Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013733.1 Kokia drynarioides strain JFW-HI SEQ_128761, 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: 202521
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:363 original size:4 final size:4
Alignment explanation
Indices: 354--425 Score: 65
Period size: 4 Copynumber: 17.5 Consensus size: 4
344 AAACACATTA
* * * * *
354 TCTT TCTT TCCTC TCTT TC-T TCTT TCTT TCCTC TCCT TCCT CCTT TCTT
1 TCTT TCTT T-CTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT
403 TCTT TCTT TCCTT TCTT TCTT TC
1 TCTT TCTT T-CTT TCTT TCTT TC
426 CCGTTTATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 3 0.05
4 43 0.77
5 10 0.18
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
TCTT
Found at i:401 original size:25 final size:20
Alignment explanation
Indices: 354--426 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
344 AAACACATTA
354 TCTTTCTTTCCTCTCTTTCT
1 TCTTTCTTTCCTCTCTTTCT
*
374 TCTTTCTTTCCTCTCCTTCCT
1 TCTTTCTTTCCTCT-CTTTCT
* *
395 CCTTTCTTT-CTTTCTTTCCTT
1 TCTTTCTTTCCTCTCTTT-C-T
416 TCTTTCTTTCC
1 TCTTTCTTTCC
427 CGTTTATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.07
20 18 0.41
21 22 0.50
22 1 0.02
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
TCTTTCTTTCCTCTCTTTCT
Found at i:629 original size:27 final size:27
Alignment explanation
Indices: 598--652 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
588 ACACCCCTTA
*
598 GTGCCGCCACT-TGATATTCCTCCATTG
1 GTGCCGCCACTACG-TATTCCTCCATTG
*
625 GTGCCGCCACTACGTGTTCCTCCATTG
1 GTGCCGCCACTACGTATTCCTCCATTG
652 G
1 G
653 GTGTCAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.13, C:0.35, G:0.22, T:0.31
Consensus pattern (27 bp):
GTGCCGCCACTACGTATTCCTCCATTG
Found at i:3600 original size:2 final size:2
Alignment explanation
Indices: 3593--3625 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3583 ATGATTAAAG
3593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3626 GTCACTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6196 original size:25 final size:24
Alignment explanation
Indices: 6167--6213 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6157 CCTTTTGCTC
6167 TCTCTAAAAACATTGTTTTTGTTTT
1 TCTCT-AAAACATTGTTTTTGTTTT
* **
6192 TCTCTCAAGTATTGTTTTTGTT
1 TCTCTAAAACATTGTTTTTGTT
6214 CTTTTGGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (24 bp):
TCTCTAAAACATTGTTTTTGTTTT
Found at i:15128 original size:5 final size:5
Alignment explanation
Indices: 15102--15162 Score: 50
Period size: 5 Copynumber: 12.2 Consensus size: 5
15092 TATCTATATG
* * * * * * *
15102 CTATG CTATG CTATA CCATA CTATA CTATG CTGTA CTATA GTATA CTAAA
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA
*
15152 ATATA CTATA C
1 CTATA CTATA C
15163 ACCCATCTCA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (5 bp):
CTATA
Found at i:15130 original size:20 final size:20
Alignment explanation
Indices: 15102--15149 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
15092 TATCTATATG
*
15102 CTATGCTATGCTATACCATA
1 CTATACTATGCTATACCATA
* *
15122 CTATACTATGCTGTACTATA
1 CTATACTATGCTATACCATA
*
15142 GTATACTA
1 CTATACTA
15150 AAATATACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
CTATACTATGCTATACCATA
Found at i:31475 original size:29 final size:29
Alignment explanation
Indices: 31436--31499 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
31426 AGTGAATCTT
31436 AAATGACTGTTTCATCAGACAAGAAATAA
1 AAATGACTGTTTCATCAGACAAGAAATAA
31465 AAATGACTGTTTCATCAGACAAGAAATAA
1 AAATGACTGTTTCATCAGACAAGAAATAA
31494 AAATGA
1 AAATGA
31500 AGAGTACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (29 bp):
AAATGACTGTTTCATCAGACAAGAAATAA
Found at i:39581 original size:144 final size:144
Alignment explanation
Indices: 39321--39617 Score: 524
Period size: 144 Copynumber: 2.1 Consensus size: 144
39311 AGTAGAAGGG
* *
39321 GAAGACCAATGGGACGAAAATGTTTAGAGAAATCAAACCAATATATATGATGACTAGGTAATAGA
1 GAAGACCAATGGGACAAAAATGTTTAGAGAAATCAAACCAATATATATAATGACTAGGTAATAGA
*
39386 AACAGAAATATATCTCCTACATTTTGAGCAATCTCAGCAACTGGAAACAAGAATATAAAGATGAA
66 AACAGAAATATACCTCCTACATTTTGAGCAATCTCAGCAACTGGAAACAAGAATATAAAGATGAA
39451 AAGCCTAATATACA
131 AAGCCTAATATACA
* *
39465 GAAGACCAATGGGACAAAAATGTTTAGAGAAATCAAAGCAATATATATAATGATTAGGTAATAGA
1 GAAGACCAATGGGACAAAAATGTTTAGAGAAATCAAACCAATATATATAATGACTAGGTAATAGA
39530 AACAGAAATATACCTCCTAC-TTTCTGAGCAATCTCAGCAACTGGAAACAAGAATATAAAGATGA
66 AACAGAAATATACCTCCTACATTT-TGAGCAATCTCAGCAACTGGAAACAAGAATATAAAGATGA
*
39594 AAAGCCTAATATATA
130 AAAGCCTAATATACA
39609 GAAGACCAA
1 GAAGACCAA
39618 AAGGACTTAC
Statistics
Matches: 146, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
143 3 0.02
144 143 0.98
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.22
Consensus pattern (144 bp):
GAAGACCAATGGGACAAAAATGTTTAGAGAAATCAAACCAATATATATAATGACTAGGTAATAGA
AACAGAAATATACCTCCTACATTTTGAGCAATCTCAGCAACTGGAAACAAGAATATAAAGATGAA
AAGCCTAATATACA
Found at i:42206 original size:20 final size:21
Alignment explanation
Indices: 42181--42222 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42171 AATTTCATAC
42181 AATATC-AACCATTAATTAAA
1 AATATCAAACCATTAATTAAA
* *
42201 AATATCAAAGCATTTATTAAA
1 AATATCAAACCATTAATTAAA
42222 A
1 A
42223 CCCTGTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (21 bp):
AATATCAAACCATTAATTAAA
Found at i:64145 original size:6 final size:6
Alignment explanation
Indices: 64134--64168 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
64124 CCATCACATT
64134 CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CCCAA
1 CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CCCAA
64169 CCCCCACCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.51, G:0.14, T:0.00
Consensus pattern (6 bp):
CCCAAG
Found at i:65363 original size:5 final size:6
Alignment explanation
Indices: 65348--65372 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
65338 TCATTCACAA
65348 TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG T
65373 CAATTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:75475 original size:2 final size:2
Alignment explanation
Indices: 75468--75492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75458 ATCATTGAGC
75468 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 A
75493 GAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76289 original size:29 final size:29
Alignment explanation
Indices: 76256--76312 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
76246 TATTTGATTT
76256 TATTTAATAATACAGGGACCAAATTGATC
1 TATTTAATAATACAGGGACCAAATTGATC
* * *
76285 TATTTAATAATAGAGGGACTAATTTGAT
1 TATTTAATAATACAGGGACCAAATTGAT
76313 AAGGTCCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (29 bp):
TATTTAATAATACAGGGACCAAATTGATC
Found at i:82060 original size:14 final size:14
Alignment explanation
Indices: 82041--82077 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
82031 TAACAACTCA
82041 TCCATCAACTATGT
1 TCCATCAACTATGT
82055 TCCATCAACTATGT
1 TCCATCAACTATGT
*
82069 TTCATCAAC
1 TCCATCAAC
82078 CATTTTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (14 bp):
TCCATCAACTATGT
Found at i:83146 original size:207 final size:201
Alignment explanation
Indices: 82795--83174 Score: 618
Period size: 207 Copynumber: 1.9 Consensus size: 201
82785 ACAGGACCAA
* * *
82795 AAACACAAGAAAAACTATACCCATGACAGAGAATAAAACCAGGGGAAAACTCATTTGGAATAGAA
1 AAACACAAGAAAAACTATACCCAAGACAGAGAAAAAAACCAGGGGAAAACTCATTTGAAATAGAA
* *
82860 AATATTGAAGAAATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
66 AACATTCAAGAAATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
* *
82925 CAAACTATATTAAGAGGAAAATAATAG-AATGCAAACTGAATTGCTTTCACTTTTATCCACAGAG
131 CAAACAAAATTAAGAGGAAAATAATAGAAAT-CAAACTGAATTGCTTTCACTTTTATCCACAGAG
82989 TATATTG
195 TATATTG
*
82996 AAACACAAGAAAAACTATACCCAAGATAGAGAAAAAAACCAGGAGAAAGGGAAAACTCATTTGAA
1 AAACACAAGAAAAACTATACCCAAGACAGAGAAAAAAACC---AG---GGGAAAACTCATTTGAA
83061 ATAGAAAACATTCAAGAAATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTA
60 ATAGAAAACATTCAAGAAATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTA
83126 AACTTTCAAACAAAATTAAGAGGAAAATAATAGAAATCAAACTGAATTG
125 AACTTTCAAACAAAATTAAGAGGAAAATAATAGAAATCAAACTGAATTG
83175 AAACATGGGC
Statistics
Matches: 164, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
201 37 0.23
204 2 0.01
207 122 0.74
208 3 0.02
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (201 bp):
AAACACAAGAAAAACTATACCCAAGACAGAGAAAAAAACCAGGGGAAAACTCATTTGAAATAGAA
AACATTCAAGAAATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
CAAACAAAATTAAGAGGAAAATAATAGAAATCAAACTGAATTGCTTTCACTTTTATCCACAGAGT
ATATTG
Found at i:89107 original size:25 final size:25
Alignment explanation
Indices: 89078--89129 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
89068 GAGGGGTAAT
*
89078 TTTTTATTTAATATTAATATAATTA
1 TTTTTATTTAATATTAATATAAATA
*
89103 TTTTTATTTGATATTAATATAAATA
1 TTTTTATTTAATATTAATATAAATA
89128 TT
1 TT
89130 GAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTATTTAATATTAATATAAATA
Found at i:106663 original size:93 final size:93
Alignment explanation
Indices: 106475--106663 Score: 247
Period size: 93 Copynumber: 2.0 Consensus size: 93
106465 CAGTTAATGT
* * ***
106475 AATATTTTATATCTAAGCTTATTTTTAATATTTAATTTGGTACTTGAATATTTTTTGTTTTAATT
1 AATATTTGATACCTAAGCTTATTTTTAATATTTAATTTGGTACTTGAATATTTTTTGTCACAATT
* * *
106540 TAGTATATAAATTATAGTTTCAATGCTC
66 AAGTATATAAATTATAGCTTAAATGCTC
106568 AATATTTGATACCTAAGCTTATTTTTAATATTTAATTTGGTACTTGAATATTTTTTTGTCACAAT
1 AATATTTGATACCTAAGCTTATTTTTAATATTTAATTTGGTACTTGAATA-TTTTTTGTCACAAT
* * *
106633 TAAGTGCT-TAAGTT-TAGCTTAAATGTTC
65 TAAGT-ATATAAATTATAGCTTAAATGCTC
106661 AAT
1 AAT
106664 TTGTTATTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 62 0.75
94 20 0.24
95 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (93 bp):
AATATTTGATACCTAAGCTTATTTTTAATATTTAATTTGGTACTTGAATATTTTTTGTCACAATT
AAGTATATAAATTATAGCTTAAATGCTC
Found at i:120501 original size:6 final size:7
Alignment explanation
Indices: 120484--120510 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
120474 AGACTTGCAA
120484 TTTTTTC
1 TTTTTTC
120491 TTTTTTC
1 TTTTTTC
120498 TTTTTTC
1 TTTTTTC
120505 TTTTTT
1 TTTTTT
120511 ATTTAATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:140694 original size:1 final size:1
Alignment explanation
Indices: 140688--140718 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
140678 CGTGTCGAAG
140688 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
140719 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:140733 original size:1 final size:1
Alignment explanation
Indices: 140729--140760 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
140719 NNNNNNNNNN
140729 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
140761 CAATTTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:141177 original size:18 final size:18
Alignment explanation
Indices: 141156--141193 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
141146 AGGATGTTTG
*
141156 AAAATAAAAAAAAA-TAA
1 AAAAAAAAAAAAAAGTAA
141173 AAAAAAAAAAAAAAGTAA
1 AAAAAAAAAAAAAAGTAA
141191 AAA
1 AAA
141194 TAGATAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAAAAAAGTAA
Found at i:141192 original size:10 final size:9
Alignment explanation
Indices: 141156--141193 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
141146 AGGATGTTTG
141156 AAAATAAAAA
1 AAAAT-AAAA
141166 AAAATAAAA
1 AAAATAAAA
141175 AAAA-AAAA
1 AAAATAAAA
141183 AAAAGTAAAA
1 AAAA-TAAAA
141193 A
1 A
141194 TAGATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.31
9 8 0.31
10 10 0.38
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (9 bp):
AAAATAAAA
Found at i:141193 original size:11 final size:10
Alignment explanation
Indices: 141156--141186 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
141146 AGGATGTTTG
141156 AAAATAAAAA
1 AAAATAAAAA
141166 AAAATAAAAA
1 AAAATAAAAA
141176 AAAA-AAAAA
1 AAAATAAAAA
141185 AA
1 AA
141187 GTAAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:148133 original size:88 final size:90
Alignment explanation
Indices: 147937--148148 Score: 216
Period size: 88 Copynumber: 2.4 Consensus size: 90
147927 CCTTACTTTT
*
147937 TTTTTTTGTGCACTCAATTGGATATTTGAACTACCAAAACGCATCAAAAAAACCCTCAAACTTAA
1 TTTTTTT-TGCACTCAATTGCATATTTGAACTACCAAAACGCATCAAAAAAACCCTCAAACTTAA
*
148002 AAAAAAAAAACAATTAAGCTCCTACA
65 AAAAAAAAAACAATTAAACTCCTACA
* ** * * * * *
148028 -TTTTTTTGCACTTAATTGCATATTTGAACTTTCAAAATGCAT-AAAAAATGCTCTCGAACTT-T
1 TTTTTTTTGCACTCAATTGCATATTTGAACTACCAAAACGCATCAAAAAA-ACCCTCAAACTTAA
*** **
148090 TTCAAAAAAACAATTAAAC-CCTTGA
65 AAAAAAAAAACAATTAAACTCCTACA
** *
148115 TTTTTTTTGCACTCAATTGGGTACTTGAACTACC
1 TTTTTTTTGCACTCAATTGCATATTTGAACTACC
148149 CCTATTTTTT
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
87 4 0.04
88 48 0.49
89 40 0.41
90 6 0.06
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (90 bp):
TTTTTTTTGCACTCAATTGCATATTTGAACTACCAAAACGCATCAAAAAAACCCTCAAACTTAAA
AAAAAAAAACAATTAAACTCCTACA
Found at i:148294 original size:29 final size:28
Alignment explanation
Indices: 148252--148340 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
148242 AATTTTTTTA
*
148252 AAATTTAATAAAAACTATAAAAAATATAT
1 AAATTTGAT-AAAACTATAAAAAATATAT
* * *
148281 AACTTTGATTAAAAATATAAAAAAAATTAT
1 AAATTTGA-TAAAACTATAAAAAATA-TAT
* * *
148311 GAAATTTTATAAAACCATAAAAAATTTAT
1 -AAATTTGATAAAACTATAAAAAATATAT
148340 A
1 A
148341 TAAAATATAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.02
29 23 0.49
30 17 0.36
31 6 0.13
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
AAATTTGATAAAACTATAAAAAATATAT
Found at i:148324 original size:30 final size:28
Alignment explanation
Indices: 148252--148362 Score: 80
Period size: 30 Copynumber: 3.8 Consensus size: 28
148242 AATTTTTTTA
*
148252 AAATTTAATAAAAACTATAAAAAATATAT
1 AAATTTAATAAAAA-TATAAAAAAAATAT
* *
148281 AACTTTGATTAAAAATATAAAAAAAATTAT
1 AAATTT-AATAAAAATATAAAAAAAA-TAT
* ** *
148311 GAAATTTTATAAAACCATAAAAAATTTATAT
1 -AAATTTAATAAAAATATAAAAAA--AATAT
*
148342 AAAATATAA-AAAAATATAAAA
1 -AAATTTAATAAAAATATAAAA
148363 TTCATAAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
29 15 0.24
30 33 0.52
31 14 0.22
32 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (28 bp):
AAATTTAATAAAAATATAAAAAAAATAT
Found at i:148338 original size:19 final size:19
Alignment explanation
Indices: 148316--148382 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
148306 ATTATGAAAT
*
148316 TTTATAAAACCATAAAAAA
1 TTTATAAAAACATAAAAAA
*
148335 TTTATATAAAATATAAAAAA
1 TTTATA-AAAACATAAAAAA
* *
148355 -ATATAAAATTCATAAAAAA
1 TTTATAAAA-ACATAAAAAA
*
148374 ATTATAAAA
1 TTTATAAAA
148383 TTATCGTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.08
19 18 0.46
20 18 0.46
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTATAAAAACATAAAAAA
Found at i:148380 original size:20 final size:20
Alignment explanation
Indices: 148317--148384 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
148307 TTATGAAATT
* *
148317 TTATAAAA-CCATAAAAAAT
1 TTATAAAATTCATAAAAAAA
*
148336 TTATATAAAAT-ATAAAAAAA
1 TTATA-AAATTCATAAAAAAA
148356 -TATAAAATTCATAAAAAAA
1 TTATAAAATTCATAAAAAAA
148375 TTATAAAATT
1 TTATAAAATT
148385 ATCGTATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.10
19 18 0.43
20 20 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTATAAAATTCATAAAAAAA
Found at i:148896 original size:89 final size:88
Alignment explanation
Indices: 148761--149015 Score: 293
Period size: 89 Copynumber: 2.9 Consensus size: 88
148751 TACCAAAAGA
* *
148761 CTTTTTCGATGCA-TTTGACAGTTCAAATACCCAATTGTGTGAAAAAATAGGGGCTTAATTGCTT
1 CTTTTT-GATGCATTTTGACAGTTCAAATACTCAATTGAGTGAAAAAATAGGGGCTTAATTGCTT
148825 TTTTTTAAAAAAAAAGTTTGAGAGT
65 TTTTTTAAAAAAAAA-TTTGAGAGT
* ** *
148850 CTTTTTGATGCATTTTGAAAGTTCAAGCACTCAATTGAGTGCAAAAAAATGCAGGGGTTTAATTG
1 CTTTTTGATGCATTTTGACAGTTCAAATACTCAATTGAGTG--AAAAAAT--AGGGGCTTAATTG
* * *
148915 -TTTTTTTT--GAAAATATTTGAGGGT
62 CTTTTTTTTAAAAAAAAATTTGAGAGT
** * *
148939 CTTTTTGATATATTTTGACAGTTCAAATACTCAAATGAGTGAAAAAAATAGGGGCTTAATTGCTA
1 CTTTTTGATGCATTTTGACAGTTCAAATACTCAATTGAGTG-AAAAAATAGGGGCTTAATTGCTT
*
149004 TTTTTGAAAAAA
65 TTTTTTAAAAAA
149016 TTTAAGAGCT
Statistics
Matches: 139, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
86 12 0.09
87 6 0.04
88 14 0.10
89 75 0.54
90 5 0.04
91 7 0.05
92 8 0.06
93 12 0.09
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (88 bp):
CTTTTTGATGCATTTTGACAGTTCAAATACTCAATTGAGTGAAAAAATAGGGGCTTAATTGCTTT
TTTTTAAAAAAAAATTTGAGAGT
Found at i:158278 original size:7 final size:7
Alignment explanation
Indices: 158266--158297 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
158256 ATCATCGTTT
158266 GCCAGTC
1 GCCAGTC
158273 GCCAGTC
1 GCCAGTC
158280 GCCAGTC
1 GCCAGTC
158287 GCCAGTC
1 GCCAGTC
158294 GCCA
1 GCCA
158298 CCCTCAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.44, G:0.28, T:0.12
Consensus pattern (7 bp):
GCCAGTC
Found at i:166017 original size:2 final size:2
Alignment explanation
Indices: 166010--166044 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
166000 GTTAATAATT
166010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
166045 TTCATGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:171866 original size:57 final size:57
Alignment explanation
Indices: 171778--171949 Score: 335
Period size: 57 Copynumber: 3.0 Consensus size: 57
171768 TTAAGTGTAG
171778 GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
1 GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
171835 GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
1 GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
*
171892 GAATGAGGTCAATGTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
1 GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
171949 G
1 G
171950 TTTTTGTGGA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 114 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (57 bp):
GAATGAGGTCAATCTGAGTGGAATTTAGTACAAATGTGTGGTAATAGTGCATGAAGA
Found at i:187029 original size:16 final size:17
Alignment explanation
Indices: 187008--187041 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
186998 ATGGGCATCA
*
187008 ATTTACATGTGCT-TGC
1 ATTTACATATGCTATGC
187024 ATTTACATATGCTATGC
1 ATTTACATATGCTATGC
187041 A
1 A
187042 CTTGATTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (17 bp):
ATTTACATATGCTATGC
Found at i:191825 original size:4 final size:4
Alignment explanation
Indices: 191816--191846 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
191806 TCTGCTCTTT
*
191816 ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
191847 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:196675 original size:6 final size:6
Alignment explanation
Indices: 196664--196702 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
196654 TGATAAAAAT
* * *
196664 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
196703 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Done.