Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009413.1 Kokia drynarioides strain JFW-HI SEQ_124120, 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: 10944
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:1146 original size:115 final size:115
Alignment explanation
Indices: 949--1165 Score: 373
Period size: 115 Copynumber: 1.9 Consensus size: 115
939 GATTTGGTTC
949 ACTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
*
1014 CAGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTAT
66 CAGGAAGCTGGAGTTCGAAGATTTGCTCACACCGAGCCCTGAGTTGGTAT
* * *
1064 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
1 ACTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
*
1129 CAGGAAGTTGG-GATTCGAAGATTTGCTCACACCGAGC
66 CAGGAAGCTGGAG-TTCGAAGATTTGCTCACACCGAGC
1166 ATGGGTTTGA
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 1 0.01
115 95 0.99
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (115 bp):
ACTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGAGTTCGAAGATTTGCTCACACCGAGCCCTGAGTTGGTAT
Found at i:1562 original size:78 final size:77
Alignment explanation
Indices: 1432--1791 Score: 420
Period size: 78 Copynumber: 4.6 Consensus size: 77
1422 TGGATAATCG
* * * * * * * * *
1432 CAATCTGCCCCGTGATCGGGGTAGGCGTTTGGTTGACGATGATTTGCGCCAAGGTCGGGGTAAGA
1 CAATCTGCCCC-AGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGGTCGGGGTAAAA
*
1497 GATCGAATGGCTGT
65 GATCAAATGGCT-T
* * * * *
1511 -AATCTACCTCTGTCTCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAAGCTCGGGGTAAAA
1 CAATCTGCCCCAG-CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGGTCGGGGTAAAA
1575 GATCAAATGGCTT
65 GATCAAATGGCTT
* * * **
1588 CAATATGCCCCAAGCTCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCTAGGTAAAA
1 CAATCTGCCCC-AGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGGTCGGGGTAAAA
1653 GATCAAATGGCTT
65 GATCAAATGGCTT
* *
1666 CAATCTGCCCCAGACTTGGGGTAAGAGATTGGTTGATGATGATCTG-CCCTAGGCTCGGGGTAAA
1 CAATCTGCCCCAG-CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGG-TCGGGGTAAA
1730 AGATCAAATGGCTT
64 AGATCAAATGGCTT
* *
1744 CAATCTGCCCCAGGCT-TGGGTAAGAGATTGGTTGACGATGATCTGCCC
1 CAATCTGCCCCA-GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCC
1792 TAGGCTTGGG
Statistics
Matches: 246, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
77 37 0.15
78 207 0.84
79 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (77 bp):
CAATCTGCCCCAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGGTCGGGGTAAAAG
ATCAAATGGCTT
Found at i:1567 original size:39 final size:39
Alignment explanation
Indices: 1524--1851 Score: 227
Period size: 39 Copynumber: 8.4 Consensus size: 39
1514 CTACCTCTGT
*
1524 CTCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAAG
1 CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
* *
1563 CTCGGGGTAAAAGATCAAATGGCTTCA--AT-A--TGCCCCAAG
1 CTCGGGGTAAGAGAT----TGG-TTGATGATGATCTGCCCCAAG
*
1602 CTCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
1 CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
** * * *
1641 CTCTAGGTAAAAGATCAAATGGCT--TCA--ATCTGCCCC-AG
1 CTCGGGGTAAGAGAT----TGGTTGATGATGATCTGCCCCAAG
* * *
1679 ACTTGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAGG
1 -CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
* * * *
1719 CTCGGGGTAAAAGATCAAATGGCT--TCA--ATCTGCCCCAGG
1 CTCGGGGTAAGAGAT----TGGTTGATGATGATCTGCCCCAAG
* * * *
1758 CT-TGGGTAAGAGATTGGTTGACGATGATCTGCCCTAGG
1 CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
* *
1796 CTTGGGGTAAGAGATTGGTTGATGATGATCTGCCCCATG
1 CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
1835 CTCGGGGTAAGAGATTG
1 CTCGGGGTAAGAGATTG
1852 ATTAACGATG
Statistics
Matches: 227, Mismatches: 33, Indels: 58
0.71 0.10 0.18
Matches are distributed among these distances:
34 7 0.03
35 7 0.03
36 3 0.01
37 3 0.01
38 25 0.11
39 160 0.70
40 1 0.00
41 5 0.02
42 2 0.01
43 11 0.05
44 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (39 bp):
CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAG
Found at i:1722 original size:156 final size:155
Alignment explanation
Indices: 1460--1791 Score: 468
Period size: 156 Copynumber: 2.1 Consensus size: 155
1450 GGGTAGGCGT
* * * * * * * * *
1460 TTGGTTGACGATGATTTGCGCCAAGGTCGGGGTAAGAGATCGAATGGCTGTAATCTACCTCTGTC
1 TTGGTTGACGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGGCTGTAATCTACCCCAGAC
*
1525 TCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTCA
66 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTCA
1590 ATATGCCCCAAGCTCGAGGTAAGAGA
131 ATATGCCCCAAGCTCG-GGTAAGAGA
* * *
1616 TTGGTTGATGATGATCTGCCCCAAGCTCTAGGTAAAAGATCAAATGGCT-TCAATCTGCCCCAGA
1 TTGGTTGACGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGGCTGT-AATCTACCCCAGA
* * *
1680 CTTGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTTC
65 CTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTC
* * *
1745 AATCTGCCCCAGGCTTGGGTAAGAGA
130 AATATGCCCCAAGCTCGGGTAAGAGA
1771 TTGGTTGACGATGATCTGCCC
1 TTGGTTGACGATGATCTGCCC
1792 TAGGCTTGGG
Statistics
Matches: 155, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
155 30 0.19
156 125 0.81
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (155 bp):
TTGGTTGACGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGGCTGTAATCTACCCCAGAC
TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTCA
ATATGCCCCAAGCTCGGGTAAGAGA
Found at i:2297 original size:50 final size:49
Alignment explanation
Indices: 2241--2570 Score: 244
Period size: 50 Copynumber: 6.6 Consensus size: 49
2231 CTAGATTTGT
*
2241 CGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATGGTCCGT
1 CGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGTCCGC
* * * **
2291 CATTGCGACTTAAACCTTTCCCTT-TTGTATCTT-TGTGGTACTGGATCTAC
1 CGTTGCGACTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTGG-TCCGC
* * * *
2341 CGTTGCGATCTTAGATCTTTCCCTTCATGTCTTC--ATGGTACTAGATTCGC
1 CGTTGCGA-CTTAAATCTTTCCCTTCTTGTCTTCTGA-GGTACT-GGTCCGC
* * * *
2391 CGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGC
1 CGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGTC-CGC
* * * * *
2442 CGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-TGTGGTACTGGATTCGT
1 CGTTGCGACTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTGG-TCCGC
* * * *
2492 TGTTGC-AGCTTAAATCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTGC
1 CGTTGCGA-CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGTCC-GC
* *
2543 CGTTGCGACTTAGACCTTTCCCTT-TTGT
1 CGTTGCGACTTAAATCTTTCCCTTCTTGT
2571 ATATTTGTGG
Statistics
Matches: 215, Mismatches: 44, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
49 34 0.16
50 99 0.46
51 75 0.35
52 7 0.03
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (49 bp):
CGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACTGGTCCGC
Found at i:2397 original size:100 final size:100
Alignment explanation
Indices: 2241--2566 Score: 256
Period size: 101 Copynumber: 3.2 Consensus size: 100
2231 CTAGATTTGT
* * * *
2241 CGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATGGTCCGTCATTGCGACTTAAAC
1 CGTTGCGACTTAGATCTTTCCCTTCATGTCTTCT-AGGTACATGATCCGCCATTGCGACTTAAAC
* * *
2306 CTTTCCCTTTTGTATCTT-TGTGGTAC-TGGATC-TAC
65 CTTTCCC-TTCGTATCTTCTGAGGTACACGG-TCTTAC
* * *
2341 CGTTGCGATCTTAGATCTTTCCCTTCATGTCTTC-ATGGTAC-TAGATTCGCCGTTGCGGCTTAA
1 CGTTGCGA-CTTAGATCTTTCCCTTCATGTCTTCTA-GGTACAT-GATCCGCCATTGCGACTTAA
* * *
2404 ATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGC
63 ACCTTTCCCTTCGTATCTTCTGAGGTACACGGTCTTAC
* * * * ***
2442 CGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-TGTGGTAC-TGGATTCGTTGTTGC-AGCTT
1 CGTTGCGACTTAGATCTTTCCCTTCATG--TCTTCT-AGGTACAT-GATCCGCCATTGCGA-CTT
* * * * *
2503 AAATCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTGC
61 AAACCTTTCCCTTCGTATCTTCTGAGGTACACGGTCTTAC
*
2543 CGTTGCGACTTAGACCTTTCCCTT
1 CGTTGCGACTTAGATCTTTCCCTT
2567 TTGTATATTT
Statistics
Matches: 193, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
99 12 0.06
100 60 0.31
101 121 0.63
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (100 bp):
CGTTGCGACTTAGATCTTTCCCTTCATGTCTTCTAGGTACATGATCCGCCATTGCGACTTAAACC
TTTCCCTTCGTATCTTCTGAGGTACACGGTCTTAC
Found at i:2504 original size:101 final size:101
Alignment explanation
Indices: 2340--2585 Score: 352
Period size: 101 Copynumber: 2.4 Consensus size: 101
2330 ACTGGATCTA
* * ** * *
2340 CCGTTGCGATCTTAGATCTTTCCCTTCATG--TCTTCATGGTACTAGATTCGCCGTTGCGGCTTA
1 CCGTTGCGA-CTTAGACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATTCGCCGTTGCAGCTTA
* *
2403 AATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTG
64 AATCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTG
**
2441 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCGTTGTTGCAGCTTAAA
1 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCGCCGTTGCAGCTTAAA
2506 TCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTG
66 TCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTG
* *
2542 CCGTTGCGACTTAGACCTTTCCCTTTTGTATATTTGTGGCACTG
1 CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTG
2586 AGACCTGTAG
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.02
100 15 0.11
101 114 0.87
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (101 bp):
CCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCGCCGTTGCAGCTTAAA
TCTTTCCCTTCGTGTCTTCTAAGGTACACGGTCCTG
Found at i:2509 original size:150 final size:149
Alignment explanation
Indices: 2206--2566 Score: 431
Period size: 150 Copynumber: 2.4 Consensus size: 149
2196 CAACTTCAAC
** * * * * *
2206 CTTTCCCCTTCAAATCTTCGTGTTACTAGATTTGTCGTTGCGACTTAAATCTTTCCCTTCTTGTC
1 CTTT-CCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTC
* *
2271 TTCTGAGGTACATGGTCCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
65 TTCTGAGGTACACGGTCCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
* *
2336 TCTACCGTTGCGATCTTAGAT
130 TCTA-CGTTGCGAGCTTAAAT
*
2357 CTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCT
1 CTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCT
* * *
2422 TCTGAGGTACACGGTCTTGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
66 TCTGAGGTACACGGTC-CGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
*
2487 T-T-CGTTGTTGCAGCTTAAAT
130 TCTACGTTG-CG-AGCTTAAAT
* * * * * *
2507 CTTTCCCTTCGTGTCTTCTAAGGTAC-ACGGTCCTGCCGTTGCGACTTAGACCTTTCCCTT
1 CTTTCCCTTCATGTCTTC-ATGGTACTA-GATTC-GCCGTTGCGACTTAAATCTTTCCCTT
2567 TTGTATATTT
Statistics
Matches: 181, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
148 5 0.03
149 1 0.01
150 94 0.52
151 58 0.32
152 23 0.13
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (149 bp):
CTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCT
TCTGAGGTACACGGTCCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGAT
CTACGTTGCGAGCTTAAAT
Found at i:9413 original size:30 final size:30
Alignment explanation
Indices: 9369--9577 Score: 80
Period size: 30 Copynumber: 7.1 Consensus size: 30
9359 GTTTGGGGGT
9369 AAAATAGTAA-TTTTGAGAGTTTCAGGGTTA
1 AAAATAG-AATTTTTGAGAGTTTCAGGGTTA
* *
9399 AAAATAGAATTTTTG-GAGGTTT-AAGGAT-
1 AAAATAGAATTTTTGAGA-GTTTCAGGGTTA
* ** * *
9427 AAAATGGTAATTTTCAAAAGTTTTAGGGTT-
1 AAAATAG-AATTTTTGAGAGTTTCAGGGTTA
* * * *
9457 AAAATTGAGATTTTGGA-AGTTT-GGGGGTA
1 AAAATAGA-ATTTTTGAGAGTTTCAGGGTTA
* * *
9486 AAAAGTA-AA-TTTTGAGAGTTTTTAAGGTCA
1 AAAA-TAGAATTTTTGAGAG-TTTCAGGGTTA
* * * * *
9516 AAAATGGGATTTTTG-GAGGTTCGGGGGT-
1 AAAATAGAATTTTTGAGAGTTTCAGGGTTA
* * *
9544 AAAATGGTAATTTTTGAAAGTTTCAGGTTTA
1 AAAATAG-AATTTTTGAGAGTTTCAGGGTTA
9575 AAA
1 AAA
9578 TCAAGATTTT
Statistics
Matches: 130, Mismatches: 33, Indels: 31
0.67 0.17 0.16
Matches are distributed among these distances:
27 5 0.04
28 20 0.15
29 44 0.34
30 53 0.41
31 8 0.06
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATAGAATTTTTGAGAGTTTCAGGGTTA
Found at i:9489 original size:29 final size:29
Alignment explanation
Indices: 9357--9745 Score: 143
Period size: 29 Copynumber: 13.2 Consensus size: 29
9347 GGGATTTCGA
*
9357 AAGTTTGGGGGT-AAAATAGTAA-TTTT-G
1 AAGTTTGGGGGTAAAAATTG-AATTTTTGG
* * *
9384 AGAGTTTCAGGGTTAAAAATAGAATTTTTGG
1 A-AGTTT-GGGGGTAAAAATTGAATTTTTGG
* ** * * ***
9415 AGGTTTAAGGAT-AAAATGGTAATTTTCAA
1 AAGTTTGGGGGTAAAAATTG-AATTTTTGG
** *
9444 AAGTTTTAGGGTTAAAATTGAGA-TTTTGG
1 AAGTTTGGGGGTAAAAATTGA-ATTTTTGG
* *
9473 AAGTTTGGGGGTAAAAAGT-AAATTTT-G
1 AAGTTTGGGGGTAAAAATTGAATTTTTGG
*** * *
9500 AGAGTTTTTAAGGTCAAAAATGGGATTTTTGG
1 A-AG-TTTGGGGGT-AAAAATTGAATTTTTGG
* * * *
9532 AGGTTCGGGGGT-AAAATGGTAATTTTTGA
1 AAGTTTGGGGGTAAAAATTG-AATTTTTGG
** * * **
9561 AAGTTTCAGGTTTAAAATCAAGATTTTTGG
1 AAGTTTGGGGGTAAAAATTGA-ATTTTTGG
* * *
9591 AAGTTCGGGGGT-AAAATGGTAATTTTTAG
1 AAGTTTGGGGGTAAAAATTG-AATTTTTGG
* * * *
9620 AAGTTTCGGAGTCAAAATTAAGATTTTTGG
1 AAGTTTGGGGGTAAAAATTGA-ATTTTTGG
*
9650 AAGTTTGAGGGTAAAAA-TGTAATTTTTGG
1 AAGTTTGGGGGTAAAAATTG-AATTTTTGG
* * *
9679 AAGTTTTGGGGTCAAAAGTTGAATTTTGGAG
1 AAGTTTGGGGGT-AAAAATTGAATTTTTG-G
* *
9710 AAGTTTGAGGGTCAAAATAT-AATTTTTGG
1 AAGTTTGGGGGTAAAAAT-TGAATTTTTGG
9739 ACAGTTT
1 A-AGTTT
9746 AGGGACGTTC
Statistics
Matches: 267, Mismatches: 69, Indels: 49
0.69 0.18 0.13
Matches are distributed among these distances:
27 4 0.01
28 25 0.09
29 108 0.40
30 106 0.40
31 22 0.08
32 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
AAGTTTGGGGGTAAAAATTGAATTTTTGG
Found at i:9693 original size:59 final size:59
Alignment explanation
Indices: 9309--9749 Score: 330
Period size: 59 Copynumber: 7.5 Consensus size: 59
9299 ACATCCGGGT
* ** * * * * *
9309 GTAAAAGGGTAATTTTTTAAAGTTTTTGGGTCAAAAATGGGA-TTTCGAAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAATTGAGATTTTTGGAAGTTTGGGG
* * * * * **
9367 GTAAAATAGTAA-TTTT-GAGAGTTTCAGGGTTAAAAAT-AGAATTTTTGGAGGTTTAAGG
1 GTAAAATGGTAATTTTTGGA-AGTTTTAGGGTCAAAATTGAG-ATTTTTGGAAGTTTGGGG
* *** *
9425 ATAAAATGGTAATTTTCAAAAGTTTTAGGGTTAAAATTGAGA-TTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAATTGAGATTTTTGGAAGTTTGGGG
* * * * * * *
9483 GTAAAA-AGTAAATTTT-GAGAGTTTTTAAGGTCAAAAATGGGATTTTTGGAGGTTCGGGG
1 GTAAAATGGTAATTTTTGGA-AG-TTTTAGGGTCAAAATTGAGATTTTTGGAAGTTTGGGG
* * * * ** *
9542 GTAAAATGGTAATTTTTGAAAGTTTCAGGTTTAAAATCAAGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAATTGAGATTTTTGGAAGTTTGGGG
* * * *
9601 GTAAAATGGTAATTTTTAGAAG-TTTCGGAGTCAAAATTAAGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTTAGG-GTCAAAATTGAGATTTTTGGAAGTTTGGGG
* * *
9660 GTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTCAAAAGTTGA-ATTTTGGAGAAGTTTGAGG
1 GT-AAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAA-TTGAGATTTTTG-GAAGTTTGGGG
*
9720 GTCAAAAT-ATAATTTTTGGACAG-TTTAGGG
1 GT-AAAATGGTAATTTTTGGA-AGTTTTAGGG
9750 ACGTTCAGGG
Statistics
Matches: 306, Mismatches: 60, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
56 3 0.01
57 29 0.09
58 69 0.23
59 141 0.46
60 61 0.20
61 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAATTGAGATTTTTGGAAGTTTGGGG
Found at i:9737 original size:31 final size:28
Alignment explanation
Indices: 9583--9745 Score: 122
Period size: 30 Copynumber: 5.5 Consensus size: 28
9573 TAAAATCAAG
*
9583 ATTTTTG-GAAGTTCGGGGGT-AAAATGGTA
1 ATTTTTGAGAAGTT-TGGGGTCAAAAT--TA
*
9612 ATTTTT-AGAAGTTTCGGAGTCAAAATTAA
1 ATTTTTGAGAAGTTT-GGGGTCAAAATT-A
*
9641 GATTTTTG-GAAGTTTGAGGGTAAAAATGTA
1 -ATTTTTGAGAAGTTTG-GGGTCAAAAT-TA
9671 ATTTTTG-GAAGTTTTGGGGTCAAAAGTTGA
1 ATTTTTGAGAAG-TTTGGGGTCAAAA-TT-A
*
9701 ATTTTGGAGAAGTTTGAGGGTCAAAATATA
1 ATTTTTGAGAAGTTTG-GGGTCAAAAT-TA
9731 ATTTTTG-GACAGTTT
1 ATTTTTGAGA-AGTTT
9746 AGGGACGTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 29
0.76 0.05 0.20
Matches are distributed among these distances:
28 1 0.01
29 40 0.36
30 56 0.50
31 15 0.13
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (28 bp):
ATTTTTGAGAAGTTTGGGGTCAAAATTA
Done.