Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002531.1 Hibiscus syriacus cultivar Beakdansim tig00005145_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: 116010
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1332 original size:85 final size:84
Alignment explanation
Indices: 1172--1402 Score: 237
Period size: 85 Copynumber: 2.7 Consensus size: 84
1162 AAAAGAAGCG
* * **
1172 CCGCAAAAGGTCGAGATCTATAGCTACGTTTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATA
1 CCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGAACAAACGTCGTAAAAGGTC-AGATAAATA
* ** *
1237 GCGCACTTTTGGGTACAAACG
64 ACGCACTTTTGGACACAAACA
** * * * *
1258 TTGCAAAAGGTCAGATCTATAGAGGCATTTTTGGAACAAACGTCGTAAAAGGTTAGATAAATAAC
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGTAAAAGGTCAGATAAATAAC
*
1323 GACATTTTTGGACACAAACA
66 G-CACTTTTGGACACAAACA
* ** * * *
1343 CCGCAAAAGGTTAGATAAATAGCGTCGTTTTTTGATACAAACGCCGTAAAAGGTCAGATA
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGA-ACAAACGTCGTAAAAGGTCAGATA
1403 TCTAGTGGCG
Statistics
Matches: 117, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
84 9 0.08
85 76 0.65
86 32 0.27
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (84 bp):
CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGTAAAAGGTCAGATAAATAAC
GCACTTTTGGACACAAACA
Found at i:1402 original size:43 final size:43
Alignment explanation
Indices: 1170--1432 Score: 208
Period size: 43 Copynumber: 6.1 Consensus size: 43
1160 CCAAAAGAAG
* ** *
1170 CGCCGCAAAAGGTCGAGATCTATAGCTACGTTTTTGGA-ACAAA
1 CGCCGCAAAAGGTC-AGATATATAGCGGCATTTTTGGATACAAA
* * * *
1213 CGTCGCAAAAGGTCGAGATCTATAGC-GCACTTTTGGGTACAAA
1 CGCCGCAAAAGGTC-AGATATATAGCGGCATTTTTGGATACAAA
** * *
1256 CGTTGCAAAAGGTCAGATCTATAGAGGCATTTTTGGA-ACAAA
1 CGCCGCAAAAGGTCAGATATATAGCGGCATTTTTGGATACAAA
* * * * * * *
1298 CGTCGTAAAAGGTTAGATAAATAACGACATTTTTGGACACAAA
1 CGCCGCAAAAGGTCAGATATATAGCGGCATTTTTGGATACAAA
* * * * * *
1341 CACCGCAAAAGGTTAGATAAATAGCGTCGTTTTTTGATACAAA
1 CGCCGCAAAAGGTCAGATATATAGCGGCATTTTTGGATACAAA
* * * * **
1384 CGCCGTAAAAGGTCAGATATCTAGTGGCGTTTTTTAATACAAA
1 CGCCGCAAAAGGTCAGATATATAGCGGCATTTTTGGATACAAA
1427 CGCCGC
1 CGCCGC
1433 TAATACCATT
Statistics
Matches: 183, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
42 51 0.28
43 132 0.72
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (43 bp):
CGCCGCAAAAGGTCAGATATATAGCGGCATTTTTGGATACAAA
Found at i:1565 original size:23 final size:22
Alignment explanation
Indices: 1539--1588 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1529 ACAACAACCA
1539 TAAATTTTA-ACAACATAATAAAT
1 TAAATTTTATA-AACATAAT-AAT
* *
1562 TAAAATTTATAAACATTATAAT
1 TAAATTTTATAAACATAATAAT
1584 TAAAT
1 TAAAT
1589 GTAATGTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTTATAAACATAATAAT
Found at i:3860 original size:2 final size:2
Alignment explanation
Indices: 3855--3981 Score: 170
Period size: 2 Copynumber: 64.5 Consensus size: 2
3845 TATATATGTA
* * *
3855 TG TG TG TG TG TG TG TG CG TG TG TG TG CG TG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
3897 TCG TG TG TG TG CG TG TG CG TG CG TG TG TG TG TG TG TG TG TG TG
1 T-G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3940 TG TG TG TG TG TG T- TG TG -G TG TG TG T- TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3979 TG T
1 TG T
3982 AGGCATGAAG
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
1 3 0.03
2 104 0.95
3 2 0.02
ACGTcount: A:0.00, C:0.06, G:0.49, T:0.46
Consensus pattern (2 bp):
TG
Found at i:4481 original size:43 final size:42
Alignment explanation
Indices: 4434--4517 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 42
4424 TGATGAAAAA
* *
4434 GGAAGAAACAAAGAGACAAAACTTCAGAATCTAAGGTACAAAG
1 GGAAGAAACAAAGAGAAAAAACTTCAG-ATCAAAGGTACAAAG
* *
4477 GGAAGCAACAAAGAGAAAAAACTTCAGATCAAAGTTACAAA
1 GGAAGAAACAAAGAGAAAAAACTTCAGATCAAAGGTACAAA
4518 TCACTGAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 12 0.32
43 25 0.68
ACGTcount: A:0.55, C:0.14, G:0.19, T:0.12
Consensus pattern (42 bp):
GGAAGAAACAAAGAGAAAAAACTTCAGATCAAAGGTACAAAG
Found at i:7188 original size:20 final size:20
Alignment explanation
Indices: 7159--7201 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
7149 ATTCCACCAC
*
7159 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
7179 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
7199 ATG
1 ATG
7202 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:8337 original size:61 final size:61
Alignment explanation
Indices: 8242--8397 Score: 228
Period size: 61 Copynumber: 2.6 Consensus size: 61
8232 TATGTATCAT
* *
8242 AGGTTTTAAAACCCCTAGGCTGGTTTCGAAACCCTTTGTCCATAATGACATTCTGCTAGAG
1 AGGTTTTAAAACCCCTAGGATGGTTTCGAAACCCTTTGTCCATAATGAAATTCTGCTAGAG
*
8303 AGGTTTTAAAACCCCTAGGATGGTTTCGAAACCCTTTGTCCATAATGAAATTCTGCTAGGG
1 AGGTTTTAAAACCCCTAGGATGGTTTCGAAACCCTTTGTCCATAATGAAATTCTGCTAGAG
*
8364 AGG-TCTAGAAACCCCTTTA-GA-GGTTTCGAAACCC
1 AGGTTTTA-AAACCCC--TAGGATGGTTTCGAAACCC
8398 CAACCCAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
60 3 0.03
61 81 0.92
62 2 0.02
63 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (61 bp):
AGGTTTTAAAACCCCTAGGATGGTTTCGAAACCCTTTGTCCATAATGAAATTCTGCTAGAG
Found at i:21139 original size:31 final size:31
Alignment explanation
Indices: 21068--21159 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
21058 AGTCGAGGGT
*
21068 TTACCTATGTTCTATGGAACATATGGACAGAA
1 TTACCTATG-TCTATCGAACATATGGACAGAA
* * *
21100 TTACCTATGTCTTTCGAGACATATGGATAGTA
1 TTACCTATGTCTATCGA-ACATATGGACAGAA
**
21132 -TACCTATGTTCTAAGGAACATATGGACA
1 TTACCTATG-TCTATCGAACATATGGACA
21160 TTTTACCTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (31 bp):
TTACCTATGTCTATCGAACATATGGACAGAA
Found at i:21167 original size:31 final size:31
Alignment explanation
Indices: 21067--21190 Score: 115
Period size: 31 Copynumber: 4.0 Consensus size: 31
21057 GAGTCGAGGG
21067 TTTACCTATGTTCTATGGAACATATGGACAGA
1 TTTACCTATGTTCTATGGAACATATGGACA-A
* * * * *
21099 ATTACCTATG-TCTTTCGAGACATATGGATAG
1 TTTACCTATGTTCTATGGA-ACATATGGACAA
* * *
21130 TATACCTATGTTCTAAGGAACATATGGACAT
1 TTTACCTATGTTCTATGGAACATATGGACAA
* * * *
21161 TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TTTACCTATGTTCTATGGAACATATGGACA
21191 GTTGCTGAGG
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
31 48 0.67
32 24 0.33
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTATGGAACATATGGACAA
Found at i:23218 original size:22 final size:22
Alignment explanation
Indices: 23167--23220 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
23157 TCAAAAGGGA
*
23167 AGATGTCAAATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
23189 AGATGTCGAATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
23211 AGATGTCGAA
1 AGATGTCGAA
23221 CTATGTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (22 bp):
AGATGTCGAATCTAAAGAATGT
Found at i:26901 original size:23 final size:23
Alignment explanation
Indices: 26867--26917 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
26857 TTTTATATGT
* * *
26867 CACTTCGGTGCAATTCTACGCGG
1 CACTTCGATGCAACTCTACACGG
*
26890 CACTTCGATGCAACTCTACATGG
1 CACTTCGATGCAACTCTACACGG
26913 CACTT
1 CACTT
26918 TGGTACATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (23 bp):
CACTTCGATGCAACTCTACACGG
Found at i:31723 original size:27 final size:27
Alignment explanation
Indices: 31600--31714 Score: 185
Period size: 27 Copynumber: 4.3 Consensus size: 27
31590 AGGTTCCAGA
* *
31600 GAACTATTCATGATAGTGAAATAATGG
1 GAACTATTCACGATAGTGAAATAGTGG
31627 GAACTATTCACGATAGTGAAATAGTGG
1 GAACTATTCACGATAGTGAAATAGTGG
*
31654 TAACTATTCACGATAGTGAAATAGTGG
1 GAACTATTCACGATAGTGAAATAGTGG
*
31681 TAACTATTCACGATAGTGAAATAGTGG
1 GAACTATTCACGATAGTGAAATAGTGG
*
31708 GAGCTAT
1 GAACTAT
31715 CCGTAATAGA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (27 bp):
GAACTATTCACGATAGTGAAATAGTGG
Found at i:37301 original size:17 final size:17
Alignment explanation
Indices: 37260--37302 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
37250 ATCATCTATT
*
37260 AGTAAATATATTTTTTC
1 AGTAAATATATTTTTTA
37277 AGTGAAATA-ATTTTTTA
1 AGT-AAATATATTTTTTA
37294 AGATAAATA
1 AG-TAAATA
37303 CTAGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (17 bp):
AGTAAATATATTTTTTA
Found at i:39080 original size:20 final size:20
Alignment explanation
Indices: 39057--39108 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
39047 AACGCGATCC
39057 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
39077 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
39097 CCAAAATCGCAA
1 CCAGAATCGCAA
39109 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:39125 original size:21 final size:20
Alignment explanation
Indices: 39099--39196 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
39089 ATCAGTTTCC
39099 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
39120 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
39139 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
39160 ACATAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
39182 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
39197 ACACATAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 40 0.66
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:39258 original size:20 final size:20
Alignment explanation
Indices: 39164--39532 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
39154 GATTTTACAT
* ** *
39164 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
39184 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
39204 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
39224 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
39244 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
39264 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
39284 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
39304 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
39324 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
39344 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
39364 AATCGCAATGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
39384 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
39404 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
39424 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
39444 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
39464 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
39484 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
39504 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
39524 AATCACAAC
1 AATCGCAAC
39533 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:40259 original size:24 final size:24
Alignment explanation
Indices: 40215--40261 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40205 AAATTTGGTC
*
40215 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
40239 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
40262 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:42758 original size:19 final size:19
Alignment explanation
Indices: 42736--43057 Score: 378
Period size: 19 Copynumber: 18.4 Consensus size: 19
42726 ACGGAAATAC
*
42736 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42755 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
42769 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
42789 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42803 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42822 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42841 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42855 AATCGCAATGCGAAAT-AA
1 AATCGCAATGCGAAATGAA
42873 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42892 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
*
42910 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
42924 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
42943 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42962 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42981 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
43000 AATCGCAA--CG-AA-G--
1 AATCGCAATGCGAAATGAA
43013 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
43031 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
43050 AATCGCAA
1 AATCGCAA
43058 CGAGATAATC
Statistics
Matches: 265, Mismatches: 9, Indels: 58
0.80 0.03 0.17
Matches are distributed among these distances:
13 8 0.03
14 40 0.15
15 5 0.02
16 16 0.06
17 9 0.03
18 51 0.19
19 123 0.46
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:42948 original size:121 final size:123
Alignment explanation
Indices: 42736--43038 Score: 421
Period size: 121 Copynumber: 2.5 Consensus size: 123
42726 ACGGAAATAC
* *
42736 AATCGCAACGCGAAATGAAAATCCCAAC--ATGAAAATCGCAATGCGGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACGAATGAAAATCGCAATGC-GAAATGAAAATCGCAACG
* *
42799 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAG
65 ACAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAA
42855 AATCGCAATGCGAAAT-AAAATCGCAATGCGAAATGAAAATCGCAATGCG-AATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG-AATGAAAATCGCAATGCGAAATGAAAATCGCAA
* *
42918 CGACATAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 CGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
42981 AATCGCAATGCGAAATGAAAATCGCAACGAA-G--AATCGCAATGCGAAATG-AAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAATGAAAATCGCAATGCGAAATGAAAATCGCAA
43039 TGCGAAATGA
Statistics
Matches: 166, Mismatches: 6, Indels: 22
0.86 0.03 0.11
Matches are distributed among these distances:
118 9 0.05
119 15 0.09
120 1 0.01
121 84 0.51
122 5 0.03
123 19 0.11
124 2 0.01
125 3 0.02
126 18 0.11
127 10 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (123 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
CAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAA
Found at i:43068 original size:121 final size:113
Alignment explanation
Indices: 42736--43079 Score: 317
Period size: 121 Copynumber: 2.8 Consensus size: 113
42726 ACGGAAATAC
* *
42736 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGCAA-CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAGAATCGCAATGC-GAAATGAAAATCGCAAGCG
* *
42799 AGA-GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
63 AAATGAATCGCAA--CG-AAT---AATCGCAATGCGAAATGAAAATCGCAACGAGAA
42855 AATCGCAATGCGAAAT-AAAATCGCAATGCGAAATGAAAATCGCAATGCG-AATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG-AA-G--AATCGCAATGCGAAATGAAAATCGCAA
*
42918 -CGACAT-AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
60 GCGAAATGAATCGCAA--CG-AA-T--AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
42981 AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATG-AAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAA-GCGAA
43045 ATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
65 ATG--AATCGCAACGA-ATAATCGCAATGCGAAAT
43080 TATAAACGCA
Statistics
Matches: 198, Mismatches: 5, Indels: 42
0.81 0.02 0.17
Matches are distributed among these distances:
118 10 0.05
119 17 0.09
120 1 0.01
121 99 0.50
122 6 0.03
123 21 0.11
124 5 0.03
125 3 0.02
126 26 0.13
127 10 0.05
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (113 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAAGCGAAA
TGAATCGCAACGAATAATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:43095 original size:70 final size:71
Alignment explanation
Indices: 42803--43095 Score: 429
Period size: 70 Copynumber: 4.2 Consensus size: 71
42793 GCAACGAGAG
*
42803 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
42868 AA-TAA
66 AATTAA
*
42873 AATCGCAATGCGAAATGAAAATCGCAATGCG-AATGAAAATCGCAACGACATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
42937 AATTAA
66 AATTAA
* * *
42943 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCG-CAATGCG
* **
43005 CAACGAA
65 AAATTAA
43012 GAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCG
1 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCG
43076 AAATTATA
65 AAATTA-A
*
43084 AA-CGCATTGCGA
1 AATCGCAATGCGA
43096 TTTTCATTTC
Statistics
Matches: 199, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
69 71 0.36
70 103 0.52
71 24 0.12
72 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
AATTAA
Found at i:43176 original size:19 final size:19
Alignment explanation
Indices: 43086--43168 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
43076 AAATTATAAA
43086 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
43105 CCGCATTGCGA--TTC-TCT
1 -CGCATTGCGATTTTCATTT
43122 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
43139 CGCATTGCGATTTTAATTT
1 CGCATTGCGATTTTCATTT
43158 CGCATTGCGAT
1 CGCATTGCGAT
43169 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
14 6 0.11
16 5 0.09
17 6 0.11
18 3 0.05
19 25 0.45
20 10 0.18
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:43294 original size:14 final size:14
Alignment explanation
Indices: 43275--43311 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
43265 CATCAATTAC
43275 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
43289 ACAAATCATCTTTT
1 ACAAATCAACTTTT
43303 ACAAATCAA
1 ACAAATCAA
43312 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:45272 original size:19 final size:19
Alignment explanation
Indices: 45232--45352 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
45222 TAGTTTACTT
* *
45232 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
45252 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
45271 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
45290 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
45309 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
45323 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
45342 TCGCAATGCGA
1 TCGCAACGCGA
45353 TTTTGGTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
14 9 0.10
16 4 0.05
17 4 0.05
19 57 0.66
20 13 0.15
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:45297 original size:38 final size:38
Alignment explanation
Indices: 45232--45352 Score: 153
Period size: 38 Copynumber: 3.3 Consensus size: 38
45222 TAGTTTACTT
* *
45232 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-TGAAAATCGCAACGCGAAACCAAAA
45271 TCGCAACGCGAAATGAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAACCAAAA
**
45309 TCGCAA--CGAAA-G--AATCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAACCAAAA
*
45342 TCGCAATGCGA
1 TCGCAACGCGA
45353 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
33 25 0.33
35 4 0.05
36 5 0.07
38 30 0.39
39 12 0.16
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (38 bp):
TCGCAACGCGAAATGAAAATCGCAACGCGAAACCAAAA
Found at i:45370 original size:19 final size:19
Alignment explanation
Indices: 45348--45476 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
45338 AAAATCGCAA
45348 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
45367 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
45381 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
45400 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
45414 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
45433 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
45452 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
45472 TGCGA
1 TGCGA
45477 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:45390 original size:33 final size:33
Alignment explanation
Indices: 45348--45439 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
45338 AAAATCGCAA
45348 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
45381 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
45414 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
45440 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:45966 original size:184 final size:186
Alignment explanation
Indices: 45520--46264 Score: 1425
Period size: 184 Copynumber: 4.0 Consensus size: 186
45510 TTGAATGGAT
45520 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45585 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
45650 TACTATTTCACA--G-T-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
45702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45767 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
45831 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
45886 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45951 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
46016 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
46072 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
46135 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
46200 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
46256 AAATTTACT
1 AAATTTACT
46265 AAGCAATCTA
Statistics
Matches: 555, Mismatches: 1, Indels: 11
0.98 0.00 0.02
Matches are distributed among these distances:
180 9 0.02
181 15 0.03
182 117 0.21
183 1 0.00
184 299 0.54
185 61 0.11
186 53 0.10
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:45992 original size:93 final size:93
Alignment explanation
Indices: 45520--46264 Score: 1425
Period size: 93 Copynumber: 8.1 Consensus size: 93
45510 TTGAATGGAT
45520 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45585 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
45613 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA--G-T-AAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45674 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
45702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45767 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
45795 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45858 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
45886 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
45951 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
45979 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
46044 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
46072 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
46135 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
46163 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
46228 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
46256 AAATTTACT
1 AAATTTACT
46265 AAGCAATCTA
Statistics
Matches: 643, Mismatches: 1, Indels: 16
0.97 0.00 0.02
Matches are distributed among these distances:
89 87 0.14
90 1 0.00
91 131 0.20
92 107 0.17
93 317 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:46050 original size:277 final size:278
Alignment explanation
Indices: 45520--46264 Score: 1430
Period size: 277 Copynumber: 2.7 Consensus size: 278
45510 TTGAATGGAT
45520 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
45585 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
45650 TACTATTTCACA--G-T-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
45711 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
195 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
45776 GAATTGGCAGCAACCGAAC
260 GAATTGGCAGCAACCGAAC
45795 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
45859 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
45924 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
45989 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
46054 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
46072 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
46136 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
46201 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
46265 AAGCAATCTA
Statistics
Matches: 464, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
273 102 0.22
274 15 0.03
275 24 0.05
276 23 0.05
277 300 0.65
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:47983 original size:14 final size:14
Alignment explanation
Indices: 47964--48053 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
47954 TTGAAATGAA
47964 AATCGCAACGAGAG
1 AATCGCAACGAGAG
47978 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
47995 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
48011 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
48030 AATCGCAACGAGAG
1 AATCGCAACGAGAG
48044 AATCGCAACG
1 AATCGCAACG
48054 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:48001 original size:33 final size:33
Alignment explanation
Indices: 47956--48070 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
47946 TCTTTTGGTT
47956 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
47989 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
48022 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
48055 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
48071 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:48002 original size:19 final size:18
Alignment explanation
Indices: 47963--48075 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
47953 GTTGAAATGA
47963 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
47978 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
47995 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
48011 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
48028 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
48044 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
48061 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
48076 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:48106 original size:14 final size:14
Alignment explanation
Indices: 48087--48141 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
48077 TTTGGTTTCG
48087 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
48101 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
48120 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
48134 CGTTGCGA
1 CGTTGCGA
48142 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:48119 original size:33 final size:33
Alignment explanation
Indices: 48071--48141 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
48061 AAAATCGCAA
**
48071 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
48104 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
48137 TGCGA
1 TGCGA
48142 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:48149 original size:33 final size:33
Alignment explanation
Indices: 48082--48163 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
48072 GCGATTTTGG
***
48082 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
48115 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
48148 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
48164 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:48168 original size:20 final size:20
Alignment explanation
Indices: 48094--48182 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
48084 TCGCGTTGCG
48094 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
48114 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
48127 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
48147 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
48167 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
48183 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:48304 original size:33 final size:33
Alignment explanation
Indices: 48262--48332 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
48252 AATACTAACT
*
48262 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
48295 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
48328 TGAAA
1 TGAAA
48333 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:48565 original size:22 final size:22
Alignment explanation
Indices: 48513--48567 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
48503 TGGTTGTGAG
**
48513 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
48535 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
48557 GGATTTCTTCG
1 GGATTTCTTCG
48568 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:48735 original size:20 final size:20
Alignment explanation
Indices: 48710--48902 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
48700 CTTTAAATAT
48710 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
48730 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
48752 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
48771 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
48791 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
48811 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
48831 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
48851 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
48871 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
48891 CGCGTTGCGATT
1 CGCGTTGCGATT
48903 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:48897 original size:60 final size:60
Alignment explanation
Indices: 48710--48902 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
48700 CTTTAAATAT
**
48710 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
48771 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
48831 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
48891 CGCGTTGCGATT
1 CGCGTTGCGATT
48903 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:48983 original size:20 final size:20
Alignment explanation
Indices: 48958--49009 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
48948 AAGAATCGCG
* *
48958 TTGCGATTTTTGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
48978 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
48998 TTGCGATTCTGG
1 TTGCGATTCTGG
49010 GGATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:50374 original size:31 final size:31
Alignment explanation
Indices: 50336--50416 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
50326 TTAGTTCTTA
50336 TGGTTGATTGGATTCAAGTTATATGTTATTC
1 TGGTTGATTGGATTCAAGTTATATGTTATTC
50367 TGGTTGATTGGATTCAAGTTATATGTTATTC
1 TGGTTGATTGGATTCAAGTTATATGTTATTC
*
50398 TGGTTG-TTGGTCTTCAAGT
1 TGGTTGATTGG-ATTCAAGT
50417 CTATCTTGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (31 bp):
TGGTTGATTGGATTCAAGTTATATGTTATTC
Found at i:55908 original size:2 final size:2
Alignment explanation
Indices: 55897--55932 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
55887 ATATTTAAAT
55897 TA TA -A 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 TA TA TA T
55933 TAGATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56031 original size:23 final size:23
Alignment explanation
Indices: 56005--56058 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
55995 AAATTTATTA
56005 AATTAAAATTTTAATTAGTACCT
1 AATTAAAATTTTAATTAGTACCT
56028 AATTAAAATTTTAATTAGTACCT
1 AATTAAAATTTTAATTAGTACCT
56051 AATTAAAA
1 AATTAAAA
56059 ATTAAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (23 bp):
AATTAAAATTTTAATTAGTACCT
Found at i:59128 original size:26 final size:26
Alignment explanation
Indices: 59066--59131 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
59056 ATTTTTTTGT
*
59066 TTTATTTATTTTAAATTAACCCCTGA
1 TTTATTTATTTTAAATTAACCACTGA
* * *
59092 TTTGCTTTATTTTAATTTAATCACTGA
1 TTT-ATTTATTTTAAATTAACCACTGA
*
59119 TTTATATATTTTA
1 TTTATTTATTTTA
59132 TGTTTCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTATTTATTTTAAATTAACCACTGA
Found at i:60089 original size:15 final size:17
Alignment explanation
Indices: 60065--60101 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
60055 CACACACCAA
60065 TTTTTGTCTT-AATTT-
1 TTTTTGTCTTAAATTTG
*
60080 TTTTTTTCTTAAATTTG
1 TTTTTGTCTTAAATTTG
60097 TTTTT
1 TTTTT
60102 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTGTCTTAAATTTG
Found at i:74605 original size:222 final size:222
Alignment explanation
Indices: 74219--74662 Score: 870
Period size: 222 Copynumber: 2.0 Consensus size: 222
74209 GGAAGCTATA
74219 TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
1 TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
74284 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
66 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
*
74349 GAAGAGGGAAAAATCGTATCTATTAGCAATGAAAATTTTAAATTTTAGGAACGAAATTAATAATA
131 GAAGAGGGAAAAATCGTATCTATTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
74414 GATGGGTATAACCAACAACTAGTTAGT
196 GATGGGTATAACCAACAACTAGTTAGT
74441 TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
1 TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
74506 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
66 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
*
74571 GAAGAGGGAAAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
131 GAAGAGGGAAAAATCGTATCTATTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
74636 GATGGGTATAACCAACAACTAGTTAGT
196 GATGGGTATAACCAACAACTAGTTAGT
74663 CTAGTAGGAT
Statistics
Matches: 220, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 220 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (222 bp):
TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
GAAGAGGGAAAAATCGTATCTATTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
GATGGGTATAACCAACAACTAGTTAGT
Found at i:76879 original size:18 final size:18
Alignment explanation
Indices: 76858--76906 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
76848 ATTATCAGTA
*
76858 GTCCTTCAGGACATAGTG
1 GTCCTTCGGGACATAGTG
76876 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
76894 GTCCTTCGGGACA
1 GTCCTTCGGGACA
76907 AATATTCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:79939 original size:21 final size:21
Alignment explanation
Indices: 79913--79957 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79903 GATTTCTGGG
* *
79913 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
79934 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
79955 CAA
1 CAA
79958 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:80027 original size:23 final size:22
Alignment explanation
Indices: 79983--80027 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
79973 AATGCCAGAG
*
79983 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
80005 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
80028 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:80670 original size:31 final size:31
Alignment explanation
Indices: 80632--80785 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
80622 GGGTCGAGGG
*
80632 TTACCTATGTTCTTCGGTACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
80663 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
80694 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
80725 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
80756 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
80786 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:84464 original size:21 final size:21
Alignment explanation
Indices: 84438--84482 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
84428 GATTTCTGGG
* *
84438 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
84459 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
84480 CAA
1 CAA
84483 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:84552 original size:23 final size:22
Alignment explanation
Indices: 84508--84552 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
84498 AATGCCAGAG
*
84508 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
84530 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
84553 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:85195 original size:31 final size:31
Alignment explanation
Indices: 85157--85310 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
85147 GGGTCGAGGG
* *
85157 TTACCTATGTTTTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
85188 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
85219 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
85250 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
85281 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
85311 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:88792 original size:10 final size:10
Alignment explanation
Indices: 88777--88861 Score: 90
Period size: 10 Copynumber: 8.7 Consensus size: 10
88767 CATTTAATAA
88777 ATAAACGAAC
1 ATAAACGAAC
88787 ATAAACGAAC
1 ATAAACGAAC
88797 ----ACGAAC
1 ATAAACGAAC
88803 ATAAACGAAC
1 ATAAACGAAC
* *
88813 ACAAAC-ATAA
1 ATAAACGA-AC
88823 ATGAACACGAAC
1 AT-AA-ACGAAC
88835 ATAAACGAAC
1 ATAAACGAAC
88845 ATAAACGAAC
1 ATAAACGAAC
88855 ATAAACG
1 ATAAACG
88862 TTGGAGACCC
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
6 6 0.10
9 1 0.02
10 46 0.73
11 4 0.06
12 5 0.08
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:88802 original size:16 final size:16
Alignment explanation
Indices: 88781--88845 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
88771 TAATAAATAA
88781 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
88797 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
88813 ACAAACATAAATGAAC
1 ACGAACATAAACGAAC
88829 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
88845 A
1 A
88846 TAAACGAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:92968 original size:24 final size:25
Alignment explanation
Indices: 92933--92987 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
92923 TATTATGTTA
*
92933 AACAT-ATATGAACGCACATAAACG
1 AACATAATATGAACACACATAAACG
*
92957 AACATAAT-TGAACACATATAAACG
1 AACATAATATGAACACACATAAACG
92981 AACATAA
1 AACATAA
92988 CCGAATGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (25 bp):
AACATAATATGAACACACATAAACG
Found at i:107274 original size:18 final size:18
Alignment explanation
Indices: 107251--107301 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
107241 AGGGATTATC
107251 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
107269 AGTGGTCCTTCAGCACAT
1 AGTGGTCCTTCGGGACAT
107287 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
107302 TAAATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:109208 original size:11 final size:11
Alignment explanation
Indices: 109192--109216 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109182 GGGCACACAT
109192 TTCTTGATTTC
1 TTCTTGATTTC
109203 TTCTTGATTTC
1 TTCTTGATTTC
109214 TTC
1 TTC
109217 GTGTTCATGT
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:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (11 bp):
TTCTTGATTTC
Found at i:109998 original size:32 final size:32
Alignment explanation
Indices: 109942--110017 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
109932 AGCCAATAGT
* *
109942 ATTCAAATAATGCACAGTAGAGTTAGCATGAC
1 ATTCAAATAATGCACAGCAAAGTTAGCATGAC
* *
109974 ATTCAAATAATGCACCA-CAAAGTTAGTATTAC
1 ATTCAAATAATGCA-CAGCAAAGTTAGCATGAC
*
110006 ATTCAGATAATG
1 ATTCAAATAATG
110018 TACATGAGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (32 bp):
ATTCAAATAATGCACAGCAAAGTTAGCATGAC
Found at i:115256 original size:31 final size:31
Alignment explanation
Indices: 115221--115310 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
115211 GATATCACTT
115221 CTTTCTTTTCATTTTAATTAAGATTTAGTCA
1 CTTTCTTTTCATTTTAATTAAGATTTAGTCA
115252 ----C-TTTCA-TTTAATTAAGATTTAGTCA
1 CTTTCTTTTCATTTTAATTAAGATTTAGTCA
* *
115277 CTTTCTTTTCATTTTAATTAAGATATGGTCA
1 CTTTCTTTTCATTTTAATTAAGATTTAGTCA
115308 CTT
1 CTT
115311 AAGGTTAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
25 19 0.37
26 5 0.10
27 1 0.02
29 1 0.02
30 5 0.10
31 20 0.39
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (31 bp):
CTTTCTTTTCATTTTAATTAAGATTTAGTCA
Found at i:115265 original size:25 final size:26
Alignment explanation
Indices: 115227--115285 Score: 104
Period size: 25 Copynumber: 2.3 Consensus size: 26
115217 ACTTCTTTCT
115227 TTTCATTTTAATTAAGATTTAGTCAC
1 TTTCATTTTAATTAAGATTTAGTCAC
115253 TTTCA-TTTAATTAAGATTTAGTCAC
1 TTTCATTTTAATTAAGATTTAGTCAC
115278 TTTC-TTTT
1 TTTCATTTT
115286 CATTTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTCATTTTAATTAAGATTTAGTCAC
Done.