Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016027.1 Corchorus capsularis cultivar CVL-1 contig16048, 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: 101080
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:9179 original size:3 final size:3
Alignment explanation
Indices: 9171--9211 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9161 AATCAAGCTT
9171 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9212 TTGGCATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:11748 original size:44 final size:44
Alignment explanation
Indices: 11704--11889 Score: 154
Period size: 44 Copynumber: 4.3 Consensus size: 44
11694 GAAAGATTAT
* *
11704 CAAAATTTCATAGTGTGGTTACTAAAATTTCATATAGAGGTTAT
1 CAAAATTTCATAGTGTAGTTACTAAAATTTCATATAGAGGTTAC
* *
11748 CAAAACTTCATAGTGTAGTTA-TCAAAATTTC--ATACAGGTTAC
1 CAAAATTTCATAGTGTAGTTACT-AAAATTTCATATAGAGGTTAC
** * *
11790 CAAAATTTCAT--TAAAAGTTACCAAAATTTCATA-AAAGGTTTAC
1 CAAAATTTCATAGT-GTAGTTACTAAAATTTCATATAGAGG-TTAC
* * * * *
11833 CAAAATTTCTTAG-GGATGTTAATAAAATTTCATAT-GAAAGTTAA
1 CAAAATTTCATAGTGTA-GTTACTAAAATTTCATATAG-AGGTTAC
11877 CAAAATTTCATAG
1 CAAAATTTCATAG
11890 GGAGGGAGGT
Statistics
Matches: 113, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
40 1 0.01
41 13 0.12
42 23 0.20
43 17 0.15
44 57 0.50
45 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGTGTAGTTACTAAAATTTCATATAGAGGTTAC
Found at i:11811 original size:21 final size:21
Alignment explanation
Indices: 11764--11887 Score: 101
Period size: 22 Copynumber: 5.8 Consensus size: 21
11754 TTCATAGTGT
* *
11764 AGTTATCAAAATTTCA-TACA
1 AGTTACCAAAATTTCATTAAA
*
11784 GGTTACCAAAATTTCATTAAA
1 AGTTACCAAAATTTCATTAAA
11805 AGTTACCAAAATTTCA-TAAA
1 AGTTACCAAAATTTCATTAAA
*
11825 AGGTTTACCAAAATTTC-TTAGGGA
1 A-G-TTACCAAAATTTCATTA--AA
* ** *
11849 TGTTAATAAAATTTCATATGAA
1 AGTTACCAAAATTTCAT-TAAA
*
11871 AGTTAACAAAATTTCAT
1 AGTTACCAAAATTTCAT
11888 AGGGAGGGAG
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
20 19 0.23
21 19 0.23
22 42 0.50
23 2 0.02
24 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (21 bp):
AGTTACCAAAATTTCATTAAA
Found at i:11835 original size:22 final size:21
Alignment explanation
Indices: 11680--11841 Score: 114
Period size: 22 Copynumber: 7.5 Consensus size: 21
11670 TGATAATCAA
* *
11680 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATA-AAAGGTT
* ***
11702 ATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATA-AAAGGTT
* *
11724 ACTAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATA-AAAGGTT
* * **
11746 ATCAAAACTTCAT-AGTGTAGTT
1 ACCAAAATTTCATAAAAG--GTT
* *
11768 ATCAAAATTTCAT-ACAGGTT
1 ACCAAAATTTCATAAAAGGTT
11788 ACCAAAATTTCATTAAAA-GTT
1 ACCAAAATTTCA-TAAAAGGTT
11809 ACCAAAATTTCATAAAAGGTTT
1 ACCAAAATTTCATAAAAGG-TT
11831 ACCAAAATTTC
1 ACCAAAATTTC
11842 TTAGGGATGT
Statistics
Matches: 114, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
20 22 0.19
21 17 0.15
22 75 0.66
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
ACCAAAATTTCATAAAAGGTT
Found at i:11891 original size:44 final size:43
Alignment explanation
Indices: 11683--11892 Score: 137
Period size: 44 Copynumber: 4.8 Consensus size: 43
11673 TAATCAAACC
* * * * *
11683 AAAATTACATAGAAAGATTATCAAAATTTCATAGTG-TGGTTACT
1 AAAATTTCATA-AAAG-TTACCAAAATTTCATAGGGATAGTTAAT
* * * *
11727 AAAATTTCATATAGAGGTTATCAAAACTTCATAGTG-TAGTT-AT
1 AAAATTTCATA-A-AAGTTACCAAAATTTCATAGGGATAGTTAAT
* * * **
11770 CAAAATTTCATACAGGTTACCAAAATTTCATTA---AAAGTTACC
1 -AAAATTTCATAAAAGTTACCAAAATTTCA-TAGGGATAGTTAAT
*
11812 AAAATTTCATAAAAGGTTTACCAAAATTTCTTAGGGAT-GTTAAT
1 AAAATTTCATAAAA-G-TTACCAAAATTTCATAGGGATAGTTAAT
*
11856 AAAATTTCATATGAAAGTTAACAAAATTTCATAGGGA
1 AAAATTTCATA--AAAGTTACCAAAATTTCATAGGGA
11893 GGGAGGTTAC
Statistics
Matches: 134, Mismatches: 20, Indels: 24
0.75 0.11 0.13
Matches are distributed among these distances:
41 16 0.12
42 18 0.13
43 16 0.12
44 77 0.57
45 4 0.03
46 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (43 bp):
AAAATTTCATAAAAGTTACCAAAATTTCATAGGGATAGTTAAT
Found at i:11944 original size:21 final size:22
Alignment explanation
Indices: 11915--11985 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
11905 AAATTTGTGC
11915 TTATCAAAATTTTATAGG-GAGG
1 TTATCAAAATTTTA-AGGAGAGG
11937 TTAT-AAAATTTTAAGGAGAGG
1 TTATCAAAATTTTAAGGAGAGG
11958 TTATCGAAAATATTT-A-GAGAGG
1 TTATC-AAAAT-TTTAAGGAGAGG
*
11980 ATATCA
1 TTATCA
11986 TAGTTTCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 3 0.07
21 18 0.41
22 14 0.32
23 6 0.14
24 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTTAAGGAGAGG
Found at i:12122 original size:22 final size:22
Alignment explanation
Indices: 12097--12200 Score: 118
Period size: 22 Copynumber: 4.7 Consensus size: 22
12087 TATAGGCAGA
*
12097 TTATCAAAATTTCACATTGTGG
1 TTATCAAAATTTCACAGTGTGG
* *
12119 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAGTGTGG
* *
12141 TTACCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAGTGTGG
* * *
12163 TTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCACAGTGTGG
* *
12185 CTATCAATATTTCACA
1 TTATCAAAATTTCACA
12201 TTGGAGCATG
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTGTGG
Found at i:25625 original size:14 final size:16
Alignment explanation
Indices: 25601--25634 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
25591 TAATTACTTT
25601 CTTTATAATATG-TTG
1 CTTTATAATATGTTTG
25616 CTTT-TAATATGTTTG
1 CTTTATAATATGTTTG
25631 CTTT
1 CTTT
25635 CTTAGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (16 bp):
CTTTATAATATGTTTG
Found at i:26986 original size:31 final size:31
Alignment explanation
Indices: 26946--27036 Score: 164
Period size: 31 Copynumber: 2.9 Consensus size: 31
26936 TGTTCATAAG
* *
26946 TGAACAATTATGAAGAGACTTAATTGTCTTA
1 TGAATAATTATGAAGAGACTTATTTGTCTTA
26977 TGAATAATTATGAAGAGACTTATTTGTCTTA
1 TGAATAATTATGAAGAGACTTATTTGTCTTA
27008 TGAATAATTATGAAGAGACTTATTTGTCT
1 TGAATAATTATGAAGAGACTTATTTGTCT
27037 ATAAAAAGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (31 bp):
TGAATAATTATGAAGAGACTTATTTGTCTTA
Found at i:27115 original size:37 final size:37
Alignment explanation
Indices: 27065--27135 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
27055 ATATGATTAT
* *
27065 TCATAAAGTTATGTCTATTTGCAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
27102 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
27136 GTTGATCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:29570 original size:31 final size:31
Alignment explanation
Indices: 29529--29588 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
29519 TGTTCATAAG
29529 TGAACAATTATGAAGAGACTTATTTGTCTTA
1 TGAACAATTATGAAGAGACTTATTTGTCTTA
*
29560 TGAATAATTATGAAGAGACTTATTTGTCT
1 TGAACAATTATGAAGAGACTTATTTGTCT
29589 ATAAAAGGTA
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:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (31 bp):
TGAACAATTATGAAGAGACTTATTTGTCTTA
Found at i:29667 original size:37 final size:37
Alignment explanation
Indices: 29617--29687 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
29607 ATATAATTAT
* *
29617 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
29654 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
29688 GTTGATCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:36879 original size:22 final size:22
Alignment explanation
Indices: 36837--36884 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
36827 AAATAGCAAT
*
36837 TAAAAAGAAAAAACAATTAAAC
1 TAAAAAGAAAAAACAACTAAAC
* *
36859 TAAAAATAAAACAA-AACTAAAG
1 TAAAAAGAAAA-AACAACTAAAC
36881 TAAA
1 TAAA
36885 TCTAAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (22 bp):
TAAAAAGAAAAAACAACTAAAC
Found at i:41786 original size:357 final size:356
Alignment explanation
Indices: 41132--41840 Score: 1355
Period size: 357 Copynumber: 2.0 Consensus size: 356
41122 GTTGCCAATT
*
41132 TTCTGTTTTTGGAAACAAAACAGTGAAAACATGTTTGGTATGTTGTTTCTGTTTTCAAAAATTTT
1 TTCTGTTTTTGGAAACAAAACAGTGAAAACATGTTTGGTAGGTTGTTTCTGTTTTCAAAAATTTT
41197 GGAAACAGAATCAGTGTTTTGGAAAAAAGTGGAAGCAAAAATTTTATGCTTTCATGTTTTTCCAA
66 GGAAACAGAATCAGTGTTTTGGAAAAAAGTGGAAGCAAAAATTTTATGCTTTCATGTTTTTCCAA
*
41262 AACACTTTCAAAACATAGAAGCACAGTCATGAACAGCAACTCACATACATTTTCACTTTTTTTAA
131 AACACTTTCAAAACACAGAAGCACAGTCATGAACAGCAACTCACATACATTTTCACTTTTTTTAA
41327 AAAAACCTTTTTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTTTGTTTTCAAA
196 AAAAACCTTTTTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTTTGTTTTCAAA
41392 ATATTGACAGCGCAACAAATACAAAACGAAAACGAAACAAAAACAAAAAACAGAAAAACGAAAAC
261 ATATTGACAGCGCAACAAATACAAAACGAAAACGAAACAAAAACAAAAAACAGAAAAACGAAAAC
*
41457 GATGTCAAACGGCCCCTTAATTTTACACTGA
326 GATGCCAAACGGCCCCTTAATTTTACACTGA
41488 TTCTGTTTTTGGAAACAAAACAGTGAAAACATGTTTGGTAGGTTGTTTCTGTTTTCAAAAATTTT
1 TTCTGTTTTTGGAAACAAAACAGTGAAAACATGTTTGGTAGGTTGTTTCTGTTTTCAAAAATTTT
*
41553 GGAAACAGAATCAGTGTTTTGGAAAAAAAGTGGAAGCAAAAATTTTGTGCTTTCATGTTTTTCCA
66 GGAAACAGAATCAGTGTTTTGG-AAAAAAGTGGAAGCAAAAATTTTATGCTTTCATGTTTTTCCA
*
41618 AAACACTTTCAAAACACAGAAGCACAGTCATGAACAGTAACTCACATACATTTTCACTTTTTTTA
130 AAACACTTTCAAAACACAGAAGCACAGTCATGAACAGCAACTCACATACATTTTCACTTTTTTTA
41683 AAAAAACCTTTTTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTTTGTTTTCAA
195 AAAAAACCTTTTTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTTTGTTTTCAA
*
41748 AATATTGACAGCGCAACAAATACAAAACGAAAACGAAACAAAAACAAAAAACATAAAAACGAAAA
260 AATATTGACAGCGCAACAAATACAAAACGAAAACGAAACAAAAACAAAAAACAGAAAAACGAAAA
41813 CGATGCCAAACGGCCCCTTAATTTTACA
325 CGATGCCAAACGGCCCCTTAATTTTACA
41841 GTCATGTCAA
Statistics
Matches: 346, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
356 86 0.25
357 260 0.75
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (356 bp):
TTCTGTTTTTGGAAACAAAACAGTGAAAACATGTTTGGTAGGTTGTTTCTGTTTTCAAAAATTTT
GGAAACAGAATCAGTGTTTTGGAAAAAAGTGGAAGCAAAAATTTTATGCTTTCATGTTTTTCCAA
AACACTTTCAAAACACAGAAGCACAGTCATGAACAGCAACTCACATACATTTTCACTTTTTTTAA
AAAAACCTTTTTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTTTGTTTTCAAA
ATATTGACAGCGCAACAAATACAAAACGAAAACGAAACAAAAACAAAAAACAGAAAAACGAAAAC
GATGCCAAACGGCCCCTTAATTTTACACTGA
Found at i:64328 original size:139 final size:140
Alignment explanation
Indices: 64074--64351 Score: 515
Period size: 139 Copynumber: 2.0 Consensus size: 140
64064 AAGATAATTC
64074 TTTTTAGAGAATACAATATTCAAATCTCATTACAATCAAATAATTCCTTATATGTTGTTATTAAA
1 TTTTTAGAGAATACAATATTCAAATCTCATTACAATCAAATAATTCCTTATATGTTGTTATTAAA
*
64139 AAAAAATCTTTATATGCCCAAACATCCATTGAGAAATGACCAAATAAACAAACTATAATAAACAT
66 AAAAAATCCTTATATGCCCAAACATCCATTGAGAAATGACCAAATAAACAAACTATAATAAACAT
64204 AACAAAGCCT
131 AACAAAGCCT
*
64214 TTTTTAGGGAAATACAATATTCAAATCTCATTACAATCAAATAATTCCTTATATGTTGTTA-T-A
1 TTTTTAGAG-AATACAATATTCAAATCTCATTACAATCAAATAATTCCTTATATGTTGTTATTAA
64277 AAAAAAATCCTTATATGCCCAAACATCCATTGAGAAATGACCAAATAAACAAACTATAATAAACA
65 AAAAAAATCCTTATATGCCCAAACATCCATTGAGAAATGACCAAATAAACAAACTATAATAAACA
64342 TAACAAAGCC
130 TAACAAAGCC
64352 AACAAAACCC
Statistics
Matches: 135, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
139 75 0.56
140 9 0.07
141 51 0.38
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (140 bp):
TTTTTAGAGAATACAATATTCAAATCTCATTACAATCAAATAATTCCTTATATGTTGTTATTAAA
AAAAAATCCTTATATGCCCAAACATCCATTGAGAAATGACCAAATAAACAAACTATAATAAACAT
AACAAAGCCT
Found at i:66763 original size:12 final size:12
Alignment explanation
Indices: 66746--66776 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
66736 TACTAAACAA
66746 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
66758 ATCCTCTTCAAT
1 ATCCTCCTCAAT
66770 ATCCTCC
1 ATCCTCC
66777 AAAACTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:67157 original size:87 final size:87
Alignment explanation
Indices: 66947--67168 Score: 245
Period size: 87 Copynumber: 2.6 Consensus size: 87
66937 GACCACTCCG
* * * * * * *
66947 ATTTGAATTCAAAATATCCACCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACCATAA
1 ATTTGAATTCAAAATATTCTCCACCTAATCAATTTCCAAAGATTTTGCACCATAACCAACCATAA
67012 CTCCATTAGGAAGATCACTAAA
66 CTCCATTAGGAAGATCACTAAA
* * * *
67034 ATTTGAATTCAAACTA-TCTTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCAT
1 ATTTGAATTCAAAATATTC-TCCACC-TAATCAATTTCCAAAGATTTTGCACCATAACCAACCAT
67097 AACTCCATTAGGAAGATCAC-AATCA
64 AACTCCATTAGGAAGATCACTAA--A
* * * *
67122 A-TTGAATTCAAATTATTCTCCACCTTATCAATTTCCACAGAATTTGC
1 ATTTGAATTCAAAATATTCTCCACCTAATCAATTTCCAAAGATTTTGC
67169 GCCTAAAAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
86 6 0.05
87 100 0.88
88 7 0.06
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (87 bp):
ATTTGAATTCAAAATATTCTCCACCTAATCAATTTCCAAAGATTTTGCACCATAACCAACCATAA
CTCCATTAGGAAGATCACTAAA
Found at i:69779 original size:2 final size:2
Alignment explanation
Indices: 69772--69830 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
69762 TTCGTACTTT
* * *
69772 TA TA TA TA GTA TA TA TA TA TA TA TA TT TA TA TT TA TA TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
69815 TT TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA
69831 ATTTTCGTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (2 bp):
TA
Found at i:70782 original size:68 final size:67
Alignment explanation
Indices: 70668--70804 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 67
70658 CCACCCCACA
* *
70668 CAATTACAAGAAGCTCCAAAGTGCAACCCTACACAAAAGAACCAAACCACACAAATACAACAACA
1 CAATAACAAGAAGCTCCAAAGTACAACCCTACACAAAAGAACCAAACCACACAAAT-CAACAACA
70733 AAC
65 AAC
* * *
70736 CAATAACAAGAAGCTCCAAAGTACAACCCTACATAAAAGAACCAAACCACACAAATCTACAGCAA
1 CAATAACAAGAAGCTCCAAAGTACAACCCTACACAAAAGAACCAAACCACACAAATCAACAACAA
70801 AC
66 AC
70803 CA
1 CA
70805 GAACAGAAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 11 0.17
68 53 0.83
ACGTcount: A:0.53, C:0.31, G:0.07, T:0.09
Consensus pattern (67 bp):
CAATAACAAGAAGCTCCAAAGTACAACCCTACACAAAAGAACCAAACCACACAAATCAACAACAA
AC
Found at i:76728 original size:22 final size:20
Alignment explanation
Indices: 76703--76742 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
76693 CACTTAACTT
76703 TTAAATCCGCTAATCATTTTGA
1 TTAAATCCGC-AAT-ATTTTGA
*
76725 TTAATTCCGCAATATTTT
1 TTAAATCCGCAATATTTT
76743 TCTAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (20 bp):
TTAAATCCGCAATATTTTGA
Found at i:81600 original size:4 final size:4
Alignment explanation
Indices: 81593--81623 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
81583 TATATATATA
81593 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
81624 AAATATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:87201 original size:42 final size:42
Alignment explanation
Indices: 87154--87238 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
87144 TTCAAATTTA
** *
87154 TACCTTCTTATATAA-TTCCATGTTTTCTTGACGAATTAGGTT
1 TACCTTCTTATA-AAGTTCCACATTTTCTTGACGAATGAGGTT
*
87196 TACCTTCTTATAAAGTTCCACATTTTCTTGATGAATGAGGTT
1 TACCTTCTTATAAAGTTCCACATTTTCTTGACGAATGAGGTT
87238 T
1 T
87239 CCCTGAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (42 bp):
TACCTTCTTATAAAGTTCCACATTTTCTTGACGAATGAGGTT
Found at i:94843 original size:18 final size:18
Alignment explanation
Indices: 94814--94859 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
94804 ATTCAGTATC
94814 AAATTC-AGTAGCAATAA
1 AAATTCTAGTAGCAATAA
94831 AAATTCTAGTAGCAATAA
1 AAATTCTAGTAGCAATAA
*
94849 AAATTTTAGTA
1 AAATTCTAGTA
94860 CTTAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (18 bp):
AAATTCTAGTAGCAATAA
Found at i:94868 original size:14 final size:15
Alignment explanation
Indices: 94849--94879 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
94839 GTAGCAATAA
94849 AAATTTT-AGTACTT
1 AAATTTTCAGTACTT
94863 AAATTTTCAGTACTT
1 AAATTTTCAGTACTT
94878 AA
1 AA
94880 TTTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
AAATTTTCAGTACTT
Found at i:95995 original size:13 final size:13
Alignment explanation
Indices: 95977--96019 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
95967 AGCTAAATTA
95977 AAAAAATAATTTT
1 AAAAAATAATTTT
**
95990 AAAAAATAAAATTAA
1 AAAAAAT--AATTTT
96005 AAAAAATAATTTT
1 AAAAAATAATTTT
96018 AA
1 AA
96020 GTACAAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.54
15 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:96019 original size:15 final size:15
Alignment explanation
Indices: 95976--96019 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
95966 CAGCTAAATT
95976 AAAAAAATAATTTTA
1 AAAAAAATAATTTTA
95991 AAAAATAA-AA--TTA
1 AAAAA-AATAATTTTA
96004 AAAAAAATAATTTTA
1 AAAAAAATAATTTTA
96019 A
1 A
96020 GTACAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.08
13 10 0.40
15 11 0.44
16 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAAATAATTTTA
Found at i:100361 original size:1 final size:1
Alignment explanation
Indices: 100355--100383 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
100345 TCGTTTCGTC
100355 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
100384 AAATTGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.