Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009189.1 Hibiscus syriacus cultivar Beakdansim tig00112762_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: 966119
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:352470 original size:47 final size:47
Alignment explanation
Indices: 352418--352512 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
352408 AGAGAGATAC
352418 AAAGTAATGATTTTAAGAACCAAACCAAAGGGGATGAAGATGAAACA
1 AAAGTAATGATTTTAAGAACCAAACCAAAGGGGATGAAGATGAAACA
352465 AAAGTAATGATTTTAAGAACCAAACCAAAGGGGATGAAGATGAAACA
1 AAAGTAATGATTTTAAGAACCAAACCAAAGGGGATGAAGATGAAACA
352512 A
1 A
352513 TTCAAAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.17
Consensus pattern (47 bp):
AAAGTAATGATTTTAAGAACCAAACCAAAGGGGATGAAGATGAAACA
Found at i:352494 original size:26 final size:26
Alignment explanation
Indices: 352417--352494 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
352407 TAGAGAGATA
352417 CAAAGTAATGATTTTAAGAACCAAAC
1 CAAAGTAATGATTTTAAGAACCAAAC
** * **
352443 CAAAG--GGGA--TGAAG-ATGAAAC
1 CAAAGTAATGATTTTAAGAACCAAAC
*
352464 AAAAGTAATGATTTTAAGAACCAAAC
1 CAAAGTAATGATTTTAAGAACCAAAC
352490 CAAAG
1 CAAAG
352495 GGGATGAAGA
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
21 9 0.26
22 4 0.11
23 2 0.06
24 2 0.06
25 4 0.11
26 14 0.40
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (26 bp):
CAAAGTAATGATTTTAAGAACCAAAC
Found at i:353788 original size:23 final size:23
Alignment explanation
Indices: 353758--353808 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
353748 TTCTATAATA
353758 GAATTCAATTATCTTGTTGGATG
1 GAATTCAATTATCTTGTTGGATG
353781 GAATTCAATTATCTTGTTGGATG
1 GAATTCAATTATCTTGTTGGATG
353804 GAATT
1 GAATT
353809 GAAATTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
GAATTCAATTATCTTGTTGGATG
Found at i:354571 original size:18 final size:18
Alignment explanation
Indices: 354534--354584 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
354524 TATGGAATTG
* *
354534 GATTTCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
354551 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
354569 GATTCCAATTCCTTCA
1 GATTCCAATTCCTTCA
354585 TAAACATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:363813 original size:8 final size:8
Alignment explanation
Indices: 363797--363858 Score: 70
Period size: 8 Copynumber: 7.8 Consensus size: 8
363787 TTGATAGAGT
363797 ATACATAC
1 ATACATAC
*
363805 ATGCATAC
1 ATACATAC
*
363813 ATGCATAC
1 ATACATAC
*
363821 ATGCATAC
1 ATACATAC
*
363829 ATGCATAC
1 ATACATAC
*
363837 ATGCATAC
1 ATACATAC
*
363845 ATGCATAC
1 ATACATAC
363853 ATACAT
1 ATACAT
363859 CTTTTTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 52 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (8 bp):
ATACATAC
Found at i:363893 original size:4 final size:4
Alignment explanation
Indices: 363884--364173 Score: 580
Period size: 4 Copynumber: 72.5 Consensus size: 4
363874 AATTTTTGTA
363884 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
363932 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
363980 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
364028 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
364076 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
364124 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
364172 AT
1 AT
364174 CTTTTTTCAG
Statistics
Matches: 286, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 286 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:366994 original size:37 final size:37
Alignment explanation
Indices: 366940--367022 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
366930 GGTAACCAAC
366940 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATG-TTT
* *
366977 TTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
367013 GTTGAAAAAT
1 TTTGAAAAAT
367023 GATAATGGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 12 0.29
37 29 0.69
38 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:371495 original size:37 final size:39
Alignment explanation
Indices: 371442--371515 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
371432 GGTAACCAAC
*
371442 TTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTTT
1 TTTGAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTTTT
*
371480 TTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
371516 GTTGAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 6 0.18
38 27 0.82
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (39 bp):
TTTGAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTTTT
Found at i:373542 original size:16 final size:16
Alignment explanation
Indices: 373521--373552 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
373511 TTTGTTAATA
373521 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
373537 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
373553 TAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:376291 original size:21 final size:21
Alignment explanation
Indices: 376265--376342 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
376255 GGGAGCGTCA
376265 GTGCATCGATGCATACCCATG
1 GTGCATCGATGCATACCCATG
*
376286 GTGCATCGGTGCATACCCATG
1 GTGCATCGATGCATACCCATG
**
376307 GTGCATCGATGCATAAGCATG
1 GTGCATCGATGCATACCCATG
*
376328 GTGCATCGGTGCATA
1 GTGCATCGATGCATA
376343 AGTGTAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCATACCCATG
Found at i:376446 original size:63 final size:63
Alignment explanation
Indices: 376379--376554 Score: 162
Period size: 65 Copynumber: 2.7 Consensus size: 63
376369 TTGGACCCTT
*
376379 AGTGCATCGGTGCA-CTAAGAGTGCATCGATGCATCAAGTGCATTC-ATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
376440 AG
62 AC
* * * *
376442 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
* ** *
376507 AGTGCATCGGTGCATGGTATATGCATCGATGCATGAAATGCATTCGAT
1 AGTGCATCGGTGCA-GCT-GGTGCATCGATGCATCAAATGCATTCGAT
376555 TTCAATTTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
63 36 0.39
64 6 0.06
65 46 0.49
66 5 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
Found at i:376521 original size:65 final size:64
Alignment explanation
Indices: 376399--376606 Score: 183
Period size: 65 Copynumber: 3.2 Consensus size: 64
376389 TGCACTAAGA
* *
376399 GTGCATCGATGCATCAAGTGCATTC-ATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-G
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGG-TAG
* * * *
376462 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGTA
*
376526 T
64 G
* * ** ** ** *
376527 ATGCATCGATGCATGAAATGCATTCGA--TTTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-AGCCACAGTGCATCGATGCATGG-TA
376590 G
64 G
*
376591 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
376607 CTCTAAAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
61 1 0.01
62 5 0.04
63 41 0.35
64 18 0.16
65 48 0.41
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAG
Found at i:376878 original size:3 final size:3
Alignment explanation
Indices: 376872--376974 Score: 113
Period size: 3 Copynumber: 34.7 Consensus size: 3
376862 TTTTTATCCA
* * ** *
376872 TAT TAT TAT TAT AAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
376920 TAT CAT TAT TA- TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
376964 TAAT TA- TAT TA
1 T-AT TAT TAT TA
376975 AATATATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 6 0.07
3 71 0.86
4 6 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:376917 original size:9 final size:9
Alignment explanation
Indices: 376872--376986 Score: 78
Period size: 9 Copynumber: 12.9 Consensus size: 9
376862 TTTTTATCCA
*
376872 TATTATTAT
1 TATTAATAT
*
376881 TATAAATAT
1 TATTAATAT
*
376890 TATTATTAT
1 TATTAATAT
** *
376899 CCTTATTAT
1 TATTAATAT
376908 TATTAATAT
1 TATTAATAT
376917 TATT-ATCAT
1 TATTAAT-AT
376926 TATT-ATAT
1 TATTAATAT
*
376934 TATTATTAT
1 TATTAATAT
*
376943 TA-TATTAT
1 TATTAATAT
*
376951 TATTTATTAT
1 TA-TTAATAT
376961 TATTAAT-T
1 TATTAATAT
376969 ATATTAA-AT
1 -TATTAATAT
376978 ATATTAATA
1 -TATTAATA
376987 CATAATAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
8 17 0.19
9 62 0.70
10 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTAATAT
Found at i:377469 original size:13 final size:13
Alignment explanation
Indices: 377451--377475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377441 AGGAAACAGA
377451 AAAAAACAGAGAG
1 AAAAAACAGAGAG
377464 AAAAAACAGAGA
1 AAAAAACAGAGA
377476 ACGGAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAACAGAGAG
Found at i:377492 original size:25 final size:25
Alignment explanation
Indices: 377464--377516 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
377454 AAACAGAGAG
* *
377464 AAAAAACAGAGA-ACGGAAAAGAAA
1 AAAAAACAAAGACACAGAAAAGAAA
*
377488 AAAAAACAAATACACAGAAAAGAAA
1 AAAAAACAAAGACACAGAAAAGAAA
377513 AAAA
1 AAAA
377517 TACTAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.02
Consensus pattern (25 bp):
AAAAAACAAAGACACAGAAAAGAAA
Found at i:378489 original size:23 final size:22
Alignment explanation
Indices: 378455--378533 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
378445 AACCGATGGA
378455 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-G
* * *
378478 TGCATCGGTGCACCTTC-ATGG
1 TGCATCGATGCACATTCAAGGG
* *
378499 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGG
378521 TGCATCGATGCAC
1 TGCATCGATGCAC
378534 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.33
22 16 0.35
23 15 0.33
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGG
Found at i:378549 original size:20 final size:21
Alignment explanation
Indices: 378458--378552 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
378448 CGATGGATGC
*
378458 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
378481 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
378502 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
378524 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
378544 ATCGATGCA
1 ATCGATGCA
378553 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:383881 original size:65 final size:64
Alignment explanation
Indices: 383748--383903 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
383738 TGCACTAAGA
* * * *
383748 GTGCATCGATGCATCAAGTGCATTCAATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
383812 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
383875 AT
64 -G
* *
383877 GTGCACCGATGCATGAAATGCATTCGA
1 GTGCATCGATGCATCAAATGCATTCGA
383904 CGTTCAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 27 0.35
65 47 0.61
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:385439 original size:16 final size:16
Alignment explanation
Indices: 385418--385449 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
385408 TTGATATTTA
385418 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
*
385434 ATGATTTGGTAATGAT
1 ATGATTTAGTAATGAT
385450 TACTAATAAT
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:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:385456 original size:26 final size:26
Alignment explanation
Indices: 385400--385456 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
385390 TATTAATAAT
*
385400 CTAATGATTTGATATTTAATGATTTA
1 CTAATGATATGATATTTAATGATTTA
*
385426 GTAATGATATGAT-TTGGTAATGA-TTA
1 CTAATGATATGATATT--TAATGATTTA
385452 CTAAT
1 CTAAT
385457 AATTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 18 0.69
27 6 0.23
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.46
Consensus pattern (26 bp):
CTAATGATATGATATTTAATGATTTA
Found at i:386311 original size:11 final size:11
Alignment explanation
Indices: 386287--386334 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
386277 AAGGCCCTTA
* *
386287 TTCTTCTTCTT
1 TTCTTCTCCCT
386298 TTCTTCTCCCT
1 TTCTTCTCCCT
386309 TTCCTT-T-CCT
1 TT-CTTCTCCCT
386319 TTCTTCTCCCT
1 TTCTTCTCCCT
386330 TTCTT
1 TTCTT
386335 TCTTTTCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 3 0.09
10 6 0.19
11 20 0.62
12 3 0.09
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TTCTTCTCCCT
Found at i:386322 original size:21 final size:20
Alignment explanation
Indices: 386297--386341 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
386287 TTCTTCTTCT
386297 TTTCTTCTCCCTTTCCTTTCC
1 TTTCTTCTCCCTTT-CTTTCC
*
386318 TTTCTTCTCCCTTTCTTTCT
1 TTTCTTCTCCCTTTCTTTCC
386338 TTTC
1 TTTC
386342 CCTATCTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTCTTCTCCCTTTCTTTCC
Found at i:386337 original size:15 final size:15
Alignment explanation
Indices: 386311--386355 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
386301 TTCTCCCTTT
386311 CCTTTCCTTTCTTCTC
1 CCTTT-CTTTCTTCTC
*
386327 CCTTTCTTTCTTTTC
1 CCTTTCTTTCTTCTC
*
386342 CCTATCTTTCTTCT
1 CCTTTCTTTCTTCT
386356 TACAATCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (15 bp):
CCTTTCTTTCTTCTC
Found at i:386701 original size:28 final size:27
Alignment explanation
Indices: 386630--386713 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
386620 GTGAAGGCTT
* *
386630 GGTCGCCGGGCGTGCATGGCAACCTAACA
1 GGTCG-CGGACGTGCATGGCGACCT-ACA
*
386659 TGTCGTC-GAGCGTGCATGGCGACCTACA
1 GGTCG-CGGA-CGTGCATGGCGACCTACA
*
386687 GGTCGCAGGACGTGCTTGGCGACCTAC
1 GGTCGC-GGACGTGCATGGCGACCTAC
386714 CCCTACGTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 24 0.52
29 21 0.46
ACGTcount: A:0.18, C:0.30, G:0.35, T:0.18
Consensus pattern (27 bp):
GGTCGCGGACGTGCATGGCGACCTACA
Found at i:387343 original size:22 final size:23
Alignment explanation
Indices: 387318--387366 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
387308 CTTAGGATCC
387318 TAATATATAATTTA-T-TTATATT
1 TAATATATAATTTACTATTAT-TT
*
387340 TAATTTATAATTTACTATTATTT
1 TAATATATAATTTACTATTATTT
387363 TAAT
1 TAAT
387367 TAGTTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 7 0.29
24 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATATATAATTTACTATTATTT
Found at i:388295 original size:17 final size:18
Alignment explanation
Indices: 388262--388295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
388252 CCGTTATTAG
388262 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
388280 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
388296 GATCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:388626 original size:14 final size:14
Alignment explanation
Indices: 388607--388634 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
388597 AAGTGAAAAA
388607 ATAGTTATATAATT
1 ATAGTTATATAATT
388621 ATAGTTATATAATT
1 ATAGTTATATAATT
388635 TTGTTATGAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:389778 original size:7 final size:7
Alignment explanation
Indices: 389762--389793 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
389752 GACTAAACAG
389762 ACAT-GA
1 ACATAGA
389768 ACATAGA
1 ACATAGA
389775 ACATAGA
1 ACATAGA
389782 ACATAGA
1 ACATAGA
389789 ACATA
1 ACATA
389794 TTATATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (7 bp):
ACATAGA
Found at i:393285 original size:29 final size:29
Alignment explanation
Indices: 393243--393330 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
393233 ATTTTCACCT
393243 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
* *
393272 AACTAAATAGATGTAGGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
393301 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
393330 A
1 A
393331 TTAATTTAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:396873 original size:29 final size:29
Alignment explanation
Indices: 396831--396889 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
396821 ATTTTCACCT
396831 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
396860 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
396889 A
1 A
396890 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:398117 original size:15 final size:15
Alignment explanation
Indices: 398099--398133 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
398089 TTGATGCAAT
398099 ACTGCTTGATTACCA
1 ACTGCTTGATTACCA
398114 ACTGCTTGATTACCA
1 ACTGCTTGATTACCA
398129 ACTGC
1 ACTGC
398134 GTATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (15 bp):
ACTGCTTGATTACCA
Found at i:399295 original size:109 final size:109
Alignment explanation
Indices: 399102--399468 Score: 386
Period size: 110 Copynumber: 3.3 Consensus size: 109
399092 TCATTTTCTT
* * * * * * * *
399102 GTACAATAATAATTTTAAATGATAGAGAATCTTATCTATTCACTTCTTTTTCTTTTCAATGATAC
1 GTACAATAATAATTTCAAATGACAAAGAATCATAACTATTCACATCCTTTT-TTTTCAATGATAT
* *
399167 ATCACC-CTGAATCAA-AACTTC-T-TTCAAATGAAAAATCTTATCA-G
65 ATCACCTC-AAAT-AAGAACTTCATATT-AAATGAAAAATATTAT-ATG
* * *
399211 GTACAATAATAATTTCAAATGACAAAGAATCATAACTATTCACGTCCTTTTGTTTTCAGTGATGT
1 GTACAATAATAATTTCAAATGACAAAGAATCATAACTATTCACATCCTTTT-TTTTCAATGATAT
399276 ATCACCTCAAATAAGAACTTTCATATTAAATGAAAAATATTATATG
65 ATCACCTCAAATAAGAAC-TTCATATTAAATGAAAAATATTATATG
* * * * * *
399322 GTACAATAATAATTTCAAGTGATAGAA-AATCATAATTATTCATATTCTTTTCTTTCAATGATAT
1 GTACAATAATAATTTCAAATGACA-AAGAATCATAACTATTCACATCCTTTTTTTTCAATGATAT
* * * *
399386 ATCACCTCAAATCAGAATTTTCATATTGAATGAGAAATATTATATG
65 ATCACCTCAAATAAGAA-CTTCATATTAAATGAAAAATATTATATG
* *
399432 GTACAACAATAATTTCAAATGACAAAGAATCTTAACT
1 GTACAATAATAATTTCAAATGACAAAGAATCATAACT
399469 GTTGAGTTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
108 2 0.01
109 68 0.31
110 85 0.39
111 59 0.27
112 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (109 bp):
GTACAATAATAATTTCAAATGACAAAGAATCATAACTATTCACATCCTTTTTTTTCAATGATATA
TCACCTCAAATAAGAACTTCATATTAAATGAAAAATATTATATG
Found at i:400683 original size:114 final size:111
Alignment explanation
Indices: 400529--400776 Score: 290
Period size: 113 Copynumber: 2.2 Consensus size: 111
400519 ATTCACATCC
* * * *
400529 TTTTTTTCAGTGATACAT-AACTTAAATCATAACTTCTTTCATATTAAATG-AAAATCTTATC-T
1 TTTTTTTCAGTGATATATCACCTTAAATAAGAACTTCTTTCATATTAAATGAAAAATCTTA-CAT
*
400591 AGTATAATAATAA-TTTCAAATGATATAGAA-TCATAACTATTAACGTTCTT
65 AGTATAATAA-AATTTTCAAAT--TA-A-AACTCATAACTATTAACGTCCTT
* *
400641 TTTTTTTCTAGTGATATATCACCTTAAGTAAGAACTTCTTTCATATTGAATGAAAAATCTTACAT
1 TTTTTTTC-AGTGATATATCACCTTAAATAAGAACTTCTTTCATATTAAATGAAAAATCTTACAT
* * *
400706 GGTATAATAAAATTTTCAAATTAAAACTTCATAACTATTCATGTCCTT
65 AGTATAATAAAATTTTCAAATTAAAAC-TCATAACTATTAACGTCCTT
*
400754 TTCTTTTCAGTGATATATCACCT
1 TTTTTTTCAGTGATATATCACCT
400777 CAAAACAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
111 2 0.02
112 24 0.20
113 35 0.30
114 30 0.25
115 27 0.23
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.42
Consensus pattern (111 bp):
TTTTTTTCAGTGATATATCACCTTAAATAAGAACTTCTTTCATATTAAATGAAAAATCTTACATA
GTATAATAAAATTTTCAAATTAAAACTCATAACTATTAACGTCCTT
Found at i:401596 original size:5 final size:5
Alignment explanation
Indices: 401535--401567 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
401525 TATTTGTATG
401535 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
1 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
401568 GTAATGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TGTAA
Found at i:403109 original size:21 final size:21
Alignment explanation
Indices: 403063--403110 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
403053 TTAAATATTT
* * *
403063 TTTAAAAAATAAATTATTTTA
1 TTTAAAAAAAAAATTAATGTA
*
403084 ATTAAAAAAAAAATTAATGTA
1 TTTAAAAAAAAAATTAATGTA
403105 TTTAAA
1 TTTAAA
403111 TAGAACTCGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAAAAATTAATGTA
Found at i:406760 original size:2 final size:2
Alignment explanation
Indices: 406755--406784 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
406745 TTTTAATCAT
406755 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
406785 ACGATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:410201 original size:20 final size:20
Alignment explanation
Indices: 410176--410217 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
410166 ATTTCATCTT
410176 TTCTTCCTCCTTTCTCCATC
1 TTCTTCCTCCTTTCTCCATC
*
410196 TTCTTCCTCCTTTCTTCATC
1 TTCTTCCTCCTTTCTCCATC
410216 TT
1 TT
410218 TGATAGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (20 bp):
TTCTTCCTCCTTTCTCCATC
Found at i:423992 original size:31 final size:28
Alignment explanation
Indices: 423940--424024 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
423930 CTTACTTAAG
423940 TACCTAAAATATTTTTTGTCAAAATAAC
1 TACCTAAAATATTTTTTGTCAAAATAAC
* **
423968 TACCTAAAGTAATCTTTTTGGTCAAAATAGG
1 TACCTAAAAT-AT-TTTTT-GTCAAAATAAC
* * * *
423999 TACATATAATATTTTATGTTAAAATA
1 TACCTAAAATATTTTTTGTCAAAATA
424025 GATACATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 17 0.37
29 6 0.13
30 7 0.15
31 16 0.35
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (28 bp):
TACCTAAAATATTTTTTGTCAAAATAAC
Found at i:424400 original size:15 final size:15
Alignment explanation
Indices: 424382--424432 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
424372 TCTGGAAAAA
424382 TGAATTACTGAAATT
1 TGAATTACTGAAATT
424397 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
424412 TGAATTACTGGAATT
1 TGAATTACTGAAATT
424427 TGAATT
1 TGAATT
424433 CTGGAAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:424444 original size:14 final size:15
Alignment explanation
Indices: 424363--424447 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
424353 GTTTGGCTGT
* *
424363 AATTGATTTTCTGGAA
1 AATTGAATTACTGG-A
*
424379 AAATGAATTACT-GA
1 AATTGAATTACTGGA
424393 AATTTGAATTACT-GA
1 AA-TTGAATTACTGGA
424408 AATTTGAATTACTGGA
1 AA-TTGAATTACTGGA
*
424424 ATTTGAATT-CTGGA
1 AATTGAATTACTGGA
*
424438 AAATGAATTA
1 AATTGAATTA
424448 AATTTATGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
14 15 0.25
15 32 0.54
16 12 0.20
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (15 bp):
AATTGAATTACTGGA
Found at i:424479 original size:14 final size:14
Alignment explanation
Indices: 424457--424490 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
424447 AAATTTATGG
*
424457 AAAACGTTTTCCGA
1 AAAATGTTTTCCGA
*
424471 AAAATGTTTTCCGT
1 AAAATGTTTTCCGA
424485 AAAATG
1 AAAATG
424491 AATTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Found at i:426296 original size:3 final size:3
Alignment explanation
Indices: 426288--426319 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
426278 GAATAGGGTT
426288 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
426320 ATTACAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:426575 original size:19 final size:19
Alignment explanation
Indices: 426551--426621 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
426541 GTAAATATCT
*
426551 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
426570 TTATTAGATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
426589 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
426609 TTATTAAATATAT
1 TTATTAAA-ATAT
426622 AAAAAATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:426631 original size:37 final size:41
Alignment explanation
Indices: 426558--426646 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 41
426548 TCTTTATTAA
* * * *
426558 AATATTATTAGATTATTAGATTAATATTAAATATATAA-AT
1 AATATTATTACATTATTAGAATAATATAAAAAATATAATAT
426598 AATATTATT-CATTATTA-AAT-ATATAAAAAATATAATAT
1 AATATTATTACATTATTAGAATAATATAAAAAATATAATAT
*
426636 AAATTTTATTA
1 -AATATTATTA
426647 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
37 13 0.32
38 4 0.10
39 15 0.37
40 9 0.22
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
AATATTATTACATTATTAGAATAATATAAAAAATATAATAT
Found at i:426680 original size:28 final size:28
Alignment explanation
Indices: 426581--426680 Score: 73
Period size: 28 Copynumber: 3.5 Consensus size: 28
426571 TATTAGATTA
* *
426581 ATATTAAATAT-ATAA-ATAATATTATT
1 ATATTAAATATAAAAATATAATATAATT
426607 CATTATTAAATATATAAAAAATATAATATAAATT
1 -A-TATT-AA-ATAT-AAAAATATAATAT-AATT
* *
426641 TTATTAAA-ATAAAAATATAATAT-CTT
1 ATATTAAATATAAAAATATAATATAATT
426667 ATATTATAATATAA
1 ATATTA-AATATAA
426681 TTGATTAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
26 7 0.12
27 3 0.05
28 21 0.36
29 4 0.07
30 5 0.08
31 2 0.03
32 7 0.12
33 7 0.12
34 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTAAATATAAAAATATAATATAATT
Found at i:426721 original size:19 final size:20
Alignment explanation
Indices: 426694--426734 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
426684 ATTAGTTTAT
426694 TATAGTATTAAAAATA-TAA
1 TATAGTATTAAAAATATTAA
* *
426713 TATATTATTATAAATATTAA
1 TATAGTATTAAAAATATTAA
426733 TA
1 TA
426735 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAGTATTAAAAATATTAA
Found at i:426742 original size:21 final size:20
Alignment explanation
Indices: 426699--426751 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
426689 TTTATTATAG
* *
426699 TATTAAAAATA-TAATATAT
1 TATTATAAATATTAATAAAT
426718 TATTATAAATATTAATAAAT
1 TATTATAAATATTAATAAAT
*
426738 ATATTTTAAATATT
1 -TATTATAAATATT
426752 TTAATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
21 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATAAATATTAATAAAT
Found at i:426755 original size:23 final size:23
Alignment explanation
Indices: 426706--426768 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 23
426696 TAGTATTAAA
426706 AATATAATATATTATTATAAATATT
1 AATA-AATATATT-TTATAAATATT
*
426731 AATAAATATATTTTA-AATATTTT
1 AATAAATATATTTTATAA-ATATT
*
426754 AATAATTAATATTTT
1 AATAAAT-ATATTTT
426769 GATGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 2 0.06
23 13 0.38
24 15 0.44
25 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAAATATATTTTATAAATATT
Found at i:427015 original size:42 final size:42
Alignment explanation
Indices: 426959--427053 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
426949 TTCCTCCAAC
* * * *
426959 CAAACACTGGAAAACATTTTCTGGAAAATGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
427001 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
427043 CAAACACGGGA
1 CAAACACGGGA
427054 TTCCGGGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
Found at i:441845 original size:23 final size:23
Alignment explanation
Indices: 441819--441865 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
441809 TGCCACAAAG
*
441819 GCAGAGATAAACGTGCAATACAT
1 GCAGAGATAAACGTGCAACACAT
441842 GCAGAGATAAACGTGCAACACAT
1 GCAGAGATAAACGTGCAACACAT
441865 G
1 G
441866 TTGGAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (23 bp):
GCAGAGATAAACGTGCAACACAT
Found at i:443036 original size:22 final size:23
Alignment explanation
Indices: 443008--443051 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
442998 TTTCTGTTTG
443008 GGTGTTA-TTTGTGTAAA-ATTTA
1 GGTGTTAGTTTG-GTAAATATTTA
443030 GGTGTTAGTTTGGTAAATATTT
1 GGTGTTAGTTTGGTAAATATTT
443052 GTAGAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (23 bp):
GGTGTTAGTTTGGTAAATATTTA
Found at i:447002 original size:22 final size:22
Alignment explanation
Indices: 446949--447002 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
446939 ATTCAACTGT
* *
446949 TATAACTCCTAAAATTATATTA
1 TATAACTCCTAAAATTAAATCA
* *
446971 TGTAATTCCTAAAATTAAATCA
1 TATAACTCCTAAAATTAAATCA
446993 TATAACTCCT
1 TATAACTCCT
447003 GTAACTCCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.39
Consensus pattern (22 bp):
TATAACTCCTAAAATTAAATCA
Found at i:447342 original size:12 final size:13
Alignment explanation
Indices: 447325--447353 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
447315 TATTCTTATT
447325 AAAAAACAAA-AG
1 AAAAAACAAAGAG
447337 AAAAAACAAAGAG
1 AAAAAACAAAGAG
447350 AAAA
1 AAAA
447354 GAGAACCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:453811 original size:22 final size:22
Alignment explanation
Indices: 453777--453831 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
453767 ATTCAACTGT
*
453777 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
* *
453799 TGTAATTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
453821 TATAACTCCTG
1 TATAACTCCTG
453832 TAACTCCTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:454167 original size:12 final size:13
Alignment explanation
Indices: 454150--454178 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
454140 TATTCTTATT
454150 AAAAAACAAA-AG
1 AAAAAACAAAGAG
454162 AAAAAACAAAGAG
1 AAAAAACAAAGAG
454175 AAAA
1 AAAA
454179 GAGAACCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:454320 original size:18 final size:17
Alignment explanation
Indices: 454288--454321 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
454278 AACTCAAAGG
454288 AAAAGAAAAAAAGGGAA
1 AAAAGAAAAAAAGGGAA
*
454305 AAAAGACAAAAGAGGGA
1 AAAAGA-AAAAAAGGGA
454322 GAGAGCGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAGGGAA
Found at i:458911 original size:21 final size:21
Alignment explanation
Indices: 458887--458929 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
458877 AGAGAACTTC
*
458887 AACTTATAAAATTTCAGGAGA
1 AACTAATAAAATTTCAGGAGA
*
458908 AACTAATAAAATTTTAGGAGA
1 AACTAATAAAATTTCAGGAGA
458929 A
1 A
458930 CGAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (21 bp):
AACTAATAAAATTTCAGGAGA
Found at i:466912 original size:7 final size:7
Alignment explanation
Indices: 466900--466927 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
466890 ACCAGAGGGC
466900 ATGAAGA
1 ATGAAGA
466907 ATGAAGA
1 ATGAAGA
466914 ATGAAGA
1 ATGAAGA
466921 ATGAAGA
1 ATGAAGA
466928 CTGTGCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
ATGAAGA
Found at i:470547 original size:2 final size:2
Alignment explanation
Indices: 470540--470566 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
470530 GTAAGTATCG
470540 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
470567 AGTGTTTATA
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:471378 original size:112 final size:111
Alignment explanation
Indices: 470909--471384 Score: 704
Period size: 111 Copynumber: 4.3 Consensus size: 111
470899 AAAAAGTGTT
* * *
470909 GATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATA
1 GATCCTTTTTAT-AAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATA
*
470974 ATGAAATTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
65 ATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
* * * * *
471021 TATCCTTTTTATAAACGGATCGATACTTTCAACATATCAAGTAAATTTTACCGCTTTTGTCATAA
1 GATCCTTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAA
471086 TGAAACTGGGTTTT-TCATATTTTTACATGTTATATTGTAAAGTATC
66 TGAAACT-GGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
* * * *
471132 TATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCCTTTTTTTCATAA
1 GATCCTTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAA
*
471197 TGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATC
66 TGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
* * *
471243 GATCCTTTTTATAAAAATGATCGATACTTTCAACATATCAGCTAAATTTTACCATTTTTTGTCAT
1 GATCCTTTTTATAAAAGT-ATCGATACTTTCAACATATCAGGTAAATTTTACC-GTTTTTGTCAT
* * *
471308 AATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATC
64 AATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
*
471356 GATACATTTTTAT-AAAGTATCGATACTTT
1 GAT-CCTTTTTATAAAAGTATCGATACTTT
471385 ATAGGCGCTA
Statistics
Matches: 335, Mismatches: 24, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
110 6 0.02
111 199 0.59
112 60 0.18
113 62 0.19
114 8 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (111 bp):
GATCCTTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAA
TGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
Found at i:471953 original size:110 final size:110
Alignment explanation
Indices: 471788--472127 Score: 493
Period size: 110 Copynumber: 3.1 Consensus size: 110
471778 AACTTTAAAA
* * * ** * * * **
471788 AAAGTATCAATCTTTTTTATAAAAAGTATTTATACTTTTAACATATCAGGTAAATTTTATCGGTT
1 AAAGTATCTATCATTTTTAT-AAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCCTTT
* *
471853 TGTCATAATGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
*
471899 AAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCCTTTT
1 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCCTTTT
* *
471964 TTCATAATAAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 GTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
*
472009 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATC-AGATAAATTTTACCATTT
1 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAAG-TAAATTTTACC-CTT
*
472073 TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
64 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
472120 AAAGTATC
1 AAAGTATC
472128 AGGTAAATTT
Statistics
Matches: 208, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
109 2 0.01
110 134 0.64
111 72 0.35
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (110 bp):
AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCCTTTT
GTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
Found at i:472212 original size:73 final size:73
Alignment explanation
Indices: 472050--472210 Score: 236
Period size: 73 Copynumber: 2.2 Consensus size: 73
472040 TACTTTCAAC
**
472050 ATATCAGATAAATTTTACCATTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTAT
1 ATATCAGATAAATTTTACTGTTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTAT
472115 ATTGTAAA
66 ATTGTAAA
* * * *
472123 GTATCAGGTAAATTTTACTGTTTTTGTCATACTGAAACTGGTTTTGTCATATTTTTATC-TGTTA
1 ATATCAGATAAATTTTACTGTTTTTGTCATAATGAAACTGATTTTGTCATATTTTTA-CATGTTA
472187 TATTGTAAA
65 TATTGTAAA
*
472196 ATATC-GATACATTTT
1 ATATCAGATAAATTTT
472211 TATAAAGTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 8 0.10
73 69 0.88
74 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (73 bp):
ATATCAGATAAATTTTACTGTTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTAT
ATTGTAAA
Found at i:472853 original size:111 final size:111
Alignment explanation
Indices: 472658--473358 Score: 1082
Period size: 111 Copynumber: 6.3 Consensus size: 111
472648 AACTTTAAAA
* * * * *
472658 AAAATATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTCTACCGGTT
1 AAAATATCTATCATTTTTATAAAATG-ATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
472723 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
472770 AAAATATCTATCCTTTTTATAAAATGATCGATACTTTCAACATATTAGGTAAATTTTACTGTTTT
1 AAAATATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
* * *
472835 TGTCATAATAAAATTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
*
472881 AAAGTATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCG-TTT
1 AAAATATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
* *
472945 TGTCATAATGAAACTGATTTTGTCATATTTTTACCTATTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * * *
472991 AAAGTATCGATCTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTT
1 AAAATATCTATCATTTTTAT-AAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
* *
473056 TTGTCAGAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
473103 AAAATATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGTTTT
1 AAAATATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
*
473168 TGTTATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
473214 AAAGTATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTT
1 AAAATATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
*
473279 TGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
473325 AAAATATCGATACATTTTTTATAAAGT-ATCGATA
1 AAAATATCTAT-CA-TTTTTATAAAATGATCGATA
473359 TTTTATAAGC
Statistics
Matches: 539, Mismatches: 46, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
110 62 0.12
111 372 0.69
112 94 0.17
113 11 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (111 bp):
AAAATATCTATCATTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:473868 original size:23 final size:23
Alignment explanation
Indices: 473833--473898 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
473823 CCAGTAATTA
** * *
473833 ACCTATTTTATTATATAAGTGTT
1 ACCTATTACATTATATAAGCGCT
473856 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
473879 ACCAATTACATTAAATAAGC
1 ACCTATTACATTATATAAGC
473899 AGAACCTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:473947 original size:87 final size:87
Alignment explanation
Indices: 473856--474021 Score: 242
Period size: 87 Copynumber: 1.9 Consensus size: 87
473846 TATAAGTGTT
*
473856 ACCTATTACATTATATAAGCGCTACCAATTACATTAAATAAGCAGAACCTAATATGTTATTATGC
1 ACCTATTACATTATATAAGCGCTACCAATTACATTAAATAAGCAGAACCTAATATGTTATTATAC
473921 TTGATAATGTTTCCAGTAATTA
66 TTGATAATGTTTCCAGTAATTA
** * * * ** * *
473943 ACCTATTTTATTATATAAGTGCTACCTATTACATTATATAAGTGGTACCTAATATGTTATTGTAC
1 ACCTATTACATTATATAAGCGCTACCAATTACATTAAATAAGCAGAACCTAATATGTTATTATAC
474008 TTGATAATGTTTCC
66 TTGATAATGTTTCC
474022 GGTTAAATGA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (87 bp):
ACCTATTACATTATATAAGCGCTACCAATTACATTAAATAAGCAGAACCTAATATGTTATTATAC
TTGATAATGTTTCCAGTAATTA
Found at i:473978 original size:23 final size:23
Alignment explanation
Indices: 473943--473993 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
473933 CCAGTAATTA
**
473943 ACCTATTTTATTATATAAGTGCT
1 ACCTATTACATTATATAAGTGCT
*
473966 ACCTATTACATTATATAAGTGGT
1 ACCTATTACATTATATAAGTGCT
473989 ACCTA
1 ACCTA
473994 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTGCT
Found at i:486259 original size:60 final size:60
Alignment explanation
Indices: 486177--486309 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
486167 AATGATATCA
* * * * *
486177 ATAATTTGAAGATTAATATAAAATATCTTGAAAATTT-AAGGATCAATTTAAAATAAAATT
1 ATAATTTAAAGATTAATATAAAATATATT-AAAATTTAAAAGATCAAATTAAAATAAAATC
* * * * *
486237 ATAGTTTACAGATTGATATAAAATATATTAAAGTTTAAAATATCAAATTAAAATAAAATC
1 ATAATTTAAAGATTAATATAAAATATATTAAAATTTAAAAGATCAAATTAAAATAAAATC
486297 ATAATTTAAAGAT
1 ATAATTTAAAGAT
486310 ATATTATATA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 6 0.10
60 54 0.90
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.36
Consensus pattern (60 bp):
ATAATTTAAAGATTAATATAAAATATATTAAAATTTAAAAGATCAAATTAAAATAAAATC
Found at i:489270 original size:29 final size:29
Alignment explanation
Indices: 489235--489316 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
489225 AAACTAAATT
*
489235 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
489264 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
489293 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
489317 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:494036 original size:29 final size:29
Alignment explanation
Indices: 494001--494082 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
493991 AAACTAAATT
*
494001 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
494030 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
494059 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
494083 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:495635 original size:26 final size:26
Alignment explanation
Indices: 495599--495678 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
495589 TGCTCACGTA
495599 GAATGATCGCGCGTTCTGTGAAAAGT
1 GAATGATCGCGCGTTCTGTGAAAAGT
* *
495625 GAATGATCGCGCGTTCTATGAAAAAT
1 GAATGATCGCGCGTTCTGTGAAAAGT
495651 GAATGATCGCGCGTTCTGTGAAAAGT
1 GAATGATCGCGCGTTCTGTGAAAAGT
495677 GA
1 GA
495679 TGTTAGATCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (26 bp):
GAATGATCGCGCGTTCTGTGAAAAGT
Found at i:497775 original size:63 final size:64
Alignment explanation
Indices: 497661--497798 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
497651 GTATCTTTGC
* * * * ** *
497661 AATTTGGTCATTAAAATAAATTTTCATACGTTTTAATTATATATTTTAATTT-TTCTTTA-TTAT
1 AATTTAGTCACTAAAATAAATTTTCATACATTTTAATTATACATTCAAATTTAAT-TTTATTTAT
* *
497724 AATTTAGTCACTATAATAAATTTTCATATATTTTAATT-TAGCATTCAAATTTAATTTTATTTAT
1 AATTTAGTCACTAAAATAAATTTTCATACATTTTAATTATA-CATTCAAATTTAATTTTATTTAT
497788 AATTTAGTCAC
1 AATTTAGTCAC
497799 CGTATATCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 2 0.03
63 45 0.71
64 16 0.25
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (64 bp):
AATTTAGTCACTAAAATAAATTTTCATACATTTTAATTATACATTCAAATTTAATTTTATTTAT
Found at i:498145 original size:20 final size:19
Alignment explanation
Indices: 498104--498145 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
498094 TTTAATATTT
*
498104 TAAATATTATTTATTCATA
1 TAAATATTATTTATTCAAA
498123 TAAATATATATTTGATT-AAA
1 TAAATAT-TATTT-ATTCAAA
498143 TAA
1 TAA
498146 TAATGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 10 0.50
21 3 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TAAATATTATTTATTCAAA
Found at i:498254 original size:2 final size:2
Alignment explanation
Indices: 498242--498285 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
498232 ATATGTTATT
*
498242 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
498284 TA
1 TA
498286 CTTCATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:499123 original size:17 final size:18
Alignment explanation
Indices: 499103--499139 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
499093 TCATTCAATT
499103 TTTATTATTTTT-TATCC
1 TTTATTATTTTTATATCC
499120 TTTATTATTTTTATATCC
1 TTTATTATTTTTATATCC
499138 TT
1 TT
499140 ATATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTATTTTTATATCC
Found at i:499146 original size:18 final size:17
Alignment explanation
Indices: 499104--499146 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
499094 CATTCAATTT
499104 TTAT-TATTTTTTATCC
1 TTATATATTTTTTATCC
499120 TT-TATTATTTTTATATCC
1 TTATA-TATTTTT-TATCC
499138 TTATATATT
1 TTATATATT
499147 AATGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 2 0.09
17 7 0.30
18 11 0.48
19 2 0.09
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTTTTTATCC
Found at i:503801 original size:135 final size:135
Alignment explanation
Indices: 503553--503824 Score: 454
Period size: 135 Copynumber: 2.0 Consensus size: 135
503543 AAAAAGTAAA
* *
503553 AAAAAAAGAGTTATATATTCAAAGCGTGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTACTCC
1 AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTACTCC
*
503618 ACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCATCTAATTAGTCCAATGAAGGCTA
66 ACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCATCTAATTAGTCCAATGAAGACTA
503683 ATGTC
131 ATGTC
* *
503688 AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATTGGGTATTTGGCAGTTCGGTGTTTGCTCC
1 AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTACTCC
* * ** *
503753 ACTGTGATTGTCAAGTCAAAGACATTGTGATGGGTTGAACTGTTTAATTAGTCCAATGAAGACTA
66 ACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCATCTAATTAGTCCAATGAAGACTA
503818 ATGTC
131 ATGTC
503823 AA
1 AA
503825 TAAAGCTGAA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 127 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (135 bp):
AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTACTCC
ACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCATCTAATTAGTCCAATGAAGACTA
ATGTC
Found at i:505134 original size:43 final size:43
Alignment explanation
Indices: 505086--505210 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
505076 GCCAAATCTA
* * *
505086 TTCATCAATTGCTCCAACCGATCACCATTTAGTTCTTGTACAT
1 TTCATCAATTCCTCCAACCGATCACCATTCAGTTCTTGCACAT
* * *
505129 TTCATCAATTTCTACAACCGATCACCATTCAGTTCTTGCATAT
1 TTCATCAATTCCTCCAACCGATCACCATTCAGTTCTTGCACAT
* **
505172 CTCATCAATTCCTCCAACCGATCATTATTCAGTTCTTGC
1 TTCATCAATTCCTCCAACCGATCACCATTCAGTTCTTGC
505211 CATCTACTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.37
Consensus pattern (43 bp):
TTCATCAATTCCTCCAACCGATCACCATTCAGTTCTTGCACAT
Found at i:506974 original size:55 final size:54
Alignment explanation
Indices: 506854--507066 Score: 258
Period size: 55 Copynumber: 4.0 Consensus size: 54
506844 CTGACCAGAA
* * * * *
506854 ATCTGTGCAGAAACCACAGAAAATGATGAATGT-TTGTCAAATATTTTATG-AAC
1 ATCTGTACAGAAGCCACAG-AAAGGATGAATATGTTGTCAAATATTTTACGAAAC
506907 ATCTGTGA-AGAAGCCACAAGAAAGGATGAATATGTTGTCAAATATTTTACGAAAC
1 ATCTGT-ACAGAAGCCAC-AGAAAGGATGAATATGTTGTCAAATATTTTACGAAAC
*
506962 ATCTGTACAGAAGCCACAGGAAAGGATGAATATGTGTGTCAAATGTTTT-CGAAAC
1 ATCTGTACAGAAGCCACA-GAAAGGATGAATATGT-TGTCAAATATTTTACGAAAC
** *
507017 ATCTGTACAGAAGCCAC--ACTGGATGAATGTGTTGTCAAATATTTTACGAA
1 ATCTGTACAGAAGCCACAGAAAGGATGAATATGTTGTCAAATATTTTACGAA
507067 CCAGTGATTA
Statistics
Matches: 142, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
51 12 0.08
52 16 0.11
53 25 0.18
54 20 0.14
55 57 0.40
56 12 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (54 bp):
ATCTGTACAGAAGCCACAGAAAGGATGAATATGTTGTCAAATATTTTACGAAAC
Found at i:507457 original size:22 final size:22
Alignment explanation
Indices: 507429--507486 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
507419 TACTTCTACA
507429 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
507451 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
507473 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
507487 AAACTTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:508211 original size:45 final size:45
Alignment explanation
Indices: 508147--508680 Score: 838
Period size: 45 Copynumber: 11.8 Consensus size: 45
508137 CTATTTCCCA
508147 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
508192 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCC-TCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
*
508237 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
508283 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
508328 CATCTGTATGCCCTTCAGTGCATGATGTTATTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTT-TTC-AAAACCTTCGGGT
* * *
508375 CATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
508420 CATCTGTAAGCCCTTCAGTGAATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
508465 CATCTGTAAGCCCTTCAGTGCATGATGTTATTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTT-TTC-AAAACCTTCGGGT
* *
508512 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
508557 CATCTGTAAGACCTTCAATGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
508602 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * *
508647 CATCCATAAGACCTCCAGTGCAGGATG-TTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
508681 TGAGATTTTA
Statistics
Matches: 454, Mismatches: 28, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
44 7 0.02
45 312 0.69
46 55 0.12
47 80 0.18
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:508467 original size:137 final size:136
Alignment explanation
Indices: 508147--508680 Score: 876
Period size: 137 Copynumber: 3.9 Consensus size: 136
508137 CTATTTCCCA
508147 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * * *
508212 CATGATGTTTTCAAAATCC-TCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAACC
66 CATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTC-AAAACC
*
508276 TTCGGGT
130 TTCGGAT
*
508283 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTATGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
508348 CATGATGTTATTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACC
66 CATGATGTT-TTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACC
508413 TTCGGAT
130 TTCGGAT
*
508420 CATCTGTAAGCCCTTCAGTGAATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
508485 CATGATGTTATTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACC
66 CATGATGTT-TTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACC
508550 TTCGGAT
130 TTCGGAT
* * * *
508557 CATCTGTAAGACCTTCAATGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * * *
508622 CATGATGTTTTC-AAAACCTTCGAGTCATCCATAAGACCTCCAGTGCAGGATG-TTTCAAA
66 CATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTCAAA
508681 TGAGATTTTA
Statistics
Matches: 377, Mismatches: 19, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
134 7 0.02
135 35 0.09
136 76 0.20
137 224 0.59
138 35 0.09
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (136 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACCT
TCGGAT
Found at i:508581 original size:182 final size:179
Alignment explanation
Indices: 508147--508680 Score: 838
Period size: 182 Copynumber: 2.9 Consensus size: 179
508137 CTATTTCCCA
*
508147 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTG
*
508212 CATGATGTTTTCAAAATCC-TCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAACC
66 CATGATGTTTTCAAAA-CCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACC
508276 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
128 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
508328 CATCTGTATGCCCTTCAGTGCATGATGTTATTCAAAAACCTTCGGGTCATCTATAAGACCTTCAG
1 CATCTGTAAGCCCTTCAGTGCATGATGTT-TTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAG
*
508393 TGCATGATGTTTTCAAAACCTTCGGATCATCTGTAAGCCCTTCAGTGAATGATGTTTTCAAAACC
64 TGCATGATGTTTTCAAAACCTTCGG-TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACC
508458 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATTCAAAAACCTTCGGGT
128 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTT-TTC-AAAACCTTCGGGT
* * *
508512 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGATCATCTGTAAGACCTTCAATG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTG
*
508577 CATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
66 CATGATGTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
* ** * * *
508642 CGAGTCATCCATAAGACCTCCAGTGCAGGATG-TTTCAAA
130 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
508681 TGAGATTTTA
Statistics
Matches: 328, Mismatches: 18, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
179 3 0.01
180 3 0.01
181 29 0.09
182 165 0.50
183 88 0.27
184 40 0.12
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (179 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTG
CATGATGTTTTCAAAACCTTCGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:508921 original size:3 final size:3
Alignment explanation
Indices: 508915--509003 Score: 56
Period size: 3 Copynumber: 29.3 Consensus size: 3
508905 TTCTTTTTAA
* * * * *
508915 ATT ATT ATT TTT A-A ATT ATT ATT ATT AAT ATCGT ATT ATT TTT TTGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT--T ATT ATT ATT AT-T
* * * *
508962 ATT ATT A-T ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
509004 AAAATAATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 3 0.04
3 63 0.89
4 2 0.03
5 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:508927 original size:14 final size:14
Alignment explanation
Indices: 508908--508957 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
508898 AATTTTTTTC
508908 TTTTTAAATTATTA
1 TTTTTAAATTATTA
508922 TTTTTAAATTATTA
1 TTTTTAAATTATTA
*
508936 TTATTAATATCGTATTA
1 TTTTTAA-AT--TATTA
508953 TTTTT
1 TTTTT
508958 TTGTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 20 0.65
15 2 0.06
17 9 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTTTAAATTATTA
Found at i:510031 original size:63 final size:64
Alignment explanation
Indices: 509917--510054 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
509907 GTATCTTTGC
* * * * * ** *
509917 AATTTGGTCATTAAAATCAATTTTCATATGTTTTAATTATATATTTTAATTT-TTCTTTA-TTAT
1 AATTTAGTCACTAAAATAAATTTTCATATATTTTAATTATACATTCGAATTTAAT-TTTATTTAT
*
509980 AATTTAGTCACTATAATAAATTTTCATATATTTTAATTCA-ACATTCGAATTTAATTTTATTTAT
1 AATTTAGTCACTAAAATAAATTTTCATATATTTTAATT-ATACATTCGAATTTAATTTTATTTAT
510044 AATTTAGTCAC
1 AATTTAGTCAC
510055 AGTATATCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 46 0.73
64 17 0.27
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (64 bp):
AATTTAGTCACTAAAATAAATTTTCATATATTTTAATTATACATTCGAATTTAATTTTATTTAT
Found at i:518064 original size:2 final size:2
Alignment explanation
Indices: 518053--518086 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
518043 TTTGTCAATC
518053 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
518087 TACGACATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:518261 original size:13 final size:13
Alignment explanation
Indices: 518240--518294 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
518230 AATGACGCGC
*
518240 AATGAGCGTCATA
1 AATGCGCGTCATA
518253 AATGCGCGTCATA
1 AATGCGCGTCATA
*
518266 AATGCGTGTCATA
1 AATGCGCGTCATA
*
518279 AATGTGCGTCATA
1 AATGCGCGTCATA
518292 AAT
1 AAT
518295 TTATGACGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:522557 original size:11 final size:10
Alignment explanation
Indices: 522541--522612 Score: 58
Period size: 11 Copynumber: 6.8 Consensus size: 10
522531 ACATTATACT
522541 TATAATATGTA
1 TATAATAT-TA
522552 TATAATA-TA
1 TATAATATTA
522561 TATAATATATA
1 TATAATAT-TA
*
522572 TATAGTA-TA
1 TATAATATTA
*
522581 TATAAGTATAA
1 TATAA-TATTA
522592 GTATATATATATA
1 -TATA-ATAT-TA
522605 TATAATAT
1 TATAATAT
522613 AAAATATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
9 15 0.30
10 2 0.04
11 20 0.40
12 11 0.22
13 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (10 bp):
TATAATATTA
Found at i:522561 original size:2 final size:2
Alignment explanation
Indices: 522541--522850 Score: 149
Period size: 2 Copynumber: 156.5 Consensus size: 2
522531 ACATTATACT
*
522541 TA TA -A TA TG TA TA TA -A TA TA TA TA -A TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
522581 TA TA -A GTA TA -A GTA TA TA TA TA TA TA TA -A TA TA -A AA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
522621 TA AA CTA TA TA AA CTA TA AA GTA TA TA AA T- TA TA TA CA TA TA
1 TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
522663 TA TA TA AA CTA TA TA GCA TA -A GTA TA TA TA TA AA CTA TA TA CA
1 TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* *
522706 -A TA -A GTA TA TA TA TA AA CTA TA TA GCA TA -A GTA 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
* *
522747 -A TA TA TA -A TA TA TA -A TA TA CA -A T- TA CA TA TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
522784 TA TA -A TA TA TA -A TA -A TA TA AA CTA TA TA GTA 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
* *
522825 TA TA TA TA TA TA AA TA AA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA TA T
522851 TTAAGAGAAA
Statistics
Matches: 236, Mismatches: 33, Indels: 78
0.68 0.10 0.22
Matches are distributed among these distances:
1 21 0.09
2 195 0.83
3 20 0.08
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (2 bp):
TA
Found at i:522562 original size:9 final size:9
Alignment explanation
Indices: 522550--522837 Score: 119
Period size: 9 Copynumber: 32.8 Consensus size: 9
522540 TTATAATATG
522550 TATATAATA
1 TATATAATA
522559 TATATAATA
1 TATATAATA
522568 TATAT-ATA
1 TATATAATA
522576 GTATAT-ATA
1 -TATATAATA
522585 -AGTATAAGTA
1 TA-TATAA-TA
522595 TATAT-ATA
1 TATATAATA
522603 TATATAATA
1 TATATAATA
522612 TA-A-AATA
1 TATATAATA
522619 TATA-AACTA
1 TATATAA-TA
522628 TATA-AACTA
1 TATATAA-TA
*
522637 TA-A-AGTA
1 TATATAATA
522644 TATA-AAT-
1 TATATAATA
522651 TATATACATA
1 TATATA-ATA
*
522661 TATATATAAA
1 TATATA-ATA
522671 CTATATAGCATA
1 -TATATA--ATA
522683 -AGTAT-ATA
1 TA-TATAATA
522691 TATA-AACTA
1 TATATAA-TA
*
522700 TATACAATA
1 TATATAATA
522709 -AGTAT-ATA
1 TA-TATAATA
522717 TATA-AACTA
1 TATATAA-TA
522726 TATAGCATAAGTA
1 TAT---ATAA-TA
522739 TATAT-ATA
1 TATATAATA
522747 -ATAT-ATAA
1 TATATAAT-A
522755 TATATAATA
1 TATATAATA
* * *
522764 TACAATTACA
1 TA-TATAATA
*
522774 TATATAA-G
1 TATATAATA
522782 TATAT-A-A
1 TATATAATA
522789 TATATAATA
1 TATATAATA
522798 -ATATAA-A
1 TATATAATA
*
522805 CTATATAGTA
1 -TATATAATA
522815 TATAT-ATA
1 TATATAATA
522823 TATAT-ATA
1 TATATAATA
522831 TATATAA
1 TATATAA
522838 ATAAACTATA
Statistics
Matches: 225, Mismatches: 17, Indels: 74
0.71 0.05 0.23
Matches are distributed among these distances:
7 28 0.12
8 66 0.29
9 84 0.37
10 27 0.12
11 10 0.04
12 3 0.01
13 7 0.03
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (9 bp):
TATATAATA
Found at i:522965 original size:20 final size:21
Alignment explanation
Indices: 522940--522993 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
522930 GACCAACAAA
522940 TTCGCAACGCGAATTT-CAAT
1 TTCGCAACGCGAATTTCCAAT
* *
522960 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGAATTTCCAAT
522980 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
522994 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 20 0.71
21 3 0.11
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
TTCGCAACGCGAATTTCCAAT
Found at i:523024 original size:20 final size:20
Alignment explanation
Indices: 522980--523040 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
522970 AGTTTCCAAT
*
522980 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACACGAA-A-GTCAAA
523001 -TCGCAACAC-AGAAGTCAAA
1 TTCGCAACACGA-AAGTCAAA
*
523020 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACACGAAAGTCAAA
523040 T
1 T
523041 GTTTTTACGC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 26 0.76
21 1 0.03
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
TTCGCAACACGAAAGTCAAA
Found at i:523196 original size:22 final size:22
Alignment explanation
Indices: 523171--523240 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
523161 AGGCGATATT
* * *
523171 CGTCCCAATCTCCAACGAAATC
1 CGTCCCCATTTCCGACGAAATC
523193 CGTCCCCATTTCCGACGAAATC
1 CGTCCCCATTTCCGACGAAATC
* *
523215 CATCCCCATTTCCGACAAAATC
1 CGTCCCCATTTCCGACGAAATC
523237 CGTC
1 CGTC
523241 TATCTCCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.21
Consensus pattern (22 bp):
CGTCCCCATTTCCGACGAAATC
Found at i:525749 original size:42 final size:42
Alignment explanation
Indices: 525702--525820 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
525692 GATGCACCTA
* * * * *
525702 TCATCATTCAAGAGGCGCTTCCTATCGTTCAAGAGGGCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
525744 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* * *
525786 TCATCGTTCAAGAGG-TCCTGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCT-CCCACCGTTCAAGAG
525821 CCTGATTCAC
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
41 5 0.08
42 56 0.89
43 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:525799 original size:21 final size:21
Alignment explanation
Indices: 525702--525800 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
525692 GATGCACCTA
* * *
525702 TCATCATTCAAGAGGCGCTTC
1 TCATCGTTCAAGAGGCCCCTC
*
525723 -CTATCGTTCAAGAGGGCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
525744 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
525765 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
525786 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
525801 TCCTGCCCGC
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:527272 original size:61 final size:63
Alignment explanation
Indices: 527170--527309 Score: 169
Period size: 66 Copynumber: 2.2 Consensus size: 63
527160 TTTTATATTG
* *
527170 AAAGTTGATTTG-TTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTTATTTGTA
1 AAAGTTGATTTGTTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* ** * *
527230 AAAGTTGATTTGTTTTATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTTAATTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
527295 A
63 A
527296 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
527310 GTTTCTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
60 12 0.18
61 21 0.31
64 4 0.06
66 30 0.45
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.53
Consensus pattern (63 bp):
AAAGTTGATTTGTTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:527664 original size:39 final size:39
Alignment explanation
Indices: 527610--527696 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
527600 TCAAGTTATA
*
527610 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
* *
527649 GATTTTGATTTCCTTTTGCTTGACACTATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
527688 GATTTTGAT
1 GATTTTGAT
527697 GAGTATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:528029 original size:18 final size:18
Alignment explanation
Indices: 528006--528042 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
527996 CGAAATTTAT
528006 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
528024 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
528042 A
1 A
528043 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:528462 original size:25 final size:25
Alignment explanation
Indices: 528428--528477 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
528418 ATTATTTTTC
*
528428 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
528453 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
528478 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:528610 original size:20 final size:20
Alignment explanation
Indices: 528579--528688 Score: 148
Period size: 20 Copynumber: 5.5 Consensus size: 20
528569 CGGTTTGCGA
*
528579 TTTCGGGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
528599 TATCGCGTTGCGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
* *
528619 TTTCGCGTTGCAAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
528639 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
528659 TTTCGTGTTGTGAAGTTGAC
1 TTTCGCGTTGCGAATTTGAC
528679 TTTCGCGTTG
1 TTTCGCGTTG
528689 ATCGCAACAT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:528989 original size:6 final size:6
Alignment explanation
Indices: 528980--529014 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
528970 TTGTGATTGG
**
528980 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
529015 CCTTTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:528996 original size:18 final size:18
Alignment explanation
Indices: 528973--529013 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
528963 AAGCCGGTTG
*
528973 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
528991 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
529009 TGATT
1 TGATT
529014 TCCTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:531306 original size:24 final size:24
Alignment explanation
Indices: 531272--531325 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
531262 CTATCACATC
531272 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * *
531296 ATCAAAGTCTGGGTATTGACCAGG
1 ATCAAAATCTGAGTATTGACCAAG
531320 ATCAAA
1 ATCAAA
531326 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:531473 original size:12 final size:12
Alignment explanation
Indices: 531452--531485 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
531442 GGTTGTGGGT
*
531452 TTTGAGATTGTG
1 TTTGATATTGTG
531464 TTTGATATTGTG
1 TTTGATATTGTG
*
531476 TTTGGTATTG
1 TTTGATATTG
531486 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:532404 original size:3 final size:3
Alignment explanation
Indices: 532396--532421 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
532386 GAATTGAGTT
532396 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
532422 TGGCAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:538182 original size:14 final size:14
Alignment explanation
Indices: 538163--538192 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
538153 ATATAACATT
*
538163 TTACGAAAATTGAG
1 TTACGAAAATCGAG
538177 TTACGAAAATCGAG
1 TTACGAAAATCGAG
538191 TT
1 TT
538193 GCATTCATTT
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:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (14 bp):
TTACGAAAATCGAG
Found at i:545424 original size:14 final size:14
Alignment explanation
Indices: 545405--545433 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
545395 TAGAGTAGTA
545405 GGCTGTCCCCAAAC
1 GGCTGTCCCCAAAC
545419 GGCTGTCCCCAAAC
1 GGCTGTCCCCAAAC
545433 G
1 G
545434 CTAGGTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.41, G:0.24, T:0.14
Consensus pattern (14 bp):
GGCTGTCCCCAAAC
Found at i:546429 original size:8 final size:7
Alignment explanation
Indices: 546416--546567 Score: 54
Period size: 7 Copynumber: 21.4 Consensus size: 7
546406 TATGCATACA
546416 ATATAAGT
1 ATATAA-T
546424 ATATAAT
1 ATATAAT
546431 ATA-AAT
1 ATATAAT
*
546437 ATA-CAT
1 ATATAAT
*
546443 -TATACT
1 ATATAAT
546449 -TATAAT
1 ATATAAT
*
546455 ATAT-GT
1 ATATAAT
*
546461 ATACAAT
1 ATATAAT
*
546468 GTAT-AT
1 ATATAAT
546474 ATA-AAGT
1 ATATAA-T
546481 ATATAAATT
1 ATAT-AA-T
546490 ATATAGCAT
1 ATATA--AT
546499 A-AGTATAT
1 ATA-TA-AT
546507 ATATAAT
1 ATATAAT
*
546514 ATACAAT
1 ATATAAT
*
546521 -TA-CAT
1 ATATAAT
546526 ATATAAGT
1 ATATAA-T
546534 ATATAAT
1 ATATAAT
*
546541 ATATAAGA
1 ATATAA-T
546549 ATATAAACT
1 ATAT-AA-T
546558 ATATAAT
1 ATATAAT
546565 ATA
1 ATA
546568 AGCATATATA
Statistics
Matches: 110, Mismatches: 18, Indels: 33
0.68 0.11 0.20
Matches are distributed among these distances:
5 4 0.04
6 27 0.25
7 34 0.31
8 26 0.24
9 18 0.16
10 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (7 bp):
ATATAAT
Found at i:546456 original size:37 final size:37
Alignment explanation
Indices: 546415--546543 Score: 99
Period size: 37 Copynumber: 3.5 Consensus size: 37
546405 TTATGCATAC
546415 AATATAAGTATATAATATAAATATACATTATACTTAT
1 AATATAAGTATATAATATAAATATACATTATACTTAT
* * * * * *
546452 AATATATGTATACAATGTATATATAAAGTATATAAATTAT
1 AATATAAGTATATAATATAAATATACA-T-TAT-ACTTAT
* *
546492 ATAGCATAAGTATAT-ATAT-AATATACAAT-TAC--AT
1 A-A-TATAAGTATATAATATAAATATACATTATACTTAT
546526 -ATATAAGTATATAATATA
1 AATATAAGTATATAATATA
546544 TAAGAATATA
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
31 10 0.14
32 5 0.07
34 2 0.03
36 1 0.01
37 23 0.33
38 2 0.03
39 3 0.04
40 12 0.17
41 4 0.06
42 8 0.11
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (37 bp):
AATATAAGTATATAATATAAATATACATTATACTTAT
Found at i:546476 original size:24 final size:22
Alignment explanation
Indices: 546423--546477 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
546413 ACAATATAAG
546423 TATATAATATAAATATACATTA
1 TATATAATATAAATATACATTA
**
546445 TACTTATAATATATGTATACAATGTA
1 TA--TATAATATAAATATAC-AT-TA
546471 TATATAA
1 TATATAA
546478 AGTATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
24 19 0.70
25 2 0.07
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (22 bp):
TATATAATATAAATATACATTA
Found at i:546516 original size:31 final size:28
Alignment explanation
Indices: 546471--546546 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 28
546461 ATACAATGTA
*
546471 TATATAAAGTATATAAATTATATAGCATAAG
1 TATAT-AA-TATATAAATTACATA-CATAAG
*
546502 TATATATATAATATACAATTACATATATAAG
1 TATATA-AT-ATATA-AATTACATACATAAG
546533 TATATAATATATAA
1 TATATAATATATAA
546547 GAATATAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 5 0.12
30 4 0.10
31 22 0.55
32 8 0.20
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (28 bp):
TATATAATATATAAATTACATACATAAG
Found at i:546544 original size:15 final size:16
Alignment explanation
Indices: 546524--546567 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
546514 ATACAATTAC
546524 ATATATAAGTATAT-A
1 ATATATAAGTATATAA
*
546539 ATATATAAGAATATAA
1 ATATATAAGTATATAA
546555 ACTATATAA-TATA
1 A-TATATAAGTATA
546568 AGCATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (16 bp):
ATATATAAGTATATAA
Found at i:546591 original size:2 final size:2
Alignment explanation
Indices: 546586--546616 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
546576 TACAAGTGTG
546586 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
546617 TGTAGTAGTT
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:547289 original size:2 final size:2
Alignment explanation
Indices: 547177--547273 Score: 79
Period size: 2 Copynumber: 48.0 Consensus size: 2
547167 AAAAAAATAC
* * *
547177 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
547219 TA TG TA TA CT- TA TA TA TA AA AA GTG TG TG TG 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
547262 TA TA TA TA TA TA
1 TA TA TA TA TA TA
547274 AAGTATAGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
1 1 0.01
2 78 0.98
3 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (2 bp):
TA
Found at i:547745 original size:43 final size:43
Alignment explanation
Indices: 547694--547779 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
547684 AAATTCTATA
* * *
547694 TTCCCTCTAAATTTCCAATTTCACTTTATTCCCAAAAATTTCC
1 TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
* * *
547737 TTCCCTCTAAATTCCCAAATTCTCTCTATTCTCAAAATTTTCC
1 TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
547780 AATTTTCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (43 bp):
TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
Found at i:547829 original size:2 final size:2
Alignment explanation
Indices: 547822--547846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
547812 ACTTTCAATA
547822 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
547847 AGTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:549367 original size:17 final size:17
Alignment explanation
Indices: 549332--549377 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
549322 CTAAACAAAT
* *
549332 AAATAAAAATAACGGTA
1 AAATAAAAAAAACGCTA
*
549349 AAATAAAAAAAATGCTA
1 AAATAAAAAAAACGCTA
*
549366 AAACAAAAAAAA
1 AAATAAAAAAAA
549378 GGTATGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.13
Consensus pattern (17 bp):
AAATAAAAAAAACGCTA
Found at i:553270 original size:43 final size:43
Alignment explanation
Indices: 553209--553407 Score: 113
Period size: 43 Copynumber: 4.7 Consensus size: 43
553199 AGCTCCTGTT
** * *
553209 TTTTTCAATATTACTTTTTACCTTTATAATTGAGGTCACAAAA
1 TTTTTCAATCCTATTTTTTACCTTTATAATTGAGGTCCCAAAA
* * * **
553252 TTTTTCAATCCTATTTTTTA-CTCATATAATTTAGGCCCCAATTTT
1 TTTTTCAATCCTATTTTTTACCT-TTATAATTGAGGTCCCAA--AA
** * * * *
553297 TTTTTCAATCTCGCTTTTTTACCTTTAAAATTGATG-CCCATAT
1 TTTTTCAATC-CTATTTTTTACCTTTATAATTGAGGTCCCAAAA
** * *
553340 TTTTTCAA---TATCACTTTACCTTTATAATTGAGGTCTC-TAA
1 TTTTTCAATCCTAT-TTTTTACCTTTATAATTGAGGTCCCAAAA
* * *
553380 TTTTTCAATCATAGTTTTTACTTTTATA
1 TTTTTCAATCCTATTTTTTACCTTTATA
553408 GTTTAAGCCC
Statistics
Matches: 117, Mismatches: 29, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
39 1 0.01
40 27 0.23
41 2 0.02
42 13 0.11
43 42 0.36
45 14 0.12
46 16 0.14
47 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (43 bp):
TTTTTCAATCCTATTTTTTACCTTTATAATTGAGGTCCCAAAA
Found at i:553649 original size:23 final size:23
Alignment explanation
Indices: 553606--553649 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
553596 AAACAAATTT
* *
553606 ATTTATTTATTTTCGCTCTTACA
1 ATTTAATTATTTTCGATCTTACA
553629 ATTTAATT-TTTTCGATGCTTA
1 ATTTAATTATTTTCGAT-CTTA
553650 TTATTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.57
Consensus pattern (23 bp):
ATTTAATTATTTTCGATCTTACA
Done.