Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012548.1 Corchorus capsularis cultivar CVL-1 contig12569, 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: 21237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7075 original size:36 final size:36
Alignment explanation
Indices: 7028--7101 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
7018 AAGCTCTATC
*
7028 AATACCTGTTTTCGATATTCACATGACTCGAACTCA
1 AATACATGTTTTCGATATTCACATGACTCGAACTCA
7064 AATACATGTTTTCGATATTCACATGACTCGAACTCA
1 AATACATGTTTTCGATATTCACATGACTCGAACTCA
7100 AA
1 AA
7102 ATCTTGAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (36 bp):
AATACATGTTTTCGATATTCACATGACTCGAACTCA
Found at i:18339 original size:652 final size:627
Alignment explanation
Indices: 17194--18734 Score: 1906
Period size: 652 Copynumber: 2.4 Consensus size: 627
17184 TTTTTTCCAA
* * *
17194 TTTTTTGCCACAATACTCTAAAAAATATAAAATTCAACGCCAAAAATATTGAATGGTTTTCACGC
1 TTTTTTCCCACAATACTC-AAAAAATATATAATTCAACGCCAAAAA-ATTGAAGGGTTTTCACGC
* *
17259 TTCTAATATCGTTTT-CCATTTTTATTCAAATTTATTTCTAATTAAATCGAAACAAGATTTAGAT
64 TTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGAT
*
17323 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
129 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
* * * *
17388 AAGGAGTCTTTCTGCCAAAAATCATACGAAACTGAGCCGAGGCCCCGAAACGTGTTTTTAGCCCC
194 AAGGAGTCTTTCTGCCAAAAATCATGCGAAACTAAACCGAGGCCCCGAAACGCGTTTTTAGCCCC
* * * ** *
17453 AAAATCATGATGGCTAGAACACGATTTCGGTTAAAAACTGACCCGAATTTTTTTTTTTCTGAAAT
259 AAAATC---A-CGCTAGAACACAATTTCGGCTAAAAACTGACCCGAATAATTTTTTCTCTGAAAT
* * * * *
17518 TTTTGCCACAATGCTCAGAAAAATATATAATTCAACGCTAAAAAGATTAACGGGTTTTTCACACT
320 TTTTGCCACAATACTCAAAAAAATATATAATTCAACACCAAAAAGATTAACGAGTTTTTCACACT
* *
17583 TCTACAATCTTTTTTCCATTTTTTCCTAATTAATTTCTAATTAAATAGAATCAAGATTCAGATAC
385 TCTACAATCGTTTTTCCATTTTTTCCTAATTAATTTCTAATTAAATAGAATCAAGACTCAGATAC
* * *
17648 TCGTAAAAACAAGTCCTTATATCTAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAA
450 TCATAAAAACAAGACCTTATATCTAATGCGGTTGAGATTTGGTTAGATGAATATAGATATTTCAA
** * * ** * *** *
17713 GGAGACTTCACGTTAAAAATCATGCAAAATTGAGTTGGGGCTCCAG-ATTGCG-TTTT-ACGCCA
515 GGAGACTTCACGCAAAAAATCATGCAAAACTCAGACGGAGC-CCAGAAACACGTTTTTAAC-CAA
* * *
17775 TAAATCGTGATGGTTAATACACAATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAATATTTT
578 AAAATCGTGATGGTTAATACACAATTTCGG---C-------CAAAAACTAACCCG--AA-A---T
17840 T
627 T
17841 CCTCAATTTTTCCACACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTAT
1 --T---TTTTTCC-CACAATACTC--AAAAAATATATAATTCAACGCCAAAAAATTGAAGGGT-T
* * *
17906 TTCACGC-TCTTAATTTCGTTTTCCCATTTTTATTCGAACTTATTTCTAATTAAATAGAAACAAG
57 TTCACGCTTC-TAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAG
*
17970 ATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
121 ATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATA
18035 GATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTAAACCGGTGAACCAGGGCCCCGAA
186 GATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTAAACC---G----A-GGCCCCGAA
18100 ACGCGTTTTTAGCCCCAAAA-C-CG-T-G-ACACAATTTCGGCTAAAAACTGACCCGAA-AATTT
243 ACGCGTTTTTAGCCCCAAAATCACGCTAGAACACAATTTCGGCTAAAAACTGACCCGAATAATTT
* **
18159 TTTCT-TGAAATTTTT-CCTAGAATACTCAAAAAAATATATAATTCAACACCAAAAAGATTGCCG
308 TTTCTCTGAAATTTTTGCC-ACAATACTCAAAAAAATATATAATTCAACACCAAAAAGATTAACG
* * *
18222 AGTTTTTCACGCTTCTA-ATATCGTTTTTCCATTTTTTCCTAATTAATTTTTTATTAAATAGAAT
372 AGTTTTTCACACTTCTACA-ATCGTTTTTCCATTTTTTCCTAATTAATTTCTAATTAAATAGAAT
18286 CAAGACTCAGATACTCATAAAAACAAGACCTTATATCTAATGCGGTTGAGATTTGGTTAGATGAA
436 CAAGACTCAGATACTCATAAAAACAAGACCTTATATCTAATGCGGTTGAGATTTGGTTAGATGAA
* * * * *
18351 TATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCGAAACTCAGACGGAGCCCCGAAACAC
501 TATAGATATTTCAAGGAGACTTCACGCAAAAAATCATGCAAAACTCAGACGGAGCCCAGAAACAC
* * * * *
18416 GTTTTTAACCAAAAAATCGTGATGGTTAGTATACGATTTCGGCCAAAAACTAATCTGAAATT
566 GTTTTTAACCAAAAAATCGTGATGGTTAATACACAATTTCGGCCAAAAACTAACCCGAAATT
* *
18478 TTTTTTGCCACAATACTCAAAAAATATATAATTCAACACCAAAAAATTGAAGGGTTTTTCACGCT
1 TTTTTTCCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAATTGAAGGG-TTTTCACGCT
* *
18543 TCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTATATCGAAACAAGATTCAGATG
65 TCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGATG
18608 CTCGTAAAAAACAAATCCTTAAAT-CAGATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
130 CTCGT-AAAAACAAATCCTTAAATCCA-ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
* * ** * * * *
18672 CTAGGACTCTTTCTGCCAAAAATCATGCGAAACCGATCCGGGGACCCGAAACGCGTTTGTAGC
193 CAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTAAACCGAGGCCCCGAAACGCGTTTTTAGC
18735 TTCAAAACCG
Statistics
Matches: 790, Mismatches: 77, Indels: 77
0.84 0.08 0.08
Matches are distributed among these distances:
622 20 0.03
627 1 0.00
629 108 0.14
630 91 0.12
631 10 0.01
632 6 0.01
635 1 0.00
637 2 0.00
640 1 0.00
641 2 0.00
643 10 0.01
649 1 0.00
650 1 0.00
651 6 0.01
652 219 0.28
653 60 0.08
654 74 0.09
655 144 0.18
656 1 0.00
657 1 0.00
658 1 0.00
662 2 0.00
663 28 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (627 bp):
TTTTTTCCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTCACGCTT
CTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGATGC
TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
GGAGTCTTTCTGCCAAAAATCATGCGAAACTAAACCGAGGCCCCGAAACGCGTTTTTAGCCCCAA
AATCACGCTAGAACACAATTTCGGCTAAAAACTGACCCGAATAATTTTTTCTCTGAAATTTTTGC
CACAATACTCAAAAAAATATATAATTCAACACCAAAAAGATTAACGAGTTTTTCACACTTCTACA
ATCGTTTTTCCATTTTTTCCTAATTAATTTCTAATTAAATAGAATCAAGACTCAGATACTCATAA
AAACAAGACCTTATATCTAATGCGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGAC
TTCACGCAAAAAATCATGCAAAACTCAGACGGAGCCCAGAAACACGTTTTTAACCAAAAAATCGT
GATGGTTAATACACAATTTCGGCCAAAAACTAACCCGAAATT
Found at i:18695 original size:310 final size:312
Alignment explanation
Indices: 16914--18793 Score: 1504
Period size: 332 Copynumber: 5.9 Consensus size: 312
16904 TAATTTATTG
* ** * * *
16914 CCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTT-CCATATTTT-TTCTAAATTAAT
1 CCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCAT-TTTTATTC-GAATTTAT
* * * * * *
16977 TTCTAATTAAATCGAAATTAAGATTTAGATG-TACGTAAAAACAAATGCTTAAATCCAATGTAGA
63 TTCTAATTAAATAGAAA-CAAGATTCAGATGCT-CGTAAAAACAAATCCTTAAAT-CAATGTGGC
* ** * * *
17041 TGAGATTTCGACAGATGAATAAAGATATTTCAAGGAGTC--TCAGCGCAAAAAATCATGCAAAAC
125 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGCGAAAC
** * * * *
17104 AT-AG-TTGTG-GTCCCGGAACGCG-TTTTAG-TA-AAAACCCGTGATGGTTAGTACATGATTTC
188 -TCAGACCG-GAGCCCCGAAACGCGTTTTTAGCCACAAAA--CGTGATGGTTAGTACACGATTTC
* * * * * * *
17163 GGCTAAAAACTTACTCGGAATTTTTTTCCAATTTTTTGCCACAATACTCTAAAAAATATAAAATT
249 GGCTAAAAACTAACCCGAAAATTTTTT-C----TTGT-CCACAATACTCAAAAAAATATATAATT
*
17228 CAACG
308 CAACA
* *
17233 CCAAAAATATTGAATGG-TTTTCACGCTTCTAATATCGTTTT-CCATTTTTATTCAAATTTATTT
1 CCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTT
* * *
17296 CTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
65 CTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAG
* *
17361 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATACGAAACTGAG-C
129 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTCAGAC
* * * * * *
17425 C-GAGGCCCCGAAACGTGTTTTTAGCCCCAAAATCATGATGGCTAGAACACGATTTCGGTTAAAA
194 CGGA-GCCCCGAAACGCGTTTTTAGCCACAAAA-CGTGATGGTTAGTACACGATTTCGGCTAAAA
* ** * * *
17489 ACTGACCCGAATTTTTTTTTTTCTGAAATTTTTGCCACAATGCTCAGAAAAATATATAATTCAAC
257 ACTAACCCGAA---AATTTTTTC------TTGT-CCACAATACTCAAAAAAATATATAATTCAAC
*
17554 G
312 A
* * * * * * *
17555 CTAAAAAGATT-AACGGGTTTTTCACACTTCTACA-ATCTTTTTTCCATTTTT-TCCTAATTAAT
1 CCAAAAA-ATTGAA-GGGTTTTTCACGCTTCTA-ATATCGTTTTCCCATTTTTATTCGAATTTAT
* * * * *
17617 TTCTAATTAAATAGAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCTAATGTGGTTG
63 TTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC-AATGTGGCTG
* * ** * * *
17682 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGAC-TTCACGTTAAAAATCATGCAAAATTGA
127 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC-TGCCAAAAATCATGCGAAACTCA
** * * ** * * * *
17746 G-TTGGGGCTCC-AGATTGCG-TTTTACGCCATAAATCGTGATGGTTAATACACAATTTCGGCTA
191 GACCGGAGCCCCGA-AACGCGTTTTTA-GCCACAAAACGTGATGGTTAGTACACGATTTCGG---
* * *
17808 CAATTTTGCAAAAATTGACCCGAAAATATTTTTCCTCAATTTTTCCACACAATACTCAAAAAAAA
251 C-----T--AAAAACTAACCCG-AAA-ATTTTT--TC---TTGT-C-CACAATACTC-AAAAAAA
*
17873 TATATAATTCAACG
299 TATATAATTCAACA
* * *
17887 CCAAAAAATTGAAGGGTATTTCACGC-TCTTAATTTCGTTTTCCCATTTTTATTCGAACTTATTT
1 CCAAAAAATTGAAGGGTTTTTCACGCTTC-TAATATCGTTTTCCCATTTTTATTCGAATTTATTT
*
17951 CTAATTAAATAGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
65 CTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAG
* *
18016 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACT-AAAC
129 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTCAGAC
* * *
18080 CGGTGAACCAGGGCCCCGAAACGCGTTTTTAGCCCCAAAAC-----CG-T-G-ACACAATTTCGG
194 C-G-G----A--GCCCCGAAACGCGTTTTTAGCCACAAAACGTGATGGTTAGTACACGATTTCGG
* *
18137 CTAAAAACTGACCCGAAAATTTTTTCTTGAAATTTTTCCTAGAATACTCAAAAAAATATATAATT
251 CTAAAAACTAACCCGAAAATTTTTTCTTG-------TCC-ACAATACTCAAAAAAATATATAATT
18202 CAACA
308 CAACA
** * * * * *
18207 CCAAAAAGATTGCCGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT-TCCTAATTAATTT
1 CCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTT
* * * * * * * * *
18271 TTTATTAAATAGAATCAAGACTCAGATACTCATAAAAACAAGA-CCTTATATCTAATGCGGTTGA
65 CTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAA-ATCCTTAAATC-AATGTGGCTGA
* *
18335 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCGAAACTCAGA
128 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTCAGA
* * * * *
18400 -CGGAGCCCCGAAACACGTTTTTAACCAAAAAATCGTGATGGTTAGTATACGATTTCGGCCAAAA
193 CCGGAGCCCCGAAACGCGTTTTTAGCCACAAAA-CGTGATGGTTAGTACACGATTTCGGCTAAAA
* *
18464 ACTAATCTG-AAATTTTTT-TTG-CCACAATACTC-AAAAAATATATAATTCAACA
257 ACTAACCCGAAAATTTTTTCTTGTCCACAATACTCAAAAAAATATATAATTCAACA
18516 CCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTC
1 CCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTC
* *
18581 TAATTATATCGAAACAAGATTCAGATGCTCGTAAAAAACAAATCCTTAAATCAGATGTGGCTGAG
66 TAATTAAATAGAAACAAGATTCAGATGCTCGT-AAAAACAAATCCTTAAATCA-ATGTGGCTGAG
* *
18646 ATTTGGTTAGATGAATATAGATATTTCTAGGACTCTTTCTGCCAAAAATCATGCGAAAC-C-GAT
129 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTCAGA-
* * * **
18709 CCGGGGACCCGAAACGCGTTTGTAGCTTCAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAA
193 CCGGAGCCCCGAAACGCGTTTTTAGCCACAAAA-CGTGATGGTTAGTACACGATTTCGGCTAAAA
*
18773 ACTGACCCGCTAAAATTTTTT
257 ACTAACCCG--AAAATTTTTT
18794 TCCTCAAATT
Statistics
Matches: 1279, Mismatches: 194, Indels: 183
0.77 0.12 0.11
Matches are distributed among these distances:
308 41 0.03
309 74 0.06
310 137 0.11
311 2 0.00
312 33 0.03
313 1 0.00
314 2 0.00
315 3 0.00
316 100 0.08
317 36 0.03
318 72 0.06
319 23 0.02
320 163 0.13
321 79 0.06
322 92 0.07
323 152 0.12
324 11 0.01
329 1 0.00
330 12 0.01
331 45 0.04
332 167 0.13
333 9 0.01
334 2 0.00
335 1 0.00
340 15 0.01
341 6 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (312 bp):
CCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTC
TAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAGAT
TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTCAGACCG
GAGCCCCGAAACGCGTTTTTAGCCACAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAACTA
ACCCGAAAATTTTTTCTTGTCCACAATACTCAAAAAAATATATAATTCAACA
Found at i:19002 original size:254 final size:253
Alignment explanation
Indices: 18552--19058 Score: 738
Period size: 254 Copynumber: 2.0 Consensus size: 253
18542 TTCTAATATC
*
18552 GTTTTCCCATTTTTATTCGAATTTATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAA
1 GTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * *
18617 AACAAATCCTTAAATCAGATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTAGGACTCT
66 AACAAATCCTTAAATCAGATGTGGCTGAGATATGGTTAGAAGAATATAGATATTGCAAGGACTCT
* * *
18682 TTCTGCCAAAAATCATGCGAAACCGATCCGGGGACCCGAAACGCGTTTGTAGCTTCAAAACCGTG
131 TTCTGCCAAAAATCATGCGAAACCGATCCAGGGACCCGAAACGCATTTGTAGCCTCAAAACCGTG
*
18747 ATGGTTAGTACACGATTTCGGCT-AAAACTGACCCGCTAAAATTTTTTTCCTCAAATTTTT
196 ATGGTTAGTACACGATTTCGGCTAAAAACTAACCCG---AAATTTTTTTCCTCAAATTTTT
** *
18807 GTTTTCCCATTTTTATTC-TTTATTATTTCTCATTAAATCGAAACAAGATTCAGATGCTCGT-AA
1 GTTTTCCCATTTTTATTCGAAT-TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
18870 AAACAAATCCTTAAATCCA-ATGTGGCTGAGATATGGTTAGAAGAATATAGATATTGCAAGGAGC
65 AAACAAATCCTTAAAT-CAGATGTGGCTGAGATATGGTTAGAAGAATATAGATATTGCAAGGA-C
* * * * * *
18934 -CTTTCTGCCAAAATTCATGCGAAACTGA-GCAGGGACCCCGAAATGCATTTTTAGCCTCGAAAC
128 TCTTTCTGCCAAAAATCATGCGAAACCGATCCAGGGA-CCCGAAACGCATTTGTAGCCTCAAAAC
*
18997 CGTGATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAATTTTTTTCCTGAAATTTTT
192 CGTGATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAATTTTTTTCCTCAAATTTTT
19059 TGTCACAATA
Statistics
Matches: 228, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
252 21 0.09
253 5 0.02
254 133 0.58
255 69 0.30
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (253 bp):
GTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
AACAAATCCTTAAATCAGATGTGGCTGAGATATGGTTAGAAGAATATAGATATTGCAAGGACTCT
TTCTGCCAAAAATCATGCGAAACCGATCCAGGGACCCGAAACGCATTTGTAGCCTCAAAACCGTG
ATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAATTTTTTTCCTCAAATTTTT
Found at i:19466 original size:320 final size:318
Alignment explanation
Indices: 18807--19593 Score: 889
Period size: 320 Copynumber: 2.5 Consensus size: 318
18797 TCAAATTTTT
** *
18807 GTTTTCCCATTTTTATTCTTTATTATTTCTCATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
1 GTTTTCCCATTTTT-TTAATTA--ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * *
18872 ACAAATCCTTAAATCCAATGTGGCTGAGATATGGTTAGAAGAATATAGATATTGCAAGGAGCCTT
63 ACAAATCCTT-AATCCAATG-GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* ** **
18937 TCTGCCAAAATTCATGCGAAACTGAGCAGGGACCCCGAAATGCATTTTTAGCCTCGAAACCGTGA
126 TCTGCCAAAAATCATGCGAAACTGAGCAGGGACCCCGAAACACATTTTTAGCCTAAAAACCGTGA
* **
19002 TGGTTAGTACACGATTTCGGCTAAAAACTAACCCGAAATTTTTTTCCTGAAATTTTTTGTCACAA
191 TGGTTAGTACACGATTTCGCCTAAAAACTAACCCGAAATTTTTTTCCTGAAATTTTTTACCACAA
* * * * *
19067 TACTCAGAAAAATTATATAAGTCAATACCAAAAAGATTGACGGGCTTTTCACACTTCTCATATC
256 TACTCAGAAAAA-TATATAAATCAACACCAAAAAGATTGAAGGACTTTTCACACTTCTAATATC
* ** * *
19131 ATTTTCCCA-TTTTTTAATTAATTTCTAATTAAATATAAAAAAGATTCAGATACTCGTAAAAACA
1 GTTTTCCCATTTTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * *
19195 AGTCATTACATCCAATGCGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
66 AATCCTTA-ATCCAATG-GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
* * * *
19260 -CCAAAAAATCTTGCGAAATTGAGCCGGGACCCCGAAACACGTTTTTAGCC-AAAAACCGTGATG
129 GCC-AAAAATCATGCGAAACTGAGCAGGGACCCCGAAACACATTTTTAGCCTAAAAACCGTGATG
* * *
19323 GTTAGTACATGATTTTCGCCTAAAAA-TGACCCGAAGAATTTTTTT-CT-CAATTTTTTACCACA
193 GTTAGTACACGA-TTTCGCCTAAAAACTAACCCG-A-AATTTTTTTCCTGAAATTTTTTACCACA
* * ** *
19385 ATACTCTA-AAAAA-ATA-AAATTAACGCCAAAACTATTGAAGGATTTTTCACACTTCTAATAAT
255 ATACTC-AGAAAAATATATAAATCAACACCAAAAAGATTGAAGGACTTTTCACACTTC---TAAT
19447 ATC
316 ATC
* *
19450 GTTTTCCCATTTTTTTAGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAATA
1 GTTTTCCCATTTTTTT--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
19515 CAAATCCTTAAT---AT-GGCTGAGATTTGGTTAGATGAATACAAATATTTCAAGGAGTTTTTCT
64 CAAATCCTTAATCCAATGGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
** *
19576 ATCGAAAATCATGCGAAA
129 GCCAAAAATCATGCGAAA
19594 AAGTGCCGAG
Statistics
Matches: 393, Mismatches: 57, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
316 86 0.22
317 4 0.01
318 2 0.01
319 68 0.17
320 156 0.40
321 11 0.03
322 54 0.14
323 4 0.01
324 8 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (318 bp):
GTTTTCCCATTTTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATCCTTAATCCAATGGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
CAAAAATCATGCGAAACTGAGCAGGGACCCCGAAACACATTTTTAGCCTAAAAACCGTGATGGTT
AGTACACGATTTCGCCTAAAAACTAACCCGAAATTTTTTTCCTGAAATTTTTTACCACAATACTC
AGAAAAATATATAAATCAACACCAAAAAGATTGAAGGACTTTTCACACTTCTAATATC
Found at i:20407 original size:320 final size:318
Alignment explanation
Indices: 19915--21152 Score: 1206
Period size: 320 Copynumber: 3.8 Consensus size: 318
19905 GCAATTTTGC
* * ** * *
19915 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTTCCACAATACAAAGAAAAAATTATATGATT
1 AAAAACTGACCCGAAATGTTTTTCCT-AAATTTTTGCCACAATACTCAGAAAAAA-AATATAATT
*
19980 CAACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCGAATTTTATTCA-AATT
64 CAACGCCAAAAAATTGAACGGGTTTTCACGCTTCTAATATCGTTTTCC-AATTTT-TT-ATAATT
* * * *
20044 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
126 AATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGCGG
* * *
20109 CT-ATGATTTGGGTAGATGAATATAGAAATTTCAAGAAGTATTTC-TGCCAAAAATCATGCAAAA
191 CTGA-GATTTGGTTAGATGAATATAGATATTTCAAGAAGT-TTTCACGCCAAAAATCATGCAAAA
* *
20172 CTGAGCCGTGGCCCCAAAACGCGTTTTTAGCCCCAAAACCATGATGGTTAACGTACACGATTTTG
254 CTGAGCCG-GGCACCGAAACGCGTTTTTAGCCCCAAAACC-TGATGGTTAACGTACACGATTTTG
20237 AAT
317 -AT
** * *
20240 AAAAACTGACCCGATTTTTTTTTCCTGAAATTTTTGCCCCAATACT-A-AAAAAAAATATAATTC
1 AAAAACTGACCCGAAATGTTTTTCCT-AAATTTTTGCCACAATACTCAGAAAAAAAATATAATTC
* *
20303 AACGCCAAAAAGATTG-ACGGGCTTTCACGCTTCTAACTATCGTTTT-TACATTTTTT-TAATTA
65 AACGCCAAAAA-ATTGAACGGGTTTTCACGCTTCTAA-TATCGTTTTCCA-ATTTTTTATAATTA
* * * *
20365 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCATAAAAACAAGTCCTTATATCCAATGCGGT
127 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGCGGC
* * * * *
20430 TGAGAATTGGTTGGATGAATATAGATATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAATTG
192 TGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTTTTCACGCCAAAAATCATGCAAAACTG
* * * * *
20495 AGTCGCGGCTCCGGAACGCGTTTTT--CGCCAAAGACTGTGATGGTTAGTACACGATTCCAGCTA
257 AGCCG-GGCACCGAAACGCGTTTTTAGCCCCAAA-AC-CTGATGG-T--TA-ACG--T--A-C-A
* *
20558 CAATTTTG-C
309 CGATTTTGAT
* * * * ** *
20567 AAAAACTGACTCAAAATGTTTTTCCTCAATTTTTGCCACAATAATCAGAAAAATCATACAATTCA
1 AAAAACTGACCCGAAATGTTTTTCCTAAATTTTTGCCACAATACTCAGAAAAAAAATATAATTCA
* * *
20632 ACGCCAAAAAATTGAAAGGTTTTTTCACGAATT-TAATATCGTTTTCCAA-TTTTTATTCGAATT
66 ACGCCAAAAAATTGAACGG-GTTTTCACG-CTTCTAATATCGTTTTCCAATTTTTTA-T--AATT
* * * * * * **
20695 TATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAGCAAATCCTTAAATCCAATGTTG
126 AATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGCGG
* * * *
20760 CTGTGATTTGGTTAGCTGAATATAGATATTTTAAGAAGTCTTTCTA--CCAAAAATCATGCGAAA
191 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGT-TTTC-ACGCCAAAAATCATGCAAAA
* * *
20823 CTGAGCCGGGACACCGAAACGCGTTTTGAGCCCCAAAA-CTG-T-GAT-A-GTACACGATTTCAG
254 CTGAGCCGGG-CACCGAAACGCGTTTTTAGCCCCAAAACCTGATGGTTAACGTACACGATTT-TG
*
20883 CT
317 AT
* * *
20885 AAAAACTGACCCGAAATTTTTTTTTCCTTAAATTTTTTCCACAATACTCAGAAAAAATATATAAT
1 AAAAACTGACCCGAAA--TGTTTTTCC-TAAATTTTTGCCACAATACTCAGAAAAAAAATATAAT
* * *
20950 TCAACGCCAAAAAGATTG-ACGGATTCTTAACGCTTCTAACTGTCGTTTTTCC-ATTTTTTATAA
63 TCAACGCCAAAAA-ATTGAACGGGTT-TTCACGCTTCTAA-TATCG-TTTTCCAATTTTTTATAA
* * * **
21013 ATAATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAGTCATTACGTCCAATGC
124 TTAATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGC
* * * *
21078 GGTTGAGATTTGGTTAGATGAATATAGTTATTTTAAGGAGTTTTCACGCCAAAAATCATGCAAAA
189 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTTTTCACGCCAAAAATCATGCAAAA
* *
21143 TTGAGTCGGG
254 CTGAGCCGGG
21153 GCTTTAGGAA
Statistics
Matches: 747, Mismatches: 120, Indels: 97
0.77 0.12 0.10
Matches are distributed among these distances:
316 6 0.01
317 2 0.00
318 22 0.03
319 15 0.02
320 261 0.35
321 59 0.08
322 55 0.07
323 35 0.05
324 1 0.00
325 40 0.05
326 16 0.02
327 32 0.04
328 39 0.05
329 21 0.03
330 6 0.01
331 126 0.17
332 4 0.01
333 7 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (318 bp):
AAAAACTGACCCGAAATGTTTTTCCTAAATTTTTGCCACAATACTCAGAAAAAAAATATAATTCA
ACGCCAAAAAATTGAACGGGTTTTCACGCTTCTAATATCGTTTTCCAATTTTTTATAATTAATTT
CTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGCGGCTGAG
ATTTGGTTAGATGAATATAGATATTTCAAGAAGTTTTCACGCCAAAAATCATGCAAAACTGAGCC
GGGCACCGAAACGCGTTTTTAGCCCCAAAACCTGATGGTTAACGTACACGATTTTGAT
Done.