Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010316.1 Kokia drynarioides strain JFW-HI SEQ_125178, 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: 389999
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 37 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3012 original size:59 final size:59
Alignment explanation
Indices: 2924--3366 Score: 499
Period size: 59 Copynumber: 7.6 Consensus size: 59
2914 TGAAACAGTA
* * *
2924 ATTTTGGAAAATTTTAGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAAT-GG
1 ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
* * * * **
2982 ACCTTTTGAAAGTTTTTGGGTTAAAAATGGGATTTTTGGTAGTTTTTGGGGTAAAAATGGG
1 A-TTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAGAAG-TTCGGGGGTAAAAATGGG
* * * * *
3043 ATTTTTGATAG-TTTCGGAGTCAAAATTGGG-TTTTTAGAGGTTCGGGGGTAAAAATGGG
1 ATTTTTGAAAGTTTTAGG-GTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
* * * * *
3101 ATTTTTGAAAGCTTCAGGGTTAAAAATGGGATTTTTAGTAA-TTTGGAGGTAAAAATGGA
1 ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAG-AAGTTCGGGGGTAAAAATGGG
* * * * *
3160 ATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTGA-AAGTTTTGGGGTTAAAAATGGG
1 ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAGAAG-TTCGGGGGTAAAAATGGG
*
3219 ATTTTT-AGAAG-TTTAGGGGT-AAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
1 ATTTTTGA-AAGTTTTAGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
* * *
3276 ATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTTGAAGTTC-GGGGTAAAAATGGG
1 ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
**
3334 ATTTTTGAAAGTTTCGGGGTTAAAAATGGGATT
1 ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATT
3367 GTTGAGCAAT
Statistics
Matches: 323, Mismatches: 48, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
57 41 0.13
58 99 0.31
59 148 0.46
60 32 0.10
61 3 0.01
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (59 bp):
ATTTTTGAAAGTTTTAGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGG
Found at i:3363 original size:30 final size:30
Alignment explanation
Indices: 2940--3371 Score: 423
Period size: 30 Copynumber: 14.7 Consensus size: 30
2930 GAAAATTTTA
*
2940 GGGTCAAAAATGGGATTTTT-AGAAG-TTCG
1 GGGTTAAAAATGGGATTTTTGA-AAGTTTCG
* * **
2969 GGGGTAAAAAT-GGACCTTTTGAAAGTTTTT
1 GGGTTAAAAATGGGA-TTTTTGAAAGTTTCG
** *
2999 GGGTTAAAAATGGGATTTTTGGTAGTTTTTG
1 GGGTTAAAAATGGGATTTTTGAAAG-TTTCG
*
3030 GGG-TAAAAATGGGATTTTTGATAGTTTCG
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
* * * * *
3059 GAGTCAAAATTGGG-TTTTT-AGAGGTTCG
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
* * *
3087 GGGGTAAAAATGGGATTTTTGAAAGCTTCA
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
*
3117 GGGTTAAAAATGGGATTTTTAGTAA-TTT-G
1 GGGTTAAAAATGGGATTTTT-GAAAGTTTCG
* * *
3146 GAGG-TAAAAATGGAATTTTTGGAAGTTTTG
1 G-GGTTAAAAATGGGATTTTTGAAAGTTTCG
*
3176 GGGTTAAAAATGGGA-TTTTGAAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
*
3205 GGGTTAAAAATGGGATTTTT-AGAAGTTTAG
1 GGGTTAAAAATGGGATTTTTGA-AAGTTTCG
3235 GGG-T-AAAATGGGATTTTT-AGAAG-TTCG
1 GGGTTAAAAATGGGATTTTTGA-AAGTTTCG
* * *
3262 GGGGTAAAAATGGGATTTTTGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
3292 GGGTTAAAAATGGGATTTTTTG-AAG-TTCG
1 GGGTTAAAAATGGGA-TTTTTGAAAGTTTCG
3321 GGG-TAAAAATGGGATTTTTGAAAGTTTCG
1 GGGTTAAAAATGGGATTTTTGAAAGTTTCG
*
3350 GGGTTAAAAATGGGATTGTTGA
1 GGGTTAAAAATGGGATTTTTGA
3372 GCAATTTAGG
Statistics
Matches: 341, Mismatches: 39, Indels: 45
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.04
28 57 0.17
29 113 0.33
30 140 0.41
31 19 0.06
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (30 bp):
GGGTTAAAAATGGGATTTTTGAAAGTTTCG
Found at i:4460 original size:3 final size:3
Alignment explanation
Indices: 4452--4515 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
4442 ATCATTAAAA
* * * *
4452 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT AATT ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
* *
4498 ATT A-T ATA AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
4516 ATAATATAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:4533 original size:24 final size:24
Alignment explanation
Indices: 4484--4536 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4474 TTATTATTAT
* *
4484 TATTATTAATTATGATTATATAAA
1 TATTATTAATAATGATAATATAAA
*
4508 TATTATTAATAAT-ATAATAATCAA
1 TATTATTAATAATGATAAT-ATAAA
4532 TATTA
1 TATTA
4537 ACCCTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTATTAATAATGATAATATAAA
Found at i:5236 original size:17 final size:18
Alignment explanation
Indices: 5214--5256 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5204 AACTTTATTT
5214 ATTTTAAA-TTCATAATA
1 ATTTTAAATTTCATAATA
*
5231 ATTTTAAATTTGATAATA
1 ATTTTAAATTTCATAATA
*
5249 AATTTAAA
1 ATTTTAAA
5257 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTTCATAATA
Found at i:5261 original size:6 final size:6
Alignment explanation
Indices: 5247--5306 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
5237 AATTTGATAA
* * *
5247 TAAATT TAAACT TAAATT TAAATT TAAA-A TAAATT TAAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
5294 TAAATT TAAATT T
1 TAAATT TAAATT T
5307 TTAAACAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.18
6 31 0.69
7 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:5277 original size:29 final size:29
Alignment explanation
Indices: 5233--5338 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
5223 TCATAATAAT
*
5233 TTTAAATTTGATAATAAATTTAAACTTAAA
1 TTTAAATTT-AAAATAAATTTAAACTTAAA
*
5263 TTTAAATTTAAAATAAATTTAAAATTTAAA
1 TTTAAATTTAAAATAAATTT-AAACTTAAA
* *
5293 -ATAAATTT-AAAT--TTTTAAAC--AAA
1 TTTAAATTTAAAATAAATTTAAACTTAAA
5316 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
5339 GGGGAGCTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
23 6 0.10
24 3 0.05
25 7 0.11
26 3 0.05
27 6 0.10
28 4 0.06
29 17 0.27
30 17 0.27
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTAAATTTAAAATAAATTTAAACTTAAA
Found at i:5281 original size:11 final size:11
Alignment explanation
Indices: 5265--5303 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5255 AACTTAAATT
5265 TAAATTTAAAA
1 TAAATTTAAAA
5276 TAAATTT---A
1 TAAATTTAAAA
5284 -AAATTTAAAA
1 TAAATTTAAAA
5294 TAAATTTAAA
1 TAAATTTAAA
5304 TTTTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
7 6 0.25
8 1 0.04
10 1 0.04
11 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:5281 original size:17 final size:17
Alignment explanation
Indices: 5247--5338 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 17
5237 AATTTGATAA
*
5247 TAAATTTAAACTTAAATT
1 TAAATTTAAA-ATAAATT
5265 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
5282 TAAAATTTAAAATAAATT
1 T-AAATTTAAAATAAATT
* *
5300 TAAATTTTTAAACAAATT
1 TAAA-TTTAAAATAAATT
5318 T-AATCTTAAAATAAATT
1 TAAAT-TTAAAATAAATT
5335 TAAA
1 TAAA
5339 GGGGAGCTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
16 1 0.02
17 23 0.35
18 41 0.63
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:5327 original size:35 final size:34
Alignment explanation
Indices: 5247--5338 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 34
5237 AATTTGATAA
* *
5247 TAAATTTAAACTTAAATTTAAATTTAAAATAAATT
1 TAAATTTAAA-ATAAATTTAAATTTAAAACAAATT
*
5282 TAAAATTTAAAATAAATTTAAATTTTTAAACAAATT
1 T-AAATTTAAAATAAATTTAAA-TTTAAAACAAATT
5318 T-AATCTTAAAATAAATTTAAA
1 TAAAT-TTAAAATAAATTTAAA
5339 GGGGAGCTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 3 0.06
35 27 0.53
36 21 0.41
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAAATTTAAAACAAATT
Found at i:8167 original size:52 final size:51
Alignment explanation
Indices: 8044--8190 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 51
8034 AGGTATTTGT
**
8044 TATGCAATGGCCGACACCCTTTTTATCAGATAAAAAAAATTTTGGTGTTTG
1 TATGCAATGGCCGACACCCTTTTTATCAGATAAAAAAAATTTTGGTGTTCC
* * ****
8095 TCAAGCTATGGCCGACACCCTTTTTATCAGATAAAATTTTTTTTGAGTGTCTCC
1 T-ATGCAATGGCCGACACCCTTTTTATCAGATAAAAAAAATTTTG-GTGT-TCC
* * *
8149 TATGCCATGGCCGA-ACCCTCTTTT-TCAAATAAAAAATATTTT
1 TATGCAATGGCCGACACCCT-TTTTATCAGATAAAAAAAATTTT
8191 TTTGGATGTC
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 56 0.72
53 19 0.24
54 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (51 bp):
TATGCAATGGCCGACACCCTTTTTATCAGATAAAAAAAATTTTGGTGTTCC
Found at i:8213 original size:55 final size:55
Alignment explanation
Indices: 8102--8240 Score: 155
Period size: 55 Copynumber: 2.6 Consensus size: 55
8092 TTGTCAAGCT
*
8102 ATGGCCGACACCCT-TTTTATCAGAT--AAAATTTTTTTTGAGTGTCTCCTATGCC
1 ATGGCCGACACCCTCTTTT-TCAAATAAAAAATTTTTTTTGAGTGTCTCCTATGCC
*
8155 ATGGCCGA-ACCCTCTTTTTCAAATAAAAAATATTTTTTTG-GATGTCATTC-ATGCC
1 ATGGCCGACACCCTCTTTTTCAAATAAAAAAT-TTTTTTTGAG-TGTC-TCCTATGCC
** *
8210 ATGGCTAACACCCTCTTTATCAAATAAAAAA
1 ATGGCCGACACCCTCTTTTTCAAATAAAAAA
8241 AATATTGTTG
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
52 10 0.14
53 12 0.16
54 6 0.08
55 23 0.31
56 23 0.31
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (55 bp):
ATGGCCGACACCCTCTTTTTCAAATAAAAAATTTTTTTTGAGTGTCTCCTATGCC
Found at i:9268 original size:30 final size:30
Alignment explanation
Indices: 9232--9322 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
9222 AAAATAATAG
9232 TTAGAAATTAAATTTAAAATATAAACGAAA
1 TTAGAAATTAAATTTAAAATATAAACGAAA
*
9262 TTAGAAATTAAATTTAACATATAAACGAAA
1 TTAGAAATTAAATTTAAAATATAAACGAAA
*
9292 TTAAAAATTAAATTTAAAATATAAACGAAA
1 TTAGAAATTAAATTTAAAATATAAACGAAA
9322 T
1 T
9323 AAAAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.31
Consensus pattern (30 bp):
TTAGAAATTAAATTTAAAATATAAACGAAA
Found at i:10343 original size:21 final size:20
Alignment explanation
Indices: 10319--10388 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 20
10309 AGTTAATATT
*
10319 AAAAGTATTTCATTTGTAAAAA
1 AAAAATATTTCATTTGT--AAA
**
10341 AAAAATATTTCGGAAATGTAAA
1 AAAAATATTTC--ATTTGTAAA
* *
10363 AAAATATTTTTAATTTGTAAA
1 AAAA-ATATTTCATTTGTAAA
10384 AAAAA
1 AAAAA
10389 ATCGAAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.29
22 17 0.45
23 5 0.13
24 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (20 bp):
AAAAATATTTCATTTGTAAA
Found at i:14740 original size:115 final size:113
Alignment explanation
Indices: 14559--14766 Score: 292
Period size: 115 Copynumber: 1.8 Consensus size: 113
14549 ATGATTTCGT
* * * * *
14559 AAACACCCAAAAAATATTTTTTTCCTGATAAAGGGGGTGTCAATTATTGCATGGCAAATATCCAA
1 AAACACCCAAAAAATATTTTTTTCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACCCAA
*
14624 AAAAATTATTTTTTATTCTTATTTTTTGAGTGTCAGCTATGGCTTGAC
66 AAAAATTATTTTTTATTCGTATTTTTTGAGTGTCAGCTATGGCTTGAC
** * *
14672 AAACACCCAAAAAAATAATTTTTTAT-CTGATAAAGAGGGTGTTGATCATTGTATGATAAACACC
1 AAACACCC-AAAAAAT-ATTTTTT-TCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACC
14736 CAAAAAAATTATTTTTTATTCGTATTTTTTG
63 CAAAAAAATTATTTTTTATTCGTATTTTTTG
14767 GATGTCGGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
113 8 0.10
114 7 0.09
115 66 0.80
116 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (113 bp):
AAACACCCAAAAAATATTTTTTTCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACCCAA
AAAAATTATTTTTTATTCGTATTTTTTGAGTGTCAGCTATGGCTTGAC
Found at i:14793 original size:115 final size:115
Alignment explanation
Indices: 14559--14810 Score: 289
Period size: 115 Copynumber: 2.2 Consensus size: 115
14549 ATGATTTCGT
* * * * *
14559 AAACACCC-AAAAAATATTTTTT-TCCTGATAAAGGGGGTGTCAATTATTGCATGGCAAATATCC
1 AAACACCCAAAAAAATATTTTTTATCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACCC
* *
14622 AAAAAAATTATTTTTTATTCTTATTTTTTGAGTGTCAGCTATGGCTTGAC
66 AAAAAAATTATTTTTTATTCGTATTTTTTGAGTGTCAGCTATGGCATGAC
** * *
14672 AAACACCCAAAAAAATAATTTTTTAT-CTGATAAAGAGGGTGTTGATCATTGTATGATAAACACC
1 AAACACCCAAAAAAAT-ATTTTTTATCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACC
* * **
14736 CAAAAAAATTATTTTTTATTCGTATTTTTTG-GATGTC-GGTCGTGGCATGGG
65 CAAAAAAATTATTTTTTATTCGTATTTTTTGAG-TGTCAGCT-ATGGCATGAC
**
14787 TGACACCCAAAAAAATATTTTTTA
1 AAACACCCAAAAAAATATTTTTTA
14811 AATATAAAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
113 8 0.07
114 18 0.15
115 90 0.77
116 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (115 bp):
AAACACCCAAAAAAATATTTTTTATCCTGATAAAGAGGGTGTCAATCATTGCATGACAAACACCC
AAAAAAATTATTTTTTATTCGTATTTTTTGAGTGTCAGCTATGGCATGAC
Found at i:19817 original size:11 final size:11
Alignment explanation
Indices: 19803--19827 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19793 CTACTTACTA
19803 AATAAAATTAG
1 AATAAAATTAG
19814 AATAAAATTAG
1 AATAAAATTAG
19825 AAT
1 AAT
19828 TTTTTCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
AATAAAATTAG
Found at i:22265 original size:26 final size:26
Alignment explanation
Indices: 22236--22306 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
22226 AAACATTGAG
* *
22236 ATGATATGATTATACGAAATGGTTAT
1 ATGAAATGATTACACGAAATGGTTAT
*
22262 ATGAAATGATTACATGAAATGGTTAT
1 ATGAAATGATTACACGAAATGGTTAT
* * *
22288 ATGAATTGGTTACATGAAA
1 ATGAAATGATTACACGAAA
22307 ATAGATGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (26 bp):
ATGAAATGATTACACGAAATGGTTAT
Found at i:22267 original size:13 final size:13
Alignment explanation
Indices: 22245--22306 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
22235 GATGATATGA
*
22245 TTATACGAAATGG
1 TTATATGAAATGG
*
22258 TTATATGAAATGA
1 TTATATGAAATGG
*
22271 TTACATGAAATGG
1 TTATATGAAATGG
*
22284 TTATATGAATTGG
1 TTATATGAAATGG
*
22297 TTACATGAAA
1 TTATATGAAA
22307 ATAGATGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (13 bp):
TTATATGAAATGG
Found at i:22317 original size:27 final size:26
Alignment explanation
Indices: 22259--22323 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
22249 ACGAAATGGT
* * *
22259 TATATGAAATGATTACATGAAATGGT
1 TATATGAATTGATTACATGAAATAGA
*
22285 TATATGAATTGGTTACATGAAAATAGA
1 TATATGAATTGATTACATG-AAATAGA
*
22312 TGTATGAATTGA
1 TATATGAATTGA
22324 GACATTGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (26 bp):
TATATGAATTGATTACATGAAATAGA
Found at i:26126 original size:4 final size:4
Alignment explanation
Indices: 26117--26142 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
26107 AAATGCATGA
26117 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
26143 TTTAAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:30418 original size:12 final size:12
Alignment explanation
Indices: 30401--30427 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30391 CTCCCACTTT
30401 CTTTGGCTCTTC
1 CTTTGGCTCTTC
30413 CTTTGGCTCTTC
1 CTTTGGCTCTTC
30425 CTT
1 CTT
30428 GGTTACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (12 bp):
CTTTGGCTCTTC
Found at i:41637 original size:20 final size:21
Alignment explanation
Indices: 41614--41654 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41604 TTAGTGCAAG
*
41614 CATTTTGACATG-TTTAAAAT
1 CATTTTAACATGATTTAAAAT
*
41634 CATTTTAACTTGATTTAAAAT
1 CATTTTAACATGATTTAAAAT
41655 TGTTTCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (21 bp):
CATTTTAACATGATTTAAAAT
Found at i:41765 original size:22 final size:23
Alignment explanation
Indices: 41738--41787 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
41728 TTTTGTCAAT
41738 TTTTAACTTG-CAT-TCAAAAATA
1 TTTTAACTTGTCATATC-AAAATA
* *
41760 TTTTAATTTGTTATATCAAAATA
1 TTTTAACTTGTCATATCAAAATA
41783 TTTTA
1 TTTTA
41788 TCAAATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTTAACTTGTCATATCAAAATA
Found at i:43461 original size:27 final size:28
Alignment explanation
Indices: 43421--43474 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
43411 TATTAATAAA
**
43421 TTTTTTTTTGGTCATTCAACTATTCAAC
1 TTTTTTTTTGGTCACCCAACTATTCAAC
43449 TTTTTTTTT-GTCACCCAACTATTCAA
1 TTTTTTTTTGGTCACCCAACTATTCAA
43475 AAAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTTTTTTTGGTCACCCAACTATTCAAC
Found at i:48077 original size:14 final size:14
Alignment explanation
Indices: 48060--48086 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48050 TGCTTCAACC
48060 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
48074 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
48087 CACCTTGTAT
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:49041 original size:3 final size:3
Alignment explanation
Indices: 49033--49058 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49023 TTTTTTACCA
49033 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
49059 TGCGTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:51928 original size:15 final size:16
Alignment explanation
Indices: 51892--51927 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
51882 GATGTAGGTA
51892 AAAAATATTTTATGTT
1 AAAAATATTTTATGTT
* *
51908 AAAAATGTTTTATTTT
1 AAAAATATTTTATGTT
51924 AAAA
1 AAAA
51928 TTTATTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AAAAATATTTTATGTT
Found at i:56087 original size:10 final size:11
Alignment explanation
Indices: 56067--56091 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56057 CTCCTCCTTC
56067 TTTTTCTTTTT
1 TTTTTCTTTTT
56078 TTTTTCTTTTT
1 TTTTTCTTTTT
56089 TTT
1 TTT
56092 ACATTATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:56613 original size:61 final size:63
Alignment explanation
Indices: 56537--56655 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
56527 CAATTTGTTG
* * * * *
56537 TAGATACAGCGATATTTAGA-TTTA-TTT-TTATCAATTTAATATTTAAATATTACTTTTTATT
1 TAGATACAGCAATATTT-GACATTACTTTCTTACCAAATTAATATTTAAATACTACTTTTTATT
* *
56598 TAGATACTGCAATATTTGACATTACTTTCTTACCAAATTAATATTTAGATACTACTTT
1 TAGATACAGCAATATTTGACATTACTTTCTTACCAAATTAATATTTAAATACTACTTT
56656 GTATACCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 2 0.04
61 18 0.38
62 3 0.06
63 25 0.52
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (63 bp):
TAGATACAGCAATATTTGACATTACTTTCTTACCAAATTAATATTTAAATACTACTTTTTATT
Found at i:60116 original size:24 final size:24
Alignment explanation
Indices: 60081--60132 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
60071 ATATTAGTTT
60081 TAATT-TTTT-TTTTAA-ATATTTA
1 TAATTGTTTTATTTTAATAT-TTTA
60103 T-ATTGTTTTATTTTAATATTTTA
1 TAATTGTTTTATTTTAATATTTTA
60126 TAATTGT
1 TAATTGT
60133 ATAACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 11 0.42
24 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TAATTGTTTTATTTTAATATTTTA
Found at i:69985 original size:16 final size:16
Alignment explanation
Indices: 69964--69994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
69954 AGCCCATATC
*
69964 CTGAAATGATCCAAAT
1 CTGAAATGACCCAAAT
69980 CTGAAATGACCCAAA
1 CTGAAATGACCCAAA
69995 CTTAAAATTG
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:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (16 bp):
CTGAAATGACCCAAAT
Found at i:72908 original size:20 final size:21
Alignment explanation
Indices: 72866--72909 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
72856 CAGCCGATAC
72866 ATCTCTCGTATACATGGTCAAG
1 ATCTCTCGTATACATGG-CAAG
*
72888 ATCTCTCGTATACGTGG-AAG
1 ATCTCTCGTATACATGGCAAG
72908 AT
1 AT
72910 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
22 16 0.76
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
ATCTCTCGTATACATGGCAAG
Found at i:73645 original size:2 final size:2
Alignment explanation
Indices: 73638--73664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73628 TTCAAACAGT
73638 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
73665 CCTTATAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78267 original size:21 final size:21
Alignment explanation
Indices: 78241--78317 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
78231 GGAGTTTTTA
78241 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAGTAAGACTT
78262 GTATCGGTAGAAG--AGTTACTT
1 GTATCGGTAGAAGTAAG--ACTT
* * **
78283 GTATCGGTAAAACTATCACTT
1 GTATCGGTAGAAGTAAGACTT
78304 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
78318 CTGCATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.04
21 44 0.96
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTAAGACTT
Found at i:82073 original size:18 final size:20
Alignment explanation
Indices: 82042--82079 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
82032 TTTTTTTCAT
*
82042 TTTTTTCATATCCTTTCTTC
1 TTTTTTCATATCCTCTCTTC
82062 TTTTTTC-T-TCCTCTCTTC
1 TTTTTTCATATCCTCTCTTC
82080 CCCTCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTCATATCCTCTCTTC
Found at i:94138 original size:12 final size:12
Alignment explanation
Indices: 94118--94149 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
94108 ATTTCCACTG
94118 CCTCCACCTCTA
1 CCTCCACCTCTA
*
94130 CCTCTACCTCTA
1 CCTCCACCTCTA
94142 CCTCCACC
1 CCTCCACC
94150 AACATCTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.59, G:0.00, T:0.25
Consensus pattern (12 bp):
CCTCCACCTCTA
Found at i:96155 original size:23 final size:23
Alignment explanation
Indices: 96137--96182 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 23
96127 TTATAAATTT
96137 TATAAATTAAAAAAAATAAAACA
1 TATAAATTAAAAAAAATAAAACA
96160 TATAAATTAATAAAAATATAAAA
1 TATAAATTAA-AAAAA-ATAAAA
96183 AGTTTTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 5 0.24
25 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
TATAAATTAAAAAAAATAAAACA
Found at i:96423 original size:39 final size:37
Alignment explanation
Indices: 96380--96475 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 37
96370 TTTTTTAATT
*
96380 TATATATAT-TATATTTTTTTCAAAATGTTATAGCCTTTA
1 TATATATATATATATTTTTTT-AAAAT-TTATA-ACTTTA
* *
96419 TATATATAATTGTATATTTTTTTATAATTTATAACTTTA
1 TATATAT-A-TATATATTTTTTTAAAATTTATAACTTTA
*
96458 TA-ATTTATATATATTTTT
1 TATATATATATATATTTTT
96476 GAAATAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
36 10 0.20
37 1 0.02
38 3 0.06
39 14 0.28
40 6 0.12
41 5 0.10
42 11 0.22
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (37 bp):
TATATATATATATATTTTTTTAAAATTTATAACTTTA
Found at i:96467 original size:42 final size:45
Alignment explanation
Indices: 96375--96472 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 45
96365 ATATATTTTT
*
96375 TAATTTATAT-ATATTATATTTTTTTCAAAATGTTATAGCCTTTA
1 TAATTTATATAATATTATATTTTTTTCAAAATGTTATAGACTTTA
*
96419 T-A--TATATAAT-TGTATATTTTTTT-ATAAT-TTATA-ACTTTA
1 TAATTTATATAATAT-TATATTTTTTTCAAAATGTTATAGACTTTA
96458 TAATTTATAT-ATATT
1 TAATTTATATAATATT
96473 TTTGAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
39 6 0.13
40 6 0.13
41 13 0.28
42 19 0.41
43 1 0.02
44 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (45 bp):
TAATTTATATAATATTATATTTTTTTCAAAATGTTATAGACTTTA
Found at i:100517 original size:36 final size:36
Alignment explanation
Indices: 100466--100546 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
100456 GTCATGTTGG
* * *
100466 TCACACGATCGTGTGGAATGGTTTAGCCCGTGTGGA
1 TCACACGACCATGTGGAATGGTTTAGCCCGTATGGA
*
100502 TCACACGACCATGTGGAATGGTTTAGCCTGTATGGA
1 TCACACGACCATGTGGAATGGTTTAGCCCGTATGGA
100538 TCACACGAC
1 TCACACGAC
100547 TGTGTGGTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (36 bp):
TCACACGACCATGTGGAATGGTTTAGCCCGTATGGA
Found at i:110830 original size:29 final size:29
Alignment explanation
Indices: 110798--111267 Score: 290
Period size: 30 Copynumber: 16.0 Consensus size: 29
110788 TTTTGAGAGT
* *
110798 TTCGAGATCGAAAATGGGATTTTTGGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
*
110827 TTCGGAGGT--AAAATGGTAATTTTTGGAAGG
1 TTC-GAGGTGGAAAATGG-GATTTTTGGAA-G
* *
110857 TTCGAGGT-CAAAATTAGGATTTTTGGAAG
1 TTCGAGGTGGAAAA-TGGGATTTTTGGAAG
* * *
110886 TCCGAGG-GTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTGGAAAATGG-GATTTTTGGAA-G
* ** *
110916 TTCGGGGTTAAAAATGGGATTTTTTGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
110945 TTCG-GG-GGTAAAATGGGATTTTTGGAAG
1 TTCGAGGTGG-AAAATGGGATTTTTGGAAG
* * *
110973 TT-TAGG-GGTAAAATGGTAATTTTGGAAGG
1 TTCGAGGTGG-AAAATGGGATTTTTGGAA-G
* * ** *
111002 TTTGGGGTTAAAAATGAGATTTTTGGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
111031 TTCGAGG-GGTAAAATGGTGATTTTTGGAAGG
1 TTCGAGGTGG-AAAATGG-GATTTTTGGAA-G
**
111062 TTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
111091 CTT-G-GG-GGTAAAATGGTGATTTTTGGAAGG
1 -TTCGAGGTGG-AAAATGG-GATTTTTGGAA-G
**
111121 TTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
* *
111150 TTTGAGGAT--AAAATGGTAATTTTTGGAAG
1 TTCGAGG-TGGAAAATGG-GATTTTTGGAAG
* ** *
111179 ATTCGGGGTTAAAAATGGGATTTTTGAAAG
1 -TTCGAGGTGGAAAATGGGATTTTTGGAAG
* *
111209 TTC-A-G-GGATAAATTGGTAATTTTTTGAAGG
1 TTCGAGGTGGA-AAA-TGG-GATTTTTGGAA-G
* ** *
111239 TTCGGGGTTAAAAATGGGGTTTTTGGAAG
1 TTCGAGGTGGAAAATGGGATTTTTGGAAG
111268 GTTTAGGGAC
Statistics
Matches: 348, Mismatches: 56, Indels: 74
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 71 0.20
29 105 0.30
30 119 0.34
31 43 0.12
32 4 0.01
33 1 0.00
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.34
Consensus pattern (29 bp):
TTCGAGGTGGAAAATGGGATTTTTGGAAG
Found at i:110877 original size:59 final size:59
Alignment explanation
Indices: 110808--111270 Score: 413
Period size: 59 Copynumber: 7.9 Consensus size: 59
110798 TTCGAGATCG
*
110808 AAAATGGGATTTTTGGAA-GTTCGGAGG-T-AAAATGGTAATTTTTGGAAGGTTCGAGGT
1 AAAATGGGATTTTTGGAAGGTTCGGAGGTTAAAAATGG-AATTTTTGGAAGGTTCGGGGT
* * *
110865 CAAAATTAGGATTTTTGGAA-G-TCCGAGGGT-AAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 -AAAA-TGGGATTTTTGGAAGGTTCGGAGGTTAAAAATGG-AATTTTTGGAAGGTTCGGGG-T
* * * * *
110925 AAAAATGGGATTTTTTGAA-GTTCGG-GGGT-AAAATGGGATTTTTGGAAGTTTAGGGGT
1 -AAAATGGGATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTTCGGGGT
* * *
110982 AAAATGGTAATTTTGGAAGGTTTGG-GGTTAAAAAT-GAGATTTTTGGAA-GTTCGAGGGGT
1 AAAATGGGATTTTTGGAAGGTTCGGAGGTTAAAAATGGA-ATTTTTGGAAGGTTC--GGGGT
* * *
111041 AAAATGGTGATTTTTGGAAGGTTC-GAGGTTAAAAATGGGATTTTTGGAAGCTTGGGGGT
1 AAAATGG-GATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTTCGGGGT
* * *
111100 AAAATGGTGATTTTTGGAAGGTTC-GAGGTTAAAAATGGGATTTTTGGAA-GTTTGAGGAT
1 AAAATGG-GATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTTCG-GGGT
* * * * *
111159 AAAATGGTAATTTTTGGAAGATTCGG-GGTTAAAAATGGGATTTTT-GAAAGTTCAGGGAT
1 AAAATGG-GATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTTC-GGGGT
* * * **
111218 AAATTGGTAATTTTTTGAAGGTTCGG-GGTTAAAAATGGGGTTTTTGGAAGGTT
1 AAAATGG-GATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTT
111271 TAGGGACCTT
Statistics
Matches: 352, Mismatches: 35, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
56 15 0.04
57 12 0.03
58 48 0.14
59 225 0.64
60 49 0.14
61 3 0.01
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGGTTCGGAGGTTAAAAATGGAATTTTTGGAAGGTTCGGGGT
Found at i:111193 original size:118 final size:114
Alignment explanation
Indices: 110808--111267 Score: 480
Period size: 118 Copynumber: 3.9 Consensus size: 114
110798 TTCGAGATCG
* * *
110808 AAAATGGGATTTTTGGAAGTTCGGAGG-TAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAATT
1 AAAATGGGATTTTTGGAAGTTCGG-GGTTAAAATGG-GATTTTTGGAA-GTTAGGGGT-AAAA-T
* * * * * *
110872 AG-GATTTTTGGAA-GTCCGAGGGT-AAAATGGTAATTTTTGGAAGGTTCGGGGTT
61 GGTGATTTTTGGAAGGTTCGAGGTTAAAAATGG-GATTTTTGGAA-GTTCGAGGAT
* *
110925 AAAAATGGGATTTTTTGAAGTTCGGGGGTAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGT
1 -AAAATGGGATTTTTGGAAGTTCGGGGTTAAAATGGGATTTTTGGAAG-TTAGGGGTAAAATGGT
* * * * *
110990 -AATTTTGGAAGGTTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGGT
64 GATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGA-GGAT
* *
111041 AAAATGGTGATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGCTTGGGGGTAAAATG
1 AAAATGG-GATTTTTGGAA-GTTCGGGGTT-AAAATGGGATTTTTGGAAG-TTAGGGGTAAAATG
*
111106 GTGATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGAT
62 GTGATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGAT
* * * *
111159 AAAATGGTAATTTTTGGAAGATTCGGGGTTAAAAATGGGATTTTTGAAAGTTCAGGGATAAATTG
1 AAAATGG-GATTTTTGGAAG-TTCGGGGTT-AAAATGGGATTTTTGGAAGTT-AGGGGTAAAATG
* * * *
111224 GTAATTTTTTGAAGGTTCGGGGTTAAAAATGGGGTTTTTGGAAG
62 GTGATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAG
111268 GTTTAGGGAC
Statistics
Matches: 295, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
115 23 0.08
116 34 0.12
117 35 0.12
118 162 0.55
119 41 0.14
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.35
Consensus pattern (114 bp):
AAAATGGGATTTTTGGAAGTTCGGGGTTAAAATGGGATTTTTGGAAGTTAGGGGTAAAATGGTGA
TTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGAT
Found at i:113089 original size:17 final size:16
Alignment explanation
Indices: 113069--113145 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
113059 AAATAAATTT
113069 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
113086 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
113103 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
113120 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
113137 TAAATTTAA
1 TAAATTTAA
113146 GCTGATTGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:113142 original size:34 final size:34
Alignment explanation
Indices: 113069--113145 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
113059 AAATAAATTT
* * * *
113069 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
113103 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
113137 TAAATTTAA
1 TAAATTTAA
113146 GCTGATTGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:113844 original size:197 final size:199
Alignment explanation
Indices: 113509--113977 Score: 692
Period size: 197 Copynumber: 2.3 Consensus size: 199
113499 CTTATTTTGG
* * * * *
113509 TTCGCTTCTCTATACCTCATCAAGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGC
1 TTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAAGAAGC
113574 TAACCTTTTATTACTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGAGGTTTGAAGATTTTG
66 TAACCTTTTATTACTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGAGGTTTGAAGATTTTG
*
113639 CTCGTTTCGAGCCTCGTTTAGGTTTGATTTGGTCTTCTTCTTAATATCTTGT-T-CGCATCGTTT
131 CTCGTTTCGAGCCTCGTTTAGGTTTGATTTGGTCTTCTTCTCAATATCTTGTATACGCATCGTTT
113702 TTAA
196 TTAA
*
113706 TTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAAGAAGC
1 TTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAAGAAGC
* * *
113771 TAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTG
66 TAACCTTTTATTACTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGAGGTTTGAAGATTTTG
* * *
113836 CTCGTTTCGAGCCTCTTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGTCCGGAAGATGACC
131 CTCGTTTCGAGCCTCGTTTAGGTTTGATTTGGTCTTCTTCTCAATATCTTGT-------AT-A-C
113901 GCATCGTTTTTAA
187 GCATCGTTTTTAA
* *
113914 TTCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACAC-TCTTCCGTATCTCATCAAGAAG
1 TTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTACACTTC-TCAGTATCTCATCAAGAAG
113978 ACGAATTTGG
Statistics
Matches: 244, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
197 169 0.69
205 1 0.00
207 2 0.01
208 72 0.30
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (199 bp):
TTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAAGAAGC
TAACCTTTTATTACTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGAGGTTTGAAGATTTTG
CTCGTTTCGAGCCTCGTTTAGGTTTGATTTGGTCTTCTTCTCAATATCTTGTATACGCATCGTTT
TTAA
Found at i:113972 original size:37 final size:37
Alignment explanation
Indices: 113922--113993 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
113912 AATTCGCTTC
113922 TCCGTATCTCATCAAGAAGACGAATTTGGTACACTCT
1 TCCGTATCTCATCAAGAAGACGAATTTGGTACACTCT
113959 TCCGTATCTCATCAAGAAGACGAATTTGGTACACT
1 TCCGTATCTCATCAAGAAGACGAATTTGGTACACT
113994 TCTCAATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (37 bp):
TCCGTATCTCATCAAGAAGACGAATTTGGTACACTCT
Found at i:114004 original size:37 final size:37
Alignment explanation
Indices: 113926--114006 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
113916 CGCTTCTCCG
**
113926 TATCTCATCAAGAAGACGAATTTGGTACACTCTTCCG
1 TATCTCATCAAGAAGACGAATTTGGTACACTCTTCAA
113963 TATCTCATCAAGAAGACGAATTTGGTACACT-TCTCAA
1 TATCTCATCAAGAAGACGAATTTGGTACACTCT-TCAA
114000 TATCTCA
1 TATCTCA
114007 CCAGGAAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 1 0.02
37 40 0.98
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (37 bp):
TATCTCATCAAGAAGACGAATTTGGTACACTCTTCAA
Found at i:114018 original size:245 final size:246
Alignment explanation
Indices: 113710--114217 Score: 844
Period size: 245 Copynumber: 2.1 Consensus size: 246
113700 TTTTAATTCG
* * * *
113710 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAAGAAGCTAAC
1 CTTCTCAGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAATATCTCACCAAGAAGCTAAC
113775 CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCG
66 CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCG
*
113840 TTTCGAGCCTCT-TTTGGGTTTGATTTGGTCTTCTTCT-CAGTATCTTGTCCGGAAGATGACCGC
131 TTTCGAGCCT-TGTTTAGGTTTGATTTGGTCTTCTTCTCCA-TATCTTGTCCGGAAGATGACCGC
*
113903 ATCG-TTTTTAATTCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACA
194 ATCGCTTTTTAATCCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACA
* *
113955 C-TCTTCCGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAATATCTCACCAGGAAGCTAA
1 CTTC-TCAGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAATATCTCACCAAGAAGCTAA
* *
114019 CCTTTTATTGCTTCAACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGTTTTTGCTC
65 CCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTC
* *
114084 GTTTTGGGCCTTGTTTAGGTTTGATTTGGTCTTCTTCTCCATATCTTGTCCGGAAGATGACCGCA
130 GTTTCGAGCCTTGTTTAGGTTTGATTTGGTCTTCTTCTCCATATCTTGTCCGGAAGATGACCGCA
114149 TCGCTTTTTTAATCCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACA
195 TCGC-TTTTTAATCCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACA
114202 CTTCTCAGTATCTCAT
1 CTTCTCAGTATCTCAT
114218 TAGGAAGCTA
Statistics
Matches: 245, Mismatches: 12, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
244 3 0.01
245 179 0.73
246 2 0.01
247 59 0.24
248 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (246 bp):
CTTCTCAGTATCTCATCAAGAAGACGAATTTGGTACACTTCTCAATATCTCACCAAGAAGCTAAC
CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCG
TTTCGAGCCTTGTTTAGGTTTGATTTGGTCTTCTTCTCCATATCTTGTCCGGAAGATGACCGCAT
CGCTTTTTAATCCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTACA
Found at i:126211 original size:29 final size:29
Alignment explanation
Indices: 126189--126662 Score: 406
Period size: 30 Copynumber: 16.2 Consensus size: 29
126179 TTCGAGGTCG
126189 AAAATGGGATTTTTGGAAGTTCG-GGGGT
1 AAAATGGGATTTTTGGAAGTTCGAGGGGT
**
126217 AAAATGTAATTTTTGGAAGGTTC--GGGGT
1 AAAATGGGATTTTTGGAA-GTTCGAGGGGT
126245 CAAAAATGGGATTTTTGGAAGTTCG-GGGGT
1 --AAAATGGGATTTTTGGAAGTTCGAGGGGT
** *
126275 AAAATGTAATTTTTGGAAGGTTCG-GGGTT
1 AAAATGGGATTTTTGGAA-GTTCGAGGGGT
*
126304 AAAAATGGGATTTTTGGAAGTTCGA-GAGT
1 -AAAATGGGATTTTTGGAAGTTCGAGGGGT
*
126333 AAAATGAGATTTTTGGAAGTTCG-GGGGT
1 AAAATGGGATTTTTGGAAGTTCGAGGGGT
* *
126361 AAAATGGTGA-TTTTGGATGGTTCG-GGGTT
1 AAAATGG-GATTTTTGGA-AGTTCGAGGGGT
*
126390 AAAAATAGGATTTTTGGAAGTTCGAGGGGT
1 -AAAATGGGATTTTTGGAAGTTCGAGGGGT
*
126420 AAAATGGTAATTTTTGGAAGTTCG-GGGGT
1 AAAATGG-GATTTTTGGAAGTTCGAGGGGT
*
126449 AAAATGGAGATTTTTGGAAGCTCG-GGGGT
1 AAAATGG-GATTTTTGGAAGTTCGAGGGGT
* * *
126478 AAAATGGTGTTTTTTGGAAGGTT-TAGGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGAGGGGT
*
126508 AAAAATGGGATTTTTGAAAGCTT-GAGGGGT
1 -AAAATGGGATTTTTGGAAG-TTCGAGGGGT
* *
126538 AAAATGGTAATTTTTGGAAGGTTCG-GGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGAGGGGT
* * *
126568 AAAAAAGGGATTTTTGGAAATTTGA-GGGT
1 -AAAATGGGATTTTTGGAAGTTCGAGGGGT
* * *
126597 AAAATGGTGATTTTTGAAAGGTTTG-GGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGAGGGGT
* * *
126627 AAAAATGGGAATTTTGGAAGTT-TAGGGTT
1 -AAAATGGGATTTTTGGAAGTTCGAGGGGT
126656 AAAATGG
1 AAAATGG
126663 TAATTTTTTG
Statistics
Matches: 370, Mismatches: 48, Indels: 56
0.78 0.10 0.12
Matches are distributed among these distances:
28 88 0.24
29 128 0.35
30 132 0.36
31 22 0.06
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGGT
Found at i:126485 original size:58 final size:58
Alignment explanation
Indices: 126189--126705 Score: 496
Period size: 59 Copynumber: 8.8 Consensus size: 58
126179 TTCGAGGTCG
**
126189 AAAATGG-GATTTTTGGAAGTTCGGGGGT-AAAATGTAATTTTTGGAAGGTTC-GGGGT
1 AAAATGGTGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAA-GTTCGGGGGT
** *
126245 CAAAAATGG-GATTTTTGGAAGTTCGGGGGT-AAAATGTAATTTTTGGAAGGTTCGGGGTT
1 --AAAATGGTGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAA-GTTCGGGGGT
* * *
126304 AAAAATGG-GATTTTTGGAAGTTCGAGAGT-AAAATGAGATTTTTGGAAGTTCGGGGGT
1 -AAAATGGTGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
126361 AAAATGGTGA-TTTTGGATGGTTCGGGGTTAAAAATAGGATTTTTGGAAGTTCGAGGGGT
1 AAAATGGTGATTTTTGGA-AGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCG-GGGGT
* *
126420 AAAATGGTAATTTTTGGAAGTTCGGGGGT-AAAATGGAGATTTTTGGAAGCTCGGGGGT
1 AAAATGGTGATTTTTGGAAGTTCGGGGGTAAAAATGG-GATTTTTGGAAGTTCGGGGGT
* ** * *
126478 AAAATGGTGTTTTTTGGAAGGTTTAGGGTTAAAAATGGGATTTTTGAAAGCTT-GAGGGGT
1 AAAATGGTGATTTTTGGAA-GTTCGGGGGTAAAAATGGGATTTTTGGAAG-TTCG-GGGGT
* * * * * *
126538 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAAAGGGATTTTTGGAAATTTGAGGGT
1 AAAATGGTGATTTTTGGAA-GTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * ** *
126597 AAAATGGTGATTTTTGAAAGGTTTGGGGTTAAAAATGGGAATTTTGGAAGTTTAGGGTT
1 AAAATGGTGATTTTTGGAA-GTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * ** * * *
126656 AAAATGGTAATTTTTTGAAGGTTCAAGGTTAAAAATGGGGTTTTTAGAAG
1 AAAATGGTGATTTTTGGAA-GTTCGGGGGTAAAAATGGGATTTTTGGAAG
126706 GTTTAAGGAC
Statistics
Matches: 397, Mismatches: 50, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
56 14 0.04
57 18 0.05
58 143 0.36
59 158 0.40
60 64 0.16
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (58 bp):
AAAATGGTGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:126670 original size:29 final size:28
Alignment explanation
Indices: 126189--126689 Score: 386
Period size: 29 Copynumber: 17.1 Consensus size: 28
126179 TTCGAGGTCG
* *
126189 AAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGAATTTTTGGAAGTTCGGGGTT
* *
126217 AAAATGTAATTTTTGGAAGGTTCGGGGTCA
1 AAAATGGAATTTTTGGAA-GTTCGGGGT-T
* *
126247 AAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGAATTTTTGGAAGTTCGGGGTT
*
126275 AAAATGTAATTTTTGGAAGGTTCGGGGTT
1 AAAATGGAATTTTTGGAA-GTTCGGGGTT
* *
126304 AAAAATGGGATTTTTGGAAGTTCGAGAG-T
1 -AAAATGGAATTTTTGGAAGTTCG-GGGTT
*
126333 AAAAT-GAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGA-ATTTTTGGAAGTTCGGGGTT
* *
126361 AAAATGGTGA-TTTTGGATGGTTCGGGGTT
1 AAAATGG-AATTTTTGGA-AGTTCGGGGTT
*
126390 AAAAATAGG-ATTTTTGGAAGTTCGAGGGGT
1 -AAAAT-GGAATTTTTGGAAGTTCG-GGGTT
*
126420 AAAATGGTAATTTTTGGAAGTTCGGGGGT
1 AAAATGG-AATTTTTGGAAGTTCGGGGTT
* *
126449 AAAATGGAGATTTTTGGAAGCTCGGGGGT
1 AAAATGGA-ATTTTTGGAAGTTCGGGGTT
** **
126478 AAAATGGTGTTTTTTGGAAGGTTTAGGGTT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGTT
* * *
126508 AAAAATGGGATTTTTGAAAGCTT-GAGGGGT
1 -AAAATGGAATTTTTGGAAG-TTCG-GGGTT
126538 AAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGTT
* * * *
126568 AAAAAAGGGATTTTTGGAAATTTGAGGG-T
1 -AAAATGGAATTTTTGGAAGTTCG-GGGTT
* * *
126597 AAAATGGTGATTTTTGAAAGGTTTGGGGTT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGTT
**
126627 AAAAATGGGAA-TTTTGGAAGTTTAGGGTT
1 -AAAAT-GGAATTTTTGGAAGTTCGGGGTT
* **
126656 AAAATGGTAATTTTTTGAAGGTTCAAGGTT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGTT
126686 AAAA
1 AAAA
126690 ATGGGGTTTT
Statistics
Matches: 390, Mismatches: 48, Indels: 68
0.77 0.09 0.13
Matches are distributed among these distances:
27 5 0.01
28 81 0.21
29 141 0.36
30 138 0.35
31 23 0.06
32 2 0.01
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTT
Found at i:128530 original size:17 final size:16
Alignment explanation
Indices: 128510--128586 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
128500 AAATAAATTT
128510 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
128527 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
128544 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
128561 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
128578 TAAATTTAA
1 TAAATTTAA
128587 GCTGATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:128583 original size:34 final size:34
Alignment explanation
Indices: 128510--128586 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
128500 AAATAAATTT
* * * *
128510 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
128544 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
128578 TAAATTTAA
1 TAAATTTAA
128587 GCTGATTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:129751 original size:9 final size:9
Alignment explanation
Indices: 129692--129784 Score: 55
Period size: 9 Copynumber: 10.1 Consensus size: 9
129682 ATTTATTAGA
129692 TTTTTATAT
1 TTTTTATAT
*
129701 TTTTTATAA
1 TTTTTATAT
*
129710 TATTTATA-
1 TTTTTATAT
*
129718 TTTTTATAAG
1 TTTTTAT-AT
**
129728 TTCATATACT
1 TTTTTATA-T
129738 TTTTTATAT
1 TTTTTATAT
* *
129747 TTTTTAAAAA
1 TTTTT-ATAT
*
129757 TATTTAGTA-
1 TTTTTA-TAT
*
129766 ATTTTATAT
1 TTTTTATAT
129775 TTTTTATAT
1 TTTTTATAT
129784 T
1 T
129785 ATTCTGATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
8 8 0.13
9 37 0.59
10 18 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAT
Found at i:149322 original size:24 final size:24
Alignment explanation
Indices: 149242--149329 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
149232 AGCATTAGTT
*
149242 AAATTTTT-ATAATTTTATATTTTTA
1 AAATTTTTGA-AATTTTA-AATTTTA
* ** *
149267 AATATTTTAGTGATTTTTAATTTTA
1 AA-ATTTTTGAAATTTTAAATTTTA
**
149292 ATTTTTTTGAAATTTTAAATTTTA
1 AAATTTTTGAAATTTTAAATTTTA
*
149316 AAATTTTTAAAATT
1 AAATTTTTGAAATT
149330 AATTATCACT
Statistics
Matches: 47, Mismatches: 14, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
24 28 0.60
25 9 0.19
26 10 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
AAATTTTTGAAATTTTAAATTTTA
Found at i:149801 original size:27 final size:28
Alignment explanation
Indices: 149737--149813 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
149727 TTATCAGTTC
* *
149737 TTTTAATTTGGTCACTCAATTATTGCTT
1 TTTTAATTTGGTCACTCAACTATTGATT
** *
149765 TTTTTTTTTGGTCACTTAACTATT-ATT
1 TTTTAATTTGGTCACTCAACTATTGATT
* *
149792 TTTTAATTTGATCACCCAACTA
1 TTTTAATTTGGTCACTCAACTA
149814 ATCAAGATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (28 bp):
TTTTAATTTGGTCACTCAACTATTGATT
Found at i:153925 original size:23 final size:24
Alignment explanation
Indices: 153878--153927 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
153868 TATACCGTTA
153878 TTATTTATCTGTATATTTTCTATT
1 TTATTTATCTGTATATTTTCTATT
*
153902 TTATTTAT-T-TATTTTCTTCTATT
1 TTATTTATCTGTATATT-TTCTATT
153925 TTA
1 TTA
153928 AATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (24 bp):
TTATTTATCTGTATATTTTCTATT
Found at i:154014 original size:36 final size:36
Alignment explanation
Indices: 153968--154043 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
153958 TTTCTATTTT
*
153968 ATTTTGAATAATTTTAGATAAA-AGTTGAAGATAATA
1 ATTTAGAATAATTTTAGATAAAGA-TTGAAGATAATA
154004 ATTTAGAATAATTTTAGATAAAGATTGAAGATAATA
1 ATTTAGAATAATTTTAGATAAAGATTGAAGATAATA
154040 ATTT
1 ATTT
154044 GGACATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTAGAATAATTTTAGATAAAGATTGAAGATAATA
Found at i:158091 original size:30 final size:28
Alignment explanation
Indices: 158047--158103 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
158037 TTTTATGTGA
*
158047 TTAAATTTTATCATTAAACTTTGAATTTTG
1 TTAAAGTTTATCATT-AACTTT-AATTTTG
*
158077 TTAAAGTTTGTCATTAACTTTAATTTT
1 TTAAAGTTTATCATTAACTTTAATTTT
158104 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 6 0.24
30 13 0.52
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (28 bp):
TTAAAGTTTATCATTAACTTTAATTTTG
Found at i:158458 original size:12 final size:13
Alignment explanation
Indices: 158431--158464 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
158421 ATTTTAAATT
*
158431 AAAAATGAATAGA
1 AAAAATTAATAGA
158444 AAAAATTAATA-A
1 AAAAATTAATAGA
158456 AAAAATTAA
1 AAAAATTAA
158465 CTTTAGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAAATTAATAGA
Found at i:159107 original size:18 final size:18
Alignment explanation
Indices: 159084--159126 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
159074 TCTGTGTACT
159084 TATACAATTTTTTAGTAA
1 TATACAATTTTTTAGTAA
159102 TATACAATTTTTTAGTAA
1 TATACAATTTTTTAGTAA
159120 TATACAA
1 TATACAA
159127 AAATTCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (18 bp):
TATACAATTTTTTAGTAA
Found at i:166033 original size:17 final size:18
Alignment explanation
Indices: 165998--166032 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
165988 TGTCACTATG
165998 TATATTGAAATTAAAAAA
1 TATATTGAAATTAAAAAA
166016 TATATT-AAATGTAAAAA
1 TATATTGAAAT-TAAAAA
166033 TGTGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TATATTGAAATTAAAAAA
Found at i:166626 original size:29 final size:29
Alignment explanation
Indices: 166593--166674 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
166583 GATGAGAGGG
* *
166593 GAGTAGAAGTTTCGGGGGAAAGTGAGAAA
1 GAGTAAAAGTTTCGGGGAAAAGTGAGAAA
*
166622 GAGTAAAAGTTTCGGGGAAAAGTGAGAAG
1 GAGTAAAAGTTTCGGGGAAAAGTGAGAAA
* *
166651 GAGTAAAAATTTTGGGAGAAAAGT
1 GAGTAAAAGTTTCGGG-GAAAAGT
166675 AAAAATGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 40 0.85
30 7 0.15
ACGTcount: A:0.41, C:0.02, G:0.37, T:0.20
Consensus pattern (29 bp):
GAGTAAAAGTTTCGGGGAAAAGTGAGAAA
Found at i:170705 original size:23 final size:23
Alignment explanation
Indices: 170652--170721 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
170642 TCATTAACAT
*
170652 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCGTGAACGTGTTCGATTA-A
*
170676 TGTTCGTGAACGTGTTTGATTAA
1 TGTTCGTGAACGTGTTCGATTAA
*
170699 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACGTGTTCGATTAA
170722 ATTAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACGTGTTCGATTAA
Found at i:170748 original size:23 final size:23
Alignment explanation
Indices: 170705--170750 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
170695 TTAATGTTCG
*
170705 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATGAAATTAAA
170728 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
170751 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:172436 original size:23 final size:21
Alignment explanation
Indices: 172408--172491 Score: 89
Period size: 20 Copynumber: 3.9 Consensus size: 21
172398 ATTATATTAT
172408 TGTTTTGGTTGCTTTTTTTTTAC
1 TGTTTTGGTTG--TTTTTTTTAC
* *
172431 TATTTTTGTGTTGTTTTTTTTAT
1 T-GTTTTG-GTTGTTTTTTTTAC
172454 TGTTTTGG-TGTTTTTTTTAC
1 TGTTTTGGTTGTTTTTTTTAC
* *
172474 TGTTTTAGTTGTTGTTTT
1 TGTTTTGGTTGTTTTTTT
172492 CGTGTTCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.35
21 9 0.17
22 5 0.10
23 11 0.21
24 5 0.10
25 4 0.08
ACGTcount: A:0.06, C:0.04, G:0.18, T:0.73
Consensus pattern (21 bp):
TGTTTTGGTTGTTTTTTTTAC
Found at i:172503 original size:43 final size:43
Alignment explanation
Indices: 172416--172514 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 43
172406 ATTGTTTTGG
* ** *
172416 TTGCT-TTTTTTTTACTATTTTTGTGTTGTTTTTTTTATTGTT
1 TTGCTGTTTTTTTTACTATTTTAGTGTTGTTTTTCGTATTCTT
* * *
172458 TTGGTGTTTTTTTTACTGTTTTAGTTGTTG-TTTTCGTGTTCTT
1 TTGCTGTTTTTTTTACTATTTTAG-TGTTGTTTTTCGTATTCTT
*
172501 TTGCTGTTATTTTT
1 TTGCTGTTTTTTTT
172515 GTTGCTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
42 4 0.09
43 37 0.80
44 5 0.11
ACGTcount: A:0.06, C:0.06, G:0.16, T:0.72
Consensus pattern (43 bp):
TTGCTGTTTTTTTTACTATTTTAGTGTTGTTTTTCGTATTCTT
Found at i:172755 original size:50 final size:49
Alignment explanation
Indices: 172696--172793 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 49
172686 TATCTTAGTA
* * * *
172696 TAATATTTTTTAATGTTTTTTAAAT-TTATTTATTTTTTTAATATTTGTTT
1 TAATATTTTTAAATGTATTTGAAATATTATATA-TTTTTTAA-ATTTGTTT
* *
172746 TAATGTTTTTAAATGTATTTGATATATTATATATTTTTTAAATTTGTT
1 TAATATTTTTAAATGTATTTGAAATATTATATATTTTTTAAATTTGTT
172794 ATATGTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 7 0.17
50 28 0.68
51 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (49 bp):
TAATATTTTTAAATGTATTTGAAATATTATATATTTTTTAAATTTGTTT
Found at i:172780 original size:40 final size:40
Alignment explanation
Indices: 172694--172781 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 40
172684 ACTATCTTAG
* *
172694 TATAATA-TT-TTTTAATGTTTTTTAAATTTATTTATTTT
1 TATAATATTTGTTTTAATGTTTTTTAAATGTATTTATTAT
*
172732 TTTAATATTTGTTTTAATG-TTTTTAAATGTATTTGATATAT
1 TATAATATTTGTTTTAATGTTTTTTAAATGTATTT-AT-TAT
172773 TAT-ATATTT
1 TATAATATTT
172782 TTTAAATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
38 6 0.14
39 16 0.38
40 16 0.38
41 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (40 bp):
TATAATATTTGTTTTAATGTTTTTTAAATGTATTTATTAT
Found at i:173123 original size:18 final size:16
Alignment explanation
Indices: 173100--173135 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
173090 TTAGATAACA
173100 TTATATTTTTTGAATTTT
1 TTATA-TTTTT-AATTTT
173118 TTATATTTTTAATTTT
1 TTATATTTTTAATTTT
173134 TT
1 TT
173136 CGAAAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTATATTTTTAATTTT
Found at i:173235 original size:28 final size:27
Alignment explanation
Indices: 173204--173261 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
173194 TTTTTTAAAG
173204 AAAATTAT-AATTTTTATGTTTTTTTATT
1 AAAA-TATGAATTTTT-TGTTTTTTTATT
* *
173232 AAAATATGAATTTTTTTTTTTTTTTTT
1 AAAATATGAATTTTTTGTTTTTTTATT
173259 AAA
1 AAA
173262 TTTGATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
AAAATATGAATTTTTTGTTTTTTTATT
Found at i:173736 original size:18 final size:19
Alignment explanation
Indices: 173692--173740 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
173682 TTTAAAAAAT
* *
173692 ATTTATTTTATTTTAATTTA
1 ATTTTTTTTA-TTTAATTAA
*
173712 ATATTTTTTATTT-ATTAA
1 ATTTTTTTTATTTAATTAA
173730 ATTTTTTTTAT
1 ATTTTTTTTAT
173741 ATAGTTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 14 0.56
19 3 0.12
20 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTTTATTTAATTAA
Found at i:174760 original size:7 final size:7
Alignment explanation
Indices: 174748--174776 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
174738 TTTAATACTG
174748 TAGGGTT
1 TAGGGTT
174755 TAGGGTT
1 TAGGGTT
174762 TAGGGTT
1 TAGGGTT
174769 TAGGGTT
1 TAGGGTT
174776 T
1 T
174777 GAAATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (7 bp):
TAGGGTT
Found at i:181579 original size:27 final size:27
Alignment explanation
Indices: 181522--181580 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
181512 AACAGACAGT
* *
181522 ACCAATGGTGCCTACCTGATAGGTGCA
1 ACCAATGGTGCCTACCTGACAGGGGCA
181549 ACCAATGGTGCCTACCTGACAGGCGGC-
1 ACCAATGGTGCCTACCTGACAGG-GGCA
181576 ACCAA
1 ACCAA
181581 ATTATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (27 bp):
ACCAATGGTGCCTACCTGACAGGGGCA
Found at i:187885 original size:24 final size:22
Alignment explanation
Indices: 187834--187886 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
187824 TTAATACATT
187834 TTATAATAATTAATATTTTTAA
1 TTATAATAATTAATATTTTTAA
*
187856 ATATAA-AATTATATCATTTTATAA
1 TTATAATAATTA-AT-ATTTT-TAA
187880 TTATAAT
1 TTATAAT
187887 TTATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.20
22 7 0.28
23 5 0.20
24 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAATAATTAATATTTTTAA
Found at i:191387 original size:6 final size:6
Alignment explanation
Indices: 191370--191410 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
191360 ATTTGAATTT
191370 ATTTGAA ATTTAA ATTT-- ATTATAA ATTTAA ATTTAA ATTTA
1 ATTT-AA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTTA
191411 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.10
5 1 0.03
6 20 0.65
7 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:191394 original size:11 final size:10
Alignment explanation
Indices: 191377--191416 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
191367 TTTATTTGAA
191377 ATTTAAATTT
1 ATTTAAATTT
191387 ATTATAAATTT
1 ATT-TAAATTT
191398 AAATTTAAATTT
1 --ATTTAAATTT
191410 ATTTAAA
1 ATTTAAA
191417 ATAATGTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.37
11 7 0.26
12 7 0.26
13 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:191418 original size:17 final size:17
Alignment explanation
Indices: 191359--191404 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
191349 GGCCCAATAG
*
191359 AATTTGAATTTATT-TGA
1 AATTTAAATTTATTAT-A
191376 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
191393 AATTTAAATTTA
1 AATTTAAATTTA
191405 AATTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:191418 original size:23 final size:24
Alignment explanation
Indices: 191370--191416 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
191360 ATTTGAATTT
191370 ATTTGAAATTTAAATTTATTATAA
1 ATTTGAAATTTAAATTTATTATAA
191394 ATTT-AAATTTAAATTTATT-TAA
1 ATTTGAAATTTAAATTTATTATAA
191416 A
1 A
191417 ATAATGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTGAAATTTAAATTTATTATAA
Found at i:192066 original size:3 final size:3
Alignment explanation
Indices: 192060--192138 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
192050 ATTATTATGG
* * *
192060 TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA T-A TCAT TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* * *
192105 TAA TGA CAA TAA TAA TAA TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
192139 GACATTAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:193165 original size:30 final size:30
Alignment explanation
Indices: 193129--193331 Score: 213
Period size: 29 Copynumber: 6.9 Consensus size: 30
193119 TTTGCCCTCG
* * *
193129 AACTTCCAAAAATCCCATTTTTGATCTCGA
1 AACTTCCAAAAATTCCATTTTTGACCCCGA
193159 AACTTCCAAAAATTCCATTTTT-ACCCC-A
1 AACTTCCAAAAATTCCATTTTTGACCCCGA
* *
193187 AACTTACAAAAATTCCA-TTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCGA
* * **
193216 AACTTCCAAAAATTCTAATTTT-ACCTTTG-
1 AACTTCCAAAAATTCCATTTTTGACC-CCGA
* *
193245 AACTTCCAAAAATTCCATTTTTGATCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCGA
*
193275 AACTTCCAAAAATTCCAATTTT-ACCCCTG-
1 AACTTCCAAAAATTCCATTTTTGACCCC-GA
* *
193304 AACTTCCAAAATTTCTATTTTTGACCCC
1 AACTTCCAAAAATTCCATTTTTGACCCC
193332 AAAAATCTCA
Statistics
Matches: 144, Mismatches: 21, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
27 4 0.03
28 22 0.15
29 65 0.45
30 53 0.37
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTGACCCCGA
Found at i:193344 original size:59 final size:59
Alignment explanation
Indices: 193115--193335 Score: 286
Period size: 59 Copynumber: 3.8 Consensus size: 59
193105 TCGAAAGTTA
* * * * *
193115 CAATTTT-GCCCTCGAACTTCCAAAAATCCCATTTTTGATCTCGAAACTTCCAAAAATTC
1 CAATTTTACCCCT-GAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTC
* * *
193174 CATTTTTACCCC-AAACTTACAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTC
1 CAATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTC
* ** *
193231 TAATTTTACCTTTGAACTTCCAAAAATTCCATTTTTGATCCCAAAACTTCCAAAAATTC
1 CAATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTC
* *
193290 CAATTTTACCCCTGAACTTCCAAAATTTCTATTTTTGACCCCAAAA
1 CAATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCAAAA
193336 ATCTCAAAAT
Statistics
Matches: 138, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
57 32 0.23
58 31 0.22
59 72 0.52
60 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (59 bp):
CAATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTC
Found at i:193346 original size:88 final size:86
Alignment explanation
Indices: 193162--193337 Score: 210
Period size: 88 Copynumber: 2.0 Consensus size: 86
193152 ATCTCGAAAC
*
193162 TTCCAAAAATTCCATTTTTACCCCAAACTTACAAAAATTCCATTTTGACCCCAAAACTTCCAAAA
1 TTCCAAAAATTCCATTTTTACCCAAAACTTACAAAAATTCCATTTTGACCCCAAAACTTCCAAAA
**** *
193227 ATTCTAATTTTACCTTTGAAC
66 ATTCTAATTTTACCCCAAAAA
* **
193248 TTCCAAAAATTCCATTTTTGATCCCAAAACTTCCAAAAATTCCAATTTT-ACCCCTGAACTTCCA
1 TTCCAAAAATTCCATTTTT-A-CCCAAAACTTACAAAAATTCC-ATTTTGACCCCAAAACTTCCA
* *
193312 AAATTTCTATTTTTGACCCCAAAAA
63 AAAATTCTAATTTT-ACCCCAAAAA
193337 T
1 T
193338 CTCAAAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
86 19 0.25
87 1 0.01
88 44 0.59
89 11 0.15
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (86 bp):
TTCCAAAAATTCCATTTTTACCCAAAACTTACAAAAATTCCATTTTGACCCCAAAACTTCCAAAA
ATTCTAATTTTACCCCAAAAA
Found at i:196485 original size:17 final size:17
Alignment explanation
Indices: 196465--196503 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
196455 TAAACAATGA
*
196465 ATTTTTTTCCATTTTAG
1 ATTTTTTTACATTTTAG
* *
196482 ATTTTTTTATATTTTAT
1 ATTTTTTTACATTTTAG
196499 ATTTT
1 ATTTT
196504 CTATTTATAT
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:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTTTTTACATTTTAG
Found at i:196659 original size:3 final size:3
Alignment explanation
Indices: 196651--196688 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
196641 GTTATTCCCT
196651 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
196689 GAGATTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:205852 original size:21 final size:20
Alignment explanation
Indices: 205826--205865 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
205816 TTATTTTCTC
*
205826 TCTTATCTTCTTATTATTTTA
1 TCTTATCTTCATA-TATTTTA
*
205847 TCTTATTTTCATATATTTT
1 TCTTATCTTCATATATTTT
205866 TCGAAAATTG
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:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTTATCTTCATATATTTTA
Found at i:205866 original size:21 final size:21
Alignment explanation
Indices: 205800--205866 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
205790 TTGAGAGTTG
*
205800 ATTTTTAT-TTA-TTT-ATTT
1 ATTTTTATCTTATTTTCATAT
* * *
205818 ATTTTCTCTCTTATCTTCTTAT
1 ATTTT-TATCTTATTTTCATAT
205840 -TATTTTATCTTATTTTCATAT
1 AT-TTTTATCTTATTTTCATAT
205861 ATTTTT
1 ATTTTT
205867 CGAAAATTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
18 5 0.14
19 2 0.06
20 3 0.08
21 20 0.56
22 6 0.17
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTATCTTATTTTCATAT
Found at i:206699 original size:2 final size:2
Alignment explanation
Indices: 206692--206721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
206682 TCACTCAAAA
206692 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
206722 TTTGTGTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:211659 original size:2 final size:2
Alignment explanation
Indices: 211652--211688 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
211642 ATCACCCAAA
* *
211652 TC TC TC TC TC TC TC TC TC TC TC TC TT TG TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
211689 TTTGTGTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.54
Consensus pattern (2 bp):
TC
Found at i:220648 original size:12 final size:12
Alignment explanation
Indices: 220631--220666 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
220621 CATCAAAGAA
220631 TCCTTCTAAAAC
1 TCCTTCTAAAAC
220643 TCCTTCTAAAAC
1 TCCTTCTAAAAC
220655 TCCTTCTAAAAC
1 TCCTTCTAAAAC
220667 CACACCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (12 bp):
TCCTTCTAAAAC
Found at i:222091 original size:15 final size:14
Alignment explanation
Indices: 222073--222113 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
222063 GACCAGAAAA
222073 AAGAGAAGGAAGAGG
1 AAGAGAA-GAAGAGG
222088 AAGAGAAAGAAGA-G
1 AAGAG-AAGAAGAGG
222102 AA-AGAAGAAGAG
1 AAGAGAAGAAGAG
222114 AATGACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.29
13 2 0.08
14 3 0.12
15 10 0.42
16 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AAGAGAAGAAGAGG
Found at i:222594 original size:19 final size:18
Alignment explanation
Indices: 222552--222602 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
222542 CTGTAAATAG
222552 TTTTCA-TGCATTTTATT
1 TTTTCATTGCATTTTATT
222569 TTTTCATTGCATTGTT-TT
1 TTTTCATTGCATT-TTATT
222587 TTTGTCATTGCATTTT
1 TTT-TCATTGCATTTT
222603 TGTTAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.19
18 13 0.42
19 12 0.39
ACGTcount: A:0.14, C:0.12, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTCATTGCATTTTATT
Found at i:223216 original size:18 final size:18
Alignment explanation
Indices: 223182--223224 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
223172 ATCACTTGAA
*
223182 AAAGAAAAATGAGAAAAG
1 AAAGAAAAATGAAAAAAG
223200 AAAGAAAAA-GAAAAAAAG
1 AAAGAAAAATG-AAAAAAG
223218 AAA-AAAA
1 AAAGAAAA
223225 TTTATGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAGAAAAATGAAAAAAG
Found at i:223217 original size:14 final size:15
Alignment explanation
Indices: 223193--223222 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
223183 AAGAAAAATG
223193 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
223208 AGAAAA-AAAGAAAA
1 AGAAAAGAAAGAAAA
223222 A
1 A
223223 AATTTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:248773 original size:17 final size:18
Alignment explanation
Indices: 248751--248792 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
248741 CCTCCTAAAT
**
248751 AATTAAATTTTTTTTAA-
1 AATTAAATTACTTTTAAG
248768 AATTAAATTACTTTTAAG
1 AATTAAATTACTTTTAAG
248786 AATTAAA
1 AATTAAA
248793 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
AATTAAATTACTTTTAAG
Found at i:249727 original size:6 final size:6
Alignment explanation
Indices: 249718--249748 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
249708 TTGGTTTCTC
*
249718 TTTCCA TTTCCA TTTCCA TTTCCT TTTCCA T
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA T
249749 AGTTTGTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCCA
Found at i:252694 original size:2 final size:2
Alignment explanation
Indices: 252687--252718 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
252677 AAATGTACAT
*
252687 AC AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
252719 GTATGCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:258396 original size:13 final size:15
Alignment explanation
Indices: 258373--258404 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
258363 TGCTATAGCA
258373 AACACCAAAATTT-T
1 AACACCAAAATTTAT
258387 AACA-CAAAATTTAT
1 AACACCAAAATTTAT
258401 AACA
1 AACA
258405 TTAAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (15 bp):
AACACCAAAATTTAT
Found at i:267019 original size:17 final size:16
Alignment explanation
Indices: 266955--267021 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
266945 AATGAAACAT
266955 AAAATTTT-AAAAATA
1 AAAATTTTAAAAAATA
* *
266970 TATATCTTTAAAAAATA
1 AAAAT-TTTAAAAAATA
*
266987 CAAAATTATGATAAAAATA
1 -AAAATT-TTA-AAAAATA
267006 AAAATCTTTAAAAAAT
1 AAAAT-TTTAAAAAAT
267022 GATTTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.08
16 3 0.08
17 14 0.35
18 12 0.30
19 8 0.20
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (16 bp):
AAAATTTTAAAAAATA
Found at i:268372 original size:43 final size:43
Alignment explanation
Indices: 268292--268373 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
268282 CAAACAAATT
* * * * *
268292 AACATAACAATTTCATGACAATTTAAATATTTTTAACAACGTA
1 AACATAAAAATTTCATAACAAATTAAAAATTTATAACAACGTA
268335 AACATAAAAATTTCA-AACAAATTAAAAATTTCATAACAA
1 AACATAAAAATTTCATAACAAATTAAAAATTT-ATAACAA
268374 TCCAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 13 0.39
43 20 0.61
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (43 bp):
AACATAAAAATTTCATAACAAATTAAAAATTTATAACAACGTA
Found at i:268678 original size:149 final size:147
Alignment explanation
Indices: 268469--268751 Score: 395
Period size: 149 Copynumber: 1.9 Consensus size: 147
268459 TTACGCATCA
* * * * * * *
268469 TTAATATAAAAATATATATTATAATATCATAATTGTGCATACGGTTACATATCATTAATAATTTA
1 TTAATATAAAAATATAAATTACAATAACATAATTGTACATAAGGATACATATCATTAATAATCTA
* * *
268534 TTTTAATTAAATAATGCTAATTGTATATATATTATAATCTACCATAAAGTTAGTTCCACGTTTAG
66 TATTAATTAAATAATGCTAATTGTATA-A-ATTATAATCTACCATAAAATTAGTTCCACGTTTAA
268599 GGTTTAAGCTTGTGTATCG
129 GGTTTAAGCTTGTGTATCG
* * *
268618 TTAATATAAAAATGTAAATTACAATAACATAGTTGTATATAAGGATACATATCATTAATAATCTA
1 TTAATATAAAAATATAAATTACAATAACATAATTGTACATAAGGATACATATCATTAATAATCTA
* * * *
268683 TATTAATTATATAATGTTAATTGTATAAATTATAATTTACCATAAAATTAGTTTCACGTTTAAGG
66 TATTAATTAAATAATGCTAATTGTATAAATTATAATCTACCATAAAATTAGTTCCACGTTTAAGG
268748 TTTA
131 TTTA
268752 GGTTGCATAT
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
147 37 0.32
148 1 0.01
149 79 0.68
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (147 bp):
TTAATATAAAAATATAAATTACAATAACATAATTGTACATAAGGATACATATCATTAATAATCTA
TATTAATTAAATAATGCTAATTGTATAAATTATAATCTACCATAAAATTAGTTCCACGTTTAAGG
TTTAAGCTTGTGTATCG
Found at i:270283 original size:16 final size:15
Alignment explanation
Indices: 270261--270305 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
270251 TAAAATAATT
270261 TTAAAATATAAAAAA
1 TTAAAATATAAAAAA
270276 TATAAAAT-TCAAAAAA
1 T-TAAAATAT-AAAAAA
270292 TTAAAATA-AAAAAA
1 TTAAAATATAAAAAA
270306 GTATTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 13 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
TTAAAATATAAAAAA
Found at i:270467 original size:17 final size:17
Alignment explanation
Indices: 270445--270478 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
270435 ATTTGTAAAA
270445 TATATTAAGAAAATATG
1 TATATTAAGAAAATATG
* *
270462 TATATTCATAAAATATG
1 TATATTAAGAAAATATG
270479 GAATTTAATT
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:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (17 bp):
TATATTAAGAAAATATG
Found at i:272656 original size:17 final size:17
Alignment explanation
Indices: 272639--272734 Score: 115
Period size: 17 Copynumber: 5.6 Consensus size: 17
272629 AACATGACTT
*
272639 GCATATAAACACAGCTT
1 GCATATAAACACAGCTA
*
272656 GCATATAAACATATG-TA
1 GCATATAAACACA-GCTA
*
272673 GCATATAAACATAGCTCA
1 GCATATAAACACAGCT-A
* *
272691 G-ATATAAACACATCTC
1 GCATATAAACACAGCTA
272707 GCATATAAACACAGCTA
1 GCATATAAACACAGCTA
272724 GCATATAAACA
1 GCATATAAACA
272735 TAGTTCGCAT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.03
17 63 0.93
18 3 0.04
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (17 bp):
GCATATAAACACAGCTA
Found at i:272698 original size:51 final size:51
Alignment explanation
Indices: 272641--272771 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 51
272631 CATGACTTGC
* *
272641 ATATAAACACAGCTTGCATATAAACATATG-TAGCATATAAACATAGCTCAG
1 ATATAAACACAGCTCGCATATAAACACA-GCTAGCATATAAACATAGCTCAG
* *
272692 ATATAAACACATCTCGCATATAAACACAGCTAGCATATAAACATAGTTC-G
1 ATATAAACACAGCTCGCATATAAACACAGCTAGCATATAAACATAGCTCAG
* * *
272742 CATGTAAGCACAAG-TCACATATAAACACAG
1 -ATATAAACAC-AGCTCGCATATAAACACAG
272772 TTCGTCTCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.03
51 66 0.96
52 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (51 bp):
ATATAAACACAGCTCGCATATAAACACAGCTAGCATATAAACATAGCTCAG
Found at i:272743 original size:34 final size:33
Alignment explanation
Indices: 272614--272753 Score: 133
Period size: 34 Copynumber: 4.2 Consensus size: 33
272604 TCACACATTG
* *
272614 ACACAGTTTGCATAT-AACATGACTT-GCATATAA
1 ACACAGCTAGCATATAAACAT-A-TTCGCATATAA
* *
272647 ACACAGCTTGCATATAAACATATGTAGCATATAA
1 ACACAGCTAGCATATAAACATAT-TCGCATATAA
* *
272681 ACATAGCTCAG-ATATAAACACATCTCGCATATAA
1 ACACAGCT-AGCATATAAACATAT-TCGCATATAA
*
272715 ACACAGCTAGCATATAAACATAGTTCGCATGTAA
1 ACACAGCTAGCATATAAACATA-TTCGCATATAA
*
272749 GCACA
1 ACACA
272754 AGTCACATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
32 1 0.01
33 18 0.20
34 70 0.77
35 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (33 bp):
ACACAGCTAGCATATAAACATATTCGCATATAA
Found at i:272744 original size:17 final size:17
Alignment explanation
Indices: 272639--272775 Score: 104
Period size: 17 Copynumber: 8.1 Consensus size: 17
272629 AACATGACTT
272639 GCATATAAACACAGCTT-
1 GCATATAAACACAG-TTC
* *
272656 GCATATAAACATA-TGTA
1 GCATATAAACACAGT-TC
* *
272673 GCATATAAACATAGCTC
1 GCATATAAACACAGTTC
272690 AG-ATATAAACACA-TCTC
1 -GCATATAAACACAGT-TC
* *
272707 GCATATAAACACAGCTA
1 GCATATAAACACAGTTC
*
272724 GCATATAAACATAGTTC
1 GCATATAAACACAGTTC
* *
272741 GCATGTAAGCACAAG-TC
1 GCATATAAACAC-AGTTC
*
272758 ACATATAAACACAGTTC
1 GCATATAAACACAGTTC
272775 G
1 G
272776 TCTCATAACT
Statistics
Matches: 94, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
15 1 0.01
16 4 0.04
17 86 0.91
18 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (17 bp):
GCATATAAACACAGTTC
Found at i:277488 original size:18 final size:17
Alignment explanation
Indices: 277443--277492 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
277433 CGGATAAAAC
277443 CGAATTAATTCGGTTAA
1 CGAATTAATTCGGTTAA
*
277460 CTG-ATTGAATTTGGTTAA
1 C-GAATT-AATTCGGTTAA
277478 TCGAATTAATTCGGT
1 -CGAATTAATTCGGT
277493 CGGGGTCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (17 bp):
CGAATTAATTCGGTTAA
Found at i:278393 original size:22 final size:22
Alignment explanation
Indices: 278359--278400 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
278349 GGTTTTTAGA
278359 AAAAAAGTAAAAAATCATTTTTC
1 AAAAAAGTAAAAAAT-ATTTTTC
*
278382 AAAAAA-TTAAAAATATTTT
1 AAAAAAGTAAAAAATATTTT
278401 ATAATGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAAGTAAAAAATATTTTTC
Found at i:281829 original size:67 final size:67
Alignment explanation
Indices: 281741--281871 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 67
281731 ATACTCAACA
* * *
281741 TTATGTATTTAAGTGCATTTGAATTCATATCTTTTAAATTATTATAACAATAATGATAAAATCGT
1 TTATGTATTTAAATGCATTTGAACTCATATCTTTTAAATTATTATAACAACAATGATAAAATCGT
281806 GT
66 GT
** * *
281808 TTATGTATTTAAATGTGTTTGAACTCATATTTTTTAAATTATTATAACAACAATGATACAATCG
1 TTATGTATTTAAATGCATTTGAACTCATATCTTTTAAATTATTATAACAACAATGATAAAATCG
281872 AACTTAGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (67 bp):
TTATGTATTTAAATGCATTTGAACTCATATCTTTTAAATTATTATAACAACAATGATAAAATCGT
GT
Found at i:283360 original size:119 final size:120
Alignment explanation
Indices: 283208--283444 Score: 334
Period size: 126 Copynumber: 1.9 Consensus size: 120
283198 TGGTGTTACA
* * *
283208 GGTTAATCATGTACTAATTTAGTTGAG-AAAA-AAAATAACCTCATTTTATAAAGTAAATTATAT
1 GGTTAATCATGTACTAACTTAATTGAGAAAAACAAAATAACCTCACTTTATAAAGTAAATTATAT
*
283271 TATTTTATATATTTTATATAAAAAATATAAACACTCATAATGAAATTTGTGTCACG
66 TATTTTATATATTTTATATAAAAAA-ATAAACACACATAATGAAATTTGTGTCACG
*
283327 GGTTAATCATGTACTAACTTAATTGAGAAAAAAAAACGAAAATAACCTCACTTTATACAGTAAAT
1 GGTTAATCATGTACTAACTTAATTGAG----AAAAAC-AAAATAACCTCACTTTATAAAGTAAAT
* * *
283392 TATATTTTTTTATATATTTTATATAGAAAAATAAACACACATGATGAAATTTG
61 TATATTATTTTATATATTTTATATAAAAAAATAAACACACATAATGAAATTTG
283445 AACCCATGCC
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
119 25 0.24
124 4 0.04
125 21 0.20
126 53 0.51
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (120 bp):
GGTTAATCATGTACTAACTTAATTGAGAAAAACAAAATAACCTCACTTTATAAAGTAAATTATAT
TATTTTATATATTTTATATAAAAAAATAAACACACATAATGAAATTTGTGTCACG
Found at i:285347 original size:30 final size:30
Alignment explanation
Indices: 285276--285620 Score: 370
Period size: 30 Copynumber: 11.6 Consensus size: 30
285266 TAATTTTGAG
*
285276 AGTTTTG-GGGTCGAAAATGGAGA-TTTTGGA
1 AGTTTTGAGGGT-AAAAATGGA-ATTTTTGGA
* * *
285306 AG-TTCGAGGGTAAAAATGGGATTTTTGAA
1 AGTTTTGAGGGTAAAAATGGAATTTTTGGA
285335 AGTTTTGAGGGTAAAAAAT-GAATTTTTGGA
1 AGTTTTGAGGGT-AAAAATGGAATTTTTGGA
* *
285365 AGTTTTGAGGGTAAAAATGGAAGTTTTAGA
1 AGTTTTGAGGGTAAAAATGGAATTTTTGGA
*
285395 AGTTTCGA-GGTAAAAATGGAATTTTTGGA
1 AGTTTTGAGGGTAAAAATGGAATTTTTGGA
* * *
285424 AGTTTCGAGGTTAAAAACGGAA-TTTTGGA
1 AGTTTTGAGGGTAAAAATGGAATTTTTGGA
*
285453 AGTTTCG-GGGCTAAAAATGGAATTTTTGGA
1 AGTTTTGAGGG-TAAAAATGGAATTTTTGGA
* *
285483 AGTTTCGAGGGTAAAAATTGAATTTTTGGA
1 AGTTTTGAGGGTAAAAATGGAATTTTTGGA
* *
285513 AGTTTT-ATGGGTAAAAATAGAATTTTTAGA
1 AGTTTTGA-GGGTAAAAATGGAATTTTTGGA
*
285543 AGTTTTTG-GGTTAAAAATGGAATTTTTGGA
1 AG-TTTTGAGGGTAAAAATGGAATTTTTGGA
* * *
285573 AGTTTT-AGGGGTAAAAATAGAATTCTTAGA
1 AGTTTTGA-GGGTAAAAATGGAATTTTTGGA
285603 AGTTTT-AGGGGTAAAAAT
1 AGTTTTGA-GGGTAAAAAT
285621 AAAATTATTA
Statistics
Matches: 274, Mismatches: 27, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
28 3 0.01
29 80 0.29
30 178 0.65
31 13 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (30 bp):
AGTTTTGAGGGTAAAAATGGAATTTTTGGA
Found at i:286745 original size:3 final size:3
Alignment explanation
Indices: 286720--286827 Score: 56
Period size: 3 Copynumber: 35.3 Consensus size: 3
286710 TTAATAACAT
* * * ** * * * *
286720 TTA TTA ATA CTTA TTA CTA TTA TTA TTG CCA TTA GTA TTA CTA ATG
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
286766 TTA TTA GTA ATA TTTA TTA TTA TTA TTA TTA TTA TTGA -TA TTA TTG
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* *
286812 CTA TTG TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
286828 GACTAAAGGT
Statistics
Matches: 75, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
2 1 0.01
3 69 0.92
4 5 0.07
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:287491 original size:17 final size:17
Alignment explanation
Indices: 287469--287509 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
287459 TCTTTAATTC
287469 AATTTAAAATCAATTTA
1 AATTTAAAATCAATTTA
* *
287486 AATTTAAACTTAATTTA
1 AATTTAAAATCAATTTA
287503 AATTTAA
1 AATTTAA
287510 GCTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAAATCAATTTA
Found at i:288256 original size:206 final size:201
Alignment explanation
Indices: 287889--288485 Score: 689
Period size: 206 Copynumber: 3.0 Consensus size: 201
287879 TCTGGTTTCA
* * * ** *
287889 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGACGACGACCATATCACTTGTTTTGATCCACTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGACGACCGTATCACTTGTTTCAATCCGCTT
* * * * * * *
287954 CTTTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCAGTATTTCAACAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
*
288019 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCT-GGGATTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGG-TTCGAAGATTTGCTCACA
**
288083 TCGAACGTGGGT
195 TCG-A----GCC
* * * * * * *
288095 TTGATTTGGTCTTCTTCTCAATATCTCATTAGGAAGATGACTGTATCGCTTGTTTCAATCTGCTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGACGACCGTATCACTTGTTTCAATCCGCTT
*
288160 CTCTGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
288225 TTTATTGCTTCGACATGCTTCTC-GATATCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAG-TATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACA
288289 TCGAGCC
195 TCGAGCC
* * * * * * ** * *
288296 CTAAGTTGGTATTCTTCTCTGTATCTTATCAGGAAGACGACCGCCTTATTTGTTTCAATCCGCTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGACGACCGTATCACTTGTTTCAATCCGCTT
* * * *
288361 CTCTGTACCTTATCAGGAAGANGAATTTGGTCCACTTCTCAG-AGTCTCATCAAGAAGCTAACC-
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTA-TCTCATCAGGAAGCTAACCA
* * * * *
288424 GTTTATTACTTCGACCTACTTCTTAGTATCTCATCAAGAAGCTAGGGTTCGAAGATTTGCTC
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTC
288486 TCTTTGAGCC
Statistics
Matches: 333, Mismatches: 54, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
200 54 0.16
201 107 0.32
205 2 0.01
206 168 0.50
207 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (201 bp):
TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGACGACCGTATCACTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
CGAGCC
Found at i:288608 original size:121 final size:121
Alignment explanation
Indices: 288385--288659 Score: 462
Period size: 121 Copynumber: 2.3 Consensus size: 121
288375 AGGAAGANGA
* * * *
288385 ATTTGGTCCACTTCTCAG-AGTCTCATCAAGAAGCTAACCGTTTATTACTTCGACCTACTTCTTA
1 ATTTAGTCTACTTCTCAGTA-TCTCATCAGGAAGCTAACCGTTTATTACTTCGACCTACTTCTCA
*
288449 GTATCTCATCAAGAAGCTAGGGTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCTTTG
65 GTATCTCATCAAGAAGCTAGGGTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCATTG
* *
288506 ATTTAGTCTACTTCTCAGTATCTCATCAGGAAGCTAACTGTTTATTACTTCGACCTGCTTCTCAG
1 ATTTAGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTACTTCGACCTACTTCTCAG
*
288571 TATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCATTG
66 TATCTCATCAAGAAGCTAGGGTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCATTG
288627 ATTTAGTCTACTTCTCAGTATCTCATCAGGAAG
1 ATTTAGTCTACTTCTCAGTATCTCATCAGGAAG
288660 ATGACCATAT
Statistics
Matches: 145, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
121 144 0.99
122 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (121 bp):
ATTTAGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTACTTCGACCTACTTCTCAG
TATCTCATCAAGAAGCTAGGGTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCATTG
Found at i:300503 original size:30 final size:30
Alignment explanation
Indices: 300467--300704 Score: 291
Period size: 30 Copynumber: 7.9 Consensus size: 30
300457 TGGAAGTTCG
* *
300467 AGGGTAAAAATGGGATTTTTAAAAGTTTTA
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
* * *
300497 AGGGTAAAAATAGAATTTTTAAAAGTTTCA
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
* * * *
300527 TGGGTAAAAATGGAATTTTTGGAATTTTTG
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
* *
300557 GGGGTAAAAATCGAATTTTTAGAAGTTTTA
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
*
300587 GGGGTAAAAATGGAATTTTTAGAAGTTTT-
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
*
300616 -GGAGTCAAAAATGGAATTTTTGGAAGTTTTA
1 AGG-GT-AAAAATGGAATTTTTAGAAGTTTTA
* * *
300647 AGGGTAAAAATGGAATTCTTGGAAGTTTTT
1 AGGGTAAAAATGGAATTTTTAGAAGTTTTA
*
300677 GGGGTAAAAATGGAATTTTTAGAAGTTT
1 AGGGTAAAAATGGAATTTTTAGAAGTTT
300705 CAGGGAGCCT
Statistics
Matches: 182, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
28 2 0.01
29 2 0.01
30 174 0.96
31 2 0.01
32 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
AGGGTAAAAATGGAATTTTTAGAAGTTTTA
Found at i:300545 original size:60 final size:59
Alignment explanation
Indices: 300422--300706 Score: 315
Period size: 60 Copynumber: 4.8 Consensus size: 59
300412 GGGAAAGGGT
* * * *
300422 AATTTTGAG-AGTTTTGGGGTCGAAAATGGAGA-TTTTGGAAG-TTCGAGGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGT-AAAAATGGA-ATTTTTAGAAGTTTCAAGGGTAAAAATGG
* * * * * *
300480 GATTTTTAAAAGTTTTAAGGGTAAAAATAGAATTTTTAAAAGTTTCATGGGTAAAAATGG
1 AATTTTTAGAAGTTTT-GGGGTAAAAATGGAATTTTTAGAAGTTTCAAGGGTAAAAATGG
* * * * *
300540 AATTTTTGGAATTTTTGGGGGTAAAAATCGAATTTTTAGAAGTTTTAGGGGTAAAAATGG
1 AATTTTTAGAAGTTTT-GGGGTAAAAATGGAATTTTTAGAAGTTTCAAGGGTAAAAATGG
* * *
300600 AATTTTTAGAAGTTTTGGAGTCAAAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGT-AAAAATGGAATTTTTAGAAGTTTCAAGGGTAAAAATGG
* *
300660 AATTCTTGGAAGTTTTTGGGGTAAAAATGGAATTTTTAGAAGTTTCA
1 AATTTTTAGAAG-TTTTGGGGTAAAAATGGAATTTTTAGAAGTTTCA
300707 GGGAGCCTCC
Statistics
Matches: 190, Mismatches: 31, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
58 7 0.04
59 24 0.13
60 151 0.79
61 8 0.04
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (59 bp):
AATTTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTAGAAGTTTCAAGGGTAAAAATGG
Done.