Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019634.1 Corchorus olitorius cultivar O-4 contig19667, 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: 114283
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:9870 original size:11 final size:11
Alignment explanation
Indices: 9854--9879 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9844 TGTTTCATGT
9854 AACCGAAACCG
1 AACCGAAACCG
9865 AACCGAAACCG
1 AACCGAAACCG
9876 AACC
1 AACC
9880 CTGCAAAACC
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:0.46, C:0.38, G:0.15, T:0.00
Consensus pattern (11 bp):
AACCGAAACCG
Found at i:14529 original size:332 final size:330
Alignment explanation
Indices: 13547--15651 Score: 1846
Period size: 332 Copynumber: 6.4 Consensus size: 330
13537 TACATTATCT
* * *
13547 AACCAAAACTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
1 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * * * * * * *
13612 TTAACTAGAAATTAATTTAGAAAAAATAAGTAATACAATATTAAAAGCGTGAAAAGCACTCCAAT
66 TTAATTAGAAATTAATTCA-AAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
* * * * *
13677 CTTTTTGGCGTTGAATTATATA-TTTTTATGATTATTTTAACCAAAAATTGAGGAGAAATCTATC
130 CTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTC
* * * *
13741 ATGTTAATTTTTTTGCAAAATTTTAGCCGAAATCGTGCTATAACTAACCATCACGGACTCACGGT
195 -GGGTAA-ATTTTTACAAAATTTTAGCCGAAATCGTG---T-ACT-A--A-C-C--A-TCACGGT
* * * * * **
13806 TTTTCGCTAAAAACGCGTTCCAGG-GACCCGCCTCAATTTTGCATGTTTTTTGTGACTCCGAGAC
246 TTTTGGCTAAAAACGCGTT-CAGGAGACCCGGCTCAGTTTTGCATGATTTTTG-G-CGCAAAGAC
*
13870 TACTTGAAATATCTATATTCATC
308 TCCTTGAAATATCTATATTCATC
* * *
13893 TAATCAAATTCTCAGACACATTGGATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
1 -AACCAAA-TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * * * *
13958 ATTTAATTAG-AATCTAATTTGAAAAAAATAGGAAAAACGATATTAGAAACATCAAAAGCCCTTC
64 ATTTAATTAGAAAT-TAA-TTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTC
* * * * *
14022 AATCTTTTTGACGTTGAAATATAAATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCT
127 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTT
* * ** * **
14087 TTCGGGTCAATGTTTACAAAACATTAGCCGAAATCGTGTAATAACCATCACAATTTTTGGCTAAA
192 TTCGGGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
* * * * ** * * *
14152 AAAGCATTTC-GGGGCCCCAACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTTAGATATC
257 AACGC-GTTCAGGAGACCCGGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
*
14216 CATATTCAT-
321 TATATTCATC
* ** * ** *
14225 AACATCCAATCTCAGCTGCATTTGATTTAAGGATTTGTTTTTACGAGCATCTGAATAGTGTTTCA
1 AAC--CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * * ** *
14290 ATTTAATTATAAATTAATTCAAAAATAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
64 ATTTAATTAGAAATTAATTCAAAAA-AATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
* * * * * * * * *
14355 ATATTTTTTGTGTTAAATTATTTATATTTTATGAGTATTTTATCCAAAATTTGTGGAAAAATTTT
128 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTT
** *
14420 TCGGGTAAATTTTTACAAAATTTTAGCAAAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAA
193 TCGGGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
* * ** ** *
14485 ACGTGTGTCAGG-G-CCTCGGCTCAGTTTTGCATGATTTATGGCGCCGACCCTTCTTGAAATATC
258 ACGCGT-TCAGGAGACC-CGGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
14548 TATATTCATC
321 TATATTCATC
** * * * * *
14558 TAATAAAATCTTAGCCACATTGCATTTAAGGATTTGCTTTTACGAGCATCTGAATCTTATTTTGA
1 -AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
* ** * * *
14623 TTTAATTAGAAATAAATTCGGTAAAAAT-GGAAAAATGATATTAGAAGCATGAAAAAACCCTACA
65 TTTAATTAGAAATTAATTC-AAAAAAATAGGAAAAACGATATTAGAAGCGTG-AAAAACCCTTCA
* * * * * * *
14687 ATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTT
128 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTT
* *
14752 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
193 TCGGGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
** * * * * *
14817 ACATGTTCCGGAGTCCCGGCTCAATTTT-CAAAGATTTTTGGCGCAAAGACTCCTGGAAATATCT
258 ACGCGTTCAGGAGACCCGGCTCAGTTTTGC-ATGATTTTTGGCGCAAAGACTCCTTGAAATATCT
* *
14881 ATATTTATTG
322 ATATTCA-TC
* * ** ** *
14891 AACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCCAAATCTAATTTAGAT
1 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * *
14956 TTAATTAGAAATTAATTCGGAAAGAATTGGAAAAAGACGATATTAGAAGCGT-AAAAAACCTGTC
66 TTAATTAGAAATTAATTC-AAAAAAATAGG-AAAA-ACGATATTAGAAGCGTGAAAAACCCT-TC
** * * * * * *
15020 AATCTTTTTGGTATTGAATTATATATTTTTTCTGAATAATTT-GCAAAAAAATTGAGAAAAAACT
127 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGC-CAAAAATTGAGGAAAAATT
* * *
15084 TTTCGGGT-AA---GT------TTTTAGCTGAAATCATGTACTAACCATCACGGTTTTTGGCTAA
191 TTTCGGGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* *** ** *
15139 AAACGCGTTTCAGGA-TCCCGGCTCAGTTTTGCATGATTTTTGGAAAAAAAGACTATTTGAAATG
256 AAACGCG-TTCAGGAGACCCGGCTCAGTTTTGCATGATTTTTGG-CGCAAAGACTCCTTGAAATA
*
15203 TCTATATTCATTT
319 TCTATATTCA-TC
* * * *
15216 AACCAAATCTCAGCCACAATGGATTAAAAGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGAT
1 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * **
15281 TTAATTAGAAATAAATTCAGGAAAAAATA-GAAAAATG--ATTAGAAGCGTGAAAAATGCTTCAA
66 TTAATTAGAAATTAATTCA--AAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
* * *
15343 TCTTTTTGGCGTTGAATTATATATATATATATG-G-A---TA---AAAAATTGA-GAAAAAATTT
129 TCTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTT
* * * *
15399 TCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT-----TTTTT-GCTAAAA
193 TCGGGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
* * * * *
15458 ACGC-TAACTGGAGACCCGGCTCAAG-TTTGGATGATTTGTGGCGTAAAGACTCCTTGAAATATC
258 ACGCGT-TCAGGAGACCCGGCTC-AGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
15521 TATATTCATC
321 TATATTCATC
* * * * *
15531 GAACCAAATCTCAGCGACATTGAATATAAGGATTTGTTTTTACGAGCATCTGAATGTTGTTTCAA
1 -AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
* * *
15596 TTTAATTAGAAATTAATTCTGAAAAAACACGGAAAAACGATATTAGAAGTGTGAAA
65 TTTAATTAGAAATTAATTC-AAAAAAATA-GGAAAAACGATATTAGAAGCGTGAAA
15652 GCGCAAAGAC
Statistics
Matches: 1442, Mismatches: 263, Indels: 134
0.78 0.14 0.07
Matches are distributed among these distances:
313 13 0.01
314 10 0.01
315 9 0.01
316 101 0.07
317 42 0.03
318 7 0.00
319 14 0.01
320 1 0.00
321 37 0.03
322 12 0.01
323 27 0.02
324 74 0.05
325 103 0.07
326 6 0.00
330 1 0.00
331 36 0.02
332 563 0.39
333 53 0.04
334 73 0.05
335 57 0.04
336 3 0.00
338 1 0.00
339 1 0.00
340 1 0.00
342 1 0.00
343 2 0.00
344 1 0.00
347 33 0.02
348 120 0.08
349 40 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
TTAATTAGAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTCG
GGTAAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
CGTTCAGGAGACCCGGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATAT
TCATC
Found at i:16252 original size:323 final size:321
Alignment explanation
Indices: 15656--16484 Score: 897
Period size: 323 Copynumber: 2.6 Consensus size: 321
15646 GTGAAAGCGC
* *
15656 AAAGACTCCTTGAAATATCTATATTCAT-TGAAGCAAATCTCAGCCACATTGGATATAAGGATTT
1 AAAGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTT
* ** * * * *
15720 GTAAAACAAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAAA-GGGAAA
65 TTATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAATGGAAAA
* * ** *
15784 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAAT
129 ACGATATTAGAAGCGTGAAAAGTCCTTCAATCTTTTTGAAGTTGAATTATATATTTCTTCTGAAT
* * *
15849 ATTTTGCAAAAAAAGAATCTACAAAAATTTTTCAGGTAAGTTTTTAGCCAAAATCGTGTACTAAT
194 ATTTGGC--AAAAAGAATCTACAAAAACTTTTCAGGTAAGTTTTTAACCAAAATCGTGTACTAAT
* *
15914 CATCACGGTTTTTGGTTAAAAACGCGTGTCGAGG-TCCAGGCTCAGTTTTGCGT-ATTTTTGGCA
257 CATCACGGTTTTTGGTTAAAAACGCGTGTCGAGGCTCC-GGCTCAATTTTGCATGATTTTTGGCA
15977 G
321 G
*
15978 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTC
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT-
* * * *
16043 TTCTTATGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGCAAAAAAAATGGAAAA
65 TTATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-AAAAAAAATGGAAAA
* * *
16108 ACGATATTAGAAGCGTGAAAAATCCTTCAAAT-TTTTTTAATTTGAATTATATAATTTCTTCTGA
129 ACGATATTAGAAGCGTGAAAAGTCCTTC-AATCTTTTTGAAGTTGAATTATAT-ATTTCTTCTGA
* * * *** *
16172 GTATTGTGGC-AAAA-AA-CTGAGGAAAAACTTTTCGGGTCAA-TTTTTAATGGAAATCGTGTAT
192 ATATT-TGGCAAAAAGAATCT-A-CAAAAACTTTTCAGGT-AAGTTTTTAACCAAAATCGTGTAC
* * * *
16233 TAA-CAATCACGGTTTTTGGTTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGGTTTTT
253 TAATC-ATCACGGTTTTTGGTTAAAAACGCGTGTCGAGGCTCCGGCTCAATTTTGCATGATTTTT
16297 GGCAG
317 GGCAG
* ** * * * * * * * *
16302 AAAGATTTTTTGAAATATTTTTATTCATCTGATCAAATCTCATCTACATTGAATTTAAGAATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT-
* * * * *
16367 TTTTTACGTGCATCTGAATCTTATTTCGGTTTAATTAGAAATTAATTCAGAAAAAATAT-GAAAA
65 TTATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAATGGAAAA
* * * ** *
16431 ATGATATTAAAAGCGTGAAAAGTCCTACAATCTTTTTGGTGTTAAATTATATAT
129 ACGATATTAGAAGCGTGAAAAGTCCTTCAATCTTTTTGAAGTTGAATTATATAT
16485 ATTGTATGAG
Statistics
Matches: 424, Mismatches: 68, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
321 2 0.00
322 69 0.16
323 170 0.40
324 162 0.38
325 18 0.04
326 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (321 bp):
AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTT
TATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAAC
GATATTAGAAGCGTGAAAAGTCCTTCAATCTTTTTGAAGTTGAATTATATATTTCTTCTGAATAT
TTGGCAAAAAGAATCTACAAAAACTTTTCAGGTAAGTTTTTAACCAAAATCGTGTACTAATCATC
ACGGTTTTTGGTTAAAAACGCGTGTCGAGGCTCCGGCTCAATTTTGCATGATTTTTGGCAG
Found at i:17369 original size:3 final size:3
Alignment explanation
Indices: 17361--17389 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17351 TTTGACATTT
17361 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17390 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17394 original size:3 final size:3
Alignment explanation
Indices: 17388--17414 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17378 ATAATAATAA
17388 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
17415 GTATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18558 original size:207 final size:203
Alignment explanation
Indices: 18171--18587 Score: 617
Period size: 207 Copynumber: 2.1 Consensus size: 203
18161 GACGAAATCA
* * * * *
18171 AATTTCTAA--GGGTAATTATTTAATATACTGACGGTGTAAATTTTGAACTCCATAAGGGGTTGT
1 AATTTCTAATTGGATAATTATTTAATACACCGACGGTGTAAATTTTGAACTCCACAAGGGGCTGT
* *
18234 GGAATTGAGACATGTTCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGG
66 GGAATTGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGG
* * *
18299 GACACATGTCACCCTTCAAGACCCGCTTATGCAGTCTGCTAAACTCCACTGACGGTGTATTTATA
131 GACACATGTCACCCTTCAAGACCCGCTTATACAGTCTACTAAACTCCACTGACGGTGTA--T-CA
18364 TATATAAACCC
193 TATATAAACCC
*
18375 AATTTCTAATTGGATAATTATTTGATACACCGACGGTGTAAATTTTGAACTCCACAAGCGGGCTG
1 AATTTCTAATTGGATAATTATTTAATACACCGACGGTGTAAATTTTGAACTCCACAAG-GGGCTG
* *
18440 TGGAGTTGACACATGTCCATTTTCTGTATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGG
65 TGGAATTGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGG
* * * *
18505 GGACACATGTCACCCTTCAAGACTCGCTTGTACAGTCTACTAAAGTTCACTGACGGTGTATCATA
130 GGACACATGTCACCCTTCAAGACCCGCTTATACAGTCTACTAAACTCCACTGACGGTGTATCATA
18570 TATAAACCC
195 TATAAACCC
18579 --TTTCTAATT
1 AATTTCTAATT
18588 ATACTTGTAC
Statistics
Matches: 193, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
202 9 0.05
204 21 0.11
205 1 0.01
206 42 0.22
207 120 0.62
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (203 bp):
AATTTCTAATTGGATAATTATTTAATACACCGACGGTGTAAATTTTGAACTCCACAAGGGGCTGT
GGAATTGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGG
GACACATGTCACCCTTCAAGACCCGCTTATACAGTCTACTAAACTCCACTGACGGTGTATCATAT
ATAAACCC
Found at i:23740 original size:35 final size:39
Alignment explanation
Indices: 23669--23746 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 39
23659 AATTAATTAC
23669 ATCTATAGATATTAATTCATTGGTCAAAAACAAAAGTAATT
1 ATCTATAGATATT-ATTCATTGGTC-AAAACAAAAGTAATT
23710 ATCTATAGATA-T-TT-ATTGGTC-AAACAAAAGTAATT
1 ATCTATAGATATTATTCATTGGTCAAAACAAAAGTAATT
23745 AT
1 AT
23747 TTTTAACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
35 16 0.43
37 7 0.19
38 2 0.05
40 1 0.03
41 11 0.30
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (39 bp):
ATCTATAGATATTATTCATTGGTCAAAACAAAAGTAATT
Found at i:31719 original size:16 final size:16
Alignment explanation
Indices: 31700--31731 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31690 AATAAATAAC
31700 AAATTAAAAGAACAAA
1 AAATTAAAAGAACAAA
31716 AAATTAAAAGAACAAA
1 AAATTAAAAGAACAAA
31732 GAAGTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAATTAAAAGAACAAA
Found at i:31887 original size:21 final size:21
Alignment explanation
Indices: 31863--31929 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
31853 AAATTAAAAG
31863 AACAAACTTAATAAATAACAA
1 AACAAACTTAATAAATAACAA
* * *
31884 AACAAAAC-GAAAAAATAGGAAAA
1 AAC-AAACTTAATAAATA--ACAA
31907 GAACAAACTTAATAAATAACAA
1 -AACAAACTTAATAAATAACAA
31929 A
1 A
31930 TTAAAATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
21 11 0.31
22 7 0.20
23 7 0.20
24 10 0.29
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (21 bp):
AACAAACTTAATAAATAACAA
Found at i:31935 original size:29 final size:29
Alignment explanation
Indices: 31903--31958 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
31893 AAAAAATAGG
31903 AAAAGAACAAACTTAATAAATAACAAATT
1 AAAAGAACAAACTTAATAAATAACAAATT
*
31932 AAAATAACAAACTTAATAAATAACAAA
1 AAAAGAACAAACTTAATAAATAACAAA
31959 ACAAAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (29 bp):
AAAAGAACAAACTTAATAAATAACAAATT
Found at i:31960 original size:17 final size:16
Alignment explanation
Indices: 31908--31958 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
31898 ATAGGAAAAG
31908 AACAAACTTAATAAAT
1 AACAAACTTAATAAAT
31924 AACAAA-TT-A-AAAT
1 AACAAACTTAATAAAT
31937 AACAAACTTAATAAAT
1 AACAAACTTAATAAAT
31953 AACAAA
1 AACAAA
31959 ACAAAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.31
14 3 0.09
15 3 0.09
16 16 0.50
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.22
Consensus pattern (16 bp):
AACAAACTTAATAAAT
Found at i:31972 original size:18 final size:18
Alignment explanation
Indices: 31949--31987 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
31939 CAAACTTAAT
31949 AAATAACAAAACAAAACG
1 AAATAACAAAACAAAACG
31967 AAATAACAAAACAAAACG
1 AAATAACAAAACAAAACG
31985 AAA
1 AAA
31988 AAGTAGGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.15, G:0.05, T:0.05
Consensus pattern (18 bp):
AAATAACAAAACAAAACG
Found at i:33286 original size:121 final size:122
Alignment explanation
Indices: 33089--33333 Score: 411
Period size: 121 Copynumber: 2.0 Consensus size: 122
33079 AAATCCAATT
* * *
33089 TTGATCTTTGAATCAAACAAATTTAAATATGACAGTAAAAATACTATCCAATGTTCCATCCAATC
1 TTGATCTTTGAATCAAACAAATTAAAATATGACAG-AAAAAAACTATACAATGTTCCATCCAATC
*
33154 AGAAAAAAGTATACATCATAACTGTCGAGTATAACTCTCAATTGCTGAATCTAAGGAG
65 AGAAAAAAGTATACATCATAACTGTCGAGCATAACTCTCAATTGCTGAATCTAAGGAG
33212 TTGATCTTTGAATCAAACAAATTAAAATATGACA-AAAAAAACTATACAATGTTCCATCCAATCA
1 TTGATCTTTGAATCAAACAAATTAAAATATGACAGAAAAAAACTATACAATGTTCCATCCAATCA
* * *
33276 GAAAGAAGTATACATCATAATTGTTGAGCATAACTCTCAATTGCTGAATCTAAGGAG
66 GAAAAAAGTATACATCATAACTGTCGAGCATAACTCTCAATTGCTGAATCTAAGGAG
33333 T
1 T
33334 AAATTACGAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
121 82 0.71
123 33 0.29
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.29
Consensus pattern (122 bp):
TTGATCTTTGAATCAAACAAATTAAAATATGACAGAAAAAAACTATACAATGTTCCATCCAATCA
GAAAAAAGTATACATCATAACTGTCGAGCATAACTCTCAATTGCTGAATCTAAGGAG
Found at i:37471 original size:37 final size:37
Alignment explanation
Indices: 37421--37495 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
37411 AATTAATTCC
*
37421 AACTTGAAAGGGTTTCTT-TTTTTGGGAAAAAAAAAAA
1 AACTTGAAAGGGTTT-TTATGTTTGGGAAAAAAAAAAA
* *
37458 AACTTGAAAGGGTTTTTATGTTTGGGAATAAAACAAA
1 AACTTGAAAGGGTTTTTATGTTTGGGAAAAAAAAAAA
37495 A
1 A
37496 TTAATAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 2 0.06
37 32 0.94
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (37 bp):
AACTTGAAAGGGTTTTTATGTTTGGGAAAAAAAAAAA
Found at i:39398 original size:16 final size:18
Alignment explanation
Indices: 39369--39410 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
39359 GTTATCATTT
39369 ATAATTTTTCTTTT-GTC
1 ATAATTTTTCTTTTGGTC
39386 ATAATTTTT-TTTTGGTC
1 ATAATTTTTCTTTTGGTC
*
39403 ACAATTTT
1 ATAATTTT
39411 ATTGACTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (18 bp):
ATAATTTTTCTTTTGGTC
Found at i:52693 original size:27 final size:28
Alignment explanation
Indices: 52655--52711 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
52645 CCCTTATTTT
52655 TACTTATTTTATG-AAAAAAAATAATAG
1 TACTTATTTTATGAAAAAAAAATAATAG
*
52682 TACTTATTTTATGAAAAAAAAATAGTAG
1 TACTTATTTTATGAAAAAAAAATAATAG
52710 TA
1 TA
52712 ATAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (28 bp):
TACTTATTTTATGAAAAAAAAATAATAG
Found at i:55974 original size:24 final size:25
Alignment explanation
Indices: 55945--55995 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
55935 ATAAATGAAC
* *
55945 AATAAAATAAATAAGCAGGA-AAAT
1 AATAAAATAAAGAAACAGGATAAAT
*
55969 AATAAAATTAAGAAACAGGATAAAT
1 AATAAAATAAAGAAACAGGATAAAT
55994 AA
1 AA
55996 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAGGATAAAT
Found at i:60783 original size:106 final size:106
Alignment explanation
Indices: 60614--60926 Score: 477
Period size: 106 Copynumber: 2.9 Consensus size: 106
60604 GAATTTGTTG
* *
60614 GACATTAACGGCTCTGCGATTGAAGATGAACTTTTTA-CGACAATAATAGGATCTTAAATACCAA
1 GACA-TAACGGCTCTGCGATTGAAGATGAACCTTTTACCGACAATAATAGGATCTTAAAAACCAA
60678 CTATTAGGGAACAGAGTTACATATGGCAGCAAATATTGGTTA
65 CTATTAGGGAACAGAGTTACATATGGCAGCAAATATTGGTTA
**
60720 GACATAACGGCTCTGCGATCAAAGATGAACCTTTTACCGACAATAATAGGATCTTAAAAACCAAC
1 GACATAACGGCTCTGCGATTGAAGATGAACCTTTTACCGACAATAATAGGATCTTAAAAACCAAC
* *
60785 TATTAGGGAACAGAGTTAAATGTGGCAGCAAATATTGGTTA
66 TATTAGGGAACAGAGTTACATATGGCAGCAAATATTGGTTA
* * *
60826 GACATAACGGCTCTGCGATTGGAGATGAACTTCTTTTACCTACAATGATAGGATCTT-AAAACCA
1 GACATAACGGCTCTGCGATTGAAGATGAAC--CTTTTACCGACAATAATAGGATCTTAAAAACCA
* * *
60890 ACAATTAGGGAACAGAGTGACATATGGCAGCCAATAT
64 ACTATTAGGGAACAGAGTTACATATGGCAGCAAATAT
60927 AGGAATCATC
Statistics
Matches: 188, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
105 29 0.15
106 97 0.52
107 39 0.21
108 23 0.12
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (106 bp):
GACATAACGGCTCTGCGATTGAAGATGAACCTTTTACCGACAATAATAGGATCTTAAAAACCAAC
TATTAGGGAACAGAGTTACATATGGCAGCAAATATTGGTTA
Found at i:65068 original size:20 final size:20
Alignment explanation
Indices: 65032--65069 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65022 ATAATTTTGA
*
65032 ATAAAAATATAAAAAATTAT
1 ATAAAAATAAAAAAAATTAT
65052 ATAAAAA-AAAAACAAATT
1 ATAAAAATAAAAA-AAATT
65070 GAATAGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAATAAAAAAAATTAT
Found at i:71712 original size:19 final size:19
Alignment explanation
Indices: 71688--71728 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
71678 CCAACACCCT
71688 AAAAAAAGCTTTTTAAGAA
1 AAAAAAAGCTTTTTAAGAA
71707 AAAAAAAGCTTTTTAAGAA
1 AAAAAAAGCTTTTTAAGAA
71726 AAA
1 AAA
71729 TACGTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAAAAAGCTTTTTAAGAA
Found at i:92476 original size:17 final size:17
Alignment explanation
Indices: 92454--92487 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
92444 ATACTCTATT
92454 AACAGATTATGCGACTC
1 AACAGATTATGCGACTC
92471 AACAGATTATGCGACTC
1 AACAGATTATGCGACTC
92488 TTGACGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
AACAGATTATGCGACTC
Found at i:100349 original size:11 final size:11
Alignment explanation
Indices: 100325--100359 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
100315 TTGATAACTC
100325 AACAAAAACAA
1 AACAAAAACAA
* *
100336 AACGAAAACGA
1 AACAAAAACAA
100347 AACAAAAACAA
1 AACAAAAACAA
100358 AA
1 AA
100360 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:104880 original size:4 final size:4
Alignment explanation
Indices: 104871--104895 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
104861 TTTAATTTAC
104871 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
104896 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:106221 original size:12 final size:12
Alignment explanation
Indices: 106204--106228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
106194 ACCAGTGCCC
106204 TTCATCTCTACA
1 TTCATCTCTACA
106216 TTCATCTCTACA
1 TTCATCTCTACA
106228 T
1 T
106229 CACTGGGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCATCTCTACA
Found at i:108019 original size:31 final size:33
Alignment explanation
Indices: 107951--108020 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
107941 CCATAAGAAG
107951 CACAG-TCACAAAATAAAAAAGAAACCAAAATC
1 CACAGCTCACAAAATAAAAAAGAAACCAAAATC
* * **
107983 AACAGCTC-CAAAATAAATAA-AAACTTAAATC
1 CACAGCTCACAAAATAAAAAAGAAACCAAAATC
108014 CACAGCT
1 CACAGCT
108021 GAAACAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 15 0.47
32 15 0.47
33 2 0.06
ACGTcount: A:0.57, C:0.23, G:0.06, T:0.14
Consensus pattern (33 bp):
CACAGCTCACAAAATAAAAAAGAAACCAAAATC
Found at i:114247 original size:2 final size:2
Alignment explanation
Indices: 114240--114283 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
114230 TTCATTCACC
* *
114240 CT CT CT CT CA CT CA 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 CT CT CT CT CT CT
114282 CT
1 CT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.05, C:0.50, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Done.