Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008038.1 Corchorus capsularis cultivar CVL-1 contig08059, 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: 75044
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:7007 original size:103 final size:103
Alignment explanation
Indices: 6872--7227 Score: 480
Period size: 103 Copynumber: 3.4 Consensus size: 103
6862 AAACTTTAGA
* ** * * *
6872 GGGGCTAAATTTAGTG-AATTAGTTTTATATTTTATCCCTAAAACCTTATAACAAAACATTATTA
1 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATACGTTATTA
* * *
6936 ATTTTGGAATTTATCCTTTAAATAAAATTTATCAATTT
66 ATTTTGGAATTTACCCTTAAAATAAAATTTATTAATTT
6974 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATACGTTATTA
1 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATACGTTATTA
* *
7039 ATTTTGAAATTTACCCTTCAAATAAAATTTATTAATTT
66 ATTTTGGAATTTACCCTTAAAATAAAATTTATTAATTT
* * *
7077 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATACCAATATGTTATTG
1 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATACGTTATTA
* *
7142 ATTTTGGAATTTACCCTTAAAACAAAATTAAAATTTTAATTT
66 ATTTTGGAATTTACCCTTAAAATAAAATT----TATTAATTT
* * * * *
7184 GGGGCTAAACTTAATGACATCAGTTTTATATCTAATTTCTAAAA
1 GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
7228 TGTTATAATA
Statistics
Matches: 227, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
102 15 0.07
103 165 0.73
107 47 0.21
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (103 bp):
GGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATACGTTATTA
ATTTTGGAATTTACCCTTAAAATAAAATTTATTAATTT
Found at i:12585 original size:16 final size:16
Alignment explanation
Indices: 12564--12600 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12554 GATAAAGTGG
*
12564 GGGTGGGGGGCGGCGT
1 GGGTGGGGGGAGGCGT
*
12580 GGGTGGGGTGAGGCGT
1 GGGTGGGGGGAGGCGT
12596 GGGTG
1 GGGTG
12601 ATTTGAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.08, G:0.73, T:0.16
Consensus pattern (16 bp):
GGGTGGGGGGAGGCGT
Found at i:33131 original size:30 final size:30
Alignment explanation
Indices: 33076--33132 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
33066 ATTCTTGCTT
*
33076 CTTGAAATAATTCTTCAATAGTCTTCATGA
1 CTTGAAATAATTCTTCAATAATCTTCATGA
*
33106 CTTGAAATCA-TCTTCAATAAATCTTCA
1 CTTGAAATAATTCTTCAAT-AATCTTCA
33133 ATCACGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
CTTGAAATAATTCTTCAATAATCTTCATGA
Found at i:35792 original size:20 final size:21
Alignment explanation
Indices: 35771--35808 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35761 AATTAATTAT
35771 TTTA-ATATTA-ATTTTTTTA
1 TTTATATATTATATTTTTTTA
35790 TTTATATATTATATTTTTT
1 TTTATATATTATATTTTTT
35809 ACTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATATATTATATTTTTTTA
Found at i:47063 original size:156 final size:161
Alignment explanation
Indices: 46776--47487 Score: 789
Period size: 167 Copynumber: 4.3 Consensus size: 161
46766 CTTAAATGAC
* * *
46776 CTAACTTTTGATTCTTGAGGTGATTAAATAACTAGA-CTTTTTGGTCATTTCTCAATTGACTTTA
1 CTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ATCTTTTTGGTCATTTCTCAATGGACTTGA
* * * ** *
46840 ATAGAGTAGTGGAATTACTAAAAGATCCTAC--CAAGGCTTGCTTTTGGAGTTAGAGAACTTATT
65 ATAGAGTAGTGGAATTAATAAAAGATCC-ACATCAAGGATTGATGATGGAGTTAGAGAACTAATT
* *
46903 TTTTTCGCCTTTTCCTACTTGGCAG-A-TT-A-
129 TTTTTCGTCTTTACCTACTTGGCAGTACTTAAT
*
46932 CTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAA
1 CTAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCAATGGACTTGAA
* * *
46997 TAGAGTAGTGAAATTAATAAAAGATCCACATCAAGGATTGATGAT-GAGCTAGAGAACTAATCTT
66 TAGAGTAGTGGAATTAATAAAAGATCCACATCAAGGATTGATGATGGAGTTAGAGAACTAATTTT
* *
47061 TTTCGTCTTTAACTACTTGACAGATTACTTAAATGT
131 TTTCGTCTTTACCTACTTGGCAG--TACTT-AA--T
* * * * * *
47097 CCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTAGTCATTTTTTAATTGACTTTA
1 -CTAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCAATGGACTTGA
* * * * * ** *
47162 ATAGAGTAATGGAATTACTAAAAGATCC-CTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATT
65 ATAGAGTAGTGGAATTAATAAAAGATCCAC-ATCAAGGATTGATGATGGAGTTAGAGAACTAATT
* *
47226 TTTTTCGTCTTTTCCTACTTGGCAGATTATTTAAATGT
129 TTTTTCGTCTTTACCTACTTGGCAG--TACTT-AA--T
* *
47264 CCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTTAATGGACTTGA
1 -CTAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCAATGGACTTGA
*
47329 ATAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGATTGATGAT-GAGTTAGAGAACTAATTT
65 ATAGAGTAGTGGAATTAATAAAAGATCCACATCAAGGATTGATGATGGAGTTAGAGAACTAA-TT
*
47393 TTTTTCGTCTTTACCTACTTGGTAGATTACTTAAATAT
129 TTTTTCGTCTTTACCTACTTGGCAG--TACTT--A-AT
* *
47431 CCTAACTTTTGATTCATT-AGGGGATTAAATAACTAAACTTTTTGCTCATTTCTCAAT
1 -CTAACTTTTGATTC-TTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCAAT
47488 TGACAAATGA
Statistics
Matches: 476, Mismatches: 60, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
155 3 0.01
156 119 0.25
157 10 0.02
159 1 0.00
160 2 0.00
162 1 0.00
165 1 0.00
166 107 0.22
167 226 0.47
168 5 0.01
169 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (161 bp):
CTAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCAATGGACTTGAA
TAGAGTAGTGGAATTAATAAAAGATCCACATCAAGGATTGATGATGGAGTTAGAGAACTAATTTT
TTTCGTCTTTACCTACTTGGCAGTACTTAAT
Found at i:47277 original size:167 final size:165
Alignment explanation
Indices: 46932--47487 Score: 799
Period size: 167 Copynumber: 3.3 Consensus size: 165
46922 TGGCAGATTA
* *
46932 CTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAA
1 CTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAA
* * *
46997 TAGAGTAGTGAAATTAATAAAAGATCCACATCAAGGATTGATGATGAGCTAGAGAACTAATCTTT
66 TAGAGTAGTGGAATTAATAAAAGATCC-CATCAAGGATTGATGATGAGTTAGAGAACTAATTTTT
* *
47062 TTCGTCTTTAACTACTTGACAGATTACTTAAATGTC
130 TTCGTCTTTACCTACTTGGCAGATTACTTAAATGTC
* * * * *
47098 CTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTAGTCATTTTTTAATTGACTTTAA
1 CTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAA
* * * * * ** *
47163 TAGAGTAATGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTT
66 TAGAGTAGTGGAATTAATAAAAGATCCC-ATCAAGGATTGATGAT-GAGTTAGAGAACTAATTTT
* *
47228 TTTCGTCTTTTCCTACTTGGCAGATTATTTAAATGTC
129 TTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTC
* * *
47265 CTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTTAATGGACTTGAA
1 CTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAA
47330 TAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGATTGATGATGAGTTAGAGAACTAATTTTT
66 TAGAGTAGTGGAATTAATAAAAGAT-CCCATCAAGGATTGATGATGAGTTAGAGAACTAA-TTTT
* *
47395 TTTCGTCTTTACCTACTTGGTAGATTACTTAAATATC
129 TTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTC
*
47432 CTAACTTTTGATTCATT-AGGGGATTAAATAACTAAACTTTTTGCTCATTTCTCAAT
1 CTAACTTTTGATTC-TTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
47488 TGACAAATGA
Statistics
Matches: 341, Mismatches: 44, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
165 1 0.00
166 107 0.31
167 228 0.67
168 5 0.01
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (165 bp):
CTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAA
TAGAGTAGTGGAATTAATAAAAGATCCCATCAAGGATTGATGATGAGTTAGAGAACTAATTTTTT
TCGTCTTTACCTACTTGGCAGATTACTTAAATGTC
Found at i:47973 original size:2 final size:2
Alignment explanation
Indices: 47966--47997 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47956 TACAGTTTTA
*
47966 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47998 GACTAGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48261 original size:16 final size:16
Alignment explanation
Indices: 48240--48270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48230 TTGAAAAATA
48240 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
48256 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
48271 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:49113 original size:202 final size:199
Alignment explanation
Indices: 48611--49282 Score: 902
Period size: 200 Copynumber: 3.4 Consensus size: 199
48601 AAAATAAGGG
* * * *
48611 TTATTACACAAATACACTGTCAATGTAAATTTTAGATTCCATAAGCAGGTTAAGAAGTTGACACA
1 TTATTATAC-AATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
* * * * *
48676 TACCCTATTTAATAATTAATTAAATAATTGATATTAATACGTATTCCCTAAGGGGACACATGTCA
65 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA-GGGACACATGTCA
** *
48741 ACCCTTAAACCATGCACGTACAGTCTGCTAAACTCCACTGA-AGGTGTATTGTATAA-TTTTTTT
129 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACA-GTGTATTGTATAATTTTTTTT
48804 TATAGGA
193 TATAGGA
** * * *
48811 TTATTATACAATACACTGTCTGTGTAAATTTTGAACTCCATAACCGGGTTAAGAAGTTGACATAT
1 TTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
* * * *
48876 ACCCTATTTCATAATTAATTAGATATTAAAATATTAATACATATTGCCTAAGAGGACACATGTCA
66 ACCCCATTTCATAATTAATTAAATATT-TAATATTAATACATATTCCCTAAG-GGACACATGTCA
** *
48941 ACCCTTAAACCCCGTGCGTGTAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTTGTTT
129 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTT-TTT
*
49006 TATATGA
193 TATAGGA
* * *
49013 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGTGGGTTAAGAAGTTGACATGA
1 TTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA-CA
* *
49078 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCCAAGGGATACATGTCAA
65 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAA
* * * *
49143 -CCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGCCTGTGTATTGCATAATTTTTCTTT-
130 CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTTTTTTA
49206 TAGGA
195 TAGGA
* * * * *
49211 TTATTATACAATATACTGTCAATATAAATTTTGGATTGCATAAGCGAGTTAAGAAGTTGACACAT
1 TTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
49276 ACCCCAT
66 ACCCCAT
49283 ATATACTACA
Statistics
Matches: 416, Mismatches: 50, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
197 9 0.02
198 59 0.14
199 76 0.18
200 140 0.34
201 17 0.04
202 88 0.21
203 27 0.06
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
TTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
ACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAAC
CCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTTTTTTAT
AGGA
Found at i:51852 original size:35 final size:34
Alignment explanation
Indices: 51787--51960 Score: 195
Period size: 35 Copynumber: 5.0 Consensus size: 34
51777 TGCATTAAAC
*
51787 AAGTCAGTAATAAGTTAATTCAGGGTAATTAAGT
1 AAGTCAGTAATAACTTAATTCAGGGTAATTAAGT
* * * *
51821 AAGTCAGTAACCAACTTAACTCAGGATAATTAAGC
1 AAGTCAGTAA-TAACTTAATTCAGGGTAATTAAGT
*
51856 AAGTCAATAATAACTTAATTCAGGGTAATTAAGT
1 AAGTCAGTAATAACTTAATTCAGGGTAATTAAGT
* * *
51890 AAATCAGTAAGTAATTTAATTCAAGGTAATTAAGT
1 AAGTCAGTAA-TAACTTAATTCAGGGTAATTAAGT
* ** *
51925 AAGTAAGGTAATTTTCTTAATTTAGGGTAATTAAGT
1 AAGTCA-GTAA-TAACTTAATTCAGGGTAATTAAGT
51961 TAGTTAAGAA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
34 38 0.33
35 54 0.47
36 23 0.20
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.33
Consensus pattern (34 bp):
AAGTCAGTAATAACTTAATTCAGGGTAATTAAGT
Found at i:51920 original size:69 final size:69
Alignment explanation
Indices: 51780--51960 Score: 204
Period size: 69 Copynumber: 2.6 Consensus size: 69
51770 GTATTCATGC
* * * *
51780 ATTAAACAAGTCAGTAATAAGTTAATTCAGGGTAATTAAGTAAGTCAGTAACCAACTTAACTCAG
1 ATTAAGCAAGTCAATAATAACTTAATTCAGGGTAATTAAGTAAATCAGTAACCAACTTAACTCAG
51845 GATA
66 GATA
** * *
51849 ATTAAGCAAGTCAATAATAACTTAATTCAGGGTAATTAAGTAAATCAGTAAGTAATTTAATTCAA
1 ATTAAGCAAGTCAATAATAACTTAATTCAGGGTAATTAAGTAAATCAGTAACCAACTTAACTC-A
51914 GG-TA
65 GGATA
* ** *
51918 ATTAAGTAAGT-AAGGTAATTTTCTTAATTTAGGGTAATTAAGT
1 ATTAAGCAAGTCAA--TAA-TAACTTAATTCAGGGTAATTAAGT
51961 TAGTTAAGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
68 2 0.02
69 67 0.70
70 6 0.06
71 21 0.22
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (69 bp):
ATTAAGCAAGTCAATAATAACTTAATTCAGGGTAATTAAGTAAATCAGTAACCAACTTAACTCAG
GATA
Found at i:51936 original size:27 final size:25
Alignment explanation
Indices: 51879--51937 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
51869 CTTAATTCAG
*
51879 GGTAATTAAGTAAATCAGTAAGTAA
1 GGTAATTAAGTAAATAAGTAAGTAA
** *
51904 TTTAATTCAAGGTAATTAAGTAAGTAA
1 GGTAATT-AA-GTAAATAAGTAAGTAA
51931 GGTAATT
1 GGTAATT
51938 TTCTTAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 5 0.19
26 2 0.08
27 19 0.73
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (25 bp):
GGTAATTAAGTAAATAAGTAAGTAA
Found at i:52034 original size:51 final size:51
Alignment explanation
Indices: 51965--52086 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
51955 TTAAGTTAGT
* * ***
51965 TAAGAAGTAAAAAGGATAATCAATAATTTG-CTTAATTTGGAGTAACTAAGG
1 TAAGAAGTAAAAATGATAATCAATAA-TCGACTTAATTCAAAGTAACTAAGG
* * *
52016 TAAGAAGTAAAAATGATAATCAGTAATCGACTTAATTCAAAGTAATTAAGT
1 TAAGAAGTAAAAATGATAATCAATAATCGACTTAATTCAAAGTAACTAAGG
* *
52067 TAAAAAGTAAAAATGGTAAT
1 TAAGAAGTAAAAATGATAAT
52087 TAGTAATAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (51 bp):
TAAGAAGTAAAAATGATAATCAATAATCGACTTAATTCAAAGTAACTAAGG
Found at i:52144 original size:40 final size:40
Alignment explanation
Indices: 52100--52179 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
52090 TAATAATTGG
52100 CTTAATTTTGGGGTAGTTAAGTTGGTTAAGAAGTAAAAGA
1 CTTAATTTTGGGGTAGTTAAGTTGGTTAAGAAGTAAAAGA
52140 CTTAATTTTGGGGTAGTTAAGTTGGTTAAGAAGTAAAAGA
1 CTTAATTTTGGGGTAGTTAAGTTGGTTAAGAAGTAAAAGA
52180 GAAAAGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (40 bp):
CTTAATTTTGGGGTAGTTAAGTTGGTTAAGAAGTAAAAGA
Found at i:52270 original size:52 final size:52
Alignment explanation
Indices: 52211--52378 Score: 180
Period size: 52 Copynumber: 3.1 Consensus size: 52
52201 TTAAGTTAAT
** * *
52211 TAAAAAAAAAGAGGGATAATAAAATGGCTTATTTCGGGGTAAATTGAGTCAG-
1 TAAAAAAAAA-AAAGATAATCAAATGGCTTATTTCAGGGTAAATTGAGTCAGA
*
52263 TAAAAAAATAAAAAAATAATCAAATGGCTTAATTT-AGGGTAAATTGAGTCAGTTAA
1 TAAAAAAA-AAAAAGATAATCAAATGGCTT-ATTTCAGGGTAAATTGAGTCAG---A
*
52319 TAAAAGAAAAAAAAAGATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCA-A
1 T-AAA-AAAAAAAAAGATAATCAAATGGCTTATTTCAGGGTAAATTGAGTCAGA
*
52372 TTAAAAA
1 TAAAAAA
52379 GGTAAAAAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
51 3 0.03
52 41 0.41
53 8 0.08
56 4 0.04
57 39 0.39
58 4 0.04
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (52 bp):
TAAAAAAAAAAAAGATAATCAAATGGCTTATTTCAGGGTAAATTGAGTCAGA
Found at i:52386 original size:57 final size:55
Alignment explanation
Indices: 52225--52409 Score: 214
Period size: 57 Copynumber: 3.4 Consensus size: 55
52215 AAAAAAGAGG
* * * * *
52225 GATAATAAAATGGCTTATTTCGGGGTAAATTGAGTC-AGTAAAAA-AATAAAAAA
1 GATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCAATTAAAAAGAAAAAAAAA
* *
52278 -ATAATCAAATGGCTTAATTTAGGGTAAATTGAGTCAGTTAATAAAAGAAAAAAAAA
1 GATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCAATT-A-AAAAGAAAAAAAAA
** *
52334 GATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCAATTAAAAAGGTAAAAAAG
1 GATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCAATTAAAAAGAAAAAAAAA
* **
52389 GATACTCAGTTGGCTTAATTC
1 GATAATCAAATGGCTTAATTC
52410 GGGATAATTA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
52 31 0.28
53 1 0.01
54 1 0.01
55 33 0.29
56 9 0.08
57 37 0.33
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (55 bp):
GATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCAATTAAAAAGAAAAAAAAA
Found at i:52439 original size:109 final size:106
Alignment explanation
Indices: 52201--52432 Score: 236
Period size: 109 Copynumber: 2.2 Consensus size: 106
52191 ATTAGCTTAG
** * *
52201 TTAAGTTAATTAA-AAAAAAAGAGGGATAATAAAATGGCTTATTTCGGGGTAAATTGAGTCAGTA
1 TTAAGTTAATTAATAAAAAAAGAAAGATAATAAAATGGCTTAATTCAGGGTAAATTGAGTCAGTA
52265 AAAAAATAAAAAAATAATCAAATGGCTTAATTTAGGGTAAA
66 AAAAAATAAAAAAATAATCAAATGGCTTAATTTAGGGTAAA
* * * * *
52306 TTGAGTCAGTTAATAAAAGAAAAAAAAAGATAATCAAATGGCTTAATTCAGGGTAAATTGAGTCA
1 TTAAGTTAATTAAT--AA-AAAAAGAAAGATAATAAAATGGCTTAATTCAGGGTAAATTGAGTC-
* ** * ** *
52371 ATTAAAAAGGTAAAAAAGGATACTCAGTTGGCTTAA-TTCGGG-ATAA
62 AGTAAAAAAATAAAAAA--ATAATCAAATGGCTTAATTTAGGGTA-AA
52417 TTAAGTTAATTAATAA
1 TTAAGTTAATTAATAA
52433 CTAAAAAGGT
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
105 10 0.10
108 2 0.02
109 41 0.41
110 15 0.15
111 18 0.18
112 14 0.14
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (106 bp):
TTAAGTTAATTAATAAAAAAAGAAAGATAATAAAATGGCTTAATTCAGGGTAAATTGAGTCAGTA
AAAAAATAAAAAAATAATCAAATGGCTTAATTTAGGGTAAA
Found at i:57428 original size:3 final size:3
Alignment explanation
Indices: 57415--57457 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
57405 TTTTGGTTCC
57415 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
57458 TTACTGTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:58569 original size:81 final size:79
Alignment explanation
Indices: 58422--58592 Score: 288
Period size: 81 Copynumber: 2.1 Consensus size: 79
58412 CACCGATTTG
*
58422 GGTGTTCAGCCGTCTTACGAGGTTGATGTCTCATAGAGACGATCGTCTTCTCGTCAAGTTATACA
1 GGTGTTCAGCCGTCTTACGAGGTTGATGTCTCATAGAGACGATCGTCTTCCCGTCAAGTTATACA
58487 GGGACACCTTGTTTA
66 -GGACACCTTGTTTA
* *
58502 GGTGTTCATCCGTTCTTACGAGGTTGATGTCTTATAGAGACGATCGTCTTCCCGTCAAGTTATAC
1 GGTGTTCAGCCG-TCTTACGAGGTTGATGTCTCATAGAGACGATCGTCTTCCCGTCAAGTTATAC
58567 AGGACACCTTGTTTA
65 AGGACACCTTGTTTA
*
58582 GGCGTTCAGCC
1 GGTGTTCAGCC
58593 ATCATACTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
80 34 0.40
81 51 0.60
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (79 bp):
GGTGTTCAGCCGTCTTACGAGGTTGATGTCTCATAGAGACGATCGTCTTCCCGTCAAGTTATACA
GGACACCTTGTTTA
Found at i:58626 original size:80 final size:81
Alignment explanation
Indices: 58425--58613 Score: 258
Period size: 81 Copynumber: 2.4 Consensus size: 81
58415 CGATTTGGGT
* * * *
58425 GTTCAGCCG-TCTTACGAGGTTGATGTCTCATAGAGACGATCGTCTTCTCGTCAAGTTATACAGG
1 GTTCAGCCGATCATACGAGGTAGATGTCTTATAGAGACGATCGTCTTCCCGTCAAGTTATACAGG
*
58489 GACACCTTGTTTAGGT
66 GACACCTTGTTTAGGC
* * * *
58505 GTTCATCCGTTCTTACGAGGTTGATGTCTTATAGAGACGATCGTCTTCCCGTCAAGTTATACA-G
1 GTTCAGCCGATCATACGAGGTAGATGTCTTATAGAGACGATCGTCTTCCCGTCAAGTTATACAGG
58569 GACACCTTGTTTAGGC
66 GACACCTTGTTTAGGC
* *
58585 GTTCAGCC-ATCATACTATGTAGATGTCTT
1 GTTCAGCCGATCATACGAGGTAGATGTCTT
58614 GTTTAAGACG
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
79 16 0.16
80 31 0.32
81 51 0.52
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (81 bp):
GTTCAGCCGATCATACGAGGTAGATGTCTTATAGAGACGATCGTCTTCCCGTCAAGTTATACAGG
GACACCTTGTTTAGGC
Found at i:66832 original size:26 final size:26
Alignment explanation
Indices: 66791--66841 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
66781 AAAATCAATT
66791 ATAAAGAAAACAAATTAAA-CTAAAA
1 ATAAAGAAAACAAATTAAATCTAAAA
*
66816 ATAAAGCAAAGCAAATTAAATCTAAA
1 ATAAAG-AAAACAAATTAAATCTAAA
66842 TCTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.18
Consensus pattern (26 bp):
ATAAAGAAAACAAATTAAATCTAAAA
Found at i:69106 original size:19 final size:19
Alignment explanation
Indices: 69068--69104 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
69058 CTCCTCTTGC
69068 ATGAAAAACACTCTTTTTT
1 ATGAAAAACACTCTTTTTT
*
69087 ATGAAAAA-ATTCTTTTTT
1 ATGAAAAACACTCTTTTTT
69105 TAACTACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (19 bp):
ATGAAAAACACTCTTTTTT
Done.