Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003862.1 Kokia drynarioides strain JFW-HI SEQ_116893, 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: 86125
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:3169 original size:16 final size:16
Alignment explanation
Indices: 3148--3185 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3138 TTGAATCGAG
*
3148 TCGAATAAGATAGAAT
1 TCGAATAAAATAGAAT
*
3164 TCGAATAAAATCGAAT
1 TCGAATAAAATAGAAT
3180 T-GAATA
1 TCGAATA
3186 TATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (16 bp):
TCGAATAAAATAGAAT
Found at i:6097 original size:59 final size:59
Alignment explanation
Indices: 6026--6156 Score: 262
Period size: 59 Copynumber: 2.2 Consensus size: 59
6016 CTTCAGGCAA
6026 TTCATGTTAATTTATTACGTTGTTTTCATCGTATAGAACTTTCCTTGTGGAAGGGAAGG
1 TTCATGTTAATTTATTACGTTGTTTTCATCGTATAGAACTTTCCTTGTGGAAGGGAAGG
6085 TTCATGTTAATTTATTACGTTGTTTTCATCGTATAGAACTTTCCTTGTGGAAGGGAAGG
1 TTCATGTTAATTTATTACGTTGTTTTCATCGTATAGAACTTTCCTTGTGGAAGGGAAGG
6144 TTCATGTTAATTT
1 TTCATGTTAATTT
6157 CCTATTCCAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (59 bp):
TTCATGTTAATTTATTACGTTGTTTTCATCGTATAGAACTTTCCTTGTGGAAGGGAAGG
Found at i:11223 original size:20 final size:20
Alignment explanation
Indices: 11179--11225 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
11169 TCCAATTTTT
* *
11179 TATTTTTTTATTAATATATG
1 TATTTTATTATTAATATATA
11199 T-TTTTATT-TTAATATATTA
1 TATTTTATTATTAATATA-TA
11218 TATTTTAT
1 TATTTTAT
11226 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTATTATTAATATATA
Found at i:14209 original size:54 final size:54
Alignment explanation
Indices: 14125--14229 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
14115 ACAAGGACAC
* *
14125 ACCTAGGCCAAAAATCAAACCAGAAACTCCAACAATTAGCCCCACCACTAACAA
1 ACCTAGGCCAAAAACCAAACCACAAACTCCAACAATTAGCCCCACCACTAACAA
* * *
14179 ACCTAGGCTAAGAACCAAACCACAAGCTCCAACAATTAGCCCCACCACTAA
1 ACCTAGGCCAAAAACCAAACCACAAACTCCAACAATTAGCCCCACCACTAA
14230 TCCTCTAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (54 bp):
ACCTAGGCCAAAAACCAAACCACAAACTCCAACAATTAGCCCCACCACTAACAA
Found at i:16714 original size:19 final size:19
Alignment explanation
Indices: 16675--16734 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
16665 TCAAAAAAAA
*
16675 TATTAAAAATTATATAAGAAT
1 TATT-AAAATTTTA-AAGAAT
16696 TATTAAAATTTTAAAGAAT
1 TATTAAAATTTTAAAGAAT
16715 T-TATAAAATTATTAAA-AAT
1 TAT-TAAAATT-TTAAAGAAT
16734 T
1 T
16735 TTGAAATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 13 0.36
21 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TATTAAAATTTTAAAGAAT
Found at i:16719 original size:29 final size:29
Alignment explanation
Indices: 16670--16736 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
16660 AATTATCAAA
*
16670 AAAAATATTAAAAATTATATAAGAATTATT
1 AAAAATTTTAAAAATTATATAA-AATTATT
16700 -AAAATTTTAAAGAATT-TATAAAATTATT
1 AAAAATTTTAAA-AATTATATAAAATTATT
16728 AAAAATTTT
1 AAAAATTTT
16737 GAAATAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.21
29 23 0.68
30 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAAATTTTAAAAATTATATAAAATTATT
Found at i:16735 original size:19 final size:19
Alignment explanation
Indices: 16670--16735 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
16660 AATTATCAAA
16670 AAAAATATTA-AAAATTATAT
1 AAAAAT-TTATAAAATTAT-T
*
16690 AAGAA-TTATTAAAATT-TT
1 AAAAATTTA-TAAAATTATT
16708 AAAGAATTTATAAAATTATT
1 AAA-AATTTATAAAATTATT
16728 AAAAATTT
1 AAAAATTT
16736 TGAAATAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.15
19 15 0.38
20 18 0.46
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATTTATAAAATTATT
Found at i:16752 original size:28 final size:28
Alignment explanation
Indices: 16689--16756 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
16679 AAAAATTATA
*
16689 TAAGAATTATT-AAAATTTTAAAGAATT
1 TAAGAATTATTAAAAATTTTAAAGAATG
* *
16716 TATAAAATTATTAAAAATTTTGAAATAA-G
1 TA-AGAATTATTAAAAATTTT-AAAGAATG
16745 TAAGAATTATTA
1 TAAGAATTATTA
16757 TATTTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.06
28 17 0.50
29 10 0.29
30 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
TAAGAATTATTAAAAATTTTAAAGAATG
Found at i:16767 original size:8 final size:8
Alignment explanation
Indices: 16754--16787 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16744 GTAAGAATTA
16754 TTATATTT
1 TTATATTT
16762 TTATATTT
1 TTATATTT
*
16770 TTATAATT
1 TTATATTT
*
16778 CTATATTT
1 TTATATTT
16786 TT
1 TT
16788 TATAAGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATATTT
Found at i:21251 original size:136 final size:133
Alignment explanation
Indices: 20927--21609 Score: 697
Period size: 136 Copynumber: 5.1 Consensus size: 133
20917 AGATATCCTT
* * *
20927 TCTTTGTCATGAGTGGTTTA-CTTTTGAGA-TTAGGATCCCATTCAT-TACT-TTCTGAATTTCA
1 TCTTTGTCATGAGTGGTTTACCTTTT-AGATTTAGGAT-CCATCCATGTACTCTT-TGAGTTACA
** * * *
20988 GATATGATCATATGAATCACATGGAGTCCG-TTTTATCCATTTGACTTATATGTTGTGTCTCTCT
63 GATATGATCATACAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATG--GTGTCTCTC-
21052 TTCCC-AAA
125 TTCCCTAAA
* * *
21060 TCTTTTGTCAGGAGTAGTTTACCTTTTAGATTTAGGATCC--CAATGATTACTCTTTGAGTTACA
1 TC-TTTGTCATGAGTGGTTTACCTTTTAGATTTAGGATCCATCCATG--TACTCTTTGAGTTACA
* * *
21123 GATATGATCATACAAATTGCATGGAGTTCGCTTTTTTCCATTTGGCTTATATGGTGCCTCTCTTC
63 GATATGATCATACAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTC
21188 CCTAAA
128 CCTAAA
* * *
21194 TCTTTGTCTTGAGTGGTTTATCTTTTAGATTTAGGATCCATCCGATGATCACTCTTTGAGTTATA
1 TCTTTGTCATGAGTGGTTTACCTTTTAGATTTAGGATCCATCC-ATG-T-ACTCTTTGAGTTACA
* *
21259 GATATGATCATACGAAA-CTCATGGAGTCTGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTT
63 GATATGATCATAC-AAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTT
21323 CCCTAAA
127 CCCTAAA
* * * * * *
21330 TCTTTGTCTTGAGTGGTTTATCTTTTAGATTTAGGATCCATTCAT-TGCT-TTCTGAATTACGGA
1 TCTTTGTCATGAGTGGTTTACCTTTTAGATTTAGGATCCATCCATGTACTCTT-TGAGTTACAGA
** * * * * *
21393 TACAATCACACGAATGGCATGGA-------TTTATCCATTTGACTTATATGTTGTGTCTCTCTTC
65 TATGATCATACAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATG--GTGTCTCTCTTC
*
21451 CCCAAA
128 CCTAAA
* * * *
21457 TCTTTTGTCACGAATGGTTTACCTTTTAGATTTAGGATCC--CAATGGTCACTCTCTGAGTTACA
1 TC-TTTGTCATGAGTGGTTTACCTTTTAGATTTAGGATCCATCCAT-GT-ACTCTTTGAGTTACA
*
21520 GATATGATCATGCAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTC
63 GATATGATCATACAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTC
21585 CCTAAA
128 CCTAAA
21591 TCTTTGTC-TCGAGTGGTTT
1 TCTTTGTCAT-GAGTGGTTT
21610 TAGATTTAGG
Statistics
Matches: 458, Mismatches: 61, Indels: 62
0.79 0.10 0.11
Matches are distributed among these distances:
125 19 0.04
126 2 0.00
127 19 0.04
128 34 0.07
129 28 0.06
130 1 0.00
131 4 0.01
132 26 0.06
133 55 0.12
134 53 0.12
135 52 0.11
136 162 0.35
137 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (133 bp):
TCTTTGTCATGAGTGGTTTACCTTTTAGATTTAGGATCCATCCATGTACTCTTTGAGTTACAGAT
ATGATCATACAAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTCCCT
AAA
Found at i:21517 original size:261 final size:259
Alignment explanation
Indices: 20927--21772 Score: 818
Period size: 261 Copynumber: 3.3 Consensus size: 259
20917 AGATATCCTT
* * * * * *
20927 TCTTTGTCATGAGTGGTTTA-CTTTTGAGA-TTAGGATCCCATTCATTACTTTCTGAATT-TCAG
1 TCTTTGTCACGAGTGGTTTACCTTTT-AGATTTAGGATCCCAATGATCACTCTCTGAGTTAT-AG
* * * *
20989 ATATGATCATATGAATCACATGGAGTCCG-TTTTATCCATTTGACTTATATGTTGTGTCTCTCTT
64 ATATGATCATACGAAACACATGGAGTCCGCTTTTTTCCATTTGGCTTATATG--GTGTCTCTC-T
** * * *
21053 TCCC-AAATCTTTTGTCAGGAGTAGTTTACCTTTTAGATTTAGGATCCCAATGATTACTCTT-TG
126 TCCCTAAATC-TTTGTCTCGAGTGGTTTA-CTTTTAGATTTAGGAT-CCATTCATTACT-TTCTG
* * * * * * *
21116 AGTTACAGATATGATCATACAAATTGCATGGAGTTCGCTTTTTTCCATTTGGCTTATATG--GTG
187 AATTACGGATACGATCACACAAATAGCATGGA-------TTTATCCATTTGACTTATATGTTGTG
* *
21179 CCTCTCTTCCCTAAA
245 TCTCTCTTCCCCAAA
** * * *
21194 TCTTTGTCTTGAGTGGTTTATCTTTTAGATTTAGGATCCATCCGATGATCACTCTTTGAGTTATA
1 TCTTTGTCACGAGTGGTTTACCTTTTAGATTTAGGAT-C--CCAATGATCACTCTCTGAGTTATA
* *
21259 GATATGATCATACGAAACTCATGGAGTCTGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTC
63 GATATGATCATACGAAACACATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTC
* *
21324 CCTAAATCTTTGTCTTGAGTGGTTTATCTTTTAGATTTAGGATCCATTCATTGCTTTCTGAATTA
128 CCTAAATCTTTGTCTCGAGTGGTTTA-CTTTTAGATTTAGGATCCATTCATTACTTTCTGAATTA
* * *
21389 CGGATACAATCACACGAATGGCATGGATTTATCCATTTGACTTATATGTTGTGTCTCTCTTCCCC
192 CGGATACGATCACACAAATAGCATGGATTTATCCATTTGACTTATATGTTGTGTCTCTCTTCCCC
21454 AAA
257 AAA
* * *
21457 TCTTTTGTCACGAATGGTTTACCTTTTAGATTTAGGATCCCAATGGTCACTCTCTGAGTTACAGA
1 TC-TTTGTCACGAGTGGTTTACCTTTTAGATTTAGGATCCCAATGATCACTCTCTGAGTTATAGA
* *
21522 TATGATCATGC-AAATCGCATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTCC
65 TATGATCATACGAAA-CACATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTCC
* * *
21586 CTAAATCTTTGTCTCGAGTGG-----TTTTAGATTTAGGATACATTCATCACTTTCTGAATTATG
129 CTAAATCTTTGTCTCGAGTGGTTTACTTTTAGATTTAGGATCCATTCATTACTTTCTGAATTACG
* ** *
21646 GATACGATCACACAAATAGCAT-GA---AGTCCATTTTA--TCCAT-TTGACT-TATCTCTTCCC
194 GATACGATCACACAAATAGCATGGATTTA-TCCATTTGACTTATATGTTG--TGTCTCTCTTCCC
21703 CAAA
256 CAAA
* * * ** * *
21707 TCTTTGTTACGAGTGATTTACCTTTTAGATTTAGGATCCCATTGATTGCTTTCTGAGTTATGGAT
1 TCTTTGTCACGAGTGGTTTACCTTTTAGATTTAGGATCCCAATGATCACTCTCTGAGTTATAGAT
21772 A
66 A
21773 CAATCTTACA
Statistics
Matches: 498, Mismatches: 65, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
249 57 0.11
250 19 0.04
251 2 0.00
252 8 0.02
254 2 0.00
255 54 0.11
260 3 0.01
261 118 0.24
263 19 0.04
264 31 0.06
267 24 0.05
268 48 0.10
269 37 0.07
270 14 0.03
271 41 0.08
272 21 0.04
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (259 bp):
TCTTTGTCACGAGTGGTTTACCTTTTAGATTTAGGATCCCAATGATCACTCTCTGAGTTATAGAT
ATGATCATACGAAACACATGGAGTCCGCTTTTTTCCATTTGGCTTATATGGTGTCTCTCTTCCCT
AAATCTTTGTCTCGAGTGGTTTACTTTTAGATTTAGGATCCATTCATTACTTTCTGAATTACGGA
TACGATCACACAAATAGCATGGATTTATCCATTTGACTTATATGTTGTGTCTCTCTTCCCCAAA
Found at i:22800 original size:21 final size:21
Alignment explanation
Indices: 22759--22802 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22749 TATTTAAAAT
**
22759 AAAAATATTAAATTTAAATTA
1 AAAAATATTAAAAATAAATTA
22780 AAAAAT-TTAAAAATAATATTA
1 AAAAATATTAAAAATAA-ATTA
22801 AA
1 AA
22803 TATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATATTAAAAATAAATTA
Found at i:25380 original size:22 final size:21
Alignment explanation
Indices: 25330--25382 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
25320 AAACTATATT
25330 TTAAATATTTTAATATAATCA
1 TTAAATATTTTAATATAATCA
25351 TTAAATATTTGTAAT-TAAAT-A
1 TTAAATATTT-TAATAT-AATCA
25372 TTAACATATTT
1 TTAA-ATATTT
25383 ATATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TTAAATATTTTAATATAATCA
Found at i:51962 original size:22 final size:22
Alignment explanation
Indices: 51916--51977 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
51906 TTATTTTTTA
** *
51916 AAAAAATAG-AATTTTAGAATT
1 AAAAAATAGAAAGATTAAAATT
51937 -AAAAATAGAAAGATTAAAATT
1 AAAAAATAGAAAGATTAAAATT
* *
51958 AAAAAATATAGAGATTAAAA
1 AAAAAATAGAAAGATTAAAA
51978 GTGTAATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 8 0.24
21 9 0.26
22 17 0.50
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (22 bp):
AAAAAATAGAAAGATTAAAATT
Found at i:56187 original size:32 final size:31
Alignment explanation
Indices: 56146--56209 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
56136 ATCATAAAAA
56146 AAATATGGACTAA-AGTTTATCCAGATTCATTT
1 AAATATGGAC-AACA-TTTATCCAGATTCATTT
* *
56178 AAATCTGGACAACTATTTATCTAGATTCATTT
1 AAATATGGACAAC-ATTTATCCAGATTCATTT
56210 TAACCATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.07
32 25 0.89
33 1 0.04
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (31 bp):
AAATATGGACAACATTTATCCAGATTCATTT
Found at i:58648 original size:24 final size:24
Alignment explanation
Indices: 58612--58686 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
58602 AGAAATAATC
* * *
58612 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
58636 TTTCAATTCAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
58660 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
58684 TTT
1 TTT
58687 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:58695 original size:24 final size:24
Alignment explanation
Indices: 58628--58698 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
58618 TTAAACTTTG
* *
58628 TTTAATTGTTTCAATTC-AACTCTG
1 TTTATTTGTTTCAA-TCAAACTCTA
*
58652 TTTATTTGTTTCAATTAAACTCTA
1 TTTATTTGTTTCAATCAAACTCTA
* *
58676 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
58699 TATTAGTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTCTA
Found at i:59635 original size:23 final size:23
Alignment explanation
Indices: 59592--59659 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
59582 AGTGTTGGGG
*
59592 AAACAGTAGGCACACATAGTG-A
1 AAACAGTAGGCACACACAGTGCA
*
59614 AAATCAGTAGGCACACGCAGTGCA
1 AAA-CAGTAGGCACACACAGTGCA
* *
59638 AAACAATAAGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
59660 TGAACAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 3 0.08
23 32 0.82
24 4 0.10
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGTAGGCACACACAGTGCA
Found at i:59665 original size:23 final size:23
Alignment explanation
Indices: 59592--59675 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
59582 AGTGTTGGGG
* * *
59592 AAACAGTAGGCACACATAGTG-A
1 AAACAATAAGCACACACAGTGCA
* * *
59614 AAATCAGTAGGCACACGCAGTGCA
1 AAA-CAATAAGCACACACAGTGCA
*
59638 AAACAATAAGCACACACAGTGCT
1 AAACAATAAGCACACACAGTGCA
*
59661 GAACAATAAGCACAC
1 AAACAATAAGCACAC
59676 TAATGTTTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.06
23 46 0.87
24 4 0.08
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (23 bp):
AAACAATAAGCACACACAGTGCA
Found at i:62059 original size:23 final size:25
Alignment explanation
Indices: 62019--62064 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
62009 CTTTATACAC
*
62019 TTTTAAAAATATTTAAA-TAATTCT
1 TTTTAAAAATATTAAAATTAATTCT
62043 TTTTAAAAAT-TTAAAATTAATT
1 TTTTAAAAATATTAAAATTAATT
62065 AATTATTGAC
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:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTAAAAATATTAAAATTAATTCT
Found at i:63091 original size:21 final size:21
Alignment explanation
Indices: 63067--63117 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
63057 AACAATAATA
63067 ATAATAATTTAATGAAATAGT
1 ATAATAATTTAATGAAATAGT
63088 ATAATAATTTAATGAAATAGT
1 ATAATAATTTAATGAAATAGT
63109 ATAATAATT
1 ATAATAATT
63118 AAATTGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (21 bp):
ATAATAATTTAATGAAATAGT
Found at i:63750 original size:13 final size:15
Alignment explanation
Indices: 63715--63752 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
63705 ATATTAAAAT
63715 ATTAATATTTTGTAG
1 ATTAATATTTTGTAG
*
63730 ATTAATATTTTTTA-
1 ATTAATATTTTGTAG
63744 A-TAATATTT
1 ATTAATATTT
63753 AAAAATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
ATTAATATTTTGTAG
Found at i:64863 original size:9 final size:9
Alignment explanation
Indices: 64849--64873 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64839 TCACGTCTAA
64849 AATATTTTT
1 AATATTTTT
64858 AATATTTTT
1 AATATTTTT
64867 AATATTT
1 AATATTT
64874 ACAACGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AATATTTTT
Found at i:79180 original size:84 final size:83
Alignment explanation
Indices: 79030--79560 Score: 634
Period size: 84 Copynumber: 6.3 Consensus size: 83
79020 TAGATATAGC
* * *
79030 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATATGAGGATTGGGGAGTTTTGTTAACAAAAG
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATA-AAGGATTGGAGAGTTTTGTCAACAAAAG
*
79095 GTTTTCAGGCAGC-GATTCT
65 GTTTCCAGGCAGCAG-TTCT
* * * * *
79114 AAAATAATTATCCTCCAGCTCCTTAGTAAGTTGATCAAAAGATTGGAGAGTTTTGTCAACAGAAG
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGAT-AAAGGATTGGAGAGTTTTGTCAACAAAAG
* *
79179 GTTTCCAGGCCGCAATTCT
65 GTTTCCAGGCAGCAGTTCT
* * * * * *
79198 AGAATATTTATCCTCCAACTCCTTGGCAGGTTGATCAGAGGATTGAAGAGTTTTGTCGACAAAAG
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGAT-AAAGGATTGGAGAGTTTTGTCAACAAAAG
79263 GTTTCCAGGCAGCAGTTCT
65 GTTTCCAGGCAGCAGTTCT
* * *
79282 AGAATATTTATCCTCCACCTCTTTAGCAAATTGATAAGAGGATT-GAGGAGTTTTGTCAACAAAA
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATAA-AGGATTGGA-GAGTTTTGTCAACAAAA
*
79346 GATTTCCAGGCAGCAGTTCT
64 GGTTTCCAGGCAGCAGTTCT
* * * *
79366 AGAATATTTATCCTCCAGCTCCTTAACAAGTTGAGAAGATGATTGGGGAGTTTTGTCAACAAAAG
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATAA-AGGATTGGAGAGTTTTGTCAACAAAAG
*
79431 ATTTCCAGGCAGCAGTTCT
65 GTTTCCAGGCAGCAGTTCT
* * * * * * * *
79450 AGAATATTTATCCTCCAGCTCCTTAACAAGTTGAGAAGATGATTGGGGGGTTTTATTAATAAAAG
1 AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATAA-AGGATTGGAGAGTTTTGTCAACAAAAG
*
79515 GTTTCCAAGCAGCAGTTCT
65 GTTTCCAGGCAGCAGTTCT
* * *
79534 AGAATATATATCCTCCAGTTGCTTAGC
1 AGAATATTTATCCTCCAGCTCCTTAGC
79561 CACTTGAGAA
Statistics
Matches: 392, Mismatches: 50, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
83 2 0.01
84 388 0.99
85 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (83 bp):
AGAATATTTATCCTCCAGCTCCTTAGCAAGTTGATAAAGGATTGGAGAGTTTTGTCAACAAAAGG
TTTCCAGGCAGCAGTTCT
Found at i:80358 original size:89 final size:89
Alignment explanation
Indices: 80264--80531 Score: 509
Period size: 89 Copynumber: 3.0 Consensus size: 89
80254 GACATATATG
80264 AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
1 AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
*
80329 TCATTAATGAAATCAATTATTGCA
66 CCATTAATGAAATCAATTATTGCA
80353 AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
1 AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
80418 CCATTAATGAAATCAATTATTGCA
66 CCATTAATGAAATCAATTATTGCA
*
80442 AAAAAAATATTAAAAGAGGAGTAATTGCACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
1 AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
*
80507 CCATTAATGAAATCAGTTATTGCA
66 CCATTAATGAAATCAATTATTGCA
80531 A
1 A
80532 TACGGGTTTA
Statistics
Matches: 176, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 176 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (89 bp):
AAAAAAATATTAAAAGAGGAGTAATTGTACCAACATGGATACCAATAGTGGAGAGGTTATCCCTA
CCATTAATGAAATCAATTATTGCA
Found at i:84049 original size:30 final size:29
Alignment explanation
Indices: 84009--84078 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
83999 GTTAATAATT
*
84009 TATAAGAATTGAATC-AAATTAAAATTTCATG
1 TATAA-AATTGAA-CAAAATT-AAAGTTCATG
*
84040 TATAAAATTGCACAAAATTAAAGTTCATG
1 TATAAAATTGAACAAAATTAAAGTTCATG
*
84069 TATATAATTG
1 TATAAAATTG
84079 CACATTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.54
30 11 0.31
31 5 0.14
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (29 bp):
TATAAAATTGAACAAAATTAAAGTTCATG
Found at i:84067 original size:29 final size:30
Alignment explanation
Indices: 84024--84082 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
84014 GAATTGAATC
*
84024 AAATTAAAATTTCATGTATAAAATTGCACA
1 AAATTAAAAGTTCATGTATAAAATTGCACA
*
84054 AAATT-AAAGTTCATGTATATAATTGCACA
1 AAATTAAAAGTTCATGTATAAAATTGCACA
84083 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AAATTAAAAGTTCATGTATAAAATTGCACA
Found at i:84096 original size:31 final size:29
Alignment explanation
Indices: 84034--84103 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
84024 AAATTAAAAT
**
84034 TTCATGTATAAAATTGCACAAAATTAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
* *
84063 TTCATGTATATAATTGCACATTAAACCATAG
1 TTCATGTATAAAATTGCACA--AAACCAAAG
84094 TTCATGTATA
1 TTCATGTATA
84104 GTTTTGGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Done.