Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2724
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: 46148
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:1079 original size:2 final size:2
Alignment explanation
Indices: 1066--1106 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1056 CCAAAACAAA
*
1066 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1107 GTTAACCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:8713 original size:2 final size:2
Alignment explanation
Indices: 8706--8748 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
8696 GAAGGTTAAC
*
8706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8748 T
1 T
8749 TTTGTTTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13756 original size:59 final size:57
Alignment explanation
Indices: 13687--13935 Score: 229
Period size: 59 Copynumber: 4.3 Consensus size: 57
13677 GTATTTTAGT
* * * *
13687 GTCATCTAGGTTATTTTCGATAATCTAGGGACCATTTAGTAATTTCTCA-ACACTGTAGG
1 GTCATTTAGGTTATTTT--ATAATCTAGGGACCATTTAGCAATTT-TCATACATTCTAGG
* * *
13746 GTCATTTAGGTTAGTTTTTATAATCTAGGGACCATTTAGTAATTTTTATACATTTTAGG
1 GTCATTTAGGTTA--TTTTATAATCTAGGGACCATTTAGCAATTTTCATACATTCTAGG
** * * *
13805 GTCATTTAGGCAATTTT-TCA--TAGGGATCATTTAGCAATTTTCATACATTCTAGA
1 GTCATTTAGGTTATTTTATAATCTAGGGACCATTTAGCAATTTTCATACATTCTAGG
* * * *
13859 GTTATTTAGGTTATTTTCCATAATCTAGAGACCATTTAGCAA-TTTCATACATTTTAGA
1 GTCATTTAGGTTATTTT--ATAATCTAGGGACCATTTAGCAATTTTCATACATTCTAGG
*
13917 GTCTTTTAAGGTTAGTTTT
1 GTCATTT-AGGTTA-TTTT
13936 GTACCTACAA
Statistics
Matches: 159, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
54 43 0.27
56 2 0.01
57 6 0.04
58 22 0.14
59 78 0.49
60 4 0.03
61 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (57 bp):
GTCATTTAGGTTATTTTATAATCTAGGGACCATTTAGCAATTTTCATACATTCTAGG
Found at i:13774 original size:29 final size:30
Alignment explanation
Indices: 13742--13875 Score: 90
Period size: 30 Copynumber: 4.7 Consensus size: 30
13732 CTCAACACTG
*
13742 TAGGGTCATTTAGGTTAGTTTTTATA-A-TC
1 TAGGGTCATTTAGG-TAATTTTTATACATTC
* *
13771 TAGGGACCATTTA-GTAATTTTTATACATTT
1 TAGGG-TCATTTAGGTAATTTTTATACATTC
*
13801 TAGGGTCATTTAGGCAA-TTTT-T-CA---
1 TAGGGTCATTTAGGTAATTTTTATACATTC
* *
13825 TAGGGATCATTTA-GCAATTTTCATACATTC
1 TAGGG-TCATTTAGGTAATTTTTATACATTC
* * *
13855 TAGAGTTATTTAGGTTATTTT
1 TAGGGTCATTTAGGTAATTTT
13876 CCATAATCTA
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
24 9 0.11
25 10 0.12
26 1 0.01
27 4 0.05
28 11 0.13
29 23 0.28
30 25 0.30
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (30 bp):
TAGGGTCATTTAGGTAATTTTTATACATTC
Found at i:13805 original size:30 final size:29
Alignment explanation
Indices: 13709--13822 Score: 83
Period size: 30 Copynumber: 3.9 Consensus size: 29
13699 ATTTTCGATA
*
13709 ATCTAGGGACCATTTA-GTAATTTCTCA-AC
1 ATCTAGGG-CCATTTAGGTAATTT-TTATAC
* * *
13738 ACTGTAGGGTCATTTAGGTTAGTTTTTATA-
1 A-TCTAGGGCCATTTAGG-TAATTTTTATAC
13768 ATCTAGGGACCATTTA-GTAATTTTTATAC
1 ATCTAGGG-CCATTTAGGTAATTTTTATAC
* * *
13797 ATTTTAGGGTCATTTAGGCAATTTTT
1 A-TCTAGGGCCATTTAGGTAATTTTT
13823 CATAGGGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
28 10 0.15
29 21 0.31
30 30 0.45
31 6 0.09
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (29 bp):
ATCTAGGGCCATTTAGGTAATTTTTATAC
Found at i:13849 original size:23 final size:24
Alignment explanation
Indices: 13801--13849 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
13791 TTATACATTT
13801 TAGGGTCATTTAGGCAATTTTTCA
1 TAGGGTCATTTAGGCAATTTTTCA
13825 TAGGGATCATTTA-GCAA-TTTTCA
1 TAGGG-TCATTTAGGCAATTTTTCA
13848 TA
1 TA
13850 CATTCTAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.33
24 9 0.38
25 7 0.29
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (24 bp):
TAGGGTCATTTAGGCAATTTTTCA
Found at i:13871 original size:113 final size:112
Alignment explanation
Indices: 13712--13924 Score: 277
Period size: 113 Copynumber: 1.9 Consensus size: 112
13702 TTCGATAATC
* * * * *
13712 TAGGGACCATTTAGTAATTTCTCAACACTGTAGGGTCATTTAGGTTAGTTTT-TATAATCTAGGG
1 TAGGGACCATTTAGCAATTTCTCAACACTCTAGAGTCATTTAGGTTA-TTTTCCATAATCTAGAG
* * *
13776 ACCATTTAGTAATTTTTATACATTTTAGGGTCATTTAGGCAATTTTTCA
65 ACCATTTAGCAA-TTTCATACATTTTAGAGTCATTTAGGCAATTTTTCA
* * *
13825 TAGGGATCATTTAGCAATTT-TCATACATTCTAGAGTTATTTAGGTTATTTTCCATAATCTAGAG
1 TAGGGACCATTTAGCAATTTCTCA-ACACTCTAGAGTCATTTAGGTTATTTTCCATAATCTAGAG
*
13889 ACCATTTAGCAATTTCATACATTTTAGAGTCTTTTA
65 ACCATTTAGCAATTTCATACATTTTAGAGTCATTTA
13925 AGGTTAGTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
112 28 0.33
113 58 0.67
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (112 bp):
TAGGGACCATTTAGCAATTTCTCAACACTCTAGAGTCATTTAGGTTATTTTCCATAATCTAGAGA
CCATTTAGCAATTTCATACATTTTAGAGTCATTTAGGCAATTTTTCA
Found at i:13875 original size:54 final size:54
Alignment explanation
Indices: 13771--13924 Score: 148
Period size: 54 Copynumber: 2.8 Consensus size: 54
13761 TTTTATAATC
* * * * *
13771 TAGGGACCATTTAGTAATTTTTATACATTTTAGGGTCATTTAGGCAATTTTTCA
1 TAGGGACCATTTAGCAATTTTCATACATTCTAGAGTCATTTAGGCAATTTTCCA
* * **
13825 TAGGGATCATTTAGCAATTTTCATACATTCTAGAGTTATTTAGGTTATTTTCCATAA
1 TAGGGACCATTTAGCAATTTTCATACATTCTAGAGTCATTTAGGCAATTTTCC---A
* * *
13882 TCTAGAGACCATTTAGCAA-TTTCATACATTTTAGAGTCTTTTA
1 --TAGGGACCATTTAGCAATTTTCATACATTCTAGAGTCATTTA
13925 AGGTTAGTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
54 44 0.54
57 1 0.01
58 21 0.26
59 15 0.19
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (54 bp):
TAGGGACCATTTAGCAATTTTCATACATTCTAGAGTCATTTAGGCAATTTTCCA
Found at i:13903 original size:29 final size:29
Alignment explanation
Indices: 13832--13917 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
13822 TCATAGGGAT
*
13832 CATTTAGCAATTTTCATACATTCTAGAGT
1 CATTTAGCAATTTTCATACATTCTAGAGC
* **
13861 TATTTAGGTTATTTTCCATA-A-TCTAGAGAC
1 CATTTA-GCAATTTT-CATACATTCTAGAG-C
*
13891 CATTTAGCAA-TTTCATACATTTTAGAG
1 CATTTAGCAATTTTCATACATTCTAGAG
13918 TCTTTTAAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 20 0.45
30 12 0.27
31 4 0.09
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (29 bp):
CATTTAGCAATTTTCATACATTCTAGAGC
Found at i:14089 original size:49 final size:49
Alignment explanation
Indices: 13945--14183 Score: 173
Period size: 49 Copynumber: 4.9 Consensus size: 49
13935 TGTACCTACA
** * *
13945 ATCAAAATTGAATCTTTTAAGGTTAGTTTTATAATTTTTATCAAAATTG
1 ATCAAAATTGAATCTTTTAAGGTTAGTTTTATACCTTTCATCAAAACTG
* * * ** *
13994 A-CTAAAATCGAATCTTTTAAGGTTAGTTTTGTACGTACCGTCAAAACTG
1 ATC-AAAATTGAATCTTTTAAGGTTAGTTTTATACCTTTCATCAAAACTG
* * *
14043 ATCAAAATTGAGTTTTTTAAGGTTAGTTTTATACCTTTCATTAAAACT-
1 ATCAAAATTGAATCTTTTAAGGTTAGTTTTATACCTTTCATCAAAACTG
* * ** * * * **
14091 AACCAAA-TGAGCCTTTTAGGGTTAGTTTTGTA-TTTTCCATCAAAACCA
1 ATCAAAATTGAATCTTTTAAGGTTAGTTTTATACCTTT-CATCAAAACTG
* * * * * *
14139 ACCAAAATCGTATCTTTTAGGGTTAG-TTTGTACTTTTCATCAAAA
1 ATCAAAATTGAATCTTTTAAGGTTAGTTTTATACCTTTCATCAAAA
14184 TAGACCTCAA
Statistics
Matches: 151, Mismatches: 33, Indels: 13
0.77 0.17 0.07
Matches are distributed among these distances:
46 3 0.02
47 29 0.19
48 25 0.17
49 93 0.62
50 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (49 bp):
ATCAAAATTGAATCTTTTAAGGTTAGTTTTATACCTTTCATCAAAACTG
Found at i:14145 original size:96 final size:98
Alignment explanation
Indices: 13947--14183 Score: 230
Period size: 96 Copynumber: 2.4 Consensus size: 98
13937 TACCTACAAT
* * * * *
13947 CAAAATTGAATCTTTTAAGGTTAGTTTTATAATTTTTATCAAAATTGACTAAAATCGAATCTTTT
1 CAAAATTGAATCTTTTAAGGTTAGTTTTATAACTTTCATCAAAACTAACTAAAATCGAACCTTTT
* ** *
14012 AAGGTTAGTTTTGTACGTACCGTCAAAACTGAT
66 AAGGTTAGTTTTGTACGTACCATCAAAACCAAC
* * * * * *
14045 CAAAATTGAGTTTTTTAAGGTTAGTTTTATACCTTTCATTAAAACTAAC-CAAAT-GAGCCTTTT
1 CAAAATTGAATCTTTTAAGGTTAGTTTTATAACTTTCATCAAAACTAACTAAAATCGAACCTTTT
* ** *
14108 AGGGTTAGTTTTGTATTTTCCATCAAAACCAAC
66 AAGGTTAGTTTTGTACGTACCATCAAAACCAAC
* * * *
14141 CAAAATCGTATCTTTTAGGGTTAG-TTTGT-ACTTTTCATCAAAA
1 CAAAATTGAATCTTTTAAGGTTAGTTTTATAAC-TTTCATCAAAA
14184 TAGACCTCAA
Statistics
Matches: 111, Mismatches: 27, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
94 1 0.01
95 14 0.13
96 51 0.46
97 4 0.04
98 41 0.37
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (98 bp):
CAAAATTGAATCTTTTAAGGTTAGTTTTATAACTTTCATCAAAACTAACTAAAATCGAACCTTTT
AAGGTTAGTTTTGTACGTACCATCAAAACCAAC
Found at i:18845 original size:156 final size:155
Alignment explanation
Indices: 18508--19003 Score: 574
Period size: 156 Copynumber: 3.2 Consensus size: 155
18498 CTAAGTTCAA
* * * **
18508 AAAAAATTATGAAAATGCCCTTAGGGGATACCTTCGACGTAGAAGTACCCGATACCTTTAAA-AG
1 AAAAAATTATGAAAATGCCCATAGGGGATACTTTCGACGTAGAAGTACTCGATACCCCTAAAGA-
* * *
18572 ACTTAAAAATGATTATAAATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAAAC
65 ACTTAAAAAGGATTATAAATGGGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAGAC
* * * *
18637 -CTGGTGACAATCTATGACTCGATTCT
130 TC-GGTGACAACCTAGGATTCAATTCT
** * *
18663 AAAAAATTACCAAAATGCCCATAGGGGATATTTTCGACGTAGAAGTGCTCGATACCCCTAAAGAA
1 AAAAAATTATGAAAATGCCCATAGGGGATACTTTCGACGTAGAAGTACTCGATACCCCTAAAGAA
* * *
18728 CTTAAAAAGGATTATAAATTGGGATGAACTTATCCTAAATACTCACCTTCAGTATAAAAGCAGAC
66 CTTAAAAAGGATTATAAA-TGGGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAGAC
* *
18793 TCGGTAACAACCTAGGATTCAATTTT
130 TCGGTGACAACCTAGGATTCAATTCT
* ** * *
18819 AAAAAATTATGAAAATACCCCCAGGGGATACTTTCGACGTAGAAGTACTCGATACCCCCAAAGGA
1 AAAAAATTATGAAAATGCCCATAGGGGATACTTTCGACGTAGAAGTACTCGATACCCCTAAAGAA
* * * *
18884 CTTAACAAGGA-TATAGATGGGATGAGCCTATCCTAAAT-CTCACCTTCGGCATAAAAG-TGCAC
66 CTTAAAAAGGATTATAAATGGGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAG-AC
* **
18946 TCAGTGACAACCTAGGATTCGGTTCT
130 TCGGTGACAACCTAGGATTCAATTCT
*
18972 AAAAAAATT-TCAAAAATGCCC-TAGGGGTATAC
1 -AAAAAATTAT-GAAAATGCCCATAGGGG-ATAC
19004 ATTTGATATG
Statistics
Matches: 289, Mismatches: 45, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
152 1 0.00
153 46 0.16
154 39 0.13
155 76 0.26
156 126 0.44
157 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (155 bp):
AAAAAATTATGAAAATGCCCATAGGGGATACTTTCGACGTAGAAGTACTCGATACCCCTAAAGAA
CTTAAAAAGGATTATAAATGGGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAGACT
CGGTGACAACCTAGGATTCAATTCT
Found at i:20351 original size:20 final size:20
Alignment explanation
Indices: 20259--20336 Score: 131
Period size: 20 Copynumber: 3.9 Consensus size: 20
20249 GTTGAACTCA
20259 ATGTATCGATACATTTATGG
1 ATGTATCGATACATTTATGG
20279 ATGTATCGATACATTTATGG
1 ATGTATCGATACATTTATGG
*
20299 ATGTATCGATACATTT-TGA
1 ATGTATCGATACATTTATGG
20318 ATTGTATCGATACATTTAT
1 A-TGTATCGATACATTTAT
20337 ATGTGTACCG
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 3 0.05
20 51 0.93
21 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTATGG
Found at i:20435 original size:21 final size:21
Alignment explanation
Indices: 20392--20447 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
20382 GCCAATAAAG
* * *
20392 TGTATCGATACA-ATACATTA
1 TGTATCAATACATTTACATAA
*
20412 TGTATCAATATATTTACATAA
1 TGTATCAATACATTTACATAA
*
20433 TGTATCGATACATTT
1 TGTATCAATACATTT
20448 CAACTTGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (21 bp):
TGTATCAATACATTTACATAA
Found at i:22524 original size:78 final size:78
Alignment explanation
Indices: 22395--22550 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
22385 AGAGGAGGAG
22395 AGATAAGTAGGGATGGGCAGGGGTAGGCAAGGGTACTTGGTAGAGTGAAATGAGGACTGTTGTCG
1 AGATAAGTAGGGATGGGCAGGGGTAGGCAAGGGTACTTGGTAGAGTGAAATGAGGACTGTTGTCG
22460 AATAGATTGTGAA
66 AATAGATTGTGAA
22473 AGATAAGTAGGGATGGGCAGGGGTAGGCAAGGGTACTTGGTAGAGTGAAATGAGGACTGTTGTCG
1 AGATAAGTAGGGATGGGCAGGGGTAGGCAAGGGTACTTGGTAGAGTGAAATGAGGACTGTTGTCG
22538 AATAGATTGTGAA
66 AATAGATTGTGAA
22551 CGGGTGTTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.40, T:0.23
Consensus pattern (78 bp):
AGATAAGTAGGGATGGGCAGGGGTAGGCAAGGGTACTTGGTAGAGTGAAATGAGGACTGTTGTCG
AATAGATTGTGAA
Found at i:27198 original size:98 final size:98
Alignment explanation
Indices: 27029--27260 Score: 410
Period size: 98 Copynumber: 2.4 Consensus size: 98
27019 TTTTTGATTG
* *
27029 AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGGGGTGGGAGTGTCCCCGACAATGATAATTTA
1 AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGAGATGGGAGTGTCCCCGACAATGATAATTTA
27094 GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
66 GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
*
27127 AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGAGATTGGAGTGTCCCCGACAATGATAATTTA
1 AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGAGATGGGAGTGTCCCCGACAATGATAATTTA
27192 GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
66 GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
* * *
27225 AAAAATGGGGTTGGAGTATCCCCTCGGAGGAATGAG
1 AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGAG
27261 GTTAGAGTAT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 128 1.00
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (98 bp):
AAAAACGAGGTTGGAGTATCCCCTTGGAGGAATGAGATGGGAGTGTCCCCGACAATGATAATTTA
GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
Found at i:29582 original size:90 final size:91
Alignment explanation
Indices: 29408--29582 Score: 273
Period size: 90 Copynumber: 1.9 Consensus size: 91
29398 TTTTAACTAG
*
29408 ATGTATCGATACATTAAAAAATATATTGATACATCTTGGTAAAAAGACAAAATGTATCGATAAAT
1 ATGTATCGATACATTAAAAAATATATCGATACATCTTGGTAAAAAGACAAAATGTATCGATAAAT
*
29473 TGAAGAATGTATCGATACATTCATAC
66 TGAAAAATGTATCGATACATTCATAC
* * * *
29499 ATGTATCGATACATTGAAAAATATATCGATACAT-TTGGGT-AAAAGATAGAATGTATCGATACA
1 ATGTATCGATACATTAAAAAATATATCGATACATCTT-GGTAAAAAGACAAAATGTATCGATAAA
29562 TTGAAAAATGTATCGATACAT
65 TTGAAAAATGTATCGATACAT
29583 CTCGGTAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
90 42 0.55
91 35 0.45
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAATATATCGATACATCTTGGTAAAAAGACAAAATGTATCGATAAAT
TGAAAAATGTATCGATACATTCATAC
Found at i:29595 original size:24 final size:20
Alignment explanation
Indices: 29456--29582 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
29446 GTAAAAAGAC
*
29456 AAAATGTATCGATAAATTGA
1 AAAATGTATCGATACATTGA
* *
29476 AGAATGTATCGATACATTCA
1 AAAATGTATCGATACATTGA
* *
29496 TACATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
*
29516 AAAATATATCGATACATTTGGGTAAAA
1 AAAATGTATCGATACA-TT--G----A
29543 GATAGAATGTATCGATACATTGA
1 -A-A-AATGTATCGATACATTGA
29566 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
29583 CTCGGTAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
20 61 0.71
21 3 0.03
22 1 0.01
23 2 0.02
27 2 0.02
28 1 0.01
29 3 0.03
30 13 0.15
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:30614 original size:28 final size:27
Alignment explanation
Indices: 30574--30993 Score: 383
Period size: 28 Copynumber: 14.9 Consensus size: 27
30564 GTTTCGAGTA
*
30574 CCACTAACTTGTGGGCTTTAAAATGGTG
1 CCACTGACTTGTGGGCTTTAAAA-GGTG
* *
30602 CCACTAACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTT-AAAAGGTG
* *
30630 CCACTAACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTT-AAAAGGTG
* *
30658 CCACTAACTTGTGGGCTTTGAGAGAGGTTG
1 CCACTGACTTGTGGGCTTT-A-AAAGG-TG
*
30688 CCACCGACTTGTGTGGGC-TTAAAAGGGTG
1 CCACTGAC-T-TGTGGGCTTTAAAA-GGTG
* * * *
30717 CCACTAATTTGTGGGCTTTGAGAATGATG
1 CCACTGACTTGTGGGCTTT-A-AAAGGTG
**
30746 CCACTGACTCATGGGCTTTGAAAAGGTG
1 CCACTGACTTGTGGGCTTT-AAAAGGTG
* *
30774 CCACTGACTTGTGAGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTAAAAGG-TG
* * *
30802 CCACTGACATGTGGGTTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTT-AAAAGGTG
*
30830 CCACTGACTTGTGGGCTTTGAAAAGATG
1 CCACTGACTTGTGGGCTTT-AAAAGGTG
* *
30858 CCACTGACTTGTGGGCTTTGAATGGATG
1 CCACTGACTTGTGGGCTTTAAAAGG-TG
* * *
30886 CCACTAACTTATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTAAAAGG-TG
* *
30914 CCAGTGACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTAAAAGG-TG
*
30942 CCACTGACTTGTGGGCTTTGAGAAGGATG
1 CCACTGACTTGTGGGCTTT-AAAAGG-TG
* *
30971 CCACTGACTTGTGGACTCTAAAA
1 CCACTGACTTGTGGGCTTTAAAA
30994 AGGGTCGTAT
Statistics
Matches: 334, Mismatches: 45, Indels: 26
0.82 0.11 0.06
Matches are distributed among these distances:
27 15 0.04
28 232 0.69
29 64 0.19
30 13 0.04
31 3 0.01
32 7 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (27 bp):
CCACTGACTTGTGGGCTTTAAAAGGTG
Found at i:30660 original size:56 final size:56
Alignment explanation
Indices: 30574--30984 Score: 536
Period size: 56 Copynumber: 7.2 Consensus size: 56
30564 GTTTCGAGTA
* * * *
30574 CCACTAACTTGTGGGCTTTAAAATGGTGCCACTAACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
* *
30630 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAGAGAGGTTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGA-A-AGGATG
* * * *
30688 CCACCGACTTGTGTGGGC-TTAAAAGGGTGCCACTAATTTGTGGGCTTTGAGAATGATG
1 CCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGA-AAGGATG
** * * *
30746 CCACTGACTCATGGGCTTTGAAAAGGTGCCACTGACTTGTGAGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
* * * *
30802 CCACTGACATGTGGGTTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
* * *
30858 CCACTGACTTGTGGGCTTTGAATGGATGCCACTAACTTATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
* * *
30914 CCAGTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGA-AAGGATG
30971 CCACTGACTTGTGG
1 CCACTGACTTGTGG
30985 ACTCTAAAAA
Statistics
Matches: 312, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
56 201 0.64
57 49 0.16
58 22 0.07
59 33 0.11
60 7 0.02
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (56 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
Found at i:30852 original size:84 final size:84
Alignment explanation
Indices: 30574--30984 Score: 522
Period size: 84 Copynumber: 4.8 Consensus size: 84
30564 GTTTCGAGTA
* * *
30574 CCACTAACTTGTGGGCTTT-AAAATGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAAC
1 CCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAAC
*
30638 TTGTGGGCTTTGAAAGGGTG
65 TTGTGGGCTTTGAAAGGATG
* * * * *
30658 CCACTAACTTGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGC-TTAAAAGGGTGCCACT
1 CCACTGACTTGTGGGCTTTGA-AAAGG-TGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACT
* *
30722 AATTTGTGGGCTTTGAGAATGATG
62 AACTTGTGGGCTTTGA-AAGGATG
** * * *
30746 CCACTGACTCATGGGCTTTGAAAAGGTGCCACTGACTTGTGAGCTTTGAAAGGATGCCACTGACA
1 CCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
* *
30811 TGTGGGTTTTGAAAGGGTG
66 TGTGGGCTTTGAAAGGATG
* *
30830 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAATGGATGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
*
30895 TATGGGCTTTGAAAGGATG
66 TGTGGGCTTTGAAAGGATG
* *
30914 CCAGTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGA
1 CCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTAA
30978 CTTGTGG
64 CTTGTGG
30985 ACTCTAAAAA
Statistics
Matches: 282, Mismatches: 36, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
83 4 0.01
84 146 0.52
85 48 0.17
86 19 0.07
87 35 0.12
88 30 0.11
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (84 bp):
CCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
TGTGGGCTTTGAAAGGATG
Done.