Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000230.1 Hibiscus syriacus cultivar Beakdansim tig00000400_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: 88005
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3869 original size:64 final size:65
Alignment explanation
Indices: 3736--3912 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 65
3726 GTTGGACCTT
* * * *
3736 AGTGCATCGGTGCACTAAGA-GTGCATCGACGCATC-AA-GCATTCGATG-TTTCAAAATAGCCA
1 AGTGCATCGATGCA-TAGGATGGGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCA
3797 G
65 G
*
3798 AGTGCATCGATGCAT-GGCTGGGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGATGCATAGGATGGGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGC-C
*
3860 TG
64 AG
* * * *
3862 AGTGCATCGATGCATAGTATGTGCATCGATGCATGAAATGTATTCGATGTT
1 AGTGCATCGATGCATAGGATGGGCATCGATGCATCAAATGCATTCGATGTT
3913 CAATTTATTC
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
60 1 0.01
61 14 0.14
62 15 0.15
63 11 0.11
64 23 0.24
65 33 0.34
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (65 bp):
AGTGCATCGATGCATAGGATGGGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAG
Found at i:4970 original size:21 final size:19
Alignment explanation
Indices: 4929--4976 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
4919 GAGTTCATAA
*
4929 TTTTTTTTTGTTTTTATTC
1 TTTTTTTTTGTTTTTAGTC
*
4948 TTTTTTCTTTGTCTTTTGGTC
1 TTTTTT-TTTGT-TTTTAGTC
4969 TTTATTTT
1 TTT-TTTT
4977 ATAATACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 10 0.42
22 3 0.12
ACGTcount: A:0.04, C:0.08, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTAGTC
Found at i:10349 original size:45 final size:45
Alignment explanation
Indices: 9944--10328 Score: 558
Period size: 45 Copynumber: 8.6 Consensus size: 45
9934 CATTATGCCT
* * * * *
9944 TTTCATTTATAGCATCTTTTCAT-ACGATAATGCATCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* * *
9988 TTTCAATTATGGCATCCTTTCGTGCCTATAATGCACCCATATGTA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
**
10033 TTT-ACATTATGGCATTATTTCATGCCGATAATGCACCCATATGCA
1 TTTCA-ATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* * **
10078 TTTCAATTATGGCATCATTTCAAGATGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* ** *
10123 TTTCAATTATGACATCCTTTCATGTTGATAATGCACCCATAAGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
10168 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
*
10213 TTTCAATTATGGCATCCTTTCATGTCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
*
10258 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
*
10303 TTTCAATTATGACATCCTTTCATGCC
1 TTTCAATTATGGCATCCTTTCATGCC
10329 TGTTATGCAA
Statistics
Matches: 307, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
44 20 0.07
45 286 0.93
46 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (45 bp):
TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
Found at i:10557 original size:68 final size:68
Alignment explanation
Indices: 10388--10642 Score: 377
Period size: 68 Copynumber: 3.8 Consensus size: 68
10378 TATTTAACCG
* * * * * * *
10388 TTCATCTAAATTGCATAATTGACACGTTTCTATGAAATGCATAGTAAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
10453 CC-
66 CCT
* * *
10455 TTCATCTAACTGGCATGATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACATAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
10520 CCT
66 CCT
* *
10523 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTGAAAGTCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
10588 CCT
66 CCT
* *
10591 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCATAGTTAGGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
10643 TTAATCTTGT
Statistics
Matches: 170, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 57 0.34
68 113 0.66
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:10933 original size:58 final size:58
Alignment explanation
Indices: 10863--11105 Score: 423
Period size: 58 Copynumber: 4.2 Consensus size: 58
10853 TTTCCTATAT
* * *
10863 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTGGCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
10921 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
* *
10979 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTACCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
* *
11037 AGAAATTCATTCACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
11095 GGAAATTCATA
1 GGAAATTCATA
11106 TTGTTGAGTT
Statistics
Matches: 174, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 174 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATGCCCAATAC
Found at i:20283 original size:58 final size:58
Alignment explanation
Indices: 20205--20415 Score: 332
Period size: 58 Copynumber: 3.6 Consensus size: 58
20195 GTTTTAAGCA
*
20205 CATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCTAATACGGAAATT
1 CATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCAAATACGGAAATT
* * * **
20263 CATACACTTAATATGGATTTCTTAACTTTTTGCACACAAAGTGCCCAATACAAAAATT
1 CATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCAAATACGGAAATT
* *
20321 CATACACTTAGTATGGATTTCTTAACTTTTTGCACACAAAGTACCAAATACGGAAATT
1 CATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCAAATACGGAAATT
* *
20379 CATACGCTTAGTATGAATTTCTTAACTTTTTGTACAC
1 CATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
20416 TTGGTTCCAT
Statistics
Matches: 140, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 140 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (58 bp):
CATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCAAATACGGAAATT
Found at i:20844 original size:20 final size:21
Alignment explanation
Indices: 20819--20871 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
20809 CTGTGCTCAA
20819 TGGTATCGATACCAT-CCTCC
1 TGGTATCGATACCATCCCTCC
**
20839 TGGTATCGATA-C-TCCCTTT
1 TGGTATCGATACCATCCCTCC
20858 TGGTATCGATACCA
1 TGGTATCGATACCA
20872 CTTGAATCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (21 bp):
TGGTATCGATACCATCCCTCC
Found at i:24460 original size:45 final size:45
Alignment explanation
Indices: 24410--24731 Score: 400
Period size: 45 Copynumber: 7.2 Consensus size: 45
24400 TATAGCCTCT
*
24410 TTTCATACCGATAATGCACCCATATGCATTTCAATTATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGAATCC
* * * * *
24455 TTTCATGCCTATAATGCACCCATATGAATTTGAATTATGGCATCA
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGAATCC
* * *
24500 TTTCATGCCGATAGTGCACCCATATGCATTTCAATTAT-AACATCA
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGA-ATCC
* *
24545 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCT
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGAATCC
** **
24590 TTTCATGCTAATAATGCACCCATGCGCATTTCAATTAT-GACATCC
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGA-ATCC
* * *
24635 TTTTATGCCGATAATGCACCCATATGCATTTAAATTAT-GACATCT
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGA-ATCC
* *
24680 TTTCATGCCAATAATGCACCCATATGCATTTCAATTACGGCAA-CC
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG-AATCC
24725 TTTCATG
1 TTTCATG
24732 TCTTTTATAC
Statistics
Matches: 238, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.00
45 234 0.98
46 2 0.01
47 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (45 bp):
TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGAATCC
Found at i:24519 original size:90 final size:90
Alignment explanation
Indices: 24407--24731 Score: 463
Period size: 90 Copynumber: 3.6 Consensus size: 90
24397 ATTTATAGCC
* * *
24407 TCTTTTCATACCGATAATGCACCCATATGCATTTCAATTATGGA-ATCCTTTCATGCCTATAATG
1 TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTAT-GACATCCTTTCATGCCGATAATG
* *
24471 CACCCATATGAATTTGAATTATGGCA
65 CACCCATATGCATTTAAATTATGGCA
* * * * *
24497 TCATTTCATGCCGATAGTGCACCCATATGCATTTCAATTATAACATCATTTCATGCCGATAATGC
1 TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATGCCGATAATGC
*
24562 ACCCATATGCATTTCAATTATGGCA
66 ACCCATATGCATTTAAATTATGGCA
* ** *
24587 TCTTTTCATGCTAATAATGCACCCATGCGCATTTCAATTATGACATCCTTTTATGCCGATAATGC
1 TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATGCCGATAATGC
*
24652 ACCCATATGCATTTAAATTATGACA
66 ACCCATATGCATTTAAATTATGGCA
* * *
24677 TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTACGGCAACCTTTCATG
1 TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATG
24732 TCTTTTATAC
Statistics
Matches: 208, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
89 1 0.00
90 207 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (90 bp):
TCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATGCCGATAATGC
ACCCATATGCATTTAAATTATGGCA
Found at i:24643 original size:135 final size:135
Alignment explanation
Indices: 24410--24731 Score: 475
Period size: 135 Copynumber: 2.4 Consensus size: 135
24400 TATAGCCTCT
* *
24410 TTTCATACCGATAATGCACCCATATGCATTTCAATTATGGAATCCTTTCATGCCTATAATGCACC
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCTATAATGCACC
* * * * *
24475 CATATGAATTTGAATTATGGCATCATTTCATGCCGATAGTGCACCCATATGCATTTCAATTATAA
66 CATACGAATTTCAATTATGACATCATTTCATGCCGATAATGCACCCATATGCATTTAAATTATAA
24540 CATCA
131 CATCA
*
24545 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCTTTTCATG-CTAATAATGCAC
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCT-ATAATGCAC
* * * * *
24609 CCATGCGCATTTCAATTATGACATCCTTTTATGCCGATAATGCACCCATATGCATTTAAATTATG
65 CCATACGAATTTCAATTATGACATCATTTCATGCCGATAATGCACCCATATGCATTTAAATTATA
*
24674 ACATCT
130 ACATCA
* * *
24680 TTTCATGCCAATAATGCACCCATATGCATTTCAATTACGGCAACCTTTCATG
1 TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
24732 TCTTTTATAC
Statistics
Matches: 168, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
134 2 0.01
135 166 0.99
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (135 bp):
TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCTATAATGCACC
CATACGAATTTCAATTATGACATCATTTCATGCCGATAATGCACCCATATGCATTTAAATTATAA
CATCA
Found at i:24887 original size:68 final size:68
Alignment explanation
Indices: 24793--25189 Score: 508
Period size: 68 Copynumber: 5.8 Consensus size: 68
24783 TATTTAATCG
* * * * * * *
24793 TTCATCTAAATGACATAATTGACACCTTTCTGTTATATGCACAGTCAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
24858 TCT
66 CCT
** * * *
24861 TTCATCTAACTGGCATGATTCCCACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACCTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
24926 CCT
66 CCT
* * *
24929 TTCATCGAACTGGCATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCTCAAAGACAAAGGC
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCT------CAAAGGC
24994 ACTTAGCCT
60 ACTTAGCCT
* *
25003 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTCGAG-CTCAAAGACACTTA
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAG-GCCTCAAAGGCACTTA
25067 GCCT
65 GCCT
* * *
25071 TTCATCTAACTGGAATGATTGACACATTTCTATCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
25136 CCT
66 CCT
* * *
25139 TCCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCC
25190 GTTAATCTTG
Statistics
Matches: 288, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
67 1 0.00
68 225 0.78
74 61 0.21
75 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:25039 original size:142 final size:136
Alignment explanation
Indices: 24829--25189 Score: 499
Period size: 142 Copynumber: 2.6 Consensus size: 136
24819 TTTCTGTTAT
* * **
24829 ATGCACAGTCAGGCCTCAAAGGCACTTAGTCTTTCATCTAACTGGCATGATTCCCACCTTTCTGT
1 ATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGT
* * * *
24894 CAAATGCATAGTTAGGCCTCAAAGGCACCTAGCCTTTCATCGAACTGGCATAATTGACACCTTTC
66 CAAATGCACAGTTAGGCCTCAAAGACACCTAGCCTTTCATCGAACTGGAATAATTGACACATTTC
24959 TACCAA
131 TACCAA
24965 ATGCACAGTTAGGCCTCAAAGACAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCT
1 ATGCACAGTTAGGCCT------CAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCT
* * * * *
25030 TTCTATCAAATGCACAGTTCGAG-CTCAAAGACACTTAGCCTTTCATCTAACTGGAATGATTGAC
60 TTCTGTCAAATGCACAGTTAG-GCCTCAAAGACACCTAGCCTTTCATCGAACTGGAATAATTGAC
*
25094 ACATTTCTATCAA
124 ACATTTCTACCAA
* * *
25107 ATGCATAGTTAGGCCTCAAAGGCACTTAGCCTTCCATCTAACTGGCATGATTGACACATTTCTGT
1 ATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGT
25172 CAAATGCACAGTTAGGCC
66 CAAATGCACAGTTAGGCC
25190 GTTAATCTTG
Statistics
Matches: 198, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
135 1 0.01
136 76 0.38
142 120 0.61
143 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (136 bp):
ATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGT
CAAATGCACAGTTAGGCCTCAAAGACACCTAGCCTTTCATCGAACTGGAATAATTGACACATTTC
TACCAA
Found at i:25162 original size:210 final size:210
Alignment explanation
Indices: 24793--25189 Score: 582
Period size: 210 Copynumber: 1.9 Consensus size: 210
24783 TATTTAATCG
* * * *
24793 TTCATCTAAATGACATAATTGACACCTTTCTGTTATATGCACAGTCAGGCCTCAAAGGCACTTAG
1 TTCATCTAAATGACATAATTGACACCTTTCTATCAAATGCACAGTCAGGCCTCAAAGACACTTAG
* * * * *
24858 TCTTTCATCTAACTGGCATGATTCCCACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACC
66 CCTTTCATCTAACTGGAATGATTCACACATTTCTATCAAATGCATAGTTAGGCCTCAAAGGCACC
* *
24923 TAGCCTTTCATCGAACTGGCATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCTCAAAGAC
131 TAGCCTTCCATCGAACTGGCATAATTGACACATTTCTACCAAATGCACAGTTAGGCCTCAAAGAC
24988 AAAGGCACTTAGCCT
196 AAAGGCACTTAGCCT
* * *
25003 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGTTC-GAG-CTCAAAGACACTT
1 TTCATCTAAATGACATAATTGACACCTTTCTATCAAATGCACAG-TCAG-GCCTCAAAGACACTT
*
25066 AGCCTTTCATCTAACTGGAATGATTGACACATTTCTATCAAATGCATAGTTAGGCCTCAAAGGCA
64 AGCCTTTCATCTAACTGGAATGATTCACACATTTCTATCAAATGCATAGTTAGGCCTCAAAGGCA
* * * **
25131 CTTAGCCTTCCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCC
129 CCTAGCCTTCCATCGAACTGGCATAATTGACACATTTCTACCAAATGCACAGTTAGGCC
25190 GTTAATCTTG
Statistics
Matches: 165, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
210 162 0.98
211 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (210 bp):
TTCATCTAAATGACATAATTGACACCTTTCTATCAAATGCACAGTCAGGCCTCAAAGACACTTAG
CCTTTCATCTAACTGGAATGATTCACACATTTCTATCAAATGCATAGTTAGGCCTCAAAGGCACC
TAGCCTTCCATCGAACTGGCATAATTGACACATTTCTACCAAATGCACAGTTAGGCCTCAAAGAC
AAAGGCACTTAGCCT
Found at i:25483 original size:58 final size:58
Alignment explanation
Indices: 25413--25779 Score: 628
Period size: 58 Copynumber: 6.3 Consensus size: 58
25403 TTCCGTACAA
*
25413 AAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
25471 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAA-TGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
* * * *
25528 AAATTAATACACTAAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCACAATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
*
25586 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACTCAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
*
25644 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
* * * *
25702 AAATTCATACACTTAGTATGAATTTCTAAACTTTTTGCGCACAAAATGCCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
25760 AAATTCATACACTTAGTATG
1 AAATTCATACACTTAGTATG
25780 TGTAACCCCC
Statistics
Matches: 291, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
57 55 0.19
58 236 0.81
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGG
Found at i:27302 original size:11 final size:10
Alignment explanation
Indices: 27273--27311 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
27263 CGGTTCGAAC
*
27273 CGGTCGAAAT
1 CGGTCAAAAT
27283 CGGTCAAAAT
1 CGGTCAAAAT
27293 CGGTTCAAAAT
1 CGG-TCAAAAT
27304 CGGTCAAA
1 CGGTCAAA
27312 CTGGTTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (10 bp):
CGGTCAAAAT
Found at i:35720 original size:19 final size:21
Alignment explanation
Indices: 35676--35727 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
35666 CCCCCACCAT
*
35676 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
35698 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
35717 GGTACCGATAC
1 GGTATCGATAC
35728 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:39771 original size:21 final size:21
Alignment explanation
Indices: 39736--39778 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
39726 AATATACTTA
*
39736 TATTATATAATATATTT-TTT
1 TATTACATAATATATTTGTTT
39756 TATTACATATATATATTTGTTT
1 TATTACATA-ATATATTTGTTT
39778 T
1 T
39779 GCAGTCTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 8 0.40
22 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTACATAATATATTTGTTT
Found at i:41541 original size:4 final size:4
Alignment explanation
Indices: 41516--41593 Score: 61
Period size: 4 Copynumber: 19.0 Consensus size: 4
41506 TTTTATCATC
* * * *
41516 ATTT -TTT ATTT TTTT AATTT ATTT ATTT ATTC CTTT CATTT GACTT ATTT
1 ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT -ATTT -ATTT ATTT
*
41566 A-GT ATTTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT
41594 CTTCTAACAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
3 5 0.09
4 42 0.72
5 11 0.19
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:44810 original size:7 final size:6
Alignment explanation
Indices: 44774--44816 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
44764 TATATTTTGC
* *
44774 ATTTTT ATATTTC ATGTTT ATTTTT ATTTTT ATTTTTT ATTTT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT A-TTTTT ATTTT
44817 CCATGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:44810 original size:13 final size:13
Alignment explanation
Indices: 44774--44816 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
44764 TATATTTTGC
* *
44774 ATTTTTATATTTC
1 ATTTTTATTTTTT
*
44787 ATGTTTA-TTTTT
1 ATTTTTATTTTTT
44799 ATTTTTATTTTTT
1 ATTTTTATTTTTT
44812 ATTTT
1 ATTTT
44817 CCATGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:51996 original size:64 final size:64
Alignment explanation
Indices: 51921--52046 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
51911 AATACTTCGC
* * **
51921 TTAGGATGAAAACCCGAGAGGGC-ATCCTATGTTGAAAAAAAAAGAAAAAAAAAGAGAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCT-CTAAATTGAAAAAAAAAGAAAAAAAAAGAGAAAAACGT
* * * *
51985 TTAGGGTGAAAACCCGAAAGGGCGCTCTAAATTGAAAAAAAGAGAGAAAAAAATAGAAAAAC
1 TTAGGATGAAAACCCGAAAGGGCGCTCTAAATTGAAAAAAAAAGAAAAAAAAAGAGAAAAAC
52047 AAACGAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 52 0.98
65 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.13
Consensus pattern (64 bp):
TTAGGATGAAAACCCGAAAGGGCGCTCTAAATTGAAAAAAAAAGAAAAAAAAAGAGAAAAACGT
Found at i:53172 original size:94 final size:94
Alignment explanation
Indices: 53011--53479 Score: 902
Period size: 94 Copynumber: 5.0 Consensus size: 94
53001 AGCTCCAGAA
53011 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53076 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
* *
53105 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53170 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
*
53199 CCAATTTAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53264 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
53293 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53358 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
*
53387 CCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53452 GGGACCGCTGGTTGTCAATAAACAATTT
66 GGGACCGCTGGTTGTCAATAAACAATTT
53480 TCCAGCTCCA
Statistics
Matches: 368, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 368 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:53220 original size:51 final size:51
Alignment explanation
Indices: 53153--53408 Score: 202
Period size: 51 Copynumber: 5.3 Consensus size: 51
53143 ACAATGCAAG
*
53153 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* *** ** * * * *
53204 TTAAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*
53247 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*** ** * * * *
53298 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*
53341 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
53392 TTCAACTTCACAACGAA
1 TTCAACTTCACAACGAA
53409 TGATATTGGA
Statistics
Matches: 146, Mismatches: 43, Indels: 32
0.66 0.19 0.14
Matches are distributed among these distances:
43 39 0.27
44 6 0.04
45 6 0.04
46 14 0.10
48 14 0.10
49 6 0.04
50 6 0.04
51 55 0.38
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (51 bp):
TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
Found at i:53328 original size:188 final size:188
Alignment explanation
Indices: 52806--53479 Score: 1141
Period size: 188 Copynumber: 3.5 Consensus size: 188
52796 TTACCTAGAG
*
52806 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
52871 GGGACCGCTGGTTGTCAATAAACAATTTCAAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 GGGACCGCTGGTTGTCAATAAACAATTTC-----CCAATTTCAACTTCACAACGAAGGATATTGG
*
52936 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
126 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA--TT--
53001 AGCTCC
187 ---T-C
53007 AGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
53072 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAGCGAAGGATATTGGA
62 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGA
*
53137 CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
127 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
53199 CCAATTTAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53264 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
53329 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
131 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
53387 CCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53452 GGGACCGCTGGTTGTCAATAAACAATTT
66 GGGACCGCTGGTTGTCAATAAACAATTT
53480 TCCAGCTCCA
Statistics
Matches: 460, Mismatches: 9, Indels: 17
0.95 0.02 0.03
Matches are distributed among these distances:
188 276 0.60
192 1 0.00
193 1 0.00
198 2 0.00
200 87 0.19
205 93 0.20
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (188 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:53421 original size:282 final size:287
Alignment explanation
Indices: 52806--53479 Score: 1151
Period size: 282 Copynumber: 2.3 Consensus size: 287
52796 TTACCTAGAG
*
52806 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
52871 GGGACCGCTGGTTGTCAATAAACAATTTCAAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 GGGACCGCTGGTTGTCAATAAACAATTTC---A-CCAATTTAAACTTCACAACGAAGGATATTGG
*
52936 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
127 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTT--
53001 AGCTCCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
189 --CTCC---ACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
53066 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
249 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* *
53105 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53170 GGGACCGCTGGTTGTCAATAAACAATTTC-CCAATTTAAACTTCACAACGAAGGATATTGGACTC
66 GGGACCGCTGGTTGTCAATAAACAATTTCACCAATTTAAACTTCACAACGAAGGATATTGGACTC
53234 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TT-T-C-CC
131 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCCACC
53295 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
196 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
53360 GACCGCTGGTTGTCAATAAACAATTTC
261 GACCGCTGGTTGTCAATAAACAATTTC
*
53387 CCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53452 GGGACCGCTGGTTGTCAATAAACAATTT
66 GGGACCGCTGGTTGTCAATAAACAATTT
53480 TCCAGCTCCA
Statistics
Matches: 367, Mismatches: 8, Indels: 17
0.94 0.02 0.04
Matches are distributed among these distances:
282 184 0.50
286 1 0.00
287 1 0.00
292 2 0.01
294 88 0.24
299 91 0.25
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (287 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCACCAATTTAAACTTCACAACGAAGGATATTGGACTC
CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCCACC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAATTTC
Found at i:53960 original size:18 final size:18
Alignment explanation
Indices: 53918--53953 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53908 TGTCTTTTTG
*
53918 ATATTATATAATATACTT
1 ATATTATATAATATATTT
53936 ATATTATATAATATATTT
1 ATATTATATAATATATTT
53954 TTTTTATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATATAATATATTT
Found at i:62718 original size:18 final size:18
Alignment explanation
Indices: 62695--62743 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
62685 TTAATATGTG
62695 TCTGATTACTGTAAAACA
1 TCTGATTACTGTAAAACA
*
62713 TCTGATATA-TGT-AAATA
1 TCTGAT-TACTGTAAAACA
*
62730 TCTGATAACTGTAA
1 TCTGATTACTGTAA
62744 TAATCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 13 0.50
18 10 0.38
19 2 0.08
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (18 bp):
TCTGATTACTGTAAAACA
Found at i:62734 original size:17 final size:17
Alignment explanation
Indices: 62712--62770 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
62702 ACTGTAAAAC
62712 ATCTGATATATGTAAAT
1 ATCTGATATATGTAAAT
62729 ATCTGATA-ACTGT-AAT
1 ATCTGATATA-TGTAAAT
* *
62745 AATCTAATATCTGTAAAT
1 -ATCTGATATATGTAAAT
62763 ATCTGATA
1 ATCTGATA
62771 ACAGTGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.11
17 28 0.80
18 3 0.09
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (17 bp):
ATCTGATATATGTAAAT
Found at i:62765 original size:34 final size:35
Alignment explanation
Indices: 62695--62772 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 35
62685 TTAATATGTG
* *
62695 TCTGATTACTGTAAAACATCTGATATATGTAAATA
1 TCTGATAACTGTAAAACATCTAATATATGTAAATA
* *
62730 TCTGATAACTGTAATA-ATCTAATATCTGTAAATA
1 TCTGATAACTGTAAAACATCTAATATATGTAAATA
62764 TCTGATAAC
1 TCTGATAAC
62773 AGTGAAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 25 0.64
35 14 0.36
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (35 bp):
TCTGATAACTGTAAAACATCTAATATATGTAAATA
Found at i:65899 original size:16 final size:16
Alignment explanation
Indices: 65863--65945 Score: 94
Period size: 16 Copynumber: 5.2 Consensus size: 16
65853 AATTATAGTT
* *
65863 GAACTGAAATCAGCCC
1 GAACCGAAATCAACCC
* * *
65879 AAACCGAAACCAACCG
1 GAACCGAAATCAACCC
65895 GAACCGAAATCAACCC
1 GAACCGAAATCAACCC
* * *
65911 GAATCAAAAGCAACCC
1 GAACCGAAATCAACCC
65927 GAACCGAAATCAACCC
1 GAACCGAAATCAACCC
65943 GAA
1 GAA
65946 TTTAATTTAC
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.46, C:0.34, G:0.14, T:0.06
Consensus pattern (16 bp):
GAACCGAAATCAACCC
Found at i:68144 original size:55 final size:55
Alignment explanation
Indices: 68070--68215 Score: 186
Period size: 55 Copynumber: 2.7 Consensus size: 55
68060 ATTGTATGAG
*
68070 TGTGTATCGGTACACTGAGGAGTGTATCGATA-CCTGCAAAACATCGAATGCCATT
1 TGTGTATCGATACACTGAGGAGTGTATCGATACCCT-CAAAACATCGAATGCCATT
* *** *
68125 TGTGTATCGATACATTGAGGAGTGTATCGATACCCTCAAAACATCGAATTTTAAT
1 TGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATT
* * * *
68180 TGTCTATCGGTACACTGAGGAGTTTATAGATACCCT
1 TGTGTATCGATACACTGAGGAGTGTATCGATACCCT
68216 TGTCATTTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 76 0.96
56 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (55 bp):
TGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATT
Found at i:68639 original size:21 final size:21
Alignment explanation
Indices: 68615--68664 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
68605 GTGTTAGGAA
*
68615 AATATGAACTTTGAA-CATGTG
1 AATATGAACTTGGAATCA-GTG
68636 AATATGAACTTGGAATCAGTG
1 AATATGAACTTGGAATCAGTG
*
68657 AATGTGAA
1 AATATGAA
68665 TATACTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (21 bp):
AATATGAACTTGGAATCAGTG
Found at i:68897 original size:21 final size:20
Alignment explanation
Indices: 68798--68890 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 20
68788 GTAGAGGGTC
*
68798 TATGTGGTCCTTCTGGAGAAT
1 TATGTGGTCCTTC-GGATAAT
*
68819 TATGTGGTCCTCCGGGATAAT
1 TATGTGGTCCTTC-GGATAAT
* *
68840 TATGTGG-CACTTCGGTGTAACCC
1 TATGTGGTC-CTTCGG-ATAA--T
68863 TATGTGGTCCTTCGAGATAAT
1 TATGTGGTCCTTCG-GATAAT
68884 TATGTGG
1 TATGTGG
68891 CACTTCGGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
20 3 0.05
21 38 0.66
23 15 0.26
24 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
TATGTGGTCCTTCGGATAAT
Found at i:74979 original size:55 final size:55
Alignment explanation
Indices: 74824--74967 Score: 207
Period size: 55 Copynumber: 2.6 Consensus size: 55
74814 GTATGAGTGC
* * * *
74824 GTATCGGGACACTGAGGAGTGTATCGATACCCATAAAATATCGAATGTCATTTGT
1 GTATCGGTACACTGAGGAGTGTATCGATACCCTTAAAATATCAAATGTCAATTGT
* * * *
74879 GTATCGGTACACTGAGGAGTGTATCTATACCCTCAAAACATCAAATGTTAATTGT
1 GTATCGGTACACTGAGGAGTGTATCGATACCCTTAAAATATCAAATGTCAATTGT
*
74934 GTATCGGTACACTGAAGAGTGTATCGATACCCTT
1 GTATCGGTACACTGAGGAGTGTATCGATACCCTT
74968 GCCATTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (55 bp):
GTATCGGTACACTGAGGAGTGTATCGATACCCTTAAAATATCAAATGTCAATTGT
Found at i:75604 original size:21 final size:21
Alignment explanation
Indices: 75547--75616 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
75537 GTAGAGGGTC
* *
75547 TATGTGGTCATTCGGGAGAAT
1 TATGTGGTCTTTCGGGACAAT
*
75568 TATGT-AT-TTCTCCGGGACAAT
1 TATGTGGTCTT-T-CGGGACAAT
*
75589 TATGTGGTCTTTCGGGACAAA
1 TATGTGGTCTTTCGGGACAAT
75610 TATGTGG
1 TATGTGG
75617 CACTTCGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 2 0.05
21 33 0.82
22 2 0.05
23 2 0.05
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
TATGTGGTCTTTCGGGACAAT
Found at i:75623 original size:21 final size:21
Alignment explanation
Indices: 75547--75682 Score: 62
Period size: 21 Copynumber: 6.3 Consensus size: 21
75537 GTAGAGGGTC
* * *
75547 TATGTGGTCATTCGGGAGAAT
1 TATGTGGTCCTTCGGGACAAA
** * * *
75568 TATGTATTTCTCCGGGACAAT
1 TATGTGGTCCTTCGGGACAAA
*
75589 TATGTGGTCTTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
*
75610 TATGTGG-CACTTCGGTG-CAACCC
1 TATGTGGTC-CTTCGG-GACAA--A
* *
75633 TATGTGGTACTTCAGTG-CAAA
1 TATGTGGTCCTTC-GGGACAAA
* * *
75654 CTATATGGTCCTTCGAGACAAT
1 -TATGTGGTCCTTCGGGACAAA
75676 TATGTGG
1 TATGTGG
75683 CACTTTGGTG
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
20 1 0.01
21 53 0.62
22 15 0.18
23 15 0.18
24 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:75662 original size:22 final size:23
Alignment explanation
Indices: 75618--75667 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
75608 AATATGTGGC
* * *
75618 ACTTCGGTGCAACCCTATGTGGT
1 ACTTCAGTGCAACACTATATGGT
75641 ACTTCAGTGCAA-ACTATATGGT
1 ACTTCAGTGCAACACTATATGGT
*
75663 CCTTC
1 ACTTC
75668 GAGACAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (23 bp):
ACTTCAGTGCAACACTATATGGT
Found at i:87709 original size:23 final size:22
Alignment explanation
Indices: 87666--87709 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
87656 CGAAATAATA
* **
87666 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAAGATTTT
87688 TATTTAATAAAAATAGAGATTT
1 TATTTAATAAAAATA-AGATTT
87710 AATTGAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAAGATTTT
Done.