Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold549
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: 67163
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.33
Warning! 6126 characters in sequence are not A, C, G, or T
Found at i:2085 original size:43 final size:43
Alignment explanation
Indices: 2038--2310 Score: 289
Period size: 43 Copynumber: 6.3 Consensus size: 43
2028 ATGTGTTGGC
* * * *
2038 CTTTAGTGGCGTTTTTGGTCAAAGCACCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
2081 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * * *
2124 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAAGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * *
2167 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * * *
2210 CTATTA-CGGCGTTTGAGGGGAAAGTGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * *
2253 CTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
2296 CTATT-GCGGCGTTTG
1 CT-TTAGCGGCGTTTG
2311 AGAAAAAAAC
Statistics
Matches: 186, Mismatches: 41, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
42 2 0.01
43 179 0.96
44 5 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:2256 original size:129 final size:129
Alignment explanation
Indices: 2038--2289 Score: 328
Period size: 129 Copynumber: 2.0 Consensus size: 129
2028 ATGTGTTGGC
* *
2038 CTTTAGTGGCGTTTTTGGTCAAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGTGGCGTTTGTGGTCAAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGAAAA
*
2103 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAAGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAAGTT
* * * * **
2167 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCTATTA-CGGCGTTTGAGGGGA
1 CTTTAGTGGCGTTTGTGGTCAAAGCACCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGAGGAAA
* * * * * * *
2231 AAGTGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
65 AAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGAT
2290 CAGGGTCTAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 2 0.02
129 100 0.95
130 3 0.03
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (129 bp):
CTTTAGTGGCGTTTGTGGTCAAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAAGTT
Found at i:2330 original size:86 final size:86
Alignment explanation
Indices: 2058--2312 Score: 359
Period size: 86 Copynumber: 3.0 Consensus size: 86
2048 GTTTTTGGTC
* * * * ** * * *
2058 AAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
*
2123 TCT-TTAGCGGCGTTTGTGGGG
66 TCTATT-GCGGCGTTTGAGGGG
* *
2144 AAAGCGCCGCTAAAGATTAAGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
*
2209 TCTATTACGGCGTTTGAGGGG
66 TCTATTGCGGCGTTTGAGGGG
* *
2230 AAAGTGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
2295 TCTATTGCGGCGTTTGAG
66 TCTATTGCGGCGTTTGAG
2313 AAAAAAACGC
Statistics
Matches: 150, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 148 0.99
87 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTGAGGGG
Found at i:2350 original size:86 final size:86
Alignment explanation
Indices: 2080--2374 Score: 312
Period size: 86 Copynumber: 3.4 Consensus size: 86
2070 AAGATAAGGG
* ** * * * *
2080 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTCT-TTAGCGGCGTTTGTGGGG
1 TCTTCAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGG
* *
2144 AAAGCGCCGCTAAAGATTAAGT
65 AAAGCGCCGCTAAAGGTTTAGT
* * * *
2166 TCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCTATTACGGCGTTTGAGGGGA
1 TCTTCAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGGA
* *
2231 AAGTGCCGCTAAA-GATTAGGT
66 AAGCGCCGCTAAAGGTTTA-GT
* ***
2252 TCTTTC-GTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGAAA
1 TC-TTCAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGG
* *
2316 AAAACGCCGTTAAAGGTCTTAG-
65 AAAGCGCCGCTAAAGGT-TTAGT
*
2338 TCTTCAGCGGCGTTTGTGCT-AGAAGCGCCGCTATAGA
1 TCTTCAGCGGCGTTTGTGGTCA-AAGCGCCGCTATAGA
2375 ACAACACCTT
Statistics
Matches: 177, Mismatches: 25, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
85 6 0.03
86 162 0.92
87 6 0.03
88 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (86 bp):
TCTTCAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGGA
AAGCGCCGCTAAAGGTTTAGT
Found at i:2517 original size:22 final size:22
Alignment explanation
Indices: 2489--2531 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2479 CTGCGGCGCT
*
2489 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
2511 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
2532 GTTTTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:5873 original size:13 final size:13
Alignment explanation
Indices: 5855--5880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5845 TCACCTTAGG
5855 CTTGCTTCTGAAC
1 CTTGCTTCTGAAC
5868 CTTGCTTCTGAAC
1 CTTGCTTCTGAAC
5881 TAGCCTAAGT
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:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
CTTGCTTCTGAAC
Found at i:7351 original size:3 final size:3
Alignment explanation
Indices: 7343--7373 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
7333 TTTAATCTTG
7343 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
7374 TACTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7516 original size:2 final size:2
Alignment explanation
Indices: 7500--7532 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7490 CATACATTTT
7500 TA TA -A TA TA -A 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 TA TA TA T
7533 GCATATACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7628 original size:26 final size:25
Alignment explanation
Indices: 7599--7658 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
7589 TTATTTTTCG
**
7599 TATATTTTACAATTTATATATATACA
1 TATATTTT-CAACATATATATATACA
* *
7625 TATATATTTCTACATATATATATCCA
1 TATAT-TTTCAACATATATATATACA
7651 TATATTTT
1 TATATTTT
7659 TATAGTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 23 0.79
27 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTTCAACATATATATATACA
Found at i:7630 original size:12 final size:12
Alignment explanation
Indices: 7613--7655 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
7603 TTTTACAATT
7613 TATATATATACA
1 TATATATATACA
*
7625 TATATATTTCTACA
1 TATATA--TATACA
*
7639 TATATATATCCA
1 TATATATATACA
7651 TATAT
1 TATAT
7656 TTTTATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATACA
Found at i:7630 original size:14 final size:14
Alignment explanation
Indices: 7613--7647 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7603 TTTTACAATT
7613 TATATATATACATA
1 TATATATATACATA
* *
7627 TATATTTCTACATA
1 TATATATATACATA
7641 TATATAT
1 TATATAT
7648 CCATATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATATATACATA
Found at i:10028 original size:23 final size:23
Alignment explanation
Indices: 9984--10029 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9974 GAGATTAGTA
* * *
9984 AATTTACAATTTGATTATTCAAT
1 AATTTACAATTTAATCACTCAAT
*
10007 AATTTATAATTTAATCACTCAAT
1 AATTTACAATTTAATCACTCAAT
10030 TATTAGTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTACAATTTAATCACTCAAT
Found at i:10033 original size:31 final size:31
Alignment explanation
Indices: 9997--10057 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
9987 TTACAATTTG
*
9997 ATTATTCAAT-AATTTATAATTTAATCACTCA
1 ATTATT-AATAAATTTATAACTTAATCACTCA
* *
10028 ATTATTAGTAAATTTATAACTTGATCACTC
1 ATTATTAATAAATTTATAACTTAATCACTC
10058 CCATGTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTATTAATAAATTTATAACTTAATCACTCA
Found at i:22734 original size:18 final size:20
Alignment explanation
Indices: 22713--22755 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
22703 ATTTATTACT
22713 TTTTTTGAAT-TT-TTAAAA
1 TTTTTTGAATGTTCTTAAAA
*
22731 TTTTTTGAATGTTCTTATAA
1 TTTTTTGAATGTTCTTAAAA
22751 TTTTT
1 TTTTT
22756 ACATTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTTGAATGTTCTTAAAA
Found at i:24725 original size:296 final size:299
Alignment explanation
Indices: 24043--24887 Score: 765
Period size: 296 Copynumber: 2.8 Consensus size: 299
24033 ATTACACATT
* * * * * *
24043 TTATCTATACTATTATTTAAA-CCTCTAACTGAGTTGTTGGTGTCATAAGCCAACCAGACACCAA
1 TTATCTATATTATTATTTAAACCCT-TGACTGA--AGTTGGTGTCATGAGTCAACCGGACACCAA
* * * *
24107 CTCGATTAGAAAAATTACTAAAATATCCTTTCATATTTAAAATAAGTTATGTTATTTGAAGATAC
63 CTTGATTAGAGAAATTACTAAAATATCCTTTCATATTTAAAATAAGTTATATTATTTAAAGATAC
** * * *
24172 TTTGGTCTTTTTTTTATTGAAAAACAATAAAAAATATATATATGATAGGATTTGAATTCATGCCA
128 TTTAATCTTTTATTTATTGAAAAACAATAAAAAATATATATATGAT--GATTTAAATCCATGCCA
* * *
24237 ATTACATTAGAAAAATCTTAAATTTACCACTCAATCAAAGCTTTGTTTTGATATTATTATACATT
191 ATTACATTAGAAAAATCTTAAAGTTACCACTCAATCAAAGCTTTATTTTGATATTATTAAACATT
* * * *
24302 ACAATTTTATTATACACACTATTATTACCTTCATCAATTGTATA
256 ACAATTTTACTATACACACTATTATTACCATCATCAAATCTATA
* * * * * *
24346 TTTATTTATATTATTATTTAAACCCTTGACTGAA-TTGGTATTATGAGTCAA-CGAAGCACTAAT
1 -TTATCTATATTATTATTTAAACCCTTGACTGAAGTTGGTGTCATGAGTCAACCGGA-CACCAAC
* * * * *
24409 TTGATTAG-GTAGATTACTAAAATATCCTCTCGTATTTAATATAAGTTATATTA-TTAAACGGTA
64 TTGATTAGAG-AAATTACTAAAATATCCTTTCATATTTAAAATAAGTTATATTATTTAAA-GATA
24472 CTTTAATCCTTTTATTT-TTG-AAAACAAT-AAAAATATGCATATTATGAT-ATTTAAATCCATG
127 CTTTAAT-CTTTTATTTATTGAAAAACAATAAAAAATAT--ATA-TATGATGATTTAAATCCATG
** * *
24533 CCAATTGTATTAG-AAAATCTTAAAGTTACCATTCAA-CTACAA-CTTTATTTTGATAACTTTTT
188 CCAATTACATTAGAAAAATCTTAAAGTTACCACTCAATC-A-AAGCTTTATTTTGAT-A-TTATT
** *
24595 AAACATTTTAATTTTACTATTCACACT-TTATTA-CATCATCAAATCTATA
249 AAACATTACAATTTTACTATACACACTATTATTACCATCATCAAATCTATA
** ** *
24644 -TATCTATATTATTATTTAAATTCTTGGGT-AAGTTGGTGTCACGAGTCAACCGGACACCAACTT
1 TTATCTATATTATTATTTAAACCCTTGACTGAAGTTGGTGTCATGAGTCAACCGGACACCAACTT
* * * * * * *
24707 GATTAGAGAAATTACTAAAATATCATTTCATATTTAAAATAAATTATATTCTTTGAGGCTATTTT
66 GATTAGAGAAATTACTAAAATATCCTTTCATATTTAAAATAAGTTATATTATTTAAAGATACTTT
* * * * * * * *
24772 AATATTTTAATTTA---AAATAATAATAAAAAATATACATTTGATGAGATATGAATTCATACCAA
131 AATCTTTT-ATTTATTGAAA-AACAATAAAAAATATATATATGAT--GATTTAAATCCATGCCAA
* * * * * * *
24834 TTGCATTAGAAAAACCTTAAATTTATCGCTCAACCAAAGCTTTATTTTAATATT
192 TTACATTAGAAAAATCTTAAAGTTACCACTCAATCAAAGCTTTATTTTGATATT
24888 TTTTACACAT
Statistics
Matches: 437, Mismatches: 77, Indels: 62
0.76 0.13 0.11
Matches are distributed among these distances:
294 5 0.01
295 10 0.02
296 107 0.24
297 40 0.09
298 76 0.17
299 40 0.09
300 40 0.09
301 77 0.18
302 14 0.03
304 25 0.06
305 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (299 bp):
TTATCTATATTATTATTTAAACCCTTGACTGAAGTTGGTGTCATGAGTCAACCGGACACCAACTT
GATTAGAGAAATTACTAAAATATCCTTTCATATTTAAAATAAGTTATATTATTTAAAGATACTTT
AATCTTTTATTTATTGAAAAACAATAAAAAATATATATATGATGATTTAAATCCATGCCAATTAC
ATTAGAAAAATCTTAAAGTTACCACTCAATCAAAGCTTTATTTTGATATTATTAAACATTACAAT
TTTACTATACACACTATTATTACCATCATCAAATCTATA
Found at i:25584 original size:841 final size:838
Alignment explanation
Indices: 23739--25600 Score: 1960
Period size: 840 Copynumber: 2.2 Consensus size: 838
23729 TAAAGTTTTA
* * * *
23739 TTTTAATATATTTTAATTCTATTATTCACACTTTATTACATTTATCAAATGTATATATCTATATT
1 TTTTTATACATTTTAATTTTA-T-TTCACACTTTATTACATTCATCAAATGTATATATCTATATT
* * *
23804 ATTATTTAAATCTCTGACCGAGTTGGTGTCACAAGTC-AACGAAGCACCAACTCGGTTAGGAAAA
64 ATTATTTAAATCT-TGACTGAGTTGGTGTCACGAGTCAAACG-AGCACCAACTTGGTTAGGAAAA
* * * *
23868 TTACTAAAATGTCCTTTTATGTTTAAAATAAGTTA-AGTTATTCAAGGATACTTTAGTTTTTTAT
127 TTACTAAAATGTCCTTTCATATTTAAAATAAGTTATA-TTATTCAAGGATACTTTAATTTTTAAT
* * * * *
23932 TTAAAAAGAATAAAAATATACACAAGATATTTGAATTCATGCCAATTGCACTAGGAAAGCCTTAA
191 TTAAAAAGAATAAAAATATACACAAGAGATATGAATTCATACCAATTGCACTAGAAAAACCTTAA
* *
23997 ATTTATCACTTAACCAAAGCTTTACTTTAATATTTTATTACACATTTTATCTATACTATTATTTA
256 ATTTATCACTCAACCAAAGCTTTACTTTAATATTTTATTACACATTTTATATATACTATTATTTA
*
24062 AACCTCTAACTGAGTTGTTGGTGTCATAAGCCAACCAGACACCAACTCGATTAGAAAAATTACTA
321 AACCTCTAACTGAG-TGTTGGTGTCATAAGCCAACCAGACACCAACTAGATTAGAAAAATTACTA
* ** ** *
24127 AAATATCCTTTCATATTTAAAATAAGTTATGTTATTTGAAGATACTTTGGTCTTTTTTTTATTGA
385 AAATATCCTTTCACATTTAAAATAAGTTACATTATTTGAAGATAC-TT-GTCTAATATTTATT-A
* * * * * *
24192 AAAACAATAAAAAATATATATATGATAGGATTTGAATTCATGCCAATTACATTAGAAAAATCTTA
447 AAAACAAT----AATATACATAGGATAGGATTTGAATCCATGCCAACTACATTAAAAAAACCTTA
* *
24257 AATTTACCACTCAATCAAAGCTTTGTTTTGATATTATTATACATTACAATTTTATTATACACACT
508 AATTTACCACTCAACCAAAACTTTGTTTTGATATTATTATACATTACAATTTTATTATACACAC-
* ** * * * *
24322 ATTATTACCTTCATCAATTGTATATTTATTTATATTATTATTTAAACCCTTGACTGAATTGGTAT
572 -TTATCACCCCCATCAATTGTATATCTATTTATACTATTATTTAAACCCCTAACTGAATTGGTAT
* ** * * * * * * *
24387 TATGAGTCAACGAAGCACTAATTTGATTAGGTAGATTACTAAAATATCCTCTCGTATTTAATATA
636 CACAAGTCAACGAAGCACCAACTCGATTAAGTAAATTACTAAAATATCCTCTCGTATTTAAAACA
* ** * *
24452 AGTTATATTATTAAACGGTACTTTAATCCTTTTATTTTTGAAAACAATAAAAATATGCATATTAT
701 AGTTATATTATTAAACGGTAATTTAATCCTTTTATTTTAAAAAACAATAAAAAAATGCATATGAT
* * *
24517 GATATTTAAATCCATGCCAATTGTATTAGAAAATCTTAAAGTTACCATTCAACTACAACTTTATT
766 GATATTTAAATCCATGCCAATTGCATTAGAAAATCTTAAAGTTAACATTCAACTAAAACTTTATT
24582 TTGATAAC
831 TTGATAAC
* *
24590 TTTTTAAACATTTTAATTTTACTATTCACACTTTATTACA-TCATCAAATCTATATATCTATATT
1 TTTTTATACATTTTAATTTTA-T-TTCACACTTTATTACATTCATCAAATGTATATATCTATATT
** * * *
24654 ATTATTTAAATTCTTGGGTAAGTTGGTGTCACGAGTCAACCG-GACACCAACTTGATTA-GAGAA
64 ATTATTTAAA-TCTTGACTGAGTTGGTGTCACGAGTCAAACGAG-CACCAACTTGGTTAGGA-AA
* * * * ** * *
24717 ATTACTAAAATATCATTTCATATTTAAAATAAATTATATTCTTTGAGGCTATTTTAATATTTTAA
126 ATTACTAAAATGTCCTTTCATATTTAAAATAAGTTATATTATTCAAGGATACTTTAAT-TTTTAA
* * * *
24782 TTTAAAATAATAATAAAAAATATACATTTGATGAGATATGAATTCATACCAATTGCATTAGAAAA
190 TTT-AAA-AAGAAT-AAAAATATACA---CAAGAGATATGAATTCATACCAATTGCACTAGAAAA
* *
24847 ACCTTAAATTTATCGCTCAACCAAAGCTTTATTTTAATATTTT-TTACACATTTTATATATACTA
249 ACCTTAAATTTATCACTCAACCAAAGCTTTACTTTAATATTTTATTACACATTTTATATATACTA
* * * * * *
24911 TTATTTAAA-CTCATAACTGA-T-TTGGTGTGATAAGTCAACCTAG-TACCAATTAGGTTAGCAA
314 TTATTTAAACCTC-TAACTGAGTGTTGGTGTCATAAGCCAACC-AGACACCAACTAGATTAGAAA
* * * *
24972 AATTACTAAAGTGTCTTTTCGCATTTAAAATAAGTTACATTATTTG-AGAGTA-TT-T-TAATAT
377 AATTACTAAAATATCCTTTCACATTTAAAATAAGTTACATTATTTGAAGA-TACTTGTCTAATAT
* * * * * *
25033 TTA-T-AAAA-GAT-ATGTGCATAGGATGGGATTTGAATCCATGCTAACTGCATTAAAAAAACCT
441 TTATTAAAAACAATAATATACATAGGATAGGATTTGAATCCATGCCAACTACATTAAAAAAACCT
* * * * * ** *
25094 TAAATTTACCACTTAGCCAAAATTTTAG-TTTGATATTGTTTATATATTTTAATTTTATTATGCA
506 TAAATTTACCACTCAACCAAAACTTT-GTTTTGATATT-ATTATACATTACAATTTTATTATACA
* *
25158 CAC-T-TCACCCCCATCAATTGTATATCTATCTATACTCACTATTATTTGAACCCCTAACTGAGT
569 CACTTATCACCCCCATCAATTGTATATCTAT-T-TA-T-ACTATTATTTAAACCCCTAACTGAAT
* ** * *
25221 TTGTATCACAAGTCAACTCAGCACCAACTCGATTAAGTAAATTACTAAAATGTCCTCTTGTATTT
630 TGGTATCACAAGTCAACGAAGCACCAACTCGATTAAGTAAATTACTAAAATATCCTCTCGTATTT
* * * *
25286 AAAACAAGTTATATTATTAGAGGGTAATTTAGT-CTTTT-TTATTAAAAAATAATAAAAAAATGT
695 AAAACAAGTTATATTATTAAACGGTAATTTAATCCTTTTATT-TTAAAAAACAATAAAAAAATG-
* *
25349 ACATATGATGA-AGTTTTAAATCCATGGCAATTGCATTAGAAAA-CTTTAAATTTAACATTCAA-
758 -CATATGATGATA--TTTAAATCCATGCCAATTGCATTAGAAAATC-TTAAAGTTAACATTCAAC
* *
25411 TCAAAATTTTATTTTGAT-AT
819 T-AAAACTTTATTTTGATAAC
* * * *
25431 TTTTTATACATTTTAATTTTATTTGCACCCTTTATTACATTCATCAATTGTATATATCTAAACTA
1 TTTTTATACATTTTAATTTTATTT-CACACTTTATTACATTCATCAAATGTATATATCTATATTA
* * *
25496 TTATTTAAACCCTTGATTGAGATGGTGTCACGAGTCAAACGAGCACCAACTTGGTTAGGAAAATT
65 TTATTTAAA-TCTTGACTGAGTTGGTGTCACGAGTCAAACGAGCACCAACTTGGTTAGGAAAATT
* * * * *
25561 ACGAATATGTCCTTCCGTATTTAAAAGAAGTTATATTATT
129 ACTAAAATGTCCTTTCATATTTAAAATAAGTTATATTATT
25601 GTCAAAACCA
Statistics
Matches: 837, Mismatches: 142, Indels: 74
0.79 0.13 0.07
Matches are distributed among these distances:
836 21 0.03
837 2 0.00
838 4 0.00
839 94 0.11
840 140 0.17
841 136 0.16
842 59 0.07
844 2 0.00
845 4 0.00
847 1 0.00
848 6 0.01
849 4 0.00
850 109 0.13
851 52 0.06
852 6 0.01
853 76 0.09
854 14 0.02
855 3 0.00
856 36 0.04
857 68 0.08
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (838 bp):
TTTTTATACATTTTAATTTTATTTCACACTTTATTACATTCATCAAATGTATATATCTATATTAT
TATTTAAATCTTGACTGAGTTGGTGTCACGAGTCAAACGAGCACCAACTTGGTTAGGAAAATTAC
TAAAATGTCCTTTCATATTTAAAATAAGTTATATTATTCAAGGATACTTTAATTTTTAATTTAAA
AAGAATAAAAATATACACAAGAGATATGAATTCATACCAATTGCACTAGAAAAACCTTAAATTTA
TCACTCAACCAAAGCTTTACTTTAATATTTTATTACACATTTTATATATACTATTATTTAAACCT
CTAACTGAGTGTTGGTGTCATAAGCCAACCAGACACCAACTAGATTAGAAAAATTACTAAAATAT
CCTTTCACATTTAAAATAAGTTACATTATTTGAAGATACTTGTCTAATATTTATTAAAAACAATA
ATATACATAGGATAGGATTTGAATCCATGCCAACTACATTAAAAAAACCTTAAATTTACCACTCA
ACCAAAACTTTGTTTTGATATTATTATACATTACAATTTTATTATACACACTTATCACCCCCATC
AATTGTATATCTATTTATACTATTATTTAAACCCCTAACTGAATTGGTATCACAAGTCAACGAAG
CACCAACTCGATTAAGTAAATTACTAAAATATCCTCTCGTATTTAAAACAAGTTATATTATTAAA
CGGTAATTTAATCCTTTTATTTTAAAAAACAATAAAAAAATGCATATGATGATATTTAAATCCAT
GCCAATTGCATTAGAAAATCTTAAAGTTAACATTCAACTAAAACTTTATTTTGATAAC
Found at i:26694 original size:2 final size:2
Alignment explanation
Indices: 26682--26711 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
26672 TAATTTAAGA
26682 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26712 CTNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27866 original size:20 final size:20
Alignment explanation
Indices: 27841--27906 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
27831 CTTGTTTACA
27841 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAATCCT
** * * *
27861 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAATCCT
27880 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAATCCT
27900 TTGATTT
1 TTGATTT
27907 CTTTCCTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
19 14 0.40
20 21 0.60
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (20 bp):
TTGATTTGATTCTCAATCCT
Found at i:27890 original size:39 final size:39
Alignment explanation
Indices: 27836--27917 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
27826 AAAATCTTGT
27836 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
*
27875 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCT
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
27914 TTAC
1 TTAC
27918 TGTTTTGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
Found at i:34291 original size:10 final size:11
Alignment explanation
Indices: 34269--34306 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
34259 GTTGCTGCGG
*
34269 AAAAGAAGAGA
1 AAAAGAGGAGA
34280 AAAAGAGG-GA
1 AAAAGAGGAGA
34290 AAAAGAGGAGA
1 AAAAGAGGAGA
34301 AAAAGA
1 AAAAGA
34307 AGGTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAAGAGGAGA
Found at i:34370 original size:19 final size:21
Alignment explanation
Indices: 34332--34370 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
34322 AATAATTGAT
*
34332 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
34353 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
34371 TTTATTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:35045 original size:18 final size:18
Alignment explanation
Indices: 35017--35061 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35007 TTGATATGGT
* *
35017 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
35035 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
35053 TGGTGGCGA
1 TGGTGGCGA
35062 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:36370 original size:33 final size:33
Alignment explanation
Indices: 36331--36405 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
36321 AAAATACCTT
36331 TTCTTTTCTTTTTTTCTCCT-TCCTTCCCTCTTC
1 TTCTTTTCTTTTTTTCTCCTCTCCTTCCCT-TTC
* * *
36364 TTCTTTTTTTTTTTTCTCTTCTCCTTTCCTTTC
1 TTCTTTTCTTTTTTTCTCCTCTCCTTCCCTTTC
36397 --CTTTTCTTT
1 TTCTTTTCTTT
36406 CCTTCTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.22
33 21 0.57
34 8 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (33 bp):
TTCTTTTCTTTTTTTCTCCTCTCCTTCCCTTTC
Found at i:36382 original size:21 final size:22
Alignment explanation
Indices: 36358--36497 Score: 121
Period size: 22 Copynumber: 6.4 Consensus size: 22
36348 CCTTCCTTCC
36358 CTCTTCTTCTTT-TTTTTTTTT
1 CTCTTCTTCTTTCTTTTTTTTT
* **
36379 CTCTTCTCCTTTCCTTTCCTTTT
1 CTCTTCTTCTTT-CTTTTTTTTT
*
36402 CT-TTCCTTCTTTCTTTCTTTTT
1 CTCTT-CTTCTTTCTTTTTTTTT
36424 -TCTTCTTCTTTCTTTCTTTTTTT
1 CTCTTCTTCTTTC-TT-TTTTTTT
* * *
36447 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTCTTTCTTTTTTTTT
36469 C-CTTCTT-TTTCTTTCTTTCTTT
1 CTCTTCTTCTTTCTTT-TTT-TTT
36491 CT-TTCTT
1 CTCTTCTT
36498 TCCCTCTCCT
Statistics
Matches: 97, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.06
21 27 0.28
22 31 0.32
23 22 0.23
24 11 0.11
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
CTCTTCTTCTTTCTTTTTTTTT
Found at i:36415 original size:4 final size:4
Alignment explanation
Indices: 36399--36499 Score: 97
Period size: 4 Copynumber: 26.0 Consensus size: 4
36389 TTCCTTTCCT
* *
36399 TTTC TTTC CTTC TTTC TTTC TTT- TTTC -TTC -TTC TTTC TTTC TTTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
36444 TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT- TTTC TTTC TTTC TTTC
1 TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
36492 TTTC TTTC
1 TTTC TTTC
36500 CCTCTCCTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
3 15 0.18
4 59 0.72
5 5 0.06
6 3 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:36444 original size:68 final size:67
Alignment explanation
Indices: 36359--36497 Score: 201
Period size: 68 Copynumber: 2.1 Consensus size: 67
36349 CTTCCTTCCC
*
36359 TCTTCTTCTTTTTTTTTTTTCTCTTCTCCTTTCCTTTCCTTTTCTT-TCCTTCTTTCTTTCTTT-
1 TCTTCTTCTTTTTTTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTCCTTCTTTCTTTCTTTC
36422 TT
66 TT
* **
36424 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCT
1 TCTTCTTC-TT-TTT-TTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTCCTTCTTTCTTTCT
36489 TTCTT
63 TTCTT
36494 TCTT
1 TCTT
36498 TCCCTCTCCT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 8 0.12
66 2 0.03
67 3 0.05
68 31 0.48
69 15 0.23
70 6 0.09
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (67 bp):
TCTTCTTCTTTTTTTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTCCTTCTTTCTTTCTTTC
TT
Found at i:36802 original size:21 final size:21
Alignment explanation
Indices: 36778--36818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36768 ACTTTATTAT
36778 TATTATATATTAT-TAGTTTTG
1 TATT-TATATTATATAGTTTTG
*
36799 TATTTATATTTTATAGTTTT
1 TATTTATATTATATAGTTTT
36819 TATAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (21 bp):
TATTTATATTATATAGTTTTG
Found at i:36819 original size:22 final size:23
Alignment explanation
Indices: 36780--36832 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
36770 TTTATTATTA
* *
36780 TTATATATTATTAGTTTTGT-AT
1 TTATATTTTATTAGTTTTATAAT
36802 TTATATTTTA-TAGTTTTTATAAT
1 TTATATTTTATTAG-TTTTATAAT
36825 TT-TATTTT
1 TTATATTTT
36833 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 20 0.74
23 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (23 bp):
TTATATTTTATTAGTTTTATAAT
Found at i:42449 original size:17 final size:18
Alignment explanation
Indices: 42416--42461 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42406 GGATTGGAAA
*
42416 TCATATTTTTGTTGTTTT
1 TCATATTTTTGTCGTTTT
42434 TCATATTTTT-TCGTTTT
1 TCATATTTTTGTCGTTTT
*
42451 TTATGATTTTT
1 TCAT-ATTTTT
42462 ATATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.72
Consensus pattern (18 bp):
TCATATTTTTGTCGTTTT
Found at i:42519 original size:3 final size:3
Alignment explanation
Indices: 42511--42536 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42501 ACCTGATTTA
42511 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
42537 ATTTATGATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:45268 original size:24 final size:24
Alignment explanation
Indices: 45234--45281 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
45224 AACAAAGAGC
*
45234 AAATTTTAAAAGAGCTCTTAGTAA
1 AAATTTCAAAAGAGCTCTTAGTAA
45258 AAATTTCAAAAGAGCTCTTAGTAA
1 AAATTTCAAAAGAGCTCTTAGTAA
45282 GCTTTCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AAATTTCAAAAGAGCTCTTAGTAA
Found at i:51535 original size:19 final size:19
Alignment explanation
Indices: 51513--51554 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
51503 TTAATAAGAT
*
51513 AAAAGTAAAGGTTTATTAC
1 AAAAGTAAAAGTTTATTAC
*
51532 AAAA-TAAAATTTTATTAC
1 AAAAGTAAAAGTTTATTAC
51550 AAAAG
1 AAAAG
51555 AGAAGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAAGTAAAAGTTTATTAC
Found at i:54151 original size:7 final size:8
Alignment explanation
Indices: 54126--54152 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54116 TTAAATTTTC
54126 TTTATGTT
1 TTTATGTT
54134 TTTATGTT
1 TTTATGTT
54142 TTTATGTT
1 TTTATGTT
54150 TTT
1 TTT
54153 TGAATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTATGTT
Found at i:56208 original size:17 final size:17
Alignment explanation
Indices: 56182--56269 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 17
56172 ACGAAAAAAA
56182 TTTA-AAACACGAGAAT
1 TTTAGAAACACGAGAAT
*
56198 TTTAGAAACACGAAAAT
1 TTTAGAAACACGAGAAT
* *
56215 TATTAAAAAAACGA-AATT
1 T-TTAGAAACACGAGAA-T
* *
56233 TTTTGAAAACACGACAAT
1 TTTAG-AAACACGAGAAT
* *
56251 TTT-GAAACATGTGAAT
1 TTTAGAAACACGAGAAT
56267 TTT
1 TTT
56270 TTTGAAAACA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
16 16 0.28
17 17 0.29
18 23 0.40
19 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTAGAAACACGAGAAT
Found at i:56230 original size:18 final size:17
Alignment explanation
Indices: 56185--56253 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
56175 AAAAAAATTT
*
56185 AAAACACGAGAATTTTA
1 AAAACACGAAAATTTTA
*
56202 GAAACACGAAAATTATTA
1 AAAACACGAAAATT-TTA
* * *
56220 AAAAAACGAAATTTTTTG
1 AAAACACGAAA-ATTTTA
*
56238 AAAACACGACAATTTT
1 AAAACACGAAAATTTT
56254 GAAACATGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 16 0.39
18 23 0.56
19 2 0.05
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (17 bp):
AAAACACGAAAATTTTA
Found at i:56452 original size:18 final size:18
Alignment explanation
Indices: 56306--56518 Score: 127
Period size: 18 Copynumber: 11.6 Consensus size: 18
56296 TAATCACCGG
56306 AATTTTTGAAAACAC-AA
1 AATTTTTGAAAACACGAA
*
56323 GGATTTTTG-AAACACGAA
1 -AATTTTTGAAAACACGAA
**
56341 TTTTTTTTG-AAACACGAA
1 -AATTTTTGAAAACACGAA
*
56359 AATTGTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
56377 ATTTTTTTTTAAAACAC-AA
1 A--ATTTTTGAAAACACGAA
* * *
56396 GGATTTGTTGAAAATAAGAA
1 -AATTT-TTGAAAACACGAA
*
56416 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
56434 AACTTTTGAAAACACG-A
1 AATTTTTGAAAACACGAA
* *
56451 AATTTTT-AAAAGACGGGA
1 AATTTTTGAAAACAC-GAA
*
56469 ATTTTTTG-AAACACGAGAA
1 AATTTTTGAAAACAC--GAA
*
56488 AATTTTGTTTGAAGACACGAA
1 AA--TT-TTTGAAAACACGAA
56509 AA-TTTTGAAA
1 AATTTTTGAAA
56519 CCCGAGGATT
Statistics
Matches: 151, Mismatches: 29, Indels: 31
0.72 0.14 0.15
Matches are distributed among these distances:
16 6 0.04
17 25 0.17
18 76 0.50
19 15 0.10
20 13 0.09
21 7 0.05
22 4 0.03
23 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:57052 original size:17 final size:16
Alignment explanation
Indices: 57029--57067 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
57019 TGTTGGGCTG
57029 TTTTTTTTT-CTGCTGC
1 TTTTTTTTTGCTGCT-C
*
57045 TCTTTTTTTGCTGCTC
1 TTTTTTTTTGCTGCTC
57061 TTTTTTT
1 TTTTTTT
57068 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.00, C:0.18, G:0.10, T:0.72
Consensus pattern (16 bp):
TTTTTTTTTGCTGCTC
Found at i:57056 original size:14 final size:13
Alignment explanation
Indices: 57031--57091 Score: 74
Period size: 14 Copynumber: 4.7 Consensus size: 13
57021 TTGGGCTGTT
57031 TTTTTTTCTGCTGC
1 TTTTTTT-TGCTGC
57045 TCTTTTTTTGCTGC
1 T-TTTTTTTGCTGC
57059 TCTTTTTTT-CT--
1 T-TTTTTTTGCTGC
57070 TTTTTTTTGCTGC
1 TTTTTTTTGCTGC
57083 TTTTTTTTG
1 TTTTTTTTG
57092 GGCTGCTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.16
11 3 0.07
13 11 0.26
14 16 0.37
15 6 0.14
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.72
Consensus pattern (13 bp):
TTTTTTTTGCTGC
Found at i:57234 original size:3 final size:3
Alignment explanation
Indices: 57221--57276 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
57211 TCCTTTTTTC
*
57221 CTT CTTT CTT CTT CTT CTG CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
57267 CTT CTT CTT C
1 CTT CTT CTT C
57277 AACACCGAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:57396 original size:24 final size:23
Alignment explanation
Indices: 57359--57409 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
57349 TTCTCTCCTC
*
57359 TTTTCTCTTATTTTCGAAGCTTT
1 TTTTCTCTTATTTTCGAAACTTT
* *
57382 TTTTCTTCTTTTTTTCGAAATTTT
1 TTTTC-TCTTATTTTCGAAACTTT
57406 TTTT
1 TTTT
57410 GATGATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.12, C:0.14, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTTCTCTTATTTTCGAAACTTT
Found at i:57775 original size:29 final size:29
Alignment explanation
Indices: 57714--57876 Score: 177
Period size: 30 Copynumber: 5.6 Consensus size: 29
57704 CAGCAAAACT
*
57714 TTTA-GGGCCAAAATGTAATTTTAAGAAAG
1 TTTAGGGGTCAAAATGTAATTTTAA-AAAG
* *
57743 TTTAGGGGTCAAAATGTAATTTTGAAAAT
1 TTTAGGGGTCAAAATGTAATTTTAAAAAG
**
57772 TTTAGGGGTCAAAATGTAA-TTTAAAATTT
1 TTTAGGGGTCAAAATGTAATTTTAAAA-AG
** * * *
57801 TTTAGGGGTTGAACTATAATTTTGAGAAAG
1 TTTAGGGGTCAAAATGTAATTTT-AAAAAG
57831 TTTAGGGGTCAAAATGTAATTTTAAAAAAG
1 TTTAGGGGTCAAAATGTAATTTT-AAAAAG
*
57861 TTTAAGGGTCAAAATG
1 TTTAGGGGTCAAAATG
57877 CAAAAAAAAT
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.05
29 42 0.38
30 60 0.54
31 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (29 bp):
TTTAGGGGTCAAAATGTAATTTTAAAAAG
Found at i:57791 original size:59 final size:58
Alignment explanation
Indices: 57708--57876 Score: 198
Period size: 59 Copynumber: 2.9 Consensus size: 58
57698 TAATGACAGC
*
57708 AAAACTTTTA-GGGCCAAAATGTAATTTTAAGAAAGTTTAGGGGTCAAAATGTAATTTTG
1 AAAA-TTTTAGGGGTCAAAATGTAATTTTAA-AAAGTTTAGGGGTCAAAATGTAATTTTG
** ** * *
57767 AAAATTTTAGGGGTCAAAATGTAA-TTTAAAATTTTTTAGGGGTTGAACTATAATTTTG
1 AAAATTTTAGGGGTCAAAATGTAATTTTAAAA-AGTTTAGGGGTCAAAATGTAATTTTG
* *
57825 AGAAAGTTTAGGGGTCAAAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATG
1 A-AAATTTTAGGGGTCAAAATGTAATTTT-AAAAAGTTTAGGGGTCAAAATG
57877 CAAAAAAAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
57 2 0.02
58 31 0.34
59 39 0.43
60 14 0.16
61 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (58 bp):
AAAATTTTAGGGGTCAAAATGTAATTTTAAAAAGTTTAGGGGTCAAAATGTAATTTTG
Found at i:58220 original size:74 final size:74
Alignment explanation
Indices: 58067--58406 Score: 432
Period size: 74 Copynumber: 4.5 Consensus size: 74
58057 GCGTGAAACC
* * *
58067 CGAGGCCCAACTCACCTCTAGCAATATGAGTTGATGTTTTTGAAAAGCA-AGAATTGAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGA-AATTGAAAAATAC
58131 CTCGACGTGACT
63 CTCGACGTGACT
* * * *
58143 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGGAAAAATATAAATTGAAAAACACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
58208 GACGTGACT
66 GACGTGACT
*
58217 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GAA-AAATAC
* * *
58282 CTCGGCATG-GT
63 CTCGACGTGACT
* * *
58293 CCGAGGCTCAATTCACCTCTCGAAATATGAGTTGATTTTTGAAAAACAGGAATTGAAAAATACCT
1 -CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCT
* *
58358 CGGCGTGACC
65 CGACGTGACT
* * *
58368 CAAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
58407 TTGANNNNNN
Statistics
Matches: 232, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
74 130 0.56
75 5 0.02
76 37 0.16
77 60 0.26
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (74 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
GACGTGACT
Found at i:58312 original size:151 final size:148
Alignment explanation
Indices: 58064--58406 Score: 438
Period size: 151 Copynumber: 2.3 Consensus size: 148
58054 TCAGCGTGAA
* * * *
58064 ACCCGAGGCCCAACTCACCTCTAGCAATATGAGTTGATGTTTTTGAAAAGCAAGAATTGAAAAAT
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAGAATTAAAAAAT
* * * *
58129 ACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGGAAAAATATAAA
64 ACCTCGACATGACTCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTGGAAAAACAGAAA
58194 TTGAAAAACACCTCGACGTG
129 TTGAAAAACACCTCGACGTG
*
58214 ACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-AGAAATTTAAAAGAA
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAG-AA-TT-AAA-AA
* * * *
58278 ATACCTCGGCATG-GTCCGAGGCTCAATTCACCTCTCGAAATATGAGTTGATTTTTGAAAAACAG
62 ATACCTCGACATGACT-CGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTGGAAAAACAG
* * *
58342 GAATTGAAAAATACCTCGGCGTG
126 AAATTGAAAAACACCTCGACGTG
* * *
58365 ACCCAAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTT
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
58407 TTGANNNNNN
Statistics
Matches: 168, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
147 2 0.01
148 13 0.08
149 2 0.01
150 37 0.22
151 114 0.68
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (148 bp):
ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAGAATTAAAAAATAC
CTCGACATGACTCGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTGGAAAAACAGAAATT
GAAAAACACCTCGACGTG
Found at i:60969 original size:9 final size:9
Alignment explanation
Indices: 60957--60998 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
60947 TGATTTTTCT
60957 TTTTTTTTG
1 TTTTTTTTG
60966 TTTTTTTTG
1 TTTTTTTTG
*
60975 -TTGTTTT-
1 TTTTTTTTG
*
60982 TTTTGTTTG
1 TTTTTTTTG
60991 TTTTTTTT
1 TTTTTTTT
60999 TGTCTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:60971 original size:12 final size:12
Alignment explanation
Indices: 60956--60999 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
60946 TTGATTTTTC
60956 TTTTTTTTTGTT
1 TTTTTTTTTGTT
*
60968 TTTTTTGTTGTT
1 TTTTTTTTTGTT
60980 TTTTTTGTTTGTT
1 TTTTTT-TTTGTT
60993 TTTTTTT
1 TTTTTTT
61000 GTCTCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:61008 original size:13 final size:12
Alignment explanation
Indices: 60957--61010 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
60947 TGATTTTTCT
60957 TTTTTTTTGTT-
1 TTTTTTTTGTTC
*
60968 TTTTTTGTTGTTT
1 TTTTTT-TTGTTC
60981 TTTTTGTTTG-T-
1 TTTTT-TTTGTTC
60992 TTTTTTTTGTCTC
1 TTTTTTTTGT-TC
61005 TTTTTT
1 TTTTTT
61011 ATTCAGGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 4 0.11
11 11 0.30
12 7 0.19
13 14 0.38
14 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTTC
Found at i:61008 original size:25 final size:25
Alignment explanation
Indices: 60953--61010 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
60943 ATCTTGATTT
60953 TTCTTTTTTTTTGTTTTTTTTGTTG
1 TTCTTTTTTTTTGTTTTTTTTGTTG
60978 TT-TTTTTTGTTTG-TTTTTTT-TTG
1 TTCTTTTTT-TTTGTTTTTTTTGTTG
61001 TCTCTTTTTT
1 T-TCTTTTTT
61011 ATTCAGGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.13
24 14 0.47
25 12 0.40
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.84
Consensus pattern (25 bp):
TTCTTTTTTTTTGTTTTTTTTGTTG
Found at i:67023 original size:8 final size:8
Alignment explanation
Indices: 67010--67065 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
67000 TTTATTTAAA
67010 AATATAAT
1 AATATAAT
67018 AATATAAT
1 AATATAAT
*
67026 -ATA-ATT
1 AATATAAT
67032 AATATAATTT
1 AATATAA--T
67042 ACAATATAAT
1 --AATATAAT
67052 AATATAAT
1 AATATAAT
67060 AATATA
1 AATATA
67066 CTTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 23 0.57
10 2 0.05
12 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATAAT
Done.