Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011967.1 Corchorus olitorius cultivar O-4 contig12000, 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: 69697
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3813 original size:25 final size:25
Alignment explanation
Indices: 3783--3830 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3773 ATGCAATGTC
3783 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
3808 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
3831 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:10188 original size:27 final size:28
Alignment explanation
Indices: 10142--10194 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
10132 GACTAATGTA
10142 TTTTTTTGTGATTTTCAATT-TTCAATT
1 TTTTTTTGTGATTTTCAATTATTCAATT
*
10169 TTTTTTTGTG-TTTTGTAATTATTCAA
1 TTTTTTTGTGATTTT-CAATTATTCAA
10195 GTGTATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 14 0.61
28 5 0.22
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (28 bp):
TTTTTTTGTGATTTTCAATTATTCAATT
Found at i:10612 original size:27 final size:27
Alignment explanation
Indices: 10574--10673 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
10564 AGTGAGCTTA
**
10574 AAATGACCAAAATGCTTCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
* *
10601 AAATGACCAAAATACCCCTGGATGTGT
1 AAATGACCAAAATGCCCCTGGATGTGC
* * **
10628 AAATGACCAAAATGCCCATAGACATGC
1 AAATGACCAAAATGCCCCTGGATGTGC
10655 AAATGACCCAAAATGCCCC
1 AAATGA-CCAAAATGCCCC
10674 ATAGATGACC
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 50 0.82
28 11 0.18
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTGC
Found at i:10756 original size:2 final size:2
Alignment explanation
Indices: 10749--10790 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10739 GGTGTCTACA
*
10749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10791 TCTTAGTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19582 original size:2 final size:2
Alignment explanation
Indices: 19577--19607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19567 TAACGTGGTG
19577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19608 TTAGGGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24245 original size:204 final size:203
Alignment explanation
Indices: 23857--25114 Score: 1259
Period size: 217 Copynumber: 5.9 Consensus size: 203
23847 TCGTTAGTTT
* **
23857 TATACTTTATATCCAAATCATTTCTCATCATCCCCAAATAATCA-AACGCACCATCCTAAAATAT
1 TATACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAA-GCACCATCCCCAAAT-T
* * * *
23921 TTTTATAGATAGACATTTGTTTATATGCCCAAAATTGGCTTTTAAACGTGTTTTAATCCATATTT
64 TTTTAGAGATTGACATTTTTTTATATACCCAAAATTGG-TTTTAAACGTGTTTTAATCCATATTT
* * * *
23986 TTATCCTAATTAATTGGAAAACCCCGTCTATATGAATTTATTGTCATCTAATAATTAAAC-GTAT
128 TCATCCTAATTAATTGAAAAACCCCGTCTATATAAATTTAGTGTCATCTAATAATTAAACAGTAT
24050 CCCCAAAGAGA
193 CCCCAAAGAGA
* *
24061 TATACTTTATACCCAAATCAGTTT-TCATCATCCCCAAATAATCATAAGCATCATCCCCAAATTT
1 TATACTTTATAACCAAATCA-TTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTT
*
24125 TTTAGA-ATTGACAATTTTTTTATATACCCAAAATTGGTTTTTCAACGTGTTTTAATCCATATTT
65 TTTAGAGATTGAC-ATTTTTTTATATACCCAAAATTGG-TTTTAAACGTGTTTTAATCCATATTT
* *
24189 TCATCCTAATTAATTGAATAAACCTCGTCTATATAAATTTAGTGTCCTCCAATAATTAAACAAAA
128 TCATCCTAATTAATTGAA-AAACCCCGTCTATATAAATTTAGTGTCAT-C--TAA-T------AA
* * *
24254 TGCAAAATTCAGTATCCTCAAAGTGA
182 T--TAAA--CAGTATCCCCAAAGAGA
* * * *
24280 TATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCACCATTCCCAAA-CTT
1 TATACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTTT
* * * *
24344 TTAGAGATTGACATATTTTTATATACCCAAAATTGGCTTAAAACGTGTTTTAATCTATATTTTCA
66 TTAGAGATTGACATTTTTTTATATACCCAAAATTGGTTTTAAACGTGTTTTAATCCATATTTTCA
24409 TCCTAATTAATTGAACAAACCCCGTCTATATAAATTTAGTGTCATCTAATAACTAAACAAAATGC
131 TCCTAATTAATTGAA-AAACCCCGTCTATATAAATTTAGTGTCATCTAATAA-T--------T--
* *
24474 AAAATTCAATATCCCCAAAGTGA
184 -AAA--CAGTATCCCCAAAGAGA
** * *
24497 TATACTTTATGTCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCTCAAA-TTT
1 TATACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTTT
* * * *
24561 TTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACGTGTTTTAATCCACATTTCCA
66 TTAGAGATTGACATTTTTTTATATACCCAAAATTGGTTTTAAACGTGTTTTAATCCATATTTTCA
* * *
24626 TCATAATTAATTGAATAAACCCCGTCTATATAAATTTATTGTCATATAATAACTAAACAAAATGC
131 TCCTAATTAATTGAA-AAACCCCGTCTATATAAATTTAGTGTCATCTAATAA-T--------T--
*
24691 AAAAATTCAGTATCCCAAAAGAGA
184 --AAA--CAGTATCCCCAAAGAGA
* * * * *
24715 TATACTTTATACCCAAATCATTTCTCATTATCCCCAAATAATCGTACGCACCATCTCCAAAATAT
1 TATACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATC-CCCAAAT-T
* * *
24780 TTTTATAGATTGACATTTGTTTATATGCCCAAAATTGGCTTTTAAACGTGTTTTAATCCATATTT
64 TTTTAGAGATTGACATTTTTTTATATACCCAAAATTGG-TTTTAAACGTGTTTTAATCCATATTT
* * * *
24845 TTATCATAATTAATTGAATAAACCCCATCTATATAAATTTAGTGTCCTCTAATAATTAAACAAAA
128 TCATCCTAATTAATTGAA-AAACCCCGTCTATATAAATTTAGTGTCATCTAATAA-T--------
*
24910 TGCAAAATTCAGTATCCCCATAATGATA
183 T---AAA--CAGTATCCCCA-AA-GAGA
* *
24938 TACGTACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCACCATCCCCAAATT
1 TA--TACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATT
* * * *
25003 TTTTAGAGATTGACATTTTTTTATATACCCAAATTTGGCTTAAAACGTGTTGTAATCCATATTTT
64 TTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGTTTTAAACGTGTTTTAATCCATATTTT
25068 CATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCAT
129 CATCCTAATTAATTGAA-AAACCCCGTCTATATAAATTTAGTGTCAT
25115 AAAAAAAATA
Statistics
Matches: 918, Mismatches: 96, Indels: 62
0.85 0.09 0.06
Matches are distributed among these distances:
202 5 0.01
203 70 0.08
204 76 0.08
205 6 0.01
207 5 0.01
208 2 0.00
213 1 0.00
214 6 0.01
216 4 0.00
217 265 0.29
218 104 0.11
219 75 0.08
221 52 0.06
222 151 0.16
223 40 0.04
224 6 0.01
225 50 0.05
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (203 bp):
TATACTTTATAACCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTTT
TTAGAGATTGACATTTTTTTATATACCCAAAATTGGTTTTAAACGTGTTTTAATCCATATTTTCA
TCCTAATTAATTGAAAAACCCCGTCTATATAAATTTAGTGTCATCTAATAATTAAACAGTATCCC
CAAAGAGA
Found at i:24437 original size:217 final size:217
Alignment explanation
Indices: 24046--25114 Score: 1561
Period size: 217 Copynumber: 4.9 Consensus size: 217
24036 ATAATTAAAC
* * * *
24046 GTATCCCCAAAGAGATATACTTTATACCCAAATCAGTTT-TCATCATCCCCAAATAATCATAAGC
1 GTATCCCCAAAGTGATATACTTTATAACCAAATCA-TTTCTCATTATCCCCAAATAATCATATGC
* * * **
24110 ATCATCCCCAAATTTTTTAGA-ATTGACAATTTTTTTATATACCCAAAATTGGTTTTTCAACGTG
65 ACCATTCCCAAA-TTTTTAGAGATTGAC-ATTTTTTTATATACCCAAAATTGG-CTTAAAACGTG
* * *
24174 TTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCTCGTCTATATAAATTTAGTGTCCTCC
127 TTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCATCT
*
24239 AATAATTAAACAAAATGCAAAATTCA
192 AATAACTAAACAAAATGCAAAATTCA
*
24265 GTATCCTCAAAGTGATATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCA
1 GTATCCCCAAAGTGATATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCA
* *
24330 CCATTCCCAAACTTTTAGAGATTGACATATTTTTATATACCCAAAATTGGCTTAAAACGTGTTTT
66 CCATTCCCAAATTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACGTGTTTT
* *
24395 AATCTATATTTTCATCCTAATTAATTGAACAAACCCCGTCTATATAAATTTAGTGTCATCTAATA
131 AATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCATCTAATA
24460 ACTAAACAAAATGCAAAATTCA
196 ACTAAACAAAATGCAAAATTCA
* ** *
24482 ATATCCCCAAAGTGATATACTTTATGTCCAAATCATTTCTCATCATCCCCAAATAATCATATGCA
1 GTATCCCCAAAGTGATATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCA
24547 CCA-TCCTCAAATTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACGTGTTT
66 CCATTCC-CAAATTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACGTGTTT
* * * * *
24611 TAATCCACATTTCCATCATAATTAATTGAATAAACCCCGTCTATATAAATTTATTGTCATATAAT
130 TAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCATCTAAT
24676 AACTAAACAAAATGCAAAAATTCA
195 AACTAAACAAAATGC-AAAATTCA
* * * * *
24700 GTATCCCAAAAGAGATATACTTTATACCCAAATCATTTCTCATTATCCCCAAATAATCGTACGCA
1 GTATCCCCAAAGTGATATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCA
* * * * *
24765 CCATCTCCAAAATATTTTTATAGATTGACATTTGTTTATATGCCCAAAATTGGCTTTTAAACGTG
66 CCAT-TCC-CAA-ATTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGC-TTAAAACGTG
* * * *
24830 TTTTAATCCATATTTTTATCATAATTAATTGAATAAACCCCATCTATATAAATTTAGTGTCCTCT
127 TTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCATCT
*
24895 AATAATTAAACAAAATGCAAAATTCA
192 AATAACTAAACAAAATGCAAAATTCA
24921 GTATCCCCATAA-TGATATACGTACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCAT
1 GTATCCCCA-AAGTG--ATA--TACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCAT
* *
24985 ATGCACCATCCCCAAATTTTTTAGAGATTGACATTTTTTTATATACCCAAATTTGGCTTAAAACG
61 ATGCACCATTCCCAAA-TTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACG
*
25050 TGTTGTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCAT
125 TGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCAT
25115 AAAAAAAATA
Statistics
Matches: 765, Mismatches: 71, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
216 3 0.00
217 284 0.37
218 101 0.13
219 71 0.09
220 5 0.01
221 55 0.07
222 154 0.20
223 41 0.05
224 2 0.00
225 49 0.06
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (217 bp):
GTATCCCCAAAGTGATATACTTTATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCA
CCATTCCCAAATTTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAACGTGTTTT
AATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCATCTAATA
ACTAAACAAAATGCAAAATTCA
Found at i:24893 original size:656 final size:643
Alignment explanation
Indices: 23857--25114 Score: 1877
Period size: 656 Copynumber: 1.9 Consensus size: 643
23847 TCGTTAGTTT
23857 TATACTTTATATCCAAATCATTTCTCATCATCCCCAAATAATCAAACGCACCATCCTAAAATATT
1 TATACTTTATATCCAAATCATTTCTCATCATCCCCAAATAATCAAACGCACCATCCTAAAATATT
* * * * *
23922 TTTATAGATAGACATTTGTTTATATGCCCAAAATTGGCTTTTAAACGTGTTTTAATCCATATTTT
66 TTTAGAGATAGACATTTGTTTATATACCCAAAATTGGCTTTAAAACGTGTTTTAATCCACATTTC
* * * * *
23987 TATCCTAATTAATTGGAAAACCCCGTCTATATGAATTTATTGTCATCTAATAATTAAACGTATCC
131 CATCATAATTAATTGAAAAACCCCGTCTATATAAATTTATTGTCATATAATAATTAAACGTATCC
* *
24052 CCAAAGAGATATACTTTATACCCAAATCAGTTTTCATCATCCCCAAATAATCATAAGCATCATCC
196 CAAAAGAGATATACTTTATACCCAAATCAGTTTTCATCATCCCCAAATAATCATAAGCACCATCC
* * * *
24117 CCAAATTTTTTAGAATTGACAATTTTTTTATATACCCAAAATTGGTTTTTCAACGTGTTTTAATC
261 CAAAATTTTTTAGAATTGACAATTTGTTTATATACCCAAAATTGGCTTTTAAACGTGTTTTAATC
* * *
24182 CATATTTTCATCCTAATTAATTGAATAAACCTCGTCTATATAAATTTAGTGTCCTCCAATAATTA
326 CATATTTTCATCATAATTAATTGAATAAACCCCATCTATATAAATTTAGTGTCCTCCAATAATTA
*
24247 AACAAAATGCAAAATTCAGTATCCTCA-AAGTG-ATA-TACTTTATAACCAAATCATTTCTCATT
391 AACAAAATGCAAAATTCAGTATCCCCATAA-TGAATACTACTTTATAACCAAATCATTTCTCATT
*
24309 ATCCCCAAATAATCATATGCACCATTCCCAAA-CTTTTAGAGATTGACATATTTTTATATACCCA
455 ATCCCCAAATAATCATATGCACCATCCCCAAATCTTTTAGAGATTGACATATTTTTATATACCCA
* *
24373 AAATTGGCTTAAAACGTGTTTTAATCTATATTTTCATCCTAATTAATTGAACAAACCCCGTCTAT
520 AAATTGGCTTAAAACGTGTTGTAATCCATATTTTCATCCTAATTAATTGAACAAACCCCGTCTAT
24438 ATAAATTTAGTGTCATCTAATAACTAAACAAAATGCAAAATTCAATATCCCCAAAGTGA
585 ATAAATTTAGTGTCATCTAATAACTAAACAAAATGCAAAATTCAATATCCCCAAAGTGA
* * * *
24497 TATACTTTATGTCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCT-CAA-ATT
1 TATACTTTATATCCAAATCATTTCTCATCATCCCCAAATAATCAAACGCACCATCCTAAAATATT
* *
24560 TTTAGAGATTGACATTTTTTTATATACCCAAAATTGGC-TTAAAACGTGTTTTAATCCACATTTC
66 TTTAGAGATAGACATTTGTTTATATACCCAAAATTGGCTTTAAAACGTGTTTTAATCCACATTTC
24624 CATCATAATTAATTGAATAAACCCCGTCTATATAAATTTATTGTCATATAATAACTAAACAAAAT
131 CATCATAATTAATTGAA-AAACCCCGTCTATATAAATTTATTGTCATATAATAA-T--------T
*
24689 GCAAAAATTCAGTATCCCAAAAGAGATATACTTTATACCCAAATCA-TTTCTCATTATCCCCAAA
186 ----AAA--C-GTATCCCAAAAGAGATATACTTTATACCCAAATCAGTTT-TCATCATCCCCAAA
* * * *
24753 TAATCGTACGCACCATCTCCAAAATATTTTTATAGATTGAC-ATTTGTTTATATGCCCAAAATTG
243 TAATCATAAGCACCATC-CCAAAAT-TTTTTAGA-ATTGACAATTTGTTTATATACCCAAAATTG
*
24817 GCTTTTAAACGTGTTTTAATCCATATTTTTATCATAATTAATTGAATAAACCCCATCTATATAAA
305 GCTTTTAAACGTGTTTTAATCCATATTTTCATCATAATTAATTGAATAAACCCCATCTATATAAA
*
24882 TTTAGTGTCCTCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCATAATGATATACGTACTT
370 TTTAGTGTCCTCCAATAATTAAACAAAATGCAAAATTCAGTATCCCCATAATGA-ATAC-TACTT
*
24947 TATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGA
433 TATAACCAAATCATTTCTCATTATCCCCAAATAATCATATGCACCATCCCCAAATCTTTTAGAGA
* *
25012 TTGACATTTTTTTATATACCCAAATTTGGCTTAAAACGTGTTGTAATCCATATTTTCATCCTAAT
498 TTGACATATTTTTATATACCCAAAATTGGCTTAAAACGTGTTGTAATCCATATTTTCATCCTAAT
*
25077 TAATTGAATAAACCCCGTCTATATAAATTTAGTGTCAT
563 TAATTGAACAAACCCCGTCTATATAAATTTAGTGTCAT
25115 AAAAAAAATA
Statistics
Matches: 551, Mismatches: 40, Indels: 33
0.88 0.06 0.05
Matches are distributed among these distances:
637 37 0.07
638 71 0.13
639 3 0.01
640 54 0.10
647 1 0.00
651 3 0.01
653 4 0.01
654 61 0.11
655 6 0.01
656 135 0.25
657 8 0.01
658 3 0.01
660 58 0.11
661 107 0.19
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (643 bp):
TATACTTTATATCCAAATCATTTCTCATCATCCCCAAATAATCAAACGCACCATCCTAAAATATT
TTTAGAGATAGACATTTGTTTATATACCCAAAATTGGCTTTAAAACGTGTTTTAATCCACATTTC
CATCATAATTAATTGAAAAACCCCGTCTATATAAATTTATTGTCATATAATAATTAAACGTATCC
CAAAAGAGATATACTTTATACCCAAATCAGTTTTCATCATCCCCAAATAATCATAAGCACCATCC
CAAAATTTTTTAGAATTGACAATTTGTTTATATACCCAAAATTGGCTTTTAAACGTGTTTTAATC
CATATTTTCATCATAATTAATTGAATAAACCCCATCTATATAAATTTAGTGTCCTCCAATAATTA
AACAAAATGCAAAATTCAGTATCCCCATAATGAATACTACTTTATAACCAAATCATTTCTCATTA
TCCCCAAATAATCATATGCACCATCCCCAAATCTTTTAGAGATTGACATATTTTTATATACCCAA
AATTGGCTTAAAACGTGTTGTAATCCATATTTTCATCCTAATTAATTGAACAAACCCCGTCTATA
TAAATTTAGTGTCATCTAATAACTAAACAAAATGCAAAATTCAATATCCCCAAAGTGA
Found at i:27238 original size:39 final size:39
Alignment explanation
Indices: 27184--27364 Score: 247
Period size: 39 Copynumber: 4.7 Consensus size: 39
27174 TAGCCAACAA
* * *
27184 TTAACCCCCTGAGGCATGGGTCCACTATTACCAATCATT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGT
* *
27223 TTAACCCCCTAAGGCACGGGTCCACTCTTACCAGTCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGT
* *
27262 TTAACCCCCTGAGGCACGAGTCCACTCTTACTAATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGT
*
27301 TTAACCCCCTGAGGCAC-GCTCCACTCTTACCAATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGT
** **
27339 TTAACCCATTGAGGCATAGGTCCACT
1 TTAACCCCCTGAGGCACGGGTCCACT
27365 ATGCACAGCC
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
38 32 0.26
39 93 0.74
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (39 bp):
TTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGT
Found at i:30949 original size:28 final size:28
Alignment explanation
Indices: 30905--30961 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
30895 TAAATTACTC
* * *
30905 ATGAGACTAAGTAAAATGTGAGAATAAA
1 ATGAGACTAAATAAAATGTAAGAACAAA
*
30933 ATGAGACTAAATGAAATGTAAGAACAAA
1 ATGAGACTAAATAAAATGTAAGAACAAA
30961 A
1 A
30962 GAAATACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.19
Consensus pattern (28 bp):
ATGAGACTAAATAAAATGTAAGAACAAA
Found at i:31009 original size:33 final size:33
Alignment explanation
Indices: 30972--31036 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
30962 GAAATACAAT
* * *
30972 CTTAATGTGACTAGAATG-GACAAAAAATATTTC
1 CTTAATCTGACTAAAATGAAAC-AAAAATATTTC
*
31005 CTTAATCTGATTAAAATGAAACAAAAATATTT
1 CTTAATCTGACTAAAATGAAACAAAAATATTT
31037 TTAGATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (33 bp):
CTTAATCTGACTAAAATGAAACAAAAATATTTC
Found at i:31881 original size:32 final size:32
Alignment explanation
Indices: 31826--31886 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
31816 TTAGTTCAAG
* *
31826 AAAACAAAAATAGGCTGCCAAAGAGAATGAGA
1 AAAACAAAAATAGGCTGCAAAAGACAATGAGA
*
31858 AAAACAAAACATAGG-TTCAAAAGACAATG
1 AAAACAAAA-ATAGGCTGCAAAAGACAATG
31887 GCATCAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.57, C:0.13, G:0.18, T:0.11
Consensus pattern (32 bp):
AAAACAAAAATAGGCTGCAAAAGACAATGAGA
Found at i:32740 original size:24 final size:25
Alignment explanation
Indices: 32687--32742 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
32677 TAATATTATT
* *
32687 ATTACTTTTTTTCATACTCATGAAGC
1 ATTAATTTTTTTCATACTCATG-AGA
32713 ATTAATTTTTTTCATACTCATG-GA
1 ATTAATTTTTTTCATACTCATGAGA
32737 ATTAAT
1 ATTAAT
32743 ATGTGCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.25
26 21 0.75
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (25 bp):
ATTAATTTTTTTCATACTCATGAGA
Found at i:35193 original size:16 final size:16
Alignment explanation
Indices: 35167--35204 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35157 GTTGAATTGA
35167 GTTGTGAGTTGTGTCTT
1 GTTGTGAGTTGT-TCTT
35184 GTTG-GAGTTGTTCTT
1 GTTGTGAGTTGTTCTT
*
35199 CTTGTG
1 GTTGTG
35205 GGAGTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.05, C:0.08, G:0.34, T:0.53
Consensus pattern (16 bp):
GTTGTGAGTTGTTCTT
Found at i:40613 original size:11 final size:11
Alignment explanation
Indices: 40597--40622 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40587 GTTTTAGATC
40597 TTTTCTTCTAG
1 TTTTCTTCTAG
40608 TTTTCTTCTAG
1 TTTTCTTCTAG
40619 TTTT
1 TTTT
40623 TAGGCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:45830 original size:26 final size:25
Alignment explanation
Indices: 45784--45849 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
45774 GGAAAAGAAA
*
45784 AAAAAGAAAAATGAAGAAAAGAA-TT
1 AAAAAGAAAAA-GAAAAAAAGAAGTT
45809 GAAAAAGAAAAAGAAAAGAAAGAAGTT
1 -AAAAAGAAAAAGAAAA-AAAGAAGTT
*
45836 AAAAATGCAAAAGA
1 AAAAA-GAAAAAGA
45850 CGGGGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 4 0.11
26 22 0.63
27 9 0.26
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (25 bp):
AAAAAGAAAAAGAAAAAAAGAAGTT
Found at i:46109 original size:39 final size:40
Alignment explanation
Indices: 46028--46110 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 40
46018 GGAATGAAAC
** * * *
46028 TTTCTTCAAAGTGTGATCTTTTCAAAAGAAAAAGATTTTT
1 TTTCTTCAAAGTGCAATCTTTTCAAAAGAAAAAAAATGTT
46068 TTTC-TCAAAGTGCAATCTTTTCAAAAGAAAAAAAATGTT
1 TTTCTTCAAAGTGCAATCTTTTCAAAAGAAAAAAAATGTT
46107 TTTC
1 TTTC
46111 AAAAAGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (40 bp):
TTTCTTCAAAGTGCAATCTTTTCAAAAGAAAAAAAATGTT
Found at i:47255 original size:54 final size:54
Alignment explanation
Indices: 47186--47341 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 54
47176 GTGTTTAAAG
*
47186 TGATACAGTGCGGTCGTTCCAAGAAGTTTTTAGAGATCAGAGTTTATCCCCAGA
1 TGATCCAGTGCGGTCGTTCCAAGAAGTTTTTAGAGATCAGAGTTTATCCCCAGA
* *
47240 TGATCCAGTGCGGTCGTTCCAAGAAGTTTTTAGAGATCAAAGTTGATCCCCAGA
1 TGATCCAGTGCGGTCGTTCCAAGAAGTTTTTAGAGATCAGAGTTTATCCCCAGA
* * ** *
47294 CGATCCAGAGTAGTCGTTCCAAGAAATTTTT-GATGATCAGAGTTTATC
1 TGATCCAGTGCGGTCGTTCCAAGAAGTTTTTAGA-GATCAGAGTTTATC
47342 TCATTTCAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 2 0.02
54 89 0.98
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (54 bp):
TGATCCAGTGCGGTCGTTCCAAGAAGTTTTTAGAGATCAGAGTTTATCCCCAGA
Found at i:47353 original size:35 final size:35
Alignment explanation
Indices: 47313--47514 Score: 278
Period size: 35 Copynumber: 5.7 Consensus size: 35
47303 GTAGTCGTTC
* * *
47313 CAAGAAATTTTTGATGATCAGAGTTTATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* *
47348 CAAGAAAGTTTTTGATGATCAGAGTTGATCTAATTT
1 CAAG-AAGTTTTCGATGATCAGAGTTGATCTCATTT
*
47384 TAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* * *
47419 CATGAAGTTTTCAATGATTAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
**
47454 CAAGAAGTTTTCGATGATCAGAGTTGATCTTGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* *
47489 CAAGAAGTTTTGGATGATCGGAGTTG
1 CAAGAAGTTTTCGATGATCAGAGTTG
47515 GTCTTCACAT
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 118 0.79
36 31 0.21
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
Found at i:50408 original size:10 final size:10
Alignment explanation
Indices: 50393--50423 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
50383 TCTATAAGAG
50393 ATTTGTTTTT
1 ATTTGTTTTT
50403 ATTTGTTTTT
1 ATTTGTTTTT
*
50413 ATTTTTTTTT
1 ATTTGTTTTT
50423 A
1 A
50424 CAAAAGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (10 bp):
ATTTGTTTTT
Found at i:50493 original size:2 final size:2
Alignment explanation
Indices: 50486--50523 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50476 AGCTGTAACA
50486 AT AT AT AT 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 AT AT AT AT
50524 TGCTGCTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55486 original size:13 final size:13
Alignment explanation
Indices: 55468--55492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55458 ATATTTCTGT
55468 TTTGCTTATATGC
1 TTTGCTTATATGC
55481 TTTGCTTATATG
1 TTTGCTTATATG
55493 ATATTAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTGCTTATATGC
Found at i:57269 original size:28 final size:28
Alignment explanation
Indices: 57241--57315 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
57231 TGATTTCCTG
*
57241 TTTTGAAGTTCCTGATTTTTAGTAGCTGT
1 TTTTGAAGTTCCTG-TTTTTAGTAGCTGA
* *
57270 TTTTGAA-TTTCTGTTTTTTAGTGGCTGA
1 TTTTGAAGTTCCTG-TTTTTAGTAGCTGA
57298 TTTTG-AGTTCCTGTTTTT
1 TTTTGAAGTTCCTGTTTTT
57316 GTGCTTTGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.15
28 27 0.68
29 7 0.17
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.57
Consensus pattern (28 bp):
TTTTGAAGTTCCTGTTTTTAGTAGCTGA
Found at i:57273 original size:14 final size:14
Alignment explanation
Indices: 57227--57316 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
57217 TGTTTTTGTC
* *
57227 TTTTTGATTTCCTG
1 TTTTTGAGTTGCTG
*
57241 -TTTTGAAGTTCCTG
1 TTTTTG-AGTTGCTG
*
57255 ATTTTT-AGTAGCTG
1 -TTTTTGAGTTGCTG
* *
57269 TTTTTGAATTTCTG
1 TTTTTGAGTTGCTG
* *
57283 TTTTTTAGTGGCTG
1 TTTTTGAGTTGCTG
* *
57297 ATTTTGAGTTCCTG
1 TTTTTGAGTTGCTG
57311 TTTTTG
1 TTTTTG
57317 TGCTTTGCAC
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
13 10 0.18
14 43 0.75
16 4 0.07
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.58
Consensus pattern (14 bp):
TTTTTGAGTTGCTG
Found at i:57380 original size:21 final size:22
Alignment explanation
Indices: 57354--57395 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
57344 GATGTAGATC
*
57354 CTGTTTTCAA-TTTCTGTTTTA
1 CTGTTTTCAAGTTCCTGTTTTA
*
57375 CTGTTTTGAAGTTCCTGTTTT
1 CTGTTTTCAAGTTCCTGTTTT
57396 TTAGTGGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (22 bp):
CTGTTTTCAAGTTCCTGTTTTA
Found at i:57400 original size:137 final size:138
Alignment explanation
Indices: 57238--57543 Score: 479
Period size: 137 Copynumber: 2.2 Consensus size: 138
57228 TTTTGATTTC
*
57238 CTGTTTTGAAGTTCCTGATTTTTAGTAGCTGTTTTTGAATTTCTGTTTTTTAGTGGCTGATTTTG
1 CTGTTTTGAAGTTCCTGTTTTTTAGTAGCTGTTTTTGAATTTCTGTTTTTTAGTGGCTGATTTTG
* * *
57303 AGTTCCTGTTTTTGTGCTTTGCACTTTCTGTTTTTTGGGTTGATGTAGATCCTGTT-TTCAATTT
66 AGTTCCTGGTTTTGTGCTTTGCACATTCTGTTTTTTAGGTTGATGTAGATCCTGTTATTCAATTT
57367 CTGTTTTA
131 CTGTTTTA
* *
57375 CTGTTTTGAAGTTCCTGTTTTTTAGTGGCTGTTTTTGAGTTTCTGTTTTTTAGTGGCTGATTTTG
1 CTGTTTTGAAGTTCCTGTTTTTTAGTAGCTGTTTTTGAATTTCTGTTTTTTAGTGGCTGATTTTG
* * *
57440 AGTTCCTGGTTTTGTGTTTTGCAGATTCTGTTTTTTAGGTTGATGTAGATCCTGTTATTTAATTT
66 AGTTCCTGGTTTTGTGCTTTGCACATTCTGTTTTTTAGGTTGATGTAGATCCTGTTATTCAATTT
57505 CTGTTTTA
131 CTGTTTTA
* ** * *
57513 TTGTTTTCCAGTTCCTGTTTTTGAGTTGCTG
1 CTGTTTTGAAGTTCCTGTTTTTTAGTAGCTG
57544 GCTGTTTTCT
Statistics
Matches: 154, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
137 113 0.73
138 41 0.27
ACGTcount: A:0.12, C:0.11, G:0.22, T:0.56
Consensus pattern (138 bp):
CTGTTTTGAAGTTCCTGTTTTTTAGTAGCTGTTTTTGAATTTCTGTTTTTTAGTGGCTGATTTTG
AGTTCCTGGTTTTGTGCTTTGCACATTCTGTTTTTTAGGTTGATGTAGATCCTGTTATTCAATTT
CTGTTTTA
Found at i:57406 original size:14 final size:14
Alignment explanation
Indices: 57389--57438 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
57379 TTTGAAGTTC
57389 CTGTTTTTTAGTGG
1 CTGTTTTTTAGTGG
* **
57403 CTGTTTTTGAGTTT
1 CTGTTTTTTAGTGG
57417 CTGTTTTTTAGTGG
1 CTGTTTTTTAGTGG
57431 CTGATTTT
1 CTG-TTTT
57439 GAGTTCCTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (14 bp):
CTGTTTTTTAGTGG
Found at i:57415 original size:28 final size:28
Alignment explanation
Indices: 57378--57452 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
57368 TGTTTTACTG
*
57378 TTTTGAAGTTCCTGTTTTTTAGTGGCTGT
1 TTTTG-AGTTCCTGTTTTTTAGTGGCTGA
*
57407 TTTTGAGTTTCTGTTTTTTAGTGGCTGA
1 TTTTGAGTTCCTGTTTTTTAGTGGCTGA
*
57435 TTTTGAGTTCCTGGTTTT
1 TTTTGAGTTCCTGTTTTT
57453 GTGTTTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 37 0.88
29 5 0.12
ACGTcount: A:0.09, C:0.09, G:0.24, T:0.57
Consensus pattern (28 bp):
TTTTGAGTTCCTGTTTTTTAGTGGCTGA
Found at i:57452 original size:14 final size:14
Alignment explanation
Indices: 57378--57453 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
57368 TGTTTTACTG
57378 TTTTGAAGTTCCTGT
1 TTTTG-AGTTCCTGT
* **
57393 TTTTTAGTGGCTGT
1 TTTTGAGTTCCTGT
*
57407 TTTTGAGTTTCTGT
1 TTTTGAGTTCCTGT
* ** *
57421 TTTTTAGTGGCTGA
1 TTTTGAGTTCCTGT
*
57435 TTTTGAGTTCCTGG
1 TTTTGAGTTCCTGT
57449 TTTTG
1 TTTTG
57454 TGTTTTGCAG
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
14 43 0.91
15 4 0.09
ACGTcount: A:0.09, C:0.09, G:0.25, T:0.57
Consensus pattern (14 bp):
TTTTGAGTTCCTGT
Found at i:58810 original size:16 final size:16
Alignment explanation
Indices: 58789--58827 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58779 ATGGTACTTC
*
58789 AAATTGAAATTGAATG
1 AAATTGAAATTCAATG
* *
58805 AAATTGAATTTCATTG
1 AAATTGAAATTCAATG
58821 AAATTGA
1 AAATTGA
58828 CTTACTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (16 bp):
AAATTGAAATTCAATG
Found at i:59259 original size:19 final size:19
Alignment explanation
Indices: 59235--59278 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
59225 AAAAGCTGAT
59235 TTGTTTGAGTGATTCTTTG
1 TTGTTTGAGTGATTCTTTG
59254 TTGTTTGAGTGATTCTTTG
1 TTGTTTGAGTGATTCTTTG
59273 TTGTTT
1 TTGTTT
59279 CTTGCCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.05, G:0.25, T:0.61
Consensus pattern (19 bp):
TTGTTTGAGTGATTCTTTG
Done.