Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009948.1 Kokia drynarioides strain JFW-HI SEQ_124693, 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: 33698
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:501 original size:4 final size:4
Alignment explanation
Indices: 481--571 Score: 85
Period size: 4 Copynumber: 22.2 Consensus size: 4
471 AACACATTAC
* * * *
481 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
* * *
529 CCTCT CCTT CTTC CTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 -CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
572 CCGTTTATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.04
4 57 0.81
5 10 0.14
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:515 original size:17 final size:17
Alignment explanation
Indices: 481--571 Score: 80
Period size: 17 Copynumber: 5.3 Consensus size: 17
471 AACACATTAC
481 CTTTCTTTCC-TT-CTT
1 CTTTCTTTCCTTTCCTT
*
496 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTTTCCTT
*
513 CTTCCTTTCTTTCTTTCCTCT
1 CTTTCTTTC---CTTTCCT-T
* *
534 CCTTC-TTCCTTTCTTT
1 CTTTCTTTCCTTTCCTT
*
550 CTTTCTTTCCTTTCTTT
1 CTTTCTTTCCTTTCCTT
567 CTTTC
1 CTTTC
572 CCGTTTATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
15 10 0.16
16 6 0.10
17 33 0.53
20 9 0.15
21 4 0.06
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCCTTTCCTT
Found at i:528 original size:25 final size:25
Alignment explanation
Indices: 494--571 Score: 122
Period size: 25 Copynumber: 3.1 Consensus size: 25
484 TCTTTCCTTC
494 TTCTTTCTTTCCTCTCCTTCTTCCT
1 TTCTTTCTTTCCTCTCCTTCTTCCT
519 TTCTTTCTTTCCTCTCCTTCTTCCT
1 TTCTTTCTTTCCTCTCCTTCTTCCT
* *
544 TTCTTTCTTT-CTTTCCTTTCTTTCT
1 TTCTTTCTTTCCTCTCC-TTCTTCCT
569 TTC
1 TTC
572 CCGTTTATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.10
25 45 0.90
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCCTCTCCTTCTTCCT
Found at i:4143 original size:17 final size:17
Alignment explanation
Indices: 4123--4159 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4113 CTCTCTTGAC
4123 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
4140 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
4157 CTT
1 CTT
4160 GAAACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:4148 original size:24 final size:24
Alignment explanation
Indices: 4103--4150 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4093 ACGGATGTTC
*
4103 AACCTTTCATCTCTCTTGACCTTT
1 AACCTTTCATCTCTCTTAACCTTT
*
4127 AACCTTTCATAT-TCTTTAACCTTT
1 AACCTTTCATCTCTC-TTAACCTTT
4151 CATATTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (24 bp):
AACCTTTCATCTCTCTTAACCTTT
Found at i:6357 original size:16 final size:17
Alignment explanation
Indices: 6324--6357 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6314 TTACAAAAAA
6324 AAAAAATCAAAATATTT
1 AAAAAATCAAAATATTT
*
6341 AAAAAATCCAAAT-TTT
1 AAAAAATCAAAATATTT
6357 A
1 A
6358 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATCAAAATATTT
Found at i:14570 original size:15 final size:15
Alignment explanation
Indices: 14540--14578 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
14530 AGATATGTTT
14540 TTTTTTCAACGGTAA
1 TTTTTTCAACGGTAA
*
14555 TTGTTTT-AACGTTAA
1 TT-TTTTCAACGGTAA
14570 TTTTTTCAA
1 TTTTTTCAA
14579 TGATTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (15 bp):
TTTTTTCAACGGTAA
Found at i:17759 original size:96 final size:95
Alignment explanation
Indices: 17574--17760 Score: 211
Period size: 96 Copynumber: 1.9 Consensus size: 95
17564 TCTTTGCGAA
* **
17574 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCG
* * *
17639 GAATCGAAGATAAGGAAACGTTGCCTCGATT
66 AAACCGAAGATAAAGAAAC-TTGCCTCGATT
* * *
17670 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGTGCA-AAT-TTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAA-G-GCACAATATTT
17733 CGAAACCCGAA-ATGAAAGAATA-TTGCCT
64 CGAAA-CCGAAGAT-AAAGAA-ACTTGCCT
17761 TGATATTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
96 60 0.78
97 13 0.17
98 4 0.05
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCG
AAACCGAAGATAAAGAAACTTGCCTCGATT
Found at i:18104 original size:29 final size:29
Alignment explanation
Indices: 18071--18378 Score: 261
Period size: 29 Copynumber: 10.5 Consensus size: 29
18061 ATTCAGGATC
*
18071 AAAAATGGGATTTTTAGAAGTTCGGGGGT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGT
* *
18100 AAAAAT-GGACCTTTT-GAAAGTTTTGGGGTT
1 AAAAATGGGA-TTTTTAG-AAG-TTTGGGGGT
* ** * *
18130 AAAAA-GGGATTTTTGGTGGTTTCGAGGTT
1 AAAAATGGGATTTTTAGAAGTTT-GGGGGT
* *
18159 AAAAATGAGATTTTTTA-AAGTTTTGGGGT
1 AAAAATGGGA-TTTTTAGAAGTTTGGGGGT
*
18188 TAAAATGGGATTTTTTAGAAGTTTGGGGGT
1 AAAAATGGGA-TTTTTAGAAGTTTGGGGGT
*
18218 -AAAATGGGATTTCTT-GAAGTTTTGGGGT
1 AAAAATGGGATTT-TTAGAAGTTTGGGGGT
** * *
18246 CAAAAATTAGATTTTTAGAAGTTCGAGGGT
1 -AAAAATGGGATTTTTAGAAGTTTGGGGGT
* * *
18276 AAAAATGGGATTTTTGGAACTTTTGGGGTT
1 AAAAATGGGATTTTTAGAA-GTTTGGGGGT
* *
18306 AAAAATGGGATTTTAAGAAGTTTTGGGGT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGT
* *
18335 CAAAATGGGATTTTT-GAAAGTTTGAGGGT
1 AAAAATGGGATTTTTAG-AAGTTTGGGGGT
*
18364 AAAAATGGAATTTTT
1 AAAAATGGGATTTTT
18379 GAACAATTTA
Statistics
Matches: 223, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
28 23 0.10
29 118 0.53
30 77 0.35
31 5 0.02
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (29 bp):
AAAAATGGGATTTTTAGAAGTTTGGGGGT
Found at i:18134 original size:59 final size:59
Alignment explanation
Indices: 18071--18378 Score: 342
Period size: 59 Copynumber: 5.3 Consensus size: 59
18061 ATTCAGGATC
*
18071 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAAT-GGACCTTTTGAAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGA-TTTTTGAAAGTTTTGGGGTT
* ** * * * *
18130 AAAAA-GGGATTTTTGGTGGTTTCGAGGTTAAAAATGAGATTTTTTAAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAG-TTCGGGGGTAAAAATGGGATTTTTGAAAGTTTTGGGGTT
* *
18189 -AAAATGGGATTTTTTAGAAGTTTGGGGGT-AAAATGGGATTTCTTG-AAGTTTTGGGGTC
1 AAAAATGGGA-TTTTTAGAAGTTCGGGGGTAAAAATGGGATTT-TTGAAAGTTTTGGGGTT
** * * *
18247 AAAAATTAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAACTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGAAAGTTTTGGGGTT
* ** *
18306 AAAAATGGGATTTTAAGAAGTTTTGGGGTCAAAATGGGATTTTTGAAAG-TTTGAGGG-T
1 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGAAAGTTTTG-GGGTT
*
18364 AAAAATGGAATTTTT
1 AAAAATGGGATTTTT
18379 GAACAATTTA
Statistics
Matches: 206, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
58 76 0.37
59 121 0.59
60 9 0.04
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (59 bp):
AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGAAAGTTTTGGGGTT
Found at i:18180 original size:88 final size:86
Alignment explanation
Indices: 18071--18381 Score: 299
Period size: 88 Copynumber: 3.5 Consensus size: 86
18061 ATTCAGGATC
* * *
18071 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAAT-GGACCTTTTGAAAGTTTTGGGGTTAAAAA
1 AAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGGA-TTTTTGAAAGTTTTGGGGTTAAAAA
** *
18135 GGGATTTTTGGTGGTTTCGAGGTT
65 GGGATTTTT-GAAGTTTTG-GGTT
* * * *
18159 AAAAATGAGATTTTTTA-AAGTTTTG-GGGTTAAAATGGGATTTTTTAGAAG-TTTGGGGGTAAA
1 AAAAATGAGA-TTTTTAGAAG-TTCGAGGGTAAAAATGGGATTTTTGA-AAGTTTTGGGGTTAAA
* *
18221 ATGGGATTTCTTGAAGTTTTGGGGTC
63 AAGGGATTT-TTGAAGTTTT-GGGTT
* * *
18247 AAAAATTAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAACTTTTGGGGTTAAAAAT
1 AAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGAAAGTTTTGGGGTTAAAAA-
* *
18312 GGGATTTTAAGAAGTTTTGGGGT
65 GGGATTTT-TGAAGTTTTGGGTT
* * * *
18335 CAAAATGGGATTTTT-GAAAGTTTGAGGGTAAAAATGGAATTTTTGAA
1 AAAAATGAGATTTTTAG-AAGTTCGAGGGTAAAAATGGGATTTTTGAA
18382 CAATTTAGGG
Statistics
Matches: 183, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
87 12 0.07
88 138 0.75
89 33 0.18
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (86 bp):
AAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGAAAGTTTTGGGGTTAAAAAG
GGATTTTTGAAGTTTTGGGTT
Found at i:18391 original size:29 final size:29
Alignment explanation
Indices: 18271--18391 Score: 106
Period size: 29 Copynumber: 4.1 Consensus size: 29
18261 TAGAAGTTCG
*
18271 AGGGTAAAAATGGGATTTTTGGAAC-TTTT
1 AGGGTAAAAATGGGATTTTT-GAACAATTT
* *
18300 GGGGTTAAAAATGGGA-TTTT-AAGAAGTTTT
1 AGGG-TAAAAATGGGATTTTTGAACAA--TTT
* * *
18330 GGGGTCAAAATGGGATTTTTGAA-AGTTT
1 AGGGTAAAAATGGGATTTTTGAACAATTT
*
18358 GAGGGTAAAAATGGAATTTTTGAACAATTT
1 -AGGGTAAAAATGGGATTTTTGAACAATTT
18388 AGGG
1 AGGG
18392 ACCCACGGGA
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.03
28 3 0.04
29 41 0.55
30 27 0.36
31 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGGGATTTTTGAACAATTT
Found at i:20220 original size:18 final size:17
Alignment explanation
Indices: 20182--20293 Score: 100
Period size: 18 Copynumber: 6.4 Consensus size: 17
20172 CTTTACTTAT
* *
20182 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
20199 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
20217 TTTAAA-CTCAAATCAAA
1 TTTAAATTTAAAAT-AAA
*
20234 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
* *
20251 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
20269 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
*
20287 CTTAAAT
1 TTTAAAT
20294 GGAGTTTGGG
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
16 4 0.05
17 29 0.39
18 42 0.56
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:21120 original size:220 final size:219
Alignment explanation
Indices: 20732--21286 Score: 842
Period size: 220 Copynumber: 2.5 Consensus size: 219
20722 AGCTAACCAC
* * * * ** * *
20732 TTTATTGCTTCGACCTGTTTTTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
1 TTTATTACTTCGACTTGCTTCTCAGTACCTCATCAGGAAGCTGGGATTCGAAGCTTTGCTCACAT
* * *
20797 TGGGCGTGAGTTTAATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGTGTCATTGGTT
66 CGAGCGTGAGTTTAGTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGTGTCATTGGTT
20862 TCAATTCGTTTCTCTGTATCTCATCAGGAAAGACGAATTTCGTCCACTTCTCCGTACCTCATCAT
131 TCAATTCGTTTCTCTGTATCTCATCAGGAAAGACGAATTTCGTCCACTTCTCCGTACCTCATCAT
20927 GAAGATGGTCAGGAAGCCAACCGT
196 GAAGATGGTCAGGAAGCCAACCGT
*
20951 TTTATTACTTCGACTTGCTTCTTAGTACCTCATCAGGAAGCTGGGATTCGAAGCTTTTGCTCACA
1 TTTATTACTTCGACTTGCTTCTCAGTACCTCATCAGGAAGCTGGGATTCGAAGC-TTTGCTCACA
* * * * * * *
21016 TCGAGCGTGACTTTGGTTCGGTCTCCTTCTTAGTATTTCATCGGGAAGATGACTGTGTCGTTGGT
65 TCGAGCGTGAGTTTAGTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGTGTCATTGGT
* *
21081 TTCAATTCGTTTCTCTGTATCTCATCAGGAAAGACGAATTTGGTCCACTTCTCCGTACCTTATCA
130 TTCAATTCGTTTCTCTGTATCTCATCAGGAAAGACGAATTTCGTCCACTTCTCCGTACCTCATCA
* *
21146 TGAAGATGGTCAGGAAGCTAACCTT
195 TGAAGATGGTCAGGAAGCCAACCGT
* * *
21171 TTTATTACTTCGACTTGCTTCTCAGTACCTCATTAGGAAGTTGGGATTCGAGGCTTTGCTCACAT
1 TTTATTACTTCGACTTGCTTCTCAGTACCTCATCAGGAAGCTGGGATTCGAAGCTTTGCTCACAT
**
21236 CGA-CGTGAGTTTAGTTTAATCTTCTTCTCAGTATCTCATCGGGAAGATGAC
66 CGAGCGTGAGTTTAGTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGAC
21287 CGCATCGCTT
Statistics
Matches: 300, Mismatches: 35, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
218 40 0.13
219 59 0.20
220 201 0.67
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (219 bp):
TTTATTACTTCGACTTGCTTCTCAGTACCTCATCAGGAAGCTGGGATTCGAAGCTTTGCTCACAT
CGAGCGTGAGTTTAGTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGTGTCATTGGTT
TCAATTCGTTTCTCTGTATCTCATCAGGAAAGACGAATTTCGTCCACTTCTCCGTACCTCATCAT
GAAGATGGTCAGGAAGCCAACCGT
Found at i:32588 original size:96 final size:95
Alignment explanation
Indices: 32414--32589 Score: 223
Period size: 96 Copynumber: 1.8 Consensus size: 95
32404 AGGATATTTG
** *
32414 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAATCGAAGAT
*
32479 AAGGAAACGTTGCCTCGATTAAGGGTATTCA
66 AAAGAAAC-TTGCCTCGATTAAGGGTATTCA
* **
32510 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTGTGTTAAGGCGCAAGT-TTTCGAAACTCGAA-
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAA-TATTTCGAAA-TCGAAG
32573 ATGAAAGAATA-TTGCCT
64 AT-AAAGAA-ACTTGCCT
32590 TGATATTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
96 57 0.83
97 11 0.16
98 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (95 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAATCGAAGAT
AAAGAAACTTGCCTCGATTAAGGGTATTCA
Found at i:32880 original size:28 final size:29
Alignment explanation
Indices: 32821--32884 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
32811 AAAATGAGAC
* *
32821 TTTTCGGATTCTCGGGGGCAAAAGTGATAA
1 TTTT-GGATTCTCGGGGACAAAACTGATAA
32851 TTTTGGATTCTCGGGGACAAAACTG-TAA
1 TTTTGGATTCTCGGGGACAAAACTGATAA
32879 TTTTGG
1 TTTTGG
32885 GAAAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 9 0.28
29 19 0.59
30 4 0.12
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTGGATTCTCGGGGACAAAACTGATAA
Found at i:33065 original size:87 final size:88
Alignment explanation
Indices: 32893--33176 Score: 258
Period size: 88 Copynumber: 3.2 Consensus size: 88
32883 GGGAAAATTT
* * * * ** *
32893 AGGGTCAAAAATGTGATTTTTAGAATTTTG-GGGTAAAAAATGGACCTTTT-GAAAGTTTTGGGG
1 AGGGT-AAAAATGAGATTTTTAGAAGTTCGAGGGT-AAAAATAGAATTTTTAG-AAGTTTCGGGG
*
32956 TTAAAAATGGGATTTTTAGAAGTTCG
63 TTAAAAATAGGATTTTTAGAAGTTCG
* * * *
32982 AGGGTAAAAAT-AGGTTTTTTGGAAGTTTCG-GGGTCAAAATAGAATTTTTAGAAG-TTCGGGGG
1 AGGGTAAAAATGA-GATTTTTAGAAG-TTCGAGGGTAAAAATAGAATTTTTAGAAGTTTCGGGGT
* *
33044 TAAAAATTGGATTTTTAGAAGTTTTG
64 TAAAAATAGGATTTTTAGAAG-TTCG
* * * * * *
33070 A-GGTTAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTTGAAGTTTTGAGGTTA
1 AGGGTAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGTTTCGGGGTTA
* *
33134 AAAATAGGATTTTTGGAAGTCCG
66 AAAATAGGATTTTTAGAAGTTCG
33157 AGGGTAAAAATG-GAATTTTT
1 AGGGTAAAAATGAG-ATTTTT
33177 GAACAATTTA
Statistics
Matches: 158, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
86 4 0.03
87 68 0.43
88 73 0.46
89 13 0.08
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (88 bp):
AGGGTAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGTTTCGGGGTTA
AAAATAGGATTTTTAGAAGTTCG
Found at i:33176 original size:58 final size:58
Alignment explanation
Indices: 32899--33179 Score: 297
Period size: 58 Copynumber: 4.8 Consensus size: 58
32889 ATTTAGGGTC
* * ** *
32899 AAAAAT-GTGATTTTTAGAATTTTG-GGGTAAAAAATGGACCTTTTGAAAGTTTTGGGGTT
1 AAAAATAG-GATTTTTAGAAGTTCGAGGGT-AAAAATGGAATTTTTG-AAGTTTTGAGGTT
* * * *
32958 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATAGG-TTTTTTGGAAGTTTCG-GGGT
1 AAAAATAGGATTTTTAGAAGTTCGAGGGTAAAAAT-GGAATTTTT-GAAGTTTTGAGGTT
* * *
33016 CAAAATAGAATTTTTAGAAGTTCGGGGGTAAAAATTGG-ATTTTTAGAAGTTTTGAGGTT
1 AAAAATAGGATTTTTAGAAGTTCGAGGGTAAAAA-TGGAATTTTT-GAAGTTTTGAGGTT
*
33075 -AAAAT-GAGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTTGAAGTTTTGAGGTT
1 AAAAATAG-GATTTTTAGAAGTTCGAGGGTAAAAAT-GGAATTTTTGAAGTTTTGAGGTT
* *
33133 AAAAATAGGATTTTTGGAAGTCCGAGGGTAAAAATGGAATTTTTGAA
1 AAAAATAGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAA
33180 CAATTTAGGG
Statistics
Matches: 191, Mismatches: 20, Indels: 23
0.82 0.09 0.10
Matches are distributed among these distances:
57 2 0.01
58 104 0.54
59 76 0.40
60 9 0.05
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
AAAAATAGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGAAGTTTTGAGGTT
Found at i:33177 original size:29 final size:28
Alignment explanation
Indices: 32893--33176 Score: 227
Period size: 29 Copynumber: 9.7 Consensus size: 28
32883 GGGAAAATTT
* *
32893 AGGGTCAAAAATGTGATTTTTAGAATTTTG
1 AGGGT-AAAAATG-GATTTTTAGAAGTTCG
* *
32923 -GGGTAAAAAATGGACCTTTT-GAAAGTTTTG
1 AGGGT-AAAAATGGA-TTTTTAG-AAG-TTCG
32953 -GGGTTAAAAATGGGATTTTTAGAAGTTCG
1 AGGG-TAAAAAT-GGATTTTTAGAAGTTCG
* *
32982 AGGGTAAAAATAGGTTTTTTGGAAGTTTCG
1 AGGGTAAAAAT-GGATTTTTAGAAG-TTCG
* *
33012 -GGGTCAAAATAGAATTTTTAGAAGTTCG
1 AGGGTAAAAAT-GGATTTTTAGAAGTTCG
* *
33040 GGGGTAAAAATTGGATTTTTAGAAGTTTTG
1 AGGGTAAAAA-TGGATTTTTAGAAG-TTCG
*
33070 A-GGTTAAAATGAGATTTTTAGAAGTTCG
1 AGGGTAAAAATG-GATTTTTAGAAGTTCG
* *
33098 AGGGTAAAAATGGGATTTTTTGAAGTTTTG
1 AGGGTAAAAAT-GGATTTTTAGAAG-TTCG
* * *
33128 AGGTTAAAAATAGGATTTTTGGAAGTCCG
1 AGGGTAAAAAT-GGATTTTTAGAAGTTCG
33157 AGGGTAAAAATGGAATTTTT
1 AGGGTAAAAATGG-ATTTTT
33177 GAACAATTTA
Statistics
Matches: 211, Mismatches: 27, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
28 15 0.07
29 134 0.64
30 57 0.27
31 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
AGGGTAAAAATGGATTTTTAGAAGTTCG
Done.