Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006092.1 Hibiscus syriacus cultivar Beakdansim tig00014442_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: 95684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15103 original size:20 final size:20
Alignment explanation
Indices: 15080--15121 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
15070 CATGGGTGGT
15080 GTGCAACATTAATGGAGTTG
1 GTGCAACATTAATGGAGTTG
* *
15100 GTGCGACATTAGTGGAGTTG
1 GTGCAACATTAATGGAGTTG
15120 GT
1 GT
15122 TGAATTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (20 bp):
GTGCAACATTAATGGAGTTG
Found at i:15957 original size:195 final size:192
Alignment explanation
Indices: 15386--15960 Score: 669
Period size: 195 Copynumber: 2.9 Consensus size: 192
15376 TTTGTTGAAG
* * * *
15386 ATGATGTTGTTCCTTCGCGTTGAGGAAATCAGTTCAATCAAGAGATAATTTG-GAGACAATATGG
1 ATGAAGTTGTTCCTTCGCGTTGAGGAAATCGGGTCAATC-AGAGATAATTTGAG-GACAATACGG
* * * *
15450 TCCCTTTGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTTGTGTTG-AGAAGATC
64 TTCCTTTGTGATGA-GAAGTCTGATTATCTGAAGATGACAATGCTCA-TTGTGATGAAG-AGATC
** * *
15514 GGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGATATCTGGTCA-TTTTCGAG
126 GGGTCAATTTGATGTTGAAGACGACACT-CTTGTCCGTGTTGAAGATATATGGTCATTTTTAGAG
15578 TAA
190 TAA
* *
15581 ATGACA-TTGTTCCTCCGCGTTGAGGAAATCGGGTCAATCAGGAGATAATTTGAGGATAATACGG
1 ATGA-AGTTGTTCCTTCGCGTTGAGGAAATCGGGTCAATCA-GAGATAATTTGAGGACAATACGG
* * * * * *
15645 TT-CTTTCGTGATGATGAAGTCTGATTTTCTGAAAATGACAATGCTCCTTCGTGGTGAGGAGATT
64 TTCCTTT-GTGATGA-GAAGTCTGATTATCTGAAGATGACAATGCTCATT-GTGATGAAGAGATC
* * *
15709 GGGTCAATTTGAT-TATGAAAACGACACTGTTGATCCGTGTTGAAGAGATATGGTCATTTTTAG-
126 GGGTCAATTTGATGT-TGAAGACGACACTCTTG-TCCGTGTTGAAGATATATGGTCATTTTTAGA
15772 GTAA
189 GTAA
*
15776 ATGAAGTTGTTCCTTTGCGTTGAGGAAATCGGGTCAATCAGTAGATAATTTGAGGACAATACGGT
1 ATGAAGTTGTTCCTTCGCGTTGAGGAAATCGGGTCAATCAG-AGATAATTTGAGGACAATACGGT
* * **
15841 TCCTTTGTGATGAGAAAGTCTGATTATCTGAAGATGACACTGCTCATATGCGATGAAGAGATCAT
65 TCCTTTGTGATGAG-AAGTCTGATTATCTGAAGATGACAATGCTCAT-TGTGATGAAGAGATCGG
** *
15906 GTCAATTTGATGTTGAAGACGACACTACTTGTTTGTGTTAAAGATATATGGTCAT
128 GTCAATTTGATGTTGAAGACGACACT-CTTGTCCGTGTTGAAGATATATGGTCAT
15961 CTAAGGGTGA
Statistics
Matches: 323, Mismatches: 41, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
194 12 0.04
195 295 0.91
196 16 0.05
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (192 bp):
ATGAAGTTGTTCCTTCGCGTTGAGGAAATCGGGTCAATCAGAGATAATTTGAGGACAATACGGTT
CCTTTGTGATGAGAAGTCTGATTATCTGAAGATGACAATGCTCATTGTGATGAAGAGATCGGGTC
AATTTGATGTTGAAGACGACACTCTTGTCCGTGTTGAAGATATATGGTCATTTTTAGAGTAA
Found at i:16898 original size:16 final size:16
Alignment explanation
Indices: 16873--16916 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16863 ACATTTCATG
*
16873 TATT-ATGTATGTATG
1 TATTGATGTATGTATA
* *
16888 TGTTGATGTATGTTTA
1 TATTGATGTATGTATA
16904 TATTGATGTATGT
1 TATTGATGTATGT
16917 TTTCTTGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
TATTGATGTATGTATA
Found at i:23604 original size:20 final size:19
Alignment explanation
Indices: 23579--23630 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
23569 TCTGGGTAGG
23579 TGCATCGATGCATTAAAGGA
1 TGCATCGATGCATT-AAGGA
* *
23599 TGCATCGATGCATTAGGGG
1 TGCATCGATGCATTAAGGA
23618 TGCATCGATGCAT
1 TGCATCGATGCAT
23631 GTATATTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCATTAAGGA
Found at i:23985 original size:74 final size:74
Alignment explanation
Indices: 23896--24048 Score: 306
Period size: 74 Copynumber: 2.1 Consensus size: 74
23886 TAGTATATTT
23896 AGTTCTAGACTTGTGATAAGTCTAGATTTAATACTTTGATATATGATTCATTTCATATTATGAAA
1 AGTTCTAGACTTGTGATAAGTCTAGATTTAATACTTTGATATATGATTCATTTCATATTATGAAA
23961 CATGATATG
66 CATGATATG
23970 AGTTCTAGACTTGTGATAAGTCTAGATTTAATACTTTGATATATGATTCATTTCATATTATGAAA
1 AGTTCTAGACTTGTGATAAGTCTAGATTTAATACTTTGATATATGATTCATTTCATATTATGAAA
24035 CATGATATG
66 CATGATATG
24044 AGTTC
1 AGTTC
24049 ATACCATATA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (74 bp):
AGTTCTAGACTTGTGATAAGTCTAGATTTAATACTTTGATATATGATTCATTTCATATTATGAAA
CATGATATG
Found at i:24712 original size:32 final size:32
Alignment explanation
Indices: 24671--24889 Score: 177
Period size: 32 Copynumber: 6.9 Consensus size: 32
24661 ATTCGAGGGT
*
24671 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTTCGGAACATATGGACAGAA
*
24703 TTACCTATG-TCTTTCGGGACATATGGACAGAA
1 TTACCTATGTTC-TTCGGAACATATGGACAGAA
* * *
24735 TTACCTAT-TTCTTTTGGGACATATGGACATAA
1 TTACCTATGTTC-TTCGGAACATATGGACAGAA
**
24767 TTACCTATG-TCTTTTGAGACATATGGAC--AA
1 TTACCTATGTTCTTCGGA-ACATATGGACAGAA
* *
24797 TATACCTATGTT-ATCAGAAACATATGGAC--AA
1 T-TACCTATGTTCTTC-GGAACATATGGACAGAA
** * *
24828 TATACCTATGTTCTAAGGAACATATAGACAG-T
1 T-TACCTATGTTCTTCGGAACATATGGACAGAA
* * *
24860 TTACCTAGGTTCTTCGGGACCTATGGACAG
1 TTACCTATGTTCTTCGGAACATATGGACAG
24890 TTGCCGAGGT
Statistics
Matches: 155, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
30 3 0.02
31 73 0.47
32 79 0.51
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGAACATATGGACAGAA
Found at i:24839 original size:31 final size:31
Alignment explanation
Indices: 24785--24866 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
24775 GTCTTTTGAG
*
24785 ACATATGGACAATATACCTATGTTATCAGAA
1 ACATATGGACAATATACCTATGTTATAAGAA
* *
24816 ACATATGGACAATATACCTATGTTCTAAGGA
1 ACATATGGACAATATACCTATGTTATAAGAA
* * *
24847 ACATATAGACAGTTTACCTA
1 ACATATGGACAATATACCTA
24867 GGTTCTTCGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (31 bp):
ACATATGGACAATATACCTATGTTATAAGAA
Found at i:28795 original size:30 final size:30
Alignment explanation
Indices: 28761--28824 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
28751 TCTTTAGTTC
28761 CCCTGATAGGTAAACTATGTTCCCCTGTTT
1 CCCTGATAGGTAAACTATGTTCCCCTGTTT
28791 CCCTGATAGGTAAACTATGTTCCCCTGTTT
1 CCCTGATAGGTAAACTATGTTCCCCTGTTT
28821 CCCT
1 CCCT
28825 TATCAGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (30 bp):
CCCTGATAGGTAAACTATGTTCCCCTGTTT
Found at i:29861 original size:32 final size:31
Alignment explanation
Indices: 29809--29918 Score: 150
Period size: 32 Copynumber: 3.5 Consensus size: 31
29799 CCCCGCCCCG
*
29809 ATTATATATATA-TATATATATATTATATTA
1 ATTATATATATATTTTATATATATTATATTA
*
29839 ATTATATATATAATTTTTTATATATTTTATATTA
1 ATTATATATAT-A--TTTTATATATATTATATTA
*
29873 ATTATATATAATATTTTATATATTTTATATTA
1 ATTATATAT-ATATTTTATATATATTATATTA
29905 ATTATATATATATT
1 ATTATATATATATT
29919 ATTTTATTAA
Statistics
Matches: 73, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
30 11 0.15
31 6 0.08
32 28 0.38
34 26 0.36
35 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTATATATATATTTTATATATATTATATTA
Found at i:29861 original size:34 final size:34
Alignment explanation
Indices: 29823--29934 Score: 153
Period size: 32 Copynumber: 3.4 Consensus size: 34
29813 TATATATATA
29823 TATATATATTATATTAATTATATATATAATTTTT
1 TATATATATTATATTAATTATATATATAATTTTT
* *
29857 TATATATTTTATATTAA-T-TATATATAATATTT
1 TATATATATTATATTAATTATATATATAATTTTT
*
29889 TATATATTTTATATTAATTATATATAT-ATTATTT
1 TATATATATTATATTAATTATATATATAATT-TTT
29923 TAT-TA-ATTATAT
1 TATATATATTATAT
29935 AATACAAACC
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
32 36 0.51
33 6 0.08
34 29 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATTATATTAATTATATATATAATTTTT
Found at i:29935 original size:2 final size:2
Alignment explanation
Indices: 29811--29917 Score: 57
Period size: 2 Copynumber: 61.5 Consensus size: 2
29801 CCGCCCCGAT
29811 TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA -A T- 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
* * *
29849 TA -A T- TT TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
29884 TA T- TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29918 TATTTTATTA
Statistics
Matches: 85, Mismatches: 4, Indels: 32
0.70 0.03 0.26
Matches are distributed among these distances:
1 16 0.19
2 69 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:30004 original size:21 final size:21
Alignment explanation
Indices: 29940--29997 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
29930 TATATAATAC
*
29940 AAACCTTAAACCCTAAACATTT
1 AAACCTTAAACCCTAAGC-TTT
29962 AAACCTTAAACCCTAAGCTTT
1 AAACCTTAAACCCTAAGCTTT
29983 AAATCC-TAAACCCTA
1 AAA-CCTTAAACCCTA
29998 GATTTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.26
Consensus pattern (21 bp):
AAACCTTAAACCCTAAGCTTT
Found at i:30755 original size:34 final size:34
Alignment explanation
Indices: 30716--30789 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
30706 AACAAGTAGG
30716 AACACATTTTTTATGTTTATTTAATAAATGAAAT
1 AACACATTTTTTATGTTTATTTAATAAATGAAAT
30750 AACACATTTTTTATGTTTATTTAATAAATGAAAT
1 AACACATTTTTTATGTTTATTTAATAAATGAAAT
30784 AACACA
1 AACACA
30790 AATAAAGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (34 bp):
AACACATTTTTTATGTTTATTTAATAAATGAAAT
Found at i:43079 original size:3 final size:3
Alignment explanation
Indices: 43071--43110 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
43061 TGATTTTTGT
43071 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
43111 TCTTTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43203 original size:16 final size:16
Alignment explanation
Indices: 43158--43203 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
43148 ATTACAATAC
*
43158 ATATATTTTAT-TATT
1 ATATATATTATATATT
*
43173 AT-TATCTTATATATT
1 ATATATATTATATATT
*
43188 ATATATATTCTATATT
1 ATATATATTATATATT
43204 TTTCAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 8 0.31
16 11 0.42
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATATTATATATT
Found at i:43969 original size:27 final size:27
Alignment explanation
Indices: 43937--43996 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
43927 TCTGCAGGCA
43937 TCTGCAACAGAAGAGGTGGACCAAAAG
1 TCTGCAACAGAAGAGGTGGACCAAAAG
**
43964 TCTGCAGTAGAAGAGGTGGACCAAAAG
1 TCTGCAACAGAAGAGGTGGACCAAAAG
43991 TCTGCA
1 TCTGCA
43997 GTCTACAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (27 bp):
TCTGCAACAGAAGAGGTGGACCAAAAG
Found at i:43997 original size:27 final size:27
Alignment explanation
Indices: 43945--43998 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
43935 CATCTGCAAC
43945 AGAAGAGGTGGACCAAAAGTCTGCAGT
1 AGAAGAGGTGGACCAAAAGTCTGCAGT
43972 AGAAGAGGTGGACCAAAAGTCTGCAGT
1 AGAAGAGGTGGACCAAAAGTCTGCAGT
43999 CTACAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (27 bp):
AGAAGAGGTGGACCAAAAGTCTGCAGT
Found at i:44125 original size:31 final size:31
Alignment explanation
Indices: 44089--44148 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
44079 AACTTAAAAG
* *
44089 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
44120 AGTTTTACAATACTTAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
44149 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:44696 original size:63 final size:59
Alignment explanation
Indices: 44614--44761 Score: 142
Period size: 63 Copynumber: 2.4 Consensus size: 59
44604 AAATAATCAA
* *
44614 AATA-AATA-TAAAATTTTAATAA-TATATAAAATAGTTTATATGATATAAAATTAAATATCTAT
1 AATATAATATTAAAATATTAATAATTATATAAAA-A-ATTA-AT-AT-TAAAATT-AATATCTAT
*
44676 AATATAATATTAAAA-ATTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTAT
1 AATATAATATTAAAATATT-A-A--TAA-TTATATAAAAAATTAATATTAAAATTAATATCTAT
44739 AATATAATATTAAAATATTAATA
1 AATATAATATTAAAATATTAATA
44762 TTTAATTTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
60 2 0.03
62 5 0.07
63 31 0.42
64 16 0.22
65 3 0.04
66 2 0.03
67 6 0.08
68 1 0.01
69 8 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (59 bp):
AATATAATATTAAAATATTAATAATTATATAAAAAATTAATATTAAAATTAATATCTAT
Found at i:44728 original size:64 final size:65
Alignment explanation
Indices: 44659--44819 Score: 245
Period size: 64 Copynumber: 2.5 Consensus size: 65
44649 TTATATGATA
*
44659 TAAAATTAAATATCTATAATATAATATTAAAA-ATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAAGTAATAT
44723 TAAAATT-AATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAAGTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAAGTAATAT
* ** *
44787 TAAAATAAAAATAAAATATAATATAAAATTAAA
1 TAAAAT-TAAAT-ATCTATAATATAATATTAAA
44820 TATAAAACCT
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
63 24 0.27
64 44 0.50
66 3 0.03
67 17 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAAGTAATAT
Found at i:44759 original size:40 final size:38
Alignment explanation
Indices: 44662--44763 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 38
44652 TATGATATAA
*
44662 AATTAAATATCTATAATA-TAATATTAAAAATTAATATTT
1 AATT-AATAT-TAAAATATTAATATTAAAAATTAATATTT
* *
44701 AATTTAT-TTAAAAAATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAATATTAATATTAAAAATTAATAT-T-T
44739 AATATAATATTAAAATATTAATATT
1 AAT-TAATATTAAAATATTAATATT
44764 TAATTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
36 16 0.30
37 9 0.17
38 6 0.11
39 7 0.13
40 15 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (38 bp):
AATTAATATTAAAATATTAATATTAAAAATTAATATTT
Found at i:44802 original size:24 final size:24
Alignment explanation
Indices: 44781--44826 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
44771 TTTAAAAAAG
44781 TAATATTAAAA-TAAAAATAAAATA
1 TAATA-TAAAATTAAAAATAAAATA
*
44805 TAATATAAAATTAAATATAAAA
1 TAATATAAAATTAAAAATAAAA
44827 CCTCTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
TAATATAAAATTAAAAATAAAATA
Found at i:44814 original size:17 final size:16
Alignment explanation
Indices: 44790--44824 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
44780 GTAATATTAA
44790 AATAAAAATAAAATAT
1 AATAAAAATAAAATAT
*
44806 AATATAAAATTAAATAT
1 AATA-AAAATAAAATAT
44823 AA
1 AA
44825 AACCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATAAAATAT
Found at i:44821 original size:12 final size:11
Alignment explanation
Indices: 44782--44826 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
44772 TTAAAAAAGT
44782 AATATTAAAATA
1 AATA-TAAAATA
*
44794 AAAATAAAATA
1 AATATAAAATA
44805 TAATATAAAATTA
1 -AATATAAAA-TA
44818 AATATAAAA
1 AATATAAAA
44827 CCTCTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 7 0.24
12 20 0.69
13 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATAAAATA
Found at i:45430 original size:24 final size:27
Alignment explanation
Indices: 45378--45430 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
45368 AATTTTGGCA
*
45378 TTTTAATCATTATTTATTTATTTGGTT
1 TTTTAATCATTATTTATTTATTTGATT
*
45405 TTTTAAT-ATT-TTT-TTTATTTTATT
1 TTTTAATCATTATTTATTTATTTGATT
45429 TT
1 TT
45431 ATTTGGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 3 0.12
26 3 0.12
27 7 0.29
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTTAATCATTATTTATTTATTTGATT
Found at i:45440 original size:17 final size:17
Alignment explanation
Indices: 45390--45447 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
45380 TTAATCATTA
*
45390 TTTA-TTTATTTGGTTT
1 TTTATTTTATTTGGTAT
*
45406 TTTAATATTT-TTT-TTAT
1 TTT-AT-TTTATTTGGTAT
45423 TTTATTTTATTTGGTAT
1 TTTATTTTATTTGGTAT
45440 TTTATTTT
1 TTTATTTT
45448 GTTTCGTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 17 0.50
18 3 0.09
19 3 0.09
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTGGTAT
Found at i:45478 original size:12 final size:12
Alignment explanation
Indices: 45463--45493 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
45453 GTCATTTATT
45463 TATTTATTTTAA
1 TATTTATTTTAA
45475 TATTTATTTTAA
1 TATTTATTTTAA
*
45487 TTTTTAT
1 TATTTAT
45494 CTATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:45539 original size:17 final size:17
Alignment explanation
Indices: 45510--45555 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
45500 TTATCCATTT
45510 TATTTGTTTTATTATTA-
1 TATTT-TTTTATTATTAG
45527 TATTTTTTCTATTATTAG
1 TATTTTTT-TATTATTAG
45545 T-TTTTTTTATT
1 TATTTTTTTATT
45556 TTACAATCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.26
17 19 0.70
18 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (17 bp):
TATTTTTTTATTATTAG
Found at i:48623 original size:7 final size:7
Alignment explanation
Indices: 48611--48680 Score: 54
Period size: 7 Copynumber: 9.6 Consensus size: 7
48601 CAATCAGAAC
48611 AAAAAGA
1 AAAAAGA
48618 AAAAAGA
1 AAAAAGA
48625 AAAAAGA
1 AAAAAGA
48632 AGAAAA-A
1 A-AAAAGA
*
48639 AGCAAAGA
1 A-AAAAGA
* *
48647 GAAAATA
1 AAAAAGA
48654 AAAAAGA
1 AAAAAGA
48661 GAAACAA-A
1 -AAA-AAGA
48669 AACAAAGA
1 AA-AAAGA
48677 AAAA
1 AAAA
48681 GTGAAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 36 0.71
8 13 0.25
9 2 0.04
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:48651 original size:29 final size:29
Alignment explanation
Indices: 48613--48681 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
48603 ATCAGAACAA
*
48613 AAAGAAAAAAGAAAAAAGA-AGAA-AAAAGC
1 AAAG-AAAAAGAAAAAAGAGA-AACAAAAAC
*
48642 AAAGAGAAAATAAAAAAGAGAAACAAAAAC
1 AAAGA-AAAAGAAAAAAGAGAAACAAAAAC
48672 AAAGAAAAAG
1 AAAGAAAAAG
48682 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 22 0.65
30 11 0.32
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (29 bp):
AAAGAAAAAGAAAAAAGAGAAACAAAAAC
Found at i:50345 original size:37 final size:35
Alignment explanation
Indices: 50304--50528 Score: 218
Period size: 36 Copynumber: 6.2 Consensus size: 35
50294 ACAAGGGGTC
*
50304 GTCTCGCTTGAGACTAATTTACTC-AAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTAAAACAAA-TTTT
* *
50341 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
* * *
50377 GTCTCTCTTGAGACAGTTTCACTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
* * * * *
50413 ATCTCTATTGAGACAATTTCCCTTGAAATAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
* * *
50449 GTCTCTCTTGAGTCAGTTTCTCTTTAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
* * *
50485 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
50521 GTCTCTCT
1 GTCTCTCT
50529 CTTGAGACGG
Statistics
Matches: 167, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
35 3 0.02
36 144 0.86
37 20 0.12
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (35 bp):
GTCTCTCTTGAGACAATTTCTCTAAAACAAATTTT
Found at i:50384 original size:36 final size:36
Alignment explanation
Indices: 50329--50554 Score: 326
Period size: 36 Copynumber: 6.2 Consensus size: 36
50319 AATTTACTCA
*
50329 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
50366 AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
50402 AAACAAATTTTATCTCTATTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
50438 AAATAAATTTTGTCTCTCTTGAGTCAGTTTCTCTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
50474 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
50510 AAACAAATTTTGTCTCTCTCTTGAGACGGTTTCCCTCG
1 AAACAAATTTTG--TCTCTCTTGAGACAGTTTCCCTTG
50548 AAACAAA
1 AAACAAA
50555 GTATTTGAAT
Statistics
Matches: 169, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 133 0.79
37 7 0.04
38 29 0.17
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:50598 original size:21 final size:21
Alignment explanation
Indices: 50572--50613 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50562 AATATGTTTT
50572 CCTTGAAACAAATTTCGTCTC
1 CCTTGAAACAAATTTCGTCTC
* *
50593 CCTTGAGACAAATTTTGTCTC
1 CCTTGAAACAAATTTCGTCTC
50614 TCATGATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
CCTTGAAACAAATTTCGTCTC
Found at i:50650 original size:86 final size:87
Alignment explanation
Indices: 50503--50688 Score: 275
Period size: 86 Copynumber: 2.1 Consensus size: 87
50493 TGAGACAGTT
* * * *
50503 TCCCTTGAAACAAATTTTGTCTCTCTCTTGAGACGGTTTCCCTCGAAACAAAGTATTTGAATATG
1 TCCCTTGAGACAAATTTTG-CTCTCTCATGAGACAGTTTCCCTCGAAACAAAATATTTGAATATG
* *
50568 TTTTCCTTGAAACAAATTTCGTC
65 CTTTCCTTGAAACAAATTTCGTA
* * *
50591 TCCCTTGAGACAAATTTTG-TCTCTCATGATACAGTTTCCCTTGAAACAAAATCTTTGAATATGC
1 TCCCTTGAGACAAATTTTGCTCTCTCATGAGACAGTTTCCCTCGAAACAAAATATTTGAATATGC
50655 TTTCCTTGAAACAAATTTCGTA
66 TTTCCTTGAAACAAATTTCGTA
50677 TCCCTTGAGACA
1 TCCCTTGAGACA
50689 GTTTCTTTGG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 71 0.80
88 18 0.20
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (87 bp):
TCCCTTGAGACAAATTTTGCTCTCTCATGAGACAGTTTCCCTCGAAACAAAATATTTGAATATGC
TTTCCTTGAAACAAATTTCGTA
Found at i:50730 original size:21 final size:21
Alignment explanation
Indices: 50706--50783 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
50696 TGGAACTAAG
50706 TTTTGTCTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAAACAAA
*
50727 TTTTGTCTCTCTTGAGAC--A
1 TTTTGTCTCTCTTGAAACAAA
*
50746 -GTT-TC-C-CTTGAAACAAAA
1 TTTTGTCTCTCTTGAAAC-AAA
*
50764 TTTTGTCTCTCTTGAGACAA
1 TTTTGTCTCTCTTGAAACAA
50784 TTTCTCTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
15 7 0.16
16 1 0.02
17 2 0.04
18 3 0.07
19 3 0.07
20 2 0.04
21 20 0.44
22 7 0.16
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (21 bp):
TTTTGTCTCTCTTGAAACAAA
Found at i:50771 original size:37 final size:37
Alignment explanation
Indices: 50716--50797 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
50706 TTTTGTCTCT
*
50716 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCC
*
50752 CTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCT
1 CTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCC
50789 CTTGAAACA
1 CTTGAAACA
50798 CCAACCTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 8 0.19
37 35 0.81
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
CTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCC
Found at i:50891 original size:69 final size:67
Alignment explanation
Indices: 50746--50896 Score: 180
Period size: 67 Copynumber: 2.2 Consensus size: 67
50736 TCTTGAGACA
* ** * * *
50746 GTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACACCAACCTTTGAAT
1 GTTTCTCTTGAAACAAAATTTTACCTCTCTGGAGACAATTTCTATTGAAACACAAACCTTTGAAT
50811 AT
66 AT
* *
50813 GTTTCTCTTGAAACAAAATTTTACCTCTCTGGAGAC-TTTTTTATTGAAACACAAAAACCCTTTG
1 GTTTCTCTTGAAACAAAATTTTACCTCTCTGGAGACAATTTCTATTGAAACAC--AAA-CCTTTG
50877 AA-ATT
63 AATA-T
50882 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
50897 CAAAAAACCT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
66 13 0.18
67 32 0.44
68 3 0.04
69 24 0.33
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAATTTTACCTCTCTGGAGACAATTTCTATTGAAACACAAACCTTTGAAT
AT
Found at i:50896 original size:33 final size:32
Alignment explanation
Indices: 50856--50942 Score: 129
Period size: 33 Copynumber: 2.7 Consensus size: 32
50846 GACTTTTTTA
*
50856 TTGAAACACAAAAACCCTTTGAAATTGTTTCTC
1 TTGAAACACAAAAA-CCTTTGAAAATGTTTCTC
*
50889 TTGAAACACAAAAAACCTTTAAAAATGTTTCTC
1 TTGAAACAC-AAAAACCTTTGAAAATGTTTCTC
*
50922 TTGAAACACAAAGACCTTTGA
1 TTGAAACACAAAAACCTTTGA
50943 GTTCGACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 10 0.20
33 34 0.69
34 5 0.10
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (32 bp):
TTGAAACACAAAAACCTTTGAAAATGTTTCTC
Found at i:52702 original size:4 final size:4
Alignment explanation
Indices: 52689--52822 Score: 57
Period size: 4 Copynumber: 32.5 Consensus size: 4
52679 CATTTTGATC
* *
52689 ATTT -TTT ATTT ATTT ATTT ATTCT ATTT TTTT AATATT -TTT ATTT -TTGC
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT -AT-TT ATTT ATTT ATT-T
* * *
52738 ATTT -TCCTT -TTT -TTT ATTTT ATTTT GTTT CTTC ATTT ATTT ATTT
1 ATTT AT--TT ATTT ATTT A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT
* *
52783 ATTT CATTT A-AT ATTT ATTT ATTT TTTT ATCTCT ATTT AT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT AT-T-T ATTT AT
52823 CCATTTTATT
Statistics
Matches: 102, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
3 15 0.15
4 58 0.57
5 24 0.24
6 5 0.05
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:52822 original size:46 final size:46
Alignment explanation
Indices: 52750--52858 Score: 105
Period size: 47 Copynumber: 2.3 Consensus size: 46
52740 TTTCCTTTTT
* **
52750 TTTATTTTATTTTGTTTCTTCATTTATTTA-TTTATTTCATTTAATA
1 TTTA-TTTATTTTTTTTCTTCATTTATCCATTTTATTTCATTTAATA
** *
52796 TTTATTTATTTTTTTATC-TCTATTTATCCATTTTATTTTTTTTATTA
1 TTTATTTATTTTTTT-TCTTC-ATTTATCCATTTTATTTCATTTAATA
*
52843 TTATATTAATTTTTTT
1 TT-TATTTATTTTTTT
52859 CTATTATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
45 12 0.23
46 13 0.25
47 15 0.29
48 12 0.23
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (46 bp):
TTTATTTATTTTTTTTCTTCATTTATCCATTTTATTTCATTTAATA
Found at i:55378 original size:66 final size:66
Alignment explanation
Indices: 55296--55427 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
55286 CTTATTTAAT
55296 ATTTTTATATCATTTCTTTAATTGATAATTCGTTCTTTTTAATTTAAACGAAAAATCACGTAATG
1 ATTTTTATATCATTTCTTTAATTGATAATTCGTTCTTTTTAATTTAAACGAAAAATCACGTAATG
55361 A
66 A
55362 ATTTTTATATCATTTCTTTAATTGATAATTCGTTCTTTTTAATTTAAACGAAAAATCACGTAATG
1 ATTTTTATATCATTTCTTTAATTGATAATTCGTTCTTTTTAATTTAAACGAAAAATCACGTAATG
55427 A
66 A
55428 TTTATTCTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (66 bp):
ATTTTTATATCATTTCTTTAATTGATAATTCGTTCTTTTTAATTTAAACGAAAAATCACGTAATG
A
Found at i:56699 original size:41 final size:40
Alignment explanation
Indices: 56642--56835 Score: 117
Period size: 40 Copynumber: 4.8 Consensus size: 40
56632 AAATGGTAGT
* *
56642 TTTAGTGGTGTTTTTATAAAAACGCCGCGATAGGGTATCA-C
1 TTTAGTGGCGTTTTTATAAAAACGCCGCAATA-GGT-TCATC
* * *
56683 TTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTTCATC
1 TTTAGTGGCGTTTTTATAAAAACGCCGCAATAGGTTCATC
* ** * *
56723 TATAGTGGCGTTTTTCCAACAAACGACGCAAT-GTGAGT-AGTAC
1 TTTAGTGGCGTTTTTATAA-AAACGCCGCAATAG-G-TTCA-T-C
* *** *
56766 TTTAGCGGCGTTTCGGTACAAACGCCGCAATAGGTTCATC
1 TTTAGTGGCGTTTTTATAAAAACGCCGCAATAGGTTCATC
** * *
56806 CATAGTGGCATTTTTCA-ACAAACGCCGCAA
1 TTTAGTGGCGTTTTT-ATAAAAACGCCGCAA
56836 CATAATAGTA
Statistics
Matches: 115, Mismatches: 29, Indels: 19
0.71 0.18 0.12
Matches are distributed among these distances:
39 3 0.03
40 42 0.37
41 41 0.36
42 15 0.13
43 14 0.12
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTATAAAAACGCCGCAATAGGTTCATC
Found at i:56786 original size:83 final size:81
Alignment explanation
Indices: 56681--56859 Score: 241
Period size: 83 Copynumber: 2.2 Consensus size: 81
56671 ATAGGGTATC
** * * *
56681 ACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTTCATCTATAGTGGCGTTTTTCCAACAAA
1 ACTTTAGCGGCGTTTCGATACAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTT-CAACAAA
** *
56746 CGACGCAATGTGAGTAGT
65 CGACGCAACAT-AATAGT
*
56764 ACTTTAGCGGCGTTTCGGTACAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCAACAAAC
1 ACTTTAGCGGCGTTTCGATACAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCAACAAAC
*
56829 GCCGCAACATAATAGT
66 GACGCAACATAATAGT
*
56845 ACTTTAGTGGCGTTT
1 ACTTTAGCGGCGTTT
56860 GTAACTATAA
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 19 0.22
82 15 0.18
83 51 0.60
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (81 bp):
ACTTTAGCGGCGTTTCGATACAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCAACAAAC
GACGCAACATAATAGT
Found at i:56872 original size:83 final size:83
Alignment explanation
Indices: 56681--56881 Score: 232
Period size: 83 Copynumber: 2.4 Consensus size: 83
56671 ATAGGGTATC
* * * *
56681 ACTTTAGCGGCGTTTTTA-TACAAACTCCGCAATAGGTTCATCTATAGTGGCGTTTTTCCAACAA
1 ACTTTAGCGGCGTTTGTACTA-AAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCCAACAA
** *
56745 ACGACGCAATGTGAGTAGT
65 ACGACGCAACATGAATAGT
56764 ACTTTAGCGGCGTTTCGGTAC--AAACGCCGCAATAGGTTCATCCATAGTGGCATTTTT-CAACA
1 ACTTTAGCGGCGTTT--GTACTAAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCCAACA
*
56826 AACGCCGCAACAT-AATAGT
64 AACGACGCAACATGAATAGT
* *
56845 ACTTTAGTGGCGTTTGTAACTATAAACGCCGTAATAG
1 ACTTTAGCGGCGTTTGT-ACTA-AAACGCCGCAATAG
56882 TAGTACTTTA
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
79 2 0.02
80 2 0.02
81 19 0.19
82 15 0.15
83 61 0.60
85 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (83 bp):
ACTTTAGCGGCGTTTGTACTAAAACGCCGCAATAGGTTCATCCATAGTGGCATTTTTCCAACAAA
CGACGCAACATGAATAGT
Found at i:58460 original size:2 final size:2
Alignment explanation
Indices: 58453--58489 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
58443 AATAAAATTG
58453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58490 CTAATTCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62081 original size:43 final size:42
Alignment explanation
Indices: 62030--62297 Score: 231
Period size: 42 Copynumber: 6.2 Consensus size: 42
62020 ATGGTAATTA
* *
62030 GCGGCGTTTATATCCAAAAACGCTGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
62073 GCAGCGTTTGTGTCAAAAAACG-CGCTATATATCTAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
*
62115 GCGGCGTTTTTTTTCTCCAAAAAC-CCGCTATAGATCTTGACCTTTT
1 GCGGCG---TTTGT-TCCAAAAACGCCGCTATAGATC-TGACCTTTT
* * * * * *
62161 GTGGCGTTTGTATCTAACAACACCACTATATATCT-ACCCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGA-CCTTTT
* * *
62204 GCGGCGTTT-TTGCTAAAAACGTCGCTATATATCTCGACCTTTT
1 GCGGCGTTTGTT-CCAAAAACGCCGCTATAGATCT-GACCTTTT
**
62247 GC-GCGTTTGTTCCAAAAACGCCGCTATAGATCTTGAATTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
62289 GCGGCGTTT
1 GCGGCGTTT
62298 TTATATCACA
Statistics
Matches: 182, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 74 0.41
43 61 0.34
44 11 0.06
45 22 0.12
46 13 0.07
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:62213 original size:89 final size:88
Alignment explanation
Indices: 62042--62299 Score: 264
Period size: 88 Copynumber: 3.0 Consensus size: 88
62032 GGCGTTTATA
* * *
62042 TCCAAAAACGCTGCTATAGATCTGACCTTTTGCAGCGTTTGTGTCAAAAAACGCGCTATATATCT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCAGCGTTTGTATCAAAAAACGCACTATATATCT
62107 AACCTTTTGCGGCGTTTTTTTTC
66 AACCTTTTGCGGCGTTTTTTTTC
** *
62130 TCCAAAAAC-CCGCTATAGATCTTGACCTTTTGTGGCGTTTGTATCTAACAACAC-CACTATATA
1 TCCAAAAACGCCGCTATAGATC-TGACCTTTTGCAGCGTTTGTATC-AA-AAAACGCACTATATA
* *
62193 TCTACCCTTTTGCGGCG--TTTTTGC
63 TCTAACCTTTTGCGGCGTTTTTTTTC
* * * * *
62217 T--AAAAACGTCGCTATATATCTCGACCTTTTGC-GCGTTTGT-TCCAAAAACGCCGCTATAGAT
1 TCCAAAAACGCCGCTATAGATCT-GACCTTTTGCAGCGTTTGTATCAAAAAACG-CACTATATAT
*
62278 CTTGAA-TTTTTGCGGCGTTTTT
64 C-T-AACCTTTTGCGGCGTTTTT
62300 ATATCACAAA
Statistics
Matches: 142, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
82 4 0.03
83 1 0.01
84 11 0.08
85 26 0.18
86 20 0.14
87 21 0.15
88 29 0.20
89 26 0.18
90 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (88 bp):
TCCAAAAACGCCGCTATAGATCTGACCTTTTGCAGCGTTTGTATCAAAAAACGCACTATATATCT
AACCTTTTGCGGCGTTTTTTTTC
Found at i:66470 original size:14 final size:15
Alignment explanation
Indices: 66442--66470 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66432 CACATATACC
66442 CATAACTTCATATCA
1 CATAACTTCATATCA
66457 CATAACTT-ATATCA
1 CATAACTTCATATCA
66471 TTTCACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (15 bp):
CATAACTTCATATCA
Found at i:83071 original size:22 final size:23
Alignment explanation
Indices: 83046--83094 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
83036 CAGGATGAAT
*
83046 CGATACCCCC-TTGCAGGGGAAC
1 CGATACCCCCTTTGAAGGGGAAC
* *
83068 CGATTCCCCCTTTGAATGGGAAC
1 CGATACCCCCTTTGAAGGGGAAC
83091 CGAT
1 CGAT
83095 TTTCGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.20
Consensus pattern (23 bp):
CGATACCCCCTTTGAAGGGGAAC
Found at i:83586 original size:13 final size:13
Alignment explanation
Indices: 83563--83605 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
83553 CTATAAATAT
83563 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
83577 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
83590 -TTAGTTTTCAAA-
1 ATT-GTTTTCAAAC
83602 ATTG
1 ATTG
83606 CTCATTAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:86318 original size:20 final size:20
Alignment explanation
Indices: 86293--86330 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
86283 GAATGCTAGA
*
86293 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
86313 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
86331 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:86859 original size:19 final size:19
Alignment explanation
Indices: 86813--86849 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
86803 ATATATGAGT
86813 TGTG-TAAATATGTAGAAA
1 TGTGTTAAATATGTAGAAA
86831 TGTGTTAAATATGT-GAAA
1 TGTGTTAAATATGTAGAAA
86849 T
1 T
86850 AGTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (19 bp):
TGTGTTAAATATGTAGAAA
Found at i:87362 original size:30 final size:30
Alignment explanation
Indices: 87328--87430 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
87318 GGTTCTTCGG
*
87328 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
87358 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
87388 GACCTCTGGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
87418 GACCTCTGGATAG
1 GACCTCTGGATAG
87431 GTCCTTCGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:91369 original size:15 final size:15
Alignment explanation
Indices: 91338--91383 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
91328 AATTTATTTA
91338 TTTATTTTATATT-TT
1 TTTATTTTAT-TTCTT
91353 TTTATTTCT-TTTCTT
1 TTTATTT-TATTTCTT
*
91368 TTTCTTTTATTTCTT
1 TTTATTTTATTTCTT
91383 T
1 T
91384 GATTTACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.11
15 23 0.85
16 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTTATTTCTT
Found at i:91377 original size:20 final size:19
Alignment explanation
Indices: 91329--91383 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
91319 TTTTGAAATA
* *
91329 ATTTATTTATTTATTTTAT
1 ATTTTTTTATTTCTTTTAT
*
91348 ATTTTTTTATTTCTTTTCT
1 ATTTTTTTATTTCTTTTAT
*
91367 TTTTCTTTTATTTCTTT
1 ATTT-TTTTATTTCTTT
91384 GATTTACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTTTATTTCTTTTAT
Found at i:91453 original size:11 final size:11
Alignment explanation
Indices: 91437--91470 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
91427 TTTTTATGTT
91437 TTTATATTATA
1 TTTATATTATA
91448 TTTATATATATA
1 TTTATAT-TATA
91460 TTATATATTAT
1 TT-TATATTAT
91471 GTTTTTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 9 0.43
13 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTATATTATA
Found at i:92334 original size:17 final size:17
Alignment explanation
Indices: 92314--92346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
92304 CTCACCAACC
*
92314 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
92331 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
92347 ATCATTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:92990 original size:19 final size:19
Alignment explanation
Indices: 92956--93019 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
92946 ATTTAGACAT
92956 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
92974 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
92993 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
93012 TTTGCATT
1 TTTGCATT
93020 CACATTAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
18 10 0.22
19 35 0.78
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Done.