Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001541.1 Kokia drynarioides strain JFW-HI SEQ_113114, 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: 6102
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:669 original size:30 final size:29
Alignment explanation
Indices: 635--869 Score: 217
Period size: 30 Copynumber: 7.9 Consensus size: 29
625 GCCAAATTTG
635 AATTTTTGGAAAGTTTGAGGGTCAAAACAT
1 AATTTTTGGAAAGTTT-AGGGTCAAAACAT
* * * *
665 AA-TTTGGGGAAGTTTGGGGGCTAAAACAT
1 AATTTTTGGAAAGTTTAGGGTC-AAAACAT
*
694 AATTTTTGGAAAGTTTAGGGGCTAAAACAT
1 AATTTTTGGAAAGTTTAGGGTC-AAAACAT
* *
724 AATTTTTGAAAAGTTTAGGGGTTAAAACAT
1 AATTTTTGGAAAGTTTA-GGGTCAAAACAT
*
754 AATTTTTGGAATGTTTAGGAGAT-AAAACAT
1 AATTTTTGGAAAGTTTAGG-G-TCAAAACAT
* *
784 AATTTTTGG-AAGTTCAAGGGCCAAAACAT
1 AATTTTTGGAAAGTT-TAGGGTCAAAACAT
* * *
813 AATTTTT-AAGAAGTTTAGAGGTTAAAATAT
1 AATTTTTGGA-AAGTTTAG-GGTCAAAACAT
* *
843 AATTTTTAGAAAGTTTGAGGGTTAAAA
1 AATTTTTGGAAAGTTT-AGGGTCAAAA
870 ATGGAATTTT
Statistics
Matches: 172, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.02
29 43 0.25
30 118 0.69
31 7 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAAAGTTTAGGGTCAAAACAT
Found at i:707 original size:59 final size:58
Alignment explanation
Indices: 635--848 Score: 225
Period size: 59 Copynumber: 3.6 Consensus size: 58
625 GCCAAATTTG
* *
635 AATTTTTGGAAAGTTTGAGGGTCAAAACATAATTTGGGGAAGTTTGGGGGCTAAAACAT
1 AATTTTTGGAAAGTTT-AGGGTCAAAACATAATTTTGGGAAGTTTAGGGGCTAAAACAT
* ** *
694 AATTTTTGGAAAGTTTAGGGGCTAAAACATAATTTTTGAAAAGTTTAGGGGTTAAAACAT
1 AATTTTTGGAAAGTTTAGGGTC-AAAACATAA-TTTTGGGAAGTTTAGGGGCTAAAACAT
* * * * *
754 AATTTTTGGAATGTTTAGGAGAT-AAAACATAATTTTTGGAAGTTCAAGGGCCAAAACAT
1 AATTTTTGGAAAGTTTAGG-G-TCAAAACATAATTTTGGGAAGTTTAGGGGCTAAAACAT
* * *
813 AATTTTT-AAGAAGTTTAGAGGTTAAAATATAATTTT
1 AATTTTTGGA-AAGTTTAG-GGTCAAAACATAATTTT
849 TAGAAAGTTT
Statistics
Matches: 130, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
58 7 0.05
59 72 0.55
60 50 0.38
61 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (58 bp):
AATTTTTGGAAAGTTTAGGGTCAAAACATAATTTTGGGAAGTTTAGGGGCTAAAACAT
Found at i:758 original size:119 final size:119
Alignment explanation
Indices: 635--869 Score: 291
Period size: 119 Copynumber: 2.0 Consensus size: 119
625 GCCAAATTTG
*** *
635 AATTTTTGGAAAGTTTGAGG-G-TCAAAACATAATTTGGGGAAGTTTGGGGGCTAAAACATAATT
1 AATTTTTGGAAAGTTT-AGGAGAT-AAAACATAATTTGGGGAAGTTCAAGGGCCAAAACATAATT
* *
698 TTT-GGAAAGTTTAGGGGCTAAAACATAATTTTT-GAAAAGTTT-AGGGGTTAAAACAT
64 TTTAAG-AAGTTTAGAGGCTAAAACATAATTTTTAG-AAAGTTTGA-GGGTTAAAACAT
* **
754 AATTTTTGGAATGTTTAGGAGATAAAACATAATTTTTGGAAGTTCAAGGGCCAAAACATAATTTT
1 AATTTTTGGAAAGTTTAGGAGATAAAACATAATTTGGGGAAGTTCAAGGGCCAAAACATAATTTT
* *
819 TAAGAAGTTTAGAGGTTAAAATATAATTTTTAGAAAGTTTGAGGGTTAAAA
66 TAAGAAGTTTAGAGGCTAAAACATAATTTTTAGAAAGTTTGAGGGTTAAAA
870 ATGGAATTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 3 0.03
119 93 0.93
120 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (119 bp):
AATTTTTGGAAAGTTTAGGAGATAAAACATAATTTGGGGAAGTTCAAGGGCCAAAACATAATTTT
TAAGAAGTTTAGAGGCTAAAACATAATTTTTAGAAAGTTTGAGGGTTAAAACAT
Found at i:827 original size:89 final size:89
Alignment explanation
Indices: 635--858 Score: 274
Period size: 89 Copynumber: 2.5 Consensus size: 89
625 GCCAAATTTG
* * ** * * *
635 AATTTTTGGAAAGTTT-GAGGGTCAAAACATAATTTGGGGAAGTTTGGGGGCTAAAACATAATTT
1 AATTTTTGAAAAGTTTAG-GGGTTAAAACATAATTTTTGGAAGTTTAGGAGATAAAACATAATTT
* * *
699 TTGGAAAGTTTAGGGGCTAAAACAT
65 TTGGAAAGTTCAAGGGCCAAAACAT
724 AATTTTTGAAAAGTTTAGGGGTTAAAACATAATTTTTGGAATGTTTAGGAGATAAAACATAATTT
1 AATTTTTGAAAAGTTTAGGGGTTAAAACATAATTTTTGGAA-GTTTAGGAGATAAAACATAATTT
789 TTGG-AAGTTCAAGGGCCAAAACAT
65 TTGGAAAGTTCAAGGGCCAAAACAT
* * *
813 AATTTTT-AAGAAGTTTAGAGGTTAAAATATAATTTTTAGAAAGTTT
1 AATTTTTGAA-AAGTTTAGGGGTTAAAACATAATTTTT-GGAAGTTT
859 GAGGGTTAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
88 2 0.02
89 88 0.75
90 28 0.24
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (89 bp):
AATTTTTGAAAAGTTTAGGGGTTAAAACATAATTTTTGGAAGTTTAGGAGATAAAACATAATTTT
TGGAAAGTTCAAGGGCCAAAACAT
Found at i:2622 original size:16 final size:15
Alignment explanation
Indices: 2601--2632 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2591 TACTAAAACT
2601 ATTTTTTTAAAATATA
1 ATTTTTTT-AAATATA
2617 ATTTTTTTAAATATA
1 ATTTTTTTAAATATA
2632 A
1 A
2633 AATTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTTTAAATATA
Found at i:2636 original size:17 final size:16
Alignment explanation
Indices: 2601--2636 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2591 TACTAAAACT
*
2601 ATTTTTTTAAAATATA
1 ATTTTTTTAAAATAAA
2617 ATTTTTTTAAATATAAA
1 ATTTTTTTAAA-ATAAA
2634 ATT
1 ATT
2637 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTTTAAAATAAA
Found at i:2739 original size:31 final size:33
Alignment explanation
Indices: 2704--2776 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
2694 CCCAATTTCA
2704 TCTTCTTCCT-CATTTTT-CATCTAACACCACT
1 TCTTCTTCCTACATTTTTCCATCTAACACCACT
* * *
2735 TCTTCTGCTTACCATTTTTCCATCTAACATCACT
1 TCTTCTTCCTA-CATTTTTCCATCTAACACCACT
2769 TCTTCTTC
1 TCTTCTTC
2777 TCACATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.23
33 7 0.20
34 20 0.57
ACGTcount: A:0.18, C:0.34, G:0.01, T:0.47
Consensus pattern (33 bp):
TCTTCTTCCTACATTTTTCCATCTAACACCACT
Found at i:3454 original size:16 final size:14
Alignment explanation
Indices: 3427--3500 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 14
3417 GATGATGATG
3427 ATTATAATTTTAAAA
1 ATTAT-ATTTTAAAA
3442 ATTTTATATTTTAAAA
1 A--TTATATTTTAAAA
3458 ATTA-ATTTT-AAA
1 ATTATATTTTAAAA
* *
3470 ATAATTTTTTAATAA
1 ATTATATTTTAA-AA
*
3485 TTCTATATTTTAAAA
1 AT-TATATTTTAAAA
3500 A
1 A
3501 AATAATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 6 0.13
13 9 0.19
14 4 0.09
15 6 0.13
16 18 0.38
17 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATTTTAAAA
Found at i:3492 original size:42 final size:41
Alignment explanation
Indices: 3434--3518 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 41
3424 ATGATTATAA
* *
3434 TTTTAAAAATTTTATATTTT-AAAAATTAATTTTAAAATAATT
1 TTTTAAAAATTCTATATTTTAAAAAAATAATTTT--AATAATT
*
3476 TTTTAATAATTCTATATTTTAAAAAAATAATTTTAATAATT
1 TTTTAAAAATTCTATATTTTAAAAAAATAATTTTAATAATT
3517 TT
1 TT
3519 AAAATGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 9 0.23
42 18 0.46
43 12 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
TTTTAAAAATTCTATATTTTAAAAAAATAATTTTAATAATT
Found at i:3505 original size:21 final size:23
Alignment explanation
Indices: 3480--3522 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3470 ATAATTTTTT
3480 AATAATTCT-AT-ATTTTAAAAA
1 AATAATTCTAATAATTTTAAAAA
*
3501 AATAATTTTAATAATTTTAAAA
1 AATAATTCTAATAATTTTAAAA
3523 TGATTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAATTCTAATAATTTTAAAAA
Found at i:4066 original size:46 final size:46
Alignment explanation
Indices: 3942--4711 Score: 545
Period size: 46 Copynumber: 16.9 Consensus size: 46
3932 AGATAATAGT
* * * * * *
3942 TTCAATTTCCCCCTCTCGA-TTAGGGGTAAAAGATTGGAAGATGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
3987 TTCAATCT-ACCC-CATG-GTT-GGGGTAAGAGATTGGATGGTGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * *
4029 TTCAATCTACCCCCCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
4075 TTCAATTTG--CCTCATGA--TCGGGGTAAGAA-ATTGGATAGTATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGAT-G-GTGTC
4119 TTCAATCTAG-CCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTC
1 TTCAATCT-GCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * * * * * *
4168 TTCAATTTGCCCCTCTTGAATTAAGGGTAAAAGATCGAATGATGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * * * * *
4214 TTCAATTTG-CCC-CATG--GTCGGGGTAAGAGATTGGGTGGTGTT
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * *
4256 TTCAATCTGCCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGAC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
4302 TTTAATCTGCCCCTTTTGACTTAGGGGTAAAAGGTTGGGTGGTGATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * * * *
4351 TTCAATTTGTCCCTCTTGACTTAGGGGTAAAATATTAGATGAT-TGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGT-C
* * * * *
4397 TTCAATCTG--CTTCATG-GTTA-GGGTAAGAGATTGGATGGTATC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* *
4439 TTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* *
4485 TTCAATCTG-CCC-CATGA--TAGGGGTAAGAA-ATTAGATAGTGTTGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGAT-G-G-TGTC
* * * *
4530 TCCAATCTACCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * *
4579 TTCAATCTACACCTCTTTACTTAGGGGTAAAAGATTAGGTGATGGT-T-
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATT--G-GATGGTGTC
* * * * *
4626 TT-AATCTGCCCCTTTTAACTTAAGGGTAAAACATTAGATGGTAG-C
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGT-GTC
* *
4671 TTCAATCTGCCCTTCTTGACTTAGGGGTAAAAGATTAGATG
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
4712 ATGATGTAAC
Statistics
Matches: 571, Mismatches: 110, Indels: 87
0.74 0.14 0.11
Matches are distributed among these distances:
42 106 0.19
43 25 0.04
44 42 0.07
45 32 0.06
46 201 0.35
47 8 0.01
48 24 0.04
49 127 0.22
50 1 0.00
51 2 0.00
52 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (46 bp):
TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
Found at i:4155 original size:90 final size:88
Alignment explanation
Indices: 3942--4180 Score: 300
Period size: 88 Copynumber: 2.7 Consensus size: 88
3932 AGATAATAGT
* * * * * * * * *
3942 TTCAATTTCCCCCTCTCGA-TTAGGGGTAAAAGATTGGAAGATGGCTTCAATCTACCCCATGGTT
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
* *
4006 GGGGTAAGAGATTGGATGGTGTC
66 GGGGTAAGAAATTGGATGATGTC
* *
4029 TTCAATCTACCCCCCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCTCATGATC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
4094 GGGGTAAGAAATTGGATAGTATGTC
66 GGGGTAAGAAATTGGAT-G-ATGTC
*
4119 TTCAATCTAGCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTG--G-CTTCAATTTGCCCC
4181 TCTTGAATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
87 15 0.12
88 54 0.42
89 1 0.01
90 46 0.35
92 1 0.01
93 13 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (88 bp):
TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
GGGGTAAGAAATTGGATGATGTC
Found at i:4313 original size:88 final size:88
Alignment explanation
Indices: 4140--4574 Score: 385
Period size: 88 Copynumber: 4.8 Consensus size: 88
4130 CCTCTTGACT
* * * *
4140 TAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTCTTGAA-TTAAGGGTAAAAGATC
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTG-CCCTCTT-AACTTAGGGGTAAAAGATT
* * * *
4204 GAATGATGGCTTCAATTTGCCCCATGG
62 GGATGGTGACTTCAATCTGCCCCATGG
* *
4231 TCGGGGTAAGAGATTGGGTGGTGTT-TTCAATCTGCCCTTCTTAACTTAGGGGTAAAAGATTGGA
1 TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTGCCC-TCTTAACTTAGGGGTAAAAGATTGGA
* * *
4295 TGGTGACTTTAATCTGCCCCTTTTGACT
65 TGGTGACTTCAATCTGCCCC--ATG--G
* * * * * * *
4323 TAGGGGTAAAAGGTTGGGTGGTGATGTCTTCAATTTGTCCCTCTTGACTTAGGGGTAAAATATTA
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTG-CCCTCTTAACTTAGGGGTAAAAGATTG
* **
4388 GATGATTG-CTTCAATCTGCTTCATGG
63 GATG-GTGACTTCAATCTGCCCCATGG
* *
4414 TTA-GGGTAAGAGATTGGATGGT-ATCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGG
1 -TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTG-CCCTCTTAACTTAGGGGTAAAAGATTGG
* *
4477 ATGGTGGCTTCAATCTGCCCCATGA
64 ATGGTGACTTCAATCTGCCCCATGG
* * * * *
4502 TAGGGGTAAGAAATTAGATAGTGTTGTCTCCAATCTACCCTTCTTAACTTAGGGGTAAAAGATTG
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTGCCC-TCTTAACTTAGGGGTAAAAGATTG
4567 GATGGTGA
63 GATGGTGA
4575 TGTCTTCAAT
Statistics
Matches: 281, Mismatches: 45, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
87 9 0.03
88 115 0.41
89 1 0.00
90 6 0.02
91 75 0.27
92 22 0.08
93 3 0.01
94 1 0.00
95 44 0.16
96 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (88 bp):
TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTGCCCTCTTAACTTAGGGGTAAAAGATTGGAT
GGTGACTTCAATCTGCCCCATGG
Found at i:4347 original size:183 final size:183
Alignment explanation
Indices: 4118--4718 Score: 562
Period size: 183 Copynumber: 3.3 Consensus size: 183
4108 GATAGTATGT
4118 CTTCAATCTAG-CCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCT
1 CTTCAATCT-GCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCT
* *
4182 CTTGAATTAAGGGTAAAAGATCGA-ATGATGGCTTCAATTTGCCCCATGGTCGGGGTAAGAGATT
65 CTTGAATTAAGGGTAAAAGAT-GAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATT
* * *
4246 GGGTGGTGTTTTCAATCTG-CCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
129 GGATGGTATCTTCAATCTGTCCC-TCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * * * *
4301 CTTTAATCTGCCCCTTTTGACTTAGGGGTAAAAGGTTGGGTGGTGATGTCTTCAATTTGTCCCTC
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTC
* * * * * ** *
4366 TTGACTTAGGGGTAAAATATTAGATGATTGCTTCAATCTGCTTCATGGTTAGGGTAAGAGATTGG
66 TTGAATTAAGGGTAAAAGATGAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGG
* *
4431 ATGGTATCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGG
131 ATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * * * * * * *
4484 CTTCAATCTG-CCC-CATGA--TAGGGGTAAGAA-ATTAGATAGTGTTGTCTCCAATCTACCCTT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGATGGTGATGTCTTCAATTTGCCCCT
* * * * * ** *
4544 CTT-AACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTACACCTCTTTACTTAGGGGTA
65 CTTGAA-TTAAGGGTAAAAGA-T-GA-GATGATGGCTTCAATCTGC-CC-C-ATGGTCA-GGGTA
* * * * * *
4608 AAAGATTAGGTGATGGT-T-TT-AATCTGCCCCTTTTAACTTAAGGGTAAAACATTAGATGGT-A
122 AGAGATT--G-GATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * *
4669 GCTTCAATCTGCCCTTCTTGACTTAGGGGTAAAAGATTAGATGATGATGT
1 -CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGT
4719 AACTTTACTC
Statistics
Matches: 339, Mismatches: 58, Indels: 35
0.78 0.13 0.08
Matches are distributed among these distances:
178 1 0.00
179 45 0.13
180 3 0.01
181 4 0.01
182 20 0.06
183 164 0.48
184 4 0.01
185 4 0.01
186 55 0.16
187 4 0.01
188 6 0.02
189 8 0.02
190 21 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (183 bp):
CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTC
TTGAATTAAGGGTAAAAGATGAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGG
ATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
Found at i:4941 original size:96 final size:94
Alignment explanation
Indices: 4770--5104 Score: 494
Period size: 96 Copynumber: 3.5 Consensus size: 94
4760 CTATTACCTT
* *
4770 TTTTGACCCACTTCTCTGTATCTCATCAGGAAGAT-GGTTTGAAGTTTCGCTCCACTTCACTGTA
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCT-CACTCCACTGTA
4834 ACCTCAGGGACATTGAGCTCTGCTTCATTG
65 ACCTCAGGGACATTGAGCTCTGCTTCATTG
*
4864 TTTTGATCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCGCTGCACTCCACTGT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGAT-GGGTTTGAAGTTTCGCT-CACTCCACTGT
4929 AACCTCAGGGACATTGAGCTCTGCTTCATTG
64 AACCTCAGGGACATTGAGCTCTGCTTCATTG
* * * *
4960 TTTTGATCCACTTCTTTGTATGTCATTAGGAAGATGGGTTTGAAGTTTCACTCTACTCCACTGTA
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTC-ACTCCACTGTA
* ** *
5025 ACC-CTAAGGATGTTGAGCTTTGCTTCATTG
65 ACCTC-AGGGACATTGAGCTCTGCTTCATTG
*
5055 TTTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTC
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGAT-GGGTTTGAAGTTTC
5105 ATTGTTGTGA
Statistics
Matches: 219, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
94 35 0.16
95 82 0.37
96 102 0.47
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (94 bp):
TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTCACTCCACTGTAA
CCTCAGGGACATTGAGCTCTGCTTCATTG
Done.