Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013785.1 Corchorus olitorius cultivar O-4 contig13818, 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: 65497
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:220 original size:27 final size:26
Alignment explanation
Indices: 189--263 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
179 AAGTGAACCT
189 AAAATGACCAAAATGCCCCTGAAAATGC
1 AAAATGACCAAAATGCCCCTG--AATGC
217 -AAATGACCAAAATGCCCCTGAATGC
1 AAAATGACCAAAATGCCCCTGAATGC
242 AAAAATGACTCAAAATGCCCCT
1 -AAAATGAC-CAAAATGCCCCT
264 AGATGACCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.11
27 27 0.61
28 12 0.27
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGAATGC
Found at i:2441 original size:19 final size:18
Alignment explanation
Indices: 2408--2443 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2398 TTTAAATAAT
2408 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
2426 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
2444 TTAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:12200 original size:19 final size:18
Alignment explanation
Indices: 12167--12202 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12157 TTGAAATAAT
12167 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
12185 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
12203 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:12210 original size:11 final size:10
Alignment explanation
Indices: 12167--12213 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
12157 TTGAAATAAT
12167 TCTTCAATGA
1 TCTTCAATGA
12177 TCTTCAA--A
1 TCTTCAATGA
*
12185 TCTTCAAATTA
1 TCTTC-AATGA
12196 TCTTCAATGA
1 TCTTCAATGA
12206 GTCTTCAA
1 -TCTTCAA
12214 ACACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:13355 original size:20 final size:21
Alignment explanation
Indices: 13316--13355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13306 TTGAGTTGAT
*
13316 TTTGAGTATAAAGGTGAAATC
1 TTTGAGTATAAAGCTGAAATC
*
13337 TTTGAGT-TAAAGCTTAAAT
1 TTTGAGTATAAAGCTGAAAT
13356 TTTTAGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (21 bp):
TTTGAGTATAAAGCTGAAATC
Found at i:14410 original size:14 final size:16
Alignment explanation
Indices: 14386--14418 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
14376 AAGAGGTAAT
14386 AAAAGGTTTTTTC-CA
1 AAAAGGTTTTTTCTCA
14401 AAAAGG-TTTTTCTCA
1 AAAAGGTTTTTTCTCA
14416 AAA
1 AAA
14419 CCATGTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
AAAAGGTTTTTTCTCA
Found at i:18669 original size:15 final size:16
Alignment explanation
Indices: 18636--18669 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18626 TTACTTTGCT
18636 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
18652 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
18667 TTG
1 TTG
18670 CATTCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:19128 original size:26 final size:25
Alignment explanation
Indices: 19069--19131 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
19059 TTGCGTTTTT
*
19069 GAAAAAAAAAAGTGTTTTTGCGTTA
1 GAAAAAAAAAAGTGTTTTTGCGTCA
*
19094 TATAAAAAAAAAGT-TTTTCTGCGTCA
1 GA-AAAAAAAAAGTGTTTT-TGCGTCA
19120 GAAATAAAAAAA
1 GAAA-AAAAAAA
19132 AATTTTCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 7 0.22
26 25 0.78
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (25 bp):
GAAAAAAAAAAGTGTTTTTGCGTCA
Found at i:21555 original size:16 final size:16
Alignment explanation
Indices: 21534--21564 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21524 TTTCTTTGCA
21534 TGCTTTGATTGATTGT
1 TGCTTTGATTGATTGT
21550 TGCTTTGATTGATTG
1 TGCTTTGATTGATTG
21565 CCTATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.26, T:0.55
Consensus pattern (16 bp):
TGCTTTGATTGATTGT
Found at i:24710 original size:15 final size:16
Alignment explanation
Indices: 24677--24716 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
24667 TTACTTTGCT
24677 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
24693 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
24708 TTGCTTTCT
1 TTGTTTTCT
24717 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:25715 original size:303 final size:303
Alignment explanation
Indices: 25163--25749 Score: 856
Period size: 303 Copynumber: 1.9 Consensus size: 303
25153 TGCTTCTCAA
* ***
25163 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTAAGGCACAGGTGTTCCACGTTTGAATACTCTTCTT
* * *
25228 TGCAATTGCTGACTCGCTTAAGTTTTTATATATAAGGTCTTCAAGAGTCTTCTTAACAAATGCAT
66 CGCAACTGCTGACTCGCTTAAGTCTTTATATATAAGGTCTTCAAGAGTCTTCTTAACAAATGCAT
* * * * * *
25293 GATGACAAAGTTTACCCAATACCTTGAGTTCACCACAACATTTCTTAGTGACAGCTCCCGTTTTG
131 GATGACAAACTTTACCCAAGACCATGAGTTCACCACAACACTTCTTAGTGACAGCTCCCGTATAG
* * * ** ** *
25358 AATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTGCAATTGTTTTCCTT
196 AATATACTTGTGAAAACCTCCCTGGAACAGGCCAGGCCCATTTTTGCCTTGCAATTATTTTCCTT
25423 AAT-AATGAAGTCGGGGTTTTCTGCTGGTGAAATGATTTCGCTT
261 AATAAAT-AAGTCGGGGTTTTCTGCTGGTGAAATGATTTCGCTT
* *
25466 GCAGAAGAAGATGGTGAAATGTCGATGACTAAGGCACATGTGTTCCATGTTTGAATACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTAAGGCACAGGTGTTCCACGTTTGAATACTCTTCTT
*
25531 CGCAACTGTTGACTCGCTTAAGTCTTTATATA-AAGGATCTTCAAGAGTCTTCTTAACAAATGCA
66 CGCAACTGCTGACTCGCTTAAGTCTTTATATATAAGG-TCTTCAAGAGTCTTCTTAACAAATGCA
* * *
25595 TCG-TGACAAACTTTACCGAAGACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTAT
130 T-GATGACAAACTTTACCCAAGACCATGAGTTCACCACAACACTTCTTAGTGACAGCTCCCGTAT
**
25659 AGAATATACTTGTGAAAACCTCCCTGGAACAGGCCAGGCCCATTTTTGCCTTGCAATTATTTTGG
194 AGAATATACTTGTGAAAACCTCCCTGGAACAGGCCAGGCCCATTTTTGCCTTGCAATTATTTTCC
*
25724 TTAATAAATAAGTCTGGGTTTTCTGC
259 TTAATAAATAAGTCGGGGTTTTCTGC
25750 AGCTGAAACG
Statistics
Matches: 251, Mismatches: 30, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
302 4 0.02
303 243 0.97
304 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATGTCGATGACTAAGGCACAGGTGTTCCACGTTTGAATACTCTTCTT
CGCAACTGCTGACTCGCTTAAGTCTTTATATATAAGGTCTTCAAGAGTCTTCTTAACAAATGCAT
GATGACAAACTTTACCCAAGACCATGAGTTCACCACAACACTTCTTAGTGACAGCTCCCGTATAG
AATATACTTGTGAAAACCTCCCTGGAACAGGCCAGGCCCATTTTTGCCTTGCAATTATTTTCCTT
AATAAATAAGTCGGGGTTTTCTGCTGGTGAAATGATTTCGCTT
Found at i:28323 original size:22 final size:20
Alignment explanation
Indices: 28290--28332 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
28280 TCTCCTAGCT
28290 TCCTTTTTTTTTTCTTTTTC
1 TCCTTTTTTTTTTCTTTTTC
28310 TCCTTATTTCTTTTTCTTTTTC
1 TCCTT-TTT-TTTTTCTTTTTC
28332 T
1 T
28333 TTTCTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TCCTTTTTTTTTTCTTTTTC
Found at i:29488 original size:30 final size:30
Alignment explanation
Indices: 29454--29515 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
29444 ATTTTTATCT
29454 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
29484 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
29514 TG
1 TG
29516 GCTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:31970 original size:10 final size:10
Alignment explanation
Indices: 31950--31979 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31940 TTTTTTTTGA
31950 CTTTC-TTTT
1 CTTTCTTTTT
31959 CTTTCTTTTT
1 CTTTCTTTTT
31969 CTTTCTTTTT
1 CTTTCTTTTT
31979 C
1 C
31980 CCTTTTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:35830 original size:18 final size:18
Alignment explanation
Indices: 35807--35841 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35797 ATCTGCTTTT
35807 GTCCCTTGATTACCTAAG
1 GTCCCTTGATTACCTAAG
35825 GTCCCTTGATTACCTAA
1 GTCCCTTGATTACCTAA
35842 CGCTTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (18 bp):
GTCCCTTGATTACCTAAG
Found at i:41742 original size:32 final size:33
Alignment explanation
Indices: 41706--41784 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
41696 AACAAGGCCA
*
41706 AAATAGCGGCGTTT-TCGTAAGGAAACACCGCT
1 AAATAGCGGCGTTTATCGTAAGGAAACACCCCT
* * ** *
41738 AAATAGCGGCATTTATTGTACTGAAACGCCCCT
1 AAATAGCGGCGTTTATCGTAAGGAAACACCCCT
*
41771 AAAAAGCGGCGTTT
1 AAATAGCGGCGTTT
41785 CTTGTACGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 13 0.34
33 25 0.66
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (33 bp):
AAATAGCGGCGTTTATCGTAAGGAAACACCCCT
Found at i:41773 original size:33 final size:33
Alignment explanation
Indices: 41726--41800 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
41716 GTTTTCGTAA
* * *
41726 GGAAACACCGCTAAATAGCGGCATTTATTGTAC
1 GGAAACGCCCCTAAAAAGCGGCATTTATTGTAC
* * *
41759 TGAAACGCCCCTAAAAAGCGGCGTTTCTTGTAC
1 GGAAACGCCCCTAAAAAGCGGCATTTATTGTAC
41792 GGAAACGCC
1 GGAAACGCC
41801 ACTATTCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (33 bp):
GGAAACGCCCCTAAAAAGCGGCATTTATTGTAC
Found at i:44251 original size:9 final size:9
Alignment explanation
Indices: 44226--44259 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
44216 GTTTAAAGAA
44226 GAGAAATTG
1 GAGAAATTG
*
44235 CAAGAAATTG
1 -GAGAAATTG
44245 GAGAAATTG
1 GAGAAATTG
44254 GAGAAA
1 GAGAAA
44260 GATTAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (9 bp):
GAGAAATTG
Found at i:53681 original size:303 final size:303
Alignment explanation
Indices: 53115--53721 Score: 885
Period size: 303 Copynumber: 2.0 Consensus size: 303
53105 TGCTTCTCAA
* * *
53115 GCAGAAGAAGATGGTGAAATGTCAATGACTTAGGCACAGGTGTTGCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCAATGACTGAGGCACAGGTGTTCCACGTTTTGGTACTCTTCTT
* * *
53180 TGCAATTATTGACTCACTTAAGTTTTTCTATATAGGGTCTTCAAGAGTCTTCTTAACAAATGCAT
66 TGCAATTATTGACTCACTTAAGTCTTTCTATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * *
53245 CGTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTG
131 CGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTGTAG
* * * * * *
53310 AATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTACAATTGTTTTCCTT
196 AATATACTTGTGAAAACCTCCCTGGAACAGGCCAGCTCCATTTTTGTCTTACAATTATTTTCCTT
* * * *
53375 AATAATCAAGTCGGGGTTTTCTGCAGGTGAAATGACTCTGCTT
261 AATAATCAAGTCGAGGTTTTCTGCAGCTGAAACGACTCCGCTT
** * *
53418 GCAGAAGAAGATGGTGAAATGTTGATGACTGAGGCACATGTGTTCCATG-TTTGGATACTCTTCT
1 GCAGAAGAAGATGGTGAAATGTCAATGACTGAGGCACAGGTGTTCCACGTTTTGG-TACTCTTCT
* ** *
53482 TTGCAATTGTTGACTTGCTTAAGTCTTTGTATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCA
65 TTGCAATTATTGACTCACTTAAGTCTTTCTATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCA
* *
53547 TCGTGACAAACTTTACCGAATACCATGAGTTCACCGCAACACTTCTTAGTGATAGCTCCGGTGTA
130 TCGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTGTA
* *
53612 GAATATACTTGTGAAAACCTCCCTGGAACAGGCCAGGCT-CATTTTTGTCTTGCAATTATTTTGC
195 GAATATACTTGTGAAAACCTCCCTGGAACAGGCCA-GCTCCATTTTTGTCTTACAATTATTTTCC
* *
53676 TTAATAATCAAGTCTAGGTTTTCTGTAGCTGAAACGACTCCGCTT
259 TTAATAATCAAGTCGAGGTTTTCTGCAGCTGAAACGACTCCGCTT
53721 G
1 G
53722 TTAAAACAAG
Statistics
Matches: 269, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
302 4 0.01
303 263 0.98
304 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATGTCAATGACTGAGGCACAGGTGTTCCACGTTTTGGTACTCTTCTT
TGCAATTATTGACTCACTTAAGTCTTTCTATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTGTAG
AATATACTTGTGAAAACCTCCCTGGAACAGGCCAGCTCCATTTTTGTCTTACAATTATTTTCCTT
AATAATCAAGTCGAGGTTTTCTGCAGCTGAAACGACTCCGCTT
Found at i:56133 original size:299 final size:300
Alignment explanation
Indices: 55587--56161 Score: 791
Period size: 299 Copynumber: 1.9 Consensus size: 300
55577 GAAGATGATG
***
55587 AAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTTTGTACTCTTCTTTGCAATTGCTGACTCA
1 AAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTTGCAA-T--TGACTCA
* * *
55652 CTTAAGTTTTTATATATAGGGTCTTCAAGAGTCTTCTTAACAAATAAATCGTGACAAACTTTAAC
63 CTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATAAATCGTGACAAACTTTAAC
* * *
55717 CAATACCTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTGAATATACTTGTGAAAA
128 CAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTATAAATATACTTGTGAAAA
* * ** ** * *
55782 CTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTAGAATTGTTTTCCTTAATAATCAAGTCGGGG
193 CCTCCCTGGCACAGGCCAGGCCCATTTTTGCCTTAGAATTATTTTCCTTAATAATCAAGTCGAGG
* *
55847 TTTTCTGCAGGTGAAATGACCCCGCTTGCAGAAGATCATGGTC
258 ATTTCTGCAGCTGAAATGACCCCGCTTGCAGAAGATCATGGTC
* * * * *
55890 AAATGTTGATGACTGAGGCACATGTGTTCCATGTTTGAATACTCTTCTTTGCCA-TGACTCGCTT
1 AAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTTGCAATTGACTCACTT
* **
55954 AAGTCTTTGTATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGACAAACTTT-ACCGA
66 AAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATAAATCGTGACAAACTTTAACC-A
56018 ATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGG-TATAATATATACTTGTGAAAAC
130 ATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTATAA-ATATACTTGTGAAAAC
* *
56082 CTCCCTGG-ACTAGGCCAGGCCCATTTTTGCCTT-GCAATTATTTTGCTTAATAATCAAGTCTAG
194 CTCCCTGGCAC-AGGCCAGGCCCATTTTTGCCTTAG-AATTATTTTCCTTAATAATCAAGTCGAG
56145 GATTTCTGCAGCTGAAA
257 GATTTCTGCAGCTGAAA
56162 CGACTCCACT
Statistics
Matches: 239, Mismatches: 29, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
298 9 0.04
299 183 0.77
303 47 0.20
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (300 bp):
AAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTTGCAATTGACTCACTT
AAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATAAATCGTGACAAACTTTAACCAA
TACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTATAAATATACTTGTGAAAACCT
CCCTGGCACAGGCCAGGCCCATTTTTGCCTTAGAATTATTTTCCTTAATAATCAAGTCGAGGATT
TCTGCAGCTGAAATGACCCCGCTTGCAGAAGATCATGGTC
Found at i:57881 original size:303 final size:303
Alignment explanation
Indices: 57333--57935 Score: 895
Period size: 303 Copynumber: 2.0 Consensus size: 303
57323 TCTCAAGCAG
*** *
57333 AAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTTTGCA
1 AAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTGAATACTCTTCTTCGCA
* * * *
57398 ATTGCTGACTGACTTAAGTTTTTATATATAGGGTGTTCAAGAGTCTTCTTAACAAATGCATCGTG
66 ATTGCTGACTGACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTG
* * * *
57463 ACAAACTTTACCCAATTCCTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTGAATA
131 ACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATA
* * * ** * * *
57528 TACTTGTGAAAACTTCCCTGGCACAGGGTAGTTCCATTTTTATTTTGCAATTGTTTTCCTTAATA
196 TACTTATGAAAACCTCCCTGGAACAGGCAAGTCCCATTTTTATCTTGCAATTATTTTCCTTAATA
** *
57593 ATCAACTCGGGGTTTTCTGCAGGTGAAATGACTCCCCTTGCAA
261 ATCAACTCGGGGTTTTCTGCAGCAGAAACGACTCCCCTTGCAA
*
57636 AAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCATGTTTGAATACTCTTCTTCGCA
1 AAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTGAATACTCTTCTTCGCA
*
57701 ATTGTTGACTCG-CTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGT
66 ATTGCTGACT-GACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGT
*
57765 GACAAACTTTACCGAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAAT
130 GACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAAT
* *
57830 ATACTTATGAAAACCTCCCTGGAACAGGCCAAG-CCCATTTTTGTCTTGCAATTATTTTGCTTAA
195 ATACTTATGAAAACCTCCCTGGAACAGG-CAAGTCCCATTTTTATCTTGCAATTATTTTCCTTAA
* * *
57894 TAATCAAGTCTGGGTTTTCTGCAGCAGAAACGACTCCGCTTG
259 TAATCAACTCGGGGTTTTCTGCAGCAGAAACGACTCCCCTTG
57936 TTAAAACAAG
Statistics
Matches: 267, Mismatches: 31, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
303 264 0.99
304 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (303 bp):
AAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTGAATACTCTTCTTCGCA
ATTGCTGACTGACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTG
ACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATA
TACTTATGAAAACCTCCCTGGAACAGGCAAGTCCCATTTTTATCTTGCAATTATTTTCCTTAATA
ATCAACTCGGGGTTTTCTGCAGCAGAAACGACTCCCCTTGCAA
Found at i:60427 original size:11 final size:11
Alignment explanation
Indices: 60411--60436 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
60401 AGATAATTTC
60411 TTTTCTTCTAG
1 TTTTCTTCTAG
60422 TTTTCTTCTAG
1 TTTTCTTCTAG
60433 TTTT
1 TTTT
60437 TAGGCAAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:61676 original size:27 final size:27
Alignment explanation
Indices: 61642--61695 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
61632 TGTTTCTGCG
61642 TCATAAAAAAAAGGTTT-TTGCGTTTT
1 TCATAAAAAAAAGGTTTCTTGCGTTTT
*
61668 TCATAAAAAAAAGTTTTCTTGCGTTTT
1 TCATAAAAAAAAGGTTTCTTGCGTTTT
61695 T
1 T
61696 AATTTATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (27 bp):
TCATAAAAAAAAGGTTTCTTGCGTTTT
Found at i:61743 original size:27 final size:28
Alignment explanation
Indices: 61705--61759 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
61695 TAATTTATTA
*
61705 GTTTTGCGTTTT-TGAAAAAAAAAATTT
1 GTTTTGCGTTTTCTAAAAAAAAAAATTT
61732 GTTTTGCGTTTTCTAAAAAAAAAAATTT
1 GTTTTGCGTTTTCTAAAAAAAAAAATTT
61760 ACTTGTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (28 bp):
GTTTTGCGTTTTCTAAAAAAAAAAATTT
Found at i:64922 original size:21 final size:21
Alignment explanation
Indices: 64867--64933 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
64857 CCAAGCCATT
* *
64867 ACCGGCCATTCACCGTGACACC
1 ACCGGCCATGC-CCGTGCCACC
** *
64889 ACCGGTTAAGCCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
*
64910 ACCGGCCATGCCCGTGCCATC
1 ACCGGCCATGCCCGTGCCACC
64931 ACC
1 ACC
64934 ATTCCAAGCC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 29 0.81
22 7 0.19
ACGTcount: A:0.19, C:0.46, G:0.21, T:0.13
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Done.