Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008885.1 Hibiscus syriacus cultivar Beakdansim tig00112131_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: 671647
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:185347 original size:20 final size:20
Alignment explanation
Indices: 185294--185349 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
185284 CAACGGGGAA
* *
185294 ATCGCAACGCGTAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
185314 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
185334 ATCGCAACTAGAAAAT
1 ATCGCAACGAGAAAAT
185350 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGGCT
Found at i:187011 original size:40 final size:42
Alignment explanation
Indices: 186952--187041 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
186942 CCTCTTCAAC
*
186952 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
186993 GATGATAG-GGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
187034 GATGACAG
1 GATGACAG
187042 GTGAGTCGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.21, C:0.16, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGTGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:187417 original size:20 final size:20
Alignment explanation
Indices: 187394--187469 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
187384 TGCAACACGA
187394 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
187414 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
187434 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
187453 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
187470 ACAAAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 14 0.28
20 36 0.72
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:187429 original size:40 final size:39
Alignment explanation
Indices: 187385--187509 Score: 111
Period size: 33 Copynumber: 3.3 Consensus size: 39
187375 GTTTACTTTT
**
187385 GCAACACGAAAATGACTATCGCAACGCGGAAATGACTATC
1 GCAACACGAAAATGACTATCGCAACGC-GAAATGAAAATC
* * * *
187425 GCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAATC
1 GCAACACGAAAATGACTATCGCAACGCGAAATGAAAATC
* *
187464 GC-A-ACGACAA--A--ATCGCAATGCGAAATGAAAATC
1 GCAACACGAAAATGACTATCGCAACGCGAAATGAAAATC
187497 GCAACGAC-AAAAT
1 GCAAC-ACGAAAAT
187510 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
33 24 0.34
34 1 0.01
35 3 0.04
36 2 0.03
37 4 0.06
38 1 0.01
39 12 0.17
40 23 0.33
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (39 bp):
GCAACACGAAAATGACTATCGCAACGCGAAATGAAAATC
Found at i:187464 original size:19 final size:19
Alignment explanation
Indices: 187442--187500 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
187432 GGAAATGGCT
187442 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
187461 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
187475 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
187494 ATCGCAA
1 ATCGCAA
187501 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:187477 original size:14 final size:14
Alignment explanation
Indices: 187458--187516 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
187448 ATGCGAAATG
187458 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
187472 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
187491 AAAATCGCAACGAC
1 AAAATCGCAACGAC
187505 AAAATCGCAACG
1 AAAATCGCAACG
187517 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:187532 original size:33 final size:33
Alignment explanation
Indices: 187442--187521 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
187432 GGAAATGGCT
187442 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
187475 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
187508 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
187522 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:187550 original size:19 final size:19
Alignment explanation
Indices: 187528--187594 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
187518 GAAACACAAA
187528 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
187547 TCGCGTTGTGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
187563 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
187580 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
187595 GTCGTTGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 18 0.50
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:187580 original size:33 final size:33
Alignment explanation
Indices: 187533--187624 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
187523 ACAAATCGCA
*
187533 TTGCGATTTTCATTTCGCGTTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
187566 TTGCAATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
187599 TTGTGATTTTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
187625 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:188203 original size:18 final size:18
Alignment explanation
Indices: 188180--188227 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
188170 CGGGTCGATC
188180 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
188198 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
188216 AGGTGATGGCTC
1 AGGTGATGGCTC
188228 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:189594 original size:20 final size:20
Alignment explanation
Indices: 189546--189604 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
189536 AATAGTTTCT
* *
189546 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
189566 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
189586 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
189605 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:189894 original size:22 final size:22
Alignment explanation
Indices: 189867--189910 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
189857 GATGGAGATA
189867 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
189889 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
189911 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:190196 original size:41 final size:41
Alignment explanation
Indices: 190077--190214 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
190067 CGTTTTAAAA
* * *
190077 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
190118 ATTGCGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
190158 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
190199 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
190215 CAAAATTCGC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.41
41 47 0.59
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:190211 original size:20 final size:20
Alignment explanation
Indices: 190097--190210 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
190087 GATTATGTAT
*
190097 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
190117 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
190137 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
190157 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
190178 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
190198 TATCGCGTTGCGA
1 TATCGCGTTGCGA
190211 TTTTCAAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:190229 original size:21 final size:21
Alignment explanation
Indices: 190200--190272 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
190190 ATAGTCAGTA
*
190200 TCGCGTTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCAAAAT
190221 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCAAAAT
* **
190242 TCGCATTGCGATTTAC-TTAT
1 TCGCATTGCGATTTTCAAAAT
190262 TCGCATTGCGA
1 TCGCATTGCGA
190273 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 13 0.27
21 35 0.73
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAAAAT
Found at i:190230 original size:41 final size:41
Alignment explanation
Indices: 190104--190232 Score: 129
Period size: 41 Copynumber: 3.2 Consensus size: 41
190094 TATTATCTCG
* * ** *
190104 TTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAGTATCG-A
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTAAAATATCGCA
* ** * *
190143 GTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 -TTGCGATAGTCAGTATCGCGTTGCGATTTTAAAATATCGCA
190185 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-AAAATATCGCA
190226 TTGCGAT
1 TTGCGAT
190233 TTTCAAAATT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
40 27 0.36
41 46 0.61
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTAAAATATCGCA
Found at i:194510 original size:20 final size:20
Alignment explanation
Indices: 194485--194523 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
194475 ATATACTAAA
194485 CAGAATAAAAGTACTAACTG
1 CAGAATAAAAGTACTAACTG
*
194505 CAGAATAACAGTACTAACT
1 CAGAATAAAAGTACTAACT
194524 AACTCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGAATAAAAGTACTAACTG
Found at i:194740 original size:43 final size:44
Alignment explanation
Indices: 194679--194789 Score: 127
Period size: 48 Copynumber: 2.5 Consensus size: 44
194669 TTTCATACTC
* *
194679 CAACATTCACCCTACTCAATTACTCTTGAAAATTT-G-CATTCAT
1 CAACATTCACCCTGCTCAATAAC-CTTGAAAATTTCGACATTCAT
* *
194722 CAACATTCACCCTGCTCAATAACCTTTAACATTTCGAATTACATTCAT
1 CAACATTCACCCTGCTCAATAACCTTGAAAATTTCG----ACATTCAT
194770 CAACATTCACCCTGCTCAAT
1 CAACATTCACCCTGCTCAAT
194790 GATTTTGCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
42 9 0.16
43 22 0.38
48 27 0.47
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (44 bp):
CAACATTCACCCTGCTCAATAACCTTGAAAATTTCGACATTCAT
Found at i:196970 original size:64 final size:64
Alignment explanation
Indices: 196887--197015 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
196877 CTATTTTCAT
* * *
196887 CCAAGCATTTATAATCTTTGTGAGAAGAGTTGTATCCAAGAAACACACATTGCCTAGATCGATA
1 CCAAACATTTATAACCTTTGTGAGAAAAGTTGTATCCAAGAAACACACATTGCCTAGATCGATA
*
196951 CCAAACATTTATAACCTTTGTGAGAAAAGTTGTATCCAAGAAACACACTTTGCCTAGATCGATA
1 CCAAACATTTATAACCTTTGTGAGAAAAGTTGTATCCAAGAAACACACATTGCCTAGATCGATA
197015 C
1 C
197016 TCCAATTTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (64 bp):
CCAAACATTTATAACCTTTGTGAGAAAAGTTGTATCCAAGAAACACACATTGCCTAGATCGATA
Found at i:199192 original size:20 final size:20
Alignment explanation
Indices: 199167--199208 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
199157 ACAAAGGTTG
199167 GATTCTCCTCAACCTGGCCA
1 GATTCTCCTCAACCTGGCCA
199187 GATTCTCCTCAACCTGGCCA
1 GATTCTCCTCAACCTGGCCA
199207 GA
1 GA
199209 CTCATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (20 bp):
GATTCTCCTCAACCTGGCCA
Found at i:200768 original size:34 final size:34
Alignment explanation
Indices: 200725--200791 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
200715 GATAAGTTTC
200725 TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
1 TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
*
200759 TCAATTTTAAAATTAGGTGGTGTGATTCATATA
1 TCAATTTTAAAATTAGGAGGTGTGATTCATATA
200792 GGAACATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (34 bp):
TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
Found at i:201252 original size:6 final size:6
Alignment explanation
Indices: 201241--201309 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
201231 TCTCGTCTCG
201241 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
201289 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
201310 AATACGTGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:201454 original size:21 final size:21
Alignment explanation
Indices: 201428--201484 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
201418 ATAACTGTAG
*
201428 ACTATCGCAACGCGATTTTGA
1 ACTATCGCAACGCGATTTTCA
201449 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
* *
201470 ATTACCGCAACGCGA
1 ACTATCGCAACGCGA
201485 AATGCAACGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:201952 original size:16 final size:17
Alignment explanation
Indices: 201923--201956 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
201913 TTGAATAAGC
201923 ACTTTTTATAGAAAAAT
1 ACTTTTTATAGAAAAAT
*
201940 ACTTTTT-TTGAAAAAT
1 ACTTTTTATAGAAAAAT
201956 A
1 A
201957 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
ACTTTTTATAGAAAAAT
Found at i:209203 original size:11 final size:12
Alignment explanation
Indices: 209174--209208 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
209164 GTTCGGAGCT
*
209174 TATTTTTTAAAA
1 TATTTTTGAAAA
209186 TATTTTTGAAAA
1 TATTTTTGAAAA
209198 TATTTTTGAAA
1 TATTTTTGAAA
209209 TATAATATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (12 bp):
TATTTTTGAAAA
Found at i:209209 original size:11 final size:11
Alignment explanation
Indices: 209177--209211 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
209167 CGGAGCTTAT
*
209177 TTTTTAAAATA
1 TTTTTGAAATA
209188 TTTTTGAAAATA
1 TTTTTG-AAATA
209200 TTTTTGAAATA
1 TTTTTGAAATA
209211 T
1 T
209212 AATATACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (11 bp):
TTTTTGAAATA
Found at i:209314 original size:36 final size:35
Alignment explanation
Indices: 209269--209396 Score: 152
Period size: 36 Copynumber: 3.6 Consensus size: 35
209259 TAAAAATCGG
* *
209269 TTTTCCAAAATATATATTATATAGTTTTTGAAAACA
1 TTTTTCAAAATATATAATATATAG-TTTTGAAAACA
209305 TTTTTCAAAATATATAATATATAGTTTTGAAAACGA
1 TTTTTCAAAATATATAATATATAGTTTTGAAAAC-A
**
209341 TCTTTAAAAAATATATACAATATATAGTTTTGAAAACA
1 T-TTTTCAAAATATAT--AATATATAGTTTTGAAAACA
*
209379 TTTTT--ATATATATAATAT
1 TTTTTCAAAATATATAATAT
209397 TTTCATTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.06
35 17 0.21
36 24 0.29
37 15 0.18
38 2 0.02
39 19 0.23
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (35 bp):
TTTTTCAAAATATATAATATATAGTTTTGAAAACA
Found at i:209392 original size:37 final size:35
Alignment explanation
Indices: 209286--209392 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 35
209276 AAATATATAT
*
209286 TATATAGTTTTTGAAAACATTTTTCAAA-ATATATAA
1 TATATAG-TTTTGAAAACATTTTT-AAATATATACAA
*
209322 TATATAGTTTTGAAAACGATCTTTAAAAAATATATACAA
1 TATATAGTTTTGAAAAC-AT-TTT--TAAATATATACAA
*
209361 TATATAGTTTTGAAAACATTTTTATATATATA
1 TATATAGTTTTGAAAACATTTTTAAATATATA
209393 ATATTTTCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
35 18 0.29
36 9 0.15
37 6 0.10
38 5 0.08
39 24 0.39
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (35 bp):
TATATAGTTTTGAAAACATTTTTAAATATATACAA
Found at i:209444 original size:15 final size:15
Alignment explanation
Indices: 209424--209462 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
209414 TTTTTATTTC
209424 TTTTTCTTTCATTCA
1 TTTTTCTTTCATTCA
209439 TTTTTCTTTCATTCA
1 TTTTTCTTTCATTCA
209454 TTTTTCTTT
1 TTTTTCTTT
209463 TTCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCTTTCATTCA
Found at i:210741 original size:4 final size:4
Alignment explanation
Indices: 210734--210803 Score: 70
Period size: 4 Copynumber: 16.8 Consensus size: 4
210724 TTAACCTGAT
* *
210734 TTTA TTTA TTTA TTTA TTTA TTTAA TCTTT TTCTA TTTT TTCTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A T-TTA TT-TA TTTA TT-TA TTTA
*
210782 TTTA -ATA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
210804 TTATTGTACA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
3 2 0.04
4 42 0.76
5 9 0.16
6 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:210798 original size:28 final size:27
Alignment explanation
Indices: 210734--210804 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
210724 TTAACCTGAT
* *
210734 TTTATTTATTTATTTATTTATTTAATC
1 TTTATTTATTTTTTTATTTATTTAATA
210761 TTT-TTCTATTTTTTCTATTTATTTAATA
1 TTTATT-TATTTTTT-TATTTATTTAATA
210789 TTTATTTATTTATTTT
1 TTTATTTATTT-TTTT
210805 TATTGTACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 10 0.26
28 21 0.55
29 5 0.13
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTATTTATTTTTTTATTTATTTAATA
Found at i:215027 original size:2 final size:2
Alignment explanation
Indices: 215016--215066 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
215006 TAAAGGCTAT
215016 TA TA -A TA TA TA TA TA TA TA TA TA TA TA 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
215057 TA TA TA TA TA
1 TA TA TA TA TA
215067 AAGTTTAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:217292 original size:15 final size:16
Alignment explanation
Indices: 217272--217303 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
217262 CAAATAACAC
217272 ATATCACATAA-ATGT
1 ATATCACATAACATGT
217287 ATATCACATAACATGT
1 ATATCACATAACATGT
217303 A
1 A
217304 ATACAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (16 bp):
ATATCACATAACATGT
Found at i:219604 original size:36 final size:37
Alignment explanation
Indices: 219486--219654 Score: 139
Period size: 38 Copynumber: 4.5 Consensus size: 37
219476 TTATTTTCAA
* **
219486 AATATATAGTTTTTAGAAAACGGTTTTTGAAAGCATAT
1 AATATATAGTTTTT-GAAAACGATTTTTGAAAATATAT
* * * * *
219524 AATACATACTTTTTAAAAATCGATTTTTGAAATTTTAT
1 AATATATAGTTTTTGAAAA-CGATTTTTGAAAATATAT
* * *
219562 ATTATATTGTTTTTGAAAAC-ATTTTTCAAAATATAT
1 AATATATAGTTTTTGAAAACGATTTTTGAAAATATAT
* *
219598 AATATATAG-TTTTGAAAATG-TTCTTTAAAAAATATATAT
1 AATATATAGTTTTTGAAAACGATT-TTT--GAAA-ATATAT
219637 AATATATAG-TTTTGAAAA
1 AATATATAGTTTTTGAAAA
219655 TATTATAATA
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
35 11 0.10
36 23 0.22
37 5 0.05
38 43 0.41
39 24 0.23
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (37 bp):
AATATATAGTTTTTGAAAACGATTTTTGAAAATATAT
Found at i:219744 original size:13 final size:13
Alignment explanation
Indices: 219726--219750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219716 CATTCATTTA
219726 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
219739 TTTTTCTTTTTT
1 TTTTTCTTTTTT
219751 AGGGTCCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:222057 original size:18 final size:17
Alignment explanation
Indices: 222034--222078 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
222024 AACATTTTCA
*
222034 GTAATCTTATTCCCGTCG
1 GTAATCTTATTCCC-ACG
*
222052 GTAATCCTATTCCCACG
1 GTAATCTTATTCCCACG
222069 GTAATCTTAT
1 GTAATCTTAT
222079 ATTCCGTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (17 bp):
GTAATCTTATTCCCACG
Found at i:229223 original size:18 final size:18
Alignment explanation
Indices: 229202--229236 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
229192 TTAACGTCTT
229202 AATGATTAAAAT-ATTAAA
1 AATGA-TAAAATAATTAAA
229220 AATGATAAAATAATTAA
1 AATGATAAAATAATTAA
229237 CCAACACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AATGATAAAATAATTAAA
Found at i:231870 original size:31 final size:32
Alignment explanation
Indices: 231834--231909 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
231824 TTAATTTTCT
*
231834 ATTTGACCCTTGAAA-CTTAGATAAAATATTA
1 ATTTGACCCTTGAAAGCTTAGATAAAATATCA
* * * *
231865 TTTTGACGCTT-AAAGTTTAGATGAAATATCA
1 ATTTGACCCTTGAAAGCTTAGATAAAATATCA
*
231896 ATTTAACCCTTGAA
1 ATTTGACCCTTGAA
231910 TTTCATATGA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 3 0.09
31 30 0.86
32 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (32 bp):
ATTTGACCCTTGAAAGCTTAGATAAAATATCA
Found at i:234962 original size:32 final size:30
Alignment explanation
Indices: 234923--234993 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
234913 ATGAACATAT
*
234923 GATATGTGAACATAAGATAATAAGTGACATGA
1 GATATGTGAACATAAGAGAAT-A-TGACATGA
* * * *
234955 GCTATGTGACCATATGAGAGTATGACATGA
1 GATATGTGAACATAAGAGAATATGACATGA
234985 GATATGTGA
1 GATATGTGA
234994 TATGTGAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 16 0.48
31 1 0.03
32 16 0.48
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (30 bp):
GATATGTGAACATAAGAGAATATGACATGA
Found at i:237336 original size:27 final size:26
Alignment explanation
Indices: 237305--237365 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
237295 GGATTGAAGG
*
237305 AAATGAACAAAATGCCCCTGAAGTGTA
1 AAATGAACAAAATGCCCC-CAAGTGTA
*
237332 AAATGACCAAAATGCCCCCAAGTGTA
1 AAATGAACAAAATGCCCCCAAGTGTA
*
237358 AAAGGAAC
1 AAATGAAC
237366 CAAAGTACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (26 bp):
AAATGAACAAAATGCCCCCAAGTGTA
Found at i:237379 original size:27 final size:26
Alignment explanation
Indices: 237325--237380 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
237315 AATGCCCCTG
* *
237325 AAGTGTAAAATGACCAAAATGCCCCC
1 AAGTGTAAAAGGACCAAAATACCCCC
* *
237351 AAGTGTAAAAGGAACCAAAGTACCTCC
1 AAGTGTAAAAGG-ACCAAAATACCCCC
237378 AAG
1 AAG
237381 CCCTAGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (26 bp):
AAGTGTAAAAGGACCAAAATACCCCC
Found at i:256579 original size:59 final size:60
Alignment explanation
Indices: 256484--256621 Score: 165
Period size: 59 Copynumber: 2.3 Consensus size: 60
256474 TAAAGTACTC
* *
256484 AAATGGTCTCCCGACTATAGGATATTAGTTTATTGAGT-CACTCGATTATTAAAAGTTATA
1 AAATGGTCACCCGACTATAGGATATTAGTTTATTGAGTCCA-TCGACTATTAAAAGTTATA
* * * * *
256544 AAATGGTC-GCCGACTATAGGGTGTT-GCTTTGTTGAGTCCATCGACTATTAACAGTTATA
1 AAATGGTCACCCGACTATAGGATATTAG-TTTATTGAGTCCATCGACTATTAAAAGTTATA
*
256603 AAATAGTCACCCGACTATA
1 AAATGGTCACCCGACTATA
256622 TATTATGTCT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
58 1 0.01
59 47 0.70
60 19 0.28
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (60 bp):
AAATGGTCACCCGACTATAGGATATTAGTTTATTGAGTCCATCGACTATTAAAAGTTATA
Found at i:258174 original size:42 final size:41
Alignment explanation
Indices: 258084--258214 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 41
258074 AAAACGTTGT
*
258084 AATAGAGTAGACATTTAGCGGCGTTTA-AGCC-CAAACGCCGC
1 AATAGAGTATA-ATTTAGCGGCGTTTATA-CCACAAACGCCGC
* * *
258125 AATAGAGTATTAATTTAGTGGCGTTTATACCACAAACACCGT
1 AATAGAGTA-TAATTTAGCGGCGTTTATACCACAAACGCCGC
* * * *
258167 AATAGAGTGGTAAATTAGCGGCATTTATACAACAAACGCCGC
1 AATAGAGT-ATAATTTAGCGGCGTTTATACCACAAACGCCGC
258209 AATAGA
1 AATAGA
258215 ATGGTAAATT
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
41 25 0.33
42 50 0.67
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (41 bp):
AATAGAGTATAATTTAGCGGCGTTTATACCACAAACGCCGC
Found at i:258220 original size:42 final size:42
Alignment explanation
Indices: 258115--258254 Score: 156
Period size: 42 Copynumber: 3.3 Consensus size: 42
258105 CGTTTAAGCC
** * * * *
258115 CAAACGCCGCAATAGAGTATTAATTTAGTGGCGTTTATACCA
1 CAAACGCCGCAATAGAGTGGTAAATTAGAGGCATTTATACAA
* * *
258157 CAAACACCGTAATAGAGTGGTAAATTAGCGGCATTTATACAA
1 CAAACGCCGCAATAGAGTGGTAAATTAGAGGCATTTATACAA
* * *
258199 CAAACGCCGCAATAGAATGGTAAATTAGAGGCCTTTATATATA
1 CAAACGCCGCAATAGAGTGGTAAATTAGAGGCATTTATACA-A
258242 -AAACGCCGCAATA
1 CAAACGCCGCAATA
258255 TGGTTGTTTA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 82 0.99
43 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (42 bp):
CAAACGCCGCAATAGAGTGGTAAATTAGAGGCATTTATACAA
Found at i:259613 original size:43 final size:41
Alignment explanation
Indices: 259516--259617 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 41
259506 ATAAATAAAG
* *
259516 GTATTTAGCGGCGTTTGTATCCAAAAACGCCGCTATATATA
1 GTATTTAGCGGCGTTTATATCCAAAAACACCGCTATATATA
*
259557 -TATCCTTTTGCGGCGTTTATATCCAAAAACACCGCTA-ATGATAA
1 GTA---TTTAGCGGCGTTTATATCCAAAAACACCGCTATAT-AT-A
259601 GTATATTAGCGGCGTTT
1 GTAT-TTAGCGGCGTTT
259618 TGTTACAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
40 2 0.04
42 3 0.06
43 42 0.84
44 1 0.02
45 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
GTATTTAGCGGCGTTTATATCCAAAAACACCGCTATATATA
Found at i:266929 original size:21 final size:21
Alignment explanation
Indices: 266905--266955 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
266895 GGAAGTAGAG
* * *
266905 AGAGAAGCAGTGGCAGTACAA
1 AGAGAAGCAGCGACAGCACAA
*
266926 AGAGAGGCAGCGACAGCACAA
1 AGAGAAGCAGCGACAGCACAA
266947 AGAGAAGCA
1 AGAGAAGCA
266956 ACATATCAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.04
Consensus pattern (21 bp):
AGAGAAGCAGCGACAGCACAA
Found at i:267333 original size:43 final size:43
Alignment explanation
Indices: 267272--267386 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
267262 TTTTGTGTTA
* *
267272 TTTAGCGGCGTTTGTATCCTGAAAACGCCGCTATATACTGACT
1 TTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACTGACC
* *
267315 TTTAGCGGTGTTTGTATCCTAAAAACGCCTCTATATACTGACC
1 TTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACTGACC
*
267358 TTTAGCGGCGTTT-T-TCATAAAAACGCCGC
1 TTTAGCGGCGTTTGTATCCTAAAAACGCCGC
267387 GAAATCGCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 13 0.20
42 1 0.02
43 51 0.78
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACTGACC
Found at i:267441 original size:43 final size:43
Alignment explanation
Indices: 267362--267687 Score: 268
Period size: 43 Copynumber: 7.6 Consensus size: 43
267352 CTGACCTTTA
* * * *
267362 GCGGCGTTTTTCATAAAAACGCCGCGAAATC-GCAACACCTATT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAA-CATCAACACCTATT
** * *
267405 GCGGCGTTTACGATAAAAACGCCGCTAAACATCAACATCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAACATCAACACCTATT
* * ** * *
267448 ACGGCATTTGTGGGAAAAACGCCGCTAAACATCAACATCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAACATCAACACCTATT
** * *
267491 GCGGCGTTTGTGGGAAAAACGCCGCTAAAAATCAACACCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAACATCAACACCTATT
* * *
267534 GTGGCGTTTGTGA-AAAAAGCGTCGCAAAACATCAACACCTATT
1 GCGGCGTTTGTGATAAAAA-CGCCGCTAAACATCAACACCTATT
* ** * * *
267577 GCGGCGTTTGT-CTGCCAGACGCCGCTAAATATCAACATCTATT
1 GCGGCGTTTGTGAT-AAAAACGCCGCTAAACATCAACACCTATT
* * *
267620 ACGGCGTTTGTCTG-T-CAAACGCCGCTAAATATCAACACCTATT
1 GCGGCGTTTG--TGATAAAAACGCCGCTAAACATCAACACCTATT
* *
267663 GCGG-GTTTTTTGTTAAAAACGCCGC
1 GCGGCG-TTTGTGATAAAAACGCCGC
267688 GAACTTTAGC
Statistics
Matches: 235, Mismatches: 38, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.01
42 8 0.03
43 221 0.94
44 2 0.01
45 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
GCGGCGTTTGTGATAAAAACGCCGCTAAACATCAACACCTATT
Found at i:267509 original size:129 final size:129
Alignment explanation
Indices: 267376--267670 Score: 333
Period size: 129 Copynumber: 2.3 Consensus size: 129
267366 CGTTTTTCAT
* ** *
267376 AAAAACGCCGCGAAATCGCAACACCTATTGCGGCGTTTACGATAAAAA-CGCCGCTAAACATCAA
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTACGA-AAAAAGCGCCGCAAAACATCAA
* * * *
267440 CATCTACTACGGCATTTGTGGGAAAAACGCCGCTAAACATCAACATCTACTGCGGCGTTTGTGGG
65 CACCTACTACGGCATTTGTCGGAAAAACGCCGCTAAACATCAACATCTACTACGGCGTTTGTCGG
* * * ** *
267505 AAAAACGCCGCTAAAAATCAACACCTACTGTGGCGTTTGTGAAAAAAGCGTCGCAAAACATCAAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTACGAAAAAAGCGCCGCAAAACATCAAC
* * * * ** * * * *
267570 ACCTATTGCGGCGTTTGTCTGCCAGACGCCGCTAAATATCAACATCTATTACGGCGTTTGTCTG
66 ACCTACTACGGCATTTGTCGGAAAAACGCCGCTAAACATCAACATCTACTACGGCGTTTGTCGG
**
267634 TCAAACGCCGCTAAATATCAACACCTATTGCGG-GTTT
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
267671 TTTGTTAAAA
Statistics
Matches: 136, Mismatches: 29, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
128 9 0.07
129 127 0.93
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (129 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTACGAAAAAAGCGCCGCAAAACATCAAC
ACCTACTACGGCATTTGTCGGAAAAACGCCGCTAAACATCAACATCTACTACGGCGTTTGTCGG
Found at i:273551 original size:3 final size:3
Alignment explanation
Indices: 273543--273574 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
273533 CTGGAAGCAA
273543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
273575 GAGAGAGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:278035 original size:12 final size:12
Alignment explanation
Indices: 278006--278054 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
277996 AATTATTAAC
278006 ATATTTAA-AAT
1 ATATTTAATAAT
*
278017 ATATTTATTAAT
1 ATATTTAATAAT
*
278029 ATTTTTAATAAT
1 ATATTTAATAAT
*
278041 ATATAATAATAAT
1 ATAT-TTAATAAT
278054 A
1 A
278055 ATAATACACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 7 0.23
12 16 0.52
13 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:278035 original size:23 final size:23
Alignment explanation
Indices: 277988--278044 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
277978 TATTTTAATA
*
277988 AAAATATTAATTATTAACATATTT
1 AAAATA-TATTTATTAACATATTT
* *
278012 AAAATATATTTATTAATATTTTT
1 AAAATATATTTATTAACATATTT
278035 AATAATATAT
1 AA-AATATAT
278045 AATAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATATTTATTAACATATTT
Found at i:278447 original size:23 final size:23
Alignment explanation
Indices: 278421--278468 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
278411 TAAATTATTC
278421 TAATATTTTTAAAAT-AATAATAT
1 TAAT-TTTTTAAAATAAATAATAT
*
278444 TAATTTTTTATAATAAATAATAT
1 TAATTTTTTAAAATAAATAATAT
278467 TA
1 TA
278469 TTTATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATTTTTTAAAATAAATAATAT
Found at i:282108 original size:32 final size:31
Alignment explanation
Indices: 282031--282122 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 31
282021 TGAAGGGCCC
* *
282031 CTATCCATATATTCCGAAGAACATAGGT-AA
1 CTATCCATATATCCCGAAGGACATAGGTAAA
* * *
282061 CTGTCCATATGTCCCGAAGGATATAGGTAATA
1 CTATCCATATATCCCGAAGGACATAGGTAA-A
*
282093 CTATCCATATATCCCGAATGACATAGGTAA
1 CTATCCATATATCCCGAAGGACATAGGTAA
282123 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 23 0.45
31 1 0.02
32 27 0.53
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (31 bp):
CTATCCATATATCCCGAAGGACATAGGTAAA
Found at i:283263 original size:21 final size:21
Alignment explanation
Indices: 283221--283300 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
283211 TAAACCCGAA
* *
283221 AATTACTTCAT-T-TCAGCTC
1 AATTGCTTCATATATCATCTC
283240 AATTGCTTCATATATCATCTC
1 AATTGCTTCATATATCATCTC
283261 AATTGCTTCATATATCATCAT-
1 AATTGCTTCATATATCATC-TC
*
283282 AATTGCTTCTTATATCATC
1 AATTGCTTCATATATCATC
283301 CCCTTTCTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 10 0.18
20 1 0.02
21 43 0.78
22 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTGCTTCATATATCATCTC
Found at i:300980 original size:58 final size:60
Alignment explanation
Indices: 300861--300981 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 60
300851 TCGGGTGATA
**
300861 ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAGCAACATCCTATAGTTTAGAGATC
1 ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAGCAACATCCTATAGTAAAGAGATC
* **
300921 ATTTTGTAACTTTTAATAGTCG-ATGACTCAA-AAAGCAATGTCCTATAGTCAAAG-GATC
1 ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAGCAACATCCTATAGT-AAAGAGATC
300979 ATT
1 ATT
300982 AATGTACTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 23 0.42
59 11 0.20
60 21 0.38
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAGCAACATCCTATAGTAAAGAGATC
Found at i:301577 original size:19 final size:19
Alignment explanation
Indices: 301555--301596 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
301545 TTTTTTAATT
301555 TTAATATATTTTTACAAGA
1 TTAATATATTTTTACAAGA
301574 TTAATATATTTTTACAAGA
1 TTAATATATTTTTACAAGA
301593 TTAA
1 TTAA
301597 GCATGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
TTAATATATTTTTACAAGA
Found at i:307926 original size:2 final size:2
Alignment explanation
Indices: 307921--307964 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
307911 TACAAAAGTA
307921 AT AT AT AT AT 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 AT AT AT AT AT
307963 AT
1 AT
307965 TTATTTAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:309115 original size:2 final size:2
Alignment explanation
Indices: 309108--309169 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
309098 TATCATGCTT
309108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
309150 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
309170 ATTGTTCGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:310986 original size:6 final size:6
Alignment explanation
Indices: 310967--311161 Score: 381
Period size: 6 Copynumber: 32.5 Consensus size: 6
310957 TCCTTGGACT
*
310967 GTATAA GTACAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
1 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
311015 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
1 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
311063 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
1 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
311111 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
1 GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA GTATAA
311159 GTA
1 GTA
311162 GGTTATATAT
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 187 1.00
ACGTcount: A:0.50, C:0.01, G:0.17, T:0.33
Consensus pattern (6 bp):
GTATAA
Found at i:318780 original size:17 final size:18
Alignment explanation
Indices: 318745--318785 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
318735 ATATTATGTA
*
318745 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
318763 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
318780 TTTACT
1 TTTACT
318786 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:321051 original size:26 final size:24
Alignment explanation
Indices: 320980--321051 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
320970 TTATATTTGT
320980 ATTTACTTTATTTTGTTTAATTGTA
1 ATTTACTTTATTTTGTTTAATT-TA
*
321005 ATTT--TTTATTATT-TTTCATTTA
1 ATTTACTTTATT-TTGTTTAATTTA
*
321027 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTTAATTT
321052 GTAGGACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 4 0.11
25 6 0.16
26 12 0.32
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTTAATTTA
Found at i:326214 original size:40 final size:40
Alignment explanation
Indices: 326159--326241 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
326149 CAGTATTACT
326159 AAAGCGGATAAAGAGATAAAAGGGCTAATTTAAAGCTTGG
1 AAAGCGGATAAAGAGATAAAAGGGCTAATTTAAAGCTTGG
326199 AAAGCGGATAAAGAGATAAAAGGGCTAATTTAAAGCTTGG
1 AAAGCGGATAAAGAGATAAAAGGGCTAATTTAAAGCTTGG
326239 AAA
1 AAA
326242 AATTTCTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.19
Consensus pattern (40 bp):
AAAGCGGATAAAGAGATAAAAGGGCTAATTTAAAGCTTGG
Found at i:327433 original size:25 final size:26
Alignment explanation
Indices: 327404--327455 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
327394 TTCATGATTT
* *
327404 TAACATCTAAAAT-TTATAAATTAAA
1 TAACATCGAAAATAATATAAATTAAA
*
327429 TAACATGGAAAATAATATAAATTAAA
1 TAACATCGAAAATAATATAAATTAAA
327455 T
1 T
327456 GTAAATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (26 bp):
TAACATCGAAAATAATATAAATTAAA
Found at i:333702 original size:2 final size:2
Alignment explanation
Indices: 333695--333725 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
333685 ATTTAACATT
333695 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
333726 TTTCTTTTTT
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:337845 original size:21 final size:21
Alignment explanation
Indices: 337805--337845 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
337795 AAAATGAAGA
* * *
337805 TGGAAGAGAAGATCAGGATGT
1 TGGAAGACAAGATAAAGATGT
337826 TGGAAGACAAGATAAAGATG
1 TGGAAGACAAGATAAAGATG
337846 GTCAAAGGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.34, T:0.17
Consensus pattern (21 bp):
TGGAAGACAAGATAAAGATGT
Found at i:345523 original size:53 final size:48
Alignment explanation
Indices: 345452--345578 Score: 128
Period size: 48 Copynumber: 2.5 Consensus size: 48
345442 GCCATCCATT
* ***
345452 ATTTCAACTTCACAACGAAAGATATCGTTTTCACTAGCAACATACAAGATTGG
1 ATTTCAACTTCACGACGAAAGATATCGTGCCCACT---AAC--ACAAGATTGG
* * * *
345505 ATTTTAACTTCACGACGAATGATATTGTGCCCACTTACACAAGATTGG
1 ATTTCAACTTCACGACGAAAGATATCGTGCCCACTAACACAAGATTGG
*
345553 ATTTCAACTTCACGACGAAGGATATC
1 ATTTCAACTTCACGACGAAAGATATC
345579 AAATTCAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
48 33 0.52
50 2 0.03
53 28 0.44
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (48 bp):
ATTTCAACTTCACGACGAAAGATATCGTGCCCACTAACACAAGATTGG
Found at i:346009 original size:21 final size:20
Alignment explanation
Indices: 345970--346045 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
345960 ATCAATTGTT
345970 CAGGGGGTACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
*
345990 CAGGGGGTACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
*
346010 CAGGGGGAACAGATTCCCTCC
1 CAGGGGGTACAGATTCCC-CC
*
346031 CAGGGGGTACCGATT
1 CAGGGGGTACAGATT
346046 ATCCCATGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 35 0.70
21 15 0.30
ACGTcount: A:0.20, C:0.33, G:0.32, T:0.16
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:346446 original size:34 final size:32
Alignment explanation
Indices: 346401--346470 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
346391 TTTTATAAAG
*
346401 GGGAAAAGTTCTAGCTTAGCCCGTGTAAAATCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
346435 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
346467 GGGA
1 GGGA
346471 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:347481 original size:3 final size:3
Alignment explanation
Indices: 347461--347506 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
347451 TAAAGAAAGG
*
347461 GAA G-A GAA GAA -AA CAA GAA GAA GAA GAA GAA -ATA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA
347504 GAA
1 GAA
347507 TGAGGACGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 5 0.13
3 32 0.84
4 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:347785 original size:18 final size:18
Alignment explanation
Indices: 347762--347809 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
347752 CATCTTGGAG
347762 TGATGAAGATGATTCCAA
1 TGATGAAGATGATTCCAA
347780 TGATGAAGATGATTCCAA
1 TGATGAAGATGATTCCAA
347798 TGATGAAGATGA
1 TGATGAAGATGA
347810 AGTAGTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (18 bp):
TGATGAAGATGATTCCAA
Found at i:349490 original size:21 final size:21
Alignment explanation
Indices: 349464--349525 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
349454 TCAAATTATT
349464 CAGGGGGTACAGATTCCCCCC
1 CAGGGGGTACAGATTCCCCCC
*
349485 CAGGGGATACAGATT-CCCCC
1 CAGGGGGTACAGATTCCCCCC
349505 CAGGGGGTATC-GATTCCCCCC
1 CAGGGGGTA-CAGATTCCCCCC
349526 TGTCTAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.16
Consensus pattern (21 bp):
CAGGGGGTACAGATTCCCCCC
Found at i:349503 original size:20 final size:20
Alignment explanation
Indices: 349464--349525 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 20
349454 TCAAATTATT
349464 CAGGGGGTACAGATTCCCCCC
1 CAGGGGGTACAGATT-CCCCC
*
349485 CAGGGGATACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
349505 CAGGGGGTATC-GATTCCCCC
1 CAGGGGGTA-CAGATTCCCCC
349525 C
1 C
349526 TGTCTAACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.16
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:350763 original size:14 final size:14
Alignment explanation
Indices: 350741--350786 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
350731 GTGATTCCTA
*
350741 ATATTCATATATAT
1 ATATACATATATAT
350755 ATATACATAT-TAT
1 ATATACATATATAT
*
350768 AATAAACATATAT-T
1 -ATATACATATATAT
350782 ATATA
1 ATATA
350787 TTTTATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.26
14 19 0.70
15 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATACATATATAT
Found at i:351957 original size:2 final size:2
Alignment explanation
Indices: 351950--351986 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
351940 ATTTAACATT
351950 TA TA TA 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
351987 TCTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:356806 original size:54 final size:54
Alignment explanation
Indices: 356743--356848 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
356733 TTAATAATTA
* *
356743 TAAGATTATATATGTTCAGAACTTTATTAATCTATTGATAACGCATACACATCT
1 TAAGATTATATATATTCAAAACTTTATTAATCTATTGATAACGCATACACATCT
356797 TAAGATTATATATATTCAAAACTTTATTAATCTATTGATAACGCATACACAT
1 TAAGATTATATATATTCAAAACTTTATTAATCTATTGATAACGCATACACAT
356849 TTTACCTACG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (54 bp):
TAAGATTATATATATTCAAAACTTTATTAATCTATTGATAACGCATACACATCT
Found at i:374930 original size:15 final size:14
Alignment explanation
Indices: 374890--374931 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
374880 TGCTTTTTGG
374890 CTTTT-TCTTTTTT
1 CTTTTCTCTTTTTT
* *
374903 CTTTTGTCCTTTTT
1 CTTTTCTCTTTTTT
374917 CTTCTTCTCTTTTTT
1 CTT-TTCTCTTTTTT
374932 TTGAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.21
14 10 0.42
15 9 0.38
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
CTTTTCTCTTTTTT
Found at i:383649 original size:16 final size:16
Alignment explanation
Indices: 383630--383667 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
383620 ATAATTACTG
383630 ATATATGTA-AAATATA
1 ATATATGTATAAA-ATA
383646 ATATATGTATAAAATA
1 ATATATGTATAAAATA
*
383662 AAATAT
1 ATATAT
383668 CACATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (16 bp):
ATATATGTATAAAATA
Found at i:386439 original size:41 final size:41
Alignment explanation
Indices: 386394--386575 Score: 271
Period size: 41 Copynumber: 4.5 Consensus size: 41
386384 ATTCGCGCTG
* * *
386394 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGGTTTTT
1 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
* *
386435 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGGTTTT-
1 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
386475 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
*
386516 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
386557 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
386576 TTTAAAAATG
Statistics
Matches: 133, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
40 39 0.29
41 93 0.70
42 1 0.01
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
Found at i:386507 original size:81 final size:82
Alignment explanation
Indices: 386394--386576 Score: 291
Period size: 81 Copynumber: 2.2 Consensus size: 82
386384 ATTCGCGCTG
* *
386394 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTTCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
386459 GTGTCGTTGCGGTTTT-
66 GTGTCGTTGCGATTTTC
*
386475 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTA
386538 CAGTGTCGTTGCGATTTTC
64 CAGTGTCGTTGCGATTTTC
386557 CATTTCGCGTTGCGATAGTT
1 CATTTCGCGTTGCGATAGTT
386577 TTAAAAATGG
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
80 1 0.01
81 74 0.78
82 20 0.21
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.39
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTGTCGTTGCGATTTTC
Found at i:386528 original size:20 final size:20
Alignment explanation
Indices: 386503--386572 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
386493 TCTACAATGT
386503 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
386523 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
386543 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
386564 CGTTGCGAT
1 CGTTGCGAT
386573 AGTTTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:387528 original size:20 final size:20
Alignment explanation
Indices: 387503--387657 Score: 80
Period size: 20 Copynumber: 7.6 Consensus size: 20
387493 TTTTAAAACT
387503 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
387523 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
387544 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
387564 ACCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
* *
387585 ATCGCAACGTGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
387605 ACCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
* *
387626 ATTGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
387646 ATCGCAACGCGA
1 ATCGCAACGCGA
387658 TTTTCAACTA
Statistics
Matches: 94, Mismatches: 34, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
18 3 0.03
19 3 0.03
20 47 0.50
21 35 0.37
22 3 0.03
23 3 0.03
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:387557 original size:41 final size:41
Alignment explanation
Indices: 387499--387682 Score: 255
Period size: 41 Copynumber: 4.5 Consensus size: 41
387489 CCATTTTTAA
* * *
387499 AACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-
1 AACTATCGCAACGCGAAATGGAAAACCGCAACG-CGATTTTC
387539 AGACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
1 A-ACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
* *
387581 AACTATCGCAACGTGAAATGAAAAACCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
* * *
387622 AACTATTGCAACGCGAAATAGAAAATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
*
387663 AACTATCGCAACGTGAAATG
1 AACTATCGCAACGCGAAATG
387683 CAGCGCGAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 2 0.02
41 125 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
AACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
Found at i:387592 original size:21 final size:21
Alignment explanation
Indices: 387566--387675 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
387556 AATGGAAAAC
387566 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
* ** * ** *
387587 CGCAACGTGA-AATGAAAAAC
1 CGCAACGCGATTTTCAACTAT
387607 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
* ** ** *
387628 TGCAACGCGAAATAGAA-AAT
1 CGCAACGCGATTTTCAACTAT
387648 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
387669 CGCAACG
1 CGCAACG
387676 TGAAATGCAG
Statistics
Matches: 61, Mismatches: 26, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 27 0.44
21 34 0.56
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:388623 original size:29 final size:29
Alignment explanation
Indices: 388566--388649 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
388556 ACATGCCTTT
* *
388566 ATTGATTTAATTTCTCAA-TCCAATGACTTA
1 ATTGATTTAA-TTCTCAATTTC-ATAACTTA
* *
388596 ATTGGTTTAATTTTCAATTTCATAACTTA
1 ATTGATTTAATTCTCAATTTCATAACTTA
*
388625 ATTGATTTAATTCTCAATTTGATAA
1 ATTGATTTAATTCTCAATTTCATAA
388650 TTTTACAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 35 0.76
30 11 0.24
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (29 bp):
ATTGATTTAATTCTCAATTTCATAACTTA
Found at i:393952 original size:13 final size:13
Alignment explanation
Indices: 393934--393964 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
393924 ATATGGTTAT
393934 ATAAGAATAGGAA
1 ATAAGAATAGGAA
393947 ATAAGAATAGGAA
1 ATAAGAATAGGAA
393960 ATAAG
1 ATAAG
393965 TTATGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (13 bp):
ATAAGAATAGGAA
Found at i:397591 original size:20 final size:20
Alignment explanation
Indices: 397553--397611 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
397543 CAGTACCGCA
*
397553 GGGGGGTATCGATTCCC-CTGT
1 GGGGGG-ATCGATTCCCTC-AT
*
397574 GGGGGGAATCGGTTCCCTCAT
1 GGGGGG-ATCGATTCCCTCAT
397595 GGGGGGATCGATTCCCT
1 GGGGGGATCGATTCCCT
397612 ATGCACCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 10 0.30
21 22 0.67
22 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:403404 original size:21 final size:21
Alignment explanation
Indices: 403378--403432 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
403368 CGTTATACAA
403378 GGGGGGAATCGGTACCCCCTC
1 GGGGGGAATCGGTACCCCCTC
*
403399 GGGGGGAATCGGTACCCCCTT
1 GGGGGGAATCGGTACCCCCTC
403420 GGGGGGAATCGGT
1 GGGGGGAATCGGT
403433 TCCCTCCGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.44, T:0.16
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTC
Found at i:417991 original size:47 final size:48
Alignment explanation
Indices: 417906--418009 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
417896 TACATATTGA
* *
417906 TAAAAATTTAATTTTAAATTATCTAAAATTCTAATAAAAAT-AAGCCTT
1 TAAAATTTTAATTTTAAATTATCTAAAAATCTAATAAAAATGAA-CCTT
*
417954 TAAAATTTTAATTTTAAATTATCTAAAAAT-TGATAAAAATGAACCTT
1 TAAAATTTTAATTTTAAATTATCTAAAAATCTAATAAAAATGAACCTT
418001 TAAAATTTT
1 TAAAATTTT
418010 TTATTCATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 22 0.42
48 30 0.58
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (48 bp):
TAAAATTTTAATTTTAAATTATCTAAAAATCTAATAAAAATGAACCTT
Found at i:419928 original size:43 final size:40
Alignment explanation
Indices: 419839--419981 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
419829 AATTAGGGGT
* * * *
419839 CTCAATTTTAAAGGTAAAAAGTGA-ATTA-AAAATTTGAGGC
1 CTCAATTATAAATGTAAAAAGTGAGATGACAAAA-TT-AAGC
419879 CTCAATTATAAATGTAAAAAGTGAGACTGACAAAATTAATGATC
1 CTCAATTATAAATGTAAAAAGTGAGA-TGACAAAATTAA-G--C
* *
419923 C-CAATTATAAA-GATAAAAAGTGTGATTACAAAATTAAGC
1 CTCAATTATAAATG-TAAAAAGTGAGATGACAAAATTAAGC
*
419962 CTCAATTATAAATATAAAAA
1 CTCAATTATAAATGTAAAAA
419982 ATAAAATTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
39 2 0.02
40 38 0.44
41 3 0.03
42 17 0.20
43 25 0.29
44 2 0.02
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (40 bp):
CTCAATTATAAATGTAAAAAGTGAGATGACAAAATTAAGC
Found at i:419979 original size:40 final size:42
Alignment explanation
Indices: 419877--419981 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
419867 AAAATTTGAG
*
419877 GCCTCAATTATAAATGTAAAAAGTGAGACTGACAAAATTAAT
1 GCCTCAATTATAAATATAAAAAGTGAGACTGACAAAATTAAT
* * *
419919 GATCC-CAATTATAAAGATAAAAAGTGTGA-TTACAAAATTAA-
1 G--CCTCAATTATAAATATAAAAAGTGAGACTGACAAAATTAAT
419960 GCCTCAATTATAAATATAAAAA
1 GCCTCAATTATAAATATAAAAA
419982 ATAAAATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
39 2 0.04
40 17 0.31
41 1 0.02
42 12 0.22
43 21 0.38
44 2 0.04
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (42 bp):
GCCTCAATTATAAATATAAAAAGTGAGACTGACAAAATTAAT
Found at i:422486 original size:22 final size:22
Alignment explanation
Indices: 422443--422488 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
422433 AATTTAATAT
*
422443 TTTAATAATTAGATAATAATGG
1 TTTAATAATTAGAAAATAATGG
*
422465 TTTAATATATTA-AAAATTATGG
1 TTTAATA-ATTAGAAAATAATGG
422487 TT
1 TT
422489 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
TTTAATAATTAGAAAATAATGG
Found at i:436581 original size:19 final size:19
Alignment explanation
Indices: 436549--436599 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
436539 AGAAGTATAA
*
436549 TTATATTT--TAATATTTG
1 TTATATTTAATAATATTAG
436566 TTATATTTAATAATATTAG
1 TTATATTTAATAATATTAG
*
436585 TTATAATTACATAAT
1 TTATATTTA-ATAAT
436600 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
19 16 0.55
20 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (19 bp):
TTATATTTAATAATATTAG
Found at i:439258 original size:17 final size:16
Alignment explanation
Indices: 439236--439271 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
439226 AATGATTAAA
439236 AAATAATATGATCGGTT
1 AAATAA-ATGATCGGTT
*
439253 AAATAAGTGATCGGTT
1 AAATAAATGATCGGTT
439269 AAA
1 AAA
439272 ATTTAGATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
AAATAAATGATCGGTT
Found at i:439360 original size:23 final size:23
Alignment explanation
Indices: 439334--439380 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
439324 AACATATTAA
*
439334 GTAGCGCTTATATAATATAATAG
1 GTAGCGCTTATATAATAAAATAG
439357 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
439380 G
1 G
439381 CATTTAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:439442 original size:87 final size:87
Alignment explanation
Indices: 439294--439456 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
439284 TATGTTATAT
* *
439294 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAAGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAAGTAGCGCTTATATAATATAATAGGT
*
439359 AGCGCTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* * *
439381 CATTTAACCAGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAAGTAGCGCTTATATAATATAATAGGT
439446 AGCACTTATAT
66 AGCACTTATAT
439457 TGACATATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAAGTAGCGCTTATATAATATAATAGGT
AGCACTTATATAATAAAATAGG
Found at i:439957 original size:199 final size:195
Alignment explanation
Indices: 439451--439970 Score: 530
Period size: 198 Copynumber: 2.6 Consensus size: 195
439441 TAGGTAGCAC
* * * * * *
439451 TTATATTGACATATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTATAAATTGACCTAT
1 TTATGTTGACCTA-TTTCTCAT-AAACCGGTATATTT-TACCGGTTACATTGTAAATTTACCTAT
* * *
439516 TACATTAT-GTATATCGGTTTCGAT-ATTTTCGGGATCGATACAATTTT-AAATGTATCGACATT
63 TACATTATAAT-TATCGGTTTCGATGATTTT-GGGATCGATAC-TTTTTAAAATGTATCGACACT
* * * * * * *
439578 TTATGCGTGCAACTCGTTTGTGCTTTATTTTGTAAAAAAGTATCGACACATATTTAAAGAGTGTC
125 TTATGCATACAACTCGTTTGTCCTTCATTTTGTAAAAAAGTATCGACACAAATTAAAAAAGTGTC
439643 GATACA
190 GATACA
* * * * * * * * * *
439649 TAATGTAGATCTATTTGCTAATTAATCAGTATATTTTAACCAGTTACATTGTAAATTTACATGTT
1 TTATGTTGACCTATTT-CTCATAAACCGGTATATTTT-ACCGGTTACATTGTAAATTTACCTATT
* * *
439714 ACATAATAATTATCGATTTCGATG-TTTCGAGGATCGATACTTTTTACAAATGTATCGACACTTT
64 ACATTATAATTATCGGTTTCGATGATTTTG-GGATCGATACTTTTTA-AAATGTATCGACACTTT
*
439778 ATGCATACACCTCGTTTG-CCATTCATTTTG-AAAAAATGTATCGACACAAATTAAAAAAGTGTC
127 ATGCATACAACTCGTTTGTCC-TTCATTTTGTAAAAAA-GTATCGACACAAATTAAAAAAGTGTC
*
439841 GATACT
190 GATACA
* *
439847 TTATGTTGACCTATTCTCTCATGAACCCGGTATATTTCTACCGGTTACATTGGAAATTTACCTAT
1 TTATGTTGACCTATT-TCTCAT-AAACCGGTATATTT-TACCGGTTACATTGTAAATTTACCTAT
* **
439912 TACATTATAATTATCGGTCTCTTTGATTTTGGGATCGATACTTTTTATAAATGTATCGA
63 TACATTATAATTATCGGTTTCGATGATTTTGGGATCGATACTTTTTA-AAATGTATCGA
439971 TACAAATCTA
Statistics
Matches: 259, Mismatches: 50, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
196 5 0.02
197 73 0.28
198 96 0.37
199 80 0.31
200 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (195 bp):
TTATGTTGACCTATTTCTCATAAACCGGTATATTTTACCGGTTACATTGTAAATTTACCTATTAC
ATTATAATTATCGGTTTCGATGATTTTGGGATCGATACTTTTTAAAATGTATCGACACTTTATGC
ATACAACTCGTTTGTCCTTCATTTTGTAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACA
Found at i:442188 original size:182 final size:182
Alignment explanation
Indices: 441881--442268 Score: 607
Period size: 182 Copynumber: 2.1 Consensus size: 182
441871 ATGAATGTCA
* * * * *
441881 ATATTGCTATGGATCGATACATTTGTATAAAGTATCGACATTTTTTAGGCGCTATTACTTCTTCT
1 ATATTGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGACACTATAACTTCTTCT
*
441946 CTTTTAAATTACGAAAGTGTCGATACTTATATTAATGTATCGACACTTTCAATATATCCGGTAGC
66 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATGTATCGACACTTTCAATATATCCGGTAGC
* * * * * *
442011 CTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCATATTATTACTTGTT
131 CGTTTACCGGTTTTATCATAAT-GACACCAGTTTTATCATATTATTACCTGTT
442063 ATATTGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGACACTATAACTTCTTCT
1 ATATTGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGACACTATAACTTCTTCT
*
442128 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGC
66 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATGTATCGACACTTTCAATATATCCGGTAGC
* *
442193 GGTTTACCGGTTTTATCATAATGACACCAGTTTTATCATATTTTTACCTGTT
131 CGTTTACCGGTTTTATCATAATGACACCAGTTTTATCATATTATTACCTGTT
* *
442245 ATATTACTATAGATCGATATATTT
1 ATATTGCTATGGATCGATATATTT
442269 TTCATTTGTA
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 187 0.99
183 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
ATATTGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGACACTATAACTTCTTCT
CTTTTAAATTACAAAAGTGTCGATACTTATATTAATGTATCGACACTTTCAATATATCCGGTAGC
CGTTTACCGGTTTTATCATAATGACACCAGTTTTATCATATTATTACCTGTT
Found at i:443267 original size:2 final size:2
Alignment explanation
Indices: 443260--443295 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
443250 ACAAGAGTAA
443260 CT CT CT 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 CT CT CT
443296 TTTGACGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:444073 original size:14 final size:15
Alignment explanation
Indices: 444050--444082 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
444040 TTATATTTAA
444050 ATTTTAAAG-AAAAT
1 ATTTTAAAGAAAAAT
*
444064 ATTTTTAAGAAAAAT
1 ATTTTAAAGAAAAAT
444079 ATTT
1 ATTT
444083 AAAAATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTTTAAAGAAAAAT
Found at i:450346 original size:35 final size:33
Alignment explanation
Indices: 450307--450384 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
450297 CTTGTATCGT
450307 TCCTTATCATATACTTAATT-TTTTTCCTGTACCAA
1 TCCTT-TCATATA-TT-ATTCTTTTTCCTGTACCAA
* *
450342 TCCTTTCACTATATTATTCTTTTTCCTGTATCAT
1 TCCTTTCA-TATATTATTCTTTTTCCTGTACCAA
450376 TCCTTTCAT
1 TCCTTTCAT
450385 TGTACTGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
33 4 0.10
34 26 0.67
35 9 0.23
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (33 bp):
TCCTTTCATATATTATTCTTTTTCCTGTACCAA
Found at i:450430 original size:16 final size:17
Alignment explanation
Indices: 450401--450432 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
450391 GTTCCTTTTT
450401 CTGTATTGATTTCTTTA
1 CTGTATTGATTTCTTTA
450418 CTGTATT-ATTTCTTT
1 CTGTATTGATTTCTTT
450433 TATTACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (17 bp):
CTGTATTGATTTCTTTA
Found at i:450434 original size:17 final size:17
Alignment explanation
Indices: 450395--450472 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
450385 TGTACTGTTC
*
450395 CTTTTTCTGTATTGATTT
1 CTTTTACTGTATT-ATTT
450413 C-TTTACTGTATTATTT
1 CTTTTACTGTATTATTT
* **
450429 CTTTTATTACATTATTT
1 CTTTTACTGTATTATTT
* * * *
450446 CTCTTATTGTATTGTAT
1 CTTTTACTGTATTATTT
450463 CTTTTACTGT
1 CTTTTACTGT
450473 TTTGTATCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 5 0.10
17 42 0.88
18 1 0.02
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.63
Consensus pattern (17 bp):
CTTTTACTGTATTATTT
Found at i:450683 original size:65 final size:65
Alignment explanation
Indices: 450603--451311 Score: 997
Period size: 65 Copynumber: 10.9 Consensus size: 65
450593 ATCTTTGCAA
* * *
450603 TATTCAATTATCACTCCACCTTATGCACCACAAAGGTACATGAGTCATATGATTGATATGTATTA
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * *
450668 TATTCAATTATCACTCCACCTCATGCACCATAAAGATACATGAGTCATATGAGTGGTATGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * * * * *
450733 TATACAATTATCACTACACATCATGCACCACAAAGATACATGAGTCATATGAGTGATCTGTACTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
*
450798 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGACTGATATGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * * *
450863 TATTCAATTATCACTTCACATCATGCACTACAAAGGTACATGAGTCATATGAGTGATATGTAATG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * * * * * * *
450928 TATACAATTATCACTCTACATCTTGCACCACAAATGTACATGAGTCATTTAAGTGATTTGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * *
450993 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTA
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * *
451058 TATTCAATTATCACTCCACCCCATGCACCACAAAGGTACACGAGTCATATGAGTGATCTGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* ** * *
451123 TATTCAATTATCACTTCACCTCATGCATGACAAAGGTACATGAGTCATATGAGTAATATGTACTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* * *
451188 TATTCAATTATCACTCCACAC-CATGCACCACAAAGGTATATGAGTCATATGAGTGATCTATATT
1 TATTCAATTATCACTCCAC-CTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
451252 G
65 G
* * * * * *
451253 TATGCAATTATCACTTCACCCCGTGCACCACAAATGTACATGAGTCATATGAGTAATAT
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATAT
451312 ATACTTGTTC
Statistics
Matches: 570, Mismatches: 72, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
64 1 0.00
65 568 1.00
66 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (65 bp):
TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
Found at i:454430 original size:34 final size:33
Alignment explanation
Indices: 454392--454501 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 33
454382 AAACCCTAAT
*
454392 TTGATTGAAAGTAGAAAGTTTATTCCATTTTATG
1 TTGATTGAAAGTAGAAAGTCTATT-CATTTTATG
*
454426 TTGATTGAAAGTCAG-AAGTCTATTCTTTTTTATG
1 TTGATTGAAAGT-AGAAAGTCTATTC-ATTTTATG
454460 TTGATTGAAAGTAGAAAGTCTATT-ATTTTATG
1 TTGATTGAAAGTAGAAAGTCTATTCATTTTATG
454492 TTGATTGAAA
1 TTGATTGAAA
454502 ATAATAAAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
32 17 0.24
33 3 0.04
34 48 0.69
35 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGATTGAAAGTAGAAAGTCTATTCATTTTATG
Found at i:461163 original size:3 final size:3
Alignment explanation
Indices: 461157--461184 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
461147 TTTTCATTTC
461157 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
461185 AATAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:462605 original size:19 final size:18
Alignment explanation
Indices: 462581--462679 Score: 59
Period size: 19 Copynumber: 5.6 Consensus size: 18
462571 GAATTTAATC
462581 ATAAATATATATAATTTTA
1 ATAAATA-ATATAATTTTA
462600 ATAAATAATAT-ATTTT-
1 ATAAATAATATAATTTTA
* *
462616 -TACATGAT-T-ATTTTA
1 ATAAATAATATAATTTTA
* *
462631 ATATATTATTATTAATATTTAA
1 ATA-AATAATA-TAAT-TTT-A
*
462653 ATACAT-ATATAATTTT-
1 ATAAATAATATAATTTTA
462669 ATAAATAATAT
1 ATAAATAATAT
462680 TTATTTATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 6 0.10
15 6 0.10
16 7 0.11
17 11 0.18
18 7 0.11
19 12 0.20
20 4 0.07
21 4 0.07
22 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (18 bp):
ATAAATAATATAATTTTA
Found at i:462616 original size:18 final size:19
Alignment explanation
Indices: 462581--462617 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
462571 GAATTTAATC
462581 ATAAATATATATAATTTTA
1 ATAAATATATATAATTTTA
*
462600 ATAAATA-ATATATTTTTA
1 ATAAATATATATAATTTTA
462618 CATGATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAATATATATAATTTTA
Found at i:463486 original size:29 final size:27
Alignment explanation
Indices: 463454--463512 Score: 57
Period size: 27 Copynumber: 2.1 Consensus size: 27
463444 TAATTATTTC
* *
463454 TTTTCAAAATTTTTATATATACT-TATTA
1 TTTTTAAAATATTT-TATATA-TATATTA
* *
463482 TTTTTATAATATTTTATATGTATATTA
1 TTTTTAAAATATTTTATATATATATTA
463509 TTTT
1 TTTT
463513 ATTAATGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 14 0.54
28 11 0.42
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTAAAATATTTTATATATATATTA
Found at i:466703 original size:15 final size:15
Alignment explanation
Indices: 466683--466714 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
466673 GATCAATACC
466683 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
466698 TTTTGCATACATTCA
1 TTTTGCATACATGCA
466713 TT
1 TT
466715 ATTTATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:474046 original size:14 final size:14
Alignment explanation
Indices: 474023--474073 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
474013 ATTATGCTTG
474023 AAGAAGAAAAAATGA
1 AAGAA-AAAAAATGA
474038 AAGAAAAAAAA-GA
1 AAGAAAAAAAATGA
*
474051 AA-AGAAAAAATG-
1 AAGAAAAAAAATGA
*
474063 ATGAAAAAAAA
1 AAGAAAAAAAA
474074 ATTAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 8 0.26
13 12 0.39
14 6 0.19
15 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (14 bp):
AAGAAAAAAAATGA
Found at i:474460 original size:18 final size:18
Alignment explanation
Indices: 474437--474471 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
474427 CAAGTTTATC
474437 TTTTTGAAATTAAATTTA
1 TTTTTGAAATTAAATTTA
*
474455 TTTTTGAAATTCAATTT
1 TTTTTGAAATTAAATTT
474472 GTTTCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTAAATTTA
Found at i:475824 original size:112 final size:111
Alignment explanation
Indices: 475627--476159 Score: 593
Period size: 112 Copynumber: 4.7 Consensus size: 111
475617 TTAGCAAGAT
* * *
475627 TTGAATCCATCACTCAATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCACTCGATGAATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGA
*
475692 AGAAGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
475739 TTGAATCCATCATTCGATGAATCAACATTTCCA-AAAGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCACTCGATGAATCAACATTTCCAGAAA-AGTTCATAATGAGAAGAACTCATCTGA
**
475803 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCAC
65 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*** * * * * * *
475851 CCAAATTCATCACTCTAGGGATCAATATTTCCAG-AAAGTTCATAATGAGAAGAACTTATCTGAA
1 TTGAATCCATCACTCGATGAATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAA
* **
475915 GAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGC
66 GAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * *
475961 ATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAATTTCATAATAAGAAG
1 TTGAATCCATCAC---------TCGAT--GAATCAACATTTCCAGA-AAAGTTCATAATGAGAAG
* *
476026 AACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGC
54 AACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
476085 TCGAATTCATCATTCGATGAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCACTCGATGAATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGA
476150 AGAAGAAGAA
65 AGAAGAAGAA
476160 TTTGTTCAAC
Statistics
Matches: 353, Mismatches: 51, Indels: 34
0.81 0.12 0.08
Matches are distributed among these distances:
110 47 0.13
111 61 0.17
112 102 0.29
113 47 0.13
115 4 0.01
119 2 0.01
121 13 0.04
123 29 0.08
124 48 0.14
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (111 bp):
TTGAATCCATCACTCGATGAATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:476036 original size:234 final size:222
Alignment explanation
Indices: 475634--476159 Score: 624
Period size: 234 Copynumber: 2.3 Consensus size: 222
475624 GATTTGAATC
*
475634 CATCACTCAATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 CATCACTCAATGGATCAATATTTCCAGA-A-AGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* * * *
475699 GAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTCGATGAATCAA
64 GAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATCCAGCAATAGATGAATCAA
*
475764 CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
129 CATTTCCAAAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
475829 AAGAACTTGTTCAACCTTTCACCCAAATT
194 AAGAACTTGTTCAACCTTTCACCCAAATT
* * * *
475858 CATCACTCTAGGGATCAATATTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
1 CATCACTCAATGGATCAATATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
* ** *
475923 AGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGAT
66 AAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGA----ATC-C---AGCA-ATAGAT
* * * *
475988 CAGCATCAACTTTTCCAGAGAA-ATTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAG
122 --GAATCAACATTTCCA-A-AAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * ** * *
476052 TTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCGAATT
183 TTCATAATGAGAAGAACTTGTTCAACCTTTCACCCAAATT
* * * *
476092 CATCATTCGATGAATTAACT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 CATCACTCAATGGATCAA-TATTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
476156 AGAA
63 AGAA
476160 TTTGTTCAAC
Statistics
Matches: 255, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
222 72 0.28
223 1 0.00
224 25 0.10
226 3 0.01
227 1 0.00
230 2 0.01
231 4 0.02
233 13 0.05
234 92 0.36
235 3 0.01
236 39 0.15
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (222 bp):
CATCACTCAATGGATCAATATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
AAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATCCAGCAATAGATGAATCAACA
TTTCCAAAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTCACCCAAATT
Found at i:476489 original size:3 final size:3
Alignment explanation
Indices: 476483--476529 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
476473 TTTTCATTTA
476483 ATT ATT ATT ATT ATT ATT GATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
476529 A
1 A
476530 CTAAATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:477970 original size:19 final size:17
Alignment explanation
Indices: 477946--477981 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
477936 GAATTTAATC
477946 ATAAATATATATAATTTTA
1 ATAAATA-ATAT-ATTTTA
477965 ATAAATAATATATTTTA
1 ATAAATAATATATTTTA
477982 CATGATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATAATATATTTTA
Found at i:481363 original size:20 final size:20
Alignment explanation
Indices: 481338--481375 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
481328 ATTAAAGAGT
481338 GTTAAAGTCAAAATTGGTGG
1 GTTAAAGTCAAAATTGGTGG
481358 GTTAAAGTCAAAATTGGT
1 GTTAAAGTCAAAATTGGT
481376 AACAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTAAAGTCAAAATTGGTGG
Found at i:494899 original size:20 final size:20
Alignment explanation
Indices: 494874--494912 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
494864 AATAATGAAA
494874 AGATAATTCCTAAAAATAAG
1 AGATAATTCCTAAAAATAAG
*
494894 AGATAATTCCTAAAGATAA
1 AGATAATTCCTAAAAATAA
494913 TTCTTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (20 bp):
AGATAATTCCTAAAAATAAG
Found at i:505672 original size:24 final size:24
Alignment explanation
Indices: 505625--505673 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
505615 TGGATTCACC
* * *
505625 TGAACTTGATTCTGAATTTTATTA
1 TGAACTCGATTCTGAATCTAATTA
*
505649 TGAACTCGATTCTGGATCTAATTA
1 TGAACTCGATTCTGAATCTAATTA
505673 T
1 T
505674 TGTTGTCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (24 bp):
TGAACTCGATTCTGAATCTAATTA
Found at i:506955 original size:27 final size:27
Alignment explanation
Indices: 506916--506991 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
506906 TTCCAGAAGG
* *
506916 TGCTGACTAGATCTTCTAGAAAACTAC
1 TGCTAACTGGATCTTCTAGAAAACTAC
* *
506943 TGCTAACTGGATCTTTTAGAAAACTGC
1 TGCTAACTGGATCTTCTAGAAAACTAC
* *
506970 TGCTAACTGTACCTTCTAGAAA
1 TGCTAACTGGATCTTCTAGAAA
506992 CTTTTACATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (27 bp):
TGCTAACTGGATCTTCTAGAAAACTAC
Done.