Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009139.1 Corchorus capsularis cultivar CVL-1 contig09160, 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: 150253
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1496 original size:218 final size:218
Alignment explanation
Indices: 1118--1544 Score: 854
Period size: 218 Copynumber: 2.0 Consensus size: 218
1108 TTGCTTCAAA
1118 TTTTTGTGTTCATTATATTTATGATGGATATACATTTGAATTTCCTTGGTTACACAGTTGCTAGG
1 TTTTTGTGTTCATTATATTTATGATGGATATACATTTGAATTTCCTTGGTTACACAGTTGCTAGG
1183 ATAAGAGATTCTGGGCAATTTAGATACTTAATAAGAAACTCTTGTTATAGGATTGCTTAAATCCT
66 ATAAGAGATTCTGGGCAATTTAGATACTTAATAAGAAACTCTTGTTATAGGATTGCTTAAATCCT
1248 TGGATACGGCTTTAGGCGAACAAAACAAGTTTTTACTAGTTAAATTTTAAATTTGTAAATTCCTC
131 TGGATACGGCTTTAGGCGAACAAAACAAGTTTTTACTAGTTAAATTTTAAATTTGTAAATTCCTC
1313 ACAGAACGCATTCCGTATCCAAG
196 ACAGAACGCATTCCGTATCCAAG
1336 TTTTTGTGTTCATTATATTTATGATGGATATACATTTGAATTTCCTTGGTTACACAGTTGCTAGG
1 TTTTTGTGTTCATTATATTTATGATGGATATACATTTGAATTTCCTTGGTTACACAGTTGCTAGG
1401 ATAAGAGATTCTGGGCAATTTAGATACTTAATAAGAAACTCTTGTTATAGGATTGCTTAAATCCT
66 ATAAGAGATTCTGGGCAATTTAGATACTTAATAAGAAACTCTTGTTATAGGATTGCTTAAATCCT
1466 TGGATACGGCTTTAGGCGAACAAAACAAGTTTTTACTAGTTAAATTTTAAATTTGTAAATTCCTC
131 TGGATACGGCTTTAGGCGAACAAAACAAGTTTTTACTAGTTAAATTTTAAATTTGTAAATTCCTC
1531 ACAGAACGCATTCC
196 ACAGAACGCATTCC
1545 TTATAGTTCA
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 209 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (218 bp):
TTTTTGTGTTCATTATATTTATGATGGATATACATTTGAATTTCCTTGGTTACACAGTTGCTAGG
ATAAGAGATTCTGGGCAATTTAGATACTTAATAAGAAACTCTTGTTATAGGATTGCTTAAATCCT
TGGATACGGCTTTAGGCGAACAAAACAAGTTTTTACTAGTTAAATTTTAAATTTGTAAATTCCTC
ACAGAACGCATTCCGTATCCAAG
Found at i:4940 original size:293 final size:293
Alignment explanation
Indices: 4413--4999 Score: 1174
Period size: 293 Copynumber: 2.0 Consensus size: 293
4403 ATAGGTGGAG
4413 TACCATGGCTGCAATTATGTCAAAGCTTCCGCATAAGCAAGGTAGTTTCTACACCAGATGGATTA
1 TACCATGGCTGCAATTATGTCAAAGCTTCCGCATAAGCAAGGTAGTTTCTACACCAGATGGATTA
4478 CAAATTTCTCAAAGTATTCTACATTTTGCTTATTTTCTAATCTATTCTTTTTCATCACTTATCAG
66 CAAATTTCTCAAAGTATTCTACATTTTGCTTATTTTCTAATCTATTCTTTTTCATCACTTATCAG
4543 CTCCACATGTTTGCTCTAAGTGTGAAAGGCTTGGGATGAATTAGGATTTTCTTTCTTGTTGATAA
131 CTCCACATGTTTGCTCTAAGTGTGAAAGGCTTGGGATGAATTAGGATTTTCTTTCTTGTTGATAA
4608 TGCTGTTACGTTGTGTAGAGACTGGTTAGGTCCACCATAGTGGCAATTAGGGTGTTTTAAAGTCT
196 TGCTGTTACGTTGTGTAGAGACTGGTTAGGTCCACCATAGTGGCAATTAGGGTGTTTTAAAGTCT
4673 TCTAGTTTGGGAATTAGATATATAAGTTCTTAA
261 TCTAGTTTGGGAATTAGATATATAAGTTCTTAA
4706 TACCATGGCTGCAATTATGTCAAAGCTTCCGCATAAGCAAGGTAGTTTCTACACCAGATGGATTA
1 TACCATGGCTGCAATTATGTCAAAGCTTCCGCATAAGCAAGGTAGTTTCTACACCAGATGGATTA
4771 CAAATTTCTCAAAGTATTCTACATTTTGCTTATTTTCTAATCTATTCTTTTTCATCACTTATCAG
66 CAAATTTCTCAAAGTATTCTACATTTTGCTTATTTTCTAATCTATTCTTTTTCATCACTTATCAG
4836 CTCCACATGTTTGCTCTAAGTGTGAAAGGCTTGGGATGAATTAGGATTTTCTTTCTTGTTGATAA
131 CTCCACATGTTTGCTCTAAGTGTGAAAGGCTTGGGATGAATTAGGATTTTCTTTCTTGTTGATAA
4901 TGCTGTTACGTTGTGTAGAGACTGGTTAGGTCCACCATAGTGGCAATTAGGGTGTTTTAAAGTCT
196 TGCTGTTACGTTGTGTAGAGACTGGTTAGGTCCACCATAGTGGCAATTAGGGTGTTTTAAAGTCT
4966 TCTAGTTTGGGAATTAGATATATAAGTTCTTAA
261 TCTAGTTTGGGAATTAGATATATAAGTTCTTAA
4999 T
1 T
5000 TAGGGCTGCA
Statistics
Matches: 294, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
293 294 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (293 bp):
TACCATGGCTGCAATTATGTCAAAGCTTCCGCATAAGCAAGGTAGTTTCTACACCAGATGGATTA
CAAATTTCTCAAAGTATTCTACATTTTGCTTATTTTCTAATCTATTCTTTTTCATCACTTATCAG
CTCCACATGTTTGCTCTAAGTGTGAAAGGCTTGGGATGAATTAGGATTTTCTTTCTTGTTGATAA
TGCTGTTACGTTGTGTAGAGACTGGTTAGGTCCACCATAGTGGCAATTAGGGTGTTTTAAAGTCT
TCTAGTTTGGGAATTAGATATATAAGTTCTTAA
Found at i:18313 original size:47 final size:47
Alignment explanation
Indices: 18242--18348 Score: 196
Period size: 47 Copynumber: 2.3 Consensus size: 47
18232 TGGTAAATCA
18242 CTTGAGTTCGAGTGGTAAACCACTTGTTTAAAATATCAGGTTTAAGT
1 CTTGAGTTCGAGTGGTAAACCACTTGTTTAAAATATCAGGTTTAAGT
*
18289 CTTGAGTTCGAGTGGTAAATCACTTGTTTAAAATATCAGGTTTAAGT
1 CTTGAGTTCGAGTGGTAAACCACTTGTTTAAAATATCAGGTTTAAGT
*
18336 TTTGAGTTCGAGT
1 CTTGAGTTCGAGT
18349 TCTATGAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (47 bp):
CTTGAGTTCGAGTGGTAAACCACTTGTTTAAAATATCAGGTTTAAGT
Found at i:20058 original size:74 final size:74
Alignment explanation
Indices: 19970--20199 Score: 388
Period size: 74 Copynumber: 3.0 Consensus size: 74
19960 ACCCTGAGTT
19970 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
20035 TAGAAGATA
66 TAGAAGATA
*
20044 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATTACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
20109 TAGAAGATA
66 TAGAAGATA
*
20118 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATACCATTCCAGCATTCCTAC
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTAT--CA--CCA--TTTCCTAC
20183 TTAGGTTAGAAGATA
60 TTAGGTTAGAAGATA
20198 TA
1 TA
20200 GAGGGAACTG
Statistics
Matches: 147, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
74 119 0.81
76 1 0.01
78 3 0.02
80 24 0.16
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (74 bp):
TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
TAGAAGATA
Found at i:22722 original size:15 final size:15
Alignment explanation
Indices: 22702--22731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22692 AATTACATCT
22702 GCTCAATAAAAGAAC
1 GCTCAATAAAAGAAC
*
22717 GCTCAATGAAAGAAC
1 GCTCAATAAAAGAAC
22732 TTTAACATGA
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:0.20, G:0.17, T:0.13
Consensus pattern (15 bp):
GCTCAATAAAAGAAC
Found at i:29198 original size:33 final size:33
Alignment explanation
Indices: 29161--29227 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29151 AAAAGCAATG
*
29161 GCTTAAACTGGTGAAACAATGGCTGCCAATAAT
1 GCTTAAACTGGAGAAACAATGGCTGCCAATAAT
29194 GCTTAAACTGGAGAAACAATGGCTGCCAATAAT
1 GCTTAAACTGGAGAAACAATGGCTGCCAATAAT
29227 G
1 G
29228 AATCAAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (33 bp):
GCTTAAACTGGAGAAACAATGGCTGCCAATAAT
Found at i:37156 original size:38 final size:38
Alignment explanation
Indices: 37105--37180 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
37095 ATCTAAGAAG
*
37105 TTTTTTTTTTTTTTCGCCAGATAATCTAAGAGGTTTCT
1 TTTTTTTTTTTTTTCGCCAGAAAATCTAAGAGGTTTCT
*
37143 TTTTTTTTTTTTTTGGCCAGAAAATCTAAGAGGTTTCT
1 TTTTTTTTTTTTTTCGCCAGAAAATCTAAGAGGTTTCT
37181 GGTAAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (38 bp):
TTTTTTTTTTTTTTCGCCAGAAAATCTAAGAGGTTTCT
Found at i:40418 original size:4 final size:4
Alignment explanation
Indices: 40409--40546 Score: 66
Period size: 4 Copynumber: 33.5 Consensus size: 4
40399 TATGTAACTA
* * * * *
40409 TTAT TTAT TTAT TTAT TTAT ATATAT ATAT TTAC ATAC TTAT TTAT CTAT
1 TTAT TTAT TTAT TTAT TTAT -T-TAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * *
40459 TTGT TTAT ATAT CTAT TTAT CTT-T TTAT TTAT CTAT TATTT TTACT TT-T
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT TTA-T TTAT
* * * *
40508 TTAT AGTTAT CTA- TTAC TTAA TTAT ATAT TTAT TTAT TT
1 TTAT --TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
40547 TAATCTTAAT
Statistics
Matches: 101, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
3 7 0.07
4 78 0.77
5 9 0.09
6 7 0.07
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (4 bp):
TTAT
Found at i:40475 original size:24 final size:23
Alignment explanation
Indices: 40410--40544 Score: 84
Period size: 24 Copynumber: 6.0 Consensus size: 23
40400 ATGTAACTAT
* * *
40410 TATTTATTTATTTATT-TATATA
1 TATTTATTTATATATTATTTATC
* *
40432 TATATATTTACATACTTATTTATC
1 TATTTATTTATATA-TTATTTATC
*
40456 TATTTGTTTATATATCTATTTATC
1 TATTTATTTATATAT-TATTTATC
* *
40480 TTTTTATTTATCTATTATTT-T-
1 TATTTATTTATATATTATTTATC
* *
40501 TACTTT-TTTATA-GTTATCTAT-
1 TA-TTTATTTATATATTATTTATC
* *
40522 TACTTAATTATATATTTATTTAT
1 TATTTATTTATATA-TTATTTAT
40545 TTTAATCTTA
Statistics
Matches: 86, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
20 7 0.08
21 14 0.16
22 15 0.17
23 15 0.17
24 35 0.41
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (23 bp):
TATTTATTTATATATTATTTATC
Found at i:44182 original size:20 final size:20
Alignment explanation
Indices: 44157--44197 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
44147 TTAATTATTG
44157 ATATGTTAAATGGGTTTTTA
1 ATATGTTAAATGGGTTTTTA
*
44177 ATATGTTAAGTGGGTTTTTA
1 ATATGTTAAATGGGTTTTTA
44197 A
1 A
44198 GACATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATATGTTAAATGGGTTTTTA
Found at i:44537 original size:29 final size:29
Alignment explanation
Indices: 44481--44537 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
44471 AAAAAAAATA
** *
44481 AAAGACGAGATTATTTTATTTTTTTATAG
1 AAAGACGAGATTATTTTATGGTTCTATAG
44510 AAAGACGAGATTATTTTATGGTTCTATA
1 AAAGACGAGATTATTTTATGGTTCTATA
44538 ATTGTTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (29 bp):
AAAGACGAGATTATTTTATGGTTCTATAG
Found at i:46415 original size:32 final size:32
Alignment explanation
Indices: 46374--46438 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
46364 GACATAGATA
* *
46374 CCAACTCAG-CTTTCTGTGGATCCTATTCCAAG
1 CCAACTCAGCCTTT-TGTGGATCCCATTCAAAG
*
46406 CCAACTCAGCCTTTTGTGGGTCCCATTCAAAG
1 CCAACTCAGCCTTTTGTGGATCCCATTCAAAG
46438 C
1 C
46439 TTAATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.29
Consensus pattern (32 bp):
CCAACTCAGCCTTTTGTGGATCCCATTCAAAG
Found at i:58029 original size:56 final size:56
Alignment explanation
Indices: 57942--58060 Score: 220
Period size: 56 Copynumber: 2.1 Consensus size: 56
57932 ATATTAAAGC
* *
57942 ATGATCATGGTAGAAATTTGAAATTCCAATAACGAATAGCACAGCATTTAATCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAATAGCACAACATTTAATCAAA
57998 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAATAGCACAACATTTAATCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAATAGCACAACATTTAATCAAA
58054 ATGATCA
1 ATGATCA
58061 CATTCAATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (56 bp):
ATGATCATGGTAGAAATTTGAAATTCAAATAACGAATAGCACAACATTTAATCAAA
Found at i:58079 original size:42 final size:42
Alignment explanation
Indices: 58020--58099 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
58010 GAAATTTGAA
*
58020 ATTCAAATAACGAATAGCACAACATTTAATCAAAATGATCAC
1 ATTCAAATAACGAATAGCACAACATATAATCAAAATGATCAC
* * *
58062 ATTCAATTAATGAATAGCACAACGTATAATCAAAATGA
1 ATTCAAATAACGAATAGCACAACATATAATCAAAATGA
58100 CAAAGGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (42 bp):
ATTCAAATAACGAATAGCACAACATATAATCAAAATGATCAC
Found at i:75222 original size:20 final size:20
Alignment explanation
Indices: 75197--75237 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
75187 CAACCCTAAG
75197 TAATACTAGGAAGCAAACAT
1 TAATACTAGGAAGCAAACAT
75217 TAATACTAGGAAGCAAACAT
1 TAATACTAGGAAGCAAACAT
75237 T
1 T
75238 GCAATCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (20 bp):
TAATACTAGGAAGCAAACAT
Found at i:101881 original size:18 final size:17
Alignment explanation
Indices: 101845--101878 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
101835 GTACAGGGAG
101845 GAAGAGGTCCAATATTT
1 GAAGAGGTCCAATATTT
101862 GAAGATGGTCCAA-ATTT
1 GAAGA-GGTCCAATATTT
101879 TGATATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (17 bp):
GAAGAGGTCCAATATTT
Found at i:105865 original size:10 final size:10
Alignment explanation
Indices: 105852--105880 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
105842 TTTTCTTTGT
105852 TTTTTTTAAA
1 TTTTTTTAAA
105862 TTTTTTTAAA
1 TTTTTTTAAA
105872 TTTTTTTAA
1 TTTTTTTAA
105881 TATTAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:105962 original size:26 final size:26
Alignment explanation
Indices: 105933--106000 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
105923 CACTTAGTTT
105933 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
105959 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
* *
105985 ATTAATTTATGATTAA
1 ATTAGTTTATGTTTAA
106001 AATGAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:106061 original size:25 final size:24
Alignment explanation
Indices: 106009--106068 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
105999 AAAATGAAAG
**
106009 AAAATGAA-TTTGAAGATTTGTTA
1 AAAATGAAGTTTGAAGAGCTGTTA
106032 AAAATGAAGTTTGAAGAAGCTGTTA
1 AAAATGAAGTTTGAAG-AGCTGTTA
* *
106057 GAAATTAAGTTT
1 AAAATGAAGTTT
106069 AGAATTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 8 0.26
24 7 0.23
25 16 0.52
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (24 bp):
AAAATGAAGTTTGAAGAGCTGTTA
Found at i:107931 original size:14 final size:14
Alignment explanation
Indices: 107912--107988 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
107902 GTTTAATAAT
107912 TATATAT-ATTGTTA
1 TATATATAATT-TTA
107926 TATATATAATTTTA
1 TATATATAATTTTA
* *
107940 TATATCTAATATTA
1 TATATATAATTTTA
***
107954 TTATTATATAAAACTA
1 -TA-TATATAATTTTA
* *
107970 TATATTTAATGTTA
1 TATATATAATTTTA
107984 TATAT
1 TATAT
107989 CTATACTATA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
14 35 0.69
15 7 0.14
16 9 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATATAATTTTA
Found at i:111164 original size:12 final size:12
Alignment explanation
Indices: 111147--111173 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
111137 ATCGTGCATT
111147 GTGGTTTGGTGG
1 GTGGTTTGGTGG
111159 GTGGTTTGGTGG
1 GTGGTTTGGTGG
111171 GTG
1 GTG
111174 AGTCTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (12 bp):
GTGGTTTGGTGG
Found at i:119824 original size:33 final size:36
Alignment explanation
Indices: 119758--119827 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
119748 AATCTTAGAA
119758 TTACAACAAGGAGTACATGATATCAGTTCGCCACAG
1 TTACAACAAGGAGTACATGATATCAGTTCGCCACAG
*
119794 TTACAACAAGGAGTACAT-CT-T-AGTTCGCCACAG
1 TTACAACAAGGAGTACATGATATCAGTTCGCCACAG
119827 T
1 T
119828 ACATACTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 13 0.39
34 1 0.03
35 1 0.03
36 18 0.55
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (36 bp):
TTACAACAAGGAGTACATGATATCAGTTCGCCACAG
Found at i:129552 original size:16 final size:17
Alignment explanation
Indices: 129528--129560 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
129518 GATGTCTCTC
129528 TCTTCTC-TTTTTCTTT
1 TCTTCTCTTTTTTCTTT
*
129544 TCTTTTCTTTTTTCTTT
1 TCTTCTCTTTTTTCTTT
129561 CTCCTCTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTCTCTTTTTTCTTT
Found at i:146195 original size:167 final size:163
Alignment explanation
Indices: 145850--146288 Score: 552
Period size: 167 Copynumber: 2.7 Consensus size: 163
145840 TGAGTCATTT
145850 GTCAATTGAGAAATGACTC-AAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGAC-CAAAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACA
* ** ** * *
145914 TTTAAGTAATCTGC---TAATTAAAGACGAAAAAGATTAGTTCTCTAACTCATCATCAATCCTTG
65 TTTAAGTAATATGCAAATAAGAAAAGACGAAAAA-ATTAGTTCTCTAACTCAAAAGCAAGCCTTG
* *
145976 ATGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 ATGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
146011 GTTC-ATTAAGAAATGACCAAAAAGATTACTTATTTAATCCACTTAAGAATCAAAAGTTAGGACA
1 G-TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACA
*
146075 TTTAATTAATATGTCAAATAAGAAAAGACGAAAAAATTAAGTTCTCTAACTCCAAAAGCAAGCCT
65 TTTAAGTAATATG-CAAATAAGAAAAGACGAAAAAATT-AGTTCTCTAACT-CAAAAGCAAGCCT
146140 TCG-TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
127 T-GAT-GGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
146178 GTCAATTGAGAAATGACCAAAAA-TTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCA
1 GTCAATTGAGAAATGACCAAAAAGTT-TAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACA
**
146242 TTTAAGTAATCA-GCCAAATGTGAAAAGACGAAAAAAATTAGTTCTCT
65 TTTAAGTAAT-ATG-CAAATAAGAAAAGACG-AAAAAATTAGTTCTCT
146289 CGCTCCTCAA
Statistics
Matches: 240, Mismatches: 24, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
160 1 0.00
161 66 0.28
162 3 0.01
164 3 0.01
165 27 0.11
166 14 0.06
167 117 0.49
168 9 0.04
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACAT
TTAAGTAATATGCAAATAAGAAAAGACGAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGAT
GGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:146736 original size:2 final size:2
Alignment explanation
Indices: 146731--146760 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
146721 TTATATTACA
146731 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
146761 CCTTCTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.