Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2090020 original size:3 final size:3
Alignment explanation
Indices: 2090012--2090058 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
2090002 TATTTCTTGT
2090012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2090059 AGTTACTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2091580 original size:18 final size:18
Alignment explanation
Indices: 2091535--2091580 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2091525 GTTTGATATC
*
2091535 GTTTAAGTTAAGTCTCAG
1 GTTTAAGTTCAGTCTCAG
2091553 GTTTAAGTTCAGTCTCAG
1 GTTTAAGTTCAGTCTCAG
2091571 GTTTAAGTTC
1 GTTTAAGTTC
2091581 TTGTGTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (18 bp):
GTTTAAGTTCAGTCTCAG
Found at i:2097464 original size:22 final size:22
Alignment explanation
Indices: 2097438--2097499 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
2097428 AGACAAGCTG
*
2097438 TTAATATCAGGAGTTATATGAT
1 TTAATTTCAGGAGTTATATGAT
* *
2097460 TTAATTTCAGGAGTTACATTAT
1 TTAATTTCAGGAGTTATATGAT
*
2097482 ATAATTTCAGGAGTTATA
1 TTAATTTCAGGAGTTATA
2097500 ACAGCTGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
TTAATTTCAGGAGTTATATGAT
Found at i:2098985 original size:3 final size:3
Alignment explanation
Indices: 2098977--2099001 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2098967 TTGTCAACTC
2098977 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2099002 TGGCAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2099576 original size:20 final size:21
Alignment explanation
Indices: 2099534--2099576 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2099524 TAATATTTTT
* *
2099534 TATATTTTAATAACTAAATAA
1 TATATTTTAATAAATAAAAAA
2099555 TATATTTTAA-AAATAAAAAA
1 TATATTTTAATAAATAAAAAA
2099575 TA
1 TA
2099577 GAACTCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATTTTAATAAATAAAAAA
Found at i:2101167 original size:19 final size:19
Alignment explanation
Indices: 2101143--2101190 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
2101133 GCAATTTGGG
2101143 TATCGATACCCAGACTTGT
1 TATCGATACCCAGACTTGT
2101162 TATCGATACCCAGACTTGT
1 TATCGATACCCAGACTTGT
2101181 TATCGATACC
1 TATCGATACC
2101191 ACAACTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (19 bp):
TATCGATACCCAGACTTGT
Found at i:2105516 original size:30 final size:31
Alignment explanation
Indices: 2105473--2105542 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
2105463 ACAAGCCTTA
* *
2105473 AGAAAA-TTTGGGGACC-ATTTTGTAATTTT
1 AGAAAAGTTAGGGGACCAATTTAGTAATTTT
*
2105502 TGAAAAGTTAGGGGACCAATTTAGTAATTTT
1 AGAAAAGTTAGGGGACCAATTTAGTAATTTT
*
2105533 AAAAAAGTTA
1 AGAAAAGTTA
2105543 TAAATAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 9 0.26
31 20 0.59
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.36
Consensus pattern (31 bp):
AGAAAAGTTAGGGGACCAATTTAGTAATTTT
Found at i:2113647 original size:23 final size:23
Alignment explanation
Indices: 2113621--2113688 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2113611 ATTATTATAT
2113621 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
2113644 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
2113667 GGTACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2113689 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2113739 original size:16 final size:17
Alignment explanation
Indices: 2113718--2113751 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2113708 GTGCACAACC
2113718 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
2113734 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
2113751 T
1 T
2113752 GTTCATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:2114996 original size:19 final size:19
Alignment explanation
Indices: 2114951--2115014 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 19
2114941 ACCCTCATGA
2114951 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--T--AG
2114974 GGGAACCGATTCCCCCTAG
1 GGGAACCGATTCCCCCTAG
* *
2114993 GGGAATCGATACCCCCCTAG
1 GGGAACCGAT-TCCCCCTAG
2115013 GG
1 GG
2115015 TTTTGGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 11 0.29
20 10 0.26
21 1 0.03
23 16 0.42
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (19 bp):
GGGAACCGATTCCCCCTAG
Found at i:2115010 original size:20 final size:19
Alignment explanation
Indices: 2114972--2115014 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2114962 CCCCCTTTGA
*
2114972 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
2114991 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
2115011 AGGG
1 AGGG
2115015 TTTTGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:2137787 original size:21 final size:22
Alignment explanation
Indices: 2137744--2137801 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
2137734 AAAACAATGA
**
2137744 AGGGATCGAT-CTTTTCTTTCG
1 AGGGATCGATCCTTTTCTCCCG
2137765 AGGGATCGATCCTTTTC-CCCG
1 AGGGATCGATCCTTTTCTCCCG
**
2137786 AGGGATTTATCCTTTT
1 AGGGATCGATCCTTTT
2137802 GAAAAAGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (22 bp):
AGGGATCGATCCTTTTCTCCCG
Found at i:2138681 original size:37 final size:37
Alignment explanation
Indices: 2138628--2138732 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2138618 TGTTTTCGTC
2138628 CTACTAGGATTCAAACTCCTAAAAATAGGATACAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATACAATT
* * * *
2138665 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATACAATT
* * * *
2138702 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2138733 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATACAATT
Found at i:2139920 original size:105 final size:105
Alignment explanation
Indices: 2139615--2140381 Score: 1130
Period size: 105 Copynumber: 7.3 Consensus size: 105
2139605 GCATTGTTCC
* * * ** * *
2139615 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * * * *
2139680 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2139721 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
2139781 CAGCGGTCCCTTCGTCGTGGAGTTAAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2139821 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2139886 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2139926 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2139991 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2140031 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2140096 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2140136 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
2140201 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2140241 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * * *
2140306 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2140347 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2140382 CGCATATGGC
Statistics
Matches: 610, Mismatches: 42, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
100 81 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 407 0.67
106 85 0.14
107 3 0.00
109 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2141125 original size:22 final size:22
Alignment explanation
Indices: 2141099--2141168 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
2141089 TTATGTTTGG
2141099 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2141121 TCAAAGGTTTGGAATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2141143 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2141165 TCAA
1 TCAA
2141169 CGATTTGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2141818 original size:21 final size:21
Alignment explanation
Indices: 2141794--2141856 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2141784 TTCTTTTTGA
2141794 TTTTTGTTCTTTCTTTTTTTC
1 TTTTTGTTCTTTCTTTTTTTC
2141815 -TTTTGTTTCTTT-TTTTTCTTC
1 TTTTTG-TTCTTTCTTTTT-TTC
**
2141836 TTTTACTTCTTTTCTTTTTTT
1 TTTTTGTTC-TTTCTTTTTTT
2141857 TCTTGATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 10 0.29
21 12 0.34
22 8 0.23
23 5 0.14
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.81
Consensus pattern (21 bp):
TTTTTGTTCTTTCTTTTTTTC
Found at i:2141825 original size:9 final size:8
Alignment explanation
Indices: 2141803--2141856 Score: 63
Period size: 8 Copynumber: 6.4 Consensus size: 8
2141793 ATTTTTGTTC
2141803 TTTCTTTT
1 TTTCTTTT
2141811 TTTCTTTT
1 TTTCTTTT
2141819 GTTTCTTTTT
1 -TTTC-TTTT
2141829 TTTCTTCTT
1 TTTCTT-TT
* *
2141838 TTACTTCT
1 TTTCTTTT
2141846 TTTCTTTT
1 TTTCTTTT
2141854 TTT
1 TTT
2141857 TCTTGATTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 20 0.51
9 15 0.38
10 4 0.10
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTCTTTT
Found at i:2141825 original size:17 final size:16
Alignment explanation
Indices: 2141803--2141856 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
2141793 ATTTTTGTTC
2141803 TTTCTTTTTTTCTTTT
1 TTTCTTTTTTTCTTTT
2141819 GTTTCTTTTTTTTCTTCTT
1 -TTTC-TTTTTTTCTT-TT
* *
2141838 TTACTTCTTTTCTTTT
1 TTTCTTTTTTTCTTTT
2141854 TTT
1 TTT
2141857 TCTTGATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.12
17 13 0.41
18 13 0.41
19 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTT
Found at i:2141832 original size:26 final size:27
Alignment explanation
Indices: 2141780--2141860 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
2141770 CTTTTTGTCC
*
2141780 CTTTTTCTTTTTGATTT-TTGTTCTTTCTT
1 CTTTTTC-TTTTG-TTTCTT-TTTTTTCTT
2141809 -TTTTTCTTTTGTTTCTTTTTTTTCTT
1 CTTTTTCTTTTGTTTCTTTTTTTTCTT
* *
2141835 CTTTTACTTCT-TTTCTTTTTTTTCTT
1 CTTTTTCTTTTGTTTCTTTTTTTTCTT
2141861 GATTGGATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 26 0.55
27 15 0.32
28 6 0.13
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (27 bp):
CTTTTTCTTTTGTTTCTTTTTTTTCTT
Found at i:2141857 original size:9 final size:9
Alignment explanation
Indices: 2141781--2141860 Score: 67
Period size: 9 Copynumber: 8.9 Consensus size: 9
2141771 TTTTTGTCCC
2141781 TTTTTCTTT
1 TTTTTCTTT
2141790 TTGATTT-TTGT
1 TT--TTTCTT-T
*
2141801 TCTTTC-TT
1 TTTTTCTTT
2141809 TTTTTCTTT
1 TTTTTCTTT
*
2141818 TGTTTCTTT
1 TTTTTCTTT
*
2141827 TTTTTCTTC
1 TTTTTCTTT
*
2141836 TTTTAC-TT
1 TTTTTCTTT
*
2141844 CTTTTCTTT
1 TTTTTCTTT
2141853 TTTTTCTT
1 TTTTTCTT
2141861 GATTGGATCT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 11 0.20
9 37 0.67
10 2 0.04
11 5 0.09
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2144888 original size:37 final size:37
Alignment explanation
Indices: 2144838--2144942 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2144828 GTGCTTGTGG
* * * *
2144838 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
2144875 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTGT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
2144912 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
2144943 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2145793 original size:17 final size:17
Alignment explanation
Indices: 2145771--2145805 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2145761 TCAAAGTAGG
2145771 CTTAACTAGCTTCATAT
1 CTTAACTAGCTTCATAT
*
2145788 CTTAACTAGCTTCTTAT
1 CTTAACTAGCTTCATAT
2145805 C
1 C
2145806 ACTAAGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (17 bp):
CTTAACTAGCTTCATAT
Found at i:2146603 original size:16 final size:16
Alignment explanation
Indices: 2146579--2146616 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2146569 TTCTTCATAA
*
2146579 TTTTTTTTATTTCT-T
1 TTTTTTTTATTACTAT
2146594 TTTTTATTTATTACTAT
1 TTTTT-TTTATTACTAT
2146611 TTTTTT
1 TTTTTT
2146617 AATACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTTATTACTAT
Found at i:2146655 original size:27 final size:24
Alignment explanation
Indices: 2146600--2146655 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
2146590 TCTTTTTTTA
2146600 TTTATTACTATTTTTTTAATACTT
1 TTTATTACTATTTTTTTAATACTT
* *
2146624 ATTATTACTATTATTTTTTATACATT
1 TTTATTACTATT-TTTTTAATAC-TT
2146650 GTTTAT
1 -TTTAT
2146656 AAGTTTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 11 0.42
25 9 0.35
26 2 0.08
27 4 0.15
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTATTACTATTTTTTTAATACTT
Found at i:2147002 original size:22 final size:22
Alignment explanation
Indices: 2146927--2147008 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
2146917 TTTTACTTCT
*
2146927 TTTATTTTCTTATTTTTTATCTTA
1 TTTATTTTCTT-TGTTTTAT-TTA
* * *
2146951 TTT-TGTTTATTCGTGTTATTTA
1 TTTAT-TTTCTTTGTTTTATTTA
* *
2146973 TGTGTTTTCTTTGTTTTATTTA
1 TTTATTTTCTTTGTTTTATTTA
*
2146995 TTTATTTTCATTGT
1 TTTATTTTCTTTGT
2147009 CTTTTTCCTC
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
22 30 0.67
23 7 0.16
24 8 0.18
ACGTcount: A:0.13, C:0.06, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTATTTTCTTTGTTTTATTTA
Found at i:2151640 original size:21 final size:21
Alignment explanation
Indices: 2151614--2151653 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2151604 CCGAAGTACC
*
2151614 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
2151635 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
2151654 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:2155561 original size:21 final size:21
Alignment explanation
Indices: 2155536--2155575 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2155526 CTCATTTCTT
2155536 TCGAGGGA-CTGATCCTTTTCC
1 TCGAGGGATC-GATCCTTTTCC
2155557 TCGAGGGATCGATCCTTTT
1 TCGAGGGATCGATCCTTTT
2155576 GAAAAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGAGGGATCGATCCTTTTCC
Found at i:2155585 original size:20 final size:20
Alignment explanation
Indices: 2155560--2155631 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
2155550 CTTTTCCTCG
2155560 AGGGATCGATCCTTTTGAAA
1 AGGGATCGATCCTTTTGAAA
** ** *
2155580 AGGGATTAATCCTTTCTCCAG
1 AGGGATCGATCCTTT-TGAAA
2155601 AGGGATCGATCCTTTTGAAA
1 AGGGATCGATCCTTTTGAAA
2155621 AGGGATCGATC
1 AGGGATCGATC
2155632 ATTTCATTTG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (20 bp):
AGGGATCGATCCTTTTGAAA
Found at i:2157186 original size:2 final size:2
Alignment explanation
Indices: 2157179--2157244 Score: 102
Period size: 2 Copynumber: 34.0 Consensus size: 2
2157169 CGTAAACTAC
2157179 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2157219 AT -T AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT
2157245 TCGTTTTGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.05
2 55 0.92
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2161225 original size:17 final size:18
Alignment explanation
Indices: 2161198--2161240 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
2161188 AAAATCTCAA
2161198 AAAAATGACATTCTTTTG
1 AAAAATGACATTCTTTTG
2161216 AAAAAT-ACATTCTTTTG
1 AAAAATGACATTCTTTTG
*
2161233 AATAATGA
1 AAAAATGA
2161241 TGATTATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (18 bp):
AAAAATGACATTCTTTTG
Found at i:2164881 original size:163 final size:163
Alignment explanation
Indices: 2164606--2164919 Score: 612
Period size: 163 Copynumber: 1.9 Consensus size: 163
2164596 AGCTACTGGG
2164606 CCAGCTACTAGGAAACCTGAAATGGAACACTCATCCCACCAGATCTGGTTTTTGTTCCGTTAGGC
1 CCAGCTACTAGGAAACCTGAAATGGAACACTCATCCCACCAGATCTGGTTTTTGTTCCGTTAGGC
2164671 ATGAATGAACCAGACAAGGACAGTATCTAAAATAGACCCTCCAAGAAATTTGAGAAGAAATGAGA
66 ATGAATGAACCAGACAAGGACAGTATCTAAAATAGACCCTCCAAGAAATTTGAGAAGAAATGAGA
2164736 TGTTTGCTGACGAAACAATCTGCTACTGGGAGA
131 TGTTTGCTGACGAAACAATCTGCTACTGGGAGA
2164769 CCAGCTACTAGGAAACCTGAAAATGGAACACTCATCCCACCAGATCTGGTTTTTGTTCCGTTAGG
1 CCAGCTACTAGGAAACCTG-AAATGGAACACTCATCCCACCAGATCTGGTTTTTGTTCCGTTAGG
2164834 CATGAATGAACCAGACAAGGACAGTA-CTAAAATAGACCCTCCAAGAAATTTGAGAAGAAATGAG
65 CATGAATGAACCAGACAAGGACAGTATCTAAAATAGACCCTCCAAGAAATTTGAGAAGAAATGAG
2164898 ATGTTTGCTGACGAAACAATCT
130 ATGTTTGCTGACGAAACAATCT
2164920 AAACTGCAAA
Statistics
Matches: 150, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 79 0.53
164 71 0.47
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (163 bp):
CCAGCTACTAGGAAACCTGAAATGGAACACTCATCCCACCAGATCTGGTTTTTGTTCCGTTAGGC
ATGAATGAACCAGACAAGGACAGTATCTAAAATAGACCCTCCAAGAAATTTGAGAAGAAATGAGA
TGTTTGCTGACGAAACAATCTGCTACTGGGAGA
Found at i:2178959 original size:28 final size:28
Alignment explanation
Indices: 2178921--2178988 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
2178911 GGATTAGGAG
*
2178921 AGAAGAAGAAGGGGTCAATGGGAGTTGA
1 AGAAGAAGAAGGGGTCAATGGGAGTTAA
2178949 AGAAGAAGAAGGGGTCAATGGGAGTTAA
1 AGAAGAAGAAGGGGTCAATGGGAGTTAA
2178977 AGAAGAAAGAAG
1 AGAAG-AAGAAG
2178989 AAGGGTTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 32 0.84
29 6 0.16
ACGTcount: A:0.46, C:0.03, G:0.40, T:0.12
Consensus pattern (28 bp):
AGAAGAAGAAGGGGTCAATGGGAGTTAA
Found at i:2184738 original size:73 final size:73
Alignment explanation
Indices: 2184598--2184743 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
2184588 AAATTTATCA
*
2184598 ATACATATATTTAAACCATCAAAATCAACATTTTCAACAATTATTTTAATTTTTTTAGCATTATC
1 ATACATATATTTAAACCATCAAAATCAACATTTTCAACAATTATTTTAATTTTTTAAGCATTATC
2184663 TACAATTC
66 TACAATTC
* * *
2184671 ATACATATATTTAAACCATCGAAATCAACATTTTCAACAATTATTTTAATTTTTTCAATC-TTCT
1 ATACATATATTTAAACCATCAAAATCAACATTTTCAACAATTATTTTAATTTTTT-AAGCATTAT
2184735 CTACAATTC
65 CTACAATTC
2184744 GTTTACTACG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 66 0.97
74 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.42
Consensus pattern (73 bp):
ATACATATATTTAAACCATCAAAATCAACATTTTCAACAATTATTTTAATTTTTTAAGCATTATC
TACAATTC
Found at i:2186990 original size:30 final size:30
Alignment explanation
Indices: 2186951--2187016 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2186941 TTAGAAAATC
2186951 ATTTGGAAAATCTTAAAATCCATTTAACTTA
1 ATTT-GAAAATCTTAAAATCCATTTAACTTA
2186982 ATTTGAAAATCTTAAAATCCATTTAACTTA
1 ATTTGAAAATCTTAAAATCCATTTAACTTA
2187012 ATTTG
1 ATTTG
2187017 TTATATCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTTGAAAATCTTAAAATCCATTTAACTTA
Found at i:2189432 original size:21 final size:21
Alignment explanation
Indices: 2189406--2189445 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2189396 CAGAACCCCA
*
2189406 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2189427 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2189446 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2189474 original size:19 final size:20
Alignment explanation
Indices: 2189428--2189487 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
2189418 TTCCCCTGTG
2189428 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
2189451 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
2189470 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2189488 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:2193333 original size:22 final size:21
Alignment explanation
Indices: 2193291--2193330 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2193281 GAGTTTGTTT
*
2193291 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2193312 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2193331 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2195575 original size:30 final size:30
Alignment explanation
Indices: 2195536--2195601 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2195526 TTAGAAAATC
2195536 ATTTGGAAAATCTTAAAATCCATTTAACTTA
1 ATTT-GAAAATCTTAAAATCCATTTAACTTA
2195567 ATTTGAAAATCTTAAAATCCATTTAACTTA
1 ATTTGAAAATCTTAAAATCCATTTAACTTA
2195597 ATTTG
1 ATTTG
2195602 TTATATCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTTGAAAATCTTAAAATCCATTTAACTTA
Found at i:2195962 original size:70 final size:70
Alignment explanation
Indices: 2195844--2196013 Score: 295
Period size: 70 Copynumber: 2.4 Consensus size: 70
2195834 AGTCAATTGG
*
2195844 GATGCTCTTCTATGTTTCTTAGCCATGTGAGATTGTTTTGTTTTCATATTTTTACTCTTTAGACT
1 GATGCTCTTCTATGTTTCTTAGCCATGTGAGATTGTTTTGTTTTCATATTTTTACTCTTTAAACT
2195909 TTTGT
66 TTTGT
*
2195914 GATGTTCTTCTATGTTTCTTAGCCATGTGAGATTGTTTTGTTTTCATATTTTTACTCTTTAAACT
1 GATGCTCTTCTATGTTTCTTAGCCATGTGAGATTGTTTTGTTTTCATATTTTTACTCTTTAAACT
2195979 TTTGT
66 TTTGT
* * *
2195984 AATGCTATTCTATGTTTCTTAGCTATGTGA
1 GATGCTCTTCTATGTTTCTTAGCCATGTGA
2196014 TTTTTTTAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 94 1.00
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.54
Consensus pattern (70 bp):
GATGCTCTTCTATGTTTCTTAGCCATGTGAGATTGTTTTGTTTTCATATTTTTACTCTTTAAACT
TTTGT
Found at i:2196270 original size:23 final size:21
Alignment explanation
Indices: 2196236--2196278 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2196226 ATATAAAAAA
2196236 TTATTTTTTATTAAATGTTTTT
1 TTATTTTTTATTAAAT-TTTTT
*
2196258 TTATATTTTTATTTAATTTTT
1 TTAT-TTTTTATTAAATTTTT
2196279 AAATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATTTTTTATTAAATTTTTT
Found at i:2201948 original size:19 final size:19
Alignment explanation
Indices: 2201908--2201949 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2201898 ATATTTTGCC
*
2201908 ATTTTAAATAAAAATAATA
1 ATTTTAAATAAAAATAAAA
*
2201927 ATTTT-AATGAAAATGAAAA
1 ATTTTAAATAAAAAT-AAAA
2201946 ATTT
1 ATTT
2201950 GTGGTCTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTTTAAATAAAAATAAAA
Found at i:2202586 original size:2 final size:2
Alignment explanation
Indices: 2202579--2202605 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2202569 CTATATTTAC
2202579 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2202606 AATTATGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2203380 original size:22 final size:22
Alignment explanation
Indices: 2203355--2203403 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2203345 ACAAACCCCT
* *
2203355 AAAACTAACCCCAAAATAACAC
1 AAAAATAAACCCAAAATAACAC
* *
2203377 AAAAATAAATCCGAAATAACAC
1 AAAAATAAACCCAAAATAACAC
2203399 AAAAA
1 AAAAA
2203404 CAGGATACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.65, C:0.22, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAATAAACCCAAAATAACAC
Done.