Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010323.1 Corchorus capsularis cultivar CVL-1 contig10344, 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: 27910
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4938 original size:15 final size:15
Alignment explanation
Indices: 4918--4953 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
4908 AGACGAATTT
4918 ACAAAAACGATATTA
1 ACAAAAACGATATTA
4933 ACAAAAACGATATTA
1 ACAAAAACGATATTA
4948 A-AAAAA
1 ACAAAAA
4954 AGAGTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (15 bp):
ACAAAAACGATATTA
Found at i:6186 original size:14 final size:13
Alignment explanation
Indices: 6158--6182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6148 AAAGTGATAC
6158 AATACAAAAATAG
1 AATACAAAAATAG
6171 AATACAAAAATA
1 AATACAAAAATA
6183 AGAACCGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
AATACAAAAATAG
Found at i:6240 original size:17 final size:17
Alignment explanation
Indices: 6206--6240 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6196 TTGTTTTTGT
*
6206 AGTCTATCTAAAAGAAA
1 AGTCTATCTAAAAAAAA
6223 AGTCTATCTAAAAAAAA
1 AGTCTATCTAAAAAAAA
6240 A
1 A
6241 AAACGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (17 bp):
AGTCTATCTAAAAAAAA
Found at i:7702 original size:329 final size:327
Alignment explanation
Indices: 6632--8908 Score: 1736
Period size: 332 Copynumber: 6.9 Consensus size: 327
6622 AGTTCAGACC
* * * * * * *
6632 ATCACGGTTTTTTGTCTAAAATCGCGTTCCGAGTACCCGGCTCAATTTTGCATGATTTTTGGCCG
1 ATCACGATTTTTTG-CTAAAAACGCATTCCGA--ACCCGACTCAGTTTTGCATTATTTTTGG-GG
* ** * * *
6697 -AAAGACTTCTTGAAATATCTATATTCATTTAACCATGTCTCAACCAAATTGCAATTTAGGATTT
62 TAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG-GATTTAGGATTT
* *
6761 GTTTTTATGAGCATCTGAATCTTATTTCGATTTAATCAGAAAATAAATTCGGGGAAAATGGAAAA
126 GTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTC-GGGAAAATGGAAAA
* *
6826 ATGAAATTAGAAGAATAAAAACCCTTCATTTTTTTTTTGCATTGAATTATAT-TTTTTTCCTGAC
190 ACGAAATTAGAAGAATAAAAACCCTTCA-ATTTTTTTTGCATTGAATTATATATTTTTTCCTGAC
* *
6890 TATTGTCGCAAAAAATTGAGGAAAAAATTTCCGGGTCTGTTTTTACAAAATTTTGGCCGAAATCG
254 TATTGTCGCAAAAAATTGAGGAAAAAATTT-CAGGTCTGTTTTTACAAAATTTTAGCCGAAATCG
* * *
6955 TTTACTAACC
318 TGTACGAACT
* *
6965 ATCACGATTTTTTGCTAAAAACACATTCC-ACAGCCCTGACTCAGTTTTGCATTATTTTTGGCGT
1 ATCACGATTTTTTGCTAAAAACGCATTCCGA-A-CCC-GACTCAGTTTTGCATTATTTTTGGGGT
* * * * * *
7029 AAAGACTTCTTGAAGTATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAAGATTTA
63 AAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAT-TTAGGATTTG
* ** *
7094 TTTTTACGAGCATCCGAATC-TAGTTTCGATTTAATTA-AAAACCAATTCGGGAAAAAAGGAAAA
127 TTTTTACGAGCATCTGAATCTTA-TTTCGATTTAATTAGAAAATAAATTCGGG-AAAATGGAAAA
* *** * *** * *
7157 ACGATATTAGAAGCGGGAAAAGCAAGTCAATTTTTTTTGCGTTGAATAATATATATTTTTTTC-G
190 ACGAAATTAGAAG-AATAAAAACCCTTCAATTTTTTTTGCATTGAAT--TATATATTTTTTCCTG
* * * * **
7221 AGTATTGTGGC-AAAATTTGAGAAAAAAAATTTC--G--TG----T-C-AGTTTTTAGCCGAAAT
252 ACTATTGTCGCAAAAAATTGAG-GAAAAAATTTCAGGTCTGTTTTTACAAAATTTTAGCCGAAAT
*
7275 CGTGTACTAA-T
316 CGTGTACGAACT
* * * * ** * * * *
7286 CATCACGGTTTTTGGTCTAAAATCGCGTTCCGGGTGCCCGGCTCAATTTTGCATGATTTTT-GGC
1 -ATCACGATTTTTTG-CTAAAAACGCATTCC--GAACCCGACTCAGTTTTGCATTATTTTTGGGG
* * * * * *
7350 CAGAAGACTTCTTGAAATATCTATATTCATTTCACCAAGTCTCAACCAGATTGGAATTTAGGATT
62 TA-AAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG-ATTTAGGATT
*
7415 TGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGGAGAAAATGGAAA
125 TGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGG-GAAAATGGAAA
* * *
7480 AATGAAATTAGAAGAATAAAAACCTTTCAATTTTTTTTGCACTGAATTATAT-TTTTTTCCTGAC
189 AACGAAATTAGAAGAATAAAAACCCTTCAATTTTTTTTGCATTGAATTATATATTTTTTCCTGAC
* * *
7544 TATTGTCACAAAAAAATTGAGG-AAAAATTTCCAAGTCTGTTTTTACAAAATTTTGGCCGAAATC
254 TATTGTCGC-AAAAAATTGAGGAAAAAATTT-CAGGTCTGTTTTTACAAAATTTTAGCCGAAATC
7608 GTGTACGAACT
317 GTGTACGAACT
*
7619 ATCACGATTTTTTGCTAAAAACACATTCCGAACCCGACTCAGTTTTGCATTATTTTTGGGGTAAA
1 ATCACGATTTTTTGCTAAAAACGCATTCCGAACCCGACTCAGTTTTGCATTATTTTTGGGGTAAA
* * * *
7684 GACTTCTTGAAGTATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAGGATTTGTTT
66 GACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAT-TTAGGATTTGTTT
7749 TTACGAGCATCTGAATCTTATTTCGATTTAATTAG-AAAT-AATTCGGGAAAATGGAAAAACGAA
130 TTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGGGAAAATGGAAAAACGAA
** * *
7812 ATTAGAAGCGTGAAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTT-CTGAATAT
195 ATTAGAAGAAT--AAAAACCCTTCAA-TTTTTTTTGCATTGAATTATATATTTTTTCCTGACTAT
* * *
7876 TG-GGCAAAAAATTTGAGGAAAAAATTTCAGGTCTGTTTTTACATAACTTTAGCCGAAAATCGTG
257 TGTCGCAAAAAA-TTGAGGAAAAAATTTCAGGTCTGTTTTTACAAAATTTTAGCCG-AAATCGTG
*
7940 TACG--TT
320 TACGAACT
* * * * ** * * * ** *
7946 ATCACAATTTTTGGCTAAAAATGCATTTCAGGGTCTCGTCTCAGTTTTTCA-TGGTTTTGGGCAT
1 ATCACGATTTTTTGCTAAAAACGCA-TTC-CGAACCCGACTCAGTTTTGCATTATTTTTGGG-GT
* *
8010 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTG
63 AAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT-AGGATTTG
* * * *
8075 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTA-CAAATAAATTCGGAAAAAAAGAATGG-
127 TTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGG----GAA-AATGGA
* * ** ** * * ** *
8138 AAAACGATATTAGATGCGTGAAAAATTCTTTAATTTTTTTGGTGTTGAATTATATAATTTTT-CT
187 AAAACGAAATTAGAAGAAT-AAAAACCCTTCAATTTTTTTTGCATTGAATTATATATTTTTTCCT
* * * * * ** * * *
8202 TAATATTGTTGCAAAGAATTAAGGAAAAAATTTTGGGTCAGTTTTTGCAAAATTTTAGTCGAAAT
251 GACTATTGTCGCAAAAAATTGAGGAAAAAATTTCAGGTCTGTTTTTACAAAATTTTAGCCGAAAT
* * *
8267 CGTATACTAACC
316 CGTGTACGAACT
* * * * * ** ** * *
8279 ATCACG-GTTTTCGCTGAAAAA-GCGTTCCTGACCCCGGCAAAGTTTCACATGATTTTTGGCGTA
1 ATCACGATTTTTTGCT-AAAAACGCATTCC-GAACCCGACTCAGTTTTGCATTATTTTTGGGGTA
* * * * *
8342 ACGACTCCTTGAAATATCTATATTCATCTTTACAAATTAATCTCAGCCACATTCGATTTAAGGAA
64 AAGACTTCTTGAAATATCTATATTCATC-TAAC-CA--AATCTCAGCCACATTGGATTT-AGG-A
* * * * *
8407 TGTTTTTTTTTACGAGCATCTGATTCTTGTTTCGATTTAATTA-AAAATTAATT-TGGAAAA---
123 --TTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGGGAAAATGG
* ** * * * * *
8467 AAAAATC-AATATTAAAAGCGTGAAAAGCCTTCAATCTTTTTGGCGTTAGAATTATATA-TTTTT
186 AAAAA-CGAA-ATTAGAAGAATAAAAACCCTTCAATTTTTTTTGCATT-GAATTATATATTTTTT
* * * * ** *
8530 --TGAGTATTGT-GACAAAGAATTAAGAAAAAAAATATTC-GGATCAATTTTTGCAAAATTTTAG
248 CCTGACTATTGTCG-CAAAAAATTGAG-GAAAAAAT-TTCAGG-TCTGTTTTTACAAAATTTTAG
* ** *
8591 CTGAAATCGTGTACTTACC
309 CCGAAATCGTGTACGAACT
* * * * * ** * * * * * *
8610 ATCACG-GTTATGGCTAAAAACGCGTTTCGGGGCCTCGGCTTAGTTTTGGATGATTTTTCGCGTA
1 ATCACGATTTTTTGCTAAAAACGC-ATTCCGAACC-CGACTCAGTTTTGCATTATTTTTGGGGTA
* * * *
8674 AATACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAACGACATTGGATTTAAGGATTTGT
64 AAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT-AGGATTTGT
* * * * **
8739 TTTTACGACCATCTTAATCTTGTTTCGATTTAATTAG-AAATTAATTCAGAAAAAAATGGAAAAA
128 TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTC-G-GGAAAATGGAAAAA
* * * * * * ** * **
8803 CGATATTAGAA-ACGTGAAGAGCCCGTCAATCTTTTCAGCCTTGAATTATATATTTTTT--TGTG
191 CGAAATTAGAAGA-AT-AAAAACCCTTCAATTTTTTTTGCATTGAATTATATATTTTTTCCTGAC
* * * * *
8865 TATTATGGCAAAAAATTGAGAAAAAAATTTCGGGTCCGTTTTTA
254 TATTGTCGCAAAAAATTGAGGAAAAAATTTCAGGTCTGTTTTTA
8909 GTCGAAATCG
Statistics
Matches: 1578, Mismatches: 273, Indels: 190
0.77 0.13 0.09
Matches are distributed among these distances:
320 7 0.00
321 22 0.01
322 37 0.02
323 147 0.09
324 41 0.03
325 47 0.03
326 27 0.02
327 36 0.02
328 89 0.06
329 303 0.19
330 96 0.06
331 248 0.16
332 308 0.20
333 68 0.04
334 26 0.02
335 28 0.02
336 1 0.00
337 1 0.00
338 46 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (327 bp):
ATCACGATTTTTTGCTAAAAACGCATTCCGAACCCGACTCAGTTTTGCATTATTTTTGGGGTAAA
GACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAGGATTTGTTTT
TACGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGGGAAAATGGAAAAACGAAA
TTAGAAGAATAAAAACCCTTCAATTTTTTTTGCATTGAATTATATATTTTTTCCTGACTATTGTC
GCAAAAAATTGAGGAAAAAATTTCAGGTCTGTTTTTACAAAATTTTAGCCGAAATCGTGTACGAA
CT
Found at i:8862 original size:331 final size:328
Alignment explanation
Indices: 6629--9112 Score: 2028
Period size: 329 Copynumber: 7.6 Consensus size: 328
6619 TGAAGTTCAG
* * * ** *
6629 ACCATCACGGTTTTTTGTCTAAAATCGCGTTCCGAGTACCCGGCTCAATTTTGCATGATTTTTGG
1 ACCATCAC-G-TTTTTGGCTAAAAACGCGTTTCG-GGGCCCGGCTCAGTTTTGCATGATTTTTGG
* ** * *
6694 CCG-AAAGACTTCTTGAAATATCTATATTCATTTAACCATGTCTCAACCAAATTGCAATTT-AGG
63 -CGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTG-GATTTAAGG
* * * * ***
6757 ATTTGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATCAGAAAATAAATTCGGGGAAAATGG
126 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAATTCGAAAAAAATGG
* * * * *
6822 AAAAATGAAATTAGAAGA-AT-AAAAACCCTTCATTTTTTTTTTGCATTGAATTATAT-TTTTTT
190 AAAAACGATATTAGAA-ACGTGAAAAACCCTTCA-ATTTTTTTTGCGTTGAATTATATATTTTTT
* * *
6884 CCTGACTATTGTCGCAAAAAATTGAG-GAAAAAATTTCCGGGTCTGTTTTTACAAAATTTTGGCC
253 --TGAGTATTGTGGCAAAAAATTGAGAGAAAAAATTT-CGGGTCTGTTTTTACAAAATTTTAGCC
*
6948 GAAATCGTTTACTA
315 GAAATCGTGTACTA
* * * * *** * *
6962 ACCATCACGATTTTTTGCTAAAAACACATTCCACAGCCCTGACTCAGTTTTGCATTATTTTTGGC
1 ACCATCACG-TTTTTGGCTAAAAACGCGTTTCGGGGCCC-GGCTCAGTTTTGCATGATTTTTGGC
* * * * * *
7027 GTAAAGACTTCTTGAAGTATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAAGATT
64 GTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATT
* * * * ** *
7092 TATTTTTACGAGCATCCGAATCTAGTTTCGATTTAATTAAAAACCAATTCGGGAAAAAA-GGAAA
129 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAA
* * * ***
7156 AACGATATTAGAAGCGGGAAAAGCAAGTCAATTTTTTTTGCGTTGAATAATATATATTTTTTTCG
193 AACGATATTAGAAACGTGAAAAACCCTTCAATTTTTTTTGCGTTGAAT--TATATATTTTTTT-G
* * **
7221 AGTATTGTGGC-AAAATTTGAGAAAAAAAATTTC--G--TG----T-C-AGTTTTTAGCCGAAAT
255 AGTATTGTGGCAAAAAATTGAGAGAAAAAATTTCGGGTCTGTTTTTACAAAATTTTAGCCGAAAT
7275 CGTGTACTA
320 CGTGTACTA
* * * *
7284 ATCATCACGGTTTTTGGTCTAAAATCGCGTTCCGGGTGCCCGGCTCAATTTTGCATGATTTTTGG
1 ACCATCAC-GTTTTTGG-CTAAAAACGCGTTTCGGG-GCCCGGCTCAGTTTTGCATGATTTTTGG
* * * * *
7349 C-CAGAAGACTTCTTGAAATATCTATATTCATTTCACCAAGTCTCAACCAGATTGGAATTT-AGG
63 CGTA-AAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGG-ATTTAAGG
* * * * *
7412 ATTTGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATTAGAAAATAAATTCGGAGAAAATGG
126 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAATTCGAAAAAAATGG
* * * * **
7477 AAAAATGAAATTAGAAGA-AT-AAAAACCTTTCAATTTTTTTTGCACTGAATTATAT-TTTTTTC
190 AAAAACGATATTAGAA-ACGTGAAAAACCCTTCAATTTTTTTTGCGTTGAATTATATATTTTTT-
* ** ** *
7539 CTGACTATTGTCACAAAAAAATTGAG-G-AAAAATTTCCAAGTCTGTTTTTACAAAATTTTGGCC
253 -TGAGTATTGTGGC-AAAAAATTGAGAGAAAAAATTT-CGGGTCTGTTTTTACAAAATTTTAGCC
*
7602 GAAATCGTGTACGA
315 GAAATCGTGTACTA
* * * * * ** * * *
7616 ACTATCACGATTTTTTGCTAAAAACAC-ATTCCGAACCCGACTCAGTTTTGCATTATTTTTGGGG
1 ACCATCACG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * *
7680 TAAAGACTTCTTGAAGTATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAGGATTT
65 TAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTT
* **
7745 GTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAA-TAATTCG-GGAAAATGGAAAAA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAA
* * *
7808 CGAAATTAGAAGCGTGAAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTTCTGAA
195 CGATATTAGAAACGTG-AAAAACCCTTCAA-TTTTTTTTGCGTTGAATTATATATTTTTT-TGAG
* * *
7873 TATTG-GGCAAAAAATTTGAG-GAAAAAATTTCAGGTCTGTTTTTACATAACTTTAGCCGAAAAT
257 TATTGTGGCAAAAAA-TTGAGAGAAAAAATTTCGGGTCTGTTTTTACAAAATTTTAGCCG-AAAT
*
7936 CGTGTACGTT
320 CGTGTAC-TA
* * * * * * * * * * *
7946 ATCA-CA-ATTTTTGGCTAAAAATGCATTTCAGGGTCTCGTCTCAGTTTTTCATGGTTTTGGGCA
1 ACCATCACGTTTTTGGCTAAAAACGCGTTTC-GGGGCCCGGCTCAGTTTTGCATGATTTTTGGCG
* * *
8009 TAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTT
65 TAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTT
* * *
8074 GTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTACAAATAAATTCGGAAAAAAAGAATGG-
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-G--AAAAA-AATGGA
** ** * * *
8138 AAAACGATATTAGATGCGTGAAAAATTCTTTAATTTTTTTGGTGTTGAATTATATAATTTTTCTT
191 AAAACGATATTAGAAACGTGAAAAACCCTTCAATTTTTTTTGCGTTGAATTATAT-ATTTTT-TT
* * * * * * * *
8203 -AATATTGTTGCAAAGAATTAAG-GAAAAAATTTTGGGTCAGTTTTTGCAAAATTTTAGTCGAAA
254 GAGTATTGTGGCAAAAAATTGAGAGAAAAAATTTCGGGTCTGTTTTTACAAAATTTTAGCCGAAA
*
8266 TCGTATACTA
319 TCGTGTACTA
* * * * ** ** **
8276 ACCATCACGGTTTTCGCTGAAAAA-GCGTTCCTGACCCCGGCAAAGTTTCACATGATTTTTGGCG
1 ACCATCACGTTTTTGGCT-AAAAACGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * * *
8340 TAACGACTCCTTGAAATATCTATATTCATCTTTACAAATTAATCTCAGCCACATTCGATTTAAGG
65 TAAAGACTTCTTGAAATATCTATATTCATC-TAAC-CA--AATCTCAACCACATTGGATTTAAGG
* * * * *
8405 AATGTTTTTTTTTACGAGCATCTGATTCTTGTTTCGATTTAATTAAAAATTAATTTG-GAAAAA-
126 -A--TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAT
* * * * *
8468 --AAAATCAATATTA-AAAGCGTG-AAAAGCCTTCAATCTTTTTGGCGTTAGAATTATATA-TTT
188 GGAAAAACGATATTAGAAA-CGTGAAAAACCCTTCAATTTTTTTTGCGTT-GAATTATATATTTT
* * * * * ** * *
8528 TTTGAGTATTGTGACAAAGAATTAAGAAAAAAAATATTCGGATCAATTTTTGCAAAATTTTAGCT
251 TTTGAGTATTGTGGCAAAAAATTGAGAGAAAAAAT-TTCGGGTCTGTTTTTACAAAATTTTAGCC
*
8593 GAAATCGTGTACTT
315 GAAATCGTGTACTA
* * * * *
8607 ACCATCACGGTTATGGCTAAAAACGCGTTTCGGGGCCTCGGCTTAGTTTTGGATGATTTTTCGCG
1 ACCATCACGTTTTTGGCTAAAAACGCGTTTCGGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCG
* * *
8672 TAAATACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAACGACATTGGATTTAAGGATTT
65 TAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTT
* *
8737 GTTTTTACGACCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAA
* * * * ** * *
8802 ACGATATTAGAAACGTGAAGAGCCCGTCAATCTTTTCAGCCTTGAATTATATATTTTTTTGTGTA
194 ACGATATTAGAAACGTGAAAAACCCTTCAATTTTTTTTGCGTTGAATTATATATTTTTTTGAGTA
* * *
8867 TTATGGCAAAAAATTGAGA-AAAAAATTTCGGGTCCG----T------TTTTAGTCGAAATCGTG
259 TTGTGGCAAAAAATTGAGAGAAAAAATTTCGGGTCTGTTTTTACAAAATTTTAGCCGAAATCGTG
8921 TACTA
324 TACTA
* * * * *
8926 ACCATCACGATTTTTGGCTAAAATCGCCTTCCGGGGTCACGGCTCTA-TTTTGCATGGTTTTTGG
1 ACCATCACG-TTTTTGGCTAAAAACGCGTTTCGGGG-CCCGGCTC-AGTTTTGCATGATTTTTGG
* ** * * * *
8990 CATCGAGAC-TCGTTGAAATATCGT-TATTGATCTAATCAAAGTCTGAGA-CATATTGGATTTAA
63 CGTAAAGACTTC-TTGAAATATC-TATATTCATCTAACCAAA-TCTCA-ACCACATTGGATTTAA
* * * *
9052 GGATTTGTTTTTATGAGTA-CTTAAATCTTGTTTCAATTTAATTAGAAATTAATTC-AAAAAA
124 GGATTTGTTTTTACGAGCATC-TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA
9113 TATGAAAGAA
Statistics
Matches: 1741, Mismatches: 319, Indels: 196
0.77 0.14 0.09
Matches are distributed among these distances:
319 36 0.02
320 76 0.04
321 88 0.05
322 38 0.02
323 158 0.09
324 33 0.02
325 47 0.03
326 27 0.02
327 32 0.02
328 77 0.04
329 312 0.18
330 90 0.05
331 254 0.15
332 303 0.17
333 64 0.04
334 30 0.02
335 28 0.02
336 1 0.00
337 1 0.00
338 46 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
ACCATCACGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGT
AAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTG
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAAC
GATATTAGAAACGTGAAAAACCCTTCAATTTTTTTTGCGTTGAATTATATATTTTTTTGAGTATT
GTGGCAAAAAATTGAGAGAAAAAATTTCGGGTCTGTTTTTACAAAATTTTAGCCGAAATCGTGTA
CTA
Found at i:9961 original size:2 final size:2
Alignment explanation
Indices: 9956--9984 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9946 TATATAGTGC
9956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9985 TTGAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12807 original size:20 final size:21
Alignment explanation
Indices: 12760--12807 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
12750 ACATGTAAAT
*
12760 AAAGAAGATCATAAAAATATAT
1 AAAGAAGATCAT-AAAATATAA
*
12782 ATAGAAGATCAT-AAATATAA
1 AAAGAAGATCATAAAATATAA
12802 AAAGAA
1 AAAGAA
12808 ATGATGGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAGAAGATCATAAAATATAA
Found at i:19348 original size:2 final size:2
Alignment explanation
Indices: 19341--19381 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19331 TCAAAACGAA
19341 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19382 AACCTAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20140 original size:64 final size:66
Alignment explanation
Indices: 20065--20190 Score: 204
Period size: 65 Copynumber: 1.9 Consensus size: 66
20055 AGTAATTAGA
20065 CCATTCATGATGTGCCT-TTTTAACCAGATT-TACTACAAACAAAACAATTTCTAA-TCAAATCA
1 CCATTCATGATGTGCCTCTTTTAACCAG-TTCTACTACAAACAAAACAATTTCTAAGTCAAATCA
20127 TT
65 TT
* *
20129 CCATTCTTGATGTGCCTCTTTTAACCAGTTCTACTACAAACAAAGCAATTTCTAAGTCAAAT
1 CCATTCATGATGTGCCTCTTTTAACCAGTTCTACTACAAACAAAACAATTTCTAAGTCAAAT
20191 TATTAATTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
64 18 0.32
65 33 0.58
66 6 0.11
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (66 bp):
CCATTCATGATGTGCCTCTTTTAACCAGTTCTACTACAAACAAAACAATTTCTAAGTCAAATCAT
T
Found at i:26321 original size:3 final size:3
Alignment explanation
Indices: 26315--26354 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
26305 TCTTCGTGGT
26315 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC G
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC G
26355 ACGAAGATCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.68, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:26620 original size:15 final size:15
Alignment explanation
Indices: 26600--26628 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26590 ATAACAATTC
26600 TTATCGGCCGGTTTG
1 TTATCGGCCGGTTTG
26615 TTATCGGCCGGTTT
1 TTATCGGCCGGTTT
26629 AAGGTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.31, T:0.41
Consensus pattern (15 bp):
TTATCGGCCGGTTTG
Done.