Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011999.1 Corchorus capsularis cultivar CVL-1 contig12020, 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: 21963
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1661 original size:96 final size:96
Alignment explanation
Indices: 1574--1852 Score: 302
Period size: 96 Copynumber: 2.9 Consensus size: 96
1564 ATTATAATTG
* * * *
1574 AGGCAGAGCGATTACGTG-TCGCGGATATTTACAATTAAGTCTTAAATGACCAAAATAATATAAA
1 AGGCAGAGAGATGACGTGCT-GCGAATATTTACAAATAAGTCTTAAATGACCAAAATAATATAAA
*
1638 TTTAGTGTGTTACACAAAAAATATTACAATCA
65 TTAAGTGTGTTACACAAAAAATATTACAATCA
* * * *
1670 AGGCAGAGAGATGATGTGCTGCGAATATTTACAAATAAGTCTTCAGTGTCCAAAATAATATAAAT
1 AGGCAGAGAGATGACGTGCTGCGAATATTTACAAATAAGTCTTAAATGACCAAAATAATATAAAT
** *
1735 TAAGTGTGTTACACAAAAAATATTGTAAACA
66 TAAGTGTGTTACACAAAAAATATTACAATCA
* ** **
1766 AGGCAGATGAG--GACGTGTCT-CG-A-ATTTACAAATAAGT-TTAAATATATAAAAATAATCCA
1 AGGCAGA-GAGATGACGTG-CTGCGAATATTTACAAATAAGTCTTAAAT-GACCAAAATAATATA
* *
1825 AATTAAGTGTGTTATACGAAAAATATTA
63 AATTAAGTGTGTTACACAAAAAATATTA
1853 AAAAAATGCA
Statistics
Matches: 155, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
92 4 0.03
93 48 0.31
94 1 0.01
95 7 0.05
96 91 0.59
97 4 0.03
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.29
Consensus pattern (96 bp):
AGGCAGAGAGATGACGTGCTGCGAATATTTACAAATAAGTCTTAAATGACCAAAATAATATAAAT
TAAGTGTGTTACACAAAAAATATTACAATCA
Found at i:1923 original size:95 final size:93
Alignment explanation
Indices: 1625--1923 Score: 216
Period size: 93 Copynumber: 3.2 Consensus size: 93
1615 TTAAATGACC
* * ** *
1625 AAAATAATATAAATTTAGTGTGTTACACAAAAAATATT-ACAATCAAGGCAGA-GA-GATGATGT
1 AAAATAATAAAAATTAAGTGTGTTACACAAAAAATATTGA-AAAAAAGGCAGATGAGGACG-TGT
* * * * **
1687 GCTGCGAATATTTACAAATAAGTCTTCAGTGT-CC
64 -CT-CG-A-ATTTACAAATAAGT-GTAAATATATA
* * *
1721 AAAATAATATAAATTAAGTGTGTTACACAAAAAATATTGTAAACAAGGCAGATGAGGACGTGTCT
1 AAAATAATAAAAATTAAGTGTGTTACACAAAAAATATTGAAAAAAAGGCAGATGAGGACGTGTCT
*
1786 CGAATTTACAAATAAGTTTAAATATATA
66 CGAATTTACAAATAAGTGTAAATATATA
** * * * *
1814 AAAATAATCCAAATTAAGTGTGTTATACGAAAAATATT-AAAAAAATGCAGAATGATGA-GTTGT
1 AAAATAATAAAAATTAAGTGTGTTACACAAAAAATATTGAAAAAAAGGCAG-ATGAGGACG-TGT
* * **
1877 CATGGATTATTACAGTTAAGTGTAAA-ATATCA
64 C-TCGAAT-TTACAAATAAGTGTAAATATAT-A
1909 AAAATAATAAAAATT
1 AAAATAATAAAAATT
1924 TTCCGTGAAA
Statistics
Matches: 170, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
92 15 0.09
93 58 0.34
94 9 0.05
95 30 0.18
96 50 0.29
97 5 0.03
98 3 0.02
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.29
Consensus pattern (93 bp):
AAAATAATAAAAATTAAGTGTGTTACACAAAAAATATTGAAAAAAAGGCAGATGAGGACGTGTCT
CGAATTTACAAATAAGTGTAAATATATA
Found at i:4255 original size:322 final size:317
Alignment explanation
Indices: 2573--7282 Score: 4711
Period size: 324 Copynumber: 14.7 Consensus size: 317
2563 TTATGGACGA
* * * * *
2573 TACACGATTTCAGCTAAAAACT-AACT-TATTTTTTTTTCTCAATTTTTTACCACAATACTCATA
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTC-ATTTTTTGCCACAATACTCATA
* * *
2636 AAAAATATATAATTCAACTCCAAAAAGATTCAAAGGTTTTTCACGCTTCTAATATCATTTTTCCA
65 AAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CA
** *
2701 TTTTTTTTCCGAATTAATTTCTAATTAAATCGATTCAAGATTCAGATGCTCATAAAAACAAATCG
129 -TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCG
* * * * * *
2766 ATAAATCCAATGTG-GTAGGAATTTGGTTCAACGAATATAGATATTTCAAGGAGTTTTTAAGCCA
193 TTAAATCCAATGTGACT-GGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCA
* *
2830 AATATCATGCAAAACTAAGCCGAGGCCCCGAAATGCGTTTTTAGCCTAAAACCGTGAAGGTTAG
257 AA-ATCATGCAAAACTGAGCCG-GGCCCCGAAATGCGTTTTTAGCC-AAAACCGTGATGGTTAG
* *
2894 TACACGATTTCGGCTACAAATTGACCTG-AATTTTTTTTCTTCATTTTTTGCCACAATACTCATA
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTC-TCATTTTTTGCCACAATACTCATA
* * *** * *
2958 AAAAATATATAATTCAACTCTAAAAAGATTAAAGAAATTTTCATGCTGCTAATATCGTTTTTCCA
65 AAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CA
* *
3023 -TTTTTTCCGAATTAATTTCTAATTAAATTGAAACAACATTCAGATGCTCGTAAAAACAAATCGT
129 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGT
* * * * *
3087 TAAATCCAATGTGGCTGGAATTTGGTTTGATGATTATAGATATATCAAGGAGTCTTTATGCCAAA
194 TAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAA
* *
3152 TATCATGCAAAACTGAGCCGTGGCCCTGAAATGCGTTTTTAG------CCGTGATAGTTAG
259 -ATCATGCAAAACTGAGCCG-GGCCCCGAAATGCGTTTTTAGCCAAAACCGTGATGGTTAG
* * * * * *
3207 TACATGATTTCGGCTAAAAACTGACCTGAATTTTTTTTTCCTCAATTTTTGCCACAAGATTAATA
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTT-CTCATTTTTTGCCACAATACTCAT-
3272 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
64 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-C
* * * * *
3337 ATTTTTTTCCGAATTAATTTCTAATTAAATTGATACAAGATTCATATGCTCGCAAAACCAAATCG
128 ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCG
* *
3402 TTAAATCCAATGTGACTGGAATTTGCTTCGATAAATATAGATATATTTCAAGGAGTCTTTACGCC
193 TTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAG--ATATTTCAAGGAGTCTTTACGCC
* * * *
3467 AAGTATCATGCAAAGCTTAGCCGGGGCCCCGAAATGCGTTTTTAGCTCAAAACCATGATGGTTAG
256 AA-AATCATGCAAAACTGAGCC-GGGCCCCGAAATGCGTTTTTAGC-CAAAACCGTGATGGTTAG
* * * * * * *
3532 TACATGATTTCGGTTAAAAACTGAACTG-AATTTTTTTTCT-AATTTTTGCCATAAGA-TGAATA
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTCATTTTTTGCCACAATACT-CATA
* *
3594 AAAAATATATAATTCAACTCCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCA
65 AAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CA
*** * * * *
3659 TTTTTTTTAAAATTAATTTCTAATTAAATCGAAACAACAATCAGATACTCGTAAAAACAAATCCT
129 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGT
* *
3724 TAAATCCAATGT-AGTTGAAATTTGGTTCGATGAATATAGAT-TTATCAAGGAGTCTTTACGCCA
194 TAAATCCAATGTGA-CTGGAATTTGGTTCGATGAATATAGATATT-TCAAGGAGTCTTTACGCC-
* * * * * *
3787 AAAATCATGCAAAGCTAAGCCGGGGCTCG-AATGCCTTTTTAGCCCAAAATCGTGATGGTTAG
256 AAAATCATGCAAAACTGAGCCGGGCCCCGAAATGCGTTTTTAG-CCAAAACCGTGATGGTTAG
* * *
3849 TACATGATTTCGGCTAAAAACATGACTTGAATTTTTATTTTCTCAATTTTTTGCCACAATACTCA
1 TACACGATTTCGGCTAAAAAC-TGACCTGAAATTTT-TTTTCTC-ATTTTTTGCCACAATACTCA
* *
3914 TAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTATTTT-ATGTTTCTAATATCGTTTTT
63 TAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGT-TTTTCACGCTTCTAATATCGTTTTT
* * * * ** *
3978 CAGTTTTTTCTGAATTAAATTCTAATTAAATCGAAACAACATTTTGATGCTCGTAAAAACTAATT
127 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAAT
* * *
4043 C-TTAAATCCAATGTGACTGGAATTTGATTCGATGAATATAGATATTTCAAGGAGTCATTACACC
191 CGTTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCC
* * *
4107 GAAAATCATGCAAACCTGAGCCAGGGCCTCGAAATGCATTTTTA-CTCGAAAACCGTGATGGTTA
256 -AAAATCATGCAAAACTGAGCC-GGGCCCCGAAATGCGTTTTTAGC-C-AAAACCGTGATGGTTA
4171 G
317 G
* *
4172 TACACGATTTCGGCTAAAAACTGATCTGAAATTTTTTTTCTCATGTTTTTTGCCATAATACTCAT
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTCA--TTTTTTGCCACAATACTCAT
* * * * *
4237 AAAAAATATATAATTCAACTCCAAAAATATTGAAGAGTTTTTAACGCTTCTAATACCGTTTTCCA
64 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCA
** *
4302 TTTTTTTCTAAATTAATTTCTAATTAAATCGATACAAGATTCAGATGCTCGTAAAAACAAATCGT
129 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGT
* *
4367 TAGATCCAATGTGACTGGAATTTGGTTTGATGAATATAGATATATTTCAAGGAGTCTTTACGCCA
194 TAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAG--ATATTTCAAGGAGTCTTTACGCCA
4432 AATATCATGC-AAACTTGAGCCGCGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAG
257 AA-ATCATGCAAAAC-TGAGCCG-GGCCCCGAAATGCGTTTTTAGCC-AAAACCGTGATGGTTAG
* * *
4496 TACACGATTTCGGCTAAAAATTGACCTGAAAATTTCTTTTCTCAATTTTTTTCCACAATACTCAT
1 TACACGATTTCGGCTAAAAACTGACCTG-AAATTTTTTTTCTC-ATTTTTTGCCACAATACTCAT
*
4561 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGAGTTTTTTCACGCTTCTAATATCGTTTTTC
64 AAAAAATATATAATTCAACTCCAAAAAGATTGAAG-GGTTTTTCACGCTTCTAATATCGTTTTTC
* * * * * *
4626 CTTTTTTCCCGAATTAAATTCTAATTAAATCGAAACAACATTCAGATTCTCGTAAAAACAAATCT
128 ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCG
* * * *
4691 TTAAATCCAATGTGACTGAAATTTTGTTCGATGAATAGAGATATTTCAAGGAGTATTT--G----
193 TTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAA
*
4750 ----A-GC----C---G--GGGCCCCGAAATGCGTTTTAAGCCAAAACCGTGATGGTTAG
258 AATCATGCAAAACTGAGCCGGGCCCCGAAATGCGTTTTTAGCCAAAACCGTGATGGTTAG
* * *
4796 TACACGATTTTCGGCTAAAAACTGAGCTGAAA--TTTTTT-TC--------CCACAATACTAATG
1 TACACGA-TTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTCATTTTTTGCCACAATACTCATA
* *
4850 AAAAATATATAATTCAACTTCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCA
65 AAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CA
* * * *
4915 TTTTTTTCCGAGTTAATTTCTAATTAAATCGATACAGGATTCAGATGATCGTAAAAACAAATCGT
129 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGT
* * *
4980 TAAATCCAATGTGACTGGAATTTGGTTTGATGAATATAGATATATTTTAAGGAGTCTTTATGCCA
194 TAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAG--ATATTTCAAGGAGTCTTTACGCCA
* * * * * *
5045 AATTTTATGC-AAACTTGAGCTTGGGCCCCGAAATGTGTTTTTAGCTAAGAATCG-GTATGGTTA
257 AA-ATCATGCAAAAC-TGAGC-CGGGCCCCGAAATGCGTTTTTAGCCAA-AACCGTG-ATGGTTA
5108 G
317 G
* * * *
5109 TACACGATTTCGGCTAAAAATTAACCTGAAAATTTTTTTTCTCTAGTTTTTGCCACAATACTCTT
1 TACACGATTTCGGCTAAAAACTGACCTG-AAATTTTTTTTCTC-ATTTTTTGCCACAATACTCAT
* * *
5174 AAAAAATAAATAATTCAACTCCAAAAATA-TGTAAGGGTTTTTCACGCTTGTAATATCGTTTTTC
64 AAAAAATATATAATTCAACTCCAAAAAGATTG-AAGGGTTTTTCACGCTTCTAATATCGTTTTT-
* * *
5238 CAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTCAGATTCTCGTAAAAACAAATC
127 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * * * * *
5303 CTTAAATCCAATGTGACTGAAATTTTGTTCGATGAATAAAGATATTTCAAGGAGTCCTTACACAA
192 GTTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGC-C
* *
5368 AAAATCATGCAAAGCTGAGTCGGGGCCCCGAAATGCGTTTTTAGCTCAAAACCGTGATGGTTAG
256 AAAATCATGCAAAACTGAG-CCGGGCCCCGAAATGCGTTTTTAGC-CAAAACCGTGATGGTTAG
*
5432 TACACGAATTTCGGCTAAAAACTGACCTGAAA-TTTTTTTCTCATTTTTTTGACACAATACTCAT
1 TACACG-ATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTCA-TTTTTTGCCACAATACTCAT
* * * ** *
5496 --AAAATATATAAATCAACTCCAAAAAGATTGAAGAGTTTCTCACATTTCTAATACCGTTTTTCC
64 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-C
* * * *
5559 ATTTTTTTTTCCGAATTAATTTTTAATTAAATCGATACAAGATTTAGATGCTTGTAAAAACAAAT
128 A--TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* *
5624 CATTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATATTTCAAGGAGTCTTTACA
191 CGTTAAATCCAATGTGACTGGAATTTGGTTCGATGAATATAG--ATATTTCAAGGAGTCTTTACG
* * * *
5689 CCAAATATCATTC-AAACTTGAGCCGGGGCCCCGAAATGCGTTTTTAGGCAAAAAC-TG-T-GAT
254 CCAAA-ATCATGCAAAAC-TGAGCC-GGGCCCCGAAATGCGTTTTTAGCCAAAACCGTGATGGTT
5750 -G
316 AG
* * * * * *
5751 TACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTCCCAATTTTTTG-CAAAATATTCAGA
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTC-ATTTTTTGCCACAATACTCATA
* * **
5815 AAAAATATATAATT-AAATCCCAAAAAAATTGAAGGGTTTTTCTTGCTTCTAATATCGTTTTTGT
65 AAAAATATATAATTCAACT-CCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTT-T
* * * **
5879 CATTTTTTT-CGAATTTATTTCTTATTAAATCGAAACAAGATTCACATGCTCGTAAAAGGAAATA
127 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-
* * * * *
5943 C-TTAAATCCATTTTGACT-AAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTT-CTG
191 CGTTAAATCCAATGTGACTGGA-ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC--
** * * * ** * *
6005 GAAAAAATCAAGCAAAACTGAGCCGGAG-CCCGAAAAGCATTTCCAGCCAAAAAACCATGATAGT
253 GCCAAAATCATGCAAAACTGAGCCGG-GCCCCGAAATGCGTTTTTAGCC--AAAACCGTGATGGT
*
6069 TAA
315 TAG
* * * * *
6072 TACACGATTTCGACTAAAAACTGACCCGAAATGCTTTTTCTCCTAATTTTTTTTG-CAAAATA-T
1 TACACGATTTCGGCTAAAAACTGACCTGAAAT--TTTTT-TTCTCA--TTTTTTGCCACAATACT
* *
6135 -TTACAAAAATATATAATTCAAAC-CCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAATATCGT
61 CATA-AAAAATATATAATTC-AACTCCAAAAAGATTGAAGGG-TTTTTCACGCTTCTAATATCG-
* * * * * **
6198 TTTTTCATTTTTTTTCAAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCATAAAAGG
122 TTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * * * * * * * *
6263 AAATCCTTAGATCCATTTTGACT-AAGATTTGATTAGATGAATGTACATATTTAAATGAGTCTTT
187 AAATCGTTAAATCCAATGTGACTGGA-ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * * *
6327 AAGGCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTCTAGCCAAAAAAATCGTGA
251 -ACGCCAAAATCATGCAAAACTGAGCCGG-GCCCCGAAATGCGTTTTTAGCC---AAAACCGTGA
6392 TGGTTAG
311 TGGTTAG
* * ** * * *
6399 TACACGATTTCGGCTAAAAACTTACCCGAAATGCTTTTTCTCAAATTTTTTG-CATAATATTCAG
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTC--ATTTTTTGCCACAATACTCAT
* * *
6463 AAAAAATATATAATTCAA-TCCCAAAAAAATTGAAGAGTTTTTCACGTTTCTAATATCGTTTTTT
64 AAAAAATATATAATTCAACT-CCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTT
*** * * * * **
6527 CATTTTTTTTTTAATTTATTTCTAATTACATCGAAACAAGATTCACATGTTCGTAAAAGGAAATC
127 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * ** * * * * *
6592 CTTAAATCCATTTTGA-TTAAGATTTGATTAGATGAATGTAGATATTTCAATGAGTCTTTATGGC
192 GTTAAATCCAATGTGACTGGA-ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTA-CGC
* * * * *
6656 AAAAATCATGCAAAACTGAGCCGAAGCCCCGAAACGTGTTTCTAGCCAAACAACCGTGATGGTTA
255 CAAAATCATGCAAAACTGAGCCG-GGCCCCGAAATGCGTTTTTAGCC-AA-AACCGTGATGGTTA
6721 G
317 G
* * * ** * * *
6722 TACACGATTTCGGCTAAAAACTAACCCGAGATGCTTTTTCTCAATTTTTTTG-CAAAATATTCAG
1 TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTC-A-TTTTTTGCCACAATACTCAT
** * * *
6786 AAAAAATATATAATTCAAAGCCAAAAA-ATTGAAGAGTTTTTCACGCTTCTGATATCATTTTTTT
64 AAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATC--GTTTTT
* * **
6850 CATTTTTTT--GAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAGGAAATC
127 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * * * * * * *
6913 CTTAAATCCATTTTGTCT-AAGATTTAGTTAGATGAAAATAGATATTTCAATGAGTCTTT-CTGG
192 GTTAAATCCAATGTGACTGGA-ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC--G
* * * * * *
6976 CAAAAATCATGCAAAACTGAGCCGAATG-CCCGAAACGCATTTCTAGCCAAAAAAAAACTGTGAT
254 CCAAAATCATGCAAAACTGAGCCG--GGCCCCGAAATGCGTTTTTAGCC-----AAAACCGTGAT
*
7040 AGTTAG
312 GGTTAG
* ** * *
7046 TACACGATTTCGGCTAAAAACTTA-CTCGAAATGCTTTTTCTCAATTTTTTTG-CAAAATATTCA
1 TACACGATTTCGGCTAAAAACTGACCT-GAAATTTTTTTTCTC-A-TTTTTTGCCACAATACTCA
* * * * * *
7109 GAAAAAATATATAACTCAA-TACCAAAAAGATTGACGGGTTTTTCACGTTTTTAATATCATTTTT
63 TAAAAAATATATAATTCAACT-CCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATC-GTTTT
* * * * *
7173 TCATTTTTTTTCCGAATTAATTCCTAATTAAACCAAAACAAGATTGAGATCCTCGTAAAAACAAA
126 TCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * **
7238 TCTTTATATCCAATGTGGCT-GAGATTTGATTATATGAATATAGAT
190 TCGTTAAATCCAATGTGACTGGA-ATTTGGTTCGATGAATATAGAT
7283 GTTTGCAAAA
Statistics
Matches: 3795, Mismatches: 424, Indels: 334
0.83 0.09 0.07
Matches are distributed among these distances:
287 26 0.01
288 137 0.04
290 16 0.00
292 1 0.00
297 2 0.00
298 5 0.00
300 27 0.01
301 42 0.01
302 3 0.00
304 1 0.00
305 1 0.00
308 1 0.00
309 1 0.00
311 2 0.00
312 43 0.01
313 58 0.02
314 28 0.01
315 84 0.02
316 124 0.03
317 61 0.02
318 187 0.05
319 77 0.02
320 261 0.07
321 498 0.13
322 524 0.14
323 283 0.07
324 595 0.16
325 562 0.15
326 22 0.01
327 123 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (317 bp):
TACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTCATTTTTTGCCACAATACTCATAA
AAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCATT
TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTA
AATCCAATGTGACTGGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAT
CATGCAAAACTGAGCCGGGCCCCGAAATGCGTTTTTAGCCAAAACCGTGATGGTTAG
Found at i:8234 original size:328 final size:322
Alignment explanation
Indices: 7585--8300 Score: 886
Period size: 328 Copynumber: 2.2 Consensus size: 322
7575 AAATCAATTT
* * * * *
7585 TGACTGAGTTTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTTCTGGCAAAAATC-ATGCAA
1 TGACTGAGATTTGGTTATATGAATATAGAT-GTTCAAGGAGTCTTTAT-GCAAAAAACTATGCAA
* * * * *
7649 AACTGAGTCGGGGCCTCGTAACGCGTTTTTAGCAAAAAAACAGTGATGACTAGTACATGATTTCG
64 AACTGAGTCGGGCCCTAGTAACGCGTTTCTAACAAAAAAACAGTGATGACTAGTACACGATTTCG
* * *
7714 GCTAAAAACTGGCTCGAAAAGTTTTTTCTTAATTTTTTGTAAAATATTCAGAAAAAATATATTAT
129 GCTAAAAACTAGCTCGAAAAGTTTTTTCTCAATTTTTTGTAAAATATTCAGAAAAAATATATAAT
* * * * *
7779 TCAATACCCAAAAGCTTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTCCTTTTTTTTCCGAT
194 TCAATACCAAAAAGATTCAAGGGCTTTTCACGCTTTTAATATCGTTTTTTCCATTTTTTTCCGAA
* * **
7844 TTAATTTCTAATTAAATTAAAACAAGATTTAGATTTTCATAAAAACAAATTTGTATATCCAATG
259 TTAATTTCTAATTAAATCAAAACAAGATTCAGACCTTCATAAAAACAAATTTGTATATCCAATG
* * *
7908 TGGCTTAGATTTGGTTATATGAATATAGATGTTTCAACGAGTCTTTATGCAAAAAACTATGCAAA
1 TGACTGAGATTTGGTTATATGAATATAGATG-TTCAAGGAGTCTTTATGCAAAAAACTATGCAAA
* * **
7973 ACTGAGTCGAGGCCCTAG-AATGCGTTTCTAACAAAAAAAAAAACCGTGATGGTTAGTACACGAT
65 ACTGAGTCG-GGCCCTAGTAACGCGTTTCTAAC----AAAAAAACAGTGATGACTAGTACACGAT
* * * *
8037 TTCGGTTAAAAATTA-ATCTGAGAAATTTATTTTCTCAATTTTTTGTAAAATATTCAGAAAAAAT
125 TTCGGCTAAAAACTAGCTC-GA-AAAGTT-TTTTCTCAATTTTTTGTAAAATATTCAGAAAAAAT
* * *
8101 ATATAATTTAATACCAAAAAGATTCACGGGCTTTTCACGCTTTTTATATCG-TTTTTCCATTTTT
187 ATATAATTCAATACCAAAAAGATTCAAGGGCTTTTCACGCTTTTAATATCGTTTTTTCCATTTTT
*
8165 TTCCGAATTAATTTCTCATTAAATCAAAACAAGATTCAGACCCTT-ATAAAAACAAATCTT-TAT
252 TTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGA-CCTTCATAAAAACAAAT-TTGTAT
8228 ATCCAATG
315 ATCCAATG
* * * * * *
8236 TGACTGAGATCTGGTTATATGAATATAGATGTTCAAGGAGTTTTTGTGCGAGAAATTATGCAAAA
1 TGACTGAGATTTGGTTATATGAATATAGATGTTCAAGGAGTCTTTATGCAAAAAACTATGCAAAA
8301 ATGGTGAGAA
Statistics
Matches: 335, Mismatches: 46, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
322 8 0.02
323 67 0.20
324 6 0.02
326 2 0.01
327 66 0.20
328 104 0.31
329 82 0.24
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (322 bp):
TGACTGAGATTTGGTTATATGAATATAGATGTTCAAGGAGTCTTTATGCAAAAAACTATGCAAAA
CTGAGTCGGGCCCTAGTAACGCGTTTCTAACAAAAAAACAGTGATGACTAGTACACGATTTCGGC
TAAAAACTAGCTCGAAAAGTTTTTTCTCAATTTTTTGTAAAATATTCAGAAAAAATATATAATTC
AATACCAAAAAGATTCAAGGGCTTTTCACGCTTTTAATATCGTTTTTTCCATTTTTTTCCGAATT
AATTTCTAATTAAATCAAAACAAGATTCAGACCTTCATAAAAACAAATTTGTATATCCAATG
Found at i:8717 original size:25 final size:25
Alignment explanation
Indices: 8666--8723 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
8656 AATCTATGAT
* **
8666 TAATTTTTCAATATTTTTTTTGCTAC
1 TAATATTTCAATATTTTTAAT-CTAC
8692 TCAATATTTCAATATTTTTAAT-TAC
1 T-AATATTTCAATATTTTTAATCTAC
8717 TAATATT
1 TAATATT
8724 ATACCCTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.21
25 4 0.14
26 1 0.04
27 17 0.61
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATATTTCAATATTTTTAATCTAC
Found at i:13907 original size:2 final size:2
Alignment explanation
Indices: 13894--13942 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
13884 TTTAGTAACC
*
13894 AT AT AC 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 AT AT
13936 ACT AT AT
1 A-T AT AT
13943 CCTTAGAGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18094 original size:6 final size:6
Alignment explanation
Indices: 18050--18083 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18040 GATGGCCCCC
* *
18050 ATGGGG ATGGGA ATGGGG ATGGGG ATGGGC ATGG
1 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGG
18084 CGGGAATGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.03, G:0.59, T:0.18
Consensus pattern (6 bp):
ATGGGG
Done.