Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015591.1 Corchorus capsularis cultivar CVL-1 contig15612, 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: 38398
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:350 original size:21 final size:21
Alignment explanation
Indices: 282--379 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
272 TGTATCTTCA
* *
282 TCTCCACCTCCACCAGTCTAT
1 TCTCCACCCCCACCAGTCTAC
* *
303 TCCCCACCGCCACCACCAGTCTCC
1 TCTCCA-C-CC-CCACCAGTCTAC
* * *
327 TCTCCACCCCCTCCTGTCTTC
1 TCTCCACCCCCACCAGTCTAC
* *
348 TCTCCTCCTCCACCAGTCTAC
1 TCTCCACCCCCACCAGTCTAC
*
369 TCACCACCCCC
1 TCTCCACCCCC
380 GCCACTTGTC
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
21 38 0.66
22 3 0.05
23 2 0.03
24 15 0.26
ACGTcount: A:0.14, C:0.57, G:0.05, T:0.23
Consensus pattern (21 bp):
TCTCCACCCCCACCAGTCTAC
Found at i:397 original size:66 final size:67
Alignment explanation
Indices: 276--406 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 67
266 AGCAGTTGTA
* * *
276 TCTTCATCTCCACCTCCACCAGTCTATTCCCCACCGCCACCACCAGTCTCCTCTCCACCCCCTCC
1 TCTTCATCTCCACCTCCACCAGTCTACTCACCACCCCCACCACCAGTCTCCTCTCCACCCCCTCC
341 TG
66 TG
* * ** *
343 TCTTC-TCTCCTCCTCCACCAGTCTACTCACCACCCCCGCCACTTGTC-CATTCTCCACCCCCTC
1 TCTTCATCTCCACCTCCACCAGTCTACTCACCACCCCCACCACCAGTCTC-CTCTCCACCCCCTC
406 C
65 C
407 ACCTGTTAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 1 0.02
66 49 0.89
67 5 0.09
ACGTcount: A:0.14, C:0.56, G:0.05, T:0.25
Consensus pattern (67 bp):
TCTTCATCTCCACCTCCACCAGTCTACTCACCACCCCCACCACCAGTCTCCTCTCCACCCCCTCC
TG
Found at i:450 original size:21 final size:22
Alignment explanation
Indices: 397--459 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
387 GTCCATTCTC
*
397 CACCCCCTCCACCTGT-TAGTT
1 CACCCCCTCCACCTGTCTACTT
* * *
418 CGCCACCACCACCTGTCT-CTT
1 CACCCCCTCCACCTGTCTACTT
*
439 CACCCCCTCCACCAGTCTACT
1 CACCCCCTCCACCTGTCTACT
460 CCCCACCACC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.16, C:0.52, G:0.08, T:0.24
Consensus pattern (22 bp):
CACCCCCTCCACCTGTCTACTT
Found at i:466 original size:24 final size:24
Alignment explanation
Indices: 288--340 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
278 TTCATCTCCA
* *
288 CCTCCACCAGTCTATTCCCCACCG
1 CCTCCACCAGTCTACTCCCCACCC
* * *
312 CCACCACCAGTCTCCTCTCCACCC
1 CCTCCACCAGTCTACTCCCCACCC
336 CCTCC
1 CCTCC
341 TGTCTTCTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.60, G:0.06, T:0.19
Consensus pattern (24 bp):
CCTCCACCAGTCTACTCCCCACCC
Found at i:466 original size:42 final size:42
Alignment explanation
Indices: 315--472 Score: 113
Period size: 42 Copynumber: 3.6 Consensus size: 42
305 CCCACCGCCA
* * * * * *
315 CCACCAGTCTCCTCTCCACCCCCTCCTGTCT-TCTCTCCTCCT
1 CCACCAGTCTACTCCCCACCACCACCTGTCTCT-TCACCCCCT
* * * *
357 CCACCAGTCTACTCACCACCCCCGCCACTTGTCCATTCTCCACCCCCT
1 CCACCAGTCTACT--CC-CCACCACCACCTGT-C--TCTTCACCCCCT
* * *
405 CCACCTGT-TAGTTCGCCACCACCACCTGTCTCTTCACCCCCT
1 CCACCAGTCTA-CTCCCCACCACCACCTGTCTCTTCACCCCCT
447 CCACCAGTCTACTCCCCACCACCACC
1 CCACCAGTCTACTCCCCACCACCACC
473 CGTATACTCT
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
42 43 0.49
43 2 0.02
44 2 0.02
45 21 0.24
46 2 0.02
47 2 0.02
48 15 0.17
49 1 0.01
ACGTcount: A:0.15, C:0.56, G:0.06, T:0.23
Consensus pattern (42 bp):
CCACCAGTCTACTCCCCACCACCACCTGTCTCTTCACCCCCT
Found at i:471 original size:21 final size:21
Alignment explanation
Indices: 420--585 Score: 97
Period size: 21 Copynumber: 7.6 Consensus size: 21
410 TGTTAGTTCG
*
420 CCACCACCACCTGTCT-CTTCAC
1 CCACCACCACCAGTCTAC-TC-C
*
442 CC-CCTCCACCAGTCTACTCC
1 CCACCACCACCAGTCTACTCC
* *
462 CCACCACCACCCGTATACTCTCC
1 CCACCACCACCAGTCTA--CTCC
* *
485 TCCACCACCTCTCCAGTC-AC-CA
1 -CCACCA-C-CACCAGTCTACTCC
*
507 CCACCACCACCAGGCTACTCC
1 CCACCACCACCAGTCTACTCC
* *
528 CCTCCACCACCCGTCTACTCACC
1 CCACCACCACCAGTCTACT--CC
* * *
551 ACCTCCACCACCAGTTTACTCA
1 -CCACCACCACCAGTCTACTCC
*
573 CCACCATCACCAG
1 CCACCACCACCAG
586 CCGTACAATC
Statistics
Matches: 112, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
19 6 0.05
20 6 0.05
21 58 0.52
22 5 0.04
23 7 0.06
24 23 0.21
25 2 0.02
26 5 0.04
ACGTcount: A:0.22, C:0.55, G:0.05, T:0.17
Consensus pattern (21 bp):
CCACCACCACCAGTCTACTCC
Found at i:490 original size:66 final size:64
Alignment explanation
Indices: 420--585 Score: 161
Period size: 66 Copynumber: 2.5 Consensus size: 64
410 TGTTAGTTCG
* * * * * *
420 CCACCACCACCTGTCTCTTCACCCCCTCCACCAGTCTACTCCCCACCACCACCCGTATACTCTCC
1 CCACCACCACCAGTCAC--CACCACCACCACCAGGCTACTCCCCACCACCACCCGTATACTCACC
*
485 T
64 A
* * *
486 CCACCACCTCTCCAGTCACCACCACCACCACCAGGCTACTCCCCTCCACCACCCGTCTACTCACC
1 CCACCA-C-CACCAGTCACCACCACCACCACCAGGCTACTCCCCACCACCACCCGTATACTCACC
551 A
64 A
* * *
552 CCTCCACCACCAGTTTACTCACCACCATCACCAG
1 CCACCACCACCAG-TCAC-CACCACCACCACCAG
586 CCGTACAATC
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 5 0.06
65 4 0.05
66 65 0.79
67 1 0.01
68 7 0.09
ACGTcount: A:0.22, C:0.55, G:0.05, T:0.17
Consensus pattern (64 bp):
CCACCACCACCAGTCACCACCACCACCACCAGGCTACTCCCCACCACCACCCGTATACTCACCA
Found at i:511 original size:45 final size:45
Alignment explanation
Indices: 462--571 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 45
452 AGTCTACTCC
* * *
462 CCACCACCACCCGTATACTCTCCTCCACCACCTC-TCCAGTCACCA
1 CCACCACCACCAGTATACTCCCCTCCACCACC-CGTCCACTCACCA
** *
507 CCACCACCACCAGGCTACTCCCCTCCACCACCCGTCTACTCACCA
1 CCACCACCACCAGTATACTCCCCTCCACCACCCGTCCACTCACCA
* *
552 CCTCCACCACCAGTTTACTC
1 CCACCACCACCAGTATACTC
572 ACCACCATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.22, C:0.55, G:0.05, T:0.17
Consensus pattern (45 bp):
CCACCACCACCAGTATACTCCCCTCCACCACCCGTCCACTCACCA
Found at i:584 original size:24 final size:24
Alignment explanation
Indices: 483--577 Score: 97
Period size: 24 Copynumber: 4.1 Consensus size: 24
473 CGTATACTCT
** * *
483 CCTCCACCACCTCTCCAGTCACCA
1 CCTCCACCACCAGTCTACTCACCA
* *
507 CCACCACCACCAGGCTACT--CC-
1 CCTCCACCACCAGTCTACTCACCA
*
528 CCTCCACCACCCGTCTACTCACCA
1 CCTCCACCACCAGTCTACTCACCA
*
552 CCTCCACCACCAGTTTACTCACCA
1 CCTCCACCACCAGTCTACTCACCA
576 CC
1 CC
578 ATCACCAGCC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 16 0.28
22 2 0.04
23 2 0.04
24 37 0.65
ACGTcount: A:0.22, C:0.57, G:0.05, T:0.16
Consensus pattern (24 bp):
CCTCCACCACCAGTCTACTCACCA
Found at i:2241 original size:26 final size:27
Alignment explanation
Indices: 2190--2242 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2180 AAAATATAAG
* *
2190 GGACAATTAAAAAGGAACAAGGGAGAT
1 GGACAATTAAAAACGAACAAGAGAGAT
2217 GGACAATTAAAAACGAACAGAGAGAG
1 GGACAATTAAAAACGAACA-AGAGAG
2243 TAATAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.53, C:0.09, G:0.28, T:0.09
Consensus pattern (27 bp):
GGACAATTAAAAACGAACAAGAGAGAT
Found at i:6667 original size:28 final size:28
Alignment explanation
Indices: 6636--6689 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6626 TTGAAGAATA
*
6636 AACCGTGAAATGC-AGATTTTGAATTTCG
1 AACCATGAAATGCTA-ATTTTGAATTTCG
*
6664 AACCATGAGATGCTAATTTTGAATTT
1 AACCATGAAATGCTAATTTTGAATTT
6690 TGATTTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (28 bp):
AACCATGAAATGCTAATTTTGAATTTCG
Found at i:6720 original size:113 final size:110
Alignment explanation
Indices: 6563--6774 Score: 302
Period size: 113 Copynumber: 1.9 Consensus size: 110
6553 ATGAAAGGAA
*
6563 ATGCAAATTTTGAAATTTGATTTTCGAACGGAATGCTGAAATGCAAGTTTTGAGTTTTGA-CTTT
1 ATGCAAATTTTGAAATTTGATTTTCGAACGGAATGCTGAAATGCAAGTTTTGAATTTTGATCTTT
*
6627 TGAAGAATAAACCGTGAAATGCAGATTTTGAATTTCGAACCATGAG
66 TGAAGAATAAACCATG-AATGCAGATTTTGAATTTCGAACCATGAG
* *
6673 ATGCTAATTTTGAATTTTGATTTTCGAA-GAATGAAATGCTGAAATGCAAGTTTTGAATTTTGAT
1 ATGCAAATTTTGAAATTTGATTTTCGAACG---G-AATGCTGAAATGCAAGTTTTGAATTTTGAT
* * *
6737 TTTTTGAAGAATGAACCATGAATGCAGCTTTTGAATTT
62 CTTTTGAAGAATAAACCATGAATGCAGATTTTGAATTT
6775 TGAATTTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
109 1 0.01
110 26 0.29
112 1 0.01
113 45 0.50
114 17 0.19
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (110 bp):
ATGCAAATTTTGAAATTTGATTTTCGAACGGAATGCTGAAATGCAAGTTTTGAATTTTGATCTTT
TGAAGAATAAACCATGAATGCAGATTTTGAATTTCGAACCATGAG
Found at i:6774 original size:42 final size:42
Alignment explanation
Indices: 6663--6787 Score: 141
Period size: 43 Copynumber: 2.9 Consensus size: 42
6653 TTTGAATTTC
*
6663 GAACCATGAGATGCTAA-TTTTGAATTTTGA-TTTTCGAAGAAT
1 GAACCATGA-ATGC-AAGTTTTGAATTTTGATTTTTTGAAGAAT
*
6705 GAAATGC-TGAAATGCAAGTTTTGAATTTTGATTTTTTGAAGAAT
1 G-AA-CCATG-AATGCAAGTTTTGAATTTTGATTTTTTGAAGAAT
6749 GAACCATGAATGC-AGCTTTTGAATTTTGAATTTTTTGAA
1 GAACCATGAATGCAAG-TTTTGAATTTTG-ATTTTTTGAA
6788 TAGTGAAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
41 2 0.03
42 21 0.29
43 35 0.49
44 14 0.19
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (42 bp):
GAACCATGAATGCAAGTTTTGAATTTTGATTTTTTGAAGAAT
Found at i:6956 original size:43 final size:42
Alignment explanation
Indices: 6892--6979 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 42
6882 AGAATGCACG
* *
6892 TTTTGAGTTTTGAAGAATGAAACAATAAAATGCATATTTTGAA
1 TTTTGAGTTTTGAAGAATGAAACAA-AAAATGCAAATTTTAAA
* *
6935 TTTTGAGTTTT-AATGAGTGAAACAAAAGATGCAAATTTTAAA
1 TTTTGAGTTTTGAA-GAATGAAACAAAAAATGCAAATTTTAAA
6977 TTT
1 TTT
6980 GGGGAACCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (42 bp):
TTTTGAGTTTTGAAGAATGAAACAAAAAATGCAAATTTTAAA
Found at i:7608 original size:37 final size:37
Alignment explanation
Indices: 7049--7591 Score: 586
Period size: 37 Copynumber: 14.7 Consensus size: 37
7039 TAACCAACAA
* *
7049 TTTGATAACAAACCTAAACAAGAATCTTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* * * *
7086 TTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAA-GAT
*
7123 TTTGACAAGAAACCTAAACAGGAATCTTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* * * *
7160 TTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAA-GAT
*
7197 TTTGATAAGAAACCTAAACAGGAGTCTTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* * * *
7234 TTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAA-GAT
*
7271 TTTCATAAGAAACCTAAACAGGAATCTTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* * * *
7308 TTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAA-GAT
*
7345 TTTGATAAGAAATCTAAACAGGAATCTTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* * * *
7382 TTTGATGAGACACCTAAACAGGGATCTTAAACAAGAA
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
*
7419 TTTGATAAGAAACCTAAACAGGAATCCTAAACAAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* *
7456 TTTGATGAA-ACACCTAAACAGGGACATC--GAACAAGGA-
1 TTTGAT-AAGAAACCTAAACA-GGA-ATCTTAAACAA-GAT
* * *
7493 TTTGATAAGACACCTAAACAGGAATCTTGAACTAGAT
1 TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
* *
7530 TTTGATGAA-ACACCTAAACATGG-ACCTTAAACAAGGA-
1 TTTGAT-AAGAAACCTAAACA-GGAATCTTAAACAA-GAT
* *
7567 TTTGATTAGAAACCTAAACAAGAAT
1 TTTGATAAGAAACCTAAACAGGAAT
7592 TTTGAATAAG
Statistics
Matches: 424, Mismatches: 61, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.01
36 17 0.04
37 380 0.90
38 21 0.05
39 3 0.01
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (37 bp):
TTTGATAAGAAACCTAAACAGGAATCTTAAACAAGAT
Found at i:7608 original size:74 final size:74
Alignment explanation
Indices: 7034--7591 Score: 909
Period size: 74 Copynumber: 7.5 Consensus size: 74
7024 CCTGAATAGA
* ** * *
7034 GACCTTAACCAACAATTTGATAACAAACCTAAACAAGAATCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7099 CTAAACAGG
66 CTAAACAGG
*
7108 GACCTTAAACAAGGATTTGACAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7173 CTAAACAGG
66 CTAAACAGG
*
7182 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAGTCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7247 CTAAACAGG
66 CTAAACAGG
*
7256 GACCTTAAACAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7321 CTAAACAGG
66 CTAAACAGG
*
7330 GACCTTAAACAAGGATTTGATAAGAAATCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7395 CTAAACAGG
66 CTAAACAGG
* * * *
7404 GATCTTAAACAAGAATTTGATAAGAAACCTAAACAGGAATCCTAAACAAGATTTTGATGAAACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
7469 CTAAACAGG
66 CTAAACAGG
* ** * * * *
7478 GACATCGAACAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACTAGATTTTGATGAAACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
*
7543 CTAAACATG
66 CTAAACAGG
* *
7552 GACCTTAAACAAGGATTTGATTAGAAACCTAAACAAGAAT
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAT
7592 TTTGAATAAG
Statistics
Matches: 451, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 451 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (74 bp):
GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
CTAAACAGG
Found at i:7790 original size:6 final size:6
Alignment explanation
Indices: 7781--7808 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7771 GTAAATGTTA
7781 ATGATT ATGATT ATGATT ATGATT ATGA
1 ATGATT ATGATT ATGATT ATGATT ATGA
7809 GATGCAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (6 bp):
ATGATT
Found at i:8671 original size:8 final size:8
Alignment explanation
Indices: 8658--8726 Score: 59
Period size: 8 Copynumber: 8.2 Consensus size: 8
8648 AACCTTTTGA
8658 TTTTTCTT
1 TTTTTCTT
8666 TTTTTCTT
1 TTTTTCTT
*
8674 TCTTTATTTCT
1 T-TTT-TCT-T
*
8685 TTTTTCTC
1 TTTTTCTT
8693 TTTTTCTT
1 TTTTTCTT
* *
8701 TGATTTCTC
1 T-TTTTCTT
8710 TTTTTCTT
1 TTTTTCTT
8718 TTTTT-TT
1 TTTTTCTT
8725 TT
1 TT
8727 AGATTGCTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
7 4 0.08
8 27 0.55
9 11 0.22
10 5 0.10
11 2 0.04
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:8694 original size:17 final size:15
Alignment explanation
Indices: 8658--8721 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
8648 AACCTTTTGA
8658 TTTT-TCTTTTT-TT
1 TTTTCTCTTTTTCTT
*
8671 CTTTCT-TTATTTCTT
1 TTTTCTCTT-TTTCTT
8686 TTTTCTCTTTTTCTT
1 TTTTCTCTTTTTCTT
8701 TGATTTCTCTTTTTCTT
1 T--TTTCTCTTTTTCTT
8718 TTTT
1 TTTT
8722 TTTTTAGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.12
14 4 0.09
15 17 0.40
16 2 0.05
17 15 0.35
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTCTTTTTCTT
Found at i:10834 original size:50 final size:50
Alignment explanation
Indices: 10759--10870 Score: 224
Period size: 50 Copynumber: 2.2 Consensus size: 50
10749 TACCTAAATT
10759 TGATTAACCATTCTAATGTTTCCTTAATGTTGAATTAAGTTCATTAATAA
1 TGATTAACCATTCTAATGTTTCCTTAATGTTGAATTAAGTTCATTAATAA
10809 TGATTAACCATTCTAATGTTTCCTTAATGTTGAATTAAGTTCATTAATAA
1 TGATTAACCATTCTAATGTTTCCTTAATGTTGAATTAAGTTCATTAATAA
10859 TGATTAACCATT
1 TGATTAACCATT
10871 AGTCTTCATC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (50 bp):
TGATTAACCATTCTAATGTTTCCTTAATGTTGAATTAAGTTCATTAATAA
Found at i:29548 original size:19 final size:21
Alignment explanation
Indices: 29524--29571 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
29514 TCGGCAGCAT
*
29524 CCATGTGGC-TGCTGGGC-GC
1 CCATGTGGCATGCTGGGCACC
*
29543 CCATGTGGCATGCTTGGCACC
1 CCATGTGGCATGCTGGGCACC
29564 CCATGTGG
1 CCATGTGG
29572 TTAGCCTCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 7 0.28
21 9 0.36
ACGTcount: A:0.10, C:0.31, G:0.35, T:0.23
Consensus pattern (21 bp):
CCATGTGGCATGCTGGGCACC
Found at i:30752 original size:42 final size:42
Alignment explanation
Indices: 30690--30787 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
30680 TGGCCAGTTG
* * *
30690 TGGCCGG-CTTGTGCCCGGTCTTGTGCGATGGT-C-CCATGCGA
1 TGGCCGGTCATGTGCCCGGTCTTGCGCG--GCTACTCCATGCGA
*
30731 TGGCCGGTCATGTGGCCGGTCTTGCGCGGCTACTCCATGCGA
1 TGGCCGGTCATGTGCCCGGTCTTGCGCGGCTACTCCATGCGA
30773 TGGCCGGTCATGTGC
1 TGGCCGGTCATGTGC
30788 GATGGCATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
40 2 0.04
41 8 0.16
42 39 0.80
ACGTcount: A:0.08, C:0.30, G:0.37, T:0.26
Consensus pattern (42 bp):
TGGCCGGTCATGTGCCCGGTCTTGCGCGGCTACTCCATGCGA
Found at i:36131 original size:19 final size:19
Alignment explanation
Indices: 36083--36132 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
36073 GAAGAGAAAT
*
36083 TATGTGATGGTATCTAAGG
1 TATGTGATGGTATATAAGG
*
36102 T-TGTGAAGGTATATGAA-G
1 TATGTGATGGTATAT-AAGG
36120 TATGTGATGGTAT
1 TATGTGATGGTAT
36133 GTGATTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.28, C:0.02, G:0.32, T:0.38
Consensus pattern (19 bp):
TATGTGATGGTATATAAGG
Found at i:37808 original size:13 final size:13
Alignment explanation
Indices: 37775--37800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37765 CAATATTTCT
37775 GCTAATCCATGCC
1 GCTAATCCATGCC
37788 GCTAATCCATGCC
1 GCTAATCCATGCC
37801 TCTTATCCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (13 bp):
GCTAATCCATGCC
Done.