Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015154.1 Kokia drynarioides strain JFW-HI SEQ_130198, 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: 822009
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 133 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:387783 original size:21 final size:21
Alignment explanation
Indices: 387755--387807 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
387745 TTCTTTAGGA
387755 TCTTCTTCTTCCTCAGGATCCT
1 TCTTCTTCTTCCTCAGGAT-CT
** *
387777 T-TTCTTCTTATTCAGGGTCT
1 TCTTCTTCTTCCTCAGGATCT
387797 TCTTCTTCTTC
1 TCTTCTTCTTC
387808 TTCTTCTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 22 0.85
22 1 0.04
ACGTcount: A:0.08, C:0.30, G:0.09, T:0.53
Consensus pattern (21 bp):
TCTTCTTCTTCCTCAGGATCT
Found at i:388709 original size:26 final size:24
Alignment explanation
Indices: 388680--388740 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
388670 ATTTAATTAG
*
388680 TTAAAATATTAACAAGTTAAAATAAA
1 TTAAAA-ATTAACAAATT-AAATAAA
* *
388706 TTAAAGAGTTAATAAATTAAATAAA
1 TTAAA-AATTAACAAATTAAATAAA
388731 TTAAAAATTA
1 TTAAAAATTA
388741 GAAGCTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 4 0.13
25 12 0.40
26 13 0.43
27 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (24 bp):
TTAAAAATTAACAAATTAAATAAA
Found at i:395262 original size:12 final size:12
Alignment explanation
Indices: 395245--395269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
395235 TACATGAACA
395245 TGCCCAGAATTG
1 TGCCCAGAATTG
395257 TGCCCAGAATTG
1 TGCCCAGAATTG
395269 T
1 T
395270 TGGCGCATCT
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TGCCCAGAATTG
Found at i:396071 original size:16 final size:16
Alignment explanation
Indices: 396050--396080 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
396040 TTGTGGATCC
396050 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
396066 CATTTTATCTTTATT
1 CATTTTACCTTTATT
396081 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:398904 original size:3 final size:3
Alignment explanation
Indices: 398898--398926 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
398888 ATTATTATTA
398898 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
398927 ATTTAATTAA
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:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:400238 original size:18 final size:18
Alignment explanation
Indices: 400196--400238 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
400186 CCAGCTTCGG
*
400196 TGGTGGAGTCGCCGCATA
1 TGGTGGCGTCGCCGCATA
400214 TGGTGGCGTCGCCGCATA
1 TGGTGGCGTCGCCGCATA
400232 TGGTGGC
1 TGGTGGC
400239 CGAAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (18 bp):
TGGTGGCGTCGCCGCATA
Found at i:400524 original size:22 final size:21
Alignment explanation
Indices: 400486--400534 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
400476 TTTGAAATAG
*
400486 TTAAAAAATCAAAATTTT-GT
1 TTAAAAAATCAAAATTTTCCT
*
400506 TTAAAAAATTTAAACATTTTCCT
1 TTAAAAAA-TCAAA-ATTTTCCT
400529 TTAAAA
1 TTAAAA
400535 TGACTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
22 5 0.21
23 7 0.29
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAAAATCAAAATTTTCCT
Found at i:401605 original size:75 final size:75
Alignment explanation
Indices: 401512--401670 Score: 239
Period size: 75 Copynumber: 2.1 Consensus size: 75
401502 CATATTAAAA
* * * * *
401512 AAAAGAAAATTAGGATTATTCCCTTATTAATAGAGAAGGCAAATAGAAAGTTTGAAAAATGAATT
1 AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
401577 ATATTCTTTCC
66 ATATT-TTTCC
* *
401588 AAAAGAATA-TAGGATTATTCTCTAATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATT
1 AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
401652 ATATTTTTCC
66 ATATTTTTCC
401662 AAAAGAATA
1 AAAAGAATA
401671 ATAATTTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
74 14 0.18
75 54 0.71
76 8 0.11
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (75 bp):
AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
ATATTTTTCC
Found at i:401678 original size:19 final size:20
Alignment explanation
Indices: 401642--401679 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
401632 GAAAGTTAGA
* *
401642 AAAAGGAATTATATTTTTCC
1 AAAAGGAATAATAATTTTCC
401662 AAAA-GAATAATAATTTTC
1 AAAAGGAATAATAATTTTC
401680 ATATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (20 bp):
AAAAGGAATAATAATTTTCC
Found at i:401835 original size:139 final size:137
Alignment explanation
Indices: 401648--401915 Score: 392
Period size: 139 Copynumber: 1.9 Consensus size: 137
401638 TAGAAAAAGG
* *
401648 AATTATATTTTTCCAAAAGAATAATAATTTTCATATATTTTATATTTTGACTGAAATTAATTAAT
1 AATTATATTTTTCAAAAAGAATAATAATTTTCATATATTTTATATTTTGACCGAAATTAATTAAT
* * * *
401713 ATAATTATTTATATTAATAAATTCAGAAAAATATATACAATCAATATTTTGTATGGAATCAAATT
66 AAAATTATTTATAGTAATAAATTCAGAAAAATATATACAATCAATATTTTGAAT-AAATCAAATT
401778 CATATATC
130 CATATATC
* * * *
401786 AATTATATTCTTTCAAAAAGAATATTAATTTTCATGTCTTTTATGTTTTGACCGAAATTAATTAA
1 AATTATATT-TTTCAAAAAGAATAATAATTTTCATATATTTTATATTTTGACCGAAATTAATTAA
* * * *
401851 TAAAATTGTTTATAGTAATAAATTCGGTAAAATATATACAATTAATATTTTGAATAAATCAAATT
65 TAAAATTATTTATAGTAATAAATTCAGAAAAATATATACAATCAATATTTTGAATAAATCAAATT
401916 ATGTTCCCTA
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 18 0.16
139 97 0.84
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (137 bp):
AATTATATTTTTCAAAAAGAATAATAATTTTCATATATTTTATATTTTGACCGAAATTAATTAAT
AAAATTATTTATAGTAATAAATTCAGAAAAATATATACAATCAATATTTTGAATAAATCAAATTC
ATATATC
Found at i:405460 original size:5 final size:5
Alignment explanation
Indices: 405450--405505 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
405440 TTCTGTTTGG
* * *
405450 AAGAA AAGAA AAGAA ACA-AA AAGAA AA-AA ATGAA AAGGA ACGAA AAGAA
1 AAGAA AAGAA AAGAA A-AGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
405499 AAGAA AA
1 AAGAA AA
405506 TATATGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 4 0.10
5 37 0.88
6 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:405484 original size:24 final size:23
Alignment explanation
Indices: 405453--405500 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
405443 TGTTTGGAAG
405453 AAAAGAAAAGAAACAAAAAGAAA
1 AAAAGAAAAGAAACAAAAAGAAA
* *
405476 AAAATGAAAAGGAACGAAAAGAAA
1 AAAA-GAAAAGAAACAAAAAGAAA
405500 A
1 A
405501 GAAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAGAAACAAAAAGAAA
Found at i:410423 original size:17 final size:17
Alignment explanation
Indices: 410377--410434 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
410367 ATATATATGG
**
410377 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* **
410394 AGATGCAGCGACAATAA
1 AAATGCAATGACAATAA
*
410411 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
410428 TAATGCA
1 AAATGCA
410435 CGAACAATTA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:410434 original size:34 final size:34
Alignment explanation
Indices: 410377--410442 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
410367 ATATATATGG
*
410377 AAATGCAATGACAATGTAGATGCAGCG-ACAATAA
1 AAATGCAATGACAATATAGATGCA-CGAACAATAA
*
410411 AAATGCAATGACATTAATA-ATGCACGAACAAT
1 AAATGCAATGACAAT-ATAGATGCACGAACAAT
410443 TATACTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.07
34 24 0.86
35 2 0.07
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCACGAACAATAA
Found at i:420486 original size:29 final size:29
Alignment explanation
Indices: 420444--420507 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
420434 ATTTGGTCGT
420444 CCATGGAAATATGATAGAGATGTGCAACA
1 CCATGGAAATATGATAGAGATGTGCAACA
420473 CCATGGAAATATGATAGAGATGTGCAACA
1 CCATGGAAATATGATAGAGATGTGCAACA
420502 CCATGG
1 CCATGG
420508 CAAGCTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (29 bp):
CCATGGAAATATGATAGAGATGTGCAACA
Found at i:428453 original size:30 final size:30
Alignment explanation
Indices: 428419--428513 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
428409 CAACTTAACA
*
428419 AACAAATATCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
*
428449 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
428479 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
428509 AACAA
1 AACAA
428514 TGAAATAAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:429734 original size:138 final size:138
Alignment explanation
Indices: 429486--429760 Score: 444
Period size: 138 Copynumber: 2.0 Consensus size: 138
429476 TAGAAAAGGA
* *
429486 ATTATATTCTTTCCAAAAGAATATTAATTTCCGTGCCTTTCACATTTTAACCGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTCACATTTTAACCAAAATTAATTAAT
*
429551 ATAACTGTTTATATTAATAAATTCAGTAAAATATTTACAAATAATATTTTGTATGAATAAAATTC
66 ATAACTGTTTATATTAATAAATTCAGTAAAATATATACAAATAATATTTTGTATGAATAAAATTC
429616 ATATATTG
131 ATATATTG
* * * *
429624 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATC-TTTTGACTAAAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTCA-CATTTTAACCAAAATTAATTAA
* * *
429688 TATAACTGTTTATATTAATAAATTCAGTAAAATGTATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAAATAATATTTTGTATGAATAAAATT
429753 CATATATT
130 CATATATT
429761 AATTTTACCT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
138 125 0.99
139 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (138 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTCACATTTTAACCAAAATTAATTAAT
ATAACTGTTTATATTAATAAATTCAGTAAAATATATACAAATAATATTTTGTATGAATAAAATTC
ATATATTG
Found at i:431788 original size:17 final size:17
Alignment explanation
Indices: 431746--431778 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
431736 TTAGAGAAGG
*
431746 CATAGGGAGCTTTGTCA
1 CATAGGAAGCTTTGTCA
431763 CATAGGAAGCTTTGTC
1 CATAGGAAGCTTTGTC
431779 GCAGTGGAAG
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:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (17 bp):
CATAGGAAGCTTTGTCA
Found at i:435915 original size:261 final size:262
Alignment explanation
Indices: 435450--435971 Score: 895
Period size: 261 Copynumber: 2.0 Consensus size: 262
435440 CATCGTCTGA
** *
435450 AAAATTTGTAGGGTTGACCCGACATGCTCTTGAAACTTGATTATTAAACCCTTATTTTACTCGAT
1 AAAATTTGTAGGGTTGACCCGACATGCTCCCGAAACTCGATTATTAAACCCTTATTTTACTCGAT
*
435515 TTTAAACCCCAAAACCCTAATATTTCATGCCAGTTATATATACCAAACTAACCTAAACTTATTTT
66 TTTAAACCCCAAAACCCTAATATTTCATGCCAATTATATATACCAAACTAACCTAAACTTATTTT
* * * *
435580 CTAACACTAAACACTTTCAAATCTCTCTCAATTCTTCATCTCTTTTCTCTCTTTAAAGCCTAGAA
131 CTAACACTAAACACTTTCAAAACTCTCTCAATCCTTCATCTCTTTTCTCTCTTAAAAACCTAGAA
435645 CCCCAAAACTCTACCATTCCTC-AAGAAGGCTCCGTTCTATCATTCAATGGCTTGATCTCGTCCT
196 CCCCAAAACTCTACCATTCCTCAAAG-AGGCTCCGTTCTATCATTCAATGGCTTGATCTCGTCCT
435709 CTT
260 CTT
435712 AAAATTTGTAGGGTTGACCCGACATGCTCCCGAAACTCGATTATTAAACCCTTATTTTACTCGAT
1 AAAATTTGTAGGGTTGACCCGACATGCTCCCGAAACTCGATTATTAAACCCTTATTTTACTCGAT
*
435777 TTTAAACCCTAAAA-CCTAATATTTCATGCCAATTATATATACCAAACTAACCTAAACTTATTTT
66 TTTAAACCCCAAAACCCTAATATTTCATGCCAATTATATATACCAAACTAACCTAAACTTATTTT
* *
435841 CTAACACTAAACTCTTTCAAAACTCTCTCAATCCTTTATCTCTTTTCTCTCTTAAAAACCTAGAA
131 CTAACACTAAACACTTTCAAAACTCTCTCAATCCTTCATCTCTTTTCTCTCTTAAAAACCTAGAA
* * *
435906 CCCCAAAACTCTACCATTCCTCAAAGATGCTCTGTTCTATCATTTAATGGCTTGATCTCGTCCTC
196 CCCCAAAACTCTACCATTCCTCAAAGAGGCTCCGTTCTATCATTCAATGGCTTGATCTCGTCCTC
435971 T
261 T
435972 CAACAATGCA
Statistics
Matches: 245, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
261 167 0.68
262 78 0.32
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (262 bp):
AAAATTTGTAGGGTTGACCCGACATGCTCCCGAAACTCGATTATTAAACCCTTATTTTACTCGAT
TTTAAACCCCAAAACCCTAATATTTCATGCCAATTATATATACCAAACTAACCTAAACTTATTTT
CTAACACTAAACACTTTCAAAACTCTCTCAATCCTTCATCTCTTTTCTCTCTTAAAAACCTAGAA
CCCCAAAACTCTACCATTCCTCAAAGAGGCTCCGTTCTATCATTCAATGGCTTGATCTCGTCCTC
TT
Found at i:445203 original size:52 final size:52
Alignment explanation
Indices: 445125--445299 Score: 235
Period size: 52 Copynumber: 3.4 Consensus size: 52
445115 TGTGTCATCT
* * *
445125 TGTGTCATCAAGAGTATACGAATCCTTTACGGATTATGAGATCCGATGACTA
1 TGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTA
* *
445177 TGTGTCATCGTGAGTATATGAATCCTTTAAAGG-TTATGAGGTCCGATGACTA
1 TGTGTCATCATGAGTATATGAATCCTTT-ACGGATTATGAGGTCCGATGACTA
* * ** *
445229 TGTGTCATCATGAGTATTTGAATCCTTTACAGATTATGAGGTTTGATGACAA
1 TGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTA
*
445281 TGTGTCATCATCAGTATAT
1 TGTGTCATCATGAGTATAT
445300 AATTCCCAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
51 2 0.02
52 102 0.95
53 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (52 bp):
TGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTA
Found at i:445227 original size:114 final size:112
Alignment explanation
Indices: 445013--445237 Score: 342
Period size: 114 Copynumber: 2.0 Consensus size: 112
445003 CCGATGACTA
** * *
445013 TGTGTCATCGTGAGTATAAGAATCCCTTACGAATTATGAGGTCCGATGACTGTGTCATTGTGAGT
1 TGTGTCATCAAGAGTATAAGAATCCCTTACGAATTATGAGATCCGATGACTGTGTCATCGTGAGT
* *
445078 ATGTGAATCCTTTACAGATTATGAGGTCCGATGACTATGTGTCATCT
66 ATATGAATCCTTTAAAGATTATGAGGTCCGATGACTATGTGTCATCT
* * *
445125 TGTGTCATCAAGAGTATACGAATCCTTTACGGATTATGAGATCCGATGACTATGTGTCATCGTGA
1 TGTGTCATCAAGAGTATAAGAATCCCTTACGAATTATGAGATCCGATGAC--TGTGTCATCGTGA
*
445190 GTATATGAATCCTTTAAAGGTTATGAGGTCCGATGACTATGTGTCATC
64 GTATATGAATCCTTTAAAGATTATGAGGTCCGATGACTATGTGTCATC
445238 ATGAGTATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 44 0.44
114 57 0.56
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (112 bp):
TGTGTCATCAAGAGTATAAGAATCCCTTACGAATTATGAGATCCGATGACTGTGTCATCGTGAGT
ATATGAATCCTTTAAAGATTATGAGGTCCGATGACTATGTGTCATCT
Found at i:445323 original size:104 final size:103
Alignment explanation
Indices: 445125--445341 Score: 233
Period size: 104 Copynumber: 2.1 Consensus size: 103
445115 TGTGTCATCT
* * * *
445125 TGTGTCATCAAGAGTATACGAATCCTTTACGGATTATGAGATCCGATGACTATGTGTCATCGTGA
1 TGTGTCATCAAGAGTATACGAATCCTTTACAGATTATGAGATCCGATGACAATGTGTCATCATCA
* *
445190 GTATATGAATCCTTTAAAGGTTATGAGGTCCGATGACTA
66 GTATATGAATCC-TCAAAGGTTATAAGGTCCGATGACTA
* ** * **
445229 TGTGTCATCATGAGTATTTGAATCCTTTACAGATTATGAGGTTTGATGACAATGTGTCATCATCA
1 TGTGTCATCAAGAGTATACGAATCCTTTACAGATTATGAGATCCGATGACAATGTGTCATCATCA
* *
445294 GTATAT-AATTCC-CAATATGGATTA-AAGGTCTGATGACTC
66 GTATATGAA-TCCTCAA-A-GG-TTATAAGGTCCGATGACTA
*
445333 TATGTCATC
1 TGTGTCATC
445342 GTGAATATAA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
102 2 0.02
103 3 0.03
104 86 0.91
105 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (103 bp):
TGTGTCATCAAGAGTATACGAATCCTTTACAGATTATGAGATCCGATGACAATGTGTCATCATCA
GTATATGAATCCTCAAAGGTTATAAGGTCCGATGACTA
Found at i:446078 original size:21 final size:21
Alignment explanation
Indices: 446035--446086 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
446025 TAGGGGTGAA
* * *
446035 ACTTGTATCGTTAGAAGAGTC
1 ACTTGTATCGATAGAACACTC
*
446056 ACTTGTATCGATAGAACTCTC
1 ACTTGTATCGATAGAACACTC
*
446077 ACATGTATCG
1 ACTTGTATCG
446087 GTAAAAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGATAGAACACTC
Found at i:455673 original size:15 final size:15
Alignment explanation
Indices: 455653--455686 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
455643 GGAACTAAAT
455653 AGGAGAAGGAGGAAG
1 AGGAGAAGGAGGAAG
*
455668 AGGAGAAGGATGAAG
1 AGGAGAAGGAGGAAG
455683 AGGA
1 AGGA
455687 TGTAGATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (15 bp):
AGGAGAAGGAGGAAG
Found at i:464682 original size:52 final size:52
Alignment explanation
Indices: 464594--464781 Score: 238
Period size: 52 Copynumber: 3.6 Consensus size: 52
464584 TAAATGAAAA
* *
464594 AGGTCTGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
464646 AGATCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * ** *
464698 AGGTCCAATGACTATGTGTCATTGTGAGTATAT-AATTCCCAATACGGATTA-A
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAA-T-CCTTTACGGATTATG
*
464750 AGGTCCGAAGACT-TAGTGTCATCGTGAGTATA
1 AGGTCCGATGACTAT-GTGTCATCGTGAGTATA
464782 AAAAATGCAT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
51 3 0.03
52 106 0.89
53 10 0.08
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:464874 original size:19 final size:19
Alignment explanation
Indices: 464847--464888 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
464837 GATTTTACAA
*
464847 CTATTTAAGTTTGTTAAAT
1 CTATATAAGTTTGTTAAAT
464866 CTATATAAGTTTGTTAAAT
1 CTATATAAGTTTGTTAAAT
464885 CTAT
1 CTAT
464889 TTAACTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (19 bp):
CTATATAAGTTTGTTAAAT
Found at i:468908 original size:6 final size:6
Alignment explanation
Indices: 468897--468946 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
468887 AGGCAACCCA
*
468897 ATTTTT ATTTTT ATTTATT -TTATTT ATTTTT ATTTTT AGTTTT AGTTTTT
1 ATTTTT ATTTTT ATTT-TT ATT-TTT ATTTTT ATTTTT ATTTTT A-TTTTT
468947 TTCTTGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 29 0.76
7 9 0.24
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:468915 original size:10 final size:10
Alignment explanation
Indices: 468900--468931 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
468890 CAACCCAATT
468900 TTTATTTTTA
1 TTTATTTTTA
468910 TTTA-TTTTA
1 TTTATTTTTA
468919 TTTATTTTTA
1 TTTATTTTTA
468929 TTT
1 TTT
468932 TTAGTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:468919 original size:15 final size:15
Alignment explanation
Indices: 468899--468932 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
468889 GCAACCCAAT
468899 TTTTATTT-TTATTTA
1 TTTTATTTATT-TTTA
468914 TTTTATTTATTTTTA
1 TTTTATTTATTTTTA
468929 TTTT
1 TTTT
468933 TAGTTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTATTTTTA
Found at i:468940 original size:31 final size:32
Alignment explanation
Indices: 468897--468958 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
468887 AGGCAACCCA
*
468897 ATTTTTATTTTTA-TTTATTTTATT-TATTTTT
1 ATTTTTAGTTTTAGTTT-TTTTATTGTATTTTT
*
468928 ATTTTTAGTTTTAGTTTTTTTCTTGTATTTT
1 ATTTTTAGTTTTAGTTTTTTTATTGTATTTT
468959 AATAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (32 bp):
ATTTTTAGTTTTAGTTTTTTTATTGTATTTTT
Found at i:469492 original size:13 final size:13
Alignment explanation
Indices: 469476--469503 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
469466 CAAAACTTAT
469476 TTTTGACACTTGA
1 TTTTGACACTTGA
469489 TTTTGACACTTGA
1 TTTTGACACTTGA
469502 TT
1 TT
469504 ATTTTTCCTA
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:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTTGACACTTGA
Found at i:470433 original size:11 final size:11
Alignment explanation
Indices: 470419--470451 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
470409 TAGAATATTG
470419 TTTATATTTAT
1 TTTATATTTAT
*
470430 TTTATATTTAA
1 TTTATATTTAT
470441 TTTATATTTAT
1 TTTATATTTAT
470452 CTTCTAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:470469 original size:6 final size:6
Alignment explanation
Indices: 470419--470451 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
470409 TAGAATATTG
470419 TTTATA TTTAT- TTTATA TTTA-A TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
470452 CTTCTAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:475219 original size:37 final size:37
Alignment explanation
Indices: 475169--475242 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
475159 TCATTCTTAT
*
475169 TAAAAATGTGCTTTATGTCAATAGTCTTAAGCATAAC
1 TAAAAATGTGCTTTATGCCAATAGTCTTAAGCATAAC
*
475206 TAAAAATGTGCTTTATGCCAATGGTCTTAAGCATAAC
1 TAAAAATGTGCTTTATGCCAATAGTCTTAAGCATAAC
475243 CTCCTTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (37 bp):
TAAAAATGTGCTTTATGCCAATAGTCTTAAGCATAAC
Found at i:481064 original size:144 final size:144
Alignment explanation
Indices: 480804--481092 Score: 533
Period size: 144 Copynumber: 2.0 Consensus size: 144
480794 GATCATAAGT
* *
480804 CCTTCAAATTATTTTCAAAGTGTTTGACAAATAAACTGTTAAAAAGCCTTGAAATAACTTAGTTT
1 CCTTCAAATTATTTTCAAAGTGTTGGACAAATAAACTGTTAAAAAGCCTTGAAATAACCTAGTTT
*
480869 TTAACACAATTTTTGAAGTCTGGAAGACTTCTACTGATACTTAGTGGAAAAGTATCGGTAGAACG
66 TTAACACAATTTTTGAAGTCTGGAAGACTTCTACCGATACTTAGTGGAAAAGTATCGGTAGAACG
480934 CAAGGTAGAAAAAC
131 CAAGGTAGAAAAAC
480948 CCTTCAAATTATTTTCAAAGTGTTGGACAAATAAACTGTTAAAAAGCCTTGAAATAACCTAGTTT
1 CCTTCAAATTATTTTCAAAGTGTTGGACAAATAAACTGTTAAAAAGCCTTGAAATAACCTAGTTT
* *
481013 TTAACACAATTTTTGAAGTTTGGAAGACTTCTACCGATACTTAGTGGAAAAGTATCGGTATAACG
66 TTAACACAATTTTTGAAGTCTGGAAGACTTCTACCGATACTTAGTGGAAAAGTATCGGTAGAACG
481078 CAAGGTAGAAAAAC
131 CAAGGTAGAAAAAC
481092 C
1 C
481093 TTTGTATATG
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 140 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (144 bp):
CCTTCAAATTATTTTCAAAGTGTTGGACAAATAAACTGTTAAAAAGCCTTGAAATAACCTAGTTT
TTAACACAATTTTTGAAGTCTGGAAGACTTCTACCGATACTTAGTGGAAAAGTATCGGTAGAACG
CAAGGTAGAAAAAC
Found at i:483321 original size:31 final size:31
Alignment explanation
Indices: 483231--483322 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
483221 TAGACATATT
* * *
483231 TGTTATTAGTGGCAGTTTATTTGCAAATAAA
1 TGTTATCAGTGGCAGTTTATATGCAAATCAA
* *
483262 TGTTATCAATGGCAGTTTATATACAAATCAA
1 TGTTATCAGTGGCAGTTTATATGCAAATCAA
*
483293 TGTTATCAGTGGCAGTTTATCTGCAAATCA
1 TGTTATCAGTGGCAGTTTATATGCAAATCA
483323 GTGGTGGCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (31 bp):
TGTTATCAGTGGCAGTTTATATGCAAATCAA
Found at i:484964 original size:37 final size:38
Alignment explanation
Indices: 484784--484966 Score: 178
Period size: 38 Copynumber: 4.9 Consensus size: 38
484774 AAATAAATAT
* *
484784 CCCGATGAACACC-AGCACGATGGCCTACTAGGCATAAAG
1 CCCGAT-AACACCGA-CACGAAGGCCTGCTAGGCATAAAG
*
484823 CCCGATAACACCGACACGAAGGCTTGCTAGGCATAAAG
1 CCCGATAACACCGACACGAAGGCCTGCTAGGCATAAAG
* ** * *
484861 CCCAATAACATAGACACGAAGGCCCGCTAGGCATGAAG
1 CCCGATAACACCGACACGAAGGCCTGCTAGGCATAAAG
* * ** *
484899 -CCGAT-ATACC-AGCACGAAAGCCAACTAGGCATCAAG
1 CCCGATAACACCGA-CACGAAGGCCTGCTAGGCATAAAG
*
484935 CCCGAT-ACACCGACATGAAGGCCTGCTAGGCA
1 CCCGATAACACCGACACGAAGGCCTGCTAGGCA
484967 CATAACTCAA
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
35 1 0.01
36 22 0.19
37 28 0.24
38 60 0.51
39 7 0.06
ACGTcount: A:0.34, C:0.31, G:0.23, T:0.12
Consensus pattern (38 bp):
CCCGATAACACCGACACGAAGGCCTGCTAGGCATAAAG
Found at i:484999 original size:37 final size:37
Alignment explanation
Indices: 484955--485054 Score: 146
Period size: 37 Copynumber: 2.7 Consensus size: 37
484945 CGACATGAAG
*
484955 GCCTGCTAGGCACATAACTCAATTACACTGGCACGAA
1 GCCTGCTAGGCACATAACCCAATTACACTGGCACGAA
* *
484992 GCTTGCTAGGCACATATCCCAATTACACTGGCACGAA
1 GCCTGCTAGGCACATAACCCAATTACACTGGCACGAA
* * *
485029 GCCTGTTAGGCACATACCCCGATTAC
1 GCCTGCTAGGCACATAACCCAATTAC
485055 TTAAATGCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (37 bp):
GCCTGCTAGGCACATAACCCAATTACACTGGCACGAA
Found at i:486868 original size:14 final size:16
Alignment explanation
Indices: 486834--486868 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
486824 TAGAGAATTA
486834 TGAAATCTATAGATAG
1 TGAAATCTATAGATAG
486850 TGAAA-CTATAGAT-G
1 TGAAATCTATAGATAG
486864 TGAAA
1 TGAAA
486869 ACAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 8 0.42
16 5 0.26
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (16 bp):
TGAAATCTATAGATAG
Found at i:486870 original size:15 final size:15
Alignment explanation
Indices: 486815--486870 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
486805 TCTTTAGCAT
*
486815 TGTGAAAACTAGAGAA
1 TGTGAAAACTATAG-A
* *
486831 TTATGAAATCTATAGA
1 -TGTGAAAACTATAGA
486847 TAGTG-AAACTATAGA
1 T-GTGAAAACTATAGA
486862 TGTGAAAAC
1 TGTGAAAAC
486871 AATAAAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 3 0.09
15 15 0.47
16 3 0.09
17 11 0.34
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
TGTGAAAACTATAGA
Found at i:489342 original size:54 final size:54
Alignment explanation
Indices: 489260--489367 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
489250 TGTAAAGTTT
489260 TATAAACCTTTAAGATCCTTAACAGGTGATGGTTACGGATTTTGGGTGTTACAC
1 TATAAACCTTTAAGATCCTTAACAGGTGATGGTTACGGATTTTGGGTGTTACAC
489314 TATAAACCTTTAAGATCCTTAACAGGTGATGGTTACGGATTTTGGGTGTTACAC
1 TATAAACCTTTAAGATCCTTAACAGGTGATGGTTACGGATTTTGGGTGTTACAC
489368 CACATCTCGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (54 bp):
TATAAACCTTTAAGATCCTTAACAGGTGATGGTTACGGATTTTGGGTGTTACAC
Found at i:491090 original size:26 final size:26
Alignment explanation
Indices: 491054--491107 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
491044 GTTTACCTCT
491054 AGAACTTGAGGTTGAATTCGGTATTA
1 AGAACTTGAGGTTGAATTCGGTATTA
491080 AGAACTTGAGGTTGAATTCGGTATTA
1 AGAACTTGAGGTTGAATTCGGTATTA
491106 AG
1 AG
491108 TTGTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.33
Consensus pattern (26 bp):
AGAACTTGAGGTTGAATTCGGTATTA
Found at i:494218 original size:20 final size:21
Alignment explanation
Indices: 494180--494221 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
494170 GCTTAGTGCT
494180 TTGCGAACTATAAGATAATATG
1 TTGCGAACTAT-AGATAATATG
494202 TTGCGAACTAT-GATAATATG
1 TTGCGAACTATAGATAATATG
494222 GCTAATTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TTGCGAACTATAGATAATATG
Found at i:494254 original size:24 final size:24
Alignment explanation
Indices: 494225--494272 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
494215 TAATATGGCT
494225 AATTGCGAGCTCTTGTGAACTATG
1 AATTGCGAGCTCTTGTGAACTATG
* *
494249 AATTGCGAGCTTTTGTGAATTATG
1 AATTGCGAGCTCTTGTGAACTATG
494273 CATTTCGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (24 bp):
AATTGCGAGCTCTTGTGAACTATG
Found at i:499071 original size:17 final size:17
Alignment explanation
Indices: 499049--499088 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
499039 TTTTCTACAT
*
499049 TTTTTTCGACAATTGAA
1 TTTTTTCAACAATTGAA
*
499066 TTTTTTTAACAATTGAA
1 TTTTTTCAACAATTGAA
499083 TTTTTT
1 TTTTTT
499089 TTAACAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTTTTCAACAATTGAA
Found at i:499089 original size:17 final size:17
Alignment explanation
Indices: 499047--499095 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
499037 CTTTTTCTAC
*
499047 ATTTTTTTCGACAATTGA
1 ATTTTTTT-AACAATTGA
499065 ATTTTTTTAACAATTGA
1 ATTTTTTTAACAATTGA
499082 ATTTTTTTTAACAA
1 A-TTTTTTTAACAA
499096 CATACAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTTTTTAACAATTGA
Found at i:502155 original size:37 final size:35
Alignment explanation
Indices: 502106--502176 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
502096 ATTTCAAAAA
502106 TAATATTATTTTAATAGT-TTAATATTAAATTTAATT
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATT
*
502142 TAATACTTATTTTAATAGTATTTTATTAATTTAAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAAT
502177 ATTCATGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 13 0.41
37 17 0.53
38 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (35 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATT
Found at i:502179 original size:11 final size:11
Alignment explanation
Indices: 502106--502212 Score: 51
Period size: 12 Copynumber: 9.4 Consensus size: 11
502096 ATTTCAAAAA
*
502106 TAATATTATTT
1 TAATATTAATT
502117 TAATAGTTTAATAT
1 TAATA--TTAAT-T
502131 TAA-ATTTAATT
1 TAATA-TTAATT
*
502142 TAATACTTATTT
1 TAATA-TTAATT
*
502154 TAATAGT-ATT
1 TAATATTAATT
502164 T--TATTAATT
1 TAATATTAATT
*
502173 TAATATTCATGT
1 TAATATTAAT-T
* *
502185 GATATCTTAATAT
1 TA-ATATTAAT-T
*
502198 TAATTTTAATT
1 TAATATTAATT
502209 TAAT
1 TAAT
502213 TTTTGTCATG
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 3 0.04
11 21 0.28
12 26 0.35
13 13 0.18
14 4 0.05
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:503811 original size:21 final size:21
Alignment explanation
Indices: 503781--503827 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
503771 ACGTGAGTGA
*
503781 AGTTTTATTACATGATCTGTC
1 AGTTTGATTACATGATCTGTC
503802 AGTTTGATTACATGATCTGTC
1 AGTTTGATTACATGATCTGTC
503823 AGTTT
1 AGTTT
503828 TATACCTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (21 bp):
AGTTTGATTACATGATCTGTC
Found at i:506677 original size:27 final size:26
Alignment explanation
Indices: 506640--506693 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
506630 TGCACCTACA
*
506640 TTTTTTTCTTTATGCCTATGTCTATG
1 TTTTTTTCTTTATGCCCATGTCTATG
506666 TTTTCTTTCTTTATGCCCATGTCTATG
1 TTTT-TTTCTTTATGCCCATGTCTATG
506693 T
1 T
506694 ACTATTGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.59
Consensus pattern (26 bp):
TTTTTTTCTTTATGCCCATGTCTATG
Found at i:507230 original size:20 final size:20
Alignment explanation
Indices: 507205--507279 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
507195 ACAATTTTAA
*
507205 AATCAAGTTAAAATTATTTT
1 AATCAAGTCAAAATTATTTT
* *
507225 AATCAAGTCAAAATCATTTG
1 AATCAAGTCAAAATTATTTT
* *
507245 AA-CAAATCAAAATGATTTT
1 AATCAAGTCAAAATTATTTT
*
507264 CAAACAAGTCAAAATT
1 -AATCAAGTCAAAATT
507280 GCTCCAGGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 14 0.31
20 21 0.47
21 10 0.22
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
AATCAAGTCAAAATTATTTT
Found at i:507275 original size:21 final size:20
Alignment explanation
Indices: 507198--507278 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
507188 TTTTGAAACA
* *
507198 ATTTTAAAATCAAGTTAAAATT
1 ATTTT-AAA-CAAGTCAAAATC
*
507220 ATTTTAATCAAGTCAAAATC
1 ATTTTAAACAAGTCAAAATC
* * *
507240 A-TTTGAACAAATCAAAATG
1 ATTTTAAACAAGTCAAAATC
507259 ATTTTCAAACAAGTCAAAAT
1 ATTTT-AAACAAGTCAAAAT
507279 TGCTCCAGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.31
20 14 0.29
21 14 0.29
22 5 0.10
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTTTAAACAAGTCAAAATC
Found at i:517121 original size:65 final size:65
Alignment explanation
Indices: 517017--517148 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
517007 CAGAATAATT
517017 TATTCTGAAAAAATTCAACATAATATATAGGGAAAGCATGCCACTGATTAGGTATGAAATTCCCA
1 TATTCTGAAAAAATTCAACATAATATATAGGGAAAGCATGCCACTGATTAGGTATGAAATTCCCA
517082 TATTCTGAAAAAATTCAACATAATATATAGGGAAAGCATGCCACTGATTAGGTATGAAATTCCCA
1 TATTCTGAAAAAATTCAACATAATATATAGGGAAAGCATGCCACTGATTAGGTATGAAATTCCCA
517147 TA
1 TA
517149 ATTGATGCAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (65 bp):
TATTCTGAAAAAATTCAACATAATATATAGGGAAAGCATGCCACTGATTAGGTATGAAATTCCCA
Found at i:517255 original size:21 final size:21
Alignment explanation
Indices: 517231--517272 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
517221 CCTAAATTAT
517231 CTCCAAATCCCTAATTGACAG
1 CTCCAAATCCCTAATTGACAG
* *
517252 CTCCAAATCTCTTATTGACAG
1 CTCCAAATCCCTAATTGACAG
517273 ATTATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
CTCCAAATCCCTAATTGACAG
Found at i:521619 original size:19 final size:21
Alignment explanation
Indices: 521578--521623 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
521568 TATTCTCTTA
*
521578 TAAAAAATTATAAAATTATGT
1 TAAAAAATTATAAAACTATGT
521599 TAAAAAATTAT-AAACTA-GT
1 TAAAAAATTATAAAACTATGT
521618 TAAAAA
1 TAAAAA
521624 CTTTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAAAAATTATAAAACTATGT
Found at i:538741 original size:17 final size:17
Alignment explanation
Indices: 538713--538758 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
538703 TTGGAATAAA
538713 AATATTATTTTTGCATATT
1 AATA-TATTTTTG-ATATT
538732 AATA-ATTTTTTGATATT
1 AATATA-TTTTTGATATT
538749 AATATATTTT
1 AATATATTTT
538759 GTCCCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 14 0.56
18 7 0.28
19 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
AATATATTTTTGATATT
Found at i:538743 original size:18 final size:18
Alignment explanation
Indices: 538720--538758 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
538710 AAAAATATTA
538720 TTTTTGCATATTAATA-AT
1 TTTTTG-ATATTAATATAT
538738 TTTTTGATATTAATATAT
1 TTTTTGATATTAATATAT
538756 TTT
1 TTT
538759 GTCCCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTTGATATTAATATAT
Found at i:539997 original size:80 final size:80
Alignment explanation
Indices: 539853--540009 Score: 215
Period size: 80 Copynumber: 2.0 Consensus size: 80
539843 GGGCGCAAAA
* * * * * * *
539853 TCGTCGGTTAATCTAACTAGAGCTGGGCTCATTTATCGCGGTTTATTAGCTAGGCACTGGGTGCC
1 TCGTCGGTTAATCCAACTAGAGCTAGGATCATTAATCGCGGTTTATCAGCTAGGCACCGAGTGCC
*
539918 ATGAATTGACGAGTT
66 AAGAATTGACGAGTT
* *
539933 TCGTTGGTTAATCCAACTAGAGCTAGGATCATTAATCGCGGTTTATCCGCTAGGCACCGAGTGCC
1 TCGTCGGTTAATCCAACTAGAGCTAGGATCATTAATCGCGGTTTATCAGCTAGGCACCGAGTGCC
*
539998 AAGAGTTGACGA
66 AAGAATTGACGA
540010 AATGATTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (80 bp):
TCGTCGGTTAATCCAACTAGAGCTAGGATCATTAATCGCGGTTTATCAGCTAGGCACCGAGTGCC
AAGAATTGACGAGTT
Found at i:541129 original size:75 final size:75
Alignment explanation
Indices: 541006--541156 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 75
540996 TTTTTTGAGG
* * * *
541006 AGGCATCAGTTGAGGGATTGGGTCATGTGGCTGATATTCTAAGGGAGTATGAACTTTGTTCTGGT
1 AGGCATCAGTTGAGGGATTGGGTCACGTGGCTGATATCCTAAGGGAGTATGAACTCTGTTCTAGT
*
541071 CAGTAGATTA
66 CAGAAGATTA
* * *
541081 AGGCATTAGTTGAGGGATTGGGTCACGTGGTTGATATCCTAAGGGAGTATGAGCTCTGTTCTAGT
1 AGGCATCAGTTGAGGGATTGGGTCACGTGGCTGATATCCTAAGGGAGTATGAACTCTGTTCTAGT
*
541146 TAGAAGATTA
66 CAGAAGATTA
541156 A
1 A
541157 CTTTGCGAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.32
Consensus pattern (75 bp):
AGGCATCAGTTGAGGGATTGGGTCACGTGGCTGATATCCTAAGGGAGTATGAACTCTGTTCTAGT
CAGAAGATTA
Found at i:545804 original size:20 final size:20
Alignment explanation
Indices: 545760--545805 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
545750 CTGTTCAAAA
*
545760 AATAATATTATTTTAATAGTT
1 AATAATATTAATTTAATA-TT
545781 -ATAATATTAAATTTAAT-TT
1 AATAATATT-AATTTAATATT
545800 AATAAT
1 AATAAT
545806 TATCTTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 13 0.59
21 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATAATATTAATTTAATATT
Found at i:550879 original size:101 final size:101
Alignment explanation
Indices: 550728--551418 Score: 531
Period size: 101 Copynumber: 6.9 Consensus size: 101
550718 TCAACCCGAC
* * * * *
550728 CCACTACAACTTTAGGG-G-TATAGGATTTGGTTTTGTAGCTTCAATTTGATCCACTATAACTT-
1 CCACTACAACTTCAGGGAGATA-AAGATTTGCTTTTGTAGCTTCAATCTGATCCACTACAACTTC
* * *
550790 AGTGGATATAGGATTTGACGTCGTAGCTTCATGTTTCT
65 AG-GGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
* * * *
550828 CCACTACAACTTTAGGGAGATAAAGATTTGCTTTTGTATCTTCAATCTGATCCATTGCAACTTCA
1 CCACTACAACTTCAGGGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTACAACTTCA
* *
550893 AGGATATAGGATTTGATGTCGTAGCTTCATATTGCT
66 GGGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
* * * * * ** * ** *
550929 CCACTATAACTTCAAGGAGATAAAGGTTCT-CTTTTGTAGTTTTAATCCAACCCTTTATAACTTT
1 CCACTACAACTTCAGGGAGATAAAGATT-TGCTTTTGTAGCTTCAATCTGATCCACTACAAC-TT
* * * * *
550993 AAGGG-TATAGGATTTGGTTTTGTAGCTTCATCCTGCT
64 CAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
* * * * * ** ** *
551030 CTACTGCAACTTAAGAGAGATAACGATTTGCTTTCATAGCTTCAATCCAATCCACTGCAACTTCA
1 CCACTACAACTTCAGGGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTACAACTTCA
* * * *
551095 GGGATATAAGATTTGATGTCGTAGCTTTATTTTGAT
66 GGGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
* * * * * **
551131 CCACTACAACTTCAGGGAGGTAAAAATTTGCATTTT-TAGTTTCAATCTGACCCATTGTAACTTC
1 CCACTACAACTTCAGGGAGATAAAGATTTGC-TTTTGTAGCTTCAATCTGATCCACTACAACTTC
* * * * * * * *
551195 TGGGGTATATGACTTGGTTTTGTAGCTTCATCCTGCT
65 AGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
* * * * * ** *
551232 CTATTATAACTTCAGAGAGATAAGGATTTGCTTTCATAGCTTCAAT-TCGATCCACTACAACTTT
1 CCACTACAACTTCAGGGAGATAAAGATTTGCTTTTGTAGCTTCAATCT-GATCCACTACAACTTC
*
551296 AGGGATATAGGATTTGATGTGGTAGCTTCATCTTGCAT
65 AGGGATATAGGATTTGATGTCGTAGCTTCATCTTGC-T
* * * * * * * * *
551334 -TACTGCAACTTCAGAGAGATAAATATTTGCTATTGTAGTTTTAGTTTGATCC-CTACAACTTCA
1 CCACTACAACTTCAGGGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTACAACTTCA
*
551397 AGGATATATGG--TTGATGTCGTA
66 GGGATATA-GGATTTGATGTCGTA
551419 CTGATCCCTC
Statistics
Matches: 460, Mismatches: 118, Indels: 27
0.76 0.20 0.04
Matches are distributed among these distances:
99 10 0.02
100 45 0.10
101 391 0.85
102 14 0.03
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (101 bp):
CCACTACAACTTCAGGGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTACAACTTCA
GGGATATAGGATTTGATGTCGTAGCTTCATCTTGCT
Found at i:550941 original size:50 final size:49
Alignment explanation
Indices: 550728--550946 Score: 161
Period size: 50 Copynumber: 4.4 Consensus size: 49
550718 TCAACCCGAC
* * * * * *
550728 CCACTACAACTTTAGGGGTATAGGATTTGGTTTTGTAGCTTCAATTTGAT
1 CCACTACAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCAA-TTGAT
* * * * **
550778 CCACTATAACTT-AGTGGATATAGGATTTGACGTCGTAGCTTCATGTTTCT
1 CCACTACAACTTCA-AGGATATAGGATTTGATGTCGTAGCTTCA-ATTGAT
* * * * * * * *
550828 CCACTACAACTTTAGGGAGATAAAGATTTGCTTTTGTATCTTCAATCTGAT
1 CCACTACAACTTCAAGGATAT-AGGATTTGATGTCGTAGCTTCAAT-TGAT
* * *
550879 CCATTGCAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCATATTGCT
1 CCACTACAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCA-ATTGAT
*
550929 CCACTATAACTTCAAGGA
1 CCACTACAACTTCAAGGA
550947 GATAAAGGTT
Statistics
Matches: 127, Mismatches: 36, Indels: 12
0.73 0.21 0.07
Matches are distributed among these distances:
49 1 0.01
50 89 0.70
51 37 0.29
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (49 bp):
CCACTACAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCAATTGAT
Found at i:551110 original size:202 final size:202
Alignment explanation
Indices: 550812--551363 Score: 628
Period size: 202 Copynumber: 2.7 Consensus size: 202
550802 ATTTGACGTC
** * * * * ** * *
550812 GTAGCTTCATGTTTCTCCACTACAACTTTAGGGAGATAAAGATTTGCTTTTGTATCTTCAATCTG
1 GTAGCTTCATCCTGCTCTACTACAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCG
* * *
550877 ATCCATTGCAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCATATTGCTCCACTATAACTTC
66 ATCCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATATTGCTCCACTACAACTTC
** * *
550942 AAGGAGATAAAGGTTCT-C-TTTTGTAGTTTTAATCCAACCCTTTATAACTT-TAAGGGTATAGG
131 AAGGAGATAAAAATT-TGCATTTT-TAGTTTCAATCCAACCCATTATAACTTCT-AGGGTATAGG
*
551004 ATTTGGTTTT
193 ACTTGGTTTT
* * *
551014 GTAGCTTCATCCTGCTCTACTGCAACTTAAGAGAGATAACGATTTGCTTTCATAGCTTCAATCCA
1 GTAGCTTCATCCTGCTCTACTACAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCG
* * * *
551079 ATCCACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTTATTTTGATCCACTACAACTTC
66 ATCCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATATTGCTCCACTACAACTTC
* * ** * * *
551144 AGGGAGGTAAAAATTTGCATTTTTAGTTTCAATCTGACCCATTGTAACTTCTGGGGTATATGACT
131 AAGGAGATAAAAATTTGCATTTTTAGTTTCAATCCAACCCATTATAACTTCTAGGGTATAGGACT
551209 TGGTTTT
196 TGGTTTT
* * * * *
551216 GTAGCTTCATCCTGCTCTATTATAACTTCAGAGAGATAAGGATTTGCTTTCATAGCTTCAATTCG
1 GTAGCTTCATCCTGCTCTACTACAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCG
* * * * * *
551281 ATCCACTACAACTTTAGGGATATAGGATTTGATGTGGTAGCTTCATCTTGCAT-TACTGCAACTT
66 ATCCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATATTGC-TCCACTACAACTT
*
551345 C-AGAGAGATAAATATTTGC
130 CAAG-GAGATAAAAATTTGC
551364 TATTGTAGTT
Statistics
Matches: 294, Mismatches: 51, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
201 2 0.01
202 286 0.97
203 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (202 bp):
GTAGCTTCATCCTGCTCTACTACAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCG
ATCCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATATTGCTCCACTACAACTTC
AAGGAGATAAAAATTTGCATTTTTAGTTTCAATCCAACCCATTATAACTTCTAGGGTATAGGACT
TGGTTTT
Found at i:551310 original size:303 final size:303
Alignment explanation
Indices: 550776--551364 Score: 674
Period size: 303 Copynumber: 1.9 Consensus size: 303
550766 CTTCAATTTG
* * * *
550776 ATCCACTATAACTTAGTGGATATAGGATTTGACGTCGTAGCTTCATGTTTCTCCACTACAACTTT
1 ATCCACTACAACTTAGTGGATATAAGATTTGACGTCGTAGCTTCATGTTTATCCACTACAACTTC
* * *
550841 AGGGAGATAAAGATTTGCTTTTGTATCTTCAATCTGATCCATTGCAACTTCAAGGATATAGGATT
66 AGGGAGATAAAAATTTGCTTTTGTATCTTCAATCTGACCCATTGCAACTTCAAGGATATAGGACT
* ** *
550906 TGATGTCGTAGCTTCATATTGCTCCACTATAACTTCAAGGAGATAAAGGTTCTCTTTTGTAGTTT
131 TGATGTCGTAGCTTCATACTGCTCCACTATAACTTCAAGGAGATAAAGGTTCTCTTTCATAGCTT
* ** * * * *
550971 TAATCCAACCCTTTATAACTTTAAGGGTATAGGATTTGGTTTTGTAGCTTCATCCTGC-TCTACT
196 CAATCCAACCCACTACAACTTTAAGGGTATAGGATTTGATGTGGTAGCTTCATCCTGCAT-TACT
*
551035 GCAACTTAAGAGAGATAACGATTTGCTTTCATAGCTTCAATCCA
260 GCAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCA
* * *
551079 ATCCACTGCAACTTCAG-GGATATAAGATTTGATGTCGTAGCTTTAT-TTTGATCCACTACAACT
1 ATCCACTACAACTT-AGTGGATATAAGATTTGACGTCGTAGCTTCATGTTT-ATCCACTACAACT
* * ** * *
551142 TCAGGGAGGTAAAAATTTGCATTTT-TAGT-TTCAATCTGACCCATTGTAACTTCTGGGGTATAT
64 TCAGGGAGATAAAAATTTGC-TTTTGTA-TCTTCAATCTGACCCATTGCAACTTCAAGGATATAG
* * * * * *
551205 GACTTGGTTTTGTAGCTTCATCCTGCTCTATTATAACTTC-AGAGAGAT-AAGGATT-TGCTTTC
127 GACTTGATGTCGTAGCTTCATACTGCTCCACTATAACTTCAAG-GAGATAAAGG-TTCT-CTTTC
* * * *
551267 ATAGCTTCAATTCGATCCACTACAACTTT-AGGGATATAGGATTTGATGTGGTAGCTTCATCTTG
189 ATAGCTTCAATCCAACCCACTACAACTTTAAGGG-TATAGGATTTGATGTGGTAGCTTCATCCTG
* *
551331 CATTACTGCAACTTCAGAGAGATAAATATTTGCT
253 CATTACTGCAACTTAAGAGAGATAAAGATTTGCT
551365 ATTGTAGTTT
Statistics
Matches: 237, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
302 14 0.06
303 215 0.91
304 8 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (303 bp):
ATCCACTACAACTTAGTGGATATAAGATTTGACGTCGTAGCTTCATGTTTATCCACTACAACTTC
AGGGAGATAAAAATTTGCTTTTGTATCTTCAATCTGACCCATTGCAACTTCAAGGATATAGGACT
TGATGTCGTAGCTTCATACTGCTCCACTATAACTTCAAGGAGATAAAGGTTCTCTTTCATAGCTT
CAATCCAACCCACTACAACTTTAAGGGTATAGGATTTGATGTGGTAGCTTCATCCTGCATTACTG
CAACTTAAGAGAGATAAAGATTTGCTTTCATAGCTTCAATCCA
Found at i:557837 original size:37 final size:37
Alignment explanation
Indices: 557784--557909 Score: 146
Period size: 37 Copynumber: 3.4 Consensus size: 37
557774 TTGCAAATAA
* * * * *
557784 GTATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGT
1 GTATTCGAGCTATGTGCCTAGCAGGCTTTGTGCTGGT
* *
557821 GTATTCGAGCTATGTGCTTAGCAGGCTTTGTGCTGGA
1 GTATTCGAGCTATGTGCCTAGCAGGCTTTGTGCTGGT
* * *
557858 GTATTCGAGCTATATGCCTAACAAGCTTTGTGCTGGT
1 GTATTCGAGCTATGTGCCTAGCAGGCTTTGTGCTGGT
557895 GTATTC-AGGCTATGT
1 GTATTCGA-GCTATGT
557910 AGCAGGCTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
36 1 0.01
37 74 0.99
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (37 bp):
GTATTCGAGCTATGTGCCTAGCAGGCTTTGTGCTGGT
Found at i:573104 original size:29 final size:29
Alignment explanation
Indices: 573072--573131 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
573062 ATAAATAAAT
573072 AAAATAAAATGAAAA-CCAAATTGCAAAGA
1 AAAATAAAAT-AAAACCCAAATTGCAAAGA
*
573101 AAAATAAAATAAAACCCAAATTGGAAAGA
1 AAAATAAAATAAAACCCAAATTGCAAAGA
573130 AA
1 AA
573132 TAATTCCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (29 bp):
AAAATAAAATAAAACCCAAATTGCAAAGA
Found at i:582807 original size:14 final size:14
Alignment explanation
Indices: 582788--582819 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
582778 TGAATTCAAA
582788 AGAAAGTTGTAAAG
1 AGAAAGTTGTAAAG
*
582802 AGAAAGTTGTAGAG
1 AGAAAGTTGTAAAG
582816 AGAA
1 AGAA
582820 TTCTCTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (14 bp):
AGAAAGTTGTAAAG
Found at i:585606 original size:21 final size:21
Alignment explanation
Indices: 585567--585612 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
585557 ATACAATATG
* *
585567 ATAATGACAAAATAAAAATAC
1 ATAATGAAAAAATAAAAATAA
585588 ATAATTGAAAAAAT-AAAATAA
1 ATAA-TGAAAAAATAAAAATAA
585609 ATAA
1 ATAA
585613 CACTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
ATAATGAAAAAATAAAAATAA
Found at i:585666 original size:16 final size:16
Alignment explanation
Indices: 585645--585675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
585635 AAACAAAAAA
*
585645 AAATAGTAATGATAAC
1 AAATAGAAATGATAAC
585661 AAATAGAAATGATAA
1 AAATAGAAATGATAA
585676 TACGATTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (16 bp):
AAATAGAAATGATAAC
Found at i:587876 original size:101 final size:102
Alignment explanation
Indices: 587771--588337 Score: 540
Period size: 101 Copynumber: 5.6 Consensus size: 102
587761 TTATGGGTTT
* * ** * *
587771 AAGATTTGGTTTTGTAGCTTTAATCTGATCCACTACAACTTCAGGGATATAAGATTTGATGTCAT
1 AAGATTTGCTTTTATAGCTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGATGTCGT
* *
587836 AGCTTCATCTTGATCCACTACAACTTCAAG-GAGATA
66 AGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
* * * * *
587872 AAGATTTGCTTTTTTAG-TTTCAATCCAACCCACTACAACTTCAGGGGTATAGGATTTGATTTTG
1 AAGATTTGCTTTTATAGCTTT-AATCCAATCCACTACAACTTCAGGGATATAGGATTTGATGTCG
**
587936 TAGCTTCATCTTGCTCTACTGTAACTT-AAGAGAGATA
65 TAGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
* * * *** * * *
587973 AGGATTTGCTTTCATAGCTTCAATTGGATCCACTGCAAACTTCAGGGATATAGGATTTGAAGTCA
1 AAGATTTGCTTTTATAGCTTTAATCCAATCCACTAC-AACTTCAGGGATATAGGATTTGATGTCG
* *
588038 TAGCTTCATCTTGATCCACTACAACTTCAAG-GAGATA
65 TAGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
* * * * * * * * *
588075 AAGATTTGCTTTTTTAG-TTTCAATCCAACCCACTACAACTTTAGGGGTACAGGACTTGGTTTTG
1 AAGATTTGCTTTTATAGCTTT-AATCCAATCCACTACAACTTCAGGGATATAGGATTTGATGTCG
* *
588139 TAGCTTCATCTTGCTCTATTGCAACTTC-AGAGAGATA
65 TAGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
* * * * * *
588176 AGGATTTACTTTCATAACTTCAATCCAATCCACTACAACTTCA-GGAGTATAGGATTTGATGTGG
1 AAGATTTGCTTTTATAGCTTTAATCCAATCCACTACAACTTCAGGGA-TATAGGATTTGATGTCG
*
588240 TAGCTTCATCTTGCTCTACTACAACTT-TAGAGAGATA
65 TAGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
* ** * * * *** * *
588277 AAGATTTACTACTGTAGTTTTAGTTTGATCC-CTACAACTTTAGGGATATATGATTTGATGT
1 AAGATTTGCTTTTATAGCTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGATGT
588338 TGTACTGATC
Statistics
Matches: 371, Mismatches: 84, Indels: 23
0.78 0.18 0.05
Matches are distributed among these distances:
100 34 0.09
101 254 0.68
102 80 0.22
103 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (102 bp):
AAGATTTGCTTTTATAGCTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGATGTCGT
AGCTTCATCTTGCTCTACTACAACTTCAAGAGAGATA
Found at i:587907 original size:51 final size:51
Alignment explanation
Indices: 587711--588233 Score: 218
Period size: 51 Copynumber: 10.4 Consensus size: 51
587701 ATTGTATCTC
* * * **
587711 CAAGGAGATAA-GATTTGCTTCTATAGCTTCAACCTCACCCCACTGGAACTT
1 CAAGGAGATAAGGATTTGCTTTTATAGCTTCAATC-CAACCCACTACAACTT
* * * * * * ** *
587762 TATGG-GTTTAA-GATTTGGTTTTGTAGCTTTAATCTGATCCACTACAACTT
1 CAAGGAG-ATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTACAACTT
* * * * * ** *
587812 CAGGGATATAA-GATTTGATGTCATAGCTTC-ATCTTGATCCACTACAACTT
1 CAAGGAGATAAGGATTTGCTTTTATAGCTTCAATC-CAACCCACTACAACTT
* * *
587862 CAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTT
1 CAAGGAGATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTACAACTT
* * * *** * **
587913 C-AGG-GGTATAGGATTTGATTTTGTAGCTTC-ATCTTGCTCTACTGTAACTT
1 CAAGGAGATA-AGGATTTGCTTTTATAGCTTCAATCCAAC-CCACTACAACTT
* *** * *
587963 -AAGAGAGATAAGGATTTGCTTTCATAGCTTCAATTGGATCCACTGCAAACTT
1 CAAG-GAGATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTAC-AACTT
*** * ** *
588015 C-AGG-GATATAGGATTTGAAGTCATAGCTTC-ATCTTGATCCACTACAACTT
1 CAAGGAGATA-AGGATTTGCTTTTATAGCTTCAATC-CAACCCACTACAACTT
* * *
588065 CAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTT
1 CAAGGAGATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTACAACTT
* * * * * *** * * *
588116 -TAGG-GGTACAGGACTTGGTTTTGTAGCTTC-ATCTTGCTCTATTGCAACTT
1 CAAGGAGATA-AGGATTTGCTTTTATAGCTTCAATCCAAC-CCACTACAACTT
* * * *
588166 C-AGAGAGATAAGGATTTACTTTCATAACTTCAATCCAATCCACTACAACTT
1 CAAG-GAGATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTACAACTT
588217 C-AGGAG-TATAGGATTTG
1 CAAGGAGATA-AGGATTTG
588234 ATGTGGTAGC
Statistics
Matches: 348, Mismatches: 99, Indels: 51
0.70 0.20 0.10
Matches are distributed among these distances:
49 19 0.05
50 139 0.40
51 162 0.47
52 28 0.08
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (51 bp):
CAAGGAGATAAGGATTTGCTTTTATAGCTTCAATCCAACCCACTACAACTT
Found at i:587962 original size:151 final size:151
Alignment explanation
Indices: 587618--588245 Score: 387
Period size: 151 Copynumber: 4.1 Consensus size: 151
587608 ACTCTGGAAG
** * * * *
587618 ATAAGATTTGATGATGTAG-TTTCAATCTAATCCATTGTAACTTCAAGGATATAGGATTTGATGT
1 ATAAGATTTGATTTTGTAGCTTT-AATCTGATCCACTGTAACTTCAGGGATATAAGATTTGATGT
* * * * * * * *
587682 CGTAACATCATCTTGCTCCATTGTATCTCCAAGGAGATAAGATTTGCTTCTATAGCTTCAACCTC
65 CATAGCTTCATCTTGATCCACTGCAACTTCAAGGAGATAAGATTTGCTTCTATAGCTTCAACCTC
* ** * *
587747 ACCCCACTGGAACTTTATGGGT
130 AACCCACTACAACTTCAGGGGT
* * **
587769 TTAAGATTTGGTTTTGTAGCTTTAATCTGATCCACTACAACTTCAGGGATATAAGATTTGATGTC
1 ATAAGATTTGATTTTGTAGCTTTAATCTGATCCACTGTAACTTCAGGGATATAAGATTTGATGTC
* * * * *
587834 ATAGCTTCATCTTGATCCACTACAACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATC-C
66 ATAGCTTCATCTTGATCCACTGCAACTTCAAGGAGAT-AAGATTTGCTTCTATAGCTTCAACCTC
587898 AACCCACTACAACTTCAGGGGT
130 AACCCACTACAACTTCAGGGGT
* * * * * * * * *
587920 ATAGGATTTGATTTTGTAGC-TTCATCTTGCTCTACTGTAACTTAAGAGAGATAAGGATTTGCTT
1 ATAAGATTTGATTTTGTAGCTTTAATC-TGATCCACTGTAACTTCAGGGATATAA-GATTTGATG
* * * * **
587984 TCATAGCTTCAAT-TGGATCCACTGCAAACTTCAGGGATATAGGATTTGAAGTC-ATAGCTTC-A
64 TCATAGCTTC-ATCTTGATCCACTGC-AACTTCAAGGAGATAAGATTTG-CTTCTATAGCTTCAA
* ** * *
588046 TCTTGATCCACTACAACTTCAAGGAG-
126 CCTCAACCCACTACAACTTC-AGGGGT
* * ** * ** * * * * * * *
588072 ATAAAGATTTGCTTTTTTAG-TTTCAATCCAACCCACTACAACTTTAGGGGTACAGGACTTGGTT
1 AT-AAGATTTGATTTTGTAGCTTT-AATCTGATCCACTGTAACTTCAGGGATATAAGATTTGATG
** * * * * *
588136 TTGTAGCTTCATCTTGCTCTATTGCAACTTC-AGAGAGATAAGGATTTACTT-TCATAACTTCAA
64 TCATAGCTTCATCTTGATCCACTGCAACTTCAAG-GAGATAA-GATTTGCTTCT-ATAGCTTCAA
* * *
588199 TC-CAATCCACTACAACTTCAGGAGT
126 CCTCAACCCACTACAACTTCAGGGGT
* * *
588224 ATAGGATTTGATGTGGTAGCTT
1 ATAAGATTTGATTTTGTAGCTT
588246 CATCTTGCTC
Statistics
Matches: 363, Mismatches: 94, Indels: 39
0.73 0.19 0.08
Matches are distributed among these distances:
150 6 0.02
151 168 0.46
152 134 0.37
153 52 0.14
154 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (151 bp):
ATAAGATTTGATTTTGTAGCTTTAATCTGATCCACTGTAACTTCAGGGATATAAGATTTGATGTC
ATAGCTTCATCTTGATCCACTGCAACTTCAAGGAGATAAGATTTGCTTCTATAGCTTCAACCTCA
ACCCACTACAACTTCAGGGGT
Found at i:588043 original size:203 final size:202
Alignment explanation
Indices: 587792--588283 Score: 754
Period size: 203 Copynumber: 2.4 Consensus size: 202
587782 TTGTAGCTTT
* *
587792 AATCTGATCCACTACAACTTCAGGGATATAAGATTTGATGTCATAGCTTCATCTTGATCCACTAC
1 AATCCGATCCACTACAACTTCAGGGATATAGGATTTGATGTCATAGCTTCATCTTGATCCACTAC
*
587857 AACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTTCAGGGGTAT
66 AACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTTCAGGGGTAC
* * *
587922 AGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGTAACTTAAGAGAGATAAGGATTTGCTTTCA
131 AGGACTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTAAGAGAGATAAGGATTTACTTTCA
*
587987 TAGCTTC
196 TAACTTC
** * *
587994 AATTGGATCCACTGCAAACTTCAGGGATATAGGATTTGAAGTCATAGCTTCATCTTGATCCACTA
1 AATCCGATCCACTAC-AACTTCAGGGATATAGGATTTGATGTCATAGCTTCATCTTGATCCACTA
*
588059 CAACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTTTAGGGGTA
65 CAACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTTCAGGGGTA
* * *
588124 CAGGACTTGGTTTTGTAGCTTCATCTTGCTCTATTGCAACTTCAGAGAGATAAGGATTTACTTTC
130 CAGGACTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTAAGAGAGATAAGGATTTACTTTC
588189 ATAACTTC
195 ATAACTTC
* ** * *
588197 AATCCAATCCACTACAACTTCA-GGAGTATAGGATTTGATGTGGTAGCTTCATCTTGCTCTACTA
1 AATCCGATCCACTACAACTTCAGGGA-TATAGGATTTGATGTCATAGCTTCATCTTGATCCACTA
*
588261 CAACTT-TAGAGAGATAAAGATTT
65 CAACTTCAAG-GAGATAAAGATTT
588284 ACTACTGTAG
Statistics
Matches: 263, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
201 5 0.02
202 71 0.27
203 187 0.71
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (202 bp):
AATCCGATCCACTACAACTTCAGGGATATAGGATTTGATGTCATAGCTTCATCTTGATCCACTAC
AACTTCAAGGAGATAAAGATTTGCTTTTTTAGTTTCAATCCAACCCACTACAACTTCAGGGGTAC
AGGACTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTAAGAGAGATAAGGATTTACTTTCA
TAACTTC
Found at i:591617 original size:5 final size:5
Alignment explanation
Indices: 591602--591659 Score: 64
Period size: 5 Copynumber: 11.0 Consensus size: 5
591592 TCAACCTCTC
*
591602 CTTTT CTTTTT CTTTT -TTTT TTTTT CTTTTTT CTTTT CTTTT CTTTT
1 CTTTT C-TTTT CTTTT CTTTT CTTTT C--TTTT CTTTT CTTTT CTTTT
591649 CTTTT CCTTTT
1 CTTTT -CTTTT
591660 TTGTGTGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
4 4 0.09
5 28 0.60
6 10 0.21
7 5 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:591631 original size:10 final size:10
Alignment explanation
Indices: 591602--591661 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
591592 TCAACCTCTC
591602 CTTTTCTTTTT
1 CTTTT-TTTTT
591613 CTTTTTTTTT
1 CTTTTTTTTT
*
591623 TTTTCTTTTTT
1 CTTT-TTTTTT
*
591634 CTTTTCTTTT
1 CTTTTTTTTT
*
591644 CTTTTCTTTTC
1 CTTTT-TTTTT
591655 CTTTTTT
1 CTTTTTT
591662 GTGTGAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
10 20 0.48
11 22 0.52
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:597693 original size:115 final size:115
Alignment explanation
Indices: 597491--597720 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 115
597481 TACCAGACTC
597491 ATTCGATATGCTTACCCTTGCCGAGCAAATCCAACTTTGTTCACCTTTTGTCCACTTCTCATGAG
1 ATTCGATATGCTTACCCTTGCCGAGCAAATCCAACTTTGTTCACCTTTTGTCCACTTCTCATGAG
*
597556 ATCTTTCTAATTCATTAAATCGATCCCTTTCCTTGAATTAATTAATTCTT
66 ATCTTTCTAATTCATTAAATCGATCCCTTTCCTTGAATCAATTAATTCTT
597606 ATTCGATATGCTTACCCTTGCCGAGCAAATCCAACTTTGTTCACCTTTTGTCCACTTCTCATGAG
1 ATTCGATATGCTTACCCTTGCCGAGCAAATCCAACTTTGTTCACCTTTTGTCCACTTCTCATGAG
*
597671 ATCTTTCTAATTCATTCAATCGATCCCTTTCCTTGAATCAATTAATTCTT
66 ATCTTTCTAATTCATTAAATCGATCCCTTTCCTTGAATCAATTAATTCTT
597721 TCCTTGTTCA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (115 bp):
ATTCGATATGCTTACCCTTGCCGAGCAAATCCAACTTTGTTCACCTTTTGTCCACTTCTCATGAG
ATCTTTCTAATTCATTAAATCGATCCCTTTCCTTGAATCAATTAATTCTT
Found at i:617408 original size:20 final size:21
Alignment explanation
Indices: 617372--617410 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
617362 ATTTTTGTTA
*
617372 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
617393 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
617411 AATTCCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:620323 original size:19 final size:18
Alignment explanation
Indices: 620293--620341 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
620283 TCAGTCACAT
*
620293 AGAAAAGGAAAATGAGAAAG
1 AGAAAAGAAAAAT-A-AAAG
620313 AG-AAAGAAAAAATAAAAG
1 AGAAAAG-AAAAATAAAAG
620331 AGAAAAGAAAA
1 AGAAAAGAAAA
620342 GAAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.38
19 9 0.35
20 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (18 bp):
AGAAAAGAAAAATAAAAG
Found at i:620333 original size:24 final size:26
Alignment explanation
Indices: 620301--620349 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
620291 ATAGAAAAGG
620301 AAAATGAG-AAAGAGAAAGAA-AAAAT
1 AAAATGAGAAAAGA-AAAGAAGAAAAT
620326 AAAA-GAGAAAAGAAAAGAAGAAAA
1 AAAATGAGAAAAGAAAAGAAGAAAA
620350 AATGTTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (26 bp):
AAAATGAGAAAAGAAAAGAAGAAAAT
Found at i:620336 original size:12 final size:12
Alignment explanation
Indices: 620293--620349 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
620283 TCAGTCACAT
620293 AGAAAAGGAAAATG
1 AGAAAA-GAAAA-G
620307 AG-AAAGAGAAAG
1 AGAAAAGA-AAAG
* *
620319 AAAAAATAAAAG
1 AGAAAAGAAAAG
620331 AGAAAAGAAAAG
1 AGAAAAGAAAAG
620343 AAGAAAA
1 -AGAAAA
620350 AATGTTTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 18 0.50
13 16 0.44
14 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (12 bp):
AGAAAAGAAAAG
Found at i:629625 original size:24 final size:24
Alignment explanation
Indices: 629598--629644 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
629588 TGTCATTGCA
629598 ATTTT-CTGTTAATTT-TTGTCTTTT
1 ATTTTACT-TTAATTTGTT-TCTTTT
629622 ATTTTACTTTAATTTGTTTCTTT
1 ATTTTACTTTAATTTGTTTCTTT
629645 AGTTTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (24 bp):
ATTTTACTTTAATTTGTTTCTTTT
Found at i:631375 original size:15 final size:17
Alignment explanation
Indices: 631348--631394 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 17
631338 CGTGGGTATT
*
631348 GAAGCAGAAGAAGAGAA
1 GAAGAAGAAGAAGAGAA
631365 -AAGAA-AAGAAGAGAA
1 GAAGAAGAAGAAGAGAA
631380 GGAAGAAGAAGAAGA
1 -GAAGAAGAAGAAGA
631395 CATTGCCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 5 0.19
18 7 0.27
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAAGAGAA
Found at i:631820 original size:17 final size:17
Alignment explanation
Indices: 631798--631835 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
631788 TTTTATCTAG
*
631798 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
*
631815 TTGTCACTACATTTTAC
1 TTGTCACTACATTTTAA
631832 TTGT
1 TTGT
631836 TCTCACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:644718 original size:23 final size:22
Alignment explanation
Indices: 644669--644719 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
644659 ATACGTGAAT
*
644669 AAAATAAAATAAATAACAGTAA
1 AAAATAAAATAAATAACAATAA
*
644691 TAAATACAAATAACATAA-AATAA
1 AAAATA-AAATAA-ATAACAATAA
644714 AAAATA
1 AAAATA
644720 GTAATGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAATAAAATAAATAACAATAA
Found at i:644733 original size:33 final size:33
Alignment explanation
Indices: 644666--644738 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
644656 TACATACGTG
*
644666 AATAAAATAAAATAAATAACAGTAATAAATACA
1 AATAAAATAAAATAAAAAACAGTAATAAATACA
* * *
644699 AATAACATAAAATAAAAAATAGTAAT-GATAACA
1 AATAAAATAAAATAAAAAACAGTAATAAAT-ACA
644732 AATAAAA
1 AATAAAA
644739 GTGATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (33 bp):
AATAAAATAAAATAAAAAACAGTAATAAATACA
Found at i:644968 original size:8 final size:8
Alignment explanation
Indices: 644932--645035 Score: 81
Period size: 8 Copynumber: 12.8 Consensus size: 8
644922 TAATGAATTG
644932 TAAT-AAA
1 TAATAAAA
644939 TAA-AAAA
1 TAATAAAA
* *
644946 TGATAGAA
1 TAATAAAA
644954 T-ATAAAA
1 TAATAAAA
644961 TAATAAAA
1 TAATAAAA
644969 TAATAATAA
1 TAATAA-AA
*
644978 GTGGAATAGAA
1 -T--AATAAAA
644989 T-ATAAAA
1 TAATAAAA
644996 TAAATAAAA
1 T-AATAAAA
*
645005 CAATAAAA
1 TAATAAAA
645013 TAAATAAAA
1 T-AATAAAA
645022 TAATAAAA
1 TAATAAAA
*
645030 TGATAA
1 TAATAA
645036 TAAGTGGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
7 20 0.25
8 35 0.44
9 16 0.20
10 2 0.03
11 2 0.03
12 4 0.05
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (8 bp):
TAATAAAA
Found at i:645012 original size:17 final size:17
Alignment explanation
Indices: 644990--645030 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
644980 GGAATAGAAT
644990 ATAAAATAAATAAAACA
1 ATAAAATAAATAAAACA
*
645007 ATAAAATAAATAAAATA
1 ATAAAATAAATAAAACA
645024 ATAAAAT
1 ATAAAAT
645031 GATAATAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAATAAATAAAACA
Found at i:645020 original size:61 final size:60
Alignment explanation
Indices: 644933--645049 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 60
644923 AATGAATTGT
* *
644933 AATAAATAAAAAATGATAGAATATAAAATAATAAAATAATAATAAGTGGAATAGAATATAA
1 AATAAATAAAAAATAAAAGAATATAAAATAATAAAATAATAATAAGTGGAAT-GAATATAA
* *
644994 AATAAATAAAACAATAAAATAA-ATAAAATAATAAAATGATAATAAGTGGAATGAAT
1 AATAAATAAAA-AATAAAAGAATATAAAATAATAAAATAATAATAAGTGGAATGAAT
645050 TGAAACAGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 4 0.08
61 40 0.78
62 7 0.14
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.24
Consensus pattern (60 bp):
AATAAATAAAAAATAAAAGAATATAAAATAATAAAATAATAATAAGTGGAATGAATATAA
Found at i:645274 original size:21 final size:21
Alignment explanation
Indices: 645243--645287 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
645233 GGGTAAAATT
645243 AAAATAAATT-AAAAGATAAA
1 AAAATAAATTAAAAAGATAAA
*
645263 AAAATGAAATTAAAAAGATGAA
1 AAAAT-AAATTAAAAAGATAAA
645285 AAA
1 AAA
645288 GGTGGAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAATAAATTAAAAAGATAAA
Found at i:649057 original size:23 final size:23
Alignment explanation
Indices: 649014--649058 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
649004 TGAATAAAAT
* *
649014 AAATAAATAACACTAATAAATAC
1 AAATAAATAACAATAAAAAATAC
649037 AAATAACATAA-AATAAAAAATA
1 AAATAA-ATAACAATAAAAAATA
649059 GTAATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAATAACAATAAAAAATAC
Found at i:649273 original size:27 final size:29
Alignment explanation
Indices: 649242--649314 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 29
649232 ATGACATAAG
649242 AAATAAATAAAAATAAATAAT-GAATAT-
1 AAATAAATAAAAATAAATAATAGAATATA
* *
649269 TAAT--ATATAAA-AAATAATAGAATATA
1 AAATAAATAAAAATAAATAATAGAATATA
649295 AAATAAAT-AAAAT-AATAATA
1 AAATAAATAAAAATAAATAATA
649315 AGAGGAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
24 7 0.19
25 12 0.32
26 3 0.08
27 13 0.35
28 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (29 bp):
AAATAAATAAAAATAAATAATAGAATATA
Found at i:649306 original size:24 final size:24
Alignment explanation
Indices: 649246--649311 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
649236 CATAAGAAAT
649246 AAATAAAAATAAATAAT-GAATATTA
1 AAAT-AAAA-AAATAATAGAATATTA
*
649271 ATATATAAAAAATAATAGAATA-TA
1 AAATA-AAAAAATAATAGAATATTA
649295 AAATAAATAAAATAATA
1 AAATAAA-AAAATAATA
649312 ATAAGAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 2 0.06
24 23 0.64
25 11 0.31
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (24 bp):
AAATAAAAAAATAATAGAATATTA
Found at i:649311 original size:19 final size:19
Alignment explanation
Indices: 649269--649315 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
649259 TAATGAATAT
*
649269 TAATATATAAAAAATAATA
1 TAATATATAAAAAATAAAA
*
649288 GAATATA-AAATAAATAAAA
1 TAATATATAAA-AAATAAAA
649307 TAATA-ATAA
1 TAATATATAA
649316 GAGGAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
TAATATATAAAAAATAAAA
Found at i:649551 original size:21 final size:21
Alignment explanation
Indices: 649518--649561 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
649508 AGGGTAAATT
*
649518 AAAATAAGTT-AAAAGATAAA
1 AAAATAAATTAAAAAGATAAA
649538 AAAATGAAATTAAAAAGATAAA
1 AAAAT-AAATTAAAAAGATAAA
649560 AA
1 AA
649562 GGGTGGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAATAAATTAAAAAGATAAA
Found at i:658124 original size:33 final size:34
Alignment explanation
Indices: 658086--658230 Score: 94
Period size: 33 Copynumber: 4.4 Consensus size: 34
658076 TTAATTTTTC
658086 AAATTTTGATAATTCTTAATATTAATTATAAATT
1 AAATTTTGATAATTCTTAATATTAATTATAAATT
** *
658120 -AATTTTTTTAA-T-TT-ATATTAATTAT-TATT
1 AAATTTTGATAATTCTTAATATTAATTATAAATT
** * **
658149 AAGATTTTG-TTTTTCATTTAA-ATT-CTTAT-TTTT
1 AA-ATTTTGATAATTC--TTAATATTAATTATAAATT
*
658182 CAAAATGTTGATAATTCTTAATATTAATTATAAATT
1 --AAATTTTGATAATTCTTAATATTAATTATAAATT
658218 AAATTTT-ATAATT
1 AAATTTTGATAATT
658231 TATATTAACT
Statistics
Matches: 83, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
29 3 0.04
30 13 0.16
31 8 0.10
32 1 0.01
33 26 0.31
34 19 0.23
35 11 0.13
36 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
AAATTTTGATAATTCTTAATATTAATTATAAATT
Found at i:658205 original size:98 final size:98
Alignment explanation
Indices: 658079--658260 Score: 294
Period size: 98 Copynumber: 1.9 Consensus size: 98
658069 ATTTAATTTA
* * * *
658079 ATTTTTCAAATTTTGATAATTCTTAATATTAATTATAAATTAATTTTTTTAATTTATATTAATTA
1 ATTTTTCAAATGTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAACTA
* *
658144 TTATTAAGA-TTTTGTTTTTCATTTAAATTCTT
66 TTATCAAGAGTTTTCTTTTTCATTTAAATTCTT
658176 ATTTTTCAAAATGTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAACT
1 ATTTTTC-AAATGTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAACT
658241 ATTATCAAGAGTTTTCTTTT
65 ATTATCAAGAGTTTTCTTTT
658261 AAATTCTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 7 0.09
98 62 0.81
99 8 0.10
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (98 bp):
ATTTTTCAAATGTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAACTA
TTATCAAGAGTTTTCTTTTTCATTTAAATTCTT
Found at i:658788 original size:13 final size:15
Alignment explanation
Indices: 658770--658806 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
658760 GACGAGCCTG
658770 CTACTGCTGA-GA-C
1 CTACTGCTGACGAGC
658783 CTACTGCTGACGAGC
1 CTACTGCTGACGAGC
*
658798 CTGCTGCTG
1 CTACTGCTG
658807 CCAATGCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.24
Consensus pattern (15 bp):
CTACTGCTGACGAGC
Found at i:658806 original size:15 final size:15
Alignment explanation
Indices: 658759--658806 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
658749 GACTTGTTGT
*
658759 TGACGAGCCTGCTAC
1 TGACGAGCCTGCTGC
*
658774 TG-CTGAGACCTACTGC
1 TGAC-GAG-CCTGCTGC
658790 TGACGAGCCTGCTGC
1 TGACGAGCCTGCTGC
658805 TG
1 TG
658807 CCAATGCCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.04
15 14 0.52
16 11 0.41
17 1 0.04
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (15 bp):
TGACGAGCCTGCTGC
Found at i:661000 original size:20 final size:21
Alignment explanation
Indices: 660961--661000 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
660951 TAAACCAAGC
* *
660961 ATCACTGAGTTAGGAAATGCA
1 ATCACTAAGTTAGAAAATGCA
660982 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
661001 TAAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:675020 original size:16 final size:15
Alignment explanation
Indices: 674995--675037 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
674985 TATATATATA
674995 TTTT-TTTTTTCTTCT
1 TTTTCTTTTTTC-TCT
675010 TTTTCTTTTTTCTCT
1 TTTTCTTTTTTCTCT
675025 TTTCTCATTTTTT
1 TTT-TC-TTTTTT
675038 ATAAGTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTCTCT
Found at i:675622 original size:17 final size:17
Alignment explanation
Indices: 675587--675649 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
675577 AACATTAATT
* *
675587 TACAATGAAAAATGGAAA
1 TACAATG-ACAATGAAAA
*
675605 TACAATGACAATGCAAA
1 TACAATGACAATGAAAA
* * *
675622 TGCAGTGACAATTAAAA
1 TACAATGACAATGAAAA
*
675639 TGCAATGACAA
1 TACAATGACAA
675650 AAGGGATGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 31 0.82
18 7 0.18
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19
Consensus pattern (17 bp):
TACAATGACAATGAAAA
Found at i:676101 original size:15 final size:15
Alignment explanation
Indices: 676064--676102 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
676054 TTTGCCTCAA
* *
676064 CTTCTTCCTTTCTTT
1 CTTCTTCTTTTCCTT
676079 CTTCTTCTTTTCCTT
1 CTTCTTCTTTTCCTT
676094 CTTCTTCTT
1 CTTCTTCTT
676103 CCACTTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTTCTTTTCCTT
Found at i:677459 original size:50 final size:51
Alignment explanation
Indices: 677405--677508 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 51
677395 AACTAATGGA
* * * *
677405 TTACTAAATGCATGAT-AGGATTTATGATGCATATTTAACTAA-CATGTAAG
1 TTACTAAATGCATG-TCAGGATTTATGATGCAAACTTAAATAATCATGAAAG
* **
677455 TTACTTAATGCATGTCATTATTTATGATGCAAACTTAAATAATCATGAAAG
1 TTACTAAATGCATGTCAGGATTTATGATGCAAACTTAAATAATCATGAAAG
677506 TTA
1 TTA
677509 ATGGATGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 34 0.76
51 10 0.22
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (51 bp):
TTACTAAATGCATGTCAGGATTTATGATGCAAACTTAAATAATCATGAAAG
Found at i:698882 original size:19 final size:19
Alignment explanation
Indices: 698851--698894 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
698841 AAAATTTTGC
698851 TTTTT-TTTCATTTTTGTT
1 TTTTTGTTTCATTTTTGTT
698869 GTTTTTGTTT-ATTTTTGTT
1 -TTTTTGTTTCATTTTTGTT
698888 TTTTTGT
1 TTTTTGT
698895 GTGTTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.29
19 14 0.58
20 3 0.12
ACGTcount: A:0.05, C:0.02, G:0.11, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTCATTTTTGTT
Found at i:706433 original size:34 final size:34
Alignment explanation
Indices: 706369--706437 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
706359 TTATACATAG
*
706369 ACTTTAACTTTGCCACTTAACTTACATTGTATGC
1 ACTTTAACTTTGCCACATAACTTACATTGTATGC
* * *
706403 ACTTTAACTTCT-CCACATAGCTTTCTTTGTATGC
1 ACTTTAACTT-TGCCACATAACTTACATTGTATGC
706437 A
1 A
706438 TAATAGCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (34 bp):
ACTTTAACTTTGCCACATAACTTACATTGTATGC
Found at i:707369 original size:28 final size:28
Alignment explanation
Indices: 707265--707358 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 28
707255 CCATGAATTA
* * *
707265 TTCCTTTAATAGAGCTTACCACAAAGAC
1 TTCCTTTAACAAAGCTAACCACAAAGAC
707293 TTCCTTTAACAAAGCTAACCACAAAGAC
1 TTCCTTTAACAAAGCTAACCACAAAGAC
** * *
707321 TTCCTTTAACAAAATTAGCCACAAAGGC
1 TTCCTTTAACAAAGCTAACCACAAAGAC
707349 TTCCTTTAAC
1 TTCCTTTAAC
707359 TAAGTTTGCC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.28
Consensus pattern (28 bp):
TTCCTTTAACAAAGCTAACCACAAAGAC
Found at i:708842 original size:24 final size:24
Alignment explanation
Indices: 708813--708858 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
708803 CTGAACATAT
*
708813 AATAAATAAATAGAAAATTAAATA
1 AATAAATAAATAGAAAAGTAAATA
*
708837 AATAAATAAATATAAAAGTAAA
1 AATAAATAAATAGAAAAGTAAA
708859 AAGAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
AATAAATAAATAGAAAAGTAAATA
Found at i:708881 original size:23 final size:23
Alignment explanation
Indices: 708840--708883 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
708830 TTAAATAAAT
*
708840 AAATAAATATAAAAGTAAAAAGA
1 AAATAAAAATAAAAGTAAAAAGA
708863 AAATAAAAATGAAAA-TAAAAA
1 AAATAAAAAT-AAAAGTAAAAA
708884 AATTGGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (23 bp):
AAATAAAAATAAAAGTAAAAAGA
Found at i:712147 original size:14 final size:14
Alignment explanation
Indices: 712130--712159 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
712120 TTTAAACTCT
*
712130 AAAAGATAAATCTA
1 AAAAGATAAATATA
712144 AAAAGATAAATATA
1 AAAAGATAAATATA
712158 AA
1 AA
712160 TTAAATACAA
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:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:712166 original size:11 final size:11
Alignment explanation
Indices: 712150--712182 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
712140 TCTAAAAAGA
712150 TAAATATAAAT
1 TAAATATAAAT
*
712161 TAAATACAAAT
1 TAAATATAAAT
712172 TAAATATAAAT
1 TAAATATAAAT
712183 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:714349 original size:55 final size:55
Alignment explanation
Indices: 714257--714363 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
714247 TACATCTTCT
* * * *
714257 TCCATATGATGCCATAGCCCTCTTGTCTAGATATTACATAATATGGTCTTCTTTC
1 TCCATATGATGCCATAGCCCTCTAGGCTAGATATTACACAATATGATCTTCTTTC
* * * *
714312 TCCATATGATGTCATAGCCCTCTAGGCTAGGTCTTACACGATATGATCTTCT
1 TCCATATGATGCCATAGCCCTCTAGGCTAGATATTACACAATATGATCTTCT
714364 ATTGTCATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (55 bp):
TCCATATGATGCCATAGCCCTCTAGGCTAGATATTACACAATATGATCTTCTTTC
Found at i:721972 original size:13 final size:14
Alignment explanation
Indices: 721954--721984 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
721944 TGTTAACACA
721954 ATCAGA-GTTAAAT
1 ATCAGAGGTTAAAT
721967 ATCAGAGGTTAAAT
1 ATCAGAGGTTAAAT
721981 ATCA
1 ATCA
721985 ATGTATCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (14 bp):
ATCAGAGGTTAAAT
Found at i:735086 original size:40 final size:41
Alignment explanation
Indices: 734993--735089 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
734983 AAACGATTTT
*
734993 ATAAGTTGTGTATCAGTGAAGCACCCATGAGAGATTAAGTG
1 ATAAGTTGTGTATCAGTGAAGCACCCACGAGAGATTAAGTG
* * * * * *
735034 ATAAGCTATGTATCGGTGAAGCTCCCCCGAGAGCTT-AGTG
1 ATAAGTTGTGTATCAGTGAAGCACCCACGAGAGATTAAGTG
735074 ATAAGTTGTGTATCAG
1 ATAAGTTGTGTATCAG
735090 CAAATCTCCC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (41 bp):
ATAAGTTGTGTATCAGTGAAGCACCCACGAGAGATTAAGTG
Found at i:743003 original size:21 final size:23
Alignment explanation
Indices: 742953--743003 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
742943 AGTTCCTAAA
742953 ATGGAGAAAAAAGGATGGTGAGAG
1 ATGGAGAAAAAAGGATGGT-AGAG
* *
742977 AAGGAGAAATAAGGA-GGT-GAG
1 ATGGAGAAAAAAGGATGGTAGAG
742998 ATGGAG
1 ATGGAG
743004 TGGGACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
23 3 0.12
24 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (23 bp):
ATGGAGAAAAAAGGATGGTAGAG
Found at i:745333 original size:46 final size:45
Alignment explanation
Indices: 745281--745370 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
745271 ATTGTTACTA
* * * * *
745281 ATATGATGCTGTAGTATCTTTCAACAATGGTCTTATAACATATCAG
1 ATATGATACTGTAATAGCTTTCAACAACGGTATTAT-ACATATCAG
* *
745327 ATATGATATTGTAATAGCTTTCAACTACGGTATTATACATATCA
1 ATATGATACTGTAATAGCTTTCAACAACGGTATTATACATATCA
745371 ATAAAAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 8 0.22
46 29 0.78
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (45 bp):
ATATGATACTGTAATAGCTTTCAACAACGGTATTATACATATCAG
Found at i:750072 original size:28 final size:28
Alignment explanation
Indices: 750032--750085 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
750022 AATGAGCATC
750032 ATGACCTTTGGGTCAACAGGGAGTAAGT
1 ATGACCTTTGGGTCAACAGGGAGTAAGT
750060 ATGACCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTGGGTCAACAGGGAGTAA
750086 ATCAGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAGGGAGTAAGT
Found at i:750776 original size:34 final size:36
Alignment explanation
Indices: 750738--750812 Score: 127
Period size: 34 Copynumber: 2.1 Consensus size: 36
750728 CCCATTTTTT
750738 AAATTTATTTTAAGGTTAAATTTA-TTTTAAA-TTA
1 AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTA
*
750772 AAATTTATTTTAAGTTTAAATTTATTTTTAAATTTA
1 AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTA
750808 AAATT
1 AAATT
750813 ATTCTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 23 0.61
35 7 0.18
36 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (36 bp):
AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTA
Found at i:750789 original size:6 final size:6
Alignment explanation
Indices: 750735--750828 Score: 54
Period size: 6 Copynumber: 16.3 Consensus size: 6
750725 AAACCCATTT
* * * * * *
750735 TTTAAA TTT-AT TTTAAG GTTAAA TTT-AT TTTAAA TTAAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
750780 TTTAAG TTTAAA TTTATT TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
750827 TT
1 TT
750829 AATAATGTCC
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
4 2 0.03
5 13 0.20
6 46 0.72
7 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:750822 original size:17 final size:17
Alignment explanation
Indices: 750735--750826 Score: 96
Period size: 17 Copynumber: 5.4 Consensus size: 17
750725 AAACCCATTT
* *
750735 TTTAAATTTATTTTAAG
1 TTTAAAATTATTTTAAA
* *
750752 GTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
*
750769 -TTAAAATTTATTTTAAG
1 TTTAAAA-TTATTTTAAA
*
750786 TTTAAATTTATTTTTAAA
1 TTTAAAATTA-TTTTAAA
*
750804 TTTAAAATTATTCTAAA
1 TTTAAAATTATTTTAAA
750821 TTTAAA
1 TTTAAA
750827 TTAATAATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
16 5 0.08
17 39 0.61
18 20 0.31
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:752807 original size:29 final size:29
Alignment explanation
Indices: 752735--752921 Score: 200
Period size: 29 Copynumber: 6.4 Consensus size: 29
752725 AAACTTTTCT
* *
752735 AAAATTACATTTTAACACCTAAACTTCTCA
1 AAAATTACATTTTTACCCCTAAACTTC-CA
*
752765 AAAATTAC-TCTTTTACCCCTAATCTTCCA
1 AAAATTACAT-TTTTACCCCTAAACTTCCA
*
752794 AAAATTACATTTTTA-CCCTCAAACTTCTA
1 AAAATTACATTTTTACCCCT-AAACTTCCA
* * * *
752823 AAAATTTCATTTTTGCCTC-GAACTTCCA
1 AAAATTACATTTTTACCCCTAAACTTCCA
** *
752851 AAAATTACATTTTTACCCCCGATCTTCCA
1 AAAATTACATTTTTACCCCTAAACTTCCA
*
752880 AAAATTACATTTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCCTAAACTTCCA
* *
752909 AAACTCACATTTT
1 AAAATTACATTTT
752922 GTCTCAGACT
Statistics
Matches: 134, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
28 27 0.20
29 82 0.61
30 25 0.19
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTAAACTTCCA
Done.