Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010442.1 Corchorus capsularis cultivar CVL-1 contig10463, 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: 67498
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:159 original size:30 final size:31
Alignment explanation
Indices: 124--184 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
114 TGACAATTTA
*
124 GAAATATGCTTTT-AAAA-AAGGGTACAATTG
1 GAAATATG-TTTTAAAAATAAGGATACAATTG
154 GAAATATGTTTTAAAAATAAGGATACAATTG
1 GAAATATGTTTTAAAAATAAGGATACAATTG
185 AAAAACATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 12 0.43
31 12 0.43
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGATACAATTG
Found at i:2216 original size:64 final size:64
Alignment explanation
Indices: 2110--2242 Score: 212
Period size: 64 Copynumber: 2.1 Consensus size: 64
2100 CGGTTGCTAG
* *
2110 TTAATCCAACAATGGATTTATACAAATGAGTTAGACATTTTATAAAACACTTGAAAGGCAAGAA
1 TTAAGCCAACAATGGATTTACACAAATGAGTTAGACATTTTATAAAACACTTGAAAGGCAAGAA
* * * *
2174 TTAAGCCAACAATGGATTTACACAGATGAGTTAGGCATTTTATCAAACACTTGAAAGGTAAGAA
1 TTAAGCCAACAATGGATTTACACAAATGAGTTAGACATTTTATAAAACACTTGAAAGGCAAGAA
2238 TTAAG
1 TTAAG
2243 ATAGATATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (64 bp):
TTAAGCCAACAATGGATTTACACAAATGAGTTAGACATTTTATAAAACACTTGAAAGGCAAGAA
Found at i:5523 original size:27 final size:27
Alignment explanation
Indices: 5492--5543 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
5482 ATGATTTATA
5492 AAATTAATTAT-TCATGTTA-TATATTAC
1 AAATTAA-TATGTCAT-TTATTATATTAC
5519 AAATTAATATGTCATTTATTATATT
1 AAATTAATATGTCATTTATTATATT
5544 TATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (27 bp):
AAATTAATATGTCATTTATTATATTAC
Found at i:8121 original size:2 final size:2
Alignment explanation
Indices: 8114--8138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8104 GTAGTTAGGA
8114 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8139 ATGTGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8319 original size:60 final size:59
Alignment explanation
Indices: 8211--8344 Score: 180
Period size: 60 Copynumber: 2.3 Consensus size: 59
8201 AACGTTTGTC
* *
8211 AAAATGCTCAAATAAGGACCCGATCTTTAATTTGGTCGAATAAGGGCCTAACATTATAAA
1 AAAATGCTCAAATAAGGACCCGATCTTTAATTTGGCCAAATAAGGGCCTAACATTAT-AA
* * * * *
8271 AAAATGCTCAAATAAGGACTCGGTCTTTTGATTTGGCCAAATAA-GGCCTAACGTTATCA
1 AAAATGCTCAAATAAGGACCCGATC-TTTAATTTGGCCAAATAAGGGCCTAACATTATAA
8330 AAAATGCTCAAATAA
1 AAAATGCTCAAATAA
8345 AGGTCTGACG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 16 0.24
60 35 0.53
61 15 0.23
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (59 bp):
AAAATGCTCAAATAAGGACCCGATCTTTAATTTGGCCAAATAAGGGCCTAACATTATAA
Found at i:8489 original size:60 final size:59
Alignment explanation
Indices: 8389--8552 Score: 222
Period size: 60 Copynumber: 2.7 Consensus size: 59
8379 TTTCGACGTT
*
8389 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGTACTTATTTGGCCAAATTAAAAGATT
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTA-GTACTTATTTGGCCAAATTAAAAGATC
* * * *
8449 GGGCCCTTATTTGAGCTTTTTGGCAAACGTTA-TACCCTTATTTGGTCAAATTAAAAGATC
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGTA--CTTATTTGGCCAAATTAAAAGATC
* *
8509 AGACCCTTATTTGAGCATTTTGACAAACGTTAGTCCTTTATTTG
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGTAC-TTATTTG
8553 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 86 0.96
61 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (59 bp):
AGACCCTTATTTGAGCATTTTGGCAAACGTTAGTACTTATTTGGCCAAATTAAAAGATC
Found at i:9442 original size:21 final size:21
Alignment explanation
Indices: 9418--9457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9408 TCTCACTCTC
*
9418 TCTTTCTTTTTCTTTTTTTGT
1 TCTTTCTGTTTCTTTTTTTGT
*
9439 TCTTTCTGTTTGTTTTTTT
1 TCTTTCTGTTTCTTTTTTT
9458 ATGTCTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (21 bp):
TCTTTCTGTTTCTTTTTTTGT
Found at i:14636 original size:16 final size:16
Alignment explanation
Indices: 14615--14648 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
14605 ACAATTCAGA
14615 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
14631 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
14647 AA
1 AA
14649 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:17223 original size:31 final size:31
Alignment explanation
Indices: 17183--17258 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
17173 CTCAACAAAC
** *
17183 GATCAATTTAGTCCCTGTATTCACAAGATTAG
1 GATCAATTTAGTCCCTACACTCACAAGATT-G
*
17215 G-TCAATTTAGTCCTTACACTCACAAGATTG
1 GATCAATTTAGTCCCTACACTCACAAGATTG
*
17245 GATCAATTGAGTCC
1 GATCAATTTAGTCC
17259 AACTGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 35 0.92
32 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (31 bp):
GATCAATTTAGTCCCTACACTCACAAGATTG
Found at i:25021 original size:21 final size:23
Alignment explanation
Indices: 24973--25041 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 23
24963 TAAATTGCCA
*
24973 TTACTTAAACTATTATAATTTTATT
1 TTACTTAAACT-CTAT-ATTTTATT
24998 TTACTTAAACTCTAT-TTTTA-T
1 TTACTTAAACTCTATATTTTATT
*
25019 TTAGTTAAA-TCTAATATCTTTAT
1 TTACTTAAACTCT-ATAT-TTTAT
25042 AATTACTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 3 0.08
21 11 0.29
22 6 0.16
23 4 0.11
24 3 0.08
25 11 0.29
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.55
Consensus pattern (23 bp):
TTACTTAAACTCTATATTTTATT
Found at i:25502 original size:150 final size:149
Alignment explanation
Indices: 25053--25494 Score: 737
Period size: 148 Copynumber: 3.0 Consensus size: 149
25043 ATTACTTTAA
* *
25053 TTTTATCATTTTATTATTTTTCATTAGAAACTTGGATATATTAAAATTTGTTAATATATAGTTTG
1 TTTTATCATTTTACTATTTTTCATTAAAAACTTGGATATATT-AAATTT-TTAATATATAGTTTG
*
25118 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTATATTTTTAC
64 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTAC
*
25183 CATTTTAATTTAAAAGTTTAT
129 CATTTTAATTTAAAAGATTAT
*
25204 TTTTATCA--TTACT-GTTTTCATTAAAAACTTGGATATATTAAATTTTTTAAATATATAGTTTG
1 TTTTATCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAA-TTTTT-AATATATAGTTTG
25266 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTAC
64 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTAC
*
25331 CATTTGAATTTAAAAGATTAT
129 CATTTTAATTTAAAAGATTAT
*
25352 TTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAACATTTTTAATATATAGTTTGA
1 TTTTATCATTTTACTATTTTTCATTAAAAACTTGGATATATTAA-ATTTTTAATATATAGTTTGA
* *
25417 TTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATTTTTACC
65 TTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACC
25482 ATTTTAATTTAAA
130 ATTTTAATTTAAA
25495 TGGTTATTGT
Statistics
Matches: 274, Mismatches: 11, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
147 5 0.02
148 130 0.47
149 4 0.01
150 94 0.34
151 40 0.15
152 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (149 bp):
TTTTATCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAATTTTTAATATATAGTTTGAT
TCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCA
TTTTAATTTAAAAGATTAT
Found at i:25964 original size:20 final size:20
Alignment explanation
Indices: 25926--25963 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25916 TGGTTCAGAT
*
25926 GATTTCAGGTTTGAGTTTTG
1 GATTTCAGGTTCGAGTTTTG
*
25946 GATTTCGGGTTCGA-TTTT
1 GATTTCAGGTTCGAGTTTT
25964 TTTCGGATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.13, C:0.08, G:0.29, T:0.50
Consensus pattern (20 bp):
GATTTCAGGTTCGAGTTTTG
Found at i:26279 original size:2 final size:2
Alignment explanation
Indices: 26272--26310 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26262 TAATAACTAG
*
26272 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26311 GGATAATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:26315 original size:10 final size:10
Alignment explanation
Indices: 26273--26319 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
26263 AATAACTAGT
*
26273 ATATATATAT
1 ATATATATAG
*
26283 ATATATATAT
1 ATATATATAG
26293 ATATATATAG
1 ATATATATAG
*
26303 ATATATATGG
1 ATATATATAG
26313 ATA-ATAT
1 ATATATAT
26320 GGTTAATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
9 4 0.11
10 31 0.89
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (10 bp):
ATATATATAG
Found at i:31906 original size:33 final size:33
Alignment explanation
Indices: 31860--31928 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
31850 TGCATAGCCA
*
31860 CATACCTTCTTAGTTATGTTATATACAGAATTT
1 CATACCTTCTTAGTGATGTTATATACAGAATTT
* *
31893 CATACCTTTTTAGTGATGTTGTATACAGAATTT
1 CATACCTTCTTAGTGATGTTATATACAGAATTT
31926 CAT
1 CAT
31929 TTCCATCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (33 bp):
CATACCTTCTTAGTGATGTTATATACAGAATTT
Found at i:33803 original size:58 final size:58
Alignment explanation
Indices: 33733--33848 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
33723 CCTTTTCCCC
*
33733 TATAGTTTGATCTGTCAATTCACTCTGGCTCCTATTACGTCTTTACTCCACATAATCA
1 TATAGTTCGATCTGTCAATTCACTCTGGCTCCTATTACGTCTTTACTCCACATAATCA
*
33791 TATAGTTCGATCTGTCAATTCACTCTGGCTCCTATTACTTCTTTACTCCACATAATCA
1 TATAGTTCGATCTGTCAATTCACTCTGGCTCCTATTACGTCTTTACTCCACATAATCA
33849 GATAATCCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (58 bp):
TATAGTTCGATCTGTCAATTCACTCTGGCTCCTATTACGTCTTTACTCCACATAATCA
Found at i:36842 original size:53 final size:53
Alignment explanation
Indices: 36783--36886 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
36773 CAAGCAAATC
36783 CTAAATATTTGAATCTTAATAAAAAGATTGAGA-TTTCACCAACAAAATATATA
1 CTAAATATTTGAATCTTAATAAAAAGATTGA-ATTTTCACCAACAAAATATATA
*
36836 CTAAATATTTGAATCTTAATAAAAAGATTGAATTTTCACTAACAAAATATA
1 CTAAATATTTGAATCTTAATAAAAAGATTGAATTTTCACCAACAAAATATA
36887 CTATTGTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 1 0.02
53 48 0.98
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.34
Consensus pattern (53 bp):
CTAAATATTTGAATCTTAATAAAAAGATTGAATTTTCACCAACAAAATATATA
Found at i:37648 original size:23 final size:20
Alignment explanation
Indices: 37599--37650 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
37589 TTTCGTAAAG
37599 ATAA-TTTGTTACTTAAAAA
1 ATAATTTTGTTACTTAAAAA
*
37618 AAACATTTTCGTTACATTAAATAA
1 ATA-ATTTT-GTTAC-TTAAA-AA
37642 ATAATTTTG
1 ATAATTTTG
37651 GATACCGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 3 0.12
22 6 0.23
23 10 0.38
24 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (20 bp):
ATAATTTTGTTACTTAAAAA
Found at i:38213 original size:3 final size:3
Alignment explanation
Indices: 38205--38248 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
38195 ATATATATTG
*
38205 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
38249 TATTATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40933 original size:11 final size:11
Alignment explanation
Indices: 40917--40941 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40907 TCACTTTCAT
40917 GTGCATTGCAC
1 GTGCATTGCAC
40928 GTGCATTGCAC
1 GTGCATTGCAC
40939 GTG
1 GTG
40942 ACCCATCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (11 bp):
GTGCATTGCAC
Found at i:47351 original size:57 final size:57
Alignment explanation
Indices: 47263--47384 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
47253 TTTAAAGCAT
* * * *
47263 GTTTAGGAACAATTTTTTATCAAACAAGAATTCTGACCTAGTACAAATTACCTTCCA
1 GTTTAGGAACAATCTTTGATCAAACAAGAATTCCGACCTAGTACAAATTACCTTCAA
47320 GTTTAGGAACAATCTTTGATCAAACAAGAATTCCGACCTAGTACAAATTACCTTCAA
1 GTTTAGGAACAATCTTTGATCAAACAAGAATTCCGACCTAGTACAAATTACCTTCAA
*
47377 GTTAAGGA
1 GTTTAGGA
47385 CAGCTTGGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (57 bp):
GTTTAGGAACAATCTTTGATCAAACAAGAATTCCGACCTAGTACAAATTACCTTCAA
Found at i:49665 original size:16 final size:17
Alignment explanation
Indices: 49626--49667 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
49616 TACATGGGTA
49626 AATAATTTGATACACTG
1 AATAATTTGATACACTG
*
49643 TATAATTTGA-AGCACT-
1 AATAATTTGATA-CACTG
49659 AATAATTTG
1 AATAATTTG
49668 TCAACAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
AATAATTTGATACACTG
Found at i:53838 original size:3 final size:3
Alignment explanation
Indices: 53825--53875 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
53815 TTTATTTTTA
53825 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53871 -AT AAT
1 AAT AAT
53876 CATTTGATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:55941 original size:21 final size:21
Alignment explanation
Indices: 55916--55959 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55906 TATTAAGGAT
*
55916 AATATTACAAATTAAAT-AATA
1 AATATTA-AAAATAAATAAATA
55937 AATATTAAAAATAAATAAATA
1 AATATTAAAAATAAATAAATA
55958 AA
1 AA
55960 ACAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AATATTAAAAATAAATAAATA
Found at i:58451 original size:13 final size:14
Alignment explanation
Indices: 58433--58478 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
58423 TAACTATAGT
58433 ATTAAA-TCAAACA
1 ATTAAAGTCAAACA
*
58446 ATTAAAGT-AAAAA
1 ATTAAAGTCAAACA
**
58459 AAAAAAGTCAAACA
1 ATTAAAGTCAAACA
58473 ATTAAA
1 ATTAAA
58479 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (14 bp):
ATTAAAGTCAAACA
Found at i:59497 original size:31 final size:31
Alignment explanation
Indices: 59455--59525 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
59445 GTTTAATATC
* *
59455 CAAATTAGCCCC-TTAACTATCTATTTTGGGA
1 CAAATTGGCCCCATTAA-TATCTATTTTGGAA
* * *
59486 CAAATTGGCCCCATTAATTTTTTTTTTGGAA
1 CAAATTGGCCCCATTAATATCTATTTTGGAA
59517 CAAATTGGC
1 CAAATTGGC
59526 GTCTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (31 bp):
CAAATTGGCCCCATTAATATCTATTTTGGAA
Found at i:63019 original size:121 final size:120
Alignment explanation
Indices: 62863--63276 Score: 444
Period size: 121 Copynumber: 3.5 Consensus size: 120
62853 CTATTGTAGA
*
62863 TTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCTTTATAATTTCTTTATTTT
1 TTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATCTAATAT-TTTATAATTTCTTTATTTT
62928 TATCATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAAT
65 TA-CATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAAT
* * *
62985 TTTATTCTA-TTAAAACTCTATTTTCATTTAATTAAATTTAATATTTTATAATTAT-TTTATTTT
1 TTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATCTAATATTTTATAATT-TCTTTATTTT
* * * * *
63048 TACCATTTT-C-A--TTT-AA-AAGATTATTGTGAT-TGACTT---ATTTCT-ATTTGA-TAG
65 TA-CATTTTACTATTTTTCAATAA-A-AATTG-GATAT-A-TTAAAATTTTTAATAT-ACAAT
* * * *
63099 TTTAGTGTACTATTAAAGCTCTATTTTTATTCAATTAAATCTAATATCTTTATAATTTCTTTATT
1 TTTATTCTACTA--AAAACTCTATTTTCATTCAATTAAATCTAATAT-TTTATAATTTCTTTATT
* *
63164 TTTACTATTTTACTATTTTTCAATAAAAATTGGATATATTAAAGTTTTTAATATACAGT
63 TTTAC-ATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAAT
*
63223 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATAATT
1 TTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATCT-AATATTTTATAATT
63277 ATTTTTTTAC
Statistics
Matches: 237, Mismatches: 29, Indels: 53
0.74 0.09 0.17
Matches are distributed among these distances:
114 13 0.05
115 10 0.04
116 8 0.03
117 35 0.15
118 27 0.11
119 2 0.01
120 28 0.12
121 46 0.19
122 45 0.19
123 8 0.03
124 15 0.06
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (120 bp):
TTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATCTAATATTTTATAATTTCTTTATTTTT
ACATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAAT
Found at i:63138 original size:117 final size:117
Alignment explanation
Indices: 62991--63343 Score: 327
Period size: 122 Copynumber: 3.0 Consensus size: 117
62981 CAATTTTATT
62991 CTATTAAAACTCTATTTTCATTTAATTAAATTTAATATTTTATAATTATTTTATTTTTACCATTT
1 CTATTAAAACTCTATTTTCATTTAATTAAATTTAATATTTTATAATTATTTTATTTTTACCATTT
*
63056 TCATTTAAAAGATTATTGTGATTGACTTATTTCTATTTGATAGTTTAGTGTA
66 TCATTTAAAAGATTATTGTGATTGACTTATTTCTATTTGATAGTTTAATGTA
* * * * *
63108 CTATTAAAGCTCTATTTTTATTCAATTAAATCTAATATCTTTATAATT-TCTTTATTTTTACTAT
1 CTATTAAAACTCTATTTTCATTTAATTAAATTTAATAT-TTTATAATTAT-TTTATTTTTACCAT
* * * * *
63172 TTTACTATTTTTCAATAA-A-AATTG-GATAT-A-TTAAAGTTTTTAATAT-ACAGTTTTAT-T-
64 TTT-C-A--TTT-AA-AAGATTATTGTGAT-TGACTT--A-TTTCT-ATTTGATAGTTTAATGTA
* *
63229 CTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATAATTA--TT-TTTTTACCATT
1 CTA-TTAAAACTCTATTTTCATTTAATTAAATTTAATATTTTATAATTATTTTATTTTTACCATT
* * * *
63291 TTAATTTAAAATG-TTATTGTGATTGACCTGTTTCTATTTGATAATTTAATGTA
65 TTCATTTAAAA-GATTATTGTGATTGACTTATTTCTATTTGATAGTTTAATGTA
63344 TTATGATTAA
Statistics
Matches: 185, Mismatches: 27, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
112 5 0.03
113 13 0.07
114 9 0.05
115 4 0.02
116 2 0.01
117 35 0.19
118 37 0.20
119 3 0.02
120 3 0.02
121 16 0.09
122 39 0.21
123 14 0.08
124 5 0.03
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.53
Consensus pattern (117 bp):
CTATTAAAACTCTATTTTCATTTAATTAAATTTAATATTTTATAATTATTTTATTTTTACCATTT
TCATTTAAAAGATTATTGTGATTGACTTATTTCTATTTGATAGTTTAATGTA
Done.