Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1796
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: 21876
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:6038 original size:1 final size:1
Alignment explanation
Indices: 6032--6090 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
6022 CCTTCTCTTC
** * * * * *
6032 AAAAAAAAAGCAAAAAAAAAAAAACAAAAAAAAACAAAACAAAGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6091 TCTGCTTAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:6052 original size:15 final size:14
Alignment explanation
Indices: 6032--6090 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
6022 CCTTCTCTTC
*
6032 AAAAAAAAAGCAAA
1 AAAAAAAAAACAAA
6046 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
6060 AAAAAACAAAACAAA
1 AAAAAA-AAAACAAA
6075 GAAAAAGAAAAA-AAA
1 -AAAAA-AAAAACAAA
6090 A
1 A
6091 TCTGCTTAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 20 0.49
15 11 0.27
16 9 0.22
17 1 0.02
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:6059 original size:25 final size:25
Alignment explanation
Indices: 6031--6090 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
6021 ACCTTCTCTT
6031 CAAAAAAAAAGCAAAA-AAAAAAAAA
1 CAAAAAAAAA-CAAAACAAAAAAAAA
*
6056 CAAAAAAAAACAAAACAAAGAAAAA
1 CAAAAAAAAACAAAACAAAAAAAAA
*
6081 GAAAAAAAAA
1 CAAAAAAAAA
6091 TCTGCTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAACAAAACAAAAAAAAA
Found at i:7143 original size:55 final size:55
Alignment explanation
Indices: 7059--7327 Score: 450
Period size: 55 Copynumber: 4.9 Consensus size: 55
7049 TCCGCTTTTT
* *
7059 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
** *
7114 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
**
7169 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCC
*
7224 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
7279 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
7328 TTTTCTCAAA
Statistics
Matches: 202, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
54 2 0.01
55 198 0.98
56 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:7341 original size:30 final size:30
Alignment explanation
Indices: 7305--7362 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
7295 GACACCTCTT
7305 AAAGCCCACACAAGTTGGTGGCATTTTCTC
1 AAAGCCCACACAAGTTGGTGGCATTTTCTC
7335 AAAGCCCACACAAGTTGGTGGCATTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTTC
7363 CAGTCCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (30 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCTC
Found at i:7393 original size:85 final size:85
Alignment explanation
Indices: 7250--7412 Score: 299
Period size: 85 Copynumber: 1.9 Consensus size: 85
7240 GACACCTCTT
*
7250 AAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
7315 CAAGTTGGTGGCATTTTCTC
66 CAAGTTGGTGGCATTTTCTC
**
7335 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
7400 CAAGTTGGTGGCA
66 CAAGTTGGTGGCA
7413 CCTTTCAGTC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20
Consensus pattern (85 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
CAAGTTGGTGGCATTTTCTC
Found at i:7422 original size:55 final size:55
Alignment explanation
Indices: 7335--7881 Score: 712
Period size: 55 Copynumber: 9.9 Consensus size: 55
7325 GCATTTTCTC
7335 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT
1 AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTCTT
* *
7390 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT-TT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
* *
7444 CAAAGCCCACCCAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATACCTCTT
1 -AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTCTT
* * *
7500 AAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAACAGGACACCT-TT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
*
7554 CAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTC
1 -AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTCTT
* *
7610 AAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTCAAAGAGCAGGACACCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
* * * ** *
7664 AAAGCCCACACATGTTGGTGGCATTTTTCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C---ACCTCTT
* * *
7724 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACATCTCTT
1 -AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
* *
7780 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT-TT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
* * * *
7834 CAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 -AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
7882 TACAGTTTAT
Statistics
Matches: 438, Mismatches: 38, Indels: 32
0.86 0.07 0.06
Matches are distributed among these distances:
54 59 0.13
55 316 0.72
56 14 0.03
57 1 0.00
59 1 0.00
60 5 0.01
61 42 0.10
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
Found at i:7449 original size:140 final size:140
Alignment explanation
Indices: 7193--7472 Score: 508
Period size: 140 Copynumber: 2.0 Consensus size: 140
7183 AGGACACCTT
7193 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA
* *
7258 CACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGG
66 CACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGG
7323 TGGCATTTTC
131 TGGCATTTTC
7333 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA
* *
7398 CACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTG
66 CACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTG
7462 GTGGCATTTTC
130 GTGGCATTTTC
7473 CAGTCCTCAA
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
139 2 0.01
140 133 0.99
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (140 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA
CACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGG
TGGCATTTTC
Found at i:7534 original size:250 final size:250
Alignment explanation
Indices: 7085--7582 Score: 872
Period size: 250 Copynumber: 2.0 Consensus size: 250
7075 GACACCTTTT
*
7085 AAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
** *
7150 CAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTG
66 CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTG
* *
7215 GCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCA
131 GCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGCGGCACCTTCCA
*
7280 GTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCTC
196 GTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCTC
**
7335 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
*
7400 CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTG
66 CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTG
* *
7465 GCATTTTCCAGTCCTCAAAGAGCAGGATACCTCTTAAAGCCCACACAAGTTGGCGGCACCTTTCA
131 GCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGCGGCACCTTCCA
7530 GTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
196 GTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
7583 CAGTCCTCAA
Statistics
Matches: 235, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
249 2 0.01
250 233 0.99
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (250 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACA
CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTG
GCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGCGGCACCTTCCA
GTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTC
Found at i:7616 original size:305 final size:316
Alignment explanation
Indices: 7059--7881 Score: 1093
Period size: 305 Copynumber: 2.6 Consensus size: 316
7049 TCCGCTTTTT
* * *
7059 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
7124 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACA
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACA
7189 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAA
130 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTCTTAAA
* *
7253 GCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAA
194 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAA
7318 GTTGGTGGCATTT-T-CTC-A-A-A-G-C-CC-A-CACA-A-GTTGGTGGCATTTTCC
259 GTTGGTGGCATTTCTCCTCAAGACAGGACACCTACCACACATGTTGGTGGCATTTTCC
*
7364 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
* *
7429 GAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGAT
66 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGAC
* * *
7493 ACCTCTT-AAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAACAGGACACCT-TTCA
129 ACCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTT-A
**
7556 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACAC
192 AAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACAC
7621 AAGTTGGTGGCATTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACATGTTGGTGGC
257 AAGTTGGTGGCATTT-C--TCCTC-AAGA-CAGGACACC---T--A--CCACACATGTTGGTGGC
*
7686 ATTTTTC
310 ATTTTCC
* **
7693 AGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
7758 CCCAAAGAGCAGGACATCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
60 CCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGC
* * * * *
7823 AGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
124 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
7882 TACAGTTTAT
Statistics
Matches: 450, Mismatches: 30, Indels: 46
0.86 0.06 0.09
Matches are distributed among these distances:
304 8 0.02
305 241 0.54
306 5 0.01
309 1 0.00
310 3 0.01
312 1 0.00
313 1 0.00
315 1 0.00
316 1 0.00
317 1 0.00
318 2 0.00
324 1 0.00
327 4 0.01
328 1 0.00
329 32 0.07
331 1 0.00
334 6 0.01
335 135 0.30
336 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (316 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACAC
CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGC
CCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGT
TGGTGGCATTTCTCCTCAAGACAGGACACCTACCACACATGTTGGTGGCATTTTCC
Found at i:8715 original size:19 final size:16
Alignment explanation
Indices: 8692--8773 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 16
8682 ATTCAACGAT
8692 TTGTATCGATACATAA
1 TTGTATCGATACATAA
8708 GTTTTGTATCGATAC--AA
1 ---TTGTATCGATACATAA
8725 -TGTATCGATAC--AA
1 TTGTATCGATACATAA
8738 -TGTATCGATACATAAGTA
1 TTGTATCGATACAT-A--A
8756 TTGTATCGATACATAA
1 TTGTATCGATACATAA
8772 TT
1 TT
8774 ATCTACTGCC
Statistics
Matches: 57, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
13 24 0.42
16 4 0.07
17 2 0.04
18 2 0.04
19 25 0.44
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (16 bp):
TTGTATCGATACATAA
Found at i:8730 original size:13 final size:13
Alignment explanation
Indices: 8712--8749 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
8702 ACATAAGTTT
8712 TGTATCGATACAA
1 TGTATCGATACAA
8725 TGTATCGATACAA
1 TGTATCGATACAA
8738 TGTATCGATACA
1 TGTATCGATACA
8750 TAAGTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8829 original size:13 final size:13
Alignment explanation
Indices: 8811--8836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8801 CATTTTTCTG
8811 TGTATCGATACAT
1 TGTATCGATACAT
8824 TGTATCGATACAT
1 TGTATCGATACAT
8837 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8833 original size:33 final size:33
Alignment explanation
Indices: 8791--8857 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8781 GCCAAGGAAA
***
8791 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
8824 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
8857 T
1 T
8858 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:11241 original size:51 final size:53
Alignment explanation
Indices: 11180--11509 Score: 186
Period size: 52 Copynumber: 6.3 Consensus size: 53
11170 AATTCTCCAC
* * * *
11180 AATCGAGGATATTCTAACTCCGATTTTATTTTC-AAAACACTAA-TT-TTCTAT
1 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTCTTC-AT
11231 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAT
1 AATCGGGGATACTCTAACTCCGATTTTATTTCC-AAAAACACCAATTTCTTCAT
* * * * * * ***
11285 AATCGGGGATACTCCAACCCCG--TTAATCAT-CAAGGATACTCCAACCCCGTT-AT
1 AATCGGGGATACTCTAACTCCGATTTTAT-TTCCAA--AAACACCAATTTC-TTCAT
** * * * * *
11338 TTTCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTT-TTCCAC
1 AATC--GGGGATACTCTAACTCCGATTTTATTTC-CAAAAACACCAATTTCTT-CAT
* * * *
11392 AATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTT--T
1 AATCGGGGATACTCTAACTCC-GATTTTATTTCCAAAAACACCAA-TTT-CTTCAT
* * *
11444 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTT-TTCAC
1 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
*
11496 AATCGAGGATACTC
1 AATCGGGGATACTC
11510 CAACCTCGTT
Statistics
Matches: 216, Mismatches: 37, Indels: 51
0.71 0.12 0.17
Matches are distributed among these distances:
50 2 0.01
51 35 0.16
52 78 0.36
53 37 0.17
54 37 0.17
55 22 0.10
56 2 0.01
57 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (53 bp):
AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
Found at i:11497 original size:104 final size:103
Alignment explanation
Indices: 11177--11512 Score: 297
Period size: 104 Copynumber: 3.2 Consensus size: 103
11167 ATCAATTCTC
* * * * *
11177 CACAATCGAGGATATTCTAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
11241 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * * ** * ** **
11282 CATAATCGGGGATACTCCAACCCCG-TTAATCATCAAGGATACTCCAA--CCCCGTTATTTTCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAA--A-ACACCAATTTTCC-TT-TAATC--
* * *
11344 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
11388 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
11453 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
11493 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
11513 CCTCGTTATT
Statistics
Matches: 178, Mismatches: 37, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
103 8 0.04
104 44 0.25
105 32 0.18
106 19 0.11
107 41 0.23
108 4 0.02
109 30 0.17
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:11533 original size:28 final size:28
Alignment explanation
Indices: 11497--11573 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
11487 ATTTTTCACA
* * *
11497 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
11525 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
11553 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
11574 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:11542 original size:212 final size:212
Alignment explanation
Indices: 11175--11580 Score: 593
Period size: 212 Copynumber: 1.9 Consensus size: 212
11165 TTATCAATTC
* * *
11175 TCCACAATCGAGGATATTCTAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
11240 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
11305 CGTTAATCATCAAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCAAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
11370 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
11387 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
11451 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * **
11514 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCAAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
11579 AT
193 AT
11581 TCCCAAAATA
Statistics
Matches: 172, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
211 30 0.17
212 107 0.62
213 35 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCAAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:11640 original size:107 final size:107
Alignment explanation
Indices: 11235--11644 Score: 262
Period size: 107 Copynumber: 3.8 Consensus size: 107
11225 TTCTATAATC
* * * * * *
11235 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * ** * *
11300 AACCCCGTTAATCATCAAGGATACTCCAACCCCGTTATTTTCGA
64 AACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * * *
11344 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
* * * ***** * * ** * *
11407 AATCCTGGT-TTTATTTTCAAAACGCCAATTTTCCTTTA-AT-C--
64 AACCCCGTTATTTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
11448 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
11513 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
11556 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
11620 CCCCGTTATTT-TCGAAGGGATACTC
66 CCCCGTTATTTATCG--GGGATACTC
11645 TAATCCCGAT
Statistics
Matches: 231, Mismatches: 56, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
104 45 0.19
105 24 0.10
106 25 0.11
107 90 0.39
108 30 0.13
109 17 0.07
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:12789 original size:21 final size:20
Alignment explanation
Indices: 12760--12811 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
12750 TCTATAATTG
*
12760 GTATTGATACAAATAGTAAAT
1 GTATCGATACAAA-AGTAAAT
* *
12781 GTATCGATACATAAGTGAAT
1 GTATCGATACAAAAGTAAAT
12801 GTATCGATACA
1 GTATCGATACA
12812 TGCCTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACAAAAGTAAAT
Found at i:12905 original size:20 final size:22
Alignment explanation
Indices: 12860--12911 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
12850 AGGAAGGAAA
*
12860 TGTATCGATACATGCTCACAAT
1 TGTATCGATACATGATCACAAT
*
12882 TGTATCGATACATTATC-C-AT
1 TGTATCGATACATGATCACAAT
12902 TGTATCGATA
1 TGTATCGATA
12912 TATTCTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.43
21 1 0.04
22 15 0.54
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (22 bp):
TGTATCGATACATGATCACAAT
Found at i:17877 original size:16 final size:16
Alignment explanation
Indices: 17835--17878 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
17825 TAAAAAAAAT
*
17835 CCAAACCCGAAAGAAC
1 CCAAACCCGAGAGAAC
*
17851 CCAAACTCGAGAGAAC
1 CCAAACCCGAGAGAAC
*
17867 CCGAACCCGAGA
1 CCAAACCCGAGA
17879 CTGACCTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.36, G:0.18, T:0.02
Consensus pattern (16 bp):
CCAAACCCGAGAGAAC
Found at i:18371 original size:16 final size:15
Alignment explanation
Indices: 18350--18379 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18340 ATGTTACACT
18350 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
18366 TAGAATAGAATATA
1 TAGAATAGAATATA
18380 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:19309 original size:16 final size:16
Alignment explanation
Indices: 19287--19373 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
19277 CCGACCCGAA
19287 CCCGAACCCGAATAAG
1 CCCGAACCCGAATAAG
* **
19303 CCTGAACCTAAATAAG
1 CCCGAACCCGAATAAG
*
19319 CCCGAACCCGAAAAAG
1 CCCGAACCCGAATAAG
* *
19335 CCCGAACCTGAATGAG
1 CCCGAACCCGAATAAG
*
19351 CCCGAACCCGAATGAG
1 CCCGAACCCGAATAAG
*
19367 CCTGAAC
1 CCCGAAC
19374 TTGAACCTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.37, C:0.34, G:0.20, T:0.09
Consensus pattern (16 bp):
CCCGAACCCGAATAAG
Found at i:19328 original size:32 final size:32
Alignment explanation
Indices: 19287--19373 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
19277 CCGACCCGAA
19287 CCCGAACCCGAATAAGCCTGAACCTAAATAAG
1 CCCGAACCCGAATAAGCCTGAACCTAAATAAG
* * * *
19319 CCCGAACCCGAAAAAGCCCGAACCTGAATGAG
1 CCCGAACCCGAATAAGCCTGAACCTAAATAAG
*
19351 CCCGAACCCGAATGAGCCTGAAC
1 CCCGAACCCGAATAAGCCTGAAC
19374 TTGAACCTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.37, C:0.34, G:0.20, T:0.09
Consensus pattern (32 bp):
CCCGAACCCGAATAAGCCTGAACCTAAATAAG
Found at i:20761 original size:20 final size:21
Alignment explanation
Indices: 20731--20771 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20721 TGCATTTTGG
20731 AAATGAAATGTA-TCGATACAT
1 AAATGAAATGTAGT-GATACAT
20752 AAAT-AAATGTAGTGATACAT
1 AAATGAAATGTAGTGATACAT
20772 TTACTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (21 bp):
AAATGAAATGTAGTGATACAT
Found at i:20804 original size:20 final size:20
Alignment explanation
Indices: 20779--20829 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
20769 CATTTACTAT
20779 TTGTATCAATACATTATTCA
1 TTGTATCAATACATTATTCA
20799 TTGTATCAATACATTATTCA
1 TTGTATCAATACATTATTCA
20819 TTGTATCAATA
1 TTGTATCAATA
20830 TATTCTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
TTGTATCAATACATTATTCA
Done.