Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012325.1 Corchorus capsularis cultivar CVL-1 contig12346, 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: 93084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:223 original size:2 final size:2
Alignment explanation
Indices: 216--254 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
206 TATATCAAAC
216 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
255 CTTATCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6900 original size:32 final size:32
Alignment explanation
Indices: 6856--6918 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
6846 ATATATTATG
*
6856 TATTGTGTATGAATGTATTAGAAGAAAATATA
1 TATTATGTATGAATGTATTAGAAGAAAATATA
6888 TATTATGTATGAATGTATTAGAAGAAAATAT
1 TATTATGTATGAATGTATTAGAAGAAAATAT
6919 GCAATATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.38
Consensus pattern (32 bp):
TATTATGTATGAATGTATTAGAAGAAAATATA
Found at i:7935 original size:15 final size:15
Alignment explanation
Indices: 7915--7946 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7905 GAATGGTACT
7915 AATTAGAAGATAAGG
1 AATTAGAAGATAAGG
*
7930 AATTAGAAGATTAGG
1 AATTAGAAGATAAGG
7945 AA
1 AA
7947 GAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (15 bp):
AATTAGAAGATAAGG
Found at i:9367 original size:29 final size:28
Alignment explanation
Indices: 9293--9368 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
9283 TTAACCTAAG
*
9293 GGGGCAAAACATCCCAAAAATTGAAATTCA
1 GGGGCAAAAC-GCCC-AAAATTGAAATTCA
* * * *
9323 GGAGCAAAATGTCCAAAATTGAAGTTCA
1 GGGGCAAAACGCCCAAAATTGAAATTCA
9351 GGGGACAAAACGCCCAAA
1 GGGG-CAAAACGCCCAAA
9369 CGCTATAAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 16 0.43
29 13 0.35
30 8 0.22
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (28 bp):
GGGGCAAAACGCCCAAAATTGAAATTCA
Found at i:9782 original size:90 final size:89
Alignment explanation
Indices: 9598--9788 Score: 246
Period size: 90 Copynumber: 2.1 Consensus size: 89
9588 ATGAAGTCTT
9598 ATAATTTTTGGTTCACATAACAATTTTCGGACAGTTTTTGTAGTTATTTATAAAGTTTCCTATGT
1 ATAATTTTTGGTTCACATAACAATTTTCGGACAGTTTTTGTAGTTATTTATAAAGTTTCCTATGT
* **
9663 TCTATAAATTATAAGTTTCCTATTT
66 TCTATAAATTATAAGATT-CTATGG
**
9688 ATAATTTTTGGTTC-CAATAACAATTTTCGGATGGTTTTTGTAGTTATCTATTTATAAAGTTTCC
1 ATAATTTTTGGTTCAC-ATAACAATTTTCGGACAGTTTTTGTAG---T-TATTTATAAAGTTTCC
9752 TATGTTCTATAAATTATAA-ATT-TA-GG
61 TATGTTCTATAAATTATAAGATTCTATGG
9778 ATAATTATTTG
1 ATAATT-TTTG
9789 ATACACCGAC
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
89 1 0.01
90 45 0.50
91 6 0.07
93 3 0.03
94 35 0.39
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (89 bp):
ATAATTTTTGGTTCACATAACAATTTTCGGACAGTTTTTGTAGTTATTTATAAAGTTTCCTATGT
TCTATAAATTATAAGATTCTATGG
Found at i:10500 original size:31 final size:31
Alignment explanation
Indices: 10459--10518 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
10449 AACTTTATGT
*
10459 TTTCCGATTGTACCCTTTATTTTCATATATA
1 TTTCCAATTGTACCCTTTATTTTCATATATA
10490 TTTCCAATTGTACCCTTTATTTTCATATA
1 TTTCCAATTGTACCCTTTATTTTCATATA
10519 CTCCCTCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTATTTTCATATATA
Found at i:10805 original size:2 final size:2
Alignment explanation
Indices: 10798--10822 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10788 CTTTGACCGG
10798 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
10823 CACACACACT
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:11518 original size:22 final size:22
Alignment explanation
Indices: 11456--11527 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
11446 AGGGGGATGA
* * *
11456 ATTAA-ATTTTATTGTGTGATT
1 ATTAAGATTTCATAGTGTGGTT
* *
11477 ATCAAAATTTCATAGTGTGGTT
1 ATTAAGATTTCATAGTGTGGTT
11499 ATTAAGATTTCATAGTGTGGTT
1 ATTAAGATTTCATAGTGTGGTT
*
11521 TTTAAGA
1 ATTAAGA
11528 GGGATGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 4 0.09
22 39 0.91
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
ATTAAGATTTCATAGTGTGGTT
Found at i:11587 original size:21 final size:21
Alignment explanation
Indices: 11561--11615 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
11551 TGGGGTAATC
*
11561 TAAATTTCTTAGTATGGTTAA
1 TAAATTTCATAGTATGGTTAA
* * *
11582 TAAATTTGATAGTTTGGTTAT
1 TAAATTTCATAGTATGGTTAA
*
11603 TAAAATTACATAG
1 T-AAATTTCATAG
11616 GGAGGTTATC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (21 bp):
TAAATTTCATAGTATGGTTAA
Found at i:11622 original size:22 final size:22
Alignment explanation
Indices: 11597--11850 Score: 123
Period size: 22 Copynumber: 11.6 Consensus size: 22
11587 TTGATAGTTT
*
11597 GGTTATTAAAATTACATAGGGA
1 GGTTATCAAAATTACATAGGGA
** *
11619 GGTTATCGTAATTACATTGTGGA
1 GGTTATCAAAATTACATAG-GGA
*
11642 -GTTATCAAAATTTA-ATA-GTA
1 GGTTATCAAAA-TTACATAGGGA
* * *
11662 TGGTTTTCAAAATTTCGTAGGGA
1 -GGTTATCAAAATTACATAGGGA
* * * *
11685 GATTAACAAAATTCCGTAAGGGA
1 GGTTATCAAAATTACAT-AGGGA
* * *
11708 TGTTATAAAAATTTCATAGGGA
1 GGTTATCAAAATTACATAGGGA
*
11730 GGTTATCAAAATTTCATAGGGTA
1 GGTTATCAAAATTACATAGGG-A
*
11753 -GTTATCAAAATTTCATGAGGTGA
1 GGTTATCAAAATTACAT-AGG-GA
*
11776 --TTATCAAAATTTCAT---GA
1 GGTTATCAAAATTACATAGGGA
* * **
11793 GATTATCAAAATTGCA-AAAGA
1 GGTTATCAAAATTACATAGGGA
** * *
11814 GGGTTATCAAAATTTTACAGAGA
1 -GGTTATCAAAATTACATAGGGA
11837 GGTTTATCAAAATT
1 GG-TTATCAAAATT
11851 TTATAATGAG
Statistics
Matches: 185, Mismatches: 29, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.01
19 13 0.07
20 2 0.01
21 4 0.02
22 119 0.64
23 44 0.24
24 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTACATAGGGA
Found at i:11767 original size:44 final size:43
Alignment explanation
Indices: 11597--11895 Score: 164
Period size: 44 Copynumber: 6.8 Consensus size: 43
11587 TTGATAGTTT
* * ** * *
11597 GGTTATTAAAATTACATAGGGAGGTTATCGTAATTACATTGTGGA
1 GGTTATCAAAATTTCATAGGGA-GTTATCAAAATTTCATAG-GGA
* * * *
11642 -GTTATCAAAATTTAATA-GTATGGTTTTCAAAATTTCGTAGGGA
1 GGTTATCAAAATTTCATAGGGA--GTTATCAAAATTTCATAGGGA
* * * * *
11685 GATTAACAAAATTCCGTAAGGGATGTTATAAAAATTTCATAGGGA
1 GGTTATCAAAATTTCAT-AGGGA-GTTATCAAAATTTCATAGGGA
11730 GGTTATCAAAATTTCATAGGGTAGTTATCAAAATTTCATGAGGTGA
1 GGTTATCAAAATTTCATAGGG-AGTTATCAAAATTTCAT-AGG-GA
* * **
11776 --TTATCAAAATTTCAT-GAGA-TTATCAAAATTGCA-AAAGA
1 GGTTATCAAAATTTCATAGGGAGTTATCAAAATTTCATAGGGA
* * * * **
11814 GGGTTATCAAAATTTTACAGAGAGGTTTATCAAAATTTTATAATGA
1 -GGTTATCAAAATTTCATAGGGA-G-TTATCAAAATTTCATAGGGA
* * * *
11860 GGTT-TCACAATTTTATAGGAAGGTGATCAAAATTTC
1 GGTTATCAAAATTTCATAGGGA-GTTATCAAAATTTC
11896 GTAGTGTGCT
Statistics
Matches: 199, Mismatches: 40, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
41 26 0.13
42 5 0.03
43 18 0.09
44 87 0.44
45 52 0.26
46 8 0.04
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGGAGTTATCAAAATTTCATAGGGA
Found at i:11799 original size:41 final size:43
Alignment explanation
Indices: 11639--11851 Score: 145
Period size: 45 Copynumber: 4.9 Consensus size: 43
11629 ATTACATTGT
* * * *
11639 GGAGTTATCAAAATTTAATAGTA-TGGTTTTCAAAATTTCGTAG
1 GGAGTTATCAAAATTTCATAG-AGTAGTTATCAAAATTTCATAG
* * * * *
11682 GGAGATTAACAAAATTCCGTA-AGGGATGTTATAAAAATTTCATAG
1 GGAG-TTATCAAAATTTCATAGA-GTA-GTTATCAAAATTTCATAG
*
11727 GGAGGTTATCAAAATTTCATAGGGTAGTTATCAAAATTTCATGAG
1 GGA-GTTATCAAAATTTCATAGAGTAGTTATCAAAATTTCAT-AG
* *
11772 GTGA-TTATCAAAATTTCAT-GAG-A-TTATCAAAATTGCAAAAG
1 G-GAGTTATCAAAATTTCATAGAGTAGTTATCAAAATTTC-ATAG
* *
11813 AGG-GTTATCAAAATTTTACAGAG-AGGTTTATCAAAATTT
1 -GGAGTTATCAAAATTTCATAGAGTA-G-TTATCAAAATTT
11852 TATAATGAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 28
0.73 0.11 0.15
Matches are distributed among these distances:
41 28 0.21
42 8 0.06
43 6 0.04
44 42 0.31
45 47 0.35
46 3 0.02
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (43 bp):
GGAGTTATCAAAATTTCATAGAGTAGTTATCAAAATTTCATAG
Found at i:11861 original size:23 final size:21
Alignment explanation
Indices: 11709--11894 Score: 103
Period size: 22 Copynumber: 8.6 Consensus size: 21
11699 CGTAAGGGAT
* * *
11709 GTTATAAAAATTTCATAGGGAG
1 GTTATCAAAATTTTATA-AGAG
* *
11731 GTTATCAAAATTTCAT-AGGG
1 GTTATCAAAATTTTATAAGAG
* *
11751 TAGTTATCAAAATTTCATGAG-G
1 --GTTATCAAAATTTTATAAGAG
*
11773 TGATTATCAAAATTTCAT--GAG
1 -G-TTATCAAAATTTTATAAGAG
* ** *
11794 ATTATCAAAATTGCAAAAGAGG
1 GTTATCAAAATTTTATAAGA-G
*
11816 GTTATCAAAATTTTACAGAGAG
1 GTTATCAAAATTTTATA-AGAG
11838 GTTTATCAAAATTTTATAATGAG
1 G-TTATCAAAATTTTATAA-GAG
* *
11861 GTT-TCACAATTTTATAGGAAG
1 GTTATCAAAATTTTATAAG-AG
*
11882 GTGATCAAAATTT
1 GTTATCAAAATTT
11895 CGTAGTGTGC
Statistics
Matches: 135, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
19 13 0.10
20 4 0.03
21 20 0.15
22 74 0.55
23 24 0.18
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTTATAAGAG
Found at i:11917 original size:44 final size:44
Alignment explanation
Indices: 11869--11959 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
11859 AGGTTTCACA
*
11869 ATTTTATAGGAAGGTGATCAAAATTTCGTAGTGTGCTTACCAAC
1 ATTTTATAGGAAGGTGATCAAAATTTCGTAATGTGCTTACCAAC
11913 ATTTTATAGGAAGGTGATCAAAATTTCGTAATGTGCTTACCAAC
1 ATTTTATAGGAAGGTGATCAAAATTTCGTAATGTGCTTACCAAC
11957 ATT
1 ATT
11960 CCACATGGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (44 bp):
ATTTTATAGGAAGGTGATCAAAATTTCGTAATGTGCTTACCAAC
Found at i:12039 original size:22 final size:21
Alignment explanation
Indices: 11991--12039 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
11981 ATCATTTTGT
11991 GCTTATCAAATTTCATAACGA
1 GCTTATCAAATTTCATAACGA
*
12012 GGTTATCAAAATTTCATAA-GCA
1 GCTTATC-AAATTTCATAACG-A
12034 GCTTAT
1 GCTTAT
12040 TACATTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (21 bp):
GCTTATCAAATTTCATAACGA
Found at i:12217 original size:22 final size:22
Alignment explanation
Indices: 12190--12267 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
12180 TTTGATGTCG
12190 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
12212 TTATCAAATTTTCATA-TG-GA
1 TTATCAAAATTTCATAGTGTGA
* * * *
12232 TGTCATTAAAATTTTATGGTGTAA
1 T-T-ATCAAAATTTCATAGTGTGA
12256 TTATCAAAATTT
1 TTATCAAAATTT
12268 AATATAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
20 3 0.07
21 3 0.07
22 34 0.76
23 3 0.07
24 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:12347 original size:15 final size:15
Alignment explanation
Indices: 12327--12356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12317 AAGCTAGAAC
*
12327 TAGTAATTTATAAAT
1 TAGTAATTTAAAAAT
12342 TAGTAATTTAAAAAT
1 TAGTAATTTAAAAAT
12357 GACCCAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TAGTAATTTAAAAAT
Found at i:13579 original size:24 final size:24
Alignment explanation
Indices: 13547--13596 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
13537 CCAATATCCT
13547 AACGGCGGTGAAATCAAGGAAATC
1 AACGGCGGTGAAATCAAGGAAATC
13571 AACGGCGGTGAAATCAAGGAAATC
1 AACGGCGGTGAAATCAAGGAAATC
13595 AA
1 AA
13597 AGGGTGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (24 bp):
AACGGCGGTGAAATCAAGGAAATC
Found at i:17206 original size:30 final size:29
Alignment explanation
Indices: 17172--17228 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
17162 AATATCATAT
*
17172 TTTATATAATAT-ATATTATAAGTATATAGA
1 TTTATA-AATATAATATGATAA-TATATAGA
17202 TTTATAAATATAATATGATAATATATA
1 TTTATAAATATAATATGATAATATATA
17229 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTATAAATATAATATGATAATATATAGA
Found at i:18493 original size:21 final size:21
Alignment explanation
Indices: 18447--18504 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
18437 TGGTCTGTTA
18447 CTGTTTTGATCAATTTCTAAT
1 CTGTTTTGATCAATTTCTAAT
* * *
18468 ATGTTTTGATTAGTTTC-AATT
1 CTGTTTTGATCAATTTCTAA-T
* *
18489 CTGTTCTAATCAATTT
1 CTGTTTTGATCAATTT
18505 GGAATTGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
CTGTTTTGATCAATTTCTAAT
Found at i:21236 original size:13 final size:13
Alignment explanation
Indices: 21218--21243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21208 TTCTGTCTTA
21218 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
21231 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
21244 GCTGCTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
CTGTTTTTGAGTT
Found at i:23747 original size:14 final size:14
Alignment explanation
Indices: 23728--23755 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23718 CTTTTCCCTT
23728 TTTAGCATTTACCG
1 TTTAGCATTTACCG
23742 TTTAGCATTTACCG
1 TTTAGCATTTACCG
23756 ATTGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTAGCATTTACCG
Found at i:48020 original size:22 final size:23
Alignment explanation
Indices: 47916--48021 Score: 89
Period size: 22 Copynumber: 4.8 Consensus size: 23
47906 ATTAAACATC
47916 CTTATGAAATTTTGATAAT-TGTA
1 CTTATGAAATTTTGATAATCT-TA
* * * *
47939 C-TATGAAATTGTGATTACCTTG
1 CTTATGAAATTTTGATAATCTTA
*
47961 C-TATGAAATTTTGAAAATC--A
1 CTTATGAAATTTTGATAATCTTA
* *
47981 CATTATGAAATCTAGATAATCTT-
1 C-TTATGAAATTTTGATAATCTTA
48004 CTTATGAAATTTTGATAA
1 CTTATGAAATTTTGATAA
48022 CCTCTCTAAG
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
22 60 0.94
23 3 0.05
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (23 bp):
CTTATGAAATTTTGATAATCTTA
Found at i:48101 original size:22 final size:22
Alignment explanation
Indices: 48076--48119 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
48066 TTGATAGCCT
*
48076 TCCCTATGAAATATTGAAAACC
1 TCCCGATGAAATATTGAAAACC
* *
48098 TCCCGATGAAATTTTGATAACC
1 TCCCGATGAAATATTGAAAACC
48120 ATTTAATGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (22 bp):
TCCCGATGAAATATTGAAAACC
Found at i:48132 original size:22 final size:22
Alignment explanation
Indices: 48107--48185 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
48097 CTCCCGATGA
48107 AATTTTGATAACCATTTAATGG
1 AATTTTGATAACCATTTAATGG
*
48129 AATTTTGATAA-C-TGTACTATGG
1 AATTTTGATAACCATTTA--ATGG
*
48151 AATTTTGATAACTTCA-TT-ATGA
1 AATTTTGATAAC--CATTTAATGG
48173 AATTTTGATAACC
1 AATTTTGATAACC
48186 TTCATATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
20 4 0.08
21 1 0.02
22 41 0.85
25 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (22 bp):
AATTTTGATAACCATTTAATGG
Found at i:48197 original size:22 final size:22
Alignment explanation
Indices: 48129--48202 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
48119 CATTTAATGG
* **
48129 AATTTTGATAACTGT-ACTATGG
1 AATTTTGATAACT-TCATTATAA
*
48151 AATTTTGATAACTTCATTATGA
1 AATTTTGATAACTTCATTATAA
48173 AATTTTGATAACCTTCA-TATAA
1 AATTTTGATAA-CTTCATTATAA
48195 AATTTTGA
1 AATTTTGA
48203 CAAGCACCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
21 1 0.02
22 41 0.87
23 5 0.11
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
AATTTTGATAACTTCATTATAA
Found at i:48330 original size:22 final size:21
Alignment explanation
Indices: 48305--49237 Score: 363
Period size: 22 Copynumber: 42.6 Consensus size: 21
48295 TCACACTGTA
*
48305 AAATTTTGATAATCTCCTTATG
1 AAATTTTGATAACCTCC-TATG
* *
48327 AAATTTTAATAAACCTCCGTATA
1 AAATTTTGAT-AACCTCC-TATG
**
48350 AAATTTTTGATAATTTCCGTAATG
1 AAA-TTTTGATAACCTCC-T-ATG
*
48374 AAATTTTAATAACCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
** * * *
48396 ATTTTTTTATAACATCATTATG
1 AAATTTTGATAACCTC-CTATG
*
48418 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAACC-TCCTATG
* * * ***
48440 AAATATTAATCTACAAACTATG
1 AAATTTTGAT-AACCTCCTATG
* *
48462 GAATTTTGATACACAC-ACTATG
1 AAATTTTGATA-AC-CTCCTATG
* *
48484 AAATTTTGATAACCACACTTTG
1 AAATTTTGATAACCTC-CTATG
* *
48506 AGATTTTGATAA-CTACATTAT-
1 AAATTTTGATAACCT-C-CTATG
48527 AAATTTTTGATAACCTCCTATG
1 AAA-TTTTGATAACCTCCTATG
* * *
48549 AAATTTTGA-AAACTACAATGTG
1 AAATTTTGATAACCT-C-CTATG
* * *
48571 AAATTTCGATAACGTCCCTTTG
1 AAATTTTGATAACCT-CCTATG
** *
48593 AAATTCCGATAACCTCCCTATA
1 AAATTTTGATAACCT-CCTATG
*
48615 AAATTTTGAAAACCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
* * * * *
48637 AAATTTAGATTACCTTACAATA
1 AAATTTTGATAACC-TCCTATG
48659 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACC-TCCTATG
* * *
48681 AAATTTTGGTAA-TTACATTATG
1 AAATTTTGATAACCT-C-CTATG
* * *
48703 AAATTTTGAT-GCATCTCTTTG
1 AAATTTTGATAACCTC-CTATG
* *
48724 -AA-----AT-ACCACAATATG
1 AAATTTTGATAACCTC-CTATG
** *
48739 AAATTTTGATAATTATACTATG
1 AAATTTTGATAA-CCTCCTATG
* *
48761 AAATTTCGATAACCTCTTTATG
1 AAATTTTGATAACCTC-CTATG
48783 AAATTTTGATAACCGTCCTATG
1 AAATTTTGATAACC-TCCTATG
* * * * *
48805 ATATTTTGTTATCCTCTCTGTA
1 AAATTTTGATAACCTC-CTATG
* * *
48827 AAATTTTGATAATCACACTGTG
1 AAATTTTGATAACCTC-CTATG
** *
48849 AAATTTCAACAACCT-CTATG
1 AAATTTTGATAACCTCCTATG
* * *
48869 AAATTTTGATAATCACACTGTG
1 AAATTTTGATAACCTC-CTATG
* *
48891 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTC-CTATG
* *
48913 AAATTCTGATAACCTCGATATG
1 AAATTTTGATAACCTC-CTATG
* *
48935 AAATTTTGATAACCTTCTTATA
1 AAATTTTGATAACC-TCCTATG
* *
48957 AAATTTTGATAACCTTTCTATA
1 AAATTTTGATAACC-TCCTATG
* * *
48979 AAATTTTAATAACCTGATCCCGATT
1 AAATTTTGATAACC---T-CCTATG
* * *
49004 AAATTTTAATAACCACTCTTTAATT
1 AAATTTTGATAA-C-CTC-CT-ATG
*
49029 ATAATTTTGATAACCTTCCTATA
1 A-AATTTTGATAACC-TCCTATG
* ** *
49052 AAATTTTGCTAGTCGCACTATG
1 AAATTTTGATAACCTC-CTATG
*
49074 AAATTTTGATAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
49096 AAATTTTGAT-ACC-CCTATG
1 AAATTTTGATAACCTCCTATG
* * *
49115 AAATTTTGGTAA-CACCTATA
1 AAATTTTGATAACCTCCTATG
* *
49135 AAATTTTGAAAACTTCCCTATG
1 AAATTTTGATAACCT-CCTATG
* *
49157 AAATTATGATAACCATACTATG
1 AAATTTTGATAACC-TCCTATG
*
49179 AAATTTTGA-AGACCATACTATG
1 AAATTTTGATA-ACC-TCCTATG
* * *
49201 ATATTGAGTGATAACATCCTTATG
1 AAATT--TTGATAACCTCC-TATG
49225 AAATTTTGATAAC
1 AAATTTTGATAAC
49238 TACATAGAGA
Statistics
Matches: 686, Mismatches: 168, Indels: 114
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.01
16 2 0.00
19 16 0.02
20 38 0.06
21 30 0.04
22 476 0.69
23 52 0.08
24 30 0.04
25 23 0.03
26 11 0.02
27 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATG
Found at i:48353 original size:23 final size:22
Alignment explanation
Indices: 48303--48390 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 22
48293 AATCACACTG
* * *
48303 TAAAATTTTGATAATCTCCTTA
1 TAAAATTTTAATAACCTCCGTA
*
48325 TGAAATTTTAATAAACCTCCGTA
1 TAAAATTTTAAT-AACCTCCGTA
* **
48348 TAAAATTTTTGATAATTTCCGTAA
1 TAAAA-TTTTAATAACCTCCGT-A
*
48372 TGAAATTTTAATAACCTCC
1 TAAAATTTTAATAACCTCC
48391 CTATGATTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
22 10 0.20
23 30 0.59
24 11 0.22
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.41
Consensus pattern (22 bp):
TAAAATTTTAATAACCTCCGTA
Found at i:48362 original size:46 final size:46
Alignment explanation
Indices: 48303--48429 Score: 136
Period size: 46 Copynumber: 2.8 Consensus size: 46
48293 AATCACACTG
*
48303 TAAAA-TTTTGATAATCTCCTTATGAAATTTTAATAAACCTCCGTA
1 TAAAATTTTTGATAATCTCCTTATGAAATTTTAATAAACCTCCCTA
* *
48348 TAAAATTTTTGATAATTTCCGTAATGAAATTTTAAT-AACCTCCCTA
1 TAAAATTTTTGATAATCTCC-TTATGAAATTTTAATAAACCTCCCTA
* * * * *
48394 T-GATTTTTTTATAA-CATCATTATGAAATTTTGATAA
1 TAAAATTTTTGATAATC-TCCTTATGAAATTTTAATAA
48430 CCATCTTATG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
44 13 0.19
45 18 0.26
46 23 0.34
47 14 0.21
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (46 bp):
TAAAATTTTTGATAATCTCCTTATGAAATTTTAATAAACCTCCCTA
Found at i:48573 original size:87 final size:88
Alignment explanation
Indices: 48482--48642 Score: 200
Period size: 87 Copynumber: 1.8 Consensus size: 88
48472 ACACACACTA
* * ** * * *
48482 TGAAATTTTGATAACCACACTTTGAGATTTTGATAA-CTACATTATAAATTTTTGATAACCT-CC
1 TGAAATTTCGATAACCACACTTTGAAATTCCGATAACCT-CACTATAAAATTTTGAAAACCTCCC
48545 TATGAAATTTTGAAAACTACAATG
65 TATGAAATTTTGAAAACTACAATG
** * *
48569 TGAAATTTCGATAACGTCCCTTTGAAATTCCGATAACCTCCCTATAAAATTTTGAAAACCTCCCT
1 TGAAATTTCGATAACCACACTTTGAAATTCCGATAACCTCACTATAAAATTTTGAAAACCTCCCT
48634 ATGAAATTT
66 ATGAAATTT
48643 AGATTACCTT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
87 47 0.77
88 14 0.23
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (88 bp):
TGAAATTTCGATAACCACACTTTGAAATTCCGATAACCTCACTATAAAATTTTGAAAACCTCCCT
ATGAAATTTTGAAAACTACAATG
Found at i:48707 original size:44 final size:44
Alignment explanation
Indices: 48080--49187 Score: 291
Period size: 44 Copynumber: 25.3 Consensus size: 44
48070 TAGCCTTCCC
* * *
48080 TATGAAATATTGAAAACCTCCCGATGAAATTTTGATAAC--CATT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACA-T
* ** * *
48123 TAATGGAATTTTGATAA-CTGTACTATGGAATTTTGATAACTTCAT
1 T-ATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAACTACAT
* * * * **
48168 TATGAAATTTTGATAACCTTCATATAAAATTTTGACAAGC-ACCG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CTACAT
* * * ** * * * *
48212 TATGCAATTTAGATAATCTCTATGTGAAATGTTGGTAAGCACACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-C-TACAT
*** * * * * *
48258 TATGAAAAACTGATAACCTTCCTA-AAAATGTTAATAA-TCACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACT-ACAT
* * * * * **
48301 TGTAAAATTTTGATAATCTCCTTATGAAATTTTAATAAACCT-CCG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AA-CTACAT
* ** * * **
48346 TATAAAATTTTTGATAATTTCCGTAATGAAATTTTAATAACCT-CCC
1 TATGAAA-TTTTGATAACCTCCCT-ATGAAATTTTGATAA-CTACAT
** * * ** *
48392 TATGATTTTTTTATAACATCATTATGAAATTTTGATAACCATC-T
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTA-CAT
* * * *** * *
48436 TATGAAATATTAATCTA-CAAACTATGGAATTTTGATACAC-ACAC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGATA-ACTACAT
* * * *
48480 TATGAAATTTTGATAACCACACTTTGAGATTTTGATAACTACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* *
48524 TAT-AAATTTTTGATAACCT-CCTATGAAATTTTGAAAACTACAA
1 TATGAAA-TTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* * * * ** **
48567 TGTGAAATTTCGATAACGTCCCTTTGAAATTCCGATAACCT-CCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CTACAT
* * * *
48611 TATAAAATTTTGAAAACCTCCCTATGAAATTTAGATTACCTTACA-
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAAC-TACAT
* * * *
48656 -ATAAAATTTTGATAACCTTCCTATGAAATTTTGGTAATTACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* * * * * *
48699 TATGAAATTTTGAT-GCATCTCTTTG-AA-----AT-ACCACAA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* ** * *
48735 TATGAAATTTTGATAA-TTATACTATGAAATTTCGATAACCT-CTT
1 TATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAA-CTACAT
* * *
48779 TATGAAATTTTGATAACCGT-CCTATGATATTTTGTTATCCT-C-T
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATA-ACTACAT
* * * * * * * * *
48822 CTGTAAAATTTTGATAATCACACTGTGAAA-TTT--CAACAACCT
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* * * * *
48864 CTATGAAATTTTGATAATCACACTGTGAAATTTTGATAA-TCACAC
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACT-ACAT
* ** *
48909 TATGAAATTCTGATAACCTCGATATGAAATTTTGATAACCTTC-T
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CTACAT
* ** * * **
48953 TATAAAATTTTGATAACCTTTCTATAAAATTTTAATAACCTGATCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CT-A-CAT
* * * ** * * *
49000 GATTAAATTTTAATAACCACTCTTTAATTATAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAA-C-CTCCCT-ATGA-AATTTTGATAA-CTACAT
* * ** * * **
49048 TATAAAATTTTGCTAGTCGCACTATGAAATTTTGATAATCT-CCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CTACAT
* *
49092 TATGAAATTTTGAT-A-C-CCCTATGAAATTTTGGTAAC-AC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
* * * * * * *
49131 TATAAAATTTTGAAAACTTCCCTATGAAATTATGATAACCATAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
49175 TATGAAATTTTGA
1 TATGAAATTTTGA
49188 AGACCATACT
Statistics
Matches: 789, Mismatches: 208, Indels: 135
0.70 0.18 0.12
Matches are distributed among these distances:
36 19 0.02
37 5 0.01
38 2 0.00
39 13 0.02
40 4 0.01
41 19 0.02
42 54 0.07
43 80 0.10
44 429 0.54
45 53 0.07
46 50 0.06
47 27 0.03
48 13 0.02
49 5 0.01
50 3 0.00
51 13 0.02
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACTACAT
Found at i:48897 original size:64 final size:65
Alignment explanation
Indices: 48822--48946 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
48812 GTTATCCTCT
*
48822 CTGTAAAATTTTGATAATCACACTGTGAAATT-TCAACAACCTC-TATGAAATTTTGATAATCAC
1 CTGTAAAATTTTGATAATCACACTATGAAATTCT-AACAACCTCATATGAAATTTTGATAATCAC
48885 A
65 A
* * *
48886 CTGTGAAATTTTGATAATCACACTATGAAATTCTGATAACCTCGATATGAAATTTTGATAA
1 CTGTAAAATTTTGATAATCACACTATGAAATTCTAACAACCTC-ATATGAAATTTTGATAA
48947 CCTTCTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
64 37 0.69
65 1 0.02
66 16 0.30
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (65 bp):
CTGTAAAATTTTGATAATCACACTATGAAATTCTAACAACCTCATATGAAATTTTGATAATCACA
Found at i:48916 original size:130 final size:130
Alignment explanation
Indices: 48735--48968 Score: 310
Period size: 130 Copynumber: 1.8 Consensus size: 130
48725 AATACCACAA
* * * ** *
48735 TATGAAATTTTGATAATTATACTATGAAATTTCGATAACCTCTTTATGAAATTTTGATAACCGTC
1 TATGAAATTTTGATAATCACACTATGAAATTTCGATAACCACACTATGAAATTCTGATAACC-TC
* * * * *
48800 -CTATGATATTTTGTTATCC-TCTCTGTAAAATTTTGATAATCACACTGTGAAATTTCAACAACC
65 GATATGAAATTTTGATAACCTTCT-TATAAAATTTTGATAATCACACTGTGAAATTTCAACAACC
48863 TC
129 TC
* * *
48865 TATGAAATTTTGATAATCACACTGTGAAATTTTGATAATCACACTATGAAATTCTGATAACCTCG
1 TATGAAATTTTGATAATCACACTATGAAATTTCGATAACCACACTATGAAATTCTGATAACCTCG
48930 ATATGAAATTTTGATAACCTTCTTATAAAATTTTGATAA
66 ATATGAAATTTTGATAACCTTCTTATAAAATTTTGATAA
48969 CCTTTCTATA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
129 2 0.02
130 83 0.94
131 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (130 bp):
TATGAAATTTTGATAATCACACTATGAAATTTCGATAACCACACTATGAAATTCTGATAACCTCG
ATATGAAATTTTGATAACCTTCTTATAAAATTTTGATAATCACACTGTGAAATTTCAACAACCTC
Found at i:49138 original size:20 final size:19
Alignment explanation
Indices: 49069--49143 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 19
49059 GCTAGTCGCA
*
49069 CTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGAT-A-C-AC
*
49091 CTATGAAATTTTGATACCC
1 CTATGAAATTTTGATACAC
*
49110 CTATGAAATTTTGGTAACAC
1 CTATGAAATTTTGAT-ACAC
*
49130 CTATAAAATTTTGA
1 CTATGAAATTTTGA
49144 AAACTTCCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.33
20 16 0.33
21 1 0.02
22 15 0.31
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (19 bp):
CTATGAAATTTTGATACAC
Found at i:49153 original size:61 final size:63
Alignment explanation
Indices: 49069--49186 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 63
49059 GCTAGTCGCA
* * * *
49069 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGAT-ACC-CCTATGAAATTTTGGTAACAC
1 CTATAAAATTTTGAAAATCTCCCTATGAAATTATGATAACCAACTATGAAATTTTGGTAACAC
49130 CTATAAAATTTTGAAAA-CTTCCCTATGAAATTATGATAACCATACTATGAAATTTTG
1 CTATAAAATTTTGAAAATC-TCCCTATGAAATTATGATAACCA-ACTATGAAATTTTG
49187 AAGACCATAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 1 0.02
61 32 0.65
62 3 0.06
64 13 0.27
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (63 bp):
CTATAAAATTTTGAAAATCTCCCTATGAAATTATGATAACCAACTATGAAATTTTGGTAACAC
Found at i:49878 original size:24 final size:25
Alignment explanation
Indices: 49851--49901 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
49841 AATTGAAATT
*
49851 TTATAATT-ATTTTAAATAGTA-AAA
1 TTAT-ATTAATTTTAAATAATAGAAA
*
49875 TTATATTAATTTTTAATAATAGAAA
1 TTATATTAATTTTAAATAATAGAAA
49900 TT
1 TT
49902 CAGAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.13
24 15 0.65
25 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTATATTAATTTTAAATAATAGAAA
Found at i:63311 original size:15 final size:15
Alignment explanation
Indices: 63288--63336 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
63278 AGGGAACCCT
* *
63288 TTTCCTTCCTTCTCA
1 TTTCTTTCCTTCCCA
*
63303 TTTCTTTCC-TCCCC
1 TTTCTTTCCTTCCCA
63317 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCA
63333 TTTC
1 TTTC
63337 CTCTCTACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 19 0.68
16 5 0.18
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCTTTCCTTCCCA
Found at i:64352 original size:27 final size:27
Alignment explanation
Indices: 64314--64374 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
64304 AATGTCATCC
**
64314 AAATCAATTACAAAATATAACCAATCT
1 AAATCAATTACAAAATATAACCAAAAT
64341 AAATCAATTACAAAATATAACCAAAAT
1 AAATCAATTACAAAATATAACCAAAAT
64368 AAATCAA
1 AAATCAA
64375 GTAGAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (27 bp):
AAATCAATTACAAAATATAACCAAAAT
Found at i:67716 original size:23 final size:24
Alignment explanation
Indices: 67670--67716 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
67660 TTCCTTTATT
*
67670 TTTATTTATTTTTCATTTTCTAAA
1 TTTATTTATGTTTCATTTTCTAAA
* *
67694 TTTATTT-TGTTTGATTTTTTAAA
1 TTTATTTATGTTTCATTTTCTAAA
67717 AAAGCTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATTTATGTTTCATTTTCTAAA
Found at i:79611 original size:14 final size:14
Alignment explanation
Indices: 79592--79619 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
79582 CTAGGCCCTT
79592 CTGTTTGTATTAAG
1 CTGTTTGTATTAAG
79606 CTGTTTGTATTAAG
1 CTGTTTGTATTAAG
79620 AATTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
CTGTTTGTATTAAG
Found at i:80460 original size:12 final size:11
Alignment explanation
Indices: 80443--80476 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
80433 AAGTAAAGTC
80443 TAATTATATAAT
1 TAATTA-ATAAT
80455 TAATTAATATAT
1 TAATTAATA-AT
80467 TAATTAATAA
1 TAATTAATAA
80477 ATATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTAATAAT
Found at i:80470 original size:16 final size:16
Alignment explanation
Indices: 80447--80502 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
80437 AAAGTCTAAT
80447 TATA-TAATTAATTAA
1 TATATTAATTAATTAA
*
80462 TATATTAATTAATAAA
1 TATATTAATTAATTAA
**
80478 TAT-TATAAAAAATTAA
1 TATAT-TAATTAATTAA
*
80494 AATATTAAT
1 TATATTAAT
80503 GGAATAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 5 0.16
16 26 0.81
17 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATTAATTAATTAA
Found at i:82901 original size:24 final size:25
Alignment explanation
Indices: 82869--82916 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
82859 ATCTAAAGTT
* *
82869 ATAAAAAAAAGA-TACAGTGATTAC
1 ATAAAAAAAAAATTACACTGATTAC
82893 ATAAAAAAAAAATTACACTGATTA
1 ATAAAAAAAAAATTACACTGATTA
82917 TTCAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (25 bp):
ATAAAAAAAAAATTACACTGATTAC
Found at i:82964 original size:2 final size:2
Alignment explanation
Indices: 82957--82985 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82947 TCAATAACGT
82957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82986 TTGTTAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83260 original size:60 final size:61
Alignment explanation
Indices: 83166--83286 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 61
83156 TAACAACAAG
* *
83166 GGAGAATTCCTCTTAGGTGTATTGGATTTCAAAAGAATCAATAGTTGGTGGTATGGTGAAA
1 GGAGAATTCCTCTTAGGCGTATTGGACTTCAAAAGAATCAATAGTTGGTGGTATGGTGAAA
83227 GGAGAATTCCTCTTA-GCGTATTGGACTTCAAAAGAATCAATAGTTGGTGGTATGGTGAAA
1 GGAGAATTCCTCTTAGGCGTATTGGACTTCAAAAGAATCAATAGTTGGTGGTATGGTGAAA
83287 ATTAATCAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 43 0.74
61 15 0.26
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (61 bp):
GGAGAATTCCTCTTAGGCGTATTGGACTTCAAAAGAATCAATAGTTGGTGGTATGGTGAAA
Found at i:84880 original size:15 final size:15
Alignment explanation
Indices: 84860--84889 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
84850 ACTGCCACCG
*
84860 CTTGATTTCCTTGAT
1 CTTGATTTCCCTGAT
84875 CTTGATTTCCCTGAT
1 CTTGATTTCCCTGAT
84890 GTTAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
CTTGATTTCCCTGAT
Found at i:91084 original size:49 final size:49
Alignment explanation
Indices: 91012--91120 Score: 209
Period size: 49 Copynumber: 2.2 Consensus size: 49
91002 AACAAATTAC
*
91012 TGTCTCTTTCCTAGTTTTTCGTCTTTCCAAACTTAGTCATCAACTAATT
1 TGTCTCTTTCCTAGTTCTTCGTCTTTCCAAACTTAGTCATCAACTAATT
91061 TGTCTCTTTCCTAGTTCTTCGTCTTTCCAAACTTAGTCATCAACTAATT
1 TGTCTCTTTCCTAGTTCTTCGTCTTTCCAAACTTAGTCATCAACTAATT
91110 TGTCTCTTTCC
1 TGTCTCTTTCC
91121 AACTAATTGG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (49 bp):
TGTCTCTTTCCTAGTTCTTCGTCTTTCCAAACTTAGTCATCAACTAATT
Found at i:92928 original size:8 final size:10
Alignment explanation
Indices: 92906--92932 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
92896 AACTTCAAAC
92906 CTCTCAAATT
1 CTCTCAAATT
92916 CTCTCAAATT
1 CTCTCAAATT
92926 CTCTCAA
1 CTCTCAA
92933 CCTTCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (10 bp):
CTCTCAAATT
Done.