Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007777.1 Hibiscus syriacus cultivar Beakdansim tig00110059_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: 1720799
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:406038 original size:17 final size:17
Alignment explanation
Indices: 405984--406043 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
405974 TACCCGATTA
**
405984 CCGGGTACCATCAAAAT
1 CCGGGTACCCGCAAAAT
* **
406001 TCGGGTACCCG-ATTA-
1 CCGGGTACCCGCAAAAT
406016 CCGGGTACCCGCAAAAT
1 CCGGGTACCCGCAAAAT
406033 CCGGGTACCCG
1 CCGGGTACCCG
406044 ATTACCGGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 10 0.30
16 4 0.12
17 19 0.58
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (17 bp):
CCGGGTACCCGCAAAAT
Found at i:406067 original size:32 final size:32
Alignment explanation
Indices: 405970--406070 Score: 150
Period size: 32 Copynumber: 3.2 Consensus size: 32
405960 AAACGGGTAT
*
405970 CGGGTACCCGATTACCGGGTACCA-TCAAAATT
1 CGGGTACCCGATTACCGGGTACCAGT-AAAATC
* *
406002 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCAGTAAAATC
*
406034 CGGGTACCCGATTACCGGGTACCAGTAACATC
1 CGGGTACCCGATTACCGGGTACCAGTAAAATC
406066 CGGGT
1 CGGGT
406071 CGGGACACGG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCAGTAAAATC
Found at i:406125 original size:16 final size:16
Alignment explanation
Indices: 406096--406133 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
406086 GAAATCGTCG
*
406096 ACCCGGAAATTCCGGGT
1 ACCC-GAAAATCCGGGT
406113 ACCCGAAAATCCGGGT
1 ACCCGAAAATCCGGGT
406129 ACCCG
1 ACCCG
406134 GATTTGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (16 bp):
ACCCGAAAATCCGGGT
Found at i:410372 original size:21 final size:21
Alignment explanation
Indices: 410348--410394 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
410338 GAAATTGGAC
*
410348 CGATCCC-TTTGTAAAAATGAT
1 CGATCCCATTT-TAAAAAGGAT
*
410369 CGATCCCATTTTCAAAAGGAT
1 CGATCCCATTTTAAAAAGGAT
410390 CGATC
1 CGATC
410395 TATTTTTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATCCCATTTTAAAAAGGAT
Found at i:412759 original size:21 final size:21
Alignment explanation
Indices: 412735--412793 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
412725 ATTTTTGGCT
412735 CAAAGGATCGATCCCTTTGAC
1 CAAAGGATCGATCCCTTTGAC
*
412756 CAAAGGATCAATCCCTTTGAC
1 CAAAGGATCGATCCCTTTGAC
412777 CAAAGGATCGATCCCTT
1 CAAAGGATCGATCCCTT
412794 GGATTCCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
CAAAGGATCGATCCCTTTGAC
Found at i:413841 original size:14 final size:13
Alignment explanation
Indices: 413814--413838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
413804 CAACTATCAA
413814 CATCTTATTTTTC
1 CATCTTATTTTTC
413827 CATCTTATTTTT
1 CATCTTATTTTT
413839 TCCTCTAAAT
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:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (13 bp):
CATCTTATTTTTC
Found at i:416607 original size:18 final size:18
Alignment explanation
Indices: 416563--416616 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
416553 TCATCACGAT
416563 ATGAAGACTTAAGCAAAG
1 ATGAAGACTTAAGCAAAG
*
416581 ATAAAGACTTAAGCAAAG
1 ATGAAGACTTAAGCAAAG
* *
416599 ATGAGGACTCAA-CAAAG
1 ATGAAGACTTAAGCAAAG
416616 A
1 A
416617 AAATGAAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.52, C:0.13, G:0.20, T:0.15
Consensus pattern (18 bp):
ATGAAGACTTAAGCAAAG
Found at i:417288 original size:42 final size:42
Alignment explanation
Indices: 417164--417288 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
417154 TTCAACCTTG
* * *
417164 GCTCATCCATCACATAAGGAGTTGGATCATCATAAACATTTC
1 GCTCATCCATCACAAAAGGAGTTGGATCAACATCAACATTTC
* * * *
417206 ACTCGTCGATCACATAAA-GAGTTGGATCAATATCAACATTTC
1 GCTCATCCATCACA-AAAGGAGTTGGATCAACATCAACATTTC
* * *
417248 GCTCATCCATCACAAAAGGAGTTAGATCAGCATCACCATTT
1 GCTCATCCATCACAAAAGGAGTTGGATCAACATCAACATTT
417289 TGATCAATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.04
42 62 0.93
43 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (42 bp):
GCTCATCCATCACAAAAGGAGTTGGATCAACATCAACATTTC
Found at i:420144 original size:3 final size:3
Alignment explanation
Indices: 420136--420498 Score: 627
Period size: 3 Copynumber: 122.7 Consensus size: 3
420126 GAATGACTCT
420136 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420183 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420229 ATA ATA A-A ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420275 ATA ATAA ATA AT- ATA AT- ATA ATA AT- ATA ATA ATA ATA ATA TATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
420319 ATA ATA ATA ATA ATAA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
420366 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420413 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420461 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
420499 CTGTGTCAAT
Statistics
Matches: 347, Mismatches: 0, Indels: 26
0.93 0.00 0.07
Matches are distributed among these distances:
2 18 0.05
3 317 0.91
4 12 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:423791 original size:22 final size:25
Alignment explanation
Indices: 423761--423817 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
423751 AAAATTACGA
423761 ATAATATTACT-AT-TAAAAATAAAT
1 ATAATA-TACTAATATAAAAATAAAT
423785 ATAATTAATACTAATATAAAAATAAAT
1 ATAA-T-ATACTAATATAAAAATAAAT
423812 ATAATA
1 ATAATA
423818 GTATGACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 4 0.14
25 6 0.21
26 4 0.14
27 15 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATACTAATATAAAAATAAAT
Found at i:425275 original size:122 final size:124
Alignment explanation
Indices: 425141--425387 Score: 464
Period size: 122 Copynumber: 2.0 Consensus size: 124
425131 CACTTCACTT
425141 AAAAAAAAGTTAAAAAGATTATTTTAAAATTTGAAATCTCAAATTAAATAATTTGAATAAGAACT
1 AAAAAAAAGTTAAAAAGATTATTTTAAAATTTGAAATCTCAAATTAAATAATTTGAATAAGAACT
425206 TTATCAAACTCA-AATTGATCGAG-AAAAAAAT-AACAATTTAAATCTATCAAACTTAAA
66 TTATCAAACT-AGAATTGATCGAGAAAAAAAATCAACAATTTAAATCTATCAAACTTAAA
425263 AAAAAAAAGTTAAAAAGATTATTTTAAAATTTGAAATCTCAAATTAAATAATTTGAATAAGAACT
1 AAAAAAAAGTTAAAAAGATTATTTTAAAATTTGAAATCTCAAATTAAATAATTTGAATAAGAACT
425328 TTATCAAACTAGAATTGATCGAGAAAAAAAATCAACAATTTAAATCTATCAAACTTAAA
66 TTATCAAACTAGAATTGATCGAGAAAAAAAATCAACAATTTAAATCTATCAAACTTAAA
425387 A
1 A
425388 TGAACATAAC
Statistics
Matches: 122, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
121 1 0.01
122 86 0.70
123 8 0.07
124 27 0.22
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (124 bp):
AAAAAAAAGTTAAAAAGATTATTTTAAAATTTGAAATCTCAAATTAAATAATTTGAATAAGAACT
TTATCAAACTAGAATTGATCGAGAAAAAAAATCAACAATTTAAATCTATCAAACTTAAA
Found at i:427704 original size:2 final size:2
Alignment explanation
Indices: 427697--427745 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
427687 CAAAATAAAC
427697 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
427739 AT AT AT A
1 AT AT AT A
427746 AAAGCTATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:427927 original size:25 final size:24
Alignment explanation
Indices: 427899--427958 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
427889 TCATAATATC
*
427899 ATCCAAATAAGAAAATATCCACAAT
1 ATCCAAATAACAAAATATCCA-AAT
* *
427924 ATCCAAATATCCATAATATCCAAAT
1 ATCCAAATA-ACAAAATATCCAAAT
427949 ATCCAAATAA
1 ATCCAAATAA
427959 TCTATAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.23
Consensus pattern (24 bp):
ATCCAAATAACAAAATATCCAAAT
Found at i:427931 original size:17 final size:16
Alignment explanation
Indices: 427911--427957 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 16
427901 CCAAATAAGA
427911 AAATATCCACAATATCC
1 AAATATCCA-AATATCC
427928 AAATATCCATAATATCC
1 AAATATCCA-AATATCC
427945 AAATATCCAAATA
1 AAATATCCAAATA
427958 ATCTATAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATCCAAATATCC
Found at i:427932 original size:8 final size:8
Alignment explanation
Indices: 427911--427957 Score: 76
Period size: 8 Copynumber: 5.6 Consensus size: 8
427901 CCAAATAAGA
427911 AAATATCC
1 AAATATCC
427919 ACAATATCC
1 A-AATATCC
427928 AAATATCC
1 AAATATCC
427936 ATAATATCC
1 A-AATATCC
427945 AAATATCC
1 AAATATCC
427953 AAATA
1 AAATA
427958 ATCTATAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 21 0.57
9 16 0.43
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATATCC
Found at i:429935 original size:19 final size:19
Alignment explanation
Indices: 429901--429937 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
429891 AAGGAATGTA
429901 GCATGATTTGATGATGAAT
1 GCATGATTTGATGATGAAT
429920 GCATGTATTTGA-GATGAA
1 GCATG-ATTTGATGATGAA
429938 AAGCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (19 bp):
GCATGATTTGATGATGAAT
Found at i:434015 original size:16 final size:16
Alignment explanation
Indices: 433986--434018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
433976 CTAGTCCCCT
433986 TAGGTATCCATTTTTC
1 TAGGTATCCATTTTTC
434002 TAGGATATCC-TTTTTC
1 TAGG-TATCCATTTTTC
434018 T
1 T
434019 TAGTAGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (16 bp):
TAGGTATCCATTTTTC
Found at i:437686 original size:15 final size:16
Alignment explanation
Indices: 437663--437702 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
437653 AAAATATTTT
437663 AAAT-TTAAAT-T-TA
1 AAATATTAAATATATA
437676 AAATATATAAATATATA
1 AAATAT-TAAATATATA
437693 AAATATTAAA
1 AAATATTAAA
437703 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
14 1 0.04
15 5 0.22
16 5 0.22
17 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTAAATATATA
Found at i:458172 original size:17 final size:17
Alignment explanation
Indices: 458146--458189 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
458136 TCTTACCTTT
458146 AGTATCGATACTACAAC
1 AGTATCGATACTACAAC
*
458163 AGTATTGATACTACAAC
1 AGTATCGATACTACAAC
*
458180 AATATCGATA
1 AGTATCGATA
458190 TTATTCATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (17 bp):
AGTATCGATACTACAAC
Found at i:463973 original size:16 final size:16
Alignment explanation
Indices: 463952--464009 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
463942 TAAATAAACA
*
463952 AACATAAACGAATACG
1 AACATAAACGAACACG
*
463968 AACATAAACAAACACG
1 AACATAAACGAACACG
*
463984 AACATAAATGAACACG
1 AACATAAACGAACACG
464000 AACATAAACG
1 AACATAAACG
464010 GACATAAACG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:464271 original size:12 final size:12
Alignment explanation
Indices: 464242--464279 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
464232 CTCGAGACTC
464242 GAGCTCGATTC-
1 GAGCTCGATTCT
*
464253 AAGCTCGATTCT
1 GAGCTCGATTCT
464265 GAGCTCGATTCT
1 GAGCTCGATTCT
464277 GAG
1 GAG
464280 ATCAATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (12 bp):
GAGCTCGATTCT
Found at i:464272 original size:23 final size:24
Alignment explanation
Indices: 464218--464275 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
464208 AAAAATTTAA
*
464218 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTCAAACTCGAGACTC
* **
464242 GAGCTCGATTCAAGCTCGATTCT-
1 GAGCTCGATTCAAACTCGAGACTC
464265 GAGCTCGATTC
1 GAGCTCGATTC
464276 TGAGATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (24 bp):
GAGCTCGATTCAAACTCGAGACTC
Found at i:465171 original size:10 final size:10
Alignment explanation
Indices: 465156--465203 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
465146 ATAAATGAAT
465156 GAACATAAAC
1 GAACATAAAC
465166 GAACATAACCGAAC
1 GAACAT-A---AAC
465180 GAACATAAAC
1 GAACATAAAC
*
465190 GAACATAATC
1 GAACATAAAC
465200 GAAC
1 GAAC
465204 GAACATAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:465215 original size:14 final size:14
Alignment explanation
Indices: 465163--465218 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
465153 AATGAACATA
*
465163 AACGAACATAACCG
1 AACGAACATAATCG
465177 AACGAACAT-A---
1 AACGAACATAATCG
465187 AACGAACATAATCG
1 AACGAACATAATCG
*
465201 AACGAACATAGTCG
1 AACGAACATAATCG
465215 AACG
1 AACG
465219 TTAACGAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:465226 original size:24 final size:24
Alignment explanation
Indices: 465143--465210 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
465133 AGATTGGTTA
*
465143 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
465167 AACATAACCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
465191 AACATAATCGAACGAACATA
1 AACATAATCGAACGAACATA
465211 GTCGAACGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.05
24 38 0.95
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:467632 original size:75 final size:76
Alignment explanation
Indices: 467523--467690 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 76
467513 CTAATAATTT
* *
467523 TTTTTATATA-TTTTAAATTATTATTAATGCAAGAAATACTTTTTAAATTTTA-CTTATTAACTA
1 TTTTTATATATTTTTAAATTATTATTAATGCAAGAAATAATTCTTAAATTTTATC-TATTAACTA
*
467586 TAATTTACAAC-
65 CAATTTACAACA
** * * * * *
467597 TTTTTATATATTTTTATTTTTTTGTTAATGGAAGAAATAATTCTTAATTTTTATCTCTTAACTAC
1 TTTTTATATATTTTTAAATTATTATTAATGCAAGAAATAATTCTTAAATTTTATCTATTAACTAC
467662 AATTTACAACA
66 AATTTACAACA
*
467673 TTTTGTATACATTTTTAA
1 TTTT-TATATATTTTTAA
467691 TGAAAAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
74 10 0.13
75 52 0.67
76 5 0.06
77 11 0.14
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (76 bp):
TTTTTATATATTTTTAAATTATTATTAATGCAAGAAATAATTCTTAAATTTTATCTATTAACTAC
AATTTACAACA
Found at i:468067 original size:17 final size:16
Alignment explanation
Indices: 468045--468079 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
468035 ATTAGATGAA
*
468045 AAATAAATATATTAATT
1 AAATAAATA-AATAATT
468062 AAATAAATAAATAATT
1 AAATAAATAAATAATT
468078 AA
1 AA
468080 GAAAATATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAAATAAATAATT
Found at i:471296 original size:38 final size:38
Alignment explanation
Indices: 471254--471330 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
471244 TTCCGATGCT
*
471254 ATATGAATCCTCAACCACTCTGCATTTCCGTTGCCGGA
1 ATATGAATCCTCAACCACTCTGCATTTCCATTGCCGGA
*
471292 ATATGAATCCTCAACCACTCTGCATTTCCATTGCGGGA
1 ATATGAATCCTCAACCACTCTGCATTTCCATTGCCGGA
471330 A
1 A
471331 AGTTCTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.29
Consensus pattern (38 bp):
ATATGAATCCTCAACCACTCTGCATTTCCATTGCCGGA
Found at i:484250 original size:6 final size:6
Alignment explanation
Indices: 484239--484267 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
484229 ACCTAGAGTC
484239 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
484268 CCCTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:485182 original size:13 final size:13
Alignment explanation
Indices: 485164--485190 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
485154 GTCAACAATG
485164 GCTTCTGGATGGT
1 GCTTCTGGATGGT
485177 GCTTCTGGATGGT
1 GCTTCTGGATGGT
485190 G
1 G
485191 ATTCGGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.41, T:0.37
Consensus pattern (13 bp):
GCTTCTGGATGGT
Found at i:494754 original size:21 final size:20
Alignment explanation
Indices: 494716--494754 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
494706 TAATGAATGG
*
494716 TTGTTTTTGTATGCTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
494736 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
494755 TAATTCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.03, G:0.21, T:0.67
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:495286 original size:90 final size:90
Alignment explanation
Indices: 495133--495312 Score: 333
Period size: 90 Copynumber: 2.0 Consensus size: 90
495123 AAACTCTGTC
*
495133 GGGAAAATAAGGAATAGAAGTAAGATCATCCTGAGAAGTAGACTTAAGTTTCCTAAGTGAATCCT
1 GGGAAAATAAGGAATAGAAGTAAGATCATCCTGAGAAGTAGACTTAAATTTCCTAAGTGAATCCT
495198 ATCATTCATTCCCATAGTAGCTTGT
66 ATCATTCATTCCCATAGTAGCTTGT
*
495223 GGGAAAATAAGGCATAGAAGTAAGATCATCCTGAGAAGTAGACTTAAATTTCCTAAGTGAATCCT
1 GGGAAAATAAGGAATAGAAGTAAGATCATCCTGAGAAGTAGACTTAAATTTCCTAAGTGAATCCT
*
495288 ATCATTTATTCCCATAGTAGCTTGT
66 ATCATTCATTCCCATAGTAGCTTGT
495313 TGTGTGAGTA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (90 bp):
GGGAAAATAAGGAATAGAAGTAAGATCATCCTGAGAAGTAGACTTAAATTTCCTAAGTGAATCCT
ATCATTCATTCCCATAGTAGCTTGT
Found at i:501288 original size:125 final size:127
Alignment explanation
Indices: 501066--501318 Score: 483
Period size: 125 Copynumber: 2.0 Consensus size: 127
501056 GCGTCTTGGT
501066 TGCTAGCGACGGTTAGTACAGATATTCTACCGCATCTTACTGGTCTCACGTGTTCTCTTACAACT
1 TGCTAGCGACGGTTAGTACAGATATTCTACCGCATCTTACTGGTCTCACGTGTTCTCTTACAACT
501131 GCAAAATTATATATAATGATAACGATGTTGGGTTTTTTCAAGGAT-AACT-ACAGTAGGTCA
66 GCAAAATTATATATAATGATAACGATGTTGGGTTTTTTCAAGGATAAACTAACAGTAGGTCA
501191 TGCTAGCGACGGTTAGTACAGATATTCTACCGCATCTTACTGGTCTCACGTGTTCTCTTACAACT
1 TGCTAGCGACGGTTAGTACAGATATTCTACCGCATCTTACTGGTCTCACGTGTTCTCTTACAACT
501256 GCAAAATTATATATAATGATAACGATGTTGGGTTTTTTCAAGGATAAACTACACAGTAGGTCA
66 GCAAAATTATATATAATGATAACGATGTTGGGTTTTTTCAAGGATAAACTA-ACAGTAGGTCA
501319 CTAATGTTTG
Statistics
Matches: 125, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
125 110 0.88
126 4 0.03
128 11 0.09
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (127 bp):
TGCTAGCGACGGTTAGTACAGATATTCTACCGCATCTTACTGGTCTCACGTGTTCTCTTACAACT
GCAAAATTATATATAATGATAACGATGTTGGGTTTTTTCAAGGATAAACTAACAGTAGGTCA
Found at i:502969 original size:95 final size:95
Alignment explanation
Indices: 502806--502996 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
502796 ATTGAGATAT
502806 TTTTCAAAAGATCTAAGCCATTTTTGGTATCGATACCCGGTGTAGTATCGATACCCACCTACAAG
1 TTTTCAAAAGATCTAAGCCATTTTTGGTATCGATACCCGGTGTAGTATCGATACCCACCTACAAG
502871 AGTATCAATACTCATGGTGAGTATCAATAC
66 AGTATCAATACTCATGGTGAGTATCAATAC
502901 TTTTCAAAAGATCTAAGCCATTTTTGGTATCGATACCCGGTGTAGTATCGATACCCACCTACAAG
1 TTTTCAAAAGATCTAAGCCATTTTTGGTATCGATACCCGGTGTAGTATCGATACCCACCTACAAG
*
502966 AGTATCAATACTCATGGTGAGTATCCATAC
66 AGTATCAATACTCATGGTGAGTATCAATAC
502996 T
1 T
502997 GCTAGCACAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (95 bp):
TTTTCAAAAGATCTAAGCCATTTTTGGTATCGATACCCGGTGTAGTATCGATACCCACCTACAAG
AGTATCAATACTCATGGTGAGTATCAATAC
Found at i:506752 original size:13 final size:14
Alignment explanation
Indices: 506715--506754 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
506705 GTTAACCCGC
506715 GCTGAGTCAACTCA
1 GCTGAGTCAACTCA
*
506729 GTTGAGTCAACTCA
1 GCTGAGTCAACTCA
*
506743 -CTGGGTCAACTC
1 GCTGAGTCAACTC
506755 GGTGACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (14 bp):
GCTGAGTCAACTCA
Found at i:510950 original size:31 final size:31
Alignment explanation
Indices: 510915--510975 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
510905 AATACATAAG
*
510915 ATATGATCACTTTCGTTTTTATTTAATTAAA
1 ATATGATCACTTTCATTTTTATTTAATTAAA
* *
510946 ATATGATCACTTTTATTTTTATTTATTTAA
1 ATATGATCACTTTCATTTTTATTTAATTAA
510976 GATGTGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTTATTTAATTAAA
Found at i:512623 original size:14 final size:14
Alignment explanation
Indices: 512604--512635 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
512594 TGAATTATAT
*
512604 TTTTTTTAAAAATA
1 TTTTTTGAAAAATA
512618 TTTTTTGAAAAATA
1 TTTTTTGAAAAATA
512632 TTTT
1 TTTT
512636 ACGATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTTTTGAAAAATA
Found at i:512811 original size:14 final size:14
Alignment explanation
Indices: 512780--512824 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
512770 AATAATTTAT
*
512780 TTATTATTAAAATA
1 TTATTTTTAAAATA
* *
512794 TTATTTTTATAATG
1 TTATTTTTAAAATA
*
512808 TTATTTATAAAATA
1 TTATTTTTAAAATA
512822 TTA
1 TTA
512825 AAATTGGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATTTTTAAAATA
Found at i:512879 original size:36 final size:35
Alignment explanation
Indices: 512814--512881 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
512804 AATGTTATTT
* *
512814 ATAAAATATTAAAATTGGATAAATTATTTATTGAA
1 ATAAAATATTAAAATTAGATAAATAATTTATTGAA
* *
512849 ATAAAATATTATAAATTATATTAATAATTTATT
1 ATAAAATATTA-AAATTAGATAAATAATTTATT
512882 TTATATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 11 0.39
36 17 0.61
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (35 bp):
ATAAAATATTAAAATTAGATAAATAATTTATTGAA
Found at i:512909 original size:52 final size:55
Alignment explanation
Indices: 512847--512968 Score: 128
Period size: 55 Copynumber: 2.3 Consensus size: 55
512837 TTATTTATTG
* *
512847 AAATAAAATATTATAAATTA-TATTA-ATAATTTATT-TTATATTATTAA-AATAA
1 AAATAAAATATTATAAATTATTATAATATAATTAATTATTATATTA-TAATAATAA
* * * *
512899 AAATACAATATGT-TATATTATTATAATATAATTAATTATTTTATTATAATATTAA
1 AAATAAAATAT-TATAAATTATTATAATATAATTAATTATTATATTATAATAATAA
*
512954 AAATATAATATTATA
1 AAATAAAATATTATA
512969 TTATTAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
52 16 0.28
53 5 0.09
54 13 0.23
55 23 0.40
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (55 bp):
AAATAAAATATTATAAATTATTATAATATAATTAATTATTATATTATAATAATAA
Found at i:512968 original size:22 final size:23
Alignment explanation
Indices: 512940--512986 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
512930 TTAATTATTT
512940 TATTATAATATTAAAAAT-ATAA
1 TATTATAATATTAAAAATAATAA
*
512962 TATTATATTATTAAAAATAATAA
1 TATTATAATATTAAAAATAATAA
512985 TA
1 TA
512987 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTATAATATTAAAAATAATAA
Found at i:512990 original size:32 final size:32
Alignment explanation
Indices: 512923--512992 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
512913 ATATTATTAT
* * *
512923 AATATAATTAATTATTTTATTATAATATTAAA
1 AATATAATTAATTATATTATTAAAATAATAAA
512955 AATATAA-T-ATTATATTATTAAAAATAATAATA
1 AATATAATTAATTATATTATT-AAAATAATAA-A
512987 AATATA
1 AATATA
512993 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 10 0.30
31 9 0.27
32 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AATATAATTAATTATATTATTAAAATAATAAA
Found at i:512991 original size:22 final size:22
Alignment explanation
Indices: 512948--512991 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
512938 TTTATTATAA
*
512948 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
512970 TATTAAAAATAATAATA-AATAT
1 TATTAAAAAT-ATAATATAATAT
512992 ATTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:513053 original size:51 final size:56
Alignment explanation
Indices: 512896--513054 Score: 133
Period size: 55 Copynumber: 3.0 Consensus size: 56
512886 ATTATTAAAA
* * * * *
512896 TAAAAATACAATATGTTATATTATT-ATAAT-ATAATTAAT-TATTTTATT-ATAATAT
1 TAAAAATATAATA--TTATATGATTAAAAATAATAATAAATATATTTTATTAAT-ATTT
*
512951 TAAAAATATAATATTATATTATTAAAAATAATAATAAATATATTTTA--AATATTT
1 TAAAAATATAATATTATATGATTAAAAATAATAATAAATATATTTTATTAATATTT
* * *
513005 TAATAAT-TAATATT-T-TGATT-AAAATGATATTAAA-ATATTTTATTAATATT
1 TAAAAATATAATATTATATGATTAAAAATAATAATAAATATATTTTATTAATATT
513055 AAATTCATAA
Statistics
Matches: 90, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
49 8 0.09
50 12 0.13
51 10 0.11
52 1 0.01
53 17 0.19
54 13 0.14
55 22 0.24
56 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (56 bp):
TAAAAATATAATATTATATGATTAAAAATAATAATAAATATATTTTATTAATATTT
Found at i:517996 original size:22 final size:22
Alignment explanation
Indices: 517966--518016 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
517956 ATTCAACTGT
*
517966 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
*
517988 TGTAACTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
518010 TATAACT
1 TATAACT
518017 TCTGTAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:523827 original size:22 final size:22
Alignment explanation
Indices: 523799--523870 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
523789 TCAGCTATTA
523799 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
523821 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
* * *
523843 TAACTCCTAAAATTAAATCATA
1 TAACTCCTGAAATTATATCATG
523865 TAACTC
1 TAACTC
523871 ATGTAACTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (22 bp):
TAACTCCTGAAATTATATCATG
Found at i:524325 original size:15 final size:14
Alignment explanation
Indices: 524307--524354 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
524297 TTTTTTTTAT
524307 TTTTTTCATTTTTC
1 TTTTTTCATTTTTC
* *
524321 ATTTTTCATTTTTT
1 TTTTTTCATTTTTC
524335 TTATTTTCATTTTTC
1 TT-TTTTCATTTTTC
524350 TTTTT
1 TTTTT
524355 CTTGTGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCATTTTTC
Found at i:524342 original size:29 final size:29
Alignment explanation
Indices: 524299--524355 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
524289 AACAATATTT
*
524299 TTTTTTATTTTTTTCATTTTTCATTTTTCA
1 TTTTTTATTATTTTCATTTTTC-TTTTTCA
524329 TTTTTT-TTATTTTCATTTTTCTTTTTC
1 TTTTTTATTATTTTCATTTTTCTTTTTC
524356 TTGTGGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 14 0.54
30 6 0.23
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTTTTATTATTTTCATTTTTCTTTTTCA
Found at i:524357 original size:6 final size:7
Alignment explanation
Indices: 524308--524355 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
524298 TTTTTTTATT
524308 TTTTTCA
1 TTTTTCA
524315 TTTTTCA
1 TTTTTCA
524322 TTTTTCA
1 TTTTTCA
**
524329 TTTTTTT
1 TTTTTCA
524336 TATTTTCA
1 T-TTTTCA
524344 TTTTTC-
1 TTTTTCA
524350 TTTTTC
1 TTTTTC
524356 TTGTGGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 6 0.17
7 25 0.69
8 5 0.14
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:530944 original size:2 final size:2
Alignment explanation
Indices: 530937--530977 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
530927 ATTTATAATT
* *
530937 TA TA TA TA TA TA TA AA TA TA AA 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 TA TA T
530978 TTAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:530994 original size:24 final size:23
Alignment explanation
Indices: 530938--531025 Score: 59
Period size: 24 Copynumber: 3.7 Consensus size: 23
530928 TTTATAATTT
* * * *
530938 ATATATATATATAAATATAAATAT
1 ATATGTATATATATAT-TTAATAA
*
530962 ATATATATATATATATTTAATAAA
1 ATATGTATATATATATTTAAT-AA
* * * * *
530986 ATTTGTATACAAATAATTTAGTAT
1 ATATGTATATATAT-ATTTAATAA
531010 ATATGTATATATATAT
1 ATATGTATATATATAT
531026 CATTTTTAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
23 6 0.12
24 38 0.76
25 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.45
Consensus pattern (23 bp):
ATATGTATATATATATTTAATAA
Found at i:536554 original size:3 final size:3
Alignment explanation
Indices: 536546--536658 Score: 106
Period size: 3 Copynumber: 38.3 Consensus size: 3
536536 GACCTGAAAT
* * * * * *
536546 ATA ATA ATA ATA ATA TTT TTA ATA ATA ATA ATA TTT TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
536594 ATA TTT TTA ATA ATA ATA ATA ATA AT- ATA A-A ATA ATA ATA TTA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
536641 ATA A-A ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
536659 CAAATGGATG
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
2 6 0.07
3 83 0.90
4 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:536570 original size:18 final size:18
Alignment explanation
Indices: 536547--536614 Score: 136
Period size: 18 Copynumber: 3.8 Consensus size: 18
536537 ACCTGAAATA
536547 TAATAATAATAATATTTT
1 TAATAATAATAATATTTT
536565 TAATAATAATAATATTTT
1 TAATAATAATAATATTTT
536583 TAATAATAATAATATTTT
1 TAATAATAATAATATTTT
536601 TAATAATAATAATA
1 TAATAATAATAATA
536615 ATAATATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATAATAATATTTT
Found at i:536663 original size:16 final size:15
Alignment explanation
Indices: 536601--536658 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 15
536591 ATAATATTTT
*
536601 TAATAATAATAATAA
1 TAATAAAAATAATAA
536616 TAATATAAAATAATAA
1 TAATA-AAAATAATAA
*
536632 TATTAATAAATAA-AA
1 TAATAA-AAATAATAA
*
536647 TAATAATAATAA
1 TAATAAAAATAA
536659 CAAATGGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 19 0.51
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAAAAATAATAA
Found at i:537114 original size:122 final size:121
Alignment explanation
Indices: 536977--537527 Score: 574
Period size: 122 Copynumber: 4.7 Consensus size: 121
536967 TAGAATCAAT
536977 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
*
537042 TATGAACTTTCTCTGGAAAAATTGATGCTGGTCTATCTCCTTTTATGATAGAGTCATG
66 TATGAACTTTCTCTGGAAAAATTGATGCTGATCTA--TCCTTTTATGATAGAGTCATG
*
537100 C-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
* * * * *
537164 TATGAATTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATG
66 TATGAACTTTCTCTGGAAAAATTGATGCTGATCTA--TCCTTTTATGATAGAGTCATG
* *
537222 CAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTAC-C
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTT-CTC
* ** * **
537286 ATTATGAAC-TTCTCTGG-AAAA--G-T--TGATCCAT-C--GAATGAT-GAATTCAAA
64 ATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCCTTTTATGATAG-AGTCATG
** * * *
537334 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCTC
1 CAAAAGG-TTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CCTCTTCAGATAAGTTCTTCTC
* *** * ** *
537399 ATTATGAAC--TCTCTGG---AA---ATGCTGATCCATCAAGTGATGA-A-TTTGA-G
64 ATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCCTTTTATGATAGAGTCATG
* *
537446 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTACTTCAGATAAATTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT-CTTCAGATAAGTTCTTCTCA
537511 TTATGAACTTTCTCTGG
65 TTATGAACTTTCTCTGG
537528 CAATGGTAAT
Statistics
Matches: 376, Mismatches: 35, Indels: 44
0.83 0.08 0.10
Matches are distributed among these distances:
110 5 0.01
111 59 0.16
112 38 0.10
113 67 0.18
114 2 0.01
115 5 0.01
117 6 0.02
119 1 0.00
120 1 0.00
122 118 0.31
123 49 0.13
124 25 0.07
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (121 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCCTTTTATGATAGAGTCATG
Found at i:537356 original size:113 final size:112
Alignment explanation
Indices: 537222--537527 Score: 438
Period size: 113 Copynumber: 2.7 Consensus size: 112
537212 TAGAGTCATG
* *
537222 CAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTAC-C
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-CTC
*
537286 ATTATGAACTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAA
65 ATTATGAACTTCTCTGGAAAAGCTGATCCATC-AAGTGATGAATTCAAA
* * *
537334 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCTC
1 CAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** *
537399 ATTATGAAC-TCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAG
65 ATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
* * *
537446 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTACTTCAGATAAATTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
537511 TTATGAACTTTCTCTGG
66 TTATGAAC-TTCTCTGG
537528 CAATGGTAAT
Statistics
Matches: 173, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
111 62 0.36
112 45 0.26
113 66 0.38
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
Found at i:537495 original size:111 final size:111
Alignment explanation
Indices: 537221--537519 Score: 431
Period size: 111 Copynumber: 2.7 Consensus size: 111
537211 ATAGAGTCAT
* *
537221 GCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTAC-
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-CT
*
537285 CATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAA
65 CATTATGAAC-TCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAA
* * * *
537333 ACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCT
1 GCAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* **
537398 CATTATGAACTCTCTGGAAATGCTGATCCATC-AAGTGATGAATTTGA
65 CATTATGAACTCTCTGGAAAAGCTGATCCATCGAA-TGATGAATTCAA
* * *
537445 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTACTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
537510 ATTATGAACT
66 ATTATGAACT
537520 TTCTCTGGCA
Statistics
Matches: 167, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
111 63 0.38
112 45 0.27
113 59 0.35
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAA
Found at i:548522 original size:20 final size:22
Alignment explanation
Indices: 548476--548527 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
548466 ATTTAATACT
*
548476 TGAAAATAAAATAAAACATTAA
1 TGAAAATAATATAAAACATTAA
*
548498 T-AAAATAATAT-AAATATT-A
1 TGAAAATAATATAAAACATTAA
548517 TGAAAATAATA
1 TGAAAATAATA
548528 AGTATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 9 0.33
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
TGAAAATAATATAAAACATTAA
Found at i:550770 original size:3 final size:3
Alignment explanation
Indices: 550762--550849 Score: 92
Period size: 3 Copynumber: 30.0 Consensus size: 3
550752 ACCTGAAACG
* **
550762 TAA TAA TAA TAA TAT TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
550810 -CA TAA -AA CAA TAA TAG TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
550850 CAAATGGATG
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
2 5 0.07
3 64 0.89
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:551643 original size:31 final size:33
Alignment explanation
Indices: 551553--551650 Score: 139
Period size: 32 Copynumber: 3.1 Consensus size: 33
551543 GTTTGGCAAG
*
551553 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
551586 TTGAAAAATTCATCTT-CTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
551618 TTGGAAAATTC-T-TTGGTAGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
551649 TT
1 TT
551651 TTTCATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.03
31 17 0.29
32 25 0.43
33 14 0.24
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:556608 original size:30 final size:30
Alignment explanation
Indices: 556574--556645 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
556564 GGTTCTTCGG
* *
556574 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGAACTTTAT
556604 GACCTCTGGATAGTTACCGAGGAACTTTAT
1 GACCTCTGGATAGTTACCGAGGAACTTTAT
556634 GACCTCTGGATA
1 GACCTCTGGATA
556646 AGTCCTTCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGAACTTTAT
Found at i:558983 original size:31 final size:33
Alignment explanation
Indices: 558928--558993 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
558918 GTTTGGCAAG
* *
558928 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
558961 TTGGAAAATTC-T-TTGGTAGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
558992 TT
1 TT
558994 TTTCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.65
32 1 0.03
33 10 0.32
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
Found at i:559873 original size:7 final size:7
Alignment explanation
Indices: 559861--559890 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
559851 TCTAACCCTA
559861 CTAATTT
1 CTAATTT
559868 CTAATTT
1 CTAATTT
559875 CTAATTT
1 CTAATTT
559882 CTAATTT
1 CTAATTT
559889 CT
1 CT
559891 TACAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (7 bp):
CTAATTT
Found at i:560068 original size:19 final size:20
Alignment explanation
Indices: 560032--560073 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
560022 ATTTCAATAC
* * *
560032 TTTAATTTTCTGCTCTTT-T
1 TTTAAATTTATGCACTTTAT
560051 TTTAAATTTATGCACTTTAT
1 TTTAAATTTATGCACTTTAT
560071 TTT
1 TTT
560074 TCTTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTAAATTTATGCACTTTAT
Found at i:561135 original size:139 final size:139
Alignment explanation
Indices: 560982--561354 Score: 418
Period size: 138 Copynumber: 2.7 Consensus size: 139
560972 TTGGTCAAAG
* **
560982 TTCCCAATTAATTATTCATTTTAATAAATGGTTAAAAAATGGTTAGATTTTAATATTAGAGTTTC
1 TTCCAAATTAATTATTCATTTTAATAAATGGTTAAAAAATGGTTAGATTTTAATATTAGAGCCTC
* * ** *
561047 CTTTTTTAGGTTTATTTTCACCTTAGTCCCTTAACTTAGAGGATTTTTTA-ATTCG-AACCTCAC
66 C-ATTTTAGGTTTAATTTCACCTTAGTCCCTTAACTTAGAGGAACTTTTATATTCGTAACCGC-C
561110 TTTGCTCCAGA
129 TTTGCTCCAGA
* * * * *
561121 TTCTAAATTAATTATTTGA-TTCAATAAATAGTT-AAAAATGGTTA-ACTTTTAATATTAGAACC
1 TTCCAAATTAATTA-TTCATTTTAATAAATGGTTAAAAAATGGTTAGA-TTTTAATATTAGAGCC
* * * * * * *
561183 TCCATTTTA-GTTTAAATTTCACCTTAGTTCCTTAATTTAGGGGAACTTTTATTTTGGTTATCGC
64 TCCATTTTAGGTTT-AATTTCACCTTAGTCCCTTAACTTAGAGGAACTTTTATATTCGTAACCGC
* ** *
561247 CTTTGTTTGAGG
128 CTTTGCTCCAGA
* *
561259 TTCCAAATTAATTATTCATTTTAATGAATGGTTAAAAAATGGTTAGA-TTTAATATTAGAGGCTC
1 TTCCAAATTAATTATTCATTTTAATAAATGGTTAAAAAATGGTTAGATTTTAATATTAGAGCCTC
561323 CATTTTAGGTTTAATTTCACCTTAGTCCCTTA
66 CATTTTAGGTTTAATTTCACCTTAGTCCCTTA
561355 GTTTAGGTAA
Statistics
Matches: 193, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
136 4 0.02
137 40 0.21
138 103 0.53
139 42 0.22
140 4 0.02
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (139 bp):
TTCCAAATTAATTATTCATTTTAATAAATGGTTAAAAAATGGTTAGATTTTAATATTAGAGCCTC
CATTTTAGGTTTAATTTCACCTTAGTCCCTTAACTTAGAGGAACTTTTATATTCGTAACCGCCTT
TGCTCCAGA
Found at i:561267 original size:138 final size:137
Alignment explanation
Indices: 560952--561423 Score: 416
Period size: 138 Copynumber: 3.4 Consensus size: 137
560942 TTAAGTGAAT
* * * * * * * * * *
560952 TTTTAATTTGATCTTCGTCTTTGGTCAAAGTTCCCAATTAATTA-TTCATTTTAATAAATGGTTA
1 TTTTAATTCGGTCATCGACTTTGCTCAAGGTTCCAAATTAATTATTTGA-TTCAATAAATAGTTA
*** * *
561016 AAAAATGGTTAGATTTTAATATTAGAGTTTCCTTTTTTAGGTTTATTTTCACCTTAGTCCCTTAA
65 AAAAATGGTTAGA-TTTAATATTAGAACCTCC-ATTTTAGGTTTAATTTCACCTTAGTCCCTTAA
* **
561081 CTTAGAGGATT
128 TTTAG-GGAAC
** * * * *
561092 TTTTAATTCGAACCTC-ACTTTGCTCCAGATTCTAAATTAATTATTTGATTCAATAAATAGTT-A
1 TTTTAATTCGGTCATCGACTTTGCTCAAGGTTCCAAATTAATTATTTGATTCAATAAATAGTTAA
*
561155 AAAATGGTTA-ACTTTTAATATTAGAACCTCCATTTTA-GTTTAAATTTCACCTTAGTTCCTTAA
66 AAAATGGTTAGA--TTTAATATTAGAACCTCCATTTTAGGTTT-AATTTCACCTTAGTCCCTTAA
561218 TTTAGGGGAAC
128 TTTA-GGGAAC
* * * * * ** * * * *
561229 TTTTATTTTGGTTATCGCCTTTGTTTGAGGTTCCAAATTAATTA-TTCATTTTAATGAATGGTTA
1 TTTTAATTCGGTCATCGACTTTGCTCAAGGTTCCAAATTAATTATTTGA-TTCAATAAATAGTTA
** *
561293 AAAAATGGTTAGATTTAATATTAGAGGCTCCATTTTAGGTTTAATTTCACCTTAGTCCCTTAGTT
65 AAAAATGGTTAGATTTAATATTAGAACCTCCATTTTAGGTTTAATTTCACCTTAGTCCCTTAATT
* *
561358 TAGGTAAT
130 TAGGGAAC
* * * *
561366 TTTTAATTCGGTCCTTGATTTTGCTCAAGGTTCCAAATTGATTATTTGATTCAATAAA
1 TTTTAATTCGGTCATCGACTTTGCTCAAGGTTCCAAATTAATTATTTGATTCAATAAA
561424 ATTTATAAAA
Statistics
Matches: 264, Mismatches: 58, Indels: 23
0.77 0.17 0.07
Matches are distributed among these distances:
136 4 0.02
137 88 0.33
138 108 0.41
139 47 0.18
140 17 0.06
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (137 bp):
TTTTAATTCGGTCATCGACTTTGCTCAAGGTTCCAAATTAATTATTTGATTCAATAAATAGTTAA
AAAATGGTTAGATTTAATATTAGAACCTCCATTTTAGGTTTAATTTCACCTTAGTCCCTTAATTT
AGGGAAC
Found at i:565672 original size:23 final size:23
Alignment explanation
Indices: 565643--565691 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
565633 TAGGTGCAAT
*
565643 TTTCATGGAAACATCTTGTTTTA
1 TTTCATGGAAACATCATGTTTTA
*
565666 TTTCATGGAAGCATCATGTTTTA
1 TTTCATGGAAACATCATGTTTTA
565689 TTT
1 TTT
565692 GAATTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (23 bp):
TTTCATGGAAACATCATGTTTTA
Found at i:569914 original size:10 final size:9
Alignment explanation
Indices: 569894--569952 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
569884 CAGCTGGAAA
569894 ACCGGTTTG
1 ACCGGTTTG
569903 ACCGGTTTTG
1 ACCGG-TTTG
* *
569913 ACCAGTCTG
1 ACCGGTTTG
* *
569922 ATCGGTCTG
1 ACCGGTTTG
569931 AACCGGTTTG
1 -ACCGGTTTG
*
569941 ACCGGTCTG
1 ACCGGTTTG
569950 ACC
1 ACC
569953 CGACCGACCC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:569946 original size:19 final size:19
Alignment explanation
Indices: 569893--569950 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
569883 GCAGCTGGAA
*
569893 AACCGGTTTGACCGGTTTTG
1 AACCGGTTTGACCGG-TCTG
* * *
569913 -ACCAGTCTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
569931 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
569950 A
1 A
569951 CCCGACCGAC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 3 0.10
19 27 0.90
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:571145 original size:164 final size:165
Alignment explanation
Indices: 570845--571173 Score: 635
Period size: 165 Copynumber: 2.0 Consensus size: 165
570835 ATATGGACTT
570845 GGACTTACGGGCCTAAGGATACAAGCTCTAAAGCTTATCCTTAGGTTGGCTTCTTTTTGCTGTGT
1 GGACTTACGGGCCTAAGGATACAAGCTCTAAAGCTTATCCTTAGGTTGGCTTCTTTTTGCTGTGT
570910 GCTTAAAGTAAGCTATATGGAAAATAGTTTTGGGAACTACTGATGGTGTACAAGAAAAGGGTTTA
66 GCTTAAAGTAAGCTATATGGAAAATAGTTTTGGGAACTACTGATGGTGTACAAGAAAAGGGTTTA
570975 AAACTATGATTTTCAAAAGTT-AACTTTTTTATGA
131 AAACTATGATTTTCAAAAGTTAAACTTTTTTATGA
571009 GGACTTACGGGCCTAAGGATACAAGCTCTAAAGCTTATCCTTAGGTTGGCTTTCTTTTTGCTGTG
1 GGACTTACGGGCCTAAGGATACAAGCTCTAAAGCTTATCCTTAGGTTGGC-TTCTTTTTGCTGTG
571074 TGCTTAAAGTAAGCTATATGGAAAATAGTTTTGGGAACTACTGATGGTGTACAAGAAAAGGGTTT
65 TGCTTAAAGTAAGCTATATGGAAAATAGTTTTGGGAACTACTGATGGTGTACAAGAAAAGGGTTT
571139 -AAACTATGATTTTCAAAAGTTAAACTTTTTTATGA
130 AAAACTATGATTTTCAAAAGTTAAACTTTTTTATGA
571174 ATTTATGAGA
Statistics
Matches: 163, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
164 71 0.44
165 92 0.56
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (165 bp):
GGACTTACGGGCCTAAGGATACAAGCTCTAAAGCTTATCCTTAGGTTGGCTTCTTTTTGCTGTGT
GCTTAAAGTAAGCTATATGGAAAATAGTTTTGGGAACTACTGATGGTGTACAAGAAAAGGGTTTA
AAACTATGATTTTCAAAAGTTAAACTTTTTTATGA
Found at i:573857 original size:7 final size:7
Alignment explanation
Indices: 573845--573870 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
573835 TCTAACCCTA
573845 CTAATTT
1 CTAATTT
573852 CTAATTT
1 CTAATTT
573859 CTAATTT
1 CTAATTT
573866 CTAAT
1 CTAAT
573871 ATCTTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
CTAATTT
Found at i:575759 original size:139 final size:137
Alignment explanation
Indices: 575584--576108 Score: 535
Period size: 139 Copynumber: 3.9 Consensus size: 137
575574 AACTTAGTTA
* * * * *
575584 AATTTAGGTGAATTTTTAATTTGGTCTTCGCATTTGCTCGAGATTCCAAATTAATTATTCGTTTC
1 AATTTAGG-GAAATTTTAATTCGGTCCTCGCTTTTGCTCGAGATTCCAAATTAATTATTCATTTC
*
575649 AATAAATAGTTAAAAAAGGATTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCT
65 AATAAATAGTTAAAAATGG-TTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCT
*
575714 TAGTTCCTT
129 TAGTCCCTT
* * *
575723 AATTTAGGGAACATTTTAATTCGGTCCTTGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTTC
1 AATTTAGGGAA-ATTTTAATTCGGTCCTCGCTTTTGCTCGAGATTCCAAATTAATTATTCATTTC
* ** *
575788 AATAAATAGTTAAGAATGGTTAGGTTTTAATATTAGAGAATCCATTTTAGATTAAATTTCACCTT
65 AATAAATAGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCTT
575853 AGTCCCTT
130 AGTCCCTT
* * *
575861 TATGTT--GGAGAATTTTGAATTTGGTCCTCGCCTTTGCTCTTG-GA-TCCAAATTAATTATTCA
1 AAT-TTAGGGA-AATTTT-AATTCGGTCCTCGCTTTTGCTC--GAGATTCCAAATTAATTATTCA
* * *
575922 TTTC----AAT-G-----AATGGTTA-ATTTTAAAATTAGAGCCTCCATTTTAGGTTTAATTTCA
61 TTTCAATAAATAGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCA
575976 CCTTAGTCCCTT
126 CCTTAGTCCCTT
* * * * * *
575988 AATTTAAGAGAATTTTTAATTCAGTCCTCGCTTTTGCTTGAGGTTCCAAATTGATTATTCGA-TT
1 AATTT-AGGGAAATTTTAATTCGGTCCTCGCTTTTGCTCGAGATTCCAAATTAATTATTC-ATTT
* * * * * *
576052 CAATAAA-ATTTATAAAATTTGTTAAGTTTTAATATTAGAGTCTACATTTTAGGTTTA
64 CAATAAATAGTTA-AAAA-TGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTA
576109 GCCCTTTTAA
Statistics
Matches: 320, Mismatches: 41, Indels: 50
0.78 0.10 0.12
Matches are distributed among these distances:
125 1 0.00
126 3 0.01
127 82 0.26
128 14 0.04
129 2 0.01
131 2 0.01
133 1 0.00
134 3 0.01
137 10 0.03
138 100 0.31
139 101 0.32
140 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (137 bp):
AATTTAGGGAAATTTTAATTCGGTCCTCGCTTTTGCTCGAGATTCCAAATTAATTATTCATTTCA
ATAAATAGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCTTA
GTCCCTT
Found at i:575887 original size:138 final size:137
Alignment explanation
Indices: 575584--576108 Score: 554
Period size: 138 Copynumber: 3.9 Consensus size: 137
575574 AACTTAGTTA
* * * * * * *
575584 AATTTAGGTGAATTTTTAATTTGGTCTTCGCATTTGCTCGAGATTCCAAATTAATTATTCGTTTC
1 AATTTAGGAGAATTTTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTTC
*
575649 AATAAATAGTTAAAAAAGGATTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCT
66 AATAAA-AGTTAAAAATGG-TTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCT
*
575714 TAGTTCCTT
129 TAGTCCCTT
* *
575723 AATTTAGG-GAACATTTTAATTCGGTCCTTGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTT
1 AATTTAGGAGAA-TTTTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTT
* ** *
575787 CAATAAATAGTTAAGAATGGTTAGGTTTTAATATTAGAGAATCCATTTTAGATTAAATTTCACCT
65 CAATAAA-AGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCT
575852 TAGTCCCTT
129 TAGTCCCTT
* * * * ** * *
575861 TATGTT-GGAGAATTTTGAATTTGGTCCTCGCCTTTGCTCTTGGATCCAAATTAATTATTCATTT
1 AAT-TTAGGAGAATTTTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTT
* * *
575925 CAAT----G-----AATGGTTA-ATTTTAAAATTAGAGCCTCCATTTTAGGTTTAATTTCACCTT
65 CAATAAAAGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCTT
575980 AGTCCCTT
130 AGTCCCTT
* * * * *
575988 AATTTAAGAGAATTTTTAATTCAGTCCTCGCTTTTGCTTGAGGTTCCAAATTGATTATTCGA-TT
1 AATTTAGGAGAATTTTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTA-TCCATTT
* * * * * *
576052 CAATAAAATTTATAAAATTTGTTAAGTTTTAATATTAGAGTCTACATTTTAGGTTTA
65 CAATAAAAGTTA-AAAA-TGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTA
576109 GCCCTTTTAA
Statistics
Matches: 320, Mismatches: 49, Indels: 34
0.79 0.12 0.08
Matches are distributed among these distances:
126 2 0.01
127 93 0.29
128 10 0.03
133 1 0.00
137 2 0.01
138 109 0.34
139 103 0.32
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (137 bp):
AATTTAGGAGAATTTTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATCCATTTC
AATAAAAGTTAAAAATGGTTAGGTTTTAATATTAGAGCCTCCATTTTAGATTTAATTTCACCTTA
GTCCCTT
Found at i:576038 original size:127 final size:128
Alignment explanation
Indices: 575801--576055 Score: 320
Period size: 127 Copynumber: 2.0 Consensus size: 128
575791 AAATAGTTAA
* * *
575801 GAATGGTTAGGTTTTAATATTAGAGAATCCATTTTAGATTAAATTTCACCTTAGTCCCTTTATGT
1 GAATGGTTAGATTTTAAAATTAGAGAATCCATTTTAGATTAAATTTCACCTTAGTCCCTTAATGT
* ** *
575866 TGGAGAATTTTGAATTTGGTCCTCGCCTTTGCTCTTGGATCCAAATTAATTATTC-ATTTCAAT
66 TAGAGAATTTTGAATTCAGTCCTCGCCTTTGCTCTAGGATCCAAATTAATTATTCGA-TTCAAT
** * *
575929 GAATGGTTA-ATTTTAAAATTAGAGCCTCCATTTTAGGTTTAATTTCACCTTAGTCCCTTAAT-T
1 GAATGGTTAGATTTTAAAATTAGAGAATCCATTTTAGATTAAATTTCACCTTAGTCCCTTAATGT
* * * *
575992 TAAGAGAATTTTTAATTCAGTCCTCGCTTTTGCT-TGAGGTTCCAAATTGATTATTCGATTCAAT
66 T-AGAGAATTTTGAATTCAGTCCTCGCCTTTGCTCT-AGGATCCAAATTAATTATTCGATTCAAT
576056 AAAATTTATA
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
126 3 0.03
127 96 0.88
128 10 0.09
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (128 bp):
GAATGGTTAGATTTTAAAATTAGAGAATCCATTTTAGATTAAATTTCACCTTAGTCCCTTAATGT
TAGAGAATTTTGAATTCAGTCCTCGCCTTTGCTCTAGGATCCAAATTAATTATTCGATTCAAT
Found at i:576976 original size:6 final size:6
Alignment explanation
Indices: 576959--576993 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
576949 TCGTTAAGAA
576959 CTCGAG -TCGAG CTCGAG CTCGAG CTCGAG CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
576994 TCTATTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:577313 original size:2 final size:2
Alignment explanation
Indices: 577306--577351 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
577296 AATAAAAATG
*
577306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
577348 AT AT
1 AT AT
577352 TAAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577607 original size:22 final size:22
Alignment explanation
Indices: 577580--577626 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
577570 TCATTAATTA
577580 ACCTATTAAATGTAATGGTTAT
1 ACCTATTAAATGTAATGGTTAT
577602 ACCTATTAAATGTAATGGTTAT
1 ACCTATTAAATGTAATGGTTAT
577624 ACC
1 ACC
577627 GGTTAACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
ACCTATTAAATGTAATGGTTAT
Found at i:577632 original size:22 final size:22
Alignment explanation
Indices: 577584--577632 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
577574 TAATTAACCT
*
577584 ATTAAATGTAATGGTTATACCT
1 ATTAAATGTAATGGTTATACCG
577606 ATTAAATGTAATGGTTATACCG
1 ATTAAATGTAATGGTTATACCG
*
577628 GTTAA
1 ATTAA
577633 CGGTTCCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
ATTAAATGTAATGGTTATACCG
Found at i:583012 original size:2 final size:2
Alignment explanation
Indices: 583005--583050 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
582995 TATTTAAACA
583005 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
583047 AT AT
1 AT AT
583051 GACTAAGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:583326 original size:29 final size:27
Alignment explanation
Indices: 583238--583326 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 27
583228 AAAATGTAAT
*
583238 AATTAAAGTACTGAAATTAAAATATTGAA
1 AATTAAAGTA-TGAAATTAAAAGA-TGAA
* ** *
583267 AACTGTAAAGCAAAAAATAAAAAGATAGAA
1 AA-T-TAAAGTATGAAATTAAAAGAT-GAA
583297 AATTAAAGTAGTGAAATTAAAAGACTGAA
1 AATTAAAGTA-TGAAATTAAAAGA-TGAA
583326 A
1 A
583327 TAAAATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
28 6 0.13
29 18 0.39
30 16 0.35
31 6 0.13
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.22
Consensus pattern (27 bp):
AATTAAAGTATGAAATTAAAAGATGAA
Found at i:585042 original size:136 final size:136
Alignment explanation
Indices: 584868--585360 Score: 623
Period size: 136 Copynumber: 3.6 Consensus size: 136
584858 AGTAAAAGGC
* ** * * *
584868 TGAATAAGTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTGTGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
* * *
584933 CCT-TCTGGAAATGTTGATCCTCAAAAGAGGTGTCGCTGATTCAATTTCATATGTGATGAATTAA
66 -TTATCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTAA
584997 GGTAATGT
130 GGTAA-GT
* * *
585005 TGAACAAGTTCTT-TCATTATGAACTTCTTCTTTCTCTTCAGACGAGTTCTTCTCATTATAAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
* **
585069 CTT-TCTAGAAATACTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTAA
66 -TTATCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTAA
*
585133 GGAAAGGT
130 GGTAA-GT
*
585141 TTAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * * * * * * *
585206 TTATCTGAAAATGTTGATCCTCAAGAGAGGTTTTTCTTTCATTCAACTCCATAAGTAATTAATCA
66 TTATCTGGAAATGTTGATCCTCAAAAGAGG--TGTCGTTGATTCAACTTCATATGTGATGAATTA
*
585271 AGTTAAGAT
129 AGGTAAG-T
* *
585280 CGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
*
585345 TTCTCTGGAAATGTTG
66 TTATCTGGAAATGTTG
585361 GTGCTGATCT
Statistics
Matches: 310, Mismatches: 41, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
136 121 0.39
137 82 0.26
138 1 0.00
139 106 0.34
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (136 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
TTATCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTAAG
GTAAGT
Found at i:585447 original size:23 final size:22
Alignment explanation
Indices: 585413--585457 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
585403 TGAACAAGTT
585413 CTTCTTATTATGAACTTCTTCTC
1 CTTCTTATTATG-ACTTCTTCTC
*
585436 CTTCTTCA-TATGAGTTCTTCTC
1 CTTCTT-ATTATGACTTCTTCTC
585458 ATTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (22 bp):
CTTCTTATTATGACTTCTTCTC
Found at i:585570 original size:120 final size:121
Alignment explanation
Indices: 585281--585670 Score: 604
Period size: 120 Copynumber: 3.2 Consensus size: 121
585271 AGTTAAGATC
*
585281 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTTTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * * * * *
585345 TTCTCTGGAAATGTTGGTGCTGATCTATCTCATTCTGTGATAGAGTCGAGGAAAAGGTT
65 CT-TCTGGAAAAGTTGATGCTGATCTATCTCTTTCTATGATAGAATC-AAGCAAAGGTT
* *
585404 GAACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
585469 TTCTGGAAAAGTTGATGCTGATCTATCTCTTTTTATGATAGAATCAAGCAAAGGTT
66 TTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTATGATAGAATCAAGCAAAGGTT
*
585525 GAACAAGTTCTTCTTA-TATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
585589 TTCTGGAAAATTTGATGTTGATCTATCTCTTTCTATGATAGAATCAAGCAAAGGTT
66 TTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTATGATAGAATCAAGCAAAGGTT
585645 GAACAAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTT
585671 TCTCTGGAAA
Statistics
Matches: 248, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
120 115 0.46
121 34 0.14
122 41 0.17
123 58 0.23
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (121 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTATGATAGAATCAAGCAAAGGTT
Found at i:585711 original size:83 final size:82
Alignment explanation
Indices: 585568--585758 Score: 276
Period size: 83 Copynumber: 2.3 Consensus size: 82
585558 TCTTCAGATG
* * *
585568 AGTTCTTCTCATTATGAACTCTTCTGGAAAATTTGATGTTGATCTATCTCTTTCTATGATAGAAT
1 AGTTCTTCTCATTATGAACTTTTCTGGAAAATTTGATGCTGATCTATCTCCTTCTATGATAGAAT
585633 CAAGCAAAGGTTGAACA
66 CAAGCAAAGGTTGAACA
* *
585650 AGTTCTTCTCATTATGAACTTTCTCTGG-AAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGA
1 AGTTCTTCTCATTATGAACTTT-TCTGGAAAAT-TTGATGCTGATCTATCTCCTTCTATGATAGA
* * *
585714 GTCATGCAAATGTTGAACA
64 ATCAAGCAAAGGTTGAACA
585733 AGTTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTT-TTCT
585759 TCCTCTTCAG
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
82 25 0.26
83 72 0.73
84 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (82 bp):
AGTTCTTCTCATTATGAACTTTTCTGGAAAATTTGATGCTGATCTATCTCCTTCTATGATAGAAT
CAAGCAAAGGTTGAACA
Found at i:586025 original size:101 final size:103
Alignment explanation
Indices: 585838--586041 Score: 331
Period size: 101 Copynumber: 2.0 Consensus size: 103
585828 GGAAATGGAG
585838 TCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
1 TCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
*
585903 CCCATTATGAACTCTACCTGGAAATGTTGATCCATCGA
66 CCCATTATGAACTCTACCTGGAAATGTTGACCCATCGA
* *
585941 TCAAGCTAAA-GTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATGAGTTCTT
1 TCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
** * *
586004 CTGATTATGAACTTTATCTGGAAATGTTGACCCATCGA
66 CCCATTATGAACTCTACCTGGAAATGTTGACCCATCGA
586042 ATGATGGATC
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 57 0.61
102 28 0.30
103 9 0.10
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (103 bp):
TCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
CCCATTATGAACTCTACCTGGAAATGTTGACCCATCGA
Found at i:586870 original size:54 final size:53
Alignment explanation
Indices: 586801--586950 Score: 158
Period size: 54 Copynumber: 2.8 Consensus size: 53
586791 GTAAAACATG
* **
586801 TGACAATACATTCATCATTTCTCGTGGTTTCTGCCCAGATTTTCGTAAAGCTTT
1 TGACAACACATTCATCATTTCTCGTGGTTTCTGCCCAGATTTT-GTAAAGAATT
* * * * * *
586855 TGATAACACATTCATCTTTTCTTGTGGCTTCTGGCCAGAAGTTTGTAAAGAATT
1 TGACAACACATTCATCATTTCTCGTGGTTTCTGCCCAG-ATTTTGTAAAGAATT
* **
586909 TGACAACACATTCATCATTT-TCTGTGATTTCTGTGCAGATTT
1 TGACAACACATTCATCATTTCTC-GTGGTTTCTGCCCAGATTT
586951 CTGATCAATG
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
53 4 0.05
54 69 0.90
55 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (53 bp):
TGACAACACATTCATCATTTCTCGTGGTTTCTGCCCAGATTTTGTAAAGAATT
Found at i:587721 original size:70 final size:72
Alignment explanation
Indices: 587638--587802 Score: 201
Period size: 75 Copynumber: 2.3 Consensus size: 72
587628 GATGTGGTCC
* * *
587638 TTCAGCATGCCCCAACATTTACTGATA-TGAACGTTCAAAAT-G-TTATTCCAATTTCTGATTAA
1 TTCAGCATGCCCCAACATTTACTAATACAG-ACGTTCAAAATCGCATATTCCAATTTCTGATTAA
**
587700 AATGGGCT
65 AATAAGCT
*
587708 TTCAGCATGCCCCAACATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTCTGATT
1 TTCAGCATGCCCCAACATTTACTAATACAGACGTTCAAAAT-CG-C-ATATTCCAATTTCTGATT
*
587773 GAAATAAGCT
63 AAAATAAGCT
*
587783 TTCAGCAGGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
587803 GTTAACGTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
70 36 0.44
71 1 0.01
72 1 0.01
75 43 0.53
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (72 bp):
TTCAGCATGCCCCAACATTTACTAATACAGACGTTCAAAATCGCATATTCCAATTTCTGATTAAA
ATAAGCT
Found at i:587795 original size:75 final size:76
Alignment explanation
Indices: 587681--587880 Score: 246
Period size: 75 Copynumber: 2.7 Consensus size: 76
587671 TTCAAAATGT
* *
587681 TATTCCAATTTCTGATTAAAATGGGCTTTCAGCATGCCCCAACATTTGCTAATAC-AG-ACGTTC
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAA-ACGAGAACATTC
587744 AAAATGCGCCAA
65 AAAATGCGCCAA
** * * *
587756 TATTCCAATTTCTGATTGAAATAAGCTTTCAGCAGGCCCCAACATTTG-TTAACGTGAACATTCA
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAAACGAGAACATTCA
587820 AAATGCGCCAA
66 AAATGCGCCAA
* * * * *
587831 TATTCCTGA-TTATGATTGAAATGGGTTTTCAGCATACCCCAATATTTGCT
1 TATTCC-AATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCT
587881 TCTTGTTGAT
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
73 2 0.02
74 3 0.03
75 99 0.93
76 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (76 bp):
TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAAACGAGAACATTCA
AAATGCGCCAA
Found at i:590849 original size:72 final size:72
Alignment explanation
Indices: 590719--590853 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
590709 TATAATAGGT
* *
590719 TAGCTGAATATTATCCATAAAGCCGGGGCGATTAATCAATTGCTCTATAGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGCAT
590784 AACAAAC
66 AACAAAC
* * * *
590791 TAGCTGAATATTATCCATAAAGTCGGGGCTG-TTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAGCCGGGGC-GATTAACCAATTGCTCTAGAGGGACAACTCAAGC
590854 TTTATTATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 55 0.98
73 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGCAT
AACAAAC
Found at i:593254 original size:20 final size:20
Alignment explanation
Indices: 593226--593270 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
593216 GCAAAGATGC
* * *
593226 AAATGAAAAAATGAAAATGT
1 AAATAAAAAAATAAAAATGA
*
593246 AAATAAAAACATAAAAATGA
1 AAATAAAAAAATAAAAATGA
593266 AAATA
1 AAATA
593271 CAAATGTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (20 bp):
AAATAAAAAAATAAAAATGA
Found at i:595454 original size:22 final size:21
Alignment explanation
Indices: 595423--595468 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
595413 TTTCTTAATA
595423 TTAAAAAATAAATAT-TATTAT
1 TTAAAAAATAAATATATA-TAT
*
595444 TTAAACAAATATATATATATAT
1 TTAAA-AAATAAATATATATAT
595466 TTA
1 TTA
595469 TATGACTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAAATAAATATATATAT
Found at i:595744 original size:29 final size:28
Alignment explanation
Indices: 595670--595751 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
595660 AAAATGTAAT
* *
595670 AATTAAAGTACTGAAATTAAAATATTGAA
1 AATTAAAGTA-TGAAATTAAAAGATAGAA
* ** *
595699 AATGTAAAGCAAAAAATAAAAAGATAGAA
1 AAT-TAAAGTATGAAATTAAAAGATAGAA
595728 AATTAAAGTAGTGAAATTAAAAGA
1 AATTAAAGTA-TGAAATTAAAAGA
595752 CTGAAATAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 6 0.15
29 29 0.71
30 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.23
Consensus pattern (28 bp):
AATTAAAGTATGAAATTAAAAGATAGAA
Found at i:596365 original size:14 final size:15
Alignment explanation
Indices: 596339--596367 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
596329 CAAAATATCA
596339 TTCATTCTTTTCTCT
1 TTCATTCTTTTCTCT
596354 TTCATT-TTTTCTCT
1 TTCATTCTTTTCTCT
596368 CCCAGAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCATTCTTTTCTCT
Found at i:598300 original size:75 final size:75
Alignment explanation
Indices: 598159--598372 Score: 308
Period size: 75 Copynumber: 2.9 Consensus size: 75
598149 TAAAACATCT
* * * *
598159 TAAATCTTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATATTTA
1 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
598223 AAATAATATTC-
65 AAATAATA-TCA
* * **
598234 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTTAAATACCTAAAGTAAAGATAAAATATAA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAT-A
598299 AAATAATATCA
65 AAATAATATCA
598310 TAAAT-TTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
598373 TTGTTTAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
74 6 0.05
75 104 0.84
76 14 0.11
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AATAATATCA
Found at i:601719 original size:21 final size:21
Alignment explanation
Indices: 601693--601753 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
601683 ATCAGATTGT
601693 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
601714 CCAGGGGGAACAGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
601734 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
601754 GGGAACAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:601749 original size:20 final size:20
Alignment explanation
Indices: 601693--601753 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
601683 ATCAGATTGT
601693 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
*
601714 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
601734 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
601754 GGGAACAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:601766 original size:15 final size:15
Alignment explanation
Indices: 601746--601801 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
601736 AGGGGGTATC
601746 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
601761 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
601779 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
601794 GATTCCCC
1 GATTCCCC
601802 CTGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:601780 original size:33 final size:34
Alignment explanation
Indices: 601719--601802 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 34
601709 CCCCCCCAGG
601719 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
601754 GGGAACAGATTCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
*
601787 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
601803 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 31 0.65
34 6 0.12
35 11 0.23
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:601954 original size:21 final size:21
Alignment explanation
Indices: 601914--601954 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
601904 ATTTGAATAT
* *
601914 TATGAAGGGGTATCGGTTCCA
1 TATGAAGGGGTACCGATTCCA
601935 TATGAAGGGGTACCGATTCC
1 TATGAAGGGGTACCGATTCC
601955 CCCCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCA
Found at i:602277 original size:34 final size:32
Alignment explanation
Indices: 602238--602307 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
602228 TTTTGTAAAG
*
602238 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
602272 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
602304 GGGA
1 GGGA
602308 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:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:605315 original size:20 final size:20
Alignment explanation
Indices: 605259--605319 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
605249 ATCAGATTGT
605259 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
605279 CCTAGGTGGAACAGATTCCCC
1 CC-AGGGGGTACAGATTCCCC
605300 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
605320 GGGAACAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:605343 original size:34 final size:35
Alignment explanation
Indices: 605286--605370 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 35
605276 CCCCCTAGGT
*
605286 GGAACAGATTCCCCCCAGGGGGTATCGATTCCCCG
1 GGAACAGATTCCCCCCAGAGGGTATCGATTCCCCG
605321 GGAACAGATTCCCCCCA-AGGGTATCGATTCCCCG
1 GGAACAGATTCCCCCCAGAGGGTATCGATTCCCCG
*
605355 GGTACAGATTCCCCCC
1 GGAACAGATTCCCCCC
605371 TTGCATGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 31 0.65
35 17 0.35
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (35 bp):
GGAACAGATTCCCCCCAGAGGGTATCGATTCCCCG
Found at i:605364 original size:15 final size:15
Alignment explanation
Indices: 605312--605368 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
605302 AGGGGGTATC
*
605312 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
605327 GATTCCCCCCAAGGGTATC-
1 GATT--CCCC--GGGTA-CA
605346 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
605361 GATTCCCC
1 GATTCCCC
605369 CCTTGCATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:605510 original size:21 final size:21
Alignment explanation
Indices: 605484--605525 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
605474 ATTTGAATAT
*
605484 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
605505 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
605526 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:605587 original size:21 final size:21
Alignment explanation
Indices: 605554--605593 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
605544 TTTTTGTAGA
*
605554 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
605576 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
605594 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:605847 original size:34 final size:32
Alignment explanation
Indices: 605808--605877 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
605798 TTTTGTAAAG
*
605808 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
605842 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
605874 GGGA
1 GGGA
605878 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:611418 original size:75 final size:76
Alignment explanation
Indices: 611338--611553 Score: 301
Period size: 76 Copynumber: 2.9 Consensus size: 76
611328 TAAAACATAT
* * * *
611338 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TC
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
* *
611401 TAAATAACATTC
65 AAAATAACATCC
* *
611413 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTTAAATACCTAAAACATAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
611478 AAATAATATCC
66 AAATAACATCC
* * *
611489 AAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
611554 TGTTTAAAAT
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 5 0.04
75 50 0.40
76 70 0.56
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAACATCC
Found at i:617379 original size:60 final size:59
Alignment explanation
Indices: 617254--617386 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
617244 ATAGTTAGGT
* * ** * **
617254 GACCATTTTATAACTTTTAATAGTCGGGGGACTCAATAAAGCAACATCCTATAGTTGAG
1 GACCATTTTGTAACTGTTAATAGTCGAAGGACTCAATAAAGAAACATCCTATAGTAAAG
* ** *
617313 GAACCATTTTGTAACTGTTCATAGTCGAAGGACTCAATAAAGAAATGTCTTATAGTCAAAG
1 G-ACCATTTTGTAACTGTTAATAGTCGAAGGACTCAATAAAGAAACATCCTATAGT-AAAG
617374 GACCATTTGTGTA
1 GACCATTT-TGTA
617387 TTTTACCCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 52 0.87
61 7 0.12
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (59 bp):
GACCATTTTGTAACTGTTAATAGTCGAAGGACTCAATAAAGAAACATCCTATAGTAAAG
Found at i:624253 original size:31 final size:31
Alignment explanation
Indices: 624217--624320 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
624207 AGACTCTGGC
* * *
624217 AGGTTCAGTCGCTGCTGGTAATTCCTTGTAT
1 AGGTTCAGTCACTGTTGGTAATTCCTTATAT
* * *
624248 AGGTTCAG-CACCGATTGGTAATTCCTATCTCT
1 AGGTTCAGTCACTG-TTGGTAATTCCT-TATAT
624280 GGCAGGTTCAGTCACTGTTGGTAATTCCTTATAT
1 ---AGGTTCAGTCACTGTTGGTAATTCCTTATAT
624314 AGGTTCA
1 AGGTTCA
624321 ACACCAACTG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
30 3 0.05
31 26 0.44
32 3 0.05
34 3 0.05
35 20 0.34
36 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
AGGTTCAGTCACTGTTGGTAATTCCTTATAT
Found at i:624301 original size:35 final size:34
Alignment explanation
Indices: 624210--624309 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 34
624200 GGTATGAAGA
* *
624210 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCACTGTTGGTAATTCCTT
* * *
624244 GTAT---AGGTTCAG-CACCGATTGGTAATTCCTAT
1 CTCTGGCAGGTTCAGTCACTG-TTGGTAATTCCT-T
624276 CTCTGGCAGGTTCAGTCACTGTTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCACTGTTGGTAATTCCTT
624310 ATATAGGTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
30 3 0.06
31 19 0.37
32 3 0.06
34 3 0.06
35 20 0.38
36 4 0.08
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (34 bp):
CTCTGGCAGGTTCAGTCACTGTTGGTAATTCCTT
Found at i:629335 original size:40 final size:40
Alignment explanation
Indices: 629291--629371 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
629281 ACAAGTTCGT
629291 TCTAATTTGGTTTTTGATACCTTGTTTTGTTTTAAATAAG
1 TCTAATTTGGTTTTTGATACCTTGTTTTGTTTTAAATAAG
*
629331 TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
1 TCTAATTTGGTTTTTGATACCTTGTTTTGTTTTAAATAAG
629371 T
1 T
629372 TTTGAATGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.56
Consensus pattern (40 bp):
TCTAATTTGGTTTTTGATACCTTGTTTTGTTTTAAATAAG
Found at i:639654 original size:9 final size:9
Alignment explanation
Indices: 639642--639692 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
639632 AAAAAAGATT
639642 AAAAAATG-
1 AAAAAATGA
639650 -AAAAATGA
1 AAAAAATGA
639658 AAAAAATGA
1 AAAAAATGA
639667 AAAAAA--A
1 AAAAAATGA
*
639674 TAAAAA-GA
1 AAAAAATGA
639682 AAAAAAT-A
1 AAAAAATGA
639690 AAA
1 AAA
639693 GGAGGGTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 13 0.35
8 10 0.27
9 14 0.38
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:639678 original size:16 final size:16
Alignment explanation
Indices: 639643--639692 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
639633 AAAAAGATTA
*
639643 AAAAATGAAAAATGAA-
1 AAAAATGAAAAA-AAAT
639659 AAAAATGAAAAAAAAT
1 AAAAATGAAAAAAAAT
639675 AAAAA-G-AAAAAAAT
1 AAAAATGAAAAAAAAT
639689 AAAA
1 AAAA
639693 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.38
15 3 0.09
16 17 0.53
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAAATGAAAAAAAAT
Found at i:640988 original size:113 final size:113
Alignment explanation
Indices: 640785--641119 Score: 492
Period size: 113 Copynumber: 3.0 Consensus size: 113
640775 TTCAGGTTCG
* * **
640785 ATCCCGATTCAATGGATCAATTCCTTCAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCT
1 ATCCTGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCT
* *
640850 CTTTTATCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
66 CTTTTATCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT
*
640898 ATCCTGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCT
1 ATCCTGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCT
* * *
640963 CTTTTTTCTAAGATTTGATATTCCCTTCAAAGTAAGCGGAACAAGTCT
66 CTTTTATCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT
* * * * * *
641011 -GCTTCGATTCAATGGATTAACTTCCCCAGATCTGATAGTCCCTTCAGAGTAAGTGGAACATGTC
1 ATCCT-GATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* *
641075 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
65 TCTTTTATCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
641120 ATATCTCTTC
Statistics
Matches: 201, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
112 2 0.01
113 199 0.99
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (113 bp):
ATCCTGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCT
CTTTTATCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT
Found at i:641117 original size:48 final size:48
Alignment explanation
Indices: 641038--641147 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
641028 TAACTTCCCC
* * * ** *
641038 AGATCTGATAGTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTC-TCAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATATCTCTTCTTC-A
641086 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATATCTCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATATCTCTTCTTCA
641134 AGATTTGATATTCC
1 AGATTTGATATTCC
641148 TTGAGTGACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 53 0.96
49 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATATCTCTTCTTCA
Found at i:641396 original size:3 final size:3
Alignment explanation
Indices: 641388--641434 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
641378 CATCCTGTTC
* * *
641388 TTA TTA TTA TTA TTA -TA TTCA TTA TTA TTA ATA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
641433 TT
1 TT
641435 TTACATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:646401 original size:18 final size:18
Alignment explanation
Indices: 646378--646439 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
646368 GCATTTTTTT
646378 AATTTCAATTTGAGATTA
1 AATTTCAATTTGAGATTA
* *
646396 AATTTCAATTTCA-ATTTC
1 AATTTCAATTTGAGA-TTA
* * *
646414 AATTTTAATTTGAGTTTG
1 AATTTCAATTTGAGATTA
646432 AATTTCAA
1 AATTTCAA
646440 ATTCGGTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.97
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (18 bp):
AATTTCAATTTGAGATTA
Found at i:646405 original size:6 final size:6
Alignment explanation
Indices: 646378--646439 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
646368 GCATTTTTTT
* * * *
646378 AATTTC AATTTG AGA-TTA AATTTC AATTTC AATTTC AATTTT AATTTG
1 AATTTC AATTTC A-ATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* *
646426 AGTTTG AATTTC AA
1 AATTTC AATTTC AA
646440 ATTCGGTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 1 0.02
6 44 0.96
7 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (6 bp):
AATTTC
Found at i:647695 original size:20 final size:21
Alignment explanation
Indices: 647656--647700 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
647646 GTAAATATAA
*
647656 AGTATCGATAATTATTATTCC
1 AGTACCGATAATTATTATTCC
*
647677 AGTACCGATACTT-TTATTCC
1 AGTACCGATAATTATTATTCC
647697 AGTA
1 AGTA
647701 TGCATCTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (21 bp):
AGTACCGATAATTATTATTCC
Found at i:648047 original size:20 final size:21
Alignment explanation
Indices: 647999--648048 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
647989 ATAGGCGTAA
647999 ATACAAGTATCGATAATGTCT
1 ATACAAGTATCGATAATGTCT
* * *
648020 ATATAAGTATCGATACT-TTT
1 ATACAAGTATCGATAATGTCT
648040 ATACAAGTA
1 ATACAAGTA
648049 ACGAATTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
ATACAAGTATCGATAATGTCT
Done.