Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003726.1 Hibiscus syriacus cultivar Beakdansim tig00007967_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: 87112
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:10916 original size:29 final size:31
Alignment explanation
Indices: 10881--10939 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
10871 ATATCCTTCC
10881 ACTTTTAT-CCC-GACATTAATGGTCCTCCT
1 ACTTTTATCCCCTGACATTAATGGTCCTCCT
10910 ACTTTTATCCCCTGACATTAATGGTCCTCC
1 ACTTTTATCCCCTGACATTAATGGTCCTCC
10940 ATCTCCACGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.29
30 3 0.11
31 17 0.61
ACGTcount: A:0.20, C:0.32, G:0.10, T:0.37
Consensus pattern (31 bp):
ACTTTTATCCCCTGACATTAATGGTCCTCCT
Found at i:11494 original size:2 final size:2
Alignment explanation
Indices: 11487--11512 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11477 GTAAATTGCA
11487 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
11513 GGTGACTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20075 original size:26 final size:25
Alignment explanation
Indices: 20046--20103 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
20036 ATATGTAATC
20046 TTTAAAAATAAATTTTATAGATTATG
1 TTTAAAAAT-AATTTTATAGATTATG
* *
20072 TTTATAAAATATTTTTATATATTATG
1 TTTA-AAAATAATTTTATAGATTATG
*
20098 TATAAA
1 TTTAAA
20104 TAATTAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.75
27 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (25 bp):
TTTAAAAATAATTTTATAGATTATG
Found at i:20161 original size:14 final size:15
Alignment explanation
Indices: 20124--20206 Score: 73
Period size: 14 Copynumber: 5.5 Consensus size: 15
20114 GACAAATGCG
20124 ATTTATAAAT-ATATT
1 ATTTATAAATAATA-T
20139 ACTTTTATAAATAA-AT
1 A--TTTATAAATAATAT
20155 ATTTATAAAGTAATAT
1 ATTTATAAA-TAATAT
**
20171 ATTTATAAATTTTAT
1 ATTTATAAATAATAT
**
20186 ACATA-AAATAATAT
1 ATTTATAAATAATAT
20200 ATTTATA
1 ATTTATA
20207 TTATAAACTA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 18 0.33
15 12 0.22
16 13 0.24
17 10 0.19
18 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
ATTTATAAATAATAT
Found at i:20174 original size:16 final size:14
Alignment explanation
Indices: 20142--20180 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
20132 ATATATTACT
20142 TTTATAAATAAATA
1 TTTATAAATAAATA
20156 TTTATAAAGTAATATA
1 TTTATAAA-TAA-ATA
20172 TTTATAAAT
1 TTTATAAAT
20181 TTTATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
TTTATAAATAAATA
Found at i:20212 original size:21 final size:19
Alignment explanation
Indices: 20175--20235 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
20165 TAATATATTT
**
20175 ATAA-ATTTTATACATAAA
1 ATAATATTTTATTTATAAA
20193 ATAATATATTTATATTATAAA
1 ATAATAT-TTTAT-TTATAAA
* * *
20214 CTAATCTTTTATTTTTAAA
1 ATAATATTTTATTTATAAA
20233 ATA
1 ATA
20236 GATTATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 10 0.29
21 10 0.29
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATATTTTATTTATAAA
Found at i:20979 original size:17 final size:18
Alignment explanation
Indices: 20958--20999 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
20948 TAATAAAATA
20958 ATATATAAATAATATATTT
1 ATATATAAATAATAT-TTT
20977 ATATTATAAATAATATTTT
1 ATA-TATAAATAATATTTT
20996 ATAT
1 ATAT
21000 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATAAATAATATTTT
Found at i:20996 original size:19 final size:20
Alignment explanation
Indices: 20961--21009 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
20951 TAAAATAATA
20961 TATAAATAATATATTTATAT
1 TATAAATAATATATTTATAT
20981 TATAAATAATAT-TTTATAT
1 TATAAATAATATATTTATAT
*
21000 TTTAAA-AATA
1 TATAAATAATA
21010 AAGTATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAAATAATATATTTATAT
Found at i:21478 original size:28 final size:28
Alignment explanation
Indices: 21403--21483 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 28
21393 ATCATATAAT
*
21403 TTATTTTAAATATAATAT-AAT--TATA
1 TTATTTAAAATATAATATAAATAATATA
* **
21428 TCACATAAAA-AT-ATATAATATAATATA
1 TTATTTAAAATATAATATAA-ATAATATA
*
21455 TTATTTAAAATATAATATAAATAAAATA
1 TTATTTAAAATATAATATAAATAATATA
21483 T
1 T
21484 AAATACTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.10
24 3 0.07
25 8 0.19
27 11 0.26
28 10 0.24
29 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TTATTTAAAATATAATATAAATAATATA
Found at i:24481 original size:51 final size:50
Alignment explanation
Indices: 24426--24523 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
24416 TTAGTTTTTG
** * *
24426 ATTTAACTACTGTTCTTTTAATTT-TTGCATTTTGGTCATTATTTATTTCCT
1 ATTTAACTACT-AACTTTTAATTTCTTGCATTTTAGTAATTA-TTATTTCCT
*
24477 ATTTAACTACTAACTTTTATTTTCTTGCATTTTAGTAATTATTATTT
1 ATTTAACTACTAACTTTTAATTTCTTGCATTTTAGTAATTATTATTT
24524 TATTTTTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 15 0.37
51 26 0.63
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (50 bp):
ATTTAACTACTAACTTTTAATTTCTTGCATTTTAGTAATTATTATTTCCT
Found at i:27788 original size:9 final size:9
Alignment explanation
Indices: 27752--27818 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
27742 TGAAGAGTAC
27752 AAAAAAGCAA
1 AAAAAAG-AA
*
27762 AAAAATTG-A
1 AAAAA-AGAA
*
27771 AACAAAGAA
1 AAAAAAGAA
27780 AAAAAAGAA
1 AAAAAAGAA
*
27789 AAGAAAA-AT
1 AA-AAAAGAA
27798 AAAAAA-AA
1 AAAAAAGAA
*
27806 AACAAAGAA
1 AAAAAAGAA
27815 AAAA
1 AAAA
27819 GACAAGAAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
8 11 0.24
9 24 0.53
10 9 0.20
11 1 0.02
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:27802 original size:21 final size:21
Alignment explanation
Indices: 27778--27817 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
27768 TGAAACAAAG
*
27778 AAAAAAAAGA-AAAGAAAAAT
1 AAAAAAAAAACAAAGAAAAAT
27798 AAAAAAAAAACAAAGAAAAA
1 AAAAAAAAAACAAAGAAAAA
27818 AGACAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.88, C:0.03, G:0.07, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAACAAAGAAAAAT
Found at i:29134 original size:38 final size:38
Alignment explanation
Indices: 29082--29160 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
29072 CAAACCAGAT
* *
29082 TTTATCTCGCTTGAGATGGTTTC-ACTCGAAACAGAAGA
1 TTTATCTCGCTTGAGATAGTTTCGA-TCGAAACAAAAGA
* *
29120 TTTATTTCGGTTGAGATAGTTTCGATCGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCGATCGAAACAAAAGA
29158 TTT
1 TTT
29161 TAAGAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (38 bp):
TTTATCTCGCTTGAGATAGTTTCGATCGAAACAAAAGA
Found at i:29375 original size:99 final size:97
Alignment explanation
Indices: 29165--29380 Score: 310
Period size: 99 Copynumber: 2.2 Consensus size: 97
29155 AGATTTTAAG
* * *
29165 AAAA-TAAGCCTGATTTTTAAGGGTTTATTGATGAAGATTTTCAATGAGTTTTTAAATGAAGCTA
1 AAAACTAAGCCTGATTTTCAAGGGTTTATTGATGAAGATTTTCAATGAGTTTTTAAAGGAAACTA
**
29229 AGCCTAATTTTTAGGGGTTCCTTGAAAACCAA
66 AGCCTAATTTTTAAAGGTTCCTTGAAAACCAA
* *
29261 GAAACTAAGCCTGATTTTCAGGGGTTTATTGATGAAGATTTTTCAATGAGTTTTTAAAAGGAAAC
1 AAAACTAAGCCTGATTTTCAAGGGTTTATTGATGAAGA-TTTTCAATGAGTTTTT-AAAGGAAAC
*
29326 TAAGCCTAATTTTTAAAGGTTCCTT-AACAACTAA
64 TAAGCCTAATTTTTAAAGGTTCCTTGAA-AACCAA
*
29360 AAAACTAAGCTTGATTTTCAA
1 AAAACTAAGCCTGATTTTCAA
29381 CTTGATGAGT
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
96 3 0.03
97 31 0.30
98 18 0.17
99 53 0.50
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (97 bp):
AAAACTAAGCCTGATTTTCAAGGGTTTATTGATGAAGATTTTCAATGAGTTTTTAAAGGAAACTA
AGCCTAATTTTTAAAGGTTCCTTGAAAACCAA
Found at i:29442 original size:42 final size:41
Alignment explanation
Indices: 29375--29496 Score: 158
Period size: 42 Copynumber: 3.0 Consensus size: 41
29365 TAAGCTTGAT
*
29375 TTTCAA-CTTGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTC
1 TTTCAAGCATGATG-GTAAGTCCTTCGGGCCATCTA-TAAGTC
*
29416 TTTCGAGCATGATGTGTAAGTCCTTCGGGCCATCTATAAGTC
1 TTTCAAGCATGATG-GTAAGTCCTTCGGGCCATCTATAAGTC
* * *
29458 TTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
1 TTTCAAGCATGATGGTAAGTCCTTCGGGCCATCTATAAG
29497 ACCTTCAGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 28 0.39
42 43 0.60
43 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
TTTCAAGCATGATGGTAAGTCCTTCGGGCCATCTATAAGTC
Found at i:29457 original size:20 final size:20
Alignment explanation
Indices: 29390--29502 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 20
29380 ACTTGATGAG
29390 TAAGTCCTTCGGGCCATC-A
1 TAAGTCCTTCGGGCCATCTA
* * * * *
29409 GTAAGTCTTTCGAGCATGATGTG
1 -TAAGTCCTTCGGGC--CATCTA
29432 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGGGCCATCTA
* ** * **
29452 TAAGTCTTTCAAGCAAGATGA
1 TAAGTCCTTCGGGCCATCT-A
*
29473 TAAGTCCTTCGGGCCATCCA
1 TAAGTCCTTCGGGCCATCTA
*
29493 TAAGACCTTC
1 TAAGTCCTTC
29503 AGGTAGGATG
Statistics
Matches: 65, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 38 0.58
21 13 0.20
22 14 0.22
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCTA
Found at i:29729 original size:37 final size:36
Alignment explanation
Indices: 29660--29748 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
29650 TTGAGATTGT
*
29660 TTTCTCT-AAAAAAAGAATTTTGTCTCACTTGAGACAA
1 TTTCTCTCAAAACAAG--TTTTGTCTCACTTGAGACAA
* ** *
29697 TTTTTACTCAAAACAAGTTTTGTCTCTTTTGAGACAG
1 TTTCT-CTCAAAACAAGTTTTGTCTCACTTGAGACAA
29734 TTTCTCTCAAAACAA
1 TTTCTCTCAAAACAA
29749 AAGCTTGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 10 0.23
37 25 0.57
38 2 0.05
39 7 0.16
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (36 bp):
TTTCTCTCAAAACAAGTTTTGTCTCACTTGAGACAA
Found at i:29792 original size:63 final size:65
Alignment explanation
Indices: 29707--29866 Score: 198
Period size: 63 Copynumber: 2.5 Consensus size: 65
29697 TTTTTACTCA
* * *
29707 AAACAAGTTTTGTCTCTTTTGAGACAGTTTCTCTCAAAAC-AAAAGC-TTGAAATTGTTTCTCTT
1 AAACAA-TTTTGTCTCTCTTGAGACAGTTTCTCTCAAAACAAAAAGCTTTGAAATTATTTCCCTT
29770 G
65 G
* * ** * *
29771 AAACAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAGATTATTTCCCTTG
1 AAACAATTTTGTCTCTCTTGAGACAGTTTCTCTCAAAACAAAAAGCTTTGAAATTATTTCCCTTG
*
29836 AAACAAATTTTGTCTCTCTGGAGACAGTTTC
1 AAAC-AATTTTGTCTCTCTTGAGACAGTTTC
29867 CCTTGAAACA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 28 0.35
64 11 0.14
65 19 0.23
66 23 0.28
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (65 bp):
AAACAATTTTGTCTCTCTTGAGACAGTTTCTCTCAAAACAAAAAGCTTTGAAATTATTTCCCTTG
Found at i:29860 original size:66 final size:65
Alignment explanation
Indices: 29707--29878 Score: 213
Period size: 66 Copynumber: 2.7 Consensus size: 65
29697 TTTTTACTCA
* * ** * *
29707 AAACAAGTTTTGTCTCTTTTGAGACAGTTTCTCTCAAAAC-AAAAGCTTGAAATTGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAAGCTTGAAATTATTTCCCTTG
* * * *
29771 AAAC-AATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAGATTATTTCCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAAGC-TTGAAATTATTTCCCTT
29835 G
65 G
* *
29836 AAACAAATTTTGTCTCTCTGGAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
29879 GTTTTGTCTC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 29 0.32
64 9 0.10
65 19 0.21
66 34 0.37
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAAGCTTGAAATTATTTCCCTTG
Found at i:29898 original size:37 final size:37
Alignment explanation
Indices: 29827--30099 Score: 315
Period size: 37 Copynumber: 7.4 Consensus size: 37
29817 TTTGAGATTA
*
29827 TTTCCCTTGAAACAAA-TTTTGTCTCTCTGGAGACAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* *
29863 TTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* * *
29900 TTTCTCTT-ATAAAAAATTTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGA-AACAAA-GTTTTGTCTCTCTTGAGACAG
* * * *
29938 TTTCCCTTGAAACAAAGTTTTATCTCCCTTAAGATAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
** *
29975 TTTATCTT-ATAA-AACA-ATTTGTCTCTCTTGAGACAG
1 TTTCCCTTGA-AACAA-AGTTTTGTCTCTCTTGAGACAG
*
30011 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* * *
30048 TTTTCCTTGAAA-TAAGTTTTGTCTCTATTGAGACAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
30084 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
30100 ATGTATCTCA
Statistics
Matches: 197, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
36 78 0.40
37 88 0.45
38 30 0.15
39 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:30050 original size:73 final size:72
Alignment explanation
Indices: 29840--30099 Score: 362
Period size: 73 Copynumber: 3.5 Consensus size: 72
29830 CCCTTGAAAC
*
29840 AAATTTTGTCTCTCTGGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAGTTTCT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAGTTT-T
29905 CTTATAAA
65 CTTATAAA
* *
29913 AAATTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTAAGATAGTTT
1 AAA--TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAGTTT
29978 ATCTTATAAA
64 -TCTTATAAA
* * *
29988 ACAA-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTT
1 A-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAGTTTT
*
30052 CCTTGA-AAT
65 -CTT-ATAAA
* *
30061 AAGTTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAA
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
30100 ATGTATCTCA
Statistics
Matches: 168, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
72 2 0.01
73 96 0.57
74 1 0.01
75 67 0.40
76 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (72 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACAGTTTTC
TTATAAA
Found at i:30116 original size:36 final size:36
Alignment explanation
Indices: 29761--30099 Score: 304
Period size: 37 Copynumber: 9.5 Consensus size: 36
29751 GCTTGAAATT
* *
29761 GTTTCTCTTGAAAC-AATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * ** *
29796 ATTTCTCTTGAAACAAA-----AATCT-TTGAGATTA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CA
*
29827 -TTTCCCTTGAAACAAATTTTGTCTCTCTGGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
29862 GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
29899 GTTTCTCTT-ATAAAAAATTTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGA-AACAAA--TTTTGTCTCTCTTGAGACA
* * * *
29937 GTTTCCCTTGAAACAAAGTTTTATCTCCCTTAAGATA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
** *
29974 GTTTATCTT-ATAA-AACAATTTGTCTCTCTTGAGACA
1 GTTTCCCTTGA-AACAA-ATTTTGTCTCTCTTGAGACA
*
30010 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * * *
30047 GTTTTCCTTGAAATAAGTTTTGTCTCTATTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
30083 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
30100 ATGTATCTCA
Statistics
Matches: 244, Mismatches: 42, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
30 21 0.09
31 3 0.01
35 17 0.07
36 84 0.34
37 88 0.36
38 30 0.12
39 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:30125 original size:73 final size:73
Alignment explanation
Indices: 29831--30244 Score: 331
Period size: 73 Copynumber: 5.6 Consensus size: 73
29821 AGATTATTTC
* * *
29831 CCTTGAAACAAATTTTGTCTCTCTGGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTAAG
1 CCTTGAAAC-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAG
* *
29896 ACAGTTTCT
65 ATAGTTTTT
* * *
29905 -CTTATAAAAAATTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTA
1 CCTT-GAAACAA--TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTG
*
29969 AGATAGTTTAT
63 AGATAGTTTTT
* * * * *
29980 CTTATAAAACAA-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAG
1 CCT-TGAAACAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAG
*
30044 ACAG-TTTT
65 ATAGTTTTT
* * * * *
30052 CCTTGAAATAAGTTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAA-ATGTATCTCACTTGAG
1 CCTTGAAACAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAG
*
30116 ATGGTTTTT
65 ATAGTTTTT
* * ** * * * ** *
30125 -CTTAAAACCAACTTCATCTCGCTTAAGACAGTTTTCCTTTGAAACGAAA--TTTATCTAACTCG
1 CCTTGAAA-CAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAAC-AAAGTTTTATCTCCCTTG
*
30187 AGAT-GGTTTT
63 AGATAGTTTTT
* * * * * *
30197 CCTTAAAACCAACTTCGTCTCGCTTGAAACAACTTTCCCTTGAAACAA
1 CCTTGAAA-CAATTTTGTCTCTCTTGAGAC-AGTTTCCCTTGAAACAA
30245 GAAATTTTAT
Statistics
Matches: 283, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
71 6 0.02
72 46 0.16
73 159 0.56
74 7 0.02
75 58 0.20
76 6 0.02
77 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (73 bp):
CCTTGAAACAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAGA
TAGTTTTT
Found at i:30144 original size:36 final size:36
Alignment explanation
Indices: 30104--30223 Score: 114
Period size: 36 Copynumber: 3.3 Consensus size: 36
30094 AACAAAATGT
*
30104 ATCTCACTTGAGATGGTTTTTCTTAAAACCAACTTC
1 ATCTCACTTGAGATGGTTTTCCTTAAAACCAACTTC
* * ** * * * *
30140 ATCTCGCTTAAGACAGTTTTCCTTTGAAACGAAATTT
1 ATCTCACTTGAGATGGTTTTCC-TTAAAACCAACTTC
* *
30177 ATCTAACTCGAGATGGTTTTCCTTAAAACCAACTTC
1 ATCTCACTTGAGATGGTTTTCCTTAAAACCAACTTC
* *
30213 GTCTCGCTTGA
1 ATCTCACTTGA
30224 AACAACTTTC
Statistics
Matches: 60, Mismatches: 23, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
36 34 0.57
37 26 0.43
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (36 bp):
ATCTCACTTGAGATGGTTTTCCTTAAAACCAACTTC
Found at i:30686 original size:91 final size:91
Alignment explanation
Indices: 30529--31089 Score: 768
Period size: 91 Copynumber: 6.0 Consensus size: 91
30519 GATTAACCGA
* * *
30529 TCAACATTTCCAGTGGAGAGTTCATAATAAGAAGAACTCATCCAATAAGGGAGAAGAAGTTTATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
30594 ATGAGAAGAACTTGTTCAACCTT-GC
66 ATGAGAAGAACTTGTTCAACCTTGGC
*
30619 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGGAG-AGAAAGTTCA
1 -TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAG-AAGTTCA
* *
30683 TAATGAAAAGAACTTGTTCAAACTTGGC
64 TAATGAGAAGAACTTGTTCAACCTTGGC
* * *
30711 TCAGCATTTCCAGTGGAGATTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
* *
30776 AGGAGAAGAACTTGTTTAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGGC
* *
30802 TCAACATTTCCAGTGGAGTGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
30867 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGGC
* * *
30893 TCAACAATTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAATCATCCAATGAGGGAA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAG-----A----AC---TCATCCAATGAGGGAG
*
30958 AATAAGTTCATAATGAGAAGAACTTGTTCAACCTT-GC
54 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGC
* * *
30995 ATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTCA
1 -TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATC-CAATGAGGGAGAAGAAGTTCA
*
31060 TAATGAGAAGAACTTGTTCAACCTTAGC
64 TAATGAGAAGAACTTGTTCAACCTTGGC
31088 TC
1 TC
31090 GATTCATCAC
Statistics
Matches: 422, Mismatches: 30, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
90 2 0.00
91 281 0.67
92 48 0.11
93 2 0.00
94 2 0.00
96 1 0.00
98 1 0.00
100 2 0.00
102 2 0.00
103 81 0.19
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGC
Found at i:31018 original size:103 final size:103
Alignment explanation
Indices: 30839--31089 Score: 346
Period size: 103 Copynumber: 2.5 Consensus size: 103
30829 TGAGAAGAAC
*
30839 TCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACAATTCT
1 TCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACAATTCT
30904 AGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAA
66 AGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAA
* * *
30942 TCATCCAATGAGGGAAAATAAGTTCATAATGAGAAGAACTTGTTCAACCTT-GCATCAACATTTC
1 TCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGC-TCAACAATTC
31006 TAGTGGAGAGTTCATAATGAGAAGAACTCAT----C---
65 TAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAA
* * *
31038 TGA---AA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC
1 TCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTC
31090 GATTCATCAC
Statistics
Matches: 139, Mismatches: 7, Indels: 15
0.86 0.04 0.09
Matches are distributed among these distances:
92 42 0.30
93 4 0.03
96 2 0.01
99 1 0.01
102 2 0.01
103 88 0.63
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (103 bp):
TCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACAATTCT
AGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAA
Found at i:31281 original size:44 final size:44
Alignment explanation
Indices: 31218--31694 Score: 245
Period size: 44 Copynumber: 10.9 Consensus size: 44
31208 TTGTTCAACT
* * *
31218 TTTTTCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGATA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
* * * * * *
31262 TCTCGTTCGATTCCATCACAGAAGGAGGTGGAT--AGAT--ATTT
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGA-TA
* * * * * * * *
31303 TTTTAACTCAAATCCATCACAAAAAGA-GTCGGATCAGCATCAACT-
1 TTTT-GCTCGATTCCATCACAGAAGGAGGT-AGATCAACATCGA-TA
* * * * * *
31348 TTTTACTTGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
* * * ***
31392 TCTTGTTCGATTCCATCACAGAAGGAGGT-GAATCGACATTTTTA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAG-ATCAACATCGATA
* * * * * * * * *
31436 TTTCGCTCAAATCCATCATAGAAGGAGTTGGATTAGCATCAACT-
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGA-TA
* * * * *
31480 TTTTGCTCGATTCTATCATAGAATGAGGTAGATCATCACCGA-A
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
* * * * ***
31523 GTCTTGTTCGATTCCATCACAGAAGGAGGTGGATCAAAATTTTTA
1 -TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
* * * * *
31568 TTTTGCTCAAATCTATCACAGAAGGAGTTAGATCAACATCAACT-
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGA-TA
* * * *
31612 TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
* * * *
31656 TCTTGTTCGATTCCATCACAGAAGGAGGTGGATCGACAT
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACAT
31695 TTTTATTTGG
Statistics
Matches: 313, Mismatches: 103, Indels: 34
0.70 0.23 0.08
Matches are distributed among these distances:
40 1 0.00
41 5 0.02
42 22 0.07
43 1 0.00
44 272 0.87
45 10 0.03
46 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (44 bp):
TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGATA
Found at i:31512 original size:132 final size:132
Alignment explanation
Indices: 31212--31708 Score: 730
Period size: 132 Copynumber: 3.8 Consensus size: 132
31202 AAGAATTTGT
* * * *
31212 TCAACTTTTTTCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGATATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
* * * * * *
31277 TCACAGAAGGAGGTGGATAGATA-TTTT-TTTAACTCAAATCCATCACAAAAAGAGTCGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTAGCTCAAATCCATCACAGAAGGAGTTGGATCAG
31340 CA
131 CA
* *
31342 TCAACTTTTTACTTGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
* * * *
31407 TCACAGAAGGAGGTGAATCGACATTTTTATTTCGCTCAAATCCATCATAGAAGGAGTTGGATTAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTAGCTCAAATCCATCACAGAAGGAGTTGGATCAG
31472 CA
131 CA
* * *
31474 TCAACTTTTTGCTCGATTCTATCATAGAATGAGGTAGATCATCACCGA-AGTCTTGTTCGATTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA-TCTTGTTCGATTCC
* * * * *
31538 ATCACAGAAGGAGGTGGATCAAAATTTTTATTTTGCTCAAATCTATCACAGAAGGAGTTAGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTAGCTCAAATCCATCACAGAAGGAGTTGGATCA
*
31603 ACA
130 GCA
31606 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
*
31671 TCACAGAAGGAGGTGGATCGACATTTTTATTTGGCTCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTAGCTCA
31709 TCTATTACAT
Statistics
Matches: 328, Mismatches: 35, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
130 80 0.24
131 5 0.02
132 242 0.74
133 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (132 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTTGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTAGCTCAAATCCATCACAGAAGGAGTTGGATCAG
CA
Found at i:32217 original size:12 final size:11
Alignment explanation
Indices: 32197--32250 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 11
32187 ATTATGTTTC
*
32197 AAAATAAAAGA
1 AAAAAAAAAGA
32208 AAAAACAAAAGTA
1 AAAAA-AAAAG-A
32221 AAAGAAAAATAGA
1 AAA-AAAAA-AGA
32234 AAAAGAAAAAGA
1 AAAA-AAAAAGA
32246 AAAAA
1 AAAAA
32251 CACAATGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 5 0.14
12 13 0.35
13 15 0.41
14 4 0.11
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:32236 original size:7 final size:6
Alignment explanation
Indices: 32202--32249 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
32192 GTTTCAAAAT
*
32202 AAAAGA AAAA-A CAAAAGT AAAAGAA AAATAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA -AAAAGA AAAAG-A AAA-AGA AAAAGA AAAAGA AAAA
32250 ACACAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 1 0.03
6 26 0.72
7 7 0.19
8 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:35173 original size:12 final size:11
Alignment explanation
Indices: 35153--35206 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
35143 TTGAACCCCC
*
35153 TTTTATTTTATT
1 TTTTCTTTT-TT
35165 TTTTCTTTTTCT
1 TTTTCTTTTT-T
*
35177 TTTT-TTCTTT
1 TTTTCTTTTTT
*
35187 TTTTCTTTCTT
1 TTTTCTTTTTT
35198 TTTTCTTTT
1 TTTTCTTTT
35207 ATTCTCTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 5 0.14
11 17 0.49
12 13 0.37
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:35181 original size:8 final size:8
Alignment explanation
Indices: 35170--35199 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
35160 TTATTTTTTC
35170 TTTTTCTT
1 TTTTTCTT
35178 TTTTTCTT
1 TTTTTCTT
35186 TTTTTCTT
1 TTTTTCTT
35194 TCTTTT
1 T-TTTT
35200 TTCTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:35187 original size:19 final size:19
Alignment explanation
Indices: 35165--35211 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
35155 TTATTTTATT
35165 TTTTCTT-TTTCTTTTTTTC
1 TTTTCTTCTTTC-TTTTTTC
*
35184 TTTTTTTCTTTCTTTTTTC
1 TTTTCTTCTTTCTTTTTTC
*
35203 TTTTATTCT
1 TTTTCTTCT
35212 CTTCAGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTTTC
Found at i:35188 original size:27 final size:27
Alignment explanation
Indices: 35158--35211 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
35148 CCCCCTTTTA
*
35158 TTTTATTT-TTTC-TTTTTCTTTTTTTC
1 TTTT-TTTCTTTCTTTTTTCTTTTATTC
35184 TTTTTTTCTTTCTTTTTTCTTTTATTC
1 TTTTTTTCTTTCTTTTTTCTTTTATTC
35211 T
1 T
35212 CTTCAGGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 3 0.12
26 8 0.32
27 14 0.56
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTTTCTTTCTTTTTTCTTTTATTC
Found at i:35211 original size:8 final size:7
Alignment explanation
Indices: 35158--35211 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
35148 CCCCCTTTTA
*
35158 TTTTATT
1 TTTTCTT
35165 TTTTC-T
1 TTTTCTT
35171 TTTTCTT
1 TTTTCTT
35178 TTTT-TCT
1 TTTTCT-T
35185 TTTT-TT
1 TTTTCTT
*
35191 CTTTCTT
1 TTTTCTT
35198 TTTTCTT
1 TTTTCTT
35205 TTATTCT
1 TT-TTCT
35212 CTTCAGGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 11 0.28
7 25 0.62
8 4 0.10
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:40189 original size:22 final size:22
Alignment explanation
Indices: 40161--40215 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
40151 TTGTTTTGCA
40161 TTTTTATTTTTGTATAGTTTAC
1 TTTTTATTTTTGTATAGTTTAC
40183 TTTTTATTTTTGTATAGTTTAC
1 TTTTTATTTTTGTATAGTTTAC
**
40205 TTGATATTTTT
1 TTTTTATTTTT
40216 TATTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (22 bp):
TTTTTATTTTTGTATAGTTTAC
Found at i:47257 original size:18 final size:18
Alignment explanation
Indices: 47231--47277 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
47221 ATTTCTTAAT
*
47231 GGTGTTGTTTGAGGGAAA
1 GGTGCTGTTTGAGGGAAA
47249 GGTGCTGTTTGAGGGAAA
1 GGTGCTGTTTGAGGGAAA
*
47267 GGTGCAGTTTG
1 GGTGCTGTTTG
47278 CCTATGGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.45, T:0.32
Consensus pattern (18 bp):
GGTGCTGTTTGAGGGAAA
Found at i:49181 original size:2 final size:2
Alignment explanation
Indices: 49079--49173 Score: 181
Period size: 2 Copynumber: 47.5 Consensus size: 2
49069 ACGAAAGAGA
*
49079 AT AT GT 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
49121 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
49163 AT AT AT AT AT A
1 AT AT AT AT AT A
49174 CGTATATACA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55242 original size:42 final size:40
Alignment explanation
Indices: 55175--55254 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 40
55165 TTTGTTAAAG
* * *
55175 AATCCTACCCACACATGTTGGCTACCCAATCATGCTTTATCA
1 AATCCTACCCAAACATGATAGCTACCC-A-CATGCTTTATCA
*
55217 AATCCTACCCAAACATGATATCTACCCACATGCTTTAT
1 AATCCTACCCAAACATGATAGCTACCCACATGCTTTAT
55255 TTGAACATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 10 0.29
41 1 0.03
42 23 0.68
ACGTcount: A:0.31, C:0.33, G:0.07, T:0.29
Consensus pattern (40 bp):
AATCCTACCCAAACATGATAGCTACCCACATGCTTTATCA
Found at i:57512 original size:2 final size:2
Alignment explanation
Indices: 57505--57550 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
57495 AAATTTACTA
57505 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
57547 AT AT
1 AT AT
57551 TAAACTAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57569 original size:17 final size:17
Alignment explanation
Indices: 57547--57583 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
57537 ATATATATAT
57547 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
57564 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
57581 ATA
1 ATA
57584 GCCGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATTAAACTAAACCTA
Found at i:57967 original size:85 final size:85
Alignment explanation
Indices: 57824--58000 Score: 300
Period size: 85 Copynumber: 2.1 Consensus size: 85
57814 CTTAAAAAGA
** *
57824 GGCCCTTAAATCTCAATTTTACCACTGATCCGTAATACTTTGTTTGCTTTTTTATTGTAACAATA
1 GGCCCTTAAATCTCAATTTTACCACTGATCCACAATACTTTATTTGCTTTTTTATTGTAACAATA
57889 GTAATAAATCTAATTTTTTG
66 GTAATAAATCTAATTTTTTG
* *
57909 GGCCCTTAAATCTCAATTTTACCATTGATCCACAATGCTTTATTTGCTTTTTTATTGTAACAATA
1 GGCCCTTAAATCTCAATTTTACCACTGATCCACAATACTTTATTTGCTTTTTTATTGTAACAATA
57974 GTAATAAATCTAATTTTTTG
66 GTAATAAATCTAATTTTTTG
*
57994 GGGCCTT
1 GGCCCTT
58001 TACTATTCCG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (85 bp):
GGCCCTTAAATCTCAATTTTACCACTGATCCACAATACTTTATTTGCTTTTTTATTGTAACAATA
GTAATAAATCTAATTTTTTG
Found at i:58787 original size:30 final size:30
Alignment explanation
Indices: 58729--58791 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
58719 AAAATTAGGG
** *
58729 TATTACAATTTAGTTTTTTATAGTTTAATT
1 TATTACAATTTAGTTTTACATAGATTAATT
58759 TATTA-AATTTAGTTTTACATTAGATTAATT
1 TATTACAATTTAGTTTTACA-TAGATTAATT
58789 TAT
1 TAT
58792 AAGAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
TATTACAATTTAGTTTTACATAGATTAATT
Found at i:61004 original size:18 final size:18
Alignment explanation
Indices: 60981--61034 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
60971 AATTGGAGTG
60981 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAAGAAAAAGA
60999 CAAAAAG-AAGAAGAAAAGA
1 CAAAAAGAAAG-A-AAAAGA
61018 -AGAAAAGAAAAGAAAAA
1 CA-AAAAG-AAAGAAAAA
61035 AAGAATTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 3 0.10
18 9 0.29
19 15 0.48
20 1 0.03
21 3 0.10
ACGTcount: A:0.78, C:0.04, G:0.19, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAAGA
Found at i:61005 original size:14 final size:13
Alignment explanation
Indices: 60988--61039 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
60978 GTGCAAAAAG
60988 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
61002 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
61015 AGAAG-AAAAGAAA
1 A-AAGAAAAAGAAA
61028 AGAA-AAAAAGAA
1 A-AAGAAAAAGAA
61040 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 21 0.62
14 13 0.38
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:61009 original size:11 final size:10
Alignment explanation
Indices: 60985--61035 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
60975 GGAGTGCAAA
60985 AAGAAAGAAA-
1 AAGAAA-AAAG
60995 AAGACAAAAAG
1 AAGA-AAAAAG
61006 AAGAAGAAAAG
1 AAGAA-AAAAG
61017 AAGAAAAGAA-
1 AAGAAAA-AAG
61027 AAGAAAAAA
1 AAGAAAAAA
61036 AGAATTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 2 0.05
10 17 0.46
11 18 0.49
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:61038 original size:18 final size:18
Alignment explanation
Indices: 60983--61039 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
60973 TTGGAGTGCA
60983 AAAAG-AAAGAAAAAGACA-
1 AAAAGAAAAGAAAAA-A-AG
*
61001 AAAAGAAGAAGAAAAGAAG
1 AAAAGAA-AAGAAAAAAAG
61020 AAAAGAAAAGAAAAAAAG
1 AAAAGAAAAGAAAAAAAG
61038 AA
1 AA
61040 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 18 0.53
19 9 0.26
20 7 0.21
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAG
Found at i:70154 original size:22 final size:23
Alignment explanation
Indices: 70115--70176 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
70105 TTCCCCTGTG
70115 GGGGGAATCGGTTCCCCTTCA-AA
1 GGGGGAATCGGTT-CCCTTCATAA
*
70138 GGGGGAATCGGTTCCC-TCATGA
1 GGGGGAATCGGTTCCCTTCATAA
* *
70160 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
70177 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.09
22 18 0.53
23 13 0.38
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCTTCATAA
Found at i:70177 original size:22 final size:23
Alignment explanation
Indices: 70092--70177 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
70082 ACAGAACCCC
*
70092 AGGGGGGTATCGATTCCC-C-TG
1 AGGGGGGAATCGATTCCCTCATG
* *
70113 TGGGGGGAATCGGTTCCCCTTCA--
1 AGGGGGGAATCGATT-CCC-TCATG
* *
70136 AAGGGGGAATCGGTTCCCTCATG
1 AGGGGGGAATCGATTCCCTCATG
70159 AGGGGGG-ATCGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
70178 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 15 0.29
22 17 0.33
23 19 0.37
24 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.23
Consensus pattern (23 bp):
AGGGGGGAATCGATTCCCTCATG
Done.