Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold45
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: 1930935
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 50924 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1887586 original size:44 final size:43
Alignment explanation
Indices: 1887441--1887817 Score: 139
Period size: 44 Copynumber: 8.6 Consensus size: 43
1887431 TGTCTTCGAT
* * *
1887441 CTACTCCACTACTGCTTAGGGAGATTAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGATCTGTAA-TTTCAGC
* * * * ** * *
1887485 CTACTCCGCTGCTGCTCAGGGAAATAAG-GCTGGGGACTTC-GAT
1 CTACTCCACTACTGCTCAGGGAGATAAGATCT-GTAATTTCAG-C
* *
1887528 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTCAGC
1 CTACTCCACTACTGCTCAGGGAGATAAGATCTGTAATT-TCAGC
* * **
1887572 CTACTCCACTACTGCTCAAGGAGATAGGAT-TCACAATCTTCCA-C
1 CTACTCCACTACTGCTCAGGGAGATAAGATCT-GTAAT-TT-CAGC
* * ** * *
1887616 TTATTCCACTGTTGAC-CAGGAAGATAAGAT-TCGTAATCTTCAAC
1 CTACTCCACTACTG-CTCAGGGAGATAAGATCT-GTAAT-TTCAGC
* * *
1887660 TTA-TGCCACTATTGAC-CAGGGAGATAAGAT-TCGTAATCTTCAAC
1 CTACT-CCACTACTG-CTCAGGGAGATAAGATCT-GTAAT-TTCAGC
* * * * * * * *
1887704 CTATTCTACTGCTACCCAGGGAGATAGGA-CTTGCAATCTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGATC-TGTAAT-TTCAGC
* * * * *
1887748 CTATTCTACTGCTGCTCAGGGAGATAAG-TCTTGCAATCTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGATC-TGTAAT-TTCAGC
*
1887792 CTATTCCACTACTG-TCCAGGGAGATA
1 CTACTCCACTACTGCT-CAGGGAGATA
1887818 GGACTCACAA
Statistics
Matches: 266, Mismatches: 50, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
43 37 0.14
44 222 0.83
45 7 0.03
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (43 bp):
CTACTCCACTACTGCTCAGGGAGATAAGATCTGTAATTTCAGC
Found at i:1887829 original size:44 final size:44
Alignment explanation
Indices: 1887591--1887920 Score: 326
Period size: 44 Copynumber: 7.5 Consensus size: 44
1887581 TACTGCTCAA
* * * *
1887591 GGAGATAGGATTCACAATCTTCCACTTATTCCACTGTTGACCAG
1 GGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGTCCAG
* * ** * * ** *
1887635 GAAGATAAGATTCGTAATCTTCAACTTATGCCACTATTGACCAG
1 GGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGTCCAG
* ** * **
1887679 GGAGATAAGATTCGTAATCTTCAACCTATTCTACTGCTACCCAG
1 GGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGTCCAG
* *
1887723 GGAGATAGGACTT-GCAATCTTCAACCTATTCTACTGCTG-CTCAG
1 GGAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGTC-CAG
* ** *
1887767 GGAGATAAG-TCTTGCAATCTTCAACCTATTCCACTACTGTCCAG
1 GGAGATAGGAT-TCACAATCTTCAACCTATTCCACTGCTGTCCAG
* * * *
1887811 GGAGATAGGACTCACAATCTTCAACCTATTTCGCTGCAGTCCAG
1 GGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGTCCAG
*
1887855 GGAGATAGGATTCACAATCTTCAACCTATGT-CGCTGCTGTCCAG
1 GGAGATAGGATTCACAATCTTCAACCTAT-TCCACTGCTGTCCAG
1887899 GGAGATAGGATTCACAATCTTC
1 GGAGATAGGATTCACAATCTTC
1887921 GATCTGCTTC
Statistics
Matches: 248, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 241 0.97
45 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
GGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGTCCAG
Found at i:1889935 original size:57 final size:57
Alignment explanation
Indices: 1889847--1890020 Score: 348
Period size: 57 Copynumber: 3.1 Consensus size: 57
1889837 GGCTCTCATC
1889847 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1889904 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1889961 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1 TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
1890018 TGA
1 TGA
1890021 TTGTTTGATA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 117 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (57 bp):
TGAAATGGATTCCAATTCTTTAATATACCCTGCAATAAACCCTGATATATCTTGAAT
Found at i:1894521 original size:64 final size:63
Alignment explanation
Indices: 1894445--1894563 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 63
1894435 TAATTGATTC
*
1894445 CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTTAAACACACTAAACTTAGAAG
1 CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAACTTAGAAG
* *
1894508 CAACTAAAATAGTCACCTGCAAGCATTTATTAACAAACACATTAAAACACATTAAA
1 CAACT-AAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAA
1894564 ACACATTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 5 0.10
64 47 0.90
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.24
Consensus pattern (63 bp):
CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAACTTAGAAG
Found at i:1894576 original size:20 final size:20
Alignment explanation
Indices: 1894542--1894583 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1894532 ATTTATTAAC
*
1894542 AAACACATTAAAACACATTA
1 AAACACATTAAAACACACTA
**
1894562 AAACACATTTTAACACACTA
1 AAACACATTAAAACACACTA
1894582 AA
1 AA
1894584 CTTAATAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACACATTAAAACACACTA
Found at i:1894578 original size:10 final size:10
Alignment explanation
Indices: 1894542--1894570 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1894532 ATTTATTAAC
1894542 AAACACATTA
1 AAACACATTA
1894552 AAACACATTA
1 AAACACATTA
1894562 AAACACATT
1 AAACACATT
1894571 TTAACACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (10 bp):
AAACACATTA
Found at i:1894712 original size:34 final size:34
Alignment explanation
Indices: 1894670--1894737 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1894660 GTTGTTCTAG
*
1894670 CAATTAAATAAACT-AAGATAAGCATTTATTCCAA
1 CAATTAAATAAA-TAAAGATAAGAATTTATTCCAA
1894704 CAATTAAATAAATAAAGATAAGAATTTATTCCAA
1 CAATTAAATAAATAAAGATAAGAATTTATTCCAA
1894738 ATGAACTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (34 bp):
CAATTAAATAAATAAAGATAAGAATTTATTCCAA
Found at i:1897940 original size:24 final size:24
Alignment explanation
Indices: 1897861--1897942 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
1897851 TACAAGAAGA
1897861 TGAAAGGTTTAAGGAAGATGAAAGG
1 TGAAAGG-TTAAGGAAGATGAAAGG
* * *
1897886 CT-AAAAGTTAAAGAAGATGGAAGG
1 -TGAAAGGTTAAGGAAGATGAAAGG
* *
1897910 TGGAAGGTTAAGGGAGATGAAAGG
1 TGAAAGGTTAAGGAAGATGAAAGG
1897934 TGAAAGGTT
1 TGAAAGGTT
1897943 GAACATCCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.87
25 4 0.09
26 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.37, T:0.20
Consensus pattern (24 bp):
TGAAAGGTTAAGGAAGATGAAAGG
Found at i:1901128 original size:30 final size:30
Alignment explanation
Indices: 1901084--1901140 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1901074 AAAAATTATC
*
1901084 GAGCTGAAATTGAGCTAATTCGAGCTCTTG
1 GAGCTGAAATTGAGCTAAATCGAGCTCTTG
*
1901114 GAGCTGGAAA-TGAGCTAAATGGAGCTC
1 GAGCT-GAAATTGAGCTAAATCGAGCTC
1901141 AACGAGATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (30 bp):
GAGCTGAAATTGAGCTAAATCGAGCTCTTG
Found at i:1904191 original size:3 final size:3
Alignment explanation
Indices: 1904183--1904220 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1904173 GTTAATACTG
1904183 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1904221 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1908000 original size:25 final size:25
Alignment explanation
Indices: 1907948--1908013 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
1907938 ATAAAATACA
1907948 TCTTTACATTCATTTTTGAGAAAATAT
1 TCTTT-CATTC-TTTTTGAGAAAATAT
*
1907975 TCTTTCATTCTTTTTGA-ATAATTAT
1 TCTTTCATTCTTTTTGAGA-AAATAT
1908000 TCTTTCATTCTTTT
1 TCTTTCATTCTTTT
1908014 GAACTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 1 0.03
25 26 0.70
26 5 0.14
27 5 0.14
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.58
Consensus pattern (25 bp):
TCTTTCATTCTTTTTGAGAAAATAT
Found at i:1908686 original size:14 final size:14
Alignment explanation
Indices: 1908645--1908680 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1908635 CAAGATGAAA
1908645 GTGGAAGATCTTAT
1 GTGGAAGATCTTAT
1908659 GTGGAAGATCTTAT
1 GTGGAAGATCTTAT
1908673 GTGGAAGA
1 GTGGAAGA
1908681 CTTTATCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.31
Consensus pattern (14 bp):
GTGGAAGATCTTAT
Found at i:1908781 original size:11 final size:11
Alignment explanation
Indices: 1908767--1908828 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
1908757 AAAAAGGGTC
1908767 AAAATCAAAATA
1 AAAAT-AAAATA
*
1908779 AAAATAAAAGTG
1 AAAATAAAA-TA
* *
1908791 ATAA-AAAAGA
1 AAAATAAAATA
1908801 AAAATAAAATA
1 AAAATAAAATA
1908812 AAAATAAAACTA
1 AAAATAAAA-TA
1908824 AAAAT
1 AAAAT
1908829 GGAGAGGCCG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 3 0.07
11 22 0.54
12 16 0.39
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1908815 original size:6 final size:6
Alignment explanation
Indices: 1908767--1908828 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
1908757 AAAAAGGGTC
* *
1908767 AAAATC AAAATA AAAATA AAAGTGATAA AAAAGA AAAAT- AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAA---AT-A AAAATA AAAATA AAAATA AAAATA
*
1908818 AAACTA AAAAT
1 AAAATA AAAAT
1908829 GGAGAGGCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
5 5 0.11
6 34 0.74
7 1 0.02
9 2 0.04
10 4 0.09
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1910294 original size:44 final size:44
Alignment explanation
Indices: 1910154--1910299 Score: 215
Period size: 44 Copynumber: 3.3 Consensus size: 44
1910144 GAAGCAGATC
* *
1910154 GAAGATTGTGAA-TCCTATCTCCATGGACAGTAGTGGAATAGGTT
1 GAAGATTGT-AAGCCCTATCTCCATGGACAGCAGTGGAATAGGTT
* * *
1910198 GAAGATTGCAAGTCCTATCTCCTTGGACAGCAGTGGAATAGGTT
1 GAAGATTGTAAGCCCTATCTCCATGGACAGCAGTGGAATAGGTT
1910242 GAAGATTGTAAGCCCTATCTCTC-TGGACAGCAGTGGAATAGGTT
1 GAAGATTGTAAGCCCTATCTC-CATGGACAGCAGTGGAATAGGTT
1910286 GAAGATTGTAAGCC
1 GAAGATTGTAAGCC
1910300 TTGCCTCCCT
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
43 2 0.02
44 92 0.97
45 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
GAAGATTGTAAGCCCTATCTCCATGGACAGCAGTGGAATAGGTT
Found at i:1910675 original size:50 final size:50
Alignment explanation
Indices: 1910524--1910704 Score: 174
Period size: 50 Copynumber: 3.6 Consensus size: 50
1910514 TTGGCAATAC
* *
1910524 AGTGGAAAAGATTGAAGCTACAACAGCGAATCTTACTT--TTCAGG-TGGTGC
1 AGTGGAAAAGATTGAAGCTACAACAGTGAATCTTACTTCCTT--GGCT-GTGT
* * * ** *
1910574 AGTGGAACAGATTGAAGCCACAA-AGGTGAATCTTGCTTCCCCGACAT-TGT
1 AGTGGAAAAGATTGAAGCTACAACA-GTGAATCTTACTTCCTTGGC-TGTGT
**
1910624 AGTTAAAAAGATTGAAGCTACAACAGTGAATCTTACTTCCTTGGCTGTGT
1 AGTGGAAAAGATTGAAGCTACAACAGTGAATCTTACTTCCTTGGCTGTGT
* *
1910674 AGTGGAACAGATTGAAGCTACGACAGTGAAT
1 AGTGGAAAAGATTGAAGCTACAACAGTGAAT
1910705 ATTGTTTCCC
Statistics
Matches: 104, Mismatches: 20, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
49 2 0.02
50 100 0.96
51 1 0.01
52 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (50 bp):
AGTGGAAAAGATTGAAGCTACAACAGTGAATCTTACTTCCTTGGCTGTGT
Found at i:1910678 original size:100 final size:99
Alignment explanation
Indices: 1910529--1910740 Score: 259
Period size: 100 Copynumber: 2.1 Consensus size: 99
1910519 AATACAGTGG
1910529 AAAAGATTGAAGCTACAACAGCGAATCTTACTTTTCAGGTGGTGCAGTGGAACAGATTGAAGCCA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTTT-AGGTGGTGCAGTGGAACAGATTGAAGCCA
* * **
1910594 C-AAAGGTGAATCTTGCTTCCCCGACATTGTAGTTA
65 CGAAA-GTGAATATTGCTTCCCCAACATTACAGTTA
* *
1910629 AAAAGATTGAAGCTACAACAGTGAATCTTACTTCCTT-GGCT-GTGTAGTGGAACAGATTGAAGC
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTT--TTAGG-TGGTGCAGTGGAACAGATTGAAGC
* * * *
1910692 TACGACAGTGAATATTGTTTCCCCAATATTACAGTTA
63 CACGAAAGTGAATATTGCTTCCCCAACATTACAGTTA
*
1910729 AAAAAATTGAAG
1 AAAAGATTGAAG
1910741 AAAATAATCC
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
100 92 0.95
101 3 0.03
102 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (99 bp):
AAAAGATTGAAGCTACAACAGCGAATCTTACTTTTAGGTGGTGCAGTGGAACAGATTGAAGCCAC
GAAAGTGAATATTGCTTCCCCAACATTACAGTTA
Found at i:1910893 original size:84 final size:84
Alignment explanation
Indices: 1910751--1911281 Score: 293
Period size: 84 Copynumber: 6.3 Consensus size: 84
1910741 AAAATAATCC
* ** * *
1910751 TATCTCCCT-AAGGTTGCAGTAGAGCAGATTAAAACCAA-AGATCTTATCTCTCTGAAGTTGCAG
1 TATCTCCCTGAA-GTTGCAGTAGAGCAGA-CAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAG
* *
1910814 -AGAGCAGATTGCATACAGTCT
64 TGGAGCAGATTG-AAACAGTCT
* * *
1910835 TATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACAAATCCTATCTCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGTG
* *
1910900 GAGCGGATTAAAACCACAGATCT
66 GAGCAGATT-GAA--ACAG-TCT
* * * * * * * * *
1910923 TATCTCTCTAAAGTTGCAGTAGAGCTGATC----GTATCCAGTCTTATATCCCTGAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-CAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGT
* * *
1910984 GGAGCAGATAGAAGAAACCAATCC
65 GGAGCAGAT---TGAAA-CAGTCT
* ** * * * *
1911008 CATCTCCCTGAAGTTGCAGTAGAGCAG----ATTAAACAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGTG
* * **
1911069 AAGCAGATCGTATCCAGTCT
66 GAGCAGATTG-AAACAGTCT
* * * * * * *
1911089 TATCTCTCTGAAGTTGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGTG
**
1911154 GAGTGGATT-AAACAGATCT
66 GAGCAGATTGAAACAG-TCT
* * * * * *
1911173 TATCTCTCTAAAGTTGCAGTAGAGCAGATC----GTATCCAGTCTTATCTCCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-CAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGT
** * *
1911234 GGAGCAGACAGAAAAACCAATCC
65 GGAGCAGATTG--AAA-CAGTCT
*
1911257 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTAGAGC
1911282 GGATTAAAGC
Statistics
Matches: 338, Mismatches: 84, Indels: 50
0.72 0.18 0.11
Matches are distributed among these distances:
81 60 0.18
82 1 0.00
83 10 0.03
84 130 0.38
85 101 0.30
86 2 0.01
87 6 0.02
88 27 0.08
89 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACAAATCTTATCTCCCTGAAGTTGCAGTG
GAGCAGATTGAAACAGTCT
Found at i:1910978 original size:41 final size:41
Alignment explanation
Indices: 1910751--1911281 Score: 299
Period size: 44 Copynumber: 12.6 Consensus size: 41
1910741 AAAATAATCC
***
1910751 TATCTCCCT-AAGGTTGCAGTAGAGCAGATTAAAACCAAAGATCT
1 TATCTCCCTGAA-GTTGCAGTAGAGCAGATCGTAACC--AG-TCT
* * *
1910795 TATCTCTCTGAAGTTGCAG-AGAGCAGATTGCATA-CAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTA-ACCAGTCT
* * * * *
1910835 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACAAATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATC----GTAACCAGTCT
* * * ***
1910879 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAA-C-CAG-TCT
* * * *
1910923 TATCTCTCTAAAGTTGCAGTAGAGCTGATCGTATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAGTCT
* * * * * * *
1910964 TATATCCCTGAAGTTACAGTGGAGCAGATAGAAGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGAT---CGTAACCAGTCT
* *
1911008 CATCTCCCTGAAGTTGCAGTAGAGCAGAT--TAAACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAG-TCT
* * * *
1911048 TATCTCTCTGAAGTTACAGTAAAGCAGATCGTATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAGTCT
* * * * * *
1911089 TATCTCTCTGAAGTTGTAGTGGAGCAGACAGA-AGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGT--AG-AG-CAGATCGTAACCAGTCT
* * ** *
1911133 TATCTCCCTAAAGTTGCAGTGGAGTGGAT--TAAACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAG-TCT
* * *
1911173 TATCTCTCTAAAGTTGCAGTAGAGCAGATCGTATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAGTCT
* * * *
1911214 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATC-G--TAACCAGTCT
*
1911257 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTAGAGC
1911282 GGATTAAAGC
Statistics
Matches: 378, Mismatches: 80, Indels: 59
0.73 0.15 0.11
Matches are distributed among these distances:
39 8 0.02
40 78 0.21
41 90 0.24
42 15 0.04
43 47 0.12
44 134 0.35
45 6 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATCGTAACCAGTCT
Found at i:1911110 original size:125 final size:125
Alignment explanation
Indices: 1910737--1911344 Score: 810
Period size: 125 Copynumber: 4.8 Consensus size: 125
1910727 TAAAAAAATT
** * * *
1910737 GAAGAAAATAATCCTATCTCCCTAAGGTTGCAGTAGAGCAGATTAAAACCAAAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATT-AAA-C--AGATCTTATCTCT
* * *
1910802 CTGAAGTTGCAG-AGAGCAGATTGCATACAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
62 CTGAAGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
* *
1910865 AAAGAAACAAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATT--AA--ACAGATCTTATCTCT
* * * * *
1910930 CTAAAGTTGCAGTAGAGCTGATCGTATCCAGTCTTATATCCCTGAAGTTACAGTGGAGCAGATA
62 CTGAAGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
* * * *
1910994 GAAGAAACCAATCCCATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACAGATCTTATCTCTCTGA
1 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAACAGATCTTATCTCTCTGA
* * * *
1911059 AGTTACAGTAAAGCAGATCGTATCCAGTCTTATCTCTCTGAAGTTGTAGTGGAGCAGACA
66 AGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
* *
1911119 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAACAGATCTTATCTCTCTAA
1 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAACAGATCTTATCTCTCTGA
1911184 AGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
66 AGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
*
1911244 GAA-AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCCATAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAA--C--AGATCTTATCTCT
* * * *
1911308 CTGAATTTGCAG-AGAGTAGATCGCAT-CAGACTTATCT
62 CTGAAGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCT
1911345 TTAAAATTAT
Statistics
Matches: 426, Mismatches: 46, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
124 41 0.10
125 188 0.44
126 11 0.03
127 14 0.03
128 85 0.20
129 85 0.20
130 1 0.00
131 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (125 bp):
GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAACAGATCTTATCTCTCTGA
AGTTGCAGTAGAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
Found at i:1912707 original size:3 final size:3
Alignment explanation
Indices: 1912699--1912744 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1912689 GTTAATACTC
1912699 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1912745 AACCATGTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1919171 original size:15 final size:15
Alignment explanation
Indices: 1919153--1919184 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1919143 ACTTTCACTA
*
1919153 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
1919168 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
1919183 TT
1 TT
1919185 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:1921751 original size:6 final size:6
Alignment explanation
Indices: 1921722--1921787 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
1921712 AGTGATTTCA
* *
1921722 TTTAGTT TTTATAT TTTA-- TTTATT TTTATT TTTATTT TTTAGT TTTAGT
1 TTTA-TT TTTAT-T TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT
*
1921771 TTTAGTT TTTGTT TTTA
1 TTTA-TT TTTATT TTTA
1921788 GTTATTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
6 27 0.54
7 19 0.38
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:1921757 original size:12 final size:12
Alignment explanation
Indices: 1921722--1921787 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
1921712 AGTGATTTCA
1921722 TTTAGTTTTTATAT
1 TTTA-TTTTTAT-T
1921736 TTTA--TTTATT
1 TTTATTTTTATT
1921746 TTTATTTTTATTT
1 TTTATTTTTA-TT
* *
1921759 TTTAGTTTTAGT
1 TTTATTTTTATT
*
1921771 TTTAGTTTTTGTT
1 TTTA-TTTTTATT
1921784 TTTA
1 TTTA
1921788 GTTATTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 9 0.21
13 20 0.47
14 4 0.09
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:1921767 original size:19 final size:19
Alignment explanation
Indices: 1921740--1921790 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1921730 TTATATTTTA
* * *
1921740 TTTATTTTTATTTTTATTT
1 TTTAGTTTTAGTTTTAGTT
1921759 TTTAGTTTTAGTTTTAGTT
1 TTTAGTTTTAGTTTTAGTT
1921778 TTT-GTTTTTAGTT
1 TTTAG-TTTTAGTT
1921791 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (19 bp):
TTTAGTTTTAGTTTTAGTT
Found at i:1924939 original size:6 final size:6
Alignment explanation
Indices: 1924930--1924958 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1924920 AAATAAAATT
1924930 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1924959 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:1925012 original size:9 final size:9
Alignment explanation
Indices: 1924998--1925082 Score: 102
Period size: 9 Copynumber: 9.4 Consensus size: 9
1924988 GTAGTGATTC
1924998 AATTCGGTT
1 AATTCGGTT
1925007 AATTCGGTT
1 AATTCGGTT
1925016 AATTCAGG-T
1 AATTC-GGTT
1925025 AATTCGGTT
1 AATTCGGTT
1925034 AATTCAGG-T
1 AATTC-GGTT
*
1925043 AATCCGGTT
1 AATTCGGTT
*
1925052 AATTCGGGT
1 AATTCGGTT
*
1925061 AATCCGGTT
1 AATTCGGTT
*
1925070 AATTCGGGT
1 AATTCGGTT
1925079 AATT
1 AATT
1925083 TTTCACTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
8 4 0.06
9 57 0.88
10 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1925027 original size:18 final size:18
Alignment explanation
Indices: 1925006--1925082 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
1924996 TCAATTCGGT
1925006 TAATTCGGTTAATTCAGG
1 TAATTCGGTTAATTCAGG
1925024 TAATTCGGTTAATTCAGG
1 TAATTCGGTTAATTCAGG
* *
1925042 TAATCCGGTTAATTCGGG
1 TAATTCGGTTAATTCAGG
* *
1925060 TAATCCGGTTAATTCGGG
1 TAATTCGGTTAATTCAGG
1925078 TAATT
1 TAATT
1925083 TTTCACTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (18 bp):
TAATTCGGTTAATTCAGG
Found at i:1927924 original size:17 final size:16
Alignment explanation
Indices: 1927893--1927933 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1927883 GAAAAATAAA
*
1927893 TAAAAAAAATGAAAGT
1 TAAAAAAAATAAAAGT
1927909 TAAAAGAAAATAAAAG-
1 TAAAA-AAAATAAAAGT
1927925 -AAAAAAAAT
1 TAAAAAAAAT
1927934 TTTAATTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 5 0.22
17 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
TAAAAAAAATAAAAGT
Done.