Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2555
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: 78774
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2751 original size:20 final size:20
Alignment explanation
Indices: 2726--2779 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2716 CTACTACTAT
*
2726 TTGTATCGATACATGGT-ATA
1 TTGTATCGATACATGATGA-A
2746 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
2766 TTGTATCGATACAT
1 TTGTATCGATACAT
2780 TGCTTTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:9136 original size:20 final size:20
Alignment explanation
Indices: 9098--9137 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
9088 TTACAAATTT
9098 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
9119 CTTCATGTTTCA-TCAAAAT
1 CTTCAT-TTTCACTCAAAAT
9138 CATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:9453 original size:22 final size:20
Alignment explanation
Indices: 9409--9454 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
9399 GTAGCCACCT
* *
9409 CCAGGTCGCGATCGGCACTC
1 CCAGGTCGCAACCGGCACTC
9429 CCAGGTCGCAACCGGGCAACTC
1 CCAGGTCGCAACC-GGC-ACTC
9451 CCAG
1 CCAG
9455 ACCCACTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.20, C:0.41, G:0.28, T:0.11
Consensus pattern (20 bp):
CCAGGTCGCAACCGGCACTC
Found at i:11814 original size:33 final size:33
Alignment explanation
Indices: 11764--11838 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
11754 TATGTCAGTT
* * **
11764 AAGTGAACTAAATTGCTCATCCATGTGCTGTGA
1 AAGTGAAGTAAAGTGCTCATCCATGCACTGTGA
11797 AAGTGAAGTAAAGTGCTCATCCATGCACTGTGA
1 AAGTGAAGTAAAGTGCTCATCCATGCACTGTGA
11830 AAGTGAAGT
1 AAGTGAAGT
11839 GATCAACTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (33 bp):
AAGTGAAGTAAAGTGCTCATCCATGCACTGTGA
Found at i:25846 original size:31 final size:30
Alignment explanation
Indices: 25790--25867 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 30
25780 AGAACAATAT
* *
25790 ATGTATTGATACATTCTATTTTTTACCCAA
1 ATGTATCGATACATTTTATTTTTTACCCAA
*
25820 ATGTATCGATACATTTTATTTTTTTACCCAG
1 ATGTATCGATACATTTTA-TTTTTTACCCAA
25851 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
25868 TCAATGTATC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 16 0.36
31 28 0.64
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (30 bp):
ATGTATCGATACATTTTATTTTTTACCCAA
Found at i:29864 original size:52 final size:52
Alignment explanation
Indices: 29779--29903 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
29769 ATATGAAAAG
*
29779 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
29831 TTGCCTGCATGTGTCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
29883 TTGCCTGCATGTATCAATACA
1 TTGCCTGCATGTATCGATACA
29904 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:29916 original size:52 final size:51
Alignment explanation
Indices: 29779--29923 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
29769 ATATGAAAAG
29779 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
29831 TTGCCTGCATGTGTCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
29883 TTGCCTGCATGTATCAATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
29924 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:29930 original size:13 final size:13
Alignment explanation
Indices: 29912--29936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29902 CAAAGATCAG
29912 TGTATCGATACAA
1 TGTATCGATACAA
29925 TGTATCGATACA
1 TGTATCGATACA
29937 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:30021 original size:20 final size:19
Alignment explanation
Indices: 29975--30031 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
29965 GCAGTAGCTT
29975 ACAT-TGTATCGATACAAA
1 ACATATGTATCGATACAAA
*
29993 ACATATGTATCGATACAAC
1 ACATATGTATCGATACAAA
*
30012 ACTTTATGTATCGATACAAA
1 AC-ATATGTATCGATACAAA
30032 TCGTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 4 0.12
19 15 0.44
20 15 0.44
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (19 bp):
ACATATGTATCGATACAAA
Found at i:32005 original size:58 final size:57
Alignment explanation
Indices: 31907--32042 Score: 150
Period size: 58 Copynumber: 2.4 Consensus size: 57
31897 CGTTGCGACA
* * * * *
31907 AACCTAAATGACATCAAAAGTCTTAAAAGTGCATCCAAGTCGCTA-AGTTATGGAAAAT
1 AACCTAAATGACATCAAAAATCTTAAAAGTGCATCAAAGTCCCTAGA-TCATAG-AAAT
* *
31965 AACCTAAATGACATCAAAAATTTGTAAAATTGCAT-AAAGTCCCTAGATCATAGAAAT
1 AACCTAAATGACATCAAAAATCT-TAAAAGTGCATCAAAGTCCCTAGATCATAGAAAT
* *
32022 GACCTAGATGACATCAAAAAT
1 AACCTAAATGACATCAAAAAT
32043 GCAACCCTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 23 0.34
58 33 0.49
59 11 0.16
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (57 bp):
AACCTAAATGACATCAAAAATCTTAAAAGTGCATCAAAGTCCCTAGATCATAGAAAT
Found at i:32812 original size:45 final size:45
Alignment explanation
Indices: 32748--32835 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
32738 CATGGCACAT
**
32748 TGTATCGATACATGATGAATTGTATCGATACATTGCTTCAAACAA
1 TGTATCGATACATGATGAATTACATCGATACATTGCTTCAAACAA
32793 TGTATCGATACATGATGAATTACATCGATACATTGCTTCAAAC
1 TGTATCGATACATGATGAATTACATCGATACATTGCTTCAAAC
32836 GGCTATAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (45 bp):
TGTATCGATACATGATGAATTACATCGATACATTGCTTCAAACAA
Found at i:33377 original size:37 final size:37
Alignment explanation
Indices: 33336--33409 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
33326 ACCTTTGCCT
33336 TAAAGGTAATCAGTTCTTGTAGTGAATTGGATAACCA
1 TAAAGGTAATCAGTTCTTGTAGTGAATTGGATAACCA
33373 TAAAGGTAATCAGTTCTTGTAGTGAATTGGATAACCA
1 TAAAGGTAATCAGTTCTTGTAGTGAATTGGATAACCA
33410 CTCGACGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (37 bp):
TAAAGGTAATCAGTTCTTGTAGTGAATTGGATAACCA
Found at i:34242 original size:18 final size:19
Alignment explanation
Indices: 34215--34251 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
34205 ATTTGAAGAA
34215 ATTTTCTCTT-TTTTTTTT
1 ATTTTCTCTTCTTTTTTTT
*
34233 ATTTTTTCTTCTTTTTTTT
1 ATTTTCTCTTCTTTTTTTT
34252 GGTTTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
ATTTTCTCTTCTTTTTTTT
Found at i:38407 original size:140 final size:140
Alignment explanation
Indices: 37999--38511 Score: 589
Period size: 140 Copynumber: 3.6 Consensus size: 140
37989 TTTTTCCAAC
* * * * *
37999 CCTTTTTAAGTCCCTAAGAATCATCGGACATTTCTAAGTTGATGGTAAACCTTAGGGATATTTTA
1 CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTA
* * * * *
38064 GCATTTTCCCCAAAACCTAATCTTATAAAATTA-TCGGGTTTGCTTCTATGCTGAAGGTATGAAA
66 GCATTTTCCCTAAAACCTAATCTTATAAAACTACT-GGGTCTGCTTCTACGCTGAAGGTATGAAT
* *
38128 TAGGAATATCA
130 TAGGAGTATTA
* * * * *
38139 CCTTTTCAAGTCCCTTAGGATCACCAGGCACTTCTAAGTCGATGGTAAACCTTAGAGATGTTTTA
1 CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTA
* * * * *
38204 GCATTTTCCCTAAAACCTAATCCTATAAAACTACTAGGTCTGTTTATACGCTAAAGGTATGAATT
66 GCATTTTCCCTAAAACCTAATCTTATAAAACTACTGGGTCTGCTTCTACGCTGAAGGTATGAATT
38269 AGGAGTATTA
131 AGGAGTATTA
* *
38279 CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTGATGGATATTTTA
1 CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTA
* * *
38344 GCATTTTCCCTGAAACCTAATCTTATAAAACTACTGGGTCTACTTCTACGCCGAAGGTATGAATT
66 GCATTTTCCCTAAAACCTAATCTTATAAAACTACTGGGTCTGCTTCTACGCTGAAGGTATGAATT
* *
38409 AGAAATGGGTTTGTTTTTA
131 ----A--GG--AG-TATTA
* * ** * * *
38428 CTTTTTCAAGTCCCATAGGGTCATTGGGTACTTCTAAGTCGATGGTAAATCTTAGGGATATTTTA
1 CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTA
38493 GCATTTT-CCTCAAAACCTA
66 GCATTTTCCCT-AAAACCTA
38512 GCCCTATGAA
Statistics
Matches: 313, Mismatches: 49, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
140 231 0.74
141 1 0.00
144 1 0.00
146 2 0.01
148 4 0.01
149 74 0.24
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (140 bp):
CCTTTTCAAGTCCCTTAGAATCATCGGGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTA
GCATTTTCCCTAAAACCTAATCTTATAAAACTACTGGGTCTGCTTCTACGCTGAAGGTATGAATT
AGGAGTATTA
Found at i:40858 original size:60 final size:60
Alignment explanation
Indices: 40765--40879 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
40755 GTCCAAAAAT
* *
40765 ATGTTGAGACTAAGGCTATGAATGATTATTTGTTTTAATTTTTTATAGAAAAGAAGTAAA
1 ATGTTGAGACTAAGGCTATGAATGATTACTTGTTTTAATTTTGTATAGAAAAGAAGTAAA
* *
40825 ATGTTGAGACTAAGGCTATGAATGCTTGCTTGTTTTAATTTTGTATAGAAAAGAA
1 ATGTTGAGACTAAGGCTATGAATGATTACTTGTTTTAATTTTGTATAGAAAAGAA
40880 ATAGATAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (60 bp):
ATGTTGAGACTAAGGCTATGAATGATTACTTGTTTTAATTTTGTATAGAAAAGAAGTAAA
Found at i:41597 original size:15 final size:15
Alignment explanation
Indices: 41574--41619 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
41564 TTAAATAAAT
*
41574 TAATAATTATTTATA
1 TAATTATTATTTATA
41589 TAATTATTATTT-TA
1 TAATTATTATTTATA
41603 -AATATATTATTTATA
1 TAAT-TATTATTTATA
41618 TA
1 TA
41620 TTCATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
15 13 0.48
16 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTATTATTTATA
Found at i:44262 original size:20 final size:20
Alignment explanation
Indices: 44237--44311 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
44227 ATACATTTTC
*
44237 AATGTATTGATACATGTATG
1 AATGTATCGATACATGTATG
44257 AATGTATCGATACATGTATG
1 AATGTATCGATACATGTATG
* * *
44277 AATGTATCGATATATTTTTG
1 AATGTATCGATACATGTATG
44297 AATGTATCGATACAT
1 AATGTATCGATACAT
44312 TCTGTCTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATGTATG
Found at i:45256 original size:19 final size:19
Alignment explanation
Indices: 45218--45260 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
45208 CCTTTGATTA
45218 AGCATTTTTACTATGTTCC
1 AGCATTTTTACTATGTTCC
45237 ATGCATTTTTAAC-ATG-TCC
1 A-GCATTTTT-ACTATGTTCC
45256 AGCAT
1 AGCAT
45261 CTCATTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 11 0.50
21 2 0.09
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (19 bp):
AGCATTTTTACTATGTTCC
Found at i:47020 original size:80 final size:79
Alignment explanation
Indices: 46810--47030 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 79
46800 ATTGGATTCT
* * * * *
46810 GTGTTTTAGAAATAAAACTGAGATTAGAGTATCTCCTTGAAAATAACAGGGTTTGAGTATCCCCA
1 GTGTTTTAGAAATAAAACCGAGGTTAGAGTATCTCCTCGAAAATAACGGGGTTAGAGTATCCCCA
* *
46875 ATTGTGGAAAATCG
66 ATTATGAAAAATCG
* *
46889 GTGTTTTGGAAATAAAACCGAGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCG
1 GTGTTTTAGAAATAAAACCGAGGTTAGAGTATCTCCTCGAAAATAACGGGGTTAGAGTATCCCC-
*
46954 AA-TATGAAAAATTG
65 AATTATGAAAAATCG
* * * * *
46968 GTGTTTTAGAAAAAAAAACCGAGGTTGGAGTATCTCCTCAAAAATAATGGGGTTGGAGTATCC
1 GTGTTTTAG-AAATAAAACCGAGGTTAGAGTATCTCCTCGAAAATAACGGGGTTAGAGTATCC
47031 TTTCGAAAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 74 0.60
80 49 0.40
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
GTGTTTTAGAAATAAAACCGAGGTTAGAGTATCTCCTCGAAAATAACGGGGTTAGAGTATCCCCA
ATTATGAAAAATCG
Found at i:47021 original size:28 final size:28
Alignment explanation
Indices: 46990--47055 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
46980 AAAAAACCGA
**
46990 GGTTGGAGTAT-CTCCTCAAAAATAATGG
1 GGTTGGAGTATCCT-CTCAAAAATAACAG
* *
47018 GGTTGGAGTATCCTTTCGAAAATAACAG
1 GGTTGGAGTATCCTCTCAAAAATAACAG
47046 GGTTGGAGTA
1 GGTTGGAGTA
47056 CCCCCGATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (28 bp):
GGTTGGAGTATCCTCTCAAAAATAACAG
Found at i:47037 original size:108 final size:107
Alignment explanation
Indices: 46910--47139 Score: 293
Period size: 108 Copynumber: 2.1 Consensus size: 107
46900 ATAAAACCGA
** * *
46910 GGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGAAT-ATGAAAAATTGGTGTTT
1 GGTTAGAGTATCCTTTCGAAAATAACAGGGTTAGAGTACCCCCG-ATGATGAAAAATTGGTGTTT
*
46974 TAGAAAAAAAAACCGAGGTTGGAGTATCTCC-TCAAAAATAATGG
65 TA-AAAAAAAAACCGAGGTTGGAGTATC-CCGTCAAAAATAACGG
* * * * *
47018 GGTTGGAGTATCCTTTCGAAAATAACAGGGTTGGAGTACCCCCGATGGTGGAAGATTGGTGTTTT
1 GGTTAGAGTATCCTTTCGAAAATAACAGGGTTAGAGTACCCCCGATGATGAAAAATTGGTGTTTT
* * *
47083 AAAAATAAATCCGGGGTTGGAGTATCCCGTCAAAAATAACGG
66 AAAAAAAAAACCGAGGTTGGAGTATCCCGTCAAAAATAACGG
*
47125 GGTAAGAGTATCCTT
1 GGTTAGAGTATCCTT
47140 GGTTGTGGAA
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
106 2 0.02
107 49 0.47
108 54 0.51
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (107 bp):
GGTTAGAGTATCCTTTCGAAAATAACAGGGTTAGAGTACCCCCGATGATGAAAAATTGGTGTTTT
AAAAAAAAAACCGAGGTTGGAGTATCCCGTCAAAAATAACGG
Found at i:57365 original size:20 final size:20
Alignment explanation
Indices: 57340--57432 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
57330 GTTGAGCATA
57340 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
57360 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
57380 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
* *
57400 ATGTATTGATACAATGTC-CC
1 ATGTATCGATACAAT-TCTTC
57420 ATGTATCGATACA
1 ATGTATCGATACA
57433 TTTCACTTAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTC
Found at i:57504 original size:19 final size:19
Alignment explanation
Indices: 57461--57516 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
57451 GTGCCAGTTT
*
57461 CATGTATTGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
57481 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
57500 CATGTATCGATACAATG
1 CATGTATCGATACAATG
57517 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:57519 original size:13 final size:13
Alignment explanation
Indices: 57501--57526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57491 TACAATGAGC
57501 ATGTATCGATACA
1 ATGTATCGATACA
57514 ATGTATCGATACA
1 ATGTATCGATACA
57527 TTTGGGTGTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:60814 original size:13 final size:13
Alignment explanation
Indices: 60796--60821 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60786 CAAAATTAAT
60796 AAAATATTTTTTA
1 AAAATATTTTTTA
60809 AAAATATTTTTTA
1 AAAATATTTTTTA
60822 GTTTCTAAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATATTTTTTA
Found at i:62629 original size:15 final size:15
Alignment explanation
Indices: 62605--62640 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
62595 GCAAATTCTT
62605 AAAATTTTTCAG-GA
1 AAAATTTTTCAGAGA
62619 AAAACTTTTTCAGAGA
1 AAAA-TTTTTCAGAGA
62635 AAAATT
1 AAAATT
62641 ATTATACGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 10 0.50
16 6 0.30
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAATTTTTCAGAGA
Found at i:63619 original size:11 final size:10
Alignment explanation
Indices: 63588--63622 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
63578 TTAATTTTTT
63588 AAAAATTTCA
1 AAAAATTTCA
*
63598 GAAAATTTCA
1 AAAAATTTCA
63608 AAAAATTCTCA
1 AAAAATT-TCA
63619 AAAA
1 AAAA
63623 TAAGAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (10 bp):
AAAAATTTCA
Found at i:67830 original size:10 final size:10
Alignment explanation
Indices: 67815--67853 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
67805 GGAAACCTTA
*
67815 TTATTTTTAG
1 TTATTTTTAT
*
67825 TTATTTATTTT
1 TTATTT-TTAT
67836 TTATTTTTAT
1 TTATTTTTAT
67846 TTATTTTT
1 TTATTTTT
67854 TAAGATAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:70269 original size:167 final size:167
Alignment explanation
Indices: 69781--70492 Score: 603
Period size: 167 Copynumber: 4.3 Consensus size: 167
69771 AAAATTAAAA
* * * * * * * * * ** *
69781 TTTTCAAAACTAAATTAATGGGAATTCAATGACAATATTAGATGCATTTTGAAAATTTTAGACCA
1 TTTTAAAAACTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA
* * * * * * *
69846 A-AGAAAATCC-CCTGGAAATATTTATGAAATAGAAAACTCGATTTTTTGGAAA-AGG-GAAATT
66 AGA-AAAATCCTCCCGAAAAAATTTACGGAATAGAAAACTCGATATTTTGAAAACAGGAG-AATT
* **
69907 TTAAAGAAAAAAATCT-AAAACTCATGAAAATGAATTAAT
129 TTAAGGAAAAAAAT-TAAAAACTCATGAAAATGAAGGAAT
* *
69946 TTTTAAAAACTGATTTAATATGG-AATAAATAATAATATTTGATGAA-TTTAAAAAGTTAAAAAC
1 TTTTAAAAACTAATTTAAT-GGGAAATAAATAATAATATTTGATGAATTTTAAAAA-TTAAAAAC
* * * * * * ** *
70009 TAAGAAAAATCC-CCCAAAAAAATTTACAGAGTAGAAAACTCTATATTTCGAAAACATAAAAATT
64 CAAGAAAAATCCTCCCGAAAAAATTTACGGAATAGAAAACTCGATATTTTGAAAACAGGAGAATT
* *
70073 TGAAGG-AAAAAATTCAAAAACTAATGAAAATGAAGGAAT
129 TTAAGGAAAAAAATT-AAAAACTCATGAAAATGAAGGAAT
* * *
70112 TTTTGAAAATTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTTAAAAACTAAAAACCA
1 TTTTAAAAACTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA
*
70177 AGAAAAATCCTCTCGAAAAAATTTACGGAATAGAAAACTTC-ATATTTTGAAAACAGGAGAATTT
66 AGAAAAATCCTCCCGAAAAAATTTACGGAATAGAAAAC-TCGATATTTTGAAAACAGGAGAATTT
* *
70241 CAAGGAAAAAAATTAAAAACTCATGAAAATGAATGAAT
130 TAAGGAAAAAAATTAAAAACTCATGAAAATGAAGGAAT
* * * ** * ** *
70279 TTTTTAAAACTGATTTAATAGGAAATAAATAATAATATTTTTTGAATTTAAAAAATTTTAAACCC
1 TTTTAAAAACTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA
* * * * * *
70344 ATAAAAATCCTCCCG-AAAAATTCACGGAGA-AAAAAATCTC-ATAATTTGAAAATAAGATGAAT
66 AGAAAAATCCTCCCGAAAAAATTTACGGA-ATAGAAAA-CTCGATATTTTGAAAACAGGA-GAAT
* * * * * *
70406 TTTAA--AAGAAAGTCAATAACTCA--AATATAAAAGGAAT
128 TTTAAGGAAAAAAATTAAAAACTCATGAAAAT-GAAGGAAT
* * * * *
70443 TTTTCAAAACTAATTTGATGAGAATTAAATAATAATATTTGAAGAATTTT
1 TTTTAAAAACTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTT
70493 GATTTTTAAA
Statistics
Matches: 443, Mismatches: 88, Indels: 33
0.79 0.16 0.06
Matches are distributed among these distances:
163 4 0.01
164 54 0.12
165 100 0.23
166 122 0.28
167 153 0.35
168 10 0.02
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (167 bp):
TTTTAAAAACTAATTTAATGGGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA
AGAAAAATCCTCCCGAAAAAATTTACGGAATAGAAAACTCGATATTTTGAAAACAGGAGAATTTT
AAGGAAAAAAATTAAAAACTCATGAAAATGAAGGAAT
Found at i:72079 original size:21 final size:22
Alignment explanation
Indices: 72053--72105 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
72043 ATGGTTTAAA
* *
72053 TTAAAATATCTC-GAATAATGT
1 TTAAAAGATCTCAGAAAAATGT
72074 TTAAAAGATC-CAGAAAAATGT
1 TTAAAAGATCTCAGAAAAATGT
72095 TTAAAAGATCT
1 TTAAAAGATCT
72106 TAGTCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (22 bp):
TTAAAAGATCTCAGAAAAATGT
Found at i:73354 original size:13 final size:13
Alignment explanation
Indices: 73336--73360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73326 CATAAAGTGT
73336 TGTATCGATACAA
1 TGTATCGATACAA
73349 TGTATCGATACA
1 TGTATCGATACA
73361 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:73376 original size:32 final size:33
Alignment explanation
Indices: 73316--73381 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
73306 TTCAACGATT
73316 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
73349 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
73381 T
1 T
73382 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:73440 original size:13 final size:13
Alignment explanation
Indices: 73422--73446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73412 ATTACTCAAA
73422 TGTATCGATACAT
1 TGTATCGATACAT
73435 TGTATCGATACA
1 TGTATCGATACA
73447 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.