Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015245.1 Kokia drynarioides strain JFW-HI SEQ_130290, 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: 767229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:311131 original size:22 final size:19
Alignment explanation
Indices: 311102--311141 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
311092 TTTAATATGG
311102 AATTTTGAATTGAAGAATTTT
1 AATTTTGAATT-AA-AATTTT
311123 AATTATTGAATTAAAATTT
1 AATT-TTGAATTAAAATTT
311142 AGTATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
AATTTTGAATTAAAATTTT
Found at i:311677 original size:189 final size:195
Alignment explanation
Indices: 311236--311677 Score: 495
Period size: 189 Copynumber: 2.3 Consensus size: 195
311226 ATTTTTATTA
* * * **
311236 AATGCCTGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCATGAGTTGG
1 AATGGCTGGGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTCA
* * ** * * *
311301 GAAATGAGAAATGAATCCGATATTTGGATTACATGCCCTACAATGGCTGGTATTTATGCATAAGT
66 AAAAAGAGAAATGAATCCGATAAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAAT
* * *
311366 ACATATTCTCGACAACTCGTGTGAGCAGCATCGTTAGGGAACAATTATATGCACAAATACTGTAT
131 ACATATTCTCGACAACTCG-GTGAGCAACATCATTAGGGAACAATTATATGCACAAACACTGTAT
311431 C
195 C
* * *
311432 AATGGCTAGGCTACCACATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAG-TCA
1 AATGGCTGGGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTCA
* * * * *
311496 AAAAAGAGATATGAAT-C-TTAAATGGATTATAGGCCCTACGATGGCTGGGATTTATGCTTAAAT
66 AAAAAGAGAAATGAATCCGATAAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAAT
** * * * *
311559 GTATATTCTCGATAGCTC-GTGAGCAACATCATTAGGGGACAGTTATA-G-ACAAACA-TCGTA-
131 ACATATTCTCGACAACTCGGTGAGCAACATCATTAGGGAACAATTATATGCACAAACACT-GTAT
311619 C
195 C
* * * **
311620 TAATGGCTGGGGTACCACATACGTTGCGAGTCCTCGATAACTCAAGTGAGCAGCATCG
1 -AATGGCTGGGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
311678 AGTACTGTTA
Statistics
Matches: 207, Mismatches: 37, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
188 2 0.01
189 58 0.28
190 1 0.00
191 25 0.12
193 51 0.25
194 1 0.00
195 14 0.07
196 55 0.27
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (195 bp):
AATGGCTGGGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTCA
AAAAAGAGAAATGAATCCGATAAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAAT
ACATATTCTCGACAACTCGGTGAGCAACATCATTAGGGAACAATTATATGCACAAACACTGTATC
Found at i:312273 original size:21 final size:23
Alignment explanation
Indices: 312249--312303 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
312239 AGCTTGAGTT
312249 GTATCGGTAGTTGC-A-TCATAG-
1 GTATCGGTAGTT-CTACTCATAGA
*
312270 GTATCGTTAGTTCTACTCATAGAA
1 GTATCGGTAGTTCTACTCATAG-A
312294 GTATCGGTAG
1 GTATCGGTAG
312304 CTCGTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.43
22 6 0.21
24 9 0.32
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (23 bp):
GTATCGGTAGTTCTACTCATAGA
Found at i:323537 original size:16 final size:16
Alignment explanation
Indices: 323518--323559 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
323508 AAAGAAAAAT
*
323518 AAAGAAAAAATTATTA
1 AAAGAAAAAATTATAA
* *
323534 AAAGAAAAATTTGTAA
1 AAAGAAAAAATTATAA
323550 AAAGAAAAAA
1 AAAGAAAAAA
323560 AAATTAGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAGAAAAAATTATAA
Found at i:328858 original size:23 final size:22
Alignment explanation
Indices: 328832--328879 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
328822 AAATTATGGA
**
328832 TTTTCATAATTTTTTAATTTTTT
1 TTTTCAT-ATTTTAGAATTTTTT
328855 TTTTCATATTTTAGAATTTTTT
1 TTTTCATATTTTAGAATTTTTT
328877 TTT
1 TTT
328880 GGGAATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTCATATTTTAGAATTTTTT
Found at i:334177 original size:26 final size:26
Alignment explanation
Indices: 334146--334200 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
334136 TTGGAAGATG
*
334146 GTTTATGCTGGTAAGTTAAGGATGGT
1 GTTTATGCTGGCAAGTTAAGGATGGT
* **
334172 GTTTATGTTGGCAAGTTGGGGATGGT
1 GTTTATGCTGGCAAGTTAAGGATGGT
334198 GTT
1 GTT
334201 AATTTGTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.04, G:0.38, T:0.40
Consensus pattern (26 bp):
GTTTATGCTGGCAAGTTAAGGATGGT
Found at i:336786 original size:23 final size:25
Alignment explanation
Indices: 336759--336804 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
336749 CTAATTATGA
336759 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
336782 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
336805 TGGATCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:337915 original size:12 final size:13
Alignment explanation
Indices: 337898--337927 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
337888 ATATTTTTTG
337898 TTTTTA-ATTTAA
1 TTTTTACATTTAA
337910 TTTTTACATTTAA
1 TTTTTACATTTAA
337923 TTTTT
1 TTTTT
337928 TTATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:340075 original size:6 final size:6
Alignment explanation
Indices: 340066--340142 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
340056 AATTAGTACA
* * *
340066 TTTATT TTTATT TTTATT TTTA-T TTCATT TTCA-T TTTAGTT TTTAAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT
340113 TTTA-T TTTATT TTT-TAT TTTA-T TTTATT TT
1 TTTATT TTTATT TTTAT-T TTTATT TTTATT TT
340143 ATTATGCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
5 19 0.31
6 37 0.61
7 5 0.08
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:340083 original size:12 final size:11
Alignment explanation
Indices: 340066--340142 Score: 84
Period size: 12 Copynumber: 6.7 Consensus size: 11
340056 AATTAGTACA
340066 TTTATTTTTATT
1 TTTATTTTTA-T
340078 TTTATTTTTAT
1 TTTATTTTTAT
* *
340089 TTCATTTTCAT
1 TTTATTTTTAT
340100 TTTAGTTTTTAAT
1 TTTA-TTTTT-AT
340113 TTTA-TTTTAT
1 TTTATTTTTAT
*
340123 TTTTTATTTTAT
1 TTTAT-TTTTAT
340135 TTTATTTT
1 TTTATTTT
340143 ATTATGCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
10 5 0.09
11 20 0.36
12 24 0.44
13 6 0.11
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:340085 original size:5 final size:5
Alignment explanation
Indices: 340066--340145 Score: 70
Period size: 5 Copynumber: 14.2 Consensus size: 5
340056 AATTAGTACA
*
340066 TTTATT TTTATT TTTATT TTTAT TTCAT TTTCAT TTTAGTT TTTAAT TTTAT
1 TTTA-T TTTA-T TTTA-T TTTAT TTTAT TTT-AT TTTA--T TTT-AT TTTAT
340118 TTTATTT TTTAT TTTAT TTTAT TTTAT T
1 TTTA--T TTTAT TTTAT TTTAT TTTAT T
340146 ATGCATTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 13
0.81 0.02 0.16
Matches are distributed among these distances:
5 31 0.47
6 25 0.38
7 9 0.14
8 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:340153 original size:22 final size:23
Alignment explanation
Indices: 340106--340154 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
340096 TCATTTTAGT
* **
340106 TTTTAATTTTATTTTATTTTTTA
1 TTTTAATTTTATTTTATTATGCA
340129 TTTT-ATTTTATTTTATTATGCA
1 TTTTAATTTTATTTTATTATGCA
340151 TTTT
1 TTTT
340155 TTTATTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTAATTTTATTTTATTATGCA
Found at i:340868 original size:180 final size:179
Alignment explanation
Indices: 340560--340904 Score: 548
Period size: 180 Copynumber: 1.9 Consensus size: 179
340550 ATTTTTGAGA
* * *
340560 TATGAAAGAGTCAAGCATGATAAGTTGTCTTTAGAATTAAATATTTTAAGTTGTCTCCCTGAAAT
1 TATGAAAGAGTCAAGAATGATAACTTGTCTTCAGAATTAAATATTTTAAGTTGTCTCCCTGAAAT
* *
340625 GAAATATTATCTTCAAATTTTGATATTGCAGAATTGACATCAAAACCATAATTTTTGTGAGCTTT
66 GAAATATTATCTTCAAATTTTGAAATTGCAGAATTGACACCAAAACCATAATTTTTGTGAGCTTT
*
340690 TGAGCCTATAGAGCATATATTTTATTTCGTGCTCATACTAATCTTTAAGT
131 TGAGCCTATAGAGCAT-TATTTTATTTCATGCTCATACTAATCTTTAAGT
* * *
340740 TATGAGAGAGTCAAGAATGATAACTTGTCTTCAGAATTAAATATTTT-AGATTGTCTTCCTGAAT
1 TATGAAAGAGTCAAGAATGATAACTTGTCTTCAGAATTAAATATTTTAAG-TTGTCTCCCTGAAA
**
340804 TGAAATATTATCTTCAAATTTTGAAATTGCAGGTTTGACACCAAAACCATAATTTTTGTGAGCTT
65 TGAAATATTATCTTCAAATTTTGAAATTGCAGAATTGACACCAAAACCATAATTTTTGTGAGCTT
* *
340869 TTGAGCCTATAGAGCATTTTTTTTTTTCATGCTCAT
130 TTGAGCCTATAGAGCATTATTTTATTTCATGCTCAT
340905 GGTATTTTTG
Statistics
Matches: 151, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
179 18 0.12
180 133 0.88
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (179 bp):
TATGAAAGAGTCAAGAATGATAACTTGTCTTCAGAATTAAATATTTTAAGTTGTCTCCCTGAAAT
GAAATATTATCTTCAAATTTTGAAATTGCAGAATTGACACCAAAACCATAATTTTTGTGAGCTTT
TGAGCCTATAGAGCATTATTTTATTTCATGCTCATACTAATCTTTAAGT
Found at i:347550 original size:22 final size:22
Alignment explanation
Indices: 347524--347585 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
347514 TTAAAAATGA
* * *
347524 TAAAATTTTAATTTAATTCT-T
1 TAAAATTATAATTTAATTATCG
*
347545 TAAAAATTATAATTTTATTATCG
1 T-AAAATTATAATTTAATTATCG
347568 TAAAATTATAATTTAATT
1 TAAAATTATAATTTAATT
347586 TTAACCCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TAAAATTATAATTTAATTATCG
Found at i:348062 original size:15 final size:15
Alignment explanation
Indices: 348044--348076 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
348034 TAATTTTTAA
348044 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
348059 AAATTATTAAAAATT
1 AAATTATTAAAAATT
348074 AAA
1 AAA
348077 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:356431 original size:31 final size:33
Alignment explanation
Indices: 356386--356446 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
356376 GAGTTTTAAA
*
356386 TTAGGGTTATTG-TTT-TTAAATTTTTAGGTGT
1 TTAGGGTTAGTGTTTTATTAAATTTTTAGGTGT
* *
356417 TTAGGTTTAGTGTTTTATTTAATTTTTAGG
1 TTAGGGTTAGTGTTTTATTAAATTTTTAGG
356447 GTTCAAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 3 0.12
33 12 0.48
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.59
Consensus pattern (33 bp):
TTAGGGTTAGTGTTTTATTAAATTTTTAGGTGT
Found at i:356504 original size:29 final size:30
Alignment explanation
Indices: 356456--356512 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
356446 GGTTCAAGGG
356456 TTCTGAAAAAAAAAAATTTGACGAGATGGA
1 TTCTGAAAAAAAAAAATTTGACGAGATGGA
*
356486 TTCTG-AAAAAAAAATTTTGACGAGATG
1 TTCTGAAAAAAAAAAATTTGACGAGATG
356513 AGTTCAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (30 bp):
TTCTGAAAAAAAAAAATTTGACGAGATGGA
Found at i:359452 original size:22 final size:22
Alignment explanation
Indices: 359420--359466 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
359410 AATTATAATA
*
359420 TTTTACATTTTTACCCCAAACTT
1 TTTTACATTTTT-CCCCAAAATT
*
359443 TTTTAC-TTTTTCCCTAAAATT
1 TTTTACATTTTTCCCCAAAATT
359464 TTT
1 TTT
359467 ACTCCCCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTACATTTTTCCCCAAAATT
Found at i:360323 original size:22 final size:19
Alignment explanation
Indices: 360289--360332 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
360279 ATGTTGATTA
360289 TAAATAGGATTAATTAAGGT
1 TAAATAGGATTAATTAA-GT
360309 TAAATAAGTGATTAATTAAGT
1 TAAAT-AG-GATTAATTAAGT
360330 TAA
1 TAA
360333 TCATGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (19 bp):
TAAATAGGATTAATTAAGT
Found at i:361787 original size:40 final size:40
Alignment explanation
Indices: 361704--361789 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
361694 CTTTTCATCC
* * * *
361704 TTTTCATTTATTATCTTTTCGGATAACATTCTTTTCAATA
1 TTTTCATTTATTATCCTTCCGGATAACATTCTTTTAAAAA
* *
361744 TTTTTATTTATTATCCTTCCGGATAATA-TCTTTTTAAAAA
1 TTTTCATTTATTATCCTTCCGGATAACATTC-TTTTAAAAA
361784 TTTTCA
1 TTTTCA
361790 ACCATGATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.05
40 36 0.95
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.55
Consensus pattern (40 bp):
TTTTCATTTATTATCCTTCCGGATAACATTCTTTTAAAAA
Found at i:363389 original size:10 final size:9
Alignment explanation
Indices: 363366--363391 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
363356 AACAATTAAA
363366 TAAAAAATT
1 TAAAAAATT
363375 TAAAAAATT
1 TAAAAAATT
363384 TAAAAAAT
1 TAAAAAAT
363392 GAAATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAAATT
Found at i:366709 original size:20 final size:21
Alignment explanation
Indices: 366684--366722 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
366674 TGAAGCAAAC
366684 ATTTAGAA-TGAAAATGAGTT
1 ATTTAGAACTGAAAATGAGTT
*
366704 ATTTAGAACTGAAATTGAG
1 ATTTAGAACTGAAAATGAG
366723 AAGTTCTGTA
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:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTAGAACTGAAAATGAGTT
Found at i:370122 original size:17 final size:16
Alignment explanation
Indices: 370108--370141 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
370098 TTTAAATATT
370108 AAAA-TATAATCAATA
1 AAAATTATAATCAATA
370123 AAAATTTATAATCAATA
1 AAAA-TTATAATCAATA
370140 AA
1 AA
370142 TTTTAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
17 13 0.76
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTATAATCAATA
Found at i:372730 original size:17 final size:17
Alignment explanation
Indices: 372705--372738 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
372695 TGTAGCTTTG
* *
372705 TTTCTTCTTCTCTTCTT
1 TTTCCTCTTCTCCTCTT
372722 TTTCCTCTTCTCCTCTT
1 TTTCCTCTTCTCCTCTT
372739 CCTGTAACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCCTCTTCTCCTCTT
Found at i:379581 original size:55 final size:55
Alignment explanation
Indices: 379497--379611 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
379487 AAACAAGGGT
* * *
379497 CACACGGTCGTGCCTTAGATCATGTGCCAAACTGTGTGCATACCCGAAATACCAA
1 CACACAGTCATGCCTTAGATCATGTGCCAAACCGTGTGCATACCCGAAATACCAA
*
379552 CACACAGTCATGCCTTAGATCGTGTGCCAAACCGTGTGCATACCCGAAATACCAA
1 CACACAGTCATGCCTTAGATCATGTGCCAAACCGTGTGCATACCCGAAATACCAA
379607 CACAC
1 CACAC
379612 GGTCGTGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (55 bp):
CACACAGTCATGCCTTAGATCATGTGCCAAACCGTGTGCATACCCGAAATACCAA
Found at i:379643 original size:55 final size:55
Alignment explanation
Indices: 379515--379644 Score: 136
Period size: 55 Copynumber: 2.4 Consensus size: 55
379505 CGTGCCTTAG
* * ** *
379515 ATCATGTGCCAAACTGTGTGCATACCCGAAATACCAACACACAGTCATGCCTTAG
1 ATCATGTGACAAACCGTGTGCATACCCGAAATACCAACACACAGTCATGCCACAA
* * * * *
379570 ATCGTGTGCCAAACCGTGTGCATACCCGAAATACCAACACACGGTCGTGTCACAA
1 ATCATGTGACAAACCGTGTGCATACCCGAAATACCAACACACAGTCATGCCACAA
* *
379625 A-CTATGTGACAGATCGTGTG
1 ATC-ATGTGACAAACCGTGTG
379645 AGCATGCGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
54 1 0.02
55 61 0.98
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (55 bp):
ATCATGTGACAAACCGTGTGCATACCCGAAATACCAACACACAGTCATGCCACAA
Found at i:381153 original size:31 final size:31
Alignment explanation
Indices: 381115--381177 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
381105 TTTCTCTTTC
381115 CTTGTGAGTATTTATATCCCTCCAAATTGTA
1 CTTGTGAGTATTTATATCCCTCCAAATTGTA
381146 CTTGTGAGTATTTATATCCCTCCAAATTGTA
1 CTTGTGAGTATTTATATCCCTCCAAATTGTA
381177 C
1 C
381178 AGGTGTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (31 bp):
CTTGTGAGTATTTATATCCCTCCAAATTGTA
Found at i:382497 original size:17 final size:17
Alignment explanation
Indices: 382475--382507 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
382465 CATTAACACT
*
382475 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
382492 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
382508 GCTTACTAAC
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:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:383760 original size:38 final size:38
Alignment explanation
Indices: 383697--383780 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
383687 CCTGCAACGA
* * * *
383697 CAATTCTGGGCATGCTTATGCAGTGATAGTTTTAGGCG
1 CAATTCTGGACATGCTTATGCAGTGAAAATTCTAGGCG
* *
383735 CAATTCTGGACAT-CTTCATGTAGTGAAAATTCTGGGCG
1 CAATTCTGGACATGCTT-ATGCAGTGAAAATTCTAGGCG
383773 CAATTCTG
1 CAATTCTG
383781 AATACACTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (38 bp):
CAATTCTGGACATGCTTATGCAGTGAAAATTCTAGGCG
Found at i:385079 original size:19 final size:19
Alignment explanation
Indices: 385052--385248 Score: 225
Period size: 19 Copynumber: 10.4 Consensus size: 19
385042 CAAAACAGTA
*
385052 TATTGCTCTTACGAGCTAG
1 TATTGCTCTTACGAGCCAG
* *
385071 TATTACTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
* *
385090 CATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* **
385109 TATTGCTCTTTCGAGTTAG
1 TATTGCTCTTACGAGCCAG
*
385128 TATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
385147 TATTGCTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * *
385166 TATTACTCTTGCGAGCCAA
1 TATTGCTCTTACGAGCCAG
*
385185 TATTTG-TCTTACGAGCCAA
1 TA-TTGCTCTTACGAGCCAG
* *
385204 TATTGCTCTTGCGAGCTAG
1 TATTGCTCTTACGAGCCAG
*
385223 TATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
385242 TATTGCT
1 TATTGCT
385249 GATTCCTTTC
Statistics
Matches: 146, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
18 3 0.02
19 141 0.97
20 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:391808 original size:19 final size:19
Alignment explanation
Indices: 391784--391997 Score: 241
Period size: 19 Copynumber: 11.3 Consensus size: 19
391774 AATACAATAA
391784 ATTGCTCTTACGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
*
391803 ATTGCTCTTGCGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
* **
391822 ATTACTCTTGTGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
* * * *
391841 GTTGCTCTCACAAGCCAAT
1 ATTGCTCTTACGAGCCAGT
*
391860 ATTGCTCTTGCGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
* * *
391879 ATTGCTCTCACGAGTCAAT
1 ATTGCTCTTACGAGCCAGT
*
391898 ATTGCTCTTGCGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
* * *
391917 ATTGTTCTTGCGAGCTAGT
1 ATTGCTCTTACGAGCCAGT
* *
391936 ATTGCTCTCACGAGCTAGT
1 ATTGCTCTTACGAGCCAGT
*
391955 ATTGCTCTCACGAGCC-GT
1 ATTGCTCTTACGAGCCAGT
*
391973 ATTGCTCTCACGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
391992 ATTGCT
1 ATTGCT
391998 TATTCCTTTC
Statistics
Matches: 165, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
18 18 0.11
19 147 0.89
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (19 bp):
ATTGCTCTTACGAGCCAGT
Found at i:391873 original size:57 final size:57
Alignment explanation
Indices: 391784--391997 Score: 268
Period size: 57 Copynumber: 3.8 Consensus size: 57
391774 AATACAATAA
* * ***
391784 ATTGCTCTTACGAGCCAGTATTGCTCTTGCGAGCCAGTATTACTCTTGTGAGCCAGT
1 ATTGCTCTCACGAGCCAGTATTGCTCTTGCGAGCCAGTATTGCTCTCACGAGCCAGT
* * * * *
391841 GTTGCTCTCACAAGCCAATATTGCTCTTGCGAGCCAGTATTGCTCTCACGAGTCAAT
1 ATTGCTCTCACGAGCCAGTATTGCTCTTGCGAGCCAGTATTGCTCTCACGAGCCAGT
** * * *
391898 ATTGCTCTTGCGAGCCAGTATTGTTCTTGCGAGCTAGTATTGCTCTCACGAGCTAGT
1 ATTGCTCTCACGAGCCAGTATTGCTCTTGCGAGCCAGTATTGCTCTCACGAGCCAGT
**
391955 ATTGCTCTCACGAGCC-GTATTGCTCTCACGAGCCAGTATTGCT
1 ATTGCTCTCACGAGCCAGTATTGCTCTTGCGAGCCAGTATTGCT
391998 TATTCCTTTC
Statistics
Matches: 131, Mismatches: 26, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
56 23 0.18
57 108 0.82
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (57 bp):
ATTGCTCTCACGAGCCAGTATTGCTCTTGCGAGCCAGTATTGCTCTCACGAGCCAGT
Found at i:401660 original size:22 final size:22
Alignment explanation
Indices: 401632--401673 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
401622 ACAAAAATGA
401632 TGTTTAATTCTTTTAATTTTGG
1 TGTTTAATTCTTTTAATTTTGG
401654 TGTTTAATTCTTTTAATTTT
1 TGTTTAATTCTTTTAATTTT
401674 AACCAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (22 bp):
TGTTTAATTCTTTTAATTTTGG
Found at i:406707 original size:121 final size:121
Alignment explanation
Indices: 406493--406858 Score: 714
Period size: 121 Copynumber: 3.0 Consensus size: 121
406483 CTGCTCACAC
406493 AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
1 AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
406558 AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
66 AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
*
406614 AAGCTGTCGAGGACTCGCAACCTATGTGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
1 AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
*
406679 AAATTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
66 AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
406735 AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
1 AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
406800 AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
66 AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
406856 AAG
1 AAG
406859 TCCCAGCCAT
Statistics
Matches: 241, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 241 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (121 bp):
AAGCTGTCGAGGACTCGCAACCTATGCGGTACCCTAGCCATCGATACGGTGTTTATCTATACTGT
AAACTGTTTCCTAACGATGCTGCTCACACGAGCTATCAAGAGTATGCATAAAGCAT
Found at i:408664 original size:29 final size:29
Alignment explanation
Indices: 408622--408679 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
408612 ATTTGCGGAT
408622 GATATGAAGTACTAAAATTCAACCTGGTC
1 GATATGAAGTACTAAAATTCAACCTGGTC
408651 GATATGAAGTACTAAAATTCAACCTGGTC
1 GATATGAAGTACTAAAATTCAACCTGGTC
408680 CCTAAAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (29 bp):
GATATGAAGTACTAAAATTCAACCTGGTC
Found at i:413979 original size:30 final size:30
Alignment explanation
Indices: 413945--414002 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
413935 TTAAGCTACA
413945 TAATTTAGTCATTCAA-CACAATTTAGTCCT
1 TAATTTAGTCATT-AAGCACAATTTAGTCCT
413975 TAATTTAGTCATTAAGCACAATTTAGTC
1 TAATTTAGTCATTAAGCACAATTTAGTC
414003 ATTTTGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (30 bp):
TAATTTAGTCATTAAGCACAATTTAGTCCT
Found at i:414200 original size:82 final size:82
Alignment explanation
Indices: 414104--414270 Score: 271
Period size: 82 Copynumber: 2.0 Consensus size: 82
414094 CACAACTAAC
* * *
414104 CATAGCCGATTTCTCTTAGGTATCTATCCCACCCATACACACATTTATTTTCATAACCATACATG
1 CATAGCCGAATTCTCTTAGGTATCTATCCCACCCATACACACATTTAATTTCATAACAATACATG
*
414169 TAATTTCACCATTTTCA
66 TAATTCCACCATTTTCA
* * *
414186 CATAGCCGAATTCTCTTGGGTATCTATCTCACCCATTCACACATTTAATTTCATAACAATACATG
1 CATAGCCGAATTCTCTTAGGTATCTATCCCACCCATACACACATTTAATTTCATAACAATACATG
414251 TAATTCCACCATTTTCA
66 TAATTCCACCATTTTCA
414268 CAT
1 CAT
414271 TTTAATCCTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36
Consensus pattern (82 bp):
CATAGCCGAATTCTCTTAGGTATCTATCCCACCCATACACACATTTAATTTCATAACAATACATG
TAATTCCACCATTTTCA
Found at i:416872 original size:17 final size:17
Alignment explanation
Indices: 416841--416873 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
416831 CTTAAGGACT
416841 TTTTAATTTTATTTAAG
1 TTTTAATTTTATTTAAG
416858 TTTT-ATTTTAGTTTAA
1 TTTTAATTTTA-TTTAA
416874 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTATTTAAG
Found at i:416924 original size:31 final size:32
Alignment explanation
Indices: 416874--416936 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
416864 TTTAGTTTAA
* *
416874 TAAGTGTTTGCATCTTTAATTATGTCTTGCAT
1 TAAGTGTTTGCATCTTTAATTAAGTCATGCAT
416906 TAAGTGCTTTGC-T-TTTAATTAAGTCATGCAT
1 TAAGTG-TTTGCATCTTTAATTAAGTCATGCAT
416937 AAAAGCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 7 0.25
33 5 0.18
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.48
Consensus pattern (32 bp):
TAAGTGTTTGCATCTTTAATTAAGTCATGCAT
Found at i:417157 original size:51 final size:50
Alignment explanation
Indices: 417052--417159 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
417042 CATGCAATAT
* * * *
417052 GTAACTCACATGCTAGTTAAGTTTGCATCATAAATTATGTCAAGCACTAT
1 GTAACTCACATGATAGTTAAGTTTGCATCATAAATAAAGTCAAGCACTAA
* * ** *
417102 GTAACTCCCATGATAGTTAAAGTTTGCATCTTAAATAAAGTCTTGCATTAA
1 GTAACTCACATGATAGTT-AAGTTTGCATCATAAATAAAGTCAAGCACTAA
417153 GTAACTC
1 GTAACTC
417160 TTTTGTTCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 16 0.33
51 32 0.67
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (50 bp):
GTAACTCACATGATAGTTAAGTTTGCATCATAAATAAAGTCAAGCACTAA
Found at i:419634 original size:36 final size:36
Alignment explanation
Indices: 419565--419634 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
419555 ACATCTCGAT
** *
419565 TAATGCTAAGGAAGTGCTTACATCTTGGATAGAGAG
1 TAATGCTAAGGAAGAACTTACATATTGGATAGAGAG
** *
419601 TAATGCTAAGGAAGAACTTATGTATTGGTTAGAG
1 TAATGCTAAGGAAGAACTTACATATTGGATAGAG
419635 CATAAGGCCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (36 bp):
TAATGCTAAGGAAGAACTTACATATTGGATAGAGAG
Found at i:420485 original size:12 final size:12
Alignment explanation
Indices: 420468--420492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
420458 ATTCGTGTAT
420468 GCACACGGTCTG
1 GCACACGGTCTG
420480 GCACACGGTCTG
1 GCACACGGTCTG
420492 G
1 G
420493 GGCATGATCG
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:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (12 bp):
GCACACGGTCTG
Found at i:425018 original size:21 final size:21
Alignment explanation
Indices: 424994--425046 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
424984 ATAGATTTCT
424994 ACCGATACAAGTGATAGTTCC
1 ACCGATACAAGTGATAGTTCC
* *
425015 ACCGATATAAGTGATAGTTCT
1 ACCGATACAAGTGATAGTTCC
425036 ACCGATACAAG
1 ACCGATACAAG
425047 ATTCATCTCT
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:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (21 bp):
ACCGATACAAGTGATAGTTCC
Found at i:436439 original size:7 final size:7
Alignment explanation
Indices: 436427--436459 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
436417 TAAATCAAAT
436427 GTGTTGA
1 GTGTTGA
436434 GTGTTGA
1 GTGTTGA
436441 GTGTTGA
1 GTGTTGA
436448 GTGTTGA
1 GTGTTGA
436455 GTGTT
1 GTGTT
436460 AAATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (7 bp):
GTGTTGA
Found at i:438008 original size:52 final size:51
Alignment explanation
Indices: 437912--438091 Score: 182
Period size: 52 Copynumber: 3.5 Consensus size: 51
437902 ATTTCCTTTA
* * *** *
437912 ATACTCACGATGACACATAGTCATCTAACCTCTTGTTCCTTAAAGTAATTTT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAAACCATAAAG-AATTTT
* * * * * * *
437964 ACACTCACGATAACACATAGTCATCGGACCTCATAACCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAAACCATAAAGAATT-TT
*
438016 ATACTCACGATGACACATAATCATCGAACCTCATAAACCATAAA-AGATTTAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAAACCATAAAGA-ATTT-T
*
438068 ATACTCACGATGACACAGAGTCAT
1 ATACTCACGATGACACATAGTCAT
438092 TAGACCTTTT
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
51 3 0.03
52 101 0.97
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAAACCATAAAGAATTTT
Found at i:440974 original size:18 final size:17
Alignment explanation
Indices: 440931--440979 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
440921 CCTAATCCAA
*
440931 ATAAATAATTTAATTAT
1 ATAAATAATTTAATTAC
440948 A-AAATTAATTTATATTAC
1 ATAAA-TAATTTA-ATTAC
440966 ATAAATAATTTAAT
1 ATAAATAATTTAAT
440980 AAAAAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 12 0.43
19 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAATAATTTAATTAC
Found at i:441521 original size:13 final size:13
Alignment explanation
Indices: 441505--441535 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
441495 GATATCAGAC
441505 ATAGATAAAATAA
1 ATAGATAAAATAA
*
441518 ATAGCTAAAATAA
1 ATAGATAAAATAA
441531 ATAGA
1 ATAGA
441536 CTACTTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (13 bp):
ATAGATAAAATAA
Found at i:444234 original size:14 final size:14
Alignment explanation
Indices: 444217--444243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
444207 TTATAAAATA
444217 AAAGAACAAAAAGT
1 AAAGAACAAAAAGT
444231 AAAGAACAAAAAG
1 AAAGAACAAAAAG
444244 AATAAGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAACAAAAAGT
Found at i:449538 original size:17 final size:18
Alignment explanation
Indices: 449504--449538 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
449494 ATTTTATGAG
449504 TTTTAATTCATCTATTAA
1 TTTTAATTCATCTATTAA
*
449522 TTTTTATTCAT-TATTAA
1 TTTTAATTCATCTATTAA
449539 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATTCATCTATTAA
Found at i:450282 original size:20 final size:22
Alignment explanation
Indices: 450248--450294 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
450238 CAAATGTGTT
450248 AAAATTATTAATT-AAA-AATA
1 AAAATTATTAATTAAAATAATA
**
450268 AAAATTATTTTTTAAAATAATA
1 AAAATTATTAATTAAAATAATA
450290 AAAAT
1 AAAAT
450295 ATGTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
22 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTATTAATTAAAATAATA
Found at i:460525 original size:43 final size:43
Alignment explanation
Indices: 460446--460673 Score: 269
Period size: 43 Copynumber: 5.3 Consensus size: 43
460436 TTATTTGGAA
* *
460446 AAACGCCGTTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
460489 AAATGCCACTAAA-ATACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGA-ACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
460532 AAACACCGCTAAAGAACATGTTCTTTAGCGGGGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *** ** *
460575 AAACGCTGCTAAAGAATATGGTCAAAAGCCCCGCTTTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
460618 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
460661 AAACGCCACTAAA
1 AAACGCCGCTAAA
460674 ATTAACAAAT
Statistics
Matches: 149, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
42 1 0.01
43 147 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:471027 original size:90 final size:91
Alignment explanation
Indices: 470830--471112 Score: 405
Period size: 90 Copynumber: 3.2 Consensus size: 91
470820 ATGCTGCTAT
* * ** *
470830 CACAAGCTGTCGAGGACTCGTAATATATGCAATACCTCAACCATCGATACAATA-CTATGCATAT
1 CACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAATATCTGTGCATAT
*
470894 AACTGTTCCCTAACGATGCTG-TTCA
66 AACTGTTCCCTAACGATGATGCTTCA
* *
470919 CACAAGCTGTCGAGGACTCGCAACATATGTGGTACCTCAACCATCGATA-AGGTATCTGTGCATA
1 CACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACA-ATATCTGTGCATA
*
470983 TAACTGTTCCCTAACGATGTTGCTT-A
65 TAACTGTTCCCTAACGATGATGCTTCA
** * *
471009 CATGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAATATTTGTGCATAT
1 CACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAATATCTGTGCATAT
471074 AACTGTTCCCTAACGATGATGC-TCA
66 AACTGTTCCCTAACGATGATGCTTCA
471099 CACAAGCTGTCGAG
1 CACAAGCTGTCGAG
471113 AATATGCACT
Statistics
Matches: 171, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
88 1 0.01
89 47 0.27
90 120 0.70
91 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (91 bp):
CACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAATATCTGTGCATAT
AACTGTTCCCTAACGATGATGCTTCA
Found at i:474606 original size:9 final size:9
Alignment explanation
Indices: 474592--474650 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
474582 GTAAATGATT
474592 TTAAAATTA
1 TTAAAATTA
474601 TTAAAATTA
1 TTAAAATTA
474610 TT----TT-
1 TTAAAATTA
474614 TTAAAA-TA
1 TTAAAATTA
474622 -TAAAATTA
1 TTAAAATTA
474630 TTAAAATTA
1 TTAAAATTA
474639 TTTTAAAATTA
1 --TTAAAATTA
474650 T
1 T
474651 AATCATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.15
8 2 0.05
9 20 0.49
11 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:474612 original size:20 final size:20
Alignment explanation
Indices: 474584--474650 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
474574 TCACGTCAGT
*
474584 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
474604 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
474624 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
474644 AAATTAT
1 AAATTAT
474651 AATCATCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
20 21 0.54
21 2 0.05
22 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:475587 original size:40 final size:40
Alignment explanation
Indices: 475532--475609 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
475522 ATGATGATTA
* *
475532 TAATTTTAAAATAATTTTAATAATTTTATATTTTAAAATT
1 TAATTATAAAATAATTTCAATAATTTTATATTTTAAAATT
*
475572 TAATTATAAAATAATTTCACTAATTTTATATTTTAAAA
1 TAATTATAAAATAATTTCAATAATTTTATATTTTAAAA
475610 AAATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (40 bp):
TAATTATAAAATAATTTCAATAATTTTATATTTTAAAATT
Found at i:476372 original size:21 final size:20
Alignment explanation
Indices: 476347--476393 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
476337 TAAATATCTT
476347 ATAATTCTTAATAATTTATAA
1 ATAATTCTTAATAATTT-TAA
* * *
476368 ATAATTTTTTATAATTTTTA
1 ATAATTCTTAATAATTTTAA
476388 ATAATT
1 ATAATT
476394 ATTTGAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTCTTAATAATTTTAA
Found at i:476531 original size:20 final size:21
Alignment explanation
Indices: 476494--476541 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
476484 TGTTACTTGT
* *
476494 AATAATTTCTTATCATTTTGA
1 AATATTTTCTTATAATTTTGA
*
476515 AATATTTTC-TATAATTTTTA
1 AATATTTTCTTATAATTTTGA
476535 AATATTT
1 AATATTT
476542 GTTGATGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (21 bp):
AATATTTTCTTATAATTTTGA
Found at i:477731 original size:21 final size:21
Alignment explanation
Indices: 477690--477741 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
477680 TATTTGATTT
477690 TAATTTTTATTACTCATTTAA
1 TAATTTTTATTACTCATTTAA
477711 TAATTATTT-TTA-TCATATTAA
1 TAATT-TTTATTACTCAT-TTAA
477732 TAATTTTTAT
1 TAATTTTTAT
477742 AGCAATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTTTATTACTCATTTAA
Found at i:478463 original size:22 final size:23
Alignment explanation
Indices: 478404--478465 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
478394 TTTAATTCGA
478404 AATTAAATTATAATTTTTATAAT
1 AATTAAATTATAATTTTTATAAT
* *
478427 AATAAAAATATAATTTTGTA-AAT
1 AATTAAATTATAATTTT-TATAAT
*
478450 -ATTAAATTAAAATTTT
1 AATTAAATTATAATTTT
478466 ATTATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 13 0.39
23 18 0.55
24 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTAAATTATAATTTTTATAAT
Found at i:479516 original size:21 final size:22
Alignment explanation
Indices: 479479--479520 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
479469 ATTAATACTT
*
479479 ATATATTATAGTATTAAAGAGC
1 ATATATTATAATATTAAAGAGC
479501 ATATATTA-AATATTAAAGAG
1 ATATATTATAATATTAAAGAG
479521 GGAACAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (22 bp):
ATATATTATAATATTAAAGAGC
Found at i:491797 original size:25 final size:25
Alignment explanation
Indices: 491763--491812 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
491753 TAAGTCCCAA
*
491763 TTGTATCAACTGGTTGTAGAGTTTT
1 TTGTATCAACTGATTGTAGAGTTTT
491788 TTGTATCAACTGATTGTAGAGTTTT
1 TTGTATCAACTGATTGTAGAGTTTT
491813 AGTCTGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.48
Consensus pattern (25 bp):
TTGTATCAACTGATTGTAGAGTTTT
Found at i:492542 original size:187 final size:188
Alignment explanation
Indices: 492178--492555 Score: 625
Period size: 187 Copynumber: 2.0 Consensus size: 188
492168 TCAACAATTT
*
492178 GCAACAAATTTCCTAGTCTTAGCTCTCAAGGGATGTGACTCGGTTCTCGGTATTCAGTGGTTAAC
1 GCAACAAATTTCCTAGTCTTAGCTCTCAAGGGATGTGACTCGGTTCCCGGTATTCAGTGGTTAAC
* ** * * * *
492243 CACCTTGAGGTCCATAATTTTGGAATTTCAGTTCTCTTACTATGCAATTTGTATGCAAGGATCAT
66 CACCTTGAGGTCCATAAGTTTGGAATTTCAACTCTCTTACTATACAATTCGTATACAAGGATCAC
*
492308 TGTTGTACTTTGCAAGGAATACTTCAAGGATCCATTCAGATTATGACAGGTAATCAAA
131 TGTTGTACTTTGCAAGGAATACTTCAAGGAGCCATTCAGATTATGACAGGTAATCAAA
*
492366 GCAACAAATTTCCTAGTCTTAGCTCTCAAGGGATGTGACTTGGTTCCCGGTATTCAGTGGTTAAC
1 GCAACAAATTTCCTAGTCTTAGCTCTCAAGGGATGTGACTCGGTTCCCGGTATTCAGTGGTTAAC
*
492431 CACCTTGAGGTCCAT-AGTTTGGAATTTCAACTCTCTTACTATACAGTTCGTATACAAGGATCAC
66 CACCTTGAGGTCCATAAGTTTGGAATTTCAACTCTCTTACTATACAATTCGTATACAAGGATCAC
*
492495 TGTTGTACTTTGCAAGGAATACTTCCAA-GAGCCATTCAGATTATGACAGGTACTCAAA
131 TGTTGTACTTTGCAAGGAATACTT-CAAGGAGCCATTCAGATTATGACAGGTAATCAAA
492553 GCA
1 GCA
492556 CTAAGCTAGT
Statistics
Matches: 177, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
187 96 0.54
188 81 0.46
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (188 bp):
GCAACAAATTTCCTAGTCTTAGCTCTCAAGGGATGTGACTCGGTTCCCGGTATTCAGTGGTTAAC
CACCTTGAGGTCCATAAGTTTGGAATTTCAACTCTCTTACTATACAATTCGTATACAAGGATCAC
TGTTGTACTTTGCAAGGAATACTTCAAGGAGCCATTCAGATTATGACAGGTAATCAAA
Found at i:494628 original size:6 final size:6
Alignment explanation
Indices: 494617--494643 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
494607 AAACTTAGGT
494617 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
494644 CTAACATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:498915 original size:18 final size:18
Alignment explanation
Indices: 498892--498940 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
498882 TTATCAAAAA
* *
498892 TTTCTTTCTTTTTTTCTT
1 TTTCTTTCTTTTTCTCAT
*
498910 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCTCAT
498928 TTT-TTTCTTTTTC
1 TTTCTTTCTTTTTC
498941 AAATGACTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTTCTTTTTCTCAT
Found at i:510922 original size:51 final size:51
Alignment explanation
Indices: 510846--510948 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
510836 GGATTAGATG
* * * *
510846 CAACCGTTTGAACAAATTTGTGATGCTAGCAACTTTGCTGTAGGAGCTATC
1 CAACCATTTGAACAAATGTGTGATGCTAGCAACTTTGCTGTAGAAGATATC
*
510897 CAACCATTTGAACTAATGTGTGATGCTAGCAACTTTGCTGTAGAAGATATC
1 CAACCATTTGAACAAATGTGTGATGCTAGCAACTTTGCTGTAGAAGATATC
510948 C
1 C
510949 TAGGCCAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (51 bp):
CAACCATTTGAACAAATGTGTGATGCTAGCAACTTTGCTGTAGAAGATATC
Found at i:513170 original size:17 final size:17
Alignment explanation
Indices: 513147--513190 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
513137 TAGTTAGTTT
513147 TCATGCATTCTT-ATTG
1 TCATGCATTCTTAATTG
513163 TGCATGCATT-TTAATTG
1 T-CATGCATTCTTAATTG
513180 TCACTGCATTC
1 TCA-TGCATTC
513191 CTTTTAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (17 bp):
TCATGCATTCTTAATTG
Found at i:517150 original size:20 final size:18
Alignment explanation
Indices: 517121--517162 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
517111 AATAGTTAAA
517121 AAAAAATTAAAACTTTGTTT
1 AAAAAATTAAAA-TTT-TTT
*
517141 AAAAATTTAAAATTTTTT
1 AAAAAATTAAAATTTTTT
517159 AAAA
1 AAAA
517163 TCACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAAATTAAAATTTTTT
Found at i:517321 original size:148 final size:149
Alignment explanation
Indices: 517070--517741 Score: 733
Period size: 148 Copynumber: 4.4 Consensus size: 149
517060 TAATTAAAAC
* * * * *
517070 AAAATCATTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAAATTAAAACT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
* *
517135 TTGTTTAAAAATTTAAA--ATTT-TTTAAAATCACTAAAAAATAGATTTTTATTTTTTTAAAAAT
66 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTTTA-TTTTTT-AAAAT
* *
517197 CTGAACTTTCTTTTTTTAATG
129 CTAAACTTTCTTTTTTTAAAG
* * * * *
517218 AAAATCACTACTTTACTTAAAAATCCAGACATTTATTTCAAAATAGTT-AAAAAAAATCAAAATT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
* * *
517282 TTATTTAAAAATTTAAAC-TTTCCTTTAAAATGACTAAAAAATAAATTTTGTATTTTTTAAAATC
66 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTT-TATTTTTTAAAATC
*
517346 TAAAC--T-TTTTTTTAATG
130 TAAACTTTCTTTTTTTAAAG
* *
517363 AAAATCACTATTTTACTTAAAAATCCAAAGTTTTATTTCGAAATAGTTAAAAAAAAAAATTAAAA
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT--AAAAAAAAATCAAAA
* *
517428 CTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACA-ATTTTT-TTTTTTAAAAT
64 CTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTTTATTTTTTAAAAT
*
517491 ATAAACTTTCTCTTTTTTTTTTTTTTTTTAAAG
129 CTAAAC-TT-TC----------TTTTTTTAAAG
* *
517524 AAAATCACTATTTTACTTAAAAATACAAACTTTTATTTCGAAATAGTT--AAAAAAATCAAAATT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
* *
517587 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATGA-TTAAAAACAGATTTTTA-TTTTTAAAATCT
66 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTTTATTTTTTAAAATCT
*
517650 AAACTTTCTCTTTTTTAAAA
131 AAACTTTCT-TTTTTTAAAG
* * * * * *
517670 AAACATTACTATTTTTCTTAAAAATCAAAACTTTAATTTTCGAAATTGTTTTAAAAAAAAAAACA
1 AAA-ATCACTATTTTACTTAAAAATCCAAACTTTTA-TTTCGAAATAG--TT-AAAAAAAAATCA
517735 AAACTTT
61 AAACTTT
517742 TCCTAAGATC
Statistics
Matches: 449, Mismatches: 43, Indels: 59
0.81 0.08 0.11
Matches are distributed among these distances:
145 55 0.12
146 29 0.06
147 58 0.13
148 99 0.22
149 53 0.12
150 5 0.01
153 15 0.03
155 2 0.00
156 10 0.02
157 67 0.15
161 56 0.12
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.43
Consensus pattern (149 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
TTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTTTATTTTTTAAAATCT
AAACTTTCTTTTTTTAAAG
Found at i:517616 original size:306 final size:295
Alignment explanation
Indices: 517063--517732 Score: 793
Period size: 306 Copynumber: 2.2 Consensus size: 295
517053 AATTTTTTAA
* * *
517063 TTAAAACAAAATCATTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTT--AAAAAAAA
1 TTAAAA-AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAAAA
* *
517126 ATTAAAACTTTGTTTAAAAATTTAAAATTTTTTAAAATCACTAAAAAATAGATTTTTATTTTTTT
65 ATTAAAACTATGTTTAAAAATTTAAAATTTTTTAAAATCACTAAAAAACAGATTTTTATTTTTTT
* * * * *
517191 AAAAATCTGAACTTTCTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCCAGACATTTATTT
130 AAAAATATAAACTTTCTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATACAAACATTTATTT
517256 CAAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAA
195 CAAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTCCTTTAAAATGA-TAAAA
*
517321 AATAAATTTTGTATTTTTTAAAATCTAAAC-T-T-TTTT
259 AACAAATTTT-TA-TTTTTAAAATCTAAACTTCTCTTTT
** * *
517357 TTAATGAAAATCACTATTTTACTTAAAAATCCAAAGTTTTATTTCGAAATAGTTAAAAAAAAAAA
1 TTAAAAAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAAAAA
* *
517422 TTAAAACTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACA-A-TTTT-TTTTT
66 TTAAAACTATGTTTAAAAATTTAAA--ATTT-TTTAAAATCACTAAAAAACAGATTTTTATTTTT
*
517484 TT-AAAATATAAACTTTCTCTTTTTTTTTTTTTTTTTAAAGAAAATCACTATTTTACTTAAAAAT
128 TTAAAAATATAAAC-TT-TC----------TTTTTTTAAAGAAAATCACTACTTTACTTAAAAAT
* * * *
517548 ACAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTCT
181 ACAAACATTTATTTCAAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAAC-TTTCCT
* *
517612 TTAAAATGATTAAAAACAGATTTTTATTTTTAAAATCTAAACTTTCTCTTTT
245 TTAAAATGATAAAAAACAAATTTTTATTTTTAAAATCTAAAC-TTCTCTTTT
* * * *
517664 TTAAAAAAACATTACTATTTTTCTTAAAAATCAAAACTTTAATTTTCGAAATTGTTTTAAAAAAA
1 TTAAAAAAA-ATCACTATTTTACTTAAAAATCAAAACTTTTA-TTTCGAAATAG--TTAAAAAAA
517729 AAAA
62 AAAA
517733 CAAAACTTTT
Statistics
Matches: 318, Mismatches: 32, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
293 43 0.14
294 13 0.04
295 42 0.13
296 6 0.02
297 4 0.01
298 18 0.06
303 16 0.05
304 2 0.01
305 45 0.14
306 68 0.21
307 11 0.03
308 27 0.08
309 10 0.03
311 13 0.04
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (295 bp):
TTAAAAAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAAAAA
TTAAAACTATGTTTAAAAATTTAAAATTTTTTAAAATCACTAAAAAACAGATTTTTATTTTTTTA
AAAATATAAACTTTCTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATACAAACATTTATTTC
AAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTCCTTTAAAATGATAAAAAA
CAAATTTTTATTTTTAAAATCTAAACTTCTCTTTT
Found at i:517636 original size:157 final size:158
Alignment explanation
Indices: 517351--517665 Score: 499
Period size: 157 Copynumber: 2.0 Consensus size: 158
517341 AAATCTAAAC
* * *
517351 TTTTTTTTAATGAAAATCACTATTTTACTTAAAAATCCAAAGTTTTATTTCGAAATAGTTAAAAA
1 TTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATACAAACTTTTATTTCGAAATAGTT---AA
* *
517416 AAAAAATTAAAACTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAATTTTTT
63 AAAAAATCAAAACTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAATTTTTA
517481 TTTTTAAAATATAAACTTTCTCTTTTTTTTT
128 TTTTTAAAATATAAACTTTCTCTTTTTTTTT
517512 TTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATACAAACTTTTATTTCGAAATAGTT-AAAA
1 TTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATACAAACTTTTATTTCGAAATAGTTAAAAA
* * *
517576 AAATCAAAATTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGA-TTAAAAACAGATTTTTATT
66 AAATCAAAACTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACA-ATTTTTATT
*
517640 TTTAAAATCTAAACTTTCTCTTTTTT
130 TTTAAAATATAAACTTTCTCTTTTTT
517666 AAAAAAACAT
Statistics
Matches: 144, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
156 8 0.06
157 79 0.55
161 57 0.40
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (158 bp):
TTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATACAAACTTTTATTTCGAAATAGTTAAAAA
AAATCAAAACTATGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAATTTTTATTT
TTAAAATATAAACTTTCTCTTTTTTTTT
Found at i:518159 original size:3 final size:3
Alignment explanation
Indices: 518151--518180 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
518141 TGAAACCCTA
518151 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
518181 TGTAGGAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:519613 original size:27 final size:26
Alignment explanation
Indices: 519543--519618 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
519533 TTTATACAAA
519543 ATTT-TATTTATTTATTATTTATTTG
1 ATTTATATTTATTTATTATTTATTTG
* * *
519568 ATTTACGTAATTA-TAATTATTTATTTT
1 ATTTA--TATTTATTTATTATTTATTTG
*
519595 ATTTATATCTTATTTATTACTTAT
1 ATTTATAT-TTATTTATTATTTAT
519619 ATTCTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
25 6 0.15
26 3 0.08
27 26 0.65
28 5 0.12
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTATATTTATTTATTATTTATTTG
Found at i:519789 original size:11 final size:11
Alignment explanation
Indices: 519769--519801 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
519759 TATTGTCATG
*
519769 ATTATATTATT
1 ATTATGTTATT
519780 ATTATGTTATT
1 ATTATGTTATT
519791 ATT-TGTTATT
1 ATTATGTTATT
519801 A
1 A
519802 ATTGTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (11 bp):
ATTATGTTATT
Found at i:520614 original size:13 final size:13
Alignment explanation
Indices: 520596--520621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
520586 TTTTTGATCC
520596 TTTGCATTTTATT
1 TTTGCATTTTATT
520609 TTTGCATTTTATT
1 TTTGCATTTTATT
520622 GCTTTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TTTGCATTTTATT
Found at i:531675 original size:49 final size:49
Alignment explanation
Indices: 531610--532119 Score: 290
Period size: 49 Copynumber: 10.4 Consensus size: 49
531600 CATAGAGTTT
* * * *
531610 GAAGA-GGATAGGTTGAAGCTGCAACGGCGGACTTAACACCCTAAAATC
1 GAAGAGGGATAGATTGAAGCTGCAACGACAGACTTAACACCTTAAAATC
* *
531658 GAAGAGGGATAGATTGAAGCTGCAACGATAGATTTAACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGCTGCAACGACAGACTTAACACCTTAAAATC
* * * * * * *
531706 TTAATAGGGAAAGATTGAAGCCGCAACGGCGGATCTT-ACACCTTAAAATT
1 -GAAGAGGGATAGATTGAAGCTGCAACGACAGA-CTTAACACCTTAAAATC
* * * ** *
531756 GAAGAGGGATAGGTTGAAGCCGCAATGATGGACCTAACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGCTGCAACGACAGACTTAACACCTTAAAATC
* * *
531804 TGAAGAGGGATAGGTTGAAG-TCACAATC-ACAGAGC-TAACACCCTAAAATC
1 -GAAGAGGGATAGATTGAAGCT-GCAA-CGACAGA-CTTAACACCTTAAAATC
* * *
531854 GAAGAGGGGATAGATTGAAG-TCGTAATGAC-GAATCTAACACCTTAAAATC
1 GAAGA-GGGATAGATTGAAGCT-GCAACGACAGACT-TAACACCTTAAAATC
* * * * * *
531904 GAAGAGGGAAATATTGAAGCTGTAATGATAAATCTT-ACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGCTGCAACGACAGA-CTTAACACCTTAAAATC
* * * * * * * *
531952 TGAAGAGGGATAGGTTGAAGCTGTAATGGCAAACCTAACACCCTAAAACC
1 -GAAGAGGGATAGATTGAAGCTGCAACGACAGACTTAACACCTTAAAATC
* * * * ** ** *
532002 AAAGAGGGAAAGATTGAAGTTGTAGGGATGGATCTT-ACAGCTTAAAATC
1 GAAGAGGGATAGATTGAAGCTGCAACGACAGA-CTTAACACCTTAAAATC
* * * * * * * *
532051 GAATAGGGATAGGTTGAAG-TCGCGAGGACAGACCTAATACCCTAAAACC
1 GAAGAGGGATAGATTGAAGCT-GCAACGACAGACTTAACACCTTAAAATC
* *
532100 AAAGAGGCATAGATTGAAGC
1 GAAGAGGGATAGATTGAAGC
532120 CACGACGATG
Statistics
Matches: 358, Mismatches: 80, Indels: 46
0.74 0.17 0.10
Matches are distributed among these distances:
48 14 0.04
49 295 0.82
50 48 0.13
51 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (49 bp):
GAAGAGGGATAGATTGAAGCTGCAACGACAGACTTAACACCTTAAAATC
Found at i:531794 original size:98 final size:98
Alignment explanation
Indices: 531609--532119 Score: 379
Period size: 98 Copynumber: 5.2 Consensus size: 98
531599 TCATAGAGTT
* * * *
531609 TGAAGA-GGATAGGTTGAAGCTGCAACGGCGGA-CTTAACACCCTAAAATCGAAGAGGGATAGAT
1 TGAAGAGGGAAAGATTGAAGCTGCAACGGCGGATCTT-ACACCTTAAAATCGAAGAGGGATAGGT
* * * * **
531672 TGAAGCTGCAACGATAGATTTAACACCTTAAAAC
65 TGAAGCCGCAATGACAAACCTAACACCTTAAAAC
* * * *
531706 TTAATAGGGAAAGATTGAAGCCGCAACGGCGGATCTTACACCTTAAAATTGAAGAGGGATAGGTT
1 TGAAGAGGGAAAGATTGAAGCTGCAACGGCGGATCTTACACCTTAAAATCGAAGAGGGATAGGTT
***
531771 GAAGCCGCAATGATGGACCTAACACCTTAAAAC
66 GAAGCCGCAATGACAAACCTAACACCTTAAAAC
* * * * * * * *
531804 TGAAGAGGGATAGGTTGAAG-TCACAATC-ACAGAGCTAACACCCTAAAATCGAAGAGGGGATAG
1 TGAAGAGGGAAAGATTGAAGCT-GCAA-CGGCGGATCTTACACCTTAAAATCGAAGA-GGGATAG
* * * * *
531867 ATTGAAGTCGTAATGACGAATCTAACACCTTAAAA-
63 GTTGAAGCCGCAATGACAAACCTAACACCTTAAAAC
* * * ****
531902 TCGAAGAGGGAAATATTGAAGCTGTAATGATAAATCTTACACCTTAAAA-CTGAAGAGGGATAGG
1 T-GAAGAGGGAAAGATTGAAGCTGCAACGGCGGATCTTACACCTTAAAATC-GAAGAGGGATAGG
* * * *
531966 TTGAAGCTGTAATGGCAAACCTAACACCCTAAAAC
64 TTGAAGCCGCAATGACAAACCTAACACCTTAAAAC
** * * * * * *
532001 CAAAGAGGGAAAGATTGAAGTTG-TAGGGATGGATCTTACAGCTTAAAATCGAATAGGGATAGGT
1 TGAAGAGGGAAAGATTGAAGCTGCAACGG-CGGATCTTACACCTTAAAATCGAAGAGGGATAGGT
* * * * * *
532065 TGAAGTCGCGAGGACAGACCTAATACCCTAAAAC
65 TGAAGCCGCAATGACAAACCTAACACCTTAAAAC
** * *
532099 CAAAGAGGCATAGATTGAAGC
1 TGAAGAGGGAAAGATTGAAGC
532120 CACGACGATG
Statistics
Matches: 331, Mismatches: 71, Indels: 23
0.78 0.17 0.05
Matches are distributed among these distances:
97 6 0.02
98 245 0.74
99 79 0.24
100 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (98 bp):
TGAAGAGGGAAAGATTGAAGCTGCAACGGCGGATCTTACACCTTAAAATCGAAGAGGGATAGGTT
GAAGCCGCAATGACAAACCTAACACCTTAAAAC
Found at i:531931 original size:148 final size:147
Alignment explanation
Indices: 531643--532192 Score: 410
Period size: 147 Copynumber: 3.7 Consensus size: 147
531633 ACGGCGGACT
* * * * * ** *
531643 TAACACCCTAAAA-TCGAAGAGGGATAGATTGAAGCTGCAA-CGATAGATTTAACACCTTAAAAC
1 TAACACCTTAAAACT-GAAGAGGGATAGGTTGAAGCTACAATC-ACAAACCTAACACCCTAAAAC
** * * * * * * *
531706 TTAATAGGGAAAGATTGAAGCCGCAACGG-CGGATCTTACACCTTAAAATTGAAGAGGGATAGGT
64 CAAAGAGGGAAAGATTGAAGTCGTAA-GGACGAATCTTACACCTTAAAATCGAAGAGGGAAAGAT
**
531770 TGAAGCCGCAATGATGGACC
128 TGAAGCCGCAATGATAAACC
* * *
531790 TAACACCTTAAAACTGAAGAGGGATAGGTTGAAG-TCACAATCACAGAGCTAACACCCTAAAATC
1 TAACACCTTAAAACTGAAGAGGGATAGGTTGAAGCT-ACAATCACAAACCTAACACCCTAAAACC
* * * * *
531854 GAAGAGGGGATAGATTGAAGTCGTAATGACGAATCTAACACCTTAAAATCGAAGAGGGAAATATT
65 AAAGA-GGGAAAGATTGAAGTCGTAAGGACGAATCTTACACCTTAAAATCGAAGAGGGAAAGATT
* * *
531919 GAAGCTGTAATGATAAATC
129 GAAGCCGCAATGATAAACC
* ** **
531938 TTACACCTTAAAACTGAAGAGGGATAGGTTGAAGCTGTAATGGCAAACCTAACACCCTAAAACCA
1 TAACACCTTAAAACTGAAGAGGGATAGGTTGAAGCTACAATCACAAACCTAACACCCTAAAACCA
* * * * * * * *
532003 AAGAGGGAAAGATTGAAGTTGTAGGGATGGATCTTACAGCTTAAAATCGAATAGGGATAGGTTGA
66 AAGAGGGAAAGATTGAAGTCGTAAGGACGAATCTTACACCTTAAAATCGAAGAGGGAAAGATTGA
* * * * *
532068 AGTCGCGAGGACAGACC
131 AGCCGCAATGATAAACC
* * ** * * * * *** * * *
532085 TAATACCCTAAAACCAAAGAGGCATAGATTGAAGCCACGA-CGATGGATCTAACACCTTGAAACC
1 TAACACCTTAAAACTGAAGAGGGATAGGTTGAAGCTACAATC-ACAAACCTAACACCCTAAAACC
* *
532149 AAAGAAGGAACAGATTGAAGCCGTAACGG-CGAATCTTACACCTT
65 AAAGAGGGAA-AGATTGAAGTCGTAA-GGACGAATCTTACACCTT
532193 TAGCAAAAAA
Statistics
Matches: 313, Mismatches: 81, Indels: 17
0.76 0.20 0.04
Matches are distributed among these distances:
146 1 0.00
147 164 0.52
148 145 0.46
149 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (147 bp):
TAACACCTTAAAACTGAAGAGGGATAGGTTGAAGCTACAATCACAAACCTAACACCCTAAAACCA
AAGAGGGAAAGATTGAAGTCGTAAGGACGAATCTTACACCTTAAAATCGAAGAGGGAAAGATTGA
AGCCGCAATGATAAACC
Found at i:531990 original size:197 final size:196
Alignment explanation
Indices: 531643--532021 Score: 467
Period size: 197 Copynumber: 1.9 Consensus size: 196
531633 ACGGCGGACT
* * *
531643 TAACACCCTAAAATCGAAGAGGGATAGATTGAAGCTGCAACGATAGATTTAACACCTTAAAACTT
1 TAACACCCTAAAATCGAAGAGGGATAGATTGAAGCTGCAACGAGAGATCTAACACCTTAAAACTG
* * ** *
531708 AATAGGGAAAGATTGAAGCCGCAACGGCGGATCTTACACCTTAAAATTGAAGAGGGATAGGTTGA
66 AAGAGGGAAAGATTGAAGCCGCAACGACAAATCTTACACCTTAAAACTGAAGAGGGATAGGTTGA
*** * ** * *
531773 AGCCGCAATGATGGACCTAACACCTTAAAACTGAAGAGGGATAGGTTGAAGTCACAATCACAGAG
131 AGCCGCAATGACAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCACAATCACAGAG
531838 C
196 C
* *
531839 TAACACCCTAAAATCGAAGAGGGGATAGATTGAAG-TCGTAATGACGA-ATCTAACACCTTAAAA
1 TAACACCCTAAAATCGAAGA-GGGATAGATTGAAGCT-GCAACGA-GAGATCTAACACCTTAAAA
* * * * *
531902 -TCGAAGAGGGAAATATTGAAGCTGTAATGATAAATCTTACACCTTAAAACTGAAGAGGGATAGG
63 CT-GAAGAGGGAAAGATTGAAGCCGCAACGACAAATCTTACACCTTAAAACTGAAGAGGGATAGG
* * *
531966 TTGAAGCTGTAATGGCAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGT
127 TTGAAGCCGCAATGACAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGT
532022 TGTAGGGATG
Statistics
Matches: 153, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
196 22 0.14
197 130 0.85
198 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (196 bp):
TAACACCCTAAAATCGAAGAGGGATAGATTGAAGCTGCAACGAGAGATCTAACACCTTAAAACTG
AAGAGGGAAAGATTGAAGCCGCAACGACAAATCTTACACCTTAAAACTGAAGAGGGATAGGTTGA
AGCCGCAATGACAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCACAATCACAGAG
C
Found at i:532095 original size:246 final size:245
Alignment explanation
Indices: 531643--532118 Score: 542
Period size: 246 Copynumber: 1.9 Consensus size: 245
531633 ACGGCGGACT
* * *
531643 TAACACCCTAAAATCGAAGAGGGATAGATTGAAGCTGCAACGATAGATTTAACACCTTAAAACTT
1 TAACACCCTAAAATCGAAGAGGGAAAGATTGAAGCTGCAACGATAAATTTAACACCTTAAAACTG
* ** * * * *** * *
531708 AATAGGGAAAGATTGAAGCCGCAACGGCGGATCTTACACCTTAAAATTGAAGAGGGATAGGTTGA
66 AAGAGGGAAAGATTGAAGCCGCAACGGCAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGA
* * *
531773 AGCCGCAATGATGGACCTAACACCTTAAAACTGAAGAGGGATAGGTTGAAGTCACAATCACAGAG
131 AGCCGCAAGGATGGACCTAACACCTTAAAACTGAAGAGGGATAGGTTGAAGTCACAAGCACAGAC
* * *
531838 CTAACACCCTAAAATCGAAGAGGGGATAGATTGAAGTCGTAATGACGAATC
196 CTAACACCCTAAAACCAAAGA-GGCATAGATTGAAGTCGTAATGACGAATC
* * * *
531889 TAACACCTTAAAATCGAAGAGGGAAATATTGAAGCTGTAATGATAAATCTT-ACACCTTAAAACT
1 TAACACCCTAAAATCGAAGAGGGAAAGATTGAAGCTGCAACGATAAAT-TTAACACCTTAAAACT
* * * * *
531953 GAAGAGGGATAGGTTGAAGCTGTAATGGCAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTG
65 GAAGAGGGAAAGATTGAAGCCGCAACGGCAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTG
** * * * * * * * * *
532018 AAGTTGTAGGGATGGATCTTACAGCTTAAAA-TCGAATAGGGATAGGTTGAAGTCGCGAGGACAG
130 AAGCCGCAAGGATGGACCTAACACCTTAAAACT-GAAGAGGGATAGGTTGAAGTCACAAGCACAG
*
532082 ACCTAATACCCTAAAACCAAAGAGGCATAGATTGAAG
194 ACCTAACACCCTAAAACCAAAGAGGCATAGATTGAAG
532119 CCACGACGAT
Statistics
Matches: 187, Mismatches: 41, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
245 14 0.07
246 171 0.91
247 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (245 bp):
TAACACCCTAAAATCGAAGAGGGAAAGATTGAAGCTGCAACGATAAATTTAACACCTTAAAACTG
AAGAGGGAAAGATTGAAGCCGCAACGGCAAACCTAACACCCTAAAACCAAAGAGGGAAAGATTGA
AGCCGCAAGGATGGACCTAACACCTTAAAACTGAAGAGGGATAGGTTGAAGTCACAAGCACAGAC
CTAACACCCTAAAACCAAAGAGGCATAGATTGAAGTCGTAATGACGAATC
Found at i:533885 original size:27 final size:26
Alignment explanation
Indices: 533815--533890 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
533805 TTTATACAAA
533815 ATTT-TATTTATTTATTATTTATTTG
1 ATTTATATTTATTTATTATTTATTTG
* * *
533840 ATTTACGTAATTA-TAATTATTTATTTT
1 ATTTA--TATTTATTTATTATTTATTTG
*
533867 ATTTATATCTTATTTATTACTTAT
1 ATTTATAT-TTATTTATTATTTAT
533891 ATTCTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
25 6 0.15
26 3 0.08
27 26 0.65
28 5 0.12
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTATATTTATTTATTATTTATTTG
Found at i:535230 original size:42 final size:42
Alignment explanation
Indices: 535197--535496 Score: 345
Period size: 42 Copynumber: 7.1 Consensus size: 42
535187 CTCTAATTAT
**
535197 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCCGAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* *
535239 AATGAAAAGTAAATAGACCTCCACACATGGGCCTCTAAATG-
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * ** *
535280 AGATGAAAAGTAAATGGGCCTTCACATTTGGGCCTCTAAATGT
1 A-ATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
**
535323 AATGAAAAGTAAAT-GAGCCTCCACACCTATGCCTCTAAATGC
1 AATGAAAAGTAAATGGA-CCTCCACACCTGGGCCTCTAAATGC
* ** * *
535365 AATGAAAAGTAAATGTACCTCCACACCTAAGTCTCTAAATAC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * *
535407 AATGAAAAGTAAATGGGCC-CACACACTTGGGCCTTTAAATGC
1 AATGAAAAGTAAATGGACCTC-CACACCTGGGCCTCTAAATGC
* * **
535449 ATTGAAAAGTAAATGGGCCTCCACACCTGAACCTCTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
535491 AATGAA
1 AATGAA
535497 TGATTTCCTT
Statistics
Matches: 218, Mismatches: 34, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
41 3 0.01
42 212 0.97
43 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
Found at i:535389 original size:126 final size:124
Alignment explanation
Indices: 535184--535496 Score: 387
Period size: 126 Copynumber: 2.5 Consensus size: 124
535174 TCTATGCTTA
* * * **
535184 GGCCTCTAATTATAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCCGAATGCAATGAAAAGT
1 GGCCTCTAAATGTAATGAAAAGTAAATGG-CCTCCACACCT-AGCCTCTAAATGCAATGAAAAGT
** * ** *
535249 AAATAGACCTCCACACATGGGCCTCTAAATGA-GATGAAAAGTAAATGGGCCTTCACATTTG
64 AAATAGACCTCCACACATAAGCCTCTAAAT-ACAATGAAAAGTAAATGGGCCCACACACTTG
535310 GGCCTCTAAATGTAATGAAAAGTAAATGAGCCTCCACACCTATGCCTCTAAATGCAATGAAAAGT
1 GGCCTCTAAATGTAATGAAAAGTAAATG-GCCTCCACACCTA-GCCTCTAAATGCAATGAAAAGT
* *
535375 AAAT-GTACCTCCACACCTAAGTCTCTAAATACAATGAAAAGTAAATGGGCCCACACACTTG
64 AAATAG-ACCTCCACACATAAGCCTCTAAATACAATGAAAAGTAAATGGGCCCACACACTTG
* * * *
535436 GGCCTTTAAATGCATTGAAAAGTAAATGGGCCTCCACACCTGAACCTCTAAATGCAATGAA
1 GGCCTCTAAATGTAATGAAAAGTAAAT-GGCCTCCACACCT-AGCCTCTAAATGCAATGAA
535497 TGATTTCCTT
Statistics
Matches: 164, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
125 2 0.01
126 159 0.97
127 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (124 bp):
GGCCTCTAAATGTAATGAAAAGTAAATGGCCTCCACACCTAGCCTCTAAATGCAATGAAAAGTAA
ATAGACCTCCACACATAAGCCTCTAAATACAATGAAAAGTAAATGGGCCCACACACTTG
Found at i:543838 original size:2 final size:2
Alignment explanation
Indices: 543831--543865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
543821 ACTGACATTA
543831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
543866 GAAATGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:543906 original size:17 final size:17
Alignment explanation
Indices: 543886--543924 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
543876 GATAATGTAG
543886 ATGCAACGACAATAAAA
1 ATGCAACGACAATAAAA
* * *
543903 ATGCAATGACATTAATA
1 ATGCAACGACAATAAAA
543920 ATGCA
1 ATGCA
543925 GGGACAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (17 bp):
ATGCAACGACAATAAAA
Found at i:566903 original size:22 final size:22
Alignment explanation
Indices: 566858--566905 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
566848 CAACTAAAAT
*
566858 AAAATAAAAATAATATCAATTA
1 AAAATAAAAATAATATCAACTA
* *
566880 AAAATCAAAATAATATCACCTA
1 AAAATAAAAATAATATCAACTA
566902 AAAA
1 AAAA
566906 ACTATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATAAAAATAATATCAACTA
Found at i:574901 original size:22 final size:22
Alignment explanation
Indices: 574876--574928 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
574866 TCAACACATT
*
574876 CTTAAGCTTGCTTCCATGGCAA
1 CTTAAGCTTCCTTCCATGGCAA
*
574898 CTTAAGCTTCCTTCCATGGCAG
1 CTTAAGCTTCCTTCCATGGCAA
574920 CTTAAGCTT
1 CTTAAGCTT
574929 TTAAGGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (22 bp):
CTTAAGCTTCCTTCCATGGCAA
Found at i:582665 original size:15 final size:17
Alignment explanation
Indices: 582645--582684 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
582635 TCAATCACAT
582645 AAAAAATAG-AAA-GAA
1 AAAAAATAGAAAACGAA
582660 AAAAAAT-GAAAACGAA
1 AAAAAATAGAAAACGAA
582676 AAAATAATA
1 AAAA-AATA
582685 TATATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 10 0.48
16 7 0.33
17 3 0.14
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAATAGAAAACGAA
Found at i:587628 original size:13 final size:14
Alignment explanation
Indices: 587601--587631 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
587591 CTGAAATTTC
587601 TCAAGATTCTTGAA
1 TCAAGATTCTTGAA
587615 TCAAGATT-TTGAA
1 TCAAGATTCTTGAA
587628 TCAA
1 TCAA
587632 AGGATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (14 bp):
TCAAGATTCTTGAA
Found at i:591343 original size:50 final size:50
Alignment explanation
Indices: 591289--591387 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
591279 AAATTTTATA
591289 TTTTTTTATTATGTTTATACAAGGTTTAAAAAAGAAATGTTTGAAAAGTC
1 TTTTTTTATTATGTTTATACAAGGTTTAAAAAAGAAATGTTTGAAAAGTC
591339 TTTTTTTATTATGTTTATACAAGGTTTAAAAAAGAAATGTTTGAAAAGT
1 TTTTTTTATTATGTTTATACAAGGTTTAAAAAAGAAATGTTTGAAAAGT
591388 TCTATGTCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.44
Consensus pattern (50 bp):
TTTTTTTATTATGTTTATACAAGGTTTAAAAAAGAAATGTTTGAAAAGTC
Found at i:591662 original size:15 final size:15
Alignment explanation
Indices: 591642--591688 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
591632 TAGAGTACAG
*
591642 CTCCACCAATTCCTA
1 CTCCACCAACTCCTA
*
591657 CTCCACCAACTCCTT
1 CTCCACCAACTCCTA
* *
591672 CTCCACTAGCTCCTA
1 CTCCACCAACTCCTA
591687 CT
1 CT
591689 ACAATAGCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.49, G:0.02, T:0.28
Consensus pattern (15 bp):
CTCCACCAACTCCTA
Found at i:596324 original size:18 final size:19
Alignment explanation
Indices: 596301--596344 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
596291 TTTTTAGTTG
596301 TAATTAAATTAAAAAT-TT
1 TAATTAAATTAAAAATATT
**
596319 TAATT-AATTAAATTTATT
1 TAATTAAATTAAAAATATT
596337 TAATTAAA
1 TAATTAAA
596345 AATTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTAAATTAAAAATATT
Found at i:596349 original size:16 final size:16
Alignment explanation
Indices: 596307--596353 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 16
596297 GTTGTAATTA
*
596307 AATTAAAAATTTTAATT
1 AATTAAAAA-TTTATTT
596324 AATT--AAATTTATTT
1 AATTAAAAATTTATTT
596338 AATTAAAAATTTATTT
1 AATTAAAAATTTATTT
596354 CTATTCCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 10 0.37
17 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTAAAAATTTATTT
Found at i:599325 original size:21 final size:22
Alignment explanation
Indices: 599295--599335 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
599285 TTTTATTCAC
599295 AAAAAAATTTA-AATATAATGT
1 AAAAAAATTTAGAATATAATGT
* *
599316 AAAAAGATTTAGTATATAAT
1 AAAAAAATTTAGAATATAAT
599336 ATATAATTTT
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:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAAAATTTAGAATATAATGT
Found at i:599699 original size:19 final size:20
Alignment explanation
Indices: 599674--599730 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 20
599664 ATAAAATTAT
599674 TTTTCTCTTCTTTTTAGCAC
1 TTTTCTCTTCTTTTTAGCAC
599694 TTTCTCTCTCATCTTTTTAGCAC
1 TTT-TCTCT--TCTTTTTAGCAC
599717 -TTTCTTCTTCTTTT
1 TTTTC-TCTTCTTTT
599731 CTTCTAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 5 0.15
23 12 0.36
ACGTcount: A:0.09, C:0.26, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTCTCTTCTTTTTAGCAC
Found at i:599708 original size:23 final size:23
Alignment explanation
Indices: 599677--599721 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
599667 AAATTATTTT
*
599677 TCTCTTCTTTTTAGCACTTTCTC
1 TCTCATCTTTTTAGCACTTTCTC
599700 TCTCATCTTTTTAGCACTTTCT
1 TCTCATCTTTTTAGCACTTTCT
599722 TCTTCTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.29, G:0.04, T:0.56
Consensus pattern (23 bp):
TCTCATCTTTTTAGCACTTTCTC
Found at i:602420 original size:35 final size:35
Alignment explanation
Indices: 602380--602453 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
602370 TAAGAGATAA
* *
602380 GAAGATTATTTTTCCAGAAATTGTCAATCTAATAT
1 GAAGATTATTTTTCCAAAAATTGTCAATCCAATAT
*
602415 GAAGATTATTTTTCCAAAAATTGTCAGTCCAATAT
1 GAAGATTATTTTTCCAAAAATTGTCAATCCAATAT
602450 GAAG
1 GAAG
602454 CAAAGTGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (35 bp):
GAAGATTATTTTTCCAAAAATTGTCAATCCAATAT
Found at i:605886 original size:14 final size:14
Alignment explanation
Indices: 605863--605903 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
605853 CCGTTAACCT
*
605863 ATTGACCGTTGACC
1 ATTGATCGTTGACC
*
605877 ATTGATCGTTGATC
1 ATTGATCGTTGACC
605891 ATTGATCGTTGAC
1 ATTGATCGTTGAC
605904 TGTTGGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (14 bp):
ATTGATCGTTGACC
Found at i:616322 original size:21 final size:21
Alignment explanation
Indices: 616298--616349 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
616288 GAAGTATTTG
616298 GAAGTGTTCATGGATGACTTT
1 GAAGTGTTCATGGATGACTTT
616319 GAAGTGTTCATGGATGACTTT
1 GAAGTGTTCATGGATGACTTT
**
616340 TCAGTGTTCA
1 GAAGTGTTCA
616350 GGGACACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (21 bp):
GAAGTGTTCATGGATGACTTT
Found at i:624277 original size:17 final size:17
Alignment explanation
Indices: 624257--624289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
624247 ATGCTCAGAA
*
624257 AAAAATGAATGAAAAAT
1 AAAAATGAAAGAAAAAT
624274 AAAAATGAAAGAAAAA
1 AAAAATGAAAGAAAAA
624290 AATATATAGA
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:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAAATGAAAGAAAAAT
Found at i:629616 original size:21 final size:20
Alignment explanation
Indices: 629578--629628 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
629568 CACATTATGA
* * *
629578 TTCACATTTCCTTTTACCTT
1 TTCACTTTTACTTTTACCCT
629598 TTCACTTTTACTTGTTACCCT
1 TTCACTTTTACTT-TTACCCT
*
629619 TTCAATTTTA
1 TTCACTTTTA
629629 TGCAAGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (20 bp):
TTCACTTTTACTTTTACCCT
Found at i:631811 original size:18 final size:17
Alignment explanation
Indices: 631780--631827 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
631770 TCAGTCACCT
631780 AAAAAAGAAAAAAATGA
1 AAAAAAGAAAAAAATGA
* *
631797 GAAAAAGGAAGAAAATG-
1 -AAAAAAGAAAAAAATGA
631814 -AAAAAGAAAAAAAT
1 AAAAAAGAAAAAAAT
631828 TTGTGTATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 12 0.46
18 14 0.54
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAAAATGA
Found at i:637726 original size:24 final size:24
Alignment explanation
Indices: 637406--637895 Score: 363
Period size: 24 Copynumber: 20.3 Consensus size: 24
637396 TCATTAGCTT
* * *
637406 CTATACATTTATACTCATCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
637430 CTATACGTTTATACTCATCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* * * * **
637454 TTATACGTTTACGCTTGTCAACTT
1 CTATACGTTTATGCTCGTCAGCCA
*
637478 CTACACGTTTATGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
637502 TTATACGTTTACGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
637526 CTATATGTTTACGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
637550 CTATATGTTTATGCTCGTCAGCTTCT
1 CTATACGTTTATGCTCGTCAGC--CA
* * * * **
637576 GTATTCATTTATGCTCGTCAACTT
1 CTATACGTTTATGCTCGTCAGCCA
*
637600 CTATACATTTATGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* * * *
637624 CTATACATTTACGCTTGTCA-CCTT
1 CTATACGTTTATGCTCGTCAGCC-A
** *
637648 CTGCACGTTTATACTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* * *
637672 CTATATGTTTATGCTCATCAACCA
1 CTATACGTTTATGCTCGTCAGCCA
**
637696 CTATACGTTTATGCTCGTCAGCTT
1 CTATACGTTTATGCTCGTCAGCCA
* *
637720 CTGTACG-TTACTGCTCGTCAACCA
1 CTATACGTTTA-TGCTCGTCAGCCA
* * * *
637744 CTCTATGTTTACGCTCGTCAACCA
1 CTATACGTTTATGCTCGTCAGCCA
** * ***
637768 CTATACGTTTACACTCATCAGTTT
1 CTATACGTTTATGCTCGTCAGCCA
* * *
637792 CTATATGTTTATGCTCGTTAGCAA
1 CTATACGTTTATGCTCGTCAGCCA
* * **
637816 CTATACGTTTACGCTCATCAGCTT
1 CTATACGTTTATGCTCGTCAGCCA
* * *
637840 CTGTACATTTATGCTCGTTAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* * *
637864 CTCTATGTTTATGCTCGTCAACCA
1 CTATACGTTTATGCTCGTCAGCCA
*
637888 TTATACGT
1 CTATACGT
637896 GTCGAAACGT
Statistics
Matches: 361, Mismatches: 99, Indels: 12
0.76 0.21 0.03
Matches are distributed among these distances:
23 5 0.01
24 333 0.92
25 5 0.01
26 18 0.05
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.37
Consensus pattern (24 bp):
CTATACGTTTATGCTCGTCAGCCA
Found at i:659637 original size:24 final size:24
Alignment explanation
Indices: 659605--659654 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
659595 GTATACTGGT
659605 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
659629 TAACCATTCTGGGCTCTTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
659653 TA
1 TA
659655 TCTTGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:663860 original size:22 final size:22
Alignment explanation
Indices: 663825--663866 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
663815 TGAGCAGCAG
663825 TGTATACTGATTAACCATTCAT
1 TGTATACTGATTAACCATTCAT
* *
663847 TGTATATTGTTTAACCATTC
1 TGTATACTGATTAACCATTC
663867 TGGACTCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (22 bp):
TGTATACTGATTAACCATTCAT
Found at i:664547 original size:21 final size:21
Alignment explanation
Indices: 664501--664547 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
664491 GTTGTATCGG
* *
664501 TAGTTGAATAGCAAGTATCGA
1 TAGTTGAATAGCAAATATCAA
*
664522 CAGTTGAATAGCAAATATCAA
1 TAGTTGAATAGCAAATATCAA
664543 TAGTT
1 TAGTT
664548 CGTATACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TAGTTGAATAGCAAATATCAA
Found at i:667758 original size:101 final size:99
Alignment explanation
Indices: 667548--667758 Score: 237
Period size: 99 Copynumber: 2.1 Consensus size: 99
667538 GATAGAACGA
* * * *
667548 CAAATCCTATACCTCTAAAGTTGTAGAGGGGCGGATTAAAACGAGTACCGAACCTCAATCTCTTT
1 CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACCAGTACCAAACCTCAATCTCTCT
* * *
667613 AAAGTTGAAATGGAACGGAGCGAAGTTCTAACCT
66 AAAGATGAAATGGAACGGAGCGAAGTTCGAAACT
* ** *
667647 CAAATCCTATACCCCTAGAGTTGTAGAGGGGCGGATTAAAACTAACAGTGTCAAATCTCAATCTC
1 CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAAC---CAGTACCAAACCTCAATCTC
* * * *
667712 -CTAAAGATGTAGTGGAATGGAGTGAAGTTACGAAAC-
63 TCTAAAGATGAAATGGAACGGAGCGAAGTT-CGAAACT
667748 CAAATCCTATA
1 CAAATCCTATA
667759 TTCTTGAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
99 40 0.43
101 34 0.37
102 19 0.20
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (99 bp):
CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACCAGTACCAAACCTCAATCTCTCT
AAAGATGAAATGGAACGGAGCGAAGTTCGAAACT
Found at i:667853 original size:100 final size:100
Alignment explanation
Indices: 667734--667978 Score: 253
Period size: 100 Copynumber: 2.4 Consensus size: 100
667724 TGGAATGGAG
* * * * *
667734 TGAAGTTACGAAACCAAATCCTATATTCTTGAAGTTTCAAGGATCGGATTGAA-TCTACGAAAGT
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAAGGATCGGATTAAAGTC-ACGAAAGC
* * *** *
667798 GAATCCTTATCTCTCTGAAGTTGTTGTAGAGC-GGAA
65 AAATCCTTATCTCCCTGAAGTTACAGTAGAGCAAG-A
* * * * *
667834 TGAAGCTACAAAACAAAATCCTATACCCTTGAAGTTT-AGTGGGTTGGATTAAAGTCACGAAAGC
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCA-AGGATCGGATTAAAGTCACGAAAGC
* *
667898 AAATCTTTATCTCCCTGAAGTTACAGTGGAGCAAGA
65 AAATCCTTATCTCCCTGAAGTTACAGTAGAGCAAGA
* *
667934 TGAAGCTACAACACCAAATCCTATATCCTTGAAGTTGCAATGGAT
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAA-GGAT
667979 TAGATTGAGA
Statistics
Matches: 116, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
99 1 0.01
100 108 0.93
101 7 0.06
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (100 bp):
TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAAGGATCGGATTAAAGTCACGAAAGCA
AATCCTTATCTCCCTGAAGTTACAGTAGAGCAAGA
Found at i:668460 original size:14 final size:14
Alignment explanation
Indices: 668438--668480 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
668428 TTAACTAATT
*
668438 AATTTATAAATAAA
1 AATTAATAAATAAA
668452 AATTAATAAATAAA
1 AATTAATAAATAAA
*
668466 AACCTAAT-AATAAA
1 AA-TTAATAAATAAA
668480 A
1 A
668481 TAATCCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AATTAATAAATAAA
Found at i:672938 original size:22 final size:22
Alignment explanation
Indices: 672903--672944 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
672893 TGAGCAGCAG
672903 TGTATACTGATTAACCATTCAT
1 TGTATACTGATTAACCATTCAT
* *
672925 TGTATATTGTTTAACCATTC
1 TGTATACTGATTAACCATTC
672945 TGGACTCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (22 bp):
TGTATACTGATTAACCATTCAT
Found at i:673625 original size:21 final size:21
Alignment explanation
Indices: 673579--673625 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
673569 GTTGTATCGG
* *
673579 TAGTTGAATAGCAAGTATCGA
1 TAGTTGAATAGCAAATATCAA
*
673600 CAGTTGAATAGCAAATATCAA
1 TAGTTGAATAGCAAATATCAA
673621 TAGTT
1 TAGTT
673626 CGTATACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TAGTTGAATAGCAAATATCAA
Found at i:676836 original size:101 final size:99
Alignment explanation
Indices: 676626--676836 Score: 237
Period size: 99 Copynumber: 2.1 Consensus size: 99
676616 GATAGAACGA
* * * *
676626 CAAATCCTATACCTCTAAAGTTGTAGAGGGGCGGATTAAAACGAGTACCGAACCTCAATCTCTTT
1 CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACCAGTACCAAACCTCAATCTCTCT
* * *
676691 AAAGTTGAAATGGAACGGAGCGAAGTTCTAACCT
66 AAAGATGAAATGGAACGGAGCGAAGTTCGAAACT
* ** *
676725 CAAATCCTATACCCCTAGAGTTGTAGAGGGGCGGATTAAAACTAACAGTGTCAAATCTCAATCTC
1 CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAAC---CAGTACCAAACCTCAATCTC
* * * *
676790 -CTAAAGATGTAGTGGAATGGAGTGAAGTTACGAAAC-
63 TCTAAAGATGAAATGGAACGGAGCGAAGTT-CGAAACT
676826 CAAATCCTATA
1 CAAATCCTATA
676837 TTCTTGAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
99 40 0.43
101 34 0.37
102 19 0.20
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (99 bp):
CAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACCAGTACCAAACCTCAATCTCTCT
AAAGATGAAATGGAACGGAGCGAAGTTCGAAACT
Found at i:676931 original size:100 final size:100
Alignment explanation
Indices: 676812--677056 Score: 253
Period size: 100 Copynumber: 2.4 Consensus size: 100
676802 TGGAATGGAG
* * * * *
676812 TGAAGTTACGAAACCAAATCCTATATTCTTGAAGTTTCAAGGATCGGATTGAA-TCTACGAAAGT
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAAGGATCGGATTAAAGTC-ACGAAAGC
* * *** *
676876 GAATCCTTATCTCTCTGAAGTTGTTGTAGAGC-GGAA
65 AAATCCTTATCTCCCTGAAGTTACAGTAGAGCAAG-A
* * * * *
676912 TGAAGCTACAAAACAAAATCCTATACCCTTGAAGTTT-AGTGGGTTGGATTAAAGTCACGAAAGC
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCA-AGGATCGGATTAAAGTCACGAAAGC
* *
676976 AAATCTTTATCTCCCTGAAGTTACAGTGGAGCAAGA
65 AAATCCTTATCTCCCTGAAGTTACAGTAGAGCAAGA
* *
677012 TGAAGCTACAACACCAAATCCTATATCCTTGAAGTTGCAATGGAT
1 TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAA-GGAT
677057 TAGATTGAGA
Statistics
Matches: 116, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
99 1 0.01
100 108 0.93
101 7 0.06
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (100 bp):
TGAAGCTACAAAACCAAATCCTATATCCTTGAAGTTTCAAGGATCGGATTAAAGTCACGAAAGCA
AATCCTTATCTCCCTGAAGTTACAGTAGAGCAAGA
Found at i:677538 original size:14 final size:14
Alignment explanation
Indices: 677516--677558 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
677506 TTAACTAATT
*
677516 AATTTATAAATAAA
1 AATTAATAAATAAA
677530 AATTAATAAATAAA
1 AATTAATAAATAAA
*
677544 AACCTAAT-AATAAA
1 AA-TTAATAAATAAA
677558 A
1 A
677559 TAATCCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AATTAATAAATAAA
Found at i:681708 original size:21 final size:21
Alignment explanation
Indices: 681658--681711 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
681648 CTGGAGTTTT
* *
681658 TTGTATTGGTTGAAGCATGAC
1 TTGTATCGGTAGAAGCATGAC
* *
681679 ATGTTTCGGTAGAAGTCAT-AC
1 TTGTATCGGTAGAAG-CATGAC
681700 TTGTATCGGTAG
1 TTGTATCGGTAG
681712 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (21 bp):
TTGTATCGGTAGAAGCATGAC
Found at i:688750 original size:21 final size:21
Alignment explanation
Indices: 688698--688751 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
688688 TCGGAGTTTT
688698 TTGTATCGGTAGAAGCATGAC
1 TTGTATCGGTAGAAGCATGAC
* * *
688719 ATGTTTTGGTAGAAGTCAT-AC
1 TTGTATCGGTAGAAG-CATGAC
688740 TTGTATCGGTAG
1 TTGTATCGGTAG
688752 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGTATCGGTAGAAGCATGAC
Found at i:690258 original size:52 final size:52
Alignment explanation
Indices: 690180--690282 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
690170 AATCTACTCC
690180 GAGTGAAGGGCATTTCAATCTTTACAAAGCCACTTAAACACAAAGGATGGTT
1 GAGTGAAGGGCATTTCAATCTTTACAAAGCCACTTAAACACAAAGGATGGTT
**
690232 GAGTGAAGGGCATTTCAATCTTTACAAAGCCACTTAAACATGAAGGATGGT
1 GAGTGAAGGGCATTTCAATCTTTACAAAGCCACTTAAACACAAAGGATGGT
690283 AGCTGACTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (52 bp):
GAGTGAAGGGCATTTCAATCTTTACAAAGCCACTTAAACACAAAGGATGGTT
Found at i:692798 original size:37 final size:37
Alignment explanation
Indices: 692748--693113 Score: 430
Period size: 37 Copynumber: 9.9 Consensus size: 37
692738 TTTTAAGTAA
*
692748 TCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * *
692785 TCAGGCTATGTGCCTAGCAAGATTTGTGCCAGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * *
692822 TTAGGCTATGTACCTAGAAGGCTTCGTG-C-GTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
692857 TCAGGCTATGTGCCTAGCAGACTTCGTGTCGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * * * *
692894 TTAGGCTATGCGCTTAGCAGGCTTTGTGCTGGTGAAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * ** *
692931 TCAAGCTATGTGCCTAGTAGGCTTTATGTCGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * * * *
692968 TCAAGCTATGTGCCAAGCAGGCTTTGTGCCTGTGAAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* * *
693005 TTAAGCTATGTGCCTAGCAAGCTTCGTGCCGGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
*
693042 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCAGTGTAT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
693079 TCAGGCTATGTGCCTAGCAAGCTTCGTGTCGGTGT
1 TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
693114 TTGTTAGATT
Statistics
Matches: 278, Mismatches: 49, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
35 30 0.11
36 2 0.01
37 246 0.88
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (37 bp):
TCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTAT
Found at i:693091 original size:21 final size:20
Alignment explanation
Indices: 693030--693092 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
693020 AGCAAGCTTC
693030 GTGCCGGTGTATTCAGGCTAT
1 GTGCC-GTGTATTCAGGCTAT
*
693051 GTGCC---TA-GCAGGCT-T
1 GTGCCGTGTATTCAGGCTAT
693066 CGTGCCAGTGTATTCAGGCTAT
1 -GTGCC-GTGTATTCAGGCTAT
693088 GTGCC
1 GTGCC
693093 TAGCAAGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 1 0.03
16 11 0.33
17 2 0.06
20 2 0.06
21 16 0.48
22 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (20 bp):
GTGCCGTGTATTCAGGCTAT
Found at i:695079 original size:26 final size:26
Alignment explanation
Indices: 695050--695131 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
695040 TGTGTCATCG
695050 TGAGTATATGAATCATTTACGGATTA
1 TGAGTATATGAATCATTTACGGATTA
* * *
695076 TGAGGTATAATGACT-ATGTTTC--ATTG
1 TGA-GTAT-ATGAATCAT-TTACGGATTA
*
695102 TGAGTATATGAATTC-TTTACGGGTTA
1 TGAGTATATGAA-TCATTTACGGATTA
695128 TGAG
1 TGAG
695132 GTCCGTTGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
24 7 0.17
25 6 0.14
26 15 0.36
27 6 0.14
28 8 0.19
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (26 bp):
TGAGTATATGAATCATTTACGGATTA
Found at i:695111 original size:52 final size:51
Alignment explanation
Indices: 695027--695261 Score: 283
Period size: 52 Copynumber: 4.5 Consensus size: 51
695017 TGTTTAAAAG
*
695027 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATC-TTTACGAATTATGA
* * * * **
695079 GGTATAATGACTATGTTTCATTGTGAGTATATGAATTCTTTACGGGTTATGA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAA-TCTTTACGAATTATGA
* * * *
695131 GGTCCGTTGACTATGTGTCATCATGAGTATATGAAT-TCTTACGAATTATAA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCT-TTACGAATTATGA
* * *
695182 GGTCTGATGACTATGTATCATTGTGAGTATATGAATCCTTTACAAATTATGA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAAT-CTTTACGAATTATGA
* *
695234 GGTTTGATGACTATGTGTCATCATGAGT
1 GGTCTGATGACTATGTGTCATCGTGAGT
695262 GTTAAATGAA
Statistics
Matches: 153, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.01
51 42 0.27
52 107 0.70
53 3 0.02
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (51 bp):
GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCTTTACGAATTATGA
Done.