Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1058
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: 39052
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3031 original size:18 final size:19
Alignment explanation
Indices: 3008--3043 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2998 TAAACAAGCG
3008 ATTAATA-AAAGAAAAATT
1 ATTAATATAAAGAAAAATT
*
3026 ATTAATATAAATAAAAAT
1 ATTAATATAAAGAAAAAT
3044 CAAATTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
ATTAATATAAAGAAAAATT
Found at i:4994 original size:1 final size:1
Alignment explanation
Indices: 4988--5028 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
4978 AATCTTCAAA
* * *
4988 TTTTTTTGTTTTTTTTTTCTTTTGTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5029 ACAATTGCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (1 bp):
T
Found at i:5026 original size:16 final size:16
Alignment explanation
Indices: 4988--5026 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4978 AATCTTCAAA
4988 TTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
*
5004 TTCTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
5020 TTTTTTT
1 TTTTTTT
5027 TTACAATTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.92
Consensus pattern (16 bp):
TTTTTTTGTTTTTTTT
Found at i:18317 original size:20 final size:20
Alignment explanation
Indices: 18289--18345 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
18279 GTAAAAAGAC
18289 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTCA
* *
18309 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTCA
18329 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
18346 CTGGGCACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:20774 original size:21 final size:20
Alignment explanation
Indices: 20722--20776 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
20712 TGTTTCTGAC
20722 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
**
20742 ATGTATTAATACATTCACTT
1 ATGTATCGATACATTCACTT
20762 ATTGTATCGATACAT
1 A-TGTATCGATACAT
20777 ACTGTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:21899 original size:33 final size:34
Alignment explanation
Indices: 21788--22045 Score: 136
Period size: 35 Copynumber: 7.4 Consensus size: 34
21778 TAAATGCATT
* * * * *
21788 TTTTTAGTTCTCAAAAAAGCAAAAT-ACTTTTTCCC
1 TTTTTAGTCCTC-AAAGAGCAAGATGCCTTTTT-CA
* * *
21823 TTTTCAGTCTTCAAAGAGCATGATGCCTTTTTCCA
1 TTTTTAGTCCTCAAAGAGCAAGATGCCTTTTT-CA
*
21858 TTTTTAGTCCTCAAAGAGTAAGATGCCTTTTT-A
1 TTTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCA
* * *
21891 TTTTTAGTCCTTAAA-A-AATAGA-ACACATTTTTTCA
1 TTTTTAGTCCTCAAAGAGCA-AGATGC-C--TTTTTCA
* * * *
21926 TTTTTAATCCTTAAAGAGCAAGATGCCTAATTTCC
1 TTTTTAGTCCTCAAAGAGCAAGATGCCT-TTTTCA
* ** *
21961 TTTTTAAGTCCT-AAAAAGCAAGACACCTTCTTTCC
1 TTTTT-AGTCCTCAAAGAGCAAGATGCCTT-TTTCA
* *
21996 TTTTTAATCCTCAAAGATCACA-ATGTCTCTTTTTC-
1 TTTTTAGTCCTCAAAGAGCA-AGATG-C-CTTTTTCA
*
22031 TTTTTAATCCTCAAA
1 TTTTTAGTCCTCAAA
22046 AAGTAGGACA
Statistics
Matches: 177, Mismatches: 30, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
31 2 0.01
32 5 0.03
33 15 0.08
34 20 0.11
35 114 0.64
36 16 0.09
37 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCA
Found at i:22056 original size:70 final size:67
Alignment explanation
Indices: 21848--22056 Score: 183
Period size: 70 Copynumber: 3.0 Consensus size: 67
21838 GAGCATGATG
* * * *
21848 CCTTTTTCCATTTTTAGTCCTCAAAGAGT-AAGATGC-CTTTTTATTTTTAGTCCTTAAAAAATA
1 CCTTTTTCC-TTTTTAATCCTCAAAGA-TCAAGATGCTCTTTTTCTTTTTAATCC-TAAAAAGTA
*
21911 GAACA
63 GGACA
* * * * * *
21916 CATTTTTTCATTTTTAATCCTTAAAGAGCAAGATGC-CTAATTTCCTTTTTAAGTCCTAAAAAGC
1 C-CTTTTTCCTTTTTAATCCTCAAAGATCAAGATGCTCT--TTTTCTTTTTAA-TCCTAAAAAGT
*
21980 AAGACA
62 AGGACA
21986 CCTTCTTTCCTTTTTAATCCTCAAAGATCACA-ATGTCTCTTTTTCTTTTTAATCCTCAAAAAGT
1 CCTT-TTTCCTTTTTAATCCTCAAAGATCA-AGATG-CTCTTTTTCTTTTTAATCCT-AAAAAGT
22050 AGGACA
62 AGGACA
22056 C
1 C
22057 TTGCCTAGCT
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
68 25 0.22
69 12 0.11
70 68 0.61
71 5 0.04
72 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (67 bp):
CCTTTTTCCTTTTTAATCCTCAAAGATCAAGATGCTCTTTTTCTTTTTAATCCTAAAAAGTAGGA
CA
Found at i:22172 original size:32 final size:32
Alignment explanation
Indices: 22106--22264 Score: 104
Period size: 32 Copynumber: 5.0 Consensus size: 32
22096 CCTCCATTCC
* *
22106 CAAAAAGCAAGAAGCTTACCAACCTCAGTTCT
1 CAAAAAGCAAGAAGCTTACCAACCTCAATCCT
* *
22138 CAAATAGCAA-AAGACTTACCAACCTTAATCCT
1 CAAAAAGCAAGAAG-CTTACCAACCTCAATCCT
* * * * ** *
22170 CAAAAAGTAAGATGCCTACCTATATCAGTCCT
1 CAAAAAGCAAGAAGCTTACCAACCTCAATCCT
* * * * * *
22202 CAAAAAGTAGGATGCTTACCTATCTCAGTCCT
1 CAAAAAGCAAGAAGCTTACCAACCTCAATCCT
* * * **
22234 TAAAAAGTAAGATGCTTACCTGCCTCAATCC
1 CAAAAAGCAAGAAGCTTACCAACCTCAATCC
22265 ATGACGAGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
31 3 0.03
32 99 0.95
33 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (32 bp):
CAAAAAGCAAGAAGCTTACCAACCTCAATCCT
Found at i:22936 original size:65 final size:65
Alignment explanation
Indices: 22769--22969 Score: 172
Period size: 65 Copynumber: 3.0 Consensus size: 65
22759 TGCTATAGCC
* * * * * *
22769 TTTCTACACCACTATTCTACATAAC-AGAACCAATGGTGACAAGAGCAGCTGAGCATAGTACCTA
1 TTTCTACACCACTACTCTACATAGCAAG-ACCAAT-G-GAAAAAAGTAGTTGAGCATAGTACCTA
22833 GAG
63 GAG
* *
22836 TTTCTACACCACTACTCTACATAGCAAGACTAATGGAAAAAAGTAGTTGAGTATAGTACCTAGAG
1 TTTCTACACCACTACTCTACATAGCAAGACCAATGGAAAAAAGTAGTTGAGCATAGTACCTAGAG
* * * * ** * * *
22901 TTTCTGCACCATTACTTTGCAT-GGTAGAACCAATGGAAATAAGAGCAATTGAGCATAGTATCTA
1 TTTCTACACCACTACTCTACATAGCAAG-ACCAATGGAAA-AA-AGTAGTTGAGCATAGTACCTA
*
22965 AAG
63 GAG
22968 TT
1 TT
22970 GTCCTCTAAT
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
64 3 0.03
65 53 0.48
66 3 0.03
67 49 0.45
68 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (65 bp):
TTTCTACACCACTACTCTACATAGCAAGACCAATGGAAAAAAGTAGTTGAGCATAGTACCTAGAG
Found at i:28061 original size:15 final size:14
Alignment explanation
Indices: 28027--28073 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
28017 ATGAAACTGG
*
28027 ATTACAAAA-TAAA
1 ATTAAAAAATTAAA
28040 A-TAAAAAATCTAAA
1 ATTAAAAAAT-TAAA
28054 ATTAAAAAAATTAAA
1 ATT-AAAAAATTAAA
28069 ATTAA
1 ATTAA
28074 TAGTCATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.21
13 1 0.03
14 7 0.24
15 8 0.28
16 7 0.24
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (14 bp):
ATTAAAAAATTAAA
Found at i:30968 original size:148 final size:149
Alignment explanation
Indices: 30632--31166 Score: 582
Period size: 148 Copynumber: 3.6 Consensus size: 149
30622 CTCAGAGGTG
* * * * *
30632 CCTAGTGATCCTAAATGACTTAAAAAGGAAAAGTGAACCTACGCCTAATATGTACCCTCGGCATA
1 CCTAGTAACCCTAAAAGACTTAAAAAGGAAAAGCGAACCTACGCCTAATACGTACCCTCGGCATA
* * ** * * * *
30697 GAAGCAGCATAATAACAAATTACGACTTGATTCTAGAAAAATTATGAAAATGCCCCTATAGGTAT
66 AAAGCAACCCAGTGATAAATTAGGACTTGATTCTAGAAAAATTATGAAAATGCCCCTATAGGTAT
* *
30762 AACTTCAACATGAAAGTA-
131 ACCTTCGACATGAAAGTAT
* * * *
30780 CCTTGGTAACCCTAAAAGAATTAAAAAGGAAAACCGAACCTATGCCTAATACGTACCCTCGGCAT
1 CC-TAGTAACCCTAAAAGACTTAAAAAGGAAAAGCGAACCTACGCCTAATACGTACCCTCGGCAT
* * * *
30845 AGAAGCAACCCAGTGATAAATTAGAACTTGGTTCTA-AAAAATTATGAAAAT-CCTCCTATGGGT
65 AAAAGCAACCCAGTGATAAATTAGGACTTGATTCTAGAAAAATTATGAAAATGCC-CCTATAGGT
* *
30908 ATTCCATCGACATGAAAGTAT
129 ATACCTTCGACATGAAAGTAT
* * *
30929 CCTAGTAACCCTAAAAGACTTAAAAAGGAAAGGCAAACCTATGCCTAATACGTACCCTCGGCATA
1 CCTAGTAACCCTAAAAGACTTAAAAAGGAAAAGCGAACCTACGCCTAATACGTACCCTCGGCATA
* * * * * *
30994 AAAGCGACCTAGTGATGAATTAGGACTT-ATTTTAGAAAAA-TAAGAAAATGCCCTTATAGGTAT
66 AAAGCAACCCAGTGATAAATTAGGACTTGATTCTAGAAAAATTATGAAAATGCCCCTATAGGTAT
31057 ACCTTCGACAT-AAAGTAT
131 ACCTTCGACATGAAAGTAT
* * * * * * * *
31075 CC-CGAAAACCTTAAAGGATTTAAAAAGGAAAAACGAACCTACGCCTAATATGTACCCTCGGTAT
1 CCTAG-TAACCCTAAAAGACTTAAAAAGGAAAAGCGAACCTACGCCTAATACGTACCCTCGGCAT
**
31139 AAAAGTGACCC-GATGATAAATTAGGACT
65 AAAAGCAACCCAG-TGATAAATTAGGACT
31167 GGGATCTTAA
Statistics
Matches: 326, Mismatches: 54, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
145 2 0.01
146 81 0.25
147 32 0.10
148 129 0.40
149 82 0.25
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (149 bp):
CCTAGTAACCCTAAAAGACTTAAAAAGGAAAAGCGAACCTACGCCTAATACGTACCCTCGGCATA
AAAGCAACCCAGTGATAAATTAGGACTTGATTCTAGAAAAATTATGAAAATGCCCCTATAGGTAT
ACCTTCGACATGAAAGTAT
Found at i:31659 original size:140 final size:140
Alignment explanation
Indices: 31472--31880 Score: 513
Period size: 141 Copynumber: 2.9 Consensus size: 140
31462 TAGAAATTTC
* * * *
31472 AAAAATCTCATTCCGTACCTTAATAGAGAACTGAAAAGATAAGAAAAGTTTTCAAGATTTTTATA
1 AAAAAT-TCATTTCGTACCTTAATAGAGAAATGAAAAGATAA-AAAAGTTTTGAAGATTTCTATA
* *
31537 CCCCTAAGAAAAACCATAAGAATA-TAAAAATCTTGAAAAATTAAGACAATAATTTTTATTTAAC
64 CCCCTAAGAAAAACCATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAAC
31601 TGTTAA-TTTCTA
129 TGTTAACTTT-TA
* *
31613 AAAAATTCATTTCGTACCTTAATGGAGAAATTAAAAGATACAAAAAGTTTTGAAGATTTCTATAC
1 AAAAATTCATTTCGTACCTTAATAGAGAAATGAAAAGATA-AAAAAGTTTTGAAGATTTCTATAC
* * * * ** *
31678 CCTTACGAGAAACCAT-AGAAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTCTTGGAT
65 CCCTAAGAAAAACCATAAG-AATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAAC
*
31742 TTTTAACTTTTA
129 TGTTAACTTTTA
* * * *
31754 AGAAAATTCATTTTGTACCTTAA-CGAAAAACTGAAAATATATAAAAAGTTTTGAAGATTTCTAT
1 A-AAAATTCATTTCGTACCTTAATAGAGAAA-TGAAAAGATA-AAAAAGTTTTGAAGATTTCTAT
* *
31818 A-CCCTATGAAAAACCATAAGAATATTAGAAGTCTTGAAAAATTAAGATAATAATTTTTATTTA
63 ACCCCTAAGAAAAACCATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
31881 GTGATAAAAT
Statistics
Matches: 232, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
139 2 0.01
140 68 0.29
141 106 0.46
142 56 0.24
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (140 bp):
AAAAATTCATTTCGTACCTTAATAGAGAAATGAAAAGATAAAAAAGTTTTGAAGATTTCTATACC
CCTAAGAAAAACCATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAACTG
TTAACTTTTA
Found at i:31910 original size:8 final size:7
Alignment explanation
Indices: 31895--31933 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
31885 TAAAATAATA
31895 TTTATTT
1 TTTATTT
*
31902 ATTATTTT
1 TTTA-TTT
31910 ATTTATTT
1 -TTTATTT
31918 TTTATTT
1 TTTATTT
31925 TTTATTT
1 TTTATTT
31932 TT
1 TT
31934 AAAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 19 0.68
8 6 0.21
9 3 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTATTT
Found at i:31912 original size:12 final size:12
Alignment explanation
Indices: 31895--31932 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
31885 TAAAATAATA
31895 TTTATTTATTAT
1 TTTATTTATTAT
31907 TTTATTTATT-T
1 TTTATTTATTAT
*
31918 TTTATTTTTTAT
1 TTTATTTATTAT
31930 TTT
1 TTT
31933 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTATTAT
Found at i:31914 original size:16 final size:16
Alignment explanation
Indices: 31893--31925 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31883 GATAAAATAA
31893 TATTTATTTATTATTT
1 TATTTATTTATTATTT
*
31909 TATTTATTTTTTATTT
1 TATTTATTTATTATTT
31925 T
1 T
31926 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTATTTATTATTT
Found at i:32542 original size:17 final size:17
Alignment explanation
Indices: 32520--32570 Score: 102
Period size: 17 Copynumber: 3.0 Consensus size: 17
32510 CATGGTGTAA
32520 AATCATGAAAAACAAAT
1 AATCATGAAAAACAAAT
32537 AATCATGAAAAACAAAT
1 AATCATGAAAAACAAAT
32554 AATCATGAAAAACAAAT
1 AATCATGAAAAACAAAT
32571 GAAAACATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
AATCATGAAAAACAAAT
Found at i:32781 original size:11 final size:11
Alignment explanation
Indices: 32764--32804 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
32754 CTATATTTTC
32764 CTTTTTTCTTT
1 CTTTTTTCTTT
*
32775 ATTTTTTC--T
1 CTTTTTTCTTT
32784 CTTTTTTCTTT
1 CTTTTTTCTTT
32795 CTCTTTTTCT
1 CT-TTTTTCT
32805 CTAAGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.32
11 10 0.40
12 7 0.28
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:32786 original size:13 final size:12
Alignment explanation
Indices: 32765--32802 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
32755 TATATTTTCC
*
32765 TTTTTTCT-TTA
1 TTTTTTCTCTTT
32776 TTTTTTCTCTTT
1 TTTTTTCTCTTT
32788 TTTCTTTCTCTTT
1 TTT-TTTCTCTTT
32801 TT
1 TT
32803 CTCTAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
12 5 0.21
13 11 0.46
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:32789 original size:20 final size:21
Alignment explanation
Indices: 32759--32806 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
32749 TCTAGCTATA
32759 TTTTC-CTTTTTTCTTTAT-T
1 TTTTCTCTTTTTTCTTTATCT
*
32778 TTTTCTCTTTTTTCTTTCTCT
1 TTTTCTCTTTTTTCTTTATCT
32799 TTTTCTCT
1 TTTTCTCT
32807 AAGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 12 0.46
21 9 0.35
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTTTTTCTTTATCT
Found at i:33660 original size:162 final size:163
Alignment explanation
Indices: 33255--33816 Score: 470
Period size: 162 Copynumber: 3.4 Consensus size: 163
33245 AACATATACA
** *** * ** *
33255 AAAAAATTCAAAATTCATGAAATAAATTCAATTTTTCAAAACTGATTTAA-GGGAATCT-AATGA
1 AAAAAATGAAAAATTCATGAAATAAAAAGAATTTTTCAAAACTAATTTAATAAGAAT-TAAATAA
* * * * * * **
33318 CAATGTTAGATGAATTTTAAAAATT-TAAACTAAGAAAAATCCTCTCAAAAACATTAATGGAA-T
65 TAATATTTGATGAATTTTAAAAATTATAAAC-AAAAAAAATCC-CTCCAAAACATTTA-CAAAGT
* * * ***
33381 AGAAAACTCAGT-TTTTCGAAAATAGGAGGTTTTCCAA-
127 AAAAAACTCCGTATTTT-GAAAATAAGAAAATTT-CAAG
* * * * *
33418 AGAAAAATGAAAAACTT-AT-AAA-AATAAATGAATTTTTTAAAATTGATTTACTAAGAATTGAA
1 A-AAAAATGAAAAA-TTCATGAAATAA-AAA-GAATTTTTCAAAACTAATTTAATAAGAATTAAA
*
33480 TAATAATATTTGATGAATTTTAAAAATTATAATCCAAAAAAAATCGCC-CCAAAACATTTACAAA
62 TAATAATATTTGATGAATTTTAAAAATTATAA-ACAAAAAAAATC-CCTCCAAAACATTTACAAA
**
33544 GTAAAAAACTTTGTATTTT-AGAAAT-AGAAAATTTTCAA-
125 GTAAAAAACTCCGTATTTTGA-AAATAAGAAAA-TTTCAAG
* * * *
33582 AAAAAAT-AAAATTTCATGAAATAAAAGGAATTTTTCAAAACTAATTTAATTAGAATTAAATGAT
1 AAAAAATGAAAAATTCATGAAATAAAAAGAATTTTTCAAAACTAATTTAATAAGAATTAAATAAT
* * ** ** *
33646 AATATTTGATGAATTTTAAAAATTTTAAACTAAAAAAATCCCTTTGAAAACATTTACGGAGTAGA
66 AATATTTGATGAATTTTAAAAATTATAAACAAAAAAAATCCC-TCCAAAACATTTACAAAGTAAA
33711 AAACTCCGTATTTTGAAAATAAGAAAATTTCAAG
130 AAACTCCGTATTTTGAAAATAAGAAAATTTCAAG
**
33745 AAAAAATGAAAAATTCATGAAATAAAAAGAGCTTTTCAAAACTAATTTAA-AATGAATTAAATAA
1 AAAAAATGAAAAATTCATGAAATAAAAAGAATTTTTCAAAACTAATTTAATAA-GAATTAAATAA
*
33809 TGATATTT
65 TAATATTT
33817 AAATAATTTT
Statistics
Matches: 323, Mismatches: 53, Indels: 45
0.77 0.13 0.11
Matches are distributed among these distances:
160 2 0.01
161 12 0.04
162 103 0.32
163 31 0.10
164 97 0.30
165 59 0.18
166 17 0.05
167 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.32
Consensus pattern (163 bp):
AAAAAATGAAAAATTCATGAAATAAAAAGAATTTTTCAAAACTAATTTAATAAGAATTAAATAAT
AATATTTGATGAATTTTAAAAATTATAAACAAAAAAAATCCCTCCAAAACATTTACAAAGTAAAA
AACTCCGTATTTTGAAAATAAGAAAATTTCAAG
Found at i:34749 original size:43 final size:41
Alignment explanation
Indices: 34701--35016 Score: 109
Period size: 42 Copynumber: 7.5 Consensus size: 41
34691 TAGCCTGGTC
*
34701 AACAAAGGATAAAAATAGTTACCCATGACTAAGCTGACAGGTA
1 AACAAAGGATAAAAA-AGTTACCCA-GAATAAGCTGACAGGTA
* * * ** * *
34744 AACAAATGAGACAAAAGTTGACTGAGAATGAA-CTGACAAGTG
1 AACAAAGGATAAAAAAGTT-ACCCAGAAT-AAGCTGACAGGTA
* * * * *
34786 AACAAAGGATAAAAGGATTTACCTAGGATTAAGCTGATAGGTA
1 AACAAAGGATAAAA-AAGTTACCCA-GAATAAGCTGACAGGTA
* * * * ** * * *
34829 AATAAAGGATAAAAAGGTTGATCGAGGTTAAACCGACAAGCT-
1 AACAAAGGATAAAAAAGTT-ACCCAGAATAAGCTGAC-AGGTA
* * * * * * *
34871 AATAAAGGATAAAAAGATTTTCCTAGACTAAGCTAACACGTA
1 AACAAAGGATAAAAA-AGTTACCCAGAATAAGCTGACAGGTA
*** * ** * *
34913 AACAAAGGAT-AAAAAGATTGATTGAGATTGAA-CCAACAAGTT
1 AACAAAGGATAAAAAAG-TT-ACCCAGAAT-AAGCTGACAGGTA
* * *
34955 AACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTA
1 AACAAAGGATAAAAA-AGTTACCC-AGAATAAGCTGACAGGTA
*
34998 AACAAAGGATACAAAAGTT
1 AACAAAGGATAAAAAAGTT
35017 GAGCAGGTTT
Statistics
Matches: 195, Mismatches: 62, Indels: 33
0.67 0.21 0.11
Matches are distributed among these distances:
40 1 0.01
41 8 0.04
42 101 0.52
43 84 0.43
44 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (41 bp):
AACAAAGGATAAAAAAGTTACCCAGAATAAGCTGACAGGTA
Found at i:34799 original size:85 final size:82
Alignment explanation
Indices: 34701--35059 Score: 344
Period size: 85 Copynumber: 4.2 Consensus size: 82
34691 TAGCCTGGTC
* * * *
34701 AACAAAGGATAAAAATAGTTACCCATGACTAAGCTGACAGGTAAACAAATGAGACAAAAGTTGAC
1 AACAAAGGATAAAAAGATTTACCCA-GACTAAGCTGACAGGTAAACAAAGGATA-AAAAGTTGAC
* * *
34766 TGAGAATGAACTGACAAGT
64 TGAGATTAAACCGACAAGT
* * * * *
34785 GAACAAAGGATAAAAGGATTTACCTAGGATTAAGCTGATAGGTAAATAAAGGATAAAAAGGTTGA
1 -AACAAAGGATAAAAAGATTTACCCA-GACTAAGCTGACAGGTAAACAAAGGATAAAAA-GTTGA
*
34850 -TCGAGGTTAAACCGACAAGCT
63 CT-GAGATTAAACCGACAAG-T
* * * * * *
34871 AATAAAGGATAAAAAGATTTTCCTAGACTAAGCTAACACGTAAACAAAGGATAAAAAGATTGATT
1 AACAAAGGATAAAAAGATTTACCCAGACTAAGCTGACAGGTAAACAAAGGATAAAAAG-TTGACT
* *
34936 GAGATTGAACCAACAAGTT
65 GAGATTAAACCGACAAG-T
*
34955 AACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTAAACAAAGGATACAAAAGTTGAG
1 AACAAAGGATAAAAAGATTTACCC-AGACTAAGCTGACAGGTAAACAAAGGATA-AAAAGTTGA-
* * * *
35020 CAG-GTTTAAACTGACAAGCC
63 CTGAGATTAAACCGACAAG-T
*
35040 AACAAAGGATAAAAGGATTT
1 AACAAAGGATAAAAAGATTT
35060 TCCTAATAAC
Statistics
Matches: 225, Mismatches: 41, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
83 1 0.00
84 72 0.32
85 145 0.64
86 7 0.03
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.19
Consensus pattern (82 bp):
AACAAAGGATAAAAAGATTTACCCAGACTAAGCTGACAGGTAAACAAAGGATAAAAAGTTGACTG
AGATTAAACCGACAAGT
Found at i:34920 original size:42 final size:42
Alignment explanation
Indices: 34874--35014 Score: 135
Period size: 42 Copynumber: 3.3 Consensus size: 42
34864 ACAAGCTAAT
* * *
34874 AAAGGATAAAAAGATTTTCCTAGACTAAGCTAACACGTAAAC
1 AAAGGATAAAAAGATTTTCCAAGACTAAGCCAACAAGTAAAC
* * *
34916 AAAGGATAAAAAGATTGATT--GAGATTGAA-CCAACAAGTTAAC
1 AAAGGATAAAAAGATT--TTCCAAGACT-AAGCCAACAAGTAAAC
* * *
34958 AAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTAAAC
1 AAAGGATAAAAAGATTT-TCCAAGACTAAGCCAACAAGTAAAC
35001 AAAGGATACAAAAG
1 AAAGGATA-AAAAG
35015 TTGAGCAGGT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
40 1 0.01
42 48 0.60
43 24 0.30
44 7 0.09
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (42 bp):
AAAGGATAAAAAGATTTTCCAAGACTAAGCCAACAAGTAAAC
Found at i:34963 original size:169 final size:170
Alignment explanation
Indices: 34700--35064 Score: 450
Period size: 169 Copynumber: 2.2 Consensus size: 170
34690 GTAGCCTGGT
* * * * * * *
34700 CAACAAAGGATAAAAATAGTTACCCATGACTAAGCTGACAGGTAAACAAATGAGACAAAAGTTGA
1 CAACAAAGGATAAAAAGATTTTCCTATGACTAAGCTAACACGTAAACAAAGGAGACAAAAGTTGA
** * * * * * *
34765 CTGAGAATGAACTGACAAGTGAACAAAGGATAAAAGGATTTACCTAGGATTAAGCTGATAGGTAA
66 CTGAGAATGAACCAACAAGTGAACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTAA
* *
34830 ATAAAGGATA-AAAAGGTTGATCGAGG-TTAAACCGACAAGC
131 ACAAAGGATACAAAA-GTTGAGC-AGGTTTAAACCGACAAGC
* * *
34870 TAATAAAGGATAAAAAGATTTTCCTA-GACTAAGCTAACACGTAAACAAAGGATA-AAAAGATTG
1 CAACAAAGGATAAAAAGATTTTCCTATGACTAAGCTAACACGTAAACAAAGGAGACAAAAG-TTG
* * *
34933 ATTGAGATTGAACCAACAAGTTAACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTA
65 ACTGAGAATGAACCAACAAGTGAACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTA
*
34998 AACAAAGGATACAAAAGTTGAGCAGGTTTAAACTGACAAGC
130 AACAAAGGATACAAAAGTTGAGCAGGTTTAAACCGACAAGC
*
35039 CAACAAAGGATAAAAGGATTTTCCTA
1 CAACAAAGGATAAAAAGATTTTCCTA
35065 ATAACGTGAC
Statistics
Matches: 165, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
168 8 0.05
169 133 0.81
170 24 0.15
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (170 bp):
CAACAAAGGATAAAAAGATTTTCCTATGACTAAGCTAACACGTAAACAAAGGAGACAAAAGTTGA
CTGAGAATGAACCAACAAGTGAACAAAGGATAAAAAGATTTACCCAAGACTAAGCCGACAGGTAA
ACAAAGGATACAAAAGTTGAGCAGGTTTAAACCGACAAGC
Found at i:35361 original size:81 final size:81
Alignment explanation
Indices: 35302--35571 Score: 299
Period size: 81 Copynumber: 3.3 Consensus size: 81
35292 AGTGAAACTG
*
35302 ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACCAAAAAAGCCAACAGGTTGGAAGGGTT
1 ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACCAAAAAAGCCAACAGGTTAGAAGGGTT
*
35367 GACCAAGGCAAAACCG
66 GACCAAGGCAAAACCA
* * * * * * * *
35383 ATAAAGTCAATCAATTAAAAGGTTGGCCAAGGCAAAAGCAATAAAGCTAACTGGCTAGAAGGGTT
1 ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACCAAAAAAGCCAACAGGTTAGAAGGGTT
* * *
35448 TACTAGGGCAAAACCA
66 GACCAAGGCAAAACCA
* * * * * * * * *
35464 ATAAAGTTAACCAGTTAAAAGGTTAGCTAGGGTGAAGCCGATAAAA-CCAACAGGTTAGAAGGGT
1 ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACC-AAAAAAGCCAACAGGTTAGAAGGGT
* *
35528 TGACCAAGGCGAAACTA
65 TGACCAAGGCAAAACCA
*
35545 ATAAAGTCAACAAATTAAAAAGTTGGC
1 ATAAAGTCAACCAATTAAAAAGTTGGC
35572 TAGGGGAAAA
Statistics
Matches: 150, Mismatches: 38, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
81 146 0.97
82 4 0.03
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (81 bp):
ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACCAAAAAAGCCAACAGGTTAGAAGGGTT
GACCAAGGCAAAACCA
Found at i:35415 original size:40 final size:39
Alignment explanation
Indices: 35302--35709 Score: 167
Period size: 40 Copynumber: 10.2 Consensus size: 39
35292 AGTGAAACTG
* *
35302 ATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACCA
1 ATAAAGTCAA-CAATTAAAAGGTTGGCCAAGGCAAAACCA
* * * * * * *
35342 AAAAAGCCAACAGGTTGGAAGGGTTGACCAAGGCAAAACCG
1 ATAAAGTCAACA-ATT-AAAAGGTTGGCCAAGGCAAAACCA
*
35383 ATAAAGTCAATCAATTAAAAGGTTGGCCAAGGCAAAAGCA
1 ATAAAGTCAA-CAATTAAAAGGTTGGCCAAGGCAAAACCA
*** * ** * *
35423 ATAAAG-CTAACTGGCTAGAAGGGTTTACTAGGGCAAAACCA
1 ATAAAGTC-AAC-AATTA-AAAGGTTGGCCAAGGCAAAACCA
* * * * * ** * *
35464 ATAAAGTTAACCAGTTAAAAGGTTAGCTAGGGTGAAGCCG
1 ATAAAGTCAA-CAATTAAAAGGTTGGCCAAGGCAAAACCA
** * * * * *
35504 ATAAAACCAACAGGTTAGAAGGGTTGACCAAGGCGAAACTA
1 ATAAAGTCAACA-ATTA-AAAGGTTGGCCAAGGCAAAACCA
* * * *
35545 ATAAAGTCAACAAATTAAAAAGTTGGCTAGGGGAAAA-CA
1 ATAAAGTCAAC-AATTAAAAGGTTGGCCAAGGCAAAACCA
* * * * * *
35584 ATAAAGTCAACTAATTAAAACGTCGGCTAGGGTAAAACCC
1 ATAAAGTCAAC-AATTAAAAGGTTGGCCAAGGCAAAACCA
* * * *
35624 ATAAAG-CTAACGAGTTAGAAAGG-TGACCAAGGTAAAACTA
1 ATAAAGTC-AAC-AATTA-AAAGGTTGGCCAAGGCAAAACCA
* * * * *
35664 ATAAAGTAAACCAATTAAAAAGTTGGCCAGGGCGAAACAA
1 ATAAAGTCAA-CAATTAAAAGGTTGGCCAAGGCAAAACCA
35704 ATAAAG
1 ATAAAG
35710 CGAACGAGTT
Statistics
Matches: 270, Mismatches: 81, Indels: 34
0.70 0.21 0.09
Matches are distributed among these distances:
39 45 0.17
40 134 0.50
41 87 0.32
42 4 0.01
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (39 bp):
ATAAAGTCAACAATTAAAAGGTTGGCCAAGGCAAAACCA
Found at i:35446 original size:162 final size:161
Alignment explanation
Indices: 35278--35589 Score: 367
Period size: 162 Copynumber: 1.9 Consensus size: 161
35268 CAAAGGATTG
** ** *
35278 GAAGGGTTGACTAAAGTGAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCAAGGCGAAACC-A
1 GAAGGGTTGACTAAAGCAAAACCAATAAAGTCAACCAATTAAAAAGTTAGCCAAGGCGAAACCGA
* * *
35342 AAAAAGCCAACAGGTTGGAAGGGTTGACCAAGGCAAAACCGATAAAGTCAATC-AATTAAAAGGT
66 AAAAA-CCAACAGGTTAGAAGGGTTGACCAAGGCAAAACCAATAAAGTCAA-CAAATTAAAAAGT
35406 TGGCCAAGGCAAAAGCAATAAAGCTAACTGGCTA
129 TGGCCAAGGCAAAA-CAATAAAGCTAACTGGCTA
* ** * * * * * * *
35440 GAAGGGTTTACTAGGGCAAAACCAATAAAGTTAACCAGTTAAAAGGTTAGCTAGGGTGAAGCCGA
1 GAAGGGTTGACTAAAGCAAAACCAATAAAGTCAACCAATTAAAAAGTTAGCCAAGGCGAAACCGA
* * *
35505 TAAAACCAACAGGTTAGAAGGGTTGACCAAGGCGAAACTAATAAAGTCAACAAATTAAAAAGTTG
66 AAAAACCAACAGGTTAGAAGGGTTGACCAAGGCAAAACCAATAAAGTCAACAAATTAAAAAGTTG
* * *
35570 GCTAGGGGAAAACAATAAAG
131 GCCAAGGCAAAACAATAAAG
35590 TCAACTAATT
Statistics
Matches: 124, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
161 9 0.07
162 110 0.89
163 5 0.04
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (161 bp):
GAAGGGTTGACTAAAGCAAAACCAATAAAGTCAACCAATTAAAAAGTTAGCCAAGGCGAAACCGA
AAAAACCAACAGGTTAGAAGGGTTGACCAAGGCAAAACCAATAAAGTCAACAAATTAAAAAGTTG
GCCAAGGCAAAACAATAAAGCTAACTGGCTA
Found at i:35688 original size:119 final size:120
Alignment explanation
Indices: 35450--35709 Score: 301
Period size: 120 Copynumber: 2.2 Consensus size: 120
35440 GAAGGGTTTA
* * * * * * * *
35450 CTAGGGCAAAACCAATAAAGTTAACCAGTTAAAAGGTTAGCTAGGGTGAAGCCGATAAAACCAAC
1 CTAGGGGAAAA-CAATAAAGTCAACCAATTAAAACGTCAGCTAGGGTAAAACCCATAAAACCAAC
* * *
35515 AGGTTAGAAGGGTTGACCAAGGCGAAACTAATAAAGTCAACAAATTAAAAAGTTGG
65 AGGTTAGAAAGGTTGACCAAGGCAAAACTAATAAAGTAAACAAATTAAAAAGTTGG
* * * *
35571 CTAGGGGAAAACAATAAAGTCAACTAATTAAAACGTCGGCTAGGGTAAAACCCATAAAGCTAAC-
1 CTAGGGGAAAACAATAAAGTCAACCAATTAAAACGTCAGCTAGGGTAAAACCCATAAAACCAACA
* *
35635 GAGTTAGAAAGG-TGACCAAGGTAAAACTAATAAAGTAAACCAATTAAAAAGTTGG
66 G-GTTAGAAAGGTTGACCAAGGCAAAACTAATAAAGTAAACAAATTAAAAAGTTGG
*
35690 CCAGGGCG-AAACAAATAAAG
1 CTAGGG-GAAAAC-AATAAAG
35710 CGAACGAGTT
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
119 49 0.42
120 59 0.50
121 10 0.08
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (120 bp):
CTAGGGGAAAACAATAAAGTCAACCAATTAAAACGTCAGCTAGGGTAAAACCCATAAAACCAACA
GGTTAGAAAGGTTGACCAAGGCAAAACTAATAAAGTAAACAAATTAAAAAGTTGG
Found at i:35716 original size:80 final size:81
Alignment explanation
Indices: 35578--35769 Score: 226
Period size: 80 Copynumber: 2.4 Consensus size: 81
35568 TGGCTAGGGG
* * * * * ** *
35578 AAAAC-AATAAAGTCAACTAATTAAAACGTCGGCTAGGGTAAAACCCATAAAGCTAACGAGTTAG
1 AAAACTAATAAAGTCAACCAATTAAAAAGTTGGCCAGGGCAAAACAAATAAAGCGAACGAGTTAG
35642 AAAGG-TGACCAAGGT
66 AAAGGTTGACCAAGGT
* *
35657 AAAACTAATAAAGTAAACCAATTAAAAAGTTGGCCAGGGCGAAACAAATAAAGCGAACGAGTTAG
1 AAAACTAATAAAGTCAACCAATTAAAAAGTTGGCCAGGGCAAAACAAATAAAGCGAACGAGTTAG
* *
35722 AAGGGTTGACCAGGGT
66 AAAGGTTGACCAAGGT
* * **
35738 GAAATTGGTAAAGTCAACCAATTAAAAAGTTG
1 AAAACTAATAAAGTCAACCAATTAAAAAGTTG
35770 TATCTAATAT
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 5 0.05
80 53 0.56
81 36 0.38
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (81 bp):
AAAACTAATAAAGTCAACCAATTAAAAAGTTGGCCAGGGCAAAACAAATAAAGCGAACGAGTTAG
AAAGGTTGACCAAGGT
Done.