Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1253
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: 56562
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Found at i:2077 original size:18 final size:19
Alignment explanation
Indices: 2054--2090 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2044 TGGACACTGA
*
2054 AAGTACAAA-CAGGGCACT
1 AAGTACAAATAAGGGCACT
2072 AAGTACAAATAAGGGCACT
1 AAGTACAAATAAGGGCACT
2091 GAAGGTCGCA
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:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AAGTACAAATAAGGGCACT
Found at i:4487 original size:31 final size:31
Alignment explanation
Indices: 4443--4503 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
4433 ACGAAGTCAC
* *
4443 CAGATACAGATATGTGGCTAGGCCACCAGAA
1 CAGATACAGATATGTGGCGAAGCCACCAGAA
* *
4474 CAGATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATATGTGGCGAAGCCACCAGA
4504 TTGCAGCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (31 bp):
CAGATACAGATATGTGGCGAAGCCACCAGAA
Found at i:5200 original size:23 final size:23
Alignment explanation
Indices: 5158--5203 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5148 TCACACAAGT
*
5158 TAGTCATTTACGCACGGGGCAAA
1 TAGTCATTTACACACGGGGCAAA
* *
5181 TAGTCATTTACACCCTGGGCAAA
1 TAGTCATTTACACACGGGGCAAA
5204 ATGGTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TAGTCATTTACACACGGGGCAAA
Found at i:5286 original size:24 final size:24
Alignment explanation
Indices: 5253--5328 Score: 122
Period size: 23 Copynumber: 3.2 Consensus size: 24
5243 ATATCGGTAT
5253 TTCTACCCTACAGGGTATTTCGTAA
1 TTCTACCCTACAGGGTATTT-GTAA
5278 TTCTA-CCTACAGGGTATTTG-AA
1 TTCTACCCTACAGGGTATTTGTAA
5300 TTCTACCCTACAGGGTATTT-TAA
1 TTCTACCCTACAGGGTATTTGTAA
5323 TTCTAC
1 TTCTAC
5329 AACTTATCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.14
23 23 0.47
24 14 0.29
25 5 0.10
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (24 bp):
TTCTACCCTACAGGGTATTTGTAA
Found at i:12762 original size:27 final size:26
Alignment explanation
Indices: 12732--12878 Score: 150
Period size: 27 Copynumber: 5.5 Consensus size: 26
12722 TGGGGCAAAA
* *
12732 TGGTAATTTTACCCCACAAGGGTATCT
1 TGGTAATTCTACCCTACAAGGGTAT-T
* *
12759 TGGTAATTCTACCCTATAGGGGTATT
1 TGGTAATTCTACCCTACAAGGGTATT
* *
12785 TCGATATTTCTACCCTACAAGGGTATT
1 T-GGTAATTCTACCCTACAAGGGTATT
* * *
12812 TCGATAATTCTATCCTACAGGGGTATT
1 T-GGTAATTCTACCCTACAAGGGTATT
*
12839 TCGGTAATTCTACCCTACAAGGTTATT
1 T-GGTAATTCTACCCTACAAGGGTATT
*
12866 TCGATAATTCTAC
1 T-GGTAATTCTAC
12879 AACTTATCTA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.02
27 101 0.98
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (26 bp):
TGGTAATTCTACCCTACAAGGGTATT
Found at i:12806 original size:54 final size:54
Alignment explanation
Indices: 12737--12878 Score: 198
Period size: 54 Copynumber: 2.6 Consensus size: 54
12727 CAAAATGGTA
* * *
12737 ATTT-TACCCCACAAGGGTATCTT-GGTAATTCTACCCTATAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTAT-TTCGATAATTCTACCCTACAGGGGTATTTCGAT
* *
12790 ATTTCTACCCTACAAGGGTATTTCGATAATTCTATCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGAT
* *
12844 AATTCTACCCTACAAGGTTATTTCGATAATTCTAC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTAC
12879 AACTTATCTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
53 6 0.08
54 73 0.92
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGAT
Found at i:17497 original size:43 final size:43
Alignment explanation
Indices: 17403--17517 Score: 101
Period size: 43 Copynumber: 2.7 Consensus size: 43
17393 ATTGCGATTT
** *
17403 ACGTGTAAGACCATATCTGGGATATGGCATCGAAATGAGACTTC
1 ACGTGTAAGACCATAGATGGGATATGGCATCGAAACGAGAC-TC
* * *
17447 A--TTTAAGACCATAGATGGGCTATTGGCATCGATACGAGA-TC
1 ACGTGTAAGACCATAGATGGGATA-TGGCATCGAAACGAGACTC
* ** *
17488 ACGTGTAAGACTATATCTAGGATATGGCAT
1 ACGTGTAAGACCATAGATGGGATATGGCAT
17518 TAGTTCGGTA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
41 3 0.05
42 23 0.41
43 29 0.52
44 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
ACGTGTAAGACCATAGATGGGATATGGCATCGAAACGAGACTC
Found at i:17715 original size:15 final size:16
Alignment explanation
Indices: 17689--17718 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17679 ATGAACCTTT
17689 AGTAAGGTTATGATTG
1 AGTAAGGTTATGATTG
17705 AGTAA-GTTATGATT
1 AGTAAGGTTATGATT
17719 ACAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTAAGGTTATGATTG
Found at i:23853 original size:39 final size:39
Alignment explanation
Indices: 23799--23877 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
23789 ATCGGTTAGC
*
23799 TTTACCGATAGAGCTAGAAAGGATTCATAATGTGTTTCA
1 TTTACCGACAGAGCTAGAAAGGATTCATAATGTGTTTCA
23838 TTTACCGACAGAGCTAGAAAGGATTCATAATGTGTTTCA
1 TTTACCGACAGAGCTAGAAAGGATTCATAATGTGTTTCA
23877 T
1 T
23878 GTGTCTATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (39 bp):
TTTACCGACAGAGCTAGAAAGGATTCATAATGTGTTTCA
Found at i:25381 original size:42 final size:40
Alignment explanation
Indices: 25334--25447 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 40
25324 CTGCAATTTA
25334 CATGTAAGACCATATCTTGGATATGGCATCGATATGAGACTT
1 CATGTAAGACCATATCTTGGATATGGCATCGATATGAGA--T
* * *
25376 CATGTAAGACCATAAC-TAGACTATTGGTATCGATATGAGAT
1 CATGTAAGACCATATCTTGGA-TA-TGGCATCGATATGAGAT
*
25417 CATGTGTAAGACCATATCTGGGATATGGCAT
1 CA--TGTAAGACCATATCTTGGATATGGCAT
25448 TGGTTTGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
41 6 0.10
42 22 0.37
43 30 0.50
44 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (40 bp):
CATGTAAGACCATATCTTGGATATGGCATCGATATGAGAT
Found at i:25674 original size:89 final size:89
Alignment explanation
Indices: 25523--25701 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
25513 TTTGATGAGT
*
25523 ATGTCAAAGGTGAATTGTGTGCAAATCCAATTCAAGATGACTAAGGTATGTACATAAAACTCTTA
1 ATGTCAAAGGCGAATTGTGTGCAAATCCAATTCAAGATGACTAAGGTATGTACATAAAACTCTTA
*
25588 TGTAATGAGCTCAATATGTGAGGA
66 TGTAATGAGCTCAAAATGTGAGGA
* *
25612 ATGTCAAAGGCGAATTGTGTGCAAATCCAATTCAAGATGAGTCAGGTATGTACATAAAACTCTTA
1 ATGTCAAAGGCGAATTGTGTGCAAATCCAATTCAAGATGACTAAGGTATGTACATAAAACTCTTA
25677 TGTAATGAGCTCAAAATGTGAGGA
66 TGTAATGAGCTCAAAATGTGAGGA
25701 A
1 A
25702 CCCTTGGTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (89 bp):
ATGTCAAAGGCGAATTGTGTGCAAATCCAATTCAAGATGACTAAGGTATGTACATAAAACTCTTA
TGTAATGAGCTCAAAATGTGAGGA
Found at i:30378 original size:16 final size:16
Alignment explanation
Indices: 30357--30389 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30347 TTGTAACGCC
*
30357 CCAAAAATCTCGAAAT
1 CCAAAAATCCCGAAAT
30373 CCAAAAATCCCGAAAT
1 CCAAAAATCCCGAAAT
30389 C
1 C
30390 TTGAATTTTC
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:0.48, C:0.30, G:0.06, T:0.15
Consensus pattern (16 bp):
CCAAAAATCCCGAAAT
Found at i:31890 original size:27 final size:29
Alignment explanation
Indices: 31860--31920 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
31850 GTGAGCATGA
*
31860 ATATGAATGT-AACTAGGCCTAATGGGC-
1 ATATAAATGTGAACTAGGCCTAATGGGCT
** *
31887 ATATAAATGTGATTTGGGCCTAATGGGCT
1 ATATAAATGTGAACTAGGCCTAATGGGCT
31916 ATATA
1 ATATA
31921 CAAGTGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.32
28 14 0.50
29 5 0.18
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (29 bp):
ATATAAATGTGAACTAGGCCTAATGGGCT
Found at i:31911 original size:28 final size:29
Alignment explanation
Indices: 31875--31943 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
31865 AATGTAACTA
31875 GGCCTAATGGGC-ATATA-AATGTGATTTG
1 GGCCTAATGGGCTATATACAA-GTGATTTG
31903 GGCCTAATGGGCTATATACAAGTGATTTG
1 GGCCTAATGGGCTATATACAAGTGATTTG
**
31932 AACCTAATGGGC
1 GGCCTAATGGGC
31944 CATAGAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 12 0.32
29 23 0.62
30 2 0.05
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (29 bp):
GGCCTAATGGGCTATATACAAGTGATTTG
Found at i:35453 original size:47 final size:47
Alignment explanation
Indices: 35402--35506 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
35392 CAGTATTAAT
* *
35402 TATGTGATCAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
35449 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
35496 AATGTGATAAG
1 TATGTGATAAG
35507 TCCCGAAGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
Found at i:43623 original size:16 final size:16
Alignment explanation
Indices: 43602--43645 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
43592 ATGAATTGGC
43602 AAAAGCCGAAATGCTA
1 AAAAGCCGAAATGCTA
*
43618 AAAAGCCGAAATGCTG
1 AAAAGCCGAAATGCTA
*
43634 AAAAGTCGAAAT
1 AAAAGCCGAAAT
43646 TTGGCTACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (16 bp):
AAAAGCCGAAATGCTA
Found at i:43914 original size:29 final size:29
Alignment explanation
Indices: 43872--43928 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
43862 GTGACTAGGC
*
43872 CTAACGGGCCATATAAATGTGATTTGGGT
1 CTAACGGGCAATATAAATGTGATTTGGGT
*
43901 CTAACGGGCAATATACATGTGATTTGGG
1 CTAACGGGCAATATAAATGTGATTTGGG
43929 CCCAGTAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
CTAACGGGCAATATAAATGTGATTTGGGT
Found at i:43943 original size:29 final size:29
Alignment explanation
Indices: 43869--43952 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 29
43859 AATGTGACTA
* *
43869 GGCCTAACGGGCCATATAAATGTGATTTG
1 GGCCCAACAGGCCATATAAATGTGATTTG
* * * * *
43898 GGTCTAACGGGCAATATACATGTGATTTG
1 GGCCCAACAGGCCATATAAATGTGATTTG
** * *
43927 GGCCCAGTAGGCCATATGAATATGAT
1 GGCCCAACAGGCCATATAAATGTGAT
43953 GGGGCTTAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (29 bp):
GGCCCAACAGGCCATATAAATGTGATTTG
Found at i:46830 original size:79 final size:81
Alignment explanation
Indices: 46694--46878 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
46684 TTGAATGATG
* *
46694 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
46758 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
46773 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
46835 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
46853 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
46879 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:46892 original size:40 final size:40
Alignment explanation
Indices: 46695--46878 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
46685 TGAATGATGT
* * * *
46695 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
46735 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
46775 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
46813 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46854 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
46879 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:46900 original size:79 final size:79
Alignment explanation
Indices: 46747--46911 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
46737 GGACTAAGAT
* * **
46747 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
46812 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
46826 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
46889 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
46905 CCGAAGG
1 CCGAAGG
46912 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54737 original size:79 final size:81
Alignment explanation
Indices: 54601--54785 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
54591 TTGAATGATG
* *
54601 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
54665 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
54680 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
54742 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
54760 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54786 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:54799 original size:40 final size:40
Alignment explanation
Indices: 54602--54785 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
54592 TGAATGATGT
* * * *
54602 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
54642 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
54682 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54720 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54761 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54786 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54807 original size:79 final size:79
Alignment explanation
Indices: 54654--54818 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
54644 GGACTAAGAT
* * **
54654 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
54719 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
54733 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
54796 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
54812 CCGAAGG
1 CCGAAGG
54819 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.