Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004479.1 Kokia drynarioides strain JFW-HI SEQ_117901, 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: 71639
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3139 original size:7 final size:6
Alignment explanation
Indices: 3116--3153 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3106 GGCAACTCAA
*
3116 TTTTAT TTTTAT TTAT-T TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
3154 CTTGCATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:3153 original size:17 final size:18
Alignment explanation
Indices: 3115--3153 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3105 AGGCAACTCA
3115 ATTTTATTTTTATTTATT
1 ATTTTATTTTTATTTATT
3133 -TTTTATTTTTATTT-TT
1 ATTTTATTTTTATTTATT
3149 ATTTT
1 ATTTT
3154 CTTGCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
ATTTTATTTTTATTTATT
Found at i:4100 original size:105 final size:105
Alignment explanation
Indices: 3918--4122 Score: 313
Period size: 105 Copynumber: 2.0 Consensus size: 105
3908 AATTATGAAT
* * * *
3918 AATAATAAATTAGGAGTGTGTTGGACTGGGTAACTAGGATGGGGTGCTTGGGTTGTCATTCCATT
1 AATAATAAATTAGGAGTATGTTGGACTGAGTAACGAGGATGAGGTGCTTGGGTTGTCATTCCATT
*
3983 TCGCGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAAGA
66 TCGCGTCAAAAGGGCCAATACATTCTTAAGCAAAAAAAGA
* *
4023 AATAATAAATTAGGAGTATGTTGGGCTGAGTAACCGA-GATGAGGTGCTTGGGTTGTCATTCTAT
1 AATAATAAATTAGGAGTATGTTGGACTGAGTAA-CGAGGATGAGGTGCTTGGGTTGTCATTCCAT
* *
4087 TTCGCGTCAAAAGGGCTAATATATTCTTAAGCAAAA
65 TTCGCGTCAAAAGGGCCAATACATTCTTAAGCAAAA
4123 GAAAAAAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 88 0.98
106 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (105 bp):
AATAATAAATTAGGAGTATGTTGGACTGAGTAACGAGGATGAGGTGCTTGGGTTGTCATTCCATT
TCGCGTCAAAAGGGCCAATACATTCTTAAGCAAAAAAAGA
Found at i:4135 original size:11 final size:12
Alignment explanation
Indices: 4119--4147 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4109 ATTCTTAAGC
4119 AAAAGAAAAA-A
1 AAAAGAAAAAGA
4130 AAAAGAAAAAGA
1 AAAAGAAAAAGA
4142 AAAAGA
1 AAAAGA
4148 CGAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:4146 original size:6 final size:6
Alignment explanation
Indices: 4119--4147 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4109 ATTCTTAAGC
4119 AAAAGA AAAA-A AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
4148 CGAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:9278 original size:17 final size:17
Alignment explanation
Indices: 9258--9309 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
9248 GTAAATATAT
9258 ATAAAAAATAAAAATAA
1 ATAAAAAATAAAAATAA
* *
9275 ATAAAATACT-AAAATAT
1 ATAAAA-AATAAAAATAA
*
9292 ATAAAGAATAAAAATAA
1 ATAAAAAATAAAAATAA
9309 A
1 A
9310 CTGAGTACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
ATAAAAAATAAAAATAA
Found at i:9302 original size:34 final size:35
Alignment explanation
Indices: 9240--9367 Score: 134
Period size: 34 Copynumber: 3.6 Consensus size: 35
9230 TATGGCAAAG
* *
9240 TAAAATATGTAAATATATATAAAAAATAAAAATAAA
1 TAAAATA-CTAAATATATATAAAGAATAAAAATAAA
9276 TAAAATACTAAA-ATATATAAAGAATAAAAATAAA
1 TAAAATACTAAATATATATAAAGAATAAAAATAAA
* * * *
9310 CT-GAGTACTGTAAATATATATATAGAATAAAAGTAAA
1 -TAAAATAC--TAAATATATATAAAGAATAAAAATAAA
*
9347 CAAAATACTGAAATATATATA
1 TAAAATACT-AAATATATATA
9368 TATATACACT
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
34 25 0.32
35 6 0.08
36 22 0.29
37 24 0.31
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (35 bp):
TAAAATACTAAATATATATAAAGAATAAAAATAAA
Found at i:9369 original size:36 final size:37
Alignment explanation
Indices: 9241--9367 Score: 156
Period size: 37 Copynumber: 3.6 Consensus size: 37
9231 ATGGCAAAGT
* *
9241 AAAATA-TGTAAATATATATAAAAAATAAAAATAAAT
1 AAAATACTGTAAATATATATAAAGAATAAAAATAAAC
9277 AAAATAC--TAAA-ATATATAAAGAATAAAAATAAAC
1 AAAATACTGTAAATATATATAAAGAATAAAAATAAAC
** * * *
9311 TGAGTACTGTAAATATATATATAGAATAAAAGTAAAC
1 AAAATACTGTAAATATATATAAAGAATAAAAATAAAC
9348 AAAATACTG-AAATATATATA
1 AAAATACTGTAAATATATATA
9368 TATATACACT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
34 25 0.32
35 4 0.05
36 21 0.27
37 27 0.35
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (37 bp):
AAAATACTGTAAATATATATAAAGAATAAAAATAAAC
Found at i:9923 original size:21 final size:22
Alignment explanation
Indices: 9889--9937 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
9879 AATCAATTTT
9889 TGTGACGTTTTTTGA-ATACTTTG
1 TGTGACG-TTTTTGAGAT-CTTTG
*
9912 TGTGACG-TTTTGAGATCTTTT
1 TGTGACGTTTTTGAGATCTTTG
9933 TGTGA
1 TGTGA
9938 TGCTTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.51
Consensus pattern (22 bp):
TGTGACGTTTTTGAGATCTTTG
Found at i:12988 original size:19 final size:19
Alignment explanation
Indices: 12942--13011 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
12932 GTTGGTTAAA
*
12942 AAAAGTCAATGGTCAACGGGT
1 AAAAGTCAAT-GTTAAC-GGT
*
12963 CAAAGTCAATGATTAA-GGT
1 AAAAGTCAATG-TTAACGGT
*
12982 AAAAGTCAAAGTTAACGGT
1 AAAAGTCAATGTTAACGGT
*
13001 CAAAGTCAATG
1 AAAAGTCAATG
13012 GGTCAACGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 4 0.10
19 24 0.59
20 1 0.02
21 12 0.29
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAGTCAATGTTAACGGT
Found at i:13067 original size:20 final size:20
Alignment explanation
Indices: 13012--13070 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
13002 AAAGTCAATG
* *
13012 GGTCAACGTGTCAATAGGTC
1 GGTCAACGGGTCAATGGGTC
* *
13032 AGTCAACGGGTTAATGGGTC
1 GGTCAACGGGTCAATGGGTC
13052 GGTCAACGGGTCAATGGGT
1 GGTCAACGGGTCAATGGGT
13071 TGGGCATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (20 bp):
GGTCAACGGGTCAATGGGTC
Found at i:16930 original size:21 final size:19
Alignment explanation
Indices: 16905--16952 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
16895 GGTTGTTAAA
*
16905 AAAGTCAACGGTCAATTGGTC
1 AAAGTCAACGATCAA--GGTC
*
16926 AAAGTCAATGATCAAGGTC
1 AAAGTCAACGATCAAGGTC
16945 AAAGTCAA
1 AAAGTCAA
16953 AGTCAACGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
21 13 0.52
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAGTCAACGATCAAGGTC
Found at i:28342 original size:21 final size:21
Alignment explanation
Indices: 28301--28343 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28291 GAAGGCGCAA
*
28301 AAGAGAAGGAGAAAGATGAGG
1 AAGAGAAGGAGAAAGAAGAGG
*
28322 AAGAGAAAGGA-AATGAAGAGG
1 AAGAG-AAGGAGAAAGAAGAGG
28343 A
1 A
28344 GAAGGACGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.05
Consensus pattern (21 bp):
AAGAGAAGGAGAAAGAAGAGG
Found at i:28790 original size:18 final size:18
Alignment explanation
Indices: 28764--28801 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28754 ATGCATATCA
28764 TTTAATTGTCAT-TGCATT
1 TTTAATTGTC-TCTGCATT
*
28782 TTTATTTGTCTCTGCATT
1 TTTAATTGTCTCTGCATT
28800 TT
1 TT
28802 ACTCATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.61
Consensus pattern (18 bp):
TTTAATTGTCTCTGCATT
Found at i:39557 original size:12 final size:12
Alignment explanation
Indices: 39540--39567 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39530 ATAGACCAAC
39540 ATGCTTATGAGA
1 ATGCTTATGAGA
39552 ATGCTTATGAGA
1 ATGCTTATGAGA
39564 ATGC
1 ATGC
39568 AGTGACGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (12 bp):
ATGCTTATGAGA
Found at i:41630 original size:10 final size:9
Alignment explanation
Indices: 41608--41664 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
41598 TATGGCAAAG
*
41608 TAAAATATG
1 TAAAATATA
41617 TAAATATATA
1 TAAA-ATATA
*
41627 TAAAAAATA
1 TAAAATATA
*
41636 -AAAATAAA
1 TAAAATATA
*
41644 TAAAACAT-
1 TAAAATATA
41652 TAAAATATA
1 TAAAATATA
41661 TAAA
1 TAAA
41665 GAATAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 13 0.34
9 17 0.45
10 8 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
TAAAATATA
Found at i:41646 original size:17 final size:17
Alignment explanation
Indices: 41626--41677 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
41616 GTAAATATAT
41626 ATAAAAAATAAAAATAA
1 ATAAAAAATAAAAATAA
* * *
41643 ATAAAACATTAAAATAT
1 ATAAAAAATAAAAATAA
*
41660 ATAAAGAATAAAAATAA
1 ATAAAAAATAAAAATAA
41677 A
1 A
41678 CTAAGTACTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
ATAAAAAATAAAAATAA
Found at i:41737 original size:36 final size:36
Alignment explanation
Indices: 41609--41735 Score: 161
Period size: 37 Copynumber: 3.6 Consensus size: 36
41599 ATGGCAAAGT
* *
41609 AAAATATGTAAATATATATAAAAAATAAAAATAAAT
1 AAAATATGTAAATATATATAAAGAATAAAAATAAAC
*
41645 AAAACAT-TAAA-ATATATAAAGAATAAAAATAAAC
1 AAAATATGTAAATATATATAAAGAATAAAAATAAAC
* * *
41679 TAAGTACTGTAAATATATATATAGAATAAAAATAAAC
1 AAAATA-TGTAAATATATATAAAGAATAAAAATAAAC
41716 AAAATACTG-AAATATATATA
1 AAAATA-TGTAAATATATATA
41736 TATCATTACA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 24 0.30
35 5 0.06
36 21 0.27
37 29 0.37
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (36 bp):
AAAATATGTAAATATATATAAAGAATAAAAATAAAC
Found at i:41978 original size:76 final size:76
Alignment explanation
Indices: 41852--42005 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
41842 TGAAAATTTC
* *
41852 TTCAAAAAGGTAAAATAAAAAAAGTGTCATAGAAAGTAGAACTTTCAGTGACGATTCTGTATCAT
1 TTCAAAAAGGTAAAATAAAAAAAGCGTCACAGAAAGTAGAACTTTCAGTGACGATTCTGTATCAT
41917 GGTCAGTGACG
66 GGTCAGTGACG
*
41928 TTCAAAAAGGTAAAATAAAAAAAGCGTCACAGAAAGTAGCACTTTCAGTGACGATTCTGTATCAT
1 TTCAAAAAGGTAAAATAAAAAAAGCGTCACAGAAAGTAGAACTTTCAGTGACGATTCTGTATCAT
41993 GGTCAGTGACG
66 GGTCAGTGACG
42004 TT
1 TT
42006 TTGTAAACAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (76 bp):
TTCAAAAAGGTAAAATAAAAAAAGCGTCACAGAAAGTAGAACTTTCAGTGACGATTCTGTATCAT
GGTCAGTGACG
Found at i:42340 original size:21 final size:22
Alignment explanation
Indices: 42293--42340 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
42283 ATCAATTTCT
*
42293 GTGACGTTTTTTGAATACTTTTT
1 GTGACGTTTTTT-AATACTTTTG
42316 GTGACG-TTTTT-ATATCTTTTG
1 GTGACGTTTTTTAATA-CTTTTG
42337 GTGA
1 GTGA
42341 TACTTTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 5 0.22
23 6 0.26
ACGTcount: A:0.17, C:0.08, G:0.21, T:0.54
Consensus pattern (22 bp):
GTGACGTTTTTTAATACTTTTG
Found at i:45450 original size:13 final size:13
Alignment explanation
Indices: 45407--45454 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
45397 GGTAAATGGG
*
45407 TCAAAGTCAACGA
1 TCAAAGTCAAAGA
* * *
45420 TTAAGGTAAAAG-
1 TCAAAGTCAAAGA
45432 TCAAAGTCAAAGA
1 TCAAAGTCAAAGA
45445 TCAAAGTCAA
1 TCAAAGTCAA
45455 CGGGTCAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (13 bp):
TCAAAGTCAAAGA
Found at i:45504 original size:20 final size:20
Alignment explanation
Indices: 45479--45522 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
45469 AGTCAATAGA
*
45479 TTGGTCAACAGGTTAATGGG
1 TTGGTCAACAGGTCAATGGG
*
45499 TTGGTCAACGGGTCAATGGG
1 TTGGTCAACAGGTCAATGGG
45519 TTGG
1 TTGG
45523 GTTGGGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.39, T:0.30
Consensus pattern (20 bp):
TTGGTCAACAGGTCAATGGG
Found at i:48711 original size:18 final size:18
Alignment explanation
Indices: 48685--48722 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
48675 ATGCATATCA
48685 TTTAGTTGTCAT-TGCATT
1 TTTAGTTGTC-TCTGCATT
*
48703 TTTATTTGTCTCTGCATT
1 TTTAGTTGTCTCTGCATT
48721 TT
1 TT
48723 ACTCATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (18 bp):
TTTAGTTGTCTCTGCATT
Found at i:50344 original size:45 final size:45
Alignment explanation
Indices: 50293--50391 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
50283 TCGATTACAG
50293 CCACAACAGTCTGTGCTGCCACATATGCAAGGACGATACCATCAA
1 CCACAACAGTCTGTGCTGCCACATATGCAAGGACGATACCATCAA
50338 CCACAACAGTCTGTGCTGCCACATATGCAAGGACGATACCATCAA
1 CCACAACAGTCTGTGCTGCCACATATGCAAGGACGATACCATCAA
50383 -CATCAACAG
1 CCA-CAACAG
50392 CAGTAATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 2 0.04
45 51 0.96
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (45 bp):
CCACAACAGTCTGTGCTGCCACATATGCAAGGACGATACCATCAA
Found at i:54367 original size:103 final size:103
Alignment explanation
Indices: 54230--54437 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
54220 AGCTTGAACA
54230 TAAGGCCATGTAGGCAATCAAGCAGGTGAATATGGACTATGATGCTGTCGGAAGAAAAAGATTGT
1 TAAGGCCATGTAGGCAATCAAGCAGGTGAATATGGACTATGATGCTGTCGGAAGAAAAAGATTGT
54295 TGGACATCACTGAGCTAGAAGAAATACATCGACATGCT
66 TGGACATCACTGAGCTAGAAGAAATACATCGACATGCT
54333 TAAGGCCATGTAGGCAATCAAGCAGGTGAATATGGACTATGATGCTGTCGGAAGAAAAAGATTGT
1 TAAGGCCATGTAGGCAATCAAGCAGGTGAATATGGACTATGATGCTGTCGGAAGAAAAAGATTGT
*
54398 TGGACATCACTGAGCTAGAAGAAATACGTCGACATGCT
66 TGGACATCACTGAGCTAGAAGAAATACATCGACATGCT
54436 TA
1 TA
54438 TGAGAATGCC
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (103 bp):
TAAGGCCATGTAGGCAATCAAGCAGGTGAATATGGACTATGATGCTGTCGGAAGAAAAAGATTGT
TGGACATCACTGAGCTAGAAGAAATACATCGACATGCT
Found at i:57216 original size:37 final size:37
Alignment explanation
Indices: 57133--57710 Score: 719
Period size: 37 Copynumber: 15.7 Consensus size: 37
57123 TTACACAGTT
* * *
57133 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * * * *
57170 TTCAAGCTGTGTGGCTAGCAGGTTTAGTGCCGTTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
57207 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* *
57244 TTCAGGCTGTGTGCCTAGCAGGCTGCGTGCCAGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
*
57281 TTCAGGCTGTGTGCCTAGCAGGCTTAGTGCCGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* *
57318 TTCAGGTTGTGTGCCTAGCAGGCTTCGTGCCGGTGTT
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* *
57355 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * * * *
57392 TTCAGGCTATGCGCCTAGTAGGCTTAGTGCTGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * *
57429 TTCAGACTGTGTGCCTAGCAAGCTTCGTGCCAGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* ** * *
57466 TTCAGGCTGTATGCCTAGCACACTTAGTGCCGATGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * *
57503 TTTAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
*
57540 TTCAGGC--TGTGCCTAGTAGGCTTCGTGCCGGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
**
57575 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTTGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * * *
57612 TTCATGCTATGTGCCTAACAGGCTTCGTGCCAGTGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* * * * ** *
57649 TTTAGGTTGTGTGCTTAGCAGGCTTCATGTTGATGTA
1 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
* *
57686 TTCGGGCTATGTGCCTAGCAGGCTT
1 TTCAGGCTGTGTGCCTAGCAGGCTT
57711 TGTGTCGATG
Statistics
Matches: 461, Mismatches: 78, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
35 33 0.07
37 428 0.93
ACGTcount: A:0.14, C:0.21, G:0.32, T:0.33
Consensus pattern (37 bp):
TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
Found at i:57220 original size:21 final size:20
Alignment explanation
Indices: 57196--57332 Score: 77
Period size: 21 Copynumber: 7.2 Consensus size: 20
57186 AGCAGGTTTA
57196 GTGCCGTTGTATTCAGGCTGT
1 GTGCCG-TGTATTCAGGCTGT
*
57217 GTGCC---TA-GCAGGCT-T
1 GTGCCGTGTATTCAGGCTGT
57232 CGTGCCGGTGTATTCAGGCTGT
1 -GTGCC-GTGTATTCAGGCTGT
* *
57254 GTGCC---TA-GCAGGCTGC
1 GTGCCGTGTATTCAGGCTGT
57270 GTGCCAGTGTATTCAGGCTGT
1 GTGCC-GTGTATTCAGGCTGT
*
57291 GTGCC---TA-GCAGGCT-T
1 GTGCCGTGTATTCAGGCTGT
*
57306 AGTGCCGGTGTATTCAGGTTGT
1 -GTGCC-GTGTATTCAGGCTGT
57328 GTGCC
1 GTGCC
57333 TAGCAGGCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 38
0.65 0.07 0.28
Matches are distributed among these distances:
15 2 0.02
16 34 0.39
17 6 0.07
20 6 0.07
21 38 0.43
22 2 0.02
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.31
Consensus pattern (20 bp):
GTGCCGTGTATTCAGGCTGT
Found at i:57230 original size:16 final size:16
Alignment explanation
Indices: 57209--57304 Score: 59
Period size: 16 Copynumber: 5.4 Consensus size: 16
57199 CCGTTGTATT
57209 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
*
57225 CAGGCT-TCGTGCCGGTGTATT
1 CAGGCTGT-GTGCC----TA-G
57246 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
* *
57262 CAGGCTGCGTGCCAGTGTATT
1 CAGGCTGTGTGCC----TA-G
57283 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
57299 CAGGCT
1 CAGGCT
57305 TAGTGCCGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
15 1 0.02
16 29 0.47
17 4 0.06
20 4 0.06
21 23 0.37
22 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.35, T:0.27
Consensus pattern (16 bp):
CAGGCTGTGTGCCTAG
Found at i:57360 original size:21 final size:20
Alignment explanation
Indices: 57336--57399 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
57326 GTGTGCCTAG
57336 CAGGCTTCGTGCCGGTGTTTT
1 CAGGCTTCGTGCCGGTG-TTT
*
57357 CAGGCTTTGTGCC--TAG--T
1 CAGGCTTCGTGCCGGT-GTTT
57374 -AGGCTTCGTGCCGGTGTATT
1 CAGGCTTCGTGCCGGTGT-TT
57394 CAGGCT
1 CAGGCT
57400 ATGCGCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 11 0.32
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 17 0.50
ACGTcount: A:0.09, C:0.23, G:0.33, T:0.34
Consensus pattern (20 bp):
CAGGCTTCGTGCCGGTGTTT
Found at i:57547 original size:21 final size:21
Alignment explanation
Indices: 57521--57589 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
57511 ATGTGCCTAG
57521 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTTTGTGCCGGTGTATT
*
57542 CAGGC--TGTGCC----TAGT
1 CAGGCTTTGTGCCGGTGTATT
*
57557 -AGGCTTCGTGCCGGTGTATT
1 CAGGCTTTGTGCCGGTGTATT
*
57577 CAGGCTGTGTGCC
1 CAGGCTTTGTGCC
57590 TAGCAGGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 5 0.14
19 6 0.17
20 3 0.08
21 15 0.42
ACGTcount: A:0.10, C:0.23, G:0.35, T:0.32
Consensus pattern (21 bp):
CAGGCTTTGTGCCGGTGTATT
Found at i:61340 original size:12 final size:12
Alignment explanation
Indices: 61323--61363 Score: 66
Period size: 11 Copynumber: 3.4 Consensus size: 12
61313 CAGTCACATG
61323 AAAAAAAGAAAA
1 AAAAAAAGAAAA
61335 AAAAAAAG-AAA
1 AAAAAAAGAAAA
61346 AAAAAAAGAAGAA
1 AAAAAAAGAA-AA
61359 AAAAA
1 AAAAA
61364 TTATATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.41
12 9 0.33
13 7 0.26
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:69607 original size:16 final size:16
Alignment explanation
Indices: 69581--69619 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
69571 TACCCTAATT
*
69581 TATAA-ATGGTTATAA
1 TATAATATGGTTAAAA
69596 TATAATATGGTTAAAA
1 TATAATATGGTTAAAA
69612 TATAATAT
1 TATAATAT
69620 AAGTCCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (16 bp):
TATAATATGGTTAAAA
Found at i:70024 original size:17 final size:18
Alignment explanation
Indices: 70002--70036 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
69992 AGTAATTCTA
*
70002 TTAATTCT-TTTTATTAT
1 TTAATTCTATTTGATTAT
70019 TTAATTCTATTTGATTAT
1 TTAATTCTATTTGATTAT
70037 ATTTTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TTAATTCTATTTGATTAT
Done.