Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 17 of 17
Found at i:1770201 original size:20 final size:20
Alignment explanation
Indices: 1770136--1770211 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
1770126 ACCAAAGAAA
** *
1770136 TGTATCGATACATTAGTAAA
1 TGTATCGATACATTTCTAAT
1770156 TGTATCGATACATGCTTAC-AAT
1 TGTATCGATACAT--TT-CTAAT
*
1770178 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTAAT
*
1770198 TGTATCAATACATT
1 TGTATCGATACATT
1770212 CTGGGTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 30 0.64
22 16 0.34
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTCTAAT
Found at i:1772799 original size:95 final size:95
Alignment explanation
Indices: 1772595--1772807 Score: 225
Period size: 95 Copynumber: 2.2 Consensus size: 95
1772585 TTTTCCAAAA
*
1772595 GAATACTCCAACCCCGTTTTTAAAAATTATCAAGATTTAAACCTTAATTTTGCTTAAATTATCAT
1 GAATACTCCAACCCCGTTTTT-AAAACTATCAAGA-TTAAACCTTAATTTTGCTTAAATTATCAT
* * *
1772660 CATTAGGATACTCCAATCCCATTATTCTAAGG
64 CATGAGGATACTCCAATCCCATTAGTCCAAGG
* ** * *
1772692 GAATACTCCAACCTCGTTTTT-AAACTAGTCAAGA-TAATTCTTATTTTTGCTTAAATTGTCATC
1 GAATACTCCAACCCCGTTTTTAAAACTA-TCAAGATTAAACCTTAATTTTGCTTAAATTATCATC
* * * *
1772755 GTCGAGGATACTCCAA-CTCTATTCGTCCGAGG
65 AT-GAGGATACTCCAATC-CCATTAGTCCAAGG
* *
1772787 GGATACTCCAACCCCATTTTT
1 GAATACTCCAACCCCGTTTTT
1772808 TAACCAAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
94 27 0.28
95 44 0.45
96 6 0.06
97 20 0.21
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (95 bp):
GAATACTCCAACCCCGTTTTTAAAACTATCAAGATTAAACCTTAATTTTGCTTAAATTATCATCA
TGAGGATACTCCAATCCCATTAGTCCAAGG
Found at i:1773897 original size:20 final size:21
Alignment explanation
Indices: 1773867--1773906 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1773857 CTGGGTTTTA
*
1773867 CTCAGATGTATTGATACATTT
1 CTCAGATGTATCGATACATTT
1773888 CTCA-ATGTATCGATACATT
1 CTCAGATGTATCGATACATT
1773907 CAGACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCAGATGTATCGATACATTT
Found at i:1776076 original size:79 final size:79
Alignment explanation
Indices: 1775945--1776226 Score: 399
Period size: 79 Copynumber: 3.6 Consensus size: 79
1775935 TCATTGATGT
* * *
1775945 TTTTATTTCTAAAACACCGATTTTCCATCATCGGGGATACCCCAACCTCGTTATTTTTGAGAGGA
1 TTTTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCTCGTTATTTTTGAGAGGA
1776010 TACTCCAGCCCCAG
66 TACTCCAGCCCCAG
*
1776024 TTTTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCTCGTTATTTTTGA-AGGG
1 TTTTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCTCGTTATTTTTGAGA-GG
1776088 ATACTCCAGCCCCAG
65 ATACTCCAGCCCCAG
* * *
1776103 TTTTATTTCTAAAACATCGATTTTCTACCAACGGGGATACTCCAACC-CTATTATTTTTGAGAGG
1 TTTTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCTC-GTTATTTTTGAGAGG
* * * *
1776167 ATACTCTAACCTCGG
65 ATACTCCAGCCCCAG
* *
1776182 TTTTATTTCTAAAACACCAATTTT-TCACCATCTGGGATACTCCAA
1 TTTTATTTCTAAAACACCGATTTTCT-ACCATCGGGGATACTCCAA
1776227 TCCCGGTTTA
Statistics
Matches: 183, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
78 3 0.02
79 179 0.98
80 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCTCGTTATTTTTGAGAGGA
TACTCCAGCCCCAG
Found at i:1776234 original size:51 final size:51
Alignment explanation
Indices: 1776164--1776278 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
1776154 TATTTTTGAG
* * * *
1776164 AGGATACTCTAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACCATCT
1 AGGATACTCCAACCTCGGTTTAATTTCTAAAACACCAATTTTCCACCATCA
* * *
1776215 GGGATACTCCAATCC-CGGTTTAATTTCTAAAACATCGATTTTCCACCATCA
1 AGGATACTCCAA-CCTCGGTTTAATTTCTAAAACACCAATTTTCCACCATCA
*
1776266 AGGATACTACAAC
1 AGGATACTCCAAC
1776279 TCTATTATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 51 0.94
52 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (51 bp):
AGGATACTCCAACCTCGGTTTAATTTCTAAAACACCAATTTTCCACCATCA
Found at i:1776257 original size:130 final size:130
Alignment explanation
Indices: 1776084--1776361 Score: 360
Period size: 130 Copynumber: 2.1 Consensus size: 130
1776074 TTATTTTTGA
* * * * ** *
1776084 AGGGATACTCCAGCCCCAGTTTTATTTCTAAAACATCGATTTTCTACCAACGGGGATACTCCAAC
1 AGGGATACTCCAACCCCGGTTTAATTTCTAAAACATCGATTTTCCACCAACAAGGATACTACAAC
* * ** * *
1776149 CCTATTATTTTTG-AGAGGATACTCTAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACCAT
66 CCTATTATTTCTGAAG-GGATACTCAAACCTCAATTTTATTTCTAAAACACCAATTTTCCACAAT
1776213 C
130 C
* * *
1776214 TGGGATACTCCAATCCCGGTTTAATTTCTAAAACATCGATTTTCCACCATCAAGGATACTACAAC
1 AGGGATACTCCAACCCCGGTTTAATTTCTAAAACATCGATTTTCCACCAACAAGGATACTACAAC
* * * *
1776279 TCTATTATTTCTGAAGGGATACTCAAACTTCAATTTTATTTCTAAAACACCGATTTTCCATAATC
66 CCTATTATTTCTGAAGGGATACTCAAACCTCAATTTTATTTCTAAAACACCAATTTTCCACAATC
1776344 AGGGATACTCCAACCCCG
1 AGGGATACTCCAACCCCG
1776362 TTATTTTTGA
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
130 123 0.98
131 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (130 bp):
AGGGATACTCCAACCCCGGTTTAATTTCTAAAACATCGATTTTCCACCAACAAGGATACTACAAC
CCTATTATTTCTGAAGGGATACTCAAACCTCAATTTTATTTCTAAAACACCAATTTTCCACAATC
Found at i:1776368 original size:209 final size:207
Alignment explanation
Indices: 1776007--1776438 Score: 591
Period size: 209 Copynumber: 2.1 Consensus size: 207
1775997 ATTTTTGAGA
* * * * * *
1776007 GGATACTCCAGCCCCAGTTTTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCT
1 GGATACTCCAACCCCGGTTTAATTTCTAAAACACCGATTTTCCACCATCAAGGATACTACAACCT
* * * * * * * *
1776072 CGTTATTTTTGAAGGGATACTCCAGCCCCAGTTTTATTTCTAAAACATCGATTTTCTACCAACGG
66 CATTATTTCTGAAGGGATACTCAAACCCCAATTTTATTTCTAAAACACCGATTTTCCACCAACAG
* * *
1776137 GGATACTCCAACCCTATTATTTTTGA-GAGGATACTCTAACCTCGGTTTTATTTCTAAAACACCA
131 GGATACTCCAACCCCATTATTTTTGAGGA-GATACTCTAACCCCGATTTTATTTCTAAAACACCA
1776201 ATTTTTCACCATCT
195 ATTTTTCACCAT-T
* *
1776215 GGGATACTCCAATCCCGGTTTAATTTCTAAAACATCGATTTTCCACCATCAAGGATACTACAA-C
1 -GGATACTCCAACCCCGGTTTAATTTCTAAAACACCGATTTTCCACCATCAAGGATACTACAACC
** *
1776279 TCTATTATTTCTGAAGGGATACTCAAACTTCAATTTTATTTCTAAAACACCGATTTTCCA-TAAT
65 TC-ATTATTTCTGAAGGGATACTCAAACCCCAATTTTATTTCTAAAACACCGATTTTCCACCAA-
*
1776343 CAGGGATACTCCAACCCCGTTATTTTTGAGGAGATACTCTAACCCCGATTTTATTTCTAAAACAC
128 CAGGGATACTCCAACCCCATTATTTTTGAGGAGATACTCTAACCCCGATTTTATTTCTAAAACAC
1776408 CAATTTTTCACCATT
193 CAATTTTTCACCATT
1776423 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1776439 TTATTTTTGA
Statistics
Matches: 196, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
207 15 0.08
208 6 0.03
209 173 0.88
210 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (207 bp):
GGATACTCCAACCCCGGTTTAATTTCTAAAACACCGATTTTCCACCATCAAGGATACTACAACCT
CATTATTTCTGAAGGGATACTCAAACCCCAATTTTATTTCTAAAACACCGATTTTCCACCAACAG
GGATACTCCAACCCCATTATTTTTGAGGAGATACTCTAACCCCGATTTTATTTCTAAAACACCAA
TTTTTCACCATT
Found at i:1776463 original size:77 final size:78
Alignment explanation
Indices: 1776237--1776481 Score: 251
Period size: 79 Copynumber: 3.1 Consensus size: 78
1776227 TCCCGGTTTA
* * * * * * ** *
1776237 ATTTCTAAAACATCGATTTTCCACCATCAAGGATACTACAACTCTATTATTTCTGAAGG-GATAC
1 ATTTCTAAAACACCAATTTTCCACAAT-AGGGATACTCCAACCCCGTTATTTTTG-AGGAGATAC
* **
1776301 TCAAACTTCAATTTT
64 TCTAACCCCAATTTT
* *
1776316 ATTTCTAAAACACCGATTTTCCATAATCAGGGATACTCCAACCCCGTTATTTTTGAGGAGATACT
1 ATTTCTAAAACACCAATTTTCCACAAT-AGGGATACTCCAACCCCGTTATTTTTGAGGAGATACT
*
1776381 CTAACCCCGATTTT
65 CTAACCCCAATTTT
* * * * * *
1776395 ATTTCTAAAACACCAATTTTTCACCAT-TGGATACTCCAACCCCGTTATTTTTGAGGGGATATTT
1 ATTTCTAAAACACCAATTTTCCACAATAGGGATACTCCAACCCCGTTATTTTTGAGGAGATACTC
*
1776459 TAACCCTAATTTT
66 TAACCCCAATTTT
1776472 ATTTCTAAAA
1 ATTTCTAAAA
1776482 TATTAAATTT
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
77 54 0.38
78 3 0.02
79 85 0.60
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (78 bp):
ATTTCTAAAACACCAATTTTCCACAATAGGGATACTCCAACCCCGTTATTTTTGAGGAGATACTC
TAACCCCAATTTT
Found at i:1779648 original size:51 final size:52
Alignment explanation
Indices: 1779553--1779650 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 52
1779543 CGTTCCCCGA
* * *
1779553 TGAAAATTTTAATATTTTGGAGATAAAAATGGGGTCGGAATATCCCCGATAG
1 TGAAAATTTTAATATTTTGAAAATAAAAATGGGGTCAGAATATCCCCGATAG
* * *
1779605 TGAAAA-TTTGATATTTTGAAAATAAAAATGGGGTTAGAGTATCCCC
1 TGAAAATTTTAATATTTTGAAAATAAAAATGGGGTCAGAATATCCCC
1779651 TCGAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 34 0.85
52 6 0.15
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (52 bp):
TGAAAATTTTAATATTTTGAAAATAAAAATGGGGTCAGAATATCCCCGATAG
Found at i:1779698 original size:78 final size:78
Alignment explanation
Indices: 1779593--1779886 Score: 302
Period size: 79 Copynumber: 3.7 Consensus size: 78
1779583 GGGGTCGGAA
* * * * * **
1779593 TATCCCCGATAGTGAAAATTTGATATTTTGAAAATAAAAATGGGGTTAGAGTATCCCCTCGAAAA
1 TATCCTCGATGGTGAAAAATCGATATTTTAAAAATAAAACCGGGGTTAGAGTATCCCCT-GAAAA
* * *
1779658 TAATGGGGTTAAAG
65 TAACGGGATTAGAG
* * * ** * *
1779672 TAT-TTTGATGGTGAAAAATCAATATTTTGGAAATAAAACCGGGGTTAGAGTACCCCCTTAGAAA
1 TATCCTCGATGGTGAAAAATCGATATTTTAAAAATAAAACCGGGGTTAGAGTATCCCCTGA-AAA
1779736 TAACGGGATTAGAG
65 TAACGGGATTAGAG
* * * * *
1779750 TATCCCCAATGGTGAAAAATCGATATTTTAAAAATAGAACCGAGGTTGGAGTATCCCCTAGAAAA
1 TATCCTCGATGGTGAAAAATCGATATTTTAAAAATAAAACCGGGGTTAGAGTATCCCCT-GAAAA
* *
1779815 TAACGAGTTTAGAG
65 TAACGGGATTAGAG
* * * *
1779829 TATCCTCGATGGTGAAATATCGATATTTTAAAAATAGAACTGGGGTTGGAGTATCCCC
1 TATCCTCGATGGTGAAAAATCGATATTTTAAAAATAAAACCGGGGTTAGAGTATCCCC
1779887 GATGGTGAAA
Statistics
Matches: 178, Mismatches: 34, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 61 0.34
79 115 0.65
80 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (78 bp):
TATCCTCGATGGTGAAAAATCGATATTTTAAAAATAAAACCGGGGTTAGAGTATCCCCTGAAAAT
AACGGGATTAGAG
Found at i:1779890 original size:51 final size:51
Alignment explanation
Indices: 1779826--1779927 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
1779816 AACGAGTTTA
* *
1779826 GAGTATCCTCGATGGTGAAATATCGATATTTTAAAAATAGAA-CTGGGGTTG
1 GAGTATCCCCGATGGTGAAAAATCGATATTTTAAAAATAGAATC-GGGGTTG
*
1779877 GAGTATCCCCGATGGTGAAAAATTGATATTTTAAAAATAGAATCGGGGTTG
1 GAGTATCCCCGATGGTGAAAAATCGATATTTTAAAAATAGAATCGGGGTTG
1779928 AAGCATCCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATGGTGAAAAATCGATATTTTAAAAATAGAATCGGGGTTG
Found at i:1779905 original size:130 final size:129
Alignment explanation
Indices: 1779741--1780012 Score: 373
Period size: 130 Copynumber: 2.1 Consensus size: 129
1779731 AGAAATAACG
* * *
1779741 GGATTAGAGTATCCCCAATGGTGAAAAATCGATATTTTAAAAATAGAACCGAGGTTGGAGTATCC
1 GGATTGGAGTATCCCCAATGGTGAAAAATCGATATTTTAAAAATAGAACCGAGGTTGAAGCATCC
* * * * * *
1779806 CCTAGAAAATAACGAGTTTAGAGTATCCTCGATGGTGAAATATCGATATTTTAAAAATAGAACT
66 CCTAGAAAATAACGAGGTGAGAGTATCCTCAATGGTGAAAAATCCATATTTTAAAAATAAAACT
* * * * *
1779870 GGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATTTTAAAAATAGAATCGGGGTTGAAGCATC
1 -GGATTGGAGTATCCCCAATGGTGAAAAATCGATATTTTAAAAATAGAACCGAGGTTGAAGCATC
* * * *
1779935 CTCTCGAAAATAACGGGGTGAGAGTATCCTTAATGGTGAAAAATCCATATTTTAAAAATAAAACT
65 CCCTAGAAAATAACGAGGTGAGAGTATCCTCAATGGTGAAAAATCCATATTTTAAAAATAAAACT
1780000 GGATTGGAGTATC
1 GGATTGGAGTATC
1780013 TTTTCAAAAA
Statistics
Matches: 123, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
129 12 0.10
130 111 0.90
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (129 bp):
GGATTGGAGTATCCCCAATGGTGAAAAATCGATATTTTAAAAATAGAACCGAGGTTGAAGCATCC
CCTAGAAAATAACGAGGTGAGAGTATCCTCAATGGTGAAAAATCCATATTTTAAAAATAAAACT
Found at i:1780137 original size:28 final size:28
Alignment explanation
Indices: 1780062--1780143 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
1780052 AAATCTTGAA
* *
1780062 CAAAAA-ATCAGGGTTGGAGTATCCCCT
1 CAAAAATAACAGGATTGGAGTATCCCCT
*
1780089 CAAAAATAACAAGA-TGAGAGTATCCCCT
1 CAAAAATAACAGGATTG-GAGTATCCCCT
* *
1780117 CGAAAATAACAGGATTGGAGTGTCCCC
1 CAAAAATAACAGGATTGGAGTATCCCC
1780144 GATAGTGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 8 0.17
28 36 0.78
29 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (28 bp):
CAAAAATAACAGGATTGGAGTATCCCCT
Found at i:1782127 original size:22 final size:20
Alignment explanation
Indices: 1782078--1782133 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
1782068 AAAAACTTAG
1782078 AATGTATCGATACAATGATA
1 AATGTATCGATACAATGATA
*
1782098 AATGTATCGATACAATTATA
1 AATGTATCGATACAATGATA
1782118 AGTATGTATCGATACA
1 A--ATGTATCGATACA
1782134 TTTACTTAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 20 0.61
22 13 0.39
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATGATA
Found at i:1782918 original size:61 final size:61
Alignment explanation
Indices: 1782759--1783209 Score: 467
Period size: 61 Copynumber: 7.4 Consensus size: 61
1782749 GAGAGGCATT
* * * ** *
1782759 CTGCTCTTTGAGGACTAGAAGGTGCCACCAGCTTGTGTGGGCATTAAAATAAAAAAAGAAGTGTC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TTTAAA-AGGAAAAG--GCGTC
* *
1782824 TTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * ** *
1782885 CTAG-TCTTTAAGGACTAAAAGATGCCACCAACTTGTTTGGGCTTTAAAAGGGGAAGACGTC
1 CT-GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * * *
1782946 CTACTCTTTGAGGACTGAAAGTTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAA-GTGTC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * * * * *
1783005 TTGCTCTTTGAGGACTAGAATGTGCCACTAACTTGTGTAGGCTTTAAAAGGAGAAGGCATC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * * * * *
1783066 ATGTTCTTTGAGGACTGAAAGGTGCCATCAACTTGTGTAGGCTTTGAAAGGAAAAGTCGTC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * * * *
1783127 CTGCTCTTTTAAGACTAAAAAGTTCCACCAACTTGTGTGGGCTTTAAAAGGATAAGGCATC
1 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* *
1783188 ATGCTCTTTGAAGACTAAAAGG
1 CTGCTCTTTGAGGACTAAAAGG
1783210 ATAAAAGCTT
Statistics
Matches: 320, Mismatches: 62, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
59 45 0.14
60 4 0.01
61 219 0.68
62 1 0.00
63 7 0.02
64 5 0.02
65 39 0.12
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (61 bp):
CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
Found at i:1783100 original size:181 final size:182
Alignment explanation
Indices: 1782817--1783209 Score: 497
Period size: 181 Copynumber: 2.2 Consensus size: 182
1782807 ATAAAAAAAG
*
1782817 AAGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
1 AAGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAGGC
* * * * **
1782882 GTCCTAGTCTTTAAGGACTAAAAGATGCCACCAACTTGTTTGGGCTTTAAAAGGGGAAGACGTCC
66 ATCATAGTCTTTAAGGACTAAAAGATGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGACGTCC
* * *
1782947 TACTCTTTGAGGACT-GAAAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGA-
131 TACTCTTTGAAGACTAAAAAGTT-CCACCAACTTGTGTGGGCTTTAAAAGGAT
* * * * *
1782998 AAGTGTCTTGCTCTTTGAGGACTAGAATGTGCCACTAACTTGTGTAGGCTTTAAAAGGAGAAGGC
1 AAGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAGGC
* * * * * *
1783063 ATCAT-GTTCTTTGAGGACTGAAAGGTGCCATCAACTTGTGTAGGCTTTGAAAGGAAAAGTCGTC
66 ATCATAG-TCTTTAAGGACTAAAAGATGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGACGTC
* *
1783127 CTGCTCTTTTAAGACTAAAAAGTTCCACCAACTTGTGTGGGCTTTAAAAGGAT
130 CTACTCTTTGAAGACTAAAAAGTTCCACCAACTTGTGTGGGCTTTAAAAGGAT
* *
1783180 AAG-GCATCATGCTCTTTGAAGACTAAAAGG
1 AAGTG--TCTTGCTCTTTGAGGACTAAAAGG
1783210 ATAAAAGCTT
Statistics
Matches: 180, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
180 1 0.01
181 150 0.83
182 9 0.05
183 20 0.11
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (182 bp):
AAGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAGGC
ATCATAGTCTTTAAGGACTAAAAGATGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGACGTCC
TACTCTTTGAAGACTAAAAAGTTCCACCAACTTGTGTGGGCTTTAAAAGGAT
Found at i:1784191 original size:12 final size:12
Alignment explanation
Indices: 1784174--1784201 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1784164 CTTAAGTGGG
1784174 TTTTTTTCTTAT
1 TTTTTTTCTTAT
1784186 TTTTTTTCTTAT
1 TTTTTTTCTTAT
1784198 TTTT
1 TTTT
1784202 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTAT
Found at i:1784208 original size:16 final size:15
Alignment explanation
Indices: 1784174--1784222 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
1784164 CTTAAGTGGG
1784174 TTTTTTTCTTA---T
1 TTTTTTTCTTATTTT
1784186 TTTTTTTCTTATTTT
1 TTTTTTTCTTATTTT
* *
1784201 TGTTTTTTTTTGTTTT
1 T-TTTTTTCTTATTTT
1784217 TTTTTT
1 TTTTTT
1784223 CATTTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 11 0.35
15 7 0.23
16 13 0.42
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.88
Consensus pattern (15 bp):
TTTTTTTCTTATTTT
Found at i:1784210 original size:10 final size:10
Alignment explanation
Indices: 1784174--1784221 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1784164 CTTAAGTGGG
*
1784174 TTTTTTTCTT
1 TTTTTTTGTT
1784184 ATTTTTTT-TCT
1 -TTTTTTTGT-T
*
1784195 TATTTTTGTT
1 TTTTTTTGTT
1784205 TTTTTTTGTT
1 TTTTTTTGTT
1784215 TTTTTTT
1 TTTTTTT
1784222 TCATTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.88
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:1784218 original size:18 final size:17
Alignment explanation
Indices: 1784175--1784238 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
1784165 TTAAGTGGGT
*
1784175 TTTTTTCTTATTTTTTTTC
1 TTTTTT-TT-TTTTTTTTG
1784194 TTATTTTTGTTTTTTTTTG
1 TT-TTTTT-TTTTTTTTTG
* *
1784213 TTTTTTTTTTCATTTTGG
1 TTTTTTTTTT-TTTTTTG
1784231 TTTTTTTT
1 TTTTTTTT
1784239 AAAAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.08
18 18 0.46
19 13 0.33
20 5 0.13
ACGTcount: A:0.05, C:0.05, G:0.06, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTG
Found at i:1784237 original size:28 final size:28
Alignment explanation
Indices: 1784172--1784238 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
1784162 AACTTAAGTG
1784172 GGTTTTTTTCTTATTTTTTTTCTTATTTT
1 GGTTTTTTT-TTATTTTTTTTCTTATTTT
* *
1784201 TGTTTTTTTTTGTTTTTTTT-TTCATTTT
1 GGTTTTTTTTTATTTTTTTTCTT-ATTTT
1784229 GGTTTTTTTT
1 GGTTTTTTTT
1784239 AAAAAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.71
29 8 0.24
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.82
Consensus pattern (28 bp):
GGTTTTTTTTTATTTTTTTTCTTATTTT
Found at i:1793190 original size:22 final size:19
Alignment explanation
Indices: 1793165--1793214 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 19
1793155 ATATAAAAAT
1793165 TTATATAATATTAATTATTAA
1 TTATATAATATTAA-TA-TAA
*
1793186 CTTATA-AA-ATTTATATAA
1 -TTATATAATATTAATATAA
1793204 TTATATAATAT
1 TTATATAATAT
1793215 ATTAAATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 4 0.16
20 4 0.16
21 2 0.08
22 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATATAATATTAATATAA
Found at i:1793534 original size:22 final size:20
Alignment explanation
Indices: 1793467--1793531 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
1793457 TTAAATTAGG
1793467 TAATCTATATTTTCATATTTA
1 TAAT-TATATTTTCATATTTA
* *
1793488 T-ATTATATTTTTATATTAA
1 TAATTATATTTTCATATTTA
*
1793507 GTAATTCATGTTTTCATATTTA
1 -TAATT-ATATTTTCATATTTA
1793529 TAA
1 TAA
1793532 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 14 0.39
20 3 0.08
21 7 0.19
22 12 0.33
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (20 bp):
TAATTATATTTTCATATTTA
Found at i:1793603 original size:27 final size:25
Alignment explanation
Indices: 1793549--1793604 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
1793539 AATATTAATA
1793549 ATTTATTTTATATAAATTTTAATGT
1 ATTTATTTTATATAAATTTTAATGT
*
1793574 ATTTATATATTATATCAAATTTTTAT-T
1 ATTTAT-T-TTATAT-AAATTTTAATGT
1793601 ATTT
1 ATTT
1793605 TTACATCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 6 0.22
26 1 0.04
27 11 0.41
28 9 0.33
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTATTTTATATAAATTTTAATGT
Found at i:1793615 original size:27 final size:26
Alignment explanation
Indices: 1793558--1793643 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
1793548 AATTTATTTT
* * *
1793558 ATATAAATTTTAATGTATTTATATATT
1 ATATAAATTTTTAT-TATTTTTATATC
*
1793585 ATATCAAATTTTTATTATTTTTACATC
1 ATAT-AAATTTTTATTATTTTTATATC
* *
1793612 ATAT-TATATTTTAATATTTTTATATC
1 ATATAAAT-TTTTATTATTTTTATATC
1793638 ATATAA
1 ATATAA
1793644 TTATATCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 2 0.04
26 20 0.42
27 17 0.35
28 9 0.19
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATAAATTTTTATTATTTTTATATC
Found at i:1794823 original size:54 final size:54
Alignment explanation
Indices: 1794764--1794871 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1794754 GAAATTCCAT
1794764 AACCTTTGTTTGGAAGGAACTTAGGCGTAAAGAGATGAAAGTTACTTGGCACAG
1 AACCTTTGTTTGGAAGGAACTTAGGCGTAAAGAGATGAAAGTTACTTGGCACAG
1794818 AACCTTTGTTTGGAAGGAACTTAGGCGTAAAGAGATGAAAGTTACTTGGCACAG
1 AACCTTTGTTTGGAAGGAACTTAGGCGTAAAGAGATGAAAGTTACTTGGCACAG
1794872 GCTTGTTTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (54 bp):
AACCTTTGTTTGGAAGGAACTTAGGCGTAAAGAGATGAAAGTTACTTGGCACAG
Found at i:1801422 original size:16 final size:17
Alignment explanation
Indices: 1801401--1801435 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1801391 AATTAAACTT
1801401 AAAGTCAA-CAAAATTA
1 AAAGTCAACCAAAATTA
1801417 AAAGTCAACCAAAATTA
1 AAAGTCAACCAAAATTA
1801434 AA
1 AA
1801436 GTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAGTCAACCAAAATTA
Found at i:1801436 original size:16 final size:15
Alignment explanation
Indices: 1801399--1801437 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1801389 AAAATTAAAC
1801399 TTAAAGTCAACAAAA
1 TTAAAGTCAACAAAA
1801414 TTAAAAGTCAACCAAAA
1 TT-AAAGTCAA-CAAAA
1801431 TTAAAGT
1 TTAAAGT
1801438 TAAAAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 7 0.32
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (15 bp):
TTAAAGTCAACAAAA
Found at i:1802266 original size:19 final size:22
Alignment explanation
Indices: 1802225--1802272 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
1802215 ATTATCTAAT
1802225 TTATTTTTGTATCTTAGAATTA
1 TTATTTTTGTATCTTAGAATTA
*
1802247 TTATTTTT-TATC-TA-AGTTA
1 TTATTTTTGTATCTTAGAATTA
1802266 TTATTTT
1 TTATTTT
1802273 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 2 0.08
21 4 0.16
22 8 0.32
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (22 bp):
TTATTTTTGTATCTTAGAATTA
Found at i:1802373 original size:14 final size:15
Alignment explanation
Indices: 1802354--1802382 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1802344 TATAGTTTTC
1802354 TTTAAAAA-AAATTA
1 TTTAAAAAGAAATTA
1802368 TTTAAAAAGAAATTA
1 TTTAAAAAGAAATTA
1802383 ACTTACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TTTAAAAAGAAATTA
Found at i:1803122 original size:21 final size:22
Alignment explanation
Indices: 1803092--1803140 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1803082 GTGATTATAC
1803092 AATATAAATATAATAAAAAATA
1 AATATAAATATAATAAAAAATA
* * *
1803114 AATA-AAATATGATATAATATA
1 AATATAAATATAATAAAAAATA
1803135 AATATA
1 AATATA
1803141 TAAACGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AATATAAATATAATAAAAAATA
Found at i:1803231 original size:57 final size:57
Alignment explanation
Indices: 1803092--1803231 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 57
1803082 GTGATTATAC
* *
1803092 AATATAAATATAATAAAAAATAAATAAAATATGATATAATATAAATATATAAACGTTTCA
1 AATATAATTATAAT-AAAAAT-AATAAAATATAATATAATATAAATATATAAAC-TTTCA
* * * *
1803152 AA-AT-TTTATAATATAAATTAATAATATATAA-ATAAATATAAATATATAATA-TTTTA
1 AATATAATTATAATA-AAAATAATAAAATATAATAT-AATATAAATATATAA-ACTTTCA
1803208 AATATAATTATAATAAAAATAATA
1 AATATAATTATAATAAAAATAATA
1803232 CCAATATATT
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
56 8 0.12
57 36 0.54
58 19 0.28
59 2 0.03
60 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (57 bp):
AATATAATTATAATAAAAATAATAAAATATAATATAATATAAATATATAAACTTTCA
Found at i:1803677 original size:10 final size:11
Alignment explanation
Indices: 1803644--1803677 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1803634 TTATTTGTAA
1803644 ATATAAATTTT
1 ATATAAATTTT
1803655 ATATAATATTTT
1 ATATAA-ATTTT
1803667 A-ATAAATTTT
1 ATATAAATTTT
1803677 A
1 A
1803678 CATGATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATAAATTTT
Done.