCTACATTCTG
TAATCCATAGTATCAATAATTTCCTTTCA
Found at i:492861 original size:5 final size:5
Alignment explanation
Indices: 492844--493313 Score: 614
Period size: 5 Copynumber: 94.0 Consensus size: 5
492834 ATAAATAACT
* *
492844 ATATA ATATTA ATATA ATATA A-ATA CTATA CTATA ATA-A ATAT- ATATA
1 ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
492892 ATATAA TATATA ATGTA CA-ATA ATATA ATA-A TATATA ATATA ATAATA
1 ATAT-A -ATATA ATATA -ATATA ATATA ATATA -ATATA ATATA AT-ATA
*
492940 CTATAA TATATA ATATA ATAATA TATATA ATATA ATATA ATATA A-ATA
1 ATAT-A -ATATA ATATA AT-ATA -ATATA ATATA ATATA ATATA ATATA
492988 ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
493036 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- A-ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
493084 ATATA ATATA ATATA ATATA ATATA ATATA ATATA TATATA ATAT- A-ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
493133 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
493182 ATATA ATAT- ATATA ATAT- ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
493230 ATATA ATAAATA ATATA ATATA ATATA ATATA ATATA ATAT- ATACTA
1 ATATA AT--ATA ATATA ATATA ATATA ATATA ATATA ATATA ATA-TA
* *
493277 CATATT ATATA ATAT- ATACTA CATATT ATATA ATATA
1 -ATATA ATATA ATATA ATA-TA -ATATA ATATA ATATA
493314 TACTATATAT
Statistics
Matches: 421, Mismatches: 10, Indels: 68
0.84 0.02 0.14
Matches are distributed among these distances:
3 4 0.01
4 47 0.11
5 322 0.76
6 28 0.07
7 20 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:493110 original size:87 final size:87
Alignment explanation
Indices: 492844--493386 Score: 602
Period size: 87 Copynumber: 6.1 Consensus size: 87
492834 ATAAATAACT
* *
492844 ATATAATATTAATATAATATAA-ATACTATACTATAATA-AATAT-ATATAATATAATAT-ATAA
1 ATATAATA-T-ATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATAA
*
492905 TGTACA-ATAATATAATA-ATATATA
64 TATA-ATATAATATAATATA-ATATA
492929 ATATAATAATACTATAATATATAATATAATAATATATATAATATAATATAATATAA-ATAATATA
1 ATATAAT-ATA-TAT-A-ATATAATATAAT-ATA-ATATAATATAATATAATATAATATAATATA
492993 TATAATATAATATAATATAATATAATATA
60 -ATAATATAATATAATATAATATAATATA
493022 ATATAATATATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATAATA
1 ATATAATATATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATAATA
493087 TAATATAATATAATATAATATA
66 TAATATAATATAATATAATATA
493109 ATAT-A-ATATAT-ATATAATAT-A-ATAATATAATATAATATAATATAATATAATATAAT-ATA
1 ATATAATATATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATAAT-
493168 ATATATATAATATAATATAATAT-
65 ATA-ATATAATATAATATAATATA
493191 ATATAATATATATAATATAATATAATATAATATAATATAATATAATAAATAATATAATATAATAT
1 ATATAATATATATAATATAATATAATATAATATAATATAATATAAT--ATAATATAATAT-A-AT
*
493256 AATATAATATAATAT-ATACTACATATT
62 AATATAATATAATATAATA-TA-ATATA
* * **
493283 ATATAATATATACTACATATTATATAATAT-ATACTATATATAACAT-ATACT-ATGATAATGCA
1 ATATAATATATA-TA-ATATAATATAATATAATA-TA-ATATAATATAATA-TAAT-ATAATATA
* * *
493345 CTATATATTATATAATATACTAT-ATACTA
60 ATA-ATATAATATAATATAATATAATA-TA
*
493374 CTATAATATATAT
1 ATATAATATATAT
493387 TATACTATAA
Statistics
Matches: 408, Mismatches: 12, Indels: 71
0.83 0.02 0.14
Matches are distributed among these distances:
81 2 0.00
82 42 0.10
83 21 0.05
84 16 0.04
85 26 0.06
86 4 0.01
87 79 0.19
88 15 0.04
89 30 0.07
90 24 0.06
91 38 0.09
92 42 0.10
93 43 0.11
94 18 0.04
95 8 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (87 bp):
ATATAATATATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATAATA
TAATATAATATAATATAATATA
Found at i:493306 original size:14 final size:14
Alignment explanation
Indices: 493262--493322 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
493252 ATATAATATA
*
493262 ATATAATATATACT
1 ATATAATACATACT
* * * *
493276 ACATATTATATAAT
1 ATATAATACATACT
* *
493290 ATATACTACATATT
1 ATATAATACATACT
*
493304 ATATAATATATACT
1 ATATAATACATACT
493318 ATATA
1 ATATA
493323 TAACATATAC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAATACATACT
Found at i:495200 original size:40 final size:40
Alignment explanation
Indices: 495154--495233 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
495144 TTAGAAAATA
495154 TAGAGCGC-CTTTTTCAGGTTTTCACTCTAAACACTTTTTT
1 TAGAGCGCGC-TTTTCAGGTTTTCACTCTAAACACTTTTTT
495194 TAGAGCGCGCTTTTCAGGTTTTCACTCTAAACACTTTTTT
1 TAGAGCGCGCTTTTCAGGTTTTCACTCTAAACACTTTTTT
495234 CTGAAAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.44
Consensus pattern (40 bp):
TAGAGCGCGCTTTTCAGGTTTTCACTCTAAACACTTTTTT
Found at i:511110 original size:20 final size:20
Alignment explanation
Indices: 511085--511134 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
511075 GCCTTGAATG
511085 TGCATCGATGCACAAGGACA
1 TGCATCGATGCACAAGGACA
511105 TGCATCGATGCACAAGGACA
1 TGCATCGATGCACAAGGACA
511125 TGCATCGATG
1 TGCATCGATG
511135 AATCCGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAAGGACA
Found at i:513745 original size:20 final size:20
Alignment explanation
Indices: 513716--513753 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
513706 TTTCAAAGTG
513716 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
513736 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
513754 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:514580 original size:55 final size:55
Alignment explanation
Indices: 514480--515000 Score: 787
Period size: 55 Copynumber: 9.5 Consensus size: 55
514470 TCGATTAACT
* *
514480 CAACACCCACAAAATGCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
1 CAAC-CCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* *
514536 CAACCCCA-TAAATTTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
1 CAACCCCACGAAA-TTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
*
514591 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTACGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* *
514646 CAACCCCACGAAATTCATAATGAGTTTATGAATTTCCATATTGGGCA-TATGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATT-GGCACTATGTGTG
* * *
514701 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCCTATTGACATTATGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* * *
514756 CAACCCCACGAAATTCATAATGAGTTTATAAATTTCCGTATTGGCACTATGTGTA
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* * *
514811 TAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATTTTGGCACTATGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
*
514866 CAACCCTACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* * *
514921 CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATGTGTG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* * *
514976 CAA-CCTACGTAATTCACAATGAGTT
1 CAACCCCACGAAATTCATAATGAGTT
515001 ATTGAATGAC
Statistics
Matches: 425, Mismatches: 36, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
54 24 0.06
55 390 0.92
56 11 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (55 bp):
CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
Found at i:514678 original size:110 final size:110
Alignment explanation
Indices: 514480--515072 Score: 791
Period size: 110 Copynumber: 5.4 Consensus size: 110
514470 TCGATTAACT
* *
514480 CAACACCCACAAAATGCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCA-
1 CAAC-CCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCAC
* * *
514544 TAAATTTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
65 GAAA-TTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
*
514591 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTACGTGTGCAACCCCACG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACG
*
514656 AAATTCATAATGAGTTTATGAATTTCCATATTGGGCA-TATGTGTG
66 AAATTCATAATGAGTTTATGAATTTCCGTATT-GGCACTATGTGTG
* * *
514701 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCCTATTGACATTATGTGTGCAACCCCACG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACG
* *
514766 AAATTCATAATGAGTTTATAAATTTCCGTATTGGCACTATGTGTA
66 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * *
514811 TAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATTTTGGCACTATGTGTGCAACCCTACG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACG
*
514876 AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTG
66 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * *
514921 CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATGTGTGCAA-CCTACG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACG
* * ** * * * *
514985 TAATTCACAATGAG-TTATTGAATGACCATATCGACACTATATGTG
66 AAATTCATAATGAGTTTA-TGAATTTCCGTATTGGCACTATGTGTG
* * * * * * *
515030 C-ACCCCAAGGATTTCAAAATAAGTTTGTGAATTTTCATATTGG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
515073 TACTTAGATG
Statistics
Matches: 430, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
108 35 0.08
109 43 0.10
110 341 0.79
111 11 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (110 bp):
CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACG
AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
Found at i:514768 original size:165 final size:165
Alignment explanation
Indices: 514480--515072 Score: 809
Period size: 165 Copynumber: 3.6 Consensus size: 165
514470 TCGATTAACT
* * *
514480 CAACACCCACAAAATGCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCA-
1 CAAC-CCCACGAAATTCATAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACCCCAC
* *
514544 TAAATTTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCAT
65 GAAA-TTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCAT
* *
514609 AATGAGTTTATGAATTTTCGTATTGGCACTACGTGTG
129 AATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
*
514646 CAACCCCACGAAATTCATAATGAGTTTATGAATTTCCATATTGGGCA-TATGTGTGCAACCCCAC
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATATT-GGCACTATGTGTGCAACCCCAC
* * *
514710 GAAATTCATAATGAGTTTATGAATTTTCCTATTGACATTATGTGTGCAACCCCACGAAATTCATA
65 GAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATA
* *
514775 ATGAGTTTATAAATTTCCGTATTGGCACTATGTGTA
130 ATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * *
514811 TAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATTTTGGCACTATGTGTGCAACCCTACG
1 CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACCCCACG
*
514876 AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAA
66 AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAA
*
514941 TGAGTTTATGAATTTCCGTATTGACACTATGTGTG
131 TGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * *** * * * *
514976 CAA-CCTACGTAATTCACAATGAG-TTATTGAATGACCATATCGACACTATATGTGC-ACCCCAA
1 CAACCCCACGAAATTCATAATGAGTTTA-TGAATTTTCATATTGGCACTATGTGTGCAACCCCAC
* * * * * *
515038 GGATTTCAAAATAAGTTTGTGAATTTTCATATTGG
65 GAAATTCATAATGAGTTTATGAATTTTCGTATTGG
515073 TACTTAGATG
Statistics
Matches: 380, Mismatches: 43, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
163 37 0.10
164 42 0.11
165 290 0.76
166 11 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (165 bp):
CAACCCCACGAAATTCATAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACCCCACG
AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAA
TGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
Found at i:517598 original size:15 final size:16
Alignment explanation
Indices: 517566--517601 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
517556 CATAAACTAT
517566 ATTATATGAGATAAATG
1 ATTATATGAGA-AAATG
517583 ATTATATGAG-AAATG
1 ATTATATGAGAAAATG
517598 ATTA
1 ATTA
517602 AAGTTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
17 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (16 bp):
ATTATATGAGAAAATG
Found at i:517809 original size:21 final size:21
Alignment explanation
Indices: 517762--517829 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
517752 ATATATGAAA
*
517762 TCCTTTGGAACATATATGCGG
1 TCCTTTGGAACACATATGCGG
* * **
517783 TTCTTTGGGACACATATTTGG
1 TCCTTTGGAACACATATGCGG
* * * *
517804 TCCTTTAGAATATATATGTGG
1 TCCTTTGGAACACATATGCGG
517825 TCCTT
1 TCCTT
517830 AAGAAGAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (21 bp):
TCCTTTGGAACACATATGCGG
Found at i:517834 original size:21 final size:21
Alignment explanation
Indices: 517796--517893 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
517786 TTTGGGACAC
* *
517796 ATATTTGGTCCTTTAGAATAT
1 ATATGTGGTCCTTAAGAATAT
*
517817 ATATGTGGTCCTTAAGAAGAATT
1 ATATGTGGTCCTTAAGAA-TA-T
*
517840 ATATGTGGTCCTTCAAG-ACAT
1 ATATGTGGTCCTT-AAGAATAT
* ** *
517861 ATATGTGGTTCTTCGGGATAT
1 ATATGTGGTCCTTAAGAATAT
*
517882 ATATGAGGTCCT
1 ATATGTGGTCCT
517894 CAGGGACAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 42 0.67
22 2 0.03
23 15 0.24
24 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (21 bp):
ATATGTGGTCCTTAAGAATAT
Found at i:517846 original size:23 final size:25
Alignment explanation
Indices: 517810--517857 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
517800 TTGGTCCTTT
517810 AGAATATATATGTGGTCCTT-AAGA
1 AGAATATATATGTGGTCCTTCAAGA
517834 AGAAT-TATATGTGGTCCTTCAAGA
1 AGAATATATATGTGGTCCTTCAAGA
517858 CATATATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (25 bp):
AGAATATATATGTGGTCCTTCAAGA
Found at i:520154 original size:5 final size:5
Alignment explanation
Indices: 520131--520264 Score: 137
Period size: 5 Copynumber: 24.6 Consensus size: 5
520121 AAAATAAAAA
520131 ATAAT AATAAT ATAAAT ATAAT ATATATT ATAAT AT-AT ATATAT ATATAT
1 ATAAT -ATAAT AT-AAT ATAAT ATA-A-T ATAAT ATAAT ATA-AT ATA-AT
520181 ATATAT ATATAT ATACCAT ATAAT ACTATACT ATAAT ATAAT ATAAT ATAAT
1 ATA-AT ATA-AT ATA--AT ATAAT A-TA-A-T ATAAT ATAAT ATAAT ATAAT
520233 ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
520265 TAATGCACAA
Statistics
Matches: 117, Mismatches: 1, Indels: 21
0.84 0.01 0.15
Matches are distributed among these distances:
4 8 0.07
5 57 0.49
6 38 0.32
7 12 0.10
8 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:520158 original size:2 final size:2
Alignment explanation
Indices: 520140--520266 Score: 118
Period size: 2 Copynumber: 68.5 Consensus size: 2
520130 AATAATAATA
*
520140 AT AT AA AT AT A- AT AT AT AT -T AT A- 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
*
520179 AT AT AT AT AT AT AT AT ACC AT AT A- AT ACT AT ACT AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT A-T AT AT AT AT
520220 A- AT AT A- AT AT A- AT AT A- AT AT AT AT A- AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
520255 AT AT A- AT AT AT A
1 AT AT AT AT AT AT A
520267 ATGCACAATA
Statistics
Matches: 105, Mismatches: 4, Indels: 32
0.74 0.03 0.23
Matches are distributed among these distances:
1 13 0.12
2 87 0.83
3 5 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:520425 original size:16 final size:16
Alignment explanation
Indices: 520381--520429 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
520371 ATAATTTATA
**
520381 TATTATTATA-TAAAA
1 TATTATTATATTAATT
*
520396 TATTTTTA-ATTAATT
1 TATTATTATATTAATT
520411 TATTATTATATTAATT
1 TATTATTATATTAATT
520427 TAT
1 TAT
520430 AATATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 1 0.04
15 17 0.61
16 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATATTAATT
Found at i:522381 original size:18 final size:17
Alignment explanation
Indices: 522355--522390 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
522345 TTAAATCAAC
*
522355 TTTATATTTATTATAAA
1 TTTATATTTAATATAAA
522372 TTTATCATTTAATATAAA
1 TTTAT-ATTTAATATAAA
522390 T
1 T
522391 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATATTTAATATAAA
Found at i:523291 original size:9 final size:9
Alignment explanation
Indices: 523277--523301 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
523267 TTCGCATATA
523277 GATTTTACT
1 GATTTTACT
523286 GATTTTACT
1 GATTTTACT
523295 GATTTTA
1 GATTTTA
523302 AAATTGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (9 bp):
GATTTTACT
Found at i:523410 original size:52 final size:52
Alignment explanation
Indices: 523348--523453 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
523338 ATGAATATAA
523348 ATGAATATTACACAGATAATTTATCGAATGTTATGTTCATTTTCACCTTTAG
1 ATGAATATTACACAGATAATTTATCGAATGTTATGTTCATTTTCACCTTTAG
523400 ATGAATATTACACAGATAATTTATCGAATGTTATGTTCATTTTCACCTTTAG
1 ATGAATATTACACAGATAATTTATCGAATGTTATGTTCATTTTCACCTTTAG
523452 AT
1 AT
523454 CCAACTAATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (52 bp):
ATGAATATTACACAGATAATTTATCGAATGTTATGTTCATTTTCACCTTTAG
Found at i:523626 original size:15 final size:15
Alignment explanation
Indices: 523606--523638 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
523596 CTCTCGTACG
523606 TTAATC-TTTAAACTT
1 TTAATCATTTAAA-TT
523621 TTAATCATTTAAATT
1 TTAATCATTTAAATT
523636 TTA
1 TTA
523639 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATCATTTAAATT
Found at i:530211 original size:55 final size:55
Alignment explanation
Indices: 530122--531006 Score: 994
Period size: 55 Copynumber: 16.1 Consensus size: 55
530112 AATAAGTGAG
* * * * * *
530122 ACTTGAAAAATCTTTGAATAACGGGTCCGCTCCCTACTCTTTCAGGGAGTATAGG
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * *
530177 ACTTGAAATAATCTTC-AAAAATGGGCCCGTTCCCTATTCTTTCAGGGAGTATAGG
1 ACTTG-AACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
** ** * * * *
530232 ACTCAAACAATCTTCGAAAAATGAATCCACTCTCTATTCTTTTAGGGAGTATAGG
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * * *
530287 ACTTGAACAATCTTTGAAAAATGGGTCTGTTCCCTATTCTTTCAAGGAGTATAGG
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* *
530342 ACTTGAACAATCTTCGAAAAAATGGGTCCACTCCCTATTCTTTCATGGAGTATAGA
1 ACTTGAACAATCTTCG-AAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * ** *** *
530398 ACTCGAACAATATTC-AGAAAATGAATATTCTCCCTATTCTTTCAGGGAGTATAGG
1 ACTTGAACAATCTTCGA-AAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* *
530453 ACTTGAACAATCTTCGTAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGG
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * *
530508 ACTTGAAAAATCTTCGGAAAATGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* *
530563 ACTTGAACAATCTTCGAAAAATGAGTCTGCTCCCTATTCTTTCAGGGAGTATAGA
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* ** * *
530618 ACTCGAACAATCTTCTG-AAAATGGGTATGCTCCCTATTCTTTCAAGGAGTATAGG
1 ACTTGAACAATCTTC-GAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * * *
530673 ACTTGAACATTCTTCGAAAAACGGGTCCACTCCCTAATCTTTTAGGGAGTATAGA
1 ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * *
530728 ACTCGAACAATCTTCTG-ACAACGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
1 ACTTGAACAATCTTC-GAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * * *
530783 ACTTGAACAATCTTC-AGAAAATAGGTTCGCTCCCTCTTCTTTCAGGGGGGTGTAGA
1 ACTTGAACAATCTTCGA-AAAATGGGTCCGCTCCCTATTCTTTCA-GGGAGTATAGA
* * *
530839 ACTCGAACAATCTTCTG-AAAATGGGTTCGCTCCCTATTCTTTCAGGGAGAATAGA
1 ACTTGAACAATCTTC-GAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * *
530894 ACTAGAACAATCTTCTG-AAAATGGGTTCACTCCCTATTCTTTCAAGGAGTATAGA
1 ACTTGAACAATCTTC-GAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
* * * * *
530949 AATCGAACAATATTCTG-AAAATGGGTTCGCTCCCTATTCTTTCAGGGAGTATATA
1 ACTTGAACAATCTTC-GAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
531004 ACT
1 ACT
531007 CGATCTTGAT
Statistics
Matches: 713, Mismatches: 104, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
54 11 0.02
55 597 0.84
56 105 0.15
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (55 bp):
ACTTGAACAATCTTCGAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGA
Found at i:530544 original size:221 final size:221
Alignment explanation
Indices: 530122--531006 Score: 1098
Period size: 221 Copynumber: 4.0 Consensus size: 221
530112 AATAAGTGAG
* * * * * * * *
530122 ACTTGAAAAATCTTTG-AATAACGGGTCCGCTCCCTACTCTTTCAGGGAGTATAGGACTTGAAAT
1 ACTTGAACAATCTTCGAAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCG-AAC
* *** * **
530186 AATCTTC-AAAAATGGGCCCGTTCCCTATTCTTTCAGGGAGTATAGGACTCAAACAATCTTCGAA
65 AATCTTCTGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGAA
** * * * * * * *
530250 AAATGAATCCACTCTCTATTCTTTTAGGGAGTATAGGACTTGAACAATCTTTGAAAAATGGGTCT
130 AAATGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCGGAAAATGGGTCC
* * *
530315 GTTCCCTATTCTTTCAAGGAGTATAGG
195 GCTCCCTATTCTTTCAGGGAGTATAGA
* *
530342 ACTTGAACAATCTTCGAAAAAATGGGTCCACTCCCTATTCTTTCATGGAGTATAGAACTCGAACA
1 ACTTGAACAATCTTCGAAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACA
* * ** * *
530407 ATATTCAGAAAATGAATATTCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGTAA
66 ATCTTCTGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGAAA
* * * * *
530472 AATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAAAAATCTTCGGAAAATGAGTCCG
131 AATGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCGGAAAATGGGTCCG
530537 CTCCCTATTCTTTCAGGGAGTATAGA
196 CTCCCTATTCTTTCAGGGAGTATAGA
* *
530563 ACTTGAACAATCTTCG-AAAAATGAGTCTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACA
1 ACTTGAACAATCTTCGAAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACA
* *
530627 ATCTTCTGAAAATGGGTATGCTCCCTATTCTTTCAAGGAGTATAGGACTTGAACATTCTTCGAAA
66 ATCTTCTGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGAAA
* * * * * *
530692 AACGGGTCCACTCCCTAATCTTTTAGGGAGTATAGAACTCGAACAATCTTCTGACAACGGGTCCG
131 AATGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCGGAAAATGGGTCCG
530757 CTCCCTATTCTTTCAGGGAGTATAGA
196 CTCCCTATTCTTTCAGGGAGTATAGA
* * * * * *
530783 ACTTGAACAATCTTC-AGAAAATAGGTTCGCTCCCTCTTCTTTCAGGGGGGTGTAGAACTCGAAC
1 ACTTGAACAATCTTCGAAAAAATGGGTCCGCTCCCTATTCTTTCA-GGGAGTATAGAACTCGAAC
* * *
530847 AATCTTCTGAAAATGGGT-TCGCTCCCTATTCTTTCAGGGAGAATAGAACTAGAACAATCTTCTG
65 AATCTTCTGAAAATGGGTAT-GCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTC-G
* * * * *
530911 -AAAATGGGTTCACTCCCTATTCTTTCAAGGAGTATAGAAATCGAACAATATTCTGAAAATGGGT
128 AAAAATGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCGGAAAATGGGT
* *
530975 TCGCTCCCTATTCTTTCAGGGAGTATATA
193 CCGCTCCCTATTCTTTCAGGGAGTATAGA
531004 ACT
1 ACT
531007 CGATCTTGAT
Statistics
Matches: 577, Mismatches: 82, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
220 241 0.42
221 335 0.58
222 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (221 bp):
ACTTGAACAATCTTCGAAAAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACA
ATCTTCTGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGAAA
AATGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCGGAAAATGGGTCCG
CTCCCTATTCTTTCAGGGAGTATAGA
Found at i:535238 original size:2 final size:2
Alignment explanation
Indices: 535231--535262 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
535221 CCGGGCTTAA
535231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
535263 ATTATTGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535415 original size:14 final size:14
Alignment explanation
Indices: 535396--535423 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
535386 ACGTGGGACA
535396 CTTGCTTCATAATC
1 CTTGCTTCATAATC
535410 CTTGCTTCATAATC
1 CTTGCTTCATAATC
535424 TGGGGAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTGCTTCATAATC
Found at i:536542 original size:6 final size:6
Alignment explanation
Indices: 536533--536594 Score: 52
Period size: 6 Copynumber: 9.3 Consensus size: 6
536523 TTTATTTTTG
*
536533 TTATTT TTATTAT ATTATTC TTATTT TTATTT TAGTATTT TAGTATTT
1 TTATTT TTATT-T -TTATTT TTATTT TTATTT T--TATTT T--TATTT
*
536581 TTATTA TTATTT TT
1 TTATTT TTATTT TT
536595 CCTTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
6 28 0.58
7 1 0.02
8 19 0.40
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:536550 original size:14 final size:14
Alignment explanation
Indices: 536533--536587 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
536523 TTTATTTTTG
536533 TTATTTTTATTATA
1 TTATTTTTATTATA
*
536547 TTATTCTTATT-T-
1 TTATTTTTATTATA
*
536559 TTATTTTAGTATTTTA
1 TTATTTT--TATTATA
*
536575 GTATTTTTATTAT
1 TTATTTTTATTAT
536588 TATTTTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 6 0.18
13 1 0.03
14 19 0.58
15 1 0.03
16 6 0.18
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (14 bp):
TTATTTTTATTATA
Found at i:536556 original size:20 final size:20
Alignment explanation
Indices: 536533--536587 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
536523 TTTATTTTTG
*
536533 TTATTTTTATTATATTATTC
1 TTATTTTTATTATAGTATTC
* *
536553 TTATTTTTATTTTAGTATTT
1 TTATTTTTATTATAGTATTC
536573 TAGTATTTTTATTAT
1 T--TATTTTTATTAT
536588 TATTTTTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.62
22 11 0.38
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (20 bp):
TTATTTTTATTATAGTATTC
Found at i:536585 original size:34 final size:35
Alignment explanation
Indices: 536521--536594 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 35
536511 ATGTATATAG
* *
536521 TTTTTATTTTTGTTATTTTTATTATATTATTCTTA
1 TTTTTATTTTAGTTATTTTTATTATATTATTATTA
536556 TTTTTATTTTAG-TATTTTAGTATT-T-TTATTATTA
1 TTTTTATTTTAGTTATTTT--TATTATATTATTATTA
536590 TTTTT
1 TTTTT
536595 CCTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 19 0.54
35 12 0.34
36 4 0.11
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.74
Consensus pattern (35 bp):
TTTTTATTTTAGTTATTTTTATTATATTATTATTA
Found at i:536593 original size:20 final size:20
Alignment explanation
Indices: 536524--536593 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
536514 TATATAGTTT
*
536524 TTATTTTTGTTATTTTTATTA
1 TTATTTTAG-TATTTTTATTA
**
536545 -TATTATTCTTATTTTTATTTTA
1 TTATT-TTAGTATTTTTA--TTA
*
536567 GTATTTTAGTATTTTTATTA
1 TTATTTTAGTATTTTTATTA
536587 TTATTTT
1 TTATTTT
536594 TCCTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 21 0.52
21 2 0.05
22 13 0.32
23 4 0.10
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.73
Consensus pattern (20 bp):
TTATTTTAGTATTTTTATTA
Found at i:536641 original size:22 final size:20
Alignment explanation
Indices: 536614--536653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
536604 ACTAACTTTT
*
536614 ATTTATCTTTGTTATATATTGC
1 ATTTAT-TTTATTAT-TATTGC
536636 ATTTATTTTATTATTATT
1 ATTTATTTTATTATTATT
536654 ATATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (20 bp):
ATTTATTTTATTATTATTGC
Found at i:536683 original size:18 final size:17
Alignment explanation
Indices: 536646--536697 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
536636 ATTTATTTTA
* *
536646 TTATTATTATATTAATAT
1 TTATTTTTAT-TTTATAT
* *
536664 TTTTTTCTTTTTTTATAT
1 TTATTT-TTATTTTATAT
536682 TTATTTTTATTTTATA
1 TTATTTTTATTTTATA
536698 ATCTGACAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 9 0.33
18 15 0.56
19 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTATTTTATAT
Found at i:537390 original size:64 final size:66
Alignment explanation
Indices: 537230--537390 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 66
537220 GAATAAATTG
* ** *
537230 AACATCGAATGCAGTTTATGCATCGATGCAC-TCACCATGCATCGATGCACTCAGATTTTAATGA
1 AACATCGAATGCATTTTATGCATCGATGCACATCACCATGCATCGATGCACTCAGAGCTTAATCA
537294 A
66 A
* *
537295 AACATCGAATGCATTTTATGCATCGATGCACAT-ACCATGCATCGATGCACTTAG-GCTTATTCA
1 AACATCGAATGCATTTTATGCATCGATGCACATCACCATGCATCGATGCACTCAGAGCTTAATCA
537358 A
66 A
*
537359 AACATCGAATTCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
537391 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
64 37 0.42
65 50 0.57
66 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACATCACCATGCATCGATGCACTCAGAGCTTAATCA
A
Found at i:537405 original size:64 final size:63
Alignment explanation
Indices: 537230--537409 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
537220 GAATAAATTG
* * ** *
537230 AACATCGAATGCAGTTTATGCATCGATGCACTCACCATGCATCGATGCACTCAGATTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCA--CACTATGCATCGATGCACTCAGAGCTTAATCAA
* * *
537295 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTTAG-GCTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCAC--ACTATGCATCGATGCACTCAGAGCTTAATCAA
* *
537359 AACATCGAATTCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TA-TGCATCGATGCACT
537410 AAGTGTTCCA
Statistics
Matches: 102, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 49 0.48
65 49 0.48
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTATGCATCGATGCACTCAGAGCTTAATCAA
Found at i:539157 original size:15 final size:15
Alignment explanation
Indices: 539137--539175 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
539127 CAACATGGAG
539137 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
539152 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
539167 CGATGAAGA
1 CGATGAAGA
539176 GGAACAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (15 bp):
CGATGAAGAAGGTTC
Found at i:543251 original size:23 final size:21
Alignment explanation
Indices: 543198--543252 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
543188 ATGCATCCCT
*
543198 TTGAATGTGCATCGATACACC
1 TTGAATGTGCACCGATACACC
* * *
543219 ATGAAGGTGCACCGATGCACTCC
1 TTGAATGTGCACCGAT--ACACC
543242 TTGAATGTGCA
1 TTGAATGTGCA
543253 TCAATGCATC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 13 0.50
23 13 0.50
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (21 bp):
TTGAATGTGCACCGATACACC
Found at i:543259 original size:23 final size:23
Alignment explanation
Indices: 543180--543260 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
543170 ACACTTAACA
543180 GTGCATCAATGCA-TCCCTTTGAAT
1 GTGCATCAATGCACT-CC-TTGAAT
* * * *
543204 GTGCATCGAT--ACACCATGAAG
1 GTGCATCAATGCACTCCTTGAAT
* *
543225 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCAATGCACTCCTTGAAT
543248 GTGCATCAATGCA
1 GTGCATCAATGCA
543261 TCCGTCGGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
21 13 0.30
22 3 0.07
23 19 0.43
24 9 0.20
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (23 bp):
GTGCATCAATGCACTCCTTGAAT
Found at i:545993 original size:19 final size:19
Alignment explanation
Indices: 545969--546031 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
545959 TTATACATCA
545969 ATGCACACTTAGTGCACCG
1 ATGCACACTTAGTGCACCG
545988 ATGCACACTTAGTGCACCG
1 ATGCACACTTAGTGCACCG
* *
546007 ATGCATACTTAGTGCACCA
1 ATGCACACTTAGTGCACCG
546026 ATGCAC
1 ATGCAC
546032 TAAGTGTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (19 bp):
ATGCACACTTAGTGCACCG
Found at i:547477 original size:16 final size:17
Alignment explanation
Indices: 547451--547484 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
547441 GGTAGGAATA
547451 ATAAGCATGTGGGGTAG
1 ATAAGCATGTGGGGTAG
547468 ATAA-CATGTGGGGTAG
1 ATAAGCATGTGGGGTAG
547484 A
1 A
547485 ACTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.32, C:0.06, G:0.38, T:0.24
Consensus pattern (17 bp):
ATAAGCATGTGGGGTAG
Found at i:550649 original size:124 final size:122
Alignment explanation
Indices: 550358--551063 Score: 891
Period size: 124 Copynumber: 5.8 Consensus size: 122
550348 TTACACAAGC
* * * *
550358 TTGGATTTTAACTTCACGACGAAGGATATGCAATTTAAGGCTCAACTTCACAACGAATGGGCCAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * * * * *
550423 CCACGATTTCAATTTCACGATGAAGGATATCGTGCCAAC-AGC-ATATAACTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCAACATTACTTTAAA
*
550478 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAA-GGGACCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGG-CCA
* ** *
550542 TCCACTATTTCAACTTCACGGTGAAGGATATCGTGCCCATTAGCAACATTCATCTTTAAA
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCAACATT-A-CTTTAAA
* * **
550602 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTTAACTTCACAACGAATGGGAGAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * *
550667 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAA-TTTAC-TCAAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCAACATTACTTTAA-A
* * * * *
550723 TTGGATTTTAACTTCACAATGAAGGATATCCAATT------TTAACTTCACAACGAATGGGCCAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* *
550782 CCACGATTTCAACTTCACGACGAAGGATATCGTG-CCAGTAGCATACA--ACTTTATA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCA-ACATTACTTTAAA
* *
550837 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATAGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * * *
550902 CCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAATATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCAACATT-A-CTTTAAA
* * **
550961 TTGGATTTTAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGTTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
*
551026 CCACAATTTCAACTTCACGACGAAGGATATCGTGCCCA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
551064 ATAGATCGAC
Statistics
Matches: 510, Mismatches: 55, Indels: 38
0.85 0.09 0.06
Matches are distributed among these distances:
114 41 0.08
115 58 0.11
119 3 0.01
120 149 0.29
121 45 0.09
122 4 0.01
123 4 0.01
124 203 0.40
125 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (122 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACTAGCAACATTACTTTAAA
Found at i:551060 original size:359 final size:362
Alignment explanation
Indices: 550338--551063 Score: 1127
Period size: 359 Copynumber: 2.0 Consensus size: 362
550328 TGGACTCGAA
* * *
550338 ACAATGCAATTTACACAAGCTTGGATTTTAACTTCACGACGAAGGATATGCAATTTAAGGCTCAA
1 ACAATGCAATTTACACAAGATTGGATTTTAACTTCACAACGAAGGATATCCAATTT-A---TCAA
* *
550403 CTTCACAACGAATGGGCCACCCACGATTTCAATTTCACGATGAAGGATATCGTGCCAACAGCATA
62 CTTCACAACGAATGGGCCACCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAGCATA
*
550468 TAACTTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACG
127 CAACTTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACG
* * * **
550533 AAGGGACCATCCACTATTTCAACTTCACGGTGAAGGATATCGTGCCCATTAGCAACATTCATCTT
192 AAAGGACCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTT
* *
550598 TAAATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTTAACTTCACAACGAATGGG
257 TAAATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGG
* *
550663 AGATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCC
322 ACATCCACAATTTCAACTTCACGACGAAGGATATCGTGCCC
* *
550704 ACAA-GCAATTTACTCAAGATTGGATTTTAACTTCACAATGAAGGATATCCAATTT-T-AACTTC
1 ACAATGCAATTTACACAAGATTGGATTTTAACTTCACAACGAAGGATATCCAATTTATCAACTTC
**
550766 ACAACGAATGGGCCACCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAGTAGCATACAAC
66 ACAACGAATGGGCCACCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAGCATACAAC
* * *
550831 TTTATATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATA
131 TTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAA-A
* *
550896 GG-CCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAATATTCATCTTTAG
195 GGACCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAA
* * **
550960 ATTGGATTTTAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGTTCA
260 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGACA
551025 TCCACAATTTCAACTTCACGACGAAGGATATCGTGCCC
325 TCCACAATTTCAACTTCACGACGAAGGATATCGTGCCC
551063 A
1 A
551064 ATAGATCGAC
Statistics
Matches: 331, Mismatches: 28, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
359 278 0.84
360 3 0.01
365 46 0.14
366 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (362 bp):
ACAATGCAATTTACACAAGATTGGATTTTAACTTCACAACGAAGGATATCCAATTTATCAACTTC
ACAACGAATGGGCCACCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAGCATACAAC
TTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAG
GACCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAAA
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGACAT
CCACAATTTCAACTTCACGACGAAGGATATCGTGCCC
Found at i:552095 original size:3 final size:3
Alignment explanation
Indices: 552087--552142 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
552077 TTAAAAAATA
* *
552087 TAT TAT TAT TAT AAT AAT TATT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT
552134 TAT TAT TAT
1 TAT TAT TAT
552143 ATTTGTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:554442 original size:21 final size:21
Alignment explanation
Indices: 554417--554456 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
554407 AAGACTCTAT
554417 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
554438 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
554457 AAACAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:563460 original size:2 final size:2
Alignment explanation
Indices: 563453--563483 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
563443 AATTCATTGT
563453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563484 TTATGATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:564521 original size:34 final size:30
Alignment explanation
Indices: 564483--564551 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
564473 TTGATATAAC
564483 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
564517 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
564546 AATTTA
1 AATTTA
564552 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:564562 original size:29 final size:30
Alignment explanation
Indices: 564492--564551 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
564482 CAATTTAAGG
564492 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
564523 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
564552 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:564659 original size:22 final size:22
Alignment explanation
Indices: 564631--564689 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
564621 AGGGTGTCAA
*
564631 AGTGCATCCATGCACCCCCTGT
1 AGTGCATCCATGCACCCCCTGC
*
564653 AGTGCATCCATGCA-TCCCTGC
1 AGTGCATCCATGCACCCCCTGC
*
564674 AGTGCATCTATGCACC
1 AGTGCATCCATGCACC
564690 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (22 bp):
AGTGCATCCATGCACCCCCTGC
Found at i:564720 original size:20 final size:20
Alignment explanation
Indices: 564695--564824 Score: 64
Period size: 20 Copynumber: 6.8 Consensus size: 20
564685 GCACCTGCAC
564695 TAGTGCATCGATGCATCATA
1 TAGTGCATCGATGCATCATA
*
564715 TAGTGCATCCATGCACTCA-A
1 TAGTGCATCGATGCA-TCATA
*
564735 -A---CACCGAATGCA--AT-
1 TAGTGCATCG-ATGCATCATA
*
564749 TAGTGCATCGATGCATCCT-
1 TAGTGCATCGATGCATCATA
*
564768 TCTGTGCATCGATGCATCA-A
1 T-AGTGCATCGATGCATCATA
* * *
564788 GGTTGTGCATCCATGCATCATG
1 --TAGTGCATCGATGCATCATA
* *
564810 TTGTGCATCCATGCA
1 TAGTGCATCGATGCA
564825 CGAAGGCTGC
Statistics
Matches: 87, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
14 1 0.01
15 1 0.01
16 3 0.03
17 10 0.11
18 4 0.05
19 3 0.03
20 45 0.52
21 19 0.22
22 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
TAGTGCATCGATGCATCATA
Found at i:564796 original size:21 final size:20
Alignment explanation
Indices: 564770--564824 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
564760 TGCATCCTTC
*
564770 TGTGCATCGATGCATCAAGGT
1 TGTGCATCCATGCATC-AGGT
*
564791 TGTGCATCCATGCATCATGT
1 TGTGCATCCATGCATCAGGT
564811 TGTGCATCCATGCA
1 TGTGCATCCATGCA
564825 CGAAGGCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
TGTGCATCCATGCATCAGGT
Found at i:565297 original size:34 final size:30
Alignment explanation
Indices: 565259--565327 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
565249 TTGATATAAC
565259 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
565293 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
565322 AATTTA
1 AATTTA
565328 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Done.