Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2757
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: 154201
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:88 original size:38 final size:39
Alignment explanation
Indices: 43--119 Score: 95
Period size: 41 Copynumber: 2.0 Consensus size: 39
33 CTCACGAGCG
* *
43 AAATGCTTTGGGA-T-AGGCCGGATATAATCACTGAGCAC
1 AAATGCTTCGGGACTGAGCCCGGATATAATCACT-AGCAC
*
81 AAATGCTTCGGGACTTGAGCCCGGATATAGTCACTAGCA
1 AAATGCTTCGGGAC-TGAGCCCGGATATAATCACTAGCA
120 GAGATTAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 12 0.36
40 5 0.15
41 16 0.48
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (39 bp):
AAATGCTTCGGGACTGAGCCCGGATATAATCACTAGCAC
Found at i:11267 original size:13 final size:13
Alignment explanation
Indices: 11249--11275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11239 GGCTCGATAG
11249 GACACGCCCGTGT
1 GACACGCCCGTGT
11262 GACACGCCCGTGT
1 GACACGCCCGTGT
11275 G
1 G
11276 TAATTGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:12742 original size:40 final size:40
Alignment explanation
Indices: 12687--12883 Score: 180
Period size: 40 Copynumber: 5.1 Consensus size: 40
12677 TCGAATTTAA
* * ** *
12687 CCGGATATAGCAACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12727 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12767 CCGATT-TAGTAACTCGCACCAATGCCTTC-GG-CTTAGC
1 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
12804 CTGG-AATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
12844 CCGG--ATA-TCACTTAGCACAAA-GCCTTC-GGACTTAGC
1 CCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12880 CCGG
1 CCGG
12884 ACATCATTCG
Statistics
Matches: 134, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
36 9 0.07
37 19 0.14
38 36 0.27
39 23 0.17
40 47 0.35
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12791 original size:39 final size:39
Alignment explanation
Indices: 12706--12835 Score: 174
Period size: 38 Copynumber: 3.3 Consensus size: 39
12696 GCAACTCGTT
* *
12706 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCA
*
12746 CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
* * *
12785 CCAATGCCTTC-GG-CTTAGCCTGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCC-CGATTTAGTAACTCGCA
12823 CAAATGCCTTCGG
1 CAAATGCCTTCGG
12836 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
37 6 0.08
38 27 0.34
39 23 0.29
40 24 0.30
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:20786 original size:40 final size:40
Alignment explanation
Indices: 20723--20926 Score: 227
Period size: 40 Copynumber: 5.1 Consensus size: 40
20713 TGAAATTTAA
* ** *
20723 CCGGATATAGCAACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20763 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
20803 CCGAATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGA
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20842 CTGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
20882 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
20922 CCGGA
1 CCGGA
20927 CATCATTCGA
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.01
39 29 0.21
40 94 0.69
41 12 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:20910 original size:79 final size:80
Alignment explanation
Indices: 20770--20920 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 80
20760 AGCCCGGTTA
* * *
20770 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACCAAAGCCTTCGG
20835 G-CTTAGACTGGAAT
66 GACTTAGACTGGAAT
** * *
20849 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGAATATAGTAAC-TAGCACCAAAGCCTTC
20912 GGGACTTAG
64 GGGACTTAG
20921 CCCGGACATC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.05
79 50 0.81
80 9 0.15
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGACTGGAAT
Found at i:26557 original size:13 final size:13
Alignment explanation
Indices: 26539--26563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26529 GTATGGGTGC
26539 ACACGGCCGTGTG
1 ACACGGCCGTGTG
26552 ACACGGCCGTGT
1 ACACGGCCGTGT
26564 CTGTCTTTGT
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:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (13 bp):
ACACGGCCGTGTG
Found at i:36752 original size:14 final size:14
Alignment explanation
Indices: 36733--36760 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36723 GTTCTTCTTG
36733 ATCTATAATAGTAA
1 ATCTATAATAGTAA
36747 ATCTATAATAGTAA
1 ATCTATAATAGTAA
36761 TTTTAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
ATCTATAATAGTAA
Found at i:39182 original size:55 final size:53
Alignment explanation
Indices: 39095--39327 Score: 228
Period size: 55 Copynumber: 4.4 Consensus size: 53
39085 ATTAGGGTTT
*
39095 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGA
* * * * * *
39150 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGG-A
* * * * *
39206 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGA
*
39258 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC--A--A
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGA
*
39307 AAGGATACCACGTAAGACCAT
1 AAGGATACCATGTAAGACCAT
39328 TAAAATTCAT
Statistics
Matches: 148, Mismatches: 23, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
49 20 0.14
51 1 0.01
52 5 0.03
53 39 0.26
54 12 0.08
55 66 0.45
56 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGA
Found at i:39278 original size:53 final size:53
Alignment explanation
Indices: 39095--39302 Score: 240
Period size: 55 Copynumber: 3.8 Consensus size: 53
39085 ATTAGGGTTT
* * *
39095 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGGC
* * * *
39150 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
39205 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
39258 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
39303 TCAAAAGGAT
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
52 6 0.05
53 44 0.34
54 8 0.06
55 67 0.52
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:39301 original size:108 final size:110
Alignment explanation
Indices: 39102--39302 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
39092 TTTAAGGATA
*
39102 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGAAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGAAAGGAAACCATGTAAGA
*
39167 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * * *
39212 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGAAAGGAAACCATGTAAG
*
39274 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
39303 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGAAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:49623 original size:22 final size:23
Alignment explanation
Indices: 49581--49624 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
49571 TCTCTTTTTT
49581 TTTCTTCCACTTCATTCTCCAAAA
1 TTTCTTCCACTT-ATTCTCCAAAA
*
49605 TTTCTTCCAGTT-TTCTCCAA
1 TTTCTTCCACTTATTCTCCAA
49625 TGGCTTGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.20, C:0.32, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTCTTCCACTTATTCTCCAAAA
Found at i:51524 original size:32 final size:32
Alignment explanation
Indices: 51483--51549 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
51473 GAAGGGGGAG
51483 TAAGATTTACGCTTAGTAAGTCCATATGAAGA
1 TAAGATTTACGCTTAGTAAGTCCATATGAAGA
51515 TAAGATTTACGCTTAGTAAGTCCATATGAAGA
1 TAAGATTTACGCTTAGTAAGTCCATATGAAGA
51547 TAA
1 TAA
51550 TAAGCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (32 bp):
TAAGATTTACGCTTAGTAAGTCCATATGAAGA
Found at i:64610 original size:12 final size:12
Alignment explanation
Indices: 64588--64617 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
64578 GATTATTCAC
64588 GTAATTATTCTT
1 GTAATTATTCTT
64600 GTAATTATTCTT
1 GTAATTATTCTT
*
64612 ATAATT
1 GTAATT
64618 GCCATTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (12 bp):
GTAATTATTCTT
Found at i:74241 original size:18 final size:18
Alignment explanation
Indices: 74214--74277 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
74204 AACCGAGCCA
*
74214 TAAAATTTTTCCCAAATT
1 TAAAACTTTTCCCAAATT
***
74232 TAAAACTTTT--CAAGCCA
1 TAAAACTTTTCCCAA-ATT
*
74249 TAAAATTTTTCCCAAATT
1 TAAAACTTTTCCCAAATT
74267 TAAAACTTTTC
1 TAAAACTTTTC
74278 ATTCACATGC
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 19 0.56
19 3 0.09
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAAACTTTTCCCAAATT
Found at i:74248 original size:35 final size:35
Alignment explanation
Indices: 74209--74278 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
74199 TACAAAACCG
74209 AGCCATAAAATTTTTCCCAAATTTAAAACTTTTCA
1 AGCCATAAAATTTTTCCCAAATTTAAAACTTTTCA
74244 AGCCATAAAATTTTTCCCAAATTTAAAACTTTTCA
1 AGCCATAAAATTTTTCCCAAATTTAAAACTTTTCA
74279 TTCACATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (35 bp):
AGCCATAAAATTTTTCCCAAATTTAAAACTTTTCA
Found at i:74527 original size:16 final size:16
Alignment explanation
Indices: 74506--74539 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
74496 GACTTCATCA
74506 ACTAAATTGAGGTCGC
1 ACTAAATTGAGGTCGC
*
74522 ACTAAATTGAGGTTGC
1 ACTAAATTGAGGTCGC
74538 AC
1 AC
74540 GGCCAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (16 bp):
ACTAAATTGAGGTCGC
Found at i:74883 original size:16 final size:17
Alignment explanation
Indices: 74855--74886 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
74845 ATATATGATT
74855 TTATAATTTTTATAACC
1 TTATAATTTTTATAACC
74872 TTATAA-TTTTATAAC
1 TTATAATTTTTATAAC
74887 TAAGGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATTTTTATAACC
Found at i:83166 original size:42 final size:42
Alignment explanation
Indices: 83064--83172 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
83054 TGTTGCAAAT
* * * *
83064 GCCATATCCCAGATATGGTCTTACATGAAATATCATATCGAA
1 GCCATATCCCAGATATGGTCTTATAAGAAATATCACACCGAA
* * * *
83106 GCTATGTCCCTGACATGGTCTTATAAGAAATCA-CACACCGATA
1 GCCATATCCCAGATATGGTCTTATAAGAAAT-ATCACACCGA-A
83149 -CCATATCCCAGATATGGTCTTATA
1 GCCATATCCCAGATATGGTCTTATA
83173 TGGAATCTCA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 51 0.96
43 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTATAAGAAATATCACACCGAA
Found at i:97847 original size:68 final size:64
Alignment explanation
Indices: 97755--97976 Score: 241
Period size: 67 Copynumber: 3.4 Consensus size: 64
97745 TAATACGGGA
* *
97755 TGTATACCATGTGTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATACT
1 TGTACACCATGTGTACAAGAGAGCTACGAG--A-TAT-AAGTAGCTAGGTTGCATGGGTGATACT
97820 ATG
62 ATG
* * * *
97823 TGTACACCATGTAG-ACAAGAGAGCTACGAGATATATGTAGCTAGGTTGCATGTGTGGTTCTAGG
1 TGTACACCATGT-GTACAAGAGAGCTACGAGATATAAGTAGCTAGGTTGCATGGGTGATACTA--
97887 TG
63 TG
* * ** * **
97889 AAGGACACCATGTAAACAAGAGAGCTACGAGATA-AAGTGGCTAGGTCACATGGGTGATACTATG
1 -TGTACACCATGTGTACAAGAGAGCTACGAGATATAAGTAGCTAGGTTGCATGGGTGATACTATG
97953 TGTACACCATGTGTACAAGAGAGC
1 TGTACACCATGTGTACAAGAGAGC
97977 CAAAATTATG
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
63 20 0.15
64 26 0.20
65 3 0.02
66 24 0.18
67 29 0.22
68 27 0.21
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (64 bp):
TGTACACCATGTGTACAAGAGAGCTACGAGATATAAGTAGCTAGGTTGCATGGGTGATACTATG
Found at i:103814 original size:50 final size:49
Alignment explanation
Indices: 103684--103857 Score: 204
Period size: 50 Copynumber: 3.5 Consensus size: 49
103674 TGAGGTCGCA
* * * ** * *
103684 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCATG
1 TGTGTAGTACTAAGTGCAGGCTACAACGTGTACTAGATAA-TT-GGTCACG
* * **
103735 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACAACGTGTACTAGATAATT-GGTCACG
* *
103785 TGTGTAGTACTAAGTGCAGGCTACAACGTGTACTAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACAACGTGTACTAGATAATTGGTCACG
103834 TGTGTAGTACTAAGTGCAGGCTAC
1 TGTGTAGTACTAAGTGCAGGCTAC
103858 TATACGTACC
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
49 29 0.27
50 45 0.42
51 33 0.31
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACAACGTGTACTAGATAATTGGTCACG
Found at i:103872 original size:49 final size:50
Alignment explanation
Indices: 103676--103872 Score: 193
Period size: 50 Copynumber: 3.9 Consensus size: 50
103666 ATCTATTGTG
* * *
103676 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATACGTACCAGATAA-TT
* * ** *** ** **
103727 CGATCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATACGTACCAGATAATT
* *
103777 AGGTCACGTGTGTAGTACTAAGTGCAGGCTAC-A-ACGTGTACTAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATAC--GTACCAGATAATT
*
103827 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATACGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATACGTACCAGATA
103873 GCTTTGGCTA
Statistics
Matches: 119, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 39 0.33
50 42 0.35
51 38 0.32
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATACGTACCAGATAATT
Found at i:105811 original size:18 final size:18
Alignment explanation
Indices: 105788--105827 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
105778 CATGTGGCCT
105788 GCCCGTGTGAGCCCACAC-
1 GCCCGTGTG-GCCCACACA
*
105806 GCCCGTGTGGCTCACACA
1 GCCCGTGTGGCCCACACA
105824 GCCC
1 GCCC
105828 AATTAGGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.45, G:0.28, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGGCCCACACA
Found at i:123831 original size:17 final size:14
Alignment explanation
Indices: 123793--123822 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
123783 CACACGGTTG
123793 AGACATTAAAACCA
1 AGACATTAAAACCA
123807 AGACATTAAAACCA
1 AGACATTAAAACCA
123821 AG
1 AG
123823 CCAACATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (14 bp):
AGACATTAAAACCA
Found at i:128272 original size:33 final size:33
Alignment explanation
Indices: 128225--128312 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
128215 AGTGAATAAC
*
128225 ACAGTCTGGGCCTAAGCCCTATTCAGTATCAGT
1 ACAGTCTGGACCTAAGCCCTATTCAGTATCAGT
*
128258 ACAGTCTGGACCTAAGCCCTATTTAGTATCAGT
1 ACAGTCTGGACCTAAGCCCTATTCAGTATCAGT
*
128291 ACAGTCTGGGCCCT-AGCCCTAT
1 ACAGTCT-GGACCTAAGCCCTAT
128313 ACAATAGCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 46 0.90
34 5 0.10
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (33 bp):
ACAGTCTGGACCTAAGCCCTATTCAGTATCAGT
Found at i:128537 original size:27 final size:27
Alignment explanation
Indices: 128507--128593 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
128497 AGCATAACTG
*
128507 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
* * *
128534 CCAGTATCAGTAATTGTGGCATAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
* * * * *
128561 CCATTAACAGTGAATGTGACATAGTCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
128588 CCAGTA
1 CCAGTA
128594 TAGAACTTCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
CCAGTAACAGTAAATGTGGCAAAGCCA
Found at i:128766 original size:27 final size:27
Alignment explanation
Indices: 128736--128925 Score: 217
Period size: 27 Copynumber: 7.0 Consensus size: 27
128726 GCATAATCGA
* * * * *
128736 CATTTTATCATATAGGTGTATTACAGT
1 CATTTTATCCTACAGGGGCATTACGGT
*
128763 CATTTTACCCTACAGGGGCATTACGGT
1 CATTTTATCCTACAGGGGCATTACGGT
*
128790 CATTTTGTCCTACAGGGGCATTACGGT
1 CATTTTATCCTACAGGGGCATTACGGT
128817 CATTTTA-CTCTACAGGGGCATTACGGT
1 CATTTTATC-CTACAGGGGCATTACGGT
* *
128844 CATTTTA-CTCTACAAGGGCATTACGAT
1 CATTTTATC-CTACAGGGGCATTACGGT
* *
128871 CATTCTA-CTCTACAGGGGCATTACAGT
1 CATTTTATC-CTACAGGGGCATTACGGT
128898 CATTTTA-CTCTACAGGGGCATTACGGT
1 CATTTTATC-CTACAGGGGCATTACGGT
128925 C
1 C
128926 CTATAATGAC
Statistics
Matches: 145, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
26 1 0.01
27 144 0.99
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (27 bp):
CATTTTATCCTACAGGGGCATTACGGT
Found at i:128857 original size:81 final size:81
Alignment explanation
Indices: 128755--128925 Score: 263
Period size: 81 Copynumber: 2.1 Consensus size: 81
128745 ATATAGGTGT
* * * ** *
128755 ATTACAGTCATTTTACCCTACAGGGGCATTACGGTCATT-TTGTCCTACAGGGGCATTACGGTCA
1 ATTACGGTCATTTTACCCTACAAGGGCATTACGATCATTCTACT-CTACAGGGGCATTACAGTCA
128819 TTTTACTCTACAGGGGC
65 TTTTACTCTACAGGGGC
*
128836 ATTACGGTCATTTTACTCTACAAGGGCATTACGATCATTCTACTCTACAGGGGCATTACAGTCAT
1 ATTACGGTCATTTTACCCTACAAGGGCATTACGATCATTCTACTCTACAGGGGCATTACAGTCAT
128901 TTTACTCTACAGGGGC
66 TTTACTCTACAGGGGC
128917 ATTACGGTC
1 ATTACGGTC
128926 CTATAATGAC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 80 0.98
82 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (81 bp):
ATTACGGTCATTTTACCCTACAAGGGCATTACGATCATTCTACTCTACAGGGGCATTACAGTCAT
TTTACTCTACAGGGGC
Found at i:128922 original size:54 final size:54
Alignment explanation
Indices: 128762--128922 Score: 252
Period size: 54 Copynumber: 3.0 Consensus size: 54
128752 TGTATTACAG
* * *
128762 TCATTTTACCCTACAGGGGCATTACGGTCATTTT-GTCCTACAGGGGCATTACGG
1 TCATTTTACTCTACAGGGGCATTACGGTCATTTTACT-CTACAGGGGCATTACGA
*
128816 TCATTTTACTCTACAGGGGCATTACGGTCATTTTACTCTACAAGGGCATTACGA
1 TCATTTTACTCTACAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACGA
* *
128870 TCATTCTACTCTACAGGGGCATTACAGTCATTTTACTCTACAGGGGCATTACG
1 TCATTTTACTCTACAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACG
128923 GTCCTATAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 98 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (54 bp):
TCATTTTACTCTACAGGGGCATTACGGTCATTTTACTCTACAGGGGCATTACGA
Found at i:131100 original size:39 final size:40
Alignment explanation
Indices: 130986--131170 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
130976 GCTACTCATT
* *
130986 CAAATGCTTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
131026 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
131066 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * ** *
131105 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCTCTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
131146 CAAA-GTCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
131171 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 76 0.61
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:131156 original size:79 final size:80
Alignment explanation
Indices: 130994--131170 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
130984 TTCAAATGCT
* * *
130994 TTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGT
1 TTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGT
* *
131058 AACTCGCACCAATGCC
65 AACTAGCACCAAAGCC
** *
131074 TTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGT
1 TTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGT
** *
131137 CTCTTAGCA-CAAAGTC
65 AAC-TAGCACCAAAGCC
131153 TTCGGGACTTAGCCCGGA
1 TTCGGGACTTAGCCCGGA
131171 CATCATTCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.04
79 57 0.70
80 22 0.27
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
TTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTA
ACTAGCACCAAAGCC
Found at i:137561 original size:13 final size:13
Alignment explanation
Indices: 137543--137568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137533 GTCTTTTATT
137543 TTTATTTTATTTA
1 TTTATTTTATTTA
137556 TTTATTTTATTTA
1 TTTATTTTATTTA
137569 CTTAGTTTAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:146079 original size:22 final size:22
Alignment explanation
Indices: 146040--146090 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
146030 AATTGAGATT
*
146040 GAAAAGAATTGAAGAAAGAAGA
1 GAAAAGAATTGAAAAAAGAAGA
146062 GAAAATGAATT-AAAAAAGAA-A
1 GAAAA-GAATTGAAAAAAGAAGA
*
146083 CAAAAGAA
1 GAAAAGAA
146091 AAAAGACTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 5 0.19
22 13 0.50
23 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.10
Consensus pattern (22 bp):
GAAAAGAATTGAAAAAAGAAGA
Found at i:151997 original size:10 final size:11
Alignment explanation
Indices: 151973--152008 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
151963 TTAAACAAGT
151973 AAATAAATAAA
1 AAATAAATAAA
151984 AAATAAATAAA
1 AAATAAATAAA
*
151995 AATAAAAATAAA
1 AA-ATAAATAAA
152007 AA
1 AA
152009 CTTTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:153385 original size:27 final size:27
Alignment explanation
Indices: 153355--153406 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
153345 TCTAACTCAT
*
153355 TTTCTCTCTTCTTCAC-TTCTTTTCAAA
1 TTTCTCTCTT-TTCACATCCTTTTCAAA
*
153382 TTTCTCTGTTTTCACATCCTTTTCA
1 TTTCTCTCTTTTCACATCCTTTTCA
153407 CTCTCATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.13, C:0.29, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTCTCTCTTTTCACATCCTTTTCAAA
Done.