Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 89 of 199
Found at i:27371838 original size:24 final size:24
Alignment explanation
Indices: 27371810--27371861 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
27371800 TTTCTAGAAG
* *
27371810 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
27371834 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
27371858 ATTT
1 ATTT
27371862 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:27379552 original size:31 final size:31
Alignment explanation
Indices: 27379514--27379575 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
27379504 GGGTAACACA
27379514 CTTACGACAAGGTCGTTGGACAAGT-ACTGAT
1 CTTACGACAAGGTCGTTGGACAA-TCACTGAT
27379545 CTTACGACAAGGTCGTTGGACAATCACTGAT
1 CTTACGACAAGGTCGTTGGACAATCACTGAT
27379576 TAAGTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (31 bp):
CTTACGACAAGGTCGTTGGACAATCACTGAT
Found at i:27383056 original size:27 final size:27
Alignment explanation
Indices: 27383010--27383084 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
27383000 CAATTGTTTA
* * *
27383010 TACACAAACTCGCCAGACCTTTTGGTG
1 TACACAAACTCACCAAACCTATTGGTG
*
27383037 TACACGAACTCACCAAACCTATTGGTG
1 TACACAAACTCACCAAACCTATTGGTG
* * * *
27383064 TACGCTAGCTCACCCAACCTA
1 TACACAAACTCACCAAACCTA
27383085 CTAGTGAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (27 bp):
TACACAAACTCACCAAACCTATTGGTG
Found at i:27393822 original size:46 final size:46
Alignment explanation
Indices: 27393766--27393859 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
27393756 AAGTAACAAA
* *
27393766 AAGAAAATCAACATTCTAGAGAAGTATATATACTACACTCTTAAAC
1 AAGAAAATCAACATTCTAGAGAAGTATATACAATACACTCTTAAAC
*
27393812 AAGAAAATCAACATTCTAGAGCAGTATATACAATACACTCTTAAAC
1 AAGAAAATCAACATTCTAGAGAAGTATATACAATACACTCTTAAAC
27393858 AA
1 AA
27393860 CAGTAACCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (46 bp):
AAGAAAATCAACATTCTAGAGAAGTATATACAATACACTCTTAAAC
Found at i:27394202 original size:3 final size:3
Alignment explanation
Indices: 27394182--27394235 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
27394172 CCTCTACTTG
* * *
27394182 TTC TTG TTC TTG TTC TTC TTC ATC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
27394230 TTC TTC
1 TTC TTC
27394236 GACTATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:27399521 original size:50 final size:50
Alignment explanation
Indices: 27399444--27399690 Score: 314
Period size: 50 Copynumber: 4.9 Consensus size: 50
27399434 TCCTGTACTA
* * * * * ** * *
27399444 CCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGATG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * ** *
27399494 CCCATGCCATGCCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
27399544 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
27399594 CAAACGCCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
27399644 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
27399691 TGTTGACATG
Statistics
Matches: 173, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 173 1.00
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:27399772 original size:44 final size:44
Alignment explanation
Indices: 27399708--27399803 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
27399698 ATGGATCAAC
*
27399708 CATGGTACTTTTCCGTCAATTCTTTATTAATTGCCATGTTATAAA
1 CATGG-ACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
*
27399753 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
27399797 CATGGAC
1 CATGGAC
27399804 CTTGAGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
Found at i:27408446 original size:41 final size:42
Alignment explanation
Indices: 27408401--27408482 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
27408391 TATCACAAAA
* *
27408401 CTCACAAAAGCCCATGCTCTC-GAGGAGCACGCAGAGTGAGG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAGG
* *
27408442 CTCACAAAAGCTCATGTTCTCAAAGGAACACGCAGAGTGAG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAG
27408483 ACTTAACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 19 0.53
42 17 0.47
ACGTcount: A:0.33, C:0.27, G:0.26, T:0.15
Consensus pattern (42 bp):
CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAGG
Found at i:27412821 original size:29 final size:30
Alignment explanation
Indices: 27412762--27412819 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27412752 TCCGAGCCTT
**
27412762 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
27412792 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
27412820 AGAGTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:27413050 original size:13 final size:13
Alignment explanation
Indices: 27413032--27413062 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27413022 TTCCAGCAAC
27413032 TATGAATTTATTT
1 TATGAATTTATTT
27413045 TATGAATTTATTT
1 TATGAATTTATTT
*
27413058 GATGA
1 TATGA
27413063 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:27413232 original size:50 final size:50
Alignment explanation
Indices: 27413157--27413442 Score: 491
Period size: 50 Copynumber: 5.7 Consensus size: 50
27413147 ATTTGGGTAA
27413157 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
27413207 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
27413257 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
27413307 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
27413357 TGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
27413407 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
27413443 TTTAGCATGT
Statistics
Matches: 223, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
50 194 0.87
51 29 0.13
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:27424361 original size:19 final size:19
Alignment explanation
Indices: 27424328--27424375 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
27424318 TAAACAATTC
27424328 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
27424345 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
27424364 AATAATATAAAT
1 AATAATATAAAT
27424376 AGTAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:27432523 original size:39 final size:39
Alignment explanation
Indices: 27432480--27432613 Score: 207
Period size: 39 Copynumber: 3.4 Consensus size: 39
27432470 TTTTGTGTAC
*
27432480 TGTGATATATGCTTGAATGTTATGTGATTATATGAGTAT
1 TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
*
27432519 TGTGATATATGTTTAAATGTTATGTGATTATATGAGTAT
1 TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
* * *
27432558 TGTGATATATGATTAAATGTTATATGATTATAT-ATGTAA
1 TGTGATATATGCTTAAATGTTATGTGATTATATGA-GTAT
27432597 TGTGATATATGCTTAAA
1 TGTGATATATGCTTAAA
27432614 AGTGAATATG
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 87 0.99
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (39 bp):
TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
Found at i:27432590 original size:8 final size:8
Alignment explanation
Indices: 27432499--27432590 Score: 57
Period size: 8 Copynumber: 11.8 Consensus size: 8
27432489 TGCTTGAATG
*
27432499 TTATGTGA
1 TTATATGA
27432507 TTATATGA
1 TTATATGA
* *
27432515 GTATTGTGA
1 TTA-TATGA
*
27432524 -TATATGT
1 TTATATGA
*
27432531 TTAAATG-
1 TTATATGA
*
27432538 TTATGTGA
1 TTATATGA
27432546 TTATATGA
1 TTATATGA
* *
27432554 GTATTGTGA
1 TTA-TATGA
27432563 -TATATGA
1 TTATATGA
*
27432570 TTAAATG-
1 TTATATGA
27432577 TTATATGA
1 TTATATGA
27432585 TTATAT
1 TTATAT
27432591 ATGTAATGTG
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 18 0.28
8 38 0.59
9 8 0.12
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (8 bp):
TTATATGA
Found at i:27432634 original size:39 final size:39
Alignment explanation
Indices: 27432475--27432635 Score: 103
Period size: 39 Copynumber: 4.1 Consensus size: 39
27432465 CATGTTTTTG
* * * * * * *
27432475 TGTACTGTGATATATGCTTGAATGTTATGTGATTATATGA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATA-CA
* * * * * *
27432515 -GTATTGTGATATATGTTTAAATGTTATGTGATTATATGA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATA-CA
* * * *
27432554 -GTATTGTGATATATGATTAAATGTTATATGATTATATA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATACA
* *
27432592 TGTAATGTGATATATGCTTAAAAGTGAATATGATTA-CCA
1 TGTAATGTGATATATGATTAAAAGT-AATATGATTATACA
27432631 TGTAA
1 TGTAA
27432636 ATGAACTAGC
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 97 0.91
40 9 0.08
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (39 bp):
TGTAATGTGATATATGATTAAAAGTAATATGATTATACA
Found at i:27435604 original size:30 final size:29
Alignment explanation
Indices: 27435568--27435641 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
27435558 ACCGTCAGAC
27435568 TTAAATTTAAAAATATAAAAAGTA-AAAAAA
1 TTAAATTTAAAAATA-AAAAA-TATAAAAAA
*
27435598 TTAAATTCTTGAAAATAAAAAATATAAAAAA
1 TTAAA-T-TTAAAAATAAAAAATATAAAAAA
*
27435629 TTAAATTTCAAAA
1 TTAAATTTAAAAA
27435642 GAGTGCAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 6 0.15
30 8 0.21
31 17 0.44
32 8 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
TTAAATTTAAAAATAAAAAATATAAAAAA
Found at i:27435966 original size:20 final size:20
Alignment explanation
Indices: 27435920--27435966 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27435910 TGAATTAATC
*
27435920 AAGGTGCAATGCGGATATCT
1 AAGGTGTAATGCGGATATCT
*
27435940 AAGGTGTAATGTGGATA-CT
1 AAGGTGTAATGCGGATATCT
27435959 AGAGGTGT
1 A-AGGTGT
27435967 TTATGGGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.28
Consensus pattern (20 bp):
AAGGTGTAATGCGGATATCT
Found at i:27436412 original size:11 final size:11
Alignment explanation
Indices: 27436391--27436447 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
27436381 AAAAAACAAC
*
27436391 AACAACAAGAA
1 AACAGCAAGAA
*
27436402 AATAGCAAGAA
1 AACAGCAAGAA
* *
27436413 AACAGTAAAAAA
1 AACAG-CAAGAA
*
27436425 AAGAGCAAGAA
1 AACAGCAAGAA
27436436 AACAGCAA-AA
1 AACAGCAAGAA
27436446 AA
1 AA
27436448 GACAATAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
10 4 0.11
11 24 0.67
12 8 0.22
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.04
Consensus pattern (11 bp):
AACAGCAAGAA
Found at i:27436431 original size:23 final size:23
Alignment explanation
Indices: 27436400--27436447 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
27436390 CAACAACAAG
* *
27436400 AAAATAGCAAGAAAACAGTAAAA
1 AAAAGAGCAAGAAAACAGCAAAA
27436423 AAAAGAGCAAGAAAACAGCAAAA
1 AAAAGAGCAAGAAAACAGCAAAA
27436446 AA
1 AA
27436448 GACAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.71, C:0.10, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAAGAGCAAGAAAACAGCAAAA
Found at i:27437430 original size:21 final size:20
Alignment explanation
Indices: 27437404--27437479 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 20
27437394 ATTATATATT
27437404 AAATATATATATTTTTTAATC
1 AAATATATAT-TTTTTTAATC
27437425 AAATATATATTTTATTTTTAATC
1 AAATATATA--TT-TTTTTAATC
* *
27437448 AAATATAT-TTTTTATATATT
1 AAATATATATTTTTTTA-ATC
27437468 AAATATATATTT
1 AAATATATATTT
27437480 AATATGAGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.10
20 12 0.25
21 12 0.25
22 1 0.02
23 18 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATATATATTTTTTTAATC
Found at i:27437442 original size:23 final size:23
Alignment explanation
Indices: 27437404--27437462 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
27437394 ATTATATATT
*
27437404 AAATATATA-TAT-TTTTTAATC
1 AAATATATATTTTATTTTTAATC
27437425 AAATATATATTTTATTTTTAATC
1 AAATATATATTTTATTTTTAATC
*
27437448 AAATATATTTTTTAT
1 AAATATATATTTTAT
27437463 ATATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.26
22 2 0.06
23 23 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATATATTTTATTTTTAATC
Found at i:27437887 original size:17 final size:17
Alignment explanation
Indices: 27437865--27437899 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27437855 AATATAGAAA
*
27437865 GTAATCTTAGAAGATTT
1 GTAATCTGAGAAGATTT
*
27437882 GTAATCTGATAAGATTT
1 GTAATCTGAGAAGATTT
27437899 G
1 G
27437900 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTAATCTGAGAAGATTT
Found at i:27448538 original size:18 final size:18
Alignment explanation
Indices: 27448471--27448541 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
27448461 TTGAGCAGAT
*
27448471 ATTCTTTTAAGATTCTTTC
1 ATTCTTTTGA-ATTCTTTC
* *** *
27448490 ATTCTTTTGTA-TGAGTA
1 ATTCTTTTGAATTCTTTC
* *
27448507 ATTATTTTGGATTCTTTC
1 ATTCTTTTGAATTCTTTC
27448525 ATTCTTTTGAATTCTTT
1 ATTCTTTTGAATTCTTT
27448542 GTCAAATTAT
Statistics
Matches: 37, Mismatches: 14, Indels: 3
0.69 0.26 0.06
Matches are distributed among these distances:
17 11 0.30
18 18 0.49
19 8 0.22
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.59
Consensus pattern (18 bp):
ATTCTTTTGAATTCTTTC
Found at i:27450022 original size:3 final size:3
Alignment explanation
Indices: 27449961--27450006 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
27449951 TATCATCATC
27449961 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
27450007 AGGTTACTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27450410 original size:2 final size:2
Alignment explanation
Indices: 27450372--27450397 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27450362 TATATTATTG
27450372 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
27450398 CCTATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27456376 original size:44 final size:44
Alignment explanation
Indices: 27456305--27456613 Score: 246
Period size: 44 Copynumber: 6.9 Consensus size: 44
27456295 AGAAGATGGC
* *
27456305 AAATCTTATTTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * ** ** *
27456349 AAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * * ** *
27456393 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-A
* * * * *
27456438 GAATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTAAAGCTATAAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGC---CAA
* * ** * * *
27456485 TCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC-AGGTCATGGC--
1 --A-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
*
27456530 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * *
27456574 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAG
27456614 TTACAAGTCT
Statistics
Matches: 205, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
41 27 0.13
42 5 0.02
43 1 0.00
44 108 0.53
45 34 0.17
48 1 0.00
50 5 0.02
51 24 0.12
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
Found at i:27456548 original size:41 final size:44
Alignment explanation
Indices: 27456491--27456604 Score: 144
Period size: 41 Copynumber: 2.7 Consensus size: 44
27456481 TAAATCACAG
* * * * *
27456491 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAG-GTCATGGC-A-A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
*
27456532 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
*
27456576 ATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
27456605 GAATTAAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 29 0.46
42 4 0.06
43 1 0.02
44 29 0.46
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
Found at i:27456939 original size:44 final size:44
Alignment explanation
Indices: 27456891--27457095 Score: 159
Period size: 44 Copynumber: 4.7 Consensus size: 44
27456881 AAGTTACAAG
27456891 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * * * ** * *** *
27456935 TCTTATTTCTCTGAAATTACAGTAAAGTAGA-TCGCATCA-GG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * ***
27456976 TCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGAA--ACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AATGATGGA
* * *
27457020 TCCTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * *
27457064 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
27457096 CGCATCAGAC
Statistics
Matches: 116, Mismatches: 38, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
41 23 0.20
42 6 0.05
43 6 0.05
44 81 0.70
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
Found at i:27457156 original size:129 final size:129
Alignment explanation
Indices: 27456885--27457177 Score: 383
Period size: 129 Copynumber: 2.3 Consensus size: 129
27456875 GGATTAAAGT
* *
27456885 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGATCTTATTTCTCTGAA
1 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
** * * * *
27456950 ATTACAGTAAAGTAGATCGCATCAGGTCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGA
66 ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
* * *
27457014 AACCAA-TCCTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
1 TA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
* * * * *
27457078 AGTTGCAGTAGAGTAGATCGCATCAGACCTTATTTCCTTGAAATTACAGTGAAATAAG-TGGAAG
65 AATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTG-AAGAAGATGGAAG
*
27457142 C
129 A
* *
27457143 TACAAGTCTTATCTCCCTAAAGTTGTAGTGGAGCA
1 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
27457178 GACTGAAGAA
Statistics
Matches: 139, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
128 3 0.02
129 129 0.93
130 7 0.05
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (129 bp):
TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
Found at i:27457591 original size:14 final size:15
Alignment explanation
Indices: 27457563--27457611 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
27457553 AGGGTCCGTT
*
27457563 TGTTTGCTAGTAAAA
1 TGTTTTCTAGTAAAA
*
27457578 TGTTTTC-CGTAAAA
1 TGTTTTCTAGTAAAA
*
27457592 TGATTTCTAG-AAAA
1 TGTTTTCTAGTAAAA
27457606 TGTTTT
1 TGTTTT
27457612 ACTTTTCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (15 bp):
TGTTTTCTAGTAAAA
Found at i:27457624 original size:34 final size:35
Alignment explanation
Indices: 27457580--27457646 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
27457570 TAGTAAAATG
*
27457580 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
27457614 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
27457647 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:27458038 original size:43 final size:43
Alignment explanation
Indices: 27457977--27458063 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
27457967 TACTAGAAAT
* * * *
27457977 TAATAATAATATTATCCAAATGCATAATTAGTAGTACACCACA
1 TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
* * *
27458020 TAATAACAACATTGTCCAAGTGCATAACTAATATTACACCACA
1 TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
27458063 T
1 T
27458064 TAAAAAAGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.29
Consensus pattern (43 bp):
TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
Found at i:27471092 original size:26 final size:26
Alignment explanation
Indices: 27471061--27471125 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
27471051 TTCAAACTTT
27471061 ATTATGGTTTGTTAGCTTTTGGAAAA
1 ATTATGGTTTGTTAGCTTTTGGAAAA
27471087 ATTATGGTTTGTTAGCTTTTGGAAAA
1 ATTATGGTTTGTTAGCTTTTGGAAAA
*
27471113 ATTATGATTTGTT
1 ATTATGGTTTGTT
27471126 TAGTTCATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (26 bp):
ATTATGGTTTGTTAGCTTTTGGAAAA
Found at i:27471667 original size:16 final size:15
Alignment explanation
Indices: 27471641--27471671 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
27471631 TTTTAGAAAC
27471641 ACTTTGTATATGATA
1 ACTTTGTATATGATA
27471656 ACTTTAGTATATGATA
1 ACTTT-GTATATGATA
27471672 TGACCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTTTGTATATGATA
Found at i:27471716 original size:7 final size:7
Alignment explanation
Indices: 27471704--27471728 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27471694 AAGAAAATGT
27471704 GTTTAAA
1 GTTTAAA
27471711 GTTTAAA
1 GTTTAAA
27471718 GTTTAAA
1 GTTTAAA
27471725 GTTT
1 GTTT
27471729 GTATATGATA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
GTTTAAA
Found at i:27471779 original size:12 final size:12
Alignment explanation
Indices: 27471762--27471787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27471752 ACACGTGAGT
27471762 TGCATCTAGCAA
1 TGCATCTAGCAA
27471774 TGCATCTAGCAA
1 TGCATCTAGCAA
27471786 TG
1 TG
27471788 AGTGGCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (12 bp):
TGCATCTAGCAA
Found at i:27489540 original size:37 final size:37
Alignment explanation
Indices: 27489472--27489555 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
27489462 TGCCACATAT
* *
27489472 TGGTTTGATTAGATGGATGGACTCTATTAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTCTATTAGTCCAATA
*
27489509 TGGTGTGATTAGATGGATCGACTAT-TATAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTCTAT-TAGTCCAATA
27489546 TGGTGTGATT
1 TGGTGTGATT
27489556 GGTTGGACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (37 bp):
TGGTGTGATTAGATGGATCGACTCTATTAGTCCAATA
Found at i:27498345 original size:13 final size:13
Alignment explanation
Indices: 27498327--27498358 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27498317 TTTCCAGCAA
27498327 TTATGAATTTATT
1 TTATGAATTTATT
27498340 TTATGAATTTATT
1 TTATGAATTTATT
*
27498353 TGATGA
1 TTATGA
27498359 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:27498566 original size:50 final size:50
Alignment explanation
Indices: 27498453--27498649 Score: 277
Period size: 50 Copynumber: 3.8 Consensus size: 50
27498443 ATTTGGGTAA
* *
27498453 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
27498509 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
27498559 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
27498609 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGC
27498650 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 86 0.65
52 1 0.01
53 4 0.03
55 2 0.02
56 39 0.30
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:27498637 original size:100 final size:103
Alignment explanation
Indices: 27498453--27498649 Score: 328
Period size: 100 Copynumber: 1.9 Consensus size: 103
27498443 ATTTGGGTAA
27498453 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCCC
*
27498518 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
*
27498559 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GAG-ATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCCTA
27498621 TAAGACCATGTCTGGGACATGGCATGGGC
66 TAAGACCATGTCTGGGACATGGCATGGGC
27498650 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
100 43 0.48
103 3 0.03
105 2 0.02
106 41 0.46
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:27507436 original size:18 final size:18
Alignment explanation
Indices: 27507387--27507440 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
27507377 ATTCACCTAA
*
27507387 ACCCAATCTAAACCCAAGT
1 ACCCAATCT-AACCCAATT
** * *
27507406 ATTCAACCCAACCCAATT
1 ACCCAATCTAACCCAATT
27507424 ACCCAATCTAACCCAAT
1 ACCCAATCTAACCCAAT
27507441 CATAAAAATT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.41, C:0.39, G:0.02, T:0.19
Consensus pattern (18 bp):
ACCCAATCTAACCCAATT
Found at i:27507553 original size:9 final size:9
Alignment explanation
Indices: 27507536--27507602 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
27507526 TGTATGATTC
*
27507536 AATTAGGTT
1 AATTCGGTT
27507545 AATTCGGTT
1 AATTCGGTT
*
27507554 AATTCGGGT
1 AATTCGGTT
*
27507563 AATTCGGGT
1 AATTCGGTT
*
27507572 AATTCGGGT
1 AATTCGGTT
27507581 AATTCGGTT
1 AATTCGGTT
27507590 AATTCGGTT
1 AATTCGGTT
27507599 AATT
1 AATT
27507603 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:27514046 original size:45 final size:45
Alignment explanation
Indices: 27513990--27514084 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
27513980 TACTATGTGA
*
27513990 ACCGAACATCATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
* * * *
27514035 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCT
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
27514080 ACCGA
1 ACCGA
27514085 GTATCTGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
Found at i:27517374 original size:18 final size:18
Alignment explanation
Indices: 27517351--27517386 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27517341 GTGGACACAA
27517351 AAGCTACCATCACTTACT
1 AAGCTACCATCACTTACT
27517369 AAGCTACCATCACTTACT
1 AAGCTACCATCACTTACT
27517387 CTATCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (18 bp):
AAGCTACCATCACTTACT
Found at i:27522202 original size:88 final size:87
Alignment explanation
Indices: 27522099--27522273 Score: 237
Period size: 88 Copynumber: 2.0 Consensus size: 87
27522089 ATTAAGTCCC
* *
27522099 TTTTTTCCACTCAATTGAGCACTTGGACTTTCAAAATGTATCAAAAAGAC-CTTCGAACTTCTTT
1 TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACAC-TC-AACTTCTTT
27522163 AAAAAAAGCAATTAATCCC-CTGCT
64 AAAAAAAGCAATTAA-CCCTCTGCT
* * * * * *
27522187 TTTTTTTCACTCAATTGGGTACATGAACTTTCAAAATGTATCAAAAAGACACTCAATTTTTTTCA
1 TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACACTCAACTTCTTTAA
27522252 AAAAAGCAATTAACCCTCTGCT
66 AAAAAGCAATTAACCCTCTGCT
27522274 CTTATTAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
86 3 0.04
87 26 0.34
88 47 0.61
89 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (87 bp):
TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACACTCAACTTCTTTAA
AAAAAGCAATTAACCCTCTGCT
Found at i:27522341 original size:19 final size:18
Alignment explanation
Indices: 27522317--27522357 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
27522307 TAATAAATAA
27522317 TAAATTTTAGA-AAAATTAT
1 TAAATTTT-GATAAAATT-T
27522336 TAAATTTTGATAAAATTT
1 TAAATTTTGATAAAATTT
27522354 TAAA
1 TAAA
27522358 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TAAATTTTGATAAAATTT
Found at i:27522368 original size:17 final size:18
Alignment explanation
Indices: 27522346--27522380 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27522336 TAAATTTTGA
27522346 TAAAATTT-TAAAAAATT
1 TAAAATTTATAAAAAATT
*
27522363 TAAAATTTATTAAAAATT
1 TAAAATTTATAAAAAATT
27522381 AGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATTTATAAAAAATT
Found at i:27522669 original size:55 final size:58
Alignment explanation
Indices: 27522607--27522727 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 58
27522597 ATTTACGAAA
* *
27522607 TTTATATTTCTTTACATTTTGT-A-TTTCTTATGAC-TTTATAAAAAATTT-TAATTTT
1 TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTAT-AAAAATTTACAATTTT
* * *
27522662 TTTATATTTCTATATATTTTGTAATTTTTTTATGGCTTTTATAAAAATTTACAATTTT
1 TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTATAAAAATTTACAATTTT
27522720 TTATATAT
1 TT-TATAT
27522728 ATTTTACTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 20 0.36
56 1 0.02
57 17 0.30
58 13 0.23
59 5 0.09
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTATAAAAATTTACAATTTT
Found at i:27522721 original size:57 final size:55
Alignment explanation
Indices: 27522607--27522725 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 55
27522597 ATTTACGAAA
* *
27522607 TTTATATTTCTTTACATTTTGTATTTCTTATGACTTTATAAAAAATTTTAATTTT
1 TTTATATTTCTATACATTTTGTATTTCTTATGACTTTATAAAAAATTTTAAATTT
* * *
27522662 TTTATATTTCTATATATTTTGTAATTTTTTTATGGCTTT-TATAAAAA-TTTACAATTT
1 TTTATATTTCTATACATTTTGT-A-TTTCTTATGACTTTATA-AAAAATTTTA-AATTT
27522719 TTTATAT
1 TTTATAT
27522726 ATATTTTACT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
55 20 0.36
56 7 0.13
57 28 0.51
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (55 bp):
TTTATATTTCTATACATTTTGTATTTCTTATGACTTTATAAAAAATTTTAAATTT
Found at i:27522769 original size:20 final size:18
Alignment explanation
Indices: 27522744--27522790 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
27522734 CTACTTTTAT
27522744 ATTTTTTCTAATTTTTAATA
1 ATTTTTT-TAATTTTTAA-A
* *
27522764 ATTTTTTTTATTTTTGAA
1 ATTTTTTTAATTTTTAAA
27522782 ATTTTTTTA
1 ATTTTTTTA
27522791 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTTTAATTTTTAAA
Found at i:27522997 original size:87 final size:88
Alignment explanation
Indices: 27522858--27523078 Score: 241
Period size: 87 Copynumber: 2.5 Consensus size: 88
27522848 TAAAAGCAGT
* * * *
27522858 GGCTTAATTGCTTTTTTTGAAAATATTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACT
1 GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
* *
27522923 CAATTGAGTGCAGAAAAAAGTACA
66 CAAATGAGTCCA-AAAAAAGTACA
* * *
27522947 GGCTTAATTGC-TTTTTTGAAAAGGTTT-AAGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
*
27523010 CAAATGAGTCCAAAAAAAGAAAAAGCAA
66 CAAATGAGTCCAAAAAAAG---TA-C-A
* * *
27523038 TGGCTTAATTACTTTTTTTGAAAAAATTTG-AGGGCTTTTTG
1 -GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTG
27523079 CACCCTGAAG
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
86 7 0.06
87 41 0.38
88 14 0.13
89 12 0.11
90 1 0.01
91 1 0.01
92 10 0.09
93 22 0.20
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (88 bp):
GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
CAAATGAGTCCAAAAAAAGTACA
Found at i:27524321 original size:6 final size:6
Alignment explanation
Indices: 27524281--27524310 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
27524271 AGTAACCTCA
27524281 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
27524311 ATGCTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:27533801 original size:68 final size:68
Alignment explanation
Indices: 27533711--27534281 Score: 615
Period size: 68 Copynumber: 8.4 Consensus size: 68
27533701 GAGGTTTAAG
* * * * *
27533711 GTGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
27533776 ATT
66 ATT
* *
27533779 GTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
27533844 ATT
66 ATT
** ** ** *
27533847 GTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
27533912 ATT
66 ATT
* * *
27533915 CTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
27533980 ATT
66 ATT
* ** * ** *
27533983 GTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGTCCGCTAGGACATTAAACA-TGGGTTTA
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGG-TTA
*
27534047 CACT
65 CATT
* * * * * *
27534051 GTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACA-TGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
*
27534115 AAT
66 ATT
* ** * ** * *
27534118 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
27534183 ATT
66 ATT
* ** *** * * * * * *
27534186 GTGTAAGACCGTAAATTAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGCTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
*
27534251 AAT
66 ATT
* * *
27534254 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCGGCTATGGCAA
27534282 AGTATGGAGC
Statistics
Matches: 419, Mismatches: 82, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
67 56 0.13
68 363 0.87
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
ATT
Found at i:27533955 original size:136 final size:136
Alignment explanation
Indices: 27533711--27534281 Score: 698
Period size: 136 Copynumber: 4.2 Consensus size: 136
27533701 GAGGTTTAAG
* * * * *
27533711 GTGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* *
27533776 ATTGTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
27533841 TACATT
131 TACAAT
** *
27533847 GTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
*
27533912 ATTCTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
27533977 TACATT
131 TACAAT
* * *
27533983 GTGTAAGATCATAGCTCGAA-TATGGCAACATGTAGAGTCCGCTAGGACATTAAACA-TGGGTTT
1 GTGTAAGACCATAGCTC-AACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGG-TT
* * * * * * * *
27534046 ACACTGTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACAT-GG
64 ACATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGG
27534110 GTTACAAT
129 GTTACAAT
* * * * ** * *
27534118 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* ** *** * * * *
27534183 ATTGTGTAAGACCGTAAATTAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGC
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
27534248 TACAAT
131 TACAAT
* * *
27534254 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCAACTATGGCAA
27534282 AGTATGGAGC
Statistics
Matches: 377, Mismatches: 53, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
134 1 0.00
135 112 0.30
136 262 0.69
137 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (136 bp):
GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
TACAAT
Found at i:27534066 original size:204 final size:203
Alignment explanation
Indices: 27533712--27534281 Score: 701
Period size: 204 Copynumber: 2.8 Consensus size: 203
27533702 AGGTTTAAGG
* * * **
27533712 TGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* ** * *
27533777 TTGTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTT
66 TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
* * *
27533842 ACATTGTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGG
131 ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACA-TGG
*
27533907 GTTACATTC
195 GTTACAATC
* *
27533916 TGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* * * *
27533981 TTGTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGTCCGCTAGGACATTAAACATGGGTTT
66 TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
* * * * * * ** **
27534046 ACACTGTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACATGGG
131 ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACATGGG
*
27534111 TTACAATG
196 TTACAATC
* ** * * *
27534119 TGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* ** * * * *
27534184 TTGTGTAAGACCGTAAAT-TAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGC
66 TTGTGTAAGACCATAGCTCGAA-TATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGT
* *
27534248 TACAATGTGTAAAACCATAGCTCGACTGTGGCAA
130 TACAATGTGTAAGACCATAGCTCGACTATGGCAA
27534282 AGTATGGAGC
Statistics
Matches: 309, Mismatches: 56, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
202 2 0.01
203 144 0.47
204 163 0.53
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (203 bp):
TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACATGGG
TTACAATC
Found at i:27541933 original size:21 final size:19
Alignment explanation
Indices: 27541907--27541955 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
27541897 TGTAAAAGAC
27541907 TAATGATTCCCTTCAGTGGTA
1 TAATGATTCCCTT-AG-GGTA
*
27541928 TAATGATATTCCCTTTGGGTA
1 TAATG--ATTCCCTTAGGGTA
27541949 TAATGAT
1 TAATGAT
27541956 ATCCAAGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
21 14 0.56
22 1 0.04
23 8 0.32
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (19 bp):
TAATGATTCCCTTAGGGTA
Found at i:27541941 original size:23 final size:21
Alignment explanation
Indices: 27541912--27541957 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
27541902 AAGACTAATG
27541912 ATTCCCTTCAGTGGTATAATGAT
1 ATTCCCTT-AG-GGTATAATGAT
*
27541935 ATTCCCTTTGGGTATAATGAT
1 ATTCCCTTAGGGTATAATGAT
27541956 AT
1 AT
27541958 CCAAGCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 8 0.36
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (21 bp):
ATTCCCTTAGGGTATAATGAT
Found at i:27543865 original size:15 final size:15
Alignment explanation
Indices: 27543845--27543874 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27543835 TTCCAAATGA
27543845 TTTCATTTTCTCCAT
1 TTTCATTTTCTCCAT
*
27543860 TTTCATTTTGTCCAT
1 TTTCATTTTCTCCAT
27543875 GCAATTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTCATTTTCTCCAT
Found at i:27545333 original size:239 final size:239
Alignment explanation
Indices: 27544908--27545369 Score: 728
Period size: 239 Copynumber: 1.9 Consensus size: 239
27544898 GATATGAGCT
*
27544908 TGTGTCTATTCCATGTTGTATGAACCCGTAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* *
27544973 TGTATGTATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
66 TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
* * *
27545038 ATAGAAATAAATACAATATATTGCATGAAATGCTTTTATGTATATGATGAGGAGAAAGGAGGAAT
131 ATAGAAATAAATACAATAAATTGCATGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
27545103 ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
196 ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
* * * *
27545147 TGTGTCTATTTCGTGTTGTATGAACCCATAGTTGTGTATGAACCTGGTGACTGAGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* * * * *
27545212 TGCATATATGTTGGATGTTTATTTAGTTATAATTTGAAGTGTTAATGGGTGGTGTATTGTATGCT
66 TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
* * *
27545277 ATAGAAATAAATACAATAAATTG-ATTGAAATGCTTGTATGAATATGATGCGGAGAAATGAGGGA
131 ATAGAAATAAATACAATAAATTGCA-TGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAA
* *
27545341 TATACTTTGATGGGGTGGTTGAAGATAGG
195 TATACTTTGATGGGGTAGTTAAAGATAGG
27545370 TGAAAGCTCG
Statistics
Matches: 202, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
238 1 0.00
239 201 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (239 bp):
TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
ATAGAAATAAATACAATAAATTGCATGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
Found at i:27547984 original size:21 final size:20
Alignment explanation
Indices: 27547939--27547984 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
27547929 TTGTTGGAAT
27547939 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
27547958 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
27547979 GGTTGA
1 GGTTGA
27547985 TTGCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:27554980 original size:50 final size:50
Alignment explanation
Indices: 27554864--27555055 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 50
27554854 GATAACAACA
* * * ** * *
27554864 TGCCAAAGCCATGTCCCAGACATGATCTTATATGGGATGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
27554915 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
27554965 TGCCAACGCCATGTCCCAAACACGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
27555015 AT-TTAACGCCATGTCCCAGACATGGTCTTACATAGGACCTC
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
27555056 ATTACCCAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.02
50 85 0.71
51 30 0.25
52 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:27561642 original size:11 final size:11
Alignment explanation
Indices: 27561621--27561738 Score: 87
Period size: 11 Copynumber: 11.4 Consensus size: 11
27561611 CAAAAATTAA
27561621 AAAATATATTTT
1 AAAA-ATATTTT
27561633 AAAAATATTTT
1 AAAAATATTTT
27561644 --AAA-A--TT
1 AAAAATATTTT
*
27561650 AAAAA-AATTT
1 AAAAATATTTT
27561660 AAAAAGTATTTT
1 AAAAA-TATTTT
*
27561672 AAAAA-AATTT
1 AAAAATATTTT
27561682 -AAAA-A-TTT
1 AAAAATATTTT
27561690 AAAAA-ATTTT
1 AAAAATATTTT
27561700 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
27561713 AAAAGTATTTT
1 AAAAATATTTT
*
27561724 AAAAGTATTTT
1 AAAAATATTTT
27561735 AAAA
1 AAAA
27561739 TTAAAAAATT
Statistics
Matches: 92, Mismatches: 3, Indels: 23
0.78 0.03 0.19
Matches are distributed among these distances:
6 2 0.02
8 8 0.09
9 13 0.14
10 14 0.15
11 33 0.36
12 17 0.18
13 5 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:27561661 original size:10 final size:10
Alignment explanation
Indices: 27561644--27561705 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
27561634 AAAATATTTT
27561644 AAAA-TTAAA
1 AAAATTTAAA
27561653 AAAATTTAAA
1 AAAATTTAAA
*
27561663 AAGTATTTTAAA
1 AA--AATTTAAA
27561675 AAAATTT--A
1 AAAATTTAAA
27561683 AAAATTTAAA
1 AAAATTTAAA
*
27561693 AAATTTTAAA
1 AAAATTTAAA
27561703 AAA
1 AAA
27561706 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.18
9 4 0.09
10 24 0.53
12 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:27561676 original size:22 final size:22
Alignment explanation
Indices: 27561648--27561738 Score: 109
Period size: 22 Copynumber: 4.3 Consensus size: 22
27561638 TATTTTAAAA
27561648 TTAAAAAAATTTAAAAAGTATT
1 TTAAAAAAATTTAAAAAGTATT
27561670 TTAAAAAAATTT-AAAA--A-T
1 TTAAAAAAATTTAAAAAGTATT
*
27561688 TTAAAAAATTTTAAAAAAGTATT
1 TTAAAAAAATTT-AAAAAGTATT
** *
27561711 TTAAAAGTATTTTAAAAGTATT
1 TTAAAAAAATTTAAAAAGTATT
27561733 TTAAAA
1 TTAAAA
27561739 TTAAAAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
18 12 0.20
19 1 0.02
20 4 0.07
21 4 0.07
22 28 0.47
23 10 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAAAAAAATTTAAAAAGTATT
Found at i:27561678 original size:41 final size:40
Alignment explanation
Indices: 27561594--27561727 Score: 146
Period size: 41 Copynumber: 3.2 Consensus size: 40
27561584 ACCAAAAATT
* * *
27561594 TATTTTAAAAATTAAAACAAAAATTAAAAAATATATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAATTTAAAAAGTAT-TTTAAAAAA
27561638 TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAAA
* * *
27561678 -ATTTAAAAATTTAAAAAATTTTAAAAAAGTATTTT-AAAAG
1 TATTTTAAAA-TTAAAAAAATTT-AAAAAGTATTTTAAAAAA
27561718 TATTTTAAAA
1 TATTTTAAAA
27561728 GTATTTTAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
39 8 0.10
40 23 0.29
41 34 0.43
42 3 0.04
43 6 0.08
44 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAAA
Found at i:27565752 original size:8 final size:8
Alignment explanation
Indices: 27565739--27565770 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
27565729 TTTTCAGATC
27565739 TTATTATT
1 TTATTATT
27565747 TTATTATT
1 TTATTATT
27565755 TTATTATT
1 TTATTATT
27565763 TTATTATT
1 TTATTATT
27565771 CTGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:27572574 original size:9 final size:8
Alignment explanation
Indices: 27572545--27572595 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 8
27572535 CTAATCTTTG
27572545 ATTTA-TT
1 ATTTATTT
27572552 ATTCTATTTT
1 ATT-TA-TTT
27572562 ATTTATCTT
1 ATTTAT-TT
27572571 ATTTATTT
1 ATTTATTT
27572579 ATCTTATTT
1 AT-TTATTT
27572588 ATTTATTT
1 ATTTATTT
27572596 TGACTTGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.08
8 13 0.33
9 18 0.46
10 5 0.13
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTATTT
Found at i:27572575 original size:13 final size:13
Alignment explanation
Indices: 27572559--27572593 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
27572549 ATTATTCTAT
27572559 TTTATTTATCTTA
1 TTTATTTATCTTA
27572572 TTTATTTATCTTA
1 TTTATTTATCTTA
27572585 TTTATTTAT
1 TTTATTTAT
27572594 TTTGACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATCTTA
Found at i:27572576 original size:4 final size:4
Alignment explanation
Indices: 27572545--27572595 Score: 59
Period size: 4 Copynumber: 12.0 Consensus size: 4
27572535 CTAATCTTTG
27572545 ATTT A-TT ATTCT ATTTT ATTT ATCTT ATTT ATTT ATCTT ATTT ATTT
1 ATTT ATTT ATT-T A-TTT ATTT AT-TT ATTT ATTT AT-TT ATTT ATTT
27572592 ATTT
1 ATTT
27572596 TGACTTGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 25 0.60
5 12 0.29
6 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:27573049 original size:14 final size:14
Alignment explanation
Indices: 27572991--27573049 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
27572981 TAAATTACAT
*
27572991 TAGCCCAACAAGCC
1 TAGCCCAACTAGCC
* *
27573005 TAAACCCAATTAGCC
1 T-AGCCCAACTAGCC
*
27573020 TAAGCCCAA-TACCC
1 T-AGCCCAACTAGCC
27573034 TAGCCCAACTAGCC
1 TAGCCCAACTAGCC
27573048 TA
1 TA
27573050 AACCAGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 7 0.19
14 12 0.32
15 18 0.49
ACGTcount: A:0.36, C:0.39, G:0.10, T:0.15
Consensus pattern (14 bp):
TAGCCCAACTAGCC
Found at i:27574192 original size:20 final size:20
Alignment explanation
Indices: 27574169--27574217 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27574159 TTGTTTAAGT
* *
27574169 TTAATATATTTTTAATTTTA
1 TTAATATATTTTCAATATTA
27574189 TTAATACTA-TTTCAATATTA
1 TTAATA-TATTTTCAATATTA
27574209 -TAATATATT
1 TTAATATATT
27574218 ATTATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 15 0.60
21 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATATTTTCAATATTA
Found at i:27579493 original size:3 final size:3
Alignment explanation
Indices: 27579485--27579510 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27579475 AATTTATAAT
27579485 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
27579511 TCAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27582440 original size:23 final size:23
Alignment explanation
Indices: 27582414--27582485 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
27582404 TGTTTGTTTG
27582414 ATAAAGAAATATTACTATTTTTT
1 ATAAAGAAATATTACTATTTTTT
* * *
27582437 ATAAAGTAGTATTACT-GTTTTT
1 ATAAAGAAATATTACTATTTTTT
27582459 ATAAA-ATATATATATAACTATTTTTT
1 ATAAAGA-A-ATAT-T-ACTATTTTTT
27582485 A
1 A
27582486 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 11 0.29
23 17 0.45
24 1 0.03
25 3 0.08
26 6 0.16
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (23 bp):
ATAAAGAAATATTACTATTTTTT
Found at i:27584226 original size:15 final size:15
Alignment explanation
Indices: 27584206--27584259 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
27584196 CCTTTTTCCA
27584206 TTAAAATATTATTTT
1 TTAAAATATTATTTT
27584221 TTAAAAT-TTATTATT
1 TTAAAATATTATT-TT
** *
27584236 TT-ATTTATT-TTTA
1 TTAAAATATTATTTT
27584249 TTAAAATATTA
1 TTAAAATATTA
27584260 GACTTAGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
13 3 0.10
14 14 0.47
15 13 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAAAATATTATTTT
Found at i:27584344 original size:22 final size:22
Alignment explanation
Indices: 27584318--27584360 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
27584308 AACATTTTAA
*
27584318 ATATTACATGTACCTTTTATTG
1 ATATTACATGTACATTTTATTG
27584340 ATATTACATGTACATTTTATT
1 ATATTACATGTACATTTTATT
27584361 AAAAGACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATTACATGTACATTTTATTG
Found at i:27585209 original size:19 final size:17
Alignment explanation
Indices: 27585174--27585215 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
27585164 GTTTTTTCAC
27585174 AAAA-ATATATATATTA
1 AAAATATATATATATTA
27585190 AAAATATATATTATATTTA
1 AAAATATATA-TATA-TTA
27585209 AAAATAT
1 AAAATAT
27585216 TTATCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 4 0.17
19 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATATATATATTA
Found at i:27585508 original size:16 final size:16
Alignment explanation
Indices: 27585478--27585528 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
27585468 GGTTCATTGG
27585478 AATGGAATA-AGGTTGT
1 AATGGAATAGA-GTTGT
*
27585494 AATTGAATAGAGTTGT
1 AATGGAATAGAGTTGT
*
27585510 AATGGAATAGAGCTGT
1 AATGGAATAGAGTTGT
27585526 AAT
1 AAT
27585529 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGTTGT
Found at i:27590258 original size:50 final size:50
Alignment explanation
Indices: 27590143--27590385 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
27590133 GATAATAACA
* ** *
27590143 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
27590194 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27590244 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27590294 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
27590344 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27590386 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 145 0.81
51 33 0.19
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:27590503 original size:13 final size:13
Alignment explanation
Indices: 27590480--27590511 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
27590470 GCTTAAATTA
27590480 TCATCAAAATAAAT
1 TCAT-AAAATAAAT
27590494 TCATAAAATAAAT
1 TCATAAAATAAAT
27590507 TCATA
1 TCATA
27590512 GTTGCTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:27590760 original size:30 final size:30
Alignment explanation
Indices: 27590725--27590782 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27590715 CCTCGACTCT
*
27590725 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
27590755 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
27590783 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:27593156 original size:30 final size:30
Alignment explanation
Indices: 27593120--27593180 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
27593110 ATTTTTGAAT
27593120 TCCTTGAACTTTTCAAGGGACTCAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
*
27593150 TCCTTGAACTTTTCAAGGGACTTAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
27593180 T
1 T
27593181 GGCGTATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (30 bp):
TCCTTGAACTTTTCAAGGGACTCAGACTTA
Found at i:27604074 original size:9 final size:9
Alignment explanation
Indices: 27604037--27604238 Score: 87
Period size: 9 Copynumber: 21.9 Consensus size: 9
27604027 AATATGTGGC
27604037 AAAAATTAT
1 AAAAATTAT
* *
27604046 AAAAA-AAG
1 AAAAATTAT
*
27604054 AAAAATAAAT
1 AAAAAT-TAT
27604064 AAAAATTAT
1 AAAAATTAT
27604073 AAAAATTATT
1 AAAAATTA-T
**
27604083 AAATTTTAAT
1 AAAAATT-AT
27604093 AAAAA-TAT
1 AAAAATTAT
27604101 AAAAA-TATT
1 AAAAATTA-T
27604110 AAAAATTAT
1 AAAAATTAT
**
27604119 AAAAATCGT
1 AAAAATTAT
27604128 AAAAA-TAT
1 AAAAATTAT
*
27604136 AAAAA-AAT
1 AAAAATTAT
*
27604144 ATAAAATTGT
1 A-AAAATTAT
*
27604154 AAAATTTTAT
1 AAAA-ATTAT
*
27604164 AAAATTTTAT
1 AAAA-ATTAT
27604174 AATGTCAAA--AT
1 AA----AAATTAT
27604185 -AAAATTAT
1 AAAAATTAT
* *
27604193 AAAAAATGT
1 AAAAATTAT
*
27604202 AAAGAAATAT
1 AAA-AATTAT
*
27604212 AAAATTTAT
1 AAAAATTAT
*
27604221 AAAAAAATAT
1 -AAAAATTAT
27604231 AAAAATTA
1 AAAAATTA
27604239 ACTTACCAAA
Statistics
Matches: 149, Mismatches: 26, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
6 3 0.02
8 26 0.17
9 62 0.42
10 53 0.36
11 3 0.02
14 2 0.01
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27604076 original size:18 final size:18
Alignment explanation
Indices: 27604037--27604157 Score: 97
Period size: 18 Copynumber: 6.7 Consensus size: 18
27604027 AATATGTGGC
*
27604037 AAAAATTATAAAAA-AAG
1 AAAAATTATAAAAATAAT
* *
27604054 AAAAATAAATAAAAATTAT
1 AAAAAT-TATAAAAATAAT
**
27604073 AAAAATTATTAAATTTTAAT
1 AAAAATTA-TAAA-AATAAT
*
27604093 AAAAA-TATAAAAATATT
1 AAAAATTATAAAAATAAT
**
27604110 AAAAATTATAAAAATCGT
1 AAAAATTATAAAAATAAT
27604128 AAAAA-TATAAAAA-AAT
1 AAAAATTATAAAAATAAT
*
27604144 ATAAAATTGTAAAA
1 A-AAAATTATAAAA
27604158 TTTTATAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
16 2 0.02
17 26 0.32
18 33 0.40
19 13 0.16
20 8 0.10
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAATAAT
Found at i:27604212 original size:19 final size:19
Alignment explanation
Indices: 27604185--27604235 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
27604175 ATGTCAAAAT
* *
27604185 AAAATTATAAAAAATGTAA
1 AAAAATATAAAAAATATAA
* **
27604204 AGAAATATAAAATTTATAA
1 AAAAATATAAAAAATATAA
27604223 AAAAATATAAAAA
1 AAAAATATAAAAA
27604236 TTAACTTACC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAATATAAAAAATATAA
Found at i:27606389 original size:229 final size:229
Alignment explanation
Indices: 27605988--27606438 Score: 875
Period size: 229 Copynumber: 2.0 Consensus size: 229
27605978 AAACACAAGC
27605988 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
27606053 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
*
27606118 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTGTTTCT
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
27606183 ATATATTCCCTTTTATTCACATTTTATCATTTGA
196 ATATATTCCCTTTTATTCACATTTTATCATTTGA
*
27606217 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGATTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
*
27606282 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATTTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
27606347 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
27606412 ATATATTCCCTTTTATTCACATTTTAT
196 ATATATTCCCTTTTATTCACATTTTAT
27606439 TTAAGAAAAT
Statistics
Matches: 219, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 219 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (229 bp):
ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
ATATATTCCCTTTTATTCACATTTTATCATTTGA
Found at i:27609606 original size:79 final size:80
Alignment explanation
Indices: 27609475--27609636 Score: 290
Period size: 79 Copynumber: 2.0 Consensus size: 80
27609465 TTTAAGAGAA
* **
27609475 AGTATCAGTTTGCCCTTTGATATAATATTATATAATATTTTGGGAATAATTTATAGAAGTGCAAA
1 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
27609540 ATACTCTTGA-TCAG
66 ATACTCTTGATTCAG
27609554 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
1 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
27609619 ATACTCTTGATTCAG
66 ATACTCTTGATTCAG
27609634 AGT
1 AGT
27609637 TAAGTGGAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 72 0.91
80 7 0.09
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (80 bp):
AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
ATACTCTTGATTCAG
Found at i:27609887 original size:18 final size:18
Alignment explanation
Indices: 27609844--27609889 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27609834 CTACTAGATC
*
27609844 TTAATTTTTTTTATATAA
1 TTAATTATTTTTATATAA
*
27609862 TTACTTATTTTTAT-TAA
1 TTAATTATTTTTATATAA
27609879 TTTAATTATTT
1 -TTAATTATTT
27609890 ACAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTATTTTTATATAA
Found at i:27615880 original size:9 final size:9
Alignment explanation
Indices: 27615866--27615894 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
27615856 TTGGTTATAA
27615866 TTACAGTAT
1 TTACAGTAT
27615875 TTACAGTAT
1 TTACAGTAT
27615884 TTACAGTAT
1 TTACAGTAT
27615893 TT
1 TT
27615895 GTGATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTACAGTAT
Found at i:27616558 original size:19 final size:19
Alignment explanation
Indices: 27616534--27616633 Score: 107
Period size: 19 Copynumber: 5.1 Consensus size: 19
27616524 TTTACATTAT
27616534 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
27616553 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
*
27616572 AA-T-TAATCAA-ATGCTACAA
1 AATTATAATTAACA--CTA-AA
*
27616591 CAATTATAATTAACATTACAAA
1 -AATTATAATTAACACT--AAA
27616613 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
27616632 AA
1 AA
27616634 AAGAAAGTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 4 0.06
19 28 0.41
20 2 0.03
21 17 0.25
22 8 0.12
23 2 0.03
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (19 bp):
AATTATAATTAACACTAAA
Found at i:27616635 original size:21 final size:20
Alignment explanation
Indices: 27616534--27616634 Score: 104
Period size: 21 Copynumber: 5.1 Consensus size: 20
27616524 TTTACATTAT
27616534 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
27616553 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
* *
27616572 AA-T-TAATCAA-ATGCTACAAC
1 AATTATAATTAACA--CTA-AAA
*
27616592 AATTATAATTAACATTACAAA
1 AATTATAATTAACACTA-AAA
27616613 AATTATAATTAACACTAAAA
1 AATTATAATTAACACTAAAA
27616633 AA
1 AA
27616635 AGAAAGTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 3 0.04
19 21 0.30
20 9 0.13
21 22 0.32
22 6 0.09
23 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (20 bp):
AATTATAATTAACACTAAAA
Found at i:27618688 original size:49 final size:49
Alignment explanation
Indices: 27618631--27618734 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
27618621 TCATGTGTTA
* ** * *
27618631 TAATTTTATAAAGTGTTGAGGTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATT
27618680 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATT
27618729 TAATTT
1 TAATTT
27618735 GTTTTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATT
Found at i:27619410 original size:51 final size:51
Alignment explanation
Indices: 27619333--27619435 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
27619323 TGAAGGTGGT
*
27619333 GGCATTGGGAGCATGGAATGCTTGAAGAAATTTCTTCATGTTTCCATTAAA
1 GGCATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAA
27619384 GGCATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAA
1 GGCATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAA
27619435 G
1 G
27619436 TATCTCATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (51 bp):
GGCATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAA
Found at i:27619451 original size:4 final size:4
Alignment explanation
Indices: 27619442--27619478 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
27619432 AAAGTATCTC
27619442 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
27619479 ATAAAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:27622072 original size:20 final size:20
Alignment explanation
Indices: 27622047--27622101 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
27622037 CATAAACATT
*
27622047 AATAATTTTGTAAGAGATTC
1 AATAATTTTGTAAAAGATTC
* *
27622067 AATAATTCTGTAAAAGATTT
1 AATAATTTTGTAAAAGATTC
*
27622087 AGTAATTTTGTAAAA
1 AATAATTTTGTAAAA
27622102 AAAAAATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (20 bp):
AATAATTTTGTAAAAGATTC
Found at i:27622467 original size:20 final size:20
Alignment explanation
Indices: 27622439--27622496 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
27622429 AAATTTCGAC
*
27622439 AATTTTGTAAGGGATTCAAT
1 AATTTTGTAAGAGATTCAAT
* * *
27622459 AATTATGTAAAAGA-TCCAT
1 AATTTTGTAAGAGATTCAAT
27622478 AATTTTGTAAGAGATTCAA
1 AATTTTGTAAGAGATTCAA
27622497 CAAATTTAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (20 bp):
AATTTTGTAAGAGATTCAAT
Found at i:27623414 original size:20 final size:21
Alignment explanation
Indices: 27623376--27623418 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
27623366 TATTATTGTT
*
27623376 ACCCATGATAATTTGGACTTA
1 ACCCATGATAATTTCGACTTA
*
27623397 ACCCATTAT-ATTTCGACTTA
1 ACCCATGATAATTTCGACTTA
27623417 AC
1 AC
27623419 ATGTCATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (21 bp):
ACCCATGATAATTTCGACTTA
Found at i:27623962 original size:13 final size:12
Alignment explanation
Indices: 27623940--27623978 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
27623930 ATTGTTGTTG
27623940 TTTGATTTAAAT
1 TTTGATTTAAAT
27623952 TTTGAATTTAAAT
1 TTTG-ATTTAAAT
27623965 TTT-ATTTAGAAT
1 TTTGATTTA-AAT
27623977 TT
1 TT
27623979 ATTTTCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (12 bp):
TTTGATTTAAAT
Found at i:27628767 original size:40 final size:41
Alignment explanation
Indices: 27628672--27628779 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
27628662 GAGATTGGAG
* *
27628672 GCATGTTAAACATGCTATTGAATT-AAATATGTTACCTTAA
1 GCATGTAAAACATGCCATTGAATTGAAATATGTTACCTTAA
* *
27628712 GCATG-AGATATATGCCATTGAATTGAAAT-TGTTA-CTGTAA
1 GCATGTA-AAACATGCCATTGAATTGAAATATGTTACCT-TAA
* *
27628752 GCATGTAAAACATGCCACTGTATTGAAA
1 GCATGTAAAACATGCCATTGAATTGAAA
27628780 CTGAACTGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
39 2 0.04
40 49 0.88
41 5 0.09
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (41 bp):
GCATGTAAAACATGCCATTGAATTGAAATATGTTACCTTAA
Found at i:27630276 original size:20 final size:21
Alignment explanation
Indices: 27630238--27630277 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27630228 TGGCATGCTT
27630238 AGTGATGGTATGAAATGGTTA
1 AGTGATGGTATGAAATGGTTA
27630259 AGTGAGTGGT-TG-AATGGTT
1 AGTGA-TGGTATGAAATGGTT
27630278 TGAGTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
AGTGATGGTATGAAATGGTTA
Found at i:27633471 original size:25 final size:25
Alignment explanation
Indices: 27633423--27633471 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
27633413 CATAATTGAA
* * *
27633423 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
27633448 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
27633472 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:27633933 original size:43 final size:43
Alignment explanation
Indices: 27633867--27633952 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
27633857 TATGTGATTG
*
27633867 ATATAGAAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATAGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
* * **
27633910 ATATCGAAATGA-ACAATATGAGAAACGGTTATGAGATGAGAAA
1 ATATAGAAATGACA-AAGATGAGAAACGAATATGAGATGAGAAA
27633953 TGAGATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (43 bp):
ATATAGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
Found at i:27633978 original size:20 final size:19
Alignment explanation
Indices: 27633939--27633984 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
27633929 GAGAAACGGT
*
27633939 TATGAGATGAGAAATGAGA
1 TATGAAATGAGAAATGAGA
*
27633958 TATGAAATGATGAATTGAGA
1 TATGAAATGA-GAAATGAGA
27633978 TATGAAA
1 TATGAAA
27633985 CTTGAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (19 bp):
TATGAAATGAGAAATGAGA
Found at i:27635303 original size:49 final size:49
Alignment explanation
Indices: 27635215--27635308 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
27635205 TCAAGAAGGG
* * * ** *
27635215 ATAAATAGTGATAATTGTGTAAACAGTGGAATATTAAGTTTAGCAACGT
1 ATAAATAGTGATAATAGTGTAAACAGTGAAAGACCAAGTTGAGCAACGT
*
27635264 ATAAATAGTGATAATAGTGTAGACAGTGAAAGACCAAGTTGAGCA
1 ATAAATAGTGATAATAGTGTAAACAGTGAAAGACCAAGTTGAGCA
27635309 TTGCATAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (49 bp):
ATAAATAGTGATAATAGTGTAAACAGTGAAAGACCAAGTTGAGCAACGT
Found at i:27638907 original size:20 final size:20
Alignment explanation
Indices: 27638882--27638927 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
27638872 GAACTTTTCA
27638882 ATTTTATGAACCGTTAATTT
1 ATTTTATGAACCGTTAATTT
27638902 ATTTTATGAACCGTTAATTT
1 ATTTTATGAACCGTTAATTT
27638922 ATTTTA
1 ATTTTA
27638928 CTTCTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTTTATGAACCGTTAATTT
Found at i:27640185 original size:20 final size:20
Alignment explanation
Indices: 27640160--27640201 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27640150 GTCGAGGAAG
27640160 AAACAAGG-CGATTCAAGCAA
1 AAACAAGGACGA-TCAAGCAA
*
27640180 AAACAAGGACGATGAAGCAA
1 AAACAAGGACGATCAAGCAA
27640200 AA
1 AA
27640202 GATGGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.55, C:0.17, G:0.21, T:0.07
Consensus pattern (20 bp):
AAACAAGGACGATCAAGCAA
Found at i:27644906 original size:37 final size:37
Alignment explanation
Indices: 27644815--27644910 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
27644805 TGGAAAGTAT
* *
27644815 GCTCAATCGAGCAAATCCTACCGTTATACTGAATGAA
1 GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
* *
27644852 TCTCAATCGAGCAAATCTTACTGTTATATTGAATGAA
1 GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
*
27644889 GCTCAATCAAGCAAATCTTACT
1 GCTCAATCGAGCAAATCTTACT
27644911 TTTACACTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (37 bp):
GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
Found at i:27649170 original size:18 final size:18
Alignment explanation
Indices: 27649147--27649183 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27649137 TTTGAAAACC
27649147 TGTCAACAACAACAAATA
1 TGTCAACAACAACAAATA
27649165 TGTCAACAACAACAAATA
1 TGTCAACAACAACAAATA
27649183 T
1 T
27649184 ACTATCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.19
Consensus pattern (18 bp):
TGTCAACAACAACAAATA
Found at i:27657562 original size:25 final size:24
Alignment explanation
Indices: 27657522--27657577 Score: 103
Period size: 25 Copynumber: 2.3 Consensus size: 24
27657512 TTAAATATAT
27657522 ATAAAAATATATATTTGATTAAAA
1 ATAAAAATATATATTTGATTAAAA
27657546 ATAAAATATATATATTTGATTAAAA
1 ATAAAA-ATATATATTTGATTAAAA
27657571 ATAAAAA
1 ATAAAAA
27657578 AATTGCCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
ATAAAAATATATATTTGATTAAAA
Found at i:27657897 original size:14 final size:14
Alignment explanation
Indices: 27657867--27657896 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27657857 GTTCTAAACA
27657867 TTTAATTAATTTAT
1 TTTAATTAATTTAT
27657881 TTTAATTAATTT-T
1 TTTAATTAATTTAT
27657894 TTT
1 TTT
27657897 TCACATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTAATTTAT
Found at i:27658989 original size:30 final size:29
Alignment explanation
Indices: 27658921--27658998 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
27658911 AAGAAGAAAA
*
27658921 ATTTAACAATTTAATGATTTTAAAAAAATT
1 ATTTAATAATTTAATGA-TTTAAAAAAATT
** *
27658951 ATCAAATAATTTAATGATTTAAATAAATTT
1 ATTTAATAATTTAATGATTTAAA-AAAATT
* *
27658981 TTTTAATAATTAAATGAT
1 ATTTAATAATTTAATGAT
27658999 ATTTTATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 6 0.15
30 33 0.85
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (29 bp):
ATTTAATAATTTAATGATTTAAAAAAATT
Found at i:27660150 original size:7 final size:7
Alignment explanation
Indices: 27660134--27660162 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
27660124 AATCTAATTC
27660134 AAAA-AA
1 AAAAGAA
27660140 AAAAGAA
1 AAAAGAA
27660147 AAAAGAA
1 AAAAGAA
27660154 AAAAGAA
1 AAAAGAA
27660161 AA
1 AA
27660163 GCACAACCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:27665375 original size:2 final size:2
Alignment explanation
Indices: 27665368--27665407 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27665358 TTATACATAC
27665368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27665408 TTGTTTCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27671137 original size:8 final size:8
Alignment explanation
Indices: 27671124--27671152 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
27671114 TTTATCATAT
27671124 AAATAATA
1 AAATAATA
27671132 AAATAATA
1 AAATAATA
27671140 AAATAATA
1 AAATAATA
27671148 AAATA
1 AAATA
27671153 CATTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:27676249 original size:16 final size:17
Alignment explanation
Indices: 27676228--27676264 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
27676218 TGTTGTTTTA
27676228 ATATAAATGAATCAAT-
1 ATATAAATGAATCAATG
*
27676244 ATATAAATGTATCAATG
1 ATATAAATGAATCAATG
27676261 ATAT
1 ATAT
27676265 GATGAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (17 bp):
ATATAAATGAATCAATG
Found at i:27677555 original size:16 final size:17
Alignment explanation
Indices: 27677534--27677570 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
27677524 TGTTGTTTTA
27677534 ATATAAATGAATCAAT-
1 ATATAAATGAATCAATG
*
27677550 ATATAAATGTATCAATG
1 ATATAAATGAATCAATG
27677567 ATAT
1 ATAT
27677571 GATGAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (17 bp):
ATATAAATGAATCAATG
Found at i:27680168 original size:22 final size:22
Alignment explanation
Indices: 27680095--27680158 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
27680085 CGACTATGTT
* * *
27680095 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
27680117 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
27680139 TAACGTACTAAGCTCTCATG
1 TAACGTACTAAGCTCTCATG
27680159 TTTCACGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:27682126 original size:26 final size:26
Alignment explanation
Indices: 27682097--27682156 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
27682087 AATTCTCTAT
*
27682097 AAAGGCTTTCTTTCATATTA-GCCAC
1 AAAGGCTTTCTTTCATATTACACCAC
*
27682122 AAAAGCTTTCTTTCATATTACACCAC
1 AAAGGCTTTCTTTCATATTACACCAC
27682148 AAAGGCTTT
1 AAAGGCTTT
27682157 TCTTACCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (26 bp):
AAAGGCTTTCTTTCATATTACACCAC
Found at i:27689073 original size:24 final size:24
Alignment explanation
Indices: 27689046--27689091 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
27689036 AGAACAATCC
* *
27689046 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
27689070 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
27689092 AAAAGATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:27697179 original size:44 final size:44
Alignment explanation
Indices: 27697129--27697767 Score: 344
Period size: 44 Copynumber: 14.7 Consensus size: 44
27697119 TAACAGATCG
27697129 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * *
27697173 AGTCTTATC-CTCCTGAAGTTGCAG-CGAGGCAGACTGAAGAT-GGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AA-ATAAGCA
* * * ***
27697218 AATCTTATCTCCCAGAAGTTGCAGTGGAGCAGATTAAAGCCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAG-CA
* * * * * * * *
27697263 A-TCCTATCTCGCTGAAGCTGTAGT-GAGCGGA-TTAA-AATCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGC-A
* * * ** *
27697304 AGATCTCATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT---CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
*
27697345 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * *
27697389 AGTCTTATC-CTCCTGAAGTTGTAAT-GAGGCAGACTGAAGAT-GGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AA-ATAAGCA
* * * ***
27697434 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAG-CA
* * * * * *
27697479 A-TCCTATCTCCCTGAAGTTGCAGTGAAGCGGA-TTAA-AATCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGC-A
* * ** * ** *
27697521 AGATCTTACCTCTCTGAAGTTGCAG-AAAGCGGA-TCGCAT---CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
**
27697562 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* **
27697606 AGTCTTATC-CTCCTGAAGTTGCAATGGAGCAGACTAGGTAAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
*
27697650 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGACAGACTAAATCAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGACTAAATAAGCA
* * * **
27697694 AGTCTTATC-CTCCTGAGGTTGCAGT-GAGGCACATTAAAGTTGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAA-TAAGCA
* *
27697739 AATCTTATCTCTCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
27697768 AAGATTAGAG
Statistics
Matches: 466, Mismatches: 86, Indels: 85
0.73 0.14 0.13
Matches are distributed among these distances:
40 41 0.09
41 20 0.04
42 8 0.02
43 53 0.11
44 241 0.52
45 91 0.20
46 12 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
Found at i:27697611 original size:217 final size:217
Alignment explanation
Indices: 27697129--27697762 Score: 881
Period size: 216 Copynumber: 2.9 Consensus size: 217
27697119 TAACAGATCG
*
27697129 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
** * * *
27697194 CAGCGAGGCAGACTGAAGATGGAAAATCTTATCTCCCAGAAGTTGCAGTGGAGCAGATTAAAGCC
66 CAATGAGGCAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * *
27697259 GACAATCCTATCTCGCTGAAGCTGTAGTG-AGCGGATTAAAATCTCAGATCTCATCTCTCTGAAG
131 GACAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAG
*
27697323 TTGCAGAGAGCAGATCGCATCT
196 TTGCAGAAAGCAGATCGCATCT
27697345 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
*
27697410 TAATGAGGCAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCC
66 CAATGAGGCAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCC
*
27697475 GACAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCTCAGATCTTACCTCTCTGAAG
131 GACAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAG
*
27697540 TTGCAGAAAGCGGATCGCATCT
196 TTGCAGAAAGCAGATCGCATCT
*
27697562 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGGTAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
* * * *
27697627 CAATG-GAGCAGACT--AGGTAAGCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGACAGACTAA
66 CAATGAG-GCAGACTGAAGAT-GGCAAATCTTATCTCT-CTGAAGTTGCAGTGGAG-CAGATTAA
* * * * * ** * *
27697687 ATCAG-CAAGTCTTATC-CTCCTGAGGTTGCAGTGAGGCACATTAAAGT-TGGCAAATCTTATCT
127 AGCCGACAA-TCCTATCTC-CCTGAAGTTGCAGTGAAGCGGATTAAAATCT--CAGATCTTATCT
27697749 CTCTGAAGTTGCAG
188 CTCTGAAGTTGCAG
27697763 TGGAGAAGAT
Statistics
Matches: 379, Mismatches: 30, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
215 13 0.03
216 214 0.56
217 152 0.40
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (217 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
CAATGAGGCAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCC
GACAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAG
TTGCAGAAAGCAGATCGCATCT
Done.