Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold253
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: 843195
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 44520 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:668994 original size:77 final size:76
Alignment explanation
Indices: 668867--669079 Score: 295
Period size: 75 Copynumber: 2.8 Consensus size: 76
668857 TATCCGTTAT
* * *
668867 CGGTGGATTCAGCAGTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAACAACCCCTTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
668932 CATTCAAAAATA
66 CATT-AAAAATA
*
668944 CGGTGGAATCAGCACTTTGCAACCACCAATGAATT-GGGGAATCAGCACTTAGCAACCCC-TTTC
1 CGGTGGAATCAGCACTTAGCAACCACCAATG-ATTCGGGGAATCAGCACTTAGCAACCCCTTTTC
* *
669007 ACATTTAAGATA
65 ACATTAAAAATA
* * * * *
669019 CGCTGGGATCAACACTTAGCAACCATCAATGATTCGGGAAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
669080 GGGGGAATCA
Statistics
Matches: 121, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
74 3 0.02
75 54 0.45
76 10 0.08
77 51 0.42
78 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
CATTAAAAATA
Found at i:710118 original size:49 final size:50
Alignment explanation
Indices: 710009--710249 Score: 200
Period size: 49 Copynumber: 4.7 Consensus size: 50
709999 GATAATAACA
* * ** * * * *
710009 TGCCAAAGCCATGTCCCAGACATGGTGTTACATGGGATGTTTCCTGT-GC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATCGG
* * * * **
710058 TGCCAATGCCATATCCCAGATACGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATCGG
* * *
710108 TGCCCA-GCCATGTCCCAGACATGGTCTTATGA-GGGACATCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTA-CATGGGACATCTCATATCGG
* **
710157 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCAT-A--TC---GG
* *
710213 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
710250 TCTCATTCCC
Statistics
Matches: 155, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
49 77 0.50
50 41 0.26
53 2 0.01
56 35 0.23
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATCGG
Found at i:713955 original size:39 final size:39
Alignment explanation
Indices: 713911--714001 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
713901 TAAACATGTT
713911 TATGAGTATTGTGATATATGCTTAAATCTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATCTTATGTGATTA
* *
713950 TATGAGTATTGTGATATATGCTTATATGTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATCTTATGTGATTA
* *
713989 TATGTGTAATGTG
1 TATGAGTATTGTG
714002 TGTGATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (39 bp):
TATGAGTATTGTGATATATGCTTAAATCTTATGTGATTA
Found at i:725578 original size:14 final size:13
Alignment explanation
Indices: 725559--725609 Score: 77
Period size: 14 Copynumber: 3.8 Consensus size: 13
725549 TAGCTCTCTC
725559 TTTTTTTTTC-AA
1 TTTTTTTTTCAAA
725571 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
725584 TTTTTTTTTTCAAAA
1 -TTTTTTTTTC-AAA
725599 TTTTTTTTTCA
1 TTTTTTTTTCA
725610 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.28
13 3 0.08
14 20 0.56
15 3 0.08
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:725672 original size:14 final size:13
Alignment explanation
Indices: 725651--725697 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
725641 GGAAACTAGT
725651 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
725664 TTTTGTTTTT-GAAA
1 TTTT-TTTTTCG-AA
725678 TTTTTTTTTC-AA
1 TTTTTTTTTCGAA
725690 TTTTTTTT
1 TTTTTTTT
725698 CGAGAAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.32
13 10 0.32
14 11 0.35
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:729901 original size:15 final size:16
Alignment explanation
Indices: 729872--729902 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
729862 CTTCGCACAT
729872 AATCATGCATCAAAAA
1 AATCATGCATCAAAAA
729888 AATCATGC-TCAAAAA
1 AATCATGCATCAAAAA
729903 TACCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCATGCATCAAAAA
Found at i:730999 original size:25 final size:25
Alignment explanation
Indices: 730965--731014 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
730955 GAAACATACT
730965 TTAAAAATTCATGCAAAATGCCTTA
1 TTAAAAATTCATGCAAAATGCCTTA
**
730990 TTAAAAATTCATGCGGAATGCCTTA
1 TTAAAAATTCATGCAAAATGCCTTA
731015 GCCCCCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (25 bp):
TTAAAAATTCATGCAAAATGCCTTA
Found at i:738937 original size:13 final size:15
Alignment explanation
Indices: 738907--738943 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
738897 AAAACACCTG
738907 AAAATAAATCACAAA
1 AAAATAAATCACAAA
*
738922 AAAATAAAT-A-ATA
1 AAAATAAATCACAAA
738935 AAAATAAAT
1 AAAATAAAT
738944 TATTATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.52
14 1 0.05
15 9 0.43
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAATCACAAA
Found at i:741383 original size:13 final size:13
Alignment explanation
Indices: 741365--741389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
741355 CCGTGGCATT
741365 CTTGTTTTGTTTA
1 CTTGTTTTGTTTA
741378 CTTGTTTTGTTT
1 CTTGTTTTGTTT
741390 TGCATATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.08, G:0.16, T:0.72
Consensus pattern (13 bp):
CTTGTTTTGTTTA
Found at i:744570 original size:394 final size:393
Alignment explanation
Indices: 743835--744625 Score: 1160
Period size: 394 Copynumber: 2.0 Consensus size: 393
743825 TATCTCCCTC
* *
743835 TAAAGCACAAAATTCCATCAGTATTAATCCCAAAGTCTTCAATCAAACCATCCTCAACCTATTTA
1 TAAACCACAAAATTCCATCAATATTAATCCCAAAGTCTTCAATCAAACCATCCTCAACCTATTTA
* * *
743900 AAACGAGGTGCTAGAGTTTCATCTAAACTCTGTTTATCCTTGATTTCCTGAACCCACGCAGGCTT
66 AAACGAGGTGCTAAAGTTTCATCCAAACACTGTTTATCCTTGATTTCCTGAACCCACGCAGGCTT
* *
743965 TACTTGCAATTTAGCCAAGATACCCCCATCATCAAAAAGACCCAAGCGAGCAAACATAGCCCTCA
131 TACTTGCAATTTAGCAAAGATACCCCCATCATCAAAAAGACCCAAGCGAGCAAACAAAGCCCTCA
* * * * *
744030 AATTAGACATTGCTTTTGTAATAGCCCGTTTTTAGTGAAATCGGAATAGTGGTTTCAGGACCACA
196 AATTAGACATTGCTTTTGTAACAACCCGATTTTAATGAAATCAGAATAGTGGTTTCAGGACCACA
* *
744095 AATTAGAAGACAAAAATTTTATTTATTATTATTTTATATCCTTCAGCATGATAGTAATACCGTAT
261 AATTAGAAGACAAAAATTTTATTTATTATTATTTTATATCCTACAACATGATAGTAATACCGTAT
* * *
744160 AAAAATTTCGTTAATAGTTGA-TTTTTATTCATTTTTAATGATTTATATGTTTTTGGGATCGTTG
326 AAAAAATTC-TTAATAGTT-ATTTTTTATTCATTTTTAATGATTTATATGTTTTCGAGATCGTTG
744224 GACTT
389 GACTT
* **
744229 TAAACCACAAAATTCCATCAATATTAATCCCAAAGTCTTCAGTTGAACCATCCTCAACCTATTTA
1 TAAACCACAAAATTCCATCAATATTAATCCCAAAGTCTTCAATCAAACCATCCTCAACCTATTTA
* * * *
744294 AAATGAGGTGTTAAAGTTTCATCCAAACACTGTTTATCCTTGATTTCCTGAACCTATGCAGGCTT
66 AAACGAGGTGCTAAAGTTTCATCCAAACACTGTTTATCCTTGATTTCCTGAACCCACGCAGGCTT
* * *
744359 TACTTGCAATTTAGCAAAGATACCCCCATCATCAAAAAGACTCAAGCTAGCGAACAAAGCCCTCA
131 TACTTGCAATTTAGCAAAGATACCCCCATCATCAAAAAGACCCAAGCGAGCAAACAAAGCCCTCA
* *
744424 AATTAGACATTG-TCTTTGTAACAATCCGATTTTAATGAAATCAGAATAGTGGTTT-TGAGACCA
196 AATTAGACATTGCT-TTTGTAACAACCCGATTTTAATGAAATCAGAATAGTGGTTTCAG-GACCA
* * *
744487 CAAATCTA-AAGCCAAAAATTTTATTTTTTTATTATTTTATATCCTACAACATGATAGTAGTACC
259 CAAAT-TAGAAGACAAAAATTTTA-TTTATTATTATTTTATATCCTACAACATGATAGTAATACC
** *
744551 GTATAAAAAAATT-TTAATAGTTATTTTTTATTTGTTTTTAATGATTTATATGTTTTCGAGATTG
322 GTAT-AAAAAATTCTTAATAGTTATTTTTTATTCATTTTTAATGATTTATATGTTTTCGAGATCG
*
744615 TTGGGCTT
386 TTGGACTT
744623 TAA
1 TAA
744626 TCTAGCTAGC
Statistics
Matches: 355, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
393 3 0.01
394 303 0.85
395 42 0.12
396 7 0.02
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (393 bp):
TAAACCACAAAATTCCATCAATATTAATCCCAAAGTCTTCAATCAAACCATCCTCAACCTATTTA
AAACGAGGTGCTAAAGTTTCATCCAAACACTGTTTATCCTTGATTTCCTGAACCCACGCAGGCTT
TACTTGCAATTTAGCAAAGATACCCCCATCATCAAAAAGACCCAAGCGAGCAAACAAAGCCCTCA
AATTAGACATTGCTTTTGTAACAACCCGATTTTAATGAAATCAGAATAGTGGTTTCAGGACCACA
AATTAGAAGACAAAAATTTTATTTATTATTATTTTATATCCTACAACATGATAGTAATACCGTAT
AAAAAATTCTTAATAGTTATTTTTTATTCATTTTTAATGATTTATATGTTTTCGAGATCGTTGGA
CTT
Found at i:753295 original size:13 final size:13
Alignment explanation
Indices: 753272--753307 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
753262 AAAGACCCTA
*
753272 TTCTATTTTTCTTT
1 TTCT-TTTTTCGTT
753286 TTCTTTTTTCGTT
1 TTCTTTTTTCGTT
753299 TTCTTTTTT
1 TTCTTTTTT
753308 GTTGCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTCGTT
Found at i:753994 original size:51 final size:51
Alignment explanation
Indices: 753933--754078 Score: 143
Period size: 50 Copynumber: 2.9 Consensus size: 51
753923 GAGATTTGTT
* * *
753933 GTTGTAGCTTTAATCTATTCCATTGCACCGCCTGGGAAAGTAAGATTCGCC
1 GTTGTGGCTTTAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACC
* ** ** * * *
753984 GTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GGGGAAGCAAGATTCACC
1 GTTGTGGCTTTAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACC
* * * *
754034 GTTGTGGCTTTAATCTGTTCCACTACACCGCTTGGGAGA-TAAGAT
1 GTTGTGGCTTTAATCTATTCCACTGCACCGCCTGGGAAAGTAAGAT
754079 CTATAATTCT
Statistics
Matches: 72, Mismatches: 22, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
50 44 0.61
51 28 0.39
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (51 bp):
GTTGTGGCTTTAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACC
Found at i:754455 original size:87 final size:87
Alignment explanation
Indices: 754300--754803 Score: 740
Period size: 87 Copynumber: 5.8 Consensus size: 87
754290 GCTAATGCAA
* * * * *
754300 GAAGGCAAGACCTGCTATCTTTAACCAGCTCCACTGCACCCGATGGAGGCAAGGCTTTATTTTTG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
754365 ATCTGCTTCGCTGTTAACGCAG
66 ATCTGCTTCGCTGTTAACGCAG
* * * * * * *
754387 GAAGGCAAGATCTGGTATTTTCAACTAGCTCCCCTGCACCCGATGGAGGCAAGGCTTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
* *
754452 ATCTACTTCGCTGTTAACGTAG
66 ATCTGCTTCGCTGTTAACGCAG
* * * *
754474 GAAGGAAAGATTTGCTATCTTCAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTTG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
754539 ATCTGCTTCGCTGTTAACGCAG
66 ATCTGCTTCGCTGTTAACGCAG
* * *
754561 GATGGCAAGATCTGCTATCTTCAACCAGCT-CACTACAACTGGATAGAGGCAAGGCTTTGTTTTT
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC-CGATGGAGGCAAGGCTTTGTTTTT
*
754625 GATCTGCTTCGCTGTTAATGCAG
65 GATCTGCTTCGCTGTTAACGCAG
*
754648 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
* *
754713 ATCTGCTTCGCTATTAATGCAG
66 ATCTGCTTCGCTGTTAACGCAG
* * *
754735 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAATCGATGGAGGCAAGGCTTTGTGTTGG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
754800 ATCT
66 ATCT
754804 TCACAGATCT
Statistics
Matches: 378, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
86 8 0.02
87 361 0.96
88 9 0.02
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTG
ATCTGCTTCGCTGTTAACGCAG
Found at i:754743 original size:43 final size:43
Alignment explanation
Indices: 754607--754743 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 43
754597 AACTGGATAG
* *
754607 AGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAATGCAGGA
* * * * * * * * *
754650 AGGCAA-GATCTGCTATCTTCAACCAGCTCCACTA-CAA-CCGATGG-
1 AGGCAAGGCTTTG-T-T-TTCGATCTGCTTCGCTATTAATGC-A-GGA
754694 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAATGCAGGA
754737 AGGCAAG
1 AGGCAAG
754744 ATCTGCTATC
Statistics
Matches: 65, Mismatches: 20, Indels: 18
0.63 0.19 0.17
Matches are distributed among these distances:
42 18 0.28
43 19 0.29
44 12 0.18
45 16 0.25
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAATGCAGGA
Found at i:756049 original size:7 final size:7
Alignment explanation
Indices: 756023--756084 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
756013 TTAGCCTCTC
756023 CATTTTT
1 CATTTTT
**
756030 CATTTCC
1 CATTTTT
756037 CA-TTTT
1 CATTTTT
756043 CATTTTT
1 CATTTTT
756050 CATTTTT
1 CATTTTT
756057 CATTTTT
1 CATTTTT
*
756064 CA-TTCT
1 CATTTTT
756070 CATTTTTT
1 CA-TTTTT
756078 CATTTTT
1 CATTTTT
756085 TTTGGAACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 9 0.20
7 32 0.70
8 5 0.11
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (7 bp):
CATTTTT
Found at i:756060 original size:20 final size:20
Alignment explanation
Indices: 756023--756083 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
756013 TTAGCCTCTC
**
756023 CATTTTTCATTTCCCATTTT
1 CATTTTTCATTTTTCATTTT
756043 CATTTTTCATTTTTCATTTTT
1 CATTTTTCATTTTTCA-TTTT
*
756064 CA-TTCTCATTTTTTCATTTT
1 CATTTTTCA-TTTTTCATTTT
756084 TTTTGGAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (20 bp):
CATTTTTCATTTTTCATTTT
Found at i:758991 original size:20 final size:21
Alignment explanation
Indices: 758949--758992 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
758939 TCCTTTTGTA
758949 TTTGCTCCAGTTTCTCTAATC
1 TTTGCTCCAGTTTCTCTAATC
* * *
758970 TTTGGTCCA-TTTCTTTAGTC
1 TTTGCTCCAGTTTCTCTAATC
758990 TTT
1 TTT
758993 CGACAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.55
Consensus pattern (21 bp):
TTTGCTCCAGTTTCTCTAATC
Found at i:773571 original size:51 final size:50
Alignment explanation
Indices: 773509--773667 Score: 155
Period size: 51 Copynumber: 3.2 Consensus size: 50
773499 AGCAAATCCC
* *
773509 ATTTCCTTGGCATTGTAGTCGGACAGATTAAAGCTGAAGGCAACGAATCTT
1 ATTTCCCTGGCATTGTAG-CGGACAGATTAAAGTTGAAGGCAACGAATCTT
* * * * *
773560 ATTTCCCTGGCA-T-T-GC-AATAGATTAAAGTTCAAGGCATCAAATCTT
1 ATTTCCCTGGCATTGTAGCGGACAGATTAAAGTTGAAGGCAACGAATCTT
* * * * *
773606 ATTTCCGTGGCATTGCAGCGGAGCAAATTAAAGTTGTAGGCAGCGAATCTT
1 ATTTCCCTGGCATTGTAGCGGA-CAGATTAAAGTTGAAGGCAACGAATCTT
*
773657 ATCTCCCTGGC
1 ATTTCCCTGGC
773668 GTTAAAGTTA
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
46 35 0.41
47 2 0.02
48 1 0.01
49 3 0.04
50 2 0.02
51 42 0.49
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (50 bp):
ATTTCCCTGGCATTGTAGCGGACAGATTAAAGTTGAAGGCAACGAATCTT
Found at i:773575 original size:97 final size:98
Alignment explanation
Indices: 773424--773667 Score: 305
Period size: 97 Copynumber: 2.5 Consensus size: 98
773414 ACCGCTAAAG
* * * * *
773424 TTGTAGT-GGATCAGATTAAAGCTGAAGGCGGCGAATCTTGTTTCCCTAGAATTGCAATAGATGA
1 TTGTAGTCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCATTGCAATAGATGA
*
773488 AAGGTAAAGGCAGCAAATCCCATTTCCTTGGCA
66 AAGGTAAAGGCAGCAAATCCCATTTCCGTGGCA
* *
773521 TTGTAGTCGGA-CAGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCATTGCAATAGATTA
1 TTGTAGTCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCATTGCAATAGATGA
* * * **
773585 AAGTTCAAGGCATCAAATCTTATTTCCGTGGCA
66 AAGGTAAAGGCAGCAAATCCCATTTCCGTGGCA
* * * * *
773618 TTGCAG-CGGAGCAAATTAAAGTTGTAGGCAGCGAATCTTATCTCCCTGGC
1 TTGTAGTCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGC
773668 GTTAAAGTTA
Statistics
Matches: 127, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
96 4 0.03
97 120 0.94
98 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (98 bp):
TTGTAGTCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCATTGCAATAGATGA
AAGGTAAAGGCAGCAAATCCCATTTCCGTGGCA
Found at i:773604 original size:46 final size:46
Alignment explanation
Indices: 773436--773622 Score: 140
Period size: 46 Copynumber: 4.0 Consensus size: 46
773426 GTAGTGGATC
* ** * * * *
773436 AGATTAAAGCTGAAGGCGGCGAATCTTGTTTCCCTAGAATTGCAAT
1 AGATTAAAGCTCAAGGCAACAAATCTTATTTCCCTGGCATTGCAAT
* * * * ** * * *
773482 AGATGAAAGGTAAAGGCAGCAAATCCCATTTCCTTGGCATTGTAGTCGGAC
1 AGATTAAAGCTCAAGGCAACAAATCTTATTTCCCTGGCA-T-T-G-C-AAT
* *
773533 AGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCATTGCAAT
1 AGATTAAAGCTCAAGGCAACAAATCTTATTTCCCTGGCATTGCAAT
* * *
773579 AGATTAAAGTTCAAGGCATCAAATCTTATTTCCGTGGCATTGCA
1 AGATTAAAGCTCAAGGCAACAAATCTTATTTCCCTGGCATTGCA
773623 GCGGAGCAAA
Statistics
Matches: 108, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
46 68 0.63
47 2 0.02
48 2 0.02
49 2 0.02
50 2 0.02
51 32 0.30
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
AGATTAAAGCTCAAGGCAACAAATCTTATTTCCCTGGCATTGCAAT
Found at i:774063 original size:22 final size:22
Alignment explanation
Indices: 774029--774080 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
774019 CGATTAAATC
774029 AATAAACACCAAAGACAAAA-AAA
1 AATAAA-ACCAAAGA-AAAACAAA
* *
774052 AATAAAACCAAATAAAAACCAA
1 AATAAAACCAAAGAAAAACAAA
774074 AATAAAA
1 AATAAAA
774081 TTAAATGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.75, C:0.15, G:0.02, T:0.08
Consensus pattern (22 bp):
AATAAAACCAAAGAAAAACAAA
Found at i:786316 original size:20 final size:20
Alignment explanation
Indices: 786291--786331 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
786281 AAATGCTAAA
*
786291 CAGAGGCA-CGAATGTGCAAT
1 CAGAGGCATC-AAAGTGCAAT
786311 CAGAGGCATCAAAGTGCAAT
1 CAGAGGCATCAAAGTGCAAT
786331 C
1 C
786332 CCGTACAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.15
Consensus pattern (20 bp):
CAGAGGCATCAAAGTGCAAT
Found at i:789396 original size:29 final size:28
Alignment explanation
Indices: 789351--789406 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
789341 TTAATTAAAA
*
789351 TAATAAAATTAATTAACCTAAAATAACT
1 TAATAAAATTAATTAACATAAAATAACT
*
789379 TAATGAAATTTAATTAACATAAAATAAC
1 TAAT-AAAATTAATTAACATAAAATAAC
789407 ATATCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (28 bp):
TAATAAAATTAATTAACATAAAATAACT
Found at i:789416 original size:29 final size:29
Alignment explanation
Indices: 789350--789417 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
789340 ATTAATTAAA
* *
789350 ATAA-TAAAATTAATTAACCTAAAATAAC
1 ATAATTAAATTTAATTAACATAAAATAAC
* *
789378 TTAATGAAATTTAATTAACATAAAATAAC
1 ATAATTAAATTTAATTAACATAAAATAAC
789407 AT-ATCTAAATT
1 ATAAT-TAAATT
789418 AAGTAGTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (29 bp):
ATAATTAAATTTAATTAACATAAAATAAC
Found at i:791875 original size:29 final size:28
Alignment explanation
Indices: 791818--791897 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
791808 CTAGTGAAAA
* * *
791818 TAATTAACTTAAAATAACCTAATGAAATT
1 TAATTAGCCTAAAATAACCTAATCAAA-T
791847 TAATTAGCCTAAAATAACCTAA-CATAAT
1 TAATTAGCCTAAAATAACCTAATCA-AAT
* * *
791875 TAAGTAGTCTAAAATAACTTAAT
1 TAATTAGCCTAAAATAACCTAAT
791898 GGTGTTAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (28 bp):
TAATTAGCCTAAAATAACCTAATCAAAT
Found at i:791887 original size:28 final size:29
Alignment explanation
Indices: 791827--791897 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
791817 ATAATTAACT
* *
791827 TAAAATAACCTAATGAAATTTAATTAGCC
1 TAAAATAACCTAATCAAATTTAAGTAGCC
*
791856 TAAAATAACCTAA-CATAA-TTAAGTAGTC
1 TAAAATAACCTAATCA-AATTTAAGTAGCC
*
791884 TAAAATAACTTAAT
1 TAAAATAACCTAAT
791898 GGTGTTAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 21 0.58
29 15 0.42
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (29 bp):
TAAAATAACCTAATCAAATTTAAGTAGCC
Found at i:794154 original size:26 final size:26
Alignment explanation
Indices: 794103--794154 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
794093 ACCAATATCC
* *
794103 CAGGATAGCTGCCAGTAGTAATAATG
1 CAGGAGAGCTGCCAGTAGTAAGAATG
*
794129 CAGGAGAGCTGCCAGTAGTCAGAATG
1 CAGGAGAGCTGCCAGTAGTAAGAATG
794155 GCTAAGAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (26 bp):
CAGGAGAGCTGCCAGTAGTAAGAATG
Found at i:794202 original size:22 final size:21
Alignment explanation
Indices: 794148--794212 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
794138 TGCCAGTAGT
794148 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAA-AGCCATAAA
* *
794170 CATG-ATAGCTATAAGCTATAAA
1 CA-GAATGGCTA-AAGCCATAAA
794192 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTA-AAGCCATAA
794213 GTACAGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (21 bp):
CAGAATGGCTAAAGCCATAAA
Found at i:794281 original size:32 final size:32
Alignment explanation
Indices: 794204--794438 Score: 208
Period size: 32 Copynumber: 7.4 Consensus size: 32
794194 GAATGGCTAC
* * * *
794204 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * *
794235 AAGCCATCAATAGCAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * *
794267 CAGCCATCAGTAGCAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * * *
794299 AAACCATTAGTAACAGTGAAATAATCGGTACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* *
794331 CAGCCATC-GATAACAGTAATATGATCGGCACA
1 AAGCCATCAG-TAACAGTGATATGATCGGCACA
** *
794363 AAATCATCAGTAACGGT-ACTATGATCGGCACA
1 AAGCCATCAGTAACAGTGA-TATGATCGGCACA
* *
794395 AAGCAATCAGTAACGGT-ACTATGATCGGCACA
1 AAGCCATCAGTAACAGTGA-TATGATCGGCACA
*
794427 AAGGCATCAGTA
1 AAGCCATCAGTA
794439 GCATTGCAGC
Statistics
Matches: 167, Mismatches: 33, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
31 11 0.07
32 155 0.93
33 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTGATATGATCGGCACA
Found at i:794517 original size:27 final size:26
Alignment explanation
Indices: 794487--794546 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
794477 AGCTGCCAAC
*
794487 AACAATATATGTGGCCA-AGCCACTAGT
1 AACAATAT-TGTGG-CAGAGCCACCAGT
*
794514 AACAGTGATTGTGGCAGAGCCACCAGT
1 AACAAT-ATTGTGGCAGAGCCACCAGT
794541 -ACAATA
1 AACAATA
794547 CTTCCTCCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 1 0.04
26 6 0.21
27 19 0.68
28 2 0.07
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
AACAATATTGTGGCAGAGCCACCAGT
Found at i:794761 original size:27 final size:27
Alignment explanation
Indices: 794704--795022 Score: 408
Period size: 27 Copynumber: 11.9 Consensus size: 27
794694 TTACCCACCA
* *
794704 GGGCATTACGGTTATTTTA-CCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
*
794730 GGGCATTACGATCATTTTACCCTACAA
1 GGGCATTACGATCATTTTACCCTACAG
*
794757 GGGCATTAC-AGTTATTTTACCCTACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* * *
794784 GGGCATTACGATCATTTAACCCTAGAT
1 GGGCATTACGATCATTTTACCCTACAG
*
794811 GGGCATTACGGTCATTTTACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
794838 GGGCATTACGATCATTTTAACCTACAA
1 GGGCATTACGATCATTTTACCCTACAG
* *
794865 GGGCATTACGGTCATTTTACCCTATAG
1 GGGCATTACGATCATTTTACCCTACAG
* * * *
794892 GGGCATTATGGTCATTTTACCTTACAC
1 GGGCATTACGATCATTTTACCCTACAG
*
794919 GGGCATTACGATCATTTTACCTTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
794946 GGGCATTACGGTTATTTTACCCAACAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
794973 GGGCATTACGGTCATTTTACCCTATAG
1 GGGCATTACGATCATTTTACCCTACAG
*
795000 GGGCATTTCGATCATTTTACCCT
1 GGGCATTACGATCATTTTACCCT
795023 TCGATGGTAT
Statistics
Matches: 254, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
26 18 0.07
27 235 0.93
28 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
GGGCATTACGATCATTTTACCCTACAG
Found at i:794797 original size:54 final size:54
Alignment explanation
Indices: 794693--795049 Score: 457
Period size: 54 Copynumber: 6.6 Consensus size: 54
794683 AAAATAGTCA
* *
794693 TTTACCC-ACCAGGGCATTACGGTTATTTTA-CCTACAGGGGCATTACGATCAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* *
794745 TTTACCCTACAAGGGCATTACAGTTATTTTACCCTACAGGGGCATTACGATCAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* * *
794799 TTAACCCTAGATGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* * * *
794853 TTTAACCTACAAGGGCATTACGGTCATTTTACCCTATAGGGGCATTATGGTCAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* * * * * *
794907 TTTACCTTACACGGGCATTACGATCATTTTACCTTACAGGGGCATTACGGTTAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* * * *
794961 TTTACCCAACAGGGGCATTACGGTCATTTTACCCTATAGGGGCATTTCGATCAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
* * * * * *
795015 TTTACCCTTCGATGGTATTTCAGTCATTTTACCCT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACCCT
795050 TCTGGTGTAT
Statistics
Matches: 264, Mismatches: 39, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
52 7 0.03
53 21 0.08
54 236 0.89
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (54 bp):
TTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACGATCAT
Found at i:795059 original size:27 final size:27
Alignment explanation
Indices: 795011--795066 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
795001 GGCATTTCGA
795011 TCATTTTACCCTTCGATGGTATTTCAG
1 TCATTTTACCCTTCGATGGTATTTCAG
*
795038 TCATTTTACCCTTCTGGT-GTATTTCAG
1 TCATTTTACCCTTC-GATGGTATTTCAG
795065 TC
1 TC
795067 CAGATATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.46
Consensus pattern (27 bp):
TCATTTTACCCTTCGATGGTATTTCAG
Found at i:797135 original size:25 final size:25
Alignment explanation
Indices: 797080--797136 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
797070 TGGATAGTCC
* *
797080 ACAGCTCGTGGGAGCACACCAATTT
1 ACAGCTCGTGAGAGCACACCAATCT
** *
797105 TTAGCTCGTGAGAGCATACCAATCT
1 ACAGCTCGTGAGAGCACACCAATCT
797130 ACAGCTC
1 ACAGCTC
797137 AAATGAGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCACACCAATCT
Found at i:803881 original size:15 final size:15
Alignment explanation
Indices: 803861--803900 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
803851 GGACACACGA
*
803861 GTGTGTCACTTGGCC
1 GTGTGTCACATGGCC
*
803876 GTGTGTTACATGGCC
1 GTGTGTCACATGGCC
803891 GTGTGTCACA
1 GTGTGTCACA
803901 CACGGCTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.12, C:0.23, G:0.33, T:0.33
Consensus pattern (15 bp):
GTGTGTCACATGGCC
Found at i:806671 original size:103 final size:102
Alignment explanation
Indices: 806422--806789 Score: 574
Period size: 102 Copynumber: 3.6 Consensus size: 102
806412 ATTGCATATA
806422 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
806487 TGAAATGTGAAGGGGGTTGCTAAGTGCTAAATCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
806524 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAACTGCTAATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
806589 TTAAGTGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
* * ** * **
806627 GAGGGGTTGGTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCACATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
806692 TGAAATGTGAAGGGGGTTGCTAACTGCTGATTCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
806729 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
806790 ATAACGGTTA
Statistics
Matches: 237, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
102 149 0.63
103 88 0.37
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (102 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:808339 original size:35 final size:35
Alignment explanation
Indices: 808300--808369 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
808290 ACTCCTGAGG
808300 AATGTTTGAAATGTGATGTGTCTTTATTAAAGGAT
1 AATGTTTGAAATGTGATGTGTCTTTATTAAAGGAT
*
808335 AATGTTTGAAATGTGATGTGTCTTTATTGAAGGAT
1 AATGTTTGAAATGTGATGTGTCTTTATTAAAGGAT
808370 TCGGCATACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (35 bp):
AATGTTTGAAATGTGATGTGTCTTTATTAAAGGAT
Found at i:816553 original size:32 final size:32
Alignment explanation
Indices: 816512--816672 Score: 297
Period size: 32 Copynumber: 5.1 Consensus size: 32
816502 TCTATCATAC
816512 TTAGGCAATAAAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTT
816544 TTAGGCAATAAAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTT
*
816576 TTAGGCAATAGAATAAT-ATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTT
*
816607 TTAGGCAATAGAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTT
816639 TTAGGCAATAAAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTT
816671 TT
1 TT
816673 GACCTCAGAT
Statistics
Matches: 126, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 31 0.25
32 95 0.75
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.35
Consensus pattern (32 bp):
TTAGGCAATAAAATAATAATAAAATAAATTTT
Found at i:816614 original size:63 final size:64
Alignment explanation
Indices: 816512--816672 Score: 297
Period size: 63 Copynumber: 2.5 Consensus size: 64
816502 TCTATCATAC
816512 TTAGGCAATAAAATAATAATAAAATAAATTTTTTAGGCAATAAAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTTTTAGGCAATAAAATAATAATAAAATAAATTTT
* *
816576 TTAGGCAATAGAATAAT-ATAAAATAAATTTTTTAGGCAATAGAATAATAATAAAATAAATTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTTTTAGGCAATAAAATAATAATAAAATAAATTTT
816639 TTAGGCAATAAAATAATAATAAAATAAATTTTTT
1 TTAGGCAATAAAATAATAATAAAATAAATTTTTT
816673 GACCTCAGAT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 61 0.66
64 32 0.34
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.35
Consensus pattern (64 bp):
TTAGGCAATAAAATAATAATAAAATAAATTTTTTAGGCAATAAAATAATAATAAAATAAATTTT
Found at i:819434 original size:50 final size:50
Alignment explanation
Indices: 819359--819507 Score: 217
Period size: 50 Copynumber: 3.0 Consensus size: 50
819349 NNNNNNNNNN
*
819359 CGAGATAAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* * *
819409 CGAGATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* ** * *
819459 CGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
819508 GTACAAGAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
Found at i:833180 original size:25 final size:24
Alignment explanation
Indices: 833104--833186 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
833094 CAGCTCATGA
*
833104 GAGCATACCGATTTATAGCTCGTGA-
1 GAGCATACCGA-TCATAGCTCGT-AT
* * * **
833129 GAGCATACCAATCTACAACTCAAAT
1 GAGCATACCGATC-ATAGCTCGTAT
833154 GAGCATACCGATGCATAGCTCGTAT
1 GAGCATACCGAT-CATAGCTCGTAT
833179 GAGCATAC
1 GAGCATAC
833187 GTGTAAATAA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
24 2 0.05
25 41 0.93
26 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (24 bp):
GAGCATACCGATCATAGCTCGTAT
Found at i:837547 original size:52 final size:52
Alignment explanation
Indices: 837446--837707 Score: 264
Period size: 52 Copynumber: 5.0 Consensus size: 52
837436 GGGTATTTAG
* ** * *
837446 GGGTATTTCAGTAATTCTACCCT-TC-AGAGGTATTTCAATAGTTTTCCCATTGA
1 GGGTATTTCAGTAATT-TA-CCTGTCGA-AGGCATTTCGGTAATTTACCCATTGA
** * *
837499 GGGTATTTTGGCAATTTACCTGTCGATA-GTATTTCGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCTGTCGA-AGGCATTTCGGTAATTTACCCATTGA
* * *
837551 GGGTATTTCAGTAATTTACCTGTTGAAGGCATTTCGATAATTTACCCATTAA
1 GGGTATTTCAGTAATTTACCTGTCGAAGGCATTTCGGTAATTTACCCATTGA
* * ** *
837603 GGGTATTTCAGTAATTTACCCGTTGAAGGCATTTTAGTAATTTACCCATTTA
1 GGGTATTTCAGTAATTTACCTGTCGAAGGCATTTCGGTAATTTACCCATTGA
* *
837655 GGGTATTTCAGTAATTTACCTGTTC--AGTGTATTTTGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCTG-TCGAAG-GCATTTCGGTAATTTACCCATTGA
837707 G
1 G
837708 ACTCATAACG
Statistics
Matches: 179, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
51 6 0.03
52 157 0.88
53 16 0.09
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (52 bp):
GGGTATTTCAGTAATTTACCTGTCGAAGGCATTTCGGTAATTTACCCATTGA
Found at i:837556 original size:26 final size:26
Alignment explanation
Indices: 837446--837707 Score: 222
Period size: 26 Copynumber: 10.0 Consensus size: 26
837436 GGGTATTTAG
*
837446 GGGTATTTCAGTAATTCTACCC-TTCA
1 GGGTATTTCAGTAATT-TACCCATTGA
* * *
837472 GAGGTATTTCAATAGTTTTCCCATTGA
1 G-GGTATTTCAGTAATTTACCCATTGA
** * ** *
837499 GGGTATTTTGGCAATTTACCTGTCGA
1 GGGTATTTCAGTAATTTACCCATTGA
** *
837525 TAGTATTTCGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCATTGA
**
837551 GGGTATTTCAGTAATTTACCTGTTGA
1 GGGTATTTCAGTAATTTACCCATTGA
* * *
837577 AGGCATTTC-GATAATTTACCCATTAA
1 GGGTATTTCAG-TAATTTACCCATTGA
*
837603 GGGTATTTCAGTAATTTACCCGTTGA
1 GGGTATTTCAGTAATTTACCCATTGA
* * * *
837629 AGGCATTTTAGTAATTTACCCATTTA
1 GGGTATTTCAGTAATTTACCCATTGA
** *
837655 GGGTATTTCAGTAATTTACCTGTTCA
1 GGGTATTTCAGTAATTTACCCATTGA
* **
837681 GTGTATTTTGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCATTGA
837707 G
1 G
837708 ACTCATAACG
Statistics
Matches: 181, Mismatches: 51, Indels: 8
0.75 0.21 0.03
Matches are distributed among these distances:
25 1 0.01
26 162 0.90
27 18 0.10
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (26 bp):
GGGTATTTCAGTAATTTACCCATTGA
Found at i:842841 original size:16 final size:18
Alignment explanation
Indices: 842804--842842 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
842794 TTCTCTCTCG
*
842804 TTTCTTTTTCAATATCTT
1 TTTCTTTGTCAATATCTT
842822 TTTCTTTGTCAAT-T-TT
1 TTTCTTTGTCAATATCTT
842838 TTTCT
1 TTTCT
842843 CAATCTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTCTTTGTCAATATCTT
Found at i:842922 original size:15 final size:17
Alignment explanation
Indices: 842902--842944 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
842892 TTTTGATATC
842902 TCATTTTCATC-TT-TT
1 TCATTTTCATCATTCTT
*
842917 TCATTTTCTTCATTTCTT
1 TCATTTTCATCA-TTCTT
842935 TCATTTTCAT
1 TCATTTTCAT
842945 TTTCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (17 bp):
TCATTTTCATCATTCTT
Found at i:842931 original size:24 final size:24
Alignment explanation
Indices: 842906--842950 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
842896 GATATCTCAT
*
842906 TTTC-ATCTTTTTCATTTTCTTCA
1 TTTCTATCATTTTCATTTTCTTCA
*
842929 TTTCTTTCATTTTCATTTTCTT
1 TTTCTATCATTTTCATTTTCTT
842951 TGTTCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTATCATTTTCATTTTCTTCA
Found at i:842960 original size:24 final size:23
Alignment explanation
Indices: 842914--842958 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
842904 ATTTTCATCT
842914 TTTTCATTTTCTTCATTTCTTTCA
1 TTTTCATTTTCTT-ATTTCTTTCA
842938 TTTTCATTTTCTT-TGTTCTTT
1 TTTTCATTTTCTTAT-TTCTTT
842959 TCTCGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 6 0.30
24 13 0.65
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTCATTTTCTTATTTCTTTCA
Done.