Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016709.1 Corchorus olitorius cultivar O-4 contig16742, 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: 203331
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5815 original size:15 final size:16
Alignment explanation
Indices: 5782--5815 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5772 TTTGTTTGTT
5782 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
5798 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
5813 TTG
1 TTG
5816 ATTTATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:12455 original size:2 final size:2
Alignment explanation
Indices: 12448--12473 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12438 GTAAGGATGA
12448 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12474 CAGCACATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16021 original size:2 final size:2
Alignment explanation
Indices: 16014--16043 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16004 CTTGATGGCA
16014 AT 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 AT
16044 TTATCAGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46773 original size:3 final size:3
Alignment explanation
Indices: 46765--46807 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
46755 ACTCATCAAA
46765 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
46808 GCTGCCATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49260 original size:29 final size:29
Alignment explanation
Indices: 49216--49273 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
49206 TGAAGATTCT
49216 GGCGATTGATGACATTGGTTCATGGATGA
1 GGCGATTGATGACATTGGTTCATGGATGA
*
49245 GGCGATTGATGGCATTGGTTCATGGATGA
1 GGCGATTGATGACATTGGTTCATGGATGA
49274 TGAAGAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.36, T:0.31
Consensus pattern (29 bp):
GGCGATTGATGACATTGGTTCATGGATGA
Found at i:52933 original size:22 final size:21
Alignment explanation
Indices: 52896--52937 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
52886 ATTCTATCAT
*
52896 TATATTACTTTATTATTATTA
1 TATATTACATTATTATTATTA
52917 TATATATACATTATTATTATT
1 TATAT-TACATTATTATTATT
52938 GCTATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTACATTATTATTATTA
Found at i:57272 original size:37 final size:37
Alignment explanation
Indices: 57231--57321 Score: 173
Period size: 37 Copynumber: 2.5 Consensus size: 37
57221 GAATTCCGGC
57231 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
1 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
57268 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
1 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
*
57305 CACCCCAAGTTAGGGTG
1 CACCCCATGTTAGGGTG
57322 ATGACGACGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (37 bp):
CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
Found at i:57334 original size:37 final size:37
Alignment explanation
Indices: 57231--57336 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
57221 GAATTCCGGC
* * **
57231 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
1 CACCCCAAGTTAGGGTGATGCTGACGAAAATTTTGAT
* * **
57268 CACCCCATGTTAGGGTGGTGCTGTTGAAAATTTTGAT
1 CACCCCAAGTTAGGGTGATGCTGACGAAAATTTTGAT
57305 CACCCCAAGTTAGGGTGATGAC-GACGAAAATT
1 CACCCCAAGTTAGGGTGATG-CTGACGAAAATT
57337 AAGGGCCACC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
37 63 0.98
38 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (37 bp):
CACCCCAAGTTAGGGTGATGCTGACGAAAATTTTGAT
Found at i:58021 original size:23 final size:22
Alignment explanation
Indices: 57955--58023 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
57945 AATCCTATCT
*
57955 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
* * *
57977 TTTACAAGTTGTGATCAACCTTGTCA
1 TTTAC---TTTTCATCACCCTTGT-A
58003 TTTACTTTTCATCACCCTTGT
1 TTTACTTTTCATCACCCTTGT
58024 TGTTACAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
22 5 0.14
23 13 0.36
25 13 0.36
26 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.48
Consensus pattern (22 bp):
TTTACTTTTCATCACCCTTGTA
Found at i:59252 original size:17 final size:17
Alignment explanation
Indices: 59230--59265 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
59220 ATTCATAAAC
59230 ATAACAATATGTCACAT
1 ATAACAATATGTCACAT
59247 ATAACAATATGTCACAT
1 ATAACAATATGTCACAT
59264 AT
1 AT
59266 CCATACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
ATAACAATATGTCACAT
Found at i:59349 original size:42 final size:42
Alignment explanation
Indices: 59288--59442 Score: 234
Period size: 42 Copynumber: 3.8 Consensus size: 42
59278 GCAGGTCTAG
59288 ATTCTAAA-T-TGTGCTTCTTTTGTTATTTTTTTTTTCATAA
1 ATTCTAAATTATGTGCTTCTTTTGTTATTTTTTTTTTCATAA
*
59328 ATTGTAAATTATGTGCTTCTTTTGTTA-TTTTTTTTTCATAAA
1 ATTCTAAATTATGTGCTTCTTTTGTTATTTTTTTTTTCAT-AA
59370 ATTCTAAATTATGTGCTTCTTTTGTT-TTTTTTTTTTCATAA
1 ATTCTAAATTATGTGCTTCTTTTGTTATTTTTTTTTTCATAA
*
59411 ATTCTAAATTA--TG-TTCTTTTGTTATATTTTTT
1 ATTCTAAATTATGTGCTTCTTTTGTTATTTTTTTT
59443 CATAATTGTC
Statistics
Matches: 107, Mismatches: 3, Indels: 11
0.88 0.02 0.09
Matches are distributed among these distances:
38 10 0.09
39 9 0.08
40 7 0.07
41 26 0.24
42 55 0.51
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (42 bp):
ATTCTAAATTATGTGCTTCTTTTGTTATTTTTTTTTTCATAA
Found at i:59419 original size:83 final size:78
Alignment explanation
Indices: 59288--59447 Score: 241
Period size: 83 Copynumber: 2.0 Consensus size: 78
59278 GCAGGTCTAG
*
59288 ATTCTAAATTGTGCTTCTTTTGTTATTTTTTTTTTCATAAATTGTAAATTATGTGCTTCTTTTGT
1 ATTCTAAATTGTGCTTCTTTTGTTATTTTTTTTTTCATAAATTCTAAATTA--TG-TTCTTTTGT
*
59353 TATTTTTTTTTCATAAA
63 TA-TATTTTTTCATAAA
59370 ATTCTAAATTATGTGCTTCTTTTGTT-TTTTTTTTTTCATAAATTCTAAATTATGTTCTTTTGTT
1 ATTCTAAA-T-TGTGCTTCTTTTGTTATTTTTTTTTTCATAAATTCTAAATTATGTTCTTTTGTT
59434 ATATTTTTTCATAA
64 ATATTTTTTCATAA
59448 TTGTCTAAGT
Statistics
Matches: 74, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
79 12 0.16
80 11 0.15
81 2 0.03
82 8 0.11
83 26 0.35
84 15 0.20
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (78 bp):
ATTCTAAATTGTGCTTCTTTTGTTATTTTTTTTTTCATAAATTCTAAATTATGTTCTTTTGTTAT
ATTTTTTCATAAA
Found at i:60704 original size:32 final size:32
Alignment explanation
Indices: 60668--60732 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
60658 AAAGTATTAA
60668 TCTAGGGAATAGTGGACAGTGGAAATTAGAAT
1 TCTAGGGAATAGTGGACAGTGGAAATTAGAAT
60700 TCTAGGGAATAGTGGACAGTGGAAATTAGAAT
1 TCTAGGGAATAGTGGACAGTGGAAATTAGAAT
60732 T
1 T
60733 TGATGAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.26
Consensus pattern (32 bp):
TCTAGGGAATAGTGGACAGTGGAAATTAGAAT
Found at i:60836 original size:31 final size:31
Alignment explanation
Indices: 60801--60860 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
60791 AGAAATCAGT
60801 AGTGGAGGCAAAAGATCGGATGAGGATATGA
1 AGTGGAGGCAAAAGATCGGATGAGGATATGA
* *
60832 AGTGGAGTCAAAATATCGGATGAGGATAT
1 AGTGGAGGCAAAAGATCGGATGAGGATAT
60861 TGGAAGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (31 bp):
AGTGGAGGCAAAAGATCGGATGAGGATATGA
Found at i:64206 original size:70 final size:70
Alignment explanation
Indices: 64132--64343 Score: 424
Period size: 70 Copynumber: 3.0 Consensus size: 70
64122 TAATTTATGT
64132 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
1 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
64197 TTTCA
66 TTTCA
64202 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
1 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
64267 TTTCA
66 TTTCA
64272 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
1 CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
64337 TTTCA
66 TTTCA
64342 CA
1 CA
64344 GACAATATGG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 142 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.23
Consensus pattern (70 bp):
CACAAACTCCAAATCCAAACCCAAGAGGCTTCTCTCGTCCTGCCTTATACAGTCAAATGCAGAAG
TTTCA
Found at i:64378 original size:37 final size:37
Alignment explanation
Indices: 64328--64402 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
64318 ATACAGTCAA
64328 ATGCAGAAGTTTCACAGACAATATGGACAAAAAGAAG
1 ATGCAGAAGTTTCACAGACAATATGGACAAAAAGAAG
64365 ATGCAGAAGTTTCACAGACAATATGGACAAAAAGAAG
1 ATGCAGAAGTTTCACAGACAATATGGACAAAAAGAAG
64402 A
1 A
64403 GAGACAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.16
Consensus pattern (37 bp):
ATGCAGAAGTTTCACAGACAATATGGACAAAAAGAAG
Found at i:66380 original size:21 final size:21
Alignment explanation
Indices: 66355--66399 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
66345 GATAACCAGA
* *
66355 AAACCCACCAGCACCAGCACC
1 AAACCCACCAGAACCACCACC
* *
66376 AAACCCCCCATAACCACCACC
1 AAACCCACCAGAACCACCACC
66397 AAA
1 AAA
66400 ATCTGCAGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.51, G:0.04, T:0.02
Consensus pattern (21 bp):
AAACCCACCAGAACCACCACC
Found at i:66502 original size:9 final size:9
Alignment explanation
Indices: 66478--66529 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
66468 ACGGAGCAGG
66478 ACCAAAACC
1 ACCAAAACC
66487 ACC---ACC
1 ACCAAAACC
66493 ACCAAAACC
1 ACCAAAACC
* *
66502 ACCATAATC
1 ACCAAAACC
*
66511 ACCAAATCC
1 ACCAAAACC
66520 ACCAAAACC
1 ACCAAAACC
66529 A
1 A
66530 TCATTACCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 6 0.18
9 28 0.82
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (9 bp):
ACCAAAACC
Found at i:69872 original size:42 final size:43
Alignment explanation
Indices: 69821--69914 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
69811 AGAGCATTAC
**
69821 CTAA-ATTCTA-CACCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCACCATCTCTAAATAATTCATCAAAATAAAG
* * *
69862 CTAATATTCTACTCCTCCATCTCTAAATAATTTATCAAAGTAAAG
1 CTAATATTCTA--CCACCATCTCTAAATAATTCATCAAAATAAAG
69907 CTAATATT
1 CTAATATT
69915 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCACCATCTCTAAATAATTCATCAAAATAAAG
Found at i:79693 original size:14 final size:13
Alignment explanation
Indices: 79660--79731 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 13
79650 AACCGTTTAA
79660 TAATTATATATAT
1 TAATTATATATAT
*
79673 T-ATTATATAT-G
1 TAATTATATATAT
79684 TAATTATATATAT
1 TAATTATATATAT
*
79697 T--TAATAT-TA-
1 TAATTATATATAT
79706 TAA-TATATAT-T
1 TAATTATATATAT
*
79717 TAATTATAAATAT
1 TAATTATATATAT
79730 TA
1 TA
79732 CTAAACGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
9 1 0.02
10 6 0.13
11 10 0.22
12 24 0.52
13 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:79721 original size:33 final size:31
Alignment explanation
Indices: 79669--79730 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
79659 ATAATTATAT
*
79669 ATATTATTATATATGTAATTATATATATTTA
1 ATATTATTATATATGTAATTATAAATATTTA
*
79700 ATATTATAATATATATTTAATTATAAATATT
1 ATATTAT--TATATATGTAATTATAAATATT
79731 ACTAAACGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 7 0.26
33 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATTATTATATATGTAATTATAAATATTTA
Found at i:80090 original size:10 final size:11
Alignment explanation
Indices: 80075--80106 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
80065 GATCATAAAT
80075 TCATATATA-A
1 TCATATATATA
80085 TCATATATATA
1 TCATATATATA
80096 T-ATATATATA
1 TCATATATATA
80106 T
1 T
80107 ATCATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.90
11 2 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
TCATATATATA
Found at i:80518 original size:16 final size:15
Alignment explanation
Indices: 80483--80520 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
80473 AAACTCTTCT
80483 GAAAAAGTGCTTTTG
1 GAAAAAGTGCTTTTG
80498 GAAAAAGTGCTTTTG
1 GAAAAAGTGCTTTTG
80513 GAAAAAGT
1 GAAAAAGT
80521 TTCAATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (15 bp):
GAAAAAGTGCTTTTG
Found at i:80737 original size:3 final size:3
Alignment explanation
Indices: 80729--80807 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
80719 ACTCAGATCT
80729 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
80777 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
80808 CATCATTTAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:82356 original size:29 final size:30
Alignment explanation
Indices: 82324--82395 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
82314 ACTTGTAGTG
* * *
82324 TTTGGACGTTTTGTCTCATGAACT-TTAAT
1 TTTGGACGTTTTGTCCCATAAACTATCAAT
* *
82353 TTTGGACATTTTATCCCATAAACTATCAAT
1 TTTGGACGTTTTGTCCCATAAACTATCAAT
82383 TTTGGACGTTTTG
1 TTTGGACGTTTTG
82396 CCCCCTTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (30 bp):
TTTGGACGTTTTGTCCCATAAACTATCAAT
Found at i:89822 original size:23 final size:22
Alignment explanation
Indices: 89771--89823 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
89761 CGTTCAATGA
* *
89771 ATATTTTTAATAAATATTTTAT
1 ATATTTTTAATAAATAATATAT
*
89793 -TACTTTTTATTTAAATAATATAT
1 ATA-TTTTTA-ATAAATAATATAT
89816 ATATTTTT
1 ATATTTTT
89824 CTAACTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.08
22 6 0.24
23 15 0.60
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTAATAAATAATATAT
Found at i:95954 original size:12 final size:14
Alignment explanation
Indices: 95932--95963 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
95922 TAATTATTAT
95932 GAAAAAGAAAAA-G
1 GAAAAAGAAAAAGG
95945 GAAAAA-AAAAAGG
1 GAAAAAGAAAAAGG
95958 GAAAAA
1 GAAAAA
95964 TAATCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAGG
Found at i:99574 original size:23 final size:23
Alignment explanation
Indices: 99548--99593 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
99538 TTTATCTGAG
99548 ATAGAGATACTCTACTAATTAAA
1 ATAGAGATACTCTACTAATTAAA
99571 ATAGAGATACTCTACTAATTAAA
1 ATAGAGATACTCTACTAATTAAA
99594 GTTGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
ATAGAGATACTCTACTAATTAAA
Found at i:100025 original size:16 final size:16
Alignment explanation
Indices: 100004--100038 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
99994 AATTTTGAAA
*
100004 TAAAATTAAATTTATT
1 TAAAATTAAATTCATT
100020 TAAAATTAAATTCATT
1 TAAAATTAAATTCATT
100036 TAA
1 TAA
100039 TTTAACCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATTAAATTCATT
Found at i:101406 original size:18 final size:18
Alignment explanation
Indices: 101383--101417 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
101373 TCCAAAAGAT
101383 TCTGCCCC-ACATTGACGG
1 TCTGCCCCTA-ATTGACGG
101401 TCTGCCCCTAATTGACG
1 TCTGCCCCTAATTGACG
101418 CGAATTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.17, C:0.37, G:0.20, T:0.26
Consensus pattern (18 bp):
TCTGCCCCTAATTGACGG
Found at i:104278 original size:19 final size:19
Alignment explanation
Indices: 104258--104294 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
104248 AATTAATTAT
104258 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
104276 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
104295 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:104777 original size:19 final size:19
Alignment explanation
Indices: 104749--104788 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
104739 CCAACACAAA
104749 AAATGCATTGTTTTTAGCC
1 AAATGCATTGTTTTTAGCC
*
104768 AAATGGATTGTTTTTAGCC
1 AAATGCATTGTTTTTAGCC
104787 AA
1 AA
104789 TTTGGCTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (19 bp):
AAATGCATTGTTTTTAGCC
Found at i:119803 original size:11 final size:12
Alignment explanation
Indices: 119783--119808 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
119773 CTTAGAGTTT
119783 AAAAGAAAAAAA
1 AAAAGAAAAAAA
119795 AAAAGAAAAAAA
1 AAAAGAAAAAAA
119807 AA
1 AA
119809 GGAATCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:130632 original size:26 final size:26
Alignment explanation
Indices: 130582--130632 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
130572 TGAGCGCAAC
* * *
130582 TTTTATTTGAGACAGTTTGATTTTTT
1 TTTTATTTGAGACAATTTAACTTTTT
130608 TTTTATTTGAGACAATTTAACTTTT
1 TTTTATTTGAGACAATTTAACTTTT
130633 AAACTTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (26 bp):
TTTTATTTGAGACAATTTAACTTTTT
Found at i:138124 original size:34 final size:28
Alignment explanation
Indices: 138064--138117 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
138054 TCATGAATTT
138064 ATAAGACTATAATCATTCTTTTTGAAAA
1 ATAAGACTATAATCATTCTTTTTGAAAA
*
138092 ATAAGACTATAATCATTCTATTTGAA
1 ATAAGACTATAATCATTCTTTTTGAA
138118 CATGAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
ATAAGACTATAATCATTCTTTTTGAAAA
Found at i:140255 original size:22 final size:23
Alignment explanation
Indices: 140227--140275 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
140217 CCGTGCTTAT
140227 TTTCTC-TCAGGCCCTGCGCCAC
1 TTTCTCTTCAGGCCCTGCGCCAC
140249 TTTCTCTTATCAGGCCCTGCGCCAC
1 TTTCTC-T-TCAGGCCCTGCGCCAC
140274 TT
1 TT
140276 CTTGCAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 6 0.25
25 18 0.75
ACGTcount: A:0.10, C:0.41, G:0.16, T:0.33
Consensus pattern (23 bp):
TTTCTCTTCAGGCCCTGCGCCAC
Found at i:152294 original size:25 final size:25
Alignment explanation
Indices: 152265--152357 Score: 152
Period size: 25 Copynumber: 3.7 Consensus size: 25
152255 TATTTTTCTC
152265 TCAGGCCCTGCGCCACTTTCTTCTCA
1 TCAGGCCCTGCGCCACTTTCTT-TCA
*
152291 -CAGGCCCTGCGCCACTTTCTTTTA
1 TCAGGCCCTGCGCCACTTTCTTTCA
*
152315 TCAGGCCCTGCGCCACTTTCTTTTA
1 TCAGGCCCTGCGCCACTTTCTTTCA
152340 TCAGGCCCTGCGCCACTT
1 TCAGGCCCTGCGCCACTT
152358 CCTGCAGTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
24 2 0.03
25 63 0.97
ACGTcount: A:0.12, C:0.40, G:0.17, T:0.31
Consensus pattern (25 bp):
TCAGGCCCTGCGCCACTTTCTTTCA
Found at i:159254 original size:125 final size:125
Alignment explanation
Indices: 159032--159283 Score: 486
Period size: 125 Copynumber: 2.0 Consensus size: 125
159022 ACCCATAGTG
159032 TAGAAATCTTTATTTCTGAATGGATTGTATATAAATAAATATATCCACAGATGCAGACACAATAA
1 TAGAAATCTTTATTTCTGAATGGATTGTATATAAATAAATATATCCACAGATGCAGACACAATAA
159097 TGCAAATCCAATATTCCTTTCTGAGTGTGGAAACAAATTCCTTCAAAAATAAAACTTGAA
66 TGCAAATCCAATATTCCTTTCTGAGTGTGGAAACAAATTCCTTCAAAAATAAAACTTGAA
159157 TAGAAATCTTTATTTCTGAATGGATTGTATATAAATAAATATATCCACAGATGCAGACACAATAA
1 TAGAAATCTTTATTTCTGAATGGATTGTATATAAATAAATATATCCACAGATGCAGACACAATAA
**
159222 TGCAAATCCAATATTCCTTTCTGAGTGTGGAAACAAATTCCTTCAAAAATGTAACTTGAA
66 TGCAAATCCAATATTCCTTTCTGAGTGTGGAAACAAATTCCTTCAAAAATAAAACTTGAA
159282 TA
1 TA
159284 AAGTAAGAAC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (125 bp):
TAGAAATCTTTATTTCTGAATGGATTGTATATAAATAAATATATCCACAGATGCAGACACAATAA
TGCAAATCCAATATTCCTTTCTGAGTGTGGAAACAAATTCCTTCAAAAATAAAACTTGAA
Found at i:160493 original size:272 final size:274
Alignment explanation
Indices: 160001--160528 Score: 873
Period size: 272 Copynumber: 1.9 Consensus size: 274
159991 AGAAACTTAA
* * * *
160001 AATTTTTGGGTTGGAATCATGGGATGATTCTTTACAGTGCGACTTATAAGGCAGAGAAAACAAGC
1 AATTCTTGGGTTGAAATCATGGAATGATTCTTAACAGTGCGACTTATAAGGCAGAGAAAACAAGC
160066 ATGAAATGTTCCAAGTACACTAAATTGCTGTAAACGAATGATTGATCCATGTATAAGTTATGAGA
66 ATGAAATGTTCCAAGTACACTAAATTGCTGTAAACGAATGATTGATCCATGTATAAGTTATGAGA
* *
160131 AGAAAGTTAATCAAATTAATGATGAAGATGACGCTAAAGATCAAGTACTAGTACATTTGCAAACT
131 AAAAAGTTAATCAAATTAACGATGAAGATGACGCTAAAGATCAAGTACTAGTACATTTGCAAACT
* *
160196 AGGGGAATCCCATCACCCAATAATAGCTACAAAATCATTTCTCTC-AGAGTAATTACAGTCTGAA
196 AGGGGAAGCCCATCACCCAATAATAGCTACAAAATCAATTCTCTCAAGAGTAATTACAGTCTGAA
160260 ATGAAGACACAATC
261 ATGAAGACACAATC
160274 AATTCTTGGGTTGAAATCATGGAATGATTCTTAACAGTGCGACTTATAAGGCAGAGAAAACAAGC
1 AATTCTTGGGTTGAAATCATGGAATGATTCTTAACAGTGCGACTTATAAGGCAGAGAAAACAAGC
* * *
160339 ATGAAATG-TCCAAGTACACTAATTTGCTGTTAACGAAT-AGTTGATCCATGTATAATTTATGAG
66 ATGAAATGTTCCAAGTACACTAAATTGCTGTAAACGAATGA-TTGATCCATGTATAAGTTATGAG
* * *
160402 AAAAAAGTTAATCTATTTAACGATGAAGATGACGCTAAAGATCAAGTACTAGTATATTTGCAAAC
130 AAAAAAGTTAATCAAATTAACGATGAAGATGACGCTAAAGATCAAGTACTAGTACATTTGCAAAC
* *
160467 TATGGGCAGCCCATCACCCAATAATAGCTACAAAATCAATTCTCTCAGAGAGTAATTACAGT
195 TAGGGGAAGCCCATCACCCAATAATAGCTACAAAATCAATTCTCTCA-AGAGTAATTACAGT
160529 ACAGTCTGAA
Statistics
Matches: 236, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
271 1 0.00
272 152 0.64
273 69 0.29
274 14 0.06
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (274 bp):
AATTCTTGGGTTGAAATCATGGAATGATTCTTAACAGTGCGACTTATAAGGCAGAGAAAACAAGC
ATGAAATGTTCCAAGTACACTAAATTGCTGTAAACGAATGATTGATCCATGTATAAGTTATGAGA
AAAAAGTTAATCAAATTAACGATGAAGATGACGCTAAAGATCAAGTACTAGTACATTTGCAAACT
AGGGGAAGCCCATCACCCAATAATAGCTACAAAATCAATTCTCTCAAGAGTAATTACAGTCTGAA
ATGAAGACACAATC
Found at i:163828 original size:11 final size:12
Alignment explanation
Indices: 163802--163827 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
163792 AGCTTTTTTG
163802 TTTGCTCTGTTT
1 TTTGCTCTGTTT
163814 TTTGCTCTGTTT
1 TTTGCTCTGTTT
163826 TT
1 TT
163828 GAGAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (12 bp):
TTTGCTCTGTTT
Found at i:166721 original size:6 final size:6
Alignment explanation
Indices: 166710--166744 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
166700 CCCAACCAAC
166710 CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG CTGAA
1 CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG CTGAA
166745 AGAGAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
CTGAAG
Found at i:173891 original size:27 final size:27
Alignment explanation
Indices: 173861--173926 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
173851 CTTCTAAACT
173861 GGGACTCTGAGCTTGCTTCTTCTTAGA
1 GGGACTCTGAGCTTGCTTCTTCTTAGA
*
173888 GGGACTCTGAGCTTGCTTCTTCTTCGA
1 GGGACTCTGAGCTTGCTTCTTCTTAGA
173915 -GGAGCTCTGAGC
1 GGGA-CTCTGAGC
173927 AATTATTGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.14, C:0.24, G:0.29, T:0.33
Consensus pattern (27 bp):
GGGACTCTGAGCTTGCTTCTTCTTAGA
Found at i:178280 original size:3 final size:3
Alignment explanation
Indices: 178274--178304 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
178264 TTTCAGTCGG
178274 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
178305 CTAGCAAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:179658 original size:12 final size:12
Alignment explanation
Indices: 179641--179703 Score: 99
Period size: 12 Copynumber: 5.2 Consensus size: 12
179631 CAGAGGCAGG
179641 ACTCTTTCCTCA
1 ACTCTTTCCTCA
*
179653 ACTCTTTCTTCA
1 ACTCTTTCCTCA
*
179665 ACTCTTTCATCA
1 ACTCTTTCCTCA
179677 ACTCTTTCCTCA
1 ACTCTTTCCTCA
*
179689 ACTCTTTCTTCA
1 ACTCTTTCCTCA
179701 ACT
1 ACT
179704 GGATCTAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (12 bp):
ACTCTTTCCTCA
Found at i:179879 original size:33 final size:33
Alignment explanation
Indices: 179834--179897 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
179824 ACTTCTGCAG
* *
179834 CACTTTCTTCTACATTTTCCACAACATTTTCAA
1 CACTTTCATCTACATCTTCCACAACATTTTCAA
179867 CACTTTCATCTACATCTTCCACAACATTTTC
1 CACTTTCATCTACATCTTCCACAACATTTTC
179898 TTCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.41
Consensus pattern (33 bp):
CACTTTCATCTACATCTTCCACAACATTTTCAA
Found at i:187172 original size:17 final size:19
Alignment explanation
Indices: 187152--187195 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
187142 GAACCGAAAG
187152 AAAGAGAGAA-GAAAG-GA
1 AAAGAGAGAAGGAAAGTGA
187169 AAAG-GAAGAAGGAAAGTGA
1 AAAGAG-AGAAGGAAAGTGA
187188 AAAGAGAG
1 AAAGAGAG
187196 GTCACTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 8 0.35
18 5 0.22
19 8 0.35
20 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.02
Consensus pattern (19 bp):
AAAGAGAGAAGGAAAGTGA
Found at i:194828 original size:11 final size:11
Alignment explanation
Indices: 194813--194855 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
194803 TTTTTCAGTT
194813 TTTTTGTTTTTG
1 TTTTTG-TTTTG
*
194825 TTTTTTGTTTCG
1 -TTTTTGTTTTG
*
194837 TTTTCGTTTTG
1 TTTTTGTTTTG
194848 TTTTTGTT
1 TTTTTGTT
194856 ACGCTGTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 16 0.62
12 4 0.15
13 6 0.23
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:194868 original size:23 final size:23
Alignment explanation
Indices: 194820--194869 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
194810 GTTTTTTTGT
* * *
194820 TTTTGTTTTTTGTTTCGTTTTCG
1 TTTTGTTTTTTGTTACGCTGTCG
194843 TTTTG-TTTTTGTTACGCTGTCGG
1 TTTTGTTTTTTGTTACGCTGTC-G
194866 TTTT
1 TTTT
194870 TTGAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.02, C:0.10, G:0.20, T:0.68
Consensus pattern (23 bp):
TTTTGTTTTTTGTTACGCTGTCG
Found at i:196798 original size:54 final size:56
Alignment explanation
Indices: 196695--196824 Score: 183
Period size: 54 Copynumber: 2.4 Consensus size: 56
196685 CATCCCTAAA
* * * * *
196695 TTTGGGGTTTGATCATACGTGTACAATGATATTTTTTTGTGGTTTGACTATCAAAT
1 TTTGGGGTTTGACCATGCATGTACAATGATATGTTTTTGTGGTTTGACTATCAAAC
* *
196751 TTTGGGGTTTGACCATGCATGTATAATG-T-TGTTTTTGTGGTTTGACTATTAAAC
1 TTTGGGGTTTGACCATGCATGTACAATGATATGTTTTTGTGGTTTGACTATCAAAC
196805 TTTGGGGTTTGACCATGCAT
1 TTTGGGGTTTGACCATGCAT
196825 ATACTATCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 42 0.63
55 1 0.01
56 24 0.36
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (56 bp):
TTTGGGGTTTGACCATGCATGTACAATGATATGTTTTTGTGGTTTGACTATCAAAC
Done.