Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015126.1 Kokia drynarioides strain JFW-HI SEQ_130170, 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: 171399
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11783 original size:18 final size:17
Alignment explanation
Indices: 11748--11806 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
11738 GAAAGTTCCA
*
11748 TATTTAAA-TATTATAT
1 TATTTAAATTATAATAT
11764 TATTTAAATTACTAATAT
1 TATTTAAATTA-TAATAT
* *
11782 TATATAAATTAAAAT-T
1 TATTTAAATTATAATAT
11798 CTATTTAAA
1 -TATTTAAA
11807 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 15 0.42
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTAAATTATAATAT
Found at i:12075 original size:18 final size:17
Alignment explanation
Indices: 12039--12076 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12029 TTTAATCTTT
12039 TAAAATTTATAAAAATA
1 TAAAATTTATAAAAATA
12056 TAAAATATTA-AAATAATA
1 TAAAAT-TTATAAA-AATA
12074 TAA
1 TAA
12077 TTACATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATTTATAAAAATA
Found at i:16152 original size:42 final size:42
Alignment explanation
Indices: 16100--16210 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 42
16090 ATATAAGCTC
*
16100 TTCATCTAATCCCACCTCAATTAGGATTTATCTTTTTAGTTT
1 TTCATTTAATCCCACCTCAATTAGGATTTATCTTTTTAGTTT
16142 TTCATTTAATCCCACCTCAATTAGGATTTATCTTTTTAGTTT
1 TTCATTTAATCCCACCTCAATTAGGATTTATCTTTTTAGTTT
* *
16184 TTCATTTATTCCCACCTCAATTCGGAT
1 TTCATTTAATCCCACCTCAATTAGGAT
16211 CATTCTATTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (42 bp):
TTCATTTAATCCCACCTCAATTAGGATTTATCTTTTTAGTTT
Found at i:29366 original size:194 final size:196
Alignment explanation
Indices: 29036--29419 Score: 605
Period size: 194 Copynumber: 2.0 Consensus size: 196
29026 TGTGTTAAAA
* * *
29036 GTCTTAAATTGAAATTTTAATTCTTGGGAGGACCAAAAATGCAAATTTTCCTTTTACCAAAGGCC
1 GTCTTAAATTGAAATTTTAATTCTTGGAAGGACCAAAAATGCAAATTTTCCATGTACCAAAGGCC
* * *
29101 TGCCTGTCCCTTGGTTTCACCCCTGTTTGTATGCTATTGCTATGCATCCTCAATGTCAACGTATA
66 TACCTGTCCCTTGGTTTCACCCCTGTTTGTATGCTATTGCTATGCATCCTCAATGTCAAAGTAGA
29166 TATTTTGTTTGGATGAACTTTGATTCTTTGTTGTTTTAGATAAA-TTTTTTCCAGCTGTTGAAAG
131 TATTTTGTTTGGATGAACTTTGATTCTTTGTTGTTTTAGATAAATTTTTTTCCAGCTGTTGAAAG
29230 G
196 G
* * *
29231 GTCTTAAATTGAAATTTTAGTTCTT-GAAGG-GCATAAAATGCAAATTTTCCATGTACCGAAGGC
1 GTCTTAAATTGAAATTTTAATTCTTGGAAGGACCA-AAAATGCAAATTTTCCATGTACCAAAGGC
*
29294 CTACCTGTCCCTTGGTTTCACCCCTGTTTGTATGCTATTGCTATGTATCCAT-AATGTCAAAGTA
65 CTACCTGTCCCTTGGTTTCACCCCTGTTTGTATGCTATTGCTATGCATCC-TCAATGTCAAAGTA
* * *
29358 GATATTTTGTTTGGATGGACTTTGATTCTTTGTTGTTTTGGATAAATTTTTTTGCAGCTGTT
129 GATATTTTGTTTGGATGAACTTTGATTCTTTGTTGTTTTAGATAAATTTTTTTCCAGCTGTT
29420 TGATTGGATG
Statistics
Matches: 173, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
193 2 0.01
194 132 0.76
195 39 0.23
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (196 bp):
GTCTTAAATTGAAATTTTAATTCTTGGAAGGACCAAAAATGCAAATTTTCCATGTACCAAAGGCC
TACCTGTCCCTTGGTTTCACCCCTGTTTGTATGCTATTGCTATGCATCCTCAATGTCAAAGTAGA
TATTTTGTTTGGATGAACTTTGATTCTTTGTTGTTTTAGATAAATTTTTTTCCAGCTGTTGAAAG
G
Found at i:38802 original size:178 final size:178
Alignment explanation
Indices: 38503--38856 Score: 647
Period size: 178 Copynumber: 2.0 Consensus size: 178
38493 TTTATATTAG
* *
38503 TTACTTTTATCCCTTTTAAAAATAATAAAAATTTGATTTAATTCTTTGAATTTTATAAAAATATA
1 TTACTTTTATCCCTTTTAAAAATAATAAAAAATTGATTTAATCCTTTGAATTTTATAAAAATATA
* *
38568 AGTTATTATCGTAAAAATTACAATTTAATTTTGACATCTTCAAAGAAATTCCTGGCTTCGCCCTT
66 AGTTATTATCGTAAAAATTACAATTTAATTTCGACACCTTCAAAGAAATTCCTGGCTTCGCCCTT
38633 GAAGTAAAACGTGGATTATATTTTTATTTGAGACCTAAACTTGGTATT
131 GAAGTAAAACGTGGATTATATTTTTATTTGAGACCTAAACTTGGTATT
38681 TTACTTTTATCCCTTTTAAAAATAATAAAAAATTGATTTAATCCTTTGAATTTTATAAAAATATA
1 TTACTTTTATCCCTTTTAAAAATAATAAAAAATTGATTTAATCCTTTGAATTTTATAAAAATATA
*
38746 AGTTATTATCGTAAAAATTATAATTTAATTTCGATC-CCTTCAAAGAAATTCCTGGCTTCGCCCT
66 AGTTATTATCGTAAAAATTACAATTTAATTTCGA-CACCTTCAAAGAAATTCCTGGCTTCGCCCT
38810 TGAAGTAAAACGTGGATTATATTTTTATTTGAGACCTAAACTTGGTA
130 TGAAGTAAAACGTGGATTATATTTTTATTTGAGACCTAAACTTGGTA
38857 AGTTTCCTTG
Statistics
Matches: 170, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
178 169 0.99
179 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (178 bp):
TTACTTTTATCCCTTTTAAAAATAATAAAAAATTGATTTAATCCTTTGAATTTTATAAAAATATA
AGTTATTATCGTAAAAATTACAATTTAATTTCGACACCTTCAAAGAAATTCCTGGCTTCGCCCTT
GAAGTAAAACGTGGATTATATTTTTATTTGAGACCTAAACTTGGTATT
Found at i:50023 original size:2 final size:2
Alignment explanation
Indices: 50016--50040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50006 ATAATATGAG
50016 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
50041 ACATATTTAA
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:56794 original size:2 final size:2
Alignment explanation
Indices: 56787--56821 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
56777 ACTTCTTTAT
56787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
56822 AATAGGTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:63696 original size:21 final size:21
Alignment explanation
Indices: 63666--63705 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
63656 CATATCAAAA
* *
63666 AAAAAATTAATTTTTTTTATT
1 AAAAAATTAACTATTTTTATT
*
63687 AAAAATTTAACTATTTTTA
1 AAAAAATTAACTATTTTTA
63706 CAGTTAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAAATTAACTATTTTTATT
Found at i:78833 original size:20 final size:20
Alignment explanation
Indices: 78797--78835 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
78787 TTATCGACTA
*
78797 TATAATTATTTACATTTATC
1 TATAATTATATACATTTATC
78817 TATAATTTATATA-ATTTAT
1 TATAA-TTATATACATTTAT
78836 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAATTATATACATTTATC
Found at i:90145 original size:6 final size:6
Alignment explanation
Indices: 90113--90143 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
90103 TCATAAATTT
*
90113 ATTTCA ATTTCA ATTTCA ATTTCA AATTCA A
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA A
90144 ATATAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTCA
Found at i:90308 original size:5 final size:6
Alignment explanation
Indices: 90294--90318 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90284 CTCCTTGTTT
90294 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
90319 TATATTACCT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:102397 original size:31 final size:31
Alignment explanation
Indices: 102362--102431 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
102352 ACTTATCAAC
*
102362 TCAGTGACTTAAAT-AAGAACTTTCCAATAGT
1 TCAGTGACTTAAATGAA-AACTTTCCAATAAT
* *
102393 TCAGTGACTTAATTGAAAACTTTCGAATAAT
1 TCAGTGACTTAAATGAAAACTTTCCAATAAT
*
102424 TCAATGAC
1 TCAGTGAC
102432 CATTTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (31 bp):
TCAGTGACTTAAATGAAAACTTTCCAATAAT
Found at i:123362 original size:28 final size:28
Alignment explanation
Indices: 123330--123448 Score: 184
Period size: 28 Copynumber: 4.0 Consensus size: 28
123320 TCCATTTTGG
123330 TATTGAAATTAAGTGTTTAAAAAAACCA
1 TATTGAAATTAAGTGTTTAAAAAAACCA
123358 TATTGAAATTAAGTGTTTAAAAAAACCA
1 TATTGAAATTAAGTGTTTAAAAAAACCA
123386 TTTTGGTATTGAAATTAAGTGTTTAAAAAAACCA
1 ------TATTGAAATTAAGTGTTTAAAAAAACCA
123420 TATTGAAATTAAGTGTTTAAAAAAACCA
1 TATTGAAATTAAGTGTTTAAAAAAACCA
123448 T
1 T
123449 CTAAGCATTT
Statistics
Matches: 85, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
28 57 0.67
34 28 0.33
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (28 bp):
TATTGAAATTAAGTGTTTAAAAAAACCA
Found at i:123399 original size:62 final size:62
Alignment explanation
Indices: 123321--123448 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
123311 ATTTCAATTT
123321 CCATTTTGGTATTGAAATTAAGTGTTTAAAAAAACCATATTGAAATTAAGTGTTTAAAAAAA
1 CCATTTTGGTATTGAAATTAAGTGTTTAAAAAAACCATATTGAAATTAAGTGTTTAAAAAAA
123383 CCATTTTGGTATTGAAATTAAGTGTTTAAAAAAACCATATTGAAATTAAGTGTTTAAAAAAA
1 CCATTTTGGTATTGAAATTAAGTGTTTAAAAAAACCATATTGAAATTAAGTGTTTAAAAAAA
123445 CCAT
1 CCAT
123449 CTAAGCATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (62 bp):
CCATTTTGGTATTGAAATTAAGTGTTTAAAAAAACCATATTGAAATTAAGTGTTTAAAAAAA
Found at i:124457 original size:21 final size:22
Alignment explanation
Indices: 124431--124478 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
124421 TTAAGATTCA
*
124431 AGATTTTGAGTTT-GAGGTTCG
1 AGATTTGGAGTTTAGAGGTTCG
*
124452 AGATTTGGAGTTTAGAGTTTCG
1 AGATTTGGAGTTTAGAGGTTCG
124474 A-ATTT
1 AGATTT
124479 AAGATTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.44
Consensus pattern (22 bp):
AGATTTGGAGTTTAGAGGTTCG
Found at i:128311 original size:43 final size:43
Alignment explanation
Indices: 128264--128346 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
128254 TGACTAGTTA
*
128264 AACTATAAGAAATATGAAACCAGTAAGAAAGCAAAATGTGTTG
1 AACTATAAGAAATACGAAACCAGTAAGAAAGCAAAATGTGTTG
*
128307 AACTATAAGAAATACGAAACCAGTAAGAAAGCAACATGTG
1 AACTATAAGAAATACGAAACCAGTAAGAAAGCAAAATGTG
128347 ACACTTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (43 bp):
AACTATAAGAAATACGAAACCAGTAAGAAAGCAAAATGTGTTG
Found at i:133514 original size:14 final size:14
Alignment explanation
Indices: 133495--133525 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
133485 ACTTAAGGTA
133495 ATTTGTTTATAAGT
1 ATTTGTTTATAAGT
133509 ATTTGTTTATAAGT
1 ATTTGTTTATAAGT
133523 ATT
1 ATT
133526 AAACAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (14 bp):
ATTTGTTTATAAGT
Found at i:134234 original size:35 final size:35
Alignment explanation
Indices: 134190--134277 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
134180 ATTATTCATT
*
134190 AATATTGTTCGTGAACATGTTCAATTATATGTTCGAT-
1 AATA-TGTTCGTGAACATGTTCAATTA-A-GTTAGATG
* * *
134227 CA-ATGTTCGTGAAAATGTTCGATTAAGTTAGATG
1 AATATGTTCGTGAACATGTTCAATTAAGTTAGATG
134261 AATATGTTCGTGAACAT
1 AATATGTTCGTGAACAT
134278 TAAACAAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
33 6 0.14
34 2 0.05
35 33 0.77
36 1 0.02
37 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (35 bp):
AATATGTTCGTGAACATGTTCAATTAAGTTAGATG
Found at i:134262 original size:23 final size:23
Alignment explanation
Indices: 134218--134270 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
134208 GTTCAATTAT
*
134218 ATGTTCGATCAATGTTCGTGAAA
1 ATGTTCGATCAATGTTAGTGAAA
* *
134241 ATGTTCGATTAA-GTTAGATGAAT
1 ATGTTCGATCAATGTTAG-TGAAA
134264 ATGTTCG
1 ATGTTCG
134271 TGAACATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (23 bp):
ATGTTCGATCAATGTTAGTGAAA
Found at i:136302 original size:91 final size:88
Alignment explanation
Indices: 136192--136479 Score: 225
Period size: 91 Copynumber: 3.2 Consensus size: 88
136182 TAAAACTTAG
* * *
136192 TATTCATTATATTAT-ATTTTCCGGACATTTGAGTTTGAGTATGGGTAGAAAAAATATTTTTTAA
1 TATTTATTATATT-TCATTTTCAGGACATTTGAGCTTGAGTAT-GGTAGAAAAAATATTTTTT-A
*
136256 ACTTTCCGAGATAAATATAAAAAATAT
63 ATTTTCCG-GATAAATATAAAAAATAT
* ** * * * *
136283 TATTTATTATATTTCATTTTAAGGGTATTTGGGC-TG-G--TGGT-GCAAAAATGTTATTTAATT
1 TATTTATTATATTTCATTTTCAGGACATTTGAGCTTGAGTATGGTAGAAAAAATATTTTTTAATT
* *
136343 TTCCGGGATAACTATAAAAAATTT
66 TTCC-GGATAAATATAAAAAATAT
* ** *
136367 TATTTTTTATA-TTCATTTTTGGGCACA--TGAGCTTGAGTATGGTATTGTAAAAATATTTATTT
1 TATTTATTATATTTCATTTTCAGG-ACATTTGAGCTTGAGTATGGTA--GAAAAAATA-TT-TTT
* * *
136429 TAATTTTCCGGAATAATTATGAAAAATAG
61 TAATTTTCCGG-ATAAATATAAAAAATAT
*
136458 TATTTACTATATTTCATTTTCA
1 TATTTATTATATTTCATTTTCA
136480 TGGCGTTTGA
Statistics
Matches: 153, Mismatches: 30, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
82 4 0.03
83 12 0.08
84 35 0.23
85 13 0.08
86 7 0.05
87 1 0.01
89 8 0.05
90 7 0.05
91 58 0.38
92 8 0.05
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (88 bp):
TATTTATTATATTTCATTTTCAGGACATTTGAGCTTGAGTATGGTAGAAAAAATATTTTTTAATT
TTCCGGATAAATATAAAAAATAT
Found at i:139445 original size:54 final size:55
Alignment explanation
Indices: 139342--139451 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
139332 AAACCGGTCC
139342 TTTTTATTTGAAATTTCATCCGTTTTTTCGGTTAAAAATTGGCGTAACTGCCATG
1 TTTTTATTTGAAATTTCATCCGTTTTTTCGGTTAAAAATTGGCGTAACTGCCATG
139397 TTTTTATTTGAAATTTCATCCG-TTTTTCGGTTAAAAATTGGCGTAACTGCCATG
1 TTTTTATTTGAAATTTCATCCGTTTTTTCGGTTAAAAATTGGCGTAACTGCCATG
139451 T
1 T
139452 ATCATGTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 33 0.60
55 22 0.40
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (55 bp):
TTTTTATTTGAAATTTCATCCGTTTTTTCGGTTAAAAATTGGCGTAACTGCCATG
Found at i:144943 original size:105 final size:105
Alignment explanation
Indices: 144750--144960 Score: 246
Period size: 105 Copynumber: 2.0 Consensus size: 105
144740 TCGGTGTCTA
* * * * * *
144750 GGAGGAGAGGACTGGTTCCGGCTCTCGAGTTCAATTATGATGTTTTGTATGGGAAAGGATCAGAG
1 GGAGGAGAGGACAGATTCCGGCTCACGAGTTCAATTATGATGTTTTGTATAGGAAAGAACCAGAG
* *
144815 GATGTGAAGAATGCAAGTCTTCGGTCTACCGAGAGTATCG
66 GATGTAAAAAATGCAAGTCTTCGGTCTACCGAGAGTATCG
* * * *
144855 GGAGGAGAGGACCAGATT-CGGCTCACGAGTTGAATTGTGCTGTTTTGTATAGGAAAGAACCGGA
1 GGAGGAGAGGA-CAGATTCCGGCTCACGAGTTCAATTATGATGTTTTGTATAGGAAAGAACCAGA
* * **
144919 GGCTGTAAAAAATGTAAG-CTTTCGGTCTAGTGAGAGTATCG
65 GGATGTAAAAAATGCAAGTC-TTCGGTCTACCGAGAGTATCG
144960 G
1 G
144961 TTTGGTTTCT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
104 1 0.01
105 83 0.94
106 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (105 bp):
GGAGGAGAGGACAGATTCCGGCTCACGAGTTCAATTATGATGTTTTGTATAGGAAAGAACCAGAG
GATGTAAAAAATGCAAGTCTTCGGTCTACCGAGAGTATCG
Found at i:144956 original size:222 final size:225
Alignment explanation
Indices: 144633--145083 Score: 617
Period size: 222 Copynumber: 2.0 Consensus size: 225
144623 TTGAGCTCGA
* * *
144633 GGAGGAGCGGACCGGTTTCGGCTCACGAGTTGAATTGTGCTGATTTGTATAGGAAAGAACCGGAG
1 GGAGGAGAGGACCAGATTCGGCTCACGAGTTGAATTGTGCTGATTTGTATAGGAAAGAACCGGAG
* * *
144698 GATGTGAAAAATGCAAGCTTTCGGTCTACCGAGAGTATTGGTTCGG-TGT-CT-AGGAGGAGAGG
66 GATGTAAAAAATGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTCTACTCAGGAGGAGAGG
* * * * * *
144760 A-CTGGTTCCGGCTCTCGAGTTCAATTATGATGTTTTGTATGGGAAAGGATCAGAGGATGTGAAG
131 ATC-GATTCCGGCTCACGAGTTCAATCATGATGTCTTGTATAGGAAAGAATCAGAGGATGTGAA-
144824 AA-TGCAAG-TCTTCGGTCTACCGAGAGTATCG
194 AAGTGCAAGCT-TTCGGTCTACCGAGAGTATCG
*
144855 GGAGGAGAGGACCAGATTCGGCTCACGAGTTGAATTGTGCTGTTTTGTATAGGAAAGAACCGGAG
1 GGAGGAGAGGACCAGATTCGGCTCACGAGTTGAATTGTGCTGATTTGTATAGGAAAGAACCGGAG
* * ** *
144920 GCTGTAAAAAATGTAAGCTTTCGGTCTAGTGAGAGTATCGGTTTGGTTTCTAACTCGAGGAGGAG
66 GATGTAAAAAATGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGG-TTCT-ACTC-AGGAGGAG
* * *
144985 AGGATCGATTTCGGCTCACGAGTTGAATCATGATGTCTTGTATAGGAAAGAATCGGAGGATGTGA
128 AGGATCGATTCCGGCTCACGAGTTCAATCATGATGTCTTGTATAGGAAAGAATCAGAGGATGTGA
145050 AAAGTGCAAGCTTTCGGTCTACCGAGAGTATCG
193 AAAGTGCAAGCTTTCGGTCTACCGAGAGTATCG
145083 G
1 G
145084 TTCGGTTTCT
Statistics
Matches: 199, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
222 100 0.50
224 2 0.01
226 2 0.01
227 2 0.01
228 91 0.46
229 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.27
Consensus pattern (225 bp):
GGAGGAGAGGACCAGATTCGGCTCACGAGTTGAATTGTGCTGATTTGTATAGGAAAGAACCGGAG
GATGTAAAAAATGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTCTACTCAGGAGGAGAGG
ATCGATTCCGGCTCACGAGTTCAATCATGATGTCTTGTATAGGAAAGAATCAGAGGATGTGAAAA
GTGCAAGCTTTCGGTCTACCGAGAGTATCG
Found at i:145077 original size:123 final size:121
Alignment explanation
Indices: 144851--145255 Score: 463
Period size: 123 Copynumber: 3.3 Consensus size: 121
144841 TACCGAGAGT
144851 ATCG-GGAGGAGAGGACCAGA-TTCGGCTCACGAGTTGAATTGTGCTGTTTTGTATAGGAAAGAA
1 ATCGAGGAGGAGAGGACC-GATTTCGGCTCACGAGTTGAATTGTG-TGTTTTGTATAGGAAAGAA
* * * * * ** *
144914 CCGGAGGCTGTAAAAAATGTAAGCTTTCGGTCTAGTGAGAGTATCGGTTTGGTTTCTA
64 TCGGAGGATGTGAAAAGTGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTTCTA
* ** *
144972 ACTCGAGGAGGAGAGGATCGATTTCGGCTCACGAGTTGAATCATGATGTCTTGTATAGGAAAGAA
1 A-TCGAGGAGGAGAGGACCGATTTCGGCTCACGAGTTGAATTGTG-TGTTTTGTATAGGAAAGAA
145037 TCGGAGGATGTGAAAAGTGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTTCTA
64 TCGGAGGATGTGAAAAGTGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTTCTA
** * * * * * * *
145095 GATTAAAGAGGAGAGGATCGGTTTCGGTTCCCGAATTGAATTGTGTCGTTTTGTCTAGGAAAGAA
1 -ATCGAGGAGGAGAGGACCGATTTCGGCTCACGAGTTGAATTGTGT-GTTTTGTATAGGAAAGAA
* * * ** *
145160 TCGGATGATGTGAAAAGTGCAAGCTTCCGATCTACCGAGAGTATTAGTTCAGTTTCTA
64 TCGGAGGATGTGAAAAGTGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTTCTA
* * *
145218 ATTCGAGGAGGAGAGGACCGGTTTCGGCCCATGAGTTG
1 A-TCGAGGAGGAGAGGACCGATTTCGGCTCACGAGTTG
145256 CATTACACGA
Statistics
Matches: 239, Mismatches: 39, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
121 1 0.00
122 7 0.03
123 230 0.96
124 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (121 bp):
ATCGAGGAGGAGAGGACCGATTTCGGCTCACGAGTTGAATTGTGTGTTTTGTATAGGAAAGAATC
GGAGGATGTGAAAAGTGCAAGCTTTCGGTCTACCGAGAGTATCGGTTCGGTTTCTA
Found at i:145614 original size:60 final size:60
Alignment explanation
Indices: 145504--145617 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
145494 TAATTATTTT
* * * **
145504 TTTTTTTTTTTGTTATCTAACTATGAAAAATTACAAAATAATAGTTTAATTATTAGTAAA
1 TTTTATTTTTGGTTATCTAACTACGAAAAATTACAAAATAATAGCCTAATTATTAGTAAA
* *
145564 TTTTATTTTTGGTTATCTAATTACGAAAAATTACAAAATGATCA-CCTAATTATT
1 TTTTATTTTTGGTTATCTAACTACGAAAAATTACAAAATAAT-AGCCTAATTATT
145618 CAATTTTATC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (60 bp):
TTTTATTTTTGGTTATCTAACTACGAAAAATTACAAAATAATAGCCTAATTATTAGTAAA
Found at i:151221 original size:36 final size:36
Alignment explanation
Indices: 151139--151222 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
151129 CACCACTTCC
* *
151139 CTTCTTTCCCCTTCTTCTTCTTCTCCTCCTACTTCAT
1 CTTC-TTCCCCTTCTTCTCCATCTCCTCCTACTTCAT
* * * *
151176 CTCCCTCCCCTTCTTCTCCATCTTCT-CTTCTTTCAT
1 CTTCTTCCCCTTCTTCTCCATCTCCTCCTAC-TTCAT
151212 CTTCTTCCCCT
1 CTTCTTCCCCT
151223 GCTCCTCTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
35 3 0.08
36 32 0.84
37 3 0.08
ACGTcount: A:0.05, C:0.46, G:0.00, T:0.49
Consensus pattern (36 bp):
CTTCTTCCCCTTCTTCTCCATCTCCTCCTACTTCAT
Found at i:151238 original size:22 final size:24
Alignment explanation
Indices: 151211--151259 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
151201 TCTTCTTTCA
151211 TCTTCTTC-CCCT-GCTCCTCTCC
1 TCTTCTTCACCCTCGCTCCTCTCC
* *
151233 TCTTCTTCACTCTCGCTTCTCTCC
1 TCTTCTTCACCCTCGCTCCTCTCC
151257 TCT
1 TCT
151260 CTTTCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 3 0.13
24 12 0.52
ACGTcount: A:0.02, C:0.49, G:0.04, T:0.45
Consensus pattern (24 bp):
TCTTCTTCACCCTCGCTCCTCTCC
Found at i:151259 original size:24 final size:22
Alignment explanation
Indices: 151202--151259 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
151192 TCCATCTTCT
* *
151202 CTTCTTTCATCTTCTTCCCCTG
1 CTTCTCTCCTCTTCTTCCCCTG
* *
151224 CTCCTCTCCTCTTCTTCACTCTCG
1 CTTCTCTCCTCTTCTTC-CCCT-G
151248 CTTCTCTCCTCT
1 CTTCTCTCCTCT
151260 CTTTCCTCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 14 0.48
23 3 0.10
24 12 0.41
ACGTcount: A:0.03, C:0.47, G:0.03, T:0.47
Consensus pattern (22 bp):
CTTCTCTCCTCTTCTTCCCCTG
Found at i:160741 original size:209 final size:209
Alignment explanation
Indices: 160332--161058 Score: 1129
Period size: 206 Copynumber: 3.5 Consensus size: 209
160322 CTAAATGGAT
*
160332 ACCTCGACTAGCAAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAAT
1 ACCTCGACTA-CCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAAT
* * * *
160397 GATTTGCAATAAACTACAACGCAAACCATTTCTTTTCTTTTTTTTT-GTTAAGCCATAAGTACAA
65 GATTTGCAATAAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAA
* * *
160461 GTTAGTAAAAGAAAACACCGTATTAGTTACCAGGCTATAATTATCACAATAACGTCCTTTATTTC
130 GCTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTC
* *
160526 CTAGAATAATCCGAC
195 CTAGAATAAACAGAC
* * **
160541 ACCTGGACTACCAAAAACACAAACACTTTTATCATATGAATGACCGGTACCAAACCCGGATAACA
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
* * *
160606 ACTTGCAATCAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCTGTAAGTACAAG
66 ATTTGCAATAAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAAG
* * *
160671 CCAATAAAAGAAAACACCGTATTAGTTAACAGACTATAATTATCACAACAACGTCCTTTATTTCC
131 CTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
160736 TAGAATAAACAGAC
196 TAGAATAAACAGAC
* * * *
160750 ACCTCGACTACCAGAAACACAAACACTTTTATCATATGAATGTATGGTACCAAACCAGGATAATG
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
*
160815 ATTTGCAATAAACTACAACACAAACC--TT-TTTTTTTTTTTTTGGGTTAAGCCGTAAGTACAAG
66 ATTTGCAATAAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAAG
* *
160877 CTGGTAAAAGAAAACACCATATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
131 CTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
160942 TAGAATAAACAGAC
196 TAGAATAAACAGAC
* * *
160956 ACCTCGACTACCAAAAACACACACACTTTTATCATACGAATGAATGGTACCAAACCCGGATAATG
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
* *
161021 GTTTGCAATCAACTACAACACAAACCATTTGTTTTTTT
66 ATTTGCAATAAACTACAACACAAACCATTTGTTTTTTT
161059 CGGCTGAGTC
Statistics
Matches: 470, Mismatches: 44, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
206 190 0.40
207 2 0.00
208 93 0.20
209 185 0.39
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (209 bp):
ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
ATTTGCAATAAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAAG
CTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
TAGAATAAACAGAC
Found at i:160952 original size:206 final size:206
Alignment explanation
Indices: 160332--161058 Score: 1105
Period size: 209 Copynumber: 3.5 Consensus size: 206
160322 CTAAATGGAT
*
160332 ACCTCGACTAGCAAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAAT
1 ACCTCGACTA-CCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAAT
* * *
160397 GATTTGCAATAAACTACAACGCAAACCATTTCTTTTCTTTTTTTTTGTTAAGCCATAAGTACAAG
65 GATTTGCAATAAACTACAACACAAACCATTT-TTTT-TTTTTTTTGGTTAAGCCGTAAGTACAAG
* * *
160462 TTAGTAAAAGAAAACACCGTATTAGTTACCAGGCTATAATTATCACAATAACGTCCTTTATTTCC
128 CTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
* *
160527 TAGAATAATCCGAC
193 TAGAATAAACAGAC
* * **
160541 ACCTGGACTACCAAAAACACAAACACTTTTATCATATGAATGACCGGTACCAAACCCGGATAACA
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
* * *
160606 ACTTGCAATCAACTACAACACAAACCATTTGTTTTTTTTTTTTTTGGTTAAGCTGTAAGTACAAG
66 ATTTGCAATAAACTACAACACAAACCA--T-TTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAAG
* * *
160671 CCAATAAAAGAAAACACCGTATTAGTTAACAGACTATAATTATCACAACAACGTCCTTTATTTCC
128 CTAGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCC
160736 TAGAATAAACAGAC
193 TAGAATAAACAGAC
* * * *
160750 ACCTCGACTACCAGAAACACAAACACTTTTATCATATGAATGTATGGTACCAAACCAGGATAATG
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
160815 ATTTGCAATAAACTACAACACAAACC-TTTTTTTTTTTTTTTGGGTTAAGCCGTAAGTACAAGCT
66 ATTTGCAATAAACTACAACACAAACCATTTTTTTTTTTTTTT-GGTTAAGCCGTAAGTACAAGCT
* *
160879 GGTAAAAGAAAACACCATATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCCTA
130 AGTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCCTA
160944 GAATAAACAGAC
195 GAATAAACAGAC
* * *
160956 ACCTCGACTACCAAAAACACACACACTTTTATCATACGAATGAATGGTACCAAACCCGGATAATG
1 ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
* * *
161021 GTTTGCAATCAACTACAACACAAACCATTTGTTTTTTT
66 ATTTGCAATAAACTACAACACAAACCATTTTTTTTTTT
161059 CGGCTGAGTC
Statistics
Matches: 470, Mismatches: 43, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
205 14 0.03
206 178 0.38
207 10 0.02
208 75 0.16
209 186 0.40
210 5 0.01
211 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (206 bp):
ACCTCGACTACCAAAAACACAAACACTTTTATCATATGAATGAACGGTACCAAACCCGGATAATG
ATTTGCAATAAACTACAACACAAACCATTTTTTTTTTTTTTTGGTTAAGCCGTAAGTACAAGCTA
GTAAAAGAAAACACCGTATTAGTTAACAGGCTATAATTATCACAACAACGTCCTTTATTTCCTAG
AATAAACAGAC
Found at i:161409 original size:22 final size:22
Alignment explanation
Indices: 161362--161409 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
161352 TAGACCTAAT
* **
161362 ATGTGTGTATATATATGTATTT
1 ATGTGTGTATATATATATATCC
161384 ATGTGTGTATATATATATATCC
1 ATGTGTGTATATATATATATCC
161406 ATGT
1 ATGT
161410 AAATATGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (22 bp):
ATGTGTGTATATATATATATCC
Found at i:162211 original size:3 final size:3
Alignment explanation
Indices: 162203--162246 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
162193 CATTGTAAAG
* **
162203 GAA GAA GAA GAA GAT CTA GAA GAA -AA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
162247 AAACACTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:162243 original size:20 final size:21
Alignment explanation
Indices: 162204--162248 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
162194 ATTGTAAAGG
162204 AAGAAGAAGAAGATCTAGAAGAA
1 AAGAAGAAGAAGA--TAGAAGAA
162227 AAGAAGAAGAAGA-AGAAGAA
1 AAGAAGAAGAAGATAGAAGAA
162247 AA
1 AA
162249 ACACTTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (21 bp):
AAGAAGAAGAAGATAGAAGAA
Done.