Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003432.1 Kokia drynarioides strain JFW-HI SEQ_116208, 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: 130999
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:1424 original size:18 final size:19
Alignment explanation
Indices: 1401--1443 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1391 TCAATTGGTT
*
1401 TTTTTATTTA-TTTTGAA-A
1 TTTTTATATAGTTTT-AATA
1419 TTTTTATATAGTTTTAATA
1 TTTTTATATAGTTTTAATA
1438 TTTTTA
1 TTTTTA
1444 GAGTTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTATATAGTTTTAATA
Found at i:3666 original size:2 final size:2
Alignment explanation
Indices: 3659--3686 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3649 GCTTTGGGTC
3659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3687 GGAAGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8040 original size:89 final size:88
Alignment explanation
Indices: 7869--8041 Score: 233
Period size: 89 Copynumber: 2.0 Consensus size: 88
7859 GGGGTTCTTT
* *
7869 CAATCGTTCTTGTTGTTCCTTTCTTGCTTTCTTGGAAGGTTTCATTTACTTCAGGTAATGTTTTC
1 CAATCGTTCTTGTTGTTCCTTTCTTGCTTTCTTGAAAGGTTTCATTTACTTCAGGTAATGTTTTA
** *
7934 AGTTGGATATTTTTCATTTCATG
66 AGGGGGATATTTCTCATTTCATG
* *
7957 CAATCGTTTCTTTTTGTTCCTTTCTTG-TTTCCTTGAAAGGTTTCTTTTACTTCAGGTAATGTTT
1 CAATCG-TTCTTGTTGTTCCTTTCTTGCTTT-CTTGAAAGGTTTCATTTACTTCAGGTAATGTTT
*
8021 TAATGGGGGGT-TTTCTCATTT
64 TAA-GGGGGATATTTCTCATTT
8042 GCCATTGTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
88 9 0.12
89 61 0.82
90 4 0.05
ACGTcount: A:0.15, C:0.16, G:0.17, T:0.52
Consensus pattern (88 bp):
CAATCGTTCTTGTTGTTCCTTTCTTGCTTTCTTGAAAGGTTTCATTTACTTCAGGTAATGTTTTA
AGGGGGATATTTCTCATTTCATG
Found at i:8163 original size:64 final size:62
Alignment explanation
Indices: 8049--8181 Score: 221
Period size: 64 Copynumber: 2.1 Consensus size: 62
8039 TTTGCCATTG
* *
8049 TCTTCTCTTTTTCTTGTTATCTTGAAAGGTTTCCATTAACTTTAGGTATTGTTTTGATGGGGT
1 TCTT-TCTTTTTCTTGTTATCTTGAAAGGTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
8112 TCTTTCTTTTTACTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
1 TCTTTCTTTTT-CTTGTTATCTTGAAAGG-TTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
8176 TCTTTC
1 TCTTTC
8182 ATTTCATGCA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
62 7 0.11
63 21 0.32
64 38 0.58
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (62 bp):
TCTTTCTTTTTCTTGTTATCTTGAAAGGTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
Found at i:13899 original size:48 final size:48
Alignment explanation
Indices: 13823--13930 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
13813 TGAAGTACTT
* ** * * *
13823 AACAGAGGGCACATAAGTGCTGGGTAACAGAGGGCCCACAAAGTGCTA
1 AACAGAGGGCACAGAAGTGCTGAATAACAGAGGACACACAAAGCGCTA
* * *
13871 ATCAGAGGGCACACGAAGTGCT-AATAACAGAGGACACATATAGCGCTA
1 AACAGAGGGCACA-GAAGTGCTGAATAACAGAGGACACACAAAGCGCTA
13919 AACAGAGGGCAC
1 AACAGAGGGCAC
13931 GAAATGTGCT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
48 42 0.86
49 7 0.14
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (48 bp):
AACAGAGGGCACAGAAGTGCTGAATAACAGAGGACACACAAAGCGCTA
Found at i:13908 original size:25 final size:25
Alignment explanation
Indices: 13822--13950 Score: 94
Period size: 23 Copynumber: 5.4 Consensus size: 25
13812 CTGAAGTACT
* **
13822 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGGCACACAAAGTGCT-AA
*
13847 TAACAGAGGGCCCACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
13872 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
* * * *
13895 TAACAGAGGACACATATAGCGCT-A
1 TAACAGAGGGCACACAAAGTGCTAA
*
13919 -AACAGAGGGCACGA-AATGTGCT-A
1 TAACAGAGGGCAC-ACAAAGTGCTAA
13942 -AACAGAGGG
1 TAACAGAGGG
13951 TGCGCTAGTG
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
23 47 0.55
24 2 0.02
25 29 0.34
26 7 0.08
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.13
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:15697 original size:21 final size:21
Alignment explanation
Indices: 15673--15723 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 21
15663 GATCTTCACC
15673 AACC-AAAGTACCTTTTTCATG
1 AACCGAAAGTACC-TTTTCATG
* *
15694 AACCGTAAGTAGCTTTTCATGG
1 AACCGAAAGTACCTTTTCAT-G
15716 AAGCCGAA
1 AA-CCGAA
15724 GATAAAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 11 0.46
22 9 0.38
23 4 0.17
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (21 bp):
AACCGAAAGTACCTTTTCATG
Found at i:16052 original size:16 final size:16
Alignment explanation
Indices: 16031--16084 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
16021 GGTAAAATTT
16031 TAATTTAGGTCTTTTA
1 TAATTTAGGTCTTTTA
*****
16047 TAATTTATAAAATTT-
1 TAATTTAGGTCTTTTA
16062 TAATTTAGGTCTTTTA
1 TAATTTAGGTCTTTTA
16078 TAATTTA
1 TAATTTA
16085 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (16 bp):
TAATTTAGGTCTTTTA
Found at i:16061 original size:31 final size:31
Alignment explanation
Indices: 16023--16095 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
16013 CCTAAAATGG
16023 TAAAATTTTAATTTAGGTCTTTTATAATTTA
1 TAAAATTTTAATTTAGGTCTTTTATAATTTA
16054 TAAAATTTTAATTTAGGTCTTTTATAATTTA
1 TAAAATTTTAATTTAGGTCTTTTATAATTTA
16085 TAAAATTTTAA
1 TAAAATTTTAA
16096 ATTAATAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (31 bp):
TAAAATTTTAATTTAGGTCTTTTATAATTTA
Found at i:16098 original size:16 final size:17
Alignment explanation
Indices: 16042--16103 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 17
16032 AATTTAGGTC
16042 TTTTATAATTTATAAAA
1 TTTTATAATTTATAAAA
****
16059 -TTT-TAATTTA-GGTC
1 TTTTATAATTTATAAAA
16073 TTTTATAATTTATAAAA
1 TTTTATAATTTATAAAA
*
16090 TTTTA-AATTAATAA
1 TTTTATAATTTATAA
16104 TGGTAAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 7
0.67 0.18 0.14
Matches are distributed among these distances:
15 10 0.30
16 18 0.55
17 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTATAATTTATAAAA
Found at i:18089 original size:28 final size:28
Alignment explanation
Indices: 18057--18114 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
18047 CGATTAAAAA
*
18057 AACAGTATTCCATCATAATAATCGATTT
1 AACAGTATTCCACCATAATAATCGATTT
18085 AACAGTATTCCACCATAATAATCGATTT
1 AACAGTATTCCACCATAATAATCGATTT
18113 AA
1 AA
18115 ACATATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (28 bp):
AACAGTATTCCACCATAATAATCGATTT
Found at i:18703 original size:27 final size:26
Alignment explanation
Indices: 18656--18711 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
18646 AAATTTGGTA
*
18656 AAATTTTTTTTGAATTCTTAAAAGCT
1 AAATTTTTTTTGAATTCTTAAAAACT
*
18682 AAATTTTTTTTGAGCCTT-TTAAAAACT
1 AAATTTTTTTTGA--ATTCTTAAAAACT
18709 AAA
1 AAA
18712 AAAAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 13 0.50
27 11 0.42
28 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (26 bp):
AAATTTTTTTTGAATTCTTAAAAACT
Found at i:32704 original size:15 final size:16
Alignment explanation
Indices: 32672--32702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32662 TCTTTTTAGT
32672 TTTTTATCTCTTCAAA
1 TTTTTATCTCTTCAAA
*
32688 TTTTTATCTTTTCAA
1 TTTTTATCTCTTCAA
32703 TTAAAATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTATCTCTTCAAA
Found at i:42422 original size:8 final size:8
Alignment explanation
Indices: 42409--42435 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42399 GAAAATAATT
42409 AGATAGAG
1 AGATAGAG
42417 AGATAGAG
1 AGATAGAG
42425 AGATAGAG
1 AGATAGAG
42433 AGA
1 AGA
42436 GCAAACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.37, T:0.11
Consensus pattern (8 bp):
AGATAGAG
Found at i:45480 original size:19 final size:19
Alignment explanation
Indices: 45458--45503 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
45448 ATATAATTAA
45458 AATATATTAATTTAT-AAAT
1 AATATATTAATTT-TCAAAT
*
45477 AATATA-AAATTTTCAAAT
1 AATATATTAATTTTCAAAT
45495 AATA-ATTAA
1 AATATATTAA
45504 AGTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 15 0.65
19 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATATTAATTTTCAAAT
Found at i:53346 original size:16 final size:17
Alignment explanation
Indices: 53328--53360 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53318 ATTTTAGTTA
53328 TTTATTTAAATTTTTAT
1 TTTATTTAAATTTTTAT
*
53345 TTTTTTTAAATTTTTA
1 TTTATTTAAATTTTTA
53361 ATTCGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTAAATTTTTAT
Found at i:56403 original size:25 final size:22
Alignment explanation
Indices: 56373--56417 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
56363 TTTTAATTCA
56373 TTTATTATATATTAGTATTTTATGT
1 TTTATTATA-ATTA-T-TTTTATGT
56398 TTTATTATAATTATTTTTAT
1 TTTATTATAATTATTTTTAT
56418 CATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 4 0.20
25 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATTATAATTATTTTTATGT
Found at i:56446 original size:20 final size:19
Alignment explanation
Indices: 56428--56472 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
56418 CATATAATTA
56428 TTATATTT-TTTTACAAAT
1 TTATATTTATTTTACAAAT
*
56446 TTATATTTATTTTAC-AGT
1 TTATATTTATTTTACAAAT
56464 TTATATTTA
1 TTATATTTA
56473 ATATTCGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATATTTATTTTACAAAT
Found at i:56584 original size:81 final size:82
Alignment explanation
Indices: 56493--56656 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 82
56483 TATTCTTCTC
56493 AATAACATTATTTTCAACATTCAAATATATAATCACTATA-TTTTTTTGAAACAAATATATAATC
1 AATAACATTATTTTCAACATTCAAATATATAATCACTATATTTTTTTTGAAACAAATATATAATC
56557 ATTAATATTGTTGAGTT
66 ATTAATATTGTTGAGTT
*
56574 AATAACATTATTTTCACCATTCAAATATATAATCACTATATTTTTTTTTGAAACAAATATATAAT
1 AATAACATTATTTTCAACATTCAAATATATAATCACTATA-TTTTTTTTGAAACAAATATATAAT
56639 CATTAATATTGTTGAGTT
65 CATTAATATTGTTGAGTT
56657 TAATGATTAT
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 39 0.49
83 41 0.51
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (82 bp):
AATAACATTATTTTCAACATTCAAATATATAATCACTATATTTTTTTTGAAACAAATATATAATC
ATTAATATTGTTGAGTT
Found at i:58409 original size:23 final size:23
Alignment explanation
Indices: 58383--58551 Score: 220
Period size: 23 Copynumber: 7.3 Consensus size: 23
58373 TACTGGGCAA
*
58383 CAGTAAGCATACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCGAAT
58405 CCAGTAAGCACACACAGTGCGAAT
1 -CAGTAAGCACACACAGTGCGAAT
58429 CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTGC-GAAT
*
58452 CAGTAAGCACACACAGTG-TAAT
1 CAGTAAGCACACACAGTGCGAAT
* *
58474 CCAGTAAGTACACATAGTGCGAAT
1 -CAGTAAGCACACACAGTGCGAAT
* *
58498 CAGTAAGTACACATAGTGCGAAT
1 CAGTAAGCACACACAGTGCGAAT
58521 CAGTAAGCACACACAGTGCTGAAT
1 CAGTAAGCACACACAGTGC-GAAT
58545 -AGTAAGC
1 CAGTAAGC
58552 GCGCTAGTGT
Statistics
Matches: 133, Mismatches: 7, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
21 2 0.02
23 118 0.89
24 13 0.10
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCGAAT
Found at i:58475 original size:69 final size:68
Alignment explanation
Indices: 58381--58539 Score: 246
Period size: 69 Copynumber: 2.3 Consensus size: 68
58371 AGTACTGGGC
*
58381 AACAGTAAGCATACACAGTGCAATCCAGTAAGCACACACAGTGCGAATCAGTAAGCACACACAGT
1 AACAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAGTGCGAATCAGTAAGCACACACAGT
58446 GCTG
66 GC-G
* * * * *
58450 AACAGTAAGCACACACAGTGTAATCCAGTAAGTACACATAGTGCGAATCAGTAAGTACACATAGT
1 AACAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAGTGCGAATCAGTAAGCACACACAGT
58515 GCG
66 GCG
58518 AATCAGTAAGCACACACAGTGC
1 AA-CAGTAAGCACACACAGTGC
58540 TGAATAGTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 3 0.04
69 79 0.96
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (68 bp):
AACAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAGTGCGAATCAGTAAGCACACACAGT
GCG
Found at i:61823 original size:16 final size:17
Alignment explanation
Indices: 61789--61831 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
61779 TAAAAATTCT
*
61789 AAAATTTTTATTTTAAA
1 AAAATTTATATTTTAAA
61806 AAAATTTATATTTTAAA
1 AAAATTTATATTTTAAA
61823 AAATATTTA
1 AAA-ATTTA
61832 AAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTTATATTTTAAA
Found at i:61842 original size:10 final size:11
Alignment explanation
Indices: 61817--61848 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
61807 AAATTTATAT
61817 TTTAAAAAATA
1 TTTAAAAAATA
61828 TTTAAAAAATA
1 TTTAAAAAATA
61839 -TTAAAAAATA
1 TTTAAAAAATA
61849 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:62095 original size:14 final size:15
Alignment explanation
Indices: 62064--62097 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
62054 TTATTATTTG
*
62064 TTAATTTTTTTTACA
1 TTAATTTTATTTACA
62079 TTAATTTTATTTA-A
1 TTAATTTTATTTACA
62093 TTAAT
1 TTAAT
62098 CAACACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATTTTATTTACA
Found at i:65914 original size:3 final size:3
Alignment explanation
Indices: 65908--65947 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
65898 AAGTTAAAAA
65908 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
65948 TAAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:67558 original size:51 final size:51
Alignment explanation
Indices: 67500--67604 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
67490 GTATAATAAT
** * *
67500 AAATTTAACTCTCAATTTTTATATAT-TATATCGATTTAAT-TATAATTTTAA
1 AAATTTAACTCTCAAAATTTATAAATAT-TATCAATTTAATCT-TAATTTTAA
*
67551 AAATTTAACTCTCAAAATTTATAAATATTCTCAATTTAATCTTAATTTTAA
1 AAATTTAACTCTCAAAATTTATAAATATTATCAATTTAATCTTAATTTTAA
67602 AAA
1 AAA
67605 AAAATATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 45 0.96
52 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.47
Consensus pattern (51 bp):
AAATTTAACTCTCAAAATTTATAAATATTATCAATTTAATCTTAATTTTAA
Found at i:74491 original size:14 final size:14
Alignment explanation
Indices: 74472--74500 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
74462 TAAAATAAAC
74472 ATTTTCTAGATAGA
1 ATTTTCTAGATAGA
74486 ATTTTCTAGATAGA
1 ATTTTCTAGATAGA
74500 A
1 A
74501 AAAAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (14 bp):
ATTTTCTAGATAGA
Found at i:77266 original size:15 final size:15
Alignment explanation
Indices: 77242--77294 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
77232 AATTCTAGTC
77242 AAAAT-AAAATTAA-
1 AAAATAAAAATTAAT
77255 AAAATAACAAATTTAAT
1 AAAATAA-AAA-TTAAT
77272 CAAAAT-AAAATTAAT
1 -AAAATAAAAATTAAT
77287 AAAATAAA
1 AAAATAAA
77295 CAACTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 10 0.29
16 7 0.21
17 1 0.03
18 5 0.15
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAAAAATTAAT
Found at i:77277 original size:31 final size:33
Alignment explanation
Indices: 77222--77294 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 33
77212 TTACCCTACT
*
77222 TAAAATAAATAATTCTAGTCAAAATAAAATTAA
1 TAAAATAAATAATTCTAATCAAAATAAAATTAA
77255 -AAAATAACA-AATT-TAATCAAAATAAAATTAA
1 TAAAATAA-ATAATTCTAATCAAAATAAAATTAA
77286 TAAAATAAA
1 TAAAATAAA
77295 CAACTTTGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 18 0.49
32 18 0.49
33 1 0.03
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.27
Consensus pattern (33 bp):
TAAAATAAATAATTCTAATCAAAATAAAATTAA
Found at i:77724 original size:15 final size:14
Alignment explanation
Indices: 77704--77733 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
77694 TATTATTTTA
77704 AAATATATAACATAT
1 AAATATATAA-ATAT
77719 AAATATATAAATAT
1 AAATATATAAATAT
77733 A
1 A
77734 TAAAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:77728 original size:8 final size:8
Alignment explanation
Indices: 77704--77737 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
77694 TATTATTTTA
77704 AAATATAT
1 AAATATAT
*
77712 -AACATAT
1 AAATATAT
77719 AAATATAT
1 AAATATAT
77727 AAATATAT
1 AAATATAT
77735 AAA
1 AAA
77738 AATCTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATATAT
Found at i:84886 original size:24 final size:23
Alignment explanation
Indices: 84848--84897 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
84838 TAAACAGATG
84848 TTTAACTTTTAATTTTTTTTTATA
1 TTTAACTTTTAATTTTTTTTTA-A
84872 TTTAACCTTTT-ATTTTTTTTTAA
1 TTTAA-CTTTTAATTTTTTTTTAA
84895 TTT
1 TTT
84898 TTCATATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.16
24 16 0.64
25 5 0.20
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTAACTTTTAATTTTTTTTTAA
Found at i:91137 original size:25 final size:24
Alignment explanation
Indices: 91095--91146 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
91085 TAAAATATAA
* * *
91095 TTAAATTGTTTAATAAATATAGATT
1 TTAAATTATTAAAAAAAT-TAGATT
*
91120 TTAAATTATTAAAAAAATTATATT
1 TTAAATTATTAAAAAAATTAGATT
91144 TTA
1 TTA
91147 CATTTTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTAAATTATTAAAAAAATTAGATT
Found at i:93222 original size:23 final size:25
Alignment explanation
Indices: 93178--93224 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
93168 AATGACATAT
*
93178 AAAATAAAATAAAATGTTTATTAAA
1 AAAATAAAATAAAATGTATATTAAA
*
93203 AAAATAAAA-AATAT-TATATTAA
1 AAAATAAAATAAAATGTATATTAA
93225 CATGAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 4 0.20
25 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAAAATAAAATGTATATTAAA
Found at i:93367 original size:19 final size:17
Alignment explanation
Indices: 93343--93380 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 17
93333 AAAATTAAAG
93343 ATCAAATTTAATTAAAAAA
1 ATCAAA-TTAA-TAAAAAA
93362 ATCAAATTAATAAAAAA
1 ATCAAATTAATAAAAAA
93379 AT
1 AT
93381 ATATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
ATCAAATTAATAAAAAA
Found at i:93377 original size:18 final size:19
Alignment explanation
Indices: 93343--93379 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
93333 AAAATTAAAG
*
93343 ATCAAATTTAATTAAAAAA
1 ATCAAATTTAATAAAAAAA
93362 ATCAAA-TTAATAAAAAAA
1 ATCAAATTTAATAAAAAAA
93380 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
ATCAAATTTAATAAAAAAA
Found at i:94884 original size:11 final size:11
Alignment explanation
Indices: 94868--94898 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
94858 AAAAGAATAA
94868 AAATTTAATTC
1 AAATTTAATTC
94879 AAATTTAATTC
1 AAATTTAATTC
94890 AAATATTAA
1 AAAT-TTAA
94899 AAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTTAATTC
Found at i:96984 original size:24 final size:22
Alignment explanation
Indices: 96949--96997 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
96939 ATTTAATCCT
*
96949 TTAAAATTATAAAGATATAAACTA
1 TTAAAATGATAAA-AT-TAAACTA
*
96973 TTAAAATGATAAAATTATACTA
1 TTAAAATGATAAAATTAAACTA
96995 TTA
1 TTA
96998 CTATCATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 2 0.09
24 12 0.52
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (22 bp):
TTAAAATGATAAAATTAAACTA
Found at i:102238 original size:27 final size:27
Alignment explanation
Indices: 102197--102251 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
102187 TTAAGTCATA
* *
102197 ATTAAAATTTCAAAA-TTTGAATTTTTT
1 ATTAAAATATAAAAACTTT-AATTTTTT
*
102224 ATTAAAATATAAAAACTTTATTTTTTT
1 ATTAAAATATAAAAACTTTAATTTTTT
102251 A
1 A
102252 ATTTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTAAAATATAAAAACTTTAATTTTTT
Found at i:104247 original size:3 final size:3
Alignment explanation
Indices: 104239--104295 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
104229 TAAGTACATG
104239 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
104287 AAT AAT AAT
1 AAT AAT AAT
104296 GTACATGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:114135 original size:8 final size:8
Alignment explanation
Indices: 114122--114160 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
114112 TTGGTGAAAA
114122 TTAAAATT
1 TTAAAATT
114130 TTAAAATT
1 TTAAAATT
* *
114138 TAAAAAAT
1 TTAAAATT
*
114146 TTAAAAAT
1 TTAAAATT
114154 TTAAAAT
1 TTAAAAT
114161 AACCAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTAAAATT
Found at i:114144 original size:17 final size:17
Alignment explanation
Indices: 114124--114159 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
114114 GGTGAAAATT
*
114124 AAAATTTTAAAATTTAA
1 AAAATTTAAAAATTTAA
114141 AAAATTTAAAAATTTAA
1 AAAATTTAAAAATTTAA
114158 AA
1 AA
114160 TAACCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTTAAAAATTTAA
Found at i:114508 original size:30 final size:34
Alignment explanation
Indices: 114444--114508 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
114434 ATCATAACAA
114444 TCTATATAATATAAAATGTAACTAACTATTATTAT
1 TCTATATAATATAAAATGTAACTAACTA-TATTAT
*
114479 TCTATATAA-A-AAAATG-ACCTAACTA-ATTAT
1 TCTATATAATATAAAATGTAACTAACTATATTAT
114509 ATGTGATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 5 0.17
32 8 0.28
33 6 0.21
34 1 0.03
35 9 0.31
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (34 bp):
TCTATATAATATAAAATGTAACTAACTATATTAT
Found at i:114508 original size:33 final size:35
Alignment explanation
Indices: 114444--114508 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
114434 ATCATAACAA
114444 TCTATATAATATAAAATGTAACTAACTATTATTAT
1 TCTATATAATATAAAATGTAACTAACTATTATTAT
*
114479 TCTATATAA-A-AAAATG-ACCTAACTAATTAT
1 TCTATATAATATAAAATGTAACTAACT-ATTAT
114509 ATGTGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.25
33 11 0.39
34 1 0.04
35 9 0.32
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (35 bp):
TCTATATAATATAAAATGTAACTAACTATTATTAT
Found at i:115137 original size:12 final size:12
Alignment explanation
Indices: 115122--115146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115112 TTATTAAACA
115122 TTTTATATTTTT
1 TTTTATATTTTT
115134 TTTTATATTTTT
1 TTTTATATTTTT
115146 T
1 T
115147 AGAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATATTTTT
Found at i:116719 original size:170 final size:162
Alignment explanation
Indices: 116291--116728 Score: 524
Period size: 162 Copynumber: 2.7 Consensus size: 162
116281 TTGGTTTTGA
* * * *
116291 TTTGACAAGCATATATAATGCTATTTTCTTGGTGCGGTTTTGGTTGTGGGATTGTAGGGAAGGAA
1 TTTGACAAGCATATATAATGCTGTTTTCCTGGTGGGGTTTTGGTTGTGGGATTGTAGGGAAGAAA
* * * ** * *
116356 AAAGAGACAAAATCGACGTCGCAATTGCCATTTGTTATAGGGGAACCTGAAGAAACAGGTGAGTC
66 AAAGAGACGAAATCGACGTCGAAACTGCCATTTGCGATAGGAGAACCTGAAGAAACAGGTGACTC
*
116421 AGTTCTTAACTCGGTCATCGTTTTTTTTAGAG
131 AGTTCTTAACTCGGTCACCGTTTTTTTTAGAG
* * * **
116453 TTTGAC-TGACATATATAATGTTG-TTTCCTTGGCGGGGTTTTGGTTGTGGGATTACAGGGAAGA
1 TTTGACAAG-CATATATAATGCTGTTTTCC-TGGTGGGGTTTTGGTTGTGGGATTGTAGGGAAGA
* * *
116516 AAGAAGATACGGAATCGACGTCGAAACTGCCATTTGCGATAGGAGAACCTGAAGAAACAGGTGAC
64 AAAAAGAGACGAAATCGACGTCGAAACTGCCATTTGCGATAGGAGAACCTGAAGAAACAGGTGAC
*
116581 TCAGTTCTTAACTCGGTTACCGTTTTTTACTT-GTTTTACGG
129 TCAGTTCTTAACTCGGTCACCGTTTTTT--TTAG----A--G
* *
116622 TTTGACAAGCATATATCATGCTGTTTTCCTGGTGGGGGTTTTGGTTGTGGGATTGTAGAGAAGAA
1 TTTGACAAGCATATATAATGCTGTTTTCCTGGT-GGGGTTTTGGTTGTGGGATTGTAGGGAAGAA
*
116687 AAAAGAGACGAAATCGACGTC-AAAGCTGCCATTCGCGATAGG
65 AAAAGAGACGAAATCGACGTCGAAA-CTGCCATTTGCGATAGG
116729 GGAAACAGAA
Statistics
Matches: 230, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
161 5 0.02
162 128 0.56
163 1 0.00
164 2 0.01
167 1 0.00
169 25 0.11
170 68 0.30
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (162 bp):
TTTGACAAGCATATATAATGCTGTTTTCCTGGTGGGGTTTTGGTTGTGGGATTGTAGGGAAGAAA
AAAGAGACGAAATCGACGTCGAAACTGCCATTTGCGATAGGAGAACCTGAAGAAACAGGTGACTC
AGTTCTTAACTCGGTCACCGTTTTTTTTAGAG
Found at i:120233 original size:16 final size:16
Alignment explanation
Indices: 120212--120243 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
120202 AAGAAAAAGA
120212 ATGTACAAATTTCAGT
1 ATGTACAAATTTCAGT
120228 ATGTACAAATTTCAGT
1 ATGTACAAATTTCAGT
120244 TTGAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGTACAAATTTCAGT
Done.