Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002855.1 Hibiscus syriacus cultivar Beakdansim tig00005878_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59768
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:76 original size:21 final size:21
Alignment explanation
Indices: 52--95 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42 AAGACAATCA
*
52 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
* *
73 AGAGTCAAAGATACACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
94 AG
1 AG
96 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAG
Found at i:176 original size:33 final size:33
Alignment explanation
Indices: 129--194 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
119 AAATAGATGG
* *
129 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
162 AGTGATGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
195 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1982 original size:19 final size:19
Alignment explanation
Indices: 1958--2006 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1948 AATGTAGGGT
1958 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1977 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1996 TATTTTTGTAT
1 TAATTTTGTAT
2007 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2865 original size:400 final size:398
Alignment explanation
Indices: 2125--3298 Score: 2134
Period size: 400 Copynumber: 2.9 Consensus size: 398
2115 CAATATGGCC
*
2125 AACAGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCAAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAAA-
2190 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
2255 GAATATGTCTAAATAATGTGTCGACGCTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
* *
2320 TGAAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAAACATC
195 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
*
2385 GAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
260 -AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
* *
2450 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTATGTCGATATTTTTGGTCCAGA
324 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTAGTCCAGA
2515 ATGAATGGAA
389 ATGAATGGAA
*
2525 AACAGGGTGCAACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC-AAAA
2590 CCAAAAGTATAATGTAATATGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
65 CCAAAAGTATAATGTAATATGTAA-TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
2655 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
*
2720 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCCATCCCAAAAACAT
194 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
**
2785 CAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACAAGTTTTA
259 CAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
* *
2850 TGAGAGAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTGTCGATATTTTTATTCCAGA
324 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTAGTCCAGA
2915 ATGAATGGAA
389 ATGAATGGAA
*
2925 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAAAC
*
2990 CAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
3055 AATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
* *
3120 GGAAAACAGGGTGCAACCATAAAGTGTCGATCAATATATAAAAAGTGTCGATCCCAAAAACATCG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCA
3185 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
3250 AGAGAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATA
326 AGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
3299 CTAATTTAAA
Statistics
Matches: 748, Mismatches: 24, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
397 19 0.03
398 259 0.35
399 27 0.04
400 273 0.36
401 170 0.23
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAAAC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCA
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTAGTCCAGAAT
GAATGGAA
Found at i:2904 original size:199 final size:200
Alignment explanation
Indices: 2125--3298 Score: 2140
Period size: 199 Copynumber: 5.9 Consensus size: 200
2115 CAATATGGCC
* *
2125 AACAGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCAAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
2190 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
2255 GAATATGTCTAAATAATGTGTCGACGCTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
*
2320 TGAAA
196 TGGAA
* *
2325 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
2390 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
2455 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTATGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
2520 TGGAA
196 TGGAA
* *
2525 AACAGGGTGCAACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
2590 CCAAAAGTATAATGTAATATGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
66 CCAAAAGTATAATGTAATATGTAA-TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
2655 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
2720 ATGGAA
195 ATGGAA
*
2726 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCCATCCCAAAAACATC-AAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
**
2790 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACAAGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
2855 GAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTGTCGATATTTTTATTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
2920 TGGAA
196 TGGAA
2925 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC-AAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
*
2989 CCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
3054 GAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
3119 TGGAA
196 TGGAA
*
3124 AACAGGGTGCAACCATAAAGTGTCGATCAATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
3188 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
3253 GAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
3299 CTAATTTAAA
Statistics
Matches: 946, Mismatches: 26, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
198 19 0.02
199 453 0.48
200 307 0.32
201 167 0.18
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
TGGAA
Found at i:3802 original size:23 final size:23
Alignment explanation
Indices: 3771--3843 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3761 ATAGGTAAAA
*
3771 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3794 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3817 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3840 ATAT
1 ATAT
3844 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4230 original size:23 final size:23
Alignment explanation
Indices: 4204--4276 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
4194 ATAGGTAAAA
*
4204 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
4227 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
4250 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
4273 ATAT
1 ATAT
4277 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4402 original size:424 final size:429
Alignment explanation
Indices: 3582--4442 Score: 1509
Period size: 424 Copynumber: 2.0 Consensus size: 429
3572 TTCTCAAAGC
*
3582 TCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAA
1 TCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAAGGAAATTATTAA
3647 ATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACATAACTTT
66 ATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACATAACTTT
3712 AAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGA
131 AAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGA
* *
3777 TGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTAT
196 TGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTAT
* *
3842 ATTGTAAAGTATCTATCCTTTTTAAAATTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAA
261 ATTGTAAAGTATCTATCC----T----TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAA
*
3907 ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATGATTATAGGCGTCTA
318 ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCTA
3972 ATGATTTATTTTTTACGTTACG-ATATATTATTATTAAATTAAAAAT
383 ATGATTTATTTTTTACGTTACGAATATATTATTATTAAATTAAAAAT
4018 TCTAAATAATATTTTAT-AAATATCAAAACAATCAAATAA-TTTTTGTGCAAAGGAAATTATTAA
1 TCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAAGGAAATTATTAA
4081 ATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTT
66 ATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACATAAATTACATAACTT
*
4146 TAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC-A-ATAATAGGTAAAAATATG
130 TAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATG
4209 ATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTA
195 ATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTA
*
4274 TATTGTAAAGTATTTATCC-TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAA
260 TATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAA
*
4338 TTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTT
325 TTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCTAATGATTT
4403 ATTTTTTACGTTACGATATATATTATTATTAAATTAAAAA
390 ATTTTTTACGTTACGA-ATATATTATTATTAAATTAAAAA
4443 CAATAAACAT
Statistics
Matches: 413, Mismatches: 9, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
424 121 0.29
426 23 0.06
433 99 0.24
434 59 0.14
435 94 0.23
436 17 0.04
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (429 bp):
TCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAAGGAAATTATTAA
ATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACATAACTTT
AAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGA
TGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTAT
ATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAAT
TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCTAATGATTTA
TTTTTTACGTTACGAATATATTATTATTAAATTAAAAAT
Found at i:5341 original size:18 final size:18
Alignment explanation
Indices: 5279--5343 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
5269 TTGAAAAATA
*
5279 AAAAAATATACTATTTTT
1 AAAAAATATACTATTCTT
* **
5297 AAAAAATATTTGACAACCCTT
1 AAAAAATA--T-ACTATTCTT
5318 -AAAAATATACTATTCTT
1 AAAAAATATACTATTCTT
5335 AAAAAATAT
1 AAAAAATAT
5344 TTGAAAATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
17 6 0.17
18 17 0.47
20 8 0.22
21 5 0.14
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAAATATACTATTCTT
Found at i:6597 original size:20 final size:21
Alignment explanation
Indices: 6552--6600 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6542 GGTTAACTCG
* * *
6552 GTATTGATACCCCTCCTACGA
1 GTATCGATACCCATCCGACGA
6573 GTATCGATACCCATCCGAC-A
1 GTATCGATACCCATCCGACGA
6593 GTATCGAT
1 GTATCGAT
6601 GCTTGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (21 bp):
GTATCGATACCCATCCGACGA
Found at i:16826 original size:42 final size:42
Alignment explanation
Indices: 16734--16815 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
16724 CCTTCGAGTC
* * * *
16734 ATCAATAAGTCTTTTGAGCATGATACTTAAATCCTTTGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGCA
16776 ATCAGTAAGTCTTTCGAGCATGATGA-TTAAATCCTTCGGG
1 ATCAGTAAGTCTTTCGAGCATGAT-ACTTAAATCCTTCGGG
16816 TAATTTGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGCA
Found at i:16943 original size:42 final size:42
Alignment explanation
Indices: 16866--16965 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
16856 ATTAGTAAGT
* * * *
16866 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAATAAGCCTTCCGAGCATGATGATGAAGTCCTTCAG
* * *
16908 GCCATCAATAAGCCTTCCGATCATGGTGATTAAGTCCTTCAG
1 GCCATCAATAAGCCTTCCGAGCATGATGATGAAGTCCTTCAG
*
16950 GCCATC-TTAAGCCTTC
1 GCCATCAATAAGCCTTC
16966 ACATAAGAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
41 9 0.18
42 41 0.82
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (42 bp):
GCCATCAATAAGCCTTCCGAGCATGATGATGAAGTCCTTCAG
Found at i:17061 original size:53 final size:53
Alignment explanation
Indices: 16994--17165 Score: 283
Period size: 53 Copynumber: 3.2 Consensus size: 53
16984 AGAATCACAC
*
16994 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAACGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGG
*
17047 CAGAAGATTATTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGG
* * *
17100 CAGAAGACTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCACTAGT
1 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCC-GTAGG
17154 CAG-AGATTGTTC
1 CAGAAGATTGTTC
17166 AAAGAAGGGG
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
53 105 0.95
54 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:21266 original size:35 final size:35
Alignment explanation
Indices: 21227--21296 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
21217 GGCCGTTAAA
21227 TGATCTAATGGGACAATGACATGGCAGCCGTGCAC
1 TGATCTAATGGGACAATGACATGGCAGCCGTGCAC
21262 TGATCTAATGGGACAATGACATGGCAGCCGTGCAC
1 TGATCTAATGGGACAATGACATGGCAGCCGTGCAC
21297 CGTGACATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (35 bp):
TGATCTAATGGGACAATGACATGGCAGCCGTGCAC
Found at i:21959 original size:3 final size:3
Alignment explanation
Indices: 21945--21998 Score: 56
Period size: 3 Copynumber: 17.0 Consensus size: 3
21935 TGTCCCGGTC
*
21945 TTA TTT TTA TTA TTA TTA TTA -TA TATA TATA TATA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA -TTA TTA TTA TTA
21993 TTA TTA
1 TTA TTA
21999 CAAATCAGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 31 0.67
4 12 0.26
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:23349 original size:18 final size:18
Alignment explanation
Indices: 23326--23366 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23316 TCATATAAAT
23326 ATATTTAATTAAATTTTA
1 ATATTTAATTAAATTTTA
* **
23344 ATATTTATTTATTTTTTA
1 ATATTTAATTAAATTTTA
23362 ATATT
1 ATATT
23367 AAGAAATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTAATTAAATTTTA
Found at i:23516 original size:124 final size:125
Alignment explanation
Indices: 23341--23685 Score: 376
Period size: 135 Copynumber: 2.7 Consensus size: 125
23331 TAATTAAATT
* * **
23341 TTAATATTTATTTATTTTTTAATATTAAGAAATGG-GTCGTCTTAAGGTAACTAGATGTCATTTT
1 TTAATATTTATTTATTTTTTAATATAAAGAAATGGACT-GTCTTAAAATAACTAGATGTCATTTT
* * * *
23405 CTGTTATTTATAAATAAATAAAATATTATATTTACTTTA-TTTTATTTAAATTA-TTGTT-A
65 CTGATATTT-TAAATAAATAAAATATTACATTTAATCTATTTTTATTTAAATTATTTGTTAA
* *
23464 TTAATATTTATTTATTTTTTAATATCAAAGAAATGGACTGTCTTAAAATAACTAAATTTCATTTT
1 TTAATATTTATTTATTTTTTAATAT-AAAGAAATGGACTGTCTTAAAATAACTAGATGTCA-TTT
* *
23529 TTTGATATTTTAAATAAATAAAATATTACATTTAATCTATTTTTATTTAAATTATTTTTTAGGAA
64 TCTGATATTTTAAATAAATAAAATATTACATTTAATCTATTTTTATTTAAATTATTTGTT-----
23594 AAA
124 -AA
* * * *
23597 TTATCATATTTTTTTAATTTTTAATATTAAAGAAAT-GAGTTGTCTTAAAACAACTAGATGTCAT
1 TTA--ATATTTATTTATTTTTTAATA-TAAAGAAATGGA-CTGTCTTAAAATAACTAGATGTCAT
23661 TTTCTGATATTTTTAAATAAATAAA
62 TTTCTGATA-TTTTAAATAAATAAA
23686 TATCCTATAT
Statistics
Matches: 186, Mismatches: 19, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
123 25 0.13
124 53 0.28
125 26 0.14
126 4 0.02
133 4 0.02
134 11 0.06
135 62 0.33
136 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (125 bp):
TTAATATTTATTTATTTTTTAATATAAAGAAATGGACTGTCTTAAAATAACTAGATGTCATTTTC
TGATATTTTAAATAAATAAAATATTACATTTAATCTATTTTTATTTAAATTATTTGTTAA
Found at i:24128 original size:53 final size:53
Alignment explanation
Indices: 24048--24155 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
24038 TTTCCGCCAA
24048 GGAATATTCGTGCCCGGGCGAAAACCGGTTACGACAGCTTGGCGACTCCACTG
1 GGAATATTCGTGCCCGGGCGAAAACCGGTTACGACAGCTTGGCGACTCCACTG
* *
24101 GGAATATTCGTGCCCGGGTGAAAACCGGTTACGACAGCTTGGCGGCTCCACTG
1 GGAATATTCGTGCCCGGGCGAAAACCGGTTACGACAGCTTGGCGACTCCACTG
24154 GG
1 GG
24156 GAGACTGGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.19
Consensus pattern (53 bp):
GGAATATTCGTGCCCGGGCGAAAACCGGTTACGACAGCTTGGCGACTCCACTG
Found at i:24934 original size:28 final size:28
Alignment explanation
Indices: 24903--24956 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
24893 TATTTTTTTC
*
24903 TTTTATTTATATCTATTTTGTATATACA
1 TTTTATTTATATCTAATTTGTATATACA
* * *
24931 TTTTATTTTTCTCTAATTTGTTTATA
1 TTTTATTTATATCTAATTTGTATATA
24957 TTGATTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTATTTATATCTAATTTGTATATACA
Found at i:26278 original size:20 final size:20
Alignment explanation
Indices: 26255--26298 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
26245 CATTTGTATT
* *
26255 TTTTTATGTTTGCATTTGCA
1 TTTTTATATTTGCATTTACA
*
26275 TTTTTATATTTTCATTTACA
1 TTTTTATATTTGCATTTACA
26295 TTTT
1 TTTT
26299 CATTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTTATATTTGCATTTACA
Found at i:32176 original size:39 final size:40
Alignment explanation
Indices: 32113--32208 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 40
32103 CAGATCCATG
* * *
32113 TGGGGCATTTTGAAGGCTCACATCAGTATGAA-AAAATAT
1 TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATAT
* * *
32152 TGGGGCATTTTGAAAGCTCGCATCAATAAGAAGCAAATGT
1 TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATAT
**
32192 TGGGGCATGCTGAAAGC
1 TGGGGCATTTTGAAAGC
32209 CCATTTCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 28 0.58
40 20 0.42
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (40 bp):
TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATAT
Found at i:32273 original size:75 final size:75
Alignment explanation
Indices: 32183--32437 Score: 377
Period size: 75 Copynumber: 3.4 Consensus size: 75
32173 ATCAATAAGA
* *
32183 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGATGCGTTTTGAA
*
32248 CATTTGTATC
66 CGTTTGTATC
* * * * *
32258 AGTAAATGTTGGGGCATGCTGAAAGCCCAATTCAGTCAGAAATAGGAATGTAGATGTGTTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGATGCGTTTTGAA
32323 CGTTTGTATC
66 CGTTTGTATC
* * *
32333 AGCAAATGTTAGGGCATGCTGAAAGCCCATTTTAATAAG-AATCAGGAATGTTGATGCGTTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-AGGAATGTTGATGCGTTTTGA
32397 ACGTTTGTATC
65 ACGTTTGTATC
* *
32408 AGCAAATGCTGGGGCATGCTGAAGGCCCAT
1 AGCAAATGTTGGGGCATGCTGAAAGCCCAT
32438 ATCATCTTAT
Statistics
Matches: 160, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
74 3 0.02
75 157 0.98
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGATGCGTTTTGAA
CGTTTGTATC
Found at i:34172 original size:18 final size:18
Alignment explanation
Indices: 34149--34189 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34139 TCATATAAAT
34149 ATATTTAATTAAATTTTA
1 ATATTTAATTAAATTTTA
* **
34167 ATATTTATTTATTTTTTA
1 ATATTTAATTAAATTTTA
34185 ATATT
1 ATATT
34190 AAGAAAAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTAATTAAATTTTA
Found at i:34308 original size:124 final size:125
Alignment explanation
Indices: 34164--34408 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 125
34154 TAATTAAATT
* * ** *
34164 TTAATATTTATTTATTTTTTAATAT-TAAGAAAAGGGTCATT-TTAAGGTAACTAGATGTCCTTT
1 TTAATATTTATTTAGTTTTTAATATCAAAGAAAAGGG-CATTCTTAAAATAACTAGATGTCATTT
* * * *
34227 TCTGATATTTTTAAATAAATTAACTATTATATTTACTTTAATTTTATTTAAATTATTGTTA
65 TCTGATATTTTTAAATAAATAAAATATTATATTTAATCTAATTTTATTTAAATTATTGTTA
* *
34288 TTAATATTTATTTAGTTTTTAATATCAAAGAAATGGGCTTTCTTAAAATAACTAGATGTCATTTT
1 TTAATATTTATTTAGTTTTTAATATCAAAGAAAAGGGCATTCTTAAAATAACTAGATGTCATTTT
*
34353 CTGATATTTTTAAATAAATAAAATATTATATTTAATCTAGTTTTATTTAAATTATT
66 CTGATATTTTTAAATAAATAAAATATTATATTTAATCTAATTTTATTTAAATTATT
34409 TTTTAGGAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
124 27 0.25
125 80 0.75
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (125 bp):
TTAATATTTATTTAGTTTTTAATATCAAAGAAAAGGGCATTCTTAAAATAACTAGATGTCATTTT
CTGATATTTTTAAATAAATAAAATATTATATTTAATCTAATTTTATTTAAATTATTGTTA
Found at i:40765 original size:27 final size:27
Alignment explanation
Indices: 40735--40798 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
40725 TGCACCCTAC
*
40735 GCACGTTATCCTTAGCGCACACACCAT
1 GCACGTTATCCTTAGCACACACACCAT
*
40762 GCACGTTATCCTTGGCACACACACCAT
1 GCACGTTATCCTTAGCACACACACCAT
40789 GCACGTTATC
1 GCACGTTATC
40799 TTTCAACAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (27 bp):
GCACGTTATCCTTAGCACACACACCAT
Found at i:46121 original size:2 final size:2
Alignment explanation
Indices: 46073--46103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46063 TAATTAAAAT
46073 TA TA 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 TA TA T
46104 TAACTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47279 original size:2 final size:2
Alignment explanation
Indices: 47272--47303 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47262 GTAATCATTA
47272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47304 GAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55817 original size:15 final size:16
Alignment explanation
Indices: 55798--55839 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 16
55788 AGAAAAGAGA
55798 AAAAAGGAAAAAAAGG
1 AAAAAGGAAAAAAAGG
55814 -AAAAGG--AAAAAGG
1 AAAAAGGAAAAAAAGG
55827 AAAAAGGAAAAAA
1 AAAAAGGAAAAAA
55840 TGAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 6 0.26
16 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAGGAAAAAAAGG
Found at i:55844 original size:15 final size:15
Alignment explanation
Indices: 55798--55846 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
55788 AGAAAAGAGA
55798 AAAAAGGAAAAAAAG
1 AAAAAGGAAAAAAAG
* *
55813 GAAAAGG-AAAAAGG
1 AAAAAGGAAAAAAAG
*
55827 AAAAAGGAAAAAATG
1 AAAAAGGAAAAAAAG
55842 AAAAA
1 AAAAA
55847 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAAGGAAAAAAAG
Found at i:55852 original size:15 final size:15
Alignment explanation
Indices: 55784--55854 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
55774 ATTTTGCTTG
*
55784 AAGAAGAAAAGAGAAAA
1 AAGAA-AAAA-AGGAAA
55801 AAGGAAAAAAAGG-AA
1 AA-GAAAAAAAGGAAA
*
55816 AAG-GAAAAAGGAAA
1 AAGAAAAAAAGGAAA
* *
55830 AAGGAAAAAATGAAA
1 AAGAAAAAAAGGAAA
*
55845 AATAAAAAAA
1 AAGAAAAAAA
55855 AATGAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.16
14 6 0.13
15 21 0.47
16 2 0.04
17 6 0.13
18 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAGAAAAAAAGGAAA
Found at i:55863 original size:7 final size:7
Alignment explanation
Indices: 55807--55838 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
55797 AAAAAAGGAA
55807 AAAAAGG
1 AAAAAGG
55814 -AAAAGG
1 AAAAAGG
55820 AAAAAGG
1 AAAAAGG
55827 AAAAAGG
1 AAAAAGG
55834 AAAAA
1 AAAAA
55839 ATGAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:57147 original size:32 final size:32
Alignment explanation
Indices: 57111--57218 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
57101 TATATGAAGA
57111 AGTGAATCCATCTTAAGCCTTCACCGAAGAGT
1 AGTGAATCCATCTTAAGCCTTCACCGAAGAGT
* * *
57143 AGTGAAGCAAATCCATCTTAAGTCTTCACCGAAGCGA
1 AGT---G--AATCCATCTTAAGCCTTCACCGAAGAGT
*** * *
57180 AAAAAATCCATCTTGAGCCTTCACGGAAGAGT
1 AGTGAATCCATCTTAAGCCTTCACCGAAGAGT
57212 AGTGAAT
1 AGTGAAT
57219 TAAATCCATC
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
32 30 0.53
35 1 0.02
37 26 0.46
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (32 bp):
AGTGAATCCATCTTAAGCCTTCACCGAAGAGT
Found at i:57158 original size:37 final size:37
Alignment explanation
Indices: 57115--57449 Score: 322
Period size: 37 Copynumber: 9.1 Consensus size: 37
57105 TGAAGAAGTG
57115 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * *
57152 AATCCATCTTAAGTCTTCACCGAAGCG-A---AA-AA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * **
57184 AATCCATCTTGAGCCTTCACGGAAGAGTAGTGAATTA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * * * ****
57221 AATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCTTTC-
1 AATCCATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCA
* *
57263 GAGCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * * *
57300 AATCCCTCTTGAGCCTTCACCAAAGAGTAGTGAAGAA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * *
57337 AATTCATCTTAAGCATTCACCGAAGAGTAGTAAAGCA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
*
57374 AATCCATCTTAAGCCTTCACCGATGAGTAGTGAAGCA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* * *
57411 AATCCATTTTAAGCCTTCACCAAAGAGTAGTGAAACA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
57448 AA
1 AA
57450 CCTATTGTAA
Statistics
Matches: 238, Mismatches: 48, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
32 24 0.10
33 3 0.01
36 7 0.03
37 168 0.71
38 8 0.03
39 2 0.01
40 2 0.01
41 9 0.04
42 11 0.05
43 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (37 bp):
AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
Found at i:57399 original size:148 final size:148
Alignment explanation
Indices: 57118--57391 Score: 370
Period size: 148 Copynumber: 1.8 Consensus size: 148
57108 AGAAGTGAAT
*
57118 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGTCTTCACCGAAGCGAAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGCGAAAA
* * * * ** *
57183 AAATCCATCTTGAGCCTTCACGGAAGAGTAGTGAATTAAATCCATCAGTAAGCCTTCCGAGCATG
66 AAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTCCGAGCACG
57248 ATGATTAAGTCTTTCGAG
131 ATGATTAAGTCTTTCGAG
* * *
57266 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCCTCTTGAGCCTTCACCAAAGAGTAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACC---GA--AGC
* * *
57331 GAAGAAAATTCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATC-TTAAGCCTTC
61 GAAAAAAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTC
57392 ACCGATGAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
148 52 0.48
151 2 0.02
152 9 0.08
153 45 0.42
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (148 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGCGAAAA
AAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTCCGAGCACG
ATGATTAAGTCTTTCGAG
Found at i:57423 original size:148 final size:148
Alignment explanation
Indices: 57115--57449 Score: 358
Period size: 148 Copynumber: 2.3 Consensus size: 148
57105 TGAAGAAGTG
*
57115 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGTCTTCACCGAAGCGA
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGCGA
* * * * **
57180 AAAAAATCCATCTTGAGCCTTCACGGAAGAGTAGTGAATTAAATCCATCAGTAAGCCTTCCGAGC
66 AAAAAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTCCGAGC
* * ***
57245 ATGATGATTAAGTCTTTC
131 ACGATGAGTAAGTCAAGC
* * * *
57263 GAGCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCCTCTTGAGCCTTCACCAAAGAGT
1 AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACC---GA--
* * * *
57328 AGTGAAGAAAATTCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATC-TTAAGCCTT-
61 AGCGAAAAAAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTC
*
57391 C-A-C-CGATGAGT-AGTGAAGC
126 CGAGCACGATGAGTAAGTCAAGC
* * *
57410 AAATCCATTTTAAGCCTTCACCAAAGAGTAGTGAAACAAA
1 -AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
57450 CCTATTGTAA
Statistics
Matches: 155, Mismatches: 26, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
147 4 0.03
148 93 0.60
149 1 0.01
150 1 0.01
151 3 0.02
152 8 0.05
153 45 0.29
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (148 bp):
AATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGCGA
AAAAAATCCATCTTAAGCATTCACCGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTCCGAGC
ACGATGAGTAAGTCAAGC
Found at i:57898 original size:54 final size:54
Alignment explanation
Indices: 57826--58564 Score: 951
Period size: 54 Copynumber: 13.9 Consensus size: 54
57816 ATAATCACAA
* * *
57826 CAGAAGATTATTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * *
57880 TAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAAACCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* *
57934 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAATATGGAGCGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * *
57988 CAAAAGATTGTTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAA-CCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * **
58041 CAGAAGATTGTTCAAGTTCCTACTCCCTACAGAAAGAGGGAGCGAACATGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
** * * * * *
58095 CAGATTATTGTTTGAGTTCCTACTCCCTAAAGAAAAAAGGAGCG-ATCTGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * * * ** * *
58148 TAGAAGATTGTTCG-GTTCCTACTCCCTACAGAAAAATGGAGTTAATCCGTAGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * * * *
58201 CAGAAGATAGTTCGAGTTTCTACTCCCTAAAGAAAAAGAGAGCGAACCCGTTAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * *
58255 TAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCTGTTAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
*
58309 CAGAAGATTGTTCGAGTTCCTACTCCGTAAAGAAAGAGGGAGCGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * *
58363 GAGAATATTGTTCGAGTTCCTACTCCAT-AA-AAA-AGGGAGCGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* *
58414 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGTGGGAGCGAACCCATTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
*
58468 CAGAAGATTGTTCGAGTTCCTACTCCCT-AAGAAA-AGGGAGCGAACCCG-TAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
* * * * *
58519 TAG-ATATTGTTCGAGTT-ATACTCCCTGAAGCAAGAGGGAGCGAACC
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACC
58565 GTTTTAAGAA
Statistics
Matches: 601, Mismatches: 76, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
49 8 0.01
50 18 0.03
51 59 0.10
52 42 0.07
53 97 0.16
54 377 0.63
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (54 bp):
CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGG
Found at i:58435 original size:267 final size:265
Alignment explanation
Indices: 57826--58567 Score: 967
Period size: 267 Copynumber: 2.8 Consensus size: 265
57816 ATAATCACAA
* * * * *
57826 CAGAAGATTATTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCGTTGGTAGAAGATTGT
1 CAGAATATTGTTCGAGTTCCTACTCCAT-AA-AAA-AGGGAGCGAACCCGTTGGTAGAAGATTGT
* *
57891 TCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTA
63 TCGAGTTCCTACTCCCTAAAGAAAAATGGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTA
* * * * *
57956 CTCCCTAAAGAAATATGGAGCGAACCCGTTGGCAAAAGATTGTTCAAGTTCCTACTCCCTAAAGA
128 CTCCCTAAAGAAA-AAGGAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTACTCCCTAAAGA
* * *
58021 AAGAGGGAGTGAACCGTTGGCAGAAGATTGTTCAAGTTCCTACTCCCTACAGAAAGAGGGAGCGA
192 AAGAGGGAGCGAACCGTTAGCAGAAGATTGTTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCGA
*
58086 ACATGTTGG
257 ACACGTTGG
* * * * * *
58095 CAGATTATTGTTTGAGTTCCTACTCCCTAAAGAAAAAAGGAGCG-ATCTGTTGGTAGAAGATTGT
1 CAGAATATTGTTCGAGTTCCTACT-CC-ATA-AAAAAGGGAGCGAACCCGTTGGTAGAAGATTGT
* * * * * *
58159 TCG-GTTCCTACTCCCTACAGAAAAATGGAGTTAATCCGTAGGCAGAAGATAGTTCGAGTTTCTA
63 TCGAGTTCCTACTCCCTAAAGAAAAATGGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTA
58223 CTCCCTAAAGAAAAAGAGAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTACTCCCTAAAGA
128 CTCCCTAAAGAAAAAG-GAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTACTCCCTAAAGA
* *
58288 AAGAGGGAGCGAACCTGTTAGCAGAAGATTGTTCGAGTTCCTACTCCGTAAAGAAAGAGGGAGCG
192 AAGAGGGAGCGAACC-GTTAGCAGAAGATTGTTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCG
*
58353 AACCCGTTGG
256 AACACGTTGG
* *
58363 GAGAATATTGTTCGAGTTCCTACTCCATAAAAAAGGGAGCGAACCCGTTGGCAGAAGATTGTTCG
1 CAGAATATTGTTCGAGTTCCTACTCCATAAAAAAGGGAGCGAACCCGTTGGTAGAAGATTGTTCG
* * * *
58428 AGTTCCTACTCCCTAAAG-AAAGTGGGAGCGAACCCATTGGCAGAAGATTGTTCGAGTTCCTACT
66 AGTTCCTACTCCCTAAAGAAAAAT-GGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTACT
* * * * *
58492 CCCT-AAGAAAAGGGAGCGAACCCG-TAGTAG-ATATTGTTCGAGTT-ATACTCCCTGAAGCAAG
130 CCCTAAAGAAAAAGGAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAG
58553 AGGGAGCGAACCGTT
195 AGGGAGCGAACCGTT
58568 TTAAGAAGAT
Statistics
Matches: 412, Mismatches: 53, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
261 3 0.01
262 26 0.06
263 13 0.03
264 6 0.01
265 22 0.05
266 36 0.09
267 179 0.43
268 95 0.23
269 25 0.06
270 6 0.01
271 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (265 bp):
CAGAATATTGTTCGAGTTCCTACTCCATAAAAAAGGGAGCGAACCCGTTGGTAGAAGATTGTTCG
AGTTCCTACTCCCTAAAGAAAAATGGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTACTC
CCTAAAGAAAAAGGAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGA
GGGAGCGAACCGTTAGCAGAAGATTGTTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACAC
GTTGG
Found at i:58489 original size:321 final size:321
Alignment explanation
Indices: 57826--58518 Score: 937
Period size: 321 Copynumber: 2.2 Consensus size: 321
57816 ATAATCACAA
* * * * * *
57826 CAGAAGATTATTCAAGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCGTTGGTAGAAGATTGT
1 CAGAAGATTGTTCGAGTTCCTACTCCCT-AAGAAAAAGGGAGCAAACCCGTAGGCAGAAGATAGT
* * * *
57891 TCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAAACCGTTGGCAGAAGATTGTTCGAGTTCCTA
65 TCGAGTTCCTACTCCCTAAAGAAAAAGAGAGCGAAACCGTTAGCAGAAGATTGTTCGAGTTCCTA
* * *
57956 CTCCCTAAAGAAATATGGAGCGAACCCGTTGGCAAAAGATTGTTCAAGTTCCTACTCCCTAAAGA
130 CTCCCTAAAGAAAGAGGGAGCGAACCCGTTAGCAAAAGATTGTTCAAGTTCCTACTCCCTAAAGA
* *
58021 AAGAGGGAGTGAACCGTTGGCAGAAGATTGTTCAAGTTCCTACTCCCTACAGAAAGAGGGAGCGA
195 AAGAGGGAGCGAACCGTTGGCAGAAGATTGTTCAAGTTCCTACTCCATACAGAAAGAGGGAGCGA
* ** * * **
58086 ACATGTTGGCAGATTATTGTTTGAGTTCCTACTCCCTAAAGAAAAAAGGAGCGATCTGTTGG
260 ACACGTTGGCAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAAAAGGAGCGACCCATTGG
* * ** *
58148 TAGAAGATTGTTCG-GTTCCTACTCCCTACAGAAAAATGGAGTTAATCCGTAGGCAGAAGATAGT
1 CAGAAGATTGTTCGAGTTCCTACTCCCTA-AGAAAAAGGGAGCAAACCCGTAGGCAGAAGATAGT
* * *
58212 TCGAGTTTCTACTCCCTAAAGAAAAAGAGAGCGAACCCGTTAGTAGAAGATTGTTCGAGTTCCTA
65 TCGAGTTCCTACTCCCTAAAGAAAAAGAGAGCGAAACCGTTAGCAGAAGATTGTTCGAGTTCCTA
* * * *
58277 CTCCCTAAAGAAAGAGGGAGCGAACCTGTTAGCAGAAGATTGTTCGAGTTCCTACTCCGTAAAGA
130 CTCCCTAAAGAAAGAGGGAGCGAACCCGTTAGCAAAAGATTGTTCAAGTTCCTACTCCCTAAAGA
* * *
58342 AAGAGGGAGCGAACCCGTTGGGAGAATATTGTTCGAGTTCCTACTCCATA-A-AAA-AGGGAGCG
195 AAGAGGGAGCGAA-CCGTTGGCAGAAGATTGTTCAAGTTCCTACTCCATACAGAAAGAGGGAGCG
* ***
58404 AACCCGTTGGCAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGTGGGAGCGAACCCATTGG
259 AACACGTTGGCAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAAAAGGAGCG-ACCCATTGG
*
58468 CAGAAGATTGTTCGAGTTCCTACTCCCTAAG-AAAAGGGAGCGAACCCGTAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAGAAAAAGGGAGCAAACCCGTAG
58519 TAGATATTGT
Statistics
Matches: 321, Mismatches: 46, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
319 70 0.22
320 25 0.08
321 183 0.57
322 43 0.13
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (321 bp):
CAGAAGATTGTTCGAGTTCCTACTCCCTAAGAAAAAGGGAGCAAACCCGTAGGCAGAAGATAGTT
CGAGTTCCTACTCCCTAAAGAAAAAGAGAGCGAAACCGTTAGCAGAAGATTGTTCGAGTTCCTAC
TCCCTAAAGAAAGAGGGAGCGAACCCGTTAGCAAAAGATTGTTCAAGTTCCTACTCCCTAAAGAA
AGAGGGAGCGAACCGTTGGCAGAAGATTGTTCAAGTTCCTACTCCATACAGAAAGAGGGAGCGAA
CACGTTGGCAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAAAAGGAGCGACCCATTGG
Found at i:58854 original size:2 final size:2
Alignment explanation
Indices: 58847--58888 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
58837 ATGTAATCAT
58847 TA TA TA TA TA TA T- TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58887 TA
1 TA
58889 AATAATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58863 original size:13 final size:13
Alignment explanation
Indices: 58845--58885 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
58835 TTATGTAATC
58845 ATTATATATATAT
1 ATTATATATATAT
58858 ATTATATATATAT
1 ATTATATATATAT
58871 ATTATATATATAT
1 ATTATATATATAT
58884 AT
1 AT
58886 ATAAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Done.