Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004499.1 Hibiscus syriacus cultivar Beakdansim tig00009922_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: 94053
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:12527 original size:24 final size:24
Alignment explanation
Indices: 12473--12528 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
12463 TTTAACAAGG
*
12473 TTATTAAAAAATTAAATTAATATT
1 TTATTAAAAAATGAAATTAATATT
* * *
12497 TTTTTAAAATATGAAA-TATTATAT
1 TTATTAAAAAATGAAATTAATAT-T
12521 TTATTAAA
1 TTATTAAA
12529 TTGTTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATTAAAAAATGAAATTAATATT
Found at i:14476 original size:13 final size:12
Alignment explanation
Indices: 14420--14482 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 12
14410 CCTGATATAA
14420 AATAAAATTTAATT
1 AATAAAA-TT-ATT
*
14434 AAAAAAATGTATT
1 AATAAAAT-TATT
14447 -ATAATAATTATT
1 AATAA-AATTATT
*
14459 CATAAAATTATTT
1 AATAAAATTA-TT
14472 AATAAAATTAT
1 AATAAAATTAT
14483 ACCATTACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 13 0.31
13 22 0.52
14 7 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (12 bp):
AATAAAATTATT
Found at i:15531 original size:37 final size:37
Alignment explanation
Indices: 15460--15531 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
15450 AATATCACAC
* * *
15460 TTATATTTTTTAAATTTTAAAAGAATATTTTAAAACA
1 TTATATTTTTTAAATTTTAAAAAAAAATTCTAAAACA
15497 TTAT-TTTTTCTAAA-TTTACAAAAAAAATTCTAAAA
1 TTATATTTTT-TAAATTTTA-AAAAAAAATTCTAAAA
15532 TTCTAAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (37 bp):
TTATATTTTTTAAATTTTAAAAAAAAATTCTAAAACA
Found at i:22077 original size:30 final size:32
Alignment explanation
Indices: 22019--22079 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
22009 CGCTCTAACT
*
22019 ATTTTAAAATATTAAATATTTATATAAACATA
1 ATTTGAAAATATTAAATATTTATATAAACATA
* *
22051 ATTTGAAAATA-T-AATTTTTATTTAAACAT
1 ATTTGAAAATATTAAATATTTATATAAACAT
22080 TTAAGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 1 0.04
32 10 0.38
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTTGAAAATATTAAATATTTATATAAACATA
Found at i:26530 original size:2 final size:2
Alignment explanation
Indices: 26525--26554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26515 CCTTAAATTG
26525 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
26555 TAGTATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39374 original size:99 final size:99
Alignment explanation
Indices: 39203--39392 Score: 317
Period size: 99 Copynumber: 1.9 Consensus size: 99
39193 GATGTAGATG
* * * *
39203 AAACTAAGAAAGAAAGTGACACTGCAAGTGATTCCGAGGCAAAATCGCTGAAGAAGTCATCAAAG
1 AAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAATCATCAAAG
*
39268 AAGGTAGACTCTAGCGGTAACAATGCGGCTGATC
66 AAGGTAGACTCTAGCGGAAACAATGCGGCTGATC
*
39302 AAACTAAGAAAGAGAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAATCATCAAAG
1 AAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAATCATCAAAG
*
39367 AAGGTAGATTCTAGCGGAAACAATGC
66 AAGGTAGACTCTAGCGGAAACAATGC
39393 AGATGAATCC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (99 bp):
AAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAATCATCAAAG
AAGGTAGACTCTAGCGGAAACAATGCGGCTGATC
Found at i:48749 original size:5 final size:5
Alignment explanation
Indices: 48726--48786 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
48716 GGTAAAAACG
* *
48726 AAAAT AACAA- AATAAT AAAAT AAAAT AATAT AAAAT AAAGCAAT AATAT
1 AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT -AA--AAT AAAAT
48775 AAAAT AAAAT AA
1 AAAAT AAAAT AA
48787 TATCATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
5 35 0.76
6 6 0.13
7 2 0.04
8 3 0.07
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:48760 original size:23 final size:24
Alignment explanation
Indices: 48734--48788 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
48724 CGAAAATAAC
*
48734 AAAATAATA-AAATAAAATAATAT
1 AAAATAATAGAAATAAAATAAAAT
* *
48757 AAAATAA-AGCAATAATATAAAAT
1 AAAATAATAGAAATAAAATAAAAT
48780 AAAATAATA
1 AAAATAATA
48789 TCATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAATAGAAATAAAATAAAAT
Found at i:48788 original size:18 final size:18
Alignment explanation
Indices: 48739--48788 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
48729 ATAACAAAAT
48739 AATAAAATAAAATAATATAA
1 AATAAAAT--AATAATATAA
**
48759 AATAAAGCAATAATATAA
1 AATAAAATAATAATATAA
48777 AATAAAATAATA
1 AATAAAATAATA
48789 TCATATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 20 0.77
20 6 0.23
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAATAATATAA
Found at i:48798 original size:18 final size:16
Alignment explanation
Indices: 48743--48803 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 16
48733 CAAAATAATA
48743 AAATAAAATAATATA-
1 AAATAAAATAATATAT
48758 AAATAAAGCAATAATATA-
1 AAAT-AA--AATAATATAT
48776 AAATAAAATAATATCAT
1 AAATAAAATAATAT-AT
*
48793 ATAATATAATA
1 A-AATAAAATA
48804 GTAAAGAACC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 12 0.31
16 3 0.08
17 3 0.08
18 21 0.54
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAAAATAATATAT
Found at i:48803 original size:23 final size:23
Alignment explanation
Indices: 48729--48803 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
48719 AAAAACGAAA
* * *
48729 ATAACAAAATAATAAAATAAAAT
1 ATAATAAAATAATAACATATAAT
*
48752 A-ATATAAAATAA-AGCA-ATAAT
1 ATA-ATAAAATAATAACATATAAT
*
48773 ATAAAATAAAATAATATCATATAAT
1 AT--AATAAAATAATAACATATAAT
48798 ATAATA
1 ATAATA
48804 GTAAAGAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 22 0.54
24 4 0.10
25 7 0.17
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (23 bp):
ATAATAAAATAATAACATATAAT
Found at i:48907 original size:19 final size:19
Alignment explanation
Indices: 48883--48923 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48873 CAAACAAAAC
48883 AATTAAAAAAATATATATA
1 AATTAAAAAAATATATATA
** *
48902 AATTAATCATATATATATA
1 AATTAAAAAAATATATATA
48921 AAT
1 AAT
48924 AAGGTATAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTAAAAAAATATATATA
Found at i:49052 original size:2 final size:2
Alignment explanation
Indices: 49045--49098 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
49035 TGCTAATAAA
*
49045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49085 AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT
49099 TTGGAAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49504 original size:20 final size:20
Alignment explanation
Indices: 49467--49505 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49457 CCGCCTCGCC
*
49467 GCCGTCGTGGATCCGCGGCG
1 GCCGTCGTGCATCCGCGGCG
* *
49487 GCCGTCGTTCATCGGCGGC
1 GCCGTCGTGCATCCGCGGC
49506 CAAACACGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.36, G:0.41, T:0.18
Consensus pattern (20 bp):
GCCGTCGTGCATCCGCGGCG
Found at i:50291 original size:18 final size:18
Alignment explanation
Indices: 50258--50293 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
50248 TAATATGACC
*
50258 TATAATGTAAATACATTA
1 TATAATGTAAAGACATTA
*
50276 TATAATGTAACGACATTA
1 TATAATGTAAAGACATTA
50294 AAGGACATAT
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:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (18 bp):
TATAATGTAAAGACATTA
Found at i:50311 original size:32 final size:32
Alignment explanation
Indices: 50272--50332 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
50262 ATGTAAATAC
* *
50272 ATTATATAATGTAACGACATTAAAGGACATAT
1 ATTATATAATGCAACAACATTAAAGGACATAT
50304 ATTATATAATGCAACAACATTAAAGGACA
1 ATTATATAATGCAACAACATTAAAGGACA
50333 AAATTTGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (32 bp):
ATTATATAATGCAACAACATTAAAGGACATAT
Found at i:52267 original size:15 final size:14
Alignment explanation
Indices: 52248--52282 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
52238 ACGGGCATTA
52248 TATAAATGCTATTC
1 TATAAATGCTATTC
*
52262 TCATAAATGTTATTC
1 T-ATAAATGCTATTC
52277 TATAAA
1 TATAAA
52283 ATTTTAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (14 bp):
TATAAATGCTATTC
Found at i:57336 original size:34 final size:33
Alignment explanation
Indices: 57264--57362 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 33
57254 TTTTTCCTAC
* *
57264 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
57296 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
57330 TTTATTAGTGTTATTATATATATATATATATTT
1 TTTATTAATTTTATTATATATGTATATATATTT
57363 CCTATTTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
32 20 0.36
33 7 0.13
34 28 0.51
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:60699 original size:21 final size:21
Alignment explanation
Indices: 60674--60743 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
60664 AGGGCAAAAA
* *
60674 AAAAAAAAAGAAGCTAAAAAGG
1 AAAAAACAAGAA-CAAAAAAGG
60696 AAAAAACAAGAACAAAAAA-G
1 AAAAAACAAGAACAAAAAAGG
* * * *
60716 AAAGAACAAAAATAAAAAGGG
1 AAAAAACAAGAACAAAAAAGG
60737 AACAAAA
1 AA-AAAA
60744 AACACATACA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.41
21 9 0.23
22 14 0.36
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (21 bp):
AAAAAACAAGAACAAAAAAGG
Found at i:61364 original size:29 final size:29
Alignment explanation
Indices: 61322--61384 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
61312 CCAGTAGAGA
61322 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
61351 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
61380 AGCAT
1 AGCAT
61385 CAAATGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AGCATGCAAGCTACCCCATCAATCCTTTG
Found at i:61838 original size:18 final size:18
Alignment explanation
Indices: 61815--61850 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61805 TCAACATCAA
* *
61815 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
61833 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
61851 GGATTCAACA
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:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:62356 original size:36 final size:36
Alignment explanation
Indices: 62308--62587 Score: 317
Period size: 36 Copynumber: 8.0 Consensus size: 36
62298 ACTAGAAGAG
*
62308 TTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
62344 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
62380 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
62416 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
62452 ------ATAT-TTGA-ATAGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * ** * *
62480 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
62517 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
62552 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
62588 ACCTTTGAAT
Statistics
Matches: 204, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
28 17 0.08
29 4 0.02
30 2 0.01
34 1 0.00
35 35 0.17
36 114 0.56
37 31 0.15
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:62479 original size:100 final size:102
Alignment explanation
Indices: 62364--62551 Score: 299
Period size: 101 Copynumber: 1.9 Consensus size: 102
62354 CTTGAGACAG
*
62364 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
62428 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATAGT
66 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATAGT
* ** * *
62465 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
*
62529 TGAGACAGTTTCTCTTGAAACAA
66 TGAGACAGTTTCCCTTGAAACAA
62552 TTTCGTCTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 34 0.43
101 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATATTTGAATAGT
Found at i:62531 original size:37 final size:35
Alignment explanation
Indices: 62465--62586 Score: 156
Period size: 35 Copynumber: 3.4 Consensus size: 35
62455 TTTGAATAGT
*
62465 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAAC-AATTTCGTCTCTCTTGAGACAG
* * *
62500 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AA-TTTCGTCTCTCTTGAGACAG
*
62537 TTTCTCTTGAAACAATTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAATTTCGTCTCTCTTGAGACAG
*
62572 TTTCCCTTGAAACAA
1 TTTCTCTTGAAACAA
62587 AACCTTTGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
35 37 0.49
36 10 0.13
37 29 0.38
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (35 bp):
TTTCTCTTGAAACAATTTCGTCTCTCTTGAGACAG
Found at i:62554 original size:136 final size:136
Alignment explanation
Indices: 62334--62650 Score: 406
Period size: 136 Copynumber: 2.3 Consensus size: 136
62324 ACAGTTTCCC
* *
62334 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
* * *
62399 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAG
66 GTTTCCCTTGAAATAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTTGAATAG
62464 TTTTCT
131 TTTTCT
* * * * *
62470 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCTTGAGAC
* * *
62535 AGTTTCTCTTGAAA-CAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATT
65 AGTTTCCCTTGAAATAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTTGAA--
* *
62599 TA-TTTCCC
128 TAGTTTTCT
* * * *
62607 CT-AAAAATAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTGAAACA-AATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACA
62651 CAAAATCTTC
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
136 87 0.56
137 67 0.43
138 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (136 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
GTTTCCCTTGAAATAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTTGAATAG
TTTTCT
Found at i:62695 original size:67 final size:67
Alignment explanation
Indices: 62562--62717 Score: 192
Period size: 67 Copynumber: 2.4 Consensus size: 67
62552 TTTCGTCTAT
* * *
62562 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAAATAATTTTGTCT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTTCAAATTATTTCCCCTAAAAATAATTTTGTCT
62625 CC
66 CC
* * * *
62627 CTTGAGACAGTTACTCTTGAAACACAAAATC-TTCAAATTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTTCAAATTATTTCCCCTAAAA-ATAATTTTGTC
62691 TCC
65 TCC
* * *
62694 CTTGAAACTGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
62718 ACAGATATCT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 17 0.22
66 20 0.26
67 40 0.52
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (67 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTTCAAATTATTTCCCCTAAAAATAATTTTGTCT
CC
Found at i:62900 original size:29 final size:29
Alignment explanation
Indices: 62867--62933 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
62857 GAATGTGCAC
* *
62867 ATCAGATTTGAACATTTGAAGAATTCAAG-
1 ATCAGATTTCAAAATTTGAAG-ATTCAAGA
**
62896 ATCAGAGATCAAAATTTGAAGATTCAAGA
1 ATCAGATTTCAAAATTTGAAGATTCAAGA
62925 ATCAAGATT
1 ATC-AGATT
62934 CCAGACAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.23
29 20 0.67
30 3 0.10
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.28
Consensus pattern (29 bp):
ATCAGATTTCAAAATTTGAAGATTCAAGA
Found at i:63691 original size:105 final size:104
Alignment explanation
Indices: 63318--64390 Score: 1540
Period size: 105 Copynumber: 10.3 Consensus size: 104
63308 GCCATCCGCG
* * * * * *
63318 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
63383 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
*
63427 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
63492 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCTA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
*
63534 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63599 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
* *
63639 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63704 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
63744 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63809 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
63844 ATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63909 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
63949 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
64014 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
64049 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
64114 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
64154 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ***
64219 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTTA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
64254 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
64319 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
64360 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
64391 TGGAACAATG
Statistics
Matches: 885, Mismatches: 60, Indels: 41
0.90 0.06 0.04
Matches are distributed among these distances:
100 258 0.29
101 12 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 374 0.42
106 91 0.10
107 97 0.11
109 22 0.02
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:63927 original size:205 final size:205
Alignment explanation
Indices: 63318--64390 Score: 1610
Period size: 205 Copynumber: 5.2 Consensus size: 205
63308 GCCATCCGCG
* * * * * *
63318 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
63383 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * * *
63448 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACA
122 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* * *
63513 ATTTTCCCAATTTCAGAGCTA
186 ACTTT-CCAATCTCAGAGCCA
*
63534 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
63599 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
63664 TGGACTCCAGAAAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
63729 CCAATCTCAGAGCCA
191 CCAATCTCAGAGCCA
63744 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
63809 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
63874 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
63939 CTCAGAGCCA
196 CTCAGAGCCA
63949 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
64014 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
64079 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
64144 CCCAGAGCCA
196 CTCAGAGCCA
*
64154 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
***
64219 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTTAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * * *
64284 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
64348 GT-TCCAGAGCCA
194 ATCT-CAGAGCCA
* *
64360 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
64391 TGGAACAATG
Statistics
Matches: 808, Mismatches: 45, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
205 484 0.60
206 46 0.06
207 1 0.00
208 2 0.00
209 2 0.00
210 94 0.12
211 9 0.01
212 97 0.12
213 49 0.06
214 3 0.00
216 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:63932 original size:310 final size:311
Alignment explanation
Indices: 63318--64390 Score: 1551
Period size: 310 Copynumber: 3.4 Consensus size: 311
63308 GCCATCCGCG
* * * * *
63318 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACAACGAA
* * *
63383 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAACAAACAATTTC-CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
63448 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* * *
63513 ATTTTCCCAATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
190 ACTTT--CAA-TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAA
*
63578 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
252 GTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCAATCTCAGAGCCA
* * *
63639 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
63704 ACCGCTGCTTGTCAAC-AACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 ACCGCTGCTTGTCAACAAACAA-TTTCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
63768 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
*
63831 TC-ATTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
194 TCAATTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
63895 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC-TTCCAATCTCAGAGCCA
*
63949 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
*
64014 ACCGCTGCTTGTCAAC-AA-AATTT-C-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * *
64075 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-T
* *
64140 CAATCCCAGAGCCAATTTCAACTTCACAACGAAA-GATATTGGACTCCAGACAACGCAAGTTCAA
195 CAAT-TCAGAGCCAATTTCAACTTCACAGC-AAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* ***
64204 CTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTTC-AT-TCAGATTTA
258 CTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
* *
64254 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* * ** * *
64319 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACCGCTGCTTGTCAACAAACAATTT-CCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
64384 TTGGACT
129 TTGGACT
64391 TGGAACAATG
Statistics
Matches: 697, Mismatches: 40, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
305 171 0.25
306 8 0.01
307 11 0.02
308 4 0.01
309 7 0.01
310 276 0.40
311 42 0.06
312 1 0.00
314 3 0.00
315 2 0.00
316 3 0.00
317 95 0.14
318 49 0.07
319 3 0.00
321 22 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (311 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
AATTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
Found at i:65586 original size:16 final size:18
Alignment explanation
Indices: 65565--65597 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65555 TTTACTCATT
65565 TTTAT-CTAT-TTTTATA
1 TTTATCCTATATTTTATA
65581 TTTATCCTATATTTTAT
1 TTTATCCTATATTTTAT
65598 GTTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATCCTATATTTTATA
Found at i:68927 original size:23 final size:21
Alignment explanation
Indices: 68872--68913 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
68862 AAATAAAAAT
68872 TACAAGAATATATGACATGAG
1 TACAAGAATATATGACATGAG
68893 TACAAGAATATATGACATGAG
1 TACAAGAATATATGACATGAG
68914 ACTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (21 bp):
TACAAGAATATATGACATGAG
Found at i:75371 original size:15 final size:15
Alignment explanation
Indices: 75351--75380 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
75341 AACAGGCATT
75351 CATGTTTAACAAACA
1 CATGTTTAACAAACA
75366 CATGTTTAACAAACA
1 CATGTTTAACAAACA
75381 TGCGACTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
CATGTTTAACAAACA
Found at i:76220 original size:20 final size:20
Alignment explanation
Indices: 76197--76235 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
76187 ATATTTTATA
*
76197 AATTAATTAAAATAAATATG
1 AATTAACTAAAATAAATATG
* *
76217 AATTACCTATAATAAATAT
1 AATTAACTAAAATAAATAT
76236 ATCAGGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
AATTAACTAAAATAAATATG
Found at i:77921 original size:85 final size:85
Alignment explanation
Indices: 77778--78075 Score: 447
Period size: 85 Copynumber: 3.5 Consensus size: 85
77768 ACATGAATTT
* *
77778 TTTATGACGCGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGAC
77843 ACACATTTGTTCGTCATAAA
66 ACACATTTGTTCGTCATAAA
**
77863 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGAC
*
77928 ACACATTTGTGCGTCATAAA
66 ACACATTTGTTCGTCATAAA
* *
77948 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAA-TATGCTTGA
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAG-ATGA
*
78012 CATACATTTGTAT-GTCATAAA
65 CACACATTTGT-TCGTCATAAA
* * * **
78033 TATATGGCACGCATGTATGACTTACATTGTGTTTCATTGAAGC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGC
78076 ACACATCATT
Statistics
Matches: 195, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
84 3 0.02
85 192 0.98
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGAC
ACACATTTGTTCGTCATAAA
Found at i:78139 original size:2 final size:2
Alignment explanation
Indices: 78132--78174 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
78122 TCGTAAATTT
78132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78174 T
1 T
78175 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82822 original size:21 final size:22
Alignment explanation
Indices: 82798--82838 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
82788 GCGATTTTAG
82798 GGGAAGAGGAGGA-GGAGATGT
1 GGGAAGAGGAGGAGGGAGATGT
* *
82819 GGGACGAGGCGGAGGGAGAT
1 GGGAAGAGGAGGAGGGAGAT
82839 ACGGTGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.59, T:0.07
Consensus pattern (22 bp):
GGGAAGAGGAGGAGGGAGATGT
Found at i:84633 original size:3 final size:3
Alignment explanation
Indices: 84612--84674 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
84602 CGGGTCTTTT
* *
84612 TTA TT- TTA TT- TTAA TTA TTA TTA TTA TAA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
84656 TTA TTAA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA
84675 ATACATATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:86980 original size:24 final size:24
Alignment explanation
Indices: 86952--87001 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
86942 AATTAATTTC
86952 AAAATCACTAAT-TTTTTCAAAATA
1 AAAATCA-TAATCTTTTTCAAAATA
*
86976 AAAATCATAATCGTTTTTTAAAATA
1 AAAATCATAATC-TTTTTCAAAATA
87001 A
1 A
87002 TACTTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 7 0.30
25 12 0.52
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATCATAATCTTTTTCAAAATA
Done.