Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:294455 original size:24 final size:24
Alignment explanation
Indices: 294423--294472 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
294413 GTGTCACGTA
* *
294423 AATTTGTCCTAAAGGACCGTGTAG
1 AATTTGTCCCAAAGGACCATGTAG
*
294447 AATTTGTCCCGAAGGACCATGTAG
1 AATTTGTCCCAAAGGACCATGTAG
294471 AA
1 AA
294473 ATATCCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (24 bp):
AATTTGTCCCAAAGGACCATGTAG
Found at i:294484 original size:23 final size:24
Alignment explanation
Indices: 294434--294485 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
294424 ATTTGTCCTA
* * *
294434 AAGGACCGTGTAGAATTTGTCCCG
1 AAGGACCATGTAGAATATATCCCG
*
294458 AAGGACCATGTAGAA-ATATCCCT
1 AAGGACCATGTAGAATATATCCCG
294481 AAGGA
1 AAGGA
294486 TCACATAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (24 bp):
AAGGACCATGTAGAATATATCCCG
Found at i:296530 original size:22 final size:22
Alignment explanation
Indices: 296502--296547 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
296492 ATTTCTGGGC
* *
296502 AAGGGGAATCGGTACCCATTCA
1 AAGGGGAACCGATACCCATTCA
*
296524 AAGGGGAACCGATACCCCTTCA
1 AAGGGGAACCGATACCCATTCA
296546 AA
1 AA
296548 CGACAGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (22 bp):
AAGGGGAACCGATACCCATTCA
Found at i:296616 original size:23 final size:22
Alignment explanation
Indices: 296572--296616 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
296562 AATGCCAGAG
*
296572 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
296594 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
296617 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:297258 original size:31 final size:31
Alignment explanation
Indices: 297220--297430 Score: 342
Period size: 31 Copynumber: 6.9 Consensus size: 31
297210 GTCGAGGGTA
297220 ACCTATGTTCTTCGGGACATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGTTT
*
297251 ACCTATGTTCTTCGGGACATATGGAATGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGTTT
297282 ACCTATGTTCTTCGGGACATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGTTT
297313 ACCTATGTTCTTCGGGACATATGGACTGTTTT
1 ACCTATGTTCTTCGGGACATATGGACTG-TTT
297345 ACCTATGTTCTTC-GGACATA-GGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGTTT
297374 ACCTATGTTCTTCGGG--ATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGTTT
* *
297403 ACCTAGGTTCTTCGGAATC-TATGGACTG
1 ACCTATGTTCTTCGGGA-CATATGGACTG
297431 GTCCTTCGGG
Statistics
Matches: 170, Mismatches: 4, Indels: 12
0.91 0.02 0.06
Matches are distributed among these distances:
28 3 0.02
29 39 0.23
30 8 0.05
31 104 0.61
32 16 0.09
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
ACCTATGTTCTTCGGGACATATGGACTGTTT
Found at i:299534 original size:60 final size:59
Alignment explanation
Indices: 299416--299601 Score: 178
Period size: 60 Copynumber: 3.1 Consensus size: 59
299406 TTTGGATGGA
* * * * ** *
299416 TTTGGGGATAAAATTGAATGATCCAAAAGTTTAGGGATTAATTCAGAATGACATTCATAG
1 TTTGGGGATAAAATTGAAT-ATTCAAAAGTTTAAGGACTAATTTAGAATGGGAGTCATAG
* * *
299476 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACAAATTTAGAGTGGGAGTCATAG
1 TTTGGGGATAAAATT-GAATATTCAAAAGTTTAAGGACTAATTTAGAATGGGAGTCATAG
* * * * * *
299536 TTTTGGTATAAAATTAAATATTTAAAAG-TTAAGGAGTAATTTAAAATGAGG-GTCATAG
1 TTTGGGGATAAAATTGAATATTCAAAAGTTTAAGGACTAATTTAGAATG-GGAGTCATAG
*
299594 TTTAGGGA
1 TTTGGGGA
299602 CATGTGATGC
Statistics
Matches: 103, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
58 29 0.28
59 13 0.13
60 57 0.55
61 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.33
Consensus pattern (59 bp):
TTTGGGGATAAAATTGAATATTCAAAAGTTTAAGGACTAATTTAGAATGGGAGTCATAG
Found at i:313149 original size:42 final size:42
Alignment explanation
Indices: 313090--313176 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
313080 AAGTCGCCAA
*
313090 AGTAAGAATTTACGAGAGAGCGGTCAGAGATTTATATTGACT
1 AGTAAGAATTTACGAGAGAGCGGTAAGAGATTTATATTGACT
*
313132 AGTAAGAATTTACGAGAGAGCGGTAAGATATTTATATTGACT
1 AGTAAGAATTTACGAGAGAGCGGTAAGAGATTTATATTGACT
313174 AGT
1 AGT
313177 GAGATCAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (42 bp):
AGTAAGAATTTACGAGAGAGCGGTAAGAGATTTATATTGACT
Found at i:313158 original size:21 final size:22
Alignment explanation
Indices: 313091--313165 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 22
313081 AGTCGCCAAA
313091 GTAAGA-ATTTACGAGAGAGCG
1 GTAAGAGATTTACGAGAGAGCG
* * ** *
313112 GTCAGAGATTTA-TATTGA-CTA
1 GTAAGAGATTTACGAGAGAGC-G
313133 GTAAGA-ATTTACGAGAGAGCG
1 GTAAGAGATTTACGAGAGAGCG
*
313154 GTAAGATATTTA
1 GTAAGAGATTTA
313166 TATTGACTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
20 6 0.15
21 22 0.56
22 11 0.28
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (22 bp):
GTAAGAGATTTACGAGAGAGCG
Found at i:313827 original size:21 final size:21
Alignment explanation
Indices: 313801--313841 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
313791 ATATATGTTA
*
313801 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCATTCGGGACATC
313822 TATGTGGTCATTCGGGACAT
1 TATGTGGTCATTCGGGACAT
313842 TTTTACGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATC
Found at i:316331 original size:35 final size:36
Alignment explanation
Indices: 316281--316351 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
316271 TATGTGCAGG
*
316281 GGGAACAGATCCCCCCTG-GGGGGTATCGATTCCCC
1 GGGAACAGATCCCCCCTGAGAGGGTATCGATTCCCC
*
316316 GGGAACAGATTCCCCCTGAGAGGGTATCGATTCCCC
1 GGGAACAGATCCCCCCTGAGAGGGTATCGATTCCCC
316352 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (36 bp):
GGGAACAGATCCCCCCTGAGAGGGTATCGATTCCCC
Found at i:316682 original size:14 final size:15
Alignment explanation
Indices: 316663--316691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
316653 TACATGATAT
316663 GCATG-AACATAAGA
1 GCATGAAACATAAGA
316677 GCATGAAACATAAGA
1 GCATGAAACATAAGA
316692 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.14
Consensus pattern (15 bp):
GCATGAAACATAAGA
Found at i:319347 original size:34 final size:32
Alignment explanation
Indices: 319285--319354 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
319275 ACCTTACAAC
* *
319285 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
319317 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
319351 TCCC
1 TCCC
319355 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:319763 original size:21 final size:21
Alignment explanation
Indices: 319719--319814 Score: 151
Period size: 21 Copynumber: 4.7 Consensus size: 21
319709 TTGCAGCCTT
* *
319719 GATGCATGGATGCATGG-CAG
1 GATGCATCGATGCATGGTAAG
319739 GATGCATCGATGCATGGTAAG
1 GATGCATCGATGCATGGTAAG
319760 GATGCATCGATGCATGGTAAG
1 GATGCATCGATGCATGGTAAG
*
319781 GATGCATCGATGCATAGTAA-
1 GATGCATCGATGCATGGTAAG
319801 GATGCATCGATGCA
1 GATGCATCGATGCA
319815 CTAATTGCAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
20 30 0.42
21 42 0.58
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (21 bp):
GATGCATCGATGCATGGTAAG
Found at i:319776 original size:41 final size:41
Alignment explanation
Indices: 319719--319814 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
319709 TTGCAGCCTT
* * *
319719 GATGCATGGATGCATGG-CAGGATGCATCGATGCATGGTAA
1 GATGCATCGATGCATGGTAAGGATGCATCGATGCATAGTAA
319759 GGATGCATCGATGCATGGTAAGGATGCATCGATGCATAGTAA
1 -GATGCATCGATGCATGGTAAGGATGCATCGATGCATAGTAA
319801 GATGCATCGATGCA
1 GATGCATCGATGCA
319815 CTAATTGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 30 0.59
42 21 0.41
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (41 bp):
GATGCATCGATGCATGGTAAGGATGCATCGATGCATAGTAA
Found at i:319903 original size:21 final size:21
Alignment explanation
Indices: 319834--319934 Score: 109
Period size: 21 Copynumber: 4.8 Consensus size: 21
319824 TTCGTTGTTT
*
319834 GGATGCATGGATGCATTGCA-
1 GGATGCATGGATGCACTGCAG
* * *
319854 TGATGCATCGATGCA-T-TAG
1 GGATGCATGGATGCACTGCAG
319873 TGCAGATGCATGGATGCACTGCAG
1 -G--GATGCATGGATGCACTGCAG
319897 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCACTGCAG
*
319918 GGATGTATGGATGCACT
1 GGATGCATGGATGCACT
319935 TTGACACCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 13 0.19
21 36 0.53
22 13 0.19
23 2 0.03
24 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (21 bp):
GGATGCATGGATGCACTGCAG
Found at i:320431 original size:30 final size:31
Alignment explanation
Indices: 320355--320433 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
320345 ATAGATTTTG
*
320355 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAATCTTACTCCCCCTTACTATAGCACATC
320386 AAAATCTTACTCCCCCTTACTATAGCACATC
1 AAAATCTTACTCCCCCTTACTATAGCACATC
* *
320417 TAAAT-TTTCTCCCCCTT
1 AAAATCTTACTCCCCCTT
320434 TTTGTTAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATCTTACTCCCCCTTACTATAGCACATC
Found at i:324767 original size:20 final size:21
Alignment explanation
Indices: 324721--324775 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
324711 TTGCAGCCTT
* *
324721 GATGCATGGATGCATGGCAAG
1 GATGCATCGATGCATAGCAAG
324742 GATGCATCGATGCATAGCAA-
1 GATGCATCGATGCATAGCAAG
324762 GATGCATCGATGCA
1 GATGCATCGATGCA
324776 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATAGCAAG
Found at i:324858 original size:13 final size:13
Alignment explanation
Indices: 324840--324864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324830 TTAGTGCAGA
324840 TGCAGGGATGCAC
1 TGCAGGGATGCAC
324853 TGCAGGGATGCA
1 TGCAGGGATGCA
324865 TGGATGCACT
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:0.24, C:0.20, G:0.40, T:0.16
Consensus pattern (13 bp):
TGCAGGGATGCAC
Found at i:324975 original size:29 final size:29
Alignment explanation
Indices: 324954--325010 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
324944 AAACTTTGAA
324954 TAAATTCAATT-AAATCCAAAAACATTTTG
1 TAAATTCAATTCAAATCCAAAAACA-TTTG
*
324983 TAAATTCAATTCAAGTCCAAAAACATTT
1 TAAATTCAATTCAAATCCAAAAACATTT
325011 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAATCCAAAAACATTTG
Found at i:325004 original size:30 final size:29
Alignment explanation
Indices: 324954--325012 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
324944 AAACTTTGAA
324954 TAAATTCAATTAAATCCAAAAACATTTTG
1 TAAATTCAATTAAATCCAAAAACATTTTG
*
324983 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAATCCAAAAACATTTTG
325013 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAATCCAAAAACATTTTG
Found at i:325052 original size:2 final size:2
Alignment explanation
Indices: 325045--325087 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
325035 ATAGTTCAAC
325045 AT 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 AT
325087 A
1 A
325088 ATTTGATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:329095 original size:15 final size:15
Alignment explanation
Indices: 329043--329099 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
329033 AACCGGGTAT
329043 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* * *
329058 TGGGAACCCGAAAAATA-
1 CGGGTACCCG---ATTAC
329075 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
329090 CGGGTACCCG
1 CGGGTACCCG
329100 TAACATCCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.09
15 18 0.56
17 8 0.25
18 3 0.09
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:329169 original size:15 final size:15
Alignment explanation
Indices: 329149--329191 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
329139 CCGGAAGTTC
329149 CGGGTACCCGGAAAT
1 CGGGTACCCGGAAAT
*
329164 CGGGTACCCGAAAAT
1 CGGGTACCCGGAAAT
329179 CTGGGTACCCGGA
1 C-GGGTACCCGGA
329192 TTTGCACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.14
Consensus pattern (15 bp):
CGGGTACCCGGAAAT
Found at i:332511 original size:19 final size:19
Alignment explanation
Indices: 332449--332512 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
332439 AATAGATTGA
*
332449 AAGTATCGATACTCCTATAA-
1 AAGTATCGATACT-TTA-AAT
* **
332469 AAGTTTCGATACTTTACGT
1 AAGTATCGATACTTTAAAT
332488 AAGTATCGATACTTTAAAT
1 AAGTATCGATACTTTAAAT
*
332507 GAGTAT
1 AAGTAT
332513 GTAATGCCCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 23 0.66
20 12 0.34
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGTATCGATACTTTAAAT
Found at i:333831 original size:132 final size:132
Alignment explanation
Indices: 333597--333903 Score: 532
Period size: 132 Copynumber: 2.3 Consensus size: 132
333587 GTAAACCATT
* *
333597 AGAATAAGTTTAATAATTATAATTCTAAATACTATATTAAAAATTTTGCTTTTATGTAAAATAAT
1 AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAATTTTACTTTTATGTAAAATAAT
333662 GATATTTTTATTTACAATGTAATTTTATTTAAGAAAGATGATGAAATTGATT-A-AT-ATAT-AA
66 GATATTTTTATTTACAATGTAATTTTATTTAAGAAAGATGATGAAATT-ATTAATATAATATAAA
333723 TAA
130 TAA
333726 AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAATATTTACTTTTATATGTAAAAT
1 AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAAT-TTTAC-TTT-TATGTAAAAT
333791 AATGATATTTTTATTTACAATGTAATTTTATTTAAGAAAGATGATGAAATTATTAATATAATATA
63 AATGATATTTTTATTTACAATGTAATTTTATTTAAGAAAGATGATGAAATTATTAATATAATATA
333856 AATAA
128 AATAA
333861 AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAA
1 AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAA
333904 CATTGTCTAT
Statistics
Matches: 169, Mismatches: 2, Indels: 8
0.94 0.01 0.04
Matches are distributed among these distances:
129 43 0.25
130 4 0.02
131 6 0.04
132 62 0.37
133 2 0.01
134 4 0.02
135 48 0.28
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (132 bp):
AGAATAAGTTTAATAATTATAATTCTAAATAATATATTAAAAATTTTACTTTTATGTAAAATAAT
GATATTTTTATTTACAATGTAATTTTATTTAAGAAAGATGATGAAATTATTAATATAATATAAAT
AA
Found at i:334313 original size:3 final size:3
Alignment explanation
Indices: 334305--334332 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
334295 TGCTGATAGC
334305 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
334333 AATTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:342212 original size:28 final size:28
Alignment explanation
Indices: 342142--342212 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
342132 TTTTTATTTG
*
342142 TTTACTTTATGTATATTTTTTCATTTTCT
1 TTTACATTAT-TATATTTTTTCATTTTCT
*
342171 TTTA-ATT-TTAATATTTTTTTA-TTTCTT
1 TTTACATTATT-ATATTTTTTCATTTTC-T
342198 TTTACATTATTATAT
1 TTTACATTATTATAT
342213 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 5 0.14
27 16 0.44
28 9 0.25
29 6 0.17
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.69
Consensus pattern (28 bp):
TTTACATTATTATATTTTTTCATTTTCT
Found at i:342378 original size:18 final size:17
Alignment explanation
Indices: 342355--342395 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
342345 TCACTTTTCC
342355 ACTTTTTTCAA-TATTTT
1 ACTTTTTTCAACTA-TTT
342372 ACTTTTTTCAACTATTT
1 ACTTTTTTCAACTATTT
342389 ACTTTTT
1 ACTTTTT
342396 GACTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (17 bp):
ACTTTTTTCAACTATTT
Found at i:342529 original size:13 final size:13
Alignment explanation
Indices: 342511--342535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342501 TTCTTTGAAA
342511 ATTTATTTTCTTC
1 ATTTATTTTCTTC
342524 ATTTATTTTCTT
1 ATTTATTTTCTT
342536 TAAACTTTAT
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTTCTTC
Found at i:345564 original size:14 final size:14
Alignment explanation
Indices: 345545--345586 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
345535 TCCAATCAAG
345545 AACAAAAAGAGAAA
1 AACAAAAAGAGAAA
*
345559 AAC--AAAGAAAAA
1 AACAAAAAGAGAAA
345571 AACAAAAAGAGAAA
1 AACAAAAAGAGAAA
345585 AA
1 AA
345587 AAAGAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (14 bp):
AACAAAAAGAGAAA
Found at i:345581 original size:26 final size:25
Alignment explanation
Indices: 345545--345595 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
345535 TCCAATCAAG
345545 AACAAAAAGAGAAAAACAAAGAAAAA
1 AACAAAAAGAGAAAAA-AAAGAAAAA
345571 AACAAAAAGAGAAAAAAAAGAAAAA
1 AACAAAAAGAGAAAAAAAAGAAAAA
345596 GTAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (25 bp):
AACAAAAAGAGAAAAAAAAGAAAAA
Found at i:345585 original size:25 final size:26
Alignment explanation
Indices: 345545--345595 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
345535 TCCAATCAAG
*
345545 AACAAAAAGAGAAAAACAAAGAAAAA
1 AACAAAAAGAGAAAAAAAAAGAAAAA
345571 AACAAAAAGAG-AAAAAAAAGAAAAA
1 AACAAAAAGAGAAAAAAAAAGAAAAA
345596 GTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (26 bp):
AACAAAAAGAGAAAAAAAAAGAAAAA
Found at i:345594 original size:16 final size:15
Alignment explanation
Indices: 345562--345629 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 15
345552 AGAGAAAAAC
345562 AAAGAAAAAAACA-AA
1 AAAGAAAAAAA-AGAA
345577 AAGAGAAAAAAAAGAA
1 AA-AGAAAAAAAAGAA
345593 AAAGTAAAAATAAATGAA
1 AAAG-AAAAA-AAA-GAA
*
345611 AAATAAAGAAAAAAGAA
1 AAA-GAA-AAAAAAGAA
345628 AA
1 AA
345630 CAATACGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
15 5 0.11
16 18 0.40
17 8 0.18
18 11 0.24
19 3 0.07
ACGTcount: A:0.81, C:0.01, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:345602 original size:17 final size:17
Alignment explanation
Indices: 345566--345629 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
345556 AAAAACAAAG
*
345566 AAAAAAACAAAAAG-AGA
1 AAAAAAAGAAAAAGTA-A
345583 AAAAAAAGAAAAAGTAA
1 AAAAAAAGAAAAAGTAA
*
345600 AAATAAATGAAAAA-TAA
1 AAA-AAAAGAAAAAGTAA
345617 AGAAAAAAGAAAA
1 A-AAAAAAGAAAA
345630 CAATACGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAAGAAAAAGTAA
Found at i:347385 original size:36 final size:36
Alignment explanation
Indices: 347336--347406 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
347326 CAAAACAAAG
347336 TTTTGTCTTTCTTGAGACAGCTTCTCTTGAAACAAT
1 TTTTGTCTTTCTTGAGACAGCTTCTCTTGAAACAAT
*
347372 TTTTGT-TTCTCTTGAGACAGTTTCTCTTGAAACAA
1 TTTTGTCTT-TCTTGAGACAGCTTCTCTTGAAACAA
347407 AATCTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (36 bp):
TTTTGTCTTTCTTGAGACAGCTTCTCTTGAAACAAT
Found at i:347528 original size:36 final size:36
Alignment explanation
Indices: 347420--347580 Score: 189
Period size: 37 Copynumber: 4.4 Consensus size: 36
347410 CTTTGAATAT
* * *
347420 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
347456 GTTTCTT-TTGGAACTAAGTTTTGTCTCTCTTAAGACA
1 GTTT-TTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
347493 GTTTTTCTTGAAACAAATTTTTTCTCTTTTGAGACA
1 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
**
347529 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTTTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
347566 GTTTCTCTTGAAACA
1 GTTTTTCTTGAAACA
347581 CCAACCTTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
36 45 0.43
37 60 0.57
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:347548 original size:73 final size:73
Alignment explanation
Indices: 347420--347580 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 73
347410 CTTTGAATAT
* ** * *
347420 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
347485 TTAAGACA
66 TTAAGACA
** **
347493 GTTTTTCTTGAAACAAATTTTTTCTCTTTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
*
347558 TTGAGACA
66 TTAAGACA
*
347566 GTTTCTCTTGAAACA
1 GTTTTTCTTGAAACA
347581 CCAACCTTTG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (73 bp):
GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
TTAAGACA
Found at i:347606 original size:67 final size:68
Alignment explanation
Indices: 347529--347678 Score: 189
Period size: 67 Copynumber: 2.2 Consensus size: 68
347519 TTTTGAGACA
* * * ** *
347529 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTG-AGACAGTTTCTCTTGAAACAC-CAACCTTTGA
1 GTTTCTCTTGAAACAAAATTTTGCCTC-CCCGAAGACAGTTTCTCTTGAAACACAAAACCTTTGA
347592 ATAT-
65 A-ATC
347596 GTTTCTCTTGAAACAAAATTTTGCCTCCCCGAAGACAGTTTCTCTTGAAACACAAAAAACCTTTG
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCCGAAGACAGTTTCTCTTGAAACAC--AAAACCTTTG
347661 AAATC
64 AAATC
347666 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
347679 AACAAAAACC
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
66 2 0.03
67 45 0.62
69 2 0.03
70 23 0.32
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (68 bp):
GTTTCTCTTGAAACAAAATTTTGCCTCCCCGAAGACAGTTTCTCTTGAAACACAAAACCTTTGAA
ATC
Found at i:347675 original size:33 final size:33
Alignment explanation
Indices: 347633--347753 Score: 156
Period size: 33 Copynumber: 3.6 Consensus size: 33
347623 CCCGAAGACA
347633 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
347666 GTTTCTCTTGAAAAAC-AAAAACCTTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACC-TTTGAAATC
347699 GTTTCTCTTGAAACACAAAAAAAACCCTTTGAAAAT-
1 GTTTCTCTTGAAACAC--AAAAAA-CCTTTG-AAATC
* *
347735 ATTTATCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
347754 GACCTTCGAG
Statistics
Matches: 78, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
32 7 0.09
33 39 0.50
34 3 0.04
36 23 0.29
37 6 0.08
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:347747 original size:69 final size:66
Alignment explanation
Indices: 347633--347759 Score: 175
Period size: 69 Copynumber: 1.9 Consensus size: 66
347623 CCCGAAGACA
* *
347633 GTTTCTCTTGAAACACAAAAAACCTTTGAAATCGTTTCTCTTGAAAAACAAAAACCTTTTGAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATCATTTATCTTGAAAAACAAAAACCTTTTGAAAT
347698 C
66 C
* *
347699 GTTTCTCTTGAAACACAAAAAAAACCCTTTGAAAAT-ATTTATCTTGAAACACAAAGACCTT
1 GTTTCTCTTGAAACAC--AAAAAA-CCTTTG-AAATCATTTATCTTGAAAAACAAAAACCTT
347760 CGAGTTCAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
66 16 0.30
68 6 0.11
69 27 0.51
70 4 0.08
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (66 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATCATTTATCTTGAAAAACAAAAACCTTTTGAAAT
C
Found at i:347991 original size:86 final size:84
Alignment explanation
Indices: 347746--348008 Score: 276
Period size: 84 Copynumber: 3.1 Consensus size: 84
347736 TTTATCTTGA
* * * * *
347746 AACACAAAGACCTTCGAGTTCAACTACACTCAGCTTCAAGGGCATATCATTTGCAGTATAGCTCA
1 AACA-AAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCAAATCATTTGCAGCATAACTCA
* * * *
347811 AGGCAAGAAGGGGTATTTGCC
64 AGGTAAGAAGGGCTATCTGTC
* * * * * * * *
347832 AACAAAATACCTTCGATTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAA-
1 AACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCAAATCATTTGCAGCATAACTCAAG
*
347896 GTCGAGAAGGGCTATCTGTC
66 GT-AAGAAGGGCTATCTGTC
* * * *
347916 AACTAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGACAAATCAAATTTGCAGCATAACTCA
1 AACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCAAATC--ATTTGCAGCATAACTCA
347981 AGGTAAGAAGGGCTATCTGTC
64 AGGTAAGAAGGGCTATCTGTC
348002 AACAAAA
1 AACAAAA
348009 TTATCGAGTT
Statistics
Matches: 142, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
83 1 0.01
84 73 0.51
85 24 0.17
86 42 0.30
87 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
AACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCAAATCATTTGCAGCATAACTCAAG
GTAAGAAGGGCTATCTGTC
Found at i:350199 original size:12 final size:13
Alignment explanation
Indices: 350179--350207 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
350169 GAATCGAGAT
350179 TTTTAAATTTTAA
1 TTTTAAATTTTAA
350192 TTTT-AATTTTAA
1 TTTTAAATTTTAA
350204 TTTT
1 TTTT
350208 TTCGCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:350842 original size:21 final size:22
Alignment explanation
Indices: 350818--350876 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
350808 TAATTTTATA
350818 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
350839 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
350863 TACTATTAACTTAA
1 TA-TATTAACTTAA
350877 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:350860 original size:25 final size:27
Alignment explanation
Indices: 350804--350897 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 27
350794 AATTATATAT
* *
350804 AATATAATTTTATA-TATA-TTAACTTA
1 AATATATTTTTATATTA-ACTTAATTTA
350830 AA-ATATTTTTATATTAACTT-A-TTA
1 AATATATTTTTATATTAACTTAATTTA
350854 AATATA-TTTTACTATTAACTTAATTTAAA
1 AATATATTTTTA-TATTAACTTAATTT--A
350883 AATATATTTTT-TATT
1 AATATATTTTTATATT
350898 TTTATTTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
24 10 0.17
25 24 0.41
26 7 0.12
27 2 0.03
28 4 0.07
29 7 0.12
30 4 0.07
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATATTTTTATATTAACTTAATTTA
Found at i:350960 original size:27 final size:25
Alignment explanation
Indices: 350876--350939 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
350866 TATTAACTTA
350876 ATTTAAAAATATATTTTTTATTTTT
1 ATTTAAAAATATATTTTTTATTTTT
350901 ATTTAAAAATATATTTTTTATTTTT
1 ATTTAAAAATATATTTTTTATTTTT
350926 ATTTAAAAATATAT
1 ATTTAAAAATATAT
350940 AATTTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTAAAAATATATTTTTTATTTTT
Found at i:357150 original size:60 final size:60
Alignment explanation
Indices: 357084--357233 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
357074 AAATTAGTCT
* * * * *
357084 TTAAACTTTTAAACTTTCCAATTTCTTCCCAAAACTATTACTCTCATTCTAAATCCATCC
1 TTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATGAATATCATTCTAAATCCATCC
* * ***
357144 TTAAACTTTTTAACATTCCAATTTCATCCCTAAACTATGAATATCATTCTAAATTGGTCC
1 TTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATGAATATCATTCTAAATCCATCC
* ** * *
357204 CTAAACTTTTGTATATTCCAATTTTATCCC
1 TTAAACTTTTAAACATTCCAATTTCATCCC
357234 TAATTTCATC
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (60 bp):
TTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATGAATATCATTCTAAATCCATCC
Found at i:357234 original size:29 final size:29
Alignment explanation
Indices: 357139--357236 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
357129 ATTCTAAATC
* *
357139 CATCCTTAAACTTTT-TAACATTCCAATTT
1 CATCCCTAAACTTTTGT-ATATTCCAATTT
* * *
357168 CATCCCTAAAC-TATGAATATCATTCTAAATT
1 CATCCCTAAACTTTTG--TAT-ATTCCAATTT
**
357199 GGTCCCTAAACTTTTGTATATTCCAATTT
1 CATCCCTAAACTTTTGTATATTCCAATTT
*
357228 TATCCCTAA
1 CATCCCTAA
357237 TTTCATCCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 2 0.04
29 25 0.48
30 4 0.08
31 18 0.35
32 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
CATCCCTAAACTTTTGTATATTCCAATTT
Found at i:357509 original size:13 final size:12
Alignment explanation
Indices: 357486--357518 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
357476 TGATAGTTAT
357486 ATTTTAAAAGTA
1 ATTTTAAAAGTA
357498 ATTTTCAAAAGTA
1 ATTTT-AAAAGTA
357511 A-TTTAAAA
1 ATTTTAAAA
357519 TTCAACTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 8 0.40
13 8 0.40
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (12 bp):
ATTTTAAAAGTA
Found at i:357661 original size:15 final size:16
Alignment explanation
Indices: 357630--357668 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
357620 TACACTTATT
357630 AATATTATAATATATAA
1 AATA-TATAATATATAA
357647 AATATATAA-ATATAA
1 AATATATAATATATAA
*
357662 ATTATAT
1 AATATAT
357669 TAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATAATATATAA
Found at i:357677 original size:24 final size:24
Alignment explanation
Indices: 357590--357680 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 24
357580 TGTTATATTG
*
357590 TATATT-AAAATATAGAATTTAAAT
1 TATATTAAAAATATA-AATATAAAT
* ** *
357614 TATATTTACACTTATTAATATTATAA-
1 TATA-TTAAAAATATAAATA-TA-AAT
357640 TATA-TAAAATATATAAATATAAAT
1 TATATTAAAA-ATATAAATATAAAT
357664 TATATTAAAAATATAAA
1 TATATTAAAAATATAAA
357681 AAAATTTAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
23 2 0.04
24 20 0.39
25 17 0.33
26 10 0.20
27 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (24 bp):
TATATTAAAAATATAAATATAAAT
Found at i:363316 original size:31 final size:30
Alignment explanation
Indices: 363293--363362 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
363283 TTAGGCATGT
* *
363293 TTTTTCATTTAGGTCCTAGGTTTATTTGCTA
1 TTTTGCATTTAGGTCCTAGGTTTA-TGGCTA
*
363324 TTTTGCATTTAGGTCCTAGGTTTATTTGCTA
1 TTTTGCATTTAGGTCCTAGGTTTA-TGGCTA
363355 TTTTGCAT
1 TTTTGCAT
363363 GCTCAATTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.16, C:0.13, G:0.17, T:0.54
Consensus pattern (30 bp):
TTTTGCATTTAGGTCCTAGGTTTATGGCTA
Found at i:369324 original size:25 final size:24
Alignment explanation
Indices: 369278--369324 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
369268 TAACTATTTA
* **
369278 AATAAAATTAATCATATTAAATCT
1 AATAAAATTAATAATAGCAAATCT
369302 AATAAAACTTAATAATAGCAAAT
1 AATAAAA-TTAATAATAGCAAAT
369325 TTCATCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
AATAAAATTAATAATAGCAAATCT
Found at i:370557 original size:32 final size:31
Alignment explanation
Indices: 370516--370578 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
370506 AGGTAGAATG
*
370516 CTTAGTGTTCGATAGAAACTAAGTGAAAGATC
1 CTTAGTGTTCGAGAGAAACTAAG-GAAAGATC
*
370548 CTTAGTGTTCGAGAGAAACTAAGGGAAGATC
1 CTTAGTGTTCGAGAGAAACTAAGGAAAGATC
370579 AACGTGAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (31 bp):
CTTAGTGTTCGAGAGAAACTAAGGAAAGATC
Found at i:372562 original size:30 final size:31
Alignment explanation
Indices: 372523--372589 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
372513 GAAGGACCTA
* * * *
372523 TCCAGAGGTCATAAAGAACCTCGGT-AACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTC
* *
372553 TCCATAGGTCCCGAAGAACCTAGGTAAACTC
1 TCCATAGGTCACAAAGAACCTAGGTAAACTC
372584 TCCATA
1 TCCATA
372590 TATTCCTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTC
Found at i:372639 original size:62 final size:63
Alignment explanation
Indices: 372549--372668 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
372539 AACCTCGGTA
* * *
372549 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAA-CTCTCCATATATTCCTTAGAACATATGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAATCTATCCATATATTCCGTAGAACATATGTAT
* * *
372611 ACTGTCCATATGTCTCGAAAGAA-ATAGGTAAATCTATCCATATGTTCCGTAGAACATA
1 ACTGTCCATAGGTCCCG-AAGAACATAGGTAAATCTATCCATATATTCCGTAGAACATA
372669 AGTAAACCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 23 0.46
63 27 0.54
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAATCTATCCATATATTCCGTAGAACATATGTAT
Found at i:372674 original size:32 final size:31
Alignment explanation
Indices: 372548--372675 Score: 98
Period size: 31 Copynumber: 4.1 Consensus size: 31
372538 GAACCTCGGT
* * * *
372548 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTTCCGAAGAACATAGGTA
* * ** *
372579 AACTCTCCATATATTCCTTAGAACATATGTA
1 AACTATCCATATGTTCCGAAGAACATAGGTA
* *
372610 TACTGTCCATATG-TCTCGAAAGAA-ATAGGTA
1 AACTATCCATATGTTC-CG-AAGAACATAGGTA
* *
372641 AATCTATCCATATGTTCCGTAGAACATAAGTA
1 AA-CTATCCATATGTTCCGAAGAACATAGGTA
372673 AAC
1 AAC
372676 CATCGACTCT
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
30 2 0.03
31 46 0.62
32 24 0.32
33 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTTCCGAAGAACATAGGTA
Found at i:373038 original size:20 final size:17
Alignment explanation
Indices: 373000--373051 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 17
372990 CATATCACTC
373000 TATATCATATTCCACGTA
1 TATATCAT-TTCCACGTA
*
373018 TTCATATCATTTCACATGTA
1 -T-ATATCATTTC-CACGTA
373038 TATATCATTGTCCA
1 TATATCATT-TCCA
373052 TATGATTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
20 12 0.41
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (17 bp):
TATATCATTTCCACGTA
Found at i:375373 original size:20 final size:19
Alignment explanation
Indices: 375348--375387 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
375338 CTCAATCCCT
*
375348 TTCATTTCTTTATTCCATTA
1 TTCATTTATTTATTCC-TTA
375368 TTCATTTATTTATTCCTTA
1 TTCATTTATTTATTCCTTA
375387 T
1 T
375388 ACACAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCATTTATTTATTCCTTA
Found at i:378806 original size:18 final size:19
Alignment explanation
Indices: 378765--378808 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
378755 TGAGGGGTAT
378765 ATCGATGCACTCCATATGC
1 ATCGATGCACTCCATATGC
378784 ATCGATGCA-TCCAT-TGC
1 ATCGATGCACTCCATATGC
378801 ATTCGATG
1 A-TCGATG
378809 TTCATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (19 bp):
ATCGATGCACTCCATATGC
Found at i:382005 original size:13 final size:14
Alignment explanation
Indices: 381989--382025 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
381979 TTAAGATTTT
381989 ATTTTTGAAAAT-A
1 ATTTTTGAAAATCA
382002 ATTTTTG-AAATCA
1 ATTTTTGAAAATCA
382015 A-TTTTGAAAAT
1 ATTTTTGAAAAT
382026 TTGAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (14 bp):
ATTTTTGAAAATCA
Found at i:383883 original size:19 final size:21
Alignment explanation
Indices: 383859--383904 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
383849 TATATAGTTT
383859 TCAAAACAAC-ATAA-TTAAA
1 TCAAAACAACAATAATTTAAA
383878 TC-AAA-AACAATAATTTAAA
1 TCAAAACAACAATAATTTAAA
*
383897 ACAAAACA
1 TCAAAACA
383905 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.14
18 7 0.32
19 8 0.36
20 3 0.14
21 1 0.05
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAAACAACAATAATTTAAA
Found at i:389635 original size:18 final size:17
Alignment explanation
Indices: 389612--389645 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
389602 CGAGATCATA
*
389612 ATATTATTTTTTCATATT
1 ATATTATATTTT-ATATT
389630 ATATTATATTTTATAT
1 ATATTATATTTTATAT
389646 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:392817 original size:21 final size:20
Alignment explanation
Indices: 392774--392817 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
392764 ATCTAGTTCA
* * *
392774 ATTTAAATTAATAATAAATT
1 ATTTAAATAAAAAATAAAAT
392794 ATTTAAATAAAAATATAAAAT
1 ATTTAAATAAAAA-ATAAAAT
392815 ATT
1 ATT
392818 AGTATAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTAAATAAAAAATAAAAT
Found at i:392853 original size:17 final size:17
Alignment explanation
Indices: 392831--392879 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
392821 ATAGTTTATA
392831 ATATACACAATGAAAAT
1 ATATACACAATGAAAAT
392848 ATATAC-CAA--AAGAA-
1 ATATACACAATGAA-AAT
*
392862 ATATACACGATGAAAAT
1 ATATACACAATGAAAAT
392879 A
1 A
392880 GGTCGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
16 5 0.19
17 9 0.35
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.20
Consensus pattern (17 bp):
ATATACACAATGAAAAT
Found at i:405456 original size:2 final size:2
Alignment explanation
Indices: 405447--405484 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
405437 TAAAAAATAG
*
405447 AT AT -T AT AT AT -T AA 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
405485 TTGTCCACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:405460 original size:21 final size:23
Alignment explanation
Indices: 405434--405480 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
405424 TTTTTTGAGT
405434 TATTAAA-AAATAGATAT-TATA
1 TATTAAATAAATAGATATATATA
* *
405455 TATTAAATATATATATATATATA
1 TATTAAATAAATAGATATATATA
405478 TAT
1 TAT
405481 ATATTTGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTAAATAAATAGATATATATA
Found at i:405526 original size:17 final size:17
Alignment explanation
Indices: 405504--405536 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
405494 CAAGATCGCA
*
405504 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
405521 ATATTATATTTTATAT
1 ATATTATATTTTATAT
405537 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:405546 original size:22 final size:21
Alignment explanation
Indices: 405521--405561 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
405511 TTTTTATATT
* *
405521 ATATTATATTTTATATAAATAA
1 ATATGATA-TTTATAAAAATAA
405543 ATATGATATTTATAAAAAT
1 ATATGATATTTATAAAAAT
405562 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATGATATTTATAAAAATAA
Found at i:405939 original size:2 final size:2
Alignment explanation
Indices: 405932--405957 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
405922 TATGTTTGTA
405932 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
405958 TGTCCATAAA
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):
AT
Found at i:408396 original size:3 final size:3
Alignment explanation
Indices: 408388--408415 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
408378 TGTTGGACCA
408388 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
408416 TGGAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:411694 original size:24 final size:24
Alignment explanation
Indices: 411663--411711 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
411653 GATACACAAT
411663 ATCATCAAAAATATTA-ACATTATC
1 ATCATCAAAAATATTAGAC-TTATC
* *
411687 ATCATCAACATTATTAGACTTATC
1 ATCATCAAAAATATTAGACTTATC
411711 A
1 A
411712 ATTGTAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (24 bp):
ATCATCAAAAATATTAGACTTATC
Found at i:413336 original size:24 final size:25
Alignment explanation
Indices: 413273--413346 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 25
413263 TTCGAGATAT
*
413273 TTCTACGTGGTCA-TTCGGGACAAA
1 TTCTACGTGGTCACTTTGGGACAAA
*
413297 TTCTACGCGGTC-CTTTGGGACAAA
1 TTCTACGTGGTCACTTTGGGACAAA
413321 TTCTACGTGG-CACTTTGGTG-CAAA
1 TTCTACGTGGTCACTTTGG-GACAAA
413345 TT
1 TT
413347 ATATGAGCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.02
24 42 0.95
25 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (25 bp):
TTCTACGTGGTCACTTTGGGACAAA
Found at i:414558 original size:23 final size:23
Alignment explanation
Indices: 414509--414577 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
414499 CACCACAACT
*
414509 CGTATAAATGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
414532 CGTATAATTGCACCGAAGTGTCG
1 CGTATAATTGCACCGAAGTGCCA
* * *
414555 CGTAGAATTGTACCGTAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
414578 TATAAGATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:415293 original size:63 final size:64
Alignment explanation
Indices: 415200--415361 Score: 150
Period size: 63 Copynumber: 2.5 Consensus size: 64
415190 ATCCCTTGAC
* * * * *
415200 GGGTGCATCGATGGACTA-TCTATGCTTCGATACA-TAAATCATATTCGATGTTTGTA-TTTAAG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAA
415262 G
64 G
* * * ** *
415263 GGGTGCAGCGATGCACTACTTGTGCATCGATGCACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
** * *
415327 TAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
415362 CTTGAATAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
63 42 0.53
64 37 0.47
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
Found at i:417960 original size:136 final size:130
Alignment explanation
Indices: 417699--417945 Score: 293
Period size: 136 Copynumber: 1.8 Consensus size: 130
417689 TATTAATCGC
* *
417699 GTGATATGGAGCATTATTTTGCTCCTCTCATGCATGACCTACATGATTTGCACGTTATAAAAGTA
1 GTGATATAGAGCATTATTTTCCTCCTCTCATGCATGACCTACATGATTTGCAC-TTATAAAAGTA
* ** *
417764 GCAAATGGATGAATTATTACAGCAGTTACTTTAGAGTTTATGGGGTCAATTTAGCATTATAGTAG
65 GCAAATAGATGAATTATTACAGCAACTAATTTAGAGTTTATGGGGTCAATTTAGCATTATAGTAG
417829 T
130 T
* *
417830 GTGATATAGAGCATTA-TTTCCTCCTCTCATGCATGCATGCCTACATGATTTGCA-TTTTAATAG
1 GTGATATAGAGCATTATTTTCCTCCTCTCATGCATG-A--CCTACATGATTTGCACTTATAAAAG
* *
417893 TAGCATTGAAAATAGATGAATTATTGTC-GCAACTAATTTAGGGTTTATGGGGT
63 TAGC-----AAATAGATGAATTATT-ACAGCAACTAATTTAGAGTTTATGGGGT
417946 TAGTTTAGGG
Statistics
Matches: 97, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
130 18 0.19
131 27 0.28
133 15 0.15
136 36 0.37
137 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (130 bp):
GTGATATAGAGCATTATTTTCCTCCTCTCATGCATGACCTACATGATTTGCACTTATAAAAGTAG
CAAATAGATGAATTATTACAGCAACTAATTTAGAGTTTATGGGGTCAATTTAGCATTATAGTAGT
Found at i:418106 original size:28 final size:30
Alignment explanation
Indices: 418073--418135 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
418063 TAGTTTAAAT
418073 TATTAGTTGGTTAGTTTAAG-T-TATATTA
1 TATTAGTTGGTTAGTTTAAGTTATATATTA
*
418101 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTGGTTAGTTTAAGTTATATATTA
418131 TATTA
1 TATTA
418136 TATGAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (30 bp):
TATTAGTTGGTTAGTTTAAGTTATATATTA
Found at i:421021 original size:22 final size:21
Alignment explanation
Indices: 420983--421040 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
420973 AAAGATTTAT
420983 TATTAATATTTAATGATTTGA
1 TATTAATATTTAATGATTTGA
*
421004 TATTAATGATTTATTGATTTGA
1 TATTAAT-ATTTAATGATTTGA
*
421026 TACTAATAATTTAAT
1 TATTAAT-ATTTAAT
421041 AACGATTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TATTAATATTTAATGATTTGA
Found at i:421061 original size:24 final size:22
Alignment explanation
Indices: 421029--421079 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
421019 GATTTGATAC
*
421029 TAATAATTTAATAACGATTACTAA
1 TAATTATTTAATAACGATTA--AA
*
421053 TAATTATTTAATAATGATTAAA
1 TAATTATTTAATAACGATTAAA
421075 TAATT
1 TAATT
421080 TAATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TAATTATTTAATAACGATTAAA
Found at i:422288 original size:20 final size:21
Alignment explanation
Indices: 422251--422289 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
422241 ACATAAGTTG
422251 ATTTAAATCAAATAATAATTA
1 ATTTAAATCAAATAATAATTA
*
422272 ATTTAAAT-AATTAATAAT
1 ATTTAAATCAAATAATAAT
422290 AACATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAATCAAATAATAATTA
Found at i:422906 original size:80 final size:80
Alignment explanation
Indices: 422773--422932 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
422763 CAACTGCAAT
422773 ATATATGCCCGTGTTGCATTTAAATTTCTTGCTCCGTATACTTGCTTGGAGCTGAAATTGATTCT
1 ATATATGCCCGTGTTGCATTTAAATTTCTTGCTCCGTATACTTGCTTGGAGCTGAAATTGATTCT
422838 TCAACCATGATAACC
66 TCAACCATGATAACC
422853 ATATATGCCCGTGTTGCATTTATAA-TTCTTGCTCCGTATACTTGCTTGGAGCTGAAATTGATTC
1 ATATATGCCCGTGTTGCATTTA-AATTTCTTGCTCCGTATACTTGCTTGGAGCTGAAATTGATTC
422917 TTCAACCATGATAACC
65 TTCAACCATGATAACC
422933 TCACGCCACC
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
80 77 0.97
81 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (80 bp):
ATATATGCCCGTGTTGCATTTAAATTTCTTGCTCCGTATACTTGCTTGGAGCTGAAATTGATTCT
TCAACCATGATAACC
Found at i:429808 original size:23 final size:21
Alignment explanation
Indices: 429756--429818 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 21
429746 TTTTGGTGTA
*
429756 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
429776 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
429797 GAAGGGGAACCGATTCCCCCCT
1 G-A-GGGAACCGATTCCCCCCT
429819 AGGGTTCTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.27
21 9 0.24
22 1 0.03
23 17 0.46
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:432391 original size:22 final size:23
Alignment explanation
Indices: 432366--432409 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
432356 AATTAAGTTT
432366 TAATCTTA-AAACAATTTCGAAA
1 TAATCTTACAAACAATTTCGAAA
* **
432388 TAATTTTACAAAGTATTTCGAA
1 TAATCTTACAAACAATTTCGAA
432410 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCGAAA
Found at i:433558 original size:17 final size:18
Alignment explanation
Indices: 433524--433591 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 18
433514 TTCTTCCTTT
*
433524 CTTT-TTCCTTTCCATCAC
1 CTTTCTTCC-TTCCTTCAC
433542 CTTTCTT-CTTCCTTCAC
1 CTTTCTTCCTTCCTTCAC
433559 CTTTCTTTCTCCTTCCTTCAC
1 CTTTC--T-TCCTTCCTTCAC
*
433580 CTTTCTTGCTTC
1 CTTTCTTCCTTC
433592 TTCTTACAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 13 0.30
18 10 0.23
19 4 0.09
20 1 0.02
21 15 0.35
ACGTcount: A:0.06, C:0.40, G:0.01, T:0.53
Consensus pattern (18 bp):
CTTTCTTCCTTCCTTCAC
Found at i:433568 original size:21 final size:21
Alignment explanation
Indices: 433542--433594 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
433532 TTTCCATCAC
433542 CTTTCTTCTTCCTTCACCTTT
1 CTTTCTTCTTCCTTCACCTTT
*
433563 CTTTCTCCTTCCTTCACCTTT
1 CTTTCTTCTTCCTTCACCTTT
*
433584 CTTGCTTCTTC
1 CTTTCTTCTTC
433595 TTACAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.40, G:0.02, T:0.55
Consensus pattern (21 bp):
CTTTCTTCTTCCTTCACCTTT
Found at i:435441 original size:13 final size:13
Alignment explanation
Indices: 435419--435483 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
435409 GAACACAAAT
435419 GAACAAAATAAAC
1 GAACAAAATAAAC
* *
435432 GAACACAATAAAT
1 GAACAAAATAAAC
*
435445 GAACATAAACGTAAAT
1 GAACA-AAA--TAAAC
*
435461 GAACAAAACAAAC
1 GAACAAAATAAAC
435474 GAACATAAAT
1 GAACA-AAAT
435484 GAACATAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
13 24 0.57
14 5 0.12
15 3 0.07
16 10 0.24
ACGTcount: A:0.63, C:0.15, G:0.09, T:0.12
Consensus pattern (13 bp):
GAACAAAATAAAC
Found at i:435462 original size:42 final size:38
Alignment explanation
Indices: 435415--435497 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 38
435405 AAACGAACAC
*
435415 AAATGAACAAAATAAACGAACACAATAAATGAACATAAACGT
1 AAATGAACAAAACAAACG-A-AC-ATAAATGAACATAAAC-T
435457 AAATGAACAAAACAAACGAACATAAATGAACATAAACT
1 AAATGAACAAAACAAACGAACATAAATGAACATAAACT
435495 AAA
1 AAA
435498 ACAACAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 4 0.10
39 16 0.40
40 2 0.05
41 1 0.03
42 17 0.43
ACGTcount: A:0.64, C:0.14, G:0.08, T:0.13
Consensus pattern (38 bp):
AAATGAACAAAACAAACGAACATAAATGAACATAAACT
Found at i:435465 original size:29 final size:27
Alignment explanation
Indices: 435413--435483 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
435403 GTAAACGAAC
*
435413 ACAAATGAACA-AAATAAACGAACACA
1 ACAAATGAACATAAATAAACGAACAAA
* *
435439 ATAAATGAACATAAACGTAAATGAACAAA
1 ACAAATGAACATAAA--TAAACGAACAAA
*
435468 ACAAACGAACATAAAT
1 ACAAATGAACATAAAT
435484 GAACATAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 10 0.27
27 4 0.11
29 23 0.62
ACGTcount: A:0.63, C:0.15, G:0.08, T:0.13
Consensus pattern (27 bp):
ACAAATGAACATAAATAAACGAACAAA
Found at i:436890 original size:2 final size:2
Alignment explanation
Indices: 436883--436910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
436873 ACATATCCTA
436883 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
436911 CTACTTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446999 original size:9 final size:9
Alignment explanation
Indices: 446987--447030 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
446977 TCCATTGCCT
446987 CCACCTCCA
1 CCACCTCCA
*
446996 CCACCTCCT
1 CCACCTCCA
447005 CCACCGCTTCCA
1 CCA-C-C-TCCA
447017 CCACCTCCA
1 CCACCTCCA
447026 CCACC
1 CCACC
447031 GCTTCCAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 20 0.67
10 2 0.07
11 2 0.07
12 6 0.20
ACGTcount: A:0.18, C:0.66, G:0.02, T:0.14
Consensus pattern (9 bp):
CCACCTCCA
Found at i:447018 original size:21 final size:21
Alignment explanation
Indices: 446992--447037 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
446982 TGCCTCCACC
*
446992 TCCACCACCTCCTCCACCGCT
1 TCCACCACCTCCACCACCGCT
447013 TCCACCACCTCCACCACCGCT
1 TCCACCACCTCCACCACCGCT
447034 TCCA
1 TCCA
447038 GACCCGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.61, G:0.04, T:0.17
Consensus pattern (21 bp):
TCCACCACCTCCACCACCGCT
Found at i:447053 original size:12 final size:12
Alignment explanation
Indices: 447034--447067 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
447024 CACCACCGCT
*
447034 TCCAGACCCGTA
1 TCCAGACCCATA
*
447046 TCCGGACCCATA
1 TCCAGACCCATA
447058 TCCAGACCCA
1 TCCAGACCCA
447068 GACCCACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.15
Consensus pattern (12 bp):
TCCAGACCCATA
Found at i:447486 original size:20 final size:20
Alignment explanation
Indices: 447461--447511 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
447451 CACGGAATGT
*
447461 AAGATTACTAGT-GAAAATAA
1 AAGATTACCAGTAG-AAATAA
*
447481 AAGATTACCAGTAGGAATAA
1 AAGATTACCAGTAGAAATAA
447501 AAGATTACCAG
1 AAGATTACCAG
447512 GGAATATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTAGAAATAA
Found at i:447517 original size:18 final size:19
Alignment explanation
Indices: 447476--447517 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
447466 TACTAGTGAA
447476 AATAAAAGATTACCAGTAGG
1 AATAAAAGATTACCAG-AGG
447496 AATAAAAGATTACCAG-GG
1 AATAAAAGATTACCAGAGG
447514 AATA
1 AATA
447518 TGATTACTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (19 bp):
AATAAAAGATTACCAGAGG
Found at i:456288 original size:108 final size:107
Alignment explanation
Indices: 455872--456587 Score: 512
Period size: 108 Copynumber: 6.7 Consensus size: 107
455862 TGGTAAGCGA
* * * ** * *
455872 TTTGATAAATTTAGTGTGAATTTTATTGTTTCATTTTTAATTTTTATT-TGAAATATAAATTAAA
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTT-GTTTTTATTGT-AAATATAAATT-AT
* * * * *
455936 TAGATTAATTATTTTGA-TTTACATATTAAA-CTGTATTCGACTGG
63 TAGACTATTTATTTTGATTTTACATATTAAATC-GTATTTGAGTAG
* ** * ** *
455980 TTTGGTAAGTTTAAATTAAATTTT-TTGTGTAATTTTTATTTTTAATTTAGTTTAAAT-TATAAT
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTT-A-TT-G--TAAATATA-AAT
* * * * * *
456043 TATTATAGTATTTATTTTGATTTTACATATTAAGTTGTATTAGAGTAAAA
60 TATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGT--AG
* * * ** * * *
456093 CTTGGTAAGTTTAGTTTAAATTATATT-TTTAT-TTTTT-TGCTGA--G-CAATATAAATTATTG
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTT-TGTTTTTGTTTTTATTGTAAATATAAATTATTA
* * * *
456152 GACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGG
65 GACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAG
456195 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATTAATTA
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATT-ATTA
* * * *
456260 GACTATTTATTTTGATTTTACAAATTAAATTGTATTCGAGTGG
65 GACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAG
* * *** * * *
456303 TTTGATAATTTTAATTTTTGTATTATT-TTTAGTATAGTTT-TTTTCAATT-TAAAT-TATAATT
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGT-T--TTTGTTTT-TATTGTAAATATA-AATT
* * *
456364 ATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAG
61 ATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAG
* * * *
456411 TTTGGTAAGTTTAGTTTAAATTATA-TG--TT-TATTTG--TTTATTG-AGTAATATAATTTATT
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTA--AATATAAATTATT
*
456469 AGACTA---ATTTT-ATTTTACATATTAAATCATATTTGAGTAG
64 AGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAG
* *
456509 TTTGATAAGTTTAATTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGTAAATATAAATAAATT
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTG-TTTTTGTTTTTATTGTAAATATAAAT-TATT
456574 AGACTATTTATTTT
64 AGACTATTTATTTT
456588 TGATATAAGA
Statistics
Matches: 477, Mismatches: 87, Indels: 88
0.73 0.13 0.13
Matches are distributed among these distances:
98 48 0.10
99 7 0.01
100 4 0.01
101 4 0.01
102 42 0.09
103 15 0.03
104 54 0.11
105 19 0.04
106 9 0.02
107 29 0.06
108 149 0.31
109 13 0.03
110 23 0.05
111 29 0.06
112 3 0.01
113 27 0.06
114 2 0.00
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (107 bp):
TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATTATTAG
ACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAG
Found at i:456536 original size:314 final size:317
Alignment explanation
Indices: 455872--456587 Score: 921
Period size: 323 Copynumber: 2.2 Consensus size: 317
455862 TGGTAAGCGA
* * * ** * *
455872 TTTGATAAATTTAGTGTGAATTTTATTGTTTCATTTTTAATTTTTATT-TGAAATATAAATTAAA
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTT-GTTTTTATTGT-AAATATAAATTAAT
* * * *
455936 TAGATTAATTATTTTGATTTACATATTAAACTGTATTCGACTGGTTTGGTAAGTTTAAATTAAAT
64 TAGACTATTTATTTTGATTTACAAATTAAACTGTATTCGACTGGTTTGATAAG-TT--ATTAAAT
* * * **
456001 TTTTTGTGTAATTTTTATTTTTAATTTAGTTTAAATTATAATTATTATAGTATTTATTTTGATTT
126 TTTTTGTATAATTTTTATTTTTAATTTAATTTAAATTATAATTATTAGACAATTTATTTTGATTT
* *
456066 TACATATTAAGTTGTATTAGAGTAAAACTTGGTAAGTTTAGTTTAAATTATATTTTTATTTTTTT
191 TACATATTAAGTTGTATTAGAGT-AAACTTGGTAAGTTTAGTTTAAATTATATGTTTATTTGTTT
* * * *
456131 GCTGAGCAATATAAATTATTGGACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGG
255 ACTGAGCAATATAAATTATTAGACTAA-TATTTTTATTTTACAGATTAAATCATATTTGAGTAG
456195 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATTAATTA
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATTAATTA
* *
456260 GACTATTTATTTTGATTTTACAAATTAAATTGTATTCGAGTGGTTTGATAA-TT-TT-AA-TTTT
66 GACTATTTATTTTGA-TTTACAAATTAAACTGTATTCGACTGGTTTGATAAGTTATTAAATTTTT
* *
456321 TGTATTATTTTTAGTATAGTTT-TTTTCAATTTAAATTATAATTATTAGACAATTTATTTTGATT
130 TGTATAATTTTTA-T-T--TTTAATTT-AATTTAAATTATAATTATTAGACAATTTATTTTGATT
* **
456385 TTACATATTAAGTTGTATTTGAGT-AGTTTGGTAAGTTTAGTTTAAATTATATGTTTATTTGTTT
190 TTACATATTAAGTTGTATTAGAGTAAACTTGGTAAGTTTAGTTTAAATTATATGTTTATTTGTTT
* * * *
456449 ATTGAGTAATATAATTTATTAGACT-A-A-TTTTATTTTACATATTAAATCATATTTGAGTAG
255 ACTGAGCAATATAAATTATTAGACTAATATTTTTATTTTACAGATTAAATCATATTTGAGTAG
* *
456509 TTTGATAAGTTTAATTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGTAAATATAAATAAATT
1 TTTGATAAGTTTAGTTTAAATTTTATTGTTTTG-TTTTTGTTTTTATTGTAAATATAAATTAATT
456574 AGACTATTTATTTT
65 AGACTATTTATTTT
456588 TGATATAAGA
Statistics
Matches: 350, Mismatches: 35, Indels: 24
0.86 0.09 0.06
Matches are distributed among these distances:
314 62 0.18
315 45 0.13
316 15 0.04
317 4 0.01
318 59 0.17
319 3 0.01
320 59 0.17
321 2 0.01
322 36 0.10
323 65 0.19
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (317 bp):
TTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTGTTTTTATTGTAAATATAAATTAATTA
GACTATTTATTTTGATTTACAAATTAAACTGTATTCGACTGGTTTGATAAGTTATTAAATTTTTT
GTATAATTTTTATTTTTAATTTAATTTAAATTATAATTATTAGACAATTTATTTTGATTTTACAT
ATTAAGTTGTATTAGAGTAAACTTGGTAAGTTTAGTTTAAATTATATGTTTATTTGTTTACTGAG
CAATATAAATTATTAGACTAATATTTTTATTTTACAGATTAAATCATATTTGAGTAG
Found at i:461617 original size:16 final size:16
Alignment explanation
Indices: 461596--461634 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
461586 AATTTTTGAC
461596 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
461612 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
461628 ACTATTA
1 A-TATTA
461635 CTATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:461650 original size:17 final size:17
Alignment explanation
Indices: 461630--461664 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
461620 TTAAAGTTAC
*
461630 TATTACTATTATTATTA
1 TATTACTAATATTATTA
*
461647 TATTATTAATATTATTA
1 TATTACTAATATTATTA
461664 T
1 T
461665 TAAAATTAAA
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:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTACTAATATTATTA
Found at i:461748 original size:46 final size:46
Alignment explanation
Indices: 461681--461806 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
461671 TAAAATAATT
*
461681 ATTTTTAACATTTTTTCTAGAAATACTAAATCAATATTATTTTAAC
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
* * * *
461727 ATTTTTAAAAATTTTACTAGAAAAACTAAATCAATATTATTTTAAT
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
*
461773 AATTTTAACATTTTTACTAGAAATACTAAATCAA
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAA
461807 ATTTTGATCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (46 bp):
ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
Found at i:461982 original size:16 final size:17
Alignment explanation
Indices: 461951--461982 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
461941 ATAACTACTT
461951 ATGATTAAATTATAATA
1 ATGATTAAATTATAATA
461968 ATGATTAAA-TATAAT
1 ATGATTAAATTATAAT
461983 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGATTAAATTATAATA
Found at i:465655 original size:17 final size:17
Alignment explanation
Indices: 465627--465659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
465617 TTGAGTATTT
465627 ATATTGTAGTTTAGAATC
1 ATATTGTAGTTT-GAATC
465645 ATATT-TAGTTTGAAT
1 ATATTGTAGTTTGAAT
465660 TTGAATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATTGTAGTTTGAATC
Found at i:473222 original size:9 final size:9
Alignment explanation
Indices: 473204--473233 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
473194 TATTTTTTTT
473204 AAAAAA-AC
1 AAAAAAGAC
473212 AAAAAAGAC
1 AAAAAAGAC
473221 AAAAAAGAC
1 AAAAAAGAC
473230 AAAA
1 AAAA
473234 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAGAC
Found at i:475851 original size:9 final size:9
Alignment explanation
Indices: 475837--475863 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
475827 TAATAACTCG
475837 GATATTTCT
1 GATATTTCT
475846 GATATTTCT
1 GATATTTCT
475855 GATATTTCT
1 GATATTTCT
475864 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:478305 original size:20 final size:20
Alignment explanation
Indices: 478282--478333 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
478272 AACGCGATCC
478282 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
478302 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
478322 CCAAAATCGCAA
1 CCAGAATCGCAA
478334 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:478350 original size:21 final size:20
Alignment explanation
Indices: 478323--478422 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
478313 AATCAGTTTC
478323 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
478344 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
478365 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
478385 CCAAAATCGCAACGCGAATATG
1 -CAAAATCGCAACGCG-ATTTT
*
478407 AAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
478423 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
20 2 0.03
21 54 0.92
22 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:478423 original size:21 final size:20
Alignment explanation
Indices: 478387--478441 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
478377 GCGATTTTCC
* *
478387 AAAATCGCAACGCGAATATGA
1 AAAATCGCAACGCGAACA-CA
478408 AAAATCGCAACGCGAACACA
1 AAAATCGCAACGCGAACACA
*
478428 TAAATCGCAACGCG
1 AAAATCGCAACGCG
478442 TATCCGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAACACA
Found at i:478434 original size:20 final size:20
Alignment explanation
Indices: 478409--478582 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
478399 CGAATATGAA
* *
478409 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
478429 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
478449 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
478469 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
478489 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
478509 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
478529 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
478549 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
478570 AAATCGCAACGCG
1 AAATCGCAACGCG
478583 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:478479 original size:60 final size:60
Alignment explanation
Indices: 478409--478582 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
478399 CGAATATGAA
* *
478409 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
478469 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
478529 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
478583 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:479003 original size:33 final size:33
Alignment explanation
Indices: 478964--479034 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
478954 TTCACTTAGA
*
478964 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
478997 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
479030 TTTCA
1 TTTCA
479035 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:479173 original size:14 final size:14
Alignment explanation
Indices: 479154--479208 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
479144 AGAATGACTG
479154 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
479168 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
479187 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
479201 TCGCAACG
1 TCGCAACG
479209 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:479221 original size:33 final size:33
Alignment explanation
Indices: 479154--479224 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
479144 AGAATGACTG
***
479154 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
479187 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
479220 TCGCA
1 TCGCA
479225 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:479242 original size:19 final size:19
Alignment explanation
Indices: 479220--479317 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
479210 GAAACCAAAA
*
479220 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
479239 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
479253 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
479272 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
479286 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
479305 TCGCGTTGCGATT
1 TCGCGTTGCGATT
479318 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:479261 original size:14 final size:14
Alignment explanation
Indices: 479242--479331 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
479232 TTTCATTTCG
479242 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
479256 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
479275 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
479289 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
479306 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
479322 CGTTGCGATT
1 CGTTGCGATT
479332 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:479267 original size:33 final size:33
Alignment explanation
Indices: 479225--479339 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
479215 CAAAATCGCA
479225 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
479258 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
479291 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
479324 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
479340 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:481267 original size:185 final size:186
Alignment explanation
Indices: 481037--481418 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
481027 TAGATTGCTT
481037 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481102 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
481167 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
481222 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481287 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
481352 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
481408 AGTAAATTTAT
1 AGTAAATTTAT
481419 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:481351 original size:93 final size:93
Alignment explanation
Indices: 481037--481416 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
481027 TAGATTGCTT
*
481037 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481102 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
481130 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481194 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
481222 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481287 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
481315 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
481380 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
481408 AGTAAATTT
1 AGTAAATTT
481417 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:481500 original size:19 final size:19
Alignment explanation
Indices: 481460--481588 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
481450 TAGTTTACTT
* *
481460 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
481480 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
481499 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
481518 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
481532 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
481551 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
481565 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
481584 TCGCA
1 TCGCA
481589 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:481539 original size:33 final size:32
Alignment explanation
Indices: 481496--481588 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
481486 CGCGAAACCA
**
481496 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
481528 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
481561 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
481589 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:481586 original size:52 final size:52
Alignment explanation
Indices: 481460--481588 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
481450 TAGTTTACTT
**
481460 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
481512 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
481565 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
481589 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:481606 original size:19 final size:19
Alignment explanation
Indices: 481584--481718 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
481574 GAAACCAAAA
*
481584 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
481603 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
481619 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
481636 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
481652 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
481669 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
481688 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
481708 TCGTGTTGCGA
1 TCGCGTTGCGA
481719 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:481625 original size:14 final size:14
Alignment explanation
Indices: 481606--481662 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
481596 TTTCATTTCG
481606 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
481620 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
481637 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
481653 CGTTGCGATT
1 CGTTGCGATT
481663 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Done.