Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012000.1 Kokia drynarioides strain JFW-HI SEQ_126998, 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: 28093
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:418 original size:23 final size:22
Alignment explanation
Indices: 296--491 Score: 164
Period size: 23 Copynumber: 8.5 Consensus size: 22
286 CGAAGTACTT
296 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAAGCACACAAGTGC----GA
322 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
* *
344 ATCCAATAAGCACACACAGTGC-A
1 A-ACAGTAAGCACACA-AGTGCGA
* * * **
367 ATCAGTAGGCGCACATAGCAC-A
1 AACAGTAAGCACACA-AGTGCGA
*
389 AATCAGTAAGCACACATAGCGCGA
1 AA-CAGTAAGCACACA-AGTGCGA
*
413 AACAGTAAGCACACGAAGTGTGA
1 AACAGTAAGCACAC-AAGTGCGA
436 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
459 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
*
482 AATAGTAAGC
1 AACAGTAAGC
492 GTGCTAGCGT
Statistics
Matches: 148, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.11
23 107 0.72
24 4 0.03
26 15 0.10
27 5 0.03
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Found at i:3303 original size:168 final size:168
Alignment explanation
Indices: 3002--3360 Score: 522
Period size: 168 Copynumber: 2.1 Consensus size: 168
2992 CCAAATTCGT
* *
3002 CTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAATGATGCGATCATTTTCCTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGATCATCTTCCTGATGAGACAC
* * * * * * * *
3067 CGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATATTCAAATCTCAGCTTTCTGAT
66 CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATATTCAAACCCCAGCTTCCCGAT
* * * *
3132 GAGACACCGAGAAGCAGGT-TAAAGCAATAAACGGTTAG
131 GAGACACCGAGAAGAAGGTCGAAA-CAATAAAAGGTCAG
* *
3170 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGATCATCTTCCTGATGAGACAC
* * *
3235 TGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCCGAT
66 CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATATTCAAACCCCAGCTTCCCGAT
3300 GAGACACCGAGAAGAAGGTCGAAACAATAAAAGGTCAG
131 GAGACACCGAGAAGAAGGTCGAAACAATAAAAGGTCAG
*
3338 CTTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
3361 TGTACCAAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
168 167 0.98
169 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (168 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGATCATCTTCCTGATGAGACAC
CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATATTCAAACCCCAGCTTCCCGAT
GAGACACCGAGAAGAAGGTCGAAACAATAAAAGGTCAG
Found at i:3535 original size:205 final size:205
Alignment explanation
Indices: 3170--3565 Score: 580
Period size: 205 Copynumber: 1.9 Consensus size: 205
3160 AAACGGTTAG
* *
3170 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
* * *
3235 TGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCCGAT
66 CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
* *
3300 GAGACACCGAGAAGAAGGTCGAAACAATAAA-AGGTCAGCTTCCTGATGAGATACTGAGAAGTGT
131 AAGACACCGAGAAGAAGGTCGAAACAATAAACA-GTCAGCTTCCTGATGAGATACAGAGAAGTGT
3364 ACCAAATTCGT
195 ACCAAATTCGT
*
3375 CTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
* * * * * * *
3440 CGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATCCCATCTTCCTAAT
66 CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
* * * * *
3505 AAGACACCGAGAAGCAGGT-TAAAGCAATAAACAGTTAGCTTCTTTATGAGATACAGAGAAG
131 AAGACACCGAGAAGAAGGTCGAAA-CAATAAACAGTCAGCTTCCTGATGAGATACAGAGAAG
3566 CGGATTGAAA
Statistics
Matches: 169, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
204 3 0.02
205 165 0.98
206 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (205 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
CGAGAAGAAGACAAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
AAGACACCGAGAAGAAGGTCGAAACAATAAACAGTCAGCTTCCTGATGAGATACAGAGAAGTGTA
CCAAATTCGT
Found at i:3642 original size:373 final size:373
Alignment explanation
Indices: 2927--3938 Score: 1769
Period size: 373 Copynumber: 2.7 Consensus size: 373
2917 TCATCTTCTT
*
2927 GATGAGACACCGAGAAGCAGGTCGAAAC---AAAAGGTCAGCTTCCTGATGAGATACTGAAAAGT
1 GATGAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
* * *
2989 GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAATGATGCGATCATTTT
66 GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
*
3054 CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATATTCAAATC
131 CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATC
* * *
3119 TCAGCTTTCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACGGTTAGCTTCCTGATGAGAT
196 CCAGCTTCCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCCTGATGAGAT
* *
3184 ACAGAGAAGCGGATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACAA
261 ACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACAA
3249 AATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCC
326 AATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCC
*
3297 GATGAGACACCGAGAAGAAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
1 GATGAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
3362 GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
66 GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
3427 CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATC
131 CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATC
* * * * *
3492 CCATCTTCCTAATAAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCTTTATGAGAT
196 CCAGCTTCCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCCTGATGAGAT
*
3557 ACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCA
261 ACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACAA
* * *
3622 AATCAAACTCATGTTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCC
326 AATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCC
3670 GATGAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
1 GATGAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
*
3735 GTACCAAATTCGTCTTCTTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
66 GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
* * * *
3800 CTTGATGAGATACTGAGAAGAAGACCAGATCAAACCCACGCTCGATGTAAGCAAATCTTCAAATC
131 CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATC
3865 CCAGCTTCCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCCTGATGAGAT
196 CCAGCTTCCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCCTGATGAGAT
*
3930 ACTGAGAAG
261 ACAGAGAAG
3939 GAGGCCAAGA
Statistics
Matches: 607, Mismatches: 32, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
370 27 0.04
373 580 0.96
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (373 bp):
GATGAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAGCTTCCTGATGAGATACTGAGAAGT
GTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT
CCTGATGAGACACCGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATC
CCAGCTTCCTGATGAGACACCGAGAAGCAGGTTAAAGCAATAAACAGTTAGCTTCCTGATGAGAT
ACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACAA
AATCAAACCCACGCTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCC
Found at i:3680 original size:168 final size:168
Alignment explanation
Indices: 3375--3733 Score: 515
Period size: 168 Copynumber: 2.1 Consensus size: 168
3365 CCAAATTCGT
* *
3375 CTTCCTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGACAC
* * * * *
3440 CGAGAAGAAGACCAGATCAAACTCACGCTCGATGTAAGCAAATCTTCAAATCCCATCTTCCTAAT
66 CGAGAAGAAGACCAAATCAAACTCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
* *
3505 AAGACACCGAGAAGCAGGT-TAAAGCAATAAACA-GTTAG
131 AAGACACCGAGAAGCAGGTCGAAA-CAATAAA-AGGTCAG
* * *
3543 CTTCTTTATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGACAC
* * * * *
3608 TGAGAAGAAGACCAAATCAAACTCATGTTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCCGAT
66 CGAGAAGAAGACCAAATCAAACTCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
*
3673 GAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAG
131 AAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAG
*
3711 CTTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
3734 TGTACCAAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
167 1 0.01
168 164 0.98
169 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (168 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGACAC
CGAGAAGAAGACCAAATCAAACTCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCAAT
AAGACACCGAGAAGCAGGTCGAAACAATAAAAGGTCAG
Found at i:3908 original size:205 final size:205
Alignment explanation
Indices: 3543--3938 Score: 634
Period size: 205 Copynumber: 1.9 Consensus size: 205
3533 AAACAGTTAG
*
3543 CTTCTTTATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATAC
1 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATAC
* * * *
3608 TGAGAAGAAGACCAAATCAAACTCATGTTCGATGCAAGCAAATCTTCCAACCCCAGCTTCCCGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCGAT
3673 GAGACACCGAGAAGCAGGTCGAAACAATAAA-AGGTCAGCTTCCTGATGAGATACTGAGAAGTGT
131 GAGACACCGAGAAGCAGGTCGAAACAATAAACA-GTCAGCTTCCTGATGAGATACTGAGAAGTGT
3737 ACCAAATTCGT
195 ACCAAATTCGT
* * *
3748 CTTCTTGATGAGATACGGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCTTGATGAGATAC
1 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATAC
* * * *
3813 TGAGAAGAAGACCAGATCAAACCCACGCTCGATGTAAGCAAATCTTCAAATCCCAGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCGAT
* *
3878 GAGACACCGAGAAGCAGGT-TAAAGCAATAAACAGTTAGCTTCCTGATGAGATACTGAGAAG
131 GAGACACCGAGAAGCAGGTCGAAA-CAATAAACAGTCAGCTTCCTGATGAGATACTGAGAAG
3939 GAGGCCAAGA
Statistics
Matches: 175, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
204 3 0.02
205 171 0.98
206 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCATCTTCCTGATGAGATAC
TGAGAAGAAGACCAAATCAAACCCACGCTCGATGCAAGCAAATCTTCAAACCCCAGCTTCCCGAT
GAGACACCGAGAAGCAGGTCGAAACAATAAACAGTCAGCTTCCTGATGAGATACTGAGAAGTGTA
CCAAATTCGT
Found at i:4277 original size:6 final size:6
Alignment explanation
Indices: 4266--4346 Score: 50
Period size: 6 Copynumber: 14.2 Consensus size: 6
4256 CGGGCCCAAC
* * * *
4266 AAATTT AAATTT -ATTTT AAAATT AAGTTT --ATTCT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAATTT
4312 --ATTT AAATTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT AAATTT AAATT-T AAATTT AAATTT -AAATTT A
4347 TTTAAATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
4 9 0.16
5 6 0.10
6 31 0.53
7 12 0.21
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:4307 original size:17 final size:17
Alignment explanation
Indices: 4266--4353 Score: 74
Period size: 17 Copynumber: 5.2 Consensus size: 17
4256 CGGGCCCAAC
*
4266 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTCT
* *
4283 AAAATTAAGTTTATTCT
1 AAATTTAAATTTATTCT
*
4300 GAATTTAAATTTATT-T
1 AAATTTAAATTTATTCT
* **
4316 AAATTTATTATAAATT-T
1 AAATTTA-AATTTATTCT
4333 AAATTTAAAATTTATT-T
1 AAATTT-AAATTTATTCT
4350 AAAT
1 AAAT
4354 AATGTCCAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
16 7 0.12
17 48 0.86
18 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTCT
Found at i:4322 original size:27 final size:27
Alignment explanation
Indices: 4287--4353 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
4277 TATTTTAAAA
* * *
4287 TTAAGTTTATTCTGAATTTAAATTTAT
1 TTAAATTTATTATAAATTTAAATTTAT
4314 TTAAATTTATTATAAATTTAAATTTA-
1 TTAAATTTATTATAAATTTAAATTTAT
4340 --AAATTTATT-TAAAT
1 TTAAATTTATTATAAAT
4354 AATGTCCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 5 0.14
24 9 0.24
27 23 0.62
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (27 bp):
TTAAATTTATTATAAATTTAAATTTAT
Found at i:4331 original size:11 final size:10
Alignment explanation
Indices: 4302--4353 Score: 68
Period size: 10 Copynumber: 4.8 Consensus size: 10
4292 TTTATTCTGA
4302 ATTTAAATTT
1 ATTTAAATTT
4312 ATTTAAATTT
1 ATTTAAATTT
4322 ATTATAAATTT
1 ATT-TAAATTT
4333 AAATTTAAAATTT
1 --ATTT-AAATTT
4346 ATTTAAAT
1 ATTTAAAT
4354 AATGTCCAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 1 0.03
13 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:5032 original size:18 final size:18
Alignment explanation
Indices: 4993--5030 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
4983 ACATTAAATG
4993 AAAT-TTATTATTATTAA
1 AAATATTATTATTATTAA
5010 AAATATTATTATTAATTAA
1 AAATATTATTATT-ATTAA
5029 AA
1 AA
5031 TAAAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATTATTATTATTAA
Found at i:6250 original size:59 final size:58
Alignment explanation
Indices: 6141--6401 Score: 255
Period size: 59 Copynumber: 4.4 Consensus size: 58
6131 GGAGGTCCTT
* *
6141 AAACTATCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCG
1 AAACT-TCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATC-CATTTTTGACCTCG
* * *
6201 AAACTTCCT-AAAATTACCATTTTACCCTCGAAC-TCTAAAAATTACCATTTTTAACCTCG
1 AAACTT-CTAAAAATTACCATTTTACCCTCAAACTTCCAAAAA-T-CCATTTTTGACCTCG
* * *
6260 AACCTTCTAAAAATTACCATTTAACCC-CTAAACTCCCAAAAATCCTATTTTTGACCTCG
1 AAACTTCTAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCC-ATTTTTGACCTCG
* * * * * *
6319 AAACTTTTAAAAAAAATACCATTTTACCCTCGAACTTCCAAAAATCTCGTTTTTAACCCCG
1 AAACTTCT--AAAAATTACCATTTTACCCTCAAACTTCCAAAAATC-CATTTTTGACCTCG
*
6380 AAAC--C-AAAAATTACTATTTTAC
1 AAACTTCTAAAAATTACCATTTTAC
6402 TCCCGGATGT
Statistics
Matches: 167, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
56 15 0.09
58 12 0.07
59 80 0.48
60 14 0.08
61 44 0.26
62 2 0.01
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (58 bp):
AAACTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCATTTTTGACCTCG
Found at i:8041 original size:20 final size:20
Alignment explanation
Indices: 8018--8055 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8008 TCAAAATATT
8018 ATAAAAACTTAAAAAAATAC
1 ATAAAAACTTAAAAAAATAC
**
8038 ATAAAAGTTTAAAAAAAT
1 ATAAAAACTTAAAAAAAT
8056 TATAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (20 bp):
ATAAAAACTTAAAAAAATAC
Found at i:8060 original size:19 final size:19
Alignment explanation
Indices: 8010--8060 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
8000 TTAGAAACTC
*
8010 AAAATATTATAAAAACTTA
1 AAAAAATTATAAAAACTTA
* **
8029 AAAAAATACATAAAAGTTTA
1 AAAAAAT-TATAAAAACTTA
8049 AAAAAATTATAA
1 AAAAAATTATAA
8061 GTAATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAAAACTTA
Found at i:9894 original size:15 final size:15
Alignment explanation
Indices: 9842--9894 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
9832 GATGATATAA
*
9842 ATTTCCAAATGAATGT
1 ATTTTCAAAT-AATGT
* * *
9858 ATTTTCAACTTATAT
1 ATTTTCAAATAATGT
9873 AATTTTCAAATAATGT
1 -ATTTTCAAATAATGT
9889 ATTTTC
1 ATTTTC
9895 TACGTATTTC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (15 bp):
ATTTTCAAATAATGT
Found at i:15326 original size:20 final size:21
Alignment explanation
Indices: 15286--15327 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15276 ATACTCAAAA
*
15286 TTTGGATTTAATATAGTTATT
1 TTTGGAGTTAATATAGTTATT
15307 TTTGGAGTTAATAT-GTTATT
1 TTTGGAGTTAATATAGTTATT
15327 T
1 T
15328 ACTCTTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
TTTGGAGTTAATATAGTTATT
Found at i:24169 original size:15 final size:17
Alignment explanation
Indices: 24149--24185 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
24139 ACTTGTTATT
24149 TTTATA-TATT-CTAGA
1 TTTATACTATTACTAGA
24164 TTTATACTATTACTAGA
1 TTTATACTATTACTAGA
*
24181 ATTAT
1 TTTAT
24186 TAGAACTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTATACTATTACTAGA
Found at i:27273 original size:42 final size:42
Alignment explanation
Indices: 27175--27285 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
27165 CTTTTTCCAG
* * * *
27175 GGAGTTGCTCAGTTGCGAGGGTTGAATGAGTCTCCTGAATAT
1 GGAGATGCTCAGTTCCCAGGGTTGAATGAGTCCCCTGAATAT
* *
27217 GGAGATGCTGAGTTCCCAGGGTTGAATGAGTCCCCTGGATAT
1 GGAGATGCTCAGTTCCCAGGGTTGAATGAGTCCCCTGAATAT
* * *
27259 TGAGCTGCTCAGTTCCCATGGTTGAAT
1 GGAGATGCTCAGTTCCCAGGGTTGAAT
27286 CAGATTCATG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (42 bp):
GGAGATGCTCAGTTCCCAGGGTTGAATGAGTCCCCTGAATAT
Done.