Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004977.1 Kokia drynarioides strain JFW-HI SEQ_118711, 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: 33334
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:1537 original size:30 final size:29
Alignment explanation
Indices: 1503--1826 Score: 239
Period size: 29 Copynumber: 11.0 Consensus size: 29
1493 GTCCCGAAAT
*
1503 TTCCAAAAATCCCATTTTTAAACCCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
*
1533 TTCCAAAAATTACCA-TTTTACCCCCGAA-C
1 TTCCAAAAA-TCCCATTTTTA-CCCCGAACC
*
1562 TTCCAAAAATCCAATTTTTGACCCCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* * * * *
1592 TTCCAAAATTACTA-TTTTACCCCCAAAC
1 TTCCAAAAATCCCATTTTTACCCCGAACC
* *
1620 TTCCAAAAAATCCCATTTTAAACCCCAAACC
1 TTCC-AAAAATCCCATTTT-TACCCCGAACC
* * * *
1651 TTCAAAAAATTACCA-TTTTACCCCCAAAC
1 TTCCAAAAA-TCCCATTTTTACCCCGAACC
* *
1680 TTCCAAAAGGTCCCATTTTTTACCCCGAGCC
1 TTCCAAAA-ATCCCA-TTTTTACCCCGAACC
* * *
1711 TGCC-AAAGTCCCATTTTTCACCCCGAGCC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* * *
1740 TTCCAAAAATGACCA-TTTTACCCCCAAAC
1 TTCCAAAAAT-CCCATTTTTACCCCGAACC
* * *
1769 TTCCAAAAGTCTCATTTTTACCCCAAACC
1 TTCCAAAAATCCCATTTTTACCCCGAACC
* *
1798 TTCAAAAAATTACCA-TTTTACCCCCGAAC
1 TTCCAAAAA-TCCCATTTTTA-CCCCGAAC
1827 GTTTGAAATT
Statistics
Matches: 233, Mismatches: 43, Indels: 36
0.75 0.14 0.12
Matches are distributed among these distances:
28 22 0.09
29 111 0.48
30 64 0.27
31 36 0.15
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTTACCCCGAACC
Found at i:1588 original size:59 final size:59
Alignment explanation
Indices: 1503--1717 Score: 297
Period size: 59 Copynumber: 3.6 Consensus size: 59
1493 GTCCCGAAAT
* *
1503 TTCCAAAAATCCCATTTTTAAACCCGAACCTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAAC
* * *
1562 TTCCAAAAATCCAATTTTTGACCCCGAACCTTCC-AAAATTACTATTTTACCCCCAAAC
1 TTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAAC
* * *
1620 TTCCAAAAAATCCCATTTTAAACCCCAAACCTTCAAAAAATTACCATTTTACCCCCAAAC
1 TTCC-AAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAAC
* * * *
1680 TTCCAAAAGGTCCCATTTTTTACCCCGAGCCTGCCAAA
1 TTCCAAAA-ATCCCATTTTTAACCCCGAACCTTCCAAA
1718 GTCCCATTTT
Statistics
Matches: 135, Mismatches: 18, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
58 26 0.19
59 60 0.44
60 49 0.36
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (59 bp):
TTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAAC
Found at i:1723 original size:89 final size:87
Alignment explanation
Indices: 1630--1792 Score: 245
Period size: 89 Copynumber: 1.9 Consensus size: 87
1620 TTCCAAAAAA
*
1630 TCCCATTTTAAACCCCAAACCTTCAAAAAATTACCATTTTACCCCCAAACTTCCAAAAGGTCCCA
1 TCCCATTTTAAACCCCAAACCTTCAAAAAATGACCATTTTACCCCCAAACTTCCAAAA-GTCCCA
1695 TTTTTTACCCCGAGCCTGCCAAAG
65 -TTTTTACCCCGAGCCTGCCAAAG
** * * * *
1719 TCCCATTTTTCACCCCGAGCCTTCCAAAAATGACCATTTTACCCCCAAACTTCCAAAAGTCTCAT
1 TCCCATTTTAAACCCCAAACCTTCAAAAAATGACCATTTTACCCCCAAACTTCCAAAAGTCCCAT
1784 TTTTACCCC
66 TTTTACCCC
1793 AAACCTTCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 10 0.15
88 5 0.07
89 52 0.78
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.28
Consensus pattern (87 bp):
TCCCATTTTAAACCCCAAACCTTCAAAAAATGACCATTTTACCCCCAAACTTCCAAAAGTCCCAT
TTTTACCCCGAGCCTGCCAAAG
Found at i:1734 original size:60 final size:58
Alignment explanation
Indices: 1503--1826 Score: 268
Period size: 59 Copynumber: 5.5 Consensus size: 58
1493 GTCCCGAAAT
* *
1503 TTCCAAAAATCCCATTTTTAAACCCGAACCTTCCAAAAATTACCA-TTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTAACCCCGAACCTTCC-AAAA-TACCATTTTTACCCCCAAAC
* * *
1562 TTCCAAAAATCCAATTTTTGACCCCGAACCTTCCAAAATTACTA-TTTTACCCCCAAAC
1 TTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAA-TACCATTTTTACCCCCAAAC
* * *
1620 TTCCAAAAAATCCCATTTTAAACCCCAAACCTTCAAAAAATTACCA-TTTTACCCCCAAAC
1 TTCC-AAAAATCCCATTTTTAACCCCGAACCTTC-CAAAA-TACCATTTTTACCCCCAAAC
* * * * * * * **
1680 TTCCAAAAGGTCCCATTTTTTACCCCGAGCCTGCCAAAGTCCCATTTTTCACCCCGAGCC
1 TTCCAAAA-ATCCCATTTTTAACCCCGAACCTTCCAAAATACCATTTTT-ACCCCCAAAC
* * *
1740 TTCCAAAAATGACCA-TTTT-ACCCCCAAACTTCCAAAAGT-CTCATTTTTA-CCCCAAACC
1 TTCCAAAAAT-CCCATTTTTAACCCCGAACCTTCCAAAA-TAC-CATTTTTACCCCCAAA-C
* * *
1798 TTCAAAAAATTACCA-TTTTACCCCCGAAC
1 TTCCAAAAA-TCCCATTTTTAACCCCGAAC
1827 GTTTGAAATT
Statistics
Matches: 217, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
57 4 0.02
58 62 0.29
59 87 0.40
60 64 0.29
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (58 bp):
TTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAATACCATTTTTACCCCCAAAC
Found at i:3117 original size:153 final size:153
Alignment explanation
Indices: 2839--3142 Score: 529
Period size: 153 Copynumber: 2.0 Consensus size: 153
2829 ACAAAACCTC
* *
2839 AAAAATGTTTCAAACTTTCAAATCTGAACTTATTTTTATAAAATCATAAAATTTAGTTTGAAACA
1 AAAAATGTTTCAAACTTTCAAATCCGAAATTATTTTTATAAAATCATAAAATTTAGTTTGAAACA
* *
2904 ATTGAAGCAATTTAGAAATATTTTAAAACCATTTAGAATAATGTCATAGGAGATTGAAAGTTTTT
66 ATAGAAGCAATTTAGAAATATTTTAAAACCATTTAGAAGAATGTCATAGGAGATTGAAAGTTTTT
2969 AGGTCAAAAATGAACTTCGGTTA
131 AGGTCAAAAATGAACTTCGGTTA
2992 AAAAATGTTTCAAACTTTCAAATCCGAAATTATTTTTATAAAATCATAAAATTTAGTTTGAAACA
1 AAAAATGTTTCAAACTTTCAAATCCGAAATTATTTTTATAAAATCATAAAATTTAGTTTGAAACA
* * *
3057 ATAGAAAG-AATTTATAAATATTTTAAAACCATTTAGAAGAATTTCTTAGGAGATTGAAAGTTTT
66 ATAG-AAGCAATTTAGAAATATTTTAAAACCATTTAGAAGAATGTCATAGGAGATTGAAAGTTTT
3121 TAGGTCAAAAATGAACTTCGGT
130 TAGGTCAAAAATGAACTTCGGT
3143 GGGATCAAAC
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
153 140 0.98
154 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (153 bp):
AAAAATGTTTCAAACTTTCAAATCCGAAATTATTTTTATAAAATCATAAAATTTAGTTTGAAACA
ATAGAAGCAATTTAGAAATATTTTAAAACCATTTAGAAGAATGTCATAGGAGATTGAAAGTTTTT
AGGTCAAAAATGAACTTCGGTTA
Found at i:11724 original size:48 final size:47
Alignment explanation
Indices: 11654--11745 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 47
11644 GTTTTGAATG
11654 TAATATATTCAAAGGTGGCGGGGTTAGAGAAAAGTAGAGGTTTATAC
1 TAATATATTCAAAGGTGGCGGGGTTAGAGAAAAGTAGAGGTTTATAC
11701 TAATATTATTCAAAGGTGGCGGGGTTAGAGAAAAGTAGAGGTTTA
1 TAATA-TATTCAAAGGTGGCGGGGTTAGAGAAAAGTAGAGGTTTA
11746 AAAATTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 5 0.11
48 39 0.89
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.28
Consensus pattern (47 bp):
TAATATATTCAAAGGTGGCGGGGTTAGAGAAAAGTAGAGGTTTATAC
Found at i:13969 original size:17 final size:17
Alignment explanation
Indices: 13925--13978 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
13915 TAATTTTATT
13925 TATATT-AATTATTTAA
1 TATATTAAATTATTTAA
* * * *
13941 AATTTTAGATTATTTTA
1 TATATTAAATTATTTAA
13958 TATATTAAATTATTTGAA
1 TATATTAAATTATTT-AA
13976 TAT
1 TAT
13979 TATTTATAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TATATTAAATTATTTAA
Found at i:14026 original size:18 final size:18
Alignment explanation
Indices: 14003--14049 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
13993 ATTATAGTAA
*
14003 ATTATTTGAATATCATTT
1 ATTATTTGAATATCATAT
*
14021 ATTA-TTAAATATCATAT
1 ATTATTTGAATATCATAT
*
14038 AATATTTGAATA
1 ATTATTTGAATA
14050 AAATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (18 bp):
ATTATTTGAATATCATAT
Found at i:16247 original size:7 final size:7
Alignment explanation
Indices: 16230--16262 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
16220 TGGTGGTGGT
16230 GGAGG-A
1 GGAGGAA
16236 GGAGGAA
1 GGAGGAA
16243 GGAGGAA
1 GGAGGAA
16250 GGAGGAA
1 GGAGGAA
16257 GGAGGA
1 GGAGGA
16263 CTGTTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (7 bp):
GGAGGAA
Found at i:17410 original size:8 final size:9
Alignment explanation
Indices: 17350--17410 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
17340 CATATCCTAC
*
17350 TCTCTCTAT
1 TCTCTCAAT
* *
17359 TATCTCAAA
1 TCTCTCAAT
* *
17368 TCTCCCAAC
1 TCTCTCAAT
*
17377 TCTCTCAAC
1 TCTCTCAAT
*
17386 TCTCTTAAT
1 TCTCTCAAT
17395 TCTCTCAAT
1 TCTCTCAAT
17404 T-TCTCAA
1 TCTCTCAA
17411 GCTTTTCTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
8 6 0.14
9 36 0.86
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (9 bp):
TCTCTCAAT
Found at i:24722 original size:13 final size:13
Alignment explanation
Indices: 24704--24728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24694 TGTACATAGA
24704 ATGAAATTTTAAC
1 ATGAAATTTTAAC
24717 ATGAAATTTTAA
1 ATGAAATTTTAA
24729 AGTTTCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
ATGAAATTTTAAC
Found at i:24929 original size:6 final size:6
Alignment explanation
Indices: 24918--24958 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
24908 AGCTTTGAGA
*
24918 TATTTT TA-TTT TATTTT T-TCTT TATTTT TATTTT ATATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT -TATTTT
24959 AATCAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:24934 original size:11 final size:11
Alignment explanation
Indices: 24918--24959 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
24908 AGCTTTGAGA
24918 TATTTTTATTT
1 TATTTTTATTT
24929 TATTTTT-TCTT
1 TATTTTTAT-TT
24940 TATTTTTATTT
1 TATTTTTATTT
24951 TATATTTTA
1 TAT-TTTTA
24960 ATCAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 21 0.75
12 6 0.21
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:26134 original size:37 final size:37
Alignment explanation
Indices: 26093--26166 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
26083 AATTTTGGGA
* *
26093 AAATTTGGGGTTTAAAAATGGAACTTTTAGACATTCG
1 AAATTCGGGGTTTAAAAATGAAACTTTTAGACATTCG
26130 AAATTCGGGGTTTAAAAATGAAACTTTTAGACATTCG
1 AAATTCGGGGTTTAAAAATGAAACTTTTAGACATTCG
26167 GGATAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (37 bp):
AAATTCGGGGTTTAAAAATGAAACTTTTAGACATTCG
Found at i:26168 original size:30 final size:30
Alignment explanation
Indices: 26129--26228 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
26119 TTAGACATTC
26129 GAAATTCGGGGTTTAAAAATGAAACTTTTA
1 GAAATTCGGGGTTTAAAAATGAAACTTTTA
* * * * **
26159 GACATTC-GGGATAAAAAAGGTAAA-TTTGG
1 GAAATTCGGGGTTTAAAAATG-AAACTTTTA
* *
26188 GAAATTTTGGGGTTTAAAAATGGAACTTTTA
1 GAAA-TTCGGGGTTTAAAAATGAAACTTTTA
*
26219 GATATTCGGG
1 GAAATTCGGG
26229 ATAAAAAGGG
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
29 16 0.32
30 18 0.36
31 16 0.32
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (30 bp):
GAAATTCGGGGTTTAAAAATGAAACTTTTA
Found at i:26308 original size:59 final size:59
Alignment explanation
Indices: 26242--26510 Score: 300
Period size: 59 Copynumber: 4.5 Consensus size: 59
26232 AAAAGGGTAA
* *
26242 TTTTGGAAGTTTCGGGATCAAAAATGGGA-TTTTAGAAGTTTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCGGGAT-AAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAATGGAAT
* * * *
26301 TTTTGGAAGTTTTAGGG-TCAAAAATGAGATTTTTGGAAG-TTTGGGGGTAAAAATGAAAT
1 TTTTGGAAG-TTTCGGGAT-AAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAATGGAAT
* * *
26360 TTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGGAAT
1 TTTTGGAAG-TTTCGGGATAAAAATGGGATTTTTGGAAGTTTTGAGGGT-AAAAATGGAAT
* *
26420 TTTTAGAAG-TTCGGGGATAAAAA-GGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGAAT
1 TTTTGGAAGTTTC-GGGATAAAAATGGG-ATTTTTGGAAGTTTTGAGGGTAAAAATGGAAT
* *
26479 TTTTAGAAG-TTCGGGGATAAAAATGGAATTTT
1 TTTTGGAAGTTTC-GGGATAAAAATGGGATTTT
26511 CAGACAGTTT
Statistics
Matches: 185, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
58 4 0.02
59 139 0.75
60 42 0.23
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
TTTTGGAAGTTTCGGGATAAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAATGGAAT
Found at i:26312 original size:30 final size:29
Alignment explanation
Indices: 26202--26510 Score: 308
Period size: 30 Copynumber: 10.5 Consensus size: 29
26192 TTTTGGGGTT
* * *
26202 TAAAAATGGAACTTTTAG-A-TATTCGGGA
1 TAAAAATGGAATTTTTGGAAGT-TTCGGGG
* *
26230 TAAAAAGGGTAA-TTTTGGAAGTTTCGGGA
1 TAAAAATGG-AATTTTTGGAAGTTTCGGGG
* *
26259 TCAAAAATGGGA-TTTTAGAAGTTTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCG-GGG
**
26289 TAAAAATGGAATTTTTGGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
26318 TCAAAAAT-GAGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGA-ATTTTTGGAAGTTTCGGGG
* *
26348 TAAAAATGAAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
26377 TTAAAAATGGAATTTTTGGAAGTTTTGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
26407 TCAAAAATGGAATTTTTAGAAG-TTCGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* * *
26436 ATAAAAAGGGAATTTTTGGAAGTTTTGAGGT
1 -TAAAAATGGAATTTTTGGAAGTTTCG-GGG
*
26467 TAAAAATGGAATTTTTAGAAG-TTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
26495 ATAAAAATGGAATTTT
1 -TAAAAATGGAATTTT
26511 CAGACAGTTT
Statistics
Matches: 241, Mismatches: 25, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
28 15 0.06
29 107 0.44
30 117 0.49
31 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:26324 original size:89 final size:88
Alignment explanation
Indices: 26231--26489 Score: 310
Period size: 89 Copynumber: 2.9 Consensus size: 88
26221 TATTCGGGAT
* *
26231 AAAAAGGGTAATTTTGGAAGTTTCGGGATCAAAAATGGGA-TTTTAGAAGTTTCGAGGGTAAAAA
1 AAAAAGGG-AATTTTGGAAGTTTCGGGAT-AAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAA
26295 TGGAATTTTTGGAAGTTTTAGGGTC
64 TGGAATTTTTGGAAGTTTTAGGGTC
* * * * **
26320 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTTTG-GGGTTAAAAA
1 AAAAA-GGGAATTTTGGAAGTTTCGGGATAAAAATGGGATTTTTGGAAGTTTTGAGGG-TAAAAA
*
26384 TGGAATTTTTGGAAGTTTTGGGGTC
64 TGGAATTTTTGGAAGTTTTAGGGTC
* * *
26409 AAAAATGGAATTTTTAGAAG-TTCGGGGATAAAAA-GGGAATTTTTGGAAGTTTTGAGGTTAAAA
1 AAAAAGGGAA-TTTTGGAAGTTTC-GGGATAAAAATGGG-ATTTTTGGAAGTTTTGAGGGTAAAA
*
26472 ATGGAATTTTTAGAAGTT
63 ATGGAATTTTTGGAAGTT
26490 CGGGGATAAA
Statistics
Matches: 144, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
88 16 0.11
89 124 0.86
90 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (88 bp):
AAAAAGGGAATTTTGGAAGTTTCGGGATAAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAATG
GAATTTTTGGAAGTTTTAGGGTC
Found at i:27552 original size:3 final size:3
Alignment explanation
Indices: 27506--27537 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27496 ATTAATTAAA
*
27506 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
27538 AAACATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28312 original size:6 final size:6
Alignment explanation
Indices: 28298--28350 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
28288 AATTTGAAAA
* * *
28298 TAAATT TAAACT TAAA-T TAAAAT TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
28344 TAAATT T
1 TAAATT T
28351 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 9 0.22
6 32 0.78
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:28323 original size:17 final size:17
Alignment explanation
Indices: 28287--28387 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
28277 TAATAATTTC
* *
28287 AAATTTGAAAATAAATTT
1 AAATTT-AAATTAAAATT
*
28305 AAACTTAAATTAAAATT
1 AAATTTAAATTAAAATT
28322 AAATTTAAATTTAAAA-T
1 AAATTTAAA-TTAAAATT
*
28339 AAATTTAAATTTTAAAA-A
1 AAATTTAAA--TTAAAATT
*
28357 AAATTTAATCTTAAAA-T
1 AAATTTAA-ATTAAAATT
*
28374 AAATTTAAAATAAA
1 AAATTTAAATTAAA
28388 TTTGGGCTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
16 4 0.06
17 41 0.58
18 26 0.37
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTAAAATT
Found at i:28325 original size:23 final size:23
Alignment explanation
Indices: 28294--28350 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
28284 TTCAAATTTG
*
28294 AAAA-TAAATTTAAACTTAAATT
1 AAAATTAAATTTAAACTTAAAAT
*
28316 AAAATTAAATTTAAATTTAAAAT
1 AAAATTAAATTTAAACTTAAAAT
*
28339 AAATTTAAATTT
1 AAAATTAAATTT
28351 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTAAATTTAAACTTAAAAT
Found at i:28340 original size:58 final size:58
Alignment explanation
Indices: 28267--28390 Score: 162
Period size: 58 Copynumber: 2.2 Consensus size: 58
28257 CTTTATTTAT
* * *
28267 TTTAAATTTATAAT-AATTTCAAATTTGAAAATAAATTTAAACTTAAATTAAAATTAAA
1 TTTAAATTTAAAATAAATTT-AAATTTGAAAAAAAATTTAAACTTAAAATAAAATTAAA
* * *
28325 TTTAAATTTAAAATAAATTTAAATTTTAAAAAAAATTTAATCTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAAAAAATTTAAACTTAAAATAAAATTAAA
*
28383 -ATAAATTT
1 TTTAAATTT
28391 GGGCTTCAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 7 0.12
58 46 0.79
59 5 0.09
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (58 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAAAAAATTTAAACTTAAAATAAAATTAAA
Found at i:28361 original size:35 final size:38
Alignment explanation
Indices: 28276--28382 Score: 123
Period size: 35 Copynumber: 2.8 Consensus size: 38
28266 TTTTAAATTT
28276 ATAATAATTTCAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 ATAA-AATTT-AAATTT-AAAATAAATTTAAACTT--ATTAAA
*
28319 ATTAAATTTAAATTTAAAATAAATTTAAA-TT-TTAAA
1 ATAAAATTTAAATTTAAAATAAATTTAAACTTATTAAA
28355 A-AAAATTT-AATCTTAAAATAAATTTAAA
1 ATAAAATTTAAAT-TTAAAATAAATTTAAA
28383 ATAAATTTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
34 3 0.05
35 22 0.36
36 6 0.10
39 2 0.03
40 14 0.23
41 6 0.10
42 5 0.08
43 3 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (38 bp):
ATAAAATTTAAATTTAAAATAAATTTAAACTTATTAAA
Found at i:28381 original size:11 final size:11
Alignment explanation
Indices: 28287--28390 Score: 53
Period size: 11 Copynumber: 9.5 Consensus size: 11
28277 TAATAATTTC
28287 AAATTTGAAAAT
1 AAATTT-AAAAT
*
28299 AAATTTAAACTT
1 AAATTTAAA-AT
28311 AAA-TTAAAATT
1 AAATTTAAAA-T
28322 AAA-TT----T
1 AAATTTAAAAT
28328 AAATTTAAAAT
1 AAATTTAAAAT
*
28339 AAATTTAAATTTT
1 AAATTTAAA--AT
*
28352 AAA--AAAAATT
1 AAATTTAAAA-T
*
28362 TAATCTTAAAAT
1 AAAT-TTAAAAT
28374 AAATTTAAAAT
1 AAATTTAAAAT
28385 AAATTT
1 AAATTT
28391 GGGCTTCAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 27
0.67 0.08 0.25
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
10 3 0.04
11 40 0.56
12 14 0.20
13 8 0.11
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:30382 original size:21 final size:20
Alignment explanation
Indices: 30356--30394 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30346 ACCATTTTTT
*
30356 TCTTTTTTTTCTTTTTTTCTC
1 TCTTTTTTTT-TTCTTTTCTC
30377 TCTTTTTTTTTTCTTTTC
1 TCTTTTTTTTTTCTTTTC
30395 GAACCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TCTTTTTTTTTTCTTTTCTC
Found at i:30418 original size:13 final size:14
Alignment explanation
Indices: 30400--30428 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30390 TTTTCGAACC
30400 TTTTGCT-TTTTTT
1 TTTTGCTGTTTTTT
30413 TTTTGCTGTTTTTT
1 TTTTGCTGTTTTTT
30427 TT
1 TT
30429 CTTCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (14 bp):
TTTTGCTGTTTTTT
Done.