Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012159.1 Corchorus olitorius cultivar O-4 contig12192, 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: 52249
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:320 original size:154 final size:154
Alignment explanation
Indices: 3--3508 Score: 5422
Period size: 154 Copynumber: 22.8 Consensus size: 154
1 CC
* *
3 CCCAAAATAACAAGTGTTTCCAAATGAGTTAAAAACTTTCACAGTCGACTAATCTCACCAAAATG
1 CCCAAAATAACAAGTG-TTCCAAATGAGTTAAAAAC-TTCACAGTGGAGTAATCTCACCAAAATG
* *
68 ATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCGAAGATGATT
64 ATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGATGATT
131 CAAAACGGAACTAATGGGCCCCGATAGG
127 CAAAACGGAACTAATGGGCCCCGATAGG
* *
159 CACAAAATAACAAGTGTTCCAATTGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* ** *
224 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTCGCCAAATCGAAGACAATTCTAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
*
289 ACGGAACTAATTGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
313 CCCAAAATAACAAGTATTCCAAATGAGTTAAAAACTTCACAATGGTAGTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGG-AGTAATCTCACCAAAATGA
* * * *
378 TTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCATCGAGGATTGCCAAATTGAAGATGATTCA
65 TTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCA
442 AAACGGAACTAATGGGCCCCGATAGG
129 AAACGGAACTAATGGGCCCCGATAGG
* * *
468 CACAAAATAACAAGTGTTCCAATTGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * * *
533 TATAGTTAGGCCATAAACAATGGAAAGAAATGCATTTAGGTTTGCCAAATCGAAGACGATTTAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
598 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* * * * *
622 CCCAAAATAACAAGTATTCCAAATCATTTAAAAACTTCACACTCGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
** *
687 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCTAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
752 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
*
776 CCCAAAATAACAAGTATTCCAAATGAGTT-AAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * *
840 TATAATTAGGCCATAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCGAAGATGATTCA
66 TATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGATGATTCA
* *
903 TAACGGAACTAATGGGCCCCGATAAG
129 AAACGGAACTAATGGGCCCCGATAGG
* * *
929 CCC-AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAACTGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
** *
993 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCTAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
* **
1058 ACGGAACTAGTTTGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
1082 CCCAAAATAACAAGTATTCCAAATGAGTTAAAAACTTCACGGT-GAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
*
1146 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGGTTTGCCAAATCGAAGATGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
*
1211 ACGGAATTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
1235 ACCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACGGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * * *
1300 TATGGTTTGGCCATAAACAACT-TAAAGAAAAGC-TTCGAAGATTT-CCAAATCGAAGATGATTC
66 TATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-G-AGGTTTGCCAAATCGAAGATGATTC
* *
1362 AAAACGGAACTAATGGGCCTCGATATG
128 AAAACGGAACTAATGGGCCCCGATAGG
* * *
1389 CCCATAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
*
1454 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
1519 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
1543 ACCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * * *
1608 TATAGTTAGGCCATAAACAATGGAAAGAAATGCATTTAGGTTTGCCAAATCGAAGACGATTTAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
1673 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
1697 CCCAAAATAACAAGTATTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACGAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * *
1762 TATAGTTAGGCCATAAACAACT-TAAAGAAAATC-TTCGAGGATTGCCAAATCGAAGATGATTCA
66 TATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGATGATTCA
1825 AAACGGAACTAATGGGCCCCGATAGG
129 AAACGGAACTAATGGGCCCCGATAGG
* *
1851 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
** *
1916 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCTAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
*
1981 ACGGAACTAATTGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
*
2005 CCCAAAATAACAAGTATTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * * *
2070 TATAGTTAGGCCATAAACAACT-TAAATAAAAGC-TTCGAGGATTGCCAAATCAAAGATGATTCA
66 TATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGATGATTCA
*
2133 AAACGGAACTAAAGGGCCCCGATAGG
129 AAACGGAACTAATGGGCCCCGATAGG
* *
2159 CACAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
*
2224 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGATGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
2289 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* * *
2313 ACCAAAATAACAAGTGCTT-CAAATGAGTTAAAAACTTCACAATGGACTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTG-TTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGA
*
2377 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGATGATTCAA
65 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAA
2442 AACGGAACTAATGGGCCCCGATAGG
130 AACGGAACTAATGGGCCCCGATAGG
* * * *
2467 ACCAAAATAACAAGTGCTT-CAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTG-TTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGA
2531 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAA
65 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAA
2596 AACGGAACTAATGGGCCCCGATAGG
130 AACGGAACTAATGGGCCCCGATAGG
* * *
2621 ACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
*
2686 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGATGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
*
2751 ACGGAACTAATAGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
2775 ACCAAAAT-ACAAGTGCTT-CAAATGAGTTAAAAA-TTTACAGTGGAGTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTG-TTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGA
* * *
2837 TTATAGTTAGGCCATAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCAAAGATGATTC
65 TTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGATGATTC
2900 AAAACGGAACTAATGGGCCCCGATAGG
128 AAAACGGAACTAATGGGCCCCGATAGG
* * * * *
2927 ACCAAAATAACAAGTATTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * *
2992 TATAGTTAGGCCATAAACAATGGAAATAAAAGTATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
3057 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
3081 CCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGAGTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
3146 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
3211 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* *
3235 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
* * * ** *
3300 TATAGTTAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTGCAAAATCGAACACAATTCTAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
*
3365 ACGGAACTAATTGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGATAGG
* * * * *
3389 CCCTAAATAACAAGTATTCCAAATGGGTTAAAAACTTCAGAAG-GTAGTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCA-CAGTGGAGTAATCTCACCAAAATGA
* * * * *
3453 TTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCGTCGAGGATTGCCAAATTGAAG
65 TTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
3509 TCAGATGGCA
Statistics
Matches: 3090, Mismatches: 222, Indels: 78
0.91 0.07 0.02
Matches are distributed among these distances:
151 2 0.00
152 143 0.05
153 422 0.14
154 2328 0.75
155 179 0.06
156 16 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAA
ACGGAACTAATGGGCCCCGATAGG
Found at i:5241 original size:199 final size:199
Alignment explanation
Indices: 4894--5282 Score: 708
Period size: 199 Copynumber: 2.0 Consensus size: 199
4884 TGAGGGGGCA
*
4894 TGTAAGAGGATAGGATAGTTACTATACAACTAGGACTCTATCTTAGCATAACAAAATTTTAAATT
1 TGTAAGAGGATAGGATAGTTACTATACAACTAAGACTCTATCTTAGCATAACAAAATTTTAAATT
*
4959 CAATTTGTAAATTTGAAATTGTAATTATCTAGTTAGTTATACTCATGTAATGTGATGATGTATTT
66 CAATTTGTAAATTTGAAATTGTAATTATCTAGTTAGTTATACTCATGTAATCTGATGATGTATTT
5024 ATACATGAATAGAAACCTCAAGAGATTAAGTCTCTTTTACCCTAATCATCTCTCTAGCAACCTTT
131 ATACATGAATAGAAACCTCAAGAGATTAAGTCTCTTTTACCCTAATCATCTCTCTAGCAACCTTT
5089 ACAT
196 ACAT
* * *
5093 TGTAAGTGGATAGGGTAGTTACTATACAACTAAGACTCTCTCTTAGCATAA-AAAAGTTTTAAAT
1 TGTAAGAGGATAGGATAGTTACTATACAACTAAGACTCTATCTTAGCATAACAAAA-TTTTAAAT
5157 TCAATTTGTAAATTTGAAATTGTAATTATCTAGTTAGTTATACTCATGTAATCTGATGATGTATT
65 TCAATTTGTAAATTTGAAATTGTAATTATCTAGTTAGTTATACTCATGTAATCTGATGATGTATT
*
5222 TATACATTAATAGAAACCTCAAGAGATTAAGTCTCTTTTACCCTAATCATCTCTCTAGCAA
130 TATACATGAATAGAAACCTCAAGAGATTAAGTCTCTTTTACCCTAATCATCTCTCTAGCAA
5283 TCTCTACAAT
Statistics
Matches: 183, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
198 4 0.02
199 179 0.98
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (199 bp):
TGTAAGAGGATAGGATAGTTACTATACAACTAAGACTCTATCTTAGCATAACAAAATTTTAAATT
CAATTTGTAAATTTGAAATTGTAATTATCTAGTTAGTTATACTCATGTAATCTGATGATGTATTT
ATACATGAATAGAAACCTCAAGAGATTAAGTCTCTTTTACCCTAATCATCTCTCTAGCAACCTTT
ACAT
Found at i:9907 original size:27 final size:27
Alignment explanation
Indices: 9877--9951 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
9867 GGTAATGGAC
*
9877 CAAATGACCAAAATGCCCCTGATCATG
1 CAAATGACCAAAATGCCCCTGAACATG
*
9904 CAAATGACTAAAATGCCCCTGAACATG
1 CAAATGACCAAAATGCCCCTGAACATG
*
9931 CAAATGACCCAAAATCCCCCT
1 CAAATGA-CCAAAATGCCCCT
9952 AGGTGACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 32 0.74
28 11 0.26
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTGAACATG
Found at i:18003 original size:21 final size:21
Alignment explanation
Indices: 17977--18018 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17967 GCATCTTAGA
17977 CAACTCAGATGAGCTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
* *
17998 CAACTCCGATGGGCTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
18019 TTCTTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
CAACTCAGATGAGCTTGAAAC
Found at i:22038 original size:57 final size:57
Alignment explanation
Indices: 21947--22066 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 57
21937 GCTTATCAAA
* * *
21947 ATCAAGTTATCAAATTATCAACTCAACATTAAGTCGTCAAGAACCTTAAATTAAATT
1 ATCAAGCTATCAAATTATCAACTCAACATCAAGTCGTCAAGAACCTTAAATCAAATT
* * * * * *
22004 ATCAAGCTCTCAAGTTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATCAAATT
1 ATCAAGCTATCAAATTATCAACTCAACATCAAGTCGTCAAGAACCTTAAATCAAATT
22061 ATCAAG
1 ATCAAG
22067 TTCAAGATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (57 bp):
ATCAAGCTATCAAATTATCAACTCAACATCAAGTCGTCAAGAACCTTAAATCAAATT
Found at i:22100 original size:41 final size:42
Alignment explanation
Indices: 22018--22108 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 42
22008 AGCTCTCAAG
* * *
22018 TTATCAA-TTCAAGATCAAGTCGTCAAGACCCTTGAATCAAA
1 TTATCAAGTTCAAGATCAAGTCATCAAGACCCTCGAAGCAAA
* * *
22059 TTATCAAGTTCAAGATTAAGTCAT-TAGACTCTCGAAGCAAA
1 TTATCAAGTTCAAGATCAAGTCATCAAGACCCTCGAAGCAAA
22100 TCT-TCAAGT
1 T-TATCAAGT
22109 AGAAAGGACA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
41 27 0.64
42 15 0.36
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (42 bp):
TTATCAAGTTCAAGATCAAGTCATCAAGACCCTCGAAGCAAA
Found at i:34505 original size:20 final size:20
Alignment explanation
Indices: 34480--34522 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
34470 AACTCCATTC
34480 AGGGACTTTACTCGCAAGGG
1 AGGGACTTTACTCGCAAGGG
34500 AGGGACTTTACTCGCAAGGG
1 AGGGACTTTACTCGCAAGGG
34520 AGG
1 AGG
34523 ATAGAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.37, T:0.19
Consensus pattern (20 bp):
AGGGACTTTACTCGCAAGGG
Found at i:34993 original size:4 final size:4
Alignment explanation
Indices: 34984--35014 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
34974 CCCTAGCTAC
*
34984 ATAA ATAA ATAA GTAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
35015 TATATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:36121 original size:220 final size:218
Alignment explanation
Indices: 35732--36129 Score: 636
Period size: 220 Copynumber: 1.8 Consensus size: 218
35722 TTTAGCTACT
* * * *
35732 AGGGAAATTACTAAAAGGCCAAACTGAGGATTAATGTGGTGCCATCTTTTGGCTTTTTTTGGTTT
1 AGGGAAATCACTAAAAGGCCAAACTGAGGATTAATGCGGTGCCATCTTTTGACTTTTTTTGGTTC
* *
35797 TTTCTCATTTTTCGAATGACTAAAAAGCCCCTCTATGAGTTTCCCTCCCTTTTCCTGCTACATTT
66 TTTCTCACTTTTCGAATGACTAAAAAGCCCCTCTATGAATTTCCCTCCCTTTTCCTGCTACATTT
*
35862 TTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTAATTAATGTTTCTCCCCCCTTTTCTTTT
131 TTTTGTAATTACTAATTTCACTTCCTTAATTGCTTTTAATTAATGTTTCTCCCCCCTTTTCTTTT
35927 TTCCTCTCACCAACTCAGTACCC
196 TTCCTCTCACCAACTCAGTACCC
* * *
35950 AGGGTAATCACTAAAAGGCCAAATTGAGGGTTAATGCGGTGCCATCTTTTGACTTTTTTTGG-TC
1 AGGGAAATCACTAAAAGGCCAAACTGAGGATTAATGCGGTGCCATCTTTTGACTTTTTTTGGTTC
* * *
36014 TTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAATTTCCCCCCTTCCTTTTCCTGCTACC
66 TTTCTCACTTTTCGAATGACTAAAAAGCCCCTCTATGAATTT---CCCTCCCTTTTCCTGCTACA
*
36079 TTTTTTTGTATTTACTAATTTCACTTCCTTAATTGCTTTTAATTAATGTTT
128 TTTTTTTGTAATTACTAATTTCACTTCCTTAATTGCTTTTAATTAATGTTT
36130 AAGGCTTTAA
Statistics
Matches: 163, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
217 40 0.25
218 56 0.34
220 67 0.41
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (218 bp):
AGGGAAATCACTAAAAGGCCAAACTGAGGATTAATGCGGTGCCATCTTTTGACTTTTTTTGGTTC
TTTCTCACTTTTCGAATGACTAAAAAGCCCCTCTATGAATTTCCCTCCCTTTTCCTGCTACATTT
TTTTGTAATTACTAATTTCACTTCCTTAATTGCTTTTAATTAATGTTTCTCCCCCCTTTTCTTTT
TTCCTCTCACCAACTCAGTACCC
Found at i:36785 original size:11 final size:12
Alignment explanation
Indices: 36752--36786 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
36742 ATTTAAGTAC
36752 ATTATTTTTATA
1 ATTATTTTTATA
36764 ATTACTTTTTATA
1 ATTA-TTTTTATA
36777 A-TATTTTTAT
1 ATTATTTTTAT
36787 TTATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 6 0.27
13 9 0.41
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:43352 original size:22 final size:22
Alignment explanation
Indices: 43294--43346 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
43284 ACATTAAAAA
* *
43294 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
43316 TGGGTCGTGCTGTGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
43338 TGGGTCGTG
1 TGGGTCGTG
43347 TCGTGCTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.04, C:0.25, G:0.47, T:0.25
Consensus pattern (22 bp):
TGGGTCGTGCTGTGCCGGCACG
Found at i:43546 original size:40 final size:40
Alignment explanation
Indices: 43502--43578 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
43492 TGGGTCGTGC
43502 TGGGCTTCGTGCCGCCCGCCCATTTTGCCATCTCTAGTGT
1 TGGGCTTCGTGCCGCCCGCCCATTTTGCCATCTCTAGTGT
*
43542 TGGGCTTCGTGTCGCCCGCCCATTTTGCCATCTCTAG
1 TGGGCTTCGTGCCGCCCGCCCATTTTGCCATCTCTAG
43579 GCTTAAGCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.08, C:0.35, G:0.25, T:0.32
Consensus pattern (40 bp):
TGGGCTTCGTGCCGCCCGCCCATTTTGCCATCTCTAGTGT
Found at i:45312 original size:2 final size:2
Alignment explanation
Indices: 45305--45344 Score: 62
Period size: 2 Copynumber: 19.0 Consensus size: 2
45295 TTTCAAATAC
45305 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
45345 ACTGTGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 32 0.89
3 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Done.