Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014602.1 Kokia drynarioides strain JFW-HI SEQ_129641, 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: 80342
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:1280 original size:60 final size:61
Alignment explanation
Indices: 1164--1280 Score: 132
Period size: 60 Copynumber: 1.9 Consensus size: 61
1154 GTTTCAAGGA
* * * **
1164 CTAACTTGGACCAAAGAAAAAGTTCAAGCTCCCATGTGAAAACAATTGCCTTGTTCAGGGC
1 CTAACTTGGACCAAAAAAAAAGTTCAAGCTCCAATATGAAAACAATTGCCAAGTTCAGGGC
* *
1225 CTAACTTGGA-CAAAAAAAAAGTTC-AGGTCCAAGTATGGGAAA-AATTGCCAAGTTCA
1 CTAACTTGGACCAAAAAAAAAGTTCAAGCTCCAA-TAT-GAAAACAATTGCCAAGTTCA
1281 TGCCTCAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
59 6 0.13
60 27 0.57
61 14 0.30
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (61 bp):
CTAACTTGGACCAAAAAAAAAGTTCAAGCTCCAATATGAAAACAATTGCCAAGTTCAGGGC
Found at i:4965 original size:31 final size:31
Alignment explanation
Indices: 4927--4994 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4917 CTTATTTTCA
*
4927 AAAAAAATATAAAAT-AATTATTAAATTATTT
1 AAAAAAAT-TAAAATAAATTATTAAATTATTC
* **
4958 AAAAAAATTCATTTAAATTATTAAATTATTC
1 AAAAAAATTAAAATAAATTATTAAATTATTC
4989 AAAAAA
1 AAAAAA
4995 TTATTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAAAAATTAAAATAAATTATTAAATTATTC
Found at i:5740 original size:17 final size:16
Alignment explanation
Indices: 5720--5755 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5710 AATTTGATTA
*
5720 TTTTGAATTTTTATAAT
1 TTTTAAATTTTTA-AAT
5737 TTTTAAATTTTTAAAT
1 TTTTAAATTTTTAAAT
5753 TTT
1 TTT
5756 AATCATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTAAATTTTTAAAT
Found at i:5757 original size:7 final size:8
Alignment explanation
Indices: 5720--5755 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5710 AATTTGATTA
*
5720 TTTTGAAT
1 TTTTAAAT
5728 TTTTATAAT
1 TTTTA-AAT
5737 TTTTAAAT
1 TTTTAAAT
5745 TTTTAAAT
1 TTTTAAAT
5753 TTT
1 TTT
5756 AATCATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (8 bp):
TTTTAAAT
Found at i:7305 original size:26 final size:26
Alignment explanation
Indices: 7269--7321 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
7259 TTTTTGTCTG
7269 GTTGGTGTTCTGGAAAAGAGAAATAT
1 GTTGGTGTTCTGGAAAAGAGAAATAT
7295 GTTGGTGTTCTGGAAAAGAGAAATAT
1 GTTGGTGTTCTGGAAAAGAGAAATAT
7321 G
1 G
7322 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (26 bp):
GTTGGTGTTCTGGAAAAGAGAAATAT
Found at i:8684 original size:191 final size:191
Alignment explanation
Indices: 8360--8741 Score: 712
Period size: 191 Copynumber: 2.0 Consensus size: 191
8350 CATCTAGTGA
*
8360 CTTTTTGCTAGGCAGATCACCTCACCTTACTTTTTTCAAACTGTGGAGTTTCTGGAGAAGATGAT
1 CTTTTTGCTAGGCAGATCACCTCACCTTACTTTTGTCAAACTGTGGAGTTTCTGGAGAAGATGAT
**
8425 GTTATATTCATTCAATATTTGATGGCTCTAAGTCTAATTATGTTCATTCTCTAATTATCAGGTTT
66 GTTATATTCATTCAATATTTGATGGCTCTAAGTCTAATTATGTTCATTCTCTAACCATCAGGTTT
8490 TATGCTTTTTGCAGGGTCACATGTACATATTTGCTCATTTTATTTGCTTTTATTCCAATAT
131 TATGCTTTTTGCAGGGTCACATGTACATATTTGCTCATTTTATTTGCTTTTATTCCAATAT
*
8551 CTTTTTGCTAGGCAGATCACCTCACTTTACTTTTGTCAATA-TGTGGAGTTTCTGGAGAAGATGA
1 CTTTTTGCTAGGCAGATCACCTCACCTTACTTTTGTCAA-ACTGTGGAGTTTCTGGAGAAGATGA
8615 TGTTATATTCATTCAATATTTGATGGCTCTAAGTCTAATTATGTTCATTCTCTAACCATCAGGTT
65 TGTTATATTCATTCAATATTTGATGGCTCTAAGTCTAATTATGTTCATTCTCTAACCATCAGGTT
8680 TTATGCTTTTTGCAGGGTCACATGTACATATTTGCTCATTTTATTTGCTTTTATTCCAATAT
130 TTATGCTTTTTGCAGGGTCACATGTACATATTTGCTCATTTTATTTGCTTTTATTCCAATAT
8742 ATTAGGATTT
Statistics
Matches: 186, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
191 185 0.99
192 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (191 bp):
CTTTTTGCTAGGCAGATCACCTCACCTTACTTTTGTCAAACTGTGGAGTTTCTGGAGAAGATGAT
GTTATATTCATTCAATATTTGATGGCTCTAAGTCTAATTATGTTCATTCTCTAACCATCAGGTTT
TATGCTTTTTGCAGGGTCACATGTACATATTTGCTCATTTTATTTGCTTTTATTCCAATAT
Found at i:14618 original size:12 final size:12
Alignment explanation
Indices: 14597--14642 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
14587 TCATTAACAT
*
14597 TGTTCGTGAATA
1 TGTTCATGAATA
14609 TGTTCATGAATA
1 TGTTCATGAATA
*
14621 TGTTCAAT-TATA
1 TGTTC-ATGAATA
14633 TGTTCATGAA
1 TGTTCATGAA
14643 CATATTCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (12 bp):
TGTTCATGAATA
Found at i:14625 original size:24 final size:23
Alignment explanation
Indices: 14597--14668 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
14587 TCATTAACAT
*
14597 TGTTCGTGAATATGTTCATGAATA
1 TGTTCGT-TATATGTTCATGAATA
* *
14621 TGTTCAATTATATGTTCATGAACA
1 TGTTC-GTTATATGTTCATGAATA
* *
14645 TATTCGTT-TAATGTTCGTGAATA
1 TGTTCGTTAT-ATGTTCATGAATA
14668 T
1 T
14669 ATTCAATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.03
23 14 0.36
24 23 0.59
25 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTTCGTTATATGTTCATGAATA
Found at i:14678 original size:23 final size:23
Alignment explanation
Indices: 14608--14678 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
14598 GTTCGTGAAT
*
14608 ATGTTCATGAATATGTTCAATTA
1 ATGTTCATGAATATATTCAATTA
* **
14631 TATGTTCATGAACATATTCGTTTA
1 -ATGTTCATGAATATATTCAATTA
*
14655 ATGTTCGTGAATATATTCAATTA
1 ATGTTCATGAATATATTCAATTA
14678 A
1 A
14679 GTTAACTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.44
Consensus pattern (23 bp):
ATGTTCATGAATATATTCAATTA
Found at i:14766 original size:28 final size:30
Alignment explanation
Indices: 14709--14766 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14699 AACATTAAAC
*
14709 AAACGAACATGAACACAAATAATTTTAAAT
1 AAACGAACATGAACACAAATAATTTGAAAT
*
14739 AAACGAACATGAACA-AAA-CATTTGAAAT
1 AAACGAACATGAACACAAATAATTTGAAAT
14767 TCTTAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 8 0.31
29 3 0.12
30 15 0.58
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (30 bp):
AAACGAACATGAACACAAATAATTTGAAAT
Found at i:24969 original size:17 final size:18
Alignment explanation
Indices: 24946--25056 Score: 124
Period size: 17 Copynumber: 6.3 Consensus size: 18
24936 CCAAACTCGT
24946 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
24964 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
*
24981 TTTAAATCTATTTTAA-A
1 TTTAAATTTATTTTAAGA
24998 TTTAAATTTATTTTAAG-
1 TTTAAATTTATTTTAAGA
25015 TTTAAATTTATTTTTAA-A
1 TTTAAATTTA-TTTTAAGA
* *
25033 TTTAAAAATTATTATAA-A
1 TTT-AAATTTATTTTAAGA
25051 TTTAAA
1 TTTAAA
25057 ATAAATAAAG
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
17 44 0.54
18 31 0.38
19 6 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:24985 original size:35 final size:34
Alignment explanation
Indices: 24946--25056 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
24936 CCAAACTCGT
*
24946 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTT-AAA
* *
24981 TTTAAATCTATTTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
* *
25015 TTTAAATTTATTTTTAAATTTAAAAATTATTATAAA
1 TTTAAATTTA-TTTTAAATTT-AAATTTATTTTAAA
25051 TTTAAA
1 TTTAAA
25057 ATAAATAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
34 12 0.18
35 37 0.56
36 17 0.26
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:25008 original size:52 final size:52
Alignment explanation
Indices: 24946--25056 Score: 161
Period size: 52 Copynumber: 2.1 Consensus size: 52
24936 CCAAACTCGT
* *
24946 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTT-AAATCTATTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTTAAAAT-TATTATAAA
* *
24998 TTTAAATTTATTTTAAGTTTAAATTTATTTTTAAATTTAAAAATTATTATAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTT-AAAATTATTATAAA
25051 TTTAAA
1 TTTAAA
25057 ATAAATAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
52 35 0.66
53 14 0.26
54 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (52 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:25056 original size:6 final size:6
Alignment explanation
Indices: 24978--25038 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
24968 ATTTGTTTTA
* * * *
24978 AAATTT AAATCT -ATTTT AAATTT AAATTT -ATTTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
25024 ATTTTT AAATTT AAA
1 AAATTT AAATTT AAA
25039 AATTATTATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
5 7 0.17
6 35 0.83
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:25068 original size:52 final size:52
Alignment explanation
Indices: 24964--25068 Score: 115
Period size: 52 Copynumber: 2.0 Consensus size: 52
24954 TATTTTAAGA
* * * ** *
24964 TTAAATTTGTTTTAAAATTTAAATCTATTTTAAATTTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAATTTAAATCTATTATAAATTTAAATATAAATAAAGT
*
25016 TTAAATTTATTTTTAAATTTAAAAAT-TATTATAAATTTAAA-ATAAATAAAGT
1 TTAAATTTATTTTAAAATTT--AAATCTATTATAAATTTAAATATAAATAAAGT
25068 T
1 T
25069 CAATTACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
52 26 0.59
53 14 0.32
54 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (52 bp):
TTAAATTTATTTTAAAATTTAAATCTATTATAAATTTAAATATAAATAAAGT
Found at i:25778 original size:32 final size:34
Alignment explanation
Indices: 25742--25815 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 34
25732 ATTAATAGCA
* *
25742 ATAATAATTATT-TTAATAA-TAATAAT-TTTATT
1 ATAATAATTATTGATAATAACT-ATAATATTTAAT
25774 ATAATAA-TATTGATAATAACTATAATATTTAAT
1 ATAATAATTATTGATAATAACTATAATATTTAAT
25807 A-AATAATTA
1 ATAATAATTA
25816 ATAATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.11
32 23 0.64
33 9 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (34 bp):
ATAATAATTATTGATAATAACTATAATATTTAAT
Found at i:25779 original size:14 final size:15
Alignment explanation
Indices: 25741--25792 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
25731 TATTAATAGC
*
25741 AATAATAATTATTTT
1 AATAATAATAATTTT
25756 AATAATAATAATTTT
1 AATAATAATAATTTT
* *
25771 -ATTATAATAATATT
1 AATAATAATAATTTT
*
25785 GATAATAA
1 AATAATAA
25793 CTATAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATAATAATAATTTT
Found at i:26975 original size:59 final size:58
Alignment explanation
Indices: 26893--27237 Score: 351
Period size: 59 Copynumber: 5.9 Consensus size: 58
26883 TAAACTGTCT
* * * **
26893 AAAAAATCCACTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCGACTCTAAAACTTCC
1 AAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTCCATTTT-TACCCTCGAACTTCC
* *
26953 AAAATTTCCATTTTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
* *
27011 AAAAATTCCATTTTCGACCTCGAAACTTCCAAAAA-TCTCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTT-GACCCCAAAACTTCCAAAAATTC-CATTTTTACCCTCGAACTTCC
* * * * *
27070 AAAAATTCCATTTTGACCCTC-GAACTTCTAAAAATTCC-TTTTTACCCTTGATCTTCT
1 AAAAATTCCATTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
* * * ** *
27127 AAAAATTCCATTTTTGATCCCGAAACTTCCAAAAATCACCATTTTGCCCCT-GGA-TGTCC
1 AAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAAT-TCCATTTTTACCCTCGAACT-TCC
* * * *
27186 AAAAACTCTATTTTCGACCTCGAAAC-TCCAAAAATTCCATTTTTACCCTCGA
1 AAAAATTCCATTTT-GACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGA
27238 TCTAAAATTA
Statistics
Matches: 240, Mismatches: 34, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
57 38 0.16
58 77 0.32
59 109 0.45
60 16 0.07
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (58 bp):
AAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:27009 original size:88 final size:85
Alignment explanation
Indices: 26884--27233 Score: 298
Period size: 88 Copynumber: 4.0 Consensus size: 85
26874 GGAGGTCCCT
* * *
26884 AAACTGTCTAAAAAATCCACTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTCGACTCTAAAA
1 AAACT-TCCAAAAATTCCA-TTTTGACCCTC-GAACTTCCAAAAATTCCATTTTCGAC-CTAAAA
26948 CTTCCAAAATTTCCATTTTGACCCC
62 CTTCCAAAA-TTCCATTTTGACCCC
* * *
26973 AAAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCGACCTCGAAACT
1 -AAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTCCATTTTCGACCT-AAAACT
* *
27038 TCCAAAAATCTCATTTTTACCCTC
64 TCCAAAATTC-CATTTTGACCC-C
* * * ** *
27062 GAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCTAAAAATTCC-TTTT-TACCCTTGATCTT
1 AAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTCCATTTTCGA-CCTAAAACTT
* *
27125 CTAAAAATTCCATTTTTGATCCCG
65 C-CAAAATTCCA-TTTTGA-CCCC
* * * * * *
27149 AAACTTCCAAAAATCACCATTTTGCCCCT-GGA-TGTCCAAAAACTCTATTTTCGACCTCGAAAC
1 AAACTTCCAAAAAT-TCCATTTTGACCCTCGAACT-TCCAAAAATTCCATTTTCGACCT-AAAAC
*
27212 -TCCAAAAATTCCATTTTTACCC
63 TTCC-AAAATTCCATTTTGACCC
27234 TCGATCTAAA
Statistics
Matches: 213, Mismatches: 33, Indels: 32
0.77 0.12 0.12
Matches are distributed among these distances:
86 12 0.06
87 51 0.24
88 130 0.61
89 15 0.07
90 5 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (85 bp):
AAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTCCATTTTCGACCTAAAACTTC
CAAAATTCCATTTTGACCCC
Found at i:27235 original size:29 final size:30
Alignment explanation
Indices: 26884--27237 Score: 317
Period size: 29 Copynumber: 12.0 Consensus size: 30
26874 GGAGGTCCCT
* * *
26884 AAACTGTCTAAAAAATCCACTTTTGACCC-CA
1 AAACT-TCCAAAAATTCCA-TTTTGACCCTCG
* *
26915 AAACTTCCAAAAATTCCATTTTCGACTCT-A
1 AAACTTCCAAAAATTCCATTTT-GACCCTCG
* *
26945 AAACTTCCAAAATTTCCATTTTGACCC-CA
1 AAACTTCCAAAAATTCCATTTTGACCCTCG
* *
26974 AAACTTCCAAAAATTCTATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCCTCG
27004 -AACTTCCAAAAATTCCATTTTCGA-CCTCG
1 AAACTTCCAAAAATTCCATTTT-GACCCTCG
*
27033 AAACTTCCAAAAA-TCTCATTTTTACCCTCG
1 AAACTTCCAAAAATTC-CATTTTGACCCTCG
27063 -AACTTCCAAAAATTCCATTTTGACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCCTCG
* * *
27092 -AACTTCTAAAAATTCC-TTTTTACCCTTG
1 AAACTTCCAAAAATTCCATTTTGACCCTCG
* * *
27120 -ATCTTCTAAAAATTCCATTTTTGATCC-CG
1 AAACTTCCAAAAATTCCA-TTTTGACCCTCG
* *
27149 AAACTTCCAAAAATCACCATTTTGCCCCT-G
1 AAACTTCCAAAAAT-TCCATTTTGACCCTCG
* * *
27179 -GA-TGTCCAAAAACTCTATTTTCGA-CCTCG
1 AAACT-TCCAAAAATTCCATTTT-GACCCTCG
*
27208 AAAC-TCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCCTCG
27237 A
1 A
27238 TCTAAAATTA
Statistics
Matches: 269, Mismatches: 34, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
28 36 0.13
29 134 0.50
30 91 0.34
31 8 0.03
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTGACCCTCG
Found at i:40474 original size:14 final size:14
Alignment explanation
Indices: 40455--40482 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40445 AAAATATTGC
40455 CCAAAATGAAAATA
1 CCAAAATGAAAATA
40469 CCAAAATGAAAATA
1 CCAAAATGAAAATA
40483 AATGGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
CCAAAATGAAAATA
Found at i:49665 original size:16 final size:17
Alignment explanation
Indices: 49637--49668 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
49627 CTACAATTTC
49637 TTTGAACTTTTTTTATT
1 TTTGAACTTTTTTTATT
49654 TTTGAA-TTTTTTTAT
1 TTTGAACTTTTTTTAT
49669 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTGAACTTTTTTTATT
Found at i:51640 original size:20 final size:19
Alignment explanation
Indices: 51603--51650 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
51593 TTAATTTTAG
51603 AAATAAATTATTATAAATT
1 AAATAAATTATTATAAATT
*
51622 TAATAAATATATT-TAAAATT
1 AAATAAAT-TATTAT-AAATT
51642 AAATAAATT
1 AAATAAATT
51651 TAGACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAAATTATTATAAATT
Found at i:53085 original size:13 final size:13
Alignment explanation
Indices: 53067--53093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53057 AATTTTTTTA
53067 ATTTTTAATTAAT
1 ATTTTTAATTAAT
53080 ATTTTTAATTAAT
1 ATTTTTAATTAAT
53093 A
1 A
53094 AATATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTAATTAAT
Found at i:53914 original size:28 final size:28
Alignment explanation
Indices: 53874--53935 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
53864 AACGACGTAA
53874 CCCTTTATCGCTTTAACCTTTTCGTTTG
1 CCCTTTATCGCTTTAACCTTTTCGTTTG
53902 CCCTTTATCGCTTTAACCTTTTCGTTTG
1 CCCTTTATCGCTTTAACCTTTTCGTTTG
53930 CTCCTT
1 C-CCTT
53936 GTTATAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.50
Consensus pattern (28 bp):
CCCTTTATCGCTTTAACCTTTTCGTTTG
Found at i:54166 original size:2 final size:2
Alignment explanation
Indices: 54159--54187 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54149 TGAGCCCACA
54159 AT AT 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 AT AT A
54188 CATACTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61517 original size:29 final size:30
Alignment explanation
Indices: 61457--61520 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
61447 ACTTATTTTA
*
61457 TTGTTAATTTTGTTATCATTTTAGAGACAT
1 TTGTTAATTTTGTTATCATTTTAAAGACAT
*
61487 TTGTTAATTTTG-TA-CTATTTTAAAGATAT
1 TTGTTAATTTTGTTATC-ATTTTAAAGACAT
61516 TTGTT
1 TTGTT
61521 TATTAAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.03
29 18 0.58
30 12 0.39
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATCATTTTAAAGACAT
Found at i:69698 original size:22 final size:22
Alignment explanation
Indices: 69670--69713 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
69660 ATATTCATTA
69670 GATTCTATAGTTAGGTAAAGTG
1 GATTCTATAGTTAGGTAAAGTG
69692 GATTCTATAGTTAGGTAAAGTG
1 GATTCTATAGTTAGGTAAAGTG
69714 CCAAACTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (22 bp):
GATTCTATAGTTAGGTAAAGTG
Found at i:77080 original size:24 final size:24
Alignment explanation
Indices: 77052--77097 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
77042 TCTGCCTTTC
77052 TTCCACTCTCT-TCTTTCCTTGTCT
1 TTCCA-TCTCTGTCTTTCCTTGTCT
* *
77076 TTCCATCTTTGTCTTTTCTTGT
1 TTCCATCTCTGTCTTTCCTTGT
77098 TTTATTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.04, C:0.30, G:0.07, T:0.59
Consensus pattern (24 bp):
TTCCATCTCTGTCTTTCCTTGTCT
Done.