Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:403621 original size:22 final size:22
Alignment explanation
Indices: 403582--403623 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
403572 GGGGAAAACA
*
403582 AAAAAAAAGAAAAGAAAAAAGG
1 AAAAAAAAGAAAACAAAAAAGG
* *
403604 AAAAAAAAGCACACAAAAAA
1 AAAAAAAAGAAAACAAAAAA
403624 TGACAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAACAAAAAAGG
Found at i:409788 original size:20 final size:19
Alignment explanation
Indices: 409724--409788 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
409714 TAAATGTTTT
409724 TATGAATAGTACTATATTG
1 TATGAATAGTACTATATTG
*
409743 TATGAATAGTACTTATACTG
1 TATGAATAGTAC-TATATTG
*
409763 TATGAATAGTATCGATATTG
1 TATGAATAGTA-CTATATTG
*
409783 TGTGAA
1 TATGAA
409789 CATAGATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.30
20 27 0.68
21 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.40
Consensus pattern (19 bp):
TATGAATAGTACTATATTG
Found at i:412462 original size:20 final size:20
Alignment explanation
Indices: 412398--412462 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
412388 AAAATATTTT
*
412398 TATGAATAGTACT-ATATTG
1 TATGAATAGTACTGATATTA
* *
412417 TATGAATAGTATTGATACTA
1 TATGAATAGTACTGATATTA
412437 TATGAATAGTACTGATATTA
1 TATGAATAGTACTGATATTA
*
412457 TGTGAA
1 TATGAA
412463 CAGTGATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
TATGAATAGTACTGATATTA
Found at i:412976 original size:33 final size:34
Alignment explanation
Indices: 412913--412977 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
412903 AGGGGTTTTT
*
412913 GGTTCTAGCTAAGCCCGTGAAAAAGATAGGGAAA
1 GGTTCTAGCTAAGCCCATGAAAAAGATAGGGAAA
* *
412947 GGTTCTAGTTTAGCCCAT-AAAAA-ACTAGGGA
1 GGTTCTAGCTAAGCCCATGAAAAAGA-TAGGGA
412978 GTTATAAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 1 0.04
33 11 0.41
34 15 0.56
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (34 bp):
GGTTCTAGCTAAGCCCATGAAAAAGATAGGGAAA
Found at i:415271 original size:20 final size:20
Alignment explanation
Indices: 415234--415285 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
415224 TTATGATTAA
*
415234 TATC-ATACTGTATGAATAG
1 TATCGATACTGTATAAATAG
* *
415253 TATTGATATTGTATAAATAG
1 TATCGATACTGTATAAATAG
415273 TATCGATACTGTA
1 TATCGATACTGTA
415286 AGAGTAGTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATACTGTATAAATAG
Found at i:415293 original size:20 final size:20
Alignment explanation
Indices: 415234--415306 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
415224 TTATGATTAA
*
415234 TATC-ATACTGTATGAATAG
1 TATCGATACTGTAAGAATAG
* *
415253 TATTGATATTGTATA-AATAG
1 TATCGATACTGTA-AGAATAG
*
415273 TATCGATACTGTAAGAGTAG
1 TATCGATACTGTAAGAATAG
* *
415293 TACCAATACTGTAA
1 TATCGATACTGTAA
415307 CAACCCGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.09
20 39 0.91
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (20 bp):
TATCGATACTGTAAGAATAG
Found at i:416128 original size:29 final size:30
Alignment explanation
Indices: 416089--416240 Score: 211
Period size: 30 Copynumber: 5.2 Consensus size: 30
416079 ACCGGGTGAC
* **
416089 ATTTTGAGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
416118 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
* * *
416148 ATTTTGGGAATTTAATTTGAAGAA-GTGTT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
* *
416177 ATATTGGGAATTTAATTCG-AAAAGATGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
416206 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
416236 ATTTT
1 ATTTT
416241 AGTAATTATT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
28 3 0.03
29 51 0.48
30 53 0.50
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.39
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAAAGGTGCT
Found at i:416135 original size:30 final size:29
Alignment explanation
Indices: 416089--416240 Score: 200
Period size: 29 Copynumber: 5.2 Consensus size: 29
416079 ACCGGGTGAC
* *
416089 ATTTTGAGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
416118 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
* *
416148 ATTTTGGGAATTTAATTTGAAGAA-GTGTT
1 ATTTTGGGAATTTAATTCGAA-AAGGTGCT
* *
416177 ATATTGGGAATTTAATTCGAAAAGATGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
416206 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
416236 ATTTT
1 ATTTT
416241 AGTAATTATT
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
28 2 0.02
29 55 0.51
30 48 0.44
31 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.39
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:423386 original size:29 final size:29
Alignment explanation
Indices: 423344--423527 Score: 205
Period size: 29 Copynumber: 6.3 Consensus size: 29
423334 CCATTGACCG
* *
423344 GGTGATATTTTGGGAA-TTAATTCGAAATA
1 GGTGCTATTTTGGGAATTTAATTTGAAA-A
**
423373 GGTGCTATTTTGGGAATTTAATTCAAAAA
1 GGTGCTATTTTGGGAATTTAATTTGAAAA
*
423402 GGTGCTATTTTGGAAATTTAATTTGAAAA
1 GGTGCTATTTTGGGAATTTAATTTGAAAA
*
423431 -GTGCTATATTGGGAATTTAATTTGAAAA
1 GGTGCTATTTTGGGAATTTAATTTGAAAA
*
423459 TGTGCTATTTTGGGAATTTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTTAATTTG-AAAA
* * * *
423489 GGTG-TCATTTTAGTAA-TTATTTTAAAAA
1 GGTGCT-ATTTTGGGAATTTAATTTGAAAA
423517 GGGTGCTATTT
1 -GGTGCTATTT
423528 ATGTAAAATG
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
28 30 0.22
29 80 0.59
30 26 0.19
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTTAATTTGAAAA
Found at i:423443 original size:57 final size:58
Alignment explanation
Indices: 423344--423492 Score: 203
Period size: 57 Copynumber: 2.6 Consensus size: 58
423334 CCATTGACCG
* * *
423344 GGTGATATTTTGGGAA-TTAATTCGAAATAGGTGCTATTTTGGGAATTTAATTCAAAAA
1 GGTGCTATTTTGGGAATTTAATTTGAAA-AGGTGCTATATTGGGAATTTAATTCAAAAA
* **
423402 GGTGCTATTTTGGAAATTTAATTTGAAAA-GTGCTATATTGGGAATTTAATTTGAAAA
1 GGTGCTATTTTGGGAATTTAATTTGAAAAGGTGCTATATTGGGAATTTAATTCAAAAA
*
423459 TGTGCTATTTTGGGAATTTAATTTGAAAAAGGTG
1 GGTGCTATTTTGGGAATTTAATTTG-AAAAGGTG
423493 TCATTTTAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 48 0.60
58 19 0.24
59 13 0.16
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTTAATTTGAAAAGGTGCTATATTGGGAATTTAATTCAAAAA
Found at i:423517 original size:86 final size:86
Alignment explanation
Indices: 423353--423517 Score: 219
Period size: 86 Copynumber: 1.9 Consensus size: 86
423343 GGGTGATATT
*
423353 TTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTTAATTCAAAAAGGTGCTATTTTGGAAA
1 TTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTTAATTCAAAAAGGTGCTATTTTAGAAA
*
423418 TTTAATTTGAAAAGTGCTATA
66 TTTAATTTAAAAAGTGCTATA
* * *
423439 TTGGGAATTTAATTTGAAA-ATGTGCTATTTTGGGAATTTAATTTGAAAAAGGTG-TCATTTTAG
1 TTGGGAA-TTAATTCGAAATAGGTGCTATTTTGGGAATTTAA-TTCAAAAAGGTGCT-ATTTTAG
* *
423502 TAA-TTATTTTAAAAAG
63 AAATTTAATTTAAAAAG
423518 GGTGCTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
86 40 0.58
87 29 0.42
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (86 bp):
TTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTTAATTCAAAAAGGTGCTATTTTAGAAA
TTTAATTTAAAAAGTGCTATA
Found at i:424656 original size:20 final size:22
Alignment explanation
Indices: 424618--424657 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
424608 TTTTTGCAGA
424618 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
424640 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
424658 AAATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:426981 original size:31 final size:31
Alignment explanation
Indices: 426946--427008 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
426936 GTACCTTTTT
* * *
426946 CATATTCAAGCCATATAACTTGTACTT-TTCA
1 CATATACAAACCATATAACATGTA-TTGTTCA
*
426977 CATATACAAATCATATAACATGTATTGTTCA
1 CATATACAAACCATATAACATGTATTGTTCA
427008 C
1 C
427009 TTTTTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (31 bp):
CATATACAAACCATATAACATGTATTGTTCA
Found at i:427111 original size:26 final size:26
Alignment explanation
Indices: 427082--427148 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
427072 GTGCGCAATA
427082 TGCACTCAGAAGTGCCTCAGATAACT
1 TGCACTCAGAAGTGCCTCAGATAACT
* *
427108 TGCACTC-GAAAGTGCCTCATATCACT
1 TGCACTCAG-AAGTGCCTCAGATAACT
*
427134 TGCAC-CATAAGTGCC
1 TGCACTCAGAAGTGCC
427149 ATATAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (26 bp):
TGCACTCAGAAGTGCCTCAGATAACT
Found at i:431673 original size:21 final size:21
Alignment explanation
Indices: 431614--431673 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
431604 ACTAGTATCA
* *
431614 AAAGTTCCTTAGCACTGTACC
1 AAAGTTCCTTAGCATTGAACC
** * * *
431635 AAAACTCCATATCATTGAACT
1 AAAGTTCCTTAGCATTGAACC
431656 AAAGTTCCTTAGCATTGA
1 AAAGTTCCTTAGCATTGA
431674 TTTAGAATAT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAGTTCCTTAGCATTGAACC
Found at i:432038 original size:2 final size:2
Alignment explanation
Indices: 432031--432068 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
432021 TACCTATTTG
432031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432069 TATTACTCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441417 original size:2 final size:2
Alignment explanation
Indices: 441412--441450 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
441402 AAAAAATCAA
* *
441412 AT AT AT AT AT AT AT -T AT AT TT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
441451 TTGGTAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:442270 original size:16 final size:16
Alignment explanation
Indices: 442249--442305 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
442239 ATGTTAGTTG
442249 TTAATATTATAAGGTT
1 TTAATATTATAAGGTT
*
442265 TTAATACTTATGTTA-GTT
1 TTAATA-TTA--TAAGGTT
442283 GTTAATATTATAAGGTT
1 -TTAATATTATAAGGTT
*
442300 CTAATA
1 TTAATA
442306 CTATGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
16 13 0.39
17 6 0.18
18 6 0.18
19 8 0.24
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (16 bp):
TTAATATTATAAGGTT
Found at i:442275 original size:35 final size:35
Alignment explanation
Indices: 442233--442307 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
442223 CAAGCATTGC
*
442233 ATACTTATGTTAGTTGTTAATATTATAAGGTTTTA
1 ATACTTATGTTAGTTGTTAATATTATAAGGTTCTA
442268 ATACTTATGTTAGTTGTTAATATTATAAGGTTCTA
1 ATACTTATGTTAGTTGTTAATATTATAAGGTTCTA
442303 ATACT
1 ATACT
442308 ATGATTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.49
Consensus pattern (35 bp):
ATACTTATGTTAGTTGTTAATATTATAAGGTTCTA
Found at i:442289 original size:19 final size:18
Alignment explanation
Indices: 442237--442293 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
442227 CATTGCATAC
442237 TTATGTTAGTTGTTAATA
1 TTATGTTAGTTGTTAATA
*
442255 TTA--TAAGGTT-TTAATA
1 TTATGTTA-GTTGTTAATA
442271 CTTATGTTAGTTGTTAATA
1 -TTATGTTAGTTGTTAATA
442290 TTAT
1 TTAT
442294 AAGGTTCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 8 0.25
17 6 0.19
18 10 0.31
19 8 0.25
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (18 bp):
TTATGTTAGTTGTTAATA
Found at i:444449 original size:13 final size:14
Alignment explanation
Indices: 444412--444466 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
444402 CCTCGTATTG
444412 TTTCTGTTTTATTTAAT
1 TTTCT-TTTTA-TT-AT
*
444429 TTTTTTTTTATTA-
1 TTTCTTTTTATTAT
*
444442 TTTCTTTTT-TCAT
1 TTTCTTTTTATTAT
444455 TTTCTTTTTATT
1 TTTCTTTTTATT
444467 TCATTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 2 0.06
13 17 0.53
14 2 0.06
15 2 0.06
16 5 0.16
17 4 0.12
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTCTTTTTATTAT
Found at i:444465 original size:23 final size:26
Alignment explanation
Indices: 444430--444482 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
444420 TTATTTAATT
*
444430 TTTTTTTTATTATTTC-TTTT-TTCA
1 TTTTCTTTATTATTTCATTTTATTCA
444454 TTTTCTTT-TTATTTCATTTTATTCA
1 TTTTCTTTATTATTTCATTTTATTCA
444479 TTTT
1 TTTT
444483 TAACCTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 11 0.42
25 8 0.31
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTCTTTATTATTTCATTTTATTCA
Found at i:444468 original size:16 final size:16
Alignment explanation
Indices: 444412--444473 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
444402 CCTCGTATTG
*
444412 TTTCTGTTTTATTTAAT
1 TTTCT-TTTTATTTCAT
*
444429 TTTTTTTTTA-TT-A-
1 TTTCTTTTTATTTCAT
444442 TTTC--TTT-TTTCAT
1 TTTCTTTTTATTTCAT
444455 TTTCTTTTTATTTCAT
1 TTTCTTTTTATTTCAT
444471 TTT
1 TTT
444474 ATTCATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
11 5 0.14
12 1 0.03
13 7 0.19
14 1 0.03
15 5 0.14
16 14 0.38
17 4 0.11
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTATTTCAT
Found at i:444536 original size:18 final size:18
Alignment explanation
Indices: 444510--444545 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
444500 ATTTTATTAT
444510 TTCATTATTTTTTTCTTTA
1 TTCATTA-TTTTTTCTTTA
444529 TTCA-TATTTTTTCTTTA
1 TTCATTATTTTTTCTTTA
444546 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 2 0.12
19 4 0.24
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
TTCATTATTTTTTCTTTA
Found at i:444651 original size:10 final size:10
Alignment explanation
Indices: 444592--444660 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
444582 TGATTTACTA
* *
444592 TTTTAATTAG
1 TTTTATTTAT
444602 TTTTA-TTAT
1 TTTTATTTAT
*
444611 TTTTATTTTTT
1 TTTTA-TTTAT
444622 TGGTTTATTTAAT
1 T--TTTATTT-AT
*
444635 ATTTATTTAT
1 TTTTATTTAT
444645 TTTTATTTAT
1 TTTTATTTAT
444655 TTTTAT
1 TTTTAT
444661 CTAACATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 8 0.16
10 22 0.45
11 11 0.22
12 3 0.06
13 5 0.10
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:447133 original size:8 final size:8
Alignment explanation
Indices: 447120--447158 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
447110 GAACATTTCA
*
447120 TGCATTCT
1 TGCATTTT
447128 TGCA-TTT
1 TGCATTTT
447135 TGCATTTT
1 TGCATTTT
*
447143 TGCCTTTT
1 TGCATTTT
447151 TGCATTTT
1 TGCATTTT
447159 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:452332 original size:20 final size:20
Alignment explanation
Indices: 452309--452362 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
452299 TTTTTTGAAA
* *
452309 TTTTGGCTTTTTTGGCTCTT
1 TTTTTGCTTTTTTGCCTCTT
* *
452329 TTTTTGTTTTTTTGCCTTTT
1 TTTTTGCTTTTTTGCCTCTT
452349 TTTTTGCATTTTTT
1 TTTTTGC-TTTTTT
452363 TGTTTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.02, C:0.11, G:0.13, T:0.74
Consensus pattern (20 bp):
TTTTTGCTTTTTTGCCTCTT
Found at i:452341 original size:11 final size:11
Alignment explanation
Indices: 452335--452382 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
452325 TCTTTTTTTG
*
452335 TTTTTTTGCCTT
1 TTTTTTTG-TTT
**
452347 TTTTTTTG-CA
1 TTTTTTTGTTT
452357 TTTTTTTGTTT
1 TTTTTTTGTTT
452368 TTTTTTTGTTT
1 TTTTTTTGTTT
452379 TTTT
1 TTTT
452383 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 8 0.26
11 15 0.48
12 8 0.26
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.83
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:452368 original size:20 final size:19
Alignment explanation
Indices: 452316--452383 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
452306 AAATTTTGGC
* *
452316 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGCTTTTTTTTTG
452335 TTTTTTTGCCTTTTTTTTTG
1 TTTTTTTG-CTTTTTTTTTG
*
452355 CATTTTTTTGTTTTTTTTTTG
1 --TTTTTTTGCTTTTTTTTTG
452376 TTTTTTTG
1 TTTTTTTG
452384 AAAAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 15 0.35
20 10 0.23
21 10 0.23
22 8 0.19
ACGTcount: A:0.01, C:0.07, G:0.12, T:0.79
Consensus pattern (19 bp):
TTTTTTTGCTTTTTTTTTG
Found at i:454807 original size:22 final size:22
Alignment explanation
Indices: 454779--454822 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
454769 AGCTACCCCA
*
454779 TCAAACCTTTGAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
454801 TCAAACCATTGAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
454823 AACAAAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (22 bp):
TCAAACCATTGAGCATCAAATG
Found at i:455297 original size:32 final size:33
Alignment explanation
Indices: 455228--455300 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
455218 TGAGAAACAT
*
455228 TTGGGGCA-TCTTTGAAGATTCAACATCAAATG
1 TTGGGGCATTCTTTGAAGATTCAACATCAAATA
* * * *
455260 CTGGGGCATTTTTTGAA-ATTCAACATCGAGTA
1 TTGGGGCATTCTTTGAAGATTCAACATCAAATA
455292 TTGGGGCAT
1 TTGGGGCAT
455301 CTTAGGGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (33 bp):
TTGGGGCATTCTTTGAAGATTCAACATCAAATA
Found at i:455730 original size:37 final size:37
Alignment explanation
Indices: 455688--455786 Score: 162
Period size: 37 Copynumber: 2.7 Consensus size: 37
455678 TTAAAACACA
455688 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
* * *
455725 TTTTGTCTCTCTTGGGACAGTTTCTTTTTGAACTAAG
1 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
*
455762 TTTTATCTCCCTTGAGACAGTTTCT
1 TTTTGTCTCCCTTGAGACAGTTTCT
455787 CTTGAAACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.46
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
Found at i:456162 original size:106 final size:106
Alignment explanation
Indices: 456033--456767 Score: 1115
Period size: 106 Copynumber: 7.0 Consensus size: 106
456023 ATATCGTGCC
* *
456033 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
456098 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
456139 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
456204 AATTTCAGAGCCAGTTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
456245 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
456310 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
456351 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
456416 AATTTCGGATCCAATTTCAACTTCACGGCTAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
456457 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTG-------ACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
456515 AATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
456556 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
456621 AATTTTGGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
456662 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
456727 AATTTCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
456768 CCTCAAAACA
Statistics
Matches: 571, Mismatches: 51, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
99 88 0.15
106 483 0.85
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:458207 original size:10 final size:11
Alignment explanation
Indices: 458141--458209 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 11
458131 ATTGTTTCTG
*
458141 TTTTATTTAAT
1 TTTTATTTCAT
458152 TTTT-TTT-AT
1 TTTTATTTCAT
*
458161 TTATTATTTCTT
1 TT-TTATTTCAT
458173 TTTTCATTTTCA-
1 TTTT-A-TTTCAT
458185 TTTTATTTC-T
1 TTTTATTTCAT
458195 TTTTA-TTCAT
1 TTTTATTTCAT
458205 TTTTA
1 TTTTA
458210 ACCTTACTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
9 7 0.14
10 20 0.41
11 10 0.20
12 8 0.16
13 4 0.08
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTCAT
Found at i:458261 original size:18 final size:18
Alignment explanation
Indices: 458235--458270 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
458225 ATTTTATTAT
458235 TTCATTATTTTTTTCTTTA
1 TTCATTA-TTTTTTCTTTA
458254 TTCA-TATTTTTTCTTTA
1 TTCATTATTTTTTCTTTA
458271 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 2 0.12
19 4 0.24
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
TTCATTATTTTTTCTTTA
Found at i:458340 original size:9 final size:9
Alignment explanation
Indices: 458311--458379 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
458301 TCTCCTTTGA
*
458311 TTTACTATT
1 TTTATTATT
* *
458320 TTAATTAGT
1 TTTATTATT
458329 TTTATTATT
1 TTTATTATT
458338 TTTATT-TT
1 TTTATTATT
* *
458346 TTTGGTT-TA
1 TTT-ATTATT
458355 TTTATTTATT
1 TTTA-TTATT
458365 TTTATTTATT
1 TTTA-TTATT
458375 TTTAT
1 TTTAT
458380 CTAACATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 5 0.10
9 28 0.58
10 15 0.31
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.74
Consensus pattern (9 bp):
TTTATTATT
Found at i:458370 original size:10 final size:10
Alignment explanation
Indices: 458318--458379 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
458308 TGATTTACTA
* *
458318 TTTTAATTAG
1 TTTTATTTAT
458328 TTTTA-TTAT
1 TTTTATTTAT
458337 TTTTATTT-T
1 TTTTATTTAT
**
458346 TTTGGTTTA-
1 TTTTATTTAT
458355 -TTTATTTAT
1 TTTTATTTAT
458364 TTTTATTTAT
1 TTTTATTTAT
458374 TTTTAT
1 TTTTAT
458380 CTAACATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.14
9 15 0.35
10 22 0.51
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:458370 original size:14 final size:14
Alignment explanation
Indices: 458329--458375 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
458319 TTTAATTAGT
458329 TTTA-TTATTTTTA
1 TTTATTTATTTTTA
*
458342 TTT-TTT-TGGTTTA
1 TTTATTTAT-TTTTA
458355 TTTATTTATTTTTA
1 TTTATTTATTTTTA
458369 TTTATTT
1 TTTATTT
458376 TTATCTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.43
14 14 0.50
15 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:458865 original size:72 final size:72
Alignment explanation
Indices: 458776--458920 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
458766 CTTTGAAAGC
* *
458776 CACTCCATATTGCTGTTGACAATTTAATCATTACCTTGATCAAATCATACACTGTAATTTATTGT
1 CACTCCATATTGCTGTTGACAATTTAATCATTACCATGATCAAATCATACACTGTAATTTACTGT
458841 AAAGTAT
66 AAAGTAT
* *
458848 CACTCCATATTGTTGTTGACAATTTAATCATTACCATGATTAAATCATACACTGTAATTTACTGT
1 CACTCCATATTGCTGTTGACAATTTAATCATTACCATGATCAAATCATACACTGTAATTTACTGT
458913 AAAGTAT
66 AAAGTAT
458920 C
1 C
458921 CATGAAAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (72 bp):
CACTCCATATTGCTGTTGACAATTTAATCATTACCATGATCAAATCATACACTGTAATTTACTGT
AAAGTAT
Found at i:462133 original size:24 final size:24
Alignment explanation
Indices: 462106--462152 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
462096 ATATTTTATC
* * *
462106 TGACTTCCGATTTGAATTCTGTTT
1 TGACATCCGATCTGAAATCTGTTT
*
462130 TGACATCTGATCTGAAATCTGTT
1 TGACATCCGATCTGAAATCTGTT
462153 CTAATTCCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (24 bp):
TGACATCCGATCTGAAATCTGTTT
Found at i:462200 original size:24 final size:24
Alignment explanation
Indices: 462134--462200 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
462124 CTGTTTTGAC
* *
462134 ATCTGATCTGAAATCTGTTCTAAT
1 ATCTGATCTGAATTATGTTCTAAT
* *
462158 -TCCTGA-CTTGGATTTTGTTCTAAT
1 AT-CTGATC-TGAATTATGTTCTAAT
462182 ATCTGATCTGAATTATGTT
1 ATCTGATCTGAATTATGTT
462201 TTGTTTTCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
23 2 0.06
24 30 0.88
25 2 0.06
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (24 bp):
ATCTGATCTGAATTATGTTCTAAT
Found at i:463557 original size:18 final size:18
Alignment explanation
Indices: 463536--463570 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
463526 AATTATTATG
* *
463536 TATATCTTAACTTAAATT
1 TATATATTAAATTAAATT
463554 TATATATTAAATTAAAT
1 TATATATTAAATTAAAT
463571 ACACATCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATTAAATTAAATT
Found at i:463748 original size:60 final size:58
Alignment explanation
Indices: 463618--463760 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 58
463608 TTGCCTTGTT
* ** *
463618 AAATATATTTTATTCGTATCTTAACTAAAAATATATTTTAATATTATTTTAAATTTAA
1 AAATATATTTTATTCTTATCTTAACTAAAAATATATGCTAATATTATCTTAAATTTAA
* * * * *
463676 AAATATTTTTTTATTCTTACCTTAACTTAAAAATATATGCTATTTTTATCTTAACTTTTAA
1 AAATA-TATTTTATTCTTATCTTAAC-TAAAAATATATGCTAATATTATCTTAA-ATTTAA
*
463737 GAAA-ATATTTTATTTTTATCTTAA
1 -AAATATATTTTATTCTTATCTTAA
463761 ATTATTACAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
58 5 0.07
59 17 0.25
60 38 0.55
61 6 0.09
62 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (58 bp):
AAATATATTTTATTCTTATCTTAACTAAAAATATATGCTAATATTATCTTAAATTTAA
Found at i:463814 original size:30 final size:29
Alignment explanation
Indices: 463780--463857 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
463770 TATATTATAT
*
463780 TCTTAACTTAAAATATATACTTTATTTTTA
1 TCTTAACTTAAAA-ATATATTTTATTTTTA
*
463810 TCTTAACTACAAAAAATATATTTTATTTTTA
1 TCTTAACT--TAAAAATATATTTTATTTTTA
* *
463841 TCTTAATTTTAAAATAT
1 TCTTAACTTAAAAATAT
463858 TAAGAATAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.17
30 8 0.20
31 22 0.54
32 4 0.10
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (29 bp):
TCTTAACTTAAAAATATATTTTATTTTTA
Found at i:463835 original size:31 final size:30
Alignment explanation
Indices: 463780--463846 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
463770 TATATTATAT
* *
463780 TCTTAACTTAAAATATATACTTTATTTTTA
1 TCTTAACTCAAAAAATATACTTTATTTTTA
*
463810 TCTTAACTACAAAAAATATATTTTATTTTTA
1 TCTTAACT-CAAAAAATATACTTTATTTTTA
463841 TCTTAA
1 TCTTAA
463847 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (30 bp):
TCTTAACTCAAAAAATATACTTTATTTTTA
Found at i:463933 original size:2 final size:2
Alignment explanation
Indices: 463926--463986 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
463916 AAGAGAAGAC
463926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
463968 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
463987 TACTTTGATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:465159 original size:7 final size:7
Alignment explanation
Indices: 465147--465171 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
465137 TGATAAAAAA
465147 TATATAT
1 TATATAT
465154 TATATAT
1 TATATAT
465161 TATATAT
1 TATATAT
465168 TATA
1 TATA
465172 GTTAACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:469338 original size:12 final size:12
Alignment explanation
Indices: 469323--469392 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
469313 GATACATGAC
469323 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
469335 CTGATTTCTGAT
1 CTGAATTCTGTT
*
469347 CTGGATTCTGTT
1 CTGAATTCTGTT
*
469359 ATG-ATATCTGTT
1 CTGAAT-TCTGTT
469371 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
469383 TTGATTTCTG
1 CTGAATTCTG
469393 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:469354 original size:24 final size:24
Alignment explanation
Indices: 469286--469394 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
469276 AATTATTTTA
* * *
469286 TCTGATTTCCGACCTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
* *
469310 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
469334 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
469358 TATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
469382 TTTGATTTCTGAT
1 TCTGATTTCTGAT
469395 ATCTCCGTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 2 0.03
24 66 0.94
25 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:469364 original size:48 final size:48
Alignment explanation
Indices: 469286--469394 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
469276 AATTATTTTA
* * *
469286 TCTGATTTCCGACCTGAATTCTATTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTATTATGATATC-TGACCTGAATTCTGT
* * **
469334 TCTGATTTCTGATCTGGATTCTGTTATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTATTATGATATCTGACCTGAATTCTGT
*
469382 TTTGATTTCTGAT
1 TCTGATTTCTGAT
469395 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTATTATGATATCTGACCTGAATTCTGT
Found at i:479190 original size:181 final size:181
Alignment explanation
Indices: 478886--479249 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 181
478876 ATTTTCGGAA
478886 TTAGCACAATATAGGTATGGTTTACGGCTTCCAGTCCATGTCGCACTTCTAACATTCCAATGTAA
1 TTAGCACAATATAGGTATGGTTTACGGCTTCCAGTCCATGTCGCACTTCTAACATTCCAATGTAA
*
478951 AAGTCTACGACCTCAGTTCCAACGATATGTCACAACTGTTGGTTCAACACTACCCGTAAGCCATC
66 AAGTCTACGACCTCAGTTCCAACGATATGCCACAACTGTTGGTTCAACACTACCCGTAAGCCATC
479016 CTCACTTGAAACTTTTAAAGGGCCCATAAATTTTACTATTTGCATAACTTC
131 CTCACTTGAAACTTTTAAAGGGCCCATAAATTTTACTATTTGCATAACTTC
479067 TTAGCACAATATAGGTATGGTTTACGGCTTCCAGTCCATGTCGCACTTCTAACATTCCAATGTAA
1 TTAGCACAATATAGGTATGGTTTACGGCTTCCAGTCCATGTCGCACTTCTAACATTCCAATGTAA
479132 AAGTCTACGACCTCAGTTCCAACGATATGCCACAACTGTTGGTTCAACACTACCCGTAAGCCATC
66 AAGTCTACGACCTCAGTTCCAACGATATGCCACAACTGTTGGTTCAACACTACCCGTAAGCCATC
479197 CTCACTTGAAACTTTTAAAGGGCCCATAAATTTTACTATTTGCATAACTTC
131 CTCACTTGAAACTTTTAAAGGGCCCATAAATTTTACTATTTGCATAACTTC
479248 TT
1 TT
479250 CATAAGTAAA
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 182 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (181 bp):
TTAGCACAATATAGGTATGGTTTACGGCTTCCAGTCCATGTCGCACTTCTAACATTCCAATGTAA
AAGTCTACGACCTCAGTTCCAACGATATGCCACAACTGTTGGTTCAACACTACCCGTAAGCCATC
CTCACTTGAAACTTTTAAAGGGCCCATAAATTTTACTATTTGCATAACTTC
Found at i:482219 original size:14 final size:15
Alignment explanation
Indices: 482194--482224 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
482184 TAGATTTTTT
482194 TTAAAAATTACATTA
1 TTAAAAATTACATTA
482209 TTAAAAA-TACATTA
1 TTAAAAATTACATTA
482223 TT
1 TT
482225 GATAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAAATTACATTA
Found at i:482329 original size:23 final size:24
Alignment explanation
Indices: 482284--482330 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
482274 TTTGTAGGTT
* *
482284 AAAATTCGAGCTTGAATTAAGCTC
1 AAAATTCGAGCTTCAATCAAGCTC
*
482308 AAAA-TCGAGCTTCAATCGAGCTC
1 AAAATTCGAGCTTCAATCAAGCTC
482331 CTGAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (24 bp):
AAAATTCGAGCTTCAATCAAGCTC
Found at i:482645 original size:24 final size:26
Alignment explanation
Indices: 482598--482650 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
482588 TTGAAATTTA
*
482598 TTTCTTTACTTTAAAAGAATAATATT
1 TTTCTTAACTTTAAAAGAATAATATT
*
482624 TTTCTTAACTTTAATAAAAAT-ATATT
1 TTTCTTAACTTTAA-AAGAATAATATT
482650 T
1 T
482651 AATAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTCTTAACTTTAAAAGAATAATATT
Found at i:486039 original size:18 final size:17
Alignment explanation
Indices: 486006--486057 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
485996 GGGCCTACAA
* *
486006 AAAATATATAACAATAT
1 AAAATAAATAAAAATAT
*
486023 AAATTAAAATAAAAATA-
1 AAAAT-AAATAAAAATAT
486040 AAAATAAATAATAAATAT
1 AAAATAAATAA-AAATAT
486058 TATAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 6 0.21
17 13 0.46
18 9 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAATAAAAATAT
Found at i:486577 original size:132 final size:131
Alignment explanation
Indices: 486328--486608 Score: 323
Period size: 132 Copynumber: 2.1 Consensus size: 131
486318 ATGAAGAGTT
* * * * *
486328 CTGGCCATCTTTAGGAGTGGTGATAACTCGATTCCTACGCGATGAGGACGGCTGGTTATTTAGGG
1 CTGGCCATCTTTAGGA---ATGATAACTCGATTCCTACGCAATGAGGACGACTAGTTATCTAGGG
*
486393 GTAACACGACTCCTACGTGATGAGGATGTCGGGTCGGGGGATGACACGGTTCCTACGTGACAAGG
63 GTAACACGACTCCTACGTGATGAGGATGTCGGGTCGGGGGATGACACAGTTCCTACGTGACAAGG
*
486458 ATGG
128 ATGA
* * * *
486462 CTGGTCATCTTTAGGAATGATAACTCGTTTCCTACGTAATGAGGACGACTAGTTATCTATGGGTT
1 CTGGCCATCTTTAGGAATGATAACTCGATTCCTACGCAATGAGGACGACTAGTTATCTA-GGGGT
* * * * * **
486527 GACAC-AGCTCCTATGTGATGAGG-TGGTCTGGTCGGGGGATGACATAGTTCCTATGTGATGAGG
65 AACACGA-CTCCTACGTGATGAGGAT-GTCGGGTCGGGGGATGACACAGTTCCTACGTGACAAGG
486590 ATGA
128 ATGA
*
486594 CTTGCCATCTTTAGG
1 CTGGCCATCTTTAGG
486609 GATAATGGTT
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
131 38 0.31
132 71 0.57
134 15 0.12
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (131 bp):
CTGGCCATCTTTAGGAATGATAACTCGATTCCTACGCAATGAGGACGACTAGTTATCTAGGGGTA
ACACGACTCCTACGTGATGAGGATGTCGGGTCGGGGGATGACACAGTTCCTACGTGACAAGGATG
A
Found at i:486663 original size:36 final size:36
Alignment explanation
Indices: 486616--486748 Score: 126
Period size: 37 Copynumber: 3.6 Consensus size: 36
486606 AGGGATAATG
*
486616 GTTTCAAGGGAAACTGAGTCAAA-ACTGATTTGTTTT
1 GTTTCAAGGGAAACTGACTCAAAGA-TGATTTGTTTT
*
486652 GTTTCAAGGGAAA-TAAACTCAAAGATGATTTTTGTTTT
1 GTTTCAAGGGAAACT-GACTCAAAGATGA--TTTGTTTT
** * **
486690 GTTTCAATTGAAACAGACTCAAAGATTTCTTTGTTTT
1 GTTTCAAGGGAAACTGACTCAAAGA-TGATTTGTTTT
* *
486727 GTTTCAAGTGAAACAGACTCAA
1 GTTTCAAGGGAAACTGACTCAA
486749 TGATTTCTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.01
36 22 0.27
37 30 0.37
38 28 0.34
39 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (36 bp):
GTTTCAAGGGAAACTGACTCAAAGATGATTTGTTTT
Found at i:486732 original size:37 final size:37
Alignment explanation
Indices: 486644--486756 Score: 156
Period size: 37 Copynumber: 3.0 Consensus size: 37
486634 TCAAAACTGA
* * *
486644 TTTGTTTTGTTTCAAGGGAAATAAACTCAAAGATGATT-
1 TTTGTTTTGTTTCAAGTGAAACAGACTCAAAGAT--TTC
*
486682 TTTGTTTTGTTTCAATTGAAACAGACTCAAAGATTTC
1 TTTGTTTTGTTTCAAGTGAAACAGACTCAAAGATTTC
*
486719 TTTGTTTTGTTTCAAGTGAAACAGACTCAATGATTTC
1 TTTGTTTTGTTTCAAGTGAAACAGACTCAAAGATTTC
486756 T
1 T
486757 CAAGAAAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 2 0.03
37 36 0.53
38 30 0.44
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (37 bp):
TTTGTTTTGTTTCAAGTGAAACAGACTCAAAGATTTC
Found at i:486803 original size:21 final size:20
Alignment explanation
Indices: 486761--486804 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
486751 ATTTCTCAAG
*
486761 AAAACTGTCTCAAGAGAGAC
1 AAAACTGTCTCAAGAGAAAC
* *
486781 AAAACTTGTTTCAAGGGAAAC
1 AAAAC-TGTCTCAAGAGAAAC
486802 AAA
1 AAA
486805 CTCAAAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAACTGTCTCAAGAGAAAC
Found at i:486987 original size:30 final size:32
Alignment explanation
Indices: 486920--487007 Score: 117
Period size: 30 Copynumber: 2.8 Consensus size: 32
486910 GAAAATAAGA
* * *
486920 TTTGTTTTTAGAGAAATATACTCAAAGATTAT
1 TTTGTTTTAAGAGAAACAAACTCAAAGATTAT
*
486952 TTTGTTTTAATAGAAACAAACTCAAAGA-T-T
1 TTTGTTTTAAGAGAAACAAACTCAAAGATTAT
*
486982 TTTGTTTCAAGAGAAACAAACTCAAA
1 TTTGTTTTAAGAGAAACAAACTCAAA
487008 AATACTGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
30 25 0.50
31 1 0.02
32 24 0.48
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (32 bp):
TTTGTTTTAAGAGAAACAAACTCAAAGATTAT
Found at i:487063 original size:29 final size:29
Alignment explanation
Indices: 487027--487125 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 29
487017 TCAAAAGAGA
487027 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTGTTTCCAAAGAAACAGACT
* ** *
487055 CAAAGATTTT-TCTTCAAAAGAAATTGTCT
1 CAAAGATTTTGT-TTCCAAAGAAACAGACT
*
487084 CAAAAGACTAAGTTTTGTTTCCAAAGAAACAAACT
1 C-AAAG----A-TTTTGTTTCCAAAGAAACAGACT
487119 CAAAGAT
1 CAAAGAT
487126 AAGTTATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 17
0.67 0.11 0.22
Matches are distributed among these distances:
28 5 0.09
29 20 0.38
30 5 0.09
34 5 0.09
35 17 0.32
36 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (29 bp):
CAAAGATTTTGTTTCCAAAGAAACAGACT
Found at i:487799 original size:14 final size:14
Alignment explanation
Indices: 487780--487810 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
487770 TCATGTGTCA
487780 TGTATGTATGCATG
1 TGTATGTATGCATG
*
487794 TGTATGTATGTATG
1 TGTATGTATGCATG
487808 TGT
1 TGT
487811 TGATGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.29, T:0.48
Consensus pattern (14 bp):
TGTATGTATGCATG
Found at i:487800 original size:18 final size:19
Alignment explanation
Indices: 487771--487807 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
487761 ATGTAAATTT
487771 CATGTGTCATGTATGTATG
1 CATGTGTCATGTATGTATG
487790 CATGTGT-ATGTATGTATG
1 CATGTGTCATGTATGTATG
487808 TGTTGATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (19 bp):
CATGTGTCATGTATGTATG
Found at i:494207 original size:3 final size:3
Alignment explanation
Indices: 494201--494234 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
494191 TGTAAATTAA
494201 AAT AAT AAT AAT AAT AAT AAAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
494235 TTTTTGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:494215 original size:24 final size:24
Alignment explanation
Indices: 494185--494234 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
494175 CAAAAATATG
*
494185 TAATAAT-GTAAATTAAAATAATAA
1 TAATAATAATAAA-TAAAATAATAA
*
494209 TAATAATAATAAATAATATAATAA
1 TAATAATAATAAATAAAATAATAA
494233 TA
1 TA
494235 TTTTTGGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAATAATAATAAATAAAATAATAA
Found at i:495903 original size:18 final size:19
Alignment explanation
Indices: 495882--495924 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
495872 AAAAAAATGA
495882 CTAAAATT-TAAAATCACG
1 CTAAAATTGTAAAATCACG
*
495900 CTAAAATTGTAAAATCTCG
1 CTAAAATTGTAAAATCACG
495919 CTAAAA
1 CTAAAA
495925 GTGGGAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (19 bp):
CTAAAATTGTAAAATCACG
Found at i:497175 original size:54 final size:54
Alignment explanation
Indices: 496803--497175 Score: 458
Period size: 54 Copynumber: 6.9 Consensus size: 54
496793 GATACGTTCA
* * * * *
496803 TTCATAAACATATTATGAATTTTGTGGGTTGCACACTTAGTGCCTATACGGTCG
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
* * * * * *
496857 TTCATCAACATACGATGAATTCCGTGGCTTGCACACTTAGTTCCTATACGGTCG
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
* * * *
496911 TTCATCAACATATGATGAATTCTGTGGGTTGCACACACAGTACCTATACGGGCG
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
* * * * * *
496965 TTCATCAAAAGATTATGAATTCCGTGGGATGCACACATAGTGCCTATATGGTCT
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
* * * * *
497019 TTCATCAACATATAACGAATTCTATGGGTTGCACACATAGTGTCTATATGGTCA
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
* * *
497073 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAATGCATATATGGTCG
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
** *
497127 TTCATCAACATATGATGAATTCCATGGGTTGAACACATAGTGCCTATAT
1 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATAT
497176 TAAACTTAGT
Statistics
Matches: 272, Mismatches: 47, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 272 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTATATGGTCG
Found at i:504574 original size:12 final size:12
Alignment explanation
Indices: 504540--504577 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
504530 AAAGGTAAAC
504540 ATTTGGACATTTA
1 ATTTGG-CATTTA
*
504553 ATTTGG-ATTTT
1 ATTTGGCATTTA
504564 ATTTGGCATTTA
1 ATTTGGCATTTA
504576 AT
1 AT
504578 ATAAAAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 6 0.27
13 6 0.27
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (12 bp):
ATTTGGCATTTA
Found at i:508966 original size:17 final size:17
Alignment explanation
Indices: 508944--508979 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
508934 ATATGTGCAT
*
508944 TTGGTGAGCTAATAGAA
1 TTGGTGAGATAATAGAA
508961 TTGGTGAGATAATAGAA
1 TTGGTGAGATAATAGAA
508978 TT
1 TT
508980 AATGAACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (17 bp):
TTGGTGAGATAATAGAA
Found at i:510821 original size:17 final size:17
Alignment explanation
Indices: 510799--510834 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
510789 ATATGTGCAT
*
510799 TTGGTGAGCTAATAGAA
1 TTGGTGAGATAATAGAA
510816 TTGGTGAGATAATAGAA
1 TTGGTGAGATAATAGAA
510833 TT
1 TT
510835 AATGAACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (17 bp):
TTGGTGAGATAATAGAA
Found at i:512676 original size:17 final size:17
Alignment explanation
Indices: 512654--512689 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
512644 ATATGTGCAT
*
512654 TTGGTGAGCTAATAGAA
1 TTGGTGAGATAATAGAA
512671 TTGGTGAGATAATAGAA
1 TTGGTGAGATAATAGAA
512688 TT
1 TT
512690 AATGAACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (17 bp):
TTGGTGAGATAATAGAA
Found at i:525810 original size:19 final size:19
Alignment explanation
Indices: 525786--525842 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
525776 ATGCAAAAAT
525786 GGTATCGATACCATGCAAG
1 GGTATCGATACCATGCAAG
*
525805 GGTATC---A--ATGC-AT
1 GGTATCGATACCATGCAAG
525818 GGTATCGATACCATGCAAG
1 GGTATCGATACCATGCAAG
525837 GGTATC
1 GGTATC
525843 AATGCATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 7 0.23
14 4 0.13
16 2 0.07
18 4 0.13
19 13 0.43
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCATGCAAG
Found at i:525821 original size:32 final size:32
Alignment explanation
Indices: 525784--525863 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
525774 AAATGCAAAA
525784 ATGGTATCGATACCATGCAAGGGTATCAATGC
1 ATGGTATCGATACCATGCAAGGGTATCAATGC
525816 ATGGTATCGATACCATGCAAGGGTATCAATGC
1 ATGGTATCGATACCATGCAAGGGTATCAATGC
525848 ATGGTATCGATACCAT
1 ATGGTATCGATACCAT
525864 AGTGGAAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (32 bp):
ATGGTATCGATACCATGCAAGGGTATCAATGC
Found at i:529151 original size:29 final size:27
Alignment explanation
Indices: 529109--529168 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
529099 AATTCATCTT
529109 TTATATATATTTTAAAATT-TTAAATTATA
1 TTATATATATTTT-AAATTATT-AATTA-A
529138 TTATAT-TATATTTAAATTATTAATTAA
1 TTATATATAT-TTTAAATTATTAATTAA
529165 TTAT
1 TTAT
529169 TTCATAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.17
28 13 0.45
29 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATATATATTTTAAATTATTAATTAA
Found at i:529367 original size:24 final size:24
Alignment explanation
Indices: 529330--529384 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
529320 AATTCATCTT
529330 TTATA-TATATTTTAAAATT-TTAAA
1 TTATATTATATTTT-AAATTATT-AA
529354 TTATATTATA-TTTAAATTATTAA
1 TTATATTATATTTTAAATTATTAA
529377 TTA-ATTAT
1 TTATATTAT
529385 TTCATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.17
23 10 0.34
24 10 0.34
25 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATATTATATTTTAAATTATTAA
Found at i:529473 original size:216 final size:219
Alignment explanation
Indices: 529094--529539 Score: 826
Period size: 216 Copynumber: 2.0 Consensus size: 219
529084 TTTCAATAAT
529094 AACTAAATTCATCTTTTATATATATTTTAAAATTTTAAATTATATTATATTATATTTAAATTATT
1 AACTAAATTCATCTTTTATATATATTTTAAAATTTT-AA-TATATTATATTATATTTAAATTATT
*
529159 AATTAATTATTTCATAAAACATAATTTAAACTTATAAATATTTAAATTAATTTTATATAATCTAA
64 AATTAATTATTTCATAAAACATAATTTAAACTTATAAATATCTAAATTAATTTTATATAATCTAA
529224 TTAAATCATGTTCAATAAATAAATTATTTAATGAAATTAATTTAATGATTACAATCAAGATTTAT
129 TTAAATCATGTTCAATAAATAAATTATTTAATGAAATTAATTTAATGATTACAATCAAGATTTAT
529289 AATATAAAGATTATAATTTATATAGA
194 AATATAAAGATTATAATTTATATAGA
529315 AACTAAATTCATCTTTTATATATATTTTAAAATTTT-A-A-ATTATATTATATTTAAATTATTAA
1 AACTAAATTCATCTTTTATATATATTTTAAAATTTTAATATATTATATTATATTTAAATTATTAA
*
529377 TTAATTATTTCATAAAATATAATTTAAACTTATAAATATCTAAATTAATTTTATATAATCTAATT
66 TTAATTATTTCATAAAACATAATTTAAACTTATAAATATCTAAATTAATTTTATATAATCTAATT
529442 AAATCATGTTCAATAAATAAATTATTTAATGAAATTAATTTAATGATTACAATCAAGATTTATAA
131 AAATCATGTTCAATAAATAAATTATTTAATGAAATTAATTTAATGATTACAATCAAGATTTATAA
529507 TATAAAGATTATAATTTATATAGA
196 TATAAAGATTATAATTTATATAGA
*
529531 AAGTAAATT
1 AACTAAATT
529540 TATTAATTTA
Statistics
Matches: 222, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
216 184 0.83
217 1 0.00
219 1 0.00
221 36 0.16
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (219 bp):
AACTAAATTCATCTTTTATATATATTTTAAAATTTTAATATATTATATTATATTTAAATTATTAA
TTAATTATTTCATAAAACATAATTTAAACTTATAAATATCTAAATTAATTTTATATAATCTAATT
AAATCATGTTCAATAAATAAATTATTTAATGAAATTAATTTAATGATTACAATCAAGATTTATAA
TATAAAGATTATAATTTATATAGA
Found at i:533382 original size:20 final size:20
Alignment explanation
Indices: 533357--533397 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
533347 AAGAAGTGTT
533357 GTTACTAAGGTGTAGGTATC
1 GTTACTAAGGTGTAGGTATC
533377 GTTACTAAGGTGTAGGTATC
1 GTTACTAAGGTGTAGGTATC
533397 G
1 G
533398 ATACCAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (20 bp):
GTTACTAAGGTGTAGGTATC
Found at i:534195 original size:136 final size:137
Alignment explanation
Indices: 533918--534185 Score: 340
Period size: 136 Copynumber: 2.0 Consensus size: 137
533908 GTTATAGGTG
* * * * * * *
533918 CATTTCGATATACATTTGTATATGATGGTTATCGATCGATTTTGTTTAATGCATATGTTGCATTT
1 CATTTCGACATACGTTTGTGTATAAAGGTTATCAATCGATTTTGTTTAATACATATGTTGCATTT
* * * * *
533983 TCGTATCAATACTATGTGCAATTTCAACATTAGATGTGCAACCATGGTATTCATAATGAGTTTGT
66 TCGTATCAATACTATATGCAATTTCAACACTAGATCTGCAACCATGGAATTCATAATAAGTTTGT
534048 GAATCAC
131 GAATCAC
*
534055 CATTTTGACATACGTTTGTGTATAAAGGTTATCAATCGA-TTTGTTTAATACATATGTTGCATTT
1 CATTTCGACATACGTTTGTGTATAAAGGTTATCAATCGATTTTGTTTAATACATATGTTGCATTT
* * * ** ** *
534119 TCGTATCAGTACTATATGTACTTTCGGCACTATCTCTGCATCCATGGAATTCATAATAAGTTTGT
66 TCGTATCAATACTATATGCAATTTCAACACTAGATCTGCAACCATGGAATTCATAATAAGTTTGT
534184 GA
131 GA
534186 TTTTTCATTT
Statistics
Matches: 110, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
136 78 0.71
137 32 0.29
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (137 bp):
CATTTCGACATACGTTTGTGTATAAAGGTTATCAATCGATTTTGTTTAATACATATGTTGCATTT
TCGTATCAATACTATATGCAATTTCAACACTAGATCTGCAACCATGGAATTCATAATAAGTTTGT
GAATCAC
Found at i:534912 original size:11 final size:11
Alignment explanation
Indices: 534892--534927 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
534882 TCGAACACCT
*
534892 AAATATTTTTA
1 AAATAATTTTA
534903 AAATAATTTTA
1 AAATAATTTTA
*
534914 AAATGATTTTA
1 AAATAATTTTA
534925 AAA
1 AAA
534928 ACAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAATAATTTTA
Found at i:538716 original size:21 final size:22
Alignment explanation
Indices: 538679--538719 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
538669 TTAAATATTA
*
538679 TAAAGGAAGTATTGATACTCAT
1 TAAAGGAAGTATCGATACTCAT
538701 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTATCGATACTC
538720 CCTATCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (22 bp):
TAAAGGAAGTATCGATACTCAT
Found at i:540569 original size:12 final size:12
Alignment explanation
Indices: 540552--540600 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
540542 ATTCAGTTAT
*
540552 TATATATATATA
1 TATATATATTTA
540564 TATATATATTTA
1 TATATATATTTA
*
540576 T-T-TATAATTA
1 TATATATATTTA
*
540586 TATTTATATTTA
1 TATATATATTTA
540598 TAT
1 TAT
540601 GTGTCGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.25
11 2 0.06
12 22 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATATTTA
Found at i:541831 original size:21 final size:21
Alignment explanation
Indices: 541797--541843 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
541787 TTCTTTTCTT
*
541797 TTTTTCCTTCTTTTTGTTCCCC
1 TTTTTACTTCTTTTT-TTCCCC
*
541819 TTTTTACTT-TTTTTTTTCCC
1 TTTTTACTTCTTTTTTTCCCC
541839 TTTTT
1 TTTTT
541844 CTTAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTACTTCTTTTTTTCCCC
Found at i:542200 original size:41 final size:42
Alignment explanation
Indices: 542155--542234 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
542145 AATGTCATAT
* * * *
542155 AGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGAC
1 AGATGACCCGAAGGACTTAATCATCATACTCAAAAGACTGAC
* *
542196 AGATGACCCGAATGATTTAATCATCATACTCAAAAGACT
1 AGATGACCCGAAGGACTTAATCATCATACTCAAAAGACT
542235 TACTGATGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 15 0.47
42 17 0.53
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (42 bp):
AGATGACCCGAAGGACTTAATCATCATACTCAAAAGACTGAC
Found at i:542452 original size:263 final size:262
Alignment explanation
Indices: 541924--543295 Score: 1863
Period size: 261 Copynumber: 5.3 Consensus size: 262
541914 ACTTACCTAG
* * * * * *
541924 GAAAGATTGACAGATTACCCGAATGATTTAAGCATCA-AGCTCAAAAGGA-TTATTGATGGCC-A
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATA-CTCGAAA-GACTTACTGATGGCCGA
* *
541986 GAAGGACTTACCAATTTAGGAAATAGTTTACTAGGTAAGAAACTTTTG-AAATCGCTTTCTTACT
64 -AAGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAAC-TTTGAAAATCGCTTTCTTACT
* *
542050 TTTCAAAAATTCCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCCCATTTTT
127 TTTCAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTT
* * *
542115 CACAAACATCATATGAAAGCATCTTGTCCAAATGTCATATAGATGGCC-CGAAGGACTTATCATC
192 CACAAACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATC
542179 TTGCTC
257 TTGCTC
* * *
542185 GAAAGACTGACAGATGACCCGAATGATTTAATCATCATACTCAAAAGACTTACTGATGTCCGAAA
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGGCCGAAA
* * *
542250 GGACTTGCTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTAAAAATCGCTTTCTAACTTTTC
66 GGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTC
542315 AAAAATTTTCATTTTCTGAAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCA
131 AAAAA-TTTCATTTTCTG-AAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCA
* *
542380 CAAACATCATATGAAAGCATCTTGCCTAAAGGTCTTATAGATGGCCTCG-AGGACTTATCACCTT
194 CAAACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATCTT
*
542444 GTTC
259 GCTC
* * * * * * *
542448 GAAAGACAGAAAGATGACCCGAAAGATTTAATCATCATGCTCGAAATACTTATTGATGGCCCTAA
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGG-CCGAA
*
542513 A-GACTTACTAATTTTGGAAATAGTTTACTAGGTAAGCAACTTTGAAAATCGCTTTCTTACTTTT
65 AGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTT
* * **
542577 CAAAAATTTCATTTTTTGAAAACATTAAATGAGAAACTTTTAAAATTATTTTTCTCATTTTTCAC
130 CAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAC
* ** *
542642 AAACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGG-GTCGAACAACTTGTCATCTTG
195 AAACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATCTTG
542706 CTC
260 CTC
* *
542709 AAAAGACTGACATATGACCCGAAGGATTT-A--ATC--A-TCGAAAGACTTACTGATGGCCTG-A
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGGCC-GAA
* *
542767 AGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTACTTTT
65 AGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTT
* * *
542832 TAAAAATTTCATTTTCTGAAAACATTAAAT--GAAACTTTGGAAATTGCTTTTCTCATTTTTGAC
130 CAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAC
* * * *
542895 AAACATCATATGAAAACATCTTTCCAAAAGATCTTATAGATGGCCT-GAAGGACTTATCATCTTG
195 AAACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATCTTG
542959 CTC
260 CTC
* *
542962 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAA
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGGCCGAAA
* * *
543027 GGACTTACTAATTTTTGAAATAGTTTACTAGGTAAAAAACTTTGAAAATCTCTTTCTTACTTTT-
66 GGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTC
** *** * * * *
543091 AAAAA--AAAAAATCTGAAAACAATAAATAATAAACTTTGAAAATTGCATTTCTCATTTTTCACA
131 AAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCACA
* * * *
543154 AACATCATATGAAAGCATCTTTCCCAAAGGTCTTATGGATGGCC-CAAAAGACTTATCATCTTGC
196 AACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATCTTGC
543218 TC
261 TC
* * * *
543220 GAAAGACTGATAGATGACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTG-A
1 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGGCC-GAA
543284 AGGACTTACTAA
65 AGGACTTACTAA
543296 GTAAAAAACT
Statistics
Matches: 990, Mismatches: 98, Indels: 49
0.87 0.09 0.04
Matches are distributed among these distances:
253 112 0.11
254 6 0.01
255 105 0.11
256 19 0.02
258 168 0.17
259 82 0.08
260 9 0.01
261 238 0.24
262 24 0.02
263 220 0.22
264 7 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (262 bp):
GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTACTGATGGCCGAAA
GGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTC
AAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCACA
AACATCATATGAAAGCATCTTGCCCAAAGGTCTTATAGATGGCCTCGAAGGACTTATCATCTTGC
TC
Found at i:543029 original size:42 final size:41
Alignment explanation
Indices: 542932--543033 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
542922 AAGATCTTAT
*
542932 AGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGACTGAC
1 AGATGGCCTGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * * *
542973 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCTGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
* *
543015 TGATGGCCTAAAGGACTTA
1 AGATGGCCTGAAGGACTTA
543034 CTAATTTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
AGATGGCCTGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:551386 original size:2 final size:2
Alignment explanation
Indices: 551381--551408 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
551371 ATTTGGTTAT
551381 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
551409 CATACACGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:559995 original size:7 final size:7
Alignment explanation
Indices: 559980--560039 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
559970 TAAAAAGATA
559980 ATAATAT
1 ATAATAT
*
559987 ATAACAT
1 ATAATAT
*
559994 ATCATAT
1 ATAATAT
*
560001 ATAAAAT
1 ATAATAT
560008 AT-ATAT
1 ATAATAT
560014 -TATATAT
1 ATA-ATAT
560021 ATATATAT
1 ATA-ATAT
560029 ATATATAT
1 ATA-ATAT
560037 ATA
1 ATA
560040 TTTGTATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 1 0.02
6 3 0.07
7 22 0.50
8 18 0.41
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:560002 original size:2 final size:2
Alignment explanation
Indices: 559983--560040 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
559973 AAAGATAATA
* *
559983 AT AT AT A- AC AT AT CAT AT AT A- AA AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
560023 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
560041 TTGTATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
1 3 0.06
2 45 0.90
3 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:560005 original size:32 final size:34
Alignment explanation
Indices: 559969--560037 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
559959 ATATAGATGA
559969 ATAAAA-AGATAATA-ATATATA-ACATATCATAT
1 ATAAAATAGATAATATATATATATACATAT-ATAT
* * *
560001 ATAAAATATATATTATATATATATATATATATAT
1 ATAAAATAGATAATATATATATATACATATATAT
560035 ATA
1 ATA
560038 TATTTGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 6 0.19
33 6 0.19
34 14 0.45
35 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (34 bp):
ATAAAATAGATAATATATATATATACATATATAT
Found at i:560009 original size:9 final size:9
Alignment explanation
Indices: 559992--560039 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
559982 AATATATAAC
*
559992 ATATCATAT
1 ATATAATAT
*
560001 ATAAAATAT
1 ATATAATAT
*
560010 ATATTATAT
1 ATATAATAT
560019 ATAT-ATAT
1 ATATAATAT
560027 ATAT-ATAT
1 ATATAATAT
560035 ATATA
1 ATATA
560040 TTTGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 16 0.47
9 18 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATAATAT
Found at i:560011 original size:16 final size:16
Alignment explanation
Indices: 559992--560066 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
559982 AATATATAAC
559992 ATATCATATATAAA-AT
1 ATAT-ATATATAAATAT
560008 ATATAT-TAT--ATAT
1 ATATATATATAAATAT
*
560021 ATATATATATATATAT
1 ATATATATATAAATAT
* *
560037 ATATTTGTATAAAT-T
1 ATATATATATAAATAT
* *
560052 ATATGTAGATAAATA
1 ATATATATATAAATA
560067 CAATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 8 0.17
14 6 0.12
15 14 0.29
16 19 0.40
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (16 bp):
ATATATATATAAATAT
Found at i:561230 original size:21 final size:20
Alignment explanation
Indices: 561205--561243 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
561195 TGGGACCCGA
561205 ATTGGACTTGGATCTTGGACC
1 ATTGGACTTGGA-CTTGGACC
561226 ATTGGACTTGGACTTGGA
1 ATTGGACTTGGACTTGGA
561244 TGACCTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (20 bp):
ATTGGACTTGGACTTGGACC
Found at i:561276 original size:3 final size:3
Alignment explanation
Indices: 561268--561299 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
561258 GACCTGCAAT
561268 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
561300 TGAAAACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:561361 original size:2 final size:2
Alignment explanation
Indices: 561354--561414 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
561344 ATATTATTTT
561354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
* * *
561395 TT TA AA CTA TA TT TA TA TA T
1 TA TA TA -TA TA TA TA TA TA T
561415 TTTTCAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:561406 original size:13 final size:13
Alignment explanation
Indices: 561333--561395 Score: 71
Period size: 12 Copynumber: 5.2 Consensus size: 13
561323 ATAATCATAA
561333 ATATAATA-ATA-
1 ATATAATATATAT
* * *
561344 ATATTATTTTTAT
1 ATATAATATATAT
561357 ATAT-ATATATAT
1 ATATAATATATAT
561369 ATAT-ATATATAT
1 ATATAATATATAT
561381 ATATAATATATAT
1 ATATAATATATAT
561394 AT
1 AT
561396 TTAAACTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
11 6 0.14
12 24 0.55
13 14 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:561633 original size:21 final size:21
Alignment explanation
Indices: 561605--561653 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
561595 AATGTAAGTT
**
561605 TTATTTAATTTAAAATAT-TA
1 TTATTTAACCTAAAATATATA
561625 TTATGTTAACCTAAAATATATA
1 TTAT-TTAACCTAAAATATATA
561647 TT-TTTAA
1 TTATTTAA
561654 AAATGTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 13 0.52
22 4 0.16
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTTAACCTAAAATATATA
Found at i:564556 original size:29 final size:29
Alignment explanation
Indices: 564494--564556 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
564484 TCTTATAATC
* *
564494 GAGACCATTTTATAATTTCTAATAGTCGA
1 GAGATCATTTTATAATTTCTAATAGTCAA
*
564523 GAGATCATTTTATAATTTTTAATAGTCAA
1 GAGATCATTTTATAATTTCTAATAGTCAA
564552 GAGAT
1 GAGAT
564557 TCAACAAGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (29 bp):
GAGATCATTTTATAATTTCTAATAGTCAA
Found at i:567511 original size:15 final size:16
Alignment explanation
Indices: 567488--567520 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
567478 TATGAACATC
567488 AATAAAATAACAA-AA
1 AATAAAATAACAATAA
*
567503 AATAGAATAACAATAA
1 AATAAAATAACAATAA
567519 AA
1 AA
567521 ATAATATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AATAAAATAACAATAA
Found at i:567862 original size:207 final size:211
Alignment explanation
Indices: 567504--567913 Score: 726
Period size: 207 Copynumber: 2.0 Consensus size: 211
567494 ATAACAAAAA
*
567504 ATAGAATAACAATAAAAATAATATCTAATAAGCTCGTAAAGGAAGAATTTTGCGTTTTTTTTTTT
1 ATAGAATAACAATAAAAATAATATCTAATAAGCTCGTAAAGGAAGAATTTTGCGTTTTTTTATTT
567569 ATTCATATCTCTGTTTGAACGTCGTAAGGATTGCATCACTTCGCCAAGTGATACTTTTCACGTCC
66 ATTCATA-CTCTGTTTGAACGTCGTAAGGATTGCATCACTTCGCCAAGTGATACTTTTCACGTCC
567634 GTTCTATAAAAGACAGTGTTCTTGAAAAGTACTCGAATAAAT-AAATATCAATACCG-TTACAGA
130 GTTCTATAAAAGACAGTGTTCTTGAAAAGTACTCGAATAAATAAAATATCAATACCGTTTACAGA
567697 ATACATTCTACTTAAAC
195 ATACATTCTACTTAAAC
567714 ATAGAATAACAATAAAAATAATATCT-ATAAGCTCGTAAAAGGAAGAA-TTTGCGTTTTTTTATT
1 ATAGAATAACAATAAAAATAATATCTAATAAGCTCGT-AAAGGAAGAATTTTGCGTTTTTTTATT
567777 TA-TCATA-T-TGTTTGAACGTCGTATAGGATTGCATCACTTCGACCAAGTGATACTTTTCACGT
65 TATTCATACTCTGTTTGAACGTCGTA-AGGATTGCATCACTTCG-CCAAGTGATACTTTTCACGT
567839 CCGTTCTATAAAAGACAGTGTTCTTGAAAAGTACTCGAATAAATAAAATATCAATACCGTTTACA
128 CCGTTCTATAAAAGACAGTGTTCTTGAAAAGTACTCGAATAAATAAAATATCAATACCGTTTACA
567904 GAATACATTC
193 GAATACATTC
567914 GTCATACTTA
Statistics
Matches: 194, Mismatches: 1, Indels: 11
0.94 0.00 0.05
Matches are distributed among these distances:
205 15 0.08
206 18 0.09
207 64 0.33
208 19 0.10
209 42 0.22
210 36 0.19
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (211 bp):
ATAGAATAACAATAAAAATAATATCTAATAAGCTCGTAAAGGAAGAATTTTGCGTTTTTTTATTT
ATTCATACTCTGTTTGAACGTCGTAAGGATTGCATCACTTCGCCAAGTGATACTTTTCACGTCCG
TTCTATAAAAGACAGTGTTCTTGAAAAGTACTCGAATAAATAAAATATCAATACCGTTTACAGAA
TACATTCTACTTAAAC
Found at i:569370 original size:23 final size:23
Alignment explanation
Indices: 569334--569389 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
569324 AAAAAATTAC
*
569334 TGCTGAGAAATTTTCATTTTGAT
1 TGCTGATAAATTTTCATTTTGAT
* **
569357 TGCTGATAATTTTTTTTTTTGAT
1 TGCTGATAAATTTTCATTTTGAT
*
569380 TTCTGATAAA
1 TGCTGATAAA
569390 AAATGTTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (23 bp):
TGCTGATAAATTTTCATTTTGAT
Found at i:570303 original size:130 final size:133
Alignment explanation
Indices: 570000--570303 Score: 373
Period size: 135 Copynumber: 2.3 Consensus size: 133
569990 AGTTTGGGTC
* ** * *
570000 ATCTAAGGGTGACATGGTTCCTACGTGATGAGGATATCTAAACAGGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGAAACTGCTCATACG
* * *
570065 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACTTGGTTCCTACGCAATGAGGACAAC
66 TGATGAAGAGTTCTTGGCCATCTTT--GAAAGGCGATAACATAGTTCCTACGCAATGAGGACAAC
570130 TGGTT
129 TGGTT
* *
570135 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGAAACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGAAACTGCTCATACG
* * * **
570200 TGATGAAGAGTTCTTGGCCAT-TTT-ATA-GCGATAACATAGTTCCTACGTAATGAGGCCGGCTG
66 TGATGAAGAGTTCTTGGCCATCTTTGAAAGGCGATAACATAGTTCCTACGCAATGAGGACAACTG
570262 GTT
131 GTT
* * ** *
570265 ATCTAATGTTGACGTTG-CTCCTACATGATGAGGAGATCT
1 ATCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAGATCT
570304 GGTCAGTTGA
Statistics
Matches: 147, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
130 62 0.42
131 3 0.02
134 3 0.02
135 79 0.54
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (133 bp):
ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGAAACTGCTCATACG
TGATGAAGAGTTCTTGGCCATCTTTGAAAGGCGATAACATAGTTCCTACGCAATGAGGACAACTG
GTT
Found at i:571276 original size:23 final size:23
Alignment explanation
Indices: 571241--571284 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
571231 CTTTATTTAT
571241 TTTTTCATTTTTTTTCATTTTCC
1 TTTTTCATTTTTTTTCATTTTCC
571264 TTTTTC-TTCTTTTTTCATTTT
1 TTTTTCATT-TTTTTTCATTTT
571285 TCCATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCATTTTTTTTCATTTTCC
Found at i:571277 original size:16 final size:16
Alignment explanation
Indices: 571241--571286 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
571231 CTTTATTTAT
*
571241 TTTTTCATTTTTTTTC
1 TTTTTCATTTTTCTTC
* *
571257 ATTTTCCTTTTTCTTC
1 TTTTTCATTTTTCTTC
571273 TTTTTTCATTTTTC
1 -TTTTTCATTTTTC
571287 CATCATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTTTCTTC
Found at i:581389 original size:15 final size:16
Alignment explanation
Indices: 581371--581407 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
581361 TATGAACATC
581371 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
581386 AAATAGAATAACAATA
1 AAATAAAATAACAATA
581402 AAATAA
1 AAATAA
581408 TATCTATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:582513 original size:15 final size:15
Alignment explanation
Indices: 582493--582523 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
582483 TTAAAAATAA
582493 ACGAACATAACGAAC
1 ACGAACATAACGAAC
*
582508 ACGAACATAATGAAC
1 ACGAACATAACGAAC
582523 A
1 A
582524 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (15 bp):
ACGAACATAACGAAC
Found at i:582610 original size:16 final size:16
Alignment explanation
Indices: 582589--582646 Score: 107
Period size: 16 Copynumber: 3.6 Consensus size: 16
582579 TAATAAATAA
582589 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
582605 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
582621 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
582637 ACGAACATAA
1 ACGAACATAA
582647 CGTTGGAGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:583396 original size:14 final size:14
Alignment explanation
Indices: 583379--583434 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
583369 AATGAACATA
*
583379 AACGAACATAATCG
1 AACGAACATAACCG
583393 AACGAACAT-A---
1 AACGAACATAACCG
*
583403 AACGAACATAACCA
1 AACGAACATAACCG
583417 AACGAACATAACCG
1 AACGAACATAACCG
583431 AACG
1 AACG
583435 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:583399 original size:24 final size:24
Alignment explanation
Indices: 583359--583433 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
583349 GATTGTGTTA
*
583359 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
583383 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
583407 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
583431 AAC
1 AAC
583434 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:586844 original size:16 final size:16
Alignment explanation
Indices: 586819--586849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
586809 CTTTTTTGTT
586819 TTTCTCCCCTTTCTCG
1 TTTCTCCCCTTTCTCG
*
586835 TTTCTTCCCTTTCTC
1 TTTCTCCCCTTTCTC
586850 TGGTTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTCTCCCCTTTCTCG
Found at i:588061 original size:35 final size:35
Alignment explanation
Indices: 588022--588088 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
588012 AAATCATATA
*
588022 TATTTTCAAAAAT-T-AAATATAATATATACTATTTT
1 TATTTCCAAAAATATAAAATAT-ATAT-TACTATTTT
*
588057 TATTTCCAAAACTATAAAATATATATTACTAT
1 TATTTCCAAAAATATAAAATATATATTACTAT
588089 ATAATATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 17 0.61
36 5 0.18
37 6 0.21
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (35 bp):
TATTTCCAAAAATATAAAATATATATTACTATTTT
Found at i:589812 original size:6 final size:6
Alignment explanation
Indices: 589801--589837 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
589791 TTTAATAGCG
* *
589801 AAAATT AAAATT AAAATT AAAATT TAAATT TAAATT A
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT A
589838 CCCGATTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AAAATT
Found at i:589983 original size:13 final size:13
Alignment explanation
Indices: 589957--590050 Score: 52
Period size: 13 Copynumber: 7.4 Consensus size: 13
589947 GAAAACTATT
*
589957 ATAAAAAT-ATTA
1 ATAAAAATAAATA
589969 ATAAAAATAAATA
1 ATAAAAATAAATA
* *
589982 AT-CAAAT-AAGA
1 ATAAAAATAAATA
* ** *
589993 ATATCAAAGGAAGA
1 ATA-AAAATAAATA
*
590007 ATAAAAATTAAAAA
1 ATAAAAA-TAAATA
590021 ATAAAAATAAATA
1 ATAAAAATAAATA
*
590034 ATAATAA-AAATA
1 ATAAAAATAAATA
*
590046 TTAAA
1 ATAAA
590051 TAAACCAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
11 5 0.08
12 20 0.31
13 23 0.35
14 17 0.26
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (13 bp):
ATAAAAATAAATA
Found at i:590065 original size:2 final size:2
Alignment explanation
Indices: 590058--590085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
590048 AAATAAACCA
590058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590086 GAAATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591459 original size:36 final size:33
Alignment explanation
Indices: 591426--591699 Score: 189
Period size: 36 Copynumber: 8.3 Consensus size: 33
591416 TCCAAAATTC
*
591426 TATATAATATATATTTTCAAAAGTATTTTAAAAT
1 TATATAATATATATTTTCAAAA-TGTTTTAAAAT
* * *
591460 TATATATTATATATTTTTTTAAAATGTTTTCAAA-
1 TATATA--ATATATATTTTCAAAATGTTTTAAAAT
** * *
591494 -AT-T-ATAT-CGTTTTCAAAAATATTTTTAAAAAC
1 TATATAATATATATTTTC-AAAAT-GTTTT-AAAAT
* *
591526 TATATACTATATAATTTTTCAAAATGATTTCAAAAT
1 TATATAATATAT-A-TTTTCAAAATG-TTTTAAAAT
*
591562 TATATAATATATGTTTTCAAAATGTTTT----T
1 TATATAATATATATTTTCAAAATGTTTTAAAAT
* *
591591 T-TA-AACTATATATTTTCAAAATGTTTAAAAAAAC
1 TATATAA-TATATATTTTCAAAATGTTT--TAAAAT
591625 TATATAATATATATTTTCAAAAATGTTTTAAAA-
1 TATATAATATATATTTTC-AAAATGTTTTAAAAT
* *
591658 -ATAT-ATATTTATTTTCAAAATGTTTTAAAAAC
1 TATATAATATATATTTTCAAAATGTTTT-AAAAT
591690 TATATAATAT
1 TATATAATAT
591700 TAAATGTTTT
Statistics
Matches: 190, Mismatches: 23, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
27 2 0.01
28 25 0.13
29 11 0.06
30 14 0.07
31 18 0.09
32 5 0.03
33 11 0.06
34 27 0.14
35 24 0.13
36 40 0.21
37 8 0.04
38 5 0.03
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (33 bp):
TATATAATATATATTTTCAAAATGTTTTAAAAT
Found at i:591517 original size:64 final size:66
Alignment explanation
Indices: 591439--591566 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
591429 ATAATATATA
* * * * * *
591439 TTTTCAAAAGTA-TTTT-AAAATTATATATTATATATTTTTTTAAAATGTTTTCAAAATTATATC
1 TTTTCAAAAATATTTTTAAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATTATATC
591502 G
66 G
591503 TTTTCAAAAATATTTTTAAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATTATAT
1 TTTTCAAAAATATTTTTAAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATTATAT
591567 AATATATGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 11 0.20
65 4 0.07
66 41 0.73
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (66 bp):
TTTTCAAAAATATTTTTAAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATTATATC
G
Found at i:591624 original size:28 final size:28
Alignment explanation
Indices: 591569--591630 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
591559 AATTATATAA
* ****
591569 TATATGTTTTCAAAATGTTTTTTTAAAC
1 TATATATTTTCAAAATGTTTAAAAAAAC
591597 TATATATTTTCAAAATGTTTAAAAAAAC
1 TATATATTTTCAAAATGTTTAAAAAAAC
591625 TATATA
1 TATATA
591631 ATATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (28 bp):
TATATATTTTCAAAATGTTTAAAAAAAC
Found at i:591632 original size:63 final size:60
Alignment explanation
Indices: 591531--591731 Score: 188
Period size: 63 Copynumber: 3.1 Consensus size: 60
591521 AAAACTATAT
* * **
591531 ACTATATAATTTTTCAAAATGATTTCAAAATTATATAATATATGTTTTCAAAATGTTTTTTTAA
1 ACTATAT-A-TTTTCAAAATG-TTTAAAAACTATATAATATATGTTTTCAAAATG-TTTTAAAA
*
591595 ACTATATATTTTCAAAATGTTTAAAAAAACTATATAATATATATTTTCAAAAATGTTTTAAAA
1 ACTATATATTTTCAAAATGTTT--AAAAACTATATAATATATGTTTTC-AAAATGTTTTAAAA
* * *
591658 ATATATATTTATTTTCAAAATGTTTTAAAAACTATATAATATTAAATGTTTTCAAACAT-ATTTC
1 A-CTATA--TATTTTCAAAATG-TTTAAAAACTATATAATA-T--ATGTTTTCAAA-ATGTTTTA
591722 AAA
58 AAA
591725 ACTATAT
1 ACTATAT
591732 TATATGTTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
61 3 0.03
62 11 0.09
63 29 0.25
64 18 0.16
65 15 0.13
66 18 0.16
67 13 0.11
68 9 0.08
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (60 bp):
ACTATATATTTTCAAAATGTTTAAAAACTATATAATATATGTTTTCAAAATGTTTTAAAA
Found at i:592758 original size:84 final size:84
Alignment explanation
Indices: 592378--593155 Score: 669
Period size: 84 Copynumber: 9.4 Consensus size: 84
592368 TTATTGACAT
* * * * * * ** *
592378 ATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTAGGTTTGCC-TCTGAGCTGAATGTAATCGAA
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAA-T-GATATGCCTTC-GAGCTGAGCGTAGTCGAA
* * *
592442 CTCGGAGGTCTTCGG-TGACAG
63 CTCGAAGGTCTTTGGTTGGCAG
*** * * * * * *
592463 ATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCG-AGCTGAGCGTAGTCGAACT
*
592528 CGAGGGTC--T--TTGGCAG
65 CGAAGGTCTTTGGTTGGCAG
* * * *
592544 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
* * *
592609 AAAAG--TAT--TTGGCAG
66 GAAGGTCTTTGGTTGGCAG
* * * * *
592624 CTAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
592689 GAAGGTCTTTGGTTGGCAG
66 GAAGGTCTTTGGTTGGCAG
* * * *
592708 ATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
*
592773 GAAGGTCTTTTGG-TGACAG
66 GAAGGTC-TTTGGTTGGCAG
* * * * * * * * *
592792 ATAACCCTTCTAGTCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCG-AGCTGAGCGTAGTCGAACT
592857 CG-AGGATC--T--TTGGCAG
65 CGAAGG-TCTTTGGTTGGCAG
* * * *
592873 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
* * * *
592938 AAAGGTCTTTGTTTGGTAT
66 GAAGGTCTTTGGTTGGCAG
* * * * * * *
592957 ATAACCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCG-AGCTGAGCGTAGTCGAACT
*
593022 CGAGGGTCTTTGG-T---AG
65 CGAAGGTCTTTGGTTGGCAG
* * *
593038 ATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
* *
593103 GAAGGTCTTTTGTTGGCAA
66 GAAGGTCTTTGGTTGGCAG
* *** * *
593122 ATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATG
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
593156 TTATCTTTAA
Statistics
Matches: 568, Mismatches: 102, Indels: 47
0.79 0.14 0.07
Matches are distributed among these distances:
80 138 0.24
81 124 0.22
82 4 0.01
83 7 0.01
84 214 0.38
85 81 0.14
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (84 bp):
ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTCGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTGGCAG
Found at i:592823 original size:329 final size:327
Alignment explanation
Indices: 592437--593155 Score: 1014
Period size: 329 Copynumber: 2.2 Consensus size: 327
592427 CTGAATGTAA
* *
592437 TCGAACTCGGAGGTC-TTCGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATAT
*
592501 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* * * * * *
592566 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCAAAAG-TATTTGGCAGCTAGCC
131 ATGCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTCAAAAGTTATTTGGCAGATAACC
* * * *
592630 CTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
196 CTTCTCGACTTAAGCTATACTACAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGG
* *
592694 TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGCCTTAGAGCTGA
261 TCTTTGG-T---AGATAACCCTTCTCGACTTAAGCTATGCTACAAATAATATGCCTTAGAACTGA
592759 GCGTAG
322 GCGTAG
*
592765 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGT-CTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTA-TCCTTGAGTTATGCTGTAAATGATA
592829 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGC
65 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGC
* * * * *
592894 TATTCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTCAAAGGTCTTTGTTTGGTATAT
130 TATGCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTCAAAAG---TTATTTGGCAGAT
* *
592959 AACCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
192 AACCCTTCTCGACTTAAGCTATACTACAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* * * * *
593024 AGGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTGGAACTGA
257 AAGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCTATGCTACAAATAATATGCCTTAGAACTGA
593089 GCGTAG
322 GCGTAG
* * * * * * * *
593095 TCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATG
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATG
593156 TTATCTTTAA
Statistics
Matches: 347, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
328 14 0.04
329 152 0.44
330 105 0.30
333 43 0.12
334 33 0.10
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (327 bp):
TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATAT
GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATGCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTCAAAAGTTATTTGGCAGATAACC
CTTCTCGACTTAAGCTATACTACAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGG
TCTTTGGTAGATAACCCTTCTCGACTTAAGCTATGCTACAAATAATATGCCTTAGAACTGAGCGT
AG
Found at i:592891 original size:165 final size:164
Alignment explanation
Indices: 592378--593112 Score: 859
Period size: 165 Copynumber: 4.5 Consensus size: 164
592368 TTATTGACAT
* * * * * * ** *
592378 ATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTAGGTTTGCCTCT-GAGCTGAATGTAATCGAA
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAA-T-GATATGCCT-TAGAGCTGAGCGTAGTCGAA
* * ** * * * *
592442 CTCGGAGGTCTTCGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCCTC
63 CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTC
592507 GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
128 GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * * *
592544 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * * * * * * *
592609 AAAAGTATTT-G-G-CAGCTAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGA
66 GAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAA
* * *
592670 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
131 GCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAG
* * *
592708 ATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * *
592773 GAAGGTCTTTTGGTGACAGATAACCCTTCTAGTCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
66 GAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
*
592838 AGCTGAGTGTAATCGAACTCGAGGATCTTTGGCAG
130 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * *
592873 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTAGAGCTGACCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
* * ** * * *
592938 AAAGGTCTTTGTTTGGTATATAACCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCCTCGA
66 GAAGGTCTTTG-GTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
*
593003 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAG
130 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * *
593038 ATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
593103 GAAGGTCTTT
66 GAAGGTCTTT
593113 TGTTGGCAAA
Statistics
Matches: 479, Mismatches: 79, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
160 28 0.06
161 32 0.07
162 2 0.00
163 2 0.00
164 102 0.21
165 222 0.46
166 28 0.06
167 2 0.00
168 34 0.07
169 27 0.06
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (164 bp):
ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAA
GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
Done.