Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009426.1 Corchorus capsularis cultivar CVL-1 contig09447, 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: 33431
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:848 original size:19 final size:18
Alignment explanation
Indices: 815--850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
805 TTGAAATAAT
815 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
833 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
851 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:1515 original size:33 final size:33
Alignment explanation
Indices: 1464--1540 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
1454 AAGGATCAAA
*
1464 TGGCCGGTCTTGTGCGCCAAGCGATGGCCGGTTG
1 TGGCCGGT-TGGTGCGCCAAGCGATGGCCGGTTG
1498 TGGCCGGTTGGTGCGCCAAGCGATGGCCGGTTG
1 TGGCCGGTTGGTGCGCCAAGCGATGGCCGGTTG
1531 TGGCCGGTTG
1 TGGCCGGTTG
1541 TCCCATGCGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 34 0.81
34 8 0.19
ACGTcount: A:0.08, C:0.25, G:0.44, T:0.23
Consensus pattern (33 bp):
TGGCCGGTTGGTGCGCCAAGCGATGGCCGGTTG
Found at i:6686 original size:5 final size:5
Alignment explanation
Indices: 6676--6701 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6666 TGGTCGAAAT
6676 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
6702 AGTTTTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:7790 original size:12 final size:12
Alignment explanation
Indices: 7770--7807 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
7760 TGTGGCCGGT
*
7770 TGCTCCATGCGA
1 TGCTGCATGCGA
7782 TGCTGCATGCGA
1 TGCTGCATGCGA
7794 TGCTGCATGCGA
1 TGCTGCATGCGA
7806 TG
1 TG
7808 GCCGGTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (12 bp):
TGCTGCATGCGA
Found at i:15522 original size:35 final size:34
Alignment explanation
Indices: 15483--16081 Score: 669
Period size: 35 Copynumber: 17.7 Consensus size: 34
15473 CAGTAATAAG
*
15483 TAACTTAATTCAGGGCAATTAAGTAAGTCAGTGAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AA
* *
15518 TAACTTAATTCAAGGTAATTAAGTAAATCAG---
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * * *
15549 CAACTTAATTCAGGGTAATTAGGTAAGT-AATAGG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTA-A
* **
15583 TAACTTAATTCAGGGTAATTAAGTCAGT---TTG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
15614 TAGCTTAATTCAGGGTAATTAAGTGAAGTCAGCTAG
1 TAACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAA
* * *
15650 TAACTTAGTTCAGGGAAATTAAGTAAGGCAG---
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
15681 TAACTTAATTCAGGGTAATTAAGTAATTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
15715 TAAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
15750 TCAAATTAATTCAGGGTAATTAAGTAAGTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
15785 TCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
15820 TCAACTTAATTCAGGGTAATTAAGTAAGT---TAG
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
15852 TAGCTTACTTCAGGGTAATTAAGTAAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAA
*
15888 TAACTTAATTCAGGGTAATTAAGTAATTCA--ACA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTA-A
*
15921 TCAACTTAATTCAGGGTAATTAAGTAATTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
15956 TCAACTTAATTCAGGGTAATTAAGTAATTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
15991 TCAACTTAATTCAGGGTAATTAAGTGAGTCAG---
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
16023 CAACTTAATTCAGGGTAATTAAGT-AGTTCAATAA
1 TAACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA
*
16057 GTAACTTAGTTCAGGGTAATTAAGT
1 -TAACTTAATTCAGGGTAATTAAGT
16082 TTAGTAAGAA
Statistics
Matches: 497, Mismatches: 40, Indels: 54
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.01
31 122 0.25
32 12 0.02
33 1 0.00
34 55 0.11
35 255 0.51
36 49 0.10
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (34 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
Found at i:15866 original size:171 final size:170
Alignment explanation
Indices: 15484--16081 Score: 750
Period size: 171 Copynumber: 3.5 Consensus size: 170
15474 AGTAATAAGT
* * *
15484 AACTTAATTCAGGGCAATTAAGTAAGTCAGTGAATAACTTAATTCAAGGTAATTAAGTAAATCAG
1 AACTTAATTCAGGGTAATTAAGTAAGTCA--G--TAACTTAATTCAGGGTAATTAAGTAATTCAG
* * * ** *
15549 ---CAACTTAATTCAGGGTAATTAGGTAAGTAATAGGT-AACTTAATTCAGGGTAATTAAGTCAG
62 TAATAACTTAATTCAGGGTAATTAAGTAAGTCATACATCAACTTAATTCAGGGTAATTAAGTAAG
** * *
15610 T---TTGT-AGCTTAATTCAGGGTAATTAAGTGAAGTCAGCTAGT-
127 TCAGTAATCAACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAATC
* * *
15651 AACTTAGTTCAGGGAAATTAAGTAAGGCAGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
*
15716 AAACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATCAAATTAATTCAGGGTAATTAAGTAAGTC
66 -AACTTAATTCAGGGTAATTAAGTAAGTCA-TACATCAACTTAATTCAGGGTAATTAAGTAAGTC
15780 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
129 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
15822 AACTTAATTCAGGGTAATTAAGTAAGTTAGTAGCTTACTTCAGGGTAATTAAGTAAAGTCAGTTA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGT-AATTCAG-TA
* * *
15887 GTAACTTAATTCAGGGTAATTAAGTAATTCA-ACATCAACTTAATTCAGGGTAATTAAGTAATTC
64 ATAACTTAATTCAGGGTAATTAAGTAAGTCATACATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
15951 AGTAATCAACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
129 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
15993 AACTTAATTCAGGGTAATTAAGTGAGTCAGCAACTTAATTCAGGGTAATTAAGTAGTTCAATAAG
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAA-
*
16058 TAACTTAGTTCAGGGTAATTAAGT
65 TAACTTAATTCAGGGTAATTAAGT
16082 TTAGTAAGAA
Statistics
Matches: 379, Mismatches: 37, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
163 29 0.08
165 1 0.00
167 54 0.14
168 27 0.07
169 2 0.01
170 31 0.08
171 176 0.46
172 56 0.15
173 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (170 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
AACTTAATTCAGGGTAATTAAGTAAGTCATACATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:17890 original size:27 final size:27
Alignment explanation
Indices: 17856--17907 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17846 ACTCACCTTG
* **
17856 TCCTACTCCTTTACATTACCAAATTGT
1 TCCTACTCCTTAACAACACCAAATTGT
17883 TCCTACTCCTTAACAACACCAAATT
1 TCCTACTCCTTAACAACACCAAATT
17908 ACATCAACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.35
Consensus pattern (27 bp):
TCCTACTCCTTAACAACACCAAATTGT
Found at i:18336 original size:20 final size:21
Alignment explanation
Indices: 18311--18358 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18301 TAAAATTATC
* * *
18311 AATTAAAAAGAAAG-CAATTA
1 AATTAAAAACAAAGTAAAGTA
18331 AATTAAAAACAAAGTAAAGTA
1 AATTAAAAACAAAGTAAAGTA
18352 AATTAAA
1 AATTAAA
18359 TCTAAATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (21 bp):
AATTAAAAACAAAGTAAAGTA
Found at i:19401 original size:32 final size:32
Alignment explanation
Indices: 19317--19401 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 32
19307 GGAATTTTCT
19317 GGATTTCTGCAGAAACTTCACCAGCAGATTTG
1 GGATTTCTGCAGAAACTTCACCAGCAGATTTG
** * *
19349 GTCTTGACCT-AAGAAACTTCACCAGCAGATTTG
1 GGATT--TCTGCAGAAACTTCACCAGCAGATTTG
19382 GGATTTCTGCAGAAACTTCA
1 GGATTTCTGCAGAAACTTCA
19402 ATTTTCTGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.05
32 13 0.31
33 25 0.60
34 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (32 bp):
GGATTTCTGCAGAAACTTCACCAGCAGATTTG
Found at i:21213 original size:19 final size:19
Alignment explanation
Indices: 21168--21215 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
21158 AGTATATAGT
*
21168 AGGTGAGCATGGCCTCACC
1 AGGTGAGTATGGCCTCACC
21187 AGGTGAGTATGGCCTCACC
1 AGGTGAGTATGGCCTCACC
21206 AGGTGAGTAT
1 AGGTGAGTAT
21216 TTTATTGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (19 bp):
AGGTGAGTATGGCCTCACC
Found at i:21358 original size:89 final size:89
Alignment explanation
Indices: 21203--21485 Score: 417
Period size: 89 Copynumber: 3.2 Consensus size: 89
21193 GTATGGCCTC
* *
21203 ACCAGGTGAGTATTTTATTGGGAGAGTGTGGGTGAGTATTCTCACCAAGTGAGTATCTCACCAAG
1 ACCAGGTGAGTATTGTATTGGGTGAGTGTGGGTGAGTA-TCTCACCAAGTGAGTATCTCACCAAG
*
21268 TGAGTATTACACCAGGTGAGTATTT
65 TGAGTATTACACCAAGTGAGTATTT
* * *
21293 ACTAGGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATCTCATCAAGT
1 ACCAGGTGAGTATTGTATTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATCTCACCAAGT
*
21358 GAGTACTACACCAAGTGAGTATTT
66 GAGTATTACACCAAGTGAGTATTT
* *
21382 ACCAGGTGAGTATTGTATTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTAT-TGCACCAGG
1 ACCAGGTGAGTATTGTATTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATCT-CACCAAG
*
21446 TGAGTATT-TACCAAGTGAGTATTTGT
65 TGAGTATTACACCAAGTGAGTA-TT-T
*
21472 ACCGGGTGAGTATT
1 ACCAGGTGAGTATT
21486 TACCAGGTGA
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
88 13 0.07
89 114 0.65
90 48 0.27
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (89 bp):
ACCAGGTGAGTATTGTATTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATCTCACCAAGT
GAGTATTACACCAAGTGAGTATTT
Found at i:21390 original size:73 final size:73
Alignment explanation
Indices: 21251--21392 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 73
21241 TTCTCACCAA
* ** * * **
21251 GTGAGTATCTCACCAAGTGAGTATTACACCAGGTGAGTATTTACTAGGTGAGTATTGTACTGGGT
1 GTGAGTATCTCACCAAGTGAGTATTACACCAAGTGAGTATACACCAAGTGAGTATTGTACCAGGT
21316 GAGTGTGG
66 GAGTGTGG
*
21324 GTGAGTATCTCACCAAGTGAGTATCT-CATCAAGTGAGTACTACACCAAGTGAGTATT-TACCAG
1 GTGAGTATCTCACCAAGTGAGTAT-TACACCAAGTGAGTA-TACACCAAGTGAGTATTGTACCAG
21387 GTGAGT
64 GTGAGT
21393 ATTGTATTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
73 45 0.76
74 14 0.24
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (73 bp):
GTGAGTATCTCACCAAGTGAGTATTACACCAAGTGAGTATACACCAAGTGAGTATTGTACCAGGT
GAGTGTGG
Found at i:21417 original size:73 final size:74
Alignment explanation
Indices: 21340--21482 Score: 207
Period size: 73 Copynumber: 1.9 Consensus size: 74
21330 ATCTCACCAA
* * **
21340 GTGAGTATCTCATCAAGTGAGTACTACACCAAGTGAGTATTTACCAGGTGAGTA-TTGTATTGGG
1 GTGAGTATCTCACCAAGTGAGTACTACACCAAGTGAGTATTTACCAAGTGAGTATTTGTACCGGG
21404 TGAGTGTGG
66 TGAGTGTGG
* * * *
21413 GTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAGTATTTACCAAGTGAGTATTTGTACCGGG
1 GTGAGTATCTCACCAAGTGAGTACTACACCAAGTGAGTATTTACCAAGTGAGTATTTGTACCGGG
21478 TGAGT
66 TGAGT
21483 ATTTACCAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
73 48 0.79
74 13 0.21
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (74 bp):
GTGAGTATCTCACCAAGTGAGTACTACACCAAGTGAGTATTTACCAAGTGAGTATTTGTACCGGG
TGAGTGTGG
Found at i:21432 original size:105 final size:106
Alignment explanation
Indices: 21323--21514 Score: 273
Period size: 105 Copynumber: 1.8 Consensus size: 106
21313 GGTGAGTGTG
*
21323 GGTGAGTATCT-CACCAAGTGAGTATCTCATCAAGTGAGTA-CTACACCAAGTGAGTATTTACCA
1 GGTGAGTAT-TGCACCAAGTGAGTAT-TCACCAAGTGAGTATCTACACCAAGTGAGTATTTACCA
21386 GGTGAGTA-TTGTATTGGGTGAGTGTGGGTGAGTATCTCACCA
64 GGTGAGTATTTGTATTGGGTGAGTGTGGGTGAGTATCTCACCA
* * * ** **
21428 GGTGAGTATTGCACCAGGTGAGTATTTACCAAGTGAGTATTTGTACCGGGTGAGTATTTACCAGG
1 GGTGAGTATTGCACCAAGTGAGTATTCACCAAGTGAGTATCTACACCAAGTGAGTATTTACCAGG
21493 TGAGTATTTGTATTGGGTGAGT
66 TGAGTATTTGTATTGGGTGAGT
21515 AGGGTAGGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
104 13 0.17
105 48 0.63
106 15 0.20
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (106 bp):
GGTGAGTATTGCACCAAGTGAGTATTCACCAAGTGAGTATCTACACCAAGTGAGTATTTACCAGG
TGAGTATTTGTATTGGGTGAGTGTGGGTGAGTATCTCACCA
Found at i:21463 original size:15 final size:15
Alignment explanation
Indices: 21233--21501 Score: 117
Period size: 16 Copynumber: 17.7 Consensus size: 15
21223 GGAGAGTGTG
21233 GGTGAGTATTCTCACCA
1 GGTGAGTATT-T-ACCA
* *
21250 AGTGAGTATCTCACCA
1 GGTGAGTAT-TTACCA
* *
21266 AGTGAGTATTACACCA
1 GGTGAGTATT-TACCA
*
21282 GGTGAGTATTTACTA
1 GGTGAGTATTTACCA
**
21297 GGTGAGTATTGTACTG
1 GGTGAGTATT-TACCA
* *
21313 GGTGAG--TGT---G
1 GGTGAGTATTTACCA
*
21323 GGTGAGTATCTCACCA
1 GGTGAGTAT-TTACCA
* * *
21339 AGTGAGTATCTCATCA
1 GGTGAGTAT-TTACCA
* **
21355 AGTGAGTACTACACCA
1 GGTGAGTA-TTTACCA
*
21371 AGTGAGTATTTACCA
1 GGTGAGTATTTACCA
***
21386 GGTGAGTATTGTATTG
1 GGTGAGTATT-TACCA
* *
21402 GGTGAG--TGT---G
1 GGTGAGTATTTACCA
*
21412 GGTGAGTATCTCACCA
1 GGTGAGTAT-TTACCA
*
21428 GGTGAGTATTGCACCA
1 GGTGAGTATT-TACCA
21444 GGTGAGTATTTACCA
1 GGTGAGTATTTACCA
* *
21459 AGTGAGTATTTGTACCG
1 GGTGAGTA-TT-TACCA
21476 GGTGAGTATTTACCA
1 GGTGAGTATTTACCA
21491 GGTGAGTATTT
1 GGTGAGTATTT
21502 GTATTGGGTG
Statistics
Matches: 203, Mismatches: 29, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
10 14 0.07
12 2 0.01
13 2 0.01
14 2 0.01
15 55 0.27
16 107 0.53
17 20 0.10
18 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (15 bp):
GGTGAGTATTTACCA
Found at i:21464 original size:57 final size:57
Alignment explanation
Indices: 21356--21465 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
21346 ATCTCATCAA
* ****
21356 GTGAGTACTACACCAAGTGAGTATTTACCAGGTGAGTATTGTATTGGGTGAGTGTGG
1 GTGAGTACTACACCAAGTGAGTATTCACCAGGTGAGTATTGTACCAAGTGAGTGTGG
*
21413 GTGAGTATCT-CACCAGGTGAGTATTGCACCAGGTGAGTATT-TACCAAGTGAGT
1 GTGAGTA-CTACACCAAGTGAGTATT-CACCAGGTGAGTATTGTACCAAGTGAGT
21466 ATTTGTACCG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 29 0.64
58 16 0.36
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (57 bp):
GTGAGTACTACACCAAGTGAGTATTCACCAGGTGAGTATTGTACCAAGTGAGTGTGG
Found at i:21480 original size:17 final size:16
Alignment explanation
Indices: 21424--21500 Score: 104
Period size: 15 Copynumber: 4.9 Consensus size: 16
21414 TGAGTATCTC
*
21424 ACCAGGTGAGTATTGC
1 ACCAGGTGAGTATTGT
21440 ACCAGGTGAGTATT-T
1 ACCAGGTGAGTATTGT
*
21455 ACCAAGTGAGTATTTGT
1 ACCAGGTGAGTA-TTGT
*
21472 ACCGGGTGAGTATT-T
1 ACCAGGTGAGTATTGT
21487 ACCAGGTGAGTATT
1 ACCAGGTGAGTATT
21501 TGTATTGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
15 25 0.46
16 18 0.33
17 11 0.20
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (16 bp):
ACCAGGTGAGTATTGT
Found at i:21480 original size:32 final size:32
Alignment explanation
Indices: 21411--21515 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 32
21401 GGGTGAGTGT
* *
21411 GGGTGAGTATCTCACCAGGTGAGTA-TTGCACC
1 GGGTGAGTAT-TTACCAGGTGAGTATTTGTACC
* *
21443 AGGTGAGTATTTACCAAGTGAGTATTTGTACC
1 GGGTGAGTATTTACCAGGTGAGTATTTGTACC
**
21475 GGGTGAGTATTTACCAGGTGAGTATTTGTATT
1 GGGTGAGTATTTACCAGGTGAGTATTTGTACC
21507 GGGTGAGTA
1 GGGTGAGTA
21516 GGGTAGGAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.19
32 52 0.81
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.32
Consensus pattern (32 bp):
GGGTGAGTATTTACCAGGTGAGTATTTGTACC
Found at i:21513 original size:17 final size:17
Alignment explanation
Indices: 21428--21515 Score: 78
Period size: 15 Copynumber: 5.5 Consensus size: 17
21418 TATCTCACCA
* *
21428 GGTGAGTA-TTGCACCA
1 GGTGAGTATTTGTACCG
*
21444 GGTGAGTA-TT-TACCA
1 GGTGAGTATTTGTACCG
*
21459 AGTGAGTATTTGTACCG
1 GGTGAGTATTTGTACCG
*
21476 GGTGAGTA-TT-TACCA
1 GGTGAGTATTTGTACCG
**
21491 GGTGAGTATTTGTATTG
1 GGTGAGTATTTGTACCG
21508 GGTGAGTA
1 GGTGAGTA
21516 GGGTAGGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
15 23 0.38
16 16 0.27
17 21 0.35
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (17 bp):
GGTGAGTATTTGTACCG
Found at i:22403 original size:21 final size:19
Alignment explanation
Indices: 22371--22409 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
22361 CAATCAAGCA
22371 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
22390 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
22410 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:24260 original size:90 final size:90
Alignment explanation
Indices: 24107--24276 Score: 340
Period size: 90 Copynumber: 1.9 Consensus size: 90
24097 GAGATTGGCG
24107 CTAGTGGGGATGGAACATCAGGCAATTCCATCTTTTGAGCATACCACTGTTGAGTTTCTTCAATT
1 CTAGTGGGGATGGAACATCAGGCAATTCCATCTTTTGAGCATACCACTGTTGAGTTTCTTCAATT
24172 GCATTGATTCCATATCCTTGTGTGT
66 GCATTGATTCCATATCCTTGTGTGT
24197 CTAGTGGGGATGGAACATCAGGCAATTCCATCTTTTGAGCATACCACTGTTGAGTTTCTTCAATT
1 CTAGTGGGGATGGAACATCAGGCAATTCCATCTTTTGAGCATACCACTGTTGAGTTTCTTCAATT
24262 GCATTGATTCCATAT
66 GCATTGATTCCATAT
24277 ACTCGTGACT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (90 bp):
CTAGTGGGGATGGAACATCAGGCAATTCCATCTTTTGAGCATACCACTGTTGAGTTTCTTCAATT
GCATTGATTCCATATCCTTGTGTGT
Found at i:25507 original size:20 final size:21
Alignment explanation
Indices: 25482--25529 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
25472 TAAAATTATC
* *
25482 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
25502 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
25523 AATTAAA
1 AATTAAA
25530 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:31778 original size:13 final size:14
Alignment explanation
Indices: 31760--31793 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31750 GATTGATAAT
31760 TTTGTTAAT-ATTA
1 TTTGTTAATAATTA
31773 TTTGTTAATAATTA
1 TTTGTTAATAATTA
31787 -TTGTTAA
1 TTTGTTAA
31794 CATAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
TTTGTTAATAATTA
Found at i:33073 original size:106 final size:106
Alignment explanation
Indices: 32888--33101 Score: 320
Period size: 106 Copynumber: 2.0 Consensus size: 106
32878 AATCGAACAC
* * *
32888 AAACCTAAATCGCCAAAAATCCAAGAGCTAATCTTAAACCCAAATCAGTTCGAACCAAAGCTTCA
1 AAACCCAAATCGCCAAAAACCCAAGAGCTAACCTTAAACCCAAATCAGTTCGAACCAAAGCTTCA
* ** *
32953 ATCATAATCAAATCTTTTTGATTGGTGAAAGGAAGGGAGGG
66 ATCATAATCAAATCTTTTCGATCAGTGAAAGGAAGAGAGGG
* * * *
32994 AAACCCAAATCGCTAGAAACCCAAGAGCTAACCTTAAACCCAAATCAGTTTGAATCAAAGCTTCA
1 AAACCCAAATCGCCAAAAACCCAAGAGCTAACCTTAAACCCAAATCAGTTCGAACCAAAGCTTCA
*
33059 ATCATAATCAAATCTTTTCGATCATTGAAAGGAAGAGAGGG
66 ATCATAATCAAATCTTTTCGATCAGTGAAAGGAAGAGAGGG
33100 AA
1 AA
33102 GTTTAAGTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.22
Consensus pattern (106 bp):
AAACCCAAATCGCCAAAAACCCAAGAGCTAACCTTAAACCCAAATCAGTTCGAACCAAAGCTTCA
ATCATAATCAAATCTTTTCGATCAGTGAAAGGAAGAGAGGG
Done.