Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168126.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_37, 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: 424845
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Warning! 4000 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:296324 original size:5 final size:5
Alignment explanation
Indices: 296310--296340 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
296300 TTTTTATAAA
296310 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
296341 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:296957 original size:10 final size:10
Alignment explanation
Indices: 296942--297051 Score: 53
Period size: 10 Copynumber: 10.4 Consensus size: 10
296932 AAATATAAAT
296942 AAAAAAATAA
1 AAAAAAATAA
296952 AAAAAAATAAGA
1 AAAAAAAT-A-A
*
296964 AAAAAAATCA
1 AAAAAAATAA
* **
296974 ATACCAAT-A
1 AAAAAAATAA
296983 AAAAAAATAA
1 AAAAAAATAA
*
296993 AAAATAAACGAA
1 AAAA-AAA-TAA
* *
297005 AATATAATAA
1 AAAAAAATAA
297015 AAATATAAA-AA
1 AAA-A-AAATAA
*
297026 GTAAGAAAATAA
1 --AAAAAAATAA
*
297038 TAAAAAATAA
1 AAAAAAATAA
297048 AAAA
1 AAAA
297052 GGGAAATTAA
Statistics
Matches: 73, Mismatches: 17, Indels: 20
0.66 0.15 0.18
Matches are distributed among these distances:
9 6 0.08
10 34 0.47
11 12 0.16
12 19 0.26
13 2 0.03
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:296999 original size:48 final size:47
Alignment explanation
Indices: 296938--297051 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 47
296928 ATGAAAATAT
**
296938 AAATAAAAAAATAAAAAAAAATAAGAAAAAAAATCAATACCAA-TAA-AAA
1 AAAT-AAAAAATAAAAAAAAAT-AGAAAAAAAAT--ATAAAAAGTAAGAAA
** * *
296987 AAATAAAAAATAAACGAAAATATAATAAAAATATAAAAAGTAAGAAA
1 AAATAAAAAATAAAAAAAAATAGAAAAAAAATATAAAAAGTAAGAAA
297034 ATAATAAAAAATAAAAAA
1 A-AATAAAAAATAAAAAA
297052 GGGAAATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
45 5 0.09
46 3 0.06
47 13 0.24
48 29 0.54
49 4 0.07
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (47 bp):
AAATAAAAAATAAAAAAAAATAGAAAAAAAATATAAAAAGTAAGAAA
Found at i:297011 original size:28 final size:26
Alignment explanation
Indices: 296980--297051 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
296970 ATCAATACCA
296980 ATAAAAAAAATAAAAAATAAACGAAAAT
1 ATAAAAAAAATAAAAAAT-AA-GAAAAT
*
297008 ATAATAAAAATATAAAAAGTAAGAAAAT
1 ATAA-AAAAA-ATAAAAAATAAGAAAAT
*
297036 A-ATAAAAAATAAAAAA
1 ATAAAAAAAATAAAAAA
297052 GGGAAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 7 0.18
26 5 0.13
27 1 0.03
28 11 0.28
29 7 0.18
30 8 0.21
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (26 bp):
ATAAAAAAAATAAAAAATAAGAAAAT
Found at i:297045 original size:38 final size:37
Alignment explanation
Indices: 296933--297046 Score: 95
Period size: 38 Copynumber: 2.9 Consensus size: 37
296923 AATTTATGAA
* * *
296933 AATATAAATAAAAAAATAAAAAAAAATAAGAAAAAAAATC
1 AATAAAAAT-AAAAAA-AATAAAAAATAA-AAAAAATATC
** *
296973 AATACCAATAAAAAAAATAAAAAATAAACGAAAATAT-
1 AATAAAAATAAAAAAAATAAAAAATAAA-AAAAATATC
* *
297010 AATAAAAATATAAAAAGTAAGAAAATAATAAAAAATA
1 AATAAAAATAAAAAAAATAA-AAAATAA-AAAAAATA
297047 AAAAAGGGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 17 0.28
38 30 0.49
39 7 0.11
40 7 0.11
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.17
Consensus pattern (37 bp):
AATAAAAATAAAAAAAATAAAAAATAAAAAAAATATC
Found at i:297393 original size:17 final size:17
Alignment explanation
Indices: 297373--297427 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
297363 AAAAAAGTTT
297373 AAAACAATGAAAAAATA
1 AAAACAATGAAAAAATA
*
297390 AAAACAAAT-AAAAAATG
1 AAAAC-AATGAAAAAATA
*
297407 AAAGCATATGAAAAAA-A
1 AAAACA-ATGAAAAAATA
297424 AAAA
1 AAAA
297428 AAAGCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 21 0.68
18 9 0.29
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.11
Consensus pattern (17 bp):
AAAACAATGAAAAAATA
Found at i:297531 original size:21 final size:22
Alignment explanation
Indices: 297476--297531 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
297466 TTGAAAAAAT
297476 ATAAAATAAAAGACAATAGCAAA
1 ATAAAATAAAA-ACAATAGCAAA
* *
297499 A-AAAAGACAAAA-AATAGGAAA
1 ATAAAATA-AAAACAATAGCAAA
297520 ATAAAATAAAAA
1 ATAAAATAAAAA
297532 TAAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 13 0.46
22 11 0.39
23 4 0.14
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (22 bp):
ATAAAATAAAAACAATAGCAAA
Found at i:297704 original size:17 final size:16
Alignment explanation
Indices: 297669--297711 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
297659 AACAAAAACA
*
297669 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAATTAAG
297686 AAAATAAAAAATT-AG
1 AAAATAAAAAATTAAG
*
297701 AGAATAAAAAA
1 AAAATAAAAAA
297712 AATATAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.50
16 8 0.33
17 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAATTAAG
Found at i:298319 original size:40 final size:42
Alignment explanation
Indices: 298275--298379 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 42
298265 TTAAATAAAG
298275 AAAGAAATAAAAAATAAACCAAAATAAAAATAAA-ATAAGA-
1 AAAGAAATAAAAAATAAACCAAAATAAAAATAAACATAAGAC
* * * *
298315 AAAG-AATATAAAGTAAAAC-AAA-AAAGATAAACA-AAGTAC
1 AAAGAAATAAAAAATAAACCAAAATAAAAATAAACATAAG-AC
* *
298354 AAAAAAATAAAAAATAAACAAAAATA
1 AAAGAAATAAAAAATAAACCAAAATA
298380 CAATAAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
37 11 0.22
38 5 0.10
39 15 0.30
40 15 0.30
41 3 0.06
42 1 0.02
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (42 bp):
AAAGAAATAAAAAATAAACCAAAATAAAAATAAACATAAGAC
Found at i:298322 original size:22 final size:21
Alignment explanation
Indices: 298297--298390 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 21
298287 AATAAACCAA
*
298297 AATAAAAATAAAATAAGAAAAG
1 AATAAAAATAAAACAA-AAAAG
*
298319 AATATAAAGTAAAACAAAAAAG
1 AATA-AAAATAAAACAAAAAAG
**
298341 -ATAAACAA-AGTAC-AAAAA-
1 AATAAA-AATAAAACAAAAAAG
*
298359 AATAAAAA-ATAAACAAAAATAC
1 AATAAAAATA-AAACAAAAA-AG
298381 AATAAAAATA
1 AATAAAAATA
298391 TAAAAAGCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.05
19 12 0.21
20 9 0.16
21 5 0.09
22 17 0.30
23 11 0.19
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (21 bp):
AATAAAAATAAAACAAAAAAG
Found at i:298387 original size:28 final size:28
Alignment explanation
Indices: 298297--298396 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 28
298287 AATAAACCAA
* *
298297 AATAAAAATAAAATAAGAAA-AGAATATA-
1 AATAAAAATAAAA-AATAAACA-AAAATAC
*
298325 AAGTAAAACA-AAAAAGATAAAC-AAAGTAC
1 AA-TAAAA-ATAAAAA-ATAAACAAAAATAC
298354 AA-AAAAATAAAAAATAAACAAAAATAC
1 AATAAAAATAAAAAATAAACAAAAATAC
298381 AATAAAAATATAAAAA
1 AATAAAAATA-AAAAA
298397 GCAAGAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
26 7 0.12
27 17 0.29
28 14 0.24
29 20 0.34
30 1 0.02
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (28 bp):
AATAAAAATAAAAAATAAACAAAAATAC
Found at i:299322 original size:20 final size:20
Alignment explanation
Indices: 299299--299359 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
299289 CATAAGTAAT
*
299299 AAAAAAGAGAAAAGAAATAA
1 AAAAAAGAGAAAAGAAAAAA
* * *
299319 AAAAAACACAAAATAAAAAA
1 AAAAAAGAGAAAAGAAAAAA
299339 ATAAATAAG-GAAAAGAAAAAA
1 A-AAA-AAGAGAAAAGAAAAAA
299360 TGAGTCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 17 0.53
21 13 0.41
22 2 0.06
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAAAAGAGAAAAGAAAAAA
Found at i:299462 original size:19 final size:19
Alignment explanation
Indices: 299438--299475 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
299428 TTAAGTTTAC
299438 AAAATACAAACAAA-AATAA
1 AAAATA-AAACAAATAATAA
*
299457 AAAATATAACAAATAATAA
1 AAAATAAAACAAATAATAA
299476 GATATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAATAAAACAAATAATAA
Found at i:299515 original size:15 final size:16
Alignment explanation
Indices: 299481--299530 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
299471 AATAAGATAT
* * *
299481 AAAGATATAAAAAATC
1 AAAGATAGAAAAATTA
299497 AAAGATA-AAAAATTA
1 AAAGATAGAAAAATTA
299512 AAAGA-AGAAAAAGTTA
1 AAAGATAGAAAAA-TTA
299528 AAA
1 AAA
299531 CAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 13 0.43
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAGATAGAAAAATTA
Found at i:300232 original size:141 final size:142
Alignment explanation
Indices: 300052--300322 Score: 454
Period size: 141 Copynumber: 1.9 Consensus size: 142
300042 AGTGATAGGC
300052 ATAACAATTCCAAAAGAAAATAACAAAAATAATTATTATCACTTAACAAATTGTAATAAATAAAA
1 ATAACAATTCCAAAAGAAAATAACAAAAATAATTATTATCACTTAACAAATTGTAATAAATAAAA
* *
300117 GATTAATATTATACAATCCAAAATAATAAATAAAATAGTAAGTAATAAATAAAATAATTAAAATT
66 GATAAATATTATACAATCCAAAATAATAAATAAAATAATAAGTAATAAATAAAATAATTAAAATT
300182 ATATATAAGCCA
131 ATATATAAGCCA
* * * *
300194 ATAA-AATTCCAAAAGAAAATAATAAAGATAATTATTATCTCTTAACAAATTGTATTAAATAAAA
1 ATAACAATTCCAAAAGAAAATAACAAAAATAATTATTATCACTTAACAAATTGTAATAAATAAAA
* * *
300258 GATAAATATTATGCAATCCAAAATAGTAAATAAAATAATAAGTAATAAATAAAATAATTCAAATT
66 GATAAATATTATACAATCCAAAATAATAAATAAAATAATAAGTAATAAATAAAATAATTAAAATT
300323 GTATTAAATA
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
141 116 0.97
142 4 0.03
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (142 bp):
ATAACAATTCCAAAAGAAAATAACAAAAATAATTATTATCACTTAACAAATTGTAATAAATAAAA
GATAAATATTATACAATCCAAAATAATAAATAAAATAATAAGTAATAAATAAAATAATTAAAATT
ATATATAAGCCA
Found at i:300736 original size:19 final size:19
Alignment explanation
Indices: 300707--300752 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
300697 ATTAGTTTAT
300707 AAAATACAAACAAAAAATAA
1 AAAATA-AAACAAAAAATAA
*
300727 AAAATAAAACAAATAATAA
1 AAAATAAAACAAAAAATAA
*
300746 GAAATAA
1 AAAATAA
300753 GGATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAATAAAACAAAAAATAA
Found at i:301231 original size:25 final size:25
Alignment explanation
Indices: 301185--301232 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
301175 AAAATTTATG
*
301185 AAAATATAAATAAAAAAGAGAAATA
1 AAAATATAAATAAAAAAAAGAAATA
301210 AAAATA-AAATAAAATAAAAGAAA
1 AAAATATAAATAAAA-AAAAGAAA
301233 AAATCAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (25 bp):
AAAATATAAATAAAAAAAAGAAATA
Found at i:301513 original size:28 final size:30
Alignment explanation
Indices: 301459--301520 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
301449 ATGAAAAGAC
301459 AAAAGATTTAAAACAAAAAAAGAATAT-AA
1 AAAAGATTTAAAACAAAAAAAGAATATGAA
* ** *
301488 AAAAGTTTTAAAA-AATGAAAGCATATGAA
1 AAAAGATTTAAAACAAAAAAAGAATATGAA
301517 AAAA
1 AAAA
301521 AAAAAGCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.19
Consensus pattern (30 bp):
AAAAGATTTAAAACAAAAAAAGAATATGAA
Found at i:301809 original size:24 final size:23
Alignment explanation
Indices: 301766--301854 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 23
301756 AATTACAATT
301766 AAAAATAAACAAAA-ACAAAAAGTA
1 AAAAATAAA-AAAATA-AAAAAGTA
*
301790 AAAAAGTAAAAAAATAAAAAATTA
1 AAAAA-TAAAAAAATAAAAAAGTA
* * *
301814 GAGAATTAAAAAAATATAAAACGATA
1 -AAAAATAAAAAAATA-AAAAAG-TA
301840 AAATGAATAAAAAAA
1 AAA--AATAAAAAAA
301855 ATTTTGTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
24 26 0.51
25 14 0.27
26 2 0.04
27 9 0.18
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAAAATAAAAAAGTA
Found at i:301921 original size:24 final size:23
Alignment explanation
Indices: 301877--301950 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
301867 ATATATAAAA
*
301877 AAAACAAAAAGATATAA-AAAATC
1 AAAACAAAAA-ATAAAATAAAATC
301900 AAAGACAAAAAATAAAATAAAAGTC
1 AAA-ACAAAAAATAAAATAAAA-TC
*
301925 --AATAAAAAATATAAATAAAATC
1 AAAACAAAAAATA-AAATAAAATC
301947 AAAA
1 AAAA
301951 GAAAGTTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 11 0.26
23 17 0.40
24 13 0.30
25 2 0.05
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAACAAAAAATAAAATAAAATC
Found at i:301934 original size:22 final size:22
Alignment explanation
Indices: 301906--301948 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
301896 AATCAAAGAC
301906 AAAAAATA-AAATAAAAGTCAAT
1 AAAAAATATAAATAAAA-TCAAT
301928 AAAAAATATAAATAAAATCAA
1 AAAAAATATAAATAAAATCAA
301949 AAGAAAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAAATATAAATAAAATCAAT
Found at i:302390 original size:42 final size:41
Alignment explanation
Indices: 302335--302422 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
302325 AATAAGTACT
** * *
302335 AAAAAAGAGAAAATTTAAAAATAAG-CAAAA-ACACAATTAA
1 AAAAAAGAGAAAATGAAAAAAT-AGTCAAAAGAAAAAATTAA
302375 AAAAAAGTAAGAAAATGAAAAAATAGTCAAAAGAAAAAATTAA
1 AAAAAAG--AGAAAATGAAAAAATAGTCAAAAGAAAAAATTAA
302418 AAAAA
1 AAAAA
302423 TATAAAAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 7 0.17
41 2 0.05
42 18 0.45
43 13 0.32
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (41 bp):
AAAAAAGAGAAAATGAAAAAATAGTCAAAAGAAAAAATTAA
Found at i:302562 original size:17 final size:17
Alignment explanation
Indices: 302536--302568 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
302526 ATAAAGATAT
302536 AAAAAATTAA-AAAAAG
1 AAAAAATTAATAAAAAG
302552 AAAAAAGTTAATAAAAA
1 AAAAAA-TTAATAAAAA
302569 ATAAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAAATTAATAAAAAG
Found at i:302565 original size:28 final size:29
Alignment explanation
Indices: 302500--302587 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
302490 CAAACATAAA
* *
302500 ATATAAAATATAACAAATAATAAGAAATAAAG
1 ATATAAAAAATAA-AAACAA-AAGAAA-AAAG
*
302532 ATATAAAAAAT-TAAA-AAAAGAAAAAAG
1 ATATAAAAAATAAAAACAAAAGAAAAAAG
*
302559 TTAATAAAAAATAAAAACAAAAGAAAAAA
1 AT-ATAAAAAATAAAAACAAAAGAAAAAA
302588 TTATGGATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 5 0.10
28 15 0.31
29 5 0.10
30 14 0.29
32 10 0.20
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (29 bp):
ATATAAAAAATAAAAACAAAAGAAAAAAG
Found at i:303569 original size:21 final size:21
Alignment explanation
Indices: 303526--303592 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
303516 ATGAAATGAG
* * * *
303526 AAAATAGAAAAAAAAATACAA
1 AAAATTGAAAAACATATAAAA
303547 AAAATTGAAAAACATATAAAA
1 AAAATTGAAAAACATATAAAA
*
303568 AATAA-TAAGAAAACAATATAAAA
1 AA-AATTGA-AAAAC-ATATAAAA
303591 AA
1 AA
303593 TCAAAGACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 21 0.55
22 7 0.18
23 10 0.26
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (21 bp):
AAAATTGAAAAACATATAAAA
Found at i:303611 original size:22 final size:23
Alignment explanation
Indices: 303531--303613 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
303521 ATGAGAAAAT
* *
303531 AGAAAAAAAAATACAAAA-AAT-
1 AGAAAAAAATATAAAAAATAATA
* *
303552 TGAAAAACATATAAAAAATAATA
1 AGAAAAAAATATAAAAAATAATA
* *
303575 AGAAAACAATATAAAAAATCA-A
1 AGAAAAAAATATAAAAAATAATA
303597 AGACAAAAAAT-TAAAAA
1 AGA-AAAAAATATAAAAA
303614 TGAAAAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.28
22 13 0.26
23 23 0.46
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (23 bp):
AGAAAAAAATATAAAAAATAATA
Found at i:304100 original size:23 final size:25
Alignment explanation
Indices: 304047--304098 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
304037 AAAATTTATG
*
304047 AAAATATAAATAAAGAAAGAAATAA
1 AAAATAAAAATAAAGAAAGAAATAA
304072 AAAATAAAAATGAAA-AAAGAAA-AA
1 AAAATAAAAAT-AAAGAAAGAAATAA
304096 AAA
1 AAA
304099 TATTTATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 17 0.68
26 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (25 bp):
AAAATAAAAATAAAGAAAGAAATAA
Found at i:304244 original size:11 final size:10
Alignment explanation
Indices: 304195--304295 Score: 69
Period size: 10 Copynumber: 9.3 Consensus size: 10
304185 TAAGAAAATC
304195 AAAAATAAAA
1 AAAAATAAAA
304205 AAAGAA-AAAA
1 AAA-AATAAAA
*
304215 ATGAAATGAAATGA
1 A-AAAAT-AAA--A
304229 AAAAATAGAAA
1 AAAAATA-AAA
*
304240 AAAAATACAA
1 AAAAATAAAA
*
304250 AAAATTAAAA
1 AAAAATAAAA
*
304260 AACATATAAAA
1 AA-AAATAAAA
*
304271 AATAATAAAA
1 AAAAATAAAA
304281 AAACAATATAAA
1 AAA-AATA-AAA
304293 AAA
1 AAA
304296 TCAAACACAA
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
10 30 0.42
11 23 0.32
12 10 0.14
13 6 0.08
14 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:304245 original size:19 final size:18
Alignment explanation
Indices: 304195--304283 Score: 58
Period size: 19 Copynumber: 4.8 Consensus size: 18
304185 TAAGAAAATC
*
304195 AAAAATAAAAAAAGA--A
1 AAAAATAAAAAAAAATGA
* **
304211 AAAAATGAAATGAAATGA
1 AAAAATAAAAAAAAATGA
*
304229 AAAAATAGAAAAAAAATACA
1 AAAAATA-AAAAAAAAT-GA
*
304249 AAAAATTAAAAAACATAT-A
1 AAAAA-TAAAAAA-AAATGA
304268 AAAAATAATAAAAAAA
1 AAAAATAA-AAAAAAA
304284 CAATATAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.20
18 12 0.21
19 17 0.30
20 11 0.20
21 5 0.09
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAAAAAATGA
Found at i:304251 original size:9 final size:8
Alignment explanation
Indices: 304195--304295 Score: 60
Period size: 9 Copynumber: 11.5 Consensus size: 8
304185 TAAGAAAATC
304195 AAAAATAA
1 AAAAATAA
*
304203 AAAAAGAA
1 AAAAATAA
304211 AAAAATGAA
1 AAAAAT-AA
*
304220 ATGAAATGAA
1 A-AAAAT-AA
*
304230 AAAATAGAAA
1 AAAA-A-TAA
304240 AAAAATACA
1 AAAAATA-A
304249 AAAAATTAA
1 AAAAA-TAA
304258 AAAACATATA
1 AAAA-ATA-A
304268 AAAAATAA
1 AAAAATAA
304276 TAAAAA-AA
1 -AAAAATAA
* *
304284 CAATATAA
1 AAAAATAA
304292 AAAA
1 AAAA
304296 TCAAACACAA
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
7 3 0.04
8 20 0.27
9 27 0.37
10 23 0.32
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:304254 original size:28 final size:26
Alignment explanation
Indices: 304195--304283 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 26
304185 TAAGAAAATC
304195 AAAAATAAAAAA-AG-AAAAAAATGAA
1 AAAAATAAAAAATAGAAAAAAAAT-AA
*
304220 ATGAAATGAAAAAATAGAAAAAAAATACA
1 A-AAAAT-AAAAAATAGAAAAAAAATA-A
*
304249 AAAAATTAAAAAACATATAAAAAATAATAA
1 AAAAA-T-AAAAA-ATAGAAAAAA-AATAA
304279 AAAAA
1 AAAAA
304284 CAATATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 6 0.12
28 6 0.12
29 16 0.31
30 15 0.29
31 4 0.08
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (26 bp):
AAAAATAAAAAATAGAAAAAAAATAA
Found at i:304846 original size:19 final size:17
Alignment explanation
Indices: 304808--304921 Score: 59
Period size: 18 Copynumber: 6.1 Consensus size: 17
304798 ATAAATAAAG
* *
304808 AAATAAAAAATAAAAATA
1 AAATACAAAA-AAATATA
304826 AAATACGAAAAAAATATTAA
1 AAATAC-AAAAAAATA-T-A
*
304846 AGCAAAACAAAAAAGATAAATA
1 A--AATACAAAAAA-AT--ATA
304868 AAATACAAAAAAATATA
1 AAATACAAAAAAATATA
* *
304885 AAATATAAAATAAACA-A
1 AAATACAAAA-AAATATA
*
304902 AAATGCGATAAAAAATATA
1 AAATAC-A-AAAAAATATA
304921 A
1 A
304922 GAAGTAAGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
17 17 0.23
18 18 0.24
19 12 0.16
20 12 0.16
21 6 0.08
22 8 0.11
23 1 0.01
24 1 0.01
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (17 bp):
AAATACAAAAAAATATA
Found at i:304997 original size:34 final size:33
Alignment explanation
Indices: 304936--305023 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 33
304926 TAAGAAAATC
304936 AAAAATAAAAAAAGACAAAAATGAATTGAAATGA-AAAA
1 AAAAAT-AAAAAA-AC-AAAA--AATTGAAA-GACAAAA
*
304974 ATAGAATAAAAAAACAAAAAATTGAAAGACAAAA
1 A-AAAATAAAAAAACAAAAAATTGAAAGACAAAA
*
305008 AAAAATAAGAAAACAA
1 AAAAATAAAAAAACAA
305024 TATAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
33 15 0.33
34 13 0.29
36 4 0.09
37 2 0.04
38 7 0.16
39 4 0.09
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (33 bp):
AAAAATAAAAAAACAAAAAATTGAAAGACAAAA
Found at i:305011 original size:38 final size:37
Alignment explanation
Indices: 304969--305046 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 37
304959 AATTGAAATG
*
304969 AAAAAAT-AGAATAAAAAAACAAAAAATTGAAAGACAAA
1 AAAAAATAAGAA-AAAAAAACAAAAAA-TCAAAGACAAA
* * *
305007 AAAAAATAAGAAAACAATATAAAAAATCAAAGACAAA
1 AAAAAATAAGAAAAAAAAACAAAAAATCAAAGACAAA
305044 AAA
1 AAA
305047 TTAAAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 13 0.37
38 18 0.51
39 4 0.11
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (37 bp):
AAAAAATAAGAAAAAAAAACAAAAAATCAAAGACAAA
Found at i:305021 original size:33 final size:34
Alignment explanation
Indices: 304959--305023 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
304949 GACAAAAATG
*
304959 AATTGAAATGAAAAAATAGAATAAAAAAACAAAA
1 AATTGAAATGAAAAAATAAAATAAAAAAACAAAA
*
304993 AATTGAAA-GACAAAAA-AAAATAAGAAAACAA
1 AATTGAAATGA-AAAAATAAAATAAAAAAACAA
305024 TATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (34 bp):
AATTGAAATGAAAAAATAAAATAAAAAAACAAAA
Found at i:305039 original size:22 final size:20
Alignment explanation
Indices: 305007--305053 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
304997 GAAAGACAAA
*
305007 AAAAAATAAGA-AAACAATAT
1 AAAAAATAAGACAAAAAAT-T
305027 AAAAAATCAAAGACAAAAAATT
1 AAAAAAT--AAGACAAAAAATT
305049 AAAAA
1 AAAAA
305054 TGAGAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
22 10 0.43
23 6 0.26
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAATAAGACAAAAAATT
Found at i:305537 original size:25 final size:24
Alignment explanation
Indices: 305507--305557 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
305497 AAAGTTTATG
*
305507 AAAATATAAATAAAATAAGAAATAA
1 AAAATAAAAATAAAATAAGAAA-AA
305532 AAAATAAAAATAAAATAAGAAAAA
1 AAAATAAAAATAAAATAAGAAAAA
305556 AA
1 AA
305558 TATTCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (24 bp):
AAAATAAAAATAAAATAAGAAAAA
Found at i:305548 original size:11 final size:12
Alignment explanation
Indices: 305514--305559 Score: 60
Period size: 11 Copynumber: 3.8 Consensus size: 12
305504 ATGAAAATAT
305514 AAATAAAATAAG
1 AAATAAAATAAG
305526 AAATAAAAAATAA-
1 AAAT--AAAATAAG
305539 AAATAAAATAAG
1 AAATAAAATAAG
305551 AAA-AAAATA
1 AAATAAAATA
305560 TTCAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.42
12 7 0.23
13 4 0.13
14 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAG
Found at i:305634 original size:718 final size:718
Alignment explanation
Indices: 303919--309011 Score: 5661
Period size: 737 Copynumber: 7.0 Consensus size: 718
303909 TGTGAAAAGA
**
303919 AAAAAAATG-AAAAAGAAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAGTAAATAACCAAC
1 AAAAAAATGAAAAAAG-AAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAAC
*
303983 AACGATAAAT-AAAAAAAAGAAAAGAAAAAAGATAGAAAAATAAAAAACATGATAAAAATTTATG
65 AACGATAAATAAAAAAAAAG-ATAG--AAAA-ATA-AAAAATAAAAAACATGATAAAAATTTATG
* *
304047 AAAATATAAATAAAGAAAGAAATAAAAAATAAAAATGAAAA-AAGAAAAAAAATATTTATGCAAA
125 AAAATATAAATAAA-AAAGAAATAAAAAATAAAAAT-AAAATAAG-AAAAAAATATTAAAGCAAA
*
304111 ACAAAAAAGATAAATAAAATACAAAAGAATATAAAATATAAAATAAACAAAAATGCGATAAAGAA
187 ACAAAAAAGATAAATAAAATACAAAA-AATATAAAATATAAAATAAACAAAAATGCGATAAAAAA
* *
304176 TAAAAGAAGTAAGAAAATCAAAAATAAAAAAAGAAAAAAATGAAATGAAATGAAAAAATAGAAAA
251 TATAAGAAGTAAGAAAATCAAAAATAAAAAAAGACAAAAA-G-AATGAAATGAAAAAATAGAAAA
* * *
304241 AAAATACAAAAAATTAAAAAACATATAAAAAATAATAAAAAAACAATATAAAAAATCAAACACAA
314 AAAA-ACAAAAAATTGAAAAAC-TATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAA
*
304306 AAAATTAAAAATGACAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAAC-AA
377 AAAATTAAAAATGAGAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAA
304370 AAAAAACTATAAGAATTTAAAAATGAAAAT-AAAAATAAAAAAAAATTTGTAAAAGAATTAAGAA
442 AAAAAACTATAAGAATTTAAAAATGAAAATAAAAAAT-AAAAAAAATTTGTAAAAGAATTAAGAA
*
304434 AAGAATACAAATGAAAAGACAAGATTTATGAAAAAAAAAATCCAAGGAAGTATAAAAAAAATGGA
506 AAGAATAAAAATGAAAAGACAAGA-TT-T----------AT-----GAA--A-AAAAAAAATGGA
304499 AACAAGAAATAAAAAGAATTTTGTGAAAAAAATTAGAAAAACAAGAAAAAATAAAAAAT-AAAAG
551 AACAAGAAATAAAAAGAATTTTGTGAAAAAAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAG
*
304563 GCAAAAATATGAAACAAAATAAAAAGATAAAAAAGTATTGTAGAAATTTTTAAAACAAAGAAAAA
616 GCAAAAATATGAAACAAAATAAAAAGATAAAAAAGTATTGTAGAAAATTTTAAAACAAAGAAAAA
304628 TGTGAAAAGAAAAAAAAATATGAAAGCACATGAAAAGATAAGT
681 ----AAAA-AAAAAAAAATATGAAAGCACATGAAAAGATAAGT
* *
304671 AAAAAAATG--AAAGGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAGAAAATAACCAACA
1 AAAAAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAACA
304734 ACGATAAATAAAAAAAAAGA-A-AAAAGATAGAAAAATAAAAAACATGATAAAAATTTATGAAAA
66 ACGATAAATAAAAAAAAAGATAGAAAA-ATA-AAAAATAAAAAACATGATAAAAATTTATGAAAA
*
304797 TATAAAT---AAAGAAATAAAAAATAAAAATAAAATACGAAAAAAATATTAAAGCAAAACAAAAA
129 TATAAATAAAAAAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATTAAAGCAAAACAAAAA
304859 AGATAAATAAAATACAAAAAAATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGA
194 AGATAAATAAAATAC-AAAAAATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGA
304924 AGTAAGAAAATCAAAAATAAAAAAAGACAAAAATGAATTGAAATGAAAAAATAGAATAAAAAAAC
258 AGTAAGAAAATCAAAAATAAAAAAAGACAAAAA-GAA-TGAAATGAAAAAATAGAA-AAAAAAAC
*
304989 AAAAAATTGAAAGAC-A-AAAAAA-AATAAGAAAACAATATAAAAAATCAAAGACAAAAAATTAA
320 AAAAAATTGAAAAACTATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAAAAATTAA
*
305051 AAATGAGAAAAGTTAATGCAAAATAAAAACGAAAACAAAAGAAGAAAATGCAACAAAAAAAAACT
385 AAATGAGAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAAAAAAACT
*
305116 ATAAGAATTTAAAAATGAAAATAAAAAATAAAAAAAATTTCTAAAAGAATTAAGAAAAGAATAAA
450 ATAAGAATTTAAAAATGAAAATAAAAAATAAAAAAAATTTGTAAAAGAATTAAGAAAAGAATAAA
* *
305181 AATGAAAAGACAACATTTATG-AAAAAAAAAATGGAAACAAGAAATAAAAAGAATTTTGAGAAAA
515 AATGAAAAGACAAGATTTATGAAAAAAAAAAATGGAAACAAGAAATAAAAAGAATTTTGTGAAAA
*
305245 AAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAGGC-AAAATACGAAACAAAATAAAAAGATA
580 AAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATA
* *
305309 AAAAAGTATTGTAGAAAATTTTAAAACAAAGAAAAAAAGAAAAAAAAAATATGAAAGCACATAAA
645 AAAAAGTATTGTAGAAAATTTTAAAACAAAGAAAAAAAAAAAAAAAAAATATGAAAGCACATGAA
305374 AAGATAAGT
710 AAGATAAGT
* *
305383 AAAAAAATGAAAAAAGAAAAAGTGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAGCA
1 AAAAAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAACA
*
305448 ACGATAAATAAAAAAAAAGATAGAAAAATAAAAAATAAAAAACATGATAAAAGTTTATGAAAATA
66 ACGATAAATAAAAAAAAAGATAGAAAAATAAAAAATAAAAAACATGATAAAAATTTATGAAAATA
305513 TAAATAAAATAAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATTCAAA-CAAAACAAAAA
131 TAAATAAAA-AAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATT-AAAGCAAAACAAAAA
305577 AGATAAATAAAATACAAAAGAATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGA
194 AGATAAATAAAATACAAAA-AATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGA
* *
305642 AGTAAGAAAATCAAAAATAAAAAAAGAC--AAA-AATGAAAT---CAAAT-G-AAAAAATACAAA
258 AGTAAGAAAATCAAAAATAAAAAAAGACAAAAAGAATGAAATGAAAAAATAGAAAAAAAAACAAA
* * *
305699 AATTTGAAAAAC-CTAAAAAATAATAAGAAAACAATATAAAAAATCAAAG--AGAAAATTAAAAA
323 AAATTGAAAAACTATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAAAAATTAAAAA
305761 TGAG--AAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAAAAAAAACTAT
388 TGAGAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAAC-AAAAAAAAACTAT
* *
305824 AGGAATTTAAAAATGAAAATAAGAAATAAAAAGAAATTTGTAAAAGAATTAAGAAAAGAATAAAA
452 AAGAATTTAAAAATGAAAATAAAAAATAAAAA-AAATTTGTAAAAGAATTAAGAAAAGAATAAAA
*
305889 ATGAAAAGACAAGATTTATGAAAAAAAAAAAATGGAAACAAGAAATAAAGAGAATTTTGTGAAAA
516 ATGAAAAGACAAGATTTATG-AAAAAAAAAAATGGAAACAAGAAATAAAAAGAATTTTGTGAAAA
305954 AAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATA
580 AAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATA
* ** *
306019 AAAAAGTATTGTA-CAAA-TTTAAAA-AAA-AAATGTGAAAAGAAAAAAAATATGAAAGCACATG
645 AAAAAGTATTGTAGAAAATTTTAAAACAAAGAAA--AAAAAAAAAAAAAAATATGAAAGCACATG
306080 AAAAGATAAGT
708 AAAAGATAAGT
* * *
306091 AAAAAAATGAAAAAGGATAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAGCA
1 AAAAAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAACA
*
306156 ACGATAGATAAAAAAAAAAAGAAAAAAGATAGAAAAATAAAAAAATAAAAAACATGATAAAAATT
66 AC----GAT----AAATAAA-AAAAAAGATAGAAAAAT-AAAAAATAAAAAACATGATAAAAATT
*
306221 TATGAAAATATAAAT---AAAG-AAT---AAATAAAAATAAAATTAG-AAAAAATATTAAAGCAA
121 TATGAAAATATAAATAAAAAAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATTAAAGCAA
* *
306278 AACAAAAATAAATAAATAAAATACAAAAATATATAAAATATAAAATAAACAAAAATACGATAAAA
186 AACAAAAA-AGATAAATAAAATACAAAAA-ATATAAAATATAAAATAAACAAAAATGCGATAAAA
* *
306343 CATATAAAAAGTAAGAAAATCAAAAATAAAAAAAGAC--AAA-AATGAAATGAAAAAATACG-AA
249 AATATAAGAAGTAAGAAAATCAAAAATAAAAAAAGACAAAAAGAATGAAATGAAAAAATA-GAAA
* *
306404 AAAATACAAAAAATTGAAAGAC-ATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAA
313 AAAAAACAAAAAATTGAAAAACTATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAA
*
306468 AAATTAAAAATGATAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAA
378 AAATTAAAAATGAGAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAA
* *
306533 AAAAACTATAAGAATTTAAAAATGAAAATAAGAACA-AAAAAAAATTTGTAAAAAAATTAAGAAA
443 AAAAACTATAAGAATTTAAAAATGAAAATAA-AAAATAAAAAAAATTTGTAAAAGAATTAAGAAA
* *
306597 AGAATAAAAATGAAAA-AAAAGATTTATAAAAAAAAATCCAAGTATAAAAAAAAATGGAAACAAG
507 AGAATAAAAATGAAAAGACAAGA-TT-T--------AT----G-AAAAAAAAAAATGGAAACAAG
* * * *
306661 AAATAAAAAGAATTTTGTGAAAAAAATTAGAAAAATAGGAAAAAATAAGAAATGAAGAGGCAAAA
557 AAATAAAAAGAATTTTGTGAAAAAAATTAGAAAAACAAGAAAAAATAAAAAATGAAAAGGCAAAA
306726 ATATGAAACAAAATAAAAAGATAAAAAAGTATTGTA-AAAATTTTTAAAACAAAGAAAAATGTGA
622 ATATGAAACAAAATAAAAAGATAAAAAAGTATTGTAGAAAA-TTTTAAAACAAAGAAAAA----A
*
306790 AAAGAAAAAAAAATATTAAAGCACATGAAAAGATAAGT
682 AAA-AAAAAAAAATATGAAAGCACATGAAAAGATAAGT
* *
306828 AAAAAAATG-AAAAAGAAAAAAGAGTTAATGAAAAATTATAAAAATAATACAAAAAATAACAAAC
1 AAAAAAATGAAAAAAG-AAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAAC
* *
306892 AACGATAAAT--AAAAAAAG--A-AAAGATAAAAAATTAAAAAACAAGAT--AAATTTATGAAAA
65 AACGATAAATAAAAAAAAAGATAGAAAAATAAAAAA-TAAAAAACATGATAAAAATTTATGAAAA
* * *
306950 TATAAATAAAAAAAGAAAT-AAAAAT-ATAAT-AAAT-A-TAATAAATATTAAAGCAAAACAAAA
129 TATAAAT-AAAAAAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATTAAAGCAAAACAAAA
*
307010 AAGATAAATAAAATAC-AAAAATATAAAATATAAAATAAACAAAAATGCGATAAAAAA-AT-ATA
193 AAGATAAATAAAATACAAAAAATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGA
* *
307072 AGTAAGAAAATCAAAAAT-------G------A-AATGAAATGAGAAAATAGAAAACAAATACAA
258 AGTAAGAAAATCAAAAATAAAAAAAGACAAAAAGAATGAAATGAAAAAATAGAAAA-AAAAACAA
* *
307123 AAAATTGAAAAACATATAAAAAATAGTAATAAAACAATATAAAAAATCAAAGACAAAAAATTAAA
322 AAAATTGAAAAAC-TATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAAAAATTAAA
* * * * *
307188 AATAAGAAAAATTAATGCAAAATAAAAATAAAAACAAAAGAACAAAATGCAAC-AAAAAAAACTG
386 AATGAGAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAAAAAAACTA
* * *
307252 TAAGAATTTAAAAATGAAAAT-AGAAATAAAAGAAATTTGTAAAAGGATTAAGAAAAGAATAAAA
451 TAAGAATTTAAAAATGAAAATAAAAAATAAAAAAAATTTGTAAAAGAATTAAGAAAAGAATAAAA
* * *
307316 ATGAAAAGACAAGATTTATG-AAAAAAAAAAT--CAA-AAGAAGT----ATAA-------AAAAA
516 ATGAAAAGACAAGATTTATGAAAAAAAAAAATGGAAACAAGAAATAAAAAGAATTTTGTGAAAAA
* * * *
307366 AA-T-G-GAAACGAA-AAAAAATAAAAAATGAACAGGCAAAAATATGAAACAAGATAAAATGATA
581 AATTAGAAAAAC-AAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATA
* * *
307427 AAAAAGTTTTGTAGAAATTTTTAAAACAAA-AAAAAATGTGAAACCCAAAAAAAATATGAAAGCA
645 AAAAAGTATTGTAGAAAATTTTAAAACAAAGAAAAAA----AAA--AAAAAAAAATATGAAAGCA
307491 CATGAAAAGATAAGTAAAAAAAT
704 CATGAAAAGATAAG--------T
307514 GAAAAATTTAAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAA
1 ---AAA---AAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAA
* * * *
307579 CCAACAACGATAAAAAAAAAAAGATAAAAGATAAAAAAATAAAAAATAAAAAACACGATAAAATT
60 CCAACAACGAT---AAATAAAA-A-AAAAGATAGAAAAATAAAAAATAAAAAACATGATAAAAAT
307644 TTATGAAAATATAAATAAAGAAAGAAATAAAAAATAAACCAAAATAAAAAATGAAAAAAAAAAAA
120 TTATGAAAATATAAATAAA-AAAGAAATAAAAAAT--A--AAAAT--AAAAT-----------AA
* * *
307709 GAAAAAAATATTGAAGCAAAACAAAAAAGTTGAATAAAATACAAAAAAATATAAAATATAAAATA
167 GAAAAAAATATTAAAGCAAAACAAAAAAGATAAATAAAATAC-AAAAAATATAAAATATAAAATA
* * * *
307774 AACAAAAATGCAAT-AAAAATATAAAAAGTAAGAAAATCAAAAAT-AAAAAATA-AAAAAG-A-C
231 AACAAAAATGCGATAAAAAATATAAGAAGTAAGAAAATCAAAAATAAAAAAAGACAAAAAGAATG
* *
307834 AAATGAAATGAAAT--AAGAAAATACAAAAAATTGAAAAACATATAAAAAATAATAAGAAAACAA
296 AAATGAAA--AAATAGAAAAAAAAACAAAAAATTGAAAAAC-TATAAAAAATAATAAGAAAACAA
*
307897 TATAAAAAATCAAAGACAAAAAATTAAAAATGAAAAAAGTTAATGCAAAAT-----T-------A
358 TATAAAAAATCAAAGACAAAAAATTAAAAATGAGAAAAGTTAATGCAAAATAAAAATGAAAACAA
* *
307950 AA-ATG--AA---AACAAAAAAAAACTATAAGAATTTAAAAATGAATATAAAAAATAAAAAGAAA
423 AAGAAGAAAATGCAACAAAAAAAAACTATAAGAATTTAAAAATGAAAATAAAAAATAAAAA-AAA
* * ** * * ** *
308009 TTTGTAAAATAA-AAATGAAAAGACA-AGATTTATGAAAA-AAAATAATCCGACGAAGTATAAAA
487 TTTGTAAAAGAATTAA-GAAAAGA-ATA-A-AAATGAAAAGACAA-GAT-TTATGAA--A-AAAA
* * * * **
308071 AAAATGAAAACAGGAAATAAAGAGAATTTTATGAAAAAAATTAGAAAATGAAGAAAAAATAAAAA
543 AAAATGGAAACAAGAAATAAAAAGAATTTTGTGAAAAAAATTAGAAAAACAAGAAAAAAT-AAAA
* * * *
308136 AATGAAGAGGCAAAAATATGAAATAAAATAAAAAGATGAAAAAAGTTTTGTAGAAATTTTTAAAA
607 AATGAAAAGGCAAAAATATGAAACAAAATAAAAAGAT-AAAAAAGTATTGTAGAAAATTTTAAAA
* *
308201 CAAAGAAAAATGTGAAAAAAAAAAAATATGAAAGCACATGAAAAGATGAGT
671 CAAAGAAAAA---AAAAAAAAAAAAATATGAAAGCACATGAAAAGATAAGT
308252 AAAAAAATGAAAAACTTAAAAGGAAAAAGGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACA
1 AAAAAAATG-----------A--AAAAA-GAAAAAGAGTTAATGAAAAATTATAAAAATAAAACA
* *
308317 AAAAATAACCAACAAAGATAAATAAATAAGGAAGAGAAAAAAGACAGAAAAATTAAAAAACT-AA
52 AAAAATAACCAACAACG----ATAAAT----AA-A-AAAAAAGATAGAAAAA-TAAAAAA-TAAA
* *
308381 AAACATGATAAAAATTTATAAAAATATAAATAAAGAAAGAAATAAGAAATAAAATTAAAATTAAA
105 AAACATGATAAAAATTTATGAAAATATAAATAAA-AAAGAAAT----AA-AAAA-TAAAAATAAA
*
308446 ATTAA-AAAAAAATATTAAAGCAAAACAAAAAAGATAAATAAAAGAC----AA-A-AAAATATAA
163 A-TAAGAAAAAAATATTAAAGCAAAACAAAAAAGATAAATAAAATACAAAAAATATAAAATATAA
* ** *
308504 AATAAACAAAAATACGATAAAAAATAT---TTGTAAGAAAATCAAAAATACAAAAATG------A
227 AATAAACAAAAATGCGATAAAAAATATAAGAAGTAAGAAAATCAAAAATA-AAAAAAGACAAAAA
* *
308560 -AATGAAATGAGAAAAT--AAAAAAAAAC--AAAATTAAAAAACATATAAAAAAATAATAAGAAA
291 GAATGAAATGAAAAAATAGAAAAAAAAACAAAAAATTGAAAAAC-TAT-AAAAAATAATAAGAAA
308620 ACAATATAAAAAATCAAAGAC--AAAATTAAAAATGAGAAAAGTTAATGCAAAATAAAAATGAAA
354 ACAATATAAAAAATCAAAGACAAAAAATTAAAAATGAGAAAAGTTAATGCAAAATAAAAATGAAA
* *
308683 ACAAAAGAAGAAAATGCAACAAAAAAAAAAACGATAAGAATTTAAAAATGAAAATAAGAAATAAA
419 ACAAAAGAAGAAAATGCAAC--AAAAAAAAACTATAAGAATTTAAAAATGAAAATAAAAAATAAA
*
308748 AAAAA-TTGTAAAAAAATTAAGAAAAGAATAAAAAT--AAAGACAAAAGATTTATGAAAAACAAA
482 AAAAATTTGTAAAAGAATTAAGAAAAGAATAAAAATGAAAAGAC--AAGATTTATGAAAAA-AAA
* * *
308810 AAATTCAAGGAAGTGTAAAAAAAATGGAAACAAGAAATAAAAATAACTGTGAAAAAAATTAGAAA
544 AAA-T---GGAA----ACAAGAAAT--AAA-AAG-AAT-----T--TTGTGAAAAAAATTAGAAA
* * * *
308875 AATAAGAAAAAATAAAAAATGAAGAGGCAAAAATATGAAATAAAATAAAAAG----AAAAGTTTT
590 AACAAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATAAAAAAGTATT
* * * *
308936 GTAAAAAATTTTAAAACAAAGAAAAAAGTGAAAACAAAAAAAAAATGAAAGCACATTAAAAAAAT
655 GTAGAAAATTTTAAAACAAAGAAAAAA---AAAA-AAAAAAAATATGAAAGCACA-TGAAAAGAT
309001 AAGT
715 AAGT
309005 AAAAAAA
1 AAAAAAA
309012 ATTTTAAAAG
Statistics
Matches: 3818, Mismatches: 233, Indels: 579
0.82 0.05 0.13
Matches are distributed among these distances:
673 1 0.00
677 8 0.00
678 103 0.03
679 5 0.00
680 1 0.00
681 7 0.00
686 1 0.00
688 3 0.00
689 3 0.00
692 64 0.02
693 8 0.00
695 13 0.00
697 3 0.00
698 1 0.00
699 5 0.00
701 15 0.00
702 14 0.00
703 27 0.01
704 6 0.00
705 44 0.01
706 46 0.01
707 89 0.02
708 117 0.03
709 160 0.04
710 221 0.06
711 36 0.01
712 145 0.04
713 17 0.00
714 114 0.03
715 64 0.02
716 18 0.00
717 207 0.05
718 225 0.06
719 53 0.01
720 51 0.01
721 34 0.01
722 64 0.02
723 26 0.01
724 26 0.01
725 101 0.03
726 40 0.01
727 78 0.02
728 37 0.01
729 14 0.00
730 128 0.03
731 2 0.00
732 36 0.01
733 6 0.00
734 33 0.01
735 12 0.00
736 15 0.00
737 276 0.07
738 106 0.03
739 13 0.00
740 13 0.00
741 194 0.05
742 42 0.01
743 29 0.01
744 6 0.00
745 50 0.01
746 147 0.04
747 40 0.01
748 37 0.01
749 8 0.00
750 63 0.02
751 64 0.02
752 83 0.02
753 20 0.01
754 4 0.00
755 1 0.00
756 42 0.01
757 32 0.01
758 1 0.00
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (718 bp):
AAAAAAATGAAAAAAGAAAAAGAGTTAATGAAAAATTATAAAAATAAAACAAAAAATAACCAACA
ACGATAAATAAAAAAAAAGATAGAAAAATAAAAAATAAAAAACATGATAAAAATTTATGAAAATA
TAAATAAAAAAGAAATAAAAAATAAAAATAAAATAAGAAAAAAATATTAAAGCAAAACAAAAAAG
ATAAATAAAATACAAAAAATATAAAATATAAAATAAACAAAAATGCGATAAAAAATATAAGAAGT
AAGAAAATCAAAAATAAAAAAAGACAAAAAGAATGAAATGAAAAAATAGAAAAAAAAACAAAAAA
TTGAAAAACTATAAAAAATAATAAGAAAACAATATAAAAAATCAAAGACAAAAAATTAAAAATGA
GAAAAGTTAATGCAAAATAAAAATGAAAACAAAAGAAGAAAATGCAACAAAAAAAAACTATAAGA
ATTTAAAAATGAAAATAAAAAATAAAAAAAATTTGTAAAAGAATTAAGAAAAGAATAAAAATGAA
AAGACAAGATTTATGAAAAAAAAAAATGGAAACAAGAAATAAAAAGAATTTTGTGAAAAAAATTA
GAAAAACAAGAAAAAATAAAAAATGAAAAGGCAAAAATATGAAACAAAATAAAAAGATAAAAAAG
TATTGTAGAAAATTTTAAAACAAAGAAAAAAAAAAAAAAAAAATATGAAAGCACATGAAAAGATA
AGT
Found at i:305748 original size:22 final size:21
Alignment explanation
Indices: 305712--305760 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
305702 TTGAAAAACC
305712 TAAAAAATAATAAGAAAACAAT
1 TAAAAAATAATAAGAAAA-AAT
* *
305734 ATAAAAAATCA-AAGAGAAAAT
1 -TAAAAAATAATAAGAAAAAAT
305755 TAAAAA
1 TAAAAA
305761 TGAGAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 6 0.25
23 9 0.38
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.16
Consensus pattern (21 bp):
TAAAAAATAATAAGAAAAAAT
Found at i:306186 original size:25 final size:25
Alignment explanation
Indices: 306158--306218 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
306148 AACCAGCAAC
306158 GATAGATAAAAAAAAAAAGAAAAAA
1 GATAGATAAAAAAAAAAAGAAAAAA
*
306183 GATAGA-AAAATAAAAAAATAAAAAA
1 GATAGATAAAA-AAAAAAAGAAAAAA
*
306208 CAT-GATAAAAA
1 GATAGATAAAAA
306219 TTTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.11
Consensus pattern (25 bp):
GATAGATAAAAAAAAAAAGAAAAAA
Found at i:306197 original size:16 final size:15
Alignment explanation
Indices: 306165--306207 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
306155 AACGATAGAT
*
306165 AAAAA-AAAAAAGAA
1 AAAAATAAAAAATAA
306179 AAAAGATAGAAAAATAA
1 AAAA-ATA-AAAAATAA
306196 AAAAATAAAAAA
1 AAAAATAAAAAA
306208 CATGATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 4 0.16
17 11 0.44
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:306313 original size:17 final size:17
Alignment explanation
Indices: 306287--306331 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
306277 AAACAAAAAT
306287 AAATAAATAAAATACAA
1 AAATAAATAAAATACAA
* *
306304 AAATATATAAAATA-TA
1 AAATAAATAAAATACAA
*
306320 AAATAAACAAAA
1 AAATAAATAAAA
306332 ATACGATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAATACAA
Found at i:306347 original size:29 final size:24
Alignment explanation
Indices: 306293--306351 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 24
306283 AAATAAATAA
*
306293 ATAAAATACAAAAATATATAAAAT
1 ATAAAATACAAAAATAGATAAAAT
306317 ATAAAATAAACAAAAATACGATAAAACAT
1 ATAAAAT--ACAAAAATA-GAT-AAA-AT
306346 ATAAAA
1 ATAAAA
306352 AGTAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.24
26 9 0.31
27 2 0.07
28 3 0.10
29 8 0.28
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (24 bp):
ATAAAATACAAAAATAGATAAAAT
Found at i:306367 original size:36 final size:34
Alignment explanation
Indices: 306287--306376 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 34
306277 AAACAAAAAT
* *
306287 AAATAAA-TAAAATACAAAAATATATAAAATATA
1 AAATAAACAAAAATACAAAAACATATAAAATATA
306320 AAATAAACAAAAATACGATAAAACATATAAAA-AGTA
1 AAATAAACAAAAATAC-A-AAAACATATAAAATA-TA
* *
306356 AGAA-AATCAAAAATAAAAAAA
1 A-AATAAACAAAAATACAAAAA
306377 GACAAAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
33 7 0.15
34 11 0.23
35 3 0.06
36 25 0.52
37 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (34 bp):
AAATAAACAAAAATACAAAAACATATAAAATATA
Found at i:306390 original size:21 final size:22
Alignment explanation
Indices: 306366--306406 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
306356 AGAAAATCAA
306366 AAATAAAAAAAGAC-AAAAATG
1 AAATAAAAAAAGACGAAAAATG
* *
306387 AAATGAAAAAATACGAAAAA
1 AAATAAAAAAAGACGAAAAA
306407 ATACAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (22 bp):
AAATAAAAAAAGACGAAAAATG
Found at i:306444 original size:39 final size:37
Alignment explanation
Indices: 306392--306470 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
306382 AAATGAAATG
* *
306392 AAAAAATACGAAAA-AATACAAAAAATTGAAAGACATAA
1 AAAAAATAAGAAAACAATACAAAAAA-TCAAAGACA-AA
*
306430 AAAATAATAAGAAAACAATATAAAAAATCAAAGACAAA
1 AAAA-AATAAGAAAACAATACAAAAAATCAAAGACAAA
306468 AAA
1 AAA
306471 TTAAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 9 0.25
39 17 0.47
40 10 0.28
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (37 bp):
AAAAAATAAGAAAACAATACAAAAAATCAAAGACAAA
Found at i:306463 original size:22 final size:24
Alignment explanation
Indices: 306426--306477 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
306416 ATTGAAAGAC
*
306426 ATAAAAAATAATAAGA-AAACAAT
1 ATAAAAAATAATAAGACAAAAAAT
*
306449 ATAAAAAATCA-AAGACAAAAAAT
1 ATAAAAAATAATAAGACAAAAAAT
306472 -TAAAAA
1 ATAAAAA
306478 TGATAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (24 bp):
ATAAAAAATAATAAGACAAAAAAT
Found at i:306935 original size:20 final size:19
Alignment explanation
Indices: 306878--306939 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
306868 AAAATAATAC
*
306878 AAAAAATAACAAACAACGAT
1 AAAAAATAAAAAACAA-GAT
306898 AAATAAA-AAAAGAA-AAGAT
1 AAA-AAATAAAA-AACAAGAT
306917 AAAAAATTAAAAAACAAGAT
1 AAAAAA-TAAAAAACAAGAT
306937 AAA
1 AAA
306940 TTTATGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 3 0.08
19 8 0.22
20 20 0.56
21 5 0.14
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.11
Consensus pattern (19 bp):
AAAAAATAAAAAACAAGAT
Found at i:307125 original size:19 final size:20
Alignment explanation
Indices: 307103--307168 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
307093 ATGAAATGAG
307103 AAAATAG-AAAACAAATACAA
1 AAAATAGAAAAACAAATA-AA
* *
307123 AAAATTGAAAAACATAT-AA
1 AAAATAGAAAAACAAATAAA
307142 AAAATAGTAATAAAACAATATAAA
1 AAAATAG--A-AAAACAA-ATAAA
307166 AAA
1 AAA
307169 TCAAAGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.22
20 6 0.17
21 9 0.25
22 6 0.17
23 2 0.06
24 5 0.14
ACGTcount: A:0.73, C:0.06, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAATAGAAAAACAAATAAA
Found at i:307132 original size:20 final size:19
Alignment explanation
Indices: 307103--307148 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
307093 ATGAAATGAG
307103 AAAATAGAAAACAAATACAA
1 AAAATAGAAAA-AAATACAA
* * *
307123 AAAATTGAAAAACATATAA
1 AAAATAGAAAAAAATACAA
307142 AAAATAG
1 AAAATAG
307149 TAATAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAATAGAAAAAAATACAA
Found at i:307620 original size:15 final size:16
Alignment explanation
Indices: 307590--307631 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
307580 CAACAACGAT
307590 AAAAA-AAAAAAGATA
1 AAAAATAAAAAAGATA
*
307605 AAAGATAAAAAA-ATA
1 AAAAATAAAAAAGATA
307620 AAAAATAAAAAA
1 AAAAATAAAAAA
307632 CACGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAATAAAAAAGATA
Found at i:307629 original size:6 final size:7
Alignment explanation
Indices: 307588--307830 Score: 58
Period size: 7 Copynumber: 30.1 Consensus size: 7
307578 ACCAACAACG
307588 ATAAAAA
1 ATAAAAA
307595 A-AAAAA
1 ATAAAAA
*
307601 GATAAAAG
1 -ATAAAAA
307609 ATAAAAAA
1 AT-AAAAA
307617 ATAAAAA
1 ATAAAAA
307624 ATAAAAA
1 ATAAAAA
*
307631 ACACGATAAA
1 ATA--A-AAA
307641 ATTTTATGAAAA
1 A---TA--AAAA
307653 TATAAATAA
1 -ATAAA-AA
*
307662 AGAAAGAA
1 ATAAA-AA
307670 ATAAAAA
1 ATAAAAA
307677 ATAAACCAAA
1 AT-AA--AAA
307687 ATAAAAA
1 ATAAAAA
307694 ATGAAAAA
1 AT-AAAAA
*
307702 AAAAAAA
1 ATAAAAA
*
307709 GAAAAAAA
1 -ATAAAAA
307717 TATTGAAGCAAA
1 -A-T-AA--AAA
*
307729 ACAAAAA
1 ATAAAAA
307736 AGTTGAATAAA
1 A--T-AA-AAA
307747 ATACAAAAAA
1 AT--AA-AAA
*
307757 ATATAAA
1 ATAAAAA
*
307764 ATATAAA
1 ATAAAAA
307771 ATAAACAA
1 ATAAA-AA
**
307779 A-AATGCA
1 ATAA-AAA
307786 ATAAAAA
1 ATAAAAA
307793 TATAAAAA
1 -ATAAAAA
*
307801 GTAAGAAA
1 ATAA-AAA
*
307809 ATCAAAA
1 ATAAAAA
307816 ATAAAAA
1 ATAAAAA
307823 ATAAAAA
1 ATAAAAA
307830 A
1 A
307831 GACAAATGAA
Statistics
Matches: 181, Mismatches: 25, Indels: 60
0.68 0.09 0.23
Matches are distributed among these distances:
6 5 0.03
7 75 0.41
8 56 0.31
9 8 0.04
10 22 0.12
11 5 0.03
12 6 0.03
13 4 0.02
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (7 bp):
ATAAAAA
Found at i:307630 original size:34 final size:34
Alignment explanation
Indices: 307592--307705 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 34
307582 ACAACGATAA
*
307592 AAAAAAAAAGATAAAAGATAAAAAAATAAAAAAT
1 AAAAAAAAAGATAAAAAATAAAAAAATAAAAAAT
* * ** ** *
307626 AAAAAACACGATAAAATTTTATGAAAAT-ATAAAT
1 AAAAAAAAAGATAAAA-AATAAAAAAATAAAAAAT
*
307660 AAAGAAAGAA-ATAAAAAATAAACCAAAATAAAAAAT
1 AAA-AAAAAAGATAAAAAATAAA--AAAATAAAAAAT
307696 GAAAAAAAAA
1 -AAAAAAAAA
307706 AAAGAAAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
33 2 0.03
34 28 0.47
35 16 0.27
36 10 0.17
37 3 0.05
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (34 bp):
AAAAAAAAAGATAAAAAATAAAAAAATAAAAAAT
Found at i:307704 original size:17 final size:17
Alignment explanation
Indices: 307668--307708 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
307658 ATAAAGAAAG
*
307668 AAATAAAAAATAAACCA
1 AAATAAAAAATAAACAA
307685 AAATAAAAAATGAAA-AA
1 AAATAAAAAAT-AAACAA
307702 AAA-AAAA
1 AAATAAAA
307709 GAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (17 bp):
AAATAAAAAATAAACAA
Found at i:307705 original size:13 final size:13
Alignment explanation
Indices: 307664--307716 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
307654 ATAAATAAAG
307664 AAAGAAATAAAAAA
1 AAAGAAA-AAAAAA
* *
307678 TAAACCAAAATAAAA
1 -AAA-GAAAAAAAAA
*
307693 AATGAAAAAAAAA
1 AAAGAAAAAAAAA
307706 AAAGAAAAAAA
1 AAAGAAAAAAA
307717 TATTGAAGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 18 0.58
14 2 0.06
15 8 0.26
16 3 0.10
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.08
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:307716 original size:29 final size:31
Alignment explanation
Indices: 307649--307718 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
307639 AAATTTTATG
* *
307649 AAAATATAAATAAAGAAAGAAATAAAAAATA
1 AAAAAATAAATAAAGAAAGAAATAAAAAAGA
307680 AACCAAAATAAA-AAATGAAA-AAA-AAAAAAGA
1 AA--AAAATAAATAAA-GAAAGAAATAAAAAAGA
307711 AAAAAATA
1 AAAAAATA
307719 TTGAAGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
29 6 0.18
31 11 0.32
32 6 0.18
33 11 0.32
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (31 bp):
AAAAAATAAATAAAGAAAGAAATAAAAAAGA
Found at i:307741 original size:19 final size:20
Alignment explanation
Indices: 307719--307756 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
307709 GAAAAAAATA
*
307719 TTGAAGCAAA-ACAAAAAAG
1 TTGAAGAAAATACAAAAAAG
*
307738 TTGAATAAAATACAAAAAA
1 TTGAAGAAAATACAAAAAA
307757 ATATAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.16
Consensus pattern (20 bp):
TTGAAGAAAATACAAAAAAG
Found at i:307764 original size:17 final size:17
Alignment explanation
Indices: 307742--307799 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
307732 AAAAAGTTGA
307742 ATAAAATACAAAAAAAT
1 ATAAAATACAAAAAAAT
* *
307759 ATAAAATATAAAATAAAC
1 ATAAAATACAAAA-AAAT
*
307777 A-AAAATGCAATAAAAAT
1 ATAAAATACAA-AAAAAT
307794 ATAAAA
1 ATAAAA
307800 AGTAAGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 23 0.70
18 10 0.30
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (17 bp):
ATAAAATACAAAAAAAT
Found at i:307815 original size:35 final size:34
Alignment explanation
Indices: 307744--307823 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
307734 AAAGTTGAAT
307744 AAAATACAAAAAAATATAAAATATAAAATAAACA
1 AAAATACAAAAAAATATAAAATATAAAATAAACA
* *
307778 AAAATGCAATAAAAATATAAAA-AGTAAGAA-AATCA
1 AAAATACAA-AAAAATATAAAATA-TAA-AATAAACA
307813 AAAATA-AAAAA
1 AAAATACAAAAA
307824 TAAAAAAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 3 0.08
34 11 0.28
35 24 0.60
36 2 0.05
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (34 bp):
AAAATACAAAAAAATATAAAATATAAAATAAACA
Found at i:307836 original size:22 final size:24
Alignment explanation
Indices: 307788--307836 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
307778 AAAATGCAAT
*
307788 AAAAATATAAAAAGTAAGAAAATC
1 AAAAATATAAAAAGTAAGAAAAAC
307812 AAAAATA-AAAAA-TAA-AAAAGAC
1 AAAAATATAAAAAGTAAGAAAA-AC
307834 AAA
1 AAA
307837 TGAAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 7 0.30
23 5 0.22
24 7 0.30
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAATATAAAAAGTAAGAAAAAC
Found at i:307868 original size:23 final size:22
Alignment explanation
Indices: 307821--307869 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
307811 CAAAAATAAA
307821 AAATAAAAAAGACAAATGAAATG
1 AAATAAAAAAGACAAA-GAAATG
*
307844 AAATAAGAAAATACAAA-AAATTG
1 AAATAA-AAAAGACAAAGAAA-TG
307867 AAA
1 AAA
307870 AACATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 11 0.48
24 9 0.39
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAGACAAAGAAATG
Found at i:307924 original size:22 final size:23
Alignment explanation
Indices: 307866--307926 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
307856 ACAAAAAATT
*
307866 GAAAAACATATAAAAAATAATAA
1 GAAAAAAATATAAAAAATAATAA
* *
307889 GAAAACAATATAAAAAATCA-AA
1 GAAAAAAATATAAAAAATAATAA
307911 GACAAAAAAT-TAAAAA
1 GA-AAAAAATATAAAAA
307927 TGAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.15
Consensus pattern (23 bp):
GAAAAAAATATAAAAAATAATAA
Found at i:308002 original size:19 final size:19
Alignment explanation
Indices: 307980--308027 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
307970 TATAAGAATT
307980 TAAAAATGAATATAAAAAA
1 TAAAAATGAATATAAAAAA
* **
307999 TAAAAA-GAAATTTGTAAAA
1 TAAAAATG-AATATAAAAAA
308018 TAAAAATGAA
1 TAAAAATGAA
308028 AAGACAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (19 bp):
TAAAAATGAATATAAAAAA
Found at i:308129 original size:19 final size:19
Alignment explanation
Indices: 308105--308143 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
308095 AATTTTATGA
* *
308105 AAAAAATTAGAAAATGAAG
1 AAAAAATAAAAAAATGAAG
308124 AAAAAATAAAAAAATGAAG
1 AAAAAATAAAAAAATGAAG
308143 A
1 A
308144 GGCAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAAAATAAAAAAATGAAG
Found at i:308512 original size:19 final size:19
Alignment explanation
Indices: 308400--308515 Score: 68
Period size: 19 Copynumber: 6.2 Consensus size: 19
308390 AAAAATTTAT
*
308400 AAAAATAT-AAATAAAGAA
1 AAAAATATAAAATAAACAA
* *
308418 AGAAATA-AGAAATAAA-AT
1 AAAAATATA-AAATAAACAA
* *
308436 TAAAAT-TAAAATTAA-AA
1 AAAAATATAAAATAAACAA
308453 AAAAATATTAAAGCA-AAACAA
1 AAAAATA-TAAA--ATAAACAA
308474 AAAAGATA-AATAA-AAGACAA
1 AAAA-ATATAA-AATAA-ACAA
308494 AAAAATATAAAATAAACAA
1 AAAAATATAAAATAAACAA
308513 AAA
1 AAA
308516 TACGATAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
17 12 0.16
18 12 0.16
19 26 0.34
20 16 0.21
21 8 0.10
22 3 0.04
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAATATAAAATAAACAA
Found at i:308605 original size:11 final size:11
Alignment explanation
Indices: 308591--308632 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
308581 AAAACAAAAT
308591 TAAAAAACATA
1 TAAAAAACATA
308602 TAAAAAA-ATAA
1 TAAAAAACAT-A
308613 TAAGAAAACAATA
1 TAA-AAAAC-ATA
308626 TAAAAAA
1 TAAAAAA
308633 TCAAAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.07
11 11 0.41
12 8 0.30
13 4 0.15
14 2 0.07
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (11 bp):
TAAAAAACATA
Found at i:308659 original size:27 final size:26
Alignment explanation
Indices: 308628--308680 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
308618 AAACAATATA
*
308628 AAAAATCAAAGACAAAATTAAAAATGAG
1 AAAAGTCAAAG-CAAAA-TAAAAATGAG
* *
308656 AAAAGTTAATGCAAAATAAAAATGA
1 AAAAGTCAAAGCAAAATAAAAATGA
308681 AAACAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 5 0.23
28 8 0.36
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (26 bp):
AAAAGTCAAAGCAAAATAAAAATGAG
Found at i:308899 original size:18 final size:19
Alignment explanation
Indices: 308862--308899 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
308852 ATAACTGTGA
308862 AAAAAATTAGAAAAATAAG
1 AAAAAATTAGAAAAATAAG
308881 AAAAAA-TA-AAAAATGAAG
1 AAAAAATTAGAAAAAT-AAG
308899 A
1 A
308900 GGCAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAATTAGAAAAATAAG
Found at i:308960 original size:19 final size:19
Alignment explanation
Indices: 308938--308982 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
308928 AAAGTTTTGT
* * *
308938 AAAAAATTTTAAAACAAAG
1 AAAAAATGTGAAAACAAAA
308957 AAAAAA-GTGAAAACAAAA
1 AAAAAATGTGAAAACAAAA
308975 AAAAAATG
1 AAAAAATG
308983 AAAGCACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAAAATGTGAAAACAAAA
Found at i:308977 original size:17 final size:18
Alignment explanation
Indices: 308948--308985 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
308938 AAAAAATTTT
*
308948 AAAACAAAGAAAAAAGTG
1 AAAACAAAGAAAAAAATG
308966 AAAACAAA-AAAAAAATG
1 AAAACAAAGAAAAAAATG
308983 AAA
1 AAA
308986 GCACATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.79, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAACAAAGAAAAAAATG
Found at i:309063 original size:8 final size:7
Alignment explanation
Indices: 309062--309124 Score: 56
Period size: 7 Copynumber: 8.6 Consensus size: 7
309052 ACAAAAATAC
309062 AATAAAA
1 AATAAAA
309069 ATATAAAA
1 A-ATAAAA
*
309077 AATCAAA
1 AATAAAA
309084 AATAAAAA
1 AAT-AAAA
309092 AATAAAA
1 AATAAAA
* *
309099 AAGACTAA
1 AATA-AAA
309107 AATAAAA
1 AATAAAA
309114 AA-AAGAA
1 AATAA-AA
309121 AATA
1 AATA
309125 TATTAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 2 0.04
7 24 0.53
8 19 0.42
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:309091 original size:23 final size:23
Alignment explanation
Indices: 309062--309116 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
309052 ACAAAAATAC
* *
309062 AATAAAAATATAAAAAA-TCAAA
1 AATAAAAAAATAAAAAAGACAAA
*
309084 AATAAAAAAATAAAAAAGACTAA
1 AATAAAAAAATAAAAAAGACAAA
309107 AATAAAAAAA
1 AATAAAAAAA
309117 AGAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (23 bp):
AATAAAAAAATAAAAAAGACAAA
Found at i:309100 original size:15 final size:14
Alignment explanation
Indices: 309035--309124 Score: 63
Period size: 15 Copynumber: 6.1 Consensus size: 14
309025 AGAGTTGATG
*
309035 AAAAACAAAAAAGAT
1 AAAAA-AAAAAAAAT
* *
309050 AAACAAAAATACAAT
1 AAA-AAAAAAAAAAT
*
309065 AAAAATATAAAAAAT
1 AAAAA-AAAAAAAAT
*
309080 CAAAAATAAAAAAAT
1 -AAAAAAAAAAAAAT
**
309095 AAAAAAGACTAAAAT
1 AAAAAA-AAAAAAAT
*
309110 AAAAAAAAGAAAAT
1 AAAAAAAAAAAAAT
309124 A
1 A
309125 TATTAAATAA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
14 14 0.24
15 37 0.64
16 7 0.12
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:309233 original size:21 final size:21
Alignment explanation
Indices: 309177--309233 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
309167 TTATACAGTC
*
309177 CAAAA-TA-ATAAAAAAAAAT
1 CAAAATTATATAATAAAAAAT
309196 CAAAATTATATTAAATAAAAAAT
1 CAAAATTATA-T-AATAAAAAAT
309219 -AAATATTATATAATA
1 CAAA-ATTATATAATA
309234 TAATTTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 5 0.16
22 5 0.16
23 15 0.47
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAATTATATAATAAAAAAT
Found at i:309236 original size:23 final size:23
Alignment explanation
Indices: 309185--309229 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
309175 TCCAAAATAA
309185 TAAA-AAAAAATCAAAATTATAT
1 TAAATAAAAAATCAAAATTATAT
309207 TAAATAAAAAAT-AAATATTATAT
1 TAAATAAAAAATCAAA-ATTATAT
309230 AATATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAATAAAAAATCAAAATTATAT
Found at i:309444 original size:50 final size:50
Alignment explanation
Indices: 309390--309491 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
309380 ATAAGGTGAT
*
309390 CTGCATTTAAGTTAAACACAAGCAACATGCCACATATATAAAGAACAATG
1 CTGCATTTAAGTTAAACACAAGCAACATCCCACATATATAAAGAACAATG
*
309440 CTGCATTTAAGTTAAACACAAGCAACATCCCACATGTATAAAGAACAATG
1 CTGCATTTAAGTTAAACACAAGCAACATCCCACATATATAAAGAACAATG
309490 CT
1 CT
309492 ATTTTAGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.23
Consensus pattern (50 bp):
CTGCATTTAAGTTAAACACAAGCAACATCCCACATATATAAAGAACAATG
Found at i:319995 original size:16 final size:16
Alignment explanation
Indices: 319971--320031 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
319961 TTTTAATTTT
*
319971 CAAAATCCCTTAAATC
1 CAAAATCCCTAAAATC
* *
319987 CAAACTCCCAAAAATC
1 CAAAATCCCTAAAATC
*
320003 CAAAATCCCTGAAATC
1 CAAAATCCCTAAAATC
*
320019 CAAAGT-CCTAAAA
1 CAAAATCCCTAAAA
320032 ATCCTAAGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 6 0.16
16 31 0.84
ACGTcount: A:0.48, C:0.31, G:0.03, T:0.18
Consensus pattern (16 bp):
CAAAATCCCTAAAATC
Found at i:320010 original size:32 final size:32
Alignment explanation
Indices: 319971--320035 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
319961 TTTTAATTTT
*
319971 CAAAATCCCTTAAATCCAAACTCCCAAAAATC
1 CAAAATCCCTGAAATCCAAACTCCCAAAAATC
* *
320003 CAAAATCCCTGAAATCCAAAGTCCTAAAAATC
1 CAAAATCCCTGAAATCCAAACTCCCAAAAATC
320035 C
1 C
320036 TAAGGACGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.18
Consensus pattern (32 bp):
CAAAATCCCTGAAATCCAAACTCCCAAAAATC
Found at i:321542 original size:3 final size:3
Alignment explanation
Indices: 321534--321560 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
321524 ATAGAATATC
321534 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
321561 TCCATTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:329722 original size:163 final size:163
Alignment explanation
Indices: 329449--329753 Score: 520
Period size: 163 Copynumber: 1.9 Consensus size: 163
329439 TGTTAAAACC
* * *
329449 TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGTTCTGTGGCGGTAGACCAGAAAGTA
1 TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
*
329514 TCAATTCAAGGTGGTTGATTCTTACAGGATAACGAGAATGAAAGGATCAAATCAGACTGGTTGCT
66 TCAATTCAAGGTGGTTGATTCTTACAGGATAACGAGAACGAAAGGATCAAATCAGACTGGTTGCT
329579 TCTGATTATATTACTTGTCATTCTATAAACACT
131 TCTGATTATATTACTTGTCATTCTATAAACACT
* *
329612 TTCAACCATTAAGGAACTAGTAGAATGAGAGATAAAAAGGATCTGTGGCGATAGACCAGAAACTA
1 TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
* * * *
329677 TCAATTCAAGGTGGTTGCTTGTTACAGTATAATGAGAACGAAAGGATCAAATCAGACTGGTTGCT
66 TCAATTCAAGGTGGTTGATTCTTACAGGATAACGAGAACGAAAGGATCAAATCAGACTGGTTGCT
329742 TCTGATTATATT
131 TCTGATTATATT
329754 GCTTATGTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 132 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (163 bp):
TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
TCAATTCAAGGTGGTTGATTCTTACAGGATAACGAGAACGAAAGGATCAAATCAGACTGGTTGCT
TCTGATTATATTACTTGTCATTCTATAAACACT
Found at i:333050 original size:19 final size:19
Alignment explanation
Indices: 333028--333066 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
333018 TATTTGTTTA
*
333028 TTAAGTTAAAATTTAAAAT
1 TTAAATTAAAATTTAAAAT
*
333047 TTAAATTCAAATTTAAAAT
1 TTAAATTAAAATTTAAAAT
333066 T
1 T
333067 GATTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TTAAATTAAAATTTAAAAT
Found at i:334379 original size:28 final size:28
Alignment explanation
Indices: 334330--334405 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
334320 CATTTTGTCT
* *
334330 TTTTTATTATTTTCTTA--ATTTGTTAA
1 TTTTAATTATTTTCTTATTTTTTGTTAA
* * *
334356 TTTTTATT-TTCTTTTTATTTTTTGTTTA
1 TTTTAATTATT-TTCTTATTTTTTGTTAA
334384 TTTTAATTATTTTCTTATTTTT
1 TTTTAATTATTTTCTTATTTTT
334406 ATTGCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
25 2 0.05
26 13 0.32
28 24 0.59
29 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTTAATTATTTTCTTATTTTTTGTTAA
Found at i:334387 original size:17 final size:17
Alignment explanation
Indices: 334330--334408 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 17
334320 CATTTTGTCT
*
334330 TTTTTATTATTTTCTTAA
1 TTTTTATTATTTT-TTTA
*
334348 TTTGTTAATT-TTTATTTTC
1 TTT-TT-ATTATTT-TTTTA
334367 TTTTTATT-TTTTGTTTA
1 TTTTTATTATTTT-TTTA
* *
334384 TTTTAATTATTTTCTTA
1 TTTTTATTATTTTTTTA
334401 TTTTTATT
1 TTTTTATT
334409 GCTTTTTCGT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.02
17 26 0.52
18 9 0.18
19 10 0.20
20 4 0.08
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATTATTTTTTTA
Found at i:334877 original size:26 final size:25
Alignment explanation
Indices: 334832--334880 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
334822 TAATTTTAAC
334832 TTTTTATTAATTTTACTTATAAATA
1 TTTTTATTAATTTTACTTATAAATA
334857 TTTTTATTATTATTTTA-TTATAAA
1 TTTTTATTA--ATTTTACTTATAAA
334881 ATCAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTATTAATTTTACTTATAAATA
Found at i:336847 original size:29 final size:28
Alignment explanation
Indices: 336815--336879 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
336805 TTTTTTATCA
* *
336815 TTTTCTTAATTTGTTAATTTTTTATTTCT
1 TTTTCTTAATTTGTTAA-TTTTTAATTAT
* ** *
336844 TTTTATTTTTTTGTTTATTTTTAATTAT
1 TTTTCTTAATTTGTTAATTTTTAATTAT
336872 TTTTCTTA
1 TTTTCTTA
336880 TTTTTATTGC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (28 bp):
TTTTCTTAATTTGTTAATTTTTAATTAT
Found at i:336848 original size:10 final size:10
Alignment explanation
Indices: 336833--336887 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
336823 ATTTGTTAAT
*
336833 TTTTTATTTC
1 TTTTTATTTA
336843 TTTTTA-TT-
1 TTTTTATTTA
*
336851 TTTTTGTTTA
1 TTTTTATTTA
*
336861 TTTTTAATTA
1 TTTTTATTTA
*
336871 TTTTT-CTTA
1 TTTTTATTTA
336880 TTTTTATT
1 TTTTTATT
336888 GCTTTTTCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 5 0.14
9 12 0.32
10 20 0.54
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:336853 original size:18 final size:18
Alignment explanation
Indices: 336832--336887 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
336822 AATTTGTTAA
*
336832 TTTTTTATTTCTTTTTAT
1 TTTTTTATTTATTTTTAT
*
336850 TTTTTTGTTTATTTTTAAT
1 TTTTTTATTTATTTTT-AT
*
336869 TATTTTT-CTTATTTTTAT
1 T-TTTTTATTTATTTTTAT
336887 T
1 T
336888 GCTTTTTCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 17 0.52
19 11 0.33
20 5 0.15
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTATTTATTTTTAT
Found at i:336883 original size:29 final size:30
Alignment explanation
Indices: 336815--336884 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
336805 TTTTTTATCA
* * *
336815 TTTTCTTA-ATTTGTTAATTTTTTATTTCT
1 TTTTCTTATTTTTGTTAATTTTTTAATTAT
* *
336844 TTTTATT-TTTTTGTTTA-TTTTTAATTAT
1 TTTTCTTATTTTTGTTAATTTTTTAATTAT
336872 TTTTCTTATTTTT
1 TTTTCTTATTTTT
336885 ATTGCTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTTCTTATTTTTGTTAATTTTTTAATTAT
Found at i:336893 original size:19 final size:19
Alignment explanation
Indices: 336843--336909 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
336833 TTTTTATTTC
336843 TTTTTATT-TTTTT-GTTTA
1 TTTTTATTATTTTTCG-TTA
336861 TTTTTAATTATTTTTC-TTA
1 TTTTT-ATTATTTTTCGTTA
*
336880 TTTTTATTGCTTTTTCGTTA
1 TTTTTATT-ATTTTTCGTTA
336900 GTATTTTATT
1 -T-TTTTATT
336910 TTATTTTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
18 8 0.20
19 17 0.41
20 8 0.20
21 1 0.02
22 7 0.17
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTATTATTTTTCGTTA
Found at i:338023 original size:19 final size:20
Alignment explanation
Indices: 337993--338037 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
337983 AATTAGTTAT
337993 AAAATATAAACAAAAAATAA
1 AAAATATAAACAAAAAATAA
*
338013 AAAATAT-AACAAATAATAA
1 AAAATATAAACAAAAAATAA
*
338032 GAAATA
1 AAAATA
338038 AAGATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATATAAACAAAAAATAA
Found at i:338062 original size:14 final size:14
Alignment explanation
Indices: 338036--338069 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
338026 TAATAAGAAA
338036 TAAAGATATAAAAAGT
1 TAAAGATA-AAAAA-T
338052 TAAAGATAAAAAAT
1 TAAAGATAAAAAAT
338066 TAAA
1 TAAA
338070 AGAAGATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 5 0.28
16 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (14 bp):
TAAAGATAAAAAAT
Found at i:338534 original size:27 final size:28
Alignment explanation
Indices: 338486--338562 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 28
338476 ATAAATAAAG
*
338486 AAAGAAATAAAA-AATAAAACAA-AA-TAA
1 AAAGAAA-AAAATAA-AAAACAATAAGAAA
338513 AAAGAAAAAAATAAAAATACAATAAGAAA
1 AAAGAAAAAAATAAAAA-ACAATAAGAAA
338542 AAAGATAAATAAAGTAAAAAA
1 AAAGA-AAA-AAA-TAAAAAA
338563 GGAAAAATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
26 7 0.17
27 13 0.31
28 2 0.05
29 7 0.17
30 3 0.07
31 4 0.10
32 6 0.14
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (28 bp):
AAAGAAAAAAATAAAAAACAATAAGAAA
Found at i:338598 original size:70 final size:69
Alignment explanation
Indices: 338471--338601 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 69
338461 AAAATTTATG
* *
338471 AAAATATAAATAAAGAAAGAAATAAAAAATAAAACAAAATAAAAAGAAAAAAATAAAAATACAAT
1 AAAAGATAAATAAAGAAAGAAAGAAAAAATAAAACAAAATAAAAAG-AAAAAATAAAAATACAAT
338536 AAGAA
65 AAGAA
* * * *
338541 AAAAGATAAATAAAGTAAA-AAAGGAAAAATACAATAAAATATAATAAG-AAAATTAAAAATA
1 AAAAGATAAATAAAG-AAAGAAAGAAAAAATAAAACAAAATA-AA-AAGAAAAAATAAAAATA
338602 ATGAATAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
70 44 0.85
71 5 0.10
72 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (69 bp):
AAAAGATAAATAAAGAAAGAAAGAAAAAATAAAACAAAATAAAAAGAAAAAATAAAAATACAATA
AGAA
Found at i:338714 original size:23 final size:22
Alignment explanation
Indices: 338676--338735 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
338666 AAAAAATTGA
338676 AAAAC-ATA-AAAGAAATAATAAG
1 AAAACAATATAAA-AAATAA-AAG
*
338698 AAAACAATATAAAAAATCAAAG
1 AAAACAATATAAAAAATAAAAG
*
338720 ACAAAAAAT-TAAAAAA
1 A-AAACAATATAAAAAA
338736 GAGAAAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 16 0.48
23 14 0.42
24 3 0.09
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (22 bp):
AAAACAATATAAAAAATAAAAG
Found at i:339202 original size:20 final size:20
Alignment explanation
Indices: 339179--339235 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
339169 GAAAAATTAT
* *
339179 AAAATAGAATAAAAAATAGG
1 AAAATAAAATAAAAAATAAG
339199 AAAA-AATAA-AAACAAATAAG
1 AAAATAA-AATAAA-AAATAAG
339219 AAAATGAAAATAAAAAA
1 AAAAT-AAAATAAAAAA
339236 GATTCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 4 0.13
20 16 0.53
21 5 0.17
22 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (20 bp):
AAAATAAAATAAAAAATAAG
Found at i:339359 original size:20 final size:20
Alignment explanation
Indices: 339336--339402 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 20
339326 CATAAAAGAT
339336 AAAATAAAATAAAAACTAAA
1 AAAATAAAATAAAAACTAAA
*
339356 AAAACAAAAT---AA-T--A
1 AAAATAAAATAAAAACTAAA
* *
339370 AAAATTAAACAAAAACTAAA
1 AAAATAAAATAAAAACTAAA
339390 AAAATAAAA-AAAA
1 AAAATAAAATAAAA
339403 TGAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
14 8 0.22
16 1 0.03
17 4 0.11
18 1 0.03
19 4 0.11
20 18 0.50
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAATAAAATAAAAACTAAA
Found at i:339391 original size:41 final size:40
Alignment explanation
Indices: 339341--339417 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
339331 AAGATAAAAT
*
339341 AAAAT-AAAAACTAAAAAAACA-AAATAATAAAAATTAAACA
1 AAAATAAAAAAATAAAAAAA-ATAAA-AATAAAAATTAAACA
*
339381 AAAACTAAAAAAATAAAAAAAATGAAAATAAAAATTA
1 AAAA-TAAAAAAATAAAAAAAATAAAAATAAAAATTA
339418 GCTAATCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
40 4 0.12
41 13 0.41
42 15 0.47
ACGTcount: A:0.78, C:0.05, G:0.01, T:0.16
Consensus pattern (40 bp):
AAAATAAAAAAATAAAAAAAATAAAAATAAAAATTAAACA
Found at i:339409 original size:35 final size:34
Alignment explanation
Indices: 339336--339413 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
339326 CATAAAAGAT
* * *
339336 AAAATAAAATAAAAACTAAAAAAACAAAATAATA
1 AAAATAAAACAAAAACTAAAAAAAAAAAAAAATA
* *
339370 AAAATTAAACAAAAACTAAAAAAATAAAAAAAATG
1 AAAATAAAACAAAAACTAAAAAAA-AAAAAAAATA
339405 AAAATAAAA
1 AAAATAAAA
339414 ATTAGCTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 22 0.59
35 15 0.41
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.14
Consensus pattern (34 bp):
AAAATAAAACAAAAACTAAAAAAAAAAAAAAATA
Found at i:339569 original size:12 final size:14
Alignment explanation
Indices: 339535--339571 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
339525 TATAGTAAAA
339535 AAAGATATAAAAATC
1 AAAGATA-AAAAATC
339550 AAAGATAAAAAAT-
1 AAAGATAAAAAATC
339563 AAA-ATAAAA
1 AAAGATAAAA
339572 GTCAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 3 0.14
14 6 0.27
15 7 0.32
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAGATAAAAAATC
Found at i:339667 original size:23 final size:22
Alignment explanation
Indices: 339624--339669 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
339614 CTGAGATTTT
* * *
339624 AAAATTGTGAAGAAGAAATAAA
1 AAAAATGTGAACAAAAAATAAA
339646 AAAAATGTGAACAAAAAGATAAA
1 AAAAATGTGAACAAAAA-ATAAA
339669 A
1 A
339670 CCAAAAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.67, C:0.02, G:0.15, T:0.15
Consensus pattern (22 bp):
AAAAATGTGAACAAAAAATAAA
Found at i:340087 original size:16 final size:17
Alignment explanation
Indices: 340068--340105 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
340058 AAAAACTAAT
340068 AAAAATGA-AAAATGAA
1 AAAAATGACAAAATGAA
*
340084 AAAAA-GACAAAATGGA
1 AAAAATGACAAAATGAA
340100 AAAAAT
1 AAAAAT
340106 AATTAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAATGACAAAATGAA
Found at i:340134 original size:7 final size:7
Alignment explanation
Indices: 340124--340201 Score: 50
Period size: 7 Copynumber: 10.9 Consensus size: 7
340114 TATAAAATAC
340124 AAAAAAT
1 AAAAAAT
340131 AAAAAA-
1 AAAAAAT
* * *
340137 ATATAAC
1 AAAAAAT
*
340144 AAATAAT
1 AAAAAAT
*
340151 AAGAAAT
1 AAAAAAT
340158 AAAGAAAT
1 AAA-AAAT
340166 AAAAAAT
1 AAAAAAT
* *
340173 CAAAGAT
1 AAAAAAT
340180 AAAAAATT
1 AAAAAA-T
*
340188 AAAAGAAG
1 AAAA-AAT
340196 AAAAAA
1 AAAAAA
340202 GTTAATACAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
6 4 0.07
7 33 0.60
8 16 0.29
9 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:340135 original size:8 final size:8
Alignment explanation
Indices: 340117--340201 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
340107 ATTAGTTTAT
340117 AAAATACAA
1 AAAATA-AA
340126 AAAATAAA
1 AAAATAAA
340134 AAAATATAA
1 AAAATA-AA
*
340143 CAAATAATA
1 AAAATAA-A
340152 AGAAATAAA
1 A-AAATAAA
*
340161 GAAAT-AA
1 AAAATAAA
*
340168 AAAAT-CA
1 AAAATAAA
*
340175 AAGATAAA
1 AAAATAAA
*
340183 AAATTAAA
1 AAAATAAA
* *
340191 AGAAGAAA
1 AAAATAAA
340199 AAA
1 AAA
340202 GTTAATACAA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
7 11 0.19
8 27 0.46
9 15 0.25
10 6 0.10
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:340172 original size:15 final size:15
Alignment explanation
Indices: 340143--340201 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
340133 AAAAATATAA
* *
340143 CAAATAATAAGAAAT
1 CAAAGAATAAAAAAT
340158 -AAAGAAATAAAAAAT
1 CAAAG-AATAAAAAAT
340173 CAAAG-ATAAAAAATT
1 CAAAGAATAAAAAA-T
* *
340188 AAAAGAAGAAAAAA
1 CAAAGAATAAAAAA
340202 GTTAATACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 11 0.31
15 14 0.39
16 11 0.31
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (15 bp):
CAAAGAATAAAAAAT
Found at i:340594 original size:16 final size:15
Alignment explanation
Indices: 340552--340594 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
340542 GAGAATGCAT
340552 AAAAAGAAAAAAAAC
1 AAAAAGAAAAAAAAC
* *
340567 AAAAAGCTAAAAAAAG
1 AAAAAG-AAAAAAAAC
*
340583 GAAAAGAAAAAA
1 AAAAAGAAAAAA
340595 GAAATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAC
Found at i:341135 original size:8 final size:9
Alignment explanation
Indices: 341114--341139 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
341104 AAATTTTTAT
341114 AAAAATAAC
1 AAAAATAAC
341123 AAAAATAAC
1 AAAAATAAC
341132 AAAAATAA
1 AAAAATAA
341140 AAGGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAC
Found at i:341524 original size:17 final size:17
Alignment explanation
Indices: 341487--341524 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
341477 AAATACAAGC
*
341487 CAAAAAAAGTAAAAAGA
1 CAAAAAAAGTAAAAAAA
341504 CAAAAAAA-TAAAAAAA
1 CAAAAAAAGTAAAAAAA
341520 TCAAA
1 -CAAA
341525 GATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (17 bp):
CAAAAAAAGTAAAAAAA
Found at i:341946 original size:18 final size:18
Alignment explanation
Indices: 341931--342067 Score: 61
Period size: 19 Copynumber: 7.3 Consensus size: 18
341921 AAAGAAATTA
341931 AAAATAAAAATAAAATAAT
1 AAAA-AAAAATAAAATAAT
**
341950 AAAAAAAAATTAAAGCAA-
1 AAAAAAAAA-TAAAATAAT
341968 AAGAAAAAAGAT-AAATAAAGT
1 AA-AAAAAA-ATAAAAT-AA-T
*
341989 ACAAAAAAATACAAA-AAT
1 AAAAAAAAATA-AAATAAT
* *
342007 ACAAAAAATATAAAAATAAG
1 A-AAAAAAAAT-AAAATAAT
*
342027 AAAATCAAAAAGAAAA-AA-
1 AAAA--AAAAATAAAATAAT
*
342045 AAAAAAAAA-AAATTGAAT
1 AAAAAAAAATAAAAT-AAT
342063 AAAAA
1 AAAAA
342068 TTTCAAAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 33
0.67 0.08 0.24
Matches are distributed among these distances:
15 3 0.03
16 5 0.05
17 2 0.02
18 20 0.22
19 38 0.42
20 15 0.16
21 8 0.09
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAAAAATAAAATAAT
Found at i:342014 original size:17 final size:16
Alignment explanation
Indices: 341991--342056 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 16
341981 AATAAAGTAC
341991 AAAAAAATACAAAAAT
1 AAAAAAATACAAAAAT
*
342007 ACAAAAAATATAAAAAT
1 A-AAAAAATACAAAAAT
* *
342024 AAGAAAAT-CAAAAAG
1 AAAAAAATACAAAAAT
342039 AAAAAAA-A-AAAAA-
1 AAAAAAATACAAAAAT
342052 AAAAA
1 AAAAA
342057 TTGAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 11 0.26
16 7 0.16
17 15 0.35
ACGTcount: A:0.83, C:0.05, G:0.03, T:0.09
Consensus pattern (16 bp):
AAAAAAATACAAAAAT
Found at i:342030 original size:9 final size:8
Alignment explanation
Indices: 341936--342057 Score: 64
Period size: 8 Copynumber: 13.8 Consensus size: 8
341926 AATTAAAAAT
341936 AAAAATAA
1 AAAAATAA
*
341944 AATAATAAAA
1 AA-AA-ATAA
341954 AAAAATTAA
1 AAAAA-TAA
*
341963 AGCAAAAGAA
1 A--AAAATAA
341973 AAAAGATAA
1 AAAA-ATAA
*
341982 ATAAAGTACAA
1 A-AAA--ATAA
*
341993 AAAAATAC
1 AAAAATAA
342001 AAAAATACA
1 AAAAATA-A
*
342010 AAAAATAT
1 AAAAATAA
342018 AAAAATAA
1 AAAAATAA
*
342026 GAAAATCAA
1 AAAAAT-AA
*
342035 AAAGAAAAA
1 AAA-AATAA
*
342044 AAAAAAAA
1 AAAAATAA
342052 AAAAAT
1 AAAAAT
342058 TGAATAAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 37 0.42
9 27 0.31
10 16 0.18
11 8 0.09
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:342172 original size:22 final size:23
Alignment explanation
Indices: 342128--342187 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
342118 AAAAAATTGA
*
342128 AAAACAA-ATAAGAAATAATAAG
1 AAAACAATATAAAAAATAATAAG
*
342150 AAAACAATATAAAAAATCA-AAG
1 AAAACAATATAAAAAATAATAAG
*
342172 ACAAAAAAT-TAAAAAA
1 A-AAACAATATAAAAAA
342188 GATAAAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (23 bp):
AAAACAATATAAAAAATAATAAG
Found at i:342398 original size:17 final size:17
Alignment explanation
Indices: 342368--342413 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
342358 AAAAAAGAAT
342368 ATAAAAAATTTTAAAAC-A
1 ATAAAAAA--TTAAAACAA
342386 ATGAAAAAATTAAAACAA
1 AT-AAAAAATTAAAACAA
342404 ATAAAAAATT
1 ATAAAAAATT
342414 TTGAAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 15 0.58
18 5 0.19
19 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAAAAAATTAAAACAA
Found at i:342410 original size:18 final size:18
Alignment explanation
Indices: 342368--342412 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
342358 AAAAAAGAAT
*
342368 ATAAAAAATTTTAAAACA
1 ATAAAAAATATTAAAACA
*
342386 ATGAAAAA-ATTAAAACAA
1 ATAAAAAATATTAAAAC-A
342404 ATAAAAAAT
1 ATAAAAAAT
342413 TTTGAAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
ATAAAAAATATTAAAACA
Found at i:342552 original size:11 final size:11
Alignment explanation
Indices: 342532--342565 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
342522 ATAAAAATTT
*
342532 TAAAATATAAA
1 TAAAAAATAAA
342543 TAAAAAATAAA
1 TAAAAAATAAA
*
342554 TGAAAAATAAA
1 TAAAAAATAAA
342565 T
1 T
342566 TAAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:342575 original size:15 final size:15
Alignment explanation
Indices: 342534--342600 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
342524 AAAAATTTTA
*
342534 AAATATAA-ATAAA-
1 AAATATAAGAAAAAT
342547 AAATA-AATGAAAAAT
1 AAATATAA-GAAAAAT
342562 AAAT-TAAGAGAAAAT
1 AAATATAAGA-AAAAT
342577 ATTAATATAAGAAAAAT
1 A--AATATAAGAAAAAT
342594 AAA-ATAA
1 AAATATAA
342601 ATACTAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
12 2 0.04
13 5 0.11
14 10 0.22
15 14 0.31
17 9 0.20
18 5 0.11
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (15 bp):
AAATATAAGAAAAAT
Found at i:342599 original size:16 final size:16
Alignment explanation
Indices: 342540--342599 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
342530 TTTAAAATAT
*
342540 AAATAAAAAATAAATGAA
1 AAATAAAATAT-AA-GAA
342558 AAAT-AAAT-TAAGAGA
1 AAATAAAATATAAGA-A
*
342573 AAATATTAATATAAGAA
1 AAATA-AAATATAAGAA
342590 AAATAAAATA
1 AAATAAAATA
342600 AATACTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 2 0.06
15 7 0.20
16 5 0.14
17 12 0.34
18 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (16 bp):
AAATAAAATATAAGAA
Found at i:342778 original size:14 final size:12
Alignment explanation
Indices: 342716--342790 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 12
342706 AGTTTAGAAT
342716 ATAAAAAGA-AAA
1 ATAAAAA-ATAAA
*
342728 ATAAAAAAT-AT
1 ATAAAAAATAAA
*
342739 ATAACAAAT---
1 ATAAAAAATAAA
*
342748 ATAGAAAA-AAA
1 ATAAAAAATAAA
342759 ATAAAAAATCAAA
1 ATAAAAAAT-AAA
342772 GATAAAAAATAAA
1 -ATAAAAAATAAA
342785 ATAAAA
1 ATAAAA
342791 GTCAATACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
9 6 0.12
11 17 0.33
12 13 0.25
13 6 0.12
14 9 0.18
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:342795 original size:25 final size:25
Alignment explanation
Indices: 342720--342790 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
342710 TAGAATATAA
* *
342720 AAAGA-AAAATAAAAAATATATAA-C
1 AAAGATAAAA-AAAAAATAAAAAATC
* *
342744 AAATATAGAAAAAAAATAAAAAATC
1 AAAGATAAAAAAAAAATAAAAAATC
342769 AAAGATAAAAAATAAAATAAAA
1 AAAGATAAAAAA-AAAATAAAA
342791 GTCAATACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
24 15 0.39
25 14 0.37
26 9 0.24
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAGATAAAAAAAAAATAAAAAATC
Found at i:343243 original size:20 final size:20
Alignment explanation
Indices: 343201--343245 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
343191 AATAAGTACT
* *
343201 AAAAAAAGAAAAAAATTAGA
1 AAAAAAACAAAAAAATAAGA
* *
343221 AAAAAAACAAAAACATAATA
1 AAAAAAACAAAAAAATAAGA
343241 AAAAA
1 AAAAA
343246 TAAAAAAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.09
Consensus pattern (20 bp):
AAAAAAACAAAAAAATAAGA
Done.