Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:265220 original size:399 final size:400
Alignment explanation
Indices: 263944--265529 Score: 2883
Period size: 399 Copynumber: 4.0 Consensus size: 400
263934 AATTTACAAT
*
263944 ATGGCAAACAGGGTGAAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
264009 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGTATACCTGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
* *
264074 ATGAGAGAATATGTGTAATATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
264139 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGA
*
264204 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAAT-TAACCGGTATAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCA
264268 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
326 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
264333 TCCAGAATGA
391 TCCAGAATGA
264343 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
264408 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
264473 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGATCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
264538 AATGAATGGCAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTAGATCCCA-
196 AATGAATGGC-AAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAG
*
264602 AAACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACC
260 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACC
*
264667 AGATTTATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATTG
325 AGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTG
264732 GTCCAGAATGA
390 GTCCAGAATGA
* *
264743 ATGGCAAACAGGGTGCAACTATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* * *
264808 TGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCAGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
264873 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
* *
264938 AATGAATTGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGA
* * *
265003 AACATTGAAACCCATAAATATAATGTAATAGGTAATTTTTTAATCTAACCGGTATAAGTATACC-
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCA
265067 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
326 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
265132 TCCAGAATGA
391 TCCAGAATGA
* *
265142 ATGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* * *
265207 TGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACTGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
265272 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
265337 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGA
265402 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATA-CA
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCA
*
265466 GGATTTATGAGAGAATAGATGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
326 -GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
265530 TTTAAATATC
Statistics
Matches: 1143, Mismatches: 39, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
398 1 0.00
399 677 0.59
400 465 0.41
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGA
AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCA
GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
TCCAGAATGA
Found at i:265481 original size:799 final size:799
Alignment explanation
Indices: 263944--265529 Score: 2899
Period size: 799 Copynumber: 2.0 Consensus size: 799
263934 AATTTACAAT
*
263944 ATGGCAAACAGGGTGAAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGAAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
* *
264009 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGTATACCTGATTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATATAACCGGTATAAGTATACCAGATTT
* *
264074 ATGAGAGAATATGTGTAATATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
* *
264139 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCAGA
*
264204 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATTAACCGGTATAAGTATACCGG
261 AACATCGAAACCCATAAATATAATGTAATAGGTAATTTTTCAATTAACCGGTATAAGTATACCGG
264269 ATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGT
326 ATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGT
* *
264334 CCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCC
391 CCAGAATGAATGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCC
264399 CAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTAT
456 CAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTAT
264464 ACCGGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
521 ACCGGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
264529 TTGATCCAGAATGAATGGCAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGT
586 TTGATCCAGAATGAATGGCAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGT
264594 AGATCCCAAAACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATA
651 AGATCCCAAAACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATA
*
264659 AGTATACCAGATTTATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGA
716 AGTATACCAGATTTATGAGAGAATAGATGTAATATATGTATCAACACTTTTTAATTTTGTGTCGA
264724 TACTATTGGTCCAGAATGA
781 TACTATTGGTCCAGAATGA
* *
264743 ATGGCAAACAGGGTGCAACTATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGAAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
* *
264808 TGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCAGATTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATATAACCGGTATAAGTATACCAGATTT
264873 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
264938 AATGAATTGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCAGA
* *
265003 AACATTGAAACCCATAAATATAATGTAATAGGTAATTTTTTAATCTAACCGGTATAAGTATACC-
261 AACATCGAAACCCATAAATATAATGTAATAGGTAATTTTTCAAT-TAACCGGTATAAGTATACCG
265067 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
325 GATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
265132 TCCAGAATGAATGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATC
390 TCCAGAATGAATGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATC
* * *
265197 CCAGAAACATTGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACTGGTATAAGTA
455 CCAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTA
265262 TACCGGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACT
520 TACCGGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACT
*
265327 ATTGGTCCAGAATGAATGGC-AAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTG
585 ATTGATCCAGAATGAATGGCAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTG
* *
265391 TCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTA
650 TAGATCCCA-AAACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTA
*
265456 TAAGTATA-CAGGATTTATGAGAGAATAGATGTAATATATGTATCGACACTTTTTAATTTTGTGT
714 TAAGTATACCA-GATTTATGAGAGAATAGATGTAATATATGTATCAACACTTTTTAATTTTGTGT
265520 CGATACTATT
778 CGATACTATT
265530 TTTAAATATC
Statistics
Matches: 759, Mismatches: 25, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
798 54 0.07
799 686 0.90
800 19 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (799 bp):
ATGGCAAACAGGGTGAAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATATAACCGGTATAAGTATACCAGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGAATGGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCAGA
AACATCGAAACCCATAAATATAATGTAATAGGTAATTTTTCAATTAACCGGTATAAGTATACCGG
ATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGT
CCAGAATGAATGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCC
CAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTAT
ACCGGATTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
TTGATCCAGAATGAATGGCAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGT
AGATCCCAAAACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATA
AGTATACCAGATTTATGAGAGAATAGATGTAATATATGTATCAACACTTTTTAATTTTGTGTCGA
TACTATTGGTCCAGAATGA
Found at i:269507 original size:20 final size:21
Alignment explanation
Indices: 269482--269536 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
269472 CGCGTGATAT
*
269482 AATCGC-ATGCGAATTAGGAA
1 AATCGCAATGCGAATTACGAA
* *
269502 AATCGCAACGCGAA-TACGTA
1 AATCGCAATGCGAATTACGAA
269522 AATCGCAATGCGAAT
1 AATCGCAATGCGAAT
269537 CTTACTATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (21 bp):
AATCGCAATGCGAATTACGAA
Found at i:270135 original size:19 final size:19
Alignment explanation
Indices: 270111--270155 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
270101 GCAACGAGAG
*
270111 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
270130 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
270149 AATCGCA
1 AATCGCA
270156 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:270173 original size:19 final size:19
Alignment explanation
Indices: 270151--270296 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
270141 GAAACCAAAA
*
270151 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
270170 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
270189 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
270203 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
270222 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
270236 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
270255 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
270275 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
270295 TC
1 TC
270297 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
16 4 0.04
17 5 0.05
19 42 0.41
20 31 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:270211 original size:14 final size:14
Alignment explanation
Indices: 270192--270247 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
270182 TTTCATTTCG
270192 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
270206 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
270225 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
270239 CGTTGCGAT
1 CGTTGCGAT
270248 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:270221 original size:33 final size:33
Alignment explanation
Indices: 270173--270271 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
270163 TTTCATTTCG
**
270173 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
270206 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
270239 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
270272 ATTATCTCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:272462 original size:21 final size:21
Alignment explanation
Indices: 272438--272504 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
272428 TCATTCCTCG
272438 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
272459 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
272480 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
272501 AGAG
1 AGAG
272505 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:272462 original size:42 final size:42
Alignment explanation
Indices: 272386--272504 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
272376 GACTCGCCTG
* * * * * * *
272386 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
272428 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
272470 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
272505 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:273900 original size:14 final size:14
Alignment explanation
Indices: 273858--273894 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
273848 GATTGTTTAA
*
273858 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
273872 GTGATTTGTAAAAT
1 TTGATTTGTAAAAT
273886 TTGATTTGT
1 TTGATTTGT
273895 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:274025 original size:19 final size:18
Alignment explanation
Indices: 274001--274062 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
273991 AAAAAGTACT
274001 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
274020 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
274034 ATCGCAACGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
274053 ATCGC-AGCGA
1 ATCGCAAGCGA
274063 GAGAATCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 1 0.03
17 5 0.15
18 2 0.06
19 15 0.44
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:274048 original size:33 final size:33
Alignment explanation
Indices: 274001--274090 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
273991 AAAAAGTACT
*
274001 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
274034 ATCGCAACGTGAAATGAAAATCGCAGCGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
274067 ATCGTAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
274091 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:274114 original size:19 final size:19
Alignment explanation
Indices: 274092--274150 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
274082 TAAATTCGCG
274092 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
* *
274111 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACA
*
274125 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
274144 TTGCGAT
1 TTGCGAT
274151 AGTAATTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
16 3 0.10
17 3 0.10
19 16 0.52
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:274158 original size:19 final size:20
Alignment explanation
Indices: 274136--274173 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
274126 TGCGATTTTC
274136 ATTTC-GCATTGCGATAGTA
1 ATTTCTGCATTGCGATAGTA
*
274155 ATTTCTGCGTTGCGATAGT
1 ATTTCTGCATTGCGATAGT
274174 CATTAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTCTGCATTGCGATAGTA
Found at i:276457 original size:12 final size:12
Alignment explanation
Indices: 276440--276464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
276430 TCTTCGGGGA
276440 CTTTTTCTTCTT
1 CTTTTTCTTCTT
276452 CTTTTTCTTCTT
1 CTTTTTCTTCTT
276464 C
1 C
276465 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:276673 original size:24 final size:24
Alignment explanation
Indices: 276639--276692 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
276629 CTGAAACATC
*
276639 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
276663 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
276687 ATCAAA
1 ATCAAA
276693 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:277535 original size:20 final size:20
Alignment explanation
Indices: 277444--277527 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
277434 GGGGAAATCA
277444 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
277464 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
** *** *
277484 CAATTCG-AAATGAAAAATTG
1 CAACGCGAAAATG-GCTATCG
277504 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
277524 CAAC
1 CAAC
277528 TAGAAAATTG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 5 0.10
20 40 0.80
21 5 0.10
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATGGCTATCG
Found at i:277578 original size:14 final size:14
Alignment explanation
Indices: 277559--277612 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
277549 GAAAATCGCA
277559 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
277573 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
277590 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
277606 TTGCGAT
1 TTGCGAT
277613 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:277578 original size:33 final size:33
Alignment explanation
Indices: 277541--277611 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
277531 AAAATTGCAA
277541 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
277574 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
277607 TGCGA
1 TGCGA
277612 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:279681 original size:39 final size:35
Alignment explanation
Indices: 279632--279751 Score: 121
Period size: 33 Copynumber: 3.5 Consensus size: 35
279622 ACGAAACTTA
279632 AAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAAAT--C-ATCGCAATGCGAAATG
279670 CAAATCGCAACGAC-AAAATCAT---AATGCGAAATG
1 -AAATCGCAACG-CGAAAATCATCGCAATGCGAAATG
279703 AAAATCGCAA--CGACAAA--ATCGCAATGCGAAATG
1 -AAATCGCAACGCGA-AAATCATCGCAATGCGAAATG
279736 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
279752 CACAAATGGC
Statistics
Matches: 72, Mismatches: 1, Indels: 22
0.76 0.01 0.23
Matches are distributed among these distances:
30 3 0.04
31 1 0.01
32 12 0.17
33 33 0.46
34 3 0.04
36 2 0.03
37 1 0.01
39 16 0.22
40 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (35 bp):
AAATCGCAACGCGAAAATCATCGCAATGCGAAATG
Found at i:279701 original size:33 final size:32
Alignment explanation
Indices: 279658--279746 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 32
279648 ATGGCTATCG
279658 CAATGCGAAATGCAAATCGCAACGACAAAATCA
1 CAATGCGAAATG-AAATCGCAACGACAAAATCA
* *
279691 TAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATG-AAATCGCAACGACAAAATCA
279724 CAATGCGAAATGAAATCGCAACG
1 CAATGCGAAATGAAATCGCAACG
279747 CGAAACACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 11 0.21
33 41 0.79
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
CAATGCGAAATGAAATCGCAACGACAAAATCA
Found at i:279782 original size:19 final size:18
Alignment explanation
Indices: 279760--279854 Score: 80
Period size: 19 Copynumber: 5.6 Consensus size: 18
279750 AACACAAATG
279760 GCATTGCGACTTTCATTTC
1 GCATTGCGA-TTTCATTTC
*
279779 GCATTGCGATTT--TGTC
1 GCATTGCGATTTCATTTC
*
279795 G--TCGCGATTTTCATTTC
1 GCATTGCGA-TTTCATTTC
*
279812 GCATTGCGATTT--TGTC
1 GCATTGCGATTTCATTTC
279828 G--TTGCGATTTTCATTTC
1 GCATTGCGA-TTTCATTTC
279845 GCATTGCGAT
1 GCATTGCGAT
279855 AGCCATTTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 7 0.12
19 20 0.33
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (18 bp):
GCATTGCGATTTCATTTC
Found at i:279812 original size:33 final size:33
Alignment explanation
Indices: 279765--279854 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
279755 AAATGGCATT
*
279765 GCGACTTTCATTTCGCATTGCGATTTTGTCGTC
1 GCGATTTTCATTTCGCATTGCGATTTTGTCGTC
*
279798 GCGATTTTCATTTCGCATTGCGATTTTGTCGTT
1 GCGATTTTCATTTCGCATTGCGATTTTGTCGTC
279831 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
279855 AGCCATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTTTGTCGTC
Found at i:279832 original size:14 final size:14
Alignment explanation
Indices: 279782--279838 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
279772 TCATTTCGCA
279782 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
* *
279796 TCGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
279813 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
279829 TTGCGATTTT
1 TTGCGATTTT
279839 CATTTCGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 15 0.44
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 5 0.15
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:279881 original size:20 final size:19
Alignment explanation
Indices: 279827--279882 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
279817 GCGATTTTGT
**
279827 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAATCATTTCG
* **
279846 CATTGCGATAGCCATTTCTG
1 CGTTGCGATAATCATTTC-G
279866 CGTTGCGATAATCATTT
1 CGTTGCGATAATCATTT
279883 TCATGTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAATCATTTCG
Found at i:280419 original size:18 final size:18
Alignment explanation
Indices: 280377--280420 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
280367 CGATCAGATG
* *
280377 ATGGCTCTAGGTGAGGTG
1 ATGGCTCTAGGCGAGGTA
* *
280395 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTAGGCGAGGTA
280413 ATGGCTCT
1 ATGGCTCT
280421 CGAAGTGGAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (18 bp):
ATGGCTCTAGGCGAGGTA
Found at i:281773 original size:20 final size:20
Alignment explanation
Indices: 281736--281793 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
281726 AATAGTTTCT
** *
281736 GAAAATGAAAATCACAACAC
1 GAAAATGACTATCGCAACAC
*
281756 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
281776 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
281794 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:282299 original size:21 final size:21
Alignment explanation
Indices: 282269--282384 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 21
282259 CGCTTTGAAA
282269 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
282290 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGATTATGT-ATT
* * *
282310 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTATT
*
282331 ATCGCATTGCGA-TA-GTAAGT
1 ATCGCATTGCGATTATGT-ATT
* *
282351 ATCTCATTGCGA-TA-GTCAAT
1 ATCGCATTGCGATTATGT-ATT
282371 ATCGCATTGCGATT
1 ATCGCATTGCGATT
282385 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
19 5 0.07
20 44 0.59
21 24 0.32
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:282332 original size:41 final size:41
Alignment explanation
Indices: 282273--282382 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
282263 TTGAAAATCG
* *
282273 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
* * *
282314 CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
*
282355 CATTGCGA-TA-GTCAATATCGCATTGCGA
1 CATTGCGATTATGT-ATTATCGCATTGCGA
282383 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.25
41 43 0.72
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (41 bp):
CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
Found at i:282358 original size:20 final size:20
Alignment explanation
Indices: 282330--282383 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
282320 GATTTTGTAT
282330 TATCGCATTGCGATAGT-AA
1 TATCGCATTGCGATAGTCAA
*
282349 GTATCTCATTGCGATAGTCAA
1 -TATCGCATTGCGATAGTCAA
282370 TATCGCATTGCGAT
1 TATCGCATTGCGAT
282384 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAA
Found at i:282381 original size:61 final size:62
Alignment explanation
Indices: 282269--282386 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
282259 CGCTTTGAAA
* * * * *
282269 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
* *
282331 ATCGCATTGCGA-TA-GTAAGTATCTCATTGCGATAGTCAATATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
282387 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 2 0.04
61 34 0.71
62 12 0.25
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
Found at i:282494 original size:21 final size:21
Alignment explanation
Indices: 282454--282494 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
282444 ACTGTAGACC
** *
282454 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
282475 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
282495 GCGAATTTGT
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:283219 original size:25 final size:26
Alignment explanation
Indices: 283172--283231 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
283162 GTTTCTTTTT
283172 TTATAAAATATTATTATTATTA-TTA
1 TTATAAAATATTATTATTATTATTTA
283197 TTATAAAATA-T-TTATTTATTTATTTA
1 TTATAAAATATTATTA-TTA-TTATTTA
*
283223 TTACAAAAT
1 TTATAAAAT
283232 CGGCCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 3 0.10
24 4 0.13
25 13 0.42
26 11 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATAAAATATTATTATTATTATTTA
Found at i:286070 original size:23 final size:23
Alignment explanation
Indices: 286039--286104 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
286029 TTATATATGA
*
286039 CACTACGGTGCATTTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGG
*
286062 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGG
*
286085 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
286105 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGTGG
Found at i:288692 original size:20 final size:18
Alignment explanation
Indices: 288669--288711 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
288659 CTCTAAATCA
* *
288669 TTTTTCAAAATTCATTTT
1 TTTTTCAAAAATAATTTT
288687 GTTTTTCAAAAATAATTTT
1 -TTTTTCAAAAATAATTTT
288706 TTTTTC
1 TTTTTC
288712 TTTCAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTCAAAAATAATTTT
Found at i:288730 original size:22 final size:22
Alignment explanation
Indices: 288669--288730 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
288659 CTCTAAATCA
288669 TTTTTC-AAAAT--TCATTTTG
1 TTTTTCAAAAATAATCATTTTG
* *
288688 TTTTTCAAAAATAAT-TTTTTT
1 TTTTTCAAAAATAATCATTTTG
288709 TTCTTTC-AAAATCAATCATTTT
1 TT-TTTCAAAAAT-AATCATTTT
288731 CAATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 6 0.18
20 5 0.15
21 11 0.32
22 8 0.24
23 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTCAAAAATAATCATTTTG
Found at i:290575 original size:49 final size:49
Alignment explanation
Indices: 290503--290675 Score: 301
Period size: 49 Copynumber: 3.5 Consensus size: 49
290493 ATTTTGCCAA
*
290503 AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
1 AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
*
290552 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
1 AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
* *
290601 AAATGCACTATTATGCATTTAACTTTCATTAGTGGCACCTTTTATACCG
1 AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
*
290650 AAATGCACCGTTATGCATTTAACTTT
1 AAATGCACCATTATGCATTTAACTTT
290676 AGCAACCTCG
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 117 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (49 bp):
AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
Found at i:292277 original size:28 final size:29
Alignment explanation
Indices: 292246--292307 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
292236 AAAGGAAAAG
292246 GATGTAAACAA-AAAACCCTTACAAGGTA
1 GATGTAAACAAGAAAACCCTTACAAGGTA
**
292274 GATGTTTACAAGAAAACCCTTACAAGGTA
1 GATGTAAACAAGAAAACCCTTACAAGGTA
292303 GATGT
1 GATGT
292308 TTACAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (29 bp):
GATGTAAACAAGAAAACCCTTACAAGGTA
Found at i:292284 original size:15 final size:15
Alignment explanation
Indices: 292264--292314 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
292254 CAAAAAACCC
292264 TTACAAGGTAGATGT
1 TTACAAGGTAGATGT
* * ***
292279 TTACAA-GAAAACCC
1 TTACAAGGTAGATGT
292293 TTACAAGGTAGATGT
1 TTACAAGGTAGATGT
292308 TTACAAG
1 TTACAAG
292315 ATTAAGCTCA
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (15 bp):
TTACAAGGTAGATGT
Found at i:292294 original size:29 final size:29
Alignment explanation
Indices: 292253--292315 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
292243 AAGGATGTAA
292253 ACAA-AAAACCCTTACAAGGTAGATGTTT
1 ACAAGAAAACCCTTACAAGGTAGATGTTT
292281 ACAAGAAAACCCTTACAAGGTAGATGTTT
1 ACAAGAAAACCCTTACAAGGTAGATGTTT
292310 ACAAGA
1 ACAAGA
292316 TTAAGCTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.22
Consensus pattern (29 bp):
ACAAGAAAACCCTTACAAGGTAGATGTTT
Found at i:298016 original size:28 final size:28
Alignment explanation
Indices: 297976--298065 Score: 125
Period size: 28 Copynumber: 3.3 Consensus size: 28
297966 TTACCCTTCC
297976 CCTCCCCAAATTAACCTGAAACACATCA
1 CCTCCCCAAATTAACCTGAAACACATCA
298004 CCTCCCCAAATTAACCTG-AA-ACATCA
1 CCTCCCCAAATTAACCTGAAACACATCA
*
298030 CAT-CCCAAATTAACCTGAAACAC-TCTA
1 CCTCCCCAAATTAACCTGAAACACATC-A
*
298057 CCTTCCCAA
1 CCTCCCCAA
298066 GTCAGCCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.25
26 12 0.21
27 7 0.12
28 23 0.41
ACGTcount: A:0.38, C:0.39, G:0.03, T:0.20
Consensus pattern (28 bp):
CCTCCCCAAATTAACCTGAAACACATCA
Found at i:298042 original size:25 final size:26
Alignment explanation
Indices: 297978--298051 Score: 114
Period size: 25 Copynumber: 2.8 Consensus size: 26
297968 ACCCTTCCCC
*
297978 TCCCCAAATTAACCTGAAACACATCACC
1 TCCCCAAATTAACCTG-AA-ACATCACA
298006 TCCCCAAATTAACCTGAAACATCACA
1 TCCCCAAATTAACCTGAAACATCACA
298032 T-CCCAAATTAACCTGAAACA
1 TCCCCAAATTAACCTGAAACA
298052 CTCTACCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 19 0.42
26 8 0.18
27 2 0.04
28 16 0.36
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (26 bp):
TCCCCAAATTAACCTGAAACATCACA
Found at i:300266 original size:2 final size:2
Alignment explanation
Indices: 300259--300294 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
300249 ATTACACATC
300259 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
300295 TGCATATGTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303043 original size:54 final size:54
Alignment explanation
Indices: 302938--303231 Score: 281
Period size: 54 Copynumber: 5.4 Consensus size: 54
302928 GCTAAGTCCG
** * * *
302938 ATTTTTAGAAGTTTCTTGATGATTTCTTCAAATGATTTTTGAAATAAACTAAGTCTA
1 ATTTTTAGGGGTTTCTTGATG---TCTTCAAATGAATTTTGAAAGAAACTAAGCCTA
302995 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAACTAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAACTAAGCCTA
*** * * * ** * *
303049 ATTTTTAGAAATTTCTCGATGTTTTCCAATGAATTTTGAAAGAAGGTAAGCATG
1 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAACTAAGCCTA
* * * * *
303103 ATTTTCAGGGGTTTCTTGAAGTTTTCAAATGAATTTGGAAAGAAGA-TAAGCCTG
1 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAA-ACTAAGCCTA
* * * *
303157 ATTTTCAGGGGTTTCTTGATGCCTTCAACTTAA-TTTGTAAA-AATGA-TAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTG-AAAGAA--ACTAAGCCTA
303211 ATTTTTAGGGGTTTCTTGATG
1 ATTTTTAGGGGTTTCTTGATG
303232 ATAATTGTAA
Statistics
Matches: 201, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
53 5 0.02
54 177 0.88
57 19 0.09
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAACTAAGCCTA
Found at i:305580 original size:3 final size:3
Alignment explanation
Indices: 305574--305618 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
305564 TTACTACGAC
305574 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
305619 CAAACCTGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:307248 original size:16 final size:17
Alignment explanation
Indices: 307229--307267 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
307219 GATTTGATTA
307229 AATTTT-GTTGTTATTT
1 AATTTTCGTTGTTATTT
*
307245 AATTTTCTTTGTTATTT
1 AATTTTCGTTGTTATTT
*
307262 CATTTT
1 AATTTT
307268 TTATCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (17 bp):
AATTTTCGTTGTTATTT
Found at i:311687 original size:18 final size:18
Alignment explanation
Indices: 311636--311687 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
311626 TAAATGTTTA
*
311636 TGAAGGAATTGGAATATG
1 TGAAGGAATTGGAATCTG
311654 TGAAGGAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
*
311672 TGAAGGAATTAGAATC
1 TGAAGGAATTGGAATC
311688 GGTCAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.38, C:0.04, G:0.31, T:0.27
Consensus pattern (18 bp):
TGAAGGAATTGGAATCTG
Found at i:312187 original size:35 final size:35
Alignment explanation
Indices: 312140--312225 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
312130 AAAACAGTCA
* * *
312140 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
312175 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
312210 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
312226 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:312219 original size:21 final size:21
Alignment explanation
Indices: 312194--312236 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
312184 TTCTAAACCC
312194 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
312215 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
312236 T
1 T
312237 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:312388 original size:16 final size:18
Alignment explanation
Indices: 312356--312389 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
312346 TATTAATGTA
312356 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
312374 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
312390 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:313060 original size:130 final size:130
Alignment explanation
Indices: 312857--313104 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
312847 AATTTTCTTC
* * *
312857 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
312922 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
312987 TAATTAGGCGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
313052 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
313105 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:314428 original size:256 final size:252
Alignment explanation
Indices: 313912--314496 Score: 718
Period size: 256 Copynumber: 2.3 Consensus size: 252
313902 TTTTTGGTCC
* * *
313912 ACCCGACCCGAATATATGAATTAGAAA-CCTAACTCGA-CC-A--TAAATAATAATAAAATTATT
1 ACCCGACCCGAATATATGAATTAGAAATCC-AACCCGACCCGACCGAAATAATAA-AAAAATATT
* * *
313972 TTTATTCAATAAAAATAGTGACTTAATTGGAAAATATATATATATAGAGGGGTATTATTGTAATT
64 TTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATATATAGAGGGGTATTATTGTAATT
* *
314037 ATTTCTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGTCGAGTATTTTTCAGCCTAAA
129 ATTTCTAAATATATAAGGTAAAATTATATATTTTTCGGGTC-GG-CGAGTATTTTTCACCCTAAA
314102 CCCGAACCCGAATATCACACTTAAAAAAAACCGACCCAACCCGACCAAAATAAAGTTTCACCCG
192 CCCGAACCCGAATATCACACTTAAAAAAAACCGACCCAACCCGACCAAAATAAAGTTT---CCG
314166 ACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTT
1 ACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGA-CCGAAATAATAAAAAAATATTT
314231 TTATTCAATAAAAACA-TG-CTTAATTGAAAAAAA-ATTATATATAGAGGGGTATTATTGTAATT
65 TTATTCAATAAAAACAGTGACTTAATTGAAAAAAATA-TATATATAGAGGGGTATTATTGTAATT
314293 ATTTCTAAATATATAAGGTAAAATTATATATATTTTCGGGTC-G-GA-TATTTTTCACCCTAAAT
129 ATTTCTAAATATATAAGGTAAAATTATATAT-TTTTCGGGTCGGCGAGTATTTTTCACCCTAAA-
* * *
314355 CCAAACTCGACCCGACCCGAATATCACACTT-AAAAAAACTGA-CTATACTCGACCAAAATAAAG
192 -C---C-CGA----ACCCGAATATCACACTTAAAAAAAACCGACCCA-ACCCGACCAAAATAAAG
314418 TTTCACCCG
247 TTT---CCG
**
314427 ACCCGACCCGAATATATGAATTAGAAATCTGACCCGA--C-A-CGAAATAATAAAAAAATATTTT
1 ACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCGAAATAATAAAAAAATATTTT
314488 TATTCAATA
66 TATTCAATA
314497 TATGAATAAG
Statistics
Matches: 299, Mismatches: 13, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
252 15 0.05
253 2 0.01
254 34 0.11
255 6 0.02
256 103 0.34
257 12 0.04
258 28 0.09
259 10 0.03
260 2 0.01
261 70 0.23
262 17 0.06
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (252 bp):
ACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCGAAATAATAAAAAAATATTTT
TATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATATATAGAGGGGTATTATTGTAATTAT
TTCTAAATATATAAGGTAAAATTATATATTTTTCGGGTCGGCGAGTATTTTTCACCCTAAACCCG
AACCCGAATATCACACTTAAAAAAAACCGACCCAACCCGACCAAAATAAAGTTTCCG
Found at i:319365 original size:2 final size:2
Alignment explanation
Indices: 319358--319391 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
319348 GTAAAATCTT
*
319358 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319392 ATTTTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:320912 original size:18 final size:18
Alignment explanation
Indices: 320891--320944 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
320881 TTTAAAAAAT
320891 TAAAATATTAAAAAT-TAA
1 TAAAA-ATTAAAAATATAA
*
320909 TAAAAA-TAAAAATACTAT
1 TAAAAATTAAAAATA-TAA
320927 TAAAAATTAAAAAATATA
1 TAAAAATT-AAAAATATA
320945 TAAGAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.23
17 1 0.03
18 13 0.42
19 3 0.10
20 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATTAAAAATATAA
Found at i:320959 original size:20 final size:21
Alignment explanation
Indices: 320914--320959 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
320904 ATTAATAAAA
*
320914 ATAAAAATACTATTAAAAATT
1 ATAAAAATACTATTAAAAACT
320935 A-AAAAATA-TA-TAAGAAACT
1 ATAAAAATACTATTAA-AAACT
320954 ATAAAA
1 ATAAAA
320960 TCTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 3 0.14
19 7 0.32
20 11 0.50
21 1 0.05
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
ATAAAAATACTATTAAAAACT
Found at i:321659 original size:19 final size:20
Alignment explanation
Indices: 321620--321659 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
321610 AATATCTAAA
*
321620 TTTTTTAATATTTTAATTTT
1 TTTTTTAATATTTTAAGTTT
*
321640 TTTTTTAA-ATTTTGAGTTT
1 TTTTTTAATATTTTAAGTTT
321659 T
1 T
321660 GAGTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTAATATTTTAAGTTT
Found at i:333671 original size:15 final size:15
Alignment explanation
Indices: 333635--333676 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
333625 GGTCTAGTCA
* *
333635 CTGAGTCAACTTGTT
1 CTGAGTCAACTCGGT
333650 C-GAGTCAACTCGGT
1 CTGAGTCAACTCGGT
333664 CTGAGTCAACTCG
1 CTGAGTCAACTCG
333677 TCCAAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (15 bp):
CTGAGTCAACTCGGT
Found at i:333686 original size:14 final size:14
Alignment explanation
Indices: 333637--333687 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
333627 TCTAGTCACT
* *
333637 GAGTCAACTTGTTC
1 GAGTCAACTCGTCC
*
333651 GAGTCAACTCGGTCT
1 GAGTCAACTC-GTCC
333666 GAGTCAACTCGTCC
1 GAGTCAACTCGTCC
*
333680 AAGTCAAC
1 GAGTCAAC
333688 CTGTTGACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (14 bp):
GAGTCAACTCGTCC
Found at i:337830 original size:14 final size:15
Alignment explanation
Indices: 337807--337847 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
337797 AATTAATATG
*
337807 GTCTATGTCAACCT-
1 GTCTAAGTCAACCTC
*
337821 GTCTGAGTCAA-CTC
1 GTCTAAGTCAACCTC
337835 GTCTAAGTCAACC
1 GTCTAAGTCAACC
337848 CATTGAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 2 0.09
14 19 0.86
15 1 0.05
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (15 bp):
GTCTAAGTCAACCTC
Found at i:340566 original size:22 final size:22
Alignment explanation
Indices: 340541--340592 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
340531 AGTTTAGAAG
*
340541 ATATCAATTAGTATACTGATAC
1 ATATCAATTAGTATACTAATAC
340563 ATATCAATTAGTATACTAATAC
1 ATATCAATTAGTATACTAATAC
340585 ATATCAAT
1 ATATCAAT
340593 GTATTACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (22 bp):
ATATCAATTAGTATACTAATAC
Found at i:341847 original size:20 final size:20
Alignment explanation
Indices: 341824--341939 Score: 91
Period size: 20 Copynumber: 6.0 Consensus size: 20
341814 GAGGGATTAT
*
341824 CAGTGGTCTTTCGGGATAAA
1 CAGTGGTCTTTCGGGACAAA
*
341844 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCTTTCGGGACAAA
*
341864 CAATGGT-TCTTCGGGAC--A
1 CAGTGGTCT-TTCGGGACAAA
* * *
341882 TAGTGGT-TCTTCGGAACAAT
1 CAGTGGTCT-TTCGGGACAAA
*
341902 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCTTTCGGGACAAA
* *
341920 TAGTGGTCCTTCGGGACAAA
1 CAGTGGTCTTTCGGGACAAA
341940 TATTCAGTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
18 31 0.40
20 46 0.60
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (20 bp):
CAGTGGTCTTTCGGGACAAA
Found at i:341890 original size:18 final size:18
Alignment explanation
Indices: 341845--341937 Score: 105
Period size: 18 Copynumber: 4.9 Consensus size: 18
341835 CGGGATAAAC
*
341845 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGAC--AT
* *
341865 AATGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
341883 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
341902 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
341921 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
341938 AATATTCAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 32 0.50
19 4 0.06
20 28 0.44
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:341894 original size:38 final size:38
Alignment explanation
Indices: 341845--341939 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
341835 CGGGATAAAC
*
341845 AGTGGTCCTTCGGGACAAACAATGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAATGGTCCTTCGGGACAT
* * * *
341883 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAATGGTCCTTCGGGACAT
341921 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
341940 TATTCAGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAACAATGGTCCTTCGGGACAT
Found at i:345530 original size:15 final size:14
Alignment explanation
Indices: 345510--345577 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 14
345500 GGTCTAGTCA
345510 CTGAGTCAACTCGGT
1 CTGAGTCAACTC-GT
345525 CTGAGTCAACAT-GT
1 CTGAGTCAAC-TCGT
*
345539 CCGAG-CTAACTCGTT
1 CTGAGTC-AACTCG-T
345554 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
345568 CCGAGTCAAC
1 CTGAGTCAAC
345578 CTGTTGACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.04
14 20 0.44
15 21 0.47
16 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:345550 original size:29 final size:29
Alignment explanation
Indices: 345517--345572 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
345507 TCACTGAGTC
345517 AACTCGGTCTGAGTCAACAT-GTCCGAGCT
1 AACTCGGTCTGAGTCAAC-TCGTCCGAGCT
*
345546 AACTCGTTCTGAGTCAACTCGTCCGAG
1 AACTCGGTCTGAGTCAACTCGTCCGAG
345573 TCAACCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (29 bp):
AACTCGGTCTGAGTCAACTCGTCCGAGCT
Found at i:345575 original size:14 final size:14
Alignment explanation
Indices: 345512--345577 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
345502 TCTAGTCACT
*
345512 GAGTCAACTCGGTCT
1 GAGTCAACTC-GTCC
345527 GAGTCAACAT-GTCC
1 GAGTCAAC-TCGTCC
*
345541 GAG-CTAACTCGTTCT
1 GAGTC-AACTCG-TCC
345556 GAGTCAACTCGTCC
1 GAGTCAACTCGTCC
345570 GAGTCAAC
1 GAGTCAAC
345578 CTGTTGACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
13 2 0.05
14 20 0.47
15 19 0.44
16 2 0.05
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (14 bp):
GAGTCAACTCGTCC
Found at i:353554 original size:22 final size:22
Alignment explanation
Indices: 353514--353590 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
353504 TTAAGTATAA
*
353514 ATATAAATATATACT-ATGAAGT
1 ATATATATATATA-TGATGAAGT
353536 ATATATATATATATGATGAATGT
1 ATATATATATATATGATGAA-GT
*
353559 -TATA-ATA-ATATGATGCATGT
1 ATATATATATATATGATG-AAGT
353579 ATATATA-ATATA
1 ATATATATATATA
353591 CATTATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 10 0.21
21 10 0.21
22 25 0.53
23 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (22 bp):
ATATATATATATATGATGAAGT
Found at i:353562 original size:20 final size:19
Alignment explanation
Indices: 353520--353585 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
353510 ATAAATATAA
* * *
353520 ATATATACTATGAAGTATAT
1 ATATATA-TATGATGAATGT
353540 ATATATATATGATGAATGT
1 ATATATATATGATGAATGT
*
353559 -TATAATAATATGATGCATGT
1 ATAT-AT-ATATGATGAATGT
353579 ATATATA
1 ATATATA
353586 ATATACATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.08
19 12 0.31
20 21 0.54
21 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (19 bp):
ATATATATATGATGAATGT
Found at i:353586 original size:20 final size:20
Alignment explanation
Indices: 353537--353589 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
353527 CTATGAAGTA
353537 TATATATATATATGATGAATG
1 TATATATA-ATATGATGAATG
*
353558 T-TATAATAATATGATGCATG
1 TATAT-ATAATATGATGAATG
353578 TATATATAATAT
1 TATATATAATAT
353590 ACATTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (20 bp):
TATATATAATATGATGAATG
Found at i:353634 original size:18 final size:18
Alignment explanation
Indices: 353611--353646 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
353601 ATGCATACAT
353611 TATATACACACACTTATA
1 TATATACACACACTTATA
353629 TATATACACACACTTATA
1 TATATACACACACTTATA
353647 AACATACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (18 bp):
TATATACACACACTTATA
Found at i:353653 original size:18 final size:18
Alignment explanation
Indices: 353614--353653 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
353604 CATACATTAT
* *
353614 ATACACACACTTATATAT
1 ATACACACACTTATAAAC
353632 ATACACACACTTATAAAC
1 ATACACACACTTATAAAC
353650 ATAC
1 ATAC
353654 GATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (18 bp):
ATACACACACTTATAAAC
Found at i:354477 original size:14 final size:14
Alignment explanation
Indices: 354426--354477 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
354416 AACATAAGTA
354426 ATATAT-GTATATG
1 ATATATGGTATATG
354439 -TATATGG-ATATG
1 ATATATGGTATATG
* **
354451 AAATATGAAATATG
1 ATATATGGTATATG
354465 ATATATGGTATAT
1 ATATATGGTATAT
354478 ATCAATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.32
13 6 0.19
14 15 0.48
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATATGGTATATG
Found at i:354691 original size:2 final size:2
Alignment explanation
Indices: 354684--354714 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
354674 ATTCATCTTT
*
354684 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
354715 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:359888 original size:35 final size:36
Alignment explanation
Indices: 359807--359913 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
359797 CAAAATCGTC
*
359807 ATTTACAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTGCAATACTAGTGGGATAACCTAATTTGAGCAT
359843 ATTTGCAATACTAGTGGGATAACCTAATTT-AGCAT
1 ATTTGCAATACTAGTGGGATAACCTAATTTGAGCAT
359878 ATTT-CTAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTGC-AATACTAGTGGGATAACCTAATTTGAGCAT
359914 TATCAACATT
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
34 1 0.01
35 33 0.49
36 34 0.50
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (36 bp):
ATTTGCAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:368562 original size:13 final size:13
Alignment explanation
Indices: 368546--368570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368536 TGTTGAATGA
368546 TGAAGTTGTTAGC
1 TGAAGTTGTTAGC
368559 TGAAGTTGTTAG
1 TGAAGTTGTTAG
368571 ATGATGTGTG
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:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (13 bp):
TGAAGTTGTTAGC
Found at i:368593 original size:12 final size:12
Alignment explanation
Indices: 368576--368600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
368566 GTTAGATGAT
368576 GTGTGTAGTTAG
1 GTGTGTAGTTAG
368588 GTGTGTAGTTAG
1 GTGTGTAGTTAG
368600 G
1 G
368601 GAAGCTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (12 bp):
GTGTGTAGTTAG
Found at i:372036 original size:60 final size:58
Alignment explanation
Indices: 371855--372041 Score: 142
Period size: 60 Copynumber: 3.1 Consensus size: 58
371845 TGTATAGTTT
* * * * * **
371855 AGGATAAAACTAGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATAAGGGTTATGGTTTG
1 AGGATAAAATTAAAATTTTC-AAAAGTTT-GGGACCAATTTAGAATAA-AGTCATAATTTG
* * * * * * *
371916 GGGATGAAATTGAAATTTTCAAAAGTTTGTGAACAAATTTAGAATGATAGTCACAATTTG
1 AGGATAAAATTAAAATTTTCAAAAGTTTG-GGACCAATTTAGAAT-AAAGTCATAATTTG
* *
371976 AGGATAAAATTAAAATATTT-AAAAGTTTAGGGACCAATTTAAAATAAAGATCATACTTTG
1 AGGATAAAATTAAAAT-TTTCAAAAGTTT-GGGACCAATTTAGAATAAAG-TCATAATTTG
*
372036 AAGATA
1 AGGATA
372042 TATGATGCAA
Statistics
Matches: 97, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
59 4 0.04
60 74 0.76
61 19 0.20
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (58 bp):
AGGATAAAATTAAAATTTTCAAAAGTTTGGGACCAATTTAGAATAAAGTCATAATTTG
Found at i:373148 original size:17 final size:17
Alignment explanation
Indices: 373126--373179 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
373116 GTATGTCTCT
373126 AATAAGATAATTATTTA
1 AATAAGATAATTATTTA
373143 AATAAGATAATTATTTA
1 AATAAGATAATTATTTA
*
373160 AATAAGATAATTACTTA
1 AATAAGATAATTATTTA
373177 AAT
1 AAT
373180 TATATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (17 bp):
AATAAGATAATTATTTA
Found at i:374417 original size:202 final size:202
Alignment explanation
Indices: 374071--374477 Score: 733
Period size: 202 Copynumber: 2.0 Consensus size: 202
374061 TATCATATAA
374071 CATGGGCATTATCATTTATAACAATTCACACCACTTGTATCATATAAACATGTAATCTCATAACT
1 CATGGGCATTATCATTTATAACAATTCACACCACTTGTATCATATAAACATGTAATCTCATAACT
*
374136 TGTTCTCTTATAGCTTGTATATCATTCTTGTATGATCTCATAAATCCTTGTATAATATTCTTGTC
66 TGTTCTCATATAGCTTGTATATCATTCTTGTATGATCTCATAAATCCTTGTATAATATTCTTGTC
*
374201 ATATAACCCATATCACATAGGTTTATATCATATAACATATAACACATATGCATGTAATCACATAG
131 ATATAACCCATATCACATAGGTTCATATCATATAACATATAACACATATGCATGTAATCACATAG
374266 ATCGTAT
196 ATCGTAT
*
374273 CATGGGCATTATCATTTATAACAGTTCACACCACTTGTATCATATAAACATGTAATCTCATAACT
1 CATGGGCATTATCATTTATAACAATTCACACCACTTGTATCATATAAACATGTAATCTCATAACT
* *
374338 TGTTCTCATGTAGCTTGTATATCATTCTTGTATGATCTCATAGATCCTTGTATAATATTCTTGTC
66 TGTTCTCATATAGCTTGTATATCATTCTTGTATGATCTCATAAATCCTTGTATAATATTCTTGTC
* * * *
374403 ATATAACCCATATCACATAGGTTCATATCATATAACATATATCACATGTGTATGTATTCACATAG
131 ATATAACCCATATCACATAGGTTCATATCATATAACATATAACACATATGCATGTAATCACATAG
374468 ATCGTAT
196 ATCGTAT
374475 CAT
1 CAT
374478 ATAGCTTATA
Statistics
Matches: 196, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
202 196 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (202 bp):
CATGGGCATTATCATTTATAACAATTCACACCACTTGTATCATATAAACATGTAATCTCATAACT
TGTTCTCATATAGCTTGTATATCATTCTTGTATGATCTCATAAATCCTTGTATAATATTCTTGTC
ATATAACCCATATCACATAGGTTCATATCATATAACATATAACACATATGCATGTAATCACATAG
ATCGTAT
Found at i:379487 original size:21 final size:21
Alignment explanation
Indices: 379458--379506 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
379448 ATTTTCCAGA
*
379458 TGCTGCAGGGTA-TCGATACCC
1 TGCTACAGGGTACT-GATACCC
379479 TGCTACA-GGTACTGATACCC
1 TGCTACAGGGTACTGATACCC
*
379499 TACTACAG
1 TGCTACAG
379507 TATTTCCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCTACAGGGTACTGATACCC
Found at i:380363 original size:31 final size:31
Alignment explanation
Indices: 380303--380384 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
380293 ATAAGAAATT
* * *
380303 TGTTCCGAAGGACCTATGT-AACTGTCCATA
1 TGTTCCGAAGAACATAGGTAAACTGTCCATA
*
380333 TGTTCCGAAGAACATAGGTAAATTGTCCATA
1 TGTTCCGAAGAACATAGGTAAACTGTCCATA
*
380364 TGTTCCGTAGAACATAGGTAA
1 TGTTCCGAAGAACATAGGTAA
380385 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 16 0.35
31 30 0.65
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (31 bp):
TGTTCCGAAGAACATAGGTAAACTGTCCATA
Found at i:381214 original size:29 final size:29
Alignment explanation
Indices: 381154--381212 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
381144 CAACCATTTA
**
381154 CAACTTTTCAAAAATTATGAATGATCCCC
1 CAACTTTTCAAAAATTAAAAATGATCCCC
* *
381183 CAACTTTTCAAAATTTACAAAATGGTCCCC
1 CAACTTTTCAAAAATTA-AAAATGATCCCC
381213 AAAATTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (29 bp):
CAACTTTTCAAAAATTAAAAATGATCCCC
Found at i:385428 original size:22 final size:23
Alignment explanation
Indices: 385381--385433 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
385371 GGATTTGGAT
* *
385381 TTTTTTTAAAAAAAATATTGAGA
1 TTTTTTAAAAAAAAATAATGAGA
385404 TTTTTTAAAAAAATAATAAT-A-A
1 TTTTTTAAAAAAA-AATAATGAGA
385426 TTTTTTAA
1 TTTTTTAA
385434 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 13 0.48
24 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAAAAAAATAATGAGA
Found at i:386212 original size:37 final size:37
Alignment explanation
Indices: 386142--386212 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
386132 TTTATTTTTT
* *
386142 AATAATTTAAAATATTATAAGATTATATTTATTTAAA
1 AATAATTTAAAATATTATAAGATTACATATATTTAAA
* *
386179 AATAATTTTAAATATTAATAATA-TACATATATTT
1 AATAATTTAAAATATT-ATAAGATTACATATATTT
386213 TATAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (37 bp):
AATAATTTAAAATATTATAAGATTACATATATTTAAA
Found at i:386220 original size:38 final size:36
Alignment explanation
Indices: 386134--386220 Score: 86
Period size: 37 Copynumber: 2.4 Consensus size: 36
386124 TGAAAATTTT
* *
386134 TATTTT-TTAATAATTTAAAATATTATAAGATTATA
1 TATTTTATAAATAATTTAAAATATTATAAGATCATA
* * * *
386169 TTTATTTAAAAATAATTTTAAATATTAATAATATACATA
1 TAT-TTTATAAATAATTTAAAATATT-ATAAGAT-CATA
386208 TATTTTATAAATA
1 TATTTTATAAATA
386221 TAATTATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
35 2 0.05
36 3 0.08
37 15 0.38
38 15 0.38
39 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
TATTTTATAAATAATTTAAAATATTATAAGATCATA
Found at i:386237 original size:232 final size:227
Alignment explanation
Indices: 385829--386288 Score: 859
Period size: 232 Copynumber: 2.0 Consensus size: 227
385819 CATGTTTGTC
385829 ATGAAAACATAATTGAGCATGCTGCTATATAATAATTATATTGCCAAGCTTATGGCATCGATTGT
1 ATGAAAACATAATTGAGCATGCTGCTATATAATAATTATATTGCCAAGCTTATGGCATCGATTGT
385894 GAAAATTTTTATTTTTTAATAATTTAAAATAATTATAAGATTATATTTATTTAAAATAATTTTAA
66 GAAAATTTTTATTTTTTAATAATTTAAAATAATTATAAGATTATATTTATTTAAAATAATTTTAA
385959 TATTAATAATATACATATATTTTATAAATATAATTATTTATAATTAAAATCTTTAAAAATAATAT
131 TATTAATAATATACATATATTTTATAAATATAATTATTTATAATTAAAATCTTTAAAAATAATAT
386024 TCATTTTAATTATCAAGATTACTATGTTCTGA
196 TCATTTTAATTATCAAGATTACTATGTTCTGA
386056 ATGAAAACATAATTGAGCATGCTGCTATATATAATAATTAGTATTGCCAAGCTTATGGCATCGAA
1 ATGAAAACATAATTGAGCATGCTGC--TATATAATAATTA-TATTGCCAAGCTTATGGCATCG-A
386121 TTGTGAAAATTTTTATTTTTTAATAATTTAAAAT-ATTATAAGATTATATTTATTTAAAAATAAT
62 TTGTGAAAATTTTTATTTTTTAATAATTTAAAATAATTATAAGATTATATTTATTT-AAAATAAT
386185 TTTAAATATTAATAATATACATATATTTTATAAATATAATTATTTATAATTAAAATCTTTAAAAA
126 TTT-AATATTAATAATATACATATATTTTATAAATATAATTATTTATAATTAAAATCTTTAAAAA
386250 TAATATTCATTTTAATTATCAAGATTACTATGTTCTGA
190 TAATATTCATTTTAATTATCAAGATTACTATGTTCTGA
386288 A
1 A
386289 AATTTTGATT
Statistics
Matches: 227, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
227 25 0.11
229 13 0.06
230 43 0.19
231 46 0.20
232 100 0.44
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (227 bp):
ATGAAAACATAATTGAGCATGCTGCTATATAATAATTATATTGCCAAGCTTATGGCATCGATTGT
GAAAATTTTTATTTTTTAATAATTTAAAATAATTATAAGATTATATTTATTTAAAATAATTTTAA
TATTAATAATATACATATATTTTATAAATATAATTATTTATAATTAAAATCTTTAAAAATAATAT
TCATTTTAATTATCAAGATTACTATGTTCTGA
Found at i:388007 original size:31 final size:30
Alignment explanation
Indices: 387953--388011 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
387943 TCATCTCATA
* *
387953 AAATATAAATTCATAATATATTAAATATTAG
1 AAATATAAAATCATAAAATATT-AATATTAG
387984 AAATATAAAAT-ATAAAATAATTAATATT
1 AAATATAAAATCATAAAAT-ATTAATATT
388012 TTATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATATAAAATCATAAAATATTAATATTAG
Found at i:388483 original size:21 final size:21
Alignment explanation
Indices: 388454--388506 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
388444 ATTCTGACTA
*
388454 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
388475 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
388496 TCGCAATGCGA
1 TCGCATTGCGA
388507 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:388755 original size:22 final size:22
Alignment explanation
Indices: 388730--388789 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
388720 ACATCCGTCC
388730 CCATCTCCGACGAAATCAGCCT
1 CCATCTCCGACGAAATCAGCCT
* **
388752 CCATCTCCGACGATATCAGTTT
1 CCATCTCCGACGAAATCAGCCT
*
388774 CCATCTCCGGCGAAAT
1 CCATCTCCGACGAAAT
388790 TATTCACGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.37, G:0.15, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGCCT
Found at i:389215 original size:20 final size:20
Alignment explanation
Indices: 389127--389217 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
389117 GCGATTCTGT
389127 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
389146 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
389166 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
389186 TGTTGTGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
389206 TGTTGCGATTTT
1 CGTTGCGATTTT
389218 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:389224 original size:20 final size:20
Alignment explanation
Indices: 389181--389224 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
389171 CGATAGTCAT
* * *
389181 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
389201 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
389221 TTTC
1 TTTC
389225 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:391112 original size:20 final size:20
Alignment explanation
Indices: 391087--391145 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
391077 AGAATAGTTT
*
391087 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
391107 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
391127 ATTATCGCAACGAGAAAAT
1 ACTATCGCAACGCGAAAAT
391146 CGCAACAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:391149 original size:14 final size:14
Alignment explanation
Indices: 391130--391173 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
391120 GAAAATGATT
*
391130 ATCGCAACGAGAAA
1 ATCGCAACAAGAAA
*
391144 ATCGCAACAACAAA
1 ATCGCAACAAGAAA
*
391158 ATCGCAACTAGAAA
1 ATCGCAACAAGAAA
391172 AT
1 AT
391174 GACTATCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
ATCGCAACAAGAAA
Found at i:391276 original size:20 final size:20
Alignment explanation
Indices: 391251--391442 Score: 225
Period size: 20 Copynumber: 9.8 Consensus size: 20
391241 GATTCTCTCG
**
391251 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
391271 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
391291 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
391311 TTGCGATAGTCATTTTCGCGCA
1 TTGCGATAGTCATTTT--CGCA
*
391333 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
391347 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
391367 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
391387 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
391407 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
391427 TTGCGATAGTTATTTT
1 TTGCGATAGTCATTTT
391443 TGCGTTGTGA
Statistics
Matches: 151, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
14 7 0.05
16 4 0.03
18 5 0.03
20 125 0.83
22 10 0.07
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:391400 original size:96 final size:95
Alignment explanation
Indices: 391236--391433 Score: 344
Period size: 96 Copynumber: 2.1 Consensus size: 95
391226 TGAAAATCGT
**
391236 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAGT
*
391301 CATTTTCGCGTTGCGATAGTCATTTTCGCG
66 CATTTTCGCATTGCGATAGTCATTTTCGCG
391331 CATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAG
1 -ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAG
*
391396 TCATTTTTGCATTGCGATAGTCATTTTCGCG
65 TCATTTTCGCATTGCGATAGTCATTTTCGCG
391427 -TTGCGAT
1 ATTGCGAT
391434 AGTTATTTTT
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 7 0.07
96 91 0.93
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (95 bp):
ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAGT
CATTTTCGCATTGCGATAGTCATTTTCGCG
Found at i:393296 original size:14 final size:14
Alignment explanation
Indices: 393277--393312 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
393267 ATTGTTTAAT
393277 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
393291 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
393305 TGATTTGT
1 TGATTTGT
393313 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:393453 original size:20 final size:20
Alignment explanation
Indices: 393414--393453 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
393404 ATGCAAAACA
* * *
393414 GACTATCGCAACGCGGAAAT
1 GACTATCACAACGAGAAAAT
393434 GACTATCACAACGAGAAAAT
1 GACTATCACAACGAGAAAAT
393454 TGCAATGCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
GACTATCACAACGAGAAAAT
Found at i:393479 original size:33 final size:34
Alignment explanation
Indices: 393418--393518 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
393408 AAAACAGACT
* * ** *
393418 ATCGCAACGCGGAAATGACTATCACAACGAGAAA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
* *
393452 ATTGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
393485 ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
393519 CTAAATTCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 28 0.48
34 30 0.52
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
Found at i:393506 original size:34 final size:33
Alignment explanation
Indices: 393418--393518 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
393408 AAAACAGACT
* ** *
393418 ATCGCAACGCGGAAATGACTATCACAACGAGAAA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAAA
* *
393452 ATTGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
393485 ATCGCAATGCGAAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAAA
393519 CTAAATTCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 29 0.50
34 29 0.50
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:393589 original size:20 final size:20
Alignment explanation
Indices: 393561--393654 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
393551 GCGATTCTCT
*
393561 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
393581 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
393601 CGCTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
393621 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
393641 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
393655 AATGAATGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 66 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:396106 original size:24 final size:24
Alignment explanation
Indices: 396072--396125 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
396062 CTGAAAAATC
396072 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
396096 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
396120 ATCAAA
1 ATCAAA
396126 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:396139 original size:24 final size:24
Alignment explanation
Indices: 396072--396139 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
396062 CTGAAAAATC
* * *
396072 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
396096 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
396120 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
396140 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:396987 original size:20 final size:20
Alignment explanation
Indices: 396962--397028 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
396952 AAATTCAATA
396962 TTGCGATAGTCAGAATCGTG
1 TTGCGATAGTCAGAATCGTG
396982 TTGCGATAGTCAGAATC-TCG
1 TTGCGATAGTCAGAATCGT-G
* *
397002 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGTG
397022 TTGCGAT
1 TTGCGAT
397029 TTACATACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGTG
Found at i:397040 original size:20 final size:20
Alignment explanation
Indices: 397015--397147 Score: 203
Period size: 20 Copynumber: 6.7 Consensus size: 20
397005 CGATAGTCAG
* *
397015 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
397035 ACTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
397055 ATTCGCAATGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
397075 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
397095 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
397115 ATTCTCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
397135 ATTCGCATTGCGA
1 ATTCGCATTGCGA
397148 ATTAGGAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:402172 original size:13 final size:14
Alignment explanation
Indices: 402154--402182 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
402144 GGGAACCAAA
402154 TATCGTTAATT-AT
1 TATCGTTAATTGAT
402167 TATCGTTAATTGAT
1 TATCGTTAATTGAT
402181 TA
1 TA
402183 GTTTAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (14 bp):
TATCGTTAATTGAT
Found at i:407831 original size:21 final size:21
Alignment explanation
Indices: 407802--407879 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 21
407792 CGTGGGAGGT
407802 ATCGATTCCC-TCAAGGAGGGA
1 ATCGATTCCCTTCAAGG-GGGA
*
407823 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGATTCCC-TTC-AAGGGGGA
* * *
407846 GTCGGTTCCCCTTCAAGGGGGT
1 ATCGATT-CCCTTCAAGGGGGA
407868 ATCGATTCCCTT
1 ATCGATTCCCTT
407880 TGCACTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 14 0.29
22 12 0.25
23 15 0.31
24 7 0.15
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (21 bp):
ATCGATTCCCTTCAAGGGGGA
Found at i:407866 original size:22 final size:22
Alignment explanation
Indices: 407812--407877 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
407802 ATCGATTCCC
407812 TCAAGGAGGGAATCGGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
* *
407835 TCAAAGGGGGAGTCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
* *
407858 TCAAGGGGGTATCGATTCCC
1 TCAAGGGGGAATCGGTTCCC
407878 TTTGCACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.41
23 18 0.49
24 4 0.11
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:415637 original size:29 final size:29
Alignment explanation
Indices: 415598--415685 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
415588 TTTTTATTCC
415598 ACCATATTTTATTCAACATCCCATGCCACT
1 ACCAT-TTTTATTCAACATCCCATGCCACT
415628 ACCATTTTTATTCAACATCCCATGCCACT
1 ACCATTTTTATTCAACATCCCATGCCACT
*
415657 ACCATTTTATATTCAATATCCCATGCCAC
1 ACCATTTT-TATTCAACATCCCATGCCAC
415686 CATGCCCCCA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 32 0.57
30 24 0.43
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34
Consensus pattern (29 bp):
ACCATTTTTATTCAACATCCCATGCCACT
Found at i:422196 original size:39 final size:39
Alignment explanation
Indices: 422137--422706 Score: 338
Period size: 39 Copynumber: 15.0 Consensus size: 39
422127 TTCTTTTTAA
* * *
422137 AGAATATTTTATCTCACTTGAGATGGTTTCTCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
*
422176 AGAAGATTTTATCTCGCTTGAGATAGTTT-TCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCT-CTCGAAAC
* * * *
422215 AGAAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCT-CTCGAAAC
* * ** * *
422255 AAGAAGA-TTTATTTCACTCAAGATTGATTT-TCT-TAAA-
1 -AGAAGATTTTATCTCGCTTGAGATAG-TTTCTCTCGAAAC
* * * * * *
422292 ACAAGA-TTTGTCTTGCTTGAGA-CGATTTTTACTCGAAAG
1 AGAAGATTTTATCTCGCTTGAGATAG-TTTCT-CTCGAAAC
* * * * * ** *
422331 AAAACATTTCATTTCACTCAAGATTGTTT-T-T--AAA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* *
422365 A-AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * *
422403 AGAAGATTTTATCTCGCTTCAGATAGTTTCACTCTAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * *
422442 AGAATATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * * * *
422481 AGAAGATTTTGTCTCGCTTGAGGTAGTTTCCCTTGACAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * *
422520 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * * * *
422559 AAAAGATTTTATCTCTCTTGAGATAATTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * ** * *
422598 --AA-ATTTTGTCTCTCTTGAGACCGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * ** * *
422634 --AA-ATTTTGTCTCTCTTGAGGCAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
* * * * *
422670 --AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
422706 A
1 A
422707 AAATCTTTGA
Statistics
Matches: 444, Mismatches: 70, Indels: 36
0.81 0.13 0.07
Matches are distributed among these distances:
33 20 0.05
34 1 0.00
35 9 0.02
36 115 0.26
37 8 0.02
38 8 0.02
39 241 0.54
40 32 0.07
41 10 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
Found at i:422321 original size:76 final size:71
Alignment explanation
Indices: 422217--422411 Score: 223
Period size: 76 Copynumber: 2.6 Consensus size: 71
422207 CTTGAAACAG
422217 AAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAAGATTG
1 AAGATT-TGTCTCGCTTGAGACA-TTTTTACTCGAAA-AAGAAGATTTCATTTCACTCAAGATTG
422281 ATTTTCTTAAAA
63 --TTT-TTAAAA
* *
422293 CAAGATTTGTCTTGCTTGAGACGATTTTTACTCGAAAGAA-AACATTTCATTTCACTCAAGATTG
1 -AAGATTTGTCTCGCTTGAGAC-ATTTTTACTCGAAA-AAGAAGATTTCATTTCACTCAAGATTG
422357 TTTTTAAAA
63 TTTTTAAAA
* * * * *
422366 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTT
1 AAGA-TTTGTCTCGCTTGAGACATTTTTACTCGAAAAAGAAGATTT
422412 TATCTCGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
71 1 0.01
72 22 0.21
73 20 0.19
74 3 0.03
75 6 0.06
76 45 0.43
77 7 0.07
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (71 bp):
AAGATTTGTCTCGCTTGAGACATTTTTACTCGAAAAAGAAGATTTCATTTCACTCAAGATTGTTT
TTAAAA
Found at i:422458 original size:78 final size:76
Alignment explanation
Indices: 422137--422598 Score: 375
Period size: 78 Copynumber: 6.0 Consensus size: 76
422127 TTCTTTTTAA
* * * * *
422137 AGAATATTTTATCTCACTTGAGATGGTTTCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTCAGATAG
422202 TTTTCCTTGAAAC
66 -TTTCCTT-AAAC
* * * * * *
422215 AGAAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGA-TTTATTTCAC-TCAAGA
1 AGAAGATTTTATCTCGCTTGAGATAG-TTTCACTCGAAAC-AGAAGATTTTATCTCGCTTC-AGA
* *
422278 TTGATTTTCTTAAA-
63 TAG-TTTCCTTAAAC
* * * * * * * * * * * *
422292 ACAAGA-TTTGTCTTGCTTGAGACGATTTTTACTCGAAAGAAAACATTTCATTTCAC-TCAAGAT
1 AGAAGATTTTATCTCGCTTGAGA-TAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTC-AGAT
*
422355 TGTTT--TTAAA-
64 AGTTTCCTTAAAC
*
422365 A-AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTCAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTCAGATAG
422429 TTTCACTCTAAAC
66 TTTC-CT-TAAAC
* * * * *
422442 AGAATATTTTATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTGTCTCGCTTGAGGTAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTCAGATAG
*
422507 TTTCCCTTGACAC
66 TTT-CCTT-AAAC
* * * * * * *
422520 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAAAAGATTTTATCTCTCTTGAGATAA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTCAGATAG
422585 TTTCCCTTGAAAC
66 TTT-CCTT-AAAC
422598 A
1 A
422599 AATTTTGTCT
Statistics
Matches: 318, Mismatches: 51, Indels: 30
0.80 0.13 0.08
Matches are distributed among these distances:
72 36 0.11
73 22 0.07
75 8 0.03
76 48 0.15
77 8 0.03
78 159 0.50
79 31 0.10
80 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (76 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTCAGATAG
TTTCCTTAAAC
Found at i:422760 original size:101 final size:102
Alignment explanation
Indices: 422506--422875 Score: 377
Period size: 101 Copynumber: 3.5 Consensus size: 102
422496 GCTTGAGGTA
* * ** *
422506 GTTTCCCTTGACACAGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAAAAGATTTTAT
1 GTTTCCCTTGA-A-ACAA-ATTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGT
* * *
422571 CTCTCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CC
60 CTCTCTTGAGACAGTTTCCCTTGAAACAAA------ATCT-TTGAGATCC
* *
422620 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGGCAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
*
422685 TGAGACAGTTTCCCTTGAAACAAAATCTTTGA-ATCT
66 TGAGACAGTTTCCCTTGAAACAAAATCTTTGAGATCC
* * * *
422721 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATAGTTTCCCTTGAAATAAGTTTTGTCTCCCT
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
* * * * *
422786 TTAGACAGTTTCTCTTGAAACACACACCTTTGAGAT-G
66 TGAGACAGTTTCCCTTGAAACA-AAATCTTTGAGATCC
* * * *
422823 GTTTCCCTTGAAACGAATTTTGTCTCTCTTTAGACAGTTTCCCTAGAAACAAA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
422876 ATCTATCTCA
Statistics
Matches: 226, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
100 1 0.00
101 84 0.37
102 57 0.25
103 2 0.01
108 34 0.15
109 2 0.01
111 31 0.14
112 3 0.01
113 1 0.00
114 11 0.05
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (102 bp):
GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATCTTTGAGATCC
Found at i:422768 original size:36 final size:36
Alignment explanation
Indices: 422721--422898 Score: 143
Period size: 36 Copynumber: 5.1 Consensus size: 36
422711 CTTTGAATCT
422721 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * * * *
422757 GTTTCCCTTGAAATAAGTTTTGTCTCCCTTTAGACA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * *
422793 GTTTCTCTTGAAACACA---CA-C-CT-TTGAGATG
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * *
422823 GTTTCCCTTGAAACGAATTTTGTCTCTCTTTAGACA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * * *
422859 GTTTCCCTAGAAACAAAATCTATCTCACTTGAGATG
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
422895 GTTT
1 GTTT
422899 TTTTTTTTAA
Statistics
Matches: 103, Mismatches: 33, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
30 19 0.18
31 1 0.01
32 1 0.01
34 1 0.01
35 2 0.02
36 79 0.77
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
Found at i:422829 original size:66 final size:66
Alignment explanation
Indices: 422749--422873 Score: 189
Period size: 66 Copynumber: 1.9 Consensus size: 66
422739 TTTATCTCTC
* * *
422749 TTGAGATAGTTTCCCTTGAAA-TAAGTTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACACACAC
1 TTGAGATAGTTTCCCTTGAAACGAA-TTTTGTCTCCCTTTAGACAGTTTCCCTAGAAACACACAC
422813 CT
65 CT
* *
422815 TTGAGATGGTTTCCCTTGAAACGAATTTTGTCTCTCTTTAGACAGTTTCCCTAGAAACA
1 TTGAGATAGTTTCCCTTGAAACGAATTTTGTCTCCCTTTAGACAGTTTCCCTAGAAACA
422874 AAATCTATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (66 bp):
TTGAGATAGTTTCCCTTGAAACGAATTTTGTCTCCCTTTAGACAGTTTCCCTAGAAACACACACC
T
Found at i:423498 original size:91 final size:90
Alignment explanation
Indices: 423388--423661 Score: 350
Period size: 91 Copynumber: 3.0 Consensus size: 90
423378 TAAGGGATTG
* *
423388 ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTTATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCAA-GAGGGAGAAGAAGTTCATAATG
** *
423453 AGAAGAACTTGTTCAACCTGGGTTTA
65 AGAAGAACTTGTTCAACCTGGCATCA
* *
423479 AGATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCAAAAAGGGAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCC-AAGAGGGAGAAGAAGTTCATAATG
* *
423544 AGAAGAACTTGTTCAATCTTGCATCA
65 AGAAGAACTTGTTCAACCTGGCATCA
* * * * *
423570 ACATTTACAGTGGAGAGTACATAATGAGAAGAACTCATCCGATAGAGGCAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCC-A-AGAGGGAGAAGAAGTTCATAAT
* * * *
423635 CAGAAGAACTTATTCAACATTGCATCA
64 GAGAAGAACTTGTTCAACCTGGCATCA
423662 CATATGGAGT
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 115 0.72
92 45 0.28
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (90 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCAAGAGGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTGGCATCA
Found at i:423557 original size:20 final size:20
Alignment explanation
Indices: 423495--423558 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
423485 CCAATGGAGA
423495 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * * *
423515 ATCCAAAAAGGGAGAAGAA---
1 GTTC-ATAA-TGAGAAGAACTT
423534 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
423554 GTTCA
1 GTTCA
423559 ATCTTGCATC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 2 0.06
20 7 0.23
21 3 0.10
22 8 0.26
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:423900 original size:30 final size:30
Alignment explanation
Indices: 423866--423949 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
423856 CCATAGTTTC
*
423866 TTCAACATCCCATTCCACTACCATTTTTTA
1 TTCAACATCCCATTCCACTACCATTTTATA
423896 TTCAACATCCCATGT-CACTACCATTTTATA
1 TTCAACATCCCAT-TCCACTACCATTTTATA
* * * *
423926 TTCAATATCACATGCCACCACCAT
1 TTCAACATCCCATTCCACTACCAT
423950 GCCCCCATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (30 bp):
TTCAACATCCCATTCCACTACCATTTTATA
Found at i:426152 original size:23 final size:23
Alignment explanation
Indices: 426118--426161 Score: 56
Period size: 21 Copynumber: 1.9 Consensus size: 23
426108 AAATATTGCT
426118 TAATAATTATTT-AC-TATAAGA
1 TAATAATTATTTCACTTATAAGA
426139 TAATATATCTATTTCACTTATAA
1 TAATA-AT-TATTTCACTTATAA
426162 TATTGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 5 0.26
24 2 0.11
25 5 0.26
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATAATTATTTCACTTATAAGA
Found at i:426961 original size:22 final size:24
Alignment explanation
Indices: 426931--426979 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
426921 AAACAGCCGA
*
426931 AAAAAGTGCCA-AAAGATATA-AG
1 AAAAAGTGCCATAAAGACATAGAG
*
426953 AAAATGTGCCATAAAGACATAGAG
1 AAAAAGTGCCATAAAGACATAGAG
426977 AAA
1 AAA
426980 CGTAATATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (24 bp):
AAAAAGTGCCATAAAGACATAGAG
Found at i:429179 original size:29 final size:29
Alignment explanation
Indices: 429147--429202 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
429137 GGACTAATCT
429147 TTTCAACTAAC-TTGATTCTTGTTGTCTTG
1 TTTCAACTAACATTGA-TCTTGTTGTCTTG
* *
429176 TTTCTACTAACATTGATCTTTTTGTCT
1 TTTCAACTAACATTGATCTTGTTGTCT
429203 GCTCTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.54
Consensus pattern (29 bp):
TTTCAACTAACATTGATCTTGTTGTCTTG
Done.