Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001193.1 Kokia drynarioides strain JFW-HI SEQ_112536, 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: 51095
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:168 original size:32 final size:32
Alignment explanation
Indices: 132--209 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
122 TTATTTTGTT
*
132 TTGGATTTTGAAATTATTATGTTTTAAAG-TAG
1 TTGGATATTGAAATTATTATG-TTTAAAGCTAG
* * *
164 TTGGATATTGAATTTATTATGTTTCAAGCTTG
1 TTGGATATTGAAATTATTATGTTTAAAGCTAG
196 TTGGATATTGAAAT
1 TTGGATATTGAAAT
210 GACTGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 6 0.15
32 34 0.85
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (32 bp):
TTGGATATTGAAATTATTATGTTTAAAGCTAG
Found at i:1181 original size:19 final size:19
Alignment explanation
Indices: 1157--1193 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1147 TGTTTAAATG
*
1157 TGGTGTAGTACTAATTATA
1 TGGTGTAATACTAATTATA
*
1176 TGGTGTAATACTAGTTAT
1 TGGTGTAATACTAATTAT
1194 GCACTTGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (19 bp):
TGGTGTAATACTAATTATA
Found at i:1359 original size:46 final size:46
Alignment explanation
Indices: 1292--1393 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
1282 ACTACTAATT
*
1292 TGTAATATTAGTTACGCACTTGGACAATATTATAGTTATCATGTGG
1 TGTAATACTAGTTACGCACTTGGACAATATTATAGTTATCATGTGG
* *
1338 TGTAATACTAGTTATGCACTTGGACAATTTTATAGTTATCATGTGG
1 TGTAATACTAGTTACGCACTTGGACAATATTATAGTTATCATGTGG
* *
1384 TCTACTACTA
1 TGTAATACTA
1394 ATTTGTAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (46 bp):
TGTAATACTAGTTACGCACTTGGACAATATTATAGTTATCATGTGG
Found at i:1634 original size:22 final size:23
Alignment explanation
Indices: 1576--1634 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
1566 AAAACAATGT
* *
1576 AAAAT-ATAAATTTAATAGATAT
1 AAAATAATAAATTAAATAGATAA
*
1598 AAAATAAACTCAATTAAATA-ATAA
1 AAAAT-AA-TAAATTAAATAGATAA
1622 AAAATAATAAATT
1 AAAATAATAAATT
1635 CTCAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 10 0.33
23 2 0.07
24 9 0.30
25 9 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAATAAATTAAATAGATAA
Found at i:2511 original size:17 final size:18
Alignment explanation
Indices: 2491--2527 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2481 AAATAAAAAA
*
2491 TAAAAT-ATTTTAAAATT
1 TAAAATGATTTAAAAATT
2508 TAAAATGATTTAAAAATT
1 TAAAATGATTTAAAAATT
2526 TA
1 TA
2528 TTTCAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TAAAATGATTTAAAAATT
Found at i:2698 original size:26 final size:26
Alignment explanation
Indices: 2666--2718 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2656 AAAACCCAAT
2666 CATCTACAACCCAAATACCCAATTAC
1 CATCTACAACCCAAATACCCAATTAC
2692 CATCTACAACCCAAATACCCAATTAC
1 CATCTACAACCCAAATACCCAATTAC
2718 C
1 C
2719 CAAATTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (26 bp):
CATCTACAACCCAAATACCCAATTAC
Found at i:4051 original size:30 final size:30
Alignment explanation
Indices: 4016--4167 Score: 130
Period size: 30 Copynumber: 5.1 Consensus size: 30
4006 GTTTTATTTT
* * *
4016 AAAATTATGTTTTAGCCCCCAAACTTTCCA
1 AAAATTATATTTTAGCCCCTAAACTTTCTA
* * *
4046 AAAATTCAAATTTGATCCCC-AAACTTTCTA
1 AAAATT-ATATTTTAGCCCCTAAACTTTCTA
** **
4076 AAAATTGCATTTTAGCCTATAAACTTTCTA
1 AAAATTATATTTTAGCCCCTAAACTTTCTA
* *
4106 AAAATTATATTTT-GATCCTTAAACTTTCTA
1 AAAATTATATTTTAG-CCCCTAAACTTTCTA
* * *
4136 AAAA-TATATTTTAACCCTTAAACTTTCCA
1 AAAATTATATTTTAGCCCCTAAACTTTCTA
4165 AAA
1 AAA
4168 TTTTGATTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
29 32 0.32
30 58 0.59
31 9 0.09
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAATTATATTTTAGCCCCTAAACTTTCTA
Found at i:4154 original size:29 final size:30
Alignment explanation
Indices: 4066--4181 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
4056 TTTGATCCCC
*
4066 AAACTTTCTAAAAAT-TGCATTTT-AGCCTAT
1 AAACTTTCTAAAAATATG-ATTTTAACCCT-T
* *
4096 AAACTTTCTAAAAATTAT-ATTTTGATCCTT
1 AAACTTTCTAAAAA-TATGATTTTAACCCTT
4126 AAACTTTCTAAAAATAT-ATTTTAACCCTT
1 AAACTTTCTAAAAATATGATTTTAACCCTT
* * *
4155 AAACTTTCCAAAATTTTGATTTTAACC
1 AAACTTTCTAAAAATATGATTTTAACC
4182 TTGTTTTTCC
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
29 27 0.36
30 43 0.57
31 5 0.07
32 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.42
Consensus pattern (30 bp):
AAACTTTCTAAAAATATGATTTTAACCCTT
Found at i:4648 original size:80 final size:80
Alignment explanation
Indices: 4544--4692 Score: 289
Period size: 80 Copynumber: 1.9 Consensus size: 80
4534 TCCTAACTTA
4544 TGGCGTATGACCTGATTTTCAATTTTCTCGAGAAAAAGATTGTTTATTTGTGAAATTTAATTTTC
1 TGGCGTATGACCTGATTTTCAATTTTCTCGAGAAAAAGATTGTTTATTTGTGAAATTTAATTTTC
4609 AAATGGTCATGTTCC
66 AAATGGTCATGTTCC
*
4624 TGGCGTATGACTTGATTTTCAATTTTCTCGAGAAAAAGATTGTTTATTTGTGAAATTTAATTTTC
1 TGGCGTATGACCTGATTTTCAATTTTCTCGAGAAAAAGATTGTTTATTTGTGAAATTTAATTTTC
4689 AAAT
66 AAAT
4693 AACTCCCAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (80 bp):
TGGCGTATGACCTGATTTTCAATTTTCTCGAGAAAAAGATTGTTTATTTGTGAAATTTAATTTTC
AAATGGTCATGTTCC
Found at i:7834 original size:58 final size:58
Alignment explanation
Indices: 7747--7859 Score: 151
Period size: 58 Copynumber: 1.9 Consensus size: 58
7737 TTAAAAAAAG
* *
7747 AAGAAAAAAAAAAGAAAAAGGGTCGAGATGAAAAAC-CGCAAAGGGGATCTTGAAACCCA
1 AAGAAAAAAAAAAGAAAAA-GGTCAAGATG-AAAACTCGCAAAGGGCATCTTGAAACCCA
7806 AAGAAAAAAGGAAAA-AAAAA-GTCAAGATGAAAACTCGCAAAGGGCATCTTGAAA
1 AAGAAAAAA--AAAAGAAAAAGGTCAAGATGAAAACTCGCAAAGGGCATCTTGAAA
7860 ATCTATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
57 5 0.10
58 26 0.53
59 9 0.18
60 5 0.10
61 4 0.08
ACGTcount: A:0.56, C:0.12, G:0.22, T:0.10
Consensus pattern (58 bp):
AAGAAAAAAAAAAGAAAAAGGTCAAGATGAAAACTCGCAAAGGGCATCTTGAAACCCA
Found at i:8476 original size:17 final size:15
Alignment explanation
Indices: 8447--8486 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
8437 ATTTCACCCG
*
8447 AAAAAAGGAAAAAGGA
1 AAAAAAAGAAAAA-GA
8463 AAAAGAAAGAAAAAGA
1 AAAA-AAAGAAAAAGA
8479 AAAAAAAG
1 AAAAAAAG
8487 GGAGTCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAGA
Found at i:8561 original size:61 final size:63
Alignment explanation
Indices: 8464--8583 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 63
8454 GAAAAAGGAA
8464 AAAGAAAGAAAAAGAAAAAAAAGGGAGTCAAGATGAAAACCCT-CAAAGGGCATCTTGAAAACC
1 AAAGAAAGAAAAAGAAAAAAAAGGGAGTCAAGATGAAAA-CCTGCAAAGGGCATCTTGAAAACC
8527 AAAGAAA-AAAAAGAAGAAAAAA-GG-GTCAAGATGAAAACCTGCAAAGGGCATCTTGAA
1 AAAGAAAGAAAAAGAA-AAAAAAGGGAGTCAAGATGAAAACCTGCAAAGGGCATCTTGAA
8584 GATCTATGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
60 3 0.05
61 29 0.53
62 10 0.18
63 13 0.24
ACGTcount: A:0.56, C:0.12, G:0.22, T:0.10
Consensus pattern (63 bp):
AAAGAAAGAAAAAGAAAAAAAAGGGAGTCAAGATGAAAACCTGCAAAGGGCATCTTGAAAACC
Found at i:9472 original size:15 final size:15
Alignment explanation
Indices: 9450--9529 Score: 85
Period size: 15 Copynumber: 5.3 Consensus size: 15
9440 TATTTCACCA
9450 AAAAAAAAAGAGAAAGG
1 AAAAAAAAAGA-AAA-G
9467 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
9482 AAAAAAAATA-AAAAG
1 AAAAAAAA-AGAAAAG
*
9497 AAAAAAGAAA-AAAGG
1 AAAAAA-AAAGAAAAG
*
9512 AAAAAAGAAG-AAAG
1 AAAAAAAAAGAAAAG
9526 AAAA
1 AAAA
9530 GGGAGAGGTC
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.16
15 31 0.54
16 6 0.11
17 11 0.19
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:9480 original size:22 final size:21
Alignment explanation
Indices: 9449--9531 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 21
9439 TTATTTCACC
9449 AAAAAA-AAAAGAGAAAGGAAA
1 AAAAAAGAAAAGA-AAAGGAAA
9470 AAAAAAGAAAAGAAAA--AAA
1 AAAAAAGAAAAGAAAAGGAAA
9489 ATAAAAAGAAAAAAGAAAAAAGGAAA
1 A-AAAAAG--AAAAG--AAAAGGAAA
*
9515 AAAGAAG-AAAGAAAAGG
1 AAAAAAGAAAAGAAAAGG
9532 GAGAGGTCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
19 4 0.08
20 12 0.23
21 9 0.17
22 15 0.28
24 4 0.08
25 5 0.09
26 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (21 bp):
AAAAAAGAAAAGAAAAGGAAA
Found at i:10956 original size:45 final size:45
Alignment explanation
Indices: 10873--11133 Score: 273
Period size: 45 Copynumber: 5.9 Consensus size: 45
10863 TTACCTTAAG
* *
10873 TCAAGAGCGGCAAATTGAAG-C-C-ATCCAATCTTTTACCCCTAA
1 TCAAGAGGGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
* **
10915 TCTAGAAAGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
1 TCAAGAGGGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
* * * *
10960 TCAAGAGGGGCAAATTGAAGCCACCATCCAAATATTTTACCCCTAG
1 TCAAGAGGGGCAAATTGAAGCCA-CAACCCAATCTTTTACCCCTAA
* * *
11006 TCAAGAGGGGCAGATTGAAG--ACCATCCAATCTTTTACCCCTAA
1 TCAAGAGGGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
* * * *
11049 TCAAGAGGGGCAGACTGAAGCCACAACCTAATCTTTTACCCTTAA
1 TCAAGAGGGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
* * * * *
11094 TCAAGAGAGGCAGATTGAGGCTATC-ATCCAATCTTTTACC
1 TCAAGAGGGGCAAATTGAAGCCA-CAACCCAATCTTTTACC
11134 TTGATCATGG
Statistics
Matches: 183, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
42 17 0.09
43 36 0.20
44 2 0.01
45 90 0.49
46 38 0.21
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (45 bp):
TCAAGAGGGGCAAATTGAAGCCACAACCCAATCTTTTACCCCTAA
Found at i:11050 original size:134 final size:132
Alignment explanation
Indices: 10871--11177 Score: 385
Period size: 134 Copynumber: 2.4 Consensus size: 132
10861 TTTTACCTTA
* *
10871 AGTCAAGAGCGGCAAATTGAAGCCATCCAATCTTTTACCCCTAATCTAGAAAGGCAAATTGAAGC
1 AGTCAAGAGCGGCAAATTGAAGCCATCCAATCTTTTACCCCTAATCAAGAAAGGCAAACTGAAGC
*
10936 CACAACCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCCACCATCCAAATATTTTACC
66 CACAACCCAATCTTTTACCCCTAATCAAGAGAGGCAAATTGAAGCCACCATCC-AATATTTTACC
11001 CCT
130 CCT
* * ** *
11004 AGTCAAGAGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGACTGAAG
1 AGTCAAGAGCGGCAAATTGAAG-CCATCCAATCTTTTACCCCTAATCAAGAAAGGCAAACTGAAG
* * * * * * *
11069 CCACAACCTAATCTTTTACCCTTAATCAAGAGAGGCAGATTGAGGCTATCATCCAATCTTTTA--
65 CCACAACCCAATCTTTTACCCCTAATCAAGAGAGGCAAATTGAAGCCACCATCCAATATTTTACC
11132 CCT
130 CCT
* *
11135 TGATCATG-G-GGCAAATTGAAG-CATCCAATC-TTTA-CCCTAATCA
1 AG-TCAAGAGCGGCAAATTGAAGCCATCCAATCTTTTACCCCTAATCA
11178 GAGGGCAGAT
Statistics
Matches: 154, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
126 9 0.06
127 4 0.03
128 9 0.06
130 11 0.07
131 5 0.03
132 4 0.03
133 28 0.18
134 84 0.55
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (132 bp):
AGTCAAGAGCGGCAAATTGAAGCCATCCAATCTTTTACCCCTAATCAAGAAAGGCAAACTGAAGC
CACAACCCAATCTTTTACCCCTAATCAAGAGAGGCAAATTGAAGCCACCATCCAATATTTTACCC
CT
Found at i:11052 original size:89 final size:89
Alignment explanation
Indices: 10873--11212 Score: 322
Period size: 89 Copynumber: 4.0 Consensus size: 89
10863 TTACCTTAAG
* * * *
10873 TCAAGAGCGGCAAATTGAAG---CCATCCAATCTTTTACCCCTAATCTAGAAAGGCAAATTGAAG
1 TCAAGAGGGGCAAATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAG
* *
10935 CCACAACCCAATCTTTTACCCCTAA
66 -CACCATCCAATCTTTTACCCCTAA
* * *
10960 TCAAGAGGGGCAAATTGAAGCCACCATCCAAATATTTTACCCCTAGTCAAGAGGGGCAGATTGAA
1 TCAAGAGGGGCAAATTGAAGCCACCATCC-AATCTTTTACCCCTAATCAAGAGAGGCAGATTGAA
11025 G-ACCATCCAATCTTTTACCCCTAA
65 GCACCATCCAATCTTTTACCCCTAA
* * * * *
11049 TCAAGAGGGGCAGACTGAAGCCA-CAACCTAATCTTTTACCCTTAATCAAGAGAGGCAGATTGAG
1 TCAAGAGGGGCAAATTGAAGCCACCATCC-AATCTTTTACCCCTAATCAAGAGAGGCAGATTGAA
* * *
11113 GCTATCATCCAATCTTTTA-CCTTGA
65 GC-ACCATCCAATCTTTTACCCCTAA
* *
11138 TC-A-TGGGGCAAATTGAAG----CATCCAATC-TTTA-CCCTAATC-AGAG-GGCAGATTAAAG
1 TCAAGAGGGGCAAATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAG
11193 -ACACA-CCAAT-TTCTTACCCC
66 CAC-CATCCAATCTT-TTACCCC
11213 AACCATGGGG
Statistics
Matches: 214, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
76 2 0.01
77 9 0.04
78 4 0.02
79 10 0.05
80 4 0.02
81 7 0.03
82 4 0.02
83 4 0.02
84 4 0.02
87 31 0.14
88 36 0.17
89 48 0.22
90 21 0.10
91 30 0.14
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (89 bp):
TCAAGAGGGGCAAATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAG
CACCATCCAATCTTTTACCCCTAA
Found at i:13689 original size:30 final size:31
Alignment explanation
Indices: 13653--13731 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
13643 TTTTTGGTCC
13653 AATTTGGTACTTAAACTTGA-AATTTTTTTT
1 AATTTGGTACTTAAACTTGACAATTTTTTTT
* *
13683 AATTTGGTACCTAAACTTGACACTTTTTTTT
1 AATTTGGTACTTAAACTTGACAATTTTTTTT
* **
13714 AAGTTATTACTTAAACTT
1 AATTTGGTACTTAAACTT
13732 TTTAAGGTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTGACAATTTTTTTT
Found at i:13713 original size:31 final size:30
Alignment explanation
Indices: 13653--13715 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
13643 TTTTTGGTCC
*
13653 AATTTGGTACTTAAACTTGAAATTTTTTTT
1 AATTTGGTACCTAAACTTGAAATTTTTTTT
*
13683 AATTTGGTACCTAAACTTGACACTTTTTTTT
1 AATTTGGTACCTAAACTTGA-AATTTTTTTT
13714 AA
1 AA
13716 GTTATTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTGAAATTTTTTTT
Found at i:13973 original size:29 final size:29
Alignment explanation
Indices: 13941--14091 Score: 88
Period size: 29 Copynumber: 5.2 Consensus size: 29
13931 AATTGAATCT
*
13941 AAAAAAAAAAGCTTAGGTACCAAATTAGG
1 AAAAAAAAAAGTTTAGGTACCAAATTAGG
*** * *
13970 AAAAATGCCACGTTTAGGTACCAAATTTGG
1 AAAAA-AAAAAGTTTAGGTACCAAATTAGG
*** *
14000 TCCAAAAAAATTTTAGGTACCAAATTAGG
1 AAAAAAAAAAGTTTAGGTACCAAATTAGG
***** * * *
14029 AAAGTGTCATGTTCAGGTACTAAATT-GG
1 AAAAAAAAAAGTTTAGGTACCAAATTAGG
*** *
14057 GTCAAAAAAAGTATAGGTACCAAATTAGG
1 AAAAAAAAAAGTTTAGGTACCAAATTAGG
14086 AAAAAA
1 AAAAAA
14092 TGTCAAATTT
Statistics
Matches: 78, Mismatches: 42, Indels: 4
0.63 0.34 0.03
Matches are distributed among these distances:
28 16 0.21
29 42 0.54
30 20 0.26
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAAAAAAAAGTTTAGGTACCAAATTAGG
Found at i:14017 original size:59 final size:58
Alignment explanation
Indices: 13944--14112 Score: 214
Period size: 59 Copynumber: 2.9 Consensus size: 58
13934 TGAATCTAAA
* * * *
13944 AAAAAAAGCTTAGGTACCAAATTAGGAAAAATGCCACGTTTAGGTACCAAATTTGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAATGTCAAGTTTAGGTACCAAATTGGGT-C
* * * * *
14003 AAAAAAATTTTAGGTACCAAATTAGG-AAAGTGTCATGTTCAGGTACTAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAATGTCAAGTTTAGGTACCAAATTGGGTC
* *
14060 AAAAAAAGTATAGGTACCAAATTAGGAAAAAATGTCAAATTTAGGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGG-AAAAATGTCAAGTTTAGGTACCAAAT
14113 ATTATAGTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 25 0.27
58 24 0.26
59 44 0.47
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAATGTCAAGTTTAGGTACCAAATTGGGTC
Found at i:14065 original size:58 final size:57
Alignment explanation
Indices: 13944--14089 Score: 193
Period size: 57 Copynumber: 2.5 Consensus size: 57
13934 TGAATCTAAA
* * *
13944 AAAAAAAGCTTAGGTACCAAATTAGGAAAAATGCCACGTTTAGGTACCAAATTTGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGG-AAAATGCCACGTTCAGGTACCAAATTGGGT-C
* * * * *
14003 AAAAAAATTTTAGGTACCAAATTAGGAAAGTGTCATGTTCAGGTACTAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAATGCCACGTTCAGGTACCAAATTGGGTC
*
14060 AAAAAAAGTATAGGTACCAAATTAGGAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAA
14090 AATGTCAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
57 28 0.37
58 24 0.32
59 24 0.32
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (57 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAATGCCACGTTCAGGTACCAAATTGGGTC
Found at i:14555 original size:72 final size:72
Alignment explanation
Indices: 14447--14591 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
14437 ATCTACATGA
14447 TTTCACACATGGACTGTATCGTAGCTCTATATTTCGATTCTACACTAGATCGAGATACAATATTC
1 TTTCACACATGGACTGTATCGTAGCTCTATATTTCGATTCTACACTAGATCGAGATACAATATTC
14512 TACTTCT
66 TACTTCT
14519 TTTCACACATGGACTGTATCGTAGCTCTATATTTCGATTCTACACTAGATCGAGATACAATATTC
1 TTTCACACATGGACTGTATCGTAGCTCTATATTTCGATTCTACACTAGATCGAGATACAATATTC
14584 TACTTCT
66 TACTTCT
14591 T
1 T
14592 ACTCCACTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (72 bp):
TTTCACACATGGACTGTATCGTAGCTCTATATTTCGATTCTACACTAGATCGAGATACAATATTC
TACTTCT
Found at i:39058 original size:26 final size:26
Alignment explanation
Indices: 38996--39059 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
38986 CTGGATCCTT
* *
38996 TGACAACTCTGGACACCTTCATGCAT
1 TGACATCTCTGGACACCTTCATGCAG
* * ** *
39022 TGATATTTCTGGACAGGTTCCTGCAG
1 TGACATCTCTGGACACCTTCATGCAG
39048 TGACATCTCTGG
1 TGACATCTCTGG
39060 GCGCAATACT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (26 bp):
TGACATCTCTGGACACCTTCATGCAG
Found at i:42754 original size:21 final size:20
Alignment explanation
Indices: 42730--42778 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
42720 ACATCAGGTC
*
42730 CTTCTCTTTTTTCTTCATTTT
1 CTTCTCTTCTTT-TTCATTTT
*
42751 CTTCCTCTTCTTTTTCCTTTT
1 CTT-CTCTTCTTTTTCATTTT
42772 CTATCTC
1 CT-TCTC
42779 CACAGGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTCTCTTCTTTTTCATTTT
Found at i:46626 original size:9 final size:9
Alignment explanation
Indices: 46612--46649 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
46602 TGGTATCAGA
46612 TTTTGGGTG
1 TTTTGGGTG
46621 TTTTGGGTG
1 TTTTGGGTG
46630 TTTTGGGTG
1 TTTTGGGTG
46639 TTTTGGGTG
1 TTTTGGGTG
46648 TT
1 TT
46650 CTTCATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (9 bp):
TTTTGGGTG
Found at i:46661 original size:19 final size:18
Alignment explanation
Indices: 46618--46661 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46608 CAGATTTTGG
**
46618 GTGTTTTGGGTGTTTTGG
1 GTGTTTTGGGTGTTTTCA
46636 GTGTTTTGGGTGTTCTTCA
1 GTGTTTTGGGTGTT-TTCA
*
46655 TTGTTTT
1 GTGTTTT
46662 CTACACTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.02, C:0.05, G:0.34, T:0.59
Consensus pattern (18 bp):
GTGTTTTGGGTGTTTTCA
Done.