Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018820.1 Corchorus olitorius cultivar O-4 contig18853, 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: 130225
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:120 original size:22 final size:22
Alignment explanation
Indices: 88--212 Score: 123
Period size: 22 Copynumber: 5.7 Consensus size: 22
78 TGAATATTTT
88 TATGAAATTTTGATAACTAACC
1 TATGAAATTTTGATAACTAACC
* * *
110 TATTAAATTTTAATAACCAACC
1 TATGAAATTTTGATAACTAACC
*
132 TATGAAATTTTGATAA-TTACC
1 TATGAAATTTTGATAACTAACC
* *
153 TATAAAATTGTGATAAACT--CC
1 TATGAAATTTTGAT-AACTAACC
*
174 ATATGAAACTTTGATAACCTAA-C
1 -TATGAAATTTTGATAA-CTAACC
*
197 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
213 ACCTTCCTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 19 0.23
22 62 0.75
23 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACTAACC
Found at i:179 original size:43 final size:44
Alignment explanation
Indices: 88--214 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 44
78 TGAATATTTT
* * *
88 TATGAAATTTTGATAACTAACCTATTAAATTTTAATAACCAACC
1 TATGAAATTTTGATAACTAACCTATAAAATTGTAATAAACAACC
* * *
132 TATGAAATTTTGATAA-TTACCTATAAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACTAACCTATAAAATTGTAATAAACAACC
* * *
174 ATATGAAACTTTGATAACCTAA-CTATGAAATTTTAATAAAC
1 -TATGAAATTTTGATAA-CTAACCTATAAAATTGTAATAAAC
215 CTTCCTATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.03
43 33 0.48
44 32 0.46
45 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACTAACCTATAAAATTGTAATAAACAACC
Found at i:3274 original size:27 final size:27
Alignment explanation
Indices: 3234--3285 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
3224 AAATTTTCCC
3234 TTATTCGTATTTTTATATATAGTATAGA
1 TTATTCGTATTTTTATATATA-TATAGA
*
3262 TTATTTGT-TTTTTATATATATATA
1 TTATTCGTATTTTTATATATATATA
3286 TATAGCTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (27 bp):
TTATTCGTATTTTTATATATATATAGA
Found at i:18805 original size:19 final size:19
Alignment explanation
Indices: 18770--18814 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
18760 TGAAATTAAT
18770 TAATTA-TTAATTAAATAA
1 TAATTATTTAATTAAATAA
* *
18788 TAATTATTTTATTGAATAA
1 TAATTATTTAATTAAATAA
*
18807 TCATTATT
1 TAATTATT
18815 AAAAATAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTATTTAATTAAATAA
Found at i:20262 original size:51 final size:50
Alignment explanation
Indices: 20160--20262 Score: 113
Period size: 51 Copynumber: 2.0 Consensus size: 50
20150 CGTTCATCAA
* **
20160 TTTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTG
1 TTTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTG
*
20210 TTTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTG
1 TTTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTG
20261 TT
1 TT
20263 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
50 10 0.22
51 34 0.76
52 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTG
Found at i:27254 original size:24 final size:24
Alignment explanation
Indices: 27222--27269 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
27212 AGTTAAAAAT
27222 TTAGAAAGTTAGAAATAATTTGAG
1 TTAGAAAGTTAGAAATAATTTGAG
*
27246 TTAGGAAGTTAGAAATAATTTGAG
1 TTAGAAAGTTAGAAATAATTTGAG
27270 AGAATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (24 bp):
TTAGAAAGTTAGAAATAATTTGAG
Found at i:28478 original size:31 final size:31
Alignment explanation
Indices: 28411--28557 Score: 134
Period size: 31 Copynumber: 4.7 Consensus size: 31
28401 GACGTGGCTT
* ** *
28411 GCCACATGTACCAAAAAGCAATATGTAGCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
* *
28442 ACCACGTGTACCAAAAAGCGACATG-AGGCAC
1 GCCACGTGTACCAAAAAGTGACATGTA-GCAC
* * *
28473 GCCACGTATACAAAAAAGTGACATGTATCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
* * * *
28504 GCCATGTGTACCCAAAAGTGACATGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTAGCAC
* **
28535 GCCATGTGTTTCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGTGACA
28558 CATGGCATGC
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.01
31 93 0.98
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACATGTAGCAC
Found at i:33337 original size:14 final size:15
Alignment explanation
Indices: 33310--33339 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
33300 CTCTCTCTCT
33310 CAAGATCAAATTAAA
1 CAAGATCAAATTAAA
33325 CAAGATC-AATTAAA
1 CAAGATCAAATTAAA
33339 C
1 C
33340 TCATAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (15 bp):
CAAGATCAAATTAAA
Found at i:38426 original size:23 final size:23
Alignment explanation
Indices: 38398--38441 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
38388 TAAAATGCAC
38398 CAAAACAGTCACCACTAACCCAT
1 CAAAACAGTCACCACTAACCCAT
38421 CAAAACAGTCACCACTAACCC
1 CAAAACAGTCACCACTAACCC
38442 TCTTCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
CAAAACAGTCACCACTAACCCAT
Found at i:39041 original size:75 final size:75
Alignment explanation
Indices: 38943--39088 Score: 177
Period size: 75 Copynumber: 1.9 Consensus size: 75
38933 TTCAAAATAT
* * * * * *
38943 TGCCTATCTTCATTGGGAAGCTCAAAA-TTAGAATTCGAAACAGCATCCTGATTAGGAAAATCAG
1 TGCCTATCATCATTAGGAAGCTCAAAATTTA-AATTCGAAACAGAAACCTGATAAAGAAAATCAG
39007 CTTCAAGATGC
65 CTTCAAGATGC
* * * **
39018 TGCCTATCATCATTATGATGCTCAAAATTTAAATTCGAATCAGAAACCTGATAAAGTGAATCAGC
1 TGCCTATCATCATTAGGAAGCTCAAAATTTAAATTCGAAACAGAAACCTGATAAAGAAAATCAGC
39083 TTCAAG
66 TTCAAG
39089 TTGTTACAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 56 0.95
76 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (75 bp):
TGCCTATCATCATTAGGAAGCTCAAAATTTAAATTCGAAACAGAAACCTGATAAAGAAAATCAGC
TTCAAGATGC
Found at i:45141 original size:69 final size:69
Alignment explanation
Indices: 45030--45167 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
45020 CGAATCCCAA
45030 CTGTATAACTCGATCCACTAATTCAGAGCCATTGAGAGTATTTTCTACTTCGGTTGAGATCAAAA
1 CTGTATAACTCGATCCACTAATTCAGAGCCATTGAGAGTATTTTCTACTTCGGTTGAGATCAAAA
45095 GAGC
66 GAGC
45099 CTGTATAACTCGATCCACTAATTCAGAGCCATTGAGAGTATTTTCTACTTCGGTTGAGATCAAAA
1 CTGTATAACTCGATCCACTAATTCAGAGCCATTGAGAGTATTTTCTACTTCGGTTGAGATCAAAA
45164 GAGC
66 GAGC
45168 AGTTTAGCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (69 bp):
CTGTATAACTCGATCCACTAATTCAGAGCCATTGAGAGTATTTTCTACTTCGGTTGAGATCAAAA
GAGC
Found at i:45213 original size:19 final size:19
Alignment explanation
Indices: 45189--45263 Score: 60
Period size: 24 Copynumber: 3.6 Consensus size: 19
45179 TGTACAAATG
45189 AGATGAGATTACACTGTAC
1 AGATGAGATTACACTGTAC
45208 AGATGAGATGAGATTACACTGTAC
1 -----AGATGAGATTACACTGTAC
* * *
45232 AGATTAGATTAGGTACTATAC
1 AGATGAGATTA--CACTGTAC
45253 AGATGAGATTA
1 AGATGAGATTA
45264 TTAGAGCAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
19 10 0.22
21 16 0.36
24 19 0.42
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (19 bp):
AGATGAGATTACACTGTAC
Found at i:45233 original size:24 final size:24
Alignment explanation
Indices: 45177--45240 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
45167 CAGTTTAGCA
*
45177 ACTGTACAAATGAGATGAGATTAC
1 ACTGTACAGATGAGATGAGATTAC
45201 ACTGTACAGATGAGATGAGATTAC
1 ACTGTACAGATGAGATGAGATTAC
*
45225 ACTGTACAGATTAGAT
1 ACTGTACAGATGAGAT
45241 TAGGTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (24 bp):
ACTGTACAGATGAGATGAGATTAC
Found at i:48343 original size:18 final size:16
Alignment explanation
Indices: 48320--48363 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
48310 GCAAAGCCCG
48320 AAGAGAGAGAGAAAGAGA
1 AAGAGAGAGAG-AAG-GA
*
48338 AAGAGAGAAAGAAGGA
1 AAGAGAGAGAGAAGGA
*
48354 AAGGGAGAGA
1 AAGAGAGAGA
48364 TGTGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 3 0.13
18 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
AAGAGAGAGAGAAGGA
Found at i:57201 original size:19 final size:19
Alignment explanation
Indices: 57141--57202 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
57131 TTGGTAAAAT
* *
57141 AAAAGTGAAAGAAAATCG-
1 AAAAGAGAAAGAAAATAGA
* *
57159 AAATGATGAAAGAAAA-AAA
1 AAAAGA-GAAAGAAAATAGA
*
57178 AAAAGAGAAAGAAAATTGA
1 AAAAGAGAAAGAAAATAGA
57197 AAAAGA
1 AAAAGA
57203 AAATAGTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (19 bp):
AAAAGAGAAAGAAAATAGA
Found at i:59505 original size:43 final size:43
Alignment explanation
Indices: 59474--59587 Score: 210
Period size: 43 Copynumber: 2.7 Consensus size: 43
59464 TTGAATAAGT
59474 TTTACTCTTCATTGCAAGAGTTCTATTTAAATGATCATCTAAA
1 TTTACTCTTCATTGCAAGAGTTCTATTTAAATGATCATCTAAA
59517 TTTACTCTTCATTGCAAGAGTTCTATTTAAATGATCATCTAAA
1 TTTACTCTTCATTGCAAGAGTTCTATTTAAATGATCATCTAAA
* *
59560 TTTACTCTTCATCGGAAGAGTTCTATTT
1 TTTACTCTTCATTGCAAGAGTTCTATTT
59588 GAATAATCTC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (43 bp):
TTTACTCTTCATTGCAAGAGTTCTATTTAAATGATCATCTAAA
Found at i:68769 original size:16 final size:16
Alignment explanation
Indices: 68748--68788 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
68738 TTACATTGTT
68748 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
68764 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
68780 TTGTTTTCT
1 TTGTTTTCT
68789 GTCAATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:76752 original size:11 final size:11
Alignment explanation
Indices: 76736--76781 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
76726 GAAGTTCGTG
76736 ATTGAAGACTT
1 ATTGAAGACTT
*
76747 ATTGAAGA-TA
1 ATTGAAGACTT
76757 ATTTGAAGAC-T
1 A-TTGAAGACTT
*
76768 ATTGAAGAATT
1 ATTGAAGACTT
76779 ATT
1 ATT
76782 TCAAGAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (11 bp):
ATTGAAGACTT
Found at i:76787 original size:22 final size:22
Alignment explanation
Indices: 76740--76787 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
76730 TTCGTGATTG
*
76740 AAGACTTATTGAAGATAATTTG
1 AAGACTTATTGAAGATAATTTC
*
76762 AAGAC-TATTGAAGAATTATTTC
1 AAGACTTATTGAAG-ATAATTTC
76784 AAGA
1 AAGA
76788 AGAAAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (22 bp):
AAGACTTATTGAAGATAATTTC
Found at i:85460 original size:11 final size:10
Alignment explanation
Indices: 85444--85490 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
85434 AAGTTCGTGT
85444 TTGAAGACTCA
1 TTGAAGA-TCA
*
85455 TTGAAGATAA
1 TTGAAGATCA
85465 TTTGAAGAT--
1 -TTGAAGATCA
85474 TTGAAGATCA
1 TTGAAGATCA
85484 TTGAAGA
1 TTGAAGA
85491 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:85479 original size:19 final size:18
Alignment explanation
Indices: 85455--85490 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
85445 TGAAGACTCA
85455 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
85474 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
85491 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:91633 original size:76 final size:76
Alignment explanation
Indices: 91504--91655 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 76
91494 TGATGAGCTA
* *
91504 TGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGGTCCTCAGACAAACCATGTGGGCACCC
1 TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCCTCAGACAAACCATGTGGGCACCC
91569 AGCTGGAGTCG
66 AGCTGGAGTCG
* ** * * *
91580 TGACACTGCCCACCTGGGTTCTCAAGC-AAACCACATGGGTGCTCAAGGC-AACCATGTGGGCGC
1 TGACACAGCCCACCTGGGTGATCAAGCGAAA-CACATGGGTCCTC-AGACAAACCATGTGGGCAC
*
91643 CCAGGTGGAGTCG
64 CCAGCTGGAGTCG
91656 GGGTCCTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 3 0.05
76 59 0.91
77 3 0.05
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCCTCAGACAAACCATGTGGGCACCC
AGCTGGAGTCG
Found at i:94698 original size:17 final size:17
Alignment explanation
Indices: 94672--94706 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
94662 TAAGAGTAAA
94672 AGCCCAAGCCCGGCCCG
1 AGCCCAAGCCCGGCCCG
*
94689 AGCCCGAGCCCGGCCCG
1 AGCCCAAGCCCGGCCCG
94706 A
1 A
94707 TTAAGGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.51, G:0.31, T:0.00
Consensus pattern (17 bp):
AGCCCAAGCCCGGCCCG
Found at i:95097 original size:10 final size:11
Alignment explanation
Indices: 95072--95100 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
95062 TAAGGCTAGG
95072 CCCGGCCCGAA
1 CCCGGCCCGAA
95083 CCCGGCCCG-A
1 CCCGGCCCGAA
95093 CCCGGCCC
1 CCCGGCCC
95101 ATGAACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.62, G:0.28, T:0.00
Consensus pattern (11 bp):
CCCGGCCCGAA
Found at i:97878 original size:16 final size:15
Alignment explanation
Indices: 97857--97886 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
97847 GTATGAATTC
97857 AAATTGGTTTCTTGAA
1 AAATTGGTTT-TTGAA
97873 AAATTGGTTTTTGA
1 AAATTGGTTTTTGA
97887 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (15 bp):
AAATTGGTTTTTGAA
Found at i:107872 original size:25 final size:26
Alignment explanation
Indices: 107824--107872 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
107814 GCCCATATTT
107824 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAATAATTAA
107850 ATTTTTTAATAA-AAAATAA-AATT
1 ATTTTTTAA-AATAAAATAATAATT
107873 CAAACATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAATAATTAA
Found at i:109337 original size:45 final size:45
Alignment explanation
Indices: 109283--109379 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
109273 CATTAATTAC
* * * ** *
109283 CTAA-ATTCTAGTATTACGTCTCTAGGTAATTCATTAAAATAAAG
1 CTAATATTCTACTACTACATCTCTAAATAATTCATCAAAATAAAG
* *
109327 CTAATATTCTACTCCTCCATCTCTAAATAATTCATCAAAATAAAG
1 CTAATATTCTACTACTACATCTCTAAATAATTCATCAAAATAAAG
*
109372 TTAATATT
1 CTAATATT
109380 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 4 0.09
45 39 0.91
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTACTACATCTCTAAATAATTCATCAAAATAAAG
Found at i:110384 original size:29 final size:30
Alignment explanation
Indices: 110334--110390 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
110324 TATATATATG
* *
110334 TATACATATAAATTATTCAATTTTATTAGA
1 TATAAATATAAATTATTCAATTATATTAGA
*
110364 TATAAATAT-AATTATTTAATTATATTA
1 TATAAATATAAATTATTCAATTATATTA
110391 TATTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (30 bp):
TATAAATATAAATTATTCAATTATATTAGA
Found at i:114987 original size:23 final size:22
Alignment explanation
Indices: 114934--114987 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
114924 GTCTTTTTAA
114934 TAATATT-AAAGCCCAACTCTT
1 TAATATTGAAAGCCCAACTCTT
* *
114955 TAACAATGAAAGCCCAAAACT-TT
1 TAATATTGAAAGCCC--AACTCTT
114978 TAATATTGAA
1 TAATATTGAA
114988 GCTTAAGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 10 0.38
24 4 0.15
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (22 bp):
TAATATTGAAAGCCCAACTCTT
Found at i:114989 original size:22 final size:21
Alignment explanation
Indices: 114934--114989 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
114924 GTCTTTTTAA
*
114934 TAATATTAAAGCCCAACTCTT
1 TAATATTGAAGCCCAACTCTT
* *
114955 TAACAATGAAAGCCCAAAACT-TT
1 TAATATTG-AAGCCC--AACTCTT
114978 TAATATTGAAGC
1 TAATATTGAAGC
114990 TTAAGCCTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.19
22 10 0.37
23 8 0.30
24 4 0.15
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (21 bp):
TAATATTGAAGCCCAACTCTT
Found at i:116853 original size:63 final size:63
Alignment explanation
Indices: 116716--116843 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
116706 GATTTAACAG
116716 TGCATATGACATATTTTTACATATGTCTTGGAATGGATGAATATTCCCAGTTGCTCCTTTGTT
1 TGCATATGACATATTTTTACATATGTCTTGGAATGGATGAATATTCCCAGTTGCTCCTTTGTT
116779 TGCATATGACATATTTTTACATATGTCTTGGAATGGATGAATATTCCCAGTTGCTCCTTTGTT
1 TGCATATGACATATTTTTACATATGTCTTGGAATGGATGAATATTCCCAGTTGCTCCTTTGTT
116842 TG
1 TG
116844 TATCAGACAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (63 bp):
TGCATATGACATATTTTTACATATGTCTTGGAATGGATGAATATTCCCAGTTGCTCCTTTGTT
Found at i:123127 original size:1 final size:1
Alignment explanation
Indices: 123121--123157 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
123111 CTGAAACATT
* *
123121 AAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
123158 GCTAGTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:123703 original size:2 final size:2
Alignment explanation
Indices: 123696--123725 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
123686 ATAGTGGTTC
123696 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
123726 ACTTTATTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:127734 original size:27 final size:27
Alignment explanation
Indices: 127696--127766 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 27
127686 TTTCATATTG
*
127696 TTTCTCTCTCTCTCTCTATCCTATTTTCTTC
1 TTTCT-TCTCTCTCTC-AT-CT-CTTTCTTC
127727 TTT-TTCTCTCATCTCATCTCTTTCTTC
1 TTTCTTCTCTC-TCTCATCTCTTTCTTC
*
127754 TTTCTTCTTTCTC
1 TTTCTTCTCTCTC
127767 CTTTCTCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
27 12 0.33
28 8 0.22
29 8 0.22
30 5 0.14
31 3 0.08
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTCTTCTCTCTCTCATCTCTTTCTTC
Found at i:127763 original size:34 final size:33
Alignment explanation
Indices: 127696--127763 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 33
127686 TTTCATATTG
127696 TTTCTCTCTCTCTCTCTATCCTATTTTCTTCTT
1 TTTCTCTCTCTCTCTCTATCCTATTTTCTTCTT
*
127729 TTTCTCTCATCTCATCTCT-TTCT-TCTTTCTTCTT
1 TTTCTCTC-TCTC-TCTCTATCCTAT-TTTCTTCTT
127763 T
1 T
127764 CTCCTTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 9 0.29
34 17 0.55
35 5 0.16
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTCTCTCTCTCTCTCTATCCTATTTTCTTCTT
Found at i:129977 original size:2 final size:2
Alignment explanation
Indices: 129970--129995 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
129960 TTTATATTGA
129970 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
129996 TATGGGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.