Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019526.1 Corchorus olitorius cultivar O-4 contig19559, 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: 148975
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:925 original size:21 final size:21
Alignment explanation
Indices: 900--942 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
890 TATCTTAGAT
900 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
921 ATAATAAATATATTTTAAATAA
1 ATAAT-AATATATTTTAAATAA
943 TCAGTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:4090 original size:29 final size:30
Alignment explanation
Indices: 4046--4112 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
4036 TGGTTTGAAA
*
4046 AGAGAAAGAGTTTGGG-GAGTA-A-TGGAGG
1 AGAGAAAGAATTTGGGTGAG-AGATTGGAGG
4074 AGAGAAGAGAATTTGGGTGAGAGATTTGGAGG
1 AGAGAA-AGAATTTGGGTGAGAGA-TTGGAGG
4106 AGAGAAA
1 AGAGAAA
4113 AGAAGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 6 0.18
29 10 0.30
30 4 0.12
31 1 0.03
32 12 0.36
ACGTcount: A:0.39, C:0.00, G:0.43, T:0.18
Consensus pattern (30 bp):
AGAGAAAGAATTTGGGTGAGAGATTGGAGG
Found at i:7568 original size:74 final size:74
Alignment explanation
Indices: 7435--7579 Score: 254
Period size: 74 Copynumber: 2.0 Consensus size: 74
7425 TTGTTAGTTT
* *
7435 CTTCACAAACTTTTGAACTATTAGCTTTTATTGGCTAATTGCTCAAATAAGGGCATGATATTTTA
1 CTTCACAAACTTTTGAACTATTAGCTTTTATTGGCTAATTGCTCAAAAAAGGACATGATATTTTA
7500 ATTTGGTTC
66 ATTTGGTTC
* *
7509 CTTCACAAACTTTTGAACTATTAGCTTTTATTGGCTAATTGCTTAAAAAAGGACCTGATATTTTA
1 CTTCACAAACTTTTGAACTATTAGCTTTTATTGGCTAATTGCTCAAAAAAGGACATGATATTTTA
7574 ATTTGG
66 ATTTGG
7580 CCAAATAAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (74 bp):
CTTCACAAACTTTTGAACTATTAGCTTTTATTGGCTAATTGCTCAAAAAAGGACATGATATTTTA
ATTTGGTTC
Found at i:13639 original size:36 final size:33
Alignment explanation
Indices: 13571--13659 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 33
13561 ACCTAGCAAT
13571 AGCATGTCCTTTGAATATTTATCAAAAAAAAAAAAA
1 AGCATGTCCTTTGAA-ATTTATC--AAAAAAAAAAA
* * * *
13607 AGCATGTCCTTTGAAATTATATGAACAGAAAAAG
1 AGCATGTCCTTTGAAATT-TATCAAAAAAAAAAA
*
13641 AGCACGTCCTTTGAAATTT
1 AGCATGTCCTTTGAAATTT
13660 TGAGCCTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 25 0.53
35 3 0.06
36 18 0.38
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (33 bp):
AGCATGTCCTTTGAAATTTATCAAAAAAAAAAA
Found at i:15349 original size:27 final size:27
Alignment explanation
Indices: 15297--15349 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
15287 AACTACTAAT
* * *
15297 AAAAAAAGGTATTTCTCTTCTACCAAA
1 AAAAAAAAGTATTTCTCTACCACCAAA
*
15324 AAAAAAAAGTATTTCTCTACCGCCAA
1 AAAAAAAAGTATTTCTCTACCACCAA
15350 GCAAACCCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (27 bp):
AAAAAAAAGTATTTCTCTACCACCAAA
Found at i:16955 original size:60 final size:61
Alignment explanation
Indices: 16861--16985 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 61
16851 CATTGCAGAT
* * * *
16861 AAGTAAGGACATAACATGTTGCCATCTATGTCTCTT-ATTGTATGTTCTGTTTTGGCATGA
1 AAGTAAGGACATAACATGTTGCCATCTATATCTCTTAATTATATATTATGTTTTGGCATGA
* * *
16921 AAGTAAGGGCATAATATGTTGCCATCTATATCTCTTAATTATATATTATGTTTTGGTATGA
1 AAGTAAGGACATAACATGTTGCCATCTATATCTCTTAATTATATATTATGTTTTGGCATGA
16982 AAGT
1 AAGT
16986 TATCACATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 33 0.58
61 24 0.42
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (61 bp):
AAGTAAGGACATAACATGTTGCCATCTATATCTCTTAATTATATATTATGTTTTGGCATGA
Found at i:27324 original size:333 final size:326
Alignment explanation
Indices: 26700--27460 Score: 827
Period size: 333 Copynumber: 2.3 Consensus size: 326
26690 ATCAAAATCG
* *
26700 AATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCTTTCAATCTTTTTGG
1 AATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGA
* *
26765 CATTAAATTATATATTTTTTACGAGTATTGTGTCAAAAAATTTAAGGAAAAATTTTTCGGGTAAG
66 CATTAAATTATATATTTTTTACGAGTATTGTGGCAAAAAATTTAAGGAAAAATATTTCGGGTAAG
* * *
26830 TTTTTGCAAAATTTTAGCCGAAATTGTGTCACAGTTTTTGACTAAAAACACGCTCCGAGGTCCCG
131 TTTTTGCAAAATTTTAGCCCAAATCGTGTCACAGTTTTTAACTAAAAACACGCTCCGAGGTCCCG
*
26895 TCTCAGTTTTGCATGATTTTTGGCACCAATACTCACTGAAATATCTATATTCATCTAACGAAATC
196 TCTCAGTTTTGCATGATTTTTGGCACCAACACTCACTGAAATATCTATATTCATCTAACGAAATC
*
26960 TCAGCAACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAAATAATATTTCGATTTAATCAT
261 TCAACAACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAAATAATATTTCGATTTAATCAT
27025 A
326 A
* *
27026 AATTAATTCA-AAAAAAA-A-GAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTTA
1 AATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGA
* * * * * * *
27088 CTTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAAA-TTGAGGAAAAAATATTTCGTGTTA
66 CATTAAATTATATATTTTTTACGAGTATTGTGGCAAAAAATTTAAGG-AAAAATATTTCGGGTAA
*
27151 GTTTTTGCAAAAATTTTAGCCCAAATCGTGTACTATCCATAACGGTTTTTAAGCTAAAAACGCGC
130 GTTTTTGC-AAAATTTTAGCCCAAATCGTGT-C-A--C---A--GTTTTTAA-CTAAAAACACGC
* * * *
27216 TCTGAGG-CCTCAGT-TCCGTTTTGCATGATTTTTTGCTCCAACACTC-CTTGAAATATCTATAT
184 TCCGAGGTCC-C-GTCTCAGTTTTGCATGATTTTTGGCACCAACACTCAC-TGAAATATCTATAT
* * * * * **
27278 AT-ATCTAACTAAATCTTAACCACAATT-TATTTAAGGATTTGTTTTTACGAGCATCAG-AATCT
246 -TCATCTAACGAAATCTCAACAAC-ATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAAATAA
* * *
27340 TGTTTCGATTTTATTAGT-
309 TATTTCGATTTAATCA-TA
* * * * * * * * *
27358 AACTAATTC-G-GAAAAATAGGAAGAACGATATTAAAAGTGTGGAAAACCC-T--ATATTTTTGG
1 AATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGA
* * *
27418 CGTTAAATTTATACATTTTTTACGACTATTGTGGCAAAAAATT
66 CATTAAA-TTATATATTTTTTACGAGTATTGTGGCAAAAAATT
27461 GAGAATTTTT
Statistics
Matches: 361, Mismatches: 50, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
321 5 0.01
322 44 0.12
323 72 0.20
324 2 0.01
325 8 0.02
326 10 0.03
327 1 0.00
330 13 0.04
331 11 0.03
332 58 0.16
333 131 0.36
334 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (326 bp):
AATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGA
CATTAAATTATATATTTTTTACGAGTATTGTGGCAAAAAATTTAAGGAAAAATATTTCGGGTAAG
TTTTTGCAAAATTTTAGCCCAAATCGTGTCACAGTTTTTAACTAAAAACACGCTCCGAGGTCCCG
TCTCAGTTTTGCATGATTTTTGGCACCAACACTCACTGAAATATCTATATTCATCTAACGAAATC
TCAACAACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAAATAATATTTCGATTTAATCAT
A
Found at i:28299 original size:330 final size:331
Alignment explanation
Indices: 27561--28377 Score: 905
Period size: 330 Copynumber: 2.5 Consensus size: 331
27551 TATCTAATCG
* * * * * * * * * *
27561 ACATTAGATTTAAGGATTTGTTTATGCGAGCATCTGAATAATG-TTTCGATTTAATCAAAAATTA
1 ACATTAGATTTAAGAATTTATTTTTACAAGCATCAGAATCATGATTGCGATTTAATCAGAAACTA
* * * * ** * *
27625 ATTCAGAAAAAAATATGAAAGACACTATTAGAAATGTGAAAAGCCCTTCAATCTTGTTGGCATTA
66 AATCAG-AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTG
* * * *
27690 AATTATATATTTTTTACGAGTATTTTTCCTCAAAAAGTTGAGGAAAAATTTTTTGGGTCAGTTTT
130 AATTATATATTTTTTACGAGTATTTTTCCTCAAAAAATTAAGAAAAAATTTTTCGGGTCAGTTTT
* *
27755 TGCAACATTTTAGCTGAAACCGTATACTAATCATCACGGTTTTTGCTAAAAACGCATTCCAGGCC
195 TGCAACATTTTAGCCGAAACCGTATAC-AACCATCACGGTTTTTGCTAAAAACGCATTCCAGGCC
* * * *
27820 CCGACTCAGTTTTACATTATTTTTGGCGCCAAACTCATTGAAATGTCTACATTCATCTAACCAAA
259 CAGACTCACTTTTACATGATTTTTGGCGCCAAACTCATTGAAATGTCTACATCCATCTAACCAAA
27885 TCTCAGCC
324 TCTCAGCC
* * ** **** *
27893 ACATTAGATTTAAGAATTTGTTTTTACGAGCATTTGAATCATGATTTTTCTTTAATCAGAAATTA
1 ACATTAGATTTAAGAATTTATTTTTACAAGCATCAGAATCATGATTGCGATTTAATCAGAAACTA
* * *
27958 AATCAGAAAAAA-A-GAAAAACAATATTAGAAGCTTGAAAATCCCTTCAATCTTTTTGGCGTTGA
66 AATCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGA
*
28021 ATTATATATTTTTTACGAGAATTTTTCCTCAAAAAATTAAGAAAAAATTTTTCGGGTCAGTTTTT
131 ATTATATATTTTTTACGAGTATTTTTCCTCAAAAAATTAAGAAAAAATTTTTCGGGTCAGTTTTT
* * *
28086 GCATA-ATTTTAGCCGAAATCGTGTAC-ACCATCACGGTTTTTTGGCTAAAAACGCATTCCGGGT
196 GCA-ACATTTTAGCCGAAACCGTATACAACCATCACGG-TTTTT-GCTAAAAACGCATTCCAGG-
* * * * * * *
28149 GCTAGA-TCACTTTTGCATGATTTTTTGCTCCAACACTCATTGAAATGTCTATATCCATCTAACT
257 CCCAGACTCACTTTTACATGATTTTTGGCGCCAA-ACTCATTGAAATGTCTACATCCATCTAACC
*
28213 AAATCTTAGCC
321 AAATCTCAGCC
* * * * **
28224 ACAATT-TATTTAAGGATTTATTTTTACAAGCATCAGAATCTTG-TTGCGATTTTATTGGAAACT
1 AC-ATTAGATTTAAGAATTTATTTTTACAAGCATCAGAATCATGATTGCGATTTAATCAGAAACT
* * ** * *
28287 AATTCGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCCTTTTAAT-TTTATTGGCATT
65 AAATCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTT-TTGGCATT
*
28351 GAATTATATATTTTTTATGAGTATTTT
129 GAATTATATATTTTTTACGAGTATTTT
28378 CATATTTTGT
Statistics
Matches: 408, Mismatches: 67, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
328 9 0.02
329 5 0.01
330 185 0.45
331 78 0.19
332 109 0.27
333 22 0.05
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (331 bp):
ACATTAGATTTAAGAATTTATTTTTACAAGCATCAGAATCATGATTGCGATTTAATCAGAAACTA
AATCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGA
ATTATATATTTTTTACGAGTATTTTTCCTCAAAAAATTAAGAAAAAATTTTTCGGGTCAGTTTTT
GCAACATTTTAGCCGAAACCGTATACAACCATCACGGTTTTTGCTAAAAACGCATTCCAGGCCCA
GACTCACTTTTACATGATTTTTGGCGCCAAACTCATTGAAATGTCTACATCCATCTAACCAAATC
TCAGCC
Found at i:29060 original size:35 final size:35
Alignment explanation
Indices: 29021--29101 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
29011 AAGTTGAGGA
29021 AAAATTTTTCGAGTTAGTTTTTGAAAAATTTTAGC
1 AAAATTTTTCGAGTTAGTTTTTGAAAAATTTTAGC
29056 AAAATTTTTCGAGTTAGTTTTTGAAAAATTTTAGC
1 AAAATTTTTCGAGTTAGTTTTTGAAAAATTTTAGC
29091 AAAATTTTTCG
1 AAAATTTTTCG
29102 GGCCTTCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.46
Consensus pattern (35 bp):
AAAATTTTTCGAGTTAGTTTTTGAAAAATTTTAGC
Found at i:32121 original size:317 final size:317
Alignment explanation
Indices: 30758--32326 Score: 1401
Period size: 317 Copynumber: 5.0 Consensus size: 317
30748 TTCGCGCTTC
* * *
30758 GAAGCGTGAAAAGCCCTTCAACATTCTTGG-AGTTGAATTATATATTTTTTATGAGTATTGTAG-
1 GAAGCGTGAAAAGCCTTTCAATATTTTTGGCA-TTGAATTATATATTTTTT-TGAGTATTGT-GT
* * * * *
30821 CCAAAAATTAAGGAAAAATCTTTCTA-GTCA-TTTTTCGCAAAATTTTAGTCGAATTTGTGTACT
63 CAAAAAATTGAGGAAAAATTTTTC-AGGTCAGTTTTT-GCAAAATTTTAGCCGAATTCGTGTACT
** * * ** ** *
30884 ATTCAT-ATCACTGTTTTTGGCTAAAAACGTGTCTCGGGGCCCCGACTCAGTTTTGCATGATTTT
126 AACCATCA-CA-T-TTTTTTGCTAAAAACGCGT-TCCAGGCCCCGGTTCAGTCTTGCATGATTTT
* * * * * *
30948 TTGCGCCAAGACTCCTTGAATTATCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAG
187 TGGCACCAAAACT-CTTGAAATATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTTAAG
** * *
31013 GATTTGTGTTTACGAGCATCAGAAA-CTTGTTTCGATTTTATTGGAAATTAGTTCAAAAAA-ATA
251 GATTTGTGTTTACGAGCATCA-AAATCTTGTTTCGATTTTATTAAAAATTAATTAAAAAAAGATA
**
31076 -GG
315 TTA
** * * *
31078 GAA-AATGATAAAGCCTTTCACTATTTTTGGTATTGAATTATATATTTTTTTACGAGTATTTTGT
1 GAAGCGTGA-AAAGCCTTTCAATATTTTTGGCATTGAATTATATATTTTTTT--GAGTATTGTGT
* * *
31142 CAAAAAAAAATTGGGGGAAAATTTTTCGGGTCAGTTTTTTTGCAAAATTTTA---G----C-TG-
63 C---AAAAAATTGAGGAAAAATTTTTCAGGTCAG--TTTTTGCAAAATTTTAGCCGAATTCGTGT
* * * * *
31198 A--AATCATCACAGTTTTTTGCTAAAAACGCGTTCCAGGCCCCGACTT-AGT-TTTCATGATTTG
123 ACTAACCATCACATTTTTTTGCTAAAAACGCGTTCCAGGCCCCG-GTTCAGTCTTGCATGATTTT
* *
31259 TGGCGCCAAGACTCATTGAAATATCTATATTC---T-AAC----CTTAGCCACATTGGATTT---
187 TGGCACCAAAACTC-TTGAAATATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTTAAG
* ** * *
31313 G---T-T-TTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTAAAAAAAAGA
251 GATTTGTGTTTACGAGCATCAAAATCTTGTTTCGATTTTATTAAAAATTAA-T-T-AAAAAAAG-
31373 AAAACAATATTA
312 ------ATATTA
* * * * * * *
31385 GAAGCGTAAAAAGCCCTTCAATGTTTTTGGCGTTGAATAATATATTTTTTGTGAGTATTGTGGCC
1 GAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTGAATTATATATTTTTT-TGAGTATTGTGTCA
* * * * * * *
31450 AAAAATTAAGGAAAAATCTTTCTGGTCAATTTTCGCAAAAATTTTAGTCGAATTCGTGTACTATC
65 AAAAATTGAGGAAAAATTTTTCAGGTCAGTTTTTGC-AAAATTTTAGCCGAATTCGTGTACTAAC
* * * * * *
31515 CATCACGGTTTTTTGGCTAAAAA-TC-TGTCTCAGGGCCCCAGCTCAGTCTTACATGATTTTTGG
129 CATCAC-ATTTTTTTGCTAAAAACGCGT-TC-CA-GGCCCCGGTTCAGTCTTGCATGATTTTTGG
* * *
31578 CACCAAGACTCCTTGAAATATCTATAATCATTTAAACAAATCTTTGCCACATTGGATTTAAGGAT
190 CACCAAAACT-CTTGAAATATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTTAAGGAT
* * * ** * *
31643 TTGTGTGTACGAGCATCAGAATCTTGTTTCGATTTTATT-AAATTTTTTTTAAAAAAGATACTA
254 TTGTGTTTACGAGCATCAAAATCTTGTTTCGATTTTATTAAAAATTAATTAAAAAAAGATATTA
* *
31706 GAAGCGTGGAAAG-CTTTCCAATATTTTTGGCATTGAATTATATATTTTTTCGAGTATTGTGTCA
1 GAAGCGTGAAAAGCCTTT-CAATATTTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGTCA
* * *
31770 AAAAATTGAGGAAAAATTTTTCAAGTCCGTTTTTGCAAAATTTTTGCCGAATTCGTGTACTAACC
65 AAAAATTGAGGAAAAATTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAATTCGTGTACTAACC
* * * * ** * * *
31835 ATCA-TTTTTTTTGCTAAAAACGGGTTCCTGACATCGGTTCTGTCTTGCATGATTTTTTGCTCCA
130 ATCACATTTTTTTGCTAAAAACGCGTTCCAGGCCCCGGTTCAGTCTTGCATGATTTTTGGCACCA
* *
31899 AAACTGCTTGAATTATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTGAAGGATTTGTG
195 AAACT-CTTGAAATATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTTAAGGATTTGTG
* *
31964 TTTACAAGCAACAAAATCTTGTTTCGATTTTATTAAAAATTAATTAAAAAAAGATATTA
259 TTTACGAGCATCAAAATCTTGTTTCGATTTTATTAAAAATTAATTAAAAAAAGATATTA
*
32023 GAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGTCAA
1 GAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGTCAA
* * *
32088 AAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCA
66 AAAATTGAGGAAAAATTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAATTCGTGTACTAACCA
* * * * * * *
32153 TCACAATTTTTTGTTTAAAACGCGTTCCAGGCCCCGCCTT-AGTTTTGCATGACTTTTGGCGCCA
131 TCACATTTTTTTGCTAAAAACGCGTTCCAGGCCCCG-GTTCAGTCTTGCATGATTTTTGGCACCA
* *
32217 AAACTCATTGAAATATCTAATATT-ATTCAAACCAAATCTTAGCCACATTGGATTTAAAGATTTG
195 AAACTC-TTGAAATATCT-ATATTCATTTAAA-CAAATCTTAGCCACATTGGATTTAAGGATTTG
* * * *
32281 TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAAT
257 TGTTTACGAGCATCAAAATCTTGTTTCGATTTTATTAAAAATTAAT
32327 ACAGAAAAAA
Statistics
Matches: 1013, Mismatches: 161, Indels: 151
0.76 0.12 0.11
Matches are distributed among these distances:
294 2 0.00
295 34 0.03
296 2 0.00
297 2 0.00
298 6 0.01
300 1 0.00
301 6 0.01
302 9 0.01
303 41 0.04
305 1 0.00
306 13 0.01
307 40 0.04
308 4 0.00
309 1 0.00
310 3 0.00
311 39 0.04
312 13 0.01
313 28 0.03
314 16 0.02
315 16 0.02
316 154 0.15
317 156 0.15
318 71 0.07
319 113 0.11
320 85 0.08
321 55 0.05
323 1 0.00
324 39 0.04
326 11 0.01
327 6 0.01
328 7 0.01
329 1 0.00
330 2 0.00
331 5 0.00
332 30 0.03
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (317 bp):
GAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGTCAA
AAAATTGAGGAAAAATTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAATTCGTGTACTAACCA
TCACATTTTTTTGCTAAAAACGCGTTCCAGGCCCCGGTTCAGTCTTGCATGATTTTTGGCACCAA
AACTCTTGAAATATCTATATTCATTTAAACAAATCTTAGCCACATTGGATTTAAGGATTTGTGTT
TACGAGCATCAAAATCTTGTTTCGATTTTATTAAAAATTAATTAAAAAAAGATATTA
Found at i:35227 original size:33 final size:34
Alignment explanation
Indices: 35190--35265 Score: 82
Period size: 38 Copynumber: 2.1 Consensus size: 34
35180 TGGATTTAAG
*
35190 GATTTGTG-TTTACGAACATCGAAATCTTGTTTT
1 GATTTGTGATTTACGAACATCCAAATCTTGTTTT
* *
35223 GATTTTATTTGATTTTACGAGCATCCAAATCTTGTTTT
1 GA--TT-TGTGA-TTTACGAACATCCAAATCTTGTTTT
35261 GATTT
1 GATTT
35266 AATTAGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
33 2 0.06
35 3 0.09
36 5 0.14
38 25 0.71
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (34 bp):
GATTTGTGATTTACGAACATCCAAATCTTGTTTT
Found at i:39069 original size:338 final size:332
Alignment explanation
Indices: 37605--39918 Score: 2907
Period size: 329 Copynumber: 7.0 Consensus size: 332
37595 CCTCTTCATT
* * * *
37605 AATGTTTTTGGCGTTGAATAATATATTTTTT-TGTGAGAATTGTGGCCAAAAATTAAAGAAAAAT
1 AATGTTTTTGGCATTGAATTATATATTTTTTAT-T-AGTATTGTGGCCAAAAATTAAGGAAAAAT
* * * *
37669 CTTCCTGGTCAATTTTCGCTAAAATTTTAGTCGAATTTGTGTACTATCCATTACGGTTTTTTGCT
64 CTTTCTGGTCAATTTTCGC-AAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCT
* * ** *
37734 AAAAACGTGTCTCGGAGTCCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCTTG-AATA
128 AAAAACGTGTTTCGG-GCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATA
* * *
37798 TCTATATTCATCTAAA-CAAATCTTAGCCACATTGGATTTAAGGATTTATGTTTACGAGCATCAG
192 TCTATATTCATC-AAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
* * * * *
37862 AATCTTTTTTCGATTTTGTTAGAAATTAATTC-AAAAAAAT-TGGAAAAACGATATTAGAAGTGT
256 AATCTTGTTTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGT
* *
37925 GGAAAGCCTTTC
321 GAAAAGCCCTTC
* ** * * * *
37937 AATATTTTTGGCATTGAATTATATATTTTTT-CGAGTATTGTGTCAAAAAATTGAGG-AAAATTT
1 AATGTTTTTGGCATTGAATTATATATTTTTTATTAGTATTGTGGCCAAAAATTAAGGAAAAATCT
* * * * * * * *
38000 TTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACCGTTTTTTGCTAAA
66 TTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAAA
** * * ** * * *
38065 AACGCATTCCGGGCGCCGGCTCAGTTTGGCATGATTTTTGGCGACAAGACTCAATGAAATATCTT
131 AACGTGTTTCGGGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATATCTA
* * *
38130 TATTCATCTAACCAAATCTTACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGGATCT
196 TATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* *
38195 TGTTTCGATTTAATTAGAAATTAATTCAAAGAAAATATG-AAAAACAATATTAGAAGCGTGAAAA
261 TGTTTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGTGAAAA
38259 GCCCTTC
326 GCCCTTC
* * * ** **
38266 AATATTTTTGGCGTTAAATTATATATTTTTTATTAGTAATT-TTTCCAAGGATTAA-GAAAAATC
1 AATGTTTTTGGCATTGAATTATATATTTTTTATTAGT-ATTGTGGCCAAAAATTAAGGAAAAATC
*
38329 -TTCTGGTCAATTTTCACAAAATTTTAGTCGAATTCGTGTACTATCCATCACGG-TTTTGGCTAA
65 TTTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAA
*
38392 AAACGTGTTTCGGGGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAAACTCATTGAAATATC
130 AAACGTGTTTC-GGGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATATC
*
38457 TATATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAAT
194 TATATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * *
38522 CTTGTTTCGATTTTATTAGTAATTAATTCAAAAAAAATATGTAAAAACAATATTATAAGCGTTAA
259 CTTGTTTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGTGAA
38587 AAGCCCTTC
324 AAGCCCTTC
* *
38596 AATGTTTTTGG-AGTTGAATTACATATTTTTTATGAGTATTGTGGCCAAAAATTAAGGAAAAATC
1 AATGTTTTTGGCA-TTGAATTATATATTTTTTATTAGTATTGTGGCCAAAAATTAAGGAAAAATC
38660 TTTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAA
65 TTTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAA
* *
38725 AAACGTGTTTCGAGGCCCCGGCTCAGTTTAACATGATTTTTGGCACCAAGACTCATTGATATATC
130 AAACGTGTTTCG-GGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATATC
* *
38790 TATATTCATCAAACCAAATCTTAACCACATTGGATTTAATGATTTGTTTTTACGAGCATCTGAAT
194 TATATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
38855 CTTATTTCGATTTTATTAAAAATTAATTCAAAAAGAAATATGAAAAAAAAAACAATATTAGAAGC
259 CTTGTTTCGATTTTATTAGAAATTAATTCAAAAA-AAATATG----AAAAAACAATATTAGAAGC
38920 GTGAAAAGCCCTTC
319 GTGAAAAGCCCTTC
* * *
38934 AATGTTTTTGGCATTGAATTACATATTTTTTATTAGTATTGTGACAAAAAATTAAGGAAAAATCT
1 AATGTTTTTGGCATTGAATTATATATTTTTTATTAGTATTGTGGCCAAAAATTAAGGAAAAATCT
* * *
38999 TTTTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCAATCATGGTTTTTGGCTAAA
66 TTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAAA
* * ** ** * * *
39064 AACGTGTCTCAGGGCCCCGACTCTTTTTTTCATGATTTTTGCCGCCAAGACTCCTTAAAATATCT
131 AACGTGTTTC-GGGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATATCT
* * * *
39129 ATATTCATCTAAA-CAAATCTTAGCCACATTGGATTTAAGGATTTATGTTTACGAGCTTCAGAAT
195 ATATTCATC-AAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * *
39193 CTTGTTTCGATTTTGTTAGAAATTAATTCAAAAAAATTA-G-AAAAACGATATTAGAAGCGTGGA
259 CTTGTTTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGTGAA
* *
39256 AAGACTTTC
324 AAGCCCTTC
* * * *
39265 AATCTTTTTGGCATTGAATTTTGATATTTTTTA-TAGTATTGT-GTCAAAAAATAGAGGAAAAAT
1 AATGTTTTTGGCATTGAATTAT-ATATTTTTTATTAGTATTGTGGCCAAAAATTA-AGGAAAAAT
* * * * * *** *
39328 TTTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTTAGTTTTTTGCT
64 CTTTCTG-GTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCT
* * * *
39392 AAAAACGCGTTCCGGGCGCCGGCTCAGTTTTAA-ATCATTTTTGGCGCCAAGACTCATTGAAATA
128 AAAAACGTGTTTCGGGCCCCGGCTCAG-TTTAACATGATTTTTGGCGCCAAGACTCATTGAAATA
* * *
39456 TATATATTCATCAAAACAAATATTAGCCACATTGGATTTAAGGATTT-TTTTTACGAGCATCTGA
192 TCTATATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
* * *
39520 ATCTTGTTTCGATTTAATTAGAAATTATTTCATAACAAAAATATTAAAAAACAATATTAGAAGCG
257 ATCTTGTTTCGATTTTATTAGAAATTAATTCA-AA-AAAAATATGAAAAAACAATATTAGAAGCG
*
39585 TGAAAAGCACTTC
320 TGAAAAGCCCTTC
* * * * *
39598 GATGTGTTTGGCGTTGAA-TAGTATATTTTTTGTGAGTATTGTGGCCAAAAATTAAGGAAAAATC
1 AATGTTTTTGGCATTGAATTA-TATATTTTTTATTAGTATTGTGGCCAAAAATTAAGGAAAAATC
* * *
39662 TTTCTGGTCAATTTTCGCAAAAATTTTAGTCGAATTTGTGTACTATCCATCTCAGTTTTTGGCTA
65 TTTCTGGTCAATTTTCGC-AAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTA
* * * ** *
39727 AAAACGTATCTCGTGGCCCCGGCTCAATTTTGCATGATTTTTTGCGCCAAGACTTC-TTGAAATA
129 AAAACGTGTTTCG-GGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGAC-TCATTGAAATA
* * *
39791 TCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTGTTTACGAGCATCAGA
192 TCTATATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
* * * *
39856 ATCTTGTATT-TATTTTATTAGAAATTAATTC-AAAAAAATA-GGAAAAACGATTTTAGAAGCGT
257 ATCTTGT-TTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGT
39918 G
321 G
39919 GAAGCCTTTC
Statistics
Matches: 1717, Mismatches: 223, Indels: 84
0.85 0.11 0.04
Matches are distributed among these distances:
327 39 0.02
328 154 0.09
329 323 0.19
330 196 0.11
331 147 0.09
332 120 0.07
333 244 0.14
334 71 0.04
335 80 0.05
336 43 0.03
337 6 0.00
338 289 0.17
339 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (332 bp):
AATGTTTTTGGCATTGAATTATATATTTTTTATTAGTATTGTGGCCAAAAATTAAGGAAAAATCT
TTCTGGTCAATTTTCGCAAAATTTTAGTCGAATTCGTGTACTATCCATCACGGTTTTTGGCTAAA
AACGTGTTTCGGGCCCCGGCTCAGTTTAACATGATTTTTGGCGCCAAGACTCATTGAAATATCTA
TATTCATCAAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
TGTTTCGATTTTATTAGAAATTAATTCAAAAAAAATATGAAAAAACAATATTAGAAGCGTGAAAA
GCCCTTC
Found at i:48242 original size:18 final size:19
Alignment explanation
Indices: 48214--48259 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
48204 TTCTCATCTA
*
48214 CTTTTTCTTTTCTTTT-TTT
1 CTTTTT-TTTTCTTTTACTT
48233 CTTTTTTTTTCTTTTACTT
1 CTTTTTTTTTCTTTTACTT
48252 CTTTTTTT
1 CTTTTTTT
48260 GTCTGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTTCTTTTACTT
Found at i:49110 original size:1 final size:1
Alignment explanation
Indices: 49104--49152 Score: 98
Period size: 1 Copynumber: 49.0 Consensus size: 1
49094 GAATGAGAAG
49104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
49153 GAACTACTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50805 original size:24 final size:24
Alignment explanation
Indices: 50761--50806 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
50751 GGGAAAAGTT
*
50761 AATCCTTGGAATTCATTCTTGTAA
1 AATCCTTGGAATTCATACTTGTAA
*
50785 AATCCTT-GATTTGCATACTTGT
1 AATCCTTGGAATT-CATACTTGT
50807 GGAATGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (24 bp):
AATCCTTGGAATTCATACTTGTAA
Found at i:55520 original size:105 final size:99
Alignment explanation
Indices: 55316--55568 Score: 336
Period size: 105 Copynumber: 2.5 Consensus size: 99
55306 AGTTTAGCTT
55316 TAATTTCACTAAGTTTAGTCCCAAATT--AATTTA-TTTTATTTTAAGGGTACAAAATTAATAAT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTATTTTTATTTTAAGGGTACAAAATTAATAA-
55378 TTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
64 TTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
*
55414 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAA-TTTATTTTTATTTTAAGGGT--A---CAAAATT
* * *
55479 AATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
59 AATAATTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
*
55519 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAATATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTAT-TTTTATTTTAAGGGT
55569 TAGAAAAATT
Statistics
Matches: 139, Mismatches: 6, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
98 26 0.19
100 2 0.01
101 4 0.03
102 19 0.14
103 27 0.19
104 15 0.11
105 35 0.25
107 11 0.08
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (99 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTATTTTTATTTTAAGGGTACAAAATTAATAATT
ATTATTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:62308 original size:33 final size:33
Alignment explanation
Indices: 62268--62363 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
62258 CTGGCTCTAC
* *
62268 AGCCACTTCTGACATCTTTTCATCTGCTTCTGA
1 AGCCACTTCTGAAATCTTTTCATCTGCCTCTGA
* * * *
62301 AGTCACTTCTGAGACCTTTTCATCAGCCTCTGA
1 AGCCACTTCTGAAATCTTTTCATCTGCCTCTGA
* *
62334 AGCCAGTTCTGAAATCTTTTCATCTTCCTC
1 AGCCACTTCTGAAATCTTTTCATCTGCCTC
62364 GAAAGCTACT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (33 bp):
AGCCACTTCTGAAATCTTTTCATCTGCCTCTGA
Found at i:83504 original size:5 final size:5
Alignment explanation
Indices: 83494--83520 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
83484 AAACAAGGGC
83494 AACAA AACAA AACAA AACAA AACAA AA
1 AACAA AACAA AACAA AACAA AACAA AA
83521 ACAAGATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:90908 original size:19 final size:19
Alignment explanation
Indices: 90884--90945 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
90874 AATAAATTGC
90884 AAAATTCCACACAATCAGA
1 AAAATTCCACACAATCAGA
** * * *
90903 AAAATTGGTA-AGAATTA-C
1 AAAATT-CCACACAATCAGA
90921 AAAATTCCACACAATCAGA
1 AAAATTCCACACAATCAGA
90940 AAAATT
1 AAAATT
90946 GCTAAGAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
17 1 0.03
18 11 0.37
19 17 0.57
20 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.21
Consensus pattern (19 bp):
AAAATTCCACACAATCAGA
Found at i:90924 original size:37 final size:37
Alignment explanation
Indices: 90878--90955 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
90868 CCATATAATA
* *
90878 AATTGCAAAATTCCACACAATCAGAAAAATTGGTAAG
1 AATTACAAAATTCCACACAATCAGAAAAATTGCTAAG
90915 AATTACAAAATTCCACACAATCAGAAAAATTGCTAAG
1 AATTACAAAATTCCACACAATCAGAAAAATTGCTAAG
90952 AATT
1 AATT
90956 TTGTCCCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (37 bp):
AATTACAAAATTCCACACAATCAGAAAAATTGCTAAG
Found at i:95522 original size:14 final size:14
Alignment explanation
Indices: 95503--95530 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95493 TTTTGAATGC
95503 AATTAGTCATATTT
1 AATTAGTCATATTT
95517 AATTAGTCATATTT
1 AATTAGTCATATTT
95531 GGCTACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
AATTAGTCATATTT
Found at i:107072 original size:17 final size:17
Alignment explanation
Indices: 107050--107083 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
107040 TTGGAGCAAC
107050 TAAATTCAAAAGTTTCA
1 TAAATTCAAAAGTTTCA
*
107067 TAAATTCAGAAGTTTCA
1 TAAATTCAAAAGTTTCA
107084 GTTTACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAATTCAAAAGTTTCA
Found at i:113581 original size:15 final size:12
Alignment explanation
Indices: 113548--113572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113538 TAATTCTTTC
113548 ATTTTTAATATG
1 ATTTTTAATATG
113560 ATTTTTAATATG
1 ATTTTTAATATG
113572 A
1 A
113573 CTATTTTTAT
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTTTTAATATG
Found at i:129800 original size:29 final size:28
Alignment explanation
Indices: 129735--129801 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
129725 TGAACATTCA
129735 CAATTTGGACGTTTTGTCCTCTAAACTC
1 CAATTTGGACGTTTTGTCCTCTAAACTC
* *
129763 TAATGTTGGACGTTTTG-CCTTCTGAACTC
1 CAAT-TTGGACGTTTTGTCC-TCTAAACTC
129792 GCAATTTGGA
1 -CAATTTGGA
129802 GTCACGTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 5 0.15
29 25 0.76
30 3 0.09
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (28 bp):
CAATTTGGACGTTTTGTCCTCTAAACTC
Found at i:131547 original size:3 final size:3
Alignment explanation
Indices: 131541--131566 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
131531 CTAAAAAAAA
131541 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
131567 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:136841 original size:29 final size:29
Alignment explanation
Indices: 136796--136866 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
136786 CCAAAATCCT
*
136796 CAAATAAGGATCC-GATCTTTTAATTTGGC
1 CAAATAA-GAGCCTGATCTTTTAATTTGGC
*
136825 TAAATAAGAGCCTGATCTTTTAATTTGGC
1 CAAATAAGAGCCTGATCTTTTAATTTGGC
*
136854 CAAATAAGGGCCT
1 CAAATAAGAGCCT
136867 AAAATTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 4 0.11
29 33 0.89
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (29 bp):
CAAATAAGAGCCTGATCTTTTAATTTGGC
Found at i:137014 original size:60 final size:60
Alignment explanation
Indices: 136942--137100 Score: 207
Period size: 60 Copynumber: 2.6 Consensus size: 60
136932 CGACAAACCT
* *
136942 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGTCCAAATTAAAAGATC-GGACCC
1 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAG-CCC
* * *
137002 TTATTTGAGCATTTTTGATAATGTTAGGCCCTTATTTGACTAAATTAAAAGATCAAGCCC
1 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAGCCC
* *
137062 TTATTTGAACATTTTAAC-AT-ACATTAGGCCCTTATTTGA
1 TTATTTGAGCATTTT--CGATAACGTTAGGCCCTTATTTGA
137101 TCAATTAGGC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
60 84 0.97
61 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAGCCC
Found at i:137037 original size:31 final size:31
Alignment explanation
Indices: 136942--137040 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
136932 CGACAAACCT
* *
136942 TTATTTGAGCATTTTCGATAACGTTAGGCCC
1 TTATTTGAGCATTTTTGATAAAGTTAGGCCC
** ** * *
136973 TTATTTGTCCA-AATT-A-AAAGATCGGACCC
1 TTATTTGAGCATTTTTGATAAAGTTAGG-CCC
*
137002 TTATTTGAGCATTTTTGATAATGTTAGGCCC
1 TTATTTGAGCATTTTTGATAAAGTTAGGCCC
137033 TTATTTGA
1 TTATTTGA
137041 CTAAATTAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 6 0.12
29 13 0.27
30 3 0.06
31 21 0.43
32 6 0.12
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (31 bp):
TTATTTGAGCATTTTTGATAAAGTTAGGCCC
Found at i:139893 original size:17 final size:17
Alignment explanation
Indices: 139871--139959 Score: 144
Period size: 17 Copynumber: 5.2 Consensus size: 17
139861 ATCACCCTCC
139871 AGATCACCAGTGATCTA
1 AGATCACCAGTGATCTA
*
139888 AGATCATCAGTGATCTA
1 AGATCACCAGTGATCTA
139905 AGATCACCAGTGATCTA
1 AGATCACCAGTGATCTA
139922 AGATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CTA
*
139939 AGATCACCAGTGATCAA
1 AGATCACCAGTGATCTA
139956 AGAT
1 AGAT
139960 TACATGGGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
16 1 0.01
17 66 0.97
18 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:141290 original size:2 final size:2
Alignment explanation
Indices: 141283--141312 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141273 AAATTTGGAC
141283 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
141313 GCTAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141498 original size:19 final size:20
Alignment explanation
Indices: 141462--141499 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
141452 GACCCACCCA
* *
141462 AAAAATGTAAAGGGAGAAAT
1 AAAAATGGAAAGGAAGAAAT
141482 AAAAATGGAAA-GAAGAAA
1 AAAAATGGAAAGGAAGAAA
141500 AAATAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.11
Consensus pattern (20 bp):
AAAAATGGAAAGGAAGAAAT
Found at i:148555 original size:6 final size:6
Alignment explanation
Indices: 148542--148571 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
148532 TTTTGTTTTG
148542 TTTT-T TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
148572 ACTACTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTAT
Done.