Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010396.1 Corchorus capsularis cultivar CVL-1 contig10417, 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: 24656
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1391 original size:670 final size:658
Alignment explanation
Indices: 1--2141 Score: 2558
Period size: 670 Copynumber: 3.2 Consensus size: 658
* * * * * *
1 AAATTGAGGAAAAATCTTTCGTGCCAATATTCGCAAAATTTTAGGCAAAATCGAGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * * *** * * *
66 CATAGTTTTA-GACTAAAAACGCGTTCCGGGGTCCTGACTCAGTTTTGCAAAATTTTTGACACTA
66 CACAGTTTTATG-CTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCA
* ** * * * *
130 AGACTCGTTGGAATATCGGTATTCATGTAACCAAATGTCAAACACATTGGATTTAAGGATTTGTT
130 AGACTCATTAAAATATCAGTATTCATCTAACCAAATCTCAGACACATTGGATTTAAGGATTTGTT
* * *
195 TTTTCGAGCATCAGAATCTTGTTTCGATATAATTAGAAATTAATCCGAAAAAAT-AGGATAAATG
195 TTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATG
* * * *
259 ATATTAGAAGCGTGAAAATCCCTTCAATCTTTATGGCGATGAATTATATATATATATATTTTTGA
260 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGC-ATGAATTATATATGTAT-TA----TGA
* * ** * * *
324 GTATTGTGGCCAAAAATTGTGGAAGCATATTTCGGGACAATTTTCGCAAAATTTTAGTCGAAATC
319 GTATTGTGGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATC
** * *
389 GTGTACTAACCATCATAG---TTTTGGGCTCCAAACGCATTCCAAGGTCCCGACTCAGTTTTGCT
384 GTG---T-ACCATCA-AGTTTTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCT
* * *
451 TGATTTTTGGCGCCTAGACTCATTAAAATATCTGTATTCATCTAACCAAATCTTGGCCACATTGG
444 TGATTTTTGGCGCCAAGACTCATTAAAATATTTGTATTCATCTAACCAAATCTCGGCCACATTGG
* *
516 ATTTAAGGATTTTTTTCTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAA
509 ATTTAAGGATTTTTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAAATTAATTCGAAA
*
581 AAATCAGGATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGG-GATGAATTATATA
574 AAAT-AGGATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATA
* *
645 GTTTTTTTGAGTTTTCTTGCCAA
638 -TTTTTTTGAGTATT-GTGCCAA
* * *
668 AAATTGAGGAAAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAGTTA-CAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * * *
732 CACAGTTTTATGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTTCTTGACTTTTGGCGCTAA
66 CACAGTTTTATGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
* *
797 GACTCATTAAAATATCAGTATTAATCTAACCAAATCTCAGTCACACTT-GATTTAAGGATTTGTT
131 GACTCATTAAAATATCAGTATTCATCTAACCAAATCTCAGACACA-TTGGATTTAAGGATTTGTT
* * * *
861 TTTACTAGCAACAGAATATTGTTTCGATTTACA-TAGAATTTAATTCGGAAAAAAATCA-GATAA
195 TTTACGAGCATCAGAATCTTGTTTCGATTTA-ATTAGAAATTAATTC-G-AAAAAATCAGGATAA
* **
924 ATGATATTGGAAGAATGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATGT-TTCATGAG
257 ATGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCA-TGAATTATATATGTATT-ATGAG
* *
988 TATTGTGGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTCAACCGAAATCG
320 TATTGTGGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCG
** * * *
1053 TGTACGCATCAGAGTTTTTTTTTTTTTTTGCGAAAAACGTGTTCTGAGGTCCCGACTCAGTTTTG
385 TGTAC-CATCA-AG------TTTTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTG
*
1118 CTTGATTTTTTGCGCCAAGACTCATTAAAATATTTGTATTCATCTAACCAAATCTCGGCCACATT
442 CTTGATTTTTGGCGCCAAGACTCATTAAAATATTTGTATTCATCTAACCAAATCTCGGCCACATT
* *
1183 GGATTTAAGGATTTTTTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAAATTAGTTCT
507 GGATTTAAGGA-TTTTTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAAATTAATTCG
*
1248 AAAAAATAGGATAAATGATACTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATA
571 AAAAAATAGGATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATA
1313 TATATTTTTTGAGTATTGTGCCCAA
636 TAT-TTTTTTGAGTATTGTG-CCAA
* *
1338 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGTAAAATTTTAGTCGAAATCGTGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
** ** * *
1403 CACAGTTTTGGGCTCCAAACGCATTCCAAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
66 CACAGTTTTATGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
* ** *
1468 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTTGGCCACATTGGATTTAAGGATTT-TTT
131 GACTCATTAAAATATCAGTATTCATCTAACCAAATCTCAGACACATTGGATTTAAGGATTTGTTT
1532 TCTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATG
196 T-TACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATG
* * * *
1597 ATATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGGGGATGAATTATATA-GTATTTTTGAGTTT
260 ATATTAGAAGCGTGAAAAGCCCTTCAAT-ATTTTTGGCATGAATTATATATGTA-TTATGAGTAT
* * * * *
1661 TCTTGCCAAAAATTGAGTAAAAATCTTTTGGGTCAATTTTCGCATAATTTTAGCCGAAATCGTAT
323 TGTGGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCG--T
* *
1726 ACTAACCATCACAG--TTTTGGGGCTAAAAACGCGTTCCG-GGATCCCGACTCAGTTTTGCTTGA
386 -GT-ACCATCA-AGTTTTTTTGGGCTAAAAACGCGTTCCGAGG-TCCCGACTCAGTTTTGCTTGA
* * * * * *
1788 TTATTGGCACCAGGACTCATTAAAATACCTT-TATTCATCTATCCAAATCTCAGCCACATTGGAT
447 TTTTTGGCGCCAAGACTCATTAAAATA-TTTGTATTCATCTAACCAAATCTCGGCCACATTGGAT
* * * * * * *
1852 TTAAGAATATGTTTTTACTAGCATCAGAATCTTGCTTCT-AGTTAAATAGAAATTAATTCGGAAA
511 TTAAGGATTTTTTTTTACGAGCATCAGAATCTTG-TTTTGATTTAATTAGAAATTAATTC-GAAA
* * ** * *
1916 AAATAGTATAAATGATATTGGAAGAATGAAAAGCCCTTTAATATTTTTGGC-ATTGAATTATATA
574 AAATAGGATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGA-TGAATTATATA
** *
1980 TTTCTCATGAGTATTGTGGACAA
638 TTT-TTTTGAGTATTGT-GCCAA
* *
2003 AAATTGAGGAAAAATCTTTCGGGTCAACTTTCGCAAAATTTTAACCGAAATCGTGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * ** *
2068 CATAGTTTT-TGGGCTAAAAACGTGTTCCGAGGTCCCGGTTCAGTTTTGCTTGATTTTTTGCGCC
66 CACAGTTTTAT--GCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCC
2132 AAGACTCATT
129 AAGACTCATT
2142 TTGCAAGGAA
Statistics
Matches: 1273, Mismatches: 158, Indels: 87
0.84 0.10 0.06
Matches are distributed among these distances:
659 2 0.00
660 8 0.01
663 62 0.05
664 46 0.04
665 244 0.19
666 204 0.16
667 60 0.05
668 59 0.05
669 164 0.13
670 254 0.20
671 159 0.12
672 1 0.00
673 8 0.01
674 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (658 bp):
AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
CACAGTTTTATGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
GACTCATTAAAATATCAGTATTCATCTAACCAAATCTCAGACACATTGGATTTAAGGATTTGTTT
TTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATGA
TATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATGAATTATATATGTATTATGAGTATTGT
GGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACC
ATCAAGTTTTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCG
CCAAGACTCATTAAAATATTTGTATTCATCTAACCAAATCTCGGCCACATTGGATTTAAGGATTT
TTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAAATTAATTCGAAAAAATAGGATAAA
TGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATATTTTTTTGAGTAT
TGTGCCAA
Found at i:1607 original size:332 final size:330
Alignment explanation
Indices: 1--2141 Score: 2636
Period size: 332 Copynumber: 6.4 Consensus size: 330
* * * * * *
1 AAATTGAGGAAAAATCTTTCGTGCCAATATTCGCAAAATTTTAGGCAAAATCGAGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * * * * *** * * *
66 CATAGTTTTAGACTAAAAACGCGTTCCGGGGTCCTGACTCAGTTTTGCAAAATTTTTGACACTAA
66 CACAGTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
* ** * * * **
131 GACTCGTTGGAATATCGGTATTCATGTAACCAAATGTCAAACACATTGGATTTAAGGATTTGTTT
131 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT-TTT
* * *
196 TTTCGAGCATCAGAATCTTGTTTCGATATAATTAGAAATTAATCCGAAAAAATAGGATAAATGAT
195 TTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGATAAATGAT
* *
261 ATTAGAAGCGTGAAAATCCCTTCAATCTTTATGGCGATGAATTATATATATATATATTTTTGAGT
260 ATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATG-A--AT-TATATATAT-TTTTTGAGT
326 ATTGTGGCCAA
320 ATTGTGGCCAA
* ** * * *
337 AAATTGTGGAAGCATATTTCGGGACAATTTTCGCAAAATTTTAGTCGAAATCGTGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* ** * * *
402 CATAGTTTTGGGCTCCAAACGCATTCCAAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCTA
66 CACAGTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
**
467 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTTGGCCACATTGGATTTAAGGATTTTTTT
131 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTTTTT
532 CTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATGA
196 -TACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAT-AGGATAAATGA
* *
597 TATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGG-GATGAATTATATAGT-TTTTTTGAGTTTT
259 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATA-TATTTTTTGAGTATT
* *
660 CTTGCCAA
323 GTGGCCAA
* * *
668 AAATTGAGGAAAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAGTTA-CAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
** * * * *
732 CACAGTTTTATGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTTCTTGACTTTTGGCGCTAA
66 CACAGTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
* * *
797 GACTCATTAAAATATCAGTATTAATCTAACCAAATCTCAGTCACACTT-GATTTAAGGATTTGTT
131 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACA-TTGGATTTAAGGATTT-TT
* * * *
861 TTTACTAGCAACAGAATATTGTTTCGATTTACA-TAGAATTTAATTCGGAAAAAAATCA-GATAA
194 TTTACGAGCATCAGAATCTTGTTTCGATTTA-ATTAGAAATTAATTC-G-AAAAAAT-AGGATAA
* ** * * **
924 ATGATATTGGAAGAATGAAAAGCCCTTCAATATTTTTGGC-ATTGAATTATATATGTTTCATGAG
255 ATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGA-TGAATTATATATATTTTTTGAG
988 TATTGTGGCCAA
319 TATTGTGGCCAA
* * * *
1000 AAATTGAGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTCAACCGAAATCGTGTAC---GCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* ** * * *
1062 CAGAGTTTTTTTTTTTTTTTGCGAAAAACGTGTTCTGAGGTCCCGACTCAGTTTTGCTTGATTTT
66 CACAG---------TTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTT
* * *
1127 TTGCGCCAAGACTCATTAAAATATTTGTATTCATCTAACCAAATCTCGGCCACATTGGATTTAAG
122 TGGCGCCAAGACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG
* * *
1192 GATTTTTTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAAATTAGTTCTAAAAAATAG
187 GA--TTTTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAG
*
1257 GATAAATGATACTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATATATTTTT
250 GATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATATATTTTT
*
1322 TGAGTATTGTGCCCAA
315 TGAGTATTGTGGCCAA
* *
1338 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGTAAAATTTTAGTCGAAATCGTGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
** * *
1403 CACAGTTTTGGGCTCCAAACGCATTCCAAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
66 CACAGTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
**
1468 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTTGGCCACATTGGATTTAAGGATTTTTTT
131 GACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTTTTT
1533 CTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATCAGGATAAATGA
196 -TACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAT-AGGATAAATGA
* * *
1598 TATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGGGGATGAATTATATAGTA-TTTTTGAGTTTT
259 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATA-TATTTTTTGAGTATT
* *
1662 CTTGCCAA
323 GTGGCCAA
* * * *
1670 AAATTGAGTAAAAATCTTTTGGGTCAATTTTCGCATAATTTTAGCCGAAATCGTATACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* *
1735 CACAGTTTTGGGGCTAAAAACGCGTTCCG-GGATCCCGACTCAGTTTTGCTTGATTATTGGCACC
66 CACAGTTTT-GGGCTAAAAACGCGTTCCGAGG-TCCCGACTCAGTTTTGCTTGATTTTTGGCGCC
* * * * * *
1799 AGGACTCATTAAAATACCTTTATTCATCTATCCAAATCTCAGCCACATTGGATTTAAGAATATGT
129 AAGACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT-TTT
* * * * * *
1864 TTTTACTAGCATCAGAATCTTGCTTCTAGTTAAATAGAAATTAATTCGGAAAAAATAGTATAAAT
193 TTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATAGGATAAAT
* ** * * **
1929 GATATTGGAAGAATGAAAAGCCCTTTAATATTTTTGGC-ATTGAATTATATAT-TTCTCATGAGT
257 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGA-TGAATTATATATATT-TTTTGAGT
*
1992 ATTGTGGACAA
320 ATTGTGGCCAA
* *
2003 AAATTGAGGAAAAATCTTTCGGGTCAACTTTCGCAAAATTTTAACCGAAATCGTGTACTAACCAT
1 AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * ** *
2068 CATAGTTTTTGGGCTAAAAACGTGTTCCGAGGTCCCGGTTCAGTTTTGCTTGATTTTTTGCGCCA
66 CACAG-TTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCA
2133 AGACTCATT
130 AGACTCATT
2142 TTGCAAGGAA
Statistics
Matches: 1563, Mismatches: 200, Indels: 87
0.84 0.11 0.05
Matches are distributed among these distances:
330 161 0.10
331 169 0.11
332 348 0.22
333 323 0.21
334 19 0.01
335 5 0.00
336 209 0.13
337 44 0.03
338 132 0.08
339 103 0.07
340 40 0.03
341 10 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (330 bp):
AAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
CACAGTTTTGGGCTAAAAACGCGTTCCGAGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAA
GACTCATTAAAATATCTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTTTTT
TACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGATAAATGATA
TTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGATGAATTATATATATTTTTTGAGTATTGTG
GCCAA
Found at i:4952 original size:122 final size:121
Alignment explanation
Indices: 4665--5084 Score: 596
Period size: 124 Copynumber: 3.4 Consensus size: 121
4655 GGCGTCAATA
*
4665 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATACATTAAAAAT
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAA-
* *
4730 TTTTAATATATCTAAGTTTTTAACGAAAAATAGTGAAATGGTAAAAATAAAATAATTAT
65 TTTTAATATATCCAAGTTTTTAA-TAAAAATAGT-AAATGGTAAAAATAAAATAATTAT
*
4789 AAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTGAAAAA
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATT-AAAAA
4854 TTTTAATATATCCAAGTTTTTAATAAAAAATAGT-AATGGTAAAAATAAAATAATTAT
65 TTTTAATATATCCAAGTTTTTAAT-AAAAATAGTAAATGGTAAAAATAAAATAATTAT
* *
4911 AAAAATATTGAATTTAGTTAAATGAAAATAGAGTTTTTAGTAGAATCAAAATATATATTAAAAA-
1 AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAT
* * * * *
4975 TTTGATATATCCAAATTTTTAATAAAAATAGTAAAATTGTAAAAATAAAGTCATTA-
66 TTTAATATATCCAAGTTTTTAATAAAAATAGT-AAATGGTAAAAATAAAATAATTAT
* * * * *
5031 AAAAGATATT-AGATTTAACTAAATAAAAATAGAGTTTTAAGTATAATAAAACTA
1 AAAA-ATATTGA-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTA
5085 CAATACTTTA
Statistics
Matches: 271, Mismatches: 19, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
119 9 0.03
120 26 0.10
121 64 0.24
122 79 0.29
124 88 0.32
125 5 0.02
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (121 bp):
AAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAT
TTTAATATATCCAAGTTTTTAATAAAAATAGTAAATGGTAAAAATAAAATAATTAT
Found at i:5586 original size:70 final size:70
Alignment explanation
Indices: 5512--5744 Score: 290
Period size: 70 Copynumber: 3.2 Consensus size: 70
5502 TTGTTTAGGT
*
5512 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATT
5576 ATTTTA
65 ATTTTA
5582 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAA-ACTAATATCCTTATAACT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATA-TAATAT-CTT-T-A-T
*
5646 ATTATATTTTACCA
61 AAT-TATTTT---A
* * * *
5660 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
*
5725 TTATA
66 TTTTA
*
5730 TTTTACAATTTTACT
1 TTTTACTATTTTACT
5745 ATTTTAGTTA
Statistics
Matches: 143, Mismatches: 9, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
69 1 0.01
70 63 0.44
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 52 0.36
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:5594 original size:78 final size:77
Alignment explanation
Indices: 5512--5750 Score: 343
Period size: 78 Copynumber: 3.2 Consensus size: 77
5502 TTGTTTAGGT
*
5512 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
5572 AAT-TATTTT--A
65 ATTATATTTTACA
5582 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAA-ACTAATATCCTTATAACT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATA-TAATATCCTTATAACT
5646 ATTATATTTTACCA
65 ATTATATTTTA-CA
* *
5660 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
5725 TTATATTTTACAA
66 TTATATTTTAC-A
5738 TTTTACTATTTTA
1 TTTTACTATTTTA
5751 GTTAAAAAAA
Statistics
Matches: 153, Mismatches: 4, Indels: 16
0.88 0.02 0.09
Matches are distributed among these distances:
69 1 0.01
70 48 0.31
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.57
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACA
Found at i:8370 original size:2 final size:2
Alignment explanation
Indices: 8358--8404 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
8348 CTCCTTAATT
*
8358 TA TA TA CTA TA TA T- TA TA AA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8399 TA TA TA
1 TA TA TA
8405 AAGTTAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15742 original size:190 final size:189
Alignment explanation
Indices: 15419--15794 Score: 707
Period size: 190 Copynumber: 2.0 Consensus size: 189
15409 GAACCAACAA
15419 ACCCCTTCCCCAACAAACAAACCCAATGAAATCTAATTACAATATAAATCTCTATATATGTCCAA
1 ACCCCTTCCCCAACAAACAAACCCAATGAAATCTAATTACAATATAAATCTCTATATATGTCCAA
15484 ACATATAAATGAGAATACAACCCAAACTAGAAACTATACCTTAAATAAACTACCAACCAAATAAA
66 ACATATAAATGAGAATACAACCCAAACTAGAAACTATACCTTAAATAAACTACCAACCAAAT-AA
15549 AAAAAACAAATTACAAAGAAACTCACATTCCGTGAGAGTTGAACCTAAGATCTCATGGTC
130 AAAAAACAAATTACAAAGAAACTCACATTCCGTGAGAGTTGAACCTAAGATCTCATGGTC
15609 ACCCCTTCCCCAACAAACAAACCCAATGAAATCTAATTACAATATAAATCTCTATATATGTCCAA
1 ACCCCTTCCCCAACAAACAAACCCAATGAAATCTAATTACAATATAAATCTCTATATATGTCCAA
* * *
15674 ACATCTAAATGAGAATACAACCCAAACTAGAAACTATACCTTAAATAAACTATCAACTAAATAAA
66 ACATATAAATGAGAATACAACCCAAACTAGAAACTATACCTTAAATAAACTACCAACCAAATAAA
*
15739 AAAAACAAATTACAGAGAAACTCACATTCCGTGAGAGTTGAACCTAAGATCTCATG
131 AAAAACAAATTACAAAGAAACTCACATTCCGTGAGAGTTGAACCTAAGATCTCATG
15795 ATCTAGGTAG
Statistics
Matches: 182, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
189 58 0.32
190 124 0.68
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.22
Consensus pattern (189 bp):
ACCCCTTCCCCAACAAACAAACCCAATGAAATCTAATTACAATATAAATCTCTATATATGTCCAA
ACATATAAATGAGAATACAACCCAAACTAGAAACTATACCTTAAATAAACTACCAACCAAATAAA
AAAAACAAATTACAAAGAAACTCACATTCCGTGAGAGTTGAACCTAAGATCTCATGGTC
Found at i:17181 original size:107 final size:104
Alignment explanation
Indices: 17033--17322 Score: 388
Period size: 107 Copynumber: 2.8 Consensus size: 104
17023 AATTTTTATC
* * * *
17033 ATAGAGTTTTAGAAATAAAATATAAAACTAATTTAATTAAGTTTAGTCCCAAATTAAAATTGTAT
1 ATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCCAAATTAAAATTATAT
*
17098 TTTCATTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTT
66 TTT-ATTTTAAGGGTAAATTCCAAAATTAATAA--TATTGTT
* * *
17140 ATAGGGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAG-CTCCAAATTAAAATTTTA
1 ATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTC-CCAAATTAAAATTATA
* * *
17204 TTTTTAGTTTAAAGGTAAATTCCATAATTAATAATATTGTT
65 -TTTTATTTTAAGGGTAAATTCCAAAATTAATAATATTGTT
* *
17245 ATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAGT-CCAAATTAAAATTAAAA
1 ATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCCAAATTAAAATT-ATA
17308 TTTTATTTTAAGGGT
65 TTTTATTTTAAGGGT
17323 TAGAAAAATT
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
103 26 0.16
104 15 0.09
105 35 0.22
106 1 0.01
107 81 0.50
108 4 0.02
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (104 bp):
ATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCCAAATTAAAATTATAT
TTTATTTTAAGGGTAAATTCCAAAATTAATAATATTGTT
Found at i:19374 original size:108 final size:108
Alignment explanation
Indices: 19185--19400 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
19175 ACAGTTATTT
19185 GGAACATAATGTTCAAAGCACCTCTGTATTTGAAGGGAGCCATTTCTGACAAGTAAATTGGAACA
1 GGAACATAATGTTCAAAGCACCTCTGTATTTGAAGGGAGCCATTTCTGACAAGTAAATTGGAACA
19250 GACTGCATGAAACAAAACCAGAAAAAGACATTTATTTCGATAC
66 GACTGCATGAAACAAAACCAGAAAAAGACATTTATTTCGATAC
19293 GGAACATAATGTTCAAAGCACCTCTGTATTTGAAGGGAGCCATTTCTGACAAGTAAATTGGAACA
1 GGAACATAATGTTCAAAGCACCTCTGTATTTGAAGGGAGCCATTTCTGACAAGTAAATTGGAACA
19358 GACTGCATGAAACAAAACCAGAAAAAGACATTTATTTCGATAC
66 GACTGCATGAAACAAAACCAGAAAAAGACATTTATTTCGATAC
19401 TTAATGCCCT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (108 bp):
GGAACATAATGTTCAAAGCACCTCTGTATTTGAAGGGAGCCATTTCTGACAAGTAAATTGGAACA
GACTGCATGAAACAAAACCAGAAAAAGACATTTATTTCGATAC
Found at i:24556 original size:30 final size:28
Alignment explanation
Indices: 24485--24562 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
24475 GAACTTACAC
*
24485 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
24513 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
24544 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
24563 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Done.