Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012852.1 Corchorus olitorius cultivar O-4 contig12885, 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: 20347
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--55 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1 TCATG
6 TA TA TA TA TA TA TA TA TA TA TA 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
48 TA TA TA TA
1 TA TA TA TA
56 CATGAATCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432 original size:21 final size:21
Alignment explanation
Indices: 408--452 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
398 TTGACACTGT
408 TTAGCAACTGTACAGATGAGA
1 TTAGCAACTGTACAGATGAGA
** * *
429 TTAGGTACTGTATATATGAGA
1 TTAGCAACTGTACAGATGAGA
450 TTA
1 TTA
453 TTAGGGCAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (21 bp):
TTAGCAACTGTACAGATGAGA
Found at i:13687 original size:332 final size:331
Alignment explanation
Indices: 12793--16302 Score: 3467
Period size: 332 Copynumber: 10.6 Consensus size: 331
12783 CCATGATGGT
* *
12793 AAAAA-TGACCCGAAAGATTTTTCCTCAATTTTT-GACAAAATTACTCATAAAATATATATAATT
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-TAAAA-TACTCATAAAAAATATATAATT
* * * *
12856 CAACGCCAAAAGGATTGAAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTCTGAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATT
* * * * *
12921 AATTTCTAATTCAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGC
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGG
* * * *
12986 CTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTGTCAAAAATCATGCAAAACA
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * * * * *
13051 GAGACGTGACCCTGGAGCGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACTATTTCGGCTAA
259 GAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
*
13116 GATTTTGC
324 AATTTTGC
* * *
13124 AAAAATTGACCCGAAAAATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-TAAAATACTCATAAAAAATATATAATTC
* ** * * * * *
13189 GACATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCGA-ATTTTTTC-AAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT-TATATTTTTTCTGAATT
*
13252 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA-TCTAATATG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTC-AATGTG
* * * * *
13316 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCAAGTAAAAC
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* ** * * * * * *
13381 TGAG-CTGAACCCCGGAATGTGGTTTTAGCTAAGAACCGTGATGGTTAGTACATGATTTCGGCTA
258 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
13445 AAATTTTGC
323 AAATTTTGC
* * *
13454 AAAAATTGACCTGAAAGATTTTTCCTCGATTTCTAGTGAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGT-AAAATACTCATAAAAAATATATAATTC
* * * * *
13519 AACACCAAAAGAAATTGAAAGCCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTAAATT
65 AACGCCAAAA-AGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATT
* * *
13584 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCATTAAATTCAGTGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGG
* * *
13649 CTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAATT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * * *
13714 GAG-CAGGGCCCCGAAATGTGTTTTTAGCCGAAAACCGTGATGGTTAGTGTACACGATTTCGGCT
259 GAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA--GTACACGATTTCGGCT
13778 AAAATTTTGC
322 AAAATTTTGC
* * *
13788 AAAAATTGACCCGAAAGATTTTATCATCAATTTTTGGCTAAAATACTCATAAAATATATATAATT
1 AAAAATTGACCCGAAAGATTTT-TCCTCAATTTTTAG-TAAAATACTCATAAAAAATATATAATT
* * * * * ** *
13853 TAACGTCAAAAAAATTGGAGGAC-TTTCACGCTTTTAATATAATTTTTCATATTTTTT-TGAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATT
* * * ** * * *
13916 AATTTCTAGTTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATTATTCAATCCAATGTAG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGG
* * * * ** ** **
13981 CTGAGATTAGATTAAATGAATATGGATATCTCAAAAAGTCTTAGCGTAAAAAATCATGCAAAACC
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA-C
** * * * * * *
14046 T-AACCGGGACACCGGAACGCGTTTTTAGCCAAAAACCATGATGATTATTATACGATTTCGGCTA
258 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* *
14110 GAATTTTAC
323 AAATTTTGC
* * * *
14119 AAAAATTGACTCGAAA-ATTATTTCCTCATTTTTTA-TCCACAATACTCATAAAAATTATATAAT
1 AAAAATTGACCCGAAAGATT-TTTCCTCAATTTTTAGT--AAAATACTCATAAAAAATATATAAT
* * * * * * * *
14182 TCGACGCCATAAATATTAAAGGGTTTTTGATGCTTCTAATATCGTTTTTCCTAT-TATTTTTC-G
63 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT--TATAT-TTTTTCTG
* * * * ***
14245 AATTGATTTCTAATTAAACCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAA-TCTAA
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTC-AA
* * * *
14308 TGTGGCTGAGATTTGGTTGGATGAATGTAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCA
189 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCA
* ** * * * * * * *
14373 ACACTGAACCGGGGTCCCGAAACGCTTTTTTAGCCAAAAACTGTGATTTCGACTAACATACACGA
254 AAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA--T-G-GTTA-GTACACGA
* *
14438 TTTCGGCTAATATTTTAC
314 TTTCGGCTAAAATTTTGC
* * * * *
14456 AAAAATTGACCAGAAATATTTTTCCTCAATTTTGGT-CTAAAATACTCATAAGATATATATAATT
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTT--TAGTAAAATACTCATAAAAAATATATAATT
* * * ** * * * * *
14520 TAACTCCAAAAA-ATTGGAGAACTTCTCTCACTTTTAATATCGTTTTTCATA-TTTTTCTAAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATT
* *
14583 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGG
* ** *
14648 CTGAGA--T--TTA-AT--ATA-A-ATATTTCGAGGAGTCTCGATGTCAAAAATCATGCAAAACT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * *
14704 GAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAACACCGTGATTGTTATTACACGATTTCGG
259 GAGTCGGGGCCCCGGAACGCGTTTTTAGC---CAAAA-ACCGTGATGGTTAGTACACGATTTCGG
*
14769 CTAAAATTTTAC
320 CTAAAATTTTGC
** * * * * * * *
14781 AAAAA-AAACCAGAAA-AATATTCTCTCAATTTTTAGCCACAATGCTTATAAAAAATATATAATT
1 AAAAATTGACCCGAAAGATTTTTC-CTCAATTTTTAG-TAAAATACTCATAAAAAATATATAATT
* * * * *
14844 CAACACCAAAAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTATTTTCTATTTTTTCCGAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATT
* * * *
14909 AGTTTCTAATTAAAACGAAACATA-ATTCAGATGTTTGT-------AA-----AAA--CAA--TG
129 AATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
* * * * * * * * *
14957 GTTGGGATTCGGTTAGATGAATATAGATATTTTAGGGAGTCTCGGTGCCAAAAATCATTCAAAAT
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
** * * * ** *
15022 TGAACCGGGG-CCCGGAACACGTTTTTGGCCAAAATCCGTGATAATTATTACACGATTTCGGCTA
258 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
15086 AAATTTTGC
323 AAATTTTGC
* * * *
15095 AAAAATTGACCCGAAAGATATCTCCTCATTTTTTAGTCATAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGT-AAAATACTCATAAAAAATATATAATTC
* * *
15160 AACGCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTTTCTGAAT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT--TATATTTTTTCTGAAT
* * *
15225 TAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
* * * * *
15290 GCTAAGATTTTATTAGATGAATATAGATTTTTCAAGGAGTGC-CGGCGCAAAAAACCATGCAAAA
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT-CTCGGCGCCAAAAATCATGCAAAA
* * * * * *
15354 CTGAGCCGGGGTCTCGAAACGCGTTTTTAGCCAAAAATCGTGATGG-T-GTACACGATTTTGGCT
257 CTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
15417 AAAATTTTGC
322 AAAATTTTGC
* * ** * * *
15427 AAAAAAATT-ACCCGAAA-TTTTTTCC-CTATTCCTGGATAAAATACTCAT-AAATATATGTAAT
1 --AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-TAAAATACTCATAAAAAATATATAAT
* * * * *
15488 TTAAAGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAAT
63 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAAT
* * * *
15552 TAATTTCTAATTAAATCGAAACAAAATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
* * * * * * *
15617 GATGAGATTTGATTAGATGAATATGGAAATCTCAAGGAGTGTTGGCGTCAAAAATCATGCAAAAC
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* * * * * *
15682 TAAGTCGGGGCCCCAGAACGCTTTTTTAGCCAAAAACTGTAATGGTTATTACACGATTTCGGCTA
258 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
*
15747 AAATTTTGT
323 AAATTTTGC
* * *** * * *
15756 AAAACTTAATTAGAAAAATATTTCCTCAATTTTTGACTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTT-AGTAAAATACTCATAAAAAATATATAATTC
* * * *
15821 AACGCCAAAAATATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTTCCTATTTTTTC-CAAT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTT-ATATTTTTTCTGAA-
* * *
15884 TTAATTTCTAATTAAAACGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGT
* * * ** *
15948 GGCTGAAACTTTGAATAGATGAATATAGATATTTCAAGTAGTCTCGAAGCCAAAAATCATACAAA
192 GGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * *
16013 ATTGAGTCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTTGTTAGTACACGATTT
256 ACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTTAGTACACGATTT
*
16078 CGGCTAAAATTTTAC
317 CGGCTAAAATTTTGC
* * * *
16093 AAAAATTGACACAAAAGATTTTTCCTCAAATTTTGGCTAAAATACTCAT-AAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-TAAAATACTCATAAAAAATATATAATTC
* * ** * * *
16157 AACGCCAAAAAGATTGGAGGGCTTTTTATACTTTTAATATCATATTTCT-TA-TTTTTCTAAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGT-TTTTTATATTTTTTCTGAATT
* *
16220 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATTCTTAAA-TCAAATGTT
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTC-AATGTG
*
16283 GCTGAGATTTGGTTAGATGA
193 GCTGAGATTTGATTAGATGA
16303 TGTAAAGTAT
Statistics
Matches: 2606, Mismatches: 467, Indels: 210
0.79 0.14 0.06
Matches are distributed among these distances:
310 7 0.00
312 3 0.00
314 46 0.02
315 90 0.03
316 4 0.00
317 47 0.02
318 17 0.01
319 42 0.02
322 1 0.00
323 5 0.00
324 50 0.02
325 59 0.02
326 103 0.04
327 165 0.06
328 12 0.00
329 37 0.01
330 256 0.10
331 295 0.11
332 524 0.20
333 339 0.13
334 201 0.08
335 73 0.03
336 76 0.03
337 149 0.06
338 3 0.00
339 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (331 bp):
AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGTAAAATACTCATAAAAAATATATAATTCA
ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTTATATTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCT
GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGA
GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTGC
Found at i:15969 original size:333 final size:328
Alignment explanation
Indices: 14969--16302 Score: 1429
Period size: 333 Copynumber: 4.0 Consensus size: 328
14959 TGGGATTCGG
* * * * * * **
14969 TTAGATGAATATAGATATTTTAGGGAGTCTCGGTGCCAAAAATCATTCAAAATTGAACCGGGGCC
1 TTAGATGAATATAGATATTTCAAGGAGTGTCGGCG-CAAAAATCATGCAAAACTGAGTCGGGGCC
* * * * * ** *
15034 CGGAACACGTTTTTGGCCAAAATCCGTGATAATTATTACACGATTTCGGCTAAAATTTTGCAAAA
65 CCGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
* * * * * * * *
15099 ATTGACCCGAAAGATATCTCCTC-ATTTTTTAGTCATAATACTCATAAAAAATATATAATTCAAC
130 ATTAATCAGAAAAATATTTCCTCAATTTTTGACT-AAAATACTCAT-AAAAATATATAATTCAAC
*
15163 GCCAAAAAGATTGAAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTTTCTGAATTAA
193 GCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA---TTTTTCTGAATTAA
* * *
15228 TTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
255 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
*
15293 -AAGATTTTA
320 GAA-ATTTGA
* * * * *
15302 TTAGATGAATATAGATTTTTCAAGGAGTGCCGGCGCAAAAAACCATGCAAAACTGAGCCGGGGTC
1 TTAGATGAATATAGATATTTCAAGGAGTGTCGGCGC-AAAAATCATGCAAAACTGAGTCGGGGCC
* *
15367 TCGAAACGCGTTTTTAGCCAAAAA-TCGTGATGG-T-GTACACGATTTTGGCTAAAATTTTGCAA
65 CCG-AACGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC--
* * * * * * * * * *
15429 AAAAATT-ACCCG-AAATTTTTTCC-CTATTCCTGGA-TAAAATACTCATAAATATATGTAATTT
126 AAAAATTAATCAGAAAAATATTTCCTCAATT-TTTGACTAAAATACTCATAAAAATATATAATTC
* *
15490 AAAGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
190 AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
* * * *
15555 TTTCTAATTAAATCGAAACAAAATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGAT
255 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
*
15620 GAGATTTGA
320 GAAATTTGA
* * * * *
15629 TTAGATGAATATGGAAATCTCAAGGAGTGTTGGCGTCAAAAATCATGCAAAACTAAGTCGGGGCC
1 TTAGATGAATATAGATATTTCAAGGAGTGTCGGCG-CAAAAATCATGCAAAACTGAGTCGGGGCC
* * * *
15694 CCAGAACGCTTTTTTAGCCAAAAACTGTAATGGTTATTACACGATTTCGGCTAAAATTTTGTAAA
65 CC-GAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* *
15759 ACTTAATTAGAAAAATATTTCCTCAATTTTTGACTAAAATACTCATAAAAAATATATAATTCAAC
129 AATTAATCAGAAAAATATTTCCTCAATTTTTGACTAAAATACTCAT-AAAAATATATAATTCAAC
* * * * *
15824 GCCAAAAATATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTTCCTATTTTT-TCCAATTTA
193 GCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATCG-TTTTTCATATTTTTCT-GAA-TTA
* *
15887 ATTTCTAATTAAAACGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTAAATCCAATGTGGC
254 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
15951 TGAAACTTTGA
319 TGAAA-TTTGA
* * * * * *
15962 ATAGATGAATATAGATATTTCAAGTAGTCTCGAAGC-CAAAAATCATACAAAATTGAGTCGGGTC
1 TTAGATGAATATAGATATTTCAAGGAGTGTCG--GCGCAAAAATCATGCAAAACTGAGTCGGGGC
16026 CCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTTGTTAGTACACGATTTCGGCTAAAATTTT
64 CCC-GAACGCGTTTTTAGCCAAAAACTGTGAT-G---GTTAGTACACGATTTCGGCTAAAATTTT
* * * * * *
16091 ACAAAAATTGA-CACAAAAGATTTTTCCTCAAATTTTGGCTAAAATACTCATAAAAATATATAAT
124 GCAAAAATTAATCAGAAAA-ATATTTCCTCAATTTTTGACTAAAATACTCATAAAAATATATAAT
* * * ** * * * *
16155 TCAACGCCAAAAAGATTGGAGGGCTTTTTATACTTTTAATATCATATTTCTTATTTTTCTAAATT
188 TCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * *
16220 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATTCTTAAATCAAATGTTG
253 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* *
16284 CTGAGATTTGG
318 CTGAAATTTGA
16295 TTAGATGA
1 TTAGATGA
16303 TGTAAAGTAT
Statistics
Matches: 844, Mismatches: 125, Indels: 64
0.82 0.12 0.06
Matches are distributed among these distances:
327 162 0.19
328 7 0.01
329 35 0.04
330 79 0.09
331 57 0.07
332 75 0.09
333 198 0.23
334 96 0.11
335 16 0.02
336 53 0.06
337 66 0.08
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (328 bp):
TTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCAAAAATCATGCAAAACTGAGTCGGGGCCC
CGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
TTAATCAGAAAAATATTTCCTCAATTTTTGACTAAAATACTCATAAAAATATATAATTCAACGCC
AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAAATT
TGA
Found at i:17020 original size:3 final size:3
Alignment explanation
Indices: 17012--17065 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
17002 TTATATATAT
17012 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17060 ATA ATA
1 ATA ATA
17066 GTAGTAGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17085 original size:15 final size:15
Alignment explanation
Indices: 17058--17109 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
17048 ATAATAATAA
17058 TAATA-ATAGTAGTAG
1 TAATATATA-TAGTAG
17073 TAATATATATAGTAG
1 TAATATATATAGTAG
17088 TAATATATATATAGTAG
1 T-A-ATATATATAGTAG
17105 TAATA
1 TAATA
17110 AGATATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.44
16 5 0.15
17 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38
Consensus pattern (15 bp):
TAATATATATAGTAG
Found at i:17097 original size:17 final size:17
Alignment explanation
Indices: 17055--17109 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
17045 ATAATAATAA
17055 TAATA-ATA-ATAGTAG
1 TAATATATATATAGTAG
*
17070 TAGTAATATATATAGTAG
1 TAAT-ATATATATAGTAG
17088 TAATATATATATAGTAG
1 TAATATATATATAGTAG
17105 TAATA
1 TAATA
17110 AGATATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 21 0.60
18 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (17 bp):
TAATATATATATAGTAG
Found at i:17930 original size:19 final size:21
Alignment explanation
Indices: 17896--17935 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
17886 AATCTGTGGG
*
17896 TTTAATAAAATTGAAG-AAAA
1 TTTAATAAAATCGAAGCAAAA
17916 TTTAA-AAAATCGAAGCAAAA
1 TTTAATAAAATCGAAGCAAAA
17936 GGGGACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.25
Consensus pattern (21 bp):
TTTAATAAAATCGAAGCAAAA
Done.