Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010998.1 Kokia drynarioides strain JFW-HI SEQ_125968, 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: 78233
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3112 original size:59 final size:56
Alignment explanation
Indices: 3029--3217 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 56
3019 AAATGGTAGT
* * *
3029 TTTTTGGAAGTATCGGGGTTAAAAATGAGATTTTTGCAAGTTCGGAGGTAAAATGGAAA
1 TTTTTGGAAGTTTAGGGG-TAAAAATG-GATTTTTGGAAGTTCGGAGGTAAAATGG-AA
*
3088 TTTTTGGAAGTTTAGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTTAGGGGT-AAAAAT-GGATTTTTGGAAGTTCGGAGGTAAAATGG-AA
* * * *
3147 GTTTTAGAAGTTTGGGGGT-AAAATGGTAATTTTTGGAAGGTTC-GAGGTCAAAAATGGGA
1 TTTTTGGAAGTTTAGGGGTAAAAATGG--ATTTTTGGAA-GTTCGGAGGT--AAAATGGAA
3206 TTTTTGGAAGTT
1 TTTTTGGAAGTT
3218 CGAGGGTAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
56 2 0.02
57 5 0.05
58 15 0.14
59 81 0.73
60 8 0.07
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (56 bp):
TTTTTGGAAGTTTAGGGGTAAAAATGGATTTTTGGAAGTTCGGAGGTAAAATGGAA
Found at i:3158 original size:88 final size:87
Alignment explanation
Indices: 3066--3240 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 87
3056 AGATTTTTGC
* *
3066 AAGTTCGGAGGTAAAATGGAAATTTTTGGAAGTTTAGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 AAGTTCGGAGGTAAAATGGAAATTTTTGGAAGGTTAGAGGTCAAAAATGGGATTTTTGGAAGTTC
*
3131 GGGGGTAAAATGGTAAGTTTTAG
66 GAGGGTAAAATGGTAA-TTTTAG
* * * *
3154 AAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
1 AAGTTCGGAGGTAAAATGGAAATTTTTGGAAGGTTAGAGGTCAAAAATGGGATTTTTGGAAGTTC
3219 GAGGGTAAAATGGTAATTTTAG
66 GAGGGTAAAATGGTAATTTTAG
3241 GAGGTTTTAG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 6 0.08
88 74 0.93
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (87 bp):
AAGTTCGGAGGTAAAATGGAAATTTTTGGAAGGTTAGAGGTCAAAAATGGGATTTTTGGAAGTTC
GAGGGTAAAATGGTAATTTTAG
Found at i:3225 original size:59 final size:60
Alignment explanation
Indices: 3148--3301 Score: 213
Period size: 59 Copynumber: 2.6 Consensus size: 60
3138 AAATGGTAAG
* *
3148 TTTTAGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGGGAT
1 TTTTAGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTCAAAAATGAGAT
* * * **
3207 TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTAGG-AGGTTTTAGGGTCAAAAATGAGAT
1 TTTTAGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTCAAAAATGAGAT
* *
3266 TTTTTGAAGTTTGAGGGTAAAATGGTAAATTTTGGA
1 TTTTAGAAGTTTGAGGGTAAAATGGTAATTTTTGGA
3302 TAGTTTAGGG
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 6 0.07
59 76 0.93
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (60 bp):
TTTTAGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTCAAAAATGAGAT
Found at i:3237 original size:29 final size:29
Alignment explanation
Indices: 3016--3306 Score: 206
Period size: 29 Copynumber: 9.8 Consensus size: 29
3006 ACATCCGGGA
*
3016 GTAAAATGGTAGTTTTTTGGAAGTATCG-GG
1 GTAAAATGGTA-ATTTTTGGAAGT-TCGAGG
*
3046 GTTAAAAAT-G-AGATTTTTGCAAGTTCG-GAG
1 G-T-AAAATGGTA-ATTTTTGGAAGTTCGAG-G
* *
3076 GTAAAATGGAAATTTTTGGAAGTT-TAGGG
1 GTAAAATGGTAATTTTTGGAAGTTCGA-GG
* *
3105 GTCAAAAATGG-GATTTTTGGAAGTTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTTCGAGG
* * * *
3135 GTAAAATGGTAAGTTTTAGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTCGAGG
3164 GTAAAATGGTAATTTTTGGAAGGTTCGA-G
1 GTAAAATGGTAATTTTTGGAA-GTTCGAGG
*
3193 GTCAAAAATGG-GATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTCGAGG
* * **
3223 GTAAAATGGTAATTTTAGGAGGTTTTAGG
1 GTAAAATGGTAATTTTTGGAAGTTCGAGG
* *
3252 GTCAAAAAT-G-AGATTTTTTGAAGTTTGAGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTCGAGG
*
3282 GTAAAATGGTAAATTTTGGATAGTT
1 GTAAAATGGTAATTTTTGGA-AGTT
3307 TAGGGATCTC
Statistics
Matches: 212, Mismatches: 27, Indels: 44
0.75 0.10 0.16
Matches are distributed among these distances:
28 24 0.11
29 89 0.42
30 73 0.34
31 21 0.10
32 5 0.02
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTCGAGG
Found at i:3299 original size:88 final size:86
Alignment explanation
Indices: 3075--3306 Score: 220
Period size: 88 Copynumber: 2.6 Consensus size: 86
3065 CAAGTTCGGA
* * * * * *
3075 GGTAAAATGGAAATTTTTGGAAGTTTAGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAA
1 GGTAAAATGG-AATTTTTGGAAGGTTCGAGGT-AAAAATGGAAATTTTGGAAGTTCGAGGGTAAA
*
3140 ATGGTAAGTTTTAGAAGTTTGGG
64 ATGGTAAGTTTTAGAAGTTTGAG
* *
3163 GGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAA
1 GGTAAAATGG-AATTTTTGGAAGGTTCGAGGT-AAAAATGGAAATTTTGGAAGTTCGAGGGTAAA
* *
3228 ATGGTAA-TTTTAGGAGGTTTTAG
64 ATGGTAAGTTTTA-GAAGTTTGAG
* *
3251 GGTCAAAAAT-GAGATTTTTTGAA-GTTTGAGGGT-AAAATGGTAAATTTTGGATAGTT
1 GGT--AAAATGGA-ATTTTTGGAAGGTTCGA-GGTAAAAATGG-AAATTTTGGA-AGTT
3307 TAGGGATCTC
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
87 12 0.10
88 91 0.73
89 17 0.14
90 5 0.04
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (86 bp):
GGTAAAATGGAATTTTTGGAAGGTTCGAGGTAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAT
GGTAAGTTTTAGAAGTTTGAG
Found at i:4378 original size:12 final size:12
Alignment explanation
Indices: 4363--4447 Score: 59
Period size: 12 Copynumber: 7.3 Consensus size: 12
4353 TTCTTTTTTA
*
4363 ATTAATGCTATT
1 ATTAATGTTATT
*
4375 ATTAATATTATT
1 ATTAATGTTATT
* *
4387 ATTGATGTCATT
1 ATTAATGTTATT
* *
4399 ATTATTGTTATC
1 ATTAATGTTATT
4411 ATTAA---TATT
1 ATTAATGTTATT
* *
4420 GTTAATGATATT
1 ATTAATGTTATT
* *
4432 AGTAATATTATT
1 ATTAATGTTATT
4444 ATTA
1 ATTA
4448 TTATTGCCAA
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
9 7 0.13
12 46 0.87
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (12 bp):
ATTAATGTTATT
Found at i:4399 original size:15 final size:15
Alignment explanation
Indices: 4381--4420 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4371 TATTATTAAT
*
4381 ATTATTATTGATGTC
1 ATTATTATTGATATC
*
4396 ATTATTATTGTTATC
1 ATTATTATTGATATC
*
4411 ATTAATATTG
1 ATTATTATTG
4421 TTAATGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTATTATTGATATC
Found at i:7197 original size:23 final size:23
Alignment explanation
Indices: 7156--7222 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
7146 TTAAGATGAC
* * *
7156 TATATAAATTTTTTTAATATATA
1 TATATAAAATTATTAAATATATA
7179 TATATAAAATTATTAAATAT-TA
1 TATATAAAATTATTAAATATATA
* *
7201 -AAATAAAATAATATAAATATAT
1 TATATAAAATTAT-TAAATATAT
7223 TTTTTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.27
22 9 0.24
23 18 0.49
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATAAAATTATTAAATATATA
Found at i:15978 original size:248 final size:246
Alignment explanation
Indices: 15545--16184 Score: 897
Period size: 248 Copynumber: 2.6 Consensus size: 246
15535 TTTTTTATAA
* *
15545 TTTAGTAACATAATATTATTAAATAAATATACTAAAAATTTATGGAAATTTTATATAGAAATGAT
1 TTTAGAAACATAATAGTATTAAATAAATATACTAAAAATTTATGGAAATTTTATATAGAAATGAT
* *
15610 ATGCTAATAAATATAATAATTTTAGCACTAAAAAAAAAATCTTAAATGGAAACTATATAATTTTT
66 ATGCTAAT-AATATAATAATTTTAGCA-T-TAAATAAAATCTTAAAT-GAAACTATATAATTTTT
*
15675 AATGAATATAATAAATGGAAAATATTCAATATATTAAATAAATATACTTTTCATCATCAATATAA
127 AATTAATATAATAAATGGAAAATATTCAATATATTAAATAAATATACTTTTCATCATCAATATAA
* *
15740 AATTTATTTTAGTTTTATAATGGAAACTTGTATTTTAAAAATAAATAAAGAA-AT
192 AATTTATTTTAGTTTTATAATGGAAAATTATATTTTAAAAATAAATAAAGAATAT
** * * *
15794 TTTA-AAATTTTTAGTAGTATTAAATAAAGATAATAAAAATTTATGGAAATTTTATATAGAAATG
1 TTTAGAAA--CATAATAGTATTAAATAAATATACTAAAAATTTATGGAAATTTTATATAGAAATG
* *
15858 ACATGCTAATATATATAATAATTTTAGCATTAAATACAATCTTAAATGAAAGCTATATAATTTTT
64 ATATGCTAATA-ATATAATAATTTTAGCATTAAATAAAATCTTAAATGAAA-CTATATAATTTTT
* * * * *
15923 AATTAACATAATAAATGGAAACTATTTAATATATTAAATAAATATATTTTTCATCATCAATATTA
127 AATTAATATAATAAATGGAAAATATTCAATATATTAAATAAATATACTTTTCATCATCAATATAA
* * ****
15988 AATTTATTTTAGTTTTATAATGGAAAATTATATTTTAAAATTAATTTTTTAATAT
192 AATTTATTTTAGTTTTATAATGGAAAATTATATTTTAAAAATAAATAAAGAATAT
* * *
16043 TTTAGTAACATAATATTATTAAATAAATATACTAAAAATTTATGGAAATTATATATAGAAATGAT
1 TTTAGAAACATAATAGTATTAAATAAATATACTAAAAATTTATGGAAATTTTATATAGAAATGAT
* * *
16108 ATGCTAATAACTAGAATAATTTTAACATTAAATAAAATCTTAAATGGAATCTATATAATTTTTAA
66 ATGCTAATAA-TATAATAATTTTAGCATTAAATAAAATCTTAAAT-GAAACTATATAATTTTTAA
16173 TTAATATAATAA
129 TTAATATAATAA
16185 TAGAAAAATA
Statistics
Matches: 344, Mismatches: 39, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
247 5 0.01
248 247 0.72
249 15 0.04
250 77 0.22
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (246 bp):
TTTAGAAACATAATAGTATTAAATAAATATACTAAAAATTTATGGAAATTTTATATAGAAATGAT
ATGCTAATAATATAATAATTTTAGCATTAAATAAAATCTTAAATGAAACTATATAATTTTTAATT
AATATAATAAATGGAAAATATTCAATATATTAAATAAATATACTTTTCATCATCAATATAAAATT
TATTTTAGTTTTATAATGGAAAATTATATTTTAAAAATAAATAAAGAATAT
Found at i:18405 original size:24 final size:24
Alignment explanation
Indices: 18373--18427 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
18363 TCAATGTTTG
*
18373 ATTGTTACAATAAGAGTATCGCTT
1 ATTGTTACAACAAGAGTATCGCTT
18397 ATTGTTACAACAAGAGTATCGCTT
1 ATTGTTACAACAAGAGTATCGCTT
18421 ATTGTTA
1 ATTGTTA
18428 ATATTATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (24 bp):
ATTGTTACAACAAGAGTATCGCTT
Found at i:22221 original size:20 final size:20
Alignment explanation
Indices: 22184--22241 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
22174 ATACCCTAGG
* * *
22184 ACTTCTACTGGTAGAACTTC
1 ACTTCTACCGATACAACTTC
*
22204 ACTTCTACCTATACAACTTC
1 ACTTCTACCGATACAACTTC
* *
22224 AGTTTTACCGATACAACT
1 ACTTCTACCGATACAACT
22242 ATGCTTTTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:25360 original size:20 final size:19
Alignment explanation
Indices: 25337--25377 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
25327 CTACTGGTAT
25337 AACTTCACTTCTACCAATAC
1 AACTTCACTTCTACC-ATAC
*
25357 AACTTCAGTTCTACCATAC
1 AACTTCACTTCTACCATAC
25376 AA
1 AA
25378 GTATGCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (19 bp):
AACTTCACTTCTACCATAC
Found at i:40992 original size:28 final size:28
Alignment explanation
Indices: 40922--40992 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
40912 GCTCATTAAG
* *
40922 GAGCTCATACTAAAGCAAAGCTAAACAAA
1 GAGCTCACA-TAAAGCAAACCTAAACAAA
* *
40951 GAGCCTGCAC--AAAGCAGACCTAAATAAA
1 GAG-CT-CACATAAAGCAAACCTAAACAAA
40979 GAGCTCACATAAAG
1 GAGCTCACATAAAG
40993 GAGATTCGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
26 3 0.09
27 2 0.06
28 22 0.65
29 3 0.09
30 2 0.06
31 2 0.06
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.13
Consensus pattern (28 bp):
GAGCTCACATAAAGCAAACCTAAACAAA
Found at i:41970 original size:44 final size:44
Alignment explanation
Indices: 41907--41996 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
41897 ATCCAAGTTT
41907 GCTGGAACACTAGCGAACCTTACTTCTCATGACCAAAATGTCTG
1 GCTGGAACACTAGCGAACCTTACTTCTCATGACCAAAATGTCTG
41951 GCTGGAACACTAGCGAACCTTACTTCTCATGACCAAAATGTCTG
1 GCTGGAACACTAGCGAACCTTACTTCTCATGACCAAAATGTCTG
41995 GC
1 GC
41997 CTCAATCTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (44 bp):
GCTGGAACACTAGCGAACCTTACTTCTCATGACCAAAATGTCTG
Found at i:49223 original size:123 final size:122
Alignment explanation
Indices: 49088--49324 Score: 386
Period size: 123 Copynumber: 1.9 Consensus size: 122
49078 GATTTCGTTA
* *
49088 AATATTAAAACATGGAAGCTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
1 AATATTAAAACATGAAAGCTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATA
* *
49153 TATTTCTTTAAAGGA-ATATTTCCATTTTAAAATGAGATATTATATAAAATGAAATTG
66 TATTTCTCTAAA-GATATATTTCCATTTTAAAATGAGATATTAAATAAAATGAAATTG
*
49210 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
1 AATATT-AAAACATGAAAGCTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
* *
49275 ATATTTCTCTAAAGATATATTTTCATTTTAATATGAGATATTAAATAAAA
65 ATATTTCTCTAAAGATATATTTCCATTTTAAAATGAGATATTAAATAAAA
49325 GGGCTACAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
122 8 0.08
123 98 0.92
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (122 bp):
AATATTAAAACATGAAAGCTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATA
TATTTCTCTAAAGATATATTTCCATTTTAAAATGAGATATTAAATAAAATGAAATTG
Found at i:60450 original size:123 final size:123
Alignment explanation
Indices: 60302--60540 Score: 328
Period size: 124 Copynumber: 1.9 Consensus size: 123
60292 GATTTCGTCA
*
60302 AATATTAAAACATGAGAGTTAATATCTTTTTT-GAAAGGATACAAT-TCTTTAATAGACCTTCCA
1 AATATTAAAACATGAGAGTTAATATCTTTTTTAGAAAGGATACAATGT-TTTAATACACCTTCCA
* *
60365 TATATTTCTTTAAAGCA-ATA-TTTCTATTTTAATACGAG-TTATTATATAAAAGAAAATTG
65 TATATTTCTCTAAAG-ATATATTTTC-ATTTTAATACGAGCTT-TTAAATAAAAGAAAATTG
* *
60424 AATATTAAAAACATG-GAAGTTGATATCTTTTTTAGAAAGGATATAATGTTTTAATACACCTTCC
1 AATATT-AAAACATGAG-AGTTAATATCTTTTTTAGAAAGGATACAATGTTTTAATACACCTTCC
*
60488 ATATATTTCTCTAAAGATATATTTTCATTTTAATATGAGCTTTTAAATAAAAG
64 ATATATTTCTCTAAAGATATATTTTCATTTTAATACGAGCTTTTAAATAAAAG
60541 GATAGATAGC
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
122 7 0.07
123 24 0.23
124 66 0.63
125 7 0.07
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (123 bp):
AATATTAAAACATGAGAGTTAATATCTTTTTTAGAAAGGATACAATGTTTTAATACACCTTCCAT
ATATTTCTCTAAAGATATATTTTCATTTTAATACGAGCTTTTAAATAAAAGAAAATTG
Found at i:62465 original size:18 final size:18
Alignment explanation
Indices: 62442--62481 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
62432 CAAATCCAAC
62442 GAGTAAGTTCGTATAATT
1 GAGTAAGTTCGTATAATT
62460 GAGTAAGTTCGTATAATT
1 GAGTAAGTTCGTATAATT
62478 -AGTA
1 GAGTA
62482 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (18 bp):
GAGTAAGTTCGTATAATT
Found at i:62537 original size:16 final size:17
Alignment explanation
Indices: 62510--62541 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
62500 ACAATAATTT
62510 TTTTATTGAATTTTAAA
1 TTTTATTGAATTTTAAA
62527 TTTTA-TGAATTTTAA
1 TTTTATTGAATTTTAA
62542 TTAAATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTATTGAATTTTAAA
Found at i:65758 original size:233 final size:228
Alignment explanation
Indices: 65343--65802 Score: 735
Period size: 233 Copynumber: 2.0 Consensus size: 228
65333 TGACTTCGAT
65343 GAGGTAAAATGTAAAAGTAATATTCTAACTTTTAAATAGCAGGTAAGTCATAGTTTATTGGTATG
1 GAGGTAAAATGTAAAAGTAATATTCTAACTTTTAAATAGCAGGTAAGTCATAGTTTATTGGTATG
* * *
65408 TTTGATAGTGAAGTCAAAATTTCTTTTTGATTTAATGAGTCGGTGCTTCATAGAACTGGTGCGAG
66 TCTGATAGTGAAGTCAAAATTTCTTTTTGATTTAATGAGTCGGTGCTTCACAGAACTGGTGAGAG
* *
65473 CTAATTCAGTGCCTTTACAACCCCTACCCCGTATTATACTCCTTATGGCATCCTTGGTTCCTCAA
131 CCAATTCAGTGCCTTTACAACCCCTACCCCGTATTATACTCCTTATGGCATCCTTGGGTCCTCAA
*
65538 TGGACTGAAATAGTTTGACAGCTTTTGATTAAA
196 GGGACTGAAATAGTTTGACAGCTTTTGATTAAA
* *
65571 GAGGTAAAATGTAAAAGTAATATTCTTACTTTTAAATAGGAGGTAAGTC-TAGTTTATTGGTTTT
1 GAGGTAAAATGTAAAAGTAATATTCTAACTTTTAAATAGCAGGTAAGTCATAGTTTATT-G----
*
65635 GTAAATGTCTGATAGTGAAGTCAAAATTTCTTTTTGATTTAATGAGTCGGTGGTTCACAGAACT-
61 GT--ATGTCTGATAGTGAAGTCAAAATTTCTTTTTGATTTAATGAGTCGGTGCTTCACAGAACTG
*
65699 GTGAGAGCCAATTCAGTGCCTTTACAACCCCTACCCCTTATTATACTCCTTATGGCATCCTTGGG
124 GTGAGAGCCAATTCAGTGCCTTTACAACCCCTACCCCGTATTATACTCCTTATGGCATCCTTGGG
* *
65764 TCCTCAAGGGATTGAAATAGTTTGACGGCTTTTGATTAA
189 TCCTCAAGGGACTGAAATAGTTTGACAGCTTTTGATTAA
65803 TTAATTAGAA
Statistics
Matches: 213, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
227 9 0.04
228 48 0.23
232 2 0.01
233 97 0.46
234 57 0.27
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (228 bp):
GAGGTAAAATGTAAAAGTAATATTCTAACTTTTAAATAGCAGGTAAGTCATAGTTTATTGGTATG
TCTGATAGTGAAGTCAAAATTTCTTTTTGATTTAATGAGTCGGTGCTTCACAGAACTGGTGAGAG
CCAATTCAGTGCCTTTACAACCCCTACCCCGTATTATACTCCTTATGGCATCCTTGGGTCCTCAA
GGGACTGAAATAGTTTGACAGCTTTTGATTAAA
Found at i:68809 original size:27 final size:27
Alignment explanation
Indices: 68767--68868 Score: 168
Period size: 27 Copynumber: 3.8 Consensus size: 27
68757 CTAAACTTTG
* *
68767 GCTCGAAAGAGGATTATTTTGTATCTA
1 GCTCGAAAGAGCATTATTCTGTATCTA
68794 GCTCGAAAGAGCATTATTCTGTATCTA
1 GCTCGAAAGAGCATTATTCTGTATCTA
*
68821 GCTCGAAAGAGCATTATTCTATATCTA
1 GCTCGAAAGAGCATTATTCTGTATCTA
*
68848 GCTCGAAAGAGCATTACTCTG
1 GCTCGAAAGAGCATTATTCTG
68869 CATTGGGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (27 bp):
GCTCGAAAGAGCATTATTCTGTATCTA
Found at i:68932 original size:27 final size:27
Alignment explanation
Indices: 68898--68967 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
68888 ACTTTCTTAA
68898 TCTA-GCTCGAATGAGCAACAATCTAT
1 TCTAGGCTCGAATGAGCAACAATCTAT
* * * *
68924 TTTGGGCTCGCATGAGCAACAATCTGT
1 TCTAGGCTCGAATGAGCAACAATCTAT
68951 TCTAGGCTCGAATGAGC
1 TCTAGGCTCGAATGAGC
68968 TATATTATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (27 bp):
TCTAGGCTCGAATGAGCAACAATCTAT
Found at i:73548 original size:2 final size:2
Alignment explanation
Indices: 73541--73566 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73531 ACCACATCTA
73541 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
73567 TAGATCGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73833 original size:61 final size:61
Alignment explanation
Indices: 73738--73862 Score: 232
Period size: 61 Copynumber: 2.0 Consensus size: 61
73728 AACTCAAGAG
*
73738 AATTACTGTCAAAATATACATGCTCAATGTCCATACATATAATTTTACCTTAGAGGAATCA
1 AATTACTGTCAAAATATACATGCTCAATGTCCATACATATAATTTTACATTAGAGGAATCA
*
73799 AATTACTGTCAAAATATACATGCTCAATGTCCATATATATAATTTTACATTAGAGGAATCA
1 AATTACTGTCAAAATATACATGCTCAATGTCCATACATATAATTTTACATTAGAGGAATCA
73860 AAT
1 AAT
73863 CGTCTAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (61 bp):
AATTACTGTCAAAATATACATGCTCAATGTCCATACATATAATTTTACATTAGAGGAATCA
Found at i:76447 original size:41 final size:41
Alignment explanation
Indices: 76326--76601 Score: 213
Period size: 41 Copynumber: 6.8 Consensus size: 41
76316 CGGCGTTTGG
* * *
76326 ATAGAAAA-CGCCGCAAAAAGT-AAAGCAATAGCGGCGCTT
1 ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* * * * **
76365 TTACATAAA-CGCTGCAAAAAAT-AGAGCAATAGCGGCGCTT
1 ATAGA-AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* *
76405 ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGTCACTT
1 ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* * * *
76446 ATGAGAAAA-CACCGCTAAAGGTCAAATCAATAGCGCCGCTT
1 AT-AGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* ** ** * * * *
76487 ATGGGCAAGTTCCGTTAAAGGTTAGCGCAATAGCGGCGCAT
1 ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* ** *
76528 ATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTT
1 ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
* *
76569 AT-GAGAAAGCCCCGCTAAAGGTCAGAGTAATAG
1 ATAGA-AAAGCGCCGCTAAAGGTCAGAGCAATAG
76602 TGGGAAAGCG
Statistics
Matches: 190, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
39 6 0.03
40 47 0.25
41 131 0.69
42 6 0.03
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.17
Consensus pattern (41 bp):
ATAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
Found at i:76657 original size:73 final size:73
Alignment explanation
Indices: 76529--76665 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 73
76519 GCGGCGCATA
* * * *
76529 TGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGAAAGCCCCGCTAAAGGTCAG
1 TGGGAAAGCGCCGCTAAAGGTCAGAGCAATAACGACGCCTATGAGAAAGCCCCGCTAAAAGTCAG
76594 AGTAATAG
66 AGTAATAG
* * * * ** *
76602 TGGGAAAGCGCTGCTAAATGTTAGAGCAATAACGATGCCTATTTGAAAGCGCCGCTAAAAGTCA
1 TGGGAAAGCGCCGCTAAAGGTCAGAGCAATAACGACGCCTATGAGAAAGCCCCGCTAAAAGTCA
76666 AAGCAATAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 53 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (73 bp):
TGGGAAAGCGCCGCTAAAGGTCAGAGCAATAACGACGCCTATGAGAAAGCCCCGCTAAAAGTCAG
AGTAATAG
Done.