Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009189.1 Hibiscus syriacus cultivar Beakdansim tig00112762_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: 966119
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 4
Found at i:555238 original size:22 final size:22
Alignment explanation
Indices: 555213--555263 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
555203 AACATTGTCG
555213 GGAAGCAATCACAAGGTTTCCC
1 GGAAGCAATCACAAGGTTTCCC
555235 GGAAGCAATCACAAGGTTTCCC
1 GGAAGCAATCACAAGGTTTCCC
*
555257 GTAAGCA
1 GGAAGCA
555264 TATTGTCGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (22 bp):
GGAAGCAATCACAAGGTTTCCC
Found at i:558178 original size:13 final size:13
Alignment explanation
Indices: 558146--558183 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
558136 AATTATAACT
*
558146 AATATATT-AATT
1 AATATATTAAATA
*
558158 ATTATATTAAATA
1 AATATATTAAATA
558171 AATATATTAAATA
1 AATATATTAAATA
558184 TATTTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATATTAAATA
Found at i:561195 original size:8 final size:8
Alignment explanation
Indices: 561182--561222 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
561172 CTCATTTTCA
561182 GAGAATTT
1 GAGAATTT
561190 GAGAATTT
1 GAGAATTT
*
561198 -AGAGTTT
1 GAGAATTT
*
561205 GGGAATTT
1 GAGAATTT
561213 GAGAATTT
1 GAGAATTT
561221 GA
1 GA
561223 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:561521 original size:128 final size:128
Alignment explanation
Indices: 561293--561921 Score: 1222
Period size: 128 Copynumber: 4.9 Consensus size: 128
561283 TAATCGGAGT
*
561293 ACTATTCACATGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
561358 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
561421 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
561486 CATTGCCATATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
561549 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
561614 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
561677 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
561742 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
561805 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
561870 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
561922 AATAAGGTAA
Statistics
Matches: 494, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 494 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:562381 original size:33 final size:34
Alignment explanation
Indices: 562320--562419 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
562310 AAATTTAATA
*
562320 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
562354 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
562387 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
562420 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:563018 original size:21 final size:21
Alignment explanation
Indices: 562930--563023 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
562920 TATGGTATAA
*
562930 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
562951 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
562972 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
562993 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
563014 AACCCTGCGG
1 AACCCTGCGG
563024 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:563053 original size:21 final size:21
Alignment explanation
Indices: 563027--563074 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
563017 CCTGCGGAGA
*
563027 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
563048 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
563069 GGGCAT
1 TGGCAT
563075 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:564843 original size:34 final size:31
Alignment explanation
Indices: 564799--564887 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
564789 TTAATAATTC
*
564799 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
564833 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
564864 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
564888 AAAATAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:564844 original size:31 final size:33
Alignment explanation
Indices: 564802--564876 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
564792 ATAATTCTAA
* * *
564802 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
564834 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
564865 ATAAAAAATAAT
1 ATAAAAAATAAT
564877 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:564893 original size:36 final size:32
Alignment explanation
Indices: 564834--564910 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 32
564824 TTATTTTAAT
* * *
564834 AAAAAAATAATATTTACATAAATATATTAATATA
1 AAAAAAATAATATTTA-A-AAAAATAATAACATA
564868 AAAAATAATAACTATTTAAAAAAATAATAACATA
1 AAAAA-AATAA-TATTTAAAAAAATAATAACATA
564902 AAAATAAAT
1 AAAA-AAAT
564911 TTCTTACCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 24 0.65
35 7 0.19
36 6 0.16
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (32 bp):
AAAAAAATAATATTTAAAAAAATAATAACATA
Found at i:570307 original size:2 final size:2
Alignment explanation
Indices: 570294--570330 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
570284 ATGCATCCAA
*
570294 AT AT AA 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 AT AT A
570331 CCATTTCCTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:570794 original size:23 final size:23
Alignment explanation
Indices: 570758--570821 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
570748 CAACTCATAT
570758 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
570781 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
**
570804 AAATGCATTGAAGTGCCA
1 AAATGCACCGAAGTGCCA
570822 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:572670 original size:19 final size:20
Alignment explanation
Indices: 572646--572693 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
572636 AATGATTTTC
*
572646 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
*
572665 TTTTGAAAGCAAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
572685 TTTTGAAAA
1 TTTTGAAAA
572694 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:581617 original size:26 final size:24
Alignment explanation
Indices: 581588--581649 Score: 56
Period size: 26 Copynumber: 2.5 Consensus size: 24
581578 TTGGTGGCCA
581588 AATTTGACCAATTTTGCCACCCCATT
1 AATTTGACCAATTTTGCCA-CCCA-T
** *
581614 AATTCCACCAA-ATTGCCACCCAT
1 AATTTGACCAATTTTGCCACCCAT
581637 AATGTTGA-CAATT
1 AAT-TTGACCAATT
581650 GATGCAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
23 7 0.25
24 6 0.21
25 6 0.21
26 9 0.32
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (24 bp):
AATTTGACCAATTTTGCCACCCAT
Found at i:587532 original size:30 final size:28
Alignment explanation
Indices: 587498--587554 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
587488 CAATTTTTTG
* *
587498 GCCCATTAGGGTATTCGGGTTTTTTATTTA
1 GCCCATTAGGATA-TCCGG-TTTTTATTTA
587528 GCCCATTAGGATATCCGGTTTTTATTT
1 GCCCATTAGGATATCCGGTTTTTATTT
587555 TGGGTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
30 12 0.48
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.46
Consensus pattern (28 bp):
GCCCATTAGGATATCCGGTTTTTATTTA
Found at i:592745 original size:2 final size:2
Alignment explanation
Indices: 592740--592773 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
592730 TAAAAAAACT
592740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
592774 AAAAAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:599425 original size:67 final size:67
Alignment explanation
Indices: 599343--599478 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 67
599333 AATGATCTAA
599343 TAGCTAAATCAAATCCCTATTTAGTACTATGAGACTATTCAATTCCAAA-TTGCAAATGGTCTAG
1 TAGCTAAATCAAATCCCTATTTAGTACTATGAGACTATTCAATTCCAAATTTGCAAATGGTCTAG
599407 TT
66 TT
599409 TAGCTAAGATCAAATCCCTATTTAGTACTATGAGACTATTCAATTCCAAATTTGCAAATGGTCTA
1 TAGCTAA-ATCAAATCCCTATTTAGTACTATGAGACTATTCAATTCCAAATTTGCAAATGGTCTA
599474 GTT
65 GTT
599477 TA
1 TA
599479 ATGCTCAGGG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 7 0.10
67 42 0.62
68 19 0.28
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (67 bp):
TAGCTAAATCAAATCCCTATTTAGTACTATGAGACTATTCAATTCCAAATTTGCAAATGGTCTAG
TT
Found at i:607253 original size:21 final size:21
Alignment explanation
Indices: 607189--607253 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
607179 ACAAATACGA
607189 TCTAAAAATCAAATCCCT-CT
1 TCTAAAAATCAAATCCCTCCT
* *
607209 TCTAAACAATGAAAT-CTTCACT
1 TCTAAA-AATCAAATCCCTC-CT
**
607231 TCTGGAAATCAAATCCCTCCT
1 TCTAAAAATCAAATCCCTCCT
607252 TC
1 TC
607254 CTATCAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 8 0.23
21 18 0.51
22 9 0.26
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (21 bp):
TCTAAAAATCAAATCCCTCCT
Found at i:610266 original size:142 final size:142
Alignment explanation
Indices: 610010--610293 Score: 568
Period size: 142 Copynumber: 2.0 Consensus size: 142
610000 TGCCACATAT
610010 TGATGTTATTGTTTCAAATAATGTGGATGGCCCTGCATGGAGATTCACGGGCTTCAATGATGCTC
1 TGATGTTATTGTTTCAAATAATGTGGATGGCCCTGCATGGAGATTCACGGGCTTCAATGATGCTC
610075 CTGAAGGAGGTCGGCGTCAAGAGTCTTGGGATTCGCTGTGTAGTTTAAATGATTTTGTGGACATG
66 CTGAAGGAGGTCGGCGTCAAGAGTCTTGGGATTCGCTGTGTAGTTTAAATGATTTTGTGGACATG
610140 TCATGGCTGTTG
131 TCATGGCTGTTG
610152 TGATGTTATTGTTTCAAATAATGTGGATGGCCCTGCATGGAGATTCACGGGCTTCAATGATGCTC
1 TGATGTTATTGTTTCAAATAATGTGGATGGCCCTGCATGGAGATTCACGGGCTTCAATGATGCTC
610217 CTGAAGGAGGTCGGCGTCAAGAGTCTTGGGATTCGCTGTGTAGTTTAAATGATTTTGTGGACATG
66 CTGAAGGAGGTCGGCGTCAAGAGTCTTGGGATTCGCTGTGTAGTTTAAATGATTTTGTGGACATG
610282 TCATGGCTGTTG
131 TCATGGCTGTTG
610294 ATGGGTGACT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (142 bp):
TGATGTTATTGTTTCAAATAATGTGGATGGCCCTGCATGGAGATTCACGGGCTTCAATGATGCTC
CTGAAGGAGGTCGGCGTCAAGAGTCTTGGGATTCGCTGTGTAGTTTAAATGATTTTGTGGACATG
TCATGGCTGTTG
Found at i:630057 original size:113 final size:113
Alignment explanation
Indices: 629878--630523 Score: 1087
Period size: 113 Copynumber: 5.7 Consensus size: 113
629868 AAGATTAACT
629878 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
629943 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
629991 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
630056 AGAATTTGTTTAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
630104 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
630169 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
630217 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
630282 AGAATTTGTTCAACCTTTTACCTGAATTCATTAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
*
630330 TTTCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * ** * *
630395 AGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACA
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
* *
630443 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
630507 AAGAAGAACTTGTTCAA
62 GAGAAGAATTTGTTCAA
630524 TAATTCTATC
Statistics
Matches: 506, Mismatches: 23, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
112 1 0.00
113 457 0.90
115 1 0.00
116 47 0.09
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCA
Found at i:630858 original size:3 final size:3
Alignment explanation
Indices: 630844--630936 Score: 152
Period size: 3 Copynumber: 31.3 Consensus size: 3
630834 TACCCATATC
* *
630844 ATT ATC ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
630892 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
630937 AATATATTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:637952 original size:2 final size:2
Alignment explanation
Indices: 637945--637971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
637935 TCAATCAATA
637945 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 A
637972 AAGAAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:640185 original size:18 final size:19
Alignment explanation
Indices: 640143--640186 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
640133 TTTGGTTTAT
* *
640143 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTACCAG-G
640163 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
640181 GGAATA
1 GGAATA
640187 GGATTACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:642677 original size:12 final size:12
Alignment explanation
Indices: 642645--642684 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
642635 TGCGGGAAAA
642645 TTAAAATC-A-T
1 TTAAAATCTATT
642655 TT-AAATCTATT
1 TTAAAATCTATT
*
642666 TTAAAATTTATT
1 TTAAAATCTATT
642678 TTAAAAT
1 TTAAAAT
642685 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:642696 original size:22 final size:22
Alignment explanation
Indices: 642671--643211 Score: 708
Period size: 22 Copynumber: 24.6 Consensus size: 22
642661 CTATTTTAAA
*
642671 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
642693 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
**
642715 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
642736 ATTTTATTTTAAAATATAGATTG
1 A-TTTATTTTAAAATATGGATTG
642759 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
642781 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
642803 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* * *
642825 AATTATTTGAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
642847 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
642869 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
642891 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
642913 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
642935 ATTTATATTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
642957 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
642979 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
643001 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* ***
643023 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
643045 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
643067 ATTTATTTTAAAATATAGAAAA
1 ATTTATTTTAAAATATGGATTG
*
643089 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
643111 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* **
643133 ATTTATTTTAAAATATGTA-AA
1 ATTTATTTTAAAATATGGATTG
643154 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
643177 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
643199 ATTTATTTTAAAA
1 ATTTATTTTAAAA
643212 AATTTATTAT
Statistics
Matches: 453, Mismatches: 62, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
21 4 0.01
22 447 0.99
23 2 0.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:643292 original size:31 final size:31
Alignment explanation
Indices: 643235--643293 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
643225 AGTTGTATGG
*
643235 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
* *
643266 ATTATTTAAATTTCGGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
643294 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:647778 original size:48 final size:48
Alignment explanation
Indices: 647721--647928 Score: 233
Period size: 48 Copynumber: 4.3 Consensus size: 48
647711 ACTGCCACTC
* * *
647721 AGGGAATATCAAATCTTGAATGAA-AGGGATTTGTTCCACTT-TTGCTGA
1 AGGGAATATCAAATCTTGAA-GAAGAGAGATTTGTTCCGCTTACT-CTGA
* * * *
647769 AGGGTATATCAAATCTTGAAGAAGAAAGACTTGTTTCGCTTACTAC-GA
1 AGGGAATATCAAATCTTGAAGAAGAGAGATTTGTTCCGCTTACT-CTGA
* *
647817 AGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGAAGAAGAGAGATTTGTTCCGCTTACTCTGA
* ** * *
647865 AGGGAATATCAAATCTTGAAGAAAAGAGACATGTTCCACTTACTCCGA
1 AGGGAATATCAAATCTTGAAGAAGAGAGATTTGTTCCGCTTACTCTGA
*
647913 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
647929 GGGGAAGTTA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
47 4 0.03
48 130 0.96
49 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGAAGAAGAGAGATTTGTTCCGCTTACTCTGA
Found at i:647852 original size:96 final size:96
Alignment explanation
Indices: 647721--647928 Score: 269
Period size: 96 Copynumber: 2.2 Consensus size: 96
647711 ACTGCCACTC
* * * *
647721 AGGGAATATCAAATCTTGAATGAAAGGGATTTGTTCCACTT-TTGCTGAAGGGTATATCAAATCT
1 AGGGAATATCAAATCTTGAATGAAAGAGATCTGTTCCACTTACT-CTGAAGGGAATATCAAATCT
* * *
647785 TGAAGAAGAA-AGACTTGTTTCGCTTACTACGA
65 TGAAGAA-AAGAGACATGTTCCACTTACTACGA
* *
647817 AGGGAATATCAAATCTTGGA-GAAGAGAGATCTGTTCCGCTTACTCTGAAGGGAATATCAAATCT
1 AGGGAATATCAAATCTTGAATGAA-AGAGATCTGTTCCACTTACTCTGAAGGGAATATCAAATCT
*
647881 TGAAGAAAAGAGACATGTTCCACTTACTCCGA
65 TGAAGAAAAGAGACATGTTCCACTTACTACGA
*
647913 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
647929 GGGGAAGTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
95 5 0.05
96 92 0.94
97 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (96 bp):
AGGGAATATCAAATCTTGAATGAAAGAGATCTGTTCCACTTACTCTGAAGGGAATATCAAATCTT
GAAGAAAAGAGACATGTTCCACTTACTACGA
Found at i:648009 original size:46 final size:46
Alignment explanation
Indices: 647951--648085 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
647941 CCATTGAATC
*
647951 GAAGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
* *
647998 GAAGAGACTTGTTCCACTTATTCTGAGGGGAATATCAAATCTTGAA
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
* *
648044 GAAGAGACATGTTCCACTTACTCTGAAGGGAATATCAGATCT
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
648086 GGGGGAGTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 77 0.95
47 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (46 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
Found at i:648085 original size:157 final size:158
Alignment explanation
Indices: 647795--648193 Score: 604
Period size: 157 Copynumber: 2.5 Consensus size: 158
647785 TGAAGAAGAA
* * * *
647795 AGACTTGTTTCGCTTACTAC-GAAGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTCCGCTTA
1 AGACTTGTTCCACTTACT-CTGAAGGGAATATCAAATCTTGGAGAAGAGA-CT-TGTTCCACTTA
647859 CTCTGAAGGGAATATCAAATCTTGAAGAAAAGAGACATGTTCCACTTACTCCGAAGGGAATATCA
63 CTCTGAAGGGAATATCAAATCTTGAAG-AAAGAGACATGTTCCACTTACTCCGAAGGGAATATCA
*
647924 GATCTGGGGAAGTTAATCCATTGAATCGAAGT
127 GATCTGGGGAAGTTAATCCATTGAATCGAAGC
*
647956 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCACTTATTC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCACTTACTC
* *
648021 TGAGGGGAATATCAAATCTTGAAG-AAGAGACATGTTCCACTTACTCTGAAGGGAATATCAGATC
66 TGAAGGGAATATCAAATCTTGAAGAAAGAGACATGTTCCACTTACTCCGAAGGGAATATCAGATC
* *
648085 TGGGGGAGTTGATCCATTGAATCGAAGC
131 TGGGGAAGTTAATCCATTGAATCGAAGC
* *
648113 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAG-A-AGAGACTTGTTCCACTTAC
**
648178 TCCCAAGGGAATATCA
64 TCTGAAGGGAATATCA
648194 GATATGGGGG
Statistics
Matches: 219, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
157 106 0.48
158 1 0.00
159 65 0.30
160 2 0.01
161 45 0.21
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (158 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCACTTACTC
TGAAGGGAATATCAAATCTTGAAGAAAGAGACATGTTCCACTTACTCCGAAGGGAATATCAGATC
TGGGGAAGTTAATCCATTGAATCGAAGC
Found at i:648209 original size:113 final size:111
Alignment explanation
Indices: 647998--648304 Score: 499
Period size: 113 Copynumber: 2.8 Consensus size: 111
647988 AAATCTTGGA
* *
647998 GAAG-AGACTTGTTCCACTTATTCTGAGGGGAATATCAAATCTTGAAGAAGAGACATGTTCCACT
1 GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGACATGTTCCACT
*
648062 TACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATC
66 TACTCTGAAGGGAATATCAGATATGGGGGAGTTGATCCATTGAATC
*
648108 GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
1 GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAG-A-AGAGACATGTTCCA
**
648173 CTTACTCCCAAGGGAATATCAGATATGGGGGAGTTGATCCATTGAATC
64 CTTACTCTGAAGGGAATATCAGATATGGGGGAGTTGATCCATTGAATC
* * * *
648221 GAAGCAGACTTGTTCCACTTACTCTGAAGGGACTATCAAATCTTGGAGAAGAGACTTGTTCCGCT
1 GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGACATGTTCCACT
648286 TACTCTGAAGGGAATATCA
66 TACTCTGAAGGGAATATCA
648305 AATCTTGAAG
Statistics
Matches: 182, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
110 4 0.02
111 72 0.40
112 2 0.01
113 104 0.57
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (111 bp):
GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGACATGTTCCACT
TACTCTGAAGGGAATATCAGATATGGGGGAGTTGATCCATTGAATC
Found at i:648293 original size:46 final size:46
Alignment explanation
Indices: 648221--648357 Score: 202
Period size: 46 Copynumber: 2.9 Consensus size: 46
648211 CCATTGAATC
* *
648221 GAAGCAGACTTGTTCCACTTACTCTGAAGGGACTATCAAATCTTGGA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
*
648268 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAA
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
* *
648314 GAAGAGAGACATATTCCACTTACTCTGAAGGGAATATCAAATCT
1 G-A-AGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
648358 AGAGAAGTTG
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 40 0.49
47 5 0.06
48 37 0.45
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (46 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
Found at i:648341 original size:48 final size:46
Alignment explanation
Indices: 648233--648357 Score: 187
Period size: 48 Copynumber: 2.7 Consensus size: 46
648223 AGCAGACTTG
* * * *
648233 TTCCACTTACTCTGAAGGGACTATCAAATCTTGGAGAAGAGACTTG
1 TTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGACATA
*
648279 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATA
1 TTCCACTTACTCTGAAGGGAATATCAAATCTTGAAG-A-AGAGACATA
648327 TTCCACTTACTCTGAAGGGAATATCAAATCT
1 TTCCACTTACTCTGAAGGGAATATCAAATCT
648358 AGAGAAGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
46 33 0.46
47 1 0.01
48 37 0.52
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (46 bp):
TTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGACATA
Found at i:649506 original size:19 final size:18
Alignment explanation
Indices: 649478--649546 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
649468 TGAATCCTCC
649478 TTTT-ATTTTTTCTTTTT
1 TTTTCATTTTTTCTTTTT
649495 TTTCTCATTTTTTCCTTTTT
1 TTT-TCATTTTTT-CTTTTT
*
649515 CTTTCA-TTTTTCATTTTTCT
1 TTTTCATTTTTTC--TTTT-T
649535 TTTTCATTTTTT
1 TTTTCATTTTTT
649547 TCAGGCGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 4 0.09
18 6 0.14
19 14 0.33
20 14 0.33
21 5 0.12
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCATTTTTTCTTTTT
Found at i:659793 original size:40 final size:40
Alignment explanation
Indices: 659744--659836 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
659734 TAAGCAAATT
**
659744 AAGAG-TCAAAATGCAAATAAAACTAATTTAAAACAAAAC
1 AAGAGATCAAAAACCAAATAAAACTAATTTAAAACAAAAC
* * * *
659783 AAGGGATCAAAAACCAAATTAGACTTATTTAAAACAAAAC
1 AAGAGATCAAAAACCAAATAAAACTAATTTAAAACAAAAC
659823 AAGAGATCAAAAAC
1 AAGAGATCAAAAAC
659837 AAAAATTAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 4 0.09
40 42 0.91
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.17
Consensus pattern (40 bp):
AAGAGATCAAAAACCAAATAAAACTAATTTAAAACAAAAC
Found at i:664932 original size:20 final size:20
Alignment explanation
Indices: 664907--664945 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
664897 AGATTACGCA
664907 GGGGGTA-CAGATTCCCCCTG
1 GGGGGTATC-GATTCCCCCTG
664927 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
664946 AATGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:666336 original size:31 final size:31
Alignment explanation
Indices: 666301--666473 Score: 256
Period size: 31 Copynumber: 5.6 Consensus size: 31
666291 GGGTCGAGGA
* *
666301 TTTACCTATGTTCTTTGGGACATATGGATTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
666332 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* *
666363 TTTACCTATGTTCTTCGGGACATATAGATTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* * *
666394 TTTACATATGTTCTTTGGGACATATAGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
666425 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* * *
666456 ATTACCGAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
666474 AATCTATGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTG
Found at i:666414 original size:93 final size:93
Alignment explanation
Indices: 666301--666473 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
666291 GGGTCGAGGA
* * * *
666301 TTTACCTATGTTCTTTGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGACTGTTT
1 TTTACATATGTTCTTTGGGACATATAGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATT
* *
666366 ACCTATGTTCTTCGGGACATATAGATTG
66 ACCGAGGTTCTTCGGGACATATAGATTG
666394 TTTACATATGTTCTTTGGGACATATAGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATT
1 TTTACATATGTTCTTTGGGACATATAGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATT
666459 ACCGAGGTTCTTCGG
66 ACCGAGGTTCTTCGG
666474 AATCTATGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (93 bp):
TTTACATATGTTCTTTGGGACATATAGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATT
ACCGAGGTTCTTCGGGACATATAGATTG
Found at i:675211 original size:23 final size:22
Alignment explanation
Indices: 675167--675211 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
675157 ATGTCTATAA
*
675167 AGCTGAAATATAGTAATTTGAT
1 AGCTGAAATATAGTAATCTGAT
*
675189 AGCTGAAATATCATTAATCTGAT
1 AGCTGAAATAT-AGTAATCTGAT
675212 CCCTTGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AGCTGAAATATAGTAATCTGAT
Found at i:681351 original size:144 final size:144
Alignment explanation
Indices: 681059--681333 Score: 369
Period size: 144 Copynumber: 1.9 Consensus size: 144
681049 GATAATTTTT
* * *
681059 TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCTTTCTTTCTTCAATTCTTCATTT
1 TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTCATTCTTCAATTCTTCATTT
* ** * * * *
681124 ATCTTAAGTCCCTTTTTTTATACCAAATTTGAGTCACATGCTCCTAAATCATAGTATAATACATG
66 ATCTTAAGTCCCTTTTTTTATACCAAATTTAAACCACATGCTCATAAATCATAATAGAATACATA
681189 TGTACTTTTACAAC
131 TGTACTTTTACAAC
*
681203 TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTT-ATTCATTCAATTTTTCATT
1 TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTCATTC-TTCAATTCTTCATT
* * * * *
681267 TATTTTAAGT-TC-TTTTTT-TACCAAATTTAAACCACATGCTCATATATTATAATAGAATACCT
65 TATCTTAAGTCCCTTTTTTTATACCAAATTTAAACCACATGCTCATAAATCATAATAGAATACAT
681329 ATGTA
130 ATGTA
681334 ACTTCAATTG
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
141 39 0.34
142 6 0.05
143 4 0.04
144 65 0.57
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (144 bp):
TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTCATTCTTCAATTCTTCATTT
ATCTTAAGTCCCTTTTTTTATACCAAATTTAAACCACATGCTCATAAATCATAATAGAATACATA
TGTACTTTTACAAC
Found at i:681523 original size:26 final size:26
Alignment explanation
Indices: 681494--681545 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
681484 ATATTTTACC
681494 CTCAAAAAAATTTCTTTAAAATATAA
1 CTCAAAAAAATTTCTTTAAAATATAA
* * *
681520 CTCAAAATACTTTCTTTGAAATATAA
1 CTCAAAAAAATTTCTTTAAAATATAA
681546 TATTATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (26 bp):
CTCAAAAAAATTTCTTTAAAATATAA
Found at i:687100 original size:18 final size:19
Alignment explanation
Indices: 687079--687119 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
687069 ATCTATGAAC
*
687079 ATAAAAGA-TTTAAGAAGA
1 ATAAAAGAGTTGAAGAAGA
*
687097 ATAAAAGAGTTGAAGAATA
1 ATAAAAGAGTTGAAGAAGA
687116 ATAA
1 ATAA
687120 CAAGGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (19 bp):
ATAAAAGAGTTGAAGAAGA
Found at i:691155 original size:17 final size:18
Alignment explanation
Indices: 691133--691166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
691123 ATGTATTCAT
691133 CTAAAAA-GATAATGGAA
1 CTAAAAATGATAATGGAA
*
691150 CTAAAAATGATGATGGA
1 CTAAAAATGATAATGGA
691167 TAGAAGACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (18 bp):
CTAAAAATGATAATGGAA
Found at i:693529 original size:16 final size:17
Alignment explanation
Indices: 693508--693543 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
693498 ATCAGAGATC
*
693508 TTATTT-TTCTTTAAAT
1 TTATTTCTTCGTTAAAT
693524 TTATTTCTTCGTTAAAT
1 TTATTTCTTCGTTAAAT
693541 TTA
1 TTA
693544 ATTATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTTCTTCGTTAAAT
Found at i:697274 original size:20 final size:20
Alignment explanation
Indices: 697251--697300 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
697241 TTGTTCATAG
* *
697251 GTATCAATACTGACCCTTTA
1 GTATCAATACTAAACCTTTA
* *
697271 GTATCGATACTAAACCTTTG
1 GTATCAATACTAAACCTTTA
697291 GTATCAATAC
1 GTATCAATAC
697301 CCACATGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCAATACTAAACCTTTA
Found at i:706049 original size:15 final size:16
Alignment explanation
Indices: 706011--706051 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
706001 ATAGAGCCTC
706011 TGAATCATTCAACATT
1 TGAATCATTCAACATT
* *
706027 TGAATCATTCAGCGTT
1 TGAATCATTCAACATT
706043 T-AATCATTC
1 TGAATCATTC
706052 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:708777 original size:20 final size:20
Alignment explanation
Indices: 708752--708902 Score: 185
Period size: 20 Copynumber: 7.4 Consensus size: 20
708742 TTTAGAAGAA
*
708752 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
708772 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
708792 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
708815 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
708835 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
708855 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
708875 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
708895 AATCGCAA
1 AATCGCAA
708903 CGTTAAATCC
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
20 93 0.83
21 3 0.03
22 2 0.02
23 14 0.12
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:708814 original size:63 final size:63
Alignment explanation
Indices: 708731--708902 Score: 233
Period size: 63 Copynumber: 2.8 Consensus size: 63
708721 GCTTTCAAGT
* *
708731 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * *
708794 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * *
708857 TCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAA
708903 CGTTAAATCC
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
60 27 0.28
61 1 0.01
62 2 0.02
63 68 0.69
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:708903 original size:20 final size:20
Alignment explanation
Indices: 708704--708904 Score: 134
Period size: 20 Copynumber: 9.7 Consensus size: 20
708694 AACGGTCAAA
708704 AGAAAATCGCAACGCGAGCTTT
1 AGAAAATCGCAACGCGA--TTT
* **
708726 -CAAGTTCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
* *
708745 AGAAGAAAATCGCAATGCGATTG
1 ---AGAAAATCGCAACGCGATTT
* * * *
708768 ATAGAATCGCAATGCGATTG
1 AGAAAATCGCAACGCGATTT
* *
708788 AGAGAGTCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
* * *
708808 AGAAGAAAATCGCAATGCGACTG
1 ---AGAAAATCGCAACGCGATTT
* *
708831 AGAGAATCGCAATGCGATTT
1 AGAAAATCGCAACGCGATTT
* * * *
708851 ATAGAATCGCAATGCGATTG
1 AGAAAATCGCAACGCGATTT
*
708871 AGAGAATCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
708891 AGAAAATCGCAACG
1 AGAAAATCGCAACG
708905 TTAAATCCAT
Statistics
Matches: 144, Mismatches: 28, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
19 3 0.02
20 99 0.69
21 13 0.09
23 29 0.20
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (20 bp):
AGAAAATCGCAACGCGATTT
Found at i:710226 original size:177 final size:175
Alignment explanation
Indices: 709830--710188 Score: 574
Period size: 177 Copynumber: 2.0 Consensus size: 175
709820 ACATATCCAC
* * * *
709830 TGCAATTTTAAGATCAGAAGGCCAAAGGATTAGTTCTTTCAAGCTATTGGCATTGTTTGTAACAA
1 TGCAATTCT-AGATCACAA-GCAAAAGGATTAGTGCTTTCAAGCTATTGGCATTGTTTGTAACAA
709895 ACATGTATAAACATGCAGTGTCTACACTTACTATGTTCCGACTACTCGAACCGTATTTTCGTTTT
64 ACATGTATAAACATGCAGTGTCTACACTTACTATGTTCCGACTACTCGAACCGTATTTTCGTTTT
709960 GGTTACCCCCAAAGATCCTGGCCATGCCAAAATCCGAAATCTTCGGA
129 GGTTACCCCCAAAGATCCTGGCCATGCCAAAATCCGAAATCTTCGGA
* * * *
710007 TGCAATTTTAAGATCAGAAGGCCAAAGGATTAGTTCTTTCAAGCTATTGGCATTGTTTGTAACAT
1 TGCAATTCT-AGATCACAA-GCAAAAGGATTAGTGCTTTCAAGCTATTGGCATTGTTTGTAACA-
710072 AACATGTATAAACATGCAGTGTCTACACTTACTATGTTCCGACTACTCGAACCGTATTTGCTTCG
63 AACATGTATAAACATGCAGTGTCTACACTTACTATGTTCCGACTACTCGAACCGTA-TT--TTCG
710137 TTTTGGTTACCCCCAAAGATCCTGGCCATGCCAAAATCCGAAATCTTCGGA
125 TTTTGGTTACCCCCAAAGATCCTGGCCATGCCAAAATCCGAAATCTTCGGA
710188 T
1 T
710189 TCATCTCTGC
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
177 64 0.36
178 56 0.31
179 2 0.01
181 56 0.31
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (175 bp):
TGCAATTCTAGATCACAAGCAAAAGGATTAGTGCTTTCAAGCTATTGGCATTGTTTGTAACAAAC
ATGTATAAACATGCAGTGTCTACACTTACTATGTTCCGACTACTCGAACCGTATTTTCGTTTTGG
TTACCCCCAAAGATCCTGGCCATGCCAAAATCCGAAATCTTCGGA
Found at i:713663 original size:19 final size:19
Alignment explanation
Indices: 713639--713675 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
713629 ATATATACAT
713639 GTAAAAATATTCTTCTTAA
1 GTAAAAATATTCTTCTTAA
713658 GTAAAAATATTCTTCTTA
1 GTAAAAATATTCTTCTTA
713676 TTTGTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
GTAAAAATATTCTTCTTAA
Found at i:716226 original size:13 final size:13
Alignment explanation
Indices: 716201--716233 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
716191 TCCTTAAAAG
716201 ATAATTT-TTTTA
1 ATAATTTATTTTA
716213 ATAATTTATTTTA
1 ATAATTTATTTTA
*
716226 ATTATTTA
1 ATAATTTA
716234 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATAATTTATTTTA
Found at i:722380 original size:42 final size:42
Alignment explanation
Indices: 722329--722566 Score: 170
Period size: 42 Copynumber: 5.7 Consensus size: 42
722319 AAAATGATAT
722329 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * *
722371 TTTAGCGGCG-TTTATAGTAA-AAATGCCGTAATAGA-TACGT--
1 TTTAGCGGCGTTTTTTA--AACAAACGCCGCAATAGAGT-GGTAA
* *
722411 TTATAGTGGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * ** * *
722454 TTTAGCGGC-ATTTTTACACAAACGCCGTGAT--AGTGTTAT
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * ** *
722493 TTATAGTGGCATTTGTTT-AACAAACGCCGCTATAGAGAAGAAA
1 TT-TAGCGGCGTTT-TTTAAACAAACGCCGCAATAGAGTGGTAA
* * *
722536 TTTAGCGGCATTTATAAAACAAACGCCGCAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAA
722567 ATAGTATTGT
Statistics
Matches: 149, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
39 8 0.05
40 10 0.07
41 60 0.40
42 62 0.42
43 9 0.06
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:722433 original size:83 final size:80
Alignment explanation
Indices: 722335--722590 Score: 280
Period size: 82 Copynumber: 3.1 Consensus size: 80
722325 ATATTTTAGC
* * * *
722335 GGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATAGTAAAAATGCCGT
1 GGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATA-AAAAAACGCCGT
722400 AATAGATACGTTTATAGT
65 AATAG-TA-GTTTATAGT
* * * *
722418 GGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTTTACACAAACGCCGTG
1 GGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATAAAAAAACGCCGTA
722483 ATAGT-GTTATTTATAGT
66 ATAGTAG---TTTATAGT
* * * ** *
722500 GGCATTTGTTTAACAAACGCCGCTATAGAGAAGAAATTTAGCGGCATTTATAAAACAAACGCCGC
1 GGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATAAAA-AAACGCCG-
*
722565 AAATAGTATTGTTTATAGT
64 TAATAGTA--GTTTATAGT
722584 GGCGTTT
1 GGCGTTT
722591 ATGCAAAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.01
81 1 0.01
82 67 0.46
83 57 0.39
84 19 0.13
87 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (80 bp):
GGCGTTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATAAAAAAACGCCGTA
ATAGTAGTTTATAGT
Found at i:724098 original size:42 final size:42
Alignment explanation
Indices: 724036--724173 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 42
724026 TTTTTTATCG
* * *
724036 AAAAACGCCGCTATAGACCACACTTTTGTGGCATTTGTATAA
1 AAAAACGCCGCCATAAACCACACTTTTATGGCATTTGTATAA
* * **
724078 AAAAACGCCGCCATAAACCACACTTTTTTACGGCGTTTACATAA
1 AAAAACGCCGCCATAAACCACAC--TTTTATGGCATTTGTATAA
* * **
724122 AAAAATGCCGCCATAAACCACACTTTTACGGCATTTGT-TTC
1 AAAAACGCCGCCATAAACCACACTTTTATGGCATTTGTATAA
724163 AAAAACGCCGC
1 AAAAACGCCGC
724174 AATATGTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 11 0.14
42 33 0.41
44 36 0.45
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCCATAAACCACACTTTTATGGCATTTGTATAA
Found at i:728418 original size:21 final size:21
Alignment explanation
Indices: 728394--728437 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
728384 AGCGGAAAAT
*
728394 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGTGGAAGCACAGAGA
*
728415 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGTGGAAGCACAGAGA
728436 GA
1 GA
728438 GACAACGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.14, G:0.41, T:0.02
Consensus pattern (21 bp):
GAAGCAGTGGAAGCACAGAGA
Found at i:728879 original size:43 final size:43
Alignment explanation
Indices: 728828--729136 Score: 266
Period size: 43 Copynumber: 7.2 Consensus size: 43
728818 CATATATTTA
* ** *
728828 GCGGCGTTTGCGCTAAAAACGCCGCTAAATCTCAACACCTATT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTACT
* ** * * *
728871 GCAGCGTTTGTGATAAAAACGCCGTTAAATATCAACATCTACT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTACT
* * * *
728914 GCGGCATTTGTGGAAAAAACGCCACTAAA-CATCAATACCTACT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATC-TCAACACCTACT
* * * **
728957 GCGGTGTTTGTGGGAAAAATGTCGCTAAAAATCAACACCTACT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTACT
* *** *
729000 GCGGCATTAACGGGAAAAACGCCGC-AAAACATCAACACCTACT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATC-TCAACACCTACT
* * * * *
729043 GCGGCGTTAG-CGGAAAAATGCCGCAAAATATCAACACCTACT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTACT
** * *
729085 GCGGCGTTTGTGAAAAAAATGCCGCTAAA-CATCAACACCTATT
1 GCGGCGTTTGTGGGAAAAACGCCGCTAAATC-TCAACACCTACT
729128 GCGGCGTTT
1 GCGGCGTTT
729137 TTTGTTGAAA
Statistics
Matches: 215, Mismatches: 45, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
42 37 0.17
43 178 0.83
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (43 bp):
GCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTACT
Found at i:728954 original size:86 final size:85
Alignment explanation
Indices: 728842--729136 Score: 349
Period size: 86 Copynumber: 3.4 Consensus size: 85
728832 CGTTTGCGCT
* * * * *
728842 AAAAACGCCGCTAAATC-TCAACACCTATTGCAGCGTTTGTGATAAAAACGCCGTTAAATATCAA
1 AAAAACGCCGCTAAA-CATCAACACCTACTGCGGCGTTTGTG-GAAAAATGCCGCTAAATATCAA
*
728906 CATCTACTGCGGCATTTGTGGA
64 CACCTACTGCGGCATTTGTGGA
* * * * *
728928 AAAAACGCCACTAAACATCAATACCTACTGCGGTGTTTGTGGGAAAAATGTCGCTAAAAATCAAC
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGT-GGAAAAATGCCGCTAAATATCAAC
*** *
728993 ACCTACTGCGGCATTAACGGG
65 ACCTACTGCGGCATTTGTGGA
* * * *
729014 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTAGCGGAAAAATGCCGCAAAATATCAACA
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGTGGAAAAATGCCGCTAAATATCAACA
* *
729079 CCTACTGCGGCGTTTGTGAA
66 CCTACTGCGGCATTTGTGGA
* *
729099 AAAAATGCCGCTAAACATCAACACCTATTGCGGCGTTT
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTT
729137 TTTGTTGAAA
Statistics
Matches: 173, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
85 71 0.41
86 101 0.58
87 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (85 bp):
AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGTGGAAAAATGCCGCTAAATATCAACA
CCTACTGCGGCATTTGTGGA
Found at i:731729 original size:60 final size:60
Alignment explanation
Indices: 731636--731780 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
731626 CATATGTCTC
* * * ** *
731636 CAAACTATGACCCTTATT-TAAATTAGTCCTTAAA-TTTCTAAAAATTTTAATTTTATCC-
1 CAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTT-TAAAAATTCCAATTTCATCCT
* * **
731694 CTAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTGAGCATTCCAATTTCATCCT
1 C-AAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAAAATTCCAATTTCATCCT
731755 CAAACTATGACTCTCATTCTAAATTA
1 CAAACTATGACTCTCATTCTAAATTA
731781 GTTCAAAGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 14 0.19
60 53 0.74
61 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
CAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAAAATTCCAATTTCATCCT
Found at i:735771 original size:212 final size:205
Alignment explanation
Indices: 735366--735782 Score: 739
Period size: 212 Copynumber: 2.0 Consensus size: 205
735356 ACCCGAATAT
735366 ATGACTTAGAAACCCGACCCGACCTGAAATAAAAAAAATTAATTCAATGAAAACAGTGACTTAAT
1 ATGACTTAGAAACCCGACCCGACCTGAAATAAAAAAAATTAATTCAATGAAAACAGTGACTTAAT
735431 TGAAAAAAATTATATGGAGTGATATTATTGTAATTATCCCTAAATATAAGATAAATTATATATTT
66 TGAAAAAAATTATATGGAGTGATATTATTGTAATTATCCCTAAATATAAGATAAATTATATATTT
735496 TCGGGTCGGGTCGGTCGGATTTTTTTACCCTAAACCCGACCCGACCCGAACAGTGCATTTAAAAA
131 TCGGGTCGGGTCGGTCGGATTTTTTTACCCTAAACCCGACCCGACCCGAACAGTGCATTTAAAAA
735561 AAACCCGACC
196 AAACCCGACC
735571 ATGACTTAGAAA-CCGACCCGACCTGAAATAAAAAAAAAATTAATTCAATGAAAACAGTGACTTA
1 ATGACTTAGAAACCCGACCCGACCTGAAAT--AAAAAAAATTAATTCAATGAAAACAGTGACTTA
735635 ATTGAAAAAAATTATATATGGAG-GATATTATTGTAATTATCCCTAAATATAAGATAAAATTATA
64 ATTGAAAAAAA-T-TATATGGAGTGATATTATTGTAATTATCCCTAAATATAAGAT-AAA-T-TA
735699 TATATTTTCGGGTCGGGTCGGGTCGGATTTTTTTTACCCTAAACCCGACCCGACCCGAACAGTGC
124 TATATTTTCGGGTCGGGTC-GGTCGGA-TTTTTTTACCCTAAACCCGACCCGACCCGAACAGTGC
735764 ATTTAAAAAAAACCCGACC
187 ATTTAAAAAAAACCCGACC
735783 CGACGACCCG
Statistics
Matches: 203, Mismatches: 0, Indels: 11
0.95 0.00 0.05
Matches are distributed among these distances:
204 17 0.08
205 12 0.06
206 44 0.22
207 33 0.16
208 12 0.06
209 1 0.00
210 21 0.10
211 7 0.03
212 56 0.28
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (205 bp):
ATGACTTAGAAACCCGACCCGACCTGAAATAAAAAAAATTAATTCAATGAAAACAGTGACTTAAT
TGAAAAAAATTATATGGAGTGATATTATTGTAATTATCCCTAAATATAAGATAAATTATATATTT
TCGGGTCGGGTCGGTCGGATTTTTTTACCCTAAACCCGACCCGACCCGAACAGTGCATTTAAAAA
AAACCCGACC
Found at i:739477 original size:23 final size:23
Alignment explanation
Indices: 739451--739519 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
739441 CACCACAGCT
*
739451 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
739474 CGTAGAATTGCACAGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
739497 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
739520 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:744705 original size:12 final size:12
Alignment explanation
Indices: 744688--744713 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
744678 CTTTTACACG
744688 TACAAACATATA
1 TACAAACATATA
744700 TACAAACATATA
1 TACAAACATATA
744712 TA
1 TA
744714 TATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (12 bp):
TACAAACATATA
Found at i:744963 original size:23 final size:23
Alignment explanation
Indices: 744937--745005 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
744927 CACCACAACT
*
744937 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
744960 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
744983 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
745006 TAATAATGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:747576 original size:21 final size:21
Alignment explanation
Indices: 747551--747653 Score: 71
Period size: 21 Copynumber: 4.7 Consensus size: 21
747541 TGAACATGTG
*
747551 AATTATATGAAAAGTGATATA
1 AATTACATGAAAAGTGATATA
* *
747572 AATTACATGAAAAGAAGCTATA
1 AATTACATGAAAAG-TGATATA
** * * * *
747594 TGTCTACATGATATGTGAACATGTG
1 AAT-TACATGAAAAGTG---ATATA
*
747619 AATTATATGAAAAGTGATATA
1 AATTACATGAAAAGTGATATA
747640 AATTACATGAAAAG
1 AATTACATGAAAAG
747654 AAGCTATATG
Statistics
Matches: 58, Mismatches: 19, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
21 29 0.50
22 7 0.12
23 9 0.16
24 10 0.17
25 3 0.05
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.30
Consensus pattern (21 bp):
AATTACATGAAAAGTGATATA
Found at i:747607 original size:68 final size:68
Alignment explanation
Indices: 747535--747681 Score: 285
Period size: 68 Copynumber: 2.1 Consensus size: 68
747525 AATATGGAAA
747535 GATATGTGAACATGTGAATTATATGAAAAGTGATATAAATTACATGAAAAGAAGCTATATGTCTA
1 GATATGTGAACATGTGAATTATATGAAAAGTGATATAAATTACATGAAAAGAAGCTATATGTCTA
747600 CAT
66 CAT
747603 GATATGTGAACATGTGAATTATATGAAAAGTGATATAAATTACATGAAAAGAAGCTATATGTCTA
1 GATATGTGAACATGTGAATTATATGAAAAGTGATATAAATTACATGAAAAGAAGCTATATGTCTA
747668 CAT
66 CAT
747671 GTATATGTGAA
1 G-ATATGTGAA
747682 AAAAAGCTAT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 69 0.88
69 9 0.12
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (68 bp):
GATATGTGAACATGTGAATTATATGAAAAGTGATATAAATTACATGAAAAGAAGCTATATGTCTA
CAT
Found at i:747846 original size:18 final size:18
Alignment explanation
Indices: 747823--747862 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
747813 TCCTTCGGGG
747823 CATAGTGGACATTAGGGA
1 CATAGTGGACATTAGGGA
* * *
747841 CATAGTGGTCCTTCGGGA
1 CATAGTGGACATTAGGGA
747859 CATA
1 CATA
747863 TGTGTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (18 bp):
CATAGTGGACATTAGGGA
Found at i:752244 original size:20 final size:20
Alignment explanation
Indices: 752219--752258 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
752209 CATGTGAATT
*
752219 TGTCCCGAAGGACCTGTGTA
1 TGTCCCGAAGGACCTATGTA
752239 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
752259 CCCCTACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:752944 original size:35 final size:35
Alignment explanation
Indices: 752885--752952 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
752875 GTTTCAAAGA
* *
752885 TGGTATCGATATTGTCCTTAAGGTATCGGTACCCT
1 TGGTATCGATAATGTCCTTAAGGTATCGATACCCT
* * *
752920 TGGTATCTATAATGTTCTTCAGGTATCGATACC
1 TGGTATCGATAATGTCCTTAAGGTATCGATACC
752953 TCATAATGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (35 bp):
TGGTATCGATAATGTCCTTAAGGTATCGATACCCT
Found at i:756563 original size:81 final size:80
Alignment explanation
Indices: 756429--756589 Score: 313
Period size: 81 Copynumber: 2.0 Consensus size: 80
756419 GAGAGTCCTG
756429 AAGAAGACCGCAAATTGATGCTTATATTAAGAGATATGGGATTTGGAACTGGGCTGAGATGGCTA
1 AAGAAGACCGCAAATTGATGCTTATATTAAGAGATATGGGATTTGGAACTGGGCTGAGATGGCTA
756494 AACCAGCAGGTGGAT
66 AACCAGCAGGTGGAT
756509 AAGAAGACCGCAAATTGACTGCTTATATTAAGAGATATGGGATTTGGAACTGGGCTGAGATGGCT
1 AAGAAGACCGCAAATTGA-TGCTTATATTAAGAGATATGGGATTTGGAACTGGGCTGAGATGGCT
756574 AAACCAGCAGGTGGAT
65 AAACCAGCAGGTGGAT
756590 TAAGCTAAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 18 0.22
81 62 0.77
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.24
Consensus pattern (80 bp):
AAGAAGACCGCAAATTGATGCTTATATTAAGAGATATGGGATTTGGAACTGGGCTGAGATGGCTA
AACCAGCAGGTGGAT
Found at i:766738 original size:2 final size:2
Alignment explanation
Indices: 766733--766779 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
766723 TTTTTATTGA
766733 AT AT AT AT AT AT A- AT AT AT AT AT AT AT A- 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
766773 AT AT AT A
1 AT AT AT A
766780 CGAACCACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:766753 original size:15 final size:15
Alignment explanation
Indices: 766733--766779 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
766723 TTTTTATTGA
766733 ATATATATATATAAT
1 ATATATATATATAAT
766748 ATATATATATATAAT
1 ATATATATATATAAT
766763 ATATATATATAT-AT
1 ATATATATATATAAT
766777 ATA
1 ATA
766780 CGAACCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:769051 original size:22 final size:23
Alignment explanation
Indices: 768998--769051 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
768988 TGATGATGTC
768998 TAATTTTATACTCTTAAAATTTTA
1 TAATTTT-TACTCTTAAAATTTTA
*
769022 TAA-CTTTACATCTT-AAA-TTTA
1 TAATTTTTAC-TCTTAAAATTTTA
769043 TAATTTTTA
1 TAATTTTTA
769052 AATTTGCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.27
22 10 0.38
23 6 0.23
24 3 0.12
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (23 bp):
TAATTTTTACTCTTAAAATTTTA
Found at i:770637 original size:19 final size:20
Alignment explanation
Indices: 770613--770663 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
770603 AATGACCAAT
770613 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
770632 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
770652 AAAATCGCAACG
1 AAAATCGCAACG
770664 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:770657 original size:20 final size:20
Alignment explanation
Indices: 770613--770870 Score: 153
Period size: 20 Copynumber: 12.6 Consensus size: 20
770603 AATGACCAAT
* *
770613 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
770632 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
770652 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
770672 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
770692 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
770713 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
770736 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
770756 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
770776 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
770799 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
770819 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
770839 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
770859 AAAATCGCAACG
1 AAAATCGCAACG
770871 TTAAAAAGAA
Statistics
Matches: 188, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.09
20 128 0.68
21 14 0.07
23 29 0.15
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:770800 original size:63 final size:63
Alignment explanation
Indices: 770717--770860 Score: 261
Period size: 63 Copynumber: 2.3 Consensus size: 63
770707 GCTTCCAAGT
* * *
770717 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
770780 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
770843 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
770861 AATCGCAACG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:770969 original size:6 final size:6
Alignment explanation
Indices: 770958--770990 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
770948 AACACGTATT
770958 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
770991 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:771740 original size:6 final size:6
Alignment explanation
Indices: 771668--771743 Score: 108
Period size: 6 Copynumber: 13.5 Consensus size: 6
771658 TCTCGTCTCG
*
771668 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
771711 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
771744 AATACGTGTC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 25 0.36
6 44 0.64
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:771856 original size:20 final size:20
Alignment explanation
Indices: 771833--772004 Score: 191
Period size: 20 Copynumber: 8.3 Consensus size: 20
771823 CTTTTGACCG
*
771833 TTGCGATTTTCTAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
771853 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
771873 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
771893 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
* *
771916 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
771936 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
771956 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
771976 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
771999 TTGCGA
1 TTGCGA
772005 ACTTGGAAGC
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
20 92 0.72
21 2 0.02
22 6 0.05
23 28 0.22
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:771877 original size:40 final size:40
Alignment explanation
Indices: 771833--771983 Score: 212
Period size: 40 Copynumber: 3.7 Consensus size: 40
771823 CTTTTGACCG
* *
771833 TTGCGATTTTCTAAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* * *
771873 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TATAAATCGCA
*
771916 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
*
771956 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTCTCAATCGCATTGCGATT
771984 TTCTTCTAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 58 0.60
41 3 0.03
42 3 0.03
43 33 0.34
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
Found at i:771920 original size:63 final size:63
Alignment explanation
Indices: 771841--771963 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 63
771831 CGTTGCGATT
* * * *
771841 TTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
1 TTCTAAATCGCATTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTTTC
* * *
771904 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT
1 TTCTAAATCGCATTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATT
771964 CTATCAATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (63 bp):
TTCTAAATCGCATTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTTTC
Found at i:771975 original size:83 final size:83
Alignment explanation
Indices: 771831--772004 Score: 303
Period size: 83 Copynumber: 2.1 Consensus size: 83
771821 TTCTTTTGAC
* * * *
771831 CGTTGCGATTTTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
771896 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
*
771914 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
771979 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
771997 CGTTGCGA
1 CGTTGCGA
772005 ACTTGGAAGC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (83 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:771996 original size:63 final size:61
Alignment explanation
Indices: 771833--772004 Score: 181
Period size: 63 Copynumber: 2.8 Consensus size: 61
771823 CTTTTGACCG
* * * *
771833 TTGCGA-TT-TTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTCTTC-AAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
* * *
771893 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGA-TTTCTTC-AAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
*
771956 TTGCGA-TTCTATC-AATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTTCT-TCAAATCGCATTGCGA--TTC-TCTAAATCGCATTGCGA
772005 ACTTGGAAGC
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
60 18 0.19
61 4 0.04
62 6 0.06
63 66 0.70
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (61 bp):
TTGCGATTTCTTCAAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
Found at i:772081 original size:20 final size:20
Alignment explanation
Indices: 771831--772108 Score: 157
Period size: 20 Copynumber: 13.6 Consensus size: 20
771821 TTCTTTTGAC
771831 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
771851 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
771871 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
771891 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
771914 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
771934 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
771954 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
771974 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
771997 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
772018 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
772036 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
772058 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
772078 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
772097 CGTTGCGATTTT
1 CGTTGCGATTTT
772109 ATTGGTCATT
Statistics
Matches: 205, Mismatches: 42, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 138 0.67
21 14 0.07
22 6 0.03
23 28 0.14
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:772098 original size:19 final size:20
Alignment explanation
Indices: 772058--772108 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
772048 TTCTTTTTAA
*
772058 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
772078 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
772097 CGTTGCGATTTT
1 CGTTGCGATTTT
772109 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:777719 original size:33 final size:35
Alignment explanation
Indices: 777682--777748 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
777672 AAGGTTTATC
777682 ATTTAAATTTAAAAT-AA-TAAATATTTA-TTAAAT
1 ATTTAAATTTAAAATAAACTAAAT-TTTACTTAAAT
**
777715 ATTTATTTTTAAAATAAACTAAATTTTACTTAAA
1 ATTTAAATTTAAAATAAACTAAATTTTACTTAAA
777749 CTAATAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 13 0.45
34 6 0.21
35 10 0.34
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (35 bp):
ATTTAAATTTAAAATAAACTAAATTTTACTTAAAT
Found at i:780027 original size:12 final size:11
Alignment explanation
Indices: 780007--780036 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
779997 ACTTTCGATC
780007 AAAAAAAACAA
1 AAAAAAAACAA
780018 AAACAAAAACAA
1 AAA-AAAAACAA
780030 AAAAAAA
1 AAAAAAA
780037 TATGAGCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:781156 original size:23 final size:23
Alignment explanation
Indices: 781130--781191 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
781120 AAGTTTTAGT
781130 ATTGGTGTGTTAATAATATTACA
1 ATTGGTGTGTTAATAATATTACA
*
781153 ATTGGTGTGTTAAT--TATTACT
1 ATTGGTGTGTTAATAATATTACA
781174 ATTGGTGTG-TAATAATAT
1 ATTGGTGTGTTAATAATAT
781192 GGAATGCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 4 0.11
21 15 0.42
22 3 0.08
23 14 0.39
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (23 bp):
ATTGGTGTGTTAATAATATTACA
Found at i:788499 original size:22 final size:24
Alignment explanation
Indices: 788469--788512 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
788459 TTTTTAATAT
*
788469 TCATATTTTTATT-AATTTAATCG
1 TCATATTTTAATTAAATTTAATCG
788492 TCAT-TTTTAATTAAATTTAAT
1 TCATATTTTAATTAAATTTAAT
788513 TCTTGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (24 bp):
TCATATTTTAATTAAATTTAATCG
Found at i:789301 original size:24 final size:24
Alignment explanation
Indices: 789269--789316 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
789259 ATATACCACC
789269 ATTTGAGGACGGGTAGGCCTTTTT
1 ATTTGAGGACGGGTAGGCCTTTTT
789293 ATTTGAGGACGGGTAGGCCTTTTT
1 ATTTGAGGACGGGTAGGCCTTTTT
789317 TATATATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (24 bp):
ATTTGAGGACGGGTAGGCCTTTTT
Found at i:790797 original size:24 final size:24
Alignment explanation
Indices: 790770--790841 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
790760 AAACGGAGAT
*
790770 ATCAAAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
790794 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
790818 ATCAGAAATCAGAAA-ATAATTCAG
1 ATCAGAAATCA-AAACAGAATTCAG
790842 GTAATGTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 37 0.95
25 2 0.05
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:790876 original size:24 final size:25
Alignment explanation
Indices: 790770--790876 Score: 71
Period size: 24 Copynumber: 4.4 Consensus size: 25
790760 AAACGGAGAT
* *
790770 ATCAAAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
790794 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
* *
790818 ATCAGAAATCAGAAAATAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * *
790842 GTAATG-TATCAGAACATAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
790867 -TCAGAAATCA
1 ATCAGAAATCA
790877 TATAAAATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.05
24 57 0.88
25 5 0.08
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.21
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:793376 original size:12 final size:13
Alignment explanation
Indices: 793347--793377 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
793337 TCGGGTCGGG
793347 TTCGGGGATTTGT
1 TTCGGGGATTTGT
793360 TTCGGGGATTT-T
1 TTCGGGGATTTGT
793372 TTCGGG
1 TTCGGG
793378 TCGGGTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.06, C:0.10, G:0.39, T:0.45
Consensus pattern (13 bp):
TTCGGGGATTTGT
Found at i:793466 original size:34 final size:34
Alignment explanation
Indices: 793427--793511 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
793417 TATATATATA
793427 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
793461 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
793495 TATATATAAAATATTTT
1 TATATATATAATATTTT
793512 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:793499 original size:25 final size:25
Alignment explanation
Indices: 793413--793482 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 25
793403 CCCCGCCCCG
*
793413 ATTATATATAT-ATA-TATATATATA
1 ATTATATATATAATATTTTATAT-TA
* *
793437 A-TAT-TTTAT-ATTTTTTATATTA
1 ATTATATATATAATATTTTATATTA
793459 ATTATATATATAATATTTTATATT
1 ATTATATATATAATATTTTATATT
793483 TTTTATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 9 0.24
23 12 0.32
24 5 0.14
25 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATATATATAATATTTTATATTA
Found at i:794809 original size:29 final size:29
Alignment explanation
Indices: 794774--794842 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
794764 GTTTATAATA
794774 TTAGACACCTAGATGAGTCAAAAAATAGT
1 TTAGACACCTAGATGAGTCAAAAAATAGT
*
794803 TTAGACATCTAGATGAGTCAAAAAATAGT
1 TTAGACACCTAGATGAGTCAAAAAATAGT
794832 TTAGACACCTA
1 TTAGACACCTA
794843 TTTAAGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (29 bp):
TTAGACACCTAGATGAGTCAAAAAATAGT
Found at i:795486 original size:21 final size:21
Alignment explanation
Indices: 795448--795488 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
795438 ATTAATAATT
*
795448 TTATTTTTATTTTTTAACTTG
1 TTATTTTTATTTTCTAACTTG
795469 TTATTTTT-TCTTTCTAACTT
1 TTATTTTTAT-TTTCTAACTT
795489 ATTTAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTATTTTCTAACTTG
Found at i:797195 original size:6 final size:6
Alignment explanation
Indices: 797184--797212 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
797174 CATGTACCTT
797184 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
797213 GTAGTAAGAC
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:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:798302 original size:21 final size:21
Alignment explanation
Indices: 798282--798423 Score: 110
Period size: 21 Copynumber: 6.9 Consensus size: 21
798272 ATTCGCGTTG
*
798282 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
798303 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
* *
798323 CATTTCACGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** * *
798344 AAAATCACGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
798364 CATTTCGCGTTGCGATAGTTA
1 CATTTCGCGTTGCGATAGTTC
* ** *
798385 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
798405 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
798424 CTACAGTTGT
Statistics
Matches: 87, Mismatches: 31, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
20 43 0.49
21 44 0.51
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:798327 original size:41 final size:41
Alignment explanation
Indices: 798282--798423 Score: 257
Period size: 41 Copynumber: 3.5 Consensus size: 41
798272 ATTCGCGTTG
798282 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
798323 CATTTCACGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
798364 CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
798405 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
798424 CTACAGTTGT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:798335 original size:20 final size:20
Alignment explanation
Indices: 798307--798420 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
798297 TAGTTGAAAA
798307 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
798327 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
798348 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
798368 TCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGAT-TTTCCATT
798389 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
798409 TCGCGTTGCGAT
1 TCGCGTTGCGAT
798421 AGTCTACAGT
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 40 0.57
21 30 0.43
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:806575 original size:22 final size:24
Alignment explanation
Indices: 806534--806579 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
806524 TGGTTATTGC
*
806534 ATATGTTATATGATATATGTGAAT
1 ATATGTTATATGATAAATGTGAAT
806558 ATATGTTATA-G-TAAATGTGAAT
1 ATATGTTATATGATAAATGTGAAT
806580 GAGTATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (24 bp):
ATATGTTATATGATAAATGTGAAT
Found at i:807768 original size:29 final size:29
Alignment explanation
Indices: 807723--807854 Score: 178
Period size: 29 Copynumber: 4.6 Consensus size: 29
807713 CCCGTTGACT
* *
807723 GGGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGTTATTTTAGTAATTATTTTTAAAA
* *
807752 GGGTGCTATTTTTGTAATTATTTTTAAAA
1 GGGTGTTATTTTAGTAATTATTTTTAAAA
*
807781 -GGTGTTATTTTAGTAATTATTTATAAAA
1 GGGTGTTATTTTAGTAATTATTTTTAAAA
*
807809 GGGTGTTATTTTCGTAATTATTTTTAAAA
1 GGGTGTTATTTTAGTAATTATTTTTAAAA
*
807838 TGGTGTTAATTTT-GTAA
1 GGGTGTT-ATTTTAGTAA
807855 AATGGTTGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
28 25 0.27
29 63 0.68
30 5 0.05
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (29 bp):
GGGTGTTATTTTAGTAATTATTTTTAAAA
Found at i:807819 original size:57 final size:58
Alignment explanation
Indices: 807724--807854 Score: 203
Period size: 57 Copynumber: 2.3 Consensus size: 58
807714 CCGTTGACTG
* * *
807724 GGTGCTATTTTAGTAATTATTTCTAAAAGGGTGCTATTTTTGTAATTATTTTTAAAA-
1 GGTGTTATTTTAGTAATTATTTATAAAAGGGTGCTATTTTCGTAATTATTTTTAAAAT
*
807781 GGTGTTATTTTAGTAATTATTTATAAAAGGGTGTTATTTTCGTAATTATTTTTAAAAT
1 GGTGTTATTTTAGTAATTATTTATAAAAGGGTGCTATTTTCGTAATTATTTTTAAAAT
807839 GGTGTTAATTTT-GTAA
1 GGTGTT-ATTTTAGTAA
807855 AATGGTTGAT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
57 53 0.78
58 10 0.15
59 5 0.07
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (58 bp):
GGTGTTATTTTAGTAATTATTTATAAAAGGGTGCTATTTTCGTAATTATTTTTAAAAT
Found at i:808523 original size:24 final size:24
Alignment explanation
Indices: 808488--808560 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
808478 ATTTTTGATG
808488 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
808512 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
808536 GGATTCTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
808560 G
1 G
808561 AATTATGTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:811996 original size:2 final size:2
Alignment explanation
Indices: 811989--812047 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
811979 AGGAGAAATG
811989 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
812031 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
812048 GGAAGATGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:812583 original size:23 final size:23
Alignment explanation
Indices: 812527--812583 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
812517 GAACTTCGGG
*
812527 GCATTTCTACGCGGCACTACGGT
1 GCATTTCTACGCGGCACTACGAT
* * *
812550 GCAATTCTACGTGGCACTTCGAT
1 GCATTTCTACGCGGCACTACGAT
*
812573 GCATTTATACG
1 GCATTTCTACG
812584 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
GCATTTCTACGCGGCACTACGAT
Found at i:820326 original size:12 final size:12
Alignment explanation
Indices: 820304--820341 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
820294 CGAAAAGGAA
820304 AAAAAAG-AAAG
1 AAAAAAGAAAAG
*
820315 AGAAAAGAAAAG
1 AAAAAAGAAAAG
*
820327 AAAAAAGAGAAG
1 AAAAAAGAAAAG
820339 AAA
1 AAA
820342 GACGTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:820333 original size:19 final size:21
Alignment explanation
Indices: 820295--820337 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
820285 GATGTTGTTC
820295 GAAAAGGAAAAAAAAGAAAGA
1 GAAAAGGAAAAAAAAGAAAGA
*
820316 GAAAA-GAAAAGAAA-AAAGA
1 GAAAAGGAAAAAAAAGAAAGA
820335 GAA
1 GAA
820338 GAAAGACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
GAAAAGGAAAAAAAAGAAAGA
Found at i:820339 original size:17 final size:16
Alignment explanation
Indices: 820295--820341 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
820285 GATGTTGTTC
*
820295 GAAAAGGAAAA-AAAA
1 GAAAAAGAAAAGAAAA
*
820310 GAAAGAGAAAAGAAAA
1 GAAAAAGAAAAGAAAA
*
820326 GAAAAAAGAGAAGAAA
1 G-AAAAAGAAAAGAAA
820342 GACGTGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 12 0.46
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAAAAGAAAAGAAAA
Found at i:840531 original size:17 final size:18
Alignment explanation
Indices: 840504--840541 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
840494 TTTAAAAATT
* *
840504 TATTGTCAAATGATTAAA
1 TATTGTCAAATAAATAAA
840522 TATT-TCAAATAAATAAA
1 TATTGTCAAATAAATAAA
840539 TAT
1 TAT
840542 ATTTAATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
TATTGTCAAATAAATAAA
Found at i:853198 original size:18 final size:18
Alignment explanation
Indices: 853170--853214 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
853160 TTCAAAATTA
*
853170 AATATTATTTTAAATAAT
1 AATATTTTTTTAAATAAT
* *
853188 TATATTTTTTTCAATAAT
1 AATATTTTTTTAAATAAT
853206 AATATTTTT
1 AATATTTTT
853215 CACCAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATTTTTTTAAATAAT
Found at i:854751 original size:13 final size:14
Alignment explanation
Indices: 854730--854762 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
854720 CGTCAATATG
*
854730 AAAAAAATAA-AAT
1 AAAACAATAATAAT
854743 AAAACAATAATAAT
1 AAAACAATAATAAT
854757 AAAACA
1 AAAACA
854763 CGCCTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAACAATAATAAT
Found at i:864291 original size:76 final size:75
Alignment explanation
Indices: 864165--864305 Score: 257
Period size: 76 Copynumber: 1.9 Consensus size: 75
864155 CGGGTTGCGG
864165 CCCGGTTCGTATACGGATAGAACCGAACATCGGTGGTCAGTGGCTTGGGAAAGAAACTGAAGAAT
1 CCCGGTTCGTATACGGATAGAACCGAACATCGGTGGTCAGTGGCTTGGGAAAGAAA-TGAAGAAT
864230 AAGACGATGGC
65 AAGACGATGGC
864241 CCCGGTTCGTATACGGATAGAACCCGAACA-CGGTGGTCAGTGGCTTGGGAAAGAAATGAAGAAT
1 CCCGGTTCGTATACGGATAGAA-CCGAACATCGGTGGTCAGTGGCTTGGGAAAGAAATGAAGAAT
864305 A
65 A
864306 TGATGGATGA
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
75 9 0.14
76 48 0.75
77 7 0.11
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.18
Consensus pattern (75 bp):
CCCGGTTCGTATACGGATAGAACCGAACATCGGTGGTCAGTGGCTTGGGAAAGAAATGAAGAATA
AGACGATGGC
Found at i:868331 original size:19 final size:19
Alignment explanation
Indices: 868307--868355 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
868297 TTTTTCCAAT
*
868307 TCGCAATGCGAATAAGTAA
1 TCGCAATGCGAATAAGGAA
* **
868326 TCGCAACGCGAATTGGGAA
1 TCGCAATGCGAATAAGGAA
868345 TCGCAATGCGA
1 TCGCAATGCGA
868356 TACTGACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (19 bp):
TCGCAATGCGAATAAGGAA
Found at i:868369 original size:20 final size:20
Alignment explanation
Indices: 868344--868458 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
868334 CGAATTGGGA
*
868344 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
868364 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
868385 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
868405 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
868425 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
868445 TTCGCAACGCGATA
1 ATCGCAACGCGATA
868459 ATACATAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:868671 original size:22 final size:22
Alignment explanation
Indices: 868643--868686 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
868633 CACTCTCTCA
868643 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
868665 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
868687 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:868987 original size:20 final size:20
Alignment explanation
Indices: 868928--868991 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
868918 GCGATTTTAG
*
868928 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
868948 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
868968 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
868988 TTTC
1 TTTC
868992 AGAAACTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:870328 original size:18 final size:18
Alignment explanation
Indices: 870307--870351 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
870297 TCCACTTCGG
*
870307 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
870325 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
870343 GAGCCATCA
1 GAGCCATCA
870352 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:872696 original size:14 final size:14
Alignment explanation
Indices: 872677--872712 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
872667 ATTGTTTAAT
872677 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
872691 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
872705 TGATTTGT
1 TGATTTGT
872713 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:872838 original size:14 final size:16
Alignment explanation
Indices: 872819--872891 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 16
872809 CGAAATGGCT
872819 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
872833 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG-AATGAAA
872852 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATGAAA
872871 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
872885 ATCGCAA
1 ATCGCAA
872892 TGCGATTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.31
15 2 0.04
16 3 0.06
17 3 0.06
18 2 0.04
19 26 0.50
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ATCGCAACGAATGAAA
Done.