Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 97 of 120
Found at i:27856740 original size:14 final size:16
Alignment explanation
Indices: 27856710--27856741 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
27856700 ATAATAAGTT
27856710 AACAAAAGTTATTAAA
1 AACAAAAGTTATTAAA
27856726 AACAAAA-TT-TTAAA
1 AACAAAAGTTATTAAA
27856740 AA
1 AA
27856742 TCTATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (16 bp):
AACAAAAGTTATTAAA
Found at i:27857692 original size:15 final size:15
Alignment explanation
Indices: 27857672--27857700 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27857662 TTATGGTTAT
27857672 AATATTAAATTATTG
1 AATATTAAATTATTG
27857687 AATATTAAATTATT
1 AATATTAAATTATT
27857701 AAGCTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATATTAAATTATTG
Found at i:27858404 original size:8 final size:8
Alignment explanation
Indices: 27858393--27858435 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
27858383 TCAAAATTTC
27858393 AAATAAGA
1 AAATAAGA
27858401 AAATAAGA
1 AAATAAGA
27858409 ACAATAA-A
1 A-AATAAGA
27858417 ATAATAAGA
1 A-AATAAGA
27858426 AAAGTAAGA
1 AAA-TAAGA
27858435 A
1 A
27858436 TAAAATAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 18 0.58
9 13 0.42
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (8 bp):
AAATAAGA
Found at i:27858441 original size:23 final size:23
Alignment explanation
Indices: 27858394--27858443 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
27858384 CAAAATTTCA
27858394 AATAAGAAAATAAGAACAATAAAAT
1 AATAAGAAAATAAG-A-AATAAAAT
27858419 AATAAGAAAAGTAAG-AATAAAAT
1 AATAAGAAAA-TAAGAAATAAAAT
27858442 AA
1 AA
27858444 GATAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.42
25 10 0.42
26 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (23 bp):
AATAAGAAAATAAGAAATAAAAT
Found at i:27858451 original size:28 final size:26
Alignment explanation
Indices: 27858394--27858458 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 26
27858384 CAAAATTTCA
*
27858394 AATAAGAAAA-TAAGAACAATAAAAT
1 AATAAGAAAAGTAAGAAAAATAAAAT
*
27858419 AATAAGAAAAGTAAGAATAAAATAAGAT
1 AATAAGAAAAGTAAG-A-AAAATAAAAT
*
27858447 AATAAAAAAAGT
1 AATAAGAAAAGT
27858459 GAATTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.29
26 4 0.12
27 1 0.03
28 19 0.56
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.17
Consensus pattern (26 bp):
AATAAGAAAAGTAAGAAAAATAAAAT
Found at i:27858591 original size:15 final size:17
Alignment explanation
Indices: 27858571--27858605 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
27858561 TGTTAAAATA
27858571 TATTTAAAAT-T-ATTT
1 TATTTAAAATATCATTT
27858586 TATTTAAAATATCATTT
1 TATTTAAAATATCATTT
27858603 TAT
1 TAT
27858606 CTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTAAAATATCATTT
Found at i:27860296 original size:21 final size:23
Alignment explanation
Indices: 27860272--27860318 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
27860262 AATTTGTGCA
27860272 TTTAAA-TAGATTTTTTT-A-AAT
1 TTTAAAGT-GATTTTTTTCATAAT
27860293 TTTAAAGTGATTTTTTTCATAAT
1 TTTAAAGTGATTTTTTTCATAAT
27860316 TTT
1 TTT
27860319 TGAAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.65
22 2 0.09
23 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTAAAGTGATTTTTTTCATAAT
Found at i:27868171 original size:21 final size:21
Alignment explanation
Indices: 27868129--27868171 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27868119 TTGAAGATTA
* * *
27868129 TAATATATTTTAAGTTTGATT
1 TAATATATTTGAAATTTAATT
*
27868150 TAATATGTTTGAAATTTAATT
1 TAATATATTTGAAATTTAATT
27868171 T
1 T
27868172 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TAATATATTTGAAATTTAATT
Found at i:27869007 original size:24 final size:24
Alignment explanation
Indices: 27868970--27869018 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
27868960 TGAGGGAGGT
27868970 AATAAAATATGCATATCAAATTAA
1 AATAAAATATGCATATCAAATTAA
*
27868994 AATATAAATA-GCATATTAAATTAA
1 AATA-AAATATGCATATCAAATTAA
27869018 A
1 A
27869019 GCTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
AATAAAATATGCATATCAAATTAA
Found at i:27871439 original size:56 final size:56
Alignment explanation
Indices: 27871362--27871473 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
27871352 GCAAAGATTG
27871362 CCTCAGGGTTCATAAGGAATTCAGCTAGTATAGGTGGAAACCTGATGATGGCCCAA
1 CCTCAGGGTTCATAAGGAATTCAGCTAGTATAGGTGGAAACCTGATGATGGCCCAA
27871418 CCTCAGGGTTCATAAGGAATTCAGCTAGTATAGGTGGAAACCTGATGATGGCCCAA
1 CCTCAGGGTTCATAAGGAATTCAGCTAGTATAGGTGGAAACCTGATGATGGCCCAA
27871474 AGGAAACACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (56 bp):
CCTCAGGGTTCATAAGGAATTCAGCTAGTATAGGTGGAAACCTGATGATGGCCCAA
Found at i:27878700 original size:22 final size:23
Alignment explanation
Indices: 27878675--27878729 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
27878665 TTTATAACAA
*
27878675 TATATTATACTATTAAA-TATAT
1 TATATTATACTACTAAATTATAT
* *
27878697 TATAATATATTACTAAATTATAT
1 TATATTATACTACTAAATTATAT
*
27878720 TTTAATTATA
1 TAT-ATTATA
27878730 ACATTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 14 0.54
23 7 0.27
24 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTATACTACTAAATTATAT
Found at i:27878738 original size:23 final size:22
Alignment explanation
Indices: 27878678--27878738 Score: 52
Period size: 23 Copynumber: 2.6 Consensus size: 22
27878668 ATAACAATAT
*
27878678 ATTATACTATTAAATATATTATA
1 ATTATAC-ATTAATTATATTATA
* *
27878701 ATATATTAC-TAAATTATATTTTA
1 AT-TA-TACATTAATTATATTATA
27878724 ATTATAACATTAATT
1 ATTAT-ACATTAATT
27878739 TTTTTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 20 0.67
24 2 0.07
25 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATACATTAATTATATTATA
Found at i:27879937 original size:20 final size:21
Alignment explanation
Indices: 27879897--27879942 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
27879887 TATTCATTTA
* *
27879897 TTTATAAATATTTTGTATGTT
1 TTTATAAATATCTTATATGTT
27879918 TTTATAAA-ATCTTATATGTT
1 TTTATAAATATCTTATATGTT
27879938 TTTAT
1 TTTAT
27879943 TGAAAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTATAAATATCTTATATGTT
Found at i:27880099 original size:60 final size:61
Alignment explanation
Indices: 27879995--27880115 Score: 140
Period size: 59 Copynumber: 2.0 Consensus size: 61
27879985 TTTAGTTTTG
* * * *
27879995 AATTTTTAAGAATAAAGATTAAATTGACATACTTTGTAAAATTGAA-AGTTAAATTAATTA
1 AATTTTTAAGAATAAAGACTAAATTGACAAAATTTATAAAATTGAATAGTTAAATTAATTA
* * *
27880055 AATTTTT-AGAATTAAA-ACTAAATTGATAAAATTTATAAATATTGAATGGTTAAATTTATTA
1 AATTTTTAAGAA-TAAAGACTAAATTGACAAAATTTATAAA-ATTGAATAGTTAAATTAATTA
27880116 TTATGCTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 22 0.43
60 17 0.33
61 12 0.24
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.40
Consensus pattern (61 bp):
AATTTTTAAGAATAAAGACTAAATTGACAAAATTTATAAAATTGAATAGTTAAATTAATTA
Found at i:27880769 original size:20 final size:20
Alignment explanation
Indices: 27880744--27880783 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27880734 TCTTGTCATC
*
27880744 ATATATTTTGAAAT-TAAAAA
1 ATATATATT-AAATGTAAAAA
27880764 ATATATATTAAATGTAAAAA
1 ATATATATTAAATGTAAAAA
27880784 TGTGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATATATATTAAATGTAAAAA
Found at i:27880974 original size:17 final size:17
Alignment explanation
Indices: 27880914--27880974 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
27880904 TCAGCATGAT
*
27880914 TAAACAATTCAATAATA
1 TAAATAATTCAATAATA
* *
27880931 TAAATAGTACAA-AATA
1 TAAATAATTCAATAATA
27880947 TAAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
27880967 TAAATAAT
1 TAAATAAT
27880975 AGACACATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.14
17 16 0.46
19 9 0.26
20 5 0.14
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:27882602 original size:13 final size:14
Alignment explanation
Indices: 27882582--27882614 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
27882572 ACTTTAAACT
27882582 CTAAACCCTAAATC
1 CTAAACCCTAAATC
27882596 C-AAACCCTAAATC
1 CTAAACCCTAAATC
27882609 CTAAAC
1 CTAAAC
27882615 ATTAAACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAACCCTAAATC
Found at i:27887932 original size:33 final size:32
Alignment explanation
Indices: 27887872--27887938 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
27887862 ATAAATGATT
27887872 ATTTAAATATAATAACTAATAATATTTAAATA
1 ATTTAAATATAATAACTAATAATATTTAAATA
27887904 ATTT-AATATAATGATACATAA-AATATTTAAATA
1 ATTTAAATATAAT-A-AC-TAATAATATTTAAATA
27887937 AT
1 AT
27887939 AAATGTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 8 0.25
32 5 0.16
33 16 0.50
34 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
ATTTAAATATAATAACTAATAATATTTAAATA
Found at i:27893674 original size:13 final size:13
Alignment explanation
Indices: 27893656--27893681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27893646 GGTTGAAATT
27893656 AAGTTACACGATC
1 AAGTTACACGATC
27893669 AAGTTACACGATC
1 AAGTTACACGATC
27893682 CAATCACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
AAGTTACACGATC
Found at i:27905982 original size:24 final size:24
Alignment explanation
Indices: 27905955--27906007 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
27905945 TCACTAAATG
27905955 ATTAAAAAT-ATAAAAAATCAATAA
1 ATTAAAAATAATAAAAAATC-ATAA
*
27905979 ATT-AAAATAATTAAAAATCATAA
1 ATTAAAAATAATAAAAAATCATAA
27906002 A-TAAAA
1 ATTAAAA
27906008 TTTAAGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 13 0.50
24 12 0.46
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
ATTAAAAATAATAAAAAATCATAA
Found at i:27913476 original size:34 final size:33
Alignment explanation
Indices: 27913410--27913477 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
27913400 ATAAGTTTAA
* *
27913410 TTATTATTTAATATAAAATAATTTAAATATATT
1 TTATTATTTAATATAAAATAATTAAAAAATATT
* *
27913443 TTATTATTTATTATGAATATAATTAAAAAATATT
1 TTATTATTTAATAT-AAAATAATTAAAAAATATT
27913477 T
1 T
27913478 AAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TTATTATTTAATATAAAATAATTAAAAAATATT
Found at i:27913546 original size:29 final size:30
Alignment explanation
Indices: 27913514--27913578 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
27913504 TTTTTAATTA
*
27913514 TTAT-TTATAAAATTATAATTATAA-TTATG
1 TTATATTATAAAA-TATAAATATAATTTATG
**
27913543 TTATATTATTTAATATAAATATAATTTATG
1 TTATATTATAAAATATAAATATAATTTATG
*
27913573 TCATAT
1 TTATAT
27913579 GAGAGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
TTATATTATAAAATATAAATATAATTTATG
Found at i:27913642 original size:20 final size:20
Alignment explanation
Indices: 27913580--27913636 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
27913570 ATGTCATATG
*
27913580 AGAGTTTAAATCGATTTAAA
1 AGAGTTTGAATCGATTTAAA
*
27913600 AGACTTTGAATCGATTTAAA
1 AGAGTTTGAATCGATTTAAA
*
27913620 AGAGTTTGAATTGATTT
1 AGAGTTTGAATCGATTT
27913637 CGAAGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (20 bp):
AGAGTTTGAATCGATTTAAA
Found at i:27914176 original size:17 final size:18
Alignment explanation
Indices: 27914146--27914179 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27914136 TTATCATTGT
27914146 TATAAAAGAATAATTAAC
1 TATAAAAGAATAATTAAC
27914164 TATAAAA-AATAATTAA
1 TATAAAAGAATAATTAA
27914180 AATAATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TATAAAAGAATAATTAAC
Found at i:27915292 original size:24 final size:23
Alignment explanation
Indices: 27915234--27915292 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
27915224 TATATAATCT
*
27915234 AATTAATTTTT-TAAATAATTAA
1 AATTAATTTTTAGAAATAATTAA
* *
27915256 TATTAATTATTTAGAAATATTTAA
1 AATTAATT-TTTAGAAATAATTAA
27915280 AATTAATATTTTA
1 AATTAAT-TTTTA
27915293 TATATTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 19 0.63
25 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTAATTTTTAGAAATAATTAA
Found at i:27915378 original size:24 final size:22
Alignment explanation
Indices: 27915290--27915378 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 22
27915280 AATTAATATT
*
27915290 TTATATATTAAAATATTAACAATAAA
1 TTAT-TATTAAAATATT-ATAAT--A
* * * *
27915316 TTA-TAATAAATTATTTTTATA
1 TTATTATTAAAATATTATAATA
27915337 TTATTATTAAAATATTATAATA
1 TTATTATTAAAATATTATAATA
*
27915359 TTAATTAATTTAAATATTAT
1 TT-ATT-ATTAAAATATTAT
27915379 TTAAATATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
21 4 0.08
22 16 0.32
23 5 0.10
24 22 0.44
26 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATTATTAAAATATTATAATA
Found at i:27917596 original size:110 final size:110
Alignment explanation
Indices: 27917476--27917677 Score: 325
Period size: 110 Copynumber: 1.8 Consensus size: 110
27917466 AATTAAGTTA
* * *
27917476 TTACAGGAAGATAGGTAAACTTGCCTTTTGGTGTCATGGCAGTTTGTTTTGTGAATGCCAACTGG
1 TTACAGGAAGATAGGTAAACTTACCTTTTGGTGTCATGCCAGTTTGTGTTGTGAATGCCAACTGG
*
27917541 GCTGGCTTGA-GAGTTTTGAGAGGCTTATTTTAGCTGCGACTTGAG
66 GCTGGCTTGAGGA-TTTTAAGAGGCTTATTTTAGCTGCGACTTGAG
* *
27917586 TTACAGGAAGATAGGTAAATTTACCTTTTTGTGTCATGCCAGTTTGTGTTGTGAATGCCAACTGG
1 TTACAGGAAGATAGGTAAACTTACCTTTTGGTGTCATGCCAGTTTGTGTTGTGAATGCCAACTGG
*
27917651 GTTGGCTTGAGGATTTTAAGAGGCTTA
66 GCTGGCTTGAGGATTTTAAGAGGCTTA
27917678 CTTAAAAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 82 0.98
111 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (110 bp):
TTACAGGAAGATAGGTAAACTTACCTTTTGGTGTCATGCCAGTTTGTGTTGTGAATGCCAACTGG
GCTGGCTTGAGGATTTTAAGAGGCTTATTTTAGCTGCGACTTGAG
Found at i:27920564 original size:2 final size:2
Alignment explanation
Indices: 27920557--27920586 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
27920547 TTTTCTCTTG
*
27920557 CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
27920587 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27923547 original size:3 final size:3
Alignment explanation
Indices: 27923539--27923585 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27923529 TTCCCTACAT
27923539 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
27923586 ATGTGTAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:27931045 original size:23 final size:24
Alignment explanation
Indices: 27931005--27931050 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
27930995 GCAAAAAAAA
*
27931005 AAAAAAAAAAGAAGAGAAGAGGAG
1 AAAAAAAAAAGAAGAGAAAAGGAG
*
27931029 AAAAAAGAAAGAA-AGAAAAGGA
1 AAAAAAAAAAGAAGAGAAAAGGA
27931051 ATTGATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAGAAGAGAAAAGGAG
Found at i:27933497 original size:348 final size:348
Alignment explanation
Indices: 27932850--27933552 Score: 1228
Period size: 348 Copynumber: 2.0 Consensus size: 348
27932840 TCCAATCCTG
* * * *
27932850 AAATCAGAATTAGGAGAGATCCTGAAGGATAGGGCTTAGTTGGGATTCTAAAAGCTTCCAAGTGC
1 AAATGAGAAGTAGGAGAGATCCTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCAAGTGA
*
27932915 AAAAGGCTGTCTGTTGTCACCATAGATGTTAGGCATTTGCCAATAGCCTTGTTGTTTTTTGGTAG
66 AAAAGGCTGTCTGTTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTGTTGTTTTTTGGTAG
* * *
27932980 TGTGCTCAACTCTTAGTTCTAGCGAGTAGTGACCATGGATCAAAGCTTCGGAAACCTCCAATATA
131 AGTGCTCAACTCTTAGTTCTAGAGAGTAGTGACCATGGATCAAAGCTTCAGAAACCTCCAATATA
27933045 AAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACT
196 AAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACT
* *
27933110 TATCTGCCCTTTAATTAAAAGTTGGATCTGTAACTGTCTCCTTGTTGCTAATTTCTTT-GAGCAA
261 TATCTGCCCTTTAAATAAAAGTTGGATCTGTAACTGTCTCCTTGTTGCTAAATTCTTTAG-GCAA
27933174 ATCCTATGTATATGAATCATTTAA
325 ATCCTATGTATATGAATCATTTAA
27933198 AAATGAGAAGTAGGAGAGATCCTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCAAGTGA
1 AAATGAGAAGTAGGAGAGATCCTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCAAGTGA
*
27933263 AAAAGGTTGTCTGTTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTGTTGTTTTTTGGTAG
66 AAAAGGCTGTCTGTTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTGTTGTTTTTTGGTAG
* * * *
27933328 AGTGCTGAACTCTTAGTTCTAGAGAGTGGTGACCATGGGTCAAAGCTTCAGAAACCTCTAATATA
131 AGTGCTCAACTCTTAGTTCTAGAGAGTAGTGACCATGGATCAAAGCTTCAGAAACCTCCAATATA
27933393 AAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACT
196 AAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACT
* * *
27933458 TATTTGCCCTTTAAATAAAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAAA
261 TATCTGCCCTTTAAATAAAAGTTGGATCTGTAACTGTCTCCTTGTTGCTAAATTCTTTAGGCAAA
27933523 TCCTATGTATATGAATCATTTAA
326 TCCTATGTATATGAATCATTTAA
27933546 AAATGAG
1 AAATGAG
27933553 TATTTCATCC
Statistics
Matches: 336, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
348 335 1.00
349 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (348 bp):
AAATGAGAAGTAGGAGAGATCCTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCAAGTGA
AAAAGGCTGTCTGTTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTGTTGTTTTTTGGTAG
AGTGCTCAACTCTTAGTTCTAGAGAGTAGTGACCATGGATCAAAGCTTCAGAAACCTCCAATATA
AAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACT
TATCTGCCCTTTAAATAAAAGTTGGATCTGTAACTGTCTCCTTGTTGCTAAATTCTTTAGGCAAA
TCCTATGTATATGAATCATTTAA
Found at i:27947023 original size:13 final size:13
Alignment explanation
Indices: 27947005--27947032 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27946995 ACCCCTATTT
27947005 ACCATTACCATTA
1 ACCATTACCATTA
27947018 ACCATTACCATTA
1 ACCATTACCATTA
27947031 AC
1 AC
27947033 TTTCTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (13 bp):
ACCATTACCATTA
Found at i:27948602 original size:4 final size:4
Alignment explanation
Indices: 27948593--27948633 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
27948583 ATCATTCTGT
27948593 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC C
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC C
27948634 CATTGCTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.51, G:0.00, T:0.24
Consensus pattern (4 bp):
CATC
Found at i:27955923 original size:23 final size:22
Alignment explanation
Indices: 27955897--27955943 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
27955887 CATAAAAATT
* *
27955897 AAAAAAAATAAGTTGTAAAGAAA
1 AAAAAAAAGAAGTT-AAAAGAAA
*
27955920 AAAATAAAGAAGTTAAAAGAAA
1 AAAAAAAAGAAGTTAAAAGAAA
27955942 AA
1 AA
27955944 TGTTATAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAAAAAGAAGTTAAAAGAAA
Found at i:27964323 original size:6 final size:7
Alignment explanation
Indices: 27964309--27964392 Score: 50
Period size: 7 Copynumber: 12.1 Consensus size: 7
27964299 AACACCAAAC
27964309 CCTTAAA
1 CCTTAAA
27964316 CC-TAAA
1 CCTTAAA
27964322 CCTTAAA
1 CCTTAAA
**
27964329 -CTTGTA
1 CCTTAAA
*
27964335 CCTCATAA
1 CCTTA-AA
*
27964343 CCCTAAA
1 CCTTAAA
27964350 CCCTTAAA
1 -CCTTAAA
27964358 CCTT-AA
1 CCTTAAA
*
27964364 CC-CAAA
1 CCTTAAA
27964370 CCTTAAAA
1 CCTT-AAA
* *
27964378 TCATAAA
1 CCTTAAA
27964385 CCTTAAA
1 CCTTAAA
27964392 C
1 C
27964393 TTGTACCTTG
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
6 18 0.32
7 23 0.41
8 15 0.27
ACGTcount: A:0.42, C:0.32, G:0.01, T:0.25
Consensus pattern (7 bp):
CCTTAAA
Found at i:27964329 original size:21 final size:21
Alignment explanation
Indices: 27964305--27964392 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
27964295 TCTAAACACC
27964305 AAACCCTTAAACCTAAACCTT
1 AAACCCTTAAACCTAAACCTT
** *
27964326 AAA--CTTGTACCTCATAACCCT
1 AAACCCTTAAACCT-A-AACCTT
* *
27964347 AAACCCTTAAACCTTAACC-C
1 AAACCCTTAAACCTAAACCTT
*
27964367 AAA-CCTTAAAATCATAAACCTT
1 AAACCCTT-AAA-CCTAAACCTT
27964389 AAAC
1 AAAC
27964393 TTGTACCTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
19 11 0.22
20 7 0.14
21 21 0.43
22 3 0.06
23 7 0.14
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (21 bp):
AAACCCTTAAACCTAAACCTT
Found at i:27964329 original size:42 final size:41
Alignment explanation
Indices: 27964279--27964370 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 41
27964269 CAAGCCCTTG
27964279 AACCTAAACTTCGAA-CTC-TAAACACC-AAACCCTTAAACCTA
1 AACCTAAACTT-GAACCTCAT-AAC-CCTAAACCCTTAAACCTA
* *
27964320 AACCTTAAACTTGTACCTCATAACCCTAAACCCTTAAACCTT
1 AACC-TAAACTTGAACCTCATAACCCTAAACCCTTAAACCTA
*
27964362 AACCCAAAC
1 AACCTAAAC
27964371 CTTAAAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
41 12 0.27
42 31 0.70
43 1 0.02
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.22
Consensus pattern (41 bp):
AACCTAAACTTGAACCTCATAACCCTAAACCCTTAAACCTA
Found at i:27969586 original size:12 final size:12
Alignment explanation
Indices: 27969560--27969601 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
27969550 TAAATGGGTT
27969560 TAATAATA--AA
1 TAATAATATTAA
27969570 T-ATAATATTAA
1 TAATAATATTAA
27969581 TAATAATATTAAA
1 TAATAATATT-AA
27969594 TAATAATA
1 TAATAATA
27969602 AAAAATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.21
10 1 0.04
11 3 0.11
12 8 0.29
13 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:27970685 original size:30 final size:30
Alignment explanation
Indices: 27970651--27970748 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
27970641 AAAATTACCA
27970651 TTTTACCCCCGAACTTTCCAAAATTCCATT
1 TTTTACCCCCGAACTTTCCAAAATTCCATT
*
27970681 TTTTA-CCCCG-A-TTTCACCAAAAATT--ATCA
1 TTTTACCCCCGAACTTT--CC-AAAATTCCAT-T
* *
27970710 TTTTACCCCCGAACTTCCCAGAATTCCATT
1 TTTTACCCCCGAACTTTCCAAAATTCCATT
*
27970740 TTTAACCCC
1 TTTTACCCC
27970749 GATTTCACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
27 3 0.06
28 3 0.06
29 17 0.31
30 26 0.48
31 3 0.06
32 2 0.04
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.35
Consensus pattern (30 bp):
TTTTACCCCCGAACTTTCCAAAATTCCATT
Found at i:27970910 original size:29 final size:28
Alignment explanation
Indices: 27970878--27970932 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
27970868 CGGTTTCACC
*
27970878 AAAATTACCATTTT-ACCCCCGAATTTCTT
1 AAAA-TACCATTTTCAACCCCG-ATTTCTT
*
27970907 AAAATCCCATTTTCAACCCCGATTTC
1 AAAATACCATTTTCAACCCCGATTTC
27970933 ACCAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATACCATTTTCAACCCCGATTTCTT
Found at i:27970911 original size:58 final size:59
Alignment explanation
Indices: 27970639--27970955 Score: 374
Period size: 59 Copynumber: 5.4 Consensus size: 59
27970629 CTGGATTGTT
*
27970639 CAAAAATTACCATTTTACCCCCGAACTTT-CCAAAAT-TCCATTTTTTACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAA-TTTCCCAAAATCT-CATTTTTAACCCCGATTTCAC
* * *
27970698 CAAAAATTATCATTTTACCCCCGAACTTCCCAGAAT-TCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATTTCCCAAAATCT-CATTTTTAACCCCGATTTCAC
* * * * * *
27970757 CAAAAATTATCATTTTACCCTCGAATTCCCCAAAATCTCATTTTCAACCTCGATTTCGC
1 CAAAAATTACCATTTTACCCCCGAATTTCCCAAAATCTCATTTTTAACCCCGATTTCAC
* * * * *
27970816 CAAAAAAATTACCATTTTACCCTCGAATTTCCCAAAATCTCGTTTTTGACCTCGGTTTCAC
1 C--AAAAATTACCATTTTACCCCCGAATTTCCCAAAATCTCATTTTTAACCCCGATTTCAC
** * *
27970877 C-AAAATTACCATTTTACCCCCGAATTTCTTAAAATCCCATTTTCAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATTTCCCAAAATCTCATTTTTAACCCCGATTTCAC
27970935 CAAAAATTA-CATTTTTACCCC
1 CAAAAATTACCA-TTTTACCCC
27970956 AAAAAATCAA
Statistics
Matches: 225, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
58 53 0.24
59 119 0.53
60 1 0.00
61 52 0.23
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAATTTCCCAAAATCTCATTTTTAACCCCGATTTCAC
Found at i:27970954 original size:29 final size:28
Alignment explanation
Indices: 27970639--27970955 Score: 138
Period size: 29 Copynumber: 10.8 Consensus size: 28
27970629 CTGGATTGTT
27970639 CAAAAATTACCA-TTTTACCCCCGAACTTT-C
1 CAAAAATTA-CATTTTTA-CCCCG-A-TTTCC
*
27970669 C-AAAATTCCATTTTTTACCCCGATTTCAC
1 CAAAAATTACA-TTTTTACCCCGATTTC-C
*
27970698 CAAAAATTATCA-TTTTACCCCCGAACTTCC
1 CAAAAATTA-CATTTTTA-CCCCG-ATTTCC
* *
27970728 C-AGAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACATTTTT-ACCCCGATTTC-C
*
27970757 CAAAAATTATCA-TTTTACCCTCGAATTCC
1 CAAAAATTA-CATTTTTACCC-CGATTTCC
* * *
27970786 CCAAAATCT-CATTTTCAACCTCGATTTCGC
1 CAAAAAT-TACATTTT-TACCCCGATTTC-C
27970816 CAAAAAAATTACCA-TTTTACCCTCGAATTTCC
1 C--AAAAATTA-CATTTTTACCC-CG-ATTTCC
* * *
27970848 C-AAAATCT-CGTTTTTGACCTCGGTTTCAC
1 CAAAAAT-TACATTTTT-ACCCCGATTTC-C
27970877 C-AAAATTACCA-TTTTACCCCCGAATTT-C
1 CAAAAATTA-CATTTTTA-CCCCG-ATTTCC
** ** *
27970905 TTAAAATCCCATTTTCAACCCCGATTTCAC
1 CAAAAATTACATTTT-TACCCCGATTTC-C
27970935 CAAAAATTACATTTTTACCCC
1 CAAAAATTACATTTTTACCCC
27970956 AAAAAATCAA
Statistics
Matches: 219, Mismatches: 31, Indels: 75
0.67 0.10 0.23
Matches are distributed among these distances:
27 3 0.01
28 25 0.11
29 98 0.45
30 62 0.28
31 12 0.05
32 12 0.05
33 7 0.03
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCGATTTCC
Found at i:27973853 original size:45 final size:44
Alignment explanation
Indices: 27973780--27973880 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 44
27973770 GTCTAAACTA
* * * *
27973780 AAAAAAATCAATCTTCTTTTGTTTAAAATAAAAATAAAATAATT
1 AAAAAAATCAATCTTATTTTCTTCAAAATAAAAATAAAAAAATT
*
27973824 AAAAAAATGTAATCTTATTTTCTTCAAAATAAAAATAAAAAAATT
1 AAAAAAAT-CAATCTTATTTTCTTCAAAATAAAAATAAAAAAATT
* *
27973869 AAATATATCAAT
1 AAAAAAATCAAT
27973881 TAAATTATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 11 0.23
45 37 0.77
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (44 bp):
AAAAAAATCAATCTTATTTTCTTCAAAATAAAAATAAAAAAATT
Found at i:27975542 original size:25 final size:25
Alignment explanation
Indices: 27975514--27975562 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
27975504 TAAATAAACT
27975514 ATTTTCTTTCAT-AAGATAGTGGATA
1 ATTTT-TTTCATAAAGATAGTGGATA
*
27975539 ATTTTTTTTATAAAGATAGTGGAT
1 ATTTTTTTCATAAAGATAGTGGAT
27975563 GATGTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTTTTTTCATAAAGATAGTGGATA
Found at i:27977015 original size:6 final size:6
Alignment explanation
Indices: 27977004--27977045 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
27976994 CAGAATACAT
27977004 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
27977046 TTAAAAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:27978744 original size:28 final size:31
Alignment explanation
Indices: 27978713--27978778 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 31
27978703 AGATTTCAAA
27978713 AATATTATTT-TA-ATTATTT-TAATTTTT-T
1 AATATT-TTTATATATTATTTATAATTTTTAT
* *
27978741 AATATTTTTATATATTCTTTATATTTTTTAT
1 AATATTTTTATATATTATTTATAATTTTTAT
27978772 AATATTT
1 AATATTT
27978779 ATGGTTAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 3 0.09
28 8 0.25
29 6 0.19
30 7 0.22
31 8 0.25
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (31 bp):
AATATTTTTATATATTATTTATAATTTTTAT
Found at i:27978749 original size:17 final size:17
Alignment explanation
Indices: 27978714--27978772 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
27978704 GATTTCAAAA
27978714 ATATTATTTTAATTATTTT
1 ATATT-TTTTAATT-TTTT
27978733 A-ATTTTTTAATATTTTT
1 ATATTTTTTAAT-TTTTT
27978750 ATATATTCTTTATATTTTTT
1 ATAT-TT-TTTA-ATTTTTT
27978770 ATA
1 ATA
27978773 ATATTTATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 12 0.34
18 6 0.17
19 3 0.09
20 12 0.34
21 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
ATATTTTTTAATTTTTT
Found at i:27978770 original size:9 final size:9
Alignment explanation
Indices: 27978714--27978772 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
27978704 GATTTCAAAA
27978714 ATATTATTTT
1 ATATT-TTTT
27978724 A-ATTATTTT
1 ATATT-TTTT
27978733 A-ATTTTTT
1 ATATTTTTT
27978741 AATATTTTTAT
1 -ATATTTTT-T
*
27978752 ATATTCTTT
1 ATATTTTTT
27978761 ATATTTTTT
1 ATATTTTTT
27978770 ATA
1 ATA
27978773 ATATTTATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 4 0.09
9 25 0.57
10 14 0.32
11 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTTT
Found at i:27978779 original size:18 final size:19
Alignment explanation
Indices: 27978742--27978780 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
27978732 TAATTTTTTA
* *
27978742 ATATTTTTATATATTCTTT
1 ATATTTTTATATAATATTT
27978761 ATATTTTT-TATAATATTT
1 ATATTTTTATATAATATTT
27978779 AT
1 AT
27978781 GGTTAGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTTTATATAATATTT
Found at i:27984159 original size:15 final size:15
Alignment explanation
Indices: 27984117--27984165 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
27984107 ACATTAAATT
27984117 AAAATTAAA-ATTAA
1 AAAATTAAATATTAA
27984131 AAAATTATAATATTAA
1 AAAATTA-AATATTAA
* *
27984147 ATATTTAAATATTGAA
1 AAAATTAAATATT-AA
27984163 AAA
1 AAA
27984166 CACTTTTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.24
15 8 0.28
16 14 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATTAAATATTAA
Found at i:27984911 original size:37 final size:37
Alignment explanation
Indices: 27984841--27984924 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 37
27984831 ACTAAAAATG
* * * *
27984841 AAGATGAACAGTAATGATTCTCTATAAAGAAAAGACA
1 AAGATGAATAGTAAAGATTCTATACAAAGAAAAGACA
* * *
27984878 AAGATGAATAGTAAAGATTCTATGCAAATAAAAGACG
1 AAGATGAATAGTAAAGATTCTATACAAAGAAAAGACA
*
27984915 GAGATGAATA
1 AAGATGAATA
27984925 ATAACGATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.21
Consensus pattern (37 bp):
AAGATGAATAGTAAAGATTCTATACAAAGAAAAGACA
Found at i:27985518 original size:35 final size:30
Alignment explanation
Indices: 27985432--27985503 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
27985422 GGGATAGCGG
*
27985432 ACAAAACAGTCACTCAACTTTCGAAAAATA
1 ACAAAACAGTCACTCAATTTTCGAAAAATA
27985462 ACAAAACAGTCACTCAATTTTCGAAAAATA
1 ACAAAACAGTCACTCAATTTTCGAAAAATA
27985492 ACAAAACAGTCA
1 ACAAAACAGTCA
27985504 TCACTAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.19
Consensus pattern (30 bp):
ACAAAACAGTCACTCAATTTTCGAAAAATA
Found at i:27985700 original size:39 final size:40
Alignment explanation
Indices: 27985647--27985726 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
27985637 AAGAGGTATG
* * *
27985647 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGCGACTCTTCAAAAAGTGTCCA
*
27985687 TCCAATTTG-AAAGGATTGCGACTCTTCAAAAAGTGTCCA
1 TCCAATATGAAAAGGATTGCGACTCTTCAAAAAGTGTCCA
27985726 T
1 T
27985727 TGAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGCGACTCTTCAAAAAGTGTCCA
Found at i:28016094 original size:15 final size:13
Alignment explanation
Indices: 28016060--28016089 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28016050 CTAACACATT
28016060 AAAAA-TATATTA
1 AAAAATTATATTA
28016072 AAAAATTATATTA
1 AAAAATTATATTA
28016085 AAAAA
1 AAAAA
28016090 CATTACCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATTATATTA
Found at i:28016240 original size:17 final size:17
Alignment explanation
Indices: 28016218--28016251 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28016208 TTGAGCTAGT
28016218 GATTTAATATAAATATG
1 GATTTAATATAAATATG
28016235 GATTTAATATAAATATG
1 GATTTAATATAAATATG
28016252 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
GATTTAATATAAATATG
Found at i:28018574 original size:4 final size:4
Alignment explanation
Indices: 28018565--28018608 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
28018555 CATTTTACAA
28018565 AGAC AGAC AGAC AGAC AGAC A-AC AGAC AG-C A-AC AGAC AAGAC AG
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC -AGAC AG
28018609 TCCACCAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 7 0.19
4 25 0.69
5 4 0.11
ACGTcount: A:0.52, C:0.25, G:0.23, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:28018591 original size:15 final size:15
Alignment explanation
Indices: 28018565--28018608 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
28018555 CATTTTACAA
28018565 AGACAGACAGACAGAC
1 AGACAGACAGACAG-C
28018581 AGACA-ACAGACAGC
1 AGACAGACAGACAGC
28018595 A-ACAGACAAGACAG
1 AGACAGAC-AGACAG
28018609 TCCACCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.12
14 4 0.15
15 14 0.54
16 5 0.19
ACGTcount: A:0.52, C:0.25, G:0.23, T:0.00
Consensus pattern (15 bp):
AGACAGACAGACAGC
Found at i:28026024 original size:87 final size:84
Alignment explanation
Indices: 28025875--28026035 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 84
28025865 TACATGCATA
* *
28025875 AGGTTGAGTTATTACTCTTAATGAGTTCATATCCCAAGTTGGGTGGTCCTATTGAGACGGACTTA
1 AGGTTGAGTTATTACTCTTAATGAATTCATATCCAAAGTTGGGTGGTCCTATTGAGACGGACTTA
28025940 AAGAATTCACTTATATGAG
66 AAGAATTCACTTATATGAG
* * *
28025959 AGGTTGAGTTTATTACTTTTAATGAATTCATATCCTAAAATTTGGGTGGTCCTATTGCGACGGAC
1 AGGTTGAG-TTATTACTCTTAATGAATTCATATCC--AAAGTTGGGTGGTCCTATTGAGACGGAC
* *
28026024 TTGATGAATTCA
63 TTAAAGAATTCA
28026036 TCGAACTTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 8 0.12
85 24 0.36
87 35 0.52
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (84 bp):
AGGTTGAGTTATTACTCTTAATGAATTCATATCCAAAGTTGGGTGGTCCTATTGAGACGGACTTA
AAGAATTCACTTATATGAG
Found at i:28030567 original size:1 final size:1
Alignment explanation
Indices: 28030563--28030592 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28030553 AAAAAAGGGC
28030563 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
28030593 AAGGTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:28031450 original size:15 final size:15
Alignment explanation
Indices: 28031430--28031481 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28031420 ACTACAAAAC
28031430 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28031445 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
28031464 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
28031479 ATT
1 ATT
28031482 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28031545 original size:16 final size:16
Alignment explanation
Indices: 28031514--28031550 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28031504 ATATGAAGAA
28031514 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
28031530 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
28031546 TATTA
1 TATTA
28031551 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:28031609 original size:16 final size:16
Alignment explanation
Indices: 28031564--28031612 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28031554 TAAAATTAAA
28031564 ATATTGAATAATTT-TT
1 ATATT-AATAATTTATT
*
28031580 AT-TT-AT-ATTAATT
1 ATATTAATAATTTATT
28031593 ATATTAATAATTTATT
1 ATATTAATAATTTATT
28031609 ATAT
1 ATAT
28031613 GATTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.11
13 6 0.22
14 2 0.07
15 4 0.15
16 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:28031622 original size:26 final size:25
Alignment explanation
Indices: 28031562--28031630 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 25
28031552 AATAAAATTA
28031562 AAATATTGAATAATTTTTATTTATATT
1 AAATATT-AATAATTTTTA-TTATATT
28031589 AATTATATTAATAATTTATTA-TATGATT
1 AA--ATATTAATAATTT-TTATTAT-ATT
*
28031617 AAATATAAATAATT
1 AAATATTAATAATT
28031631 AAATATGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 11 0.30
27 5 0.14
28 13 0.35
29 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
AAATATTAATAATTTTTATTATATT
Found at i:28036769 original size:30 final size:27
Alignment explanation
Indices: 28036735--28036798 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 27
28036725 TAGTAAAGGT
28036735 AAAATTGCACTTTTACTCC-TAAAAATGATA
1 AAAATTG-A-TTTTA-TCCTTAAAAAT-ATA
28036765 AAAATTTGATTTTATCCTTTAAAAATATA
1 AAAA-TTGATTTTATCC-TTAAAAATATA
28036794 AAAAT
1 AAAAT
28036799 ATAGGCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 12 0.39
31 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (27 bp):
AAAATTGATTTTATCCTTAAAAATATA
Found at i:28040958 original size:14 final size:14
Alignment explanation
Indices: 28040939--28040968 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28040929 ATATCCAAAC
28040939 AATAGTAATAAAAT
1 AATAGTAATAAAAT
*
28040953 AATAGTAATATAAT
1 AATAGTAATAAAAT
28040967 AA
1 AA
28040969 CGAAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAAAAT
Found at i:28040995 original size:22 final size:21
Alignment explanation
Indices: 28040970--28041032 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
28040960 ATATAATAAC
* *
28040970 GAAATGATAGCAAAACAATAGT
1 GAAAT-ATAGCAAAACAACAAT
* * *
28040992 GAAACAACAACAAAACAACAAT
1 GAAA-TATAGCAAAACAACAAT
28041014 GAAATAGTAGCAAAACAAC
1 GAAATA-TAGCAAAACAAC
28041033 CGATTCGGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (21 bp):
GAAATATAGCAAAACAACAAT
Found at i:28047047 original size:15 final size:16
Alignment explanation
Indices: 28047029--28047061 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28047019 AATACAAATT
*
28047029 TAAAGATTAAA-AAAA
1 TAAAAATTAAATAAAA
28047044 TAAAAATTAAATAAAA
1 TAAAAATTAAATAAAA
28047060 TA
1 TA
28047062 CTAAAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAATTAAATAAAA
Found at i:28047423 original size:26 final size:25
Alignment explanation
Indices: 28047393--28047458 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
28047383 AAATGTATTG
*
28047393 AAAATTTATAAAAATT-AAGAAATAT
1 AAAATTTATAAAAATTCAA-AAAAAT
28047418 ATAAATTT-TAGAAAATTCCAAAAAAAT
1 A-AAATTTATA-AAAATT-CAAAAAAAT
28047445 AAAATTTA-AAAAAT
1 AAAATTTATAAAAAT
28047459 ATATCGTGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
25 8 0.23
26 19 0.54
27 6 0.17
28 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAATTTATAAAAATTCAAAAAAAT
Found at i:28055580 original size:16 final size:19
Alignment explanation
Indices: 28055541--28055595 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 19
28055531 AAACTTTCTA
* *
28055541 TAAAAATACACTAA-AATAT
1 TAAAAATATAC-AATAATTT
28055560 TAAAAA-ATA-AAT-ATTT
1 TAAAAATATACAATAATTT
28055576 TAAAAATATACAATAATTT
1 TAAAAATATACAATAATTT
28055595 T
1 T
28055596 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 5 0.17
19 11 0.37
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATACAATAATTT
Found at i:28061183 original size:18 final size:18
Alignment explanation
Indices: 28061160--28061202 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28061150 GTTCAAGCTG
28061160 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
28061178 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
28061196 TAATTAA
1 TAATTAA
28061203 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:28064937 original size:22 final size:25
Alignment explanation
Indices: 28064912--28064965 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
28064902 GTTTTCTTCA
*
28064912 AATGATTTTAA-T-AATAA-AAAAT
1 AATGATTTCAATTAAATAATAAAAT
28064934 AATGTTATTTCAATTAAATAATAAAAT
1 AATG--ATTTCAATTAAATAATAAAAT
28064961 AATGA
1 AATGA
28064966 AAAATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
24 6 0.23
25 2 0.08
26 5 0.19
27 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AATGATTTCAATTAAATAATAAAAT
Found at i:28065122 original size:16 final size:17
Alignment explanation
Indices: 28065097--28065153 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
28065087 TTTAAGCAAA
* *
28065097 TTTTAATTTTAAT-TTT
1 TTTTATTTTTAATCATT
*
28065113 TTTTATTTTTTATCATT
1 TTTTATTTTTAATCATT
* **
28065130 TGTTATTTTTAAAGATT
1 TTTTATTTTTAATCATT
28065147 TTTTATT
1 TTTTATT
28065154 ATTTTTTGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTTATTTTTAATCATT
Found at i:28079410 original size:13 final size:13
Alignment explanation
Indices: 28079392--28079416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28079382 AATCGAAAGC
28079392 AAAAATAAGAAAT
1 AAAAATAAGAAAT
28079405 AAAAATAAGAAA
1 AAAAATAAGAAA
28079417 GGAAAAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAATAAGAAAT
Found at i:28096282 original size:33 final size:33
Alignment explanation
Indices: 28096156--28096288 Score: 115
Period size: 33 Copynumber: 4.0 Consensus size: 33
28096146 GACTAGTAGC
* * * **
28096156 AGCAGGGATGATGCCCCTATATGCAGCCTAAGT
1 AGCAGCGATGATGCCCCAATAAGCAGGTTAAGT
* ** * **
28096189 AGTAG-GAATGATGTTCAAATAAGCAGGCCAAGT
1 AGCAGCG-ATGATGCCCCAATAAGCAGGTTAAGT
* * *
28096222 AGCAGTGATGGTGCCCCTATAAGCAGGTTAAGT
1 AGCAGCGATGATGCCCCAATAAGCAGGTTAAGT
*
28096255 AGCAGCGATGATGCCCCAATAATCAGGTTAAGT
1 AGCAGCGATGATGCCCCAATAAGCAGGTTAAGT
28096288 A
1 A
28096289 TTGGGGGAAA
Statistics
Matches: 78, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
32 1 0.01
33 76 0.97
34 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (33 bp):
AGCAGCGATGATGCCCCAATAAGCAGGTTAAGT
Found at i:28096288 original size:66 final size:66
Alignment explanation
Indices: 28096156--28096281 Score: 146
Period size: 66 Copynumber: 1.9 Consensus size: 66
28096146 GACTAGTAGC
* * **
28096156 AGCAGGGATGATGCCCCTATATGCAGCCTAAGTAGTAGGAATGATGTTCAAATAAGCAGGCCAAG
1 AGCAGGGATGATGCCCCTATAAGCAGCCTAAGTAGCAGGAATGATGCCCAAATAAGCAGGCCAAG
28096221 T
66 T
* * ** * *
28096222 AGCAGTGATGGTGCCCCTATAAGCAGGTTAAGTAGCAGCG-ATGATGCCCCAATAATCAGG
1 AGCAGGGATGATGCCCCTATAAGCAGCCTAAGTAGCAG-GAATGATGCCCAAATAAGCAGG
28096282 TTAAGTATTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
66 48 0.98
67 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (66 bp):
AGCAGGGATGATGCCCCTATAAGCAGCCTAAGTAGCAGGAATGATGCCCAAATAAGCAGGCCAAG
T
Found at i:28102122 original size:29 final size:29
Alignment explanation
Indices: 28102099--28102163 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
28102089 CAAAAACGGG
*
28102099 ATTTTGGAAAGTTCGAGGGTAAAATAGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATAGGA
*
28102128 ATTTTGGAAAGTTCGGGGGTAAAAT-GGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATAGG-A
28102157 ATTTTGG
1 ATTTTGG
28102164 TGAAATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGAGGGTAAAATAGGA
Found at i:28102233 original size:86 final size:88
Alignment explanation
Indices: 28102060--28102239 Score: 203
Period size: 86 Copynumber: 2.1 Consensus size: 88
28102050 TACCCGAGGG
* * *
28102060 CAAAATGGTAATTTTGGTTGAAATTGGGTCAAAAACGGGATTTTGGAAAGTTCGAGGGTAAAATA
1 CAAAATGGTAATTTTGGTTGAAATTGGGTCAAAAACGGAATTTTGAAAACTTCGAGGGTAAAATA
*
28102125 GTAATTTTGGAAAGTTCGGGGGT
66 GTAATTTTAGAAAGTTCGGGGGT
*
28102148 -AAAATGGTAATTTTGG-TGAAATTATGGG-C-AAAATGGAATTTTGAAAAACTT-G-GGGTAAA
1 CAAAATGGTAATTTTGGTTGAAA-T-TGGGTCAAAAACGGAATTTTG-AAAACTTCGAGGGTAAA
**
28102207 A-ATGTAATTTTTAGAAAGTTTTGGGGT
63 ATA-GTAA-TTTTAGAAAGTTCGGGGGT
28102234 CAAAAT
1 CAAAAT
28102240 ACCATTTTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
84 1 0.01
85 12 0.15
86 34 0.43
87 28 0.35
88 4 0.05
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (88 bp):
CAAAATGGTAATTTTGGTTGAAATTGGGTCAAAAACGGAATTTTGAAAACTTCGAGGGTAAAATA
GTAATTTTAGAAAGTTCGGGGGT
Found at i:28103296 original size:22 final size:25
Alignment explanation
Indices: 28103268--28103329 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
28103258 TGTTTTTTAT
*
28103268 TATTAATGTTATTA-TTAATA-AA-
1 TATTAATATTATTATTTAATACAAC
28103290 TATTAATTATTATTATTTAATACAAC
1 TATTAA-TATTATTATTTAATACAAC
*
28103316 TGTTAATATTATTA
1 TATTAATATTATTA
28103330 ATATTAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 6 0.18
23 7 0.21
24 6 0.18
25 10 0.29
26 5 0.15
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
TATTAATATTATTATTTAATACAAC
Found at i:28103344 original size:10 final size:10
Alignment explanation
Indices: 28103280--28103347 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
28103270 TTAATGTTAT
*
28103280 TATTAATAAA
1 TATTAATTAA
*
28103290 TATTAATTAT
1 TATTAATTAA
*
28103300 TATTATTTAA
1 TATTAATTAA
*
28103310 TA-CAACTGTTAA
1 TATTAA---TTAA
28103322 TATT-ATTAA
1 TATTAATTAA
*
28103331 TATTAATTAC
1 TATTAATTAA
28103341 TATTAAT
1 TATTAAT
28103348 GCCGTTACTA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 9 0.20
10 29 0.64
12 7 0.16
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (10 bp):
TATTAATTAA
Found at i:28104125 original size:18 final size:20
Alignment explanation
Indices: 28104088--28104131 Score: 74
Period size: 18 Copynumber: 2.3 Consensus size: 20
28104078 CTAAATTTGA
28104088 TTAAATTTAAAAAGATAAAT
1 TTAAATTTAAAAAGATAAAT
28104108 TTAAATTT-AAAA-ATAAAT
1 TTAAATTTAAAAAGATAAAT
28104126 TTAAAT
1 TTAAAT
28104132 CAATTTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAATTTAAAAAGATAAAT
Found at i:28104150 original size:22 final size:23
Alignment explanation
Indices: 28104111--28104157 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
28104101 GATAAATTTA
28104111 AATTTAAAAATAAATTT-AAATC
1 AATTTAAAAATAAATTTAAAATC
** *
28104133 AATTTAAACCTAATTTTAAAATC
1 AATTTAAAAATAAATTTAAAATC
28104156 AA
1 AA
28104158 AGCTTAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
AATTTAAAAATAAATTTAAAATC
Found at i:28115500 original size:208 final size:209
Alignment explanation
Indices: 28115247--28115659 Score: 604
Period size: 208 Copynumber: 2.0 Consensus size: 209
28115237 GTTAAATAAT
* *
28115247 ATATTTTTTATTTAAACTATCGAATATAATTTAAATATATTAATTT-GCTAATTTAAATATTATA
1 ATATTTTTTATTTAAACTATCGAACATAATTTAAATATATTAATTTATC-AATTTAAATATTATA
* * * * *
28115311 ACAGAAAATTTTTAAATCATAATTAAAATATTTTTAATATTTTCAACATACAATATAA-TTTTAC
65 ACAGAAAATTTATAAATCATAA-TAAAAAAATTTTAACATATTCAACATACAATATAATTTTTAC
* *
28115375 TTTATTTAATTAATG-ACAAGTAACAATATTCAAAATAATAATTGATTAATATAATT-ACTTTAA
129 TTTATTTAATTAATGTA-AA-AAACAATATTCAAAAAAATAATTGATTAATATAATTAACTTTAA
28115438 TATATTAATTAAGTGATA
192 TATATTAATTAAGTGATA
* *
28115456 ATATTTATTT-TTTGAATTATCGAACATAA-TTAAATATATTAATTTATCAATTTAAATATTATA
1 ATATTT-TTTATTTAAACTATCGAACATAATTTAAATATATTAATTTATCAATTTAAATATTATA
* *
28115519 ACAGAAAATTTATAAATCATAATAAAAAAATTTTAACATATTCAACATATAATATAATTTTTATT
65 ACAGAAAATTTATAAATCATAATAAAAAAATTTTAACATATTCAACATACAATATAATTTTTACT
* *
28115584 TTATTTAATTAATGTAAAAAATATTATTCAAAAAAATAATTGATTAATATAATTAACTTTAATAT
130 TTATTTAATTAATGTAAAAAACAATATTCAAAAAAATAATTGATTAATATAATTAACTTTAATAT
28115649 ATTAATTAAGT
195 ATTAATTAAGT
28115660 TGTAATTAAA
Statistics
Matches: 184, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
207 62 0.34
208 95 0.52
209 24 0.13
210 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (209 bp):
ATATTTTTTATTTAAACTATCGAACATAATTTAAATATATTAATTTATCAATTTAAATATTATAA
CAGAAAATTTATAAATCATAATAAAAAAATTTTAACATATTCAACATACAATATAATTTTTACTT
TATTTAATTAATGTAAAAAACAATATTCAAAAAAATAATTGATTAATATAATTAACTTTAATATA
TTAATTAAGTGATA
Found at i:28115874 original size:18 final size:18
Alignment explanation
Indices: 28115839--28115875 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28115829 CTGGTTTTTC
* *
28115839 TTTGGGCCTGCTTTTGTT
1 TTTGGGCCTGATTCTGTT
28115857 TTTGGGCCTGATTCTGTT
1 TTTGGGCCTGATTCTGTT
28115875 T
1 T
28115876 GGGTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.27, T:0.54
Consensus pattern (18 bp):
TTTGGGCCTGATTCTGTT
Found at i:28116327 original size:24 final size:24
Alignment explanation
Indices: 28116300--28116370 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
28116290 TATAGTTTAA
* *
28116300 TTAATTTTTTAAATTAATATGTTT
1 TTAATTTTATAAATTAATATATTT
* * *
28116324 TTAATTGTGTAAAGTAATATATTT
1 TTAATTTTATAAATTAATATATTT
28116348 TTATATTTTCATATAATTAATAT
1 TTA-ATTTT-ATA-AATTAATAT
28116371 TTTATTCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 23 0.62
25 4 0.11
26 2 0.05
27 8 0.22
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (24 bp):
TTAATTTTATAAATTAATATATTT
Found at i:28116925 original size:24 final size:25
Alignment explanation
Indices: 28116898--28116953 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
28116888 TTTTCAAACT
28116898 AATAATTTTAAAT-TAAATATT-ATA
1 AATAATTTTAAATATAAAT-TTAATA
*
28116922 AATATTTTTAAATATAAATTTAATA
1 AATAATTTTAAATATAAATTTAATA
28116947 ATATAAT
1 A-ATAAT
28116954 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 14 0.52
25 9 0.33
26 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAATTTTAAATATAAATTTAATA
Found at i:28121022 original size:5 final size:5
Alignment explanation
Indices: 28121012--28121063 Score: 95
Period size: 5 Copynumber: 10.4 Consensus size: 5
28121002 TAATTCACAT
*
28121012 TACTA TACTA TCCTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA
1 TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA
28121062 TA
1 TA
28121064 TAAACATTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (5 bp):
TACTA
Found at i:28126501 original size:34 final size:35
Alignment explanation
Indices: 28126435--28126511 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 35
28126425 AAATATATAC
* * *
28126435 ATTTTAAATATTATAAATTTAATGATACATAAAAT
1 ATTTTAAATATTATAAATATAATAATAAATAAAAT
28126470 ATTTTAGAAT-TT-TAAATATAATAATAAATAAAAT
1 ATTTTA-AATATTATAAATATAATAATAAATAAAAT
*
28126504 -TTTAAAAT
1 ATTTTAAAT
28126512 GTAATGATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.08
33 4 0.11
34 19 0.51
35 8 0.22
36 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (35 bp):
ATTTTAAATATTATAAATATAATAATAAATAAAAT
Found at i:28126511 original size:25 final size:26
Alignment explanation
Indices: 28126477--28126538 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
28126467 AATATTTTAG
28126477 AATTTT-AAATATAATAATAAAT-AA
1 AATTTTAAAATATAATAATAAATGAA
* * *
28126501 AATTTTAAAATGTAATGATACATGAA
1 AATTTTAAAATATAATAATAAATGAA
28126527 ATATTTTAAAAT
1 A-ATTTTAAAAT
28126539 TTTAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 13 0.41
26 3 0.09
27 10 0.31
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (26 bp):
AATTTTAAAATATAATAATAAATGAA
Found at i:28126565 original size:59 final size:60
Alignment explanation
Indices: 28126440--28126585 Score: 186
Period size: 59 Copynumber: 2.5 Consensus size: 60
28126430 TATACATTTT
* * * * *
28126440 AAATATTATAAATTTAATGATACATAAAATATTTTAGAATTTTAAATATAATAATAAATA
1 AAATTTTAGAAATTTAATGATACATGAAATATTTTAAAATTTTAAATATAATAACAAATA
* * *
28126500 AAATTTTA-AAATGTAATGATACATGAAATATTTTAAAATTTTAAATATAATTACAAATG
1 AAATTTTAGAAATTTAATGATACATGAAATATTTTAAAATTTTAAATATAATAACAAATA
* **
28126559 ATATTTTAGAGTTTTAATGATACATGA
1 AAATTTTAGAAATTTAATGATACATGA
28126586 TGTCGACAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 52 0.70
60 22 0.30
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (60 bp):
AAATTTTAGAAATTTAATGATACATGAAATATTTTAAAATTTTAAATATAATAACAAATA
Found at i:28127445 original size:38 final size:38
Alignment explanation
Indices: 28127394--28127472 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
28127384 CTTAGCCTTC
28127394 CCATTTCCCAATTCCCAATTCCTAAATCAATTTCAAAA
1 CCATTTCCCAATTCCCAATTCCTAAATCAATTTCAAAA
28127432 CCATTTCCCAATTCCCAATTCCTAAATCAATTTCAAAA
1 CCATTTCCCAATTCCCAATTCCTAAATCAATTTCAAAA
28127470 CCA
1 CCA
28127473 AAAAAAACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (38 bp):
CCATTTCCCAATTCCCAATTCCTAAATCAATTTCAAAA
Found at i:28128475 original size:6 final size:6
Alignment explanation
Indices: 28128431--28128474 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
28128421 GTTTAATACT
* *
28128431 TCTTTC TCTTTC TCTTTC TCTTTC TCCTTC TCTTTC TCATTC TC
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TC
28128475 AGGTTTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.61
Consensus pattern (6 bp):
TCTTTC
Found at i:28132972 original size:5 final size:5
Alignment explanation
Indices: 28132962--28132988 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28132952 TGGTAACTCA
28132962 TCTCC TCTCC TCTCC TCTCC TCTCC TC
1 TCTCC TCTCC TCTCC TCTCC TCTCC TC
28132989 AAATCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TCTCC
Found at i:28135633 original size:2 final size:2
Alignment explanation
Indices: 28135580--28135625 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
28135570 ACACACACAC
*
28135580 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28135622 AT AT
1 AT AT
28135626 TGATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28144308 original size:74 final size:74
Alignment explanation
Indices: 28144227--28144389 Score: 290
Period size: 74 Copynumber: 2.2 Consensus size: 74
28144217 CTTTTAACTT
*
28144227 CAAATATATATATATTAGATTAAAAAGCATGAGTCGAAGAACAAATACTAGTAAATTAATATGAG
1 CAAATATATATATATTAGATTAAAAAGCATGAGTCGAAGAACAAATACTAGTAAATTAATATGAA
28144292 AAAAACAAG
66 AAAAACAAG
* *
28144301 CAAATATATATATACTAGATTAAAAAGCATGAGTTGAAGAACAAATACTAGTAAATTAATATGAA
1 CAAATATATATATATTAGATTAAAAAGCATGAGTCGAAGAACAAATACTAGTAAATTAATATGAA
28144366 AAAAACAAG
66 AAAAACAAG
*
28144375 CAAAGATATATATAT
1 CAAATATATATATAT
28144390 ATATATGCTG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 84 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (74 bp):
CAAATATATATATATTAGATTAAAAAGCATGAGTCGAAGAACAAATACTAGTAAATTAATATGAA
AAAAACAAG
Found at i:28144567 original size:30 final size:31
Alignment explanation
Indices: 28144531--28144599 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
28144521 TAAATTAGTT
*
28144531 ATGATAAAATTGTAT-TTTAACTCTTCAAAA
1 ATGATAAAATTGTATATTTAACCCTTCAAAA
* * *
28144561 ATGAT-AAATTTTTTATTTAACCCTTTAAAA
1 ATGATAAAATTGTATATTTAACCCTTCAAAA
*
28144591 ATTATAAAA
1 ATGATAAAA
28144600 GTATGCATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.22
30 22 0.69
31 3 0.09
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (31 bp):
ATGATAAAATTGTATATTTAACCCTTCAAAA
Found at i:28145035 original size:29 final size:28
Alignment explanation
Indices: 28144994--28145056 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
28144984 CACTTGTAAC
**
28144994 AAAAAAAAATTT-AGTATCAATTTGAAA
1 AAAAAAAAATTTAAGTATCAAGATGAAA
*
28145021 AAAAAAAGTAATTTAAGTATCGAGATGAAA
1 AAAAAAA--AATTTAAGTATCAAGATGAAA
28145051 AAAAAA
1 AAAAAA
28145057 TAGGTCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
29 5 0.17
30 18 0.60
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAAAAAAATTTAAGTATCAAGATGAAA
Found at i:28147911 original size:18 final size:18
Alignment explanation
Indices: 28147888--28147926 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28147878 AAACGTAGAC
28147888 AAATAAAAACTAAAA-AAA
1 AAATAAAAA-TAAAAGAAA
*
28147906 AAATAAATATAAAAGAAA
1 AAATAAAAATAAAAGAAA
28147924 AAA
1 AAA
28147927 AACTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (18 bp):
AAATAAAAATAAAAGAAA
Found at i:28147926 original size:21 final size:20
Alignment explanation
Indices: 28147899--28147944 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
28147889 AATAAAAACT
28147899 AAAAAAAAAATAAATATAAA
1 AAAAAAAAAATAAATATAAA
*
28147919 AGAAAAAAAACTAAATATAAA
1 A-AAAAAAAAATAAATATAAA
28147940 AAAAA
1 AAAAA
28147945 GGGACAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAAAAAAATAAATATAAA
Found at i:28149504 original size:22 final size:23
Alignment explanation
Indices: 28149478--28149521 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
28149468 TCAATATTCA
*
28149478 CATTTCTATTC-AATCAAATCCG
1 CATTTCAATTCGAATCAAATCCG
28149500 CATTTCAATTCTGAATCAAATC
1 CATTTCAATTC-GAATCAAATC
28149522 AATTCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (23 bp):
CATTTCAATTCGAATCAAATCCG
Found at i:28153428 original size:25 final size:25
Alignment explanation
Indices: 28153370--28153432 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
28153360 TTAGTGTCTT
* *
28153370 TTATTATTATTTGATAAGTCTTTTA
1 TTATTATTATTTTATAAGTCTTCTA
* *
28153395 ATATTATTATTTTATAA-TGTTCTA
1 TTATTATTATTTTATAAGTCTTCTA
28153419 TTATTCATTATTTT
1 TTATT-ATTATTTT
28153433 CATATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (25 bp):
TTATTATTATTTTATAAGTCTTCTA
Found at i:28153851 original size:6 final size:6
Alignment explanation
Indices: 28153842--28153925 Score: 77
Period size: 6 Copynumber: 14.5 Consensus size: 6
28153832 ATTTAGATTT
* *
28153842 ATTTAA ATTTAA ATTTAA A-TTAA ACTTTAA ATTTGA ATTT-A ATTTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA
* * * *
28153889 GTCTAA ATTT-A TTTTAA ATTTAA AATT-A ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
28153926 AAAGTCCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
5 18 0.29
6 40 0.63
7 5 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:28153859 original size:12 final size:12
Alignment explanation
Indices: 28153842--28153925 Score: 77
Period size: 11 Copynumber: 7.2 Consensus size: 12
28153832 ATTTAGATTT
28153842 ATTTAAATTTAA
1 ATTTAAATTTAA
28153854 ATTTAAA-TTAA
1 ATTTAAATTTAA
*
28153865 ACTTTAAATTTGA
1 A-TTTAAATTTAA
*
28153878 ATTT-AATTTTA
1 ATTTAAATTTAA
* *
28153889 GTCTAAATTT-A
1 ATTTAAATTTAA
*
28153900 TTTTAAATTTAA
1 ATTTAAATTTAA
*
28153912 AATT-AATTTAA
1 ATTTAAATTTAA
28153923 ATT
1 ATT
28153926 AAAGTCCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
11 31 0.53
12 24 0.41
13 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:28153872 original size:18 final size:17
Alignment explanation
Indices: 28153831--28153925 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
28153821 ATTTGATATG
* *
28153831 AATTTAGATTT-ATTTA
1 AATTTAAATTTAAATTA
28153847 AATTTAAATTTAAATTA
1 AATTTAAATTTAAATTA
* *
28153864 AACTTTAAATTTGAATTT
1 AA-TTTAAATTTAAATTA
* * * *
28153882 AATTTTAGTCTAAATTT
1 AATTTAAATTTAAATTA
*
28153899 ATTTTAAATTTAAAATT-
1 AATTTAAATTT-AAATTA
28153916 AATTTAAATT
1 AATTTAAATT
28153926 AAAGTCCAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
16 10 0.16
17 33 0.52
18 20 0.32
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:28155204 original size:12 final size:12
Alignment explanation
Indices: 28155187--28155211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28155177 CAGAGGCTAT
28155187 TAACAATATTTA
1 TAACAATATTTA
28155199 TAACAATATTTA
1 TAACAATATTTA
28155211 T
1 T
28155212 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:28157845 original size:21 final size:20
Alignment explanation
Indices: 28157816--28157854 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
28157806 ACGCCTACGA
28157816 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
28157836 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
28157855 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:28159101 original size:13 final size:13
Alignment explanation
Indices: 28159083--28159110 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28159073 AATATAGGGG
28159083 AAAATGTACCATT
1 AAAATGTACCATT
28159096 AAAATGTACCATT
1 AAAATGTACCATT
28159109 AA
1 AA
28159111 CGAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGTACCATT
Found at i:28163886 original size:18 final size:17
Alignment explanation
Indices: 28163858--28163892 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28163848 TTTTCTTTTT
*
28163858 TAAAAAAAGAAGAAGGA
1 TAAAAAAAGAAAAAGGA
28163875 TAAAACAAAGAAAAAGGA
1 TAAAA-AAAGAAAAAGGA
28163893 AAGGGAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (17 bp):
TAAAAAAAGAAAAAGGA
Found at i:28164610 original size:29 final size:29
Alignment explanation
Indices: 28164578--28164714 Score: 86
Period size: 30 Copynumber: 4.7 Consensus size: 29
28164568 AAAATTTTAG
*
28164578 AAAATTACATTTTAACCCCGAAACTTCCA
1 AAAATTACATTTTAACCCCCAAACTTCCA
* * * *
28164607 AAAATTACCATTTTTACCCCCAAATTTTCT
1 AAAATTA-CATTTTAACCCCCAAACTTCCA
** * *
28164637 AAAATCCCATTTTTAA--CCCTAA-TTTCA
1 AAAATTACA-TTTTAACCCCCAAACTTCCA
28164664 TCAAAATTACCATTTT-ACCCCCAAACTTTCC-
1 --AAAATTA-CATTTTAACCCCCAAAC-TTCCA
*
28164695 AAAATTCCATTTTTAACCCC
1 AAAATTACA-TTTTAACCCC
28164715 GATTTCACCA
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.05
28 8 0.10
29 28 0.34
30 39 0.48
32 3 0.04
ACGTcount: A:0.36, C:0.29, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCCAAACTTCCA
Found at i:28164626 original size:30 final size:29
Alignment explanation
Indices: 28164578--28165020 Score: 135
Period size: 29 Copynumber: 14.8 Consensus size: 29
28164568 AAAATTTTAG
*
28164578 AAAATTA-CATTTTAACCCCGAAACTTCCA
1 AAAATTACCATTTTTACCCCG-AACTTCCA
* * * *
28164607 AAAATTACCATTTTTACCCCCAAATTTTCT
1 AAAATTACCATTTTTA-CCCCGAACTTCCA
* * * *
28164637 AAAA-TCCCATTTTTAACCCTAA-TTTCA
1 AAAATTACCATTTTTACCCCGAACTTCCA
*
28164664 TCAAAATTACCA-TTTTACCCCCAAACTTTCC-
1 --AAAATTACCATTTTTA-CCCCGAAC-TTCCA
*
28164695 AAAATT-CCATTTTTAACCCCG-ATTTCACCA
1 AAAATTACCATTTTT-ACCCCGAACTT--CCA
28164725 AAAATTACCA-TTTTACCCTCGAACTTTCCCGA
1 AAAATTACCATTTTTACCC-CGAAC-TT-CC-A
* * *
28164757 ATTTTCCAAAATCCCATTTTTAACCCCG-ATTTCACCA
1 A------AAATTACCATTTTT-ACCCCGAACTT--CCA
* *
28164794 AAAATCATCC--TTTTACCCCTAAACTTTCC-
1 AAAATTA-CCATTTTTACCCC-GAAC-TTCCA
* *
28164823 AAAA-T-CCTATTTTTAACCCTG-ATTTCACCA
1 AAAATTACC-ATTTTT-ACCCCGAACTT--CCA
* *
28164853 AAAATCACCA-TTTTATCCCCAAACTTTCC-
1 AAAATTACCATTTTTA-CCCCGAAC-TTCCA
*
28164882 AAAATT-CCATTTTTAACCCCG-ATTTCACAA
1 AAAATTACCATTTTT-ACCCCGAACTTC-C-A
*
28164912 AAAATTATCA-TTTTATCCCCGAACTTCC-
1 AAAATTACCATTTTTA-CCCCGAACTTCCA
* *
28164940 AAAATT-CCATTTTTAACCCCG-ATTTCACC
1 AAAATTACCATTTTT-ACCCCGAACTTC-CA
28164969 AAAATTACCATTTTTACCCTCGAACTTTCC-
1 AAAATTACCATTTTTACCC-CGAAC-TTCCA
28164999 AAAATT-CCATTTTTAACCCCGA
1 AAAATTACCATTTTT-ACCCCGA
28165021 TTTCATCGAA
Statistics
Matches: 312, Mismatches: 42, Indels: 120
0.66 0.09 0.25
Matches are distributed among these distances:
26 2 0.01
27 17 0.05
28 31 0.10
29 98 0.31
30 98 0.31
31 24 0.08
32 18 0.06
37 4 0.01
38 10 0.03
39 6 0.02
40 4 0.01
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTTACCCCGAACTTCCA
Found at i:28164641 original size:59 final size:57
Alignment explanation
Indices: 28164545--28165048 Score: 372
Period size: 59 Copynumber: 8.4 Consensus size: 57
28164535 CCCCAAACAG
* ** ** *
28164545 TCCAAAAATT-GCATTTTGACCCTAAAATTTTAGAAAATTACA-TTTTAACCCCGAAACT
1 TCCAAAAATTACCATTTT-ACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCG-AA-T
* * *
28164603 TCCAAAAATTACCATTTTTACCCCCAAATTTTCTAAAATCCCATTTTTAA-CCCTAAT
1 TCCAAAAATTACCA-TTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
* * *
28164660 TTCATCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
1 TCCA--AAAATTACCATTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
* *
28164719 TCACCAAAAATTACCATTTTACCCTCGAACTTTCCCGAATTTTCCAAAATCCCATTTTTAACCCC
1 T--CCAAAAATTACCATTTTA----C---C---CCCAAATTTTCCAAAATTCCATTTTTAACCCC
*
28164784 GATT
54 GAAT
* * * * *
28164788 TCACCAAAAATCATCC-TTTTACCCCTAAACTTTCCAAAA-TCCTATTTTTAACCCTGATT
1 T--CCAAAAATTA-CCATTTTACCCCCAAATTTTCCAAAATTCC-ATTTTTAACCCCGAAT
* * * *
28164847 TCACCAAAAATCACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
1 T--CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
* * * * *
28164906 TCACAAAAAATTATCATTTTATCCCCGAA-CTTCCAAAATTCCATTTTTAACCCCGATT
1 TC-C-AAAAATTACCATTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
* * * * *
28164964 TCACCAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATT
1 TC-CAAAAATTACCA-TTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
* *
28165023 TCATCGAAATTTACCATTTTACCCCC
1 TC--CAAAAATTACCATTTTACCCCC
28165049 GAGGATCCAA
Statistics
Matches: 379, Mismatches: 40, Indels: 53
0.80 0.08 0.11
Matches are distributed among these distances:
57 14 0.04
58 92 0.24
59 192 0.51
60 23 0.06
61 2 0.01
62 1 0.00
63 1 0.00
65 1 0.00
66 1 0.00
69 50 0.13
70 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATTCCATTTTTAACCCCGAAT
Found at i:28164705 original size:58 final size:59
Alignment explanation
Indices: 28164604--28165048 Score: 434
Period size: 59 Copynumber: 7.4 Consensus size: 59
28164594 CCCGAAACTT
* * * **
28164604 CCAAAAATTACCATTTTTACCCCCAAATTTTCTAAAATCCCATTTTTAACCCTAATTTCA
1 CCAAAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
28164664 TC-AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * ** * * ***
28164722 CCAAAAATTACCATTTTACCCTCGAACTTTCCCGAATTTTCCAAAATCCCATTTTTAACCCCGAT
1 CCAAAAATTACCATTTTACCCCCAAACTTT-CC-AAAATTCC---AT----TTTTAACCCCGATT
*
28164787 T-T
57 TCA
* * * *
28164789 CACCAAAAATCATCC-TTTTACCCCTAAACTTTCCAAAA-TCCTATTTTTAACCCTGATTTCA
1 C-CAA-AAATTA-CCATTTTACCCCCAAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCA
* *
28164850 CCAAAAATCACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
28164909 CAAAAAATTATCATTTTATCCCCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
28164967 CC-AAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
28165026 TCGAAATTTACCATTTTACCCCC
1 CCAAAAATTACCATTTTACCCCC
28165049 GAGGATCCAA
Statistics
Matches: 319, Mismatches: 47, Indels: 39
0.79 0.12 0.10
Matches are distributed among these distances:
57 9 0.03
58 88 0.28
59 144 0.45
60 26 0.08
61 7 0.02
64 4 0.01
66 3 0.01
67 3 0.01
68 14 0.04
69 19 0.06
70 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:28164995 original size:117 final size:115
Alignment explanation
Indices: 28164752--28165070 Score: 392
Period size: 117 Copynumber: 2.7 Consensus size: 115
28164742 CTCGAACTTT
* * * * *
28164752 CCCGAATTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATCATCCTTTTACCCCTAAA
1 CCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATTATCATTTTACCCC-GAA
*
28164817 CTTTCCAAAA-TCCTATTTTTAACCCTGATTTCACCAAAAATCACCATTTTATC
64 C-TTCCAAAATTCC-ATTTTTAACCCCGATTTCACCAAAAATCACCATTTTATC
*
28164870 CCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAAATTATCATTTTATCCCCGAA
1 CCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC-AAAAATTATCATTTTA-CCCCGAA
*
28164935 CTTCCAAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTT-TAC
64 CTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATCACCATTTTAT-C
* * *
28164986 CCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCGAAATTTACCATTTTACCCCCGA
1 CC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATTATCATTTTA-CCCCGA
***
28165051 GGATCCAAAATTTCCATTTT
63 ACTTCCAAAA-TTCCATTTT
28165071 GCCCTCGGGT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
115 1 0.01
116 16 0.09
117 91 0.51
118 66 0.37
119 4 0.02
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (115 bp):
CCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTATCATTTTACCCCGAACT
TCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATCACCATTTTATC
Found at i:28165049 original size:30 final size:29
Alignment explanation
Indices: 28164831--28165050 Score: 172
Period size: 30 Copynumber: 7.5 Consensus size: 29
28164821 CCAAAATCCT
* *
28164831 ATTTTTAACCCTGATTTCACCAAAAATCACC
1 ATTTTTAACCCCGATTTCA-C-AAAATTACC
* *
28164862 A-TTTTATCCCCAAACTTTC-CAAAATT-CC
1 ATTTTTAACCCC-GA-TTTCACAAAATTACC
*
28164890 ATTTTTAACCCCGATTTCACAAAAAATTATC
1 ATTTTTAACCCCGATTTCAC--AAAATTACC
* *
28164921 A-TTTTATCCCCGAACTTC-CAAAATT-CC
1 ATTTTTAACCCCG-ATTTCACAAAATTACC
28164948 ATTTTTAACCCCGATTTCACCAAAATTACC
1 ATTTTTAACCCCGATTTCA-CAAAATTACC
28164978 ATTTTT-ACCCTCGAACTTTC-CAAAATT-CC
1 ATTTTTAACCC-CG-A-TTTCACAAAATTACC
*
28165007 ATTTTTAACCCCGATTTCATCGAAATTTACC
1 ATTTTTAACCCCGATTTCA-C-AAAATTACC
*
28165038 A-TTTTACCCCCGA
1 ATTTTTAACCCCGA
28165051 GGATCCAAAA
Statistics
Matches: 155, Mismatches: 14, Indels: 41
0.74 0.07 0.20
Matches are distributed among these distances:
27 14 0.09
28 22 0.14
29 36 0.23
30 63 0.41
31 12 0.08
32 8 0.05
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTTAACCCCGATTTCACAAAATTACC
Found at i:28165084 original size:28 final size:29
Alignment explanation
Indices: 28165029--28165087 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
28165019 GATTTCATCG
28165029 AAATTTACCATTTTACCCCCGAGGATCCA
1 AAATTTACCATTTTACCCCCGAGGATCCA
* *
28165058 AAATTT-CCATTTTGCCCTCG-GGTATCCA
1 AAATTTACCATTTTACCCCCGAGG-ATCCA
28165086 AA
1 AA
28165088 TGTCCCGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 19 0.70
29 6 0.22
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (29 bp):
AAATTTACCATTTTACCCCCGAGGATCCA
Found at i:28181680 original size:3 final size:3
Alignment explanation
Indices: 28181672--28181700 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28181662 GAATCAATGA
28181672 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28181701 GATCTTACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28186856 original size:21 final size:20
Alignment explanation
Indices: 28186798--28186857 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
28186788 AAAAATAGAG
*
28186798 ATTTATCCTTAATTTTATCC
1 ATTTATCCTTTATTTTATCC
* * *
28186818 AATT-TCTTTTATTCTTTACTCT
1 ATTTATCCTTTA-T-TTTA-TCC
28186840 ATTTATCCTTTATTTTAT
1 ATTTATCCTTTATTTTAT
28186858 AACAGTTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 8 0.27
22 6 0.20
23 6 0.20
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATCCTTTATTTTATCC
Found at i:28189125 original size:17 final size:17
Alignment explanation
Indices: 28189080--28189126 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
28189070 TATGACATCT
*
28189080 ATATGTAATAAAATTTAA
1 ATATG-AATAAAACTTAA
*
28189098 A-ATAAATTAAAACTTAA
1 ATATGAA-TAAAACTTAA
28189115 ATATGAATAAAA
1 ATATGAATAAAA
28189127 ATATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.08
17 17 0.71
18 5 0.21
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
ATATGAATAAAACTTAA
Found at i:28189254 original size:20 final size:20
Alignment explanation
Indices: 28189217--28189278 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
28189207 TCAAATAGTT
*
28189217 TTTTTTAATTTATAATTTTATA
1 TTTTTT-ATATAT-ATTTTATA
*
28189239 TTTTTTATATATATTTTAAA
1 TTTTTTATATATATTTTATA
* *
28189259 ATTTTTA-ATATGTTTT-TA
1 TTTTTTATATATATTTTATA
28189277 TT
1 TT
28189279 GTTAATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 13 0.38
21 5 0.15
22 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTTATATATATTTTATA
Found at i:28193958 original size:5 final size:5
Alignment explanation
Indices: 28193948--28193976 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28193938 GCAAAACCGT
28193948 GTTGG GTTGG GTTGG GTTGG GTTGG GTTG
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTTG
28193977 ACTACAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (5 bp):
GTTGG
Found at i:28194362 original size:18 final size:17
Alignment explanation
Indices: 28194339--28194381 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
28194329 GTTCAATGTG
28194339 TAATTAATATAAAATTT-T
1 TAATTAAT-T-AAATTTAT
28194357 TAATTAATTAAATTTAT
1 TAATTAATTAAATTTAT
28194374 TAAATTAA
1 T-AATTAA
28194382 AAACTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 3 0.13
18 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAATTAAATTTAT
Done.