Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007581.1 Hibiscus syriacus cultivar Beakdansim tig00021641_pilon, 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: 101734
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3636 original size:81 final size:80
Alignment explanation
Indices: 3313--3636 Score: 339
Period size: 81 Copynumber: 4.0 Consensus size: 80
3303 TTATAATTCC
* * * * *
3313 TTTAGTCTTTTACCCAAAGG-CATTTAACCTTTCATCTAACTTGCATGATTGACACTTGTCTGCC
1 TTTA-TCTTTTACTCAAAGGTC-TTTAACCGTTCATCTAACTGGCATAATTGACACTT-TCTGTC
* * *
3377 AAAGGCACCGCTAGGCTA
63 AAATGCACAGCTAGGCCA
* * **
3395 TTTATCTTTTACTTAATGGTCTTTAACCGTTCATCTAACTGAAATAATTGACACCTTTCTGTCAA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAA
*
3460 ATGCAC-GACTAGGACA
65 ATGCACAG-CTAGGCCA
* * * * * * * * *
3476 TTTATCTTTTACTCAACGGTCGTTAATCGTTCATCTAAATTGCATAACTAACATATTTCTTTCAA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAA
*
3541 ATGCACAACTAGGCCA
65 ATGCACAGCTAGGCCA
*
3557 TTTATCTTTTACTCAAAGGTCTTTAACCATTCATCTAACTGGCATAATAT-ACAGCTTTCTGTCA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAAT-TGACA-CTTTCTGTCA
3621 AATGCACAGCTAGGCC
64 AATGCACAGCTAGGCC
3637 TCAAAGGCAC
Statistics
Matches: 199, Mismatches: 38, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 189 0.95
82 9 0.05
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (80 bp):
TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACTTTCTGTCAAA
TGCACAGCTAGGCCA
Found at i:3658 original size:68 final size:68
Alignment explanation
Indices: 3586--4045 Score: 742
Period size: 68 Copynumber: 6.8 Consensus size: 68
3576 TCTTTAACCA
* *
3586 TTCATCTAACTGGCATAATAT-ACAGCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAT-TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
3650 GCCT
65 GCCT
* * *
3654 TTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGAACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3719 CCT
66 CCT
* * *
3722 TTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATACATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3787 CCT
66 CCT
* * * * *
3790 TTCATCTAACTGGCATAATTGACATCTTTCTTTCAAATACACAGTTAAGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3855 CCT
66 CCT
*
3858 TTCATCTAACTGGCATAATTGACACCTTTCTGTTAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3923 CCT
66 CCT
*
3926 TTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3991 CCT
66 CCT
** *
3994 TTCATCTAACTGGCATAATTGACACCTTTCCATCAAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
4046 ATTAATCTTT
Statistics
Matches: 362, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
67 1 0.00
68 361 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:4362 original size:55 final size:55
Alignment explanation
Indices: 4255--4460 Score: 263
Period size: 55 Copynumber: 3.7 Consensus size: 55
4245 CACTACGAAA
* * * *
4255 ATACACTTAGTATGGATTTCTTA-ATTTGCACACATAGTACCCATA-CGAAAATTC
1 ATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCG-AAATTC
* *
4309 ATACACATAGTATAAATTTCTTAGTTTTACACACATAGTGCCCATACCGAAATTC
1 ATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCGAAATTC
* * * * *
4364 ATACACTTAGTATTAACTTCTTAGTTTTGCACACATAGTGTCCGTACCGAAATTC
1 ATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCGAAATTC
*
4419 ATACACTTAGTATGAATTTCTTAAGGTTTTACACACTTAGTG
1 ATACACTTAGTATGAATTTCTT-A-GTTTTACACACATAGTG
4461 TCATTTGGTA
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
54 20 0.15
55 94 0.71
56 3 0.02
57 15 0.11
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (55 bp):
ATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCGAAATTC
Found at i:9027 original size:81 final size:81
Alignment explanation
Indices: 8909--9089 Score: 215
Period size: 81 Copynumber: 2.2 Consensus size: 81
8899 TTATAATTCC
* * * * * *
8909 TTTAGTCTTTTACCCAAAGGCATTTAACCTTTCATCTAACT-AGCATGATTGACA-CTTGTTTGC
1 TTTA-TCTTTTACTCAACGGCATTTAACCGTTCATCTAACTGA-AATAATTGACACCTT-TCTGC
**
8972 CAAATACACTTCTAGGCCA
63 CAAATACACAACTAGGCCA
*
8991 TTTATCTTTTACTCAACGGTC-TTTAACCGTTCATCTAACTGAAATAATTGACACCTTTCTGTCA
1 TTTATCTTTTACTCAACGG-CATTTAACCGTTCATCTAACTGAAATAATTGACACCTTTCTGCCA
*
9055 AATGCACAACTAGGCCA
65 AATACACAACTAGGCCA
9072 TTTATCTTTTACTCAACG
1 TTTATCTTTTACTCAACG
9090 ATCATCTAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
81 77 0.90
82 9 0.10
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGCATTTAACCGTTCATCTAACTGAAATAATTGACACCTTTCTGCCAA
ATACACAACTAGGCCA
Found at i:9138 original size:70 final size:70
Alignment explanation
Indices: 9021--9153 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 70
9011 CTTTAACCGT
* *
9021 TCATCTAACTGAAATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTTATCTTTTACTC
1 TCATCTAACTGAAATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTACTC
9086 AACGA
66 AACGA
* * *
9091 TCATCTAACT-AGCATAATTGGCACATTTCTATCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TCATCTAACTGA-AATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTAC
9154 ACAAAGTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 1 0.02
70 56 0.98
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (70 bp):
TCATCTAACTGAAATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTACTC
AACGA
Found at i:9265 original size:68 final size:68
Alignment explanation
Indices: 9171--9561 Score: 552
Period size: 68 Copynumber: 5.8 Consensus size: 68
9161 TCTTTAATCG
* ** *
9171 TTCATCTAATTGTTATAATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
9236 CCT
66 CCT
* * *
9239 TTCATCTAACTGGAATAGTTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
9304 TCT
66 CCT
* * *
9307 TTCATCTAACTGGCATAATTGACACCTTTCTGTAAAATGCACAAG-TAGGCCTCAAAGGAACATA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC-AGTTAGGCCTCAAAGGCACTTA
*
9371 ACCT
65 GCCT
* * * * *
9375 TTCATCTAACTAGCATAATTAACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAAGTACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
9440 CCT
66 CCT
* *
9443 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTGGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
9508 CCT
66 CCT
* ** *
9511 TTCATCTAACTGGC-TTATTGACACCTTTCCATCAAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
9562 ATTAATCTTT
Statistics
Matches: 285, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
67 33 0.12
68 250 0.88
69 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:17849 original size:51 final size:51
Alignment explanation
Indices: 17741--17933 Score: 253
Period size: 52 Copynumber: 3.7 Consensus size: 51
17731 TATATTATCT
* *
17741 ATGTGGGGCATCTTGAAGGCTCACATCAACAAGAAAAAGACAGAAGTAATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAAC-ATAAAAAGACAGAAGTAATCC
* *
17793 ATGTGAGGCATCTTGAAGGTTCACATCAGCATAAAAAGACAGAAGTAATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAACATAAAAAGACAGAAGTAATCC
* * * * *
17844 ATGTGAGGCATCTTTAAGGTTCACGTCAGCATGAAAAAGACAGATA-TTATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAACAT-AAAAAGACAGA-AGTAATCC
* *
17896 ATGTGGGGCATCTTGAAGGCTCACATCAACATGAAAAG
1 ATGTGAGGCATCTTGAAGGCTCACATCAACATAAAAAG
17934 GTTAAGATAT
Statistics
Matches: 126, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
51 55 0.44
52 70 0.56
53 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (51 bp):
ATGTGAGGCATCTTGAAGGCTCACATCAACATAAAAAGACAGAAGTAATCC
Found at i:17920 original size:103 final size:103
Alignment explanation
Indices: 17741--17933 Score: 271
Period size: 103 Copynumber: 1.9 Consensus size: 103
17731 TATATTATCT
*
17741 ATGTGGGGCATCTTGAAGGCTCACATCAACAAGAAAAAGACAGAAGTAATCCATGTGAGGCATCT
1 ATGTGAGGCATCTTGAAGGCTCACATCAACAAGAAAAAGACAGAAGTAATCCATGTGAGGCATCT
* *
17806 TGAAGGTTCACATCAGCATAAAAAGACAGAAGTAATCC
66 TGAAGGCTCACATCAACATAAAAAGACAGAAGTAATCC
* * * * * * *
17844 ATGTGAGGCATCTTTAAGGTTCACGTCAGCATGAAAAAGACAGATA-TTATCCATGTGGGGCATC
1 ATGTGAGGCATCTTGAAGGCTCACATCAACAAGAAAAAGACAGA-AGTAATCCATGTGAGGCATC
*
17908 TTGAAGGCTCACATCAACATGAAAAG
65 TTGAAGGCTCACATCAACATAAAAAG
17934 GTTAAGATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 77 0.99
104 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (103 bp):
ATGTGAGGCATCTTGAAGGCTCACATCAACAAGAAAAAGACAGAAGTAATCCATGTGAGGCATCT
TGAAGGCTCACATCAACATAAAAAGACAGAAGTAATCC
Found at i:19931 original size:129 final size:130
Alignment explanation
Indices: 19690--20039 Score: 336
Period size: 129 Copynumber: 2.7 Consensus size: 130
19680 TGACCTGATT
*
19690 TCCTCATCACATAGGAACCGTGTCACCTCTTTGATAACCAACCGTCCTCATCACATAGGAACCGT
1 TCCTCATCACATAGGAACCGTGTCAACTCTTTGATAACCAACCGTCCTCATCACATAGGAACCGT
* * * **
19755 GTTATCATCGTATGATGGCCAGAACTCTTCATCATGTATGAGTCGTGTCATCACCCGACTAGATC
66 GTTATCATCGTATGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCCGACTAGATC
** ** ** *
19820 TCCTCATCATGTAGGAATTGTGTCAAC-CTTTGATAACCTGCCGTCCTCATCACGTAGGAACCGT
1 TCCTCATCACATAGGAACCGTGTCAACTCTTTGATAACCAACCGTCCTCATCACATAGGAACCGT
* * ***
19884 GTTATCA-CTTATAGATGGCCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCATTGGACCT-G
66 GTTATCATCGTAT-GATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACCCGA-CTAG
19946 ATC
128 ATC
* * * * * * * * * *
19949 TCCTTATCACATATGAGCCGTGTCAA-TCCTTGATAACCAGAAC-TCTTTATCACGTATGAGCCG
1 TCCTCATCACATAGGAACCGTGTCAACTCTTTGATAACCA-ACCGTCCTCATCACATAGGAACCG
* *
20012 TGTTATCA-CCTTTAGATGGCCAGAACTC
65 TGTTATCATCGTAT-GATGGCCAGAACTC
20040 TTCACCACAT
Statistics
Matches: 178, Mismatches: 36, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
128 5 0.03
129 147 0.83
130 26 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (130 bp):
TCCTCATCACATAGGAACCGTGTCAACTCTTTGATAACCAACCGTCCTCATCACATAGGAACCGT
GTTATCATCGTATGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCCGACTAGATC
Found at i:20057 original size:46 final size:49
Alignment explanation
Indices: 19985--20095 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 49
19975 TCCTTGATAA
* * * * *
19985 CCAGAACTCTTTATCACGTATGAGCCGTGTTATCA-CCTT-T-AGATGG
1 CCAGAACTCTTCACCACATATAAGCCGAGTTATCACCCTTCTAAGATGG
20031 CCAGAACTCTTCACCACATATAAGCCGAGTTATCACCCTTCCTAAAGATGG
1 CCAGAACTCTTCACCACATATAAGCCGAGTTATCACCCTT-CT-AAGATGG
20082 CCAAGAACTCTTCA
1 CC-AGAACTCTTCA
20096 TCATTTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
46 30 0.56
47 4 0.07
49 1 0.02
51 8 0.15
52 11 0.20
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (49 bp):
CCAGAACTCTTCACCACATATAAGCCGAGTTATCACCCTTCTAAGATGG
Found at i:20404 original size:18 final size:18
Alignment explanation
Indices: 20381--20423 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20371 ATTAAGTGTT
*
20381 ATTATTTTTATTATCAGC
1 ATTATTTTAATTATCAGC
* * *
20399 ATTATTATAATTATTAGT
1 ATTATTTTAATTATCAGC
20417 ATTATTT
1 ATTATTT
20424 ACTAATGTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTATTTTAATTATCAGC
Found at i:20412 original size:21 final size:19
Alignment explanation
Indices: 20358--20414 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
20348 AATTATTATA
*
20358 ATTATTATATATTATTAAGT
1 ATTATTATA-ATTATTAAGC
* **
20378 GTTATTATTTTTATTATCAGC
1 ATTATTATAATTATTA--AGC
20399 ATTATTATAATTATTA
1 ATTATTATAATTATTA
20415 GTATTATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 6 0.21
20 7 0.25
21 15 0.54
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTATTATAATTATTAAGC
Found at i:23060 original size:48 final size:49
Alignment explanation
Indices: 22994--23088 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 49
22984 ATGAAATTCA
*
22994 CATACGGAAATTAATACACTTAGTATGGATTTCTTAA-ATTGCACACAT
1 CATACGGAAATTAATACACTTAGTATGAATTTCTTAATATTGCACACAT
* *
23042 CATACGGAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACAC
1 CATACGGAAATTAATACACTTAGTATGAATTTCTTAATATTGCACAC
23089 TGTAACACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 35 0.81
49 8 0.19
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (49 bp):
CATACGGAAATTAATACACTTAGTATGAATTTCTTAATATTGCACACAT
Found at i:23738 original size:30 final size:30
Alignment explanation
Indices: 23702--24192 Score: 937
Period size: 30 Copynumber: 16.4 Consensus size: 30
23692 CGAAGGACCG
23702 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23732 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23762 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23792 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23822 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23852 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23882 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23912 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23942 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
23972 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
* *
24002 ATCCAGAGGACATAAAGATCCTTGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
24032 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
24062 ATCCAGAGGTCATATAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
24092 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
24122 ATCCAGAGGTCATAAATATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
24152 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
24182 ATCCATAGGTC
1 ATCCAGAGGTC
24193 CAGAAGAACC
Statistics
Matches: 452, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 452 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:27892 original size:30 final size:30
Alignment explanation
Indices: 27856--28286 Score: 853
Period size: 30 Copynumber: 14.4 Consensus size: 30
27846 CGAAGGACCG
27856 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
27886 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
27916 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
27946 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
27976 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28006 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28036 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28066 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28096 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28126 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28156 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28186 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28216 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28246 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
28276 ATCCATAGGTC
1 ATCCAGAGGTC
28287 CAGAAGAACC
Statistics
Matches: 400, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 400 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:28688 original size:2 final size:2
Alignment explanation
Indices: 28676--28718 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
28666 TACACAACTC
28676 AT AT A- AT AT AT 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 AT AT AT AT AT AT
28717 AT
1 AT
28719 TGTAACATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29428 original size:55 final size:56
Alignment explanation
Indices: 29368--29476 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 56
29358 GATGTTACAC
*
29368 ACACATAGT-TCCCTTACCAAAATTCATACACTTAGTATGAATTTCTT-AGTTTTGT
1 ACACATAGTGT-CCGTACCAAAATTCATACACTTAGTATGAATTTCTTAAGTTTTGT
*
29423 ACACATAGTGTCCGTACCGAAATTCATACACTTAGTATGAATTTCTTAAGTTTT
1 ACACATAGTGTCCGTACCAAAATTCATACACTTAGTATGAATTTCTTAAGTTTT
29477 TCCACACTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
55 43 0.86
56 7 0.14
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (56 bp):
ACACATAGTGTCCGTACCAAAATTCATACACTTAGTATGAATTTCTTAAGTTTTGT
Found at i:31781 original size:6 final size:6
Alignment explanation
Indices: 31770--31798 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31760 ATTTTCTTTC
31770 TTTCTT TTTCTT TTT-TT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
31799 CATTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTCTT
Found at i:31785 original size:21 final size:21
Alignment explanation
Indices: 31766--31808 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 21
31756 GATCATTTTC
31766 TTTCTTTCTTTTTC-T--TTT
1 TTTCTTTCTTTTTCTTCATTT
31784 TTT-TTTCTTTTTCTTCATTT
1 TTTCTTTCTTTTTCTTCATTT
31804 TTTCT
1 TTTCT
31809 CTTTTCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
20 6 0.29
21 1 0.05
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTCTTTCTTTTTCTTCATTT
Found at i:31830 original size:6 final size:6
Alignment explanation
Indices: 31819--31845 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31809 CTTTTCCCTA
31819 TTTGTT TTTGTT TTTGTT TTTGTT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTT
31846 TATCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:42507 original size:71 final size:71
Alignment explanation
Indices: 42396--42553 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 71
42386 TATTCCCAGA
* *** * * * *
42396 AAAAGGATTGATCCCTTGACCAAAAGGATTAATCCTAAACTTTCTATTGTGCATAGGATCAATGT
1 AAAAGGATAGATCCCTTGGGAAAAAAGATTAATCCCAAACTTTCTATCGTGCATAGGATCAATCT
42461 CTTTTC
66 CTTTTC
* * * * *
42467 AAAATGATAGATCCCTTGGGAAAAAAGATTGATCCCAAACTTTCTGTCGTGCATATGATCGATCT
1 AAAAGGATAGATCCCTTGGGAAAAAAGATTAATCCCAAACTTTCTATCGTGCATAGGATCAATCT
42532 CTTTTC
66 CTTTTC
*
42538 AAAAGGATCGATCCCT
1 AAAAGGATAGATCCCT
42554 CAGAGAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (71 bp):
AAAAGGATAGATCCCTTGGGAAAAAAGATTAATCCCAAACTTTCTATCGTGCATAGGATCAATCT
CTTTTC
Found at i:42563 original size:71 final size:71
Alignment explanation
Indices: 42396--42573 Score: 187
Period size: 71 Copynumber: 2.5 Consensus size: 71
42386 TATTCCCAGA
* * ** * * * * *
42396 AAAAGGATTGATCCCTTGACCAAAAGGATTAATCCTAAACTTTCTATTGTGCATAGGATCAATGT
1 AAAAGGATAGATCCCTAGAGAAAAAAGATTGATCCCAAACTTTCTATCGTGCATAGGATCAATCT
42461 CTTTTC
66 CTTTTC
* * * * * *
42467 AAAATGATAGATCCCTTGGGAAAAAAGATTGATCCCAAACTTTCTGTCGTGCATATGATCGATCT
1 AAAAGGATAGATCCCTAGAGAAAAAAGATTGATCCCAAACTTTCTATCGTGCATAGGATCAATCT
42532 CTTTTC
66 CTTTTC
* *
42538 AAAAGGATCGATCCCTCAGAG-AAAAAGATCGATCCC
1 AAAAGGATAGATCCCT-AGAGAAAAAAGATTGATCCC
42574 TCGAAAGAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 86 0.98
72 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (71 bp):
AAAAGGATAGATCCCTAGAGAAAAAAGATTGATCCCAAACTTTCTATCGTGCATAGGATCAATCT
CTTTTC
Found at i:42567 original size:21 final size:19
Alignment explanation
Indices: 42538--42592 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
42528 ATCTCTTTTC
*
42538 AAAAGGATCGATCCCTCAGA
1 AAAAAGATCGATCCCTC-GA
42558 GAAAAAGATCGATCCCTCGA
1 -AAAAAGATCGATCCCTCGA
42578 AAGAAATGATCGATC
1 AA-AAA-GATCGATC
42593 ACTTTGTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 24 0.77
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (19 bp):
AAAAAGATCGATCCCTCGA
Found at i:44258 original size:20 final size:21
Alignment explanation
Indices: 44233--44281 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
44223 TTTTAAATCC
44233 AATTAAAATAA-ATT-AATTA
1 AATTAAAATAATATTAAATTA
44252 AATTTAAAA-AATATTAAATTA
1 AA-TTAAAATAATATTAAATTA
44273 AATTAAAAT
1 AATTAAAAT
44282 GAAAAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTAAAATAATATTAAATTA
Found at i:45064 original size:32 final size:32
Alignment explanation
Indices: 45019--45146 Score: 215
Period size: 32 Copynumber: 4.1 Consensus size: 32
45009 TCATTAGCAT
45019 TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
1 TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
*
45051 TTTTAAGAGTTTTGTGTTTATTTAGCATAAAA
1 TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
*
45083 TTTTAAGACTTTTGTGTTTATTTAGCATAAAT
1 TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
*
45115 TTTTAAGA--GTTGTGTTTATTTAGCATAAAA
1 TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
45145 TT
1 TT
45147 CAATAAGACT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 22 0.24
32 69 0.76
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (32 bp):
TTTTAAGACTTTTGTGTTTATTTAGCATAAAA
Found at i:67513 original size:16 final size:16
Alignment explanation
Indices: 67492--67535 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
67482 CTTAATTTCA
*
67492 TCTCAAAACCTAAAAT
1 TCTCAAACCCTAAAAT
67508 TCTCAAATCCCT-AAAT
1 TCTCAAA-CCCTAAAAT
67524 T-TCAAACCCTAA
1 TCTCAAACCCTAA
67536 TCCCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 12 0.48
17 3 0.12
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (16 bp):
TCTCAAACCCTAAAAT
Found at i:67568 original size:23 final size:22
Alignment explanation
Indices: 67513--67568 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
67503 AAAATTCTCA
*
67513 AATCCC-TAAATTTCAAACCCT
1 AATCCCTTAAATCTCAAACCCT
*
67534 AATCCCTAAAATCTCAAATACCC-
1 AATCCCTTAAATCTC-AA-ACCCT
67557 AATCCCTTAAAT
1 AATCCCTTAAAT
67569 TCATTTAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 13 0.45
24 4 0.14
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (22 bp):
AATCCCTTAAATCTCAAACCCT
Found at i:73253 original size:21 final size:21
Alignment explanation
Indices: 73229--73270 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
73219 AACTTGACCC
73229 AGGAACAAGGTCAATTTGATG
1 AGGAACAAGGTCAATTTGATG
73250 AGGAACAAGGTCAATTTGATG
1 AGGAACAAGGTCAATTTGATG
73271 TTGAATATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (21 bp):
AGGAACAAGGTCAATTTGATG
Found at i:80595 original size:22 final size:22
Alignment explanation
Indices: 80567--80732 Score: 242
Period size: 22 Copynumber: 7.5 Consensus size: 22
80557 ATTTTAAAAT
*
80567 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
***
80589 TTTATTTTAAAATATGGAAAAA
1 TTTATTTTAAAATATGGATTGA
*
80611 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
80633 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
80655 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
80677 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
80699 TTTATTTTAAAATATGGATTGC
1 TTTATTTTAAAATATGGATTGA
80721 TTTATTTTAAAA
1 TTTATTTTAAAA
80733 AATTTATTAT
Statistics
Matches: 126, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 126 1.00
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:80623 original size:44 final size:44
Alignment explanation
Indices: 80562--80732 Score: 270
Period size: 44 Copynumber: 3.9 Consensus size: 44
80552 AATCTATTTT
*
80562 AAAATTTTATTTTAAAATATAGATTGATTTATTTTAAAATATGG
1 AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGG
*
80606 AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGA
1 AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGG
*
80650 AAAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG
1 AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGG
*** * *
80694 ATTGATTTATTTTAAAATATGGATTGCTTTATTTTAAAA
1 AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAA
80733 AATTTATTAT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 119 1.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (44 bp):
AAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGG
Found at i:80813 original size:31 final size:31
Alignment explanation
Indices: 80756--80814 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
80746 AGTTGTATGG
*
80756 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
80787 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
80815 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:82468 original size:29 final size:29
Alignment explanation
Indices: 82429--82485 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
82419 TGGTAAAAAC
*
82429 AGAAACTTAAGTGACTAAAATAAAATAAA
1 AGAAACTTAAGTGACTAAAACAAAATAAA
82458 AGAAACTTAAGTGACTAAAACAAAATAA
1 AGAAACTTAAGTGACTAAAACAAAATAA
82486 CATAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (29 bp):
AGAAACTTAAGTGACTAAAACAAAATAAA
Found at i:82498 original size:29 final size:28
Alignment explanation
Indices: 82431--82520 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
82421 GTAAAAACAG
* *
82431 AAACTTAAGTGACTAAAATAAAATAAAAG
1 AAACTTAAGTGACTAAAACAAAAT-AAAT
82460 AAACTTAAGTGACTAAAACAAAATAACAT
1 AAACTTAAGTGACTAAAACAAAATAA-AT
*
82489 AAA-TTAAAGTGTC-AAAATCAGAAATAAAT
1 AAACTT-AAGTGACTAAAA-CA-AAATAAAT
82518 AAA
1 AAA
82521 ATAGGAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 8 0.15
29 40 0.74
30 6 0.11
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (28 bp):
AAACTTAAGTGACTAAAACAAAATAAAT
Found at i:83464 original size:25 final size:26
Alignment explanation
Indices: 83418--83466 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
83408 TGGCTATTAT
*
83418 TCCCCCAGTTTTCCTTTTTTCCTCAC
1 TCCCCCAGTTTTCATTTTTTCCTCAC
83444 TCCCCCA-TTTT-ATTTTCTTCCTC
1 TCCCCCAGTTTTCATTTT-TTCCTC
83467 GAAATACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.08, C:0.41, G:0.02, T:0.49
Consensus pattern (26 bp):
TCCCCCAGTTTTCATTTTTTCCTCAC
Found at i:84942 original size:201 final size:200
Alignment explanation
Indices: 84633--85070 Score: 504
Period size: 201 Copynumber: 2.2 Consensus size: 200
84623 TCGAAGGTTT
* * * * * *
84633 TTGTTGATAGATAACCCTTCTCGTCTTGAGCTATGTTGTAAATTTAACTGAGAGATAGTTCCTTG
1 TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTAACTGAGAGATAGTTCCTTA
* * * *
84698 TTGCTAAATCGCAACCAACCTAGGTCTTCTTTTTGACTTAAAGACCTCTGTTTAAAATTCAACC-
66 TTGATAAATCGCAACCAACCTAGGTATTCTTCTTGACTTAAAGACCTCAGTTTAAAATTCAACCG
* * * * * *
84762 AAAAGGTAGTTCCTCGCTGCTACCATGCAGTTGATATA-TCTTCGAGCTGAATGAAATGAAACTC
131 AAAA-ATAGTTCCTCACTGCTACCATGCAGTTGATA-AGCCCTCGAG-TGAAAGAAATCAAACTC
84826 GAAAATTC
193 GAAAATTC
* * * *
84834 TTGTTGACAGATAGTCCTTCTCGCCTTAAGCTATGCTATAAATTTGACT-ATGATATAGTTCCTT
1 TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTAACTGA-GAGATAGTTCCTT
* * * * *
84898 ATTGATAAATTGCAGCCAACCTAGGTATTCTTCTTGATTTAAAGACCTCAGTTTAAACTTTAACC
65 ATTGATAAATCGCAACCAACCTAGGTATTCTTCTTGACTTAAAGACCTCAGTTTAAAATTCAACC
* * *** * * *
84963 GAAAAATAGTTCCTTATTGCTATTGTGCGGTTGATAAGCCCTCGAGTTAAAGAAATCAAACTTGA
130 GAAAAATAGTTCCTCACTGCTACCATGCAGTTGATAAGCCCTCGAGTGAAAGAAATCAAACTCGA
*
85028 AAGTTC
195 AAATTC
*
85034 TTGTTGACAGATAGCCCTTCTCGCATTGAGCTATGCT
1 TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
85071 GCGAACAGTT
Statistics
Matches: 197, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
200 56 0.28
201 137 0.70
202 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (200 bp):
TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTAACTGAGAGATAGTTCCTTA
TTGATAAATCGCAACCAACCTAGGTATTCTTCTTGACTTAAAGACCTCAGTTTAAAATTCAACCG
AAAAATAGTTCCTCACTGCTACCATGCAGTTGATAAGCCCTCGAGTGAAAGAAATCAAACTCGAA
AATTC
Found at i:85729 original size:32 final size:32
Alignment explanation
Indices: 85654--85729 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
85644 TTCACATCAG
* * ** *
85654 GATGTTGAATCCCCAAATATGTCCCAATATTC
1 GATGTTGAATCTCCAAAAATACCCCAACATTC
*
85686 GATGTTGAATCTCCAAAAATACCCCAACATTT
1 GATGTTGAATCTCCAAAAATACCCCAACATTC
85718 GATGTTGAATCT
1 GATGTTGAATCT
85730 TTAAAGATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAAATACCCCAACATTC
Found at i:90158 original size:29 final size:29
Alignment explanation
Indices: 90116--90179 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
90106 AAATAGCAAA
* * *
90116 AACAAAAACTTAAGTGATTAAAATAAAAT
1 AACAGAAACTTAAGTGACTAAAACAAAAT
90145 AACAGAAACTTAAGTGACTAAAACAAAAT
1 AACAGAAACTTAAGTGACTAAAACAAAAT
90174 AA-AGAA
1 AACAGAA
90180 TGTAAAGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (29 bp):
AACAGAAACTTAAGTGACTAAAACAAAAT
Found at i:90188 original size:28 final size:28
Alignment explanation
Indices: 90121--90205 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
90111 GCAAAAACAA
* * *
90121 AAACTTAAGTGATTAAAATAAAATAACAG
1 AAACTAAAGTGACTAAAACAAAATAA-AG
*
90150 AAACTTAAGTGACTAAAACAAAATAAAG
1 AAACTAAAGTGACTAAAACAAAATAAAG
**
90178 AATGTAAAGTG-CTAAAATCATAAATAAA
1 AAACTAAAGTGACTAAAA-CA-AAATAAA
90206 TAAAATAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.12
28 12 0.24
29 31 0.63
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (28 bp):
AAACTAAAGTGACTAAAACAAAATAAAG
Found at i:91187 original size:27 final size:27
Alignment explanation
Indices: 91146--91208 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
91136 CCCTTTTATT
* *
91146 TTCTTCCTCGAAATGTTTCCCACTCCA
1 TTCTCCCTTGAAATGTTTCCCACTCCA
* **
91173 TTTTCCCTTGAAATGTTTCCCGTTCCA
1 TTCTCCCTTGAAATGTTTCCCACTCCA
91200 TTCTCCCTT
1 TTCTCCCTT
91209 ATCCCCCTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.35, G:0.08, T:0.43
Consensus pattern (27 bp):
TTCTCCCTTGAAATGTTTCCCACTCCA
Found at i:93811 original size:43 final size:43
Alignment explanation
Indices: 93621--93823 Score: 210
Period size: 43 Copynumber: 4.7 Consensus size: 43
93611 TAAAAAACAT
* * *
93621 CGCAATAGGTTCAGACATTTAGCGGCGTTTTT-TTACAAATGT
1 CGCAATAGGTTCAGACATTTAGCGACGTTTTTCTTACAAACGC
* * *** * *
93663 CGTAATAGGTTCAGACATTAAATAATGTTTTTCTTACAAATGC
1 CGCAATAGGTTCAGACATTTAGCGACGTTTTTCTTACAAACGC
* ** *
93706 CGCAATAGGTTCAGACATTCAGCTTCATTTTTCTTACAAACGC
1 CGCAATAGGTTCAGACATTTAGCGACGTTTTTCTTACAAACGC
* * * *
93749 CGCAATAGGTTCACACATTTAGCGGCGTTTTTCTTATAAACAC
1 CGCAATAGGTTCAGACATTTAGCGACGTTTTTCTTACAAACGC
* * *
93792 CGCAATAGTTTCAGACATTTAACGACTTTTTT
1 CGCAATAGGTTCAGACATTTAGCGACGTTTTT
93824 TTTATAAATG
Statistics
Matches: 131, Mismatches: 29, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 25 0.19
43 106 0.81
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (43 bp):
CGCAATAGGTTCAGACATTTAGCGACGTTTTTCTTACAAACGC
Found at i:93840 original size:86 final size:85
Alignment explanation
Indices: 93615--93844 Score: 226
Period size: 86 Copynumber: 2.7 Consensus size: 85
93605 TATAAATAAA
* * * * *
93615 AAACATCGCAATAGGTTCAGACATTTAGCGGCGTTTTTTTACAAATGTCGTAATAGGTTCAGACA
1 AAACACCGCAATAGGTTCAGACATTTAGCGACTTTTTTTTACAAATGTCGCAATAGGTTCACACA
* *
93680 TTAAATAATGTTTTTCTTAC
66 TTAAACAACGTTTTTCTTAC
** * ** * * *
93700 AAATGCCGCAATAGGTTCAGACATTCAGCTTCATTTTTCTTACAAACGCCGCAATAGGTTCACAC
1 AAACACCGCAATAGGTTCAGACATTTAGCGAC-TTTTTTTTACAAATGTCGCAATAGGTTCACAC
* * ** *
93765 ATTTAGCGGCGTTTTTCTTAT
65 ATTAAACAACGTTTTTCTTAC
* * * *
93786 AAACACCGCAATAGTTTCAGACATTTAACGACTTTTTTTTTATAAATGTTGCAATAGGT
1 AAACACCGCAATAGGTTCAGACATTTAGCGAC-TTTTTTTTACAAATGTCGCAATAGGT
93845 CGTGTTGAAC
Statistics
Matches: 112, Mismatches: 32, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
85 26 0.23
86 86 0.77
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (85 bp):
AAACACCGCAATAGGTTCAGACATTTAGCGACTTTTTTTTACAAATGTCGCAATAGGTTCACACA
TTAAACAACGTTTTTCTTAC
Found at i:100216 original size:3 final size:3
Alignment explanation
Indices: 100208--100970 Score: 1252
Period size: 3 Copynumber: 259.3 Consensus size: 3
100198 TTCTGGAACG
100208 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100256 TTC TTC TTC -TC TTC TTC TTC TTC TTC TT- TTC TT- TT- TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100300 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100347 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
100392 TTC TTC TTC TTC TT- TTC -TC TTC TTC TTC TTC TT- TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100437 TTC TT- TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TCTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC
100481 TT- TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100526 TTC TTTC TTC TTC TTC TTC TT- TTC TTTC TTC TTC TTC TTC TTTC TTC
1 TTC -TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC -TTC TTC
100573 TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100618 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100665 TTC TTC TTC TTC TTC TCTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC T-TC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
100712 TTTC TTC TTC TTC -TC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC
1 -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100757 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100805 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100853 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
100900 TTC TT- TTC -TC TTC TTC TTC TTC -TC TTTC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC -TTC TTC TTC
100944 TTC TTC TTC TTC TTC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
100971 ATGTGTATTT
Statistics
Matches: 725, Mismatches: 2, Indels: 66
0.91 0.00 0.08
Matches are distributed among these distances:
2 50 0.07
3 647 0.89
4 27 0.04
5 1 0.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.