Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017468.1 Corchorus olitorius cultivar O-4 contig17501, 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: 29676
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--33 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AGCAG
6 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34 CCTACTATTC
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):
AT
Found at i:1627 original size:23 final size:23
Alignment explanation
Indices: 1597--1659 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1587 GCCTTTGAAC
1597 TTTAGTTATACTTTGGCTTAAAT
1 TTTAGTTATACTTTGGCTTAAAT
** * *
1620 TTTAGTTAGGCTTGGGCTTAGAT
1 TTTAGTTATACTTTGGCTTAAAT
*
1643 TCTAGTTTATACTTTGG
1 TTTAG-TTATACTTTGG
1660 ATTTAGTTCC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (23 bp):
TTTAGTTATACTTTGGCTTAAAT
Found at i:2319 original size:19 final size:20
Alignment explanation
Indices: 2274--2319 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
2264 TCAAAATTAA
2274 CAAAAAAAGGTTTTCAAAAAT
1 CAAAAAAA-GTTTTCAAAAAT
*
2295 -ACAAAAAA-TTTTCAAAACT
1 CA-AAAAAAGTTTTCAAAAAT
2314 CAAAAA
1 CAAAAA
2320 TCAAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (20 bp):
CAAAAAAAGTTTTCAAAAAT
Found at i:2387 original size:33 final size:33
Alignment explanation
Indices: 2336--2475 Score: 154
Period size: 33 Copynumber: 4.1 Consensus size: 33
2326 AAGAATTTCA
2336 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
1 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
* * *
2369 TTAAATTTTTAATCGGGAAAGTTCCCACCGGTT
1 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
** *
2402 TTAAGTTTTTAAAAATTGGGAAAGTTCCCATTAACTT
1 TTAAGTTTTT---AATTGGGAAAGTTCCCA-CCAGTT
* *
2439 TTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTT
1 TTAAGTTTT-TAATTGGGAAAGTTCCCA-CCAGTT
2474 TT
1 TT
2476 TTTGCAAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
33 39 0.43
35 24 0.27
36 16 0.18
37 11 0.12
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (33 bp):
TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
Found at i:8739 original size:28 final size:28
Alignment explanation
Indices: 8679--8739 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
8669 GATCTTGTGA
***
8679 AGTCACCATCTCATATCAGTTTGGCAGC
1 AGTCACCATCTCATATCAGTTTCAAAGC
* *
8707 AGTCACCATCTCTTATGAGTTTCAAAGC
1 AGTCACCATCTCATATCAGTTTCAAAGC
*
8735 CGTCA
1 AGTCA
8740 GGGTTTGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (28 bp):
AGTCACCATCTCATATCAGTTTCAAAGC
Found at i:9149 original size:7 final size:7
Alignment explanation
Indices: 9134--9167 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
9124 TGATTTAAAC
*
9134 TATACAT
1 TATATAT
9141 TATATAT
1 TATATAT
9148 TATATAT
1 TATATAT
9155 TATATAT
1 TATATAT
9162 TATATA
1 TATATA
9168 AATAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:14169 original size:12 final size:12
Alignment explanation
Indices: 14152--14182 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
14142 TTTCTTTTCC
*
14152 TCCACTTGCAAT
1 TCCACTAGCAAT
14164 TCCACTAGCAAT
1 TCCACTAGCAAT
14176 TCCACTA
1 TCCACTA
14183 CGGAAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (12 bp):
TCCACTAGCAAT
Found at i:15555 original size:22 final size:22
Alignment explanation
Indices: 15510--15592 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
15500 GAGAACCTTT
* * *
15510 TTAT-AAATTTTTTTAATCTTC
1 TTATGAAATTTTGTTAACCTCC
15531 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGTTAACCTCC
* * *
15553 TTAAGGAATTTTG-AAGACCTCAC
1 TTATGAAATTTTGTTA-ACCTC-C
*
15576 -TATGAAATTTTGATAAC
1 TTATGAAATTTTGTTAAC
15593 ACTATGAGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.10
22 42 0.86
23 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.45
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACCTCC
Found at i:15597 original size:19 final size:19
Alignment explanation
Indices: 15573--15611 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
15563 TTGAAGACCT
*
15573 CACTATGAAATTTTGATAA
1 CACTATGAAATGTTGATAA
*
15592 CACTATGAGATGTTGATAA
1 CACTATGAAATGTTGATAA
15611 C
1 C
15612 CTCCATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (19 bp):
CACTATGAAATGTTGATAA
Found at i:15752 original size:23 final size:23
Alignment explanation
Indices: 15719--15765 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
15709 AAATTGTGAT
*
15719 AACCTCGCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
15742 AACCTCCCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
15765 A
1 A
15766 CCTTCTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTAATA
Found at i:15779 original size:22 final size:22
Alignment explanation
Indices: 15527--15952 Score: 137
Period size: 22 Copynumber: 19.9 Consensus size: 22
15517 TTTTTTTAAT
* *
15527 CTTCTTATGAAATTTTGTTAAC
1 CTTCCTATGAAATTTTGATAAC
* *
15549 C-TCCTTAAGGAATTTTGA-AGAC
1 CTTCC-TATGAAATTTTGATA-AC
15571 C-TCACTATGAAATTTTGATAA-
1 CTTC-CTATGAAATTTTGATAAC
* * *
15592 C--ACTATGAGATGTTGATAAC
1 CTTCCTATGAAATTTTGATAAC
* *
15612 C-TCCATATGATATATTGATAAC
1 CTTCC-TATGAAATTTTGATAAC
* ** * * *
15634 CATGATATGAAAATTTAAAAAC
1 CTTCCTATGAAATTTTGATAAC
*
15656 C-TCCATATG-AATTGTT-AGTAAT
1 CTTCC-TATGAAATT-TTGA-TAAC
* * *
15678 C-ACACTCTGAAATTTTGATAAT
1 CTTC-CTATGAAATTTTGATAAC
* *
15700 C-ACACTATGAAATTGTGATAAC
1 CTTC-CTATGAAATTTTGATAAC
* *
15722 C-TCGCTATAAAATTTTAATAAAC
1 CTTC-CTATGAAATTTTGAT-AAC
* * *
15745 CTCCCTATAAAATTTTAATAAC
1 CTTCCTATGAAATTTTGATAAC
* *
15767 CTTCTTATGAAATCTTGATAA-
1 CTTCCTATGAAATTTTGATAAC
* *
15788 ----CTA-CAAATTTTGATTAC
1 CTTCCTATGAAATTTTGATAAC
* ** *
15805 CTCCCTATGATTTTTTTATAAC
1 CTTCCTATGAAATTTTGATAAC
* *
15827 C-TCATTATGAAATTTTGTTAA-
1 CTTC-CTATGAAATTTTGATAAC
*
15848 TTTCCCTATGAAATTTTGATAAC
1 CTT-CCTATGAAATTTTGATAAC
* * *
15871 CCTCTTATGAAATTTTGA-AAA
1 CTTCCTATGAAATTTTGATAAC
**
15892 CTAAACTATGAAA-TTTGATAAC
1 CT-TCCTATGAAATTTTGATAAC
* * *
15914 CTTCATATGAAATTTTAATATC
1 CTTCCTATGAAATTTTGATAAC
*
15936 C-TCC-CTGAAATTTTGAT
1 CTTCCTATGAAATTTTGAT
15953 TACTCTATAG
Statistics
Matches: 300, Mismatches: 75, Indels: 60
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
19 15 0.05
20 12 0.04
21 31 0.10
22 199 0.66
23 30 0.10
24 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
CTTCCTATGAAATTTTGATAAC
Found at i:16061 original size:22 final size:22
Alignment explanation
Indices: 16034--16471 Score: 109
Period size: 22 Copynumber: 19.7 Consensus size: 22
16024 GAAATAATAC
* *
16034 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCAC-TT
* *
16057 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTT
**
16078 TATGAAATTTTGATAA-CTTTT
1 TATGAAATTTTGATAACCACTT
* * * * *
16099 CTATAAAATTTTGTTGACCCCTC
1 -TATGAAATTTTGATAACCACTT
**** *
16122 TATGAAATTTTGATATTTTCAT
1 TATGAAATTTTGATAACCACTT
* * *
16144 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCAC-TT
* **
16167 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCACTT
*
16188 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCACTT
* *
16208 CCTAT-AAATTTTGATAATTCGATCTC
1 --TATGAAATTTTGATAA--CCA-CTT
* * *
16234 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCACTT
*
16256 TATGAGA-TTTGATAA-C-CTT
1 TATGAAATTTTGATAACCACTT
* *
16275 CTATCAAATTTTGGT-ACTC-C-T
1 -TATGAAATTTTGATAAC-CACTT
*
16296 TATGAAATTAAGACTTTTATAA-C-CTT
1 TATGAAA-T-----TTTGATAACCACTT
**
16322 CATATGAAATTTTGATAACCACAC
1 --TATGAAATTTTGATAACCACTT
** * **
16346 TAAAAAATTTTAATAACCACAC
1 TATGAAATTTTGATAACCACTT
* **
16368 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACTT
* *
16390 TATGAAATATT-AGTAACC-TTCT
1 TATGAAATTTTGA-TAACCACT-T
* **
16412 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACTT
* **
16434 TATGAAATTCTT-ATAACCTCAC
1 TATGAAATT-TTGATAACCACTT
*
16456 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
16472 TCTCTTTGAT
Statistics
Matches: 309, Mismatches: 71, Indels: 71
0.69 0.16 0.16
Matches are distributed among these distances:
19 2 0.01
20 14 0.05
21 37 0.12
22 214 0.69
23 9 0.03
24 4 0.01
25 13 0.04
26 7 0.02
27 2 0.01
28 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTT
Found at i:16197 original size:44 final size:43
Alignment explanation
Indices: 16033--16706 Score: 232
Period size: 44 Copynumber: 15.4 Consensus size: 43
16023 AGAAATAATA
* * * *
16033 CTATGAAATTTTGGTAA-TCACATTTTGAAAATTTGATAACCTC
1 CTATGAAATTTTGATAACT-ACACTATGAAATTTTGATAACCTC
* *** * * * *
16076 TTTATGAAATTTTGATAACTTTTCTATAAAATTTTGTTGACCCC
1 -CTATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTC
** * * *
16120 TCTATGAAATTTTGATATTTTCATTATGTAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTC
* * *
16164 GCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAACTACACTATGAAATTTTGATAA-CCTC
* * *
16209 CTAT-AAATTTTGATAATTCGATCTCTATGAAATTTCGATAATCACT-
1 CTATGAAATTTTGATAA--CTA-CACTATGAAATTTTGATAA-C-CTC
* * * *
16255 CTATGAGA-TTTGATAAC--CTTCTATCAAATTTTGGT-A-CTC
1 CTATGAAATTTTGATAACTAC-ACTATGAAATTTTGATAACCTC
* * *
16294 CTTATGAAATTAAGACTTTTATAACCTTCA-TATGAAATTTTGATAACCAC
1 C-TATGAAA-T-----TTTGATAA-CTACACTATGAAATTTTGATAACCTC
** * *
16344 ACTAAAAAATTTTAATAACCACACTATGAAATTTTGATAACCTCC
1 -CTATGAAATTTTGATAACTACACTATGAAATTTTGATAACCT-C
* * * * *
16389 CTATGAAATATT-AGTAACCTTC-TTATGAAATTTTGTTAACCAC
1 CTATGAAATTTTGA-TAA-CTACACTATGAAATTTTGATAACCTC
*
16432 ACTATGAAATTCTT-ATAACCT-CACTATGACATTTTGATAA--T-
1 -CTATGAAATT-TTGATAA-CTACACTATGAAATTTTGATAACCTC
* ** * * * *
16473 C--T----CTTTGATAACCT-TTCTATAAAATTGTGATAGCCAC
1 CTATGAAATTTTGATAA-CTACACTATGAAATTTTGATAACCTC
** * ** * *
16510 ACTATGAAATTTCAATAACCTTC-CTAAAAAATTTTAATAACTTGATC
1 -CTATGAAATTTTGATAA-CTACACTATGAAATTTTGATAAC---CTC
* * *
16557 CTATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAACTACACTATGAAATTTTGATAACC-TC
* * * *
16601 CCATGAAATTTTGATAACTTC-CATATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACTACAC-TATGAAATTTTGATAACCTC
* * *
16644 ACTATGGAATTTTGATAACCT-C-CTCATGAAATTATAATAACCATC
1 -CTATGAAATTTTGATAA-CTACACT-ATGAAATTTTGATAACC-TC
*
16689 TTATGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
16707 CACATAGAGA
Statistics
Matches: 469, Mismatches: 109, Indels: 105
0.69 0.16 0.15
Matches are distributed among these distances:
33 2 0.00
34 21 0.04
38 4 0.01
39 1 0.00
40 8 0.02
41 2 0.00
42 13 0.03
43 22 0.05
44 285 0.61
45 16 0.03
46 60 0.13
47 11 0.02
48 13 0.03
49 2 0.00
50 8 0.02
51 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (43 bp):
CTATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTC
Found at i:16394 original size:66 final size:66
Alignment explanation
Indices: 16078--16710 Score: 292
Period size: 66 Copynumber: 9.3 Consensus size: 66
16068 ATAACCTCTT
**** * * * **
16078 TATGAAATTTTGATAACTTTTCTATAAAATTTTGTTGACC-CCTCTATGAAATTTTGATATTTTC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC-CTATGAAATTTTGATA-ACTC
*
16142 A-T
64 ACC
* * * * ** * *
16144 TATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA-TCTT
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTC-A
16208 CC
65 CC
* * * * * * *
16210 TAT-AAATTTTGATAATTCGATCTCTATGAAATTTCGATAATCACTCTATGAGA-TTTGATAAC-
1 TATGAAATTTTGATAA--CCA-CACTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACT
**
16272 CTTC
63 CACC
* * * * * *
16276 TATCAAATTTTGGT-ACTC-C-TTATGAAATTAAGACTTTTATAACCTTCATATGAAATTTTGAT
1 TATGAAATTTTGATAAC-CACACTATGAAA-T-----TTTGATAACCTCCCTATGAAATTTTGAT
16338 AAC-CACAC
59 AACTCAC-C
** * *
16346 TAAAAAATTTTAATAACCACACTATGAAATTTTGATAACCTCCCTATGAAATATT-AGTAAC-CT
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAACTC-
* *
16409 TCT
64 ACC
* * *
16412 TATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCACTATGACATTTTGATAATCTC
1 TATGAAATTTTGATAACCACACTATGAAATT-TTGATAACCTCCCTATGAAATTTTGATAA-CTC
16476 TTTGATAACCTTTC
64 -------A-C---C
* * * ** * ** * *
16490 TATAAAATTGTGATAGCCACACTATGAAATTTCAATAACCTTCCTAAAAAATTTTAATAACTTGA
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAC-TCA
16555 TCC
65 -CC
* *
16558 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCCC-ATGAAATTTTGATAACTTC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAAC-TC
*
16622 -CA
64 ACC
* * * *
16624 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCT-CCTCATGAAATTATAATAAC-CA
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACTCA
*
16687 TCT
65 -CC
16690 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
16711 TAGAGACAAG
Statistics
Matches: 434, Mismatches: 90, Indels: 86
0.71 0.15 0.14
Matches are distributed among these distances:
62 7 0.02
63 2 0.00
64 6 0.01
65 13 0.03
66 204 0.47
67 25 0.06
68 88 0.20
69 13 0.03
70 12 0.03
71 6 0.01
72 7 0.02
75 1 0.00
77 2 0.00
78 48 0.11
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (66 bp):
TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTCAC
C
Found at i:16585 original size:22 final size:22
Alignment explanation
Indices: 16476--16708 Score: 186
Period size: 22 Copynumber: 10.5 Consensus size: 22
16466 TGATAATCTC
* * *
16476 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATCCTATGAAAT
* *
16498 TGTGATAGCCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** * **
16520 TTCAATAACCTTCCTAAAAAAT
1 TTTGATAACCATCCTATGAAAT
* *
16542 TTTAATAACTTGATCCTATGAAAT
1 TTTGATAAC--CATCCTATGAAAT
* *
16566 TTTGGTAACCATACTATGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
16588 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
16610 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
16632 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
16654 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
16676 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
16698 TTTGATAACCA
1 TTTGATAACCA
16709 CATAGAGACA
Statistics
Matches: 165, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
21 7 0.04
22 136 0.82
23 6 0.04
24 16 0.10
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:18438 original size:293 final size:293
Alignment explanation
Indices: 17972--18558 Score: 910
Period size: 293 Copynumber: 2.0 Consensus size: 293
17962 TTTTTAGTGA
17972 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGACTTTTTTTGGT
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGACTTTTTTTGGT
* * * **
18037 CTTTTCTCACTTTTCGAGTGACTAAAAAGGCCTTTGATGAATTTCCTTTCTTACTTTTCCTCTTG
66 CTTTTCTCACCTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCTTG
* **
18102 CCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTATGTATTAATTGT
131 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGT
* * * * *
18167 GTGTGGATATTAGGATTTACCGGTTCAACTTCTCTGCTGAAATTACAAAGGATTGGTGCTATAAA
196 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTACAAAGGATTAGTGATATAAA
*
18232 TGTATCTACCCGAGTTCATTAATTTAACAATTG
261 TGTATCTACCCGAATTCATTAATTTAACAATTG
* *
18265 CTATGGAAATTACTTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTATTT
1 CTATGGAAATTACTT-AAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGACTTTTT-TTG
* *
18330 TTCTTTTCTCACCTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGC
64 GTCTTTTCTCACCTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCT-C
* *
18395 -TG-TC-TTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGAT
128 TTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAAT
* * *
18457 TGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGATGT
193 TGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTACAAAGGATTAGTGATAT
*
18522 AAATGTGTCTACCCGAATTCATTAATTTAACAATTG
258 AAATGTATCTACCCGAATTCATTAATTTAACAATTG
18558 C
1 C
18559 AATCAAGATT
Statistics
Matches: 267, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
293 161 0.60
294 45 0.17
295 60 0.22
296 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (293 bp):
CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGACTTTTTTTGGT
CTTTTCTCACCTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCTTG
CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGT
GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTACAAAGGATTAGTGATATAAA
TGTATCTACCCGAATTCATTAATTTAACAATTG
Found at i:18863 original size:27 final size:27
Alignment explanation
Indices: 18832--18888 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
18822 ACGGCTAATG
*
18832 CAATATCTTCTTTCTAA-CTGACTTAAA
1 CAATATATTCTTTCTAATC-GACTTAAA
*
18859 CAATATATTCTTTTTAATCGACTTAAA
1 CAATATATTCTTTCTAATCGACTTAAA
18886 CAA
1 CAA
18889 CTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (27 bp):
CAATATATTCTTTCTAATCGACTTAAA
Found at i:29665 original size:14 final size:14
Alignment explanation
Indices: 29646--29673 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29636 TTCACACTAA
29646 ATACCATATTCTTT
1 ATACCATATTCTTT
29660 ATACCATATTCTTT
1 ATACCATATTCTTT
29674 TTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
ATACCATATTCTTT
Done.