Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold394
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: 52390
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7711 original size:27 final size:28
Alignment explanation
Indices: 7602--7724 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
7592 GAGATTGGCG
* * * *
7602 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
7631 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
7659 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
7687 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
7714 CTGAGTGTGCG
1 CTAAGTGTGCG
7725 GACTTAATAT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 24 0.27
28 50 0.56
29 15 0.17
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:7735 original size:27 final size:27
Alignment explanation
Indices: 7627--7737 Score: 143
Period size: 28 Copynumber: 4.0 Consensus size: 27
7617 TAAATTGTAC
*
7627 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
7655 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
7683 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGATTATAT
* *
7710 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGATTATAT
7737 A
1 A
7738 CTTTTGAATC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
27 30 0.38
28 48 0.62
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGATTATAT
Found at i:29818 original size:39 final size:40
Alignment explanation
Indices: 29741--29887 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
29731 TAGCTCCTCG
* * *
29741 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
29781 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
29820 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
29860 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
29888 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:29898 original size:80 final size:80
Alignment explanation
Indices: 29787--29967 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
29777 CTCATTCAAT
* * *
29787 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
29850 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
29866 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
29930 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
29947 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29968 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:29927 original size:40 final size:40
Alignment explanation
Indices: 29784--29967 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29774 TAACTCATTC
* *
29784 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
29824 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
29864 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
29904 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
29945 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29968 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:31804 original size:72 final size:70
Alignment explanation
Indices: 31670--31826 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 70
31660 AGCCAATTTA
* *
31670 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCCCTTGGAATCACACATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCCC-T-GAATCACACATGCGACCTAGCTACATT
31735 TATCCTC
64 TATCCTC
* * **
31742 TCTCGTAGCTCTCTTGTCTACATGG-GATACATCCC-GTATCACACATGTGACCTAGCTAC-TAC
1 TCTCGTAGCTCTCTTGTCTACATGGTG-TACATCCCTGAATCACACATGCGACCTAGCTACATTT
** *
31804 ATAGTA
65 ATCCTC
31810 TCTCGTAGCTCTCTTGT
1 TCTCGTAGCTCTCTTGT
31827 ACACATGATG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
68 21 0.28
69 22 0.29
71 1 0.01
72 31 0.41
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (70 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCCCTGAATCACACATGCGACCTAGCTACATTTA
TCCTC
Found at i:40546 original size:28 final size:28
Alignment explanation
Indices: 40514--40568 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40504 AGTTGGGCTT
* *
40514 GATGGGCCATATGAATGTGATTGGGCCC
1 GATGGGCCATATGAACGAGATTGGGCCC
*
40542 GATGGGCCATGTGAACGAGATTGGGCC
1 GATGGGCCATATGAACGAGATTGGGCC
40569 TAAAGGGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (28 bp):
GATGGGCCATATGAACGAGATTGGGCCC
Found at i:40918 original size:27 final size:25
Alignment explanation
Indices: 40887--41253 Score: 250
Period size: 27 Copynumber: 13.7 Consensus size: 25
40877 TAATAAAGAG
*
40887 AAATTACTAAACTATCCTCAGTTTGTA
1 AAATTACTAAA-TACCCTC-GTTTGTA
**
40914 AAATTACCGCAATACCCTCAGTTTGTA
1 AAATTA-CTAAATACCCTC-GTTTGTA
* * *
40941 AAATTATCGAAGTACCCCCGGTTTGTA
1 AAATTA-CTAAATACCCTC-GTTTGTA
* *
40968 AAATCACCAAAATACCCTCGATTTGTA
1 AAATTA-CTAAATACCCTCG-TTTGTA
*
40995 AAATTATCGAAATACCCTCAGTTTGTA
1 AAATTA-CTAAATACCCTC-GTTTGTA
* * *
41022 AATTTATTGAAATACCCTCGATTTATA
1 AAATTACT-AAATACCCTCG-TTTGTA
* *
41049 AAATTATCAAAATACCCTCGATTGTA
1 AAATTA-CTAAATACCCTCGTTTGTA
41075 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACT-AAATACCCTCG-TTTGTA
* **
41102 AAATTACCGAAATACCCCTAATTTGTA
1 AAATTA-CTAAATA-CCCTCGTTTGTA
* * *
41129 ATATTACTAAAATACCCTCGATTGTG
1 AAATTACT-AAATACCCTCGTTTGTA
*
41155 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTACT-AAATACCCTC-GTTTGTA
*
41182 AAATTATCGAAATACCC-CTGATTTGTA
1 AAATTA-CTAAATACCCTC-G-TTTGTA
* * **
41209 AAATAACTGAAACAACCCTAATTTGTA
1 AAATTACT-AAA-TACCCTCGTTTGTA
*
41236 AAATTATCGAAATACCCT
1 AAATTA-CTAAATACCCT
41254 TGTAGTGTTA
Statistics
Matches: 270, Mismatches: 52, Indels: 37
0.75 0.14 0.10
Matches are distributed among these distances:
25 1 0.00
26 56 0.21
27 198 0.73
28 15 0.06
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (25 bp):
AAATTACTAAATACCCTCGTTTGTA
Found at i:40970 original size:54 final size:54
Alignment explanation
Indices: 40902--41253 Score: 351
Period size: 54 Copynumber: 6.6 Consensus size: 54
40892 ACTAAACTAT
** *
40902 CCTCAGTTTGTAAAATTACCGCAATACCCTC-AGTTTGTAAAATTATCGAAGTAC
1 CCTCAGTTTGTAAAATTACCAAAATACCCTCGA-TTTGTAAAATTATCGAAATAC
* * *
40956 CCCCGGTTTGTAAAATCACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
1 CCTCAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
* *** * *
41010 CCTCAGTTTGTAAATTTATTGAAATACCCTCGATTTATAAAATTATCAAAATAC
1 CCTCAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
* * *
41064 CCTC-GATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATAC
1 CCTCAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
* * * *
41117 CC-CTAATTTGTAATATTACTAAAATACCCTCGA-TTGTGAAATTA-CTGAAATAC
1 CCTC-AGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTATC-GAAATAC
* * * * *
41170 CCTCAATTTGTAAAATTATCGAAATACCC-CTGATTTGTAAAA-TAACTGAAACAAC
1 CCTCAGTTTGTAAAATTACCAAAATACCCTC-GATTTGTAAAATTATC-GAAA-TAC
* * *
41225 CCT-AATTTGTAAAATTATCGAAATACCCT
1 CCTCAGTTTGTAAAATTACCAAAATACCCT
41254 TGTAGTGTTA
Statistics
Matches: 256, Mismatches: 32, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
52 3 0.01
53 88 0.34
54 159 0.62
55 6 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (54 bp):
CCTCAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
Found at i:41100 original size:80 final size:79
Alignment explanation
Indices: 40909--41212 Score: 389
Period size: 80 Copynumber: 3.8 Consensus size: 79
40899 TATCCTCAGT
* * * * * *
40909 TTGTAAAATTACCGCAATACCCTCAGTTTGTAAAATTATCGAAGTACCCCCGGTTTGTAAAATCA
1 TTGTAAAATTACTGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCCTGATTTGTAAAATTA
40974 CCAAAATACCCTCGA
66 -CAAAATACCCTCGA
* * *
40989 TTTGTAAAATTA-TCGAAATACCCTCAGTTTGTAAATTTATTGAAATA-CCCTCGATTTATAAAA
1 -TTGTAAAATTACT-GAAATACCCTCAGTTTGTAAAATTATCGAAATACCCCT-GATTTGTAAAA
41052 TTATCAAAATACCCTCGA
63 TTA-CAAAATACCCTCGA
* * * *
41070 TTGTAAAATTACTAAAATACCCTC-GATTTGTAAAATTACCGAAATACCCCTAATTTGTAATATT
1 TTGTAAAATTACTGAAATACCCTCAG-TTTGTAAAATTATCGAAATACCCCTGATTTGTAAAATT
41134 ACTAAAATACCCTCGA
65 AC-AAAATACCCTCGA
* *
41150 TTGTGAAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAATACCCCTGATTTGTAAAAT
1 TTGTAAAATTACTGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCCTGATTTGTAAAAT
41213 AACTGAAACA
Statistics
Matches: 193, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
79 2 0.01
80 121 0.63
81 70 0.36
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (79 bp):
TTGTAAAATTACTGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCCTGATTTGTAAAATTA
CAAAATACCCTCGA
Found at i:41113 original size:107 final size:107
Alignment explanation
Indices: 40902--41253 Score: 367
Period size: 107 Copynumber: 3.3 Consensus size: 107
40892 ACTAAACTAT
* * * * *
40902 CCTCAGTTTGTAAAATTACCGCAATACCCTC-AGTTTGTAAAATTATCGAAGTACCCCCGGTTTG
1 CCTCAATTTGTAAAATTACCGAAATACCCTCGA-TTTGTAAAATTATCGAAATACCCTC-GATTG
* * *
40966 TAAAATCACCAAAATACCCTCGATTTGTAAAATTATCGAAATAC
64 TAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATAC
* * ** * *
41010 CCTCAGTTTGTAAATTTATTGAAATACCCTCGATTTATAAAATTATCAAAATACCCTCGATTGTA
1 CCTCAATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTA
41075 AAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATAC
66 AAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATAC
* ** * *
41117 CC-CTAATTTGTAATATTACTAAAATACCCTCGA-TTGTGAAATTA-CTGAAATACCCTCAATTT
1 CCTC-AATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTATC-GAAATACCCTCGA-TT
* * * *
41179 GTAAAATTA-TCGAAATACCC-CTGATTTGTAAAATAACTGAAACAAC
63 GTAAAATTACT-AAAATACCCTC-GATTTGTAAAATTACCGAAA-TAC
*
41225 CCT-AATTTGTAAAATTATCGAAATACCCT
1 CCTCAATTTGTAAAATTACCGAAATACCCT
41254 TGTAGTGTTA
Statistics
Matches: 207, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
105 1 0.00
106 23 0.11
107 130 0.63
108 52 0.25
109 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (107 bp):
CCTCAATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTA
AAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATAC
Found at i:41293 original size:27 final size:28
Alignment explanation
Indices: 41234--41312 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
41224 CCCTAATTTG
* *
41234 TAAAATTATCGAAATACCCTTGTAGTGT
1 TAAAATTACCAAAATACCCTTGTAGTGT
*
41262 T-AAATTACCAAAATATCCTTGTAGT-T
1 TAAAATTACCAAAATACCCTTGTAGTGT
* * * *
41288 TAAAATGACCGACATACCCATGTAG
1 TAAAATTACCAAAATACCCTTGTAG
41313 GGTAAGATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.93
28 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (28 bp):
TAAAATTACCAAAATACCCTTGTAGTGT
Found at i:44004 original size:51 final size:50
Alignment explanation
Indices: 43933--44162 Score: 193
Period size: 50 Copynumber: 4.6 Consensus size: 50
43923 ATTGTGAATA
* *
43933 CACGTGTGTAGTATTGAGTGCAGGCCTACTACGTGTACCATACTGTTAAGT
1 CACGTGTGTAGTACTAAGTGCAGG-CTACTACGTGTACCATACTGTTAAGT
* * * * **
43984 CGCATGTGTAGTACTAAGTGCA-GCTACTATGCGTACTCAATGACT-TCGA-T
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-C-AT-ACTGTTAAGT
* * * * *
44034 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGGTGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACT-GTTAAGT
* * * *
44084 CACGTGTGTAGTACTAAGTGCAAGCTACCTACGTGTACCAAATTGTT-GGT
1 CACGTGTGTAGTACTAAGTGCAGGCTA-CTACGTGTACCATACTGTTAAGT
* *
44134 CACCTGTGTAGTACT-AGTGCAGACTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
44163 TGCGTACAGA
Statistics
Matches: 144, Mismatches: 26, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 22 0.15
50 66 0.46
51 47 0.33
52 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGT
Found at i:48672 original size:31 final size:29
Alignment explanation
Indices: 48637--48870 Score: 114
Period size: 32 Copynumber: 7.7 Consensus size: 29
48627 TTGGTCTTGA
48637 CATATACTGGGCCGAAGCTTTCCAATAAAAT
1 CATATACTGGGCCGAAGCTTT-C-ATAAAAT
* *
48668 CATATATTGGACCGAAGCCTTTCAT-AAAT
1 CATATACTGGGCCGAAG-CTTTCATAAAAT
48697 CATAGTCACTGGGCC-AAGCTTTTCATAAAAT
1 CATA-T-ACTGGGCCGAAGC-TTTCATAAAAT
* *
48728 CATATCACCT-CGCCTGAACCTTTTCAT--AAT
1 CATAT-A-CTGGGCC-GAAGC-TTTCATAAAAT
* *
48758 CATATCACTGGGGTCGTAGCCTTTTTCAT-AAAT
1 CATAT-ACT-GGGCCGAAG-C--TTTCATAAAAT
*
48791 CATATCAGCTGGGGCGAAGCCTTTTCAT-AAAT
1 CATAT-A-CTGGGCCGAAG-C-TTTCATAAAAT
*
48823 CATATCACT-GG-CTAAGGCCTTTCAT--AAT
1 CATAT-ACTGGGCCGAA-G-CTTTCATAAAAT
48851 CATAT-CTGGGCCGAAGCTTT
1 CATATACTGGGCCGAAGCTTT
48871 ACTGTAAACG
Statistics
Matches: 172, Mismatches: 14, Indels: 39
0.76 0.06 0.17
Matches are distributed among these distances:
26 6 0.03
27 3 0.02
28 11 0.06
29 20 0.12
30 35 0.20
31 37 0.22
32 39 0.23
33 19 0.11
34 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (29 bp):
CATATACTGGGCCGAAGCTTTCATAAAAT
Found at i:48721 original size:30 final size:30
Alignment explanation
Indices: 48637--48870 Score: 191
Period size: 31 Copynumber: 7.7 Consensus size: 30
48627 TTGGTCTTGA
*
48637 CATAT-ACTGGGCCGAAGCTTTCCAATAAAAT
1 CATATCACTGGGCCGAAGCTTTTC-AT-AAAT
* * *
48668 CATAT-ATTGGACCGAAGCCTTTCATAAAT
1 CATATCACTGGGCCGAAGCTTTTCATAAAT
48697 CATAGTCACTGGGCC-AAGCTTTTCATAAAAT
1 CATA-TCACTGGGCCGAAGCTTTTCAT-AAAT
* *
48728 CATATCACCT-CGCCTGAACCTTTTCAT-AAT
1 CATATCA-CTGGGCC-GAAGCTTTTCATAAAT
* *
48758 CATATCACTGGGGTCGTAGCCTTTTTCATAAAT
1 CATATCACT-GGGCCGAAG-C-TTTTCATAAAT
*
48791 CATATCAGCTGGGGCGAAGCCTTTTCATAAAT
1 CATATCA-CTGGGCCGAAG-CTTTTCATAAAT
* *
48823 CATATCACT-GG-CTAAGGCCTTTCAT-AAT
1 CATATCACTGGGCCGAA-GCTTTTCATAAAT
48851 CATAT--CTGGGCCGAAGCTTT
1 CATATCACTGGGCCGAAGCTTT
48871 ACTGTAAACG
Statistics
Matches: 169, Mismatches: 19, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 11 0.07
29 20 0.12
30 34 0.20
31 40 0.24
32 35 0.21
33 19 0.11
34 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (30 bp):
CATATCACTGGGCCGAAGCTTTTCATAAAT
Found at i:48750 original size:61 final size:61
Alignment explanation
Indices: 48637--48833 Score: 158
Period size: 61 Copynumber: 3.2 Consensus size: 61
48627 TTGGTCTTGA
* *
48637 CATAT-ACTGGGCCGAAGCTTTCCAATAAAATCATATATTGGACCGAAGCC-TTTCATAAAT
1 CATATCACTGGGCCGAAGCTTTCCAATAAAATCATATACTCGACCGAAGCCTTTTCAT-AAT
*
48697 CATAGTCACTGGGCC-AAGCTTTTC-ATAAAATCATATCACCTCG-CCTGAA-CCTTTTCATAAT
1 CATA-TCACTGGGCCGAAGCTTTCCAATAAAATCATAT-A-CTCGACC-GAAGCCTTTTCATAAT
* * * * **
48758 CATATCACTGGGGTCGTAGCCTTTTTC-AT-AAATCATATCAGCTGGGGCGAAGCCTTTTCATAA
1 CATATCACT-GGGCCGAAG-C-TTTCCAATAAAATCATAT-A-CTCGACCGAAGCCTTTTCAT-A
48821 AT
60 AT
48823 CATATCACTGG
1 CATATCACTGG
48834 CTAAGGCCTT
Statistics
Matches: 116, Mismatches: 8, Indels: 22
0.79 0.05 0.15
Matches are distributed among these distances:
60 21 0.18
61 25 0.22
62 21 0.18
63 18 0.16
64 19 0.16
65 12 0.10
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (61 bp):
CATATCACTGGGCCGAAGCTTTCCAATAAAATCATATACTCGACCGAAGCCTTTTCATAAT
Found at i:48981 original size:43 final size:42
Alignment explanation
Indices: 48893--49057 Score: 221
Period size: 42 Copynumber: 3.9 Consensus size: 42
48883 ATGGCCTTGG
48893 CCATTTCAATATTCACATGTAATGTC-ATGGATGTATGCAAG-
1 CCATTTCAATA-TCACATGTAATGTCAATGGATGTATGCAAGC
48934 CCATTTTCAATAATCACATGTAATGTCAATGGATG-ATGCAAGC
1 CCA-TTTCAAT-ATCACATGTAATGTCAATGGATGTATGCAAGC
*
48977 CCATTTCAATATCACAATGTAAATGTCAATGAATGTACTGCAAGTC
1 CCATTTCAATATCAC-ATGT-AATGTCAATGGATGTA-TGCAAG-C
*
49023 CCATTTCAATATC-CATGTAATGTCAATGAATGTAT
1 CCATTTCAATATCACATGTAATGTCAATGGATGTAT
49058 ACGGAGGCCC
Statistics
Matches: 114, Mismatches: 1, Indels: 17
0.86 0.01 0.13
Matches are distributed among these distances:
41 8 0.07
42 40 0.35
43 40 0.35
44 5 0.04
45 7 0.06
46 14 0.12
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (42 bp):
CCATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGC
Found at i:49048 original size:86 final size:84
Alignment explanation
Indices: 48893--49050 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 84
48883 ATGGCCTTGG
*
48893 CCATTTCAATATTCACATGTAATGTCATGGATGTATGCAAGCCATTTTCAATAATCACATGTAAT
1 CCATTTCAATATTCACATGTAATGTCATGAATGTATGCAAGCCATTTTCAATAATCACATGTAAT
48958 GTCAATGGATGATGCAAGC
66 GTCAATGGATGATGCAAGC
48977 CCATTTCAATA-TCACAATGTAAATGTCAATGAATGTACTGCAAGTCCCA-TTTCAAT-ATC-CA
1 CCATTTCAATATTCAC-ATGT-AATGTC-ATGAATGTA-TGCAAG--CCATTTTCAATAATCACA
49038 TGTAATGTCAATG
60 TGTAATGTCAATG
49051 AATGTATACG
Statistics
Matches: 67, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
83 4 0.06
84 15 0.22
85 6 0.09
86 23 0.34
87 9 0.13
88 7 0.10
89 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (84 bp):
CCATTTCAATATTCACATGTAATGTCATGAATGTATGCAAGCCATTTTCAATAATCACATGTAAT
GTCAATGGATGATGCAAGC
Found at i:49100 original size:23 final size:23
Alignment explanation
Indices: 49069--49146 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
49059 CGGAGGCCCT
*
49069 AGCCTCTTTTAATAACTGGGGCAA
1 AGCC-CTTTTGATAACTGGGGCAA
*
49093 AGCCCTTTTGATAAACT-GGGTAA
1 AGCCCTTTTGAT-AACTGGGGCAA
* * *
49116 AGCCCTTTCGGT-ACTGGGGCAG
1 AGCCCTTTTGATAACTGGGGCAA
49138 AGCCCTTTT
1 AGCCCTTTT
49147 TAGCACTTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.07
22 12 0.27
23 22 0.49
24 8 0.18
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (23 bp):
AGCCCTTTTGATAACTGGGGCAA
Found at i:52081 original size:3 final size:3
Alignment explanation
Indices: 52075--52140 Score: 53
Period size: 3 Copynumber: 20.3 Consensus size: 3
52065 GGGGGGGGAG
* *
52075 GGA GGA GGTG GGA GGA -GA GGGA GGA GGA GAGA AGA GGA GGGA GGGA
1 GGA GGA GG-A GGA GGA GGA -GGA GGA GGA G-GA GGA GGA -GGA -GGA
52121 GGA GGGA GGA GGA GGA GGA G
1 GGA -GGA GGA GGA GGA GGA G
52141 AGGGAGAGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 2 0.04
3 35 0.66
4 16 0.30
ACGTcount: A:0.32, C:0.00, G:0.67, T:0.02
Consensus pattern (3 bp):
GGA
Found at i:52087 original size:10 final size:10
Alignment explanation
Indices: 52055--52314 Score: 155
Period size: 10 Copynumber: 26.8 Consensus size: 10
52045 CTGATGGTAG
52055 GGAGGGA-GA
1 GGAGGGAGGA
52064 GG-GGG-GG-
1 GGAGGGAGGA
52071 GGAGGGAGGA
1 GGAGGGAGGA
*
52081 GGTGGGAGGA
1 GGAGGGAGGA
52091 -GAGGGAGGA
1 GGAGGGAGGA
* *
52100 GGAGAGAAGA
1 GGAGGGAGGA
52110 GGAGGGAGGGA
1 GGAGGGA-GGA
52121 GGAGGGAGGA
1 GGAGGGAGGA
52131 GGA-GGAGGA
1 GGAGGGAGGA
52140 -GAGGGA-GA
1 GGAGGGAGGA
52148 GGGAGGGA-GA
1 -GGAGGGAGGA
*
52158 GGGAGGG-GGG
1 -GGAGGGAGGA
52168 GGAGGGAAGGGA
1 GGAGGG-A-GGA
*
52180 GGAGGGAAGA
1 GGAGGGAGGA
52190 GGAGGGA-GA
1 GGAGGGAGGA
*
52199 GGAGGGAGAA
1 GGAGGGAGGA
*
52209 GGGGGAGAGGA
1 GGAGG-GAGGA
52220 GAGAGGGACGG-
1 G-GAGGGA-GGA
*
52231 GTAGAGG-GG-
1 GGAG-GGAGGA
*
52240 GTAGGG-GGTA
1 GGAGGGAGG-A
52250 GG-GGGAGG-
1 GGAGGGAGGA
52258 GGAGGGAGGA
1 GGAGGGAGGA
* *
52268 GGAGGGTGGG
1 GGAGGGAGGA
52278 GGA-GG-GGA
1 GGAGGGAGGA
52286 GGGAGGGGAGGA
1 -GGA-GGGAGGA
* *
52298 -GAGGAAGGG
1 GGAGGGAGGA
52307 GGAGGGAG
1 GGAGGGAG
52315 ACCTGGTACA
Statistics
Matches: 202, Mismatches: 21, Indels: 55
0.73 0.08 0.20
Matches are distributed among these distances:
7 2 0.01
8 19 0.09
9 61 0.30
10 82 0.41
11 22 0.11
12 16 0.08
ACGTcount: A:0.28, C:0.00, G:0.70, T:0.02
Consensus pattern (10 bp):
GGAGGGAGGA
Found at i:52154 original size:78 final size:77
Alignment explanation
Indices: 52059--52314 Score: 217
Period size: 78 Copynumber: 3.3 Consensus size: 77
52049 TGGTAGGGAG
* * *
52059 GGAGAGGGGGGGGGAGGGAGGAGGTGGGAGGAGAGGGAGGAGGAGAGAAGAGGAGGGAGGGAGGA
1 GGAGAGGGAGAGGGAGGGAGGAGGTGGG-GGAGAGGGAGGAGGAGGGAAGAGGAGGGAGGGAGGA
52124 GGGAGGAGGAGGA
65 GGGAGGAGGAGGA
52137 GGAGAGGGAGAGGGAGGGAGAGGGAGG-GGGGG-GAGGGAAGGGAGGAGGGAAGAGGAGGGA--G
1 GGAGAGGGAGAGGGA-GG-GA-GGAGGTGGGGGAGAGGG-A-GGAGGAGGGAAGAGGAGGGAGGG
*
52198 AGGAGGGA-GA--AGGG
61 AGGAGGGAGGAGGAGGA
* * * *
52212 GGAGAGGAGAGAGGGACGGGTAGAGGGGGTAGGGGGTAGGGGGAGG-GGAGGGAGGAGGAGGGTG
1 GGAGAGG-GAGAGGGA--GG--GAGGAGGT-GGGGG-AGAGGGAGGAGGAGGGAAGAGGAGGGAG
52276 GG-GGAGGGGAGGGAGG-GGA
59 GGAGGA-GGGA-GGAGGAGGA
* *
52295 GGAGAGGAAGGGGGAGGGAG
1 GGAGAGGGAGAGGGAGGGAG
52315 ACCTGGTACA
Statistics
Matches: 148, Mismatches: 11, Indels: 38
0.75 0.06 0.19
Matches are distributed among these distances:
75 10 0.07
76 8 0.05
77 9 0.06
78 48 0.32
79 15 0.10
80 32 0.22
81 9 0.06
82 8 0.05
83 9 0.06
ACGTcount: A:0.28, C:0.00, G:0.70, T:0.02
Consensus pattern (77 bp):
GGAGAGGGAGAGGGAGGGAGGAGGTGGGGGAGAGGGAGGAGGAGGGAAGAGGAGGGAGGGAGGAG
GGAGGAGGAGGA
Found at i:52226 original size:31 final size:32
Alignment explanation
Indices: 52134--52227 Score: 69
Period size: 31 Copynumber: 3.1 Consensus size: 32
52124 GGGAGGAGGA
*
52134 GGAGGAGAGGGAGAGGGAGGGAGAGG-GAG--G
1 GGAGG-GAGGGAGAAGGAGGGAGAGGAGAGAAG
* * *
52164 GGGGGGAGGGA-AGGGA-GGAG-GGAAGAGGAG
1 GGAGGGAGGGAGAAGGAGGGAGAGG-AGAGAAG
52194 GGAGAGGAGGGAGAAGG-GGGAGAGGAGAG-AG
1 GGAG-GGAGGGAGAAGGAGGGAGAGGAGAGAAG
52225 GGA
1 GGA
52228 CGGGTAGAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
26 2 0.04
27 4 0.08
28 8 0.15
29 6 0.11
30 8 0.15
31 12 0.23
32 11 0.21
33 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (32 bp):
GGAGGGAGGGAGAAGGAGGGAGAGGAGAGAAG
Found at i:52261 original size:5 final size:5
Alignment explanation
Indices: 52251--52301 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
52241 TAGGGGGTAG
*
52251 GGGGA GGGGA -GGGA GGAGGA GGGTG- GGGGA GGGGA -GGGA GGGGA GGAGA
1 GGGGA GGGGA GGGGA GG-GGA GGG-GA GGGGA GGGGA GGGGA GGGGA GGGGA
52300 GG
1 GG
52302 AAGGGGGAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 9 0.22
5 25 0.62
6 6 0.15
ACGTcount: A:0.22, C:0.00, G:0.76, T:0.02
Consensus pattern (5 bp):
GGGGA
Found at i:52278 original size:25 final size:25
Alignment explanation
Indices: 52245--52296 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
52235 AGGGGGTAGG
52245 GGGTAGGGGGAGGGGAGGGAGGAGGA
1 GGGTAGGGGGAGGGGAGGGAGG-GGA
52271 GGGT-GGGGGAGGGGAGGGAGGGGA
1 GGGTAGGGGGAGGGGAGGGAGGGGA
52295 GG
1 GG
52297 AGAGGAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.77, T:0.04
Consensus pattern (25 bp):
GGGTAGGGGGAGGGGAGGGAGGGGA
Done.