Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007935.1 Hibiscus syriacus cultivar Beakdansim tig00110345_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: 1073174
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 3 of 6
Found at i:497255 original size:18 final size:19
Alignment explanation
Indices: 497205--497258 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
497195 GTCCGTTTCT
* *
497205 AGCCATTGGGATGATTTGG
1 AGCCGTTGGGATTATTTGG
*
497224 ATCCGTTGGGATTATTTGG
1 AGCCGTTGGGATTATTTGG
497243 AGCCGTT-GGATTATTT
1 AGCCGTTGGGATTATTT
497259 TTCTACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.19, C:0.11, G:0.31, T:0.39
Consensus pattern (19 bp):
AGCCGTTGGGATTATTTGG
Found at i:497314 original size:21 final size:22
Alignment explanation
Indices: 497288--497328 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
497278 ACAGGACAGG
*
497288 GAGTATTGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
*
497309 GAGTATCGGTACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
497329 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:497561 original size:20 final size:20
Alignment explanation
Indices: 497536--497605 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
497526 CTTACCTTTG
*
497536 GTATCGGTATCACGTGAACA
1 GTATCGGTACCACGTGAACA
*
497556 GTATCGGTACCACATGAACA
1 GTATCGGTACCACGTGAACA
497576 GTATCGGTACCACGTGAACA
1 GTATCGGTACCACGTGAACA
*
497596 ATATCGGTAC
1 GTATCGGTAC
497606 TTTTAATGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
GTATCGGTACCACGTGAACA
Found at i:498082 original size:20 final size:21
Alignment explanation
Indices: 498048--498103 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
498038 TATTTTAATG
498048 TATATTTAAATTTTTAGTAATTT
1 TATATTT--ATTTTTAGTAATTT
* *
498071 TAT-TTTATTTTTTGTATTTT
1 TATATTTATTTTTAGTAATTT
498091 TATATTTATTTTT
1 TATATTTATTTTT
498104 TGAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 15 0.50
21 9 0.30
22 3 0.10
23 3 0.10
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TATATTTATTTTTAGTAATTT
Found at i:498098 original size:21 final size:21
Alignment explanation
Indices: 498029--498113 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
498019 AAATTGATAA
* *
498029 TATATTTATTATTT-TAA-TG
1 TATATTTATTTTTTGTAATTT
*
498048 TATATTTAAATTTTTAGTAATTT
1 TATATTT--ATTTTTTGTAATTT
*
498071 TAT-TTTATTTTTTGTATTTT
1 TATATTTATTTTTTGTAATTT
498091 TATATTTATTTTTTG-AATATT
1 TATATTTATTTTTTGTAAT-TT
498112 TA
1 TA
498114 AACAATTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.13
20 17 0.31
21 20 0.37
22 6 0.11
23 4 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TATATTTATTTTTTGTAATTT
Found at i:498157 original size:21 final size:22
Alignment explanation
Indices: 498109--498151 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
498099 TTTTTTGAAT
*
498109 ATTTAAACAATTTTATATTTATA
1 ATTTAAA-AATATTATATTTATA
498132 ATTTAAAAATATT-TATTTAT
1 ATTTAAAAATATTATATTTAT
498152 TTTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTAAAAATATTATATTTATA
Found at i:499633 original size:20 final size:20
Alignment explanation
Indices: 499597--499636 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
499587 TGTTTGAATC
*
499597 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
499617 AAATTAATT-GTAAATTATTT
1 AAATTAATTAG-AAATTATTT
499637 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:507684 original size:24 final size:23
Alignment explanation
Indices: 507652--507702 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
507642 TTTATTTAAT
**
507652 TTTTAATTT-TAATATTTGAATAA
1 TTTTAATTTATAAT-TTAAAATAA
507675 TTTTATATTTATAATTTAAAATAA
1 TTTTA-ATTTATAATTTAAAATAA
507699 TTTT
1 TTTT
507703 TTTCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 15 0.62
25 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAATTTATAATTTAAAATAA
Found at i:508121 original size:20 final size:20
Alignment explanation
Indices: 508096--508136 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
508086 TACCATCACC
508096 AGCTTAATTGATTTTATAAG
1 AGCTTAATTGATTTTATAAG
* *
508116 AGCTTAGTTGTTTTTATAAG
1 AGCTTAATTGATTTTATAAG
508136 A
1 A
508137 TAATAATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (20 bp):
AGCTTAATTGATTTTATAAG
Found at i:508689 original size:21 final size:21
Alignment explanation
Indices: 508649--508689 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
508639 AAAAGAAAAA
*
508649 GAAAAAGAAAAGACATAATAT
1 GAAAAAGAAAAGACAAAATAT
508670 GAAAAAGAATAAGA-AAAATA
1 GAAAAAGAA-AAGACAAAATA
508690 ATAATCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (21 bp):
GAAAAAGAAAAGACAAAATAT
Found at i:508693 original size:27 final size:27
Alignment explanation
Indices: 508643--508694 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
508633 AAGAAAAAAA
*
508643 GAAAAAGAAAAAGAAAAGACATAATAT
1 GAAAAAGAAAAAGAAAAGAAATAATAT
*
508670 GAAAAAGAATAAGAAAA-ATAATAAT
1 GAAAAAGAAAAAGAAAAGA-AATAAT
508695 CAGCGGCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.71, C:0.02, G:0.13, T:0.13
Consensus pattern (27 bp):
GAAAAAGAAAAAGAAAAGAAATAATAT
Found at i:517932 original size:90 final size:89
Alignment explanation
Indices: 517773--517949 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
517763 CCTAACACAC
517773 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
517838 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
* *
517862 CCTTTTATATCCACGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
*
517927 TTTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
517950 TTTGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:523848 original size:2 final size:2
Alignment explanation
Indices: 523841--523871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
523831 CACCGTGCAA
523841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
523872 CGTTGTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:524638 original size:90 final size:89
Alignment explanation
Indices: 524476--524639 Score: 283
Period size: 90 Copynumber: 1.8 Consensus size: 89
524466 CCTAACACAC
*
524476 CCTTTTATAACCAAGTTACCCTAATCATATTATGGTTTTATTATTTCAAATTAAATAAATCTATA
1 CCTTTTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAAATAAATCTATA
524541 TTTAATTAACTAGAATTTAATAAT
66 TTTAATTAACTAGAATTTAATAAT
* *
524565 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAAATAAATCTAT
*
524630 TTTTAATTAA
65 ATTTAATTAA
524640 TTGAAATTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
89 33 0.47
90 37 0.53
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (89 bp):
CCTTTTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAAATAAATCTATA
TTTAATTAACTAGAATTTAATAAT
Found at i:530892 original size:45 final size:45
Alignment explanation
Indices: 530810--530899 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
530800 AAATGAGAGA
** *
530810 CTTAGGAAATAAGTTGGGTAATGCTGGCTATAGCTCCAACATAGT
1 CTTAGGAAATAAGTTGGGTAATGCTGAATATAACTCCAACATAGT
530855 CTTAGGAAATAAGTTGGGTAATGCT-AATAATAACTCCAACATAGT
1 CTTAGGAAATAAGTTGGGTAATGCTGAAT-ATAACTCCAACATAGT
530900 GAGGGAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
CTTAGGAAATAAGTTGGGTAATGCTGAATATAACTCCAACATAGT
Found at i:538946 original size:21 final size:20
Alignment explanation
Indices: 538921--538959 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
538911 TATCAAGGTC
*
538921 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
538942 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
538960 TCCTACAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:548671 original size:15 final size:15
Alignment explanation
Indices: 548636--548673 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
548626 CAAGTTTAGA
548636 TTTTTTAAATAAAAT
1 TTTTTTAAATAAAAT
*
548651 TATTTTTAAATAATAT
1 T-TTTTTAAATAAAAT
548667 TTTTTTA
1 TTTTTTA
548674 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTTAAATAAAAT
Found at i:555163 original size:55 final size:55
Alignment explanation
Indices: 554842--555156 Score: 477
Period size: 55 Copynumber: 5.7 Consensus size: 55
554832 CCTAATGCCA
* * *
554842 ATACGGAAATTCTTAAACTTATTATGAATTTCTTAGTTTTGAACACACGGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
* * *
554897 ATACAGAAATTCATAAAATTATTATGAATTTCTTAGTTTTGCACACACAATGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
* * * **
554952 ATACGAAAATTCATAAATTTATTATGAATTTCGTAGTTTTGCACACTTAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
* *
555007 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
* * *
555062 ATACGGAAATTCATAAACTTGTTATGAATTTCTTAGTTTGGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
*
555117 ATACGGAAATTCATAAACTTATTATGAATTTATTAGTTTT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTT
555157 TTACACATAT
Statistics
Matches: 234, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 234 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGTCC
Found at i:555569 original size:19 final size:21
Alignment explanation
Indices: 555516--555570 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
555506 GTACCCCTAC
555516 CATGGTATCGATACTTCTATA
1 CATGGTATCGATACTTCTATA
555537 CTATGGTA-CTGATAC-TCTAT-
1 C-ATGGTATC-GATACTTCTATA
555557 CATGGTATCGATAC
1 CATGGTATCGATAC
555571 CATTTCTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 11 0.35
20 2 0.06
21 7 0.23
22 11 0.35
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
CATGGTATCGATACTTCTATA
Found at i:560418 original size:51 final size:51
Alignment explanation
Indices: 560323--560420 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
560313 TCCGATAATG
** * * *
560323 CACCGTTATTCATCTAACTTGCATTAGTGTCACATTTCTACCAAAAAACTA
1 CACCGTTAGGCATCTAACTTGCATTAATGGCACATTTATACCAAAAAACTA
* *
560374 CACCGTTAGGCATCTAACTTGCATTAATGGCACCTTTATGCCAAAAA
1 CACCGTTAGGCATCTAACTTGCATTAATGGCACATTTATACCAAAAA
560421 CCACAGTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (51 bp):
CACCGTTAGGCATCTAACTTGCATTAATGGCACATTTATACCAAAAAACTA
Found at i:560703 original size:55 final size:54
Alignment explanation
Indices: 560667--561050 Score: 579
Period size: 55 Copynumber: 7.0 Consensus size: 54
560657 TTACACACCT
560667 AATGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
1 AATGCC-ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
* *
560722 AGTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
1 AATG-CCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
*
560777 AATGTCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAT
1 AATG-CCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
* * * *
560832 AGTGCTCTTACGGAAATTCATAAACTTATTATGAATTTATTAATTTTGCACACAC
1 AATGC-CATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
* * * *
560887 ATTGCCCATATGAAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACAC
1 AATG-CCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
* *
560942 AGTGCCTATACGGAAATTCATAAACTTATTATGAACTTCTTAGTTTTGCACACAC
1 AATGCC-ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
*
560997 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
1 AATG-CCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
561051 TATAGTGCCA
Statistics
Matches: 300, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
54 3 0.01
55 292 0.97
56 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (54 bp):
AATGCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
Found at i:560862 original size:165 final size:165
Alignment explanation
Indices: 560669--561050 Score: 649
Period size: 165 Copynumber: 2.3 Consensus size: 165
560659 ACACACCTAA
*
560669 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATATG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATATG
* *
560734 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGTCC-ATACGGAAATTCAT
66 AAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACACAATG-CCTATACGGAAATTCAT
* *
560798 AAACTTATTATGAATTTCTTAGTTTTGCACACATAG
130 AAACTTATTATGAACTTCTTAGTTTTGCACACACAG
* * * * *
560834 TGCTCTTACGGAAATTCATAAACTTATTATGAATTTATTAATTTTGCACACACATTGCCCATATG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATATG
*
560899 AAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACACAGTGCCTATACGGAAATTCATA
66 AAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACACAATGCCTATACGGAAATTCATA
560964 AACTTATTATGAACTTCTTAGTTTTGCACACACAG
131 AACTTATTATGAACTTCTTAGTTTTGCACACACAG
560999 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
561051 TATAGTGCCA
Statistics
Matches: 201, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
164 2 0.01
165 199 0.99
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (165 bp):
TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATATG
AAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACACAATGCCTATACGGAAATTCATA
AACTTATTATGAACTTCTTAGTTTTGCACACACAG
Found at i:564512 original size:92 final size:92
Alignment explanation
Indices: 564350--564527 Score: 311
Period size: 92 Copynumber: 1.9 Consensus size: 92
564340 AAACATACAA
564350 TTATTAAATGATTGAAGATAAATTTTATATATGTGCATGTCACCGTCATATGATTGACTAATACT
1 TTATTAAATGATTGAAGATAAATTTTATATATGTGCATGTCACCGTCATATGATTGACTAATACT
*
564415 CATGCTCGTATAAATGTGTTCTAACAC
66 AATGCTCGTATAAATGTGTTCTAACAC
* * *
564442 TTATTAAATGATTTAAGATAAGTTTTATATATGTGCATGTCACGGTCATATGATTGACTAATACT
1 TTATTAAATGATTGAAGATAAATTTTATATATGTGCATGTCACCGTCATATGATTGACTAATACT
*
564507 AATGCTCGTGTAAATGTGTTC
66 AATGCTCGTATAAATGTGTTC
564528 ACAACACGTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (92 bp):
TTATTAAATGATTGAAGATAAATTTTATATATGTGCATGTCACCGTCATATGATTGACTAATACT
AATGCTCGTATAAATGTGTTCTAACAC
Found at i:569073 original size:23 final size:22
Alignment explanation
Indices: 569031--569092 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
569021 AAAATTGTCC
* *
569031 TAAAAAT-AAATCAAATTAATGT
1 TAAAAATAAAAT-AAAATAATAT
569053 TAAACAATAAAATAAAATAATAT
1 TAAA-AATAAAATAAAATAATAT
569076 TAAATAA-ATAAATAAAA
1 TAAA-AATA-AAATAAAA
569093 GAATCAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 5 0.15
23 25 0.74
24 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAAAATAAAATAAAATAATAT
Found at i:572934 original size:21 final size:21
Alignment explanation
Indices: 572908--572952 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
572898 GATTTCTGGG
* *
572908 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
572929 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
572950 CAA
1 CAA
572953 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:573325 original size:16 final size:16
Alignment explanation
Indices: 573304--573337 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
573294 AGTCATGGAC
* *
573304 ATAATTATGTGTGGTT
1 ATAATTATATGTGATT
573320 ATAATTATATGTGATT
1 ATAATTATATGTGATT
573336 AT
1 AT
573338 CTATATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (16 bp):
ATAATTATATGTGATT
Found at i:574677 original size:149 final size:149
Alignment explanation
Indices: 574410--574867 Score: 813
Period size: 149 Copynumber: 3.1 Consensus size: 149
574400 GAGTCGAGGG
574410 TCTACGCGGTCCTTCGGGACATATGTATATTC-TTGGAACA--TGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
574472 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
574537 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
574556 TCTACGCGGTCCTTTGGGACATATGTATATTCTTTGGAATATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
574621 ACTTGATCCCTAGTATATGTATATGATTCTTAAGAAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
574686 TATGGCACTACGGTAACAAT
131 TATGGCACTACGGT-GCAAT
574706 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
574771 ACTTGAT-CCTAG--TATGTATA-GATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
574832 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
574851 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
574868 TGCAATTATA
Statistics
Matches: 299, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
145 20 0.07
146 85 0.28
147 15 0.05
149 105 0.35
150 74 0.25
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:575805 original size:19 final size:20
Alignment explanation
Indices: 575767--575817 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
575757 TTCAAAAATC
*
575767 GTTTTAAAAAACTATATATAT
1 GTTTTCAAAAAC-ATATATAT
575788 GTTTTCAAAAAC-TATATAT
1 GTTTTCAAAAACATATATAT
575807 G-TTTCAAAAAC
1 GTTTTCAAAAAC
575818 CATTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 10 0.34
19 8 0.28
21 11 0.38
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (20 bp):
GTTTTCAAAAACATATATAT
Found at i:575824 original size:52 final size:53
Alignment explanation
Indices: 575747--575850 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 53
575737 TAATATATAT
* *
575747 TATATACGTTTTCAAAAATCGTTTTAAAAAACTATA-TATATGTTTTCAAAAAC
1 TATATACGTTTTCAAAAACCATTTT-AAAAACTATATTATATGTTTTCAAAAAC
*
575800 TATATATG-TTTCAAAAACCATTTTAAAAACTATATTATATGTTTTCAAAAA
1 TATATACGTTTTCAAAAACCATTTTAAAAACTATATTATATGTTTTCAAAAA
575851 TATGTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
51 10 0.21
52 30 0.64
53 7 0.15
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (53 bp):
TATATACGTTTTCAAAAACCATTTTAAAAACTATATTATATGTTTTCAAAAAC
Found at i:575864 original size:13 final size:14
Alignment explanation
Indices: 575836--575864 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
575826 AAACTATATT
575836 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
575850 ATATGTTTT-AAAA
1 ATATGTTTTCAAAA
575863 AT
1 AT
575865 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:575916 original size:42 final size:41
Alignment explanation
Indices: 575830--575917 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
575820 TTTTAAAAAC
* *
575830 TATATTATATGTTTTCAAAAATATGTTTTAAAAATTTATAT
1 TATATTATATGTTTTCAAAAATATGTTTTAAAAATATACAT
* *
575871 TATATATATAT-TTTT-TAAAATCATTTTTTAAAAACTATACAT
1 TATAT-TATATGTTTTCAAAAAT-ATGTTTTAAAAA-TATACAT
575913 TATAT
1 TATAT
575918 GTTTTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.12
41 20 0.50
42 15 0.38
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (41 bp):
TATATTATATGTTTTCAAAAATATGTTTTAAAAATATACAT
Found at i:575940 original size:24 final size:24
Alignment explanation
Indices: 575895--575952 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
575885 TTAAAATCAT
*
575895 TTTTTAAAAACTATACATTATATG
1 TTTTTAAAAACTATACATTATATA
575919 TTTTTAAAAACTAT--ATTATATA
1 TTTTTAAAAACTATACATTATATA
575941 TATTTTCAAAAA
1 T-TTTT-AAAAA
575953 ACCATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 8 0.26
23 4 0.13
24 19 0.61
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTTAAAAACTATACATTATATA
Found at i:575976 original size:60 final size:63
Alignment explanation
Indices: 575850--576001 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 63
575840 GTTTTCAAAA
*** *
575850 ATATG-TTTTAAAAATTTATATTATATATATATTTTTTAAAATCATTTTTTAAAAACTATACATT
1 ATATGTTTTTAAAAA-TTATATTATATATATATTTCAAAAAACCA-TTTTTAAAAACTATACATT
* * *
575914 ATATGTTTTTAAAAACTATATTATATATAT-TTTCAAAAAACCA-TTTT-AAAACTTTATATT
1 ATATGTTTTTAAAAATTATATTATATATATATTTCAAAAAACCATTTTTAAAAACTATACATT
* *
575974 ATATGTTTTAAAAAATTATACTATATAT
1 ATATGTTTTTAAAAATTATATTATATAT
576002 CTTCAAAAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
60 36 0.47
61 4 0.05
63 9 0.12
64 19 0.25
65 9 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (63 bp):
ATATGTTTTTAAAAATTATATTATATATATATTTCAAAAAACCATTTTTAAAAACTATACATT
Found at i:575977 original size:36 final size:36
Alignment explanation
Indices: 575920--575988 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
575910 CATTATATGT
575920 TTTTAAAAACTATATTATATATATTTTCAAAAAACCA
1 TTTTAAAAACTATATTATATATATTTT-AAAAAACCA
* *
575957 TTTT-AAAACTTTA-TATTATATGTTTTAAAAAA
1 TTTTAAAAACTATATTA-TATATATTTTAAAAAA
575989 TTATACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.28
36 17 0.59
37 4 0.14
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATTATATATATTTTAAAAAACCA
Found at i:576001 original size:24 final size:22
Alignment explanation
Indices: 575957--575999 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
575947 CAAAAAACCA
**
575957 TTTTAAAACTTTATATTATATG
1 TTTTAAAAAATTATATTATATG
*
575979 TTTTAAAAAATTATACTATAT
1 TTTTAAAAAATTATATTATAT
576000 ATCTTCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAAAAATTATATTATATG
Found at i:580232 original size:26 final size:27
Alignment explanation
Indices: 580184--580239 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
580174 AACTATGGTT
580184 TTACATTCTTACCATTCTCCTTGGTGA
1 TTACATTCTTACCATTCTCCTTGGTGA
* *
580211 TTACATTTTTCCCATTCT-CTTGGTGA
1 TTACATTCTTACCATTCTCCTTGGTGA
580237 TTA
1 TTA
580240 GACAGAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (27 bp):
TTACATTCTTACCATTCTCCTTGGTGA
Found at i:584776 original size:20 final size:21
Alignment explanation
Indices: 584746--584789 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
584736 GAAAGTAGAA
*
584746 TTAAAATATATTGAATTTAAT
1 TTAAAATATATTAAATTTAAT
*
584767 TTAAAA-ATATTAAATTTATT
1 TTAAAATATATTAAATTTAAT
584787 TTA
1 TTA
584790 TTTTAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAAATATATTAAATTTAAT
Found at i:585150 original size:2 final size:2
Alignment explanation
Indices: 585143--585187 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
585133 AAATTGATAA
585143 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
585185 AT A
1 AT A
585188 AATAATAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:589094 original size:20 final size:20
Alignment explanation
Indices: 589049--589106 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
589039 AATAACCATT
*
589049 TGAGTATCGATAC-CAAGGT
1 TGAGTATCGATACTCAAGGG
*
589068 TGGGTATCGATACTCAAGGG
1 TGAGTATCGATACTCAAGGG
* *
589088 TGAGTATTGATACTGAAGG
1 TGAGTATCGATACTCAAGG
589107 ACACAATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (20 bp):
TGAGTATCGATACTCAAGGG
Found at i:590048 original size:2 final size:2
Alignment explanation
Indices: 590035--590071 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
590025 GATTAGGGTT
*
590035 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
590072 GTAAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:591366 original size:10 final size:10
Alignment explanation
Indices: 591351--591378 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
591341 TTTAAATAAT
591351 AAACGAACAC
1 AAACGAACAC
591361 AAACGAACAC
1 AAACGAACAC
591371 AAACGAAC
1 AAACGAAC
591379 GAACTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.29, G:0.11, T:0.00
Consensus pattern (10 bp):
AAACGAACAC
Found at i:592287 original size:11 final size:11
Alignment explanation
Indices: 592271--592337 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
592261 TTATCTATTA
* *
592271 ATAATAGTACC
1 ATAATAATAAC
592282 ATAATAATAAC
1 ATAATAATAAC
*
592293 ATAATAATAATA
1 ATAATAATAA-C
592305 ATAATATAATAAAC
1 AT-A-ATAAT-AAC
*
592319 TATACTAATAAC
1 -ATAATAATAAC
592331 ATAATAA
1 ATAATAA
592338 GATTATAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 25 0.56
12 5 0.11
13 5 0.11
14 6 0.13
15 4 0.09
ACGTcount: A:0.60, C:0.09, G:0.01, T:0.30
Consensus pattern (11 bp):
ATAATAATAAC
Found at i:592288 original size:3 final size:3
Alignment explanation
Indices: 592282--592449 Score: 91
Period size: 3 Copynumber: 56.3 Consensus size: 3
592272 TAATAGTACC
* * *
592282 ATA ATA ATA A-C ATA ATA ATA ATA ATA AT- ATA ATA A-A CT- ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
592326 ATA A-C ATA ATA A-G ATT ATA ACA GCATA ATA ATA AT- ATA A-A CATA
1 ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA -ATA
* * * *
592370 ATA ATA ATA ATA ATA ATA ATA ATA ACTA GTGCA GTA ATA ATA ACA TATT
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA AT--A ATA ATA ATA ATA -ATA
* * *
592419 ATA GTA ATA ATA ATA CTA ATA ATA TTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
592450 AAGTAATGGT
Statistics
Matches: 125, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
2 10 0.08
3 106 0.85
4 4 0.03
5 5 0.04
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:594479 original size:16 final size:18
Alignment explanation
Indices: 594458--594490 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
594448 ATACATTAAA
594458 TCGGTT-TCG-ATTTTTT
1 TCGGTTATCGAATTTTTT
594474 TCGGTTATCGAATTTTT
1 TCGGTTATCGAATTTTT
594491 GATTCGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (18 bp):
TCGGTTATCGAATTTTTT
Found at i:594873 original size:21 final size:20
Alignment explanation
Indices: 594787--594944 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
594777 AAATGACCAA
**
594787 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
594806 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
594826 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
594846 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
594867 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
594888 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
594908 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
594929 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
594945 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:594973 original size:20 final size:20
Alignment explanation
Indices: 594911--595103 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
594901 CGATTTTCCA
* ** *
594911 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
594931 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
594951 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
594971 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
594991 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
595011 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
595031 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
595051 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
595071 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
595092 AAATCGCAACGC
1 AAATCGCAACGC
595104 AATATTTAAA
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:594995 original size:60 final size:60
Alignment explanation
Indices: 594911--595103 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
594901 CGATTTTCCA
* ** * *
594911 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
594971 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
595031 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
595092 AAATCGCAACGC
1 AAATCGCAACGC
595104 AATATTTAAA
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:596182 original size:14 final size:14
Alignment explanation
Indices: 596163--596198 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
596153 ATTGTTTAAT
596163 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
596177 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
596191 TGATTTGT
1 TGATTTGT
596199 GTAATTGATG
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:596321 original size:19 final size:18
Alignment explanation
Indices: 596305--596400 Score: 128
Period size: 19 Copynumber: 5.4 Consensus size: 18
596295 AAAAATGACT
596305 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
596324 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
596342 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
596356 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
596374 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
596394 ATCGCAA
1 ATCGCAA
596401 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 8 0.12
15 1 0.01
16 8 0.12
17 1 0.01
18 20 0.29
19 22 0.32
20 9 0.13
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:596418 original size:52 final size:51
Alignment explanation
Indices: 596305--596418 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 51
596295 AAAAATGACT
596305 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGA
596356 ATCGCAATGCGAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
596408 ATCGCAATGCG
1 ATCGCAATGCG
596419 TTTATAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
50 12 0.20
51 22 0.36
52 27 0.44
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (51 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGA
Found at i:596471 original size:19 final size:19
Alignment explanation
Indices: 596447--596612 Score: 173
Period size: 19 Copynumber: 9.4 Consensus size: 19
596437 GATTCTCTCG
596447 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
596466 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
596485 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
596499 TTGCGATTTTTAATTTCGCA
1 TTGCGA-TTTTCATTTCGCA
596519 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
596538 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
596552 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
596572 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
596586 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
596605 TTGCGATT
1 TTGCGATT
596613 CTCTCGTTGC
Statistics
Matches: 122, Mismatches: 8, Indels: 34
0.74 0.05 0.21
Matches are distributed among these distances:
14 23 0.19
16 13 0.11
17 11 0.09
18 7 0.06
19 50 0.41
20 18 0.15
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:596612 original size:53 final size:52
Alignment explanation
Indices: 596425--596584 Score: 293
Period size: 53 Copynumber: 3.0 Consensus size: 52
596415 TGCGTTTATA
596425 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
596477 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTTCATTTCGCATTGCGATTTTC
596530 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
596583 AT
1 AT
596585 GTTGGGATTT
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
52 36 0.35
53 68 0.65
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:596634 original size:33 final size:33
Alignment explanation
Indices: 596425--596626 Score: 203
Period size: 33 Copynumber: 5.9 Consensus size: 33
596415 TGCGTTTATA
596425 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
596458 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *** * *
596498 GTTGCG-ATTTTTAATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
596530 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
596563 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
596597 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
596627 GTAATTTCCG
Statistics
Matches: 136, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
32 12 0.09
33 56 0.41
34 37 0.27
35 4 0.03
36 6 0.04
38 10 0.07
39 2 0.01
40 9 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:598922 original size:12 final size:12
Alignment explanation
Indices: 598905--598929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
598895 TCTTCGGGGA
598905 CTTTTTCTTCTT
1 CTTTTTCTTCTT
598917 CTTTTTCTTCTT
1 CTTTTTCTTCTT
598929 C
1 C
598930 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:599135 original size:24 final size:24
Alignment explanation
Indices: 599101--599147 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
599091 CTGAAACATC
599101 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
599125 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
599148 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:599854 original size:20 final size:20
Alignment explanation
Indices: 599826--599937 Score: 134
Period size: 20 Copynumber: 5.6 Consensus size: 20
599816 AAATTTCAGT
* *
599826 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
599846 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
599866 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
599886 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
599906 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
599926 ATTGCGATTTAC
1 GTTGCGATTTAC
599938 CCATACAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:600810 original size:14 final size:13
Alignment explanation
Indices: 600792--600867 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 13
600782 TAAAGAAAAC
*
600792 AAATAAGATAAAG
1 AAATAAAATAAAG
600805 ATAATAAAATAAAAG
1 A-AATAAAAT-AAAG
* *
600820 AAAAAAAATAAAAA
1 AAATAAAAT-AAAG
*
600834 AAATAAAATAAAT
1 AAATAAAATAAAG
*
600847 AAATAAGAT-AAG
1 AAATAAAATAAAG
600859 AAA-AAAATA
1 AAATAAAATA
600868 GTAAAGTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
11 4 0.08
12 5 0.10
13 12 0.23
14 26 0.50
15 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AAATAAAATAAAG
Found at i:600815 original size:5 final size:5
Alignment explanation
Indices: 600807--600867 Score: 58
Period size: 5 Copynumber: 12.8 Consensus size: 5
600797 AGATAAAGAT
*
600807 AATAA AATAA AAGAA AA-AA AATAA AA-AA AATAA AAT-A AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
600853 GATAA GAAAAA AATA
1 AATAA -AATAA AATA
600868 GTAAAGTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
4 16 0.34
5 28 0.60
6 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:600827 original size:9 final size:9
Alignment explanation
Indices: 600807--600864 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
600797 AGATAAAGAT
600807 AATAAAATAA
1 AATAAAA-AA
*
600817 AAGAAAAAA
1 AATAAAAAA
600826 AATAAAAAA
1 AATAAAAAA
*
600835 AATAAAATA
1 AATAAAAAA
*
600844 AATAAATAA
1 AATAAAAAA
*
600853 GATAAGAAAA
1 AATAA-AAAA
600863 AA
1 AA
600865 ATAGTAAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 29 0.74
10 10 0.26
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (9 bp):
AATAAAAAA
Found at i:600980 original size:38 final size:40
Alignment explanation
Indices: 600912--600990 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
600902 AATGAAAAAA
*
600912 ATATATATATACATCAAAGTATTAATAAAATA-AATAAGCT
1 ATATATATATACAACAAAGTATTAATAAAATAGAA-AAGCT
*
600952 ATATATATATACAACAAA-TATTTA-AAAATAGAAAAGCT
1 ATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
600990 A
1 A
600991 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (40 bp):
ATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
Found at i:601071 original size:41 final size:39
Alignment explanation
Indices: 601006--601082 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
600996 TCACTTCATC
* *
601006 GAAAGTGGGGGGCTTTAGTCAGAAAAAAAATAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAAAAAAACAAAAAGAG
* *
601045 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAAAAAAACAAAAA
601083 AATAGGTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.28
40 1 0.03
41 22 0.69
ACGTcount: A:0.51, C:0.05, G:0.27, T:0.17
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAAAAAAACAAAAAGAG
Found at i:601249 original size:2 final size:2
Alignment explanation
Indices: 601203--601233 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
601193 AAAAAAAATA
601203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
601234 AAGTTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:601397 original size:2 final size:2
Alignment explanation
Indices: 601390--601451 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
601380 ATTAAAGAAA
601390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
601431 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
601452 ATAAAAAATC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:601519 original size:18 final size:17
Alignment explanation
Indices: 601496--601538 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
601486 ATATATACGT
601496 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
601514 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
601531 ATAA-AATA
1 ATAATAATA
601539 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:603013 original size:106 final size:106
Alignment explanation
Indices: 602828--603583 Score: 1050
Period size: 106 Copynumber: 7.0 Consensus size: 106
602818 AGTATTGTTC
* * * * *
602828 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCCGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACA
* * * *
602893 GCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
602934 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACA
* *
602999 ACCAGCCGTCCCTTCGTTGTGAATTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
603040 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTATTCGCTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACA
*
603105 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
603146 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GAAAAGTGGTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAA-TTGTTTGTTGAC
603210 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
603252 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATT-GTTTGTTGAC
603317 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
603359 TGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTGGTTTGT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAACTGGAAAA-TTGTTTGT
* *
603423 TGACAACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
603469 CGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTGGTTTGT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAACTGGAAAA-TTGTTTGT
*
603533 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
603579 CGAGT
1 CGAGT
603584 GGCGCGATAT
Statistics
Matches: 595, Mismatches: 47, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
105 5 0.01
106 328 0.55
107 92 0.15
110 162 0.27
111 8 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:612798 original size:19 final size:19
Alignment explanation
Indices: 612776--612819 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
612766 AGATAAAGAG
*
612776 AATAAAATAAAAGGAAAA-A
1 AATAAAA-AAAAAGAAAATA
*
612795 AATAAAAAAAAATAAAATA
1 AATAAAAAAAAAGAAAATA
612814 AATAAA
1 AATAAA
612820 TAAGATAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (19 bp):
AATAAAAAAAAAGAAAATA
Found at i:612952 original size:38 final size:37
Alignment explanation
Indices: 612863--612962 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 37
612853 TATATATAGT
*
612863 AATATTTGAAAAATGAAAAA--TATATATATATACATCA
1 AATATTT-AAAAAT-AAAAAGCTATATATATATACAACA
*
612900 AAGTATTAATAAAATAAATAAGCTATATATATATACAACA
1 AA-TATTTA-AAAATAAA-AAGCTATATATATATACAACA
612940 AATATTTAAAAATAGAAAAGCTA
1 AATATTTAAAAATA-AAAAGCTA
612963 CCCTCTCACT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
37 6 0.11
38 23 0.43
39 7 0.13
40 18 0.33
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (37 bp):
AATATTTAAAAATAAAAAGCTATATATATATACAACA
Found at i:613053 original size:41 final size:39
Alignment explanation
Indices: 612978--613054 Score: 91
Period size: 41 Copynumber: 1.9 Consensus size: 39
612968 TCACTTCACC
* * **
612978 GAAAGTGGGGGGCTTTAGTCATAAATAAGTCAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
613017 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
613055 AATGGGTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 9 0.29
40 1 0.03
41 21 0.68
ACGTcount: A:0.47, C:0.06, G:0.27, T:0.19
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:613225 original size:2 final size:2
Alignment explanation
Indices: 613157--613209 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
613147 ATAAAAAACG
613157 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
613199 AT AT AT AT AT A
1 AT AT AT AT AT A
613210 AAGTTATAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:613437 original size:2 final size:2
Alignment explanation
Indices: 613430--613504 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
613420 CTAATTTAAA
613430 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
613472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
613505 CGTATAATAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:613541 original size:17 final size:18
Alignment explanation
Indices: 613508--613543 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
613498 ATATATACGT
*
613508 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
613526 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
613543 A
1 A
613544 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:626959 original size:31 final size:31
Alignment explanation
Indices: 626921--627029 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 31
626911 AAACTACCTA
*
626921 TTTGGTCACTTATATATTATCTCATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
** **
626952 TTTGGTCACTTGATTATTATTTAGGGTAAACTACT-T
1 TTTGGTCACTT-A-TA-TA-TTA-TCTAATTTA-TGT
626988 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
627020 TTTGGTCACT
1 TTTGGTCACT
627030 CGATTATTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
31 22 0.36
32 7 0.11
33 5 0.08
34 4 0.07
35 5 0.08
36 6 0.10
37 12 0.20
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:627007 original size:37 final size:36
Alignment explanation
Indices: 626952--627076 Score: 118
Period size: 37 Copynumber: 3.5 Consensus size: 36
626942 TCATTTATGT
626952 TTTGGTCACTTGATTATTATTTAGGGTAAACTACTTA
1 TTTGGTCACTT-ATTATTATTTAGGGTAAACTACTTA
** **
626989 TTTGGTCACTTA-TA-TA-TTA-TCTAATTTA-TGT-
1 TTTGGTCACTTATTATTATTTAGGGTAAACTACT-TA
* *
627020 TTTGGTCACTCGATTATTATTTAGGGTAAACTACCTA
1 TTTGGTCACT-TATTATTATTTAGGGTAAACTACTTA
627057 TTTGGTCACTTATATATTAT
1 TTTGGTCACTTAT-TATTAT
627077 CTAATATAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
31 11 0.16
32 7 0.10
33 5 0.07
34 4 0.06
35 5 0.07
36 9 0.13
37 27 0.40
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (36 bp):
TTTGGTCACTTATTATTATTTAGGGTAAACTACTTA
Found at i:627016 original size:68 final size:68
Alignment explanation
Indices: 626903--627168 Score: 391
Period size: 68 Copynumber: 4.0 Consensus size: 68
626893 TTAGAGATTT
* * *
626903 TTTAGGTTAAACTACCTATTTGGTCACTTATATATTATCTCATTTATGTTTTGGTCACTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
626968 TTA
66 TTA
*
626971 TTTAGGGTAAACTACTTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
627036 TTA
66 TTA
* ** *
627039 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATATAAT-TCCT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
627098 TTTA
65 ATTA
*
627102 TTTAGGGTAAACTACCTATTTGGTCACTTATATATAATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
627167 TT
66 TT
627169 TTTTTTTTCA
Statistics
Matches: 175, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
62 3 0.02
63 50 0.29
64 1 0.01
65 2 0.01
66 2 0.01
67 1 0.01
68 113 0.65
69 3 0.02
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:627142 original size:131 final size:135
Alignment explanation
Indices: 626903--627168 Score: 398
Period size: 131 Copynumber: 2.0 Consensus size: 135
626893 TTAGAGATTT
* * * ** *
626903 TTTAGGTTAAACTACCTATTTGGTCACTTATATATTATCTCATTTATGTTTTGGTCACTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAATGTCCTGATCAC-TGATTA
* *
626968 TTATTTAGGGTAAACTACTTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGA
65 TTATTTAGGGTAAACTACCTATTTGGTCACTTATATATAATCTAATTTATGTTTTGGTCACTCGA
627033 TTATTA
130 TTATTA
*
627039 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATATAAT-TCCT-AT-A-T-ATTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TAATGTCCTGATCACTGATTA
627099 TTATTTAGGGTAAACTACCTATTTGGTCACTTATATATAATCTAATTTATGTTTTGGTCACTCGA
65 TTATTTAGGGTAAACTACCTATTTGGTCACTTATATATAATCTAATTTATGTTTTGGTCACTCGA
627164 TTATT
130 TTATT
627169 TTTTTTTTCA
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
131 71 0.59
132 1 0.01
134 1 0.01
135 1 0.01
136 43 0.36
137 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (135 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAATGTCCTGATCACTGATTAT
TATTTAGGGTAAACTACCTATTTGGTCACTTATATATAATCTAATTTATGTTTTGGTCACTCGAT
TATTA
Found at i:628789 original size:18 final size:18
Alignment explanation
Indices: 628766--628800 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
628756 TATGTTATTG
628766 GAATGA-TTGATATAATTT
1 GAATGAGTTG-TATAATTT
628784 GAATGAGTTGTATAATT
1 GAATGAGTTGTATAATT
628801 ATGTTTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (18 bp):
GAATGAGTTGTATAATTT
Found at i:629601 original size:20 final size:20
Alignment explanation
Indices: 629572--629613 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
629562 CTCATGCATG
* *
629572 GAACATGCATGGAGCTTCAC
1 GAACACGCATGGAGCTGCAC
629592 GAACACGCATGGAGCTGCAC
1 GAACACGCATGGAGCTGCAC
629612 GA
1 GA
629614 GCACATGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.29, T:0.14
Consensus pattern (20 bp):
GAACACGCATGGAGCTGCAC
Found at i:631732 original size:23 final size:23
Alignment explanation
Indices: 631705--631753 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
631695 TGGTGGTTGG
631705 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
631728 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
631751 TTT
1 TTT
631754 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:633101 original size:24 final size:24
Alignment explanation
Indices: 633069--633114 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
633059 TCCAATCAAC
633069 ACCACCTTGACTGCTAGACTCAGT
1 ACCACCTTGACTGCTAGACTCAGT
* *
633093 ACCACCTTGCCTGGTAGACTCA
1 ACCACCTTGACTGCTAGACTCA
633115 ACACAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (24 bp):
ACCACCTTGACTGCTAGACTCAGT
Found at i:638242 original size:28 final size:28
Alignment explanation
Indices: 638210--638264 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
638200 TTTTGTTTAC
*
638210 ATTATGTCGTCG-AGCTAGTGCTTGAAAT
1 ATTATGTCGTCGAATC-AGTGCTTGAAAT
*
638238 ATTATGTCGTTGAATCAGTGCTTGAAA
1 ATTATGTCGTCGAATCAGTGCTTGAAA
638265 GCAACGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (28 bp):
ATTATGTCGTCGAATCAGTGCTTGAAAT
Found at i:649562 original size:18 final size:18
Alignment explanation
Indices: 649539--649574 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
649529 AGTTCGACAA
649539 AGATTCCCGATGTGGCAG
1 AGATTCCCGATGTGGCAG
**
649557 AGATTCTTGATGTGGCAG
1 AGATTCCCGATGTGGCAG
649575 GAAACTCGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
AGATTCCCGATGTGGCAG
Found at i:650582 original size:54 final size:54
Alignment explanation
Indices: 650523--650995 Score: 567
Period size: 54 Copynumber: 8.8 Consensus size: 54
650513 CCATACGATC
* * * * * * *
650523 ATTCATAAACATATTATGAATTCCGTGGTTTGCACACATAGTGTCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
* *
650577 ATTCATCAAAATATGATGAATTCCGT-ACTTTGCACAGTTAGTGCCAAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCAAAACGGTT
* * * *
650631 ATTCTTCAACATATGATGAATTCCATGATTTGCACACTTAGTGCCGAAACGATT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
* * * * *
650685 ATTCGTTAACATATGATGAATTCCGT-ACTTTGTACACTTAGTTCCAAAA-TGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCAAAACGGTT
650738 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
* * **
650792 ATTCATCAACATATGATGAATTCCGTGATTTGTACACTTATTGCCAAAATAGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
* ** * *
650846 ATTCATTAACATATGATGAATTATGT-ACTTTGCGCACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCAAAACGGTT
* *** **
650900 ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTTGAAATTGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
* * *
650954 ATTTATCAACATATGATGAATTCCTTGAATTGCACACTTAGT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGT
650996 TCCTATTTGG
Statistics
Matches: 360, Mismatches: 52, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
53 47 0.13
54 311 0.86
55 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTT
Found at i:650913 original size:215 final size:215
Alignment explanation
Indices: 650523--650995 Score: 632
Period size: 215 Copynumber: 2.2 Consensus size: 215
650513 CCATACGATC
* * * * * * *
650523 ATTCATAAACATATTATGAATTCCGTGGTTTGCACACATAGTGTCGAAATGGTTATTCATCAAAA
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTTATTCATCAAAA
* *
650588 TATGATGAATTCCGTACTTTGCACAGTTAGTGCCAAAACGGTTATTCTTCAACATATGATGAATT
66 TATGATGAATTCCGTACTTTGCACACTTAGTGCCAAAACAGTTATTCTTCAACATATGATGAATT
* *
650653 CCATGATTTGCACACTTAGTGCCGAAACGATTATTCGTTAACATATGATGAATTCCGT-ACTTTG
131 -CATGATTTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGA-TTTG
*
650717 TACACTTAGT-TCCAAAATGTT
194 CACACTTAGTGTCCAAAATGTT
*
650738 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTTATTCATCAACA
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTTATTCATCAAAA
* * *
650803 TATGATGAATTCCGTGA-TTTGTACACTTATTGCCAAAATAGTTATTCATT-AACATATGATGAA
66 TATGATGAATTCCGT-ACTTTGCACACTTAGTGCCAAAACAGTTATTC-TTCAACATATGATGAA
* * *
650866 TT-ATGTACTTTGCGCACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGATT
129 TTCATG-A-TTTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGATT
** *
650930 TGCACACTTAGTGTTGAAATTGTT
192 TGCACACTTAGTGTCCAAAATGTT
* * *
650954 ATTTATCAACATATGATGAATTCCTTGAATTGCACACTTAGT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGT
650996 TCCTATTTGG
Statistics
Matches: 227, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
213 3 0.01
214 1 0.00
215 172 0.76
216 51 0.22
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (215 bp):
ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCAAAACGGTTATTCATCAAAA
TATGATGAATTCCGTACTTTGCACACTTAGTGCCAAAACAGTTATTCTTCAACATATGATGAATT
CATGATTTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGATTTGCA
CACTTAGTGTCCAAAATGTT
Found at i:657553 original size:54 final size:55
Alignment explanation
Indices: 657503--657938 Score: 516
Period size: 54 Copynumber: 8.1 Consensus size: 55
657493 AATGCACCCG
* * * * * * *
657503 TAGTGCTC-ATACTGTTATTCATAAATATATTATGAATTTTGTGGTTTGCACACA
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
* *
657557 TAGTGCT-GAAATGGTTATTCATCAAGATATGATGAATTTCGT-ACTTTGCACACT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGA-TTTGCACACT
* * *
657611 TAGTGC-CGAAACGGTTATTCATCAACATATGATGAATTTCATGATTTTCACACT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
* **
657665 TAGTG-TCGAAACGGTTATTCATCAATATATGATGAATTCCGTGATTTGCATGCT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
*
657719 TAGTG-TCAAAACGGTTATTCATCAATATATGATGAATTTCGT-ACTTTGCACACT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGA-TTTGCACACT
* * * **
657773 GAGTGCT-GAAACGATTATTCATCAACATATGATGAA-TTCTGTGATTTGCATGCT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTC-GTGATTTGCACACT
* * * *
657827 TAGTGCT-GAAATGGTTATTCATCAACATATGATAAATTTCGTGATTTGTACACT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
* * *
657881 TAGTG-TCGAAACGGTTATTCATCAACATATGATAAATTTCGTGAATTGCACACT
1 TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
657935 TAGT
1 TAGT
657939 TCCTATTTGG
Statistics
Matches: 332, Mismatches: 39, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.02
54 321 0.97
55 6 0.02
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (55 bp):
TAGTGCTCGAAACGGTTATTCATCAATATATGATGAATTTCGTGATTTGCACACT
Found at i:658015 original size:15 final size:15
Alignment explanation
Indices: 657995--658026 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
657985 TGACTAGTAT
657995 AACATATAGTTACAC
1 AACATATAGTTACAC
658010 AACATATAGTTACAC
1 AACATATAGTTACAC
658025 AA
1 AA
658027 TTAAATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:659482 original size:17 final size:16
Alignment explanation
Indices: 659455--659506 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
659445 TTGTTGAATG
659455 ATAACTTAAACAAATTA
1 ATAA-TTAAACAAATTA
* *
659472 ATGATTTAAACATAGTTA
1 AT-AATTAAACA-AATTA
*
659490 ATAATTAAAAAAATTA
1 ATAATTAAACAAATTA
659506 A
1 A
659507 AAAAAGTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 5 0.18
17 16 0.57
18 7 0.25
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (16 bp):
ATAATTAAACAAATTA
Found at i:659735 original size:3 final size:3
Alignment explanation
Indices: 659722--659792 Score: 61
Period size: 3 Copynumber: 23.7 Consensus size: 3
659712 CTTCATTAAT
* * * * *
659722 ATC AAC ATC ATC ATC AGC ATC ATC AGC ATC ATC ATC ATC ACC ATC ACC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
** * *
659770 AAA ACC ATC ATC GTC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC AT
659793 TATCTACATG
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.24
Consensus pattern (3 bp):
ATC
Found at i:661238 original size:26 final size:26
Alignment explanation
Indices: 661209--661277 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
661199 TGTATCATCA
661209 AAAAATTAAATAATATAAACT-AAAAT
1 AAAAATTAAATAATATAAA-TAAAAAT
* * *
661235 AAAATTTTAATATTATAAATAAAAAT
1 AAAAATTAAATAATATAAATAAAAAT
*
661261 TAAAA-TAAATAAATATA
1 AAAAATTAAAT-AATATA
661278 GATTTCAACA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAATTAAATAATATAAATAAAAAT
Found at i:661751 original size:30 final size:30
Alignment explanation
Indices: 661711--661821 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
661701 AAATAAACTA
661711 TTTGAAATAAATAAATAAATTACTAATTTG
1 TTTGAAATAAATAAATAAATTACTAATTTG
** * * **
661741 TTCAAAATAAATGAATAAATAAATAAATAAACTG
1 TTTGAAAT--A--AATAAATAAATTACTAATTTG
*
661775 TTTGAAATAAATAAATAAATTACTAATTTA
1 TTTGAAATAAATAAATAAATTACTAATTTG
661805 TTTGAAATAAATAAATA
1 TTTGAAATAAATAAATA
661822 CAAAAATAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
30 39 0.61
32 2 0.03
34 23 0.36
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTGAAATAAATAAATAAATTACTAATTTG
Found at i:661761 original size:4 final size:4
Alignment explanation
Indices: 661745--661879 Score: 56
Period size: 4 Copynumber: 31.8 Consensus size: 4
661735 AATTTGTTCA
* ***
661745 AAAT AAAT GAAT AAAT AAAT AAAT AAACT GTTT GAAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT -AAAT AAAT AAAT AAAT
* * * ** * * *
661795 TACT AATTT ATTT GAAAT AAAT AAAT ACAA- AAAT AAAT AAAT TATT CGAAGT
1 AAAT AA-AT AAAT -AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT --AAAT
* *
661847 AAAT AAAT AATT CAATGT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT -AA-AT AAAT AAAT AAAT AAA
661880 AATTACCTCT
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
3 2 0.02
4 81 0.83
5 12 0.12
6 3 0.03
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:661798 original size:64 final size:64
Alignment explanation
Indices: 661701--661856 Score: 224
Period size: 64 Copynumber: 2.4 Consensus size: 64
661691 ATACCGCTTC
* *
661701 AAATAAACTATTTGAAATAAATAAATAAATTACTAATTTGTTCAAAATAAATGAATA-AATAAAT
1 AAATAAACTATTTGAAATAAATAAATAAATTACTAATTTATTCAAAATAAATAAATACAA-AAAT
* **
661765 AAATAAACTGTTTGAAATAAATAAATAAATTACTAATTTATTTGAAATAAATAAATACAAAAAT
1 AAATAAACTATTTGAAATAAATAAATAAATTACTAATTTATTCAAAATAAATAAATACAAAAAT
* * *
661829 AAATAAATTATTCGAAGTAAATAAATAA
1 AAATAAACTATTTGAAATAAATAAATAA
661857 TTCAATGTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 80 0.98
65 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.32
Consensus pattern (64 bp):
AAATAAACTATTTGAAATAAATAAATAAATTACTAATTTATTCAAAATAAATAAATACAAAAAT
Found at i:661817 original size:34 final size:34
Alignment explanation
Indices: 661715--661856 Score: 123
Period size: 34 Copynumber: 4.3 Consensus size: 34
661705 AAACTATTTG
* * * * *
661715 AAATAAATAAATAAATTACTAATTTGTTCAAAAT
1 AAATAAATAAATAAATAAATAAATTATTCGAAAT
* * * *
661749 AAATGAATAAATAAATAAATAAACTGTTTGAAAT
1 AAATAAATAAATAAATAAATAAATTATTCGAAAT
* * *
661783 AAATAAATAAAT---T-ACTAATTTATTTGAAAT
1 AAATAAATAAATAAATAAATAAATTATTCGAAAT
*
661813 AAATAAATACAA-AAATAAATAAATTATTCGAAGT
1 AAATAAATA-AATAAATAAATAAATTATTCGAAAT
661847 AAATAAATAA
1 AAATAAATAA
661857 TTCAATGTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
30 22 0.25
31 3 0.03
33 2 0.02
34 60 0.69
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (34 bp):
AAATAAATAAATAAATAAATAAATTATTCGAAAT
Found at i:661851 original size:18 final size:18
Alignment explanation
Indices: 661828--661874 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
661818 AATACAAAAA
*
661828 TAAATAAATTATTCGAA-G
1 TAAATAAATAATTC-AATG
661846 TAAATAAATAATTCAATG
1 TAAATAAATAATTCAATG
661864 TAAATAAATAA
1 TAAATAAATAA
661875 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (18 bp):
TAAATAAATAATTCAATG
Found at i:663750 original size:30 final size:29
Alignment explanation
Indices: 663714--663782 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
663704 AGATTTTATG
*
663714 TTAGGGGGATAAACTTGAATTTATAAAATT
1 TTAGGGGGA-AAACTTGAACTTATAAAATT
*
663744 TTAGGGGGCAAAATTTGAACTTATAAAATT
1 TTAGGGGG-AAAACTTGAACTTATAAAATT
*
663774 CTAGGGGGA
1 TTAGGGGGA
663783 GAAAATAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (29 bp):
TTAGGGGGAAAACTTGAACTTATAAAATT
Found at i:667590 original size:23 final size:23
Alignment explanation
Indices: 667564--667634 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
667554 CATCGAATTG
*
667564 CCACGTAGATTTTTCCTGAAGGA
1 CCACATAGATTTTTCCTGAAGGA
*
667587 CCACATACGA-TTTTCCTAAAGGA
1 CCACATA-GATTTTTCCTGAAGGA
* *
667610 GCACATAGATTTGT-CTCGAAGGA
1 CCACATAGATTTTTCCT-GAAGGA
667633 CC
1 CC
667635 GCGTAGAACC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.10
23 33 0.85
24 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (23 bp):
CCACATAGATTTTTCCTGAAGGA
Found at i:667788 original size:15 final size:15
Alignment explanation
Indices: 667770--667806 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
667760 GTCACTTAGC
667770 ACATTTTCACATAGA
1 ACATTTTCACATAGA
*
667785 ACATTTTCACGTAGA
1 ACATTTTCACATAGA
*
667800 TCATTTT
1 ACATTTT
667807 TTACTATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (15 bp):
ACATTTTCACATAGA
Found at i:667834 original size:16 final size:16
Alignment explanation
Indices: 667788--667834 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
667778 ACATAGAACA
667788 TTTTCACGTA-GATCAT
1 TTTTCACGTATGA-CAT
* *
667804 TTTTTAC-TATAACAT
1 TTTTCACGTATGACAT
667819 TTTTCACGTATGACAT
1 TTTTCACGTATGACAT
667835 ATTCACCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTTCACGTATGACAT
Found at i:667973 original size:57 final size:57
Alignment explanation
Indices: 667912--668019 Score: 126
Period size: 57 Copynumber: 1.9 Consensus size: 57
667902 GATCAATTAT
* * * *
667912 TTATAACATTTCATATCACCTTACTCAACTTATCATTTCTTCACATAGAACCTATAC
1 TTATAACATTTCATATAACATTACTAAAATTATCATTTCTTCACATAGAACCTATAC
*** * * *
667969 TTATATTGTTTCATATAACATTATTAAAATTATCATTTGTTCTCATAGAAC
1 TTATAACATTTCATATAACATTACTAAAATTATCATTTCTTCACATAGAAC
668020 ATATTCACAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
57 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (57 bp):
TTATAACATTTCATATAACATTACTAAAATTATCATTTCTTCACATAGAACCTATAC
Found at i:668057 original size:27 final size:26
Alignment explanation
Indices: 668023--668076 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
668013 ATAGAACATA
*
668023 TTCACATAA-ATCATATACTTATAATAT
1 TTCACATAATAT-ATATACATAT-ATAT
668050 TTCACATAATATATATACATATATAT
1 TTCACATAATATATATACATATATAT
668076 T
1 T
668077 CATAACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 5 0.20
27 18 0.72
28 2 0.08
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (26 bp):
TTCACATAATATATATACATATATAT
Found at i:671115 original size:20 final size:21
Alignment explanation
Indices: 671090--671138 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
671080 TGGAGCGTGG
671090 GGGGAAT-AGTACCCCCTCAT
1 GGGGAATCAGTACCCCCTCAT
* *
671110 GGGGAATCGGTTCCCCCTCAT
1 GGGGAATCAGTACCCCCTCAT
671131 GGGGAATC
1 GGGGAATC
671139 GGTTCCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.20
Consensus pattern (21 bp):
GGGGAATCAGTACCCCCTCAT
Found at i:671125 original size:21 final size:21
Alignment explanation
Indices: 671101--671145 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
671091 GGGAATAGTA
671101 CCCCCTCATGGGGAATCGGTT
1 CCCCCTCATGGGGAATCGGTT
671122 CCCCCTCATGGGGAATCGGTT
1 CCCCCTCATGGGGAATCGGTT
671143 CCC
1 CCC
671146 TAAGTGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (21 bp):
CCCCCTCATGGGGAATCGGTT
Found at i:672229 original size:18 final size:18
Alignment explanation
Indices: 672206--672251 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
672196 AGGCATTTGA
* *
672206 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
672224 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
672242 TCCTCGTGCT
1 TCCTC-TGCT
672252 GTTCTGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.00, C:0.30, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:672261 original size:18 final size:19
Alignment explanation
Indices: 672216--672266 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
672206 TCCTCTGGTT
*
672216 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
672234 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
672252 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
672267 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:673889 original size:22 final size:22
Alignment explanation
Indices: 673818--673922 Score: 133
Period size: 22 Copynumber: 4.8 Consensus size: 22
673808 CCAGAACCCC
*
673818 AGGGGGTATCGATTCCCC-TAA
1 AGGGGGTATCGATTCCCCTTCA
**
673839 AGGGGAAATC-AGTTCCCCTTCAA
1 AGGGGGTATCGA-TTCCCCTTC-A
* *
673862 AGGGGGGATCGGTTCCCCTTCA
1 AGGGGGTATCGATTCCCCTTCA
673884 AGGGGGTATCGATTCCCCTTCA
1 AGGGGGTATCGATTCCCCTTCA
673906 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
673923 TCTGCACTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
22 39 0.54
23 18 0.25
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.24
Consensus pattern (22 bp):
AGGGGGTATCGATTCCCCTTCA
Found at i:682579 original size:22 final size:22
Alignment explanation
Indices: 682548--682592 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
682538 ATTTCCTTGG
*
682548 AAACATTTCATATAAAAC-TAAT
1 AAACAATTCATA-AAAACATAAT
682570 AAACAATTCATAAAAACATAAT
1 AAACAATTCATAAAAACATAAT
682592 A
1 A
682593 TACTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACAATTCATAAAAACATAAT
Found at i:682944 original size:23 final size:23
Alignment explanation
Indices: 682918--682992 Score: 107
Period size: 23 Copynumber: 3.2 Consensus size: 23
682908 AAAGTGCCAT
*
682918 GTAGATTTGTCCCAAAGGACCGC
1 GTAGATTTGTCCCGAAGGACCGC
*
682941 GTAGAATTTGTCCCGAAGGACCAC
1 GTAG-ATTTGTCCCGAAGGACCGC
682965 GTAGGA-TTGTCCCGAAGGACCGC
1 GTA-GATTTGTCCCGAAGGACCGC
682988 GTAGA
1 GTAGA
682993 ACTATCGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
22 2 0.04
23 23 0.49
24 21 0.45
25 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (23 bp):
GTAGATTTGTCCCGAAGGACCGC
Found at i:682945 original size:47 final size:47
Alignment explanation
Indices: 682892--682993 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
682882 CCGAAGTGTT
*
682892 GCGTAGAATTT-TCACCAAAGTG-CCATGTA-GATTTGTCCCAAAGGACC
1 GCGTAGAATTTGTC-CCAAAG-GACCACGTAGGA-TTGTCCCAAAGGACC
* *
682939 GCGTAGAATTTGTCCCGAAGGACCACGTAGGATTGTCCCGAAGGACC
1 GCGTAGAATTTGTCCCAAAGGACCACGTAGGATTGTCCCAAAGGACC
682986 GCGTAGAA
1 GCGTAGAA
682994 CTATCGATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
46 1 0.02
47 44 0.90
48 4 0.08
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (47 bp):
GCGTAGAATTTGTCCCAAAGGACCACGTAGGATTGTCCCAAAGGACC
Found at i:682954 original size:24 final size:24
Alignment explanation
Indices: 682892--682993 Score: 104
Period size: 23 Copynumber: 4.3 Consensus size: 24
682882 CCGAAGTGTT
682892 GCGTAGAATTT-TCACCAAAGTG-CC
1 GCGTAGAATTTGTC-CCAAAG-GACC
**
682916 ATGTAG-ATTTGTCCCAAAGGACC
1 GCGTAGAATTTGTCCCAAAGGACC
*
682939 GCGTAGAATTTGTCCCGAAGGACC
1 GCGTAGAATTTGTCCCAAAGGACC
* * *
682963 ACGTAGGA-TTGTCCCGAAGGACC
1 GCGTAGAATTTGTCCCAAAGGACC
682986 GCGTAGAA
1 GCGTAGAA
682994 CTATCGATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 37 0.56
24 28 0.42
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (24 bp):
GCGTAGAATTTGTCCCAAAGGACC
Found at i:683175 original size:15 final size:16
Alignment explanation
Indices: 683126--683178 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
683116 ACTTAGCCCA
683126 TTTTCACATAGAACA-
1 TTTTCACATAGAACAT
* *
683141 TTTTCACGTAGATCAT
1 TTTTCACATAGAACAT
*
683157 TTTTCAC-TATAACAT
1 TTTTCACATAGAACAT
683172 TTTTCAC
1 TTTTCAC
683179 GTATGACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 26 0.79
16 7 0.21
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTTCACATAGAACAT
Found at i:683187 original size:16 final size:16
Alignment explanation
Indices: 683141--683187 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
683131 ACATAGAACA
683141 TTTTCACGTA-GATCAT
1 TTTTCACGTATGA-CAT
*
683157 TTTTCAC-TATAACAT
1 TTTTCACGTATGACAT
683172 TTTTCACGTATGACAT
1 TTTTCACGTATGACAT
683188 ATTCACCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (16 bp):
TTTTCACGTATGACAT
Found at i:683198 original size:31 final size:31
Alignment explanation
Indices: 683124--683199 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
683114 TCACTTAGCC
* *
683124 CATT-TTCACATAGAACATTTTCACGTAGAT
1 CATTATTCACCTATAACATTTTCACGTAGAT
*
683154 CATTTTTCA-CTATAACATTTTTCACGTATGA-
1 CATTATTCACCTATAACA-TTTTCACGTA-GAT
683185 CA-TATTCACCTATAA
1 CATTATTCACCTATAA
683200 TATATATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 15 0.38
31 22 0.56
32 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (31 bp):
CATTATTCACCTATAACATTTTCACGTAGAT
Found at i:683418 original size:2 final size:2
Alignment explanation
Indices: 683411--683438 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
683401 ATTTCACATA
683411 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
683439 TCATAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:683425 original size:27 final size:28
Alignment explanation
Indices: 683376--683430 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
683366 ATAGAACATA
683376 TTCACATAAATCATATACTTATA-ATAT
1 TTCACATAAATCATATACTTATATATAT
683403 TTCACATAATAT-ATATA-TATATATATAT
1 TTCACATAA-ATCATATACT-TATATATAT
683431 ATATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 1 0.04
27 18 0.72
28 6 0.24
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (28 bp):
TTCACATAAATCATATACTTATATATAT
Found at i:685704 original size:15 final size:15
Alignment explanation
Indices: 685684--685723 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
685674 ACATAATTAG
685684 GAAATGCTCTTACTA
1 GAAATGCTCTTACTA
685699 GAAATGAC-CTTACTA
1 GAAATG-CTCTTACTA
*
685714 GAAATTCTCT
1 GAAATGCTCT
685724 CACAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (15 bp):
GAAATGCTCTTACTA
Found at i:688735 original size:58 final size:59
Alignment explanation
Indices: 688635--689129 Score: 438
Period size: 58 Copynumber: 8.5 Consensus size: 59
688625 ATGGCGCCTT
* ***
688635 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATGGAGCACTGA
* * * * *
688694 GTGTGCT-AAATGATAAGGAAATTATATTGAAAATATGGATTTCCAAATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATAT-GGAGCA-CTGA
* *** *
688753 -TGTGCTAAAATGATAAGGAAATCATAATGAGTGTATAGATTTCCATATGGAGCACTGT
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATGGAGCACTGA
** * * * *
688811 GTGTGCT-AAATGATATCGAAATCATATTGAAAATATGGATTTCCAAATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATAT-GGAGCA-CTGA
* * * * ***
688870 -TTTTCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATGGAGCACTGA
* * * *
688928 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATAT-GGAGCA-CTGA
* * *** * *
688987 -TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATTTGGAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATGGAGCACTGA
* * * *
689045 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATAT-GGAGCA-CTGA
* *
689104 -TGTGCTAAAATGGTAAGGGAATCATA
1 GTGTGCTAAAATGATAAGGAAATCATA
689130 CTAATGGTAT
Statistics
Matches: 342, Mismatches: 76, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
58 179 0.52
59 163 0.48
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATGGAGCACTGA
Found at i:689141 original size:59 final size:58
Alignment explanation
Indices: 688636--689330 Score: 416
Period size: 59 Copynumber: 11.8 Consensus size: 58
688626 TGGCGCCTTG
* * * * *
688636 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCA-CTGA
1 TGTGCTAAAATGATAAGGAAATCATACTAAG-GTATGGATTTCCAGATAGG-GCATTTTA
* * ** *
688694 GTGTGCT-AAATGATAAGGAAATTATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
1 -TGTGCTAAAATGATAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCATTTTA
* * * * * * *
688753 TGTGCTAAAATGATAAGGAAATCATAATGAGTGTATAGATTTCCATAT-GGAGCACTGTG
1 TGTGCTAAAATGATAAGGAAATCATACTAAG-GTATGGATTTCCAGATAGG-GCATTTTA
** * ** *
688812 TGTGCT-AAATGATATCGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
1 TGTGCTAAAATGATAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCATTTTA
* * * * * * * *
688870 TTTTCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCA-CTGA
1 TGTGCTAAAATGATAAGGAAATCATACTAAG-GTATGGATTTCCAGATAGG-GCATTTTA
* **
688928 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
1 -TGTGCTAAAATGATAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCATTTTA
* * * * * * *
688987 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCA-TTTGGAGCA-CTAA
1 TGTGCTAAAATGATAAGGAAATCATACTAAG-GTATGGATTTCCAGATAGG-GCATTTTA
* **
689045 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
1 -TGTGCTAAAATGATAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCATTTTA
* * * ** * * *
689104 TGTGCTAAAATGGTAAGGGAATCATACTAATGGTATGGATTTTCAGATAAAGTA-ATAA
1 TGTGCTAAAATGATAAGGAAATCATACTAA-GGTATGGATTTCCAGATAGGGCATTTTA
* * * *
689162 GGGTGCTACAAA-GATAAGGAAATCATACTAACGGTATGGATTTTCACAT-GGAGCATTTCA
1 -TGTGCTA-AAATGATAAGGAAATCATACTAA-GGTATGGATTTCCAGATAGG-GCATTTTA
* * ** * * * ** * *
689222 AGTGCTAAAATGGTAACAAAATTATATTAATGGTATGAATTT-TTGAATAGGGCACTTCA
1 TGTGCTAAAATGATAAGGAAATCATACTAA-GGTATGGATTTCCAG-ATAGGGCATTTTA
* * *
689281 TGTGCTAAAATGA-AAGGGGAAGCATACTAAGCGTAT-GATTTTCCAAATAG
1 TGTGCTAAAATGATAA-GGAAATCATACTAAG-GTATGGA-TTTCCAGATAG
689331 AGCACTGAGA
Statistics
Matches: 482, Mismatches: 119, Indels: 70
0.72 0.18 0.10
Matches are distributed among these distances:
58 186 0.39
59 289 0.60
60 7 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (58 bp):
TGTGCTAAAATGATAAGGAAATCATACTAAGGTATGGATTTCCAGATAGGGCATTTTA
Found at i:689145 original size:117 final size:117
Alignment explanation
Indices: 688636--689131 Score: 866
Period size: 117 Copynumber: 4.2 Consensus size: 117
688626 TGGCGCCTTG
*
688636 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
*
688701 AAATGATAAGGAAATTATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* * *
688753 TGTGCTAAAATGATAAGGAAATCATAATGAGTGTATAGATTTCCATATGGAGCACTGTGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
**
688818 AAATGATATCGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* *
688870 TTTTCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
*
688935 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* *
688987 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATTTGGAGCACTAAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
*
689052 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
*
689104 TGTGCTAAAATGGTAAGGGAATCATACT
1 TGTGCTAAAATGGTAAGGAAATCATACT
689132 AATGGTATGG
Statistics
Matches: 361, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 361 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
Found at i:689168 original size:117 final size:117
Alignment explanation
Indices: 688636--689237 Score: 850
Period size: 117 Copynumber: 5.1 Consensus size: 117
688626 TGGCGCCTTG
* *
688636 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCT
*
688701 AAATGATAAGGAAATTATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* * **
688753 TGTGCTAAAATGATAAGGAAATCATAATGAGTGTATAGATTTCCATATGGAGCACTGTGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCT
**
688818 AAATGATATCGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* * *
688870 TTTTCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCT
*
688935 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
*
688987 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATTTGGAGCACTAAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCT
*
689052 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
* * * * * ** * * *
689104 TGTGCTAAAATGGTAAGGGAATCATACT-AATGGTATGGATTTTCAGATAAAGTAATAAGGGTGC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGT-GTATAGATTTCCATATGGAGCACTAAGTGTGC
* * ** * * *
689168 TACAAAGATAAGGAAATCATACT-AACGGTATGGATTTTCACAT-GGAGCATTTCA
65 TA-AATGATAAGGAAATCATATTGAA-AATATGGATTTCCAAATAGG-GCATTTTA
*
689222 AGTGCTAAAATGGTAA
1 TGTGCTAAAATGGTAA
689238 CAAAATTATA
Statistics
Matches: 445, Mismatches: 36, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
116 2 0.00
117 390 0.88
118 53 0.12
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCT
AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
Found at i:689404 original size:19 final size:20
Alignment explanation
Indices: 689365--689405 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
689355 AGGAAATTAC
*
689365 ATGAATTGTATGAATTTCCT
1 ATGAAATGTATGAATTTCCT
*
689385 ATGAAATGTATGGA-TTCCT
1 ATGAAATGTATGAATTTCCT
689404 AT
1 AT
689406 AGTGATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (20 bp):
ATGAAATGTATGAATTTCCT
Found at i:689640 original size:35 final size:38
Alignment explanation
Indices: 689425--690392 Score: 293
Period size: 44 Copynumber: 22.0 Consensus size: 38
689415 TAAATGAGGT
* *
689425 TAATGGAAGCATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
**
689468 TAATGGCAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
1 TAATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * *
689512 TAATGGAAGTATATTTGTAAAATAAGTTTACGAGCTTATGGAA
1 TAATGGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
*
689555 TAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
689599 TAATGGAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAA
1 TAATGGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
*
689642 TAATGGAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
*
689685 TAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* *
689729 TAATGGTAAGTATATTGGTAAAATAATCTTACGAGCTTATGGAA
1 TAATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * * *
689773 TAAATGGTAAGTGTGTTGGTAAAATAGGCTTACGAGCTTTTGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC--TT---A
* * * *
689818 TAAATGGTAAGTATGTCGGTAAAATAGGCTTACGAGCTTATGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * * *
689863 TAATGGTAAGTATATTGTTAAAATAGGCTTACGAGTTTATGAAA
1 TAATGG-AAGTATATTGGTAAAATAAGCTTACAAG-CT-T---A
* *
689907 TAAATGGTAAGTATATTGGTAAAATAGGCTTACGAGCTTATGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * *
689952 TAATGATAAGTATATTGGTAAAATAGGCTTACGAGCTTATGAAA
1 TAATG-GAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * *
689996 TAAATGGTAAGTATGTTGGTAAAATAGGCTTACGAGCTTATGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
690041 TAATGGTAAGTATATTGGTAAAAT-AGACTTACAAGCTTATGAAA
1 TAATGG-AAGTATATTGGTAAAATAAG-CTTACAAGC-T-T---A
* *
690085 TAAATCGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 T-AAT-GGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * * *
690130 TAAATGTAAGTATGTTGGTAAAATAAGTTTACGAGCTTATGGAA
1 T-AATGGAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* *
690174 TAAATGGTAAGTATATTGGTAAAATAGGCTTACGAGCTTATGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * *
690219 TAATGATAAGTATATTGGTAAAATAGGCTTACGAGCTTATGAAA
1 TAATG-GAAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
* * *
690263 TAAATGGTAAGTATGTTGGTAAAATAGGCTTACGAGCTTATGGAA
1 T-AATGG-AAGTATATTGGTAAAATAAGCTTACAAGC-T-T---A
690308 TAATGGTAAGTATATTGGTAAAAT-AGACTTACAAGCTTATGGAA
1 TAATGG-AAGTATATTGGTAAAATAAG-CTTACAAGC-T-T---A
* *
690352 TAAATCGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 T-AAT-GGAAGTATATTGGTAAAATAAGCTTACAAGCTTA
690392 T
1 T
690393 GGAATAAATG
Statistics
Matches: 848, Mismatches: 53, Indels: 51
0.89 0.06 0.05
Matches are distributed among these distances:
40 2 0.00
43 133 0.16
44 405 0.48
45 300 0.35
46 8 0.01
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (38 bp):
TAATGGAAGTATATTGGTAAAATAAGCTTACAAGCTTA
Done.