Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014755.1 Kokia drynarioides strain JFW-HI SEQ_129794, 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: 28643
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:604 original size:4 final size:4
Alignment explanation
Indices: 585--667 Score: 78
Period size: 4 Copynumber: 20.2 Consensus size: 4
575 ATACATTACT
* * * * *
585 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTTC TTTCC TCTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTT-C TTTC TTTC
*
634 TTCC TTTC TTTC TTTC TTTCC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC T
668 CGTTTATTTG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 3 0.05
4 51 0.80
5 10 0.16
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:618 original size:17 final size:17
Alignment explanation
Indices: 585--641 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
575 ATACATTACT
585 TTTCTTTCCT-T-CTTC
1 TTTCTTTCCTCTCCTTC
600 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCTCTCCTTC
617 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCTCTCCTTC
*
634 TTCCTTTC
1 TTTCTTTC
642 TTTCTTTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 10 0.26
16 1 0.03
17 28 0.72
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCTTTCCTCTCCTTC
Found at i:647 original size:29 final size:29
Alignment explanation
Indices: 596--666 Score: 54
Period size: 29 Copynumber: 2.4 Consensus size: 29
586 TTCTTTCCTT
* *
596 CTTCTTTCTTTCCTCTCCTTCTTTCTTTC
1 CTTCTTTCTTTCCTCTCCTTCTTCCTCTC
* * * * *
625 CTCTCCTTC-TTCCTTTCTTTCTTTCTTTC
1 CT-TCTTTCTTTCCTCTCCTTCTTCCTCTC
654 CTTTCTTTCTTTC
1 C-TTCTTTCTTTC
667 TCGTTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 26 0.74
30 9 0.26
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (29 bp):
CTTCTTTCTTTCCTCTCCTTCTTCCTCTC
Found at i:654 original size:17 final size:16
Alignment explanation
Indices: 585--667 Score: 86
Period size: 17 Copynumber: 5.3 Consensus size: 16
575 ATACATTACT
585 TTTCTTTCC-TTCTTC
1 TTTCTTTCCTTTCTTC
*
600 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCT-TTCTTC
617 TTTCTTTCC--TC-TC
1 TTTCTTTCCTTTCTTC
*
630 CTTC-TTCCTTTCTTTC
1 TTTCTTTCCTTTC-TTC
646 TTTCTTTCCTTTCTTTC
1 TTTCTTTCCTTTC-TTC
663 TTTCT
1 TTTCT
668 CGTTTATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
12 4 0.07
13 5 0.09
14 3 0.05
15 9 0.16
16 5 0.09
17 31 0.54
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCTTTCCTTTCTTC
Found at i:1579 original size:25 final size:25
Alignment explanation
Indices: 1548--1629 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
1538 TAAAAACATT
1548 AAAATAAATATTTCTTAACAAATTA
1 AAAATAAATATTTCTTAACAAATTA
** *
1573 AAAATAAA-ATTT-AAAAAAACATT-
1 AAAATAAATATTTCTTAACAA-ATTA
1596 AAAATAAATATTTCTTAACAAATTA
1 AAAATAAATATTTCTTAACAAATTA
1621 AAAATAAAT
1 AAAATAAAT
1630 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 12 0.26
24 14 0.30
25 21 0.45
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAATAAATATTTCTTAACAAATTA
Found at i:1651 original size:47 final size:48
Alignment explanation
Indices: 1539--1638 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
1529 TAAAAATACT
1539 AAAAACATTAAAATAAATATTTCTTAACAAATTAAAAATAAAATTTAA
1 AAAAACATTAAAATAAATATTTCTTAACAAATTAAAAATAAAATTTAA
*
1587 AAAAACATTAAAATAAATATTTCTTAACAAATTAAAAATAAATTTTAA
1 AAAAACATTAAAATAAATATTTCTTAACAAATTAAAAATAAAATTTAA
1635 AAAA
1 AAAA
1639 TATATACTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (48 bp):
AAAAACATTAAAATAAATATTTCTTAACAAATTAAAAATAAAATTTAA
Found at i:1712 original size:30 final size:30
Alignment explanation
Indices: 1678--1742 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1668 GAACTTAACA
* *
1678 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
1708 AACAAATGCCTCTACAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
1738 AACAA
1 AACAA
1743 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:3732 original size:7 final size:8
Alignment explanation
Indices: 3713--3761 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
3703 AAAATTACAA
*
3713 AAAAATTT
1 AAAAATTC
3721 AAAAATTC
1 AAAAATTC
3729 AAAAATTC
1 AAAAATTC
3737 AAAAAATTC
1 -AAAAATTC
3746 AAAAAATTC
1 -AAAAATTC
3755 AAAAATT
1 AAAAATT
3762 TATATTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
8 22 0.56
9 17 0.44
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAAATTC
Found at i:3739 original size:26 final size:27
Alignment explanation
Indices: 3701--3761 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
3691 TCACTCTCAA
*
3701 CAAAAATTACAAAAAAATT-TAAAAATT
1 CAAAAATTAC-AAAAAATTCAAAAAATT
3728 CAAAAATT-CAAAAAATTCAAAAAATT
1 CAAAAATTACAAAAAATTCAAAAAATT
3754 CAAAAATT
1 CAAAAATT
3762 TATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 8 0.25
26 16 0.50
27 8 0.25
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.25
Consensus pattern (27 bp):
CAAAAATTACAAAAAATTCAAAAAATT
Found at i:3944 original size:14 final size:15
Alignment explanation
Indices: 3920--3952 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3910 CGTTGGATTC
*
3920 AAAATTTATATTTTT
1 AAAATTTATATATTT
3935 AAAA-TTATATATTT
1 AAAATTTATATATTT
3949 AAAA
1 AAAA
3953 AAATCTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTATATATTT
Found at i:4112 original size:16 final size:16
Alignment explanation
Indices: 4091--4121 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4081 TTTGAAAAAA
4091 ATTTCAAATATATATT
1 ATTTCAAATATATATT
*
4107 ATTTCAAATTTATAT
1 ATTTCAAATATATAT
4122 GTTCTAACAT
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:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTCAAATATATATT
Found at i:4933 original size:21 final size:21
Alignment explanation
Indices: 4894--4933 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4884 AAAATTTTAA
* *
4894 AATAATTAAAATTAGTAAAAC
1 AATAATAAAAATAAGTAAAAC
*
4915 AATAATAAAAATAATTAAA
1 AATAATAAAAATAAGTAAA
4934 TAGTTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
AATAATAAAAATAAGTAAAAC
Found at i:7304 original size:30 final size:30
Alignment explanation
Indices: 7249--7506 Score: 299
Period size: 30 Copynumber: 8.7 Consensus size: 30
7239 CCCTATTTTA
* * *
7249 TTCCAAAATTGCATTATAA--CCTAAACAT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
* * **
7277 TTCTAAAATTTCATTTTGGCCCCTAAACTT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
*
7307 TCCCAAAATTACATTTTAACCCCTAAACTT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
7337 TTCCAAAATTACATTTTAACCCCTAAACTT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
7367 TTCCAAAATTACATTTTAACCCCTAAACTT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
* * *
7397 CTCCAAAATCACATTTTAACACCC-AAACCT
1 TTCCAAAATTACATTTTAAC-CCCTAAACTT
* *
7427 TTCAAAAATTGCATTTTAACCCCTAAACTT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
* * * *
7457 CTCCAAAATCACATTTTGA-CCCTAAACCT
1 TTCCAAAATTACATTTTAACCCCTAAACTT
* * *
7486 TCCCGAAATCACATTTTAACC
1 TTCCAAAATTACATTTTAACC
7507 TCGAATTCTC
Statistics
Matches: 195, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.07
29 27 0.14
30 151 0.77
31 3 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (30 bp):
TTCCAAAATTACATTTTAACCCCTAAACTT
Found at i:7392 original size:90 final size:88
Alignment explanation
Indices: 7249--7506 Score: 333
Period size: 90 Copynumber: 2.9 Consensus size: 88
7239 CCCTATTTTA
* * * * *
7249 TTCCAAAATTGCATTATAA--CCTAAACATTTCTAAAATTTCATTTTGGCCCCTAAACTTTCCCA
1 TTCCAAAATTGCATTTTAACCCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAAC-TTCCCA
* *
7312 AAATTACATTTTAACCCCTAAACTT
65 AAATCACATTTTAACCCC-AAACCT
* *
7337 TTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTCTCCA
1 TTCCAAAATTGCATTTTAACCCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTC-CCA
7402 AAATCACATTTTAACACCCAAACCT
65 AAATCACATTTTAAC-CCCAAACCT
* * * *
7427 TTCAAAAATTGCATTTTAACCCCTAAACTTCTCCAAAATCACATTTTGA-CCCTAAACCTTCCCG
1 TTCCAAAATTGCATTTTAACCCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAA-CTTCCCA
7491 AAATCACATTTTAACC
65 AAATCACATTTTAACC
7507 TCGAATTCTC
Statistics
Matches: 150, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
88 18 0.12
89 27 0.18
90 102 0.68
91 3 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (88 bp):
TTCCAAAATTGCATTTTAACCCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCCCAA
AATCACATTTTAACCCCAAACCT
Found at i:18690 original size:16 final size:16
Alignment explanation
Indices: 18669--18702 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18659 AAATTTTGAG
*
18669 CTTATTTTTTCATAAT
1 CTTATTCTTTCATAAT
18685 CTTATTCTTTCATAAT
1 CTTATTCTTTCATAAT
18701 CT
1 CT
18703 CGTTCAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (16 bp):
CTTATTCTTTCATAAT
Found at i:19726 original size:48 final size:45
Alignment explanation
Indices: 19654--19814 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 45
19644 TTTGAAAATC
* *
19654 CATCTTCCTGATTAGATATTGAGAAGTGGGTCAAAGCAATAAAGCGGT
1 CATCTTCCTGATGAGATATAGAGAAGTGGGT-AAA-CAATAAA-CGGT
*
19702 CATCTTCCTGATGAGATATAGAGAAGT-GG---AC--TAAA--TT
1 CATCTTCCTGATGAGATATAGAGAAGTGGGTAAACAATAAACGGT
* * * * *
19739 CATCTTCTTGATGAGATACAAAGAAGTGGATTAAAATAATAAACGGT
1 CATCTTCCTGATGAGATATAGAGAAGTGG-GT-AAACAATAAACGGT
*
19786 CATCTTCCTGGTGAGATATAGAGAAGTGG
1 CATCTTCCTGATGAGATATAGAGAAGTGG
19815 ACCAAATCGA
Statistics
Matches: 90, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
37 25 0.28
38 1 0.01
40 4 0.04
42 1 0.01
43 2 0.02
45 4 0.04
47 28 0.31
48 25 0.28
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
CATCTTCCTGATGAGATATAGAGAAGTGGGTAAACAATAAACGGT
Found at i:19742 original size:37 final size:37
Alignment explanation
Indices: 19701--19773 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
19691 AATAAAGCGG
* *
19701 TCATCTTCCTGATGAGATATAGAGAAGTGGACTAAAT
1 TCATCTTCCTGATGAGATACAAAGAAGTGGACTAAAT
* *
19738 TCATCTTCTTGATGAGATACAAAGAAGTGGATTAAA
1 TCATCTTCCTGATGAGATACAAAGAAGTGGACTAAA
19774 ATAATAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (37 bp):
TCATCTTCCTGATGAGATACAAAGAAGTGGACTAAAT
Found at i:19745 original size:210 final size:208
Alignment explanation
Indices: 19366--20152 Score: 909
Period size: 210 Copynumber: 3.8 Consensus size: 208
19356 TTAAAACGGC
* * * *
19366 CATCTTCCTGATAAGATACAGAGAAGTAGACCAATTCAATGAAGTGAAGCTCACAATATGAGTGA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCT--CAATACGAGTGA
* * * * *
19431 AACTTCAAAAACCCATCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAACGGTCGTC
64 AACTTCGAAAACCCATCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATC
* * * *
19496 TTCCTAATGAGATACAAAGAAGTAGACCAAATCCATCTTCCTGATGAGATACAAAGAAGCGGATT
129 TTCCTGATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATT
* *
19561 AATACAAGTGATGCGAT
194 AA-ACAA-TGAAGCGGT
* * * * * *
19578 CATCTTCCTAATGAGATATAGAGAAGTAGACCAAATCGATAAAGGGAAGCTCAATACAAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAGTGAAA
* * * *
19643 CTTTGAAAATCCATCTTCCTGATTAGATATTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTT
66 CTTCGAAAACCCATCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTT
* * * *
19708 CCTGATGAGATATAGAGAAGTGGACTAAATTCATCTTCTTGATGAGATACAAAGAAGTGGATTAA
131 CCTGATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATT-A
* *
19773 AATAAT-AAACGGT
195 AACAATGAAGCGGT
* * * * **
19786 CATCTTCCTGGTGAGATATAGAGAAGTGGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAGTGAAA
* * * * * *
19851 CTTCG-AACCCCATCTTCCTGATAAGATAGTAAGAAGTGGGCCAAAACAATAAAGTGGTCATCTT
66 CTTCGAAAACCCATCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTT
* * * * *
19915 CCTGATGAGATACAGAGAAGTGGACCAAA-TCTATCTTCCTGGTAAGATATAGAGAAGTGGATTA
131 CCTGATGAGATACAAAGAAGTGGACCAAATTC-ATCTTCCTGATGAGATACAAAGAAGTGGATTA
*
19979 AATCAATGAGGCGGT
195 AA-CAATGAAGCGGT
* *
19994 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAATGAAGCAAAGTTCAATACGAGT-AA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATC-AATGAAGCGAAGCTCAATACGAGTGAA
* * * * * ** *
20058 AGTTTC-AAACCCCTATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATGAAGCAATTAT
65 A-CTTCGAAAACCC-ATCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCAT
*
20122 CTTCCTGATGAGATACAAAGAAGTAGACCAA
128 CTTCCTGATGAGATACAAAGAAGTGGACCAA
20153 GAAATGAAGC
Statistics
Matches: 489, Mismatches: 78, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
206 5 0.01
207 107 0.22
208 107 0.22
209 29 0.06
210 195 0.40
211 2 0.00
212 44 0.09
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (208 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAGTGAAA
CTTCGAAAACCCATCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTT
CCTGATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATTAA
ACAATGAAGCGGT
Found at i:20005 original size:85 final size:85
Alignment explanation
Indices: 19862--20030 Score: 241
Period size: 85 Copynumber: 2.0 Consensus size: 85
19852 TTCGAACCCC
* *
19862 ATCTTCCTGATAAGATAGTAAGAAGTGGGCCAAAACAATAAAGTGGTCATCTTCCTGATGAGATA
1 ATCTTCCTGATAAGATAGTAAGAAGTGGACCAAAACAATAAAGCGGTCATCTTCCTGATGAGATA
*
19927 CAGAGAAGTGGACCAAATCT
66 CAGAGAAGTAGACCAAATCT
* ** * * *
19947 ATCTTCCTGGTAAGATA-TAGAGAAGTGGATTAAATCAATGAGGCGGTCATCTTCCTGATGAGAT
1 ATCTTCCTGATAAGATAGTA-AGAAGTGGACCAAAACAATAAAGCGGTCATCTTCCTGATGAGAT
20011 ACAGAGAAGTAGACCAAATC
65 ACAGAGAAGTAGACCAAATC
20031 AAATGAAGCA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 2 0.03
85 72 0.97
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (85 bp):
ATCTTCCTGATAAGATAGTAAGAAGTGGACCAAAACAATAAAGCGGTCATCTTCCTGATGAGATA
CAGAGAAGTAGACCAAATCT
Found at i:21191 original size:16 final size:16
Alignment explanation
Indices: 21170--21200 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21160 ATTTTTAATA
21170 AATAAATAATAAAGGT
1 AATAAATAATAAAGGT
21186 AATAAATAATAAAGG
1 AATAAATAATAAAGG
21201 AAGATTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (16 bp):
AATAAATAATAAAGGT
Found at i:22191 original size:29 final size:28
Alignment explanation
Indices: 22146--22373 Score: 183
Period size: 29 Copynumber: 7.9 Consensus size: 28
22136 CCCCCAAAAT
22146 TTTCCAAAATTACATTTTAGCCCTAAAC
1 TTTCCAAAATTACATTTTAGCCCTAAAC
*
22174 TTTACCAAAATTACATTTT-GACCCCAAAC
1 TTT-CCAAAATTACATTTTAG-CCCTAAAC
** * * *
22203 TTTTTTAAAATTGCATTTGATCCCTAAAC
1 -TTTCCAAAATTACATTTTAGCCCTAAAC
* *
22232 TTTCCAAAATCACATTTTGACCCCTAAACC
1 TTTCCAAAATTACATTTT-AGCCCTAAA-C
* *
22262 TTTCCAAAATTACATTTGACCCCTAAAC
1 TTTCCAAAATTACATTTTAGCCCTAAAC
*
22290 TTCTCCAAAATCACATTTT-GACCCTCAAAC
1 TT-TCCAAAATTACATTTTAG-CCCT-AAAC
* * * *
22320 CTTCTCGAAATCACATTTT-GACCTCAAAC
1 TTTC-CAAAATTACATTTTAGCCCT-AAAC
* *
22349 TTTTCTAAAATTACATTTTAACCCT
1 -TTTCCAAAATTACATTTTAGCCCT
22374 GAATTCTTTG
Statistics
Matches: 161, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
28 20 0.12
29 96 0.60
30 45 0.28
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTAGCCCTAAAC
Found at i:22228 original size:58 final size:57
Alignment explanation
Indices: 22137--22372 Score: 251
Period size: 58 Copynumber: 4.1 Consensus size: 57
22127 ATATTATGAC
* * * *
22137 CCCCAAAATTTTCCAAAATTACATTTTAGCCCTAAACTTTACCAAAATTACATTTTGA
1 CCCCAAACTTTTCCAAAATTACATTTGACCCCTAAACTTT-CCAAAATCACATTTTGA
** * *
22195 CCCCAAACTTTTTTAAAATTGCATTTGATCCCTAAACTTTCCAAAATCACATTTTGA
1 CCCCAAACTTTTCCAAAATTACATTTGACCCCTAAACTTTCCAAAATCACATTTTGA
*
22252 CCCCTAAACCTTTCCAAAATTACATTTGACCCCTAAACTTCTCCAAAATCACATTTTGA
1 CCCC-AAACTTTTCCAAAATTACATTTGACCCCTAAACTT-TCCAAAATCACATTTTGA
* * * * * * *
22311 CCCTCAAAC-CTTCTCGAAATCACATTTTGACCTC-AAACTTTTCTAAAATTACATTTTAA
1 CCC-CAAACTTTTC-CAAAATTACA-TTTGACCCCTAAAC-TTTCCAAAATCACATTTTGA
22370 CCC
1 CCC
22373 TGAATTCTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
57 20 0.13
58 67 0.44
59 55 0.36
60 11 0.07
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (57 bp):
CCCCAAACTTTTCCAAAATTACATTTGACCCCTAAACTTTCCAAAATCACATTTTGA
Found at i:22373 original size:59 final size:60
Alignment explanation
Indices: 22146--22373 Score: 227
Period size: 59 Copynumber: 3.9 Consensus size: 60
22136 CCCCCAAAAT
* * * * * *
22146 TTTCCAAAATTACATTTTAGCCCTAAACTTTACCAAAATTACATTTTGACCC-C-AAACT
1 TTTCCAAAATCACATTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCTAAACC
** ** *
22204 TTTTTAAAATTGCATTTGATCCCTAAAC-TTTCCAAAATCACATTTTGACCC-CTAAACC
1 TTTCCAAAATCACATTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCTAAACC
* *
22262 TTTCCAAAATTACATTTGACCCCTAAACTTCTCCAAAATCACATTTTGACCCTC-AAACC
1 TTTCCAAAATCACATTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCTAAACC
* * * * *
22321 -TTCTCGAAATCACATTTTGACCTC-AAACTTTTCTAAAATTACATTTTAACCCT
1 TTTC-CAAAATCACA-TTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCT
22374 GAATTCTTTG
Statistics
Matches: 145, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
57 22 0.15
58 54 0.37
59 60 0.41
60 9 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (60 bp):
TTTCCAAAATCACATTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCTAAACC
Done.