Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013166.1 Kokia drynarioides strain JFW-HI SEQ_128185, whole genome shotgun sequence
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: 90795
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:1655 original size:30 final size:30
Alignment explanation
Indices: 1621--1941 Score: 228
Period size: 30 Copynumber: 10.8 Consensus size: 30
1611 TAAAAACTAT
* *
1621 ATTTTGACCCCCAAACATTTCCAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
* * *
1651 ATTTTAACTCCTAAACTTTTCTAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
*
1681 ATTTTGA-CCCTAAACTTTTCCAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
* * *
1710 ATTTTTACGCTTAAACTTTTCCAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
* * * *
1740 ATTTT-AACCTTGAAACTTTTCCAAAATTAT
1 ATTTTGACCCCT-AAACTTTTCCAAAATCAC
* * *
1770 ATTTTGA-CCCTCGAACTTTCCCAAAATCAT
1 ATTTTGACCCCT-AAACTTTTCCAAAATCAC
* * **
1800 ATTTTGACCCTTAAATTTTTTTAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
* * * * *
1830 A-TTTAACCCCCT-AATTTTTCTAAAATTAT
1 ATTTTGA-CCCCTAAACTTTTCCAAAATCAC
* * * *
1859 ATTTT-AACCTTGAACTTTTCCAAAATCGC
1 ATTTTGACCCCTAAACTTTTCCAAAATCAC
* * *
1888 ATTTTAAGCCC-AAAC-TTTCCTAAAAACTAC
1 ATTTTGACCCCTAAACTTTTCC-AAAATC-AC
*
1918 ATTTTTA-CCCTCAAACTTTTCCAA
1 ATTTTGACCCCT-AAACTTTTCCAA
1942 CATTATGTTT
Statistics
Matches: 231, Mismatches: 47, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
28 8 0.03
29 77 0.33
30 131 0.57
31 10 0.04
32 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTTCCAAAATCAC
Found at i:1706 original size:59 final size:58
Alignment explanation
Indices: 1621--1941 Score: 270
Period size: 59 Copynumber: 5.4 Consensus size: 58
1611 TAAAAACTAT
* *
1621 ATTTTGACCCCCAAACATTTCCAAAATCACATTTTAACTCCTAAACTTTTCTAAAATCAC
1 ATTTTGA-CCCTAAACTTTTCCAAAATCACATTTTAAC-CCTAAACTTTTCTAAAATCAC
* * * *
1681 ATTTTGACCCTAAACTTTTCCAAAATTACATTTTTACGCTTAAACTTTTCCAAAATCAC
1 ATTTTGACCCTAAACTTTTCCAAAATCACATTTTAAC-CCTAAACTTTTCTAAAATCAC
* * * * * * * * *
1740 ATTTTAACCTTGAAACTTTTCCAAAATTATATTTTGACCCTCGAACTTTCCCAAAATCAT
1 ATTTTGACCCT-AAACTTTTCCAAAATCACATTTTAACCCT-AAACTTTTCTAAAATCAC
* ** * * *
1800 ATTTTGACCCTTAAATTTTTTTAAAATCACA-TTTAACCCCCT-AATTTTTCTAAAATTAT
1 ATTTTGACCC-TAAACTTTTCCAAAATCACATTTTAA--CCCTAAACTTTTCTAAAATCAC
* * * * * *
1859 ATTTTAACCTTGAACTTTTCCAAAATCGCATTTTAAGCCC-AAACTTTCCTAAAAACTAC
1 ATTTTGACCCTAAACTTTTCCAAAATCACATTTTAA-CCCTAAACTTTTCTAAAATC-AC
*
1918 ATTTTTACCCTCAAACTTTTCCAA
1 ATTTTGACCCT-AAACTTTTCCAA
1942 CATTATGTTT
Statistics
Matches: 209, Mismatches: 43, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
58 29 0.14
59 96 0.46
60 79 0.38
61 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (58 bp):
ATTTTGACCCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTTCTAAAATCAC
Found at i:1774 original size:89 final size:89
Alignment explanation
Indices: 1633--1961 Score: 306
Period size: 89 Copynumber: 3.7 Consensus size: 89
1623 TTTGACCCCC
* * * * *
1633 AAACATTTCCAAAATCACATTTTAACTCCT-AAACTTTTCTAAAATCACATTTTGACCCTAAACT
1 AAACTTTTCCAAAATCACATTTTAAC-CCTCAAACTTTTCCAAAATTATATTTTAACCCTAAACT
*
1697 TTTCCAAAATTACATTTTTACGCTT
65 TTTCCAAAATCACATTTTTACGCTT
* * * *
1722 AAACTTTTCCAAAATCACATTTTAACCTTGAAACTTTTCCAAAATTATATTTTGACCCTCGAACT
1 AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTAACCCT-AAACT
* * * *
1787 TTCCCAAAATCATATTTTGACCCTT
65 TTTCCAAAATCACATTTTTACGCTT
* ** * * * * * *
1812 AAATTTTTTTAAAATCACA-TTTAACCCCCTAATTTTTCTAAAATTATATTTTAACCTTGAACTT
1 AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTAACCCTAAACTT
* * **
1876 TTCCAAAATCGCA-TTTTAAGCCC
66 TTCCAAAATCACATTTTTACGCTT
* * * * *
1899 AAAC-TTTCCTAAAAACTACATTTTTACCCTCAAACTTTTCCAACATTATGTTTTAACCTTAAA
1 AAACTTTTCC-AAAATC-ACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTAACCCTAAA
1962 TTCTCGAAAA
Statistics
Matches: 193, Mismatches: 42, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
86 3 0.02
87 13 0.07
88 21 0.11
89 116 0.60
90 40 0.21
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (89 bp):
AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTAACCCTAAACTT
TTCCAAAATCACATTTTTACGCTT
Found at i:6639 original size:12 final size:12
Alignment explanation
Indices: 6609--6641 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6599 AGAAAACAAG
6609 AAAAAAA-GAAA
1 AAAAAAAGGAAA
6620 AAAAAAAGGAAA
1 AAAAAAAGGAAA
*
6632 AAGAAAAGGA
1 AAAAAAAGGA
6642 GGGGTCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGAAA
Found at i:7705 original size:48 final size:49
Alignment explanation
Indices: 7568--8091 Score: 281
Period size: 50 Copynumber: 10.6 Consensus size: 49
7558 AGAAACTATA
* * * * * *
7568 AAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCC-AGTACCTTAG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGA-TACCAT-G
* * * *
7618 AAGATGTGATGGGAAGGATTGAGGTCACAACAACAAACCCGATACCATG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCATG
* * * *
7667 AA-ATGTGATGGGAAAGATTGAGGTTGCAATAGTGAACCCGGTACCATG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCATG
* * * * * * *
7715 AAGATTTAAAGGGAAAGGTTGAGGCCGCAAC-GACGAACCCTG-TACCTTAA
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAG-CGAACCC-GATACCAT-G
* * ** *
7765 AAGATGTGATGGGAAGGATTGAGGTCGCAATAGCGAATTCGGTACCATG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCATG
* * * * * * * * * * * * *
7814 AA-ATTTGAAGGGGAGGATTGAGGCCACGACGGTGAATCTGGTACCTTAG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCAT-G
* * * **
7863 AAGATGTGATGGGAAAGGTTGAGGTCACAAC-GTCGAACCCGGTATTATG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAG-CGAACCCGATACCATG
* * * * * * * *
7912 AAGATTTGAAGGGAAGGATTGAGGCCGCGACAGTGAATCCGATACCTTAG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCAT-G
* * * *
7962 AAAATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCC-AGTACCATG
1 AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGA-TACCATG
* * * * ** * * *
8011 AAGATATGAAGGGAAATG-TTAAGGCCATAACGGCAAACCCGATACCTTAG
1 AAGATGTGATGGGAAA-GATTGAGGTCGCAACAGCGAACCCGATACCAT-G
* * *
8061 AAGATGTGATGGGAAAGGTTAAGGCCGCAAC
1 AAGATGTGATGGGAAAGATTGAGGTCGCAAC
8092 GATGAACCCA
Statistics
Matches: 358, Mismatches: 99, Indels: 34
0.73 0.20 0.07
Matches are distributed among these distances:
48 74 0.21
49 115 0.32
50 167 0.47
51 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (49 bp):
AAGATGTGATGGGAAAGATTGAGGTCGCAACAGCGAACCCGATACCATG
Found at i:7835 original size:147 final size:146
Alignment explanation
Indices: 7568--8075 Score: 518
Period size: 147 Copynumber: 3.4 Consensus size: 146
7558 AGAAACTATA
* * *
7568 AAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCAGTACCTTAGAAGATGTGATGGGAA
1 AAGATTTGAAGGGAAAGGTTGAGGCCACAACGGCGAACCC-GTACCTTAGAAGATGTGATGGGAA
* * * * * ** **
7633 GGATTGAGGTCACAACAACAAACCCGATACCATGAAATGTGATGGGAAAGATTGAGGTTGCAATA
65 GGATTGAGGTCGCAACAGCGAATCCGATACCATGAAATGTGATGGGAAGGATTGAGGCCGCAACG
7698 GTGAACCCGGTACCATG
130 GTGAACCCGGTACCATG
* * * *
7715 AAGATTTAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCTGTACCTTAAAAGATGTGATGGGAA
1 AAGATTTGAAGGGAAAGGTTGAGGCCACAACGGCGAACCC-GTACCTTAGAAGATGTGATGGGAA
* * * * * * * *
7780 GGATTGAGGTCGCAATAGCGAATTCGGTACCATGAAATTTGAAGGGGAGGATTGAGGCCACGACG
65 GGATTGAGGTCGCAACAGCGAATCCGATACCATGAAATGTGATGGGAAGGATTGAGGCCGCAACG
* * *
7845 GTGAATCTGGTACCTTAG
130 GTGAACCCGGTACCAT-G
* * * * * *
7863 AAGATGTGATGGGAAAGGTTGAGGTCACAACGTCGAACCCGGTA--TTATGAAGATTTGAAGGGA
1 AAGATTTGAAGGGAAAGGTTGAGGCCACAACGGCGAACCC-GTACCTTA-GAAGATGTGATGGGA
* * * *
7926 AGGATTGAGGCCGCGACAGTGAATCCGATACCTTAGAAAATGTGATGGGAAAGG-TTGAGGCCGC
64 AGGATTGAGGTCGCAACAGCGAATCCGATACCAT-G-AAATGTGATGGG-AAGGATTGAGGCCGC
* *
7990 AACGGCGAACCCAGTACCATG
126 AACGGTGAACCCGGTACCATG
* * * * *
8011 AAGATATGAAGGGAAATGTTAAGGCCATAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAA
1 AAGATTTGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCG-TACCTTAGAAGATGTGATGGGAA
8076 AGGTTAAGGC
Statistics
Matches: 290, Mismatches: 63, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
146 3 0.01
147 160 0.55
148 74 0.26
149 47 0.16
150 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.20
Consensus pattern (146 bp):
AAGATTTGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCGTACCTTAGAAGATGTGATGGGAAG
GATTGAGGTCGCAACAGCGAATCCGATACCATGAAATGTGATGGGAAGGATTGAGGCCGCAACGG
TGAACCCGGTACCATG
Found at i:7926 original size:197 final size:198
Alignment explanation
Indices: 7578--8080 Score: 506
Period size: 197 Copynumber: 2.6 Consensus size: 198
7568 AAGATTTGAA
* * * * * * *
7578 GGGAAAGGTTGAGGTCGCAACGGTGAACCCAGTACCTTAGAAGATGTGATGGG-AAGGATTGAGG
1 GGGAAAGGTTGAGGCCGCAACAGCGAACCCAGTACCAT-GAAGATATGAAGGGAAAGG-TTAAGG
* ** * * **
7642 TCACAACAACAAACCCGATACCAT-GAA-ATGTGATGGGAAAGATTGAGGTTGCAATAGTGAACC
64 CCACAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGTCACAATAGTGAACC
7705 CGGTACCATGAAGATTTAAAGGGAAAGG-TTGAGGCCGCAAC-GACGAACCCTG-TACCTTA-AA
129 CGGTACCATGAAGATTTAAAGGG-AAGGATTGAGGCCGCAACAG-CGAACCC-GATACCTTAGAA
7766 AGATGTGAT
191 A-ATGTGAT
* * ** * * * *
7775 GGG-AAGGATTGAGGTCGCAATAGCGAATTCGGTACCATGAA-ATTTGAAGGG-GAGGATTGAGG
1 GGGAAAGG-TTGAGGCCGCAACAGCGAACCCAGTACCATGAAGATATGAAGGGAAAGG-TTAAGG
* ** * * * *
7837 CCACGACGGTGAATCTGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGTCACAA-CGTCGAAC
64 CCACAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGTCACAATAGT-GAAC
** * * * *
7901 CCGGTATTATGAAGATTTGAAGGGAAGGATTGAGGCCGCGACAGTGAATCCGATACCTTAGAAAA
128 CCGGTACCATGAAGATTTAAAGGGAAGGATTGAGGCCGCAACAGCGAACCCGATACCTTAGAAAA
7966 TGTGAT
193 TGTGAT
* *
7972 GGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAATGTTAAGGCC
1 GGGAAAGGTTGAGGCCGCAACAGCGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTAAGGCC
*
8037 ATAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTT
66 ACAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTT
8081 AAGGCCGCAA
Statistics
Matches: 248, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
195 32 0.13
196 17 0.07
197 136 0.55
198 61 0.25
199 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (198 bp):
GGGAAAGGTTGAGGCCGCAACAGCGAACCCAGTACCATGAAGATATGAAGGGAAAGGTTAAGGCC
ACAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGTCACAATAGTGAACCCG
GTACCATGAAGATTTAAAGGGAAGGATTGAGGCCGCAACAGCGAACCCGATACCTTAGAAAATGT
GAT
Found at i:8091 original size:99 final size:99
Alignment explanation
Indices: 7568--8101 Score: 497
Period size: 99 Copynumber: 5.4 Consensus size: 99
7558 AGAAACTATA
* * * * * *
7568 AAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCAGTACCTTAGAAGATGTGATGGGAA
1 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCAGTACCAT-GAAGATTTGAAGGGAA
* ** * *
7633 GGATTGAGGTCACAACAACAAACCCGATACCAT-G
65 GGATTGAGGCCACAACGGCGAACCCGATACCTTAG
* * ** * * *
7667 AA-ATGTGATGGGAAAGATTGAGGTTGCAATAGTGAACCCGGTACCATGAAGATTTAAAGGGAAA
1 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCAGTACCATGAAGATTTGAAGGG-AA
* * *
7731 GG-TTGAGGCCGCAACGACGAACCCTG-TACCTTAA
65 GGATTGAGGCCACAACGGCGAACCC-GATACCTTAG
** ** * *
7765 AAGATGTGATGGG-AAGGATTGAGGTCGCAATAGCGAATTCGGTACCATGAA-ATTTGAAGGGGA
1 AAGATGTGATGGGAAAGG-TTGAGGTCGCAACGGCGAACCCAGTACCATGAAGATTTGAAGGGAA
* * * * *
7828 GGATTGAGGCCACGACGGTGAATCTGGTACCTTAG
65 GGATTGAGGCCACAACGGCGAACCCGATACCTTAG
* * * **
7863 AAGATGTGATGGGAAAGGTTGAGGTCACAACGTCGAACCCGGTATTATGAAGATTTGAAGGGAAG
1 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCAGTACCATGAAGATTTGAAGGGAAG
* * * * *
7928 GATTGAGGCCGCGACAGTGAATCCGATACCTTAG
66 GATTGAGGCCACAACGGCGAACCCGATACCTTAG
* * *
7962 AAAATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAA
1 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCAGTACCATGAAGATTTGAAGGG-AA
* * * *
8027 TG-TTAAGGCCATAACGGCAAACCCGATACCTTAG
65 GGATTGAGGCCACAACGGCGAACCCGATACCTTAG
* * **
8061 AAGATGTGATGGGAAAGGTTAAGGCCGCAACGATGAACCCA
1 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCA
8102 AAAACTACAT
Statistics
Matches: 360, Mismatches: 65, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
97 38 0.11
98 117 0.32
99 202 0.56
100 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (99 bp):
AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCAGTACCATGAAGATTTGAAGGGAAG
GATTGAGGCCACAACGGCGAACCCGATACCTTAG
Found at i:8171 original size:28 final size:30
Alignment explanation
Indices: 8102--8172 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
8092 GATGAACCCA
* * *
8102 AAAACTACATTTTTACCCTCAAACTTTTCT
1 AAAACTTCATTTTAACCCTCAAACTTCTCT
*
8132 AAAA-TTATATTTTAACCCT-AAA-TTCTCT
1 AAAACTT-CATTTTAACCCTCAAACTTCTCT
8160 AAAACTTCATTTT
1 AAAACTTCATTTT
8173 CGACCCCGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 14 0.41
29 6 0.18
30 14 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAACTTCATTTTAACCCTCAAACTTCTCT
Found at i:10739 original size:29 final size:30
Alignment explanation
Indices: 10674--10904 Score: 190
Period size: 29 Copynumber: 7.8 Consensus size: 30
10664 AGGAGTTTTC
*
10674 TAAAC-TTTTTATAAATTATATTTTAA-TC-
1 TAAACTTTTTTA-AAATCATATTTTAACTCT
*
10702 TAAACTTTTTTAAAATCATATTTTGACTCT
1 TAAACTTTTTTAAAATCATATTTTAACTCT
* * * * *
10732 TAAA-TTTTCTCAAAAATAATATTTTGACCCC
1 TAAACTTTT-T-TAAAATCATATTTTAACTCT
** * *
10763 TAATTTTTTTTAAAATCATATTTTAACCCC
1 TAAACTTTTTTAAAATCATATTTTAACTCT
*
10793 TAAA-TTTTCTTAAAATTATATTTTAAC-CTT
1 TAAACTTTT-TTAAAATCATATTTTAACTC-T
* *
10823 TAAACTTTTTAAAAATCACATTTTAACTC-
1 TAAACTTTTTTAAAATCATATTTTAACTCT
* *
10852 TAAACTTTTCTAAAATCACATTTTAAC-CT
1 TAAACTTTTTTAAAATCATATTTTAACTCT
* * *
10881 CAAACTTTTTTCAAATTATATTTT
1 TAAACTTTTTTAAAATCATATTTT
10905 TACCCTAATT
Statistics
Matches: 169, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
28 18 0.11
29 61 0.36
30 61 0.36
31 25 0.15
32 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.01, T:0.48
Consensus pattern (30 bp):
TAAACTTTTTTAAAATCATATTTTAACTCT
Found at i:10906 original size:59 final size:57
Alignment explanation
Indices: 10672--10947 Score: 223
Period size: 59 Copynumber: 4.6 Consensus size: 57
10662 TCAGGAGTTT
* * *
10672 TCTAAACTTTT-TATAAATTATATTTTAATCT-AAACTTTTTTAAAATCATATTTTGAC
1 TCTAAA-TTTTCTA-AAATCATATTTTAACCTCAAACTTTTTTAAAATCATATTTTAAC
* * * **
10729 TCTTAAATTTTCTCAAAAATAATATTTTGACCCCTAATTTTTTTTAAAATCATATTTTAACC
1 TC-TAAATTTTCT--AAAATCATATTTTAACCTC-AAACTTTTTTAAAATCATATTTTAA-C
* * * * *
10791 CCTAAATTTTCTTAAAATTATATTTTAACCTTTAAACTTTTTAAAAATCACATTTTAAC
1 TCTAAATTTTC-TAAAATCATATTTTAACC-TCAAACTTTTTTAAAATCATATTTTAAC
* * * *
10850 TCTAAACTTTTCTAAAATCACATTTTAACCTCAAACTTTTTTCAAATTATATTTTTAC
1 TCTAAA-TTTTCTAAAATCATATTTTAACCTCAAACTTTTTTAAAATCATATTTTAAC
* * * * *
10908 CCTAATTTTTTTCCAAAATCACATTTTAACCGCTAAACTT
1 TCTAA--ATTTTCTAAAATCATATTTTAACCTC-AAACTT
10948 CTCATAGTTA
Statistics
Matches: 177, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
57 6 0.03
58 31 0.18
59 58 0.33
60 48 0.27
61 31 0.18
62 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.01, T:0.46
Consensus pattern (57 bp):
TCTAAATTTTCTAAAATCATATTTTAACCTCAAACTTTTTTAAAATCATATTTTAAC
Found at i:10979 original size:59 final size:57
Alignment explanation
Indices: 10790--11001 Score: 169
Period size: 59 Copynumber: 3.6 Consensus size: 57
10780 ATATTTTAAC
* * * * * * *
10790 CCCTAAA-TTTTCTTAAAATTATATTTTAACCTTTAAACTTTTTAAAAATCACATTTTAA
1 CCCTAAACTTTTC-TAAAATCACATTTTAACC-CTAAACTTTCT-CAAATTACATTTTTA
* * *
10849 CTCTAAACTTTTCTAAAATCACATTTTAA-CCTCAAACTTTTTTCAAATTATATTTTTA
1 CCCTAAACTTTTCTAAAATCACATTTTAACCCT-AAAC-TTTCTCAAATTACATTTTTA
** * *
10907 CCCTAATTTTTTTCCAAAATCACATTTTAACCGCTAAAC-TTCTCATAGTTACATTTTTA
1 CCCTAA-ACTTTTCTAAAATCACATTTTAACC-CTAAACTTTCTCA-AATTACATTTTTA
* * *
10966 CCCTTAAAGTTTTCTAAAATTACATTTCAACCCTAA
1 CCC-TAAACTTTTCTAAAATCACATTTTAACCCTAA
11002 TTTCTTCAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
57 1 0.01
58 30 0.24
59 79 0.63
60 13 0.10
61 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.01, T:0.43
Consensus pattern (57 bp):
CCCTAAACTTTTCTAAAATCACATTTTAACCCTAAACTTTCTCAAATTACATTTTTA
Found at i:10989 original size:30 final size:30
Alignment explanation
Indices: 10702--10999 Score: 180
Period size: 30 Copynumber: 10.0 Consensus size: 30
10692 TATTTTAATC
* * * *
10702 TAAACTTTTTTAAAATCATATTTTGACTCT
1 TAAACTTTTCTAAAATCACATTTTAACCCT
* * * *
10732 TAAA-TTTTCTCAAAAATAATATTTTGACCCC
1 TAAACTTTTCT--AAAATCACATTTTAACCCT
** * * *
10763 TAATTTTTTTTAAAATCATATTTTAACCCC
1 TAAACTTTTCTAAAATCACATTTTAACCCT
* * *
10793 TAAA-TTTTCTTAAAATTATATTTTAACCTT
1 TAAACTTTTC-TAAAATCACATTTTAACCCT
*
10823 TAAACTTTT-TAAAAATCACATTTTAACTC-
1 TAAACTTTTCT-AAAATCACATTTTAACCCT
10852 TAAACTTTTCTAAAATCACATTTTAA-CCT
1 TAAACTTTTCTAAAATCACATTTTAACCCT
* * * * * *
10881 CAAACTTTTTTCAAATTATATTTTTACCC-
1 TAAACTTTTCTAAAATCACATTTTAACCCT
** *
10910 TAATTTTTTTCCAAAATCACATTTTAACCGC-
1 TAA-ACTTTTCTAAAATCACATTTTAACC-CT
* * * * *
10941 TAAACTTCTC-ATAGTTACATTTTTACCCT
1 TAAACTTTTCTAAAATCACATTTTAACCCT
* * *
10970 TAAAGTTTTCTAAAATTACATTTCAACCCT
1 TAAACTTTTCTAAAATCACATTTTAACCCT
11000 AATTTCTTCA
Statistics
Matches: 209, Mismatches: 46, Indels: 26
0.74 0.16 0.09
Matches are distributed among these distances:
28 2 0.01
29 77 0.37
30 98 0.47
31 27 0.13
32 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAACTTTTCTAAAATCACATTTTAACCCT
Found at i:15236 original size:30 final size:32
Alignment explanation
Indices: 15190--15264 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 32
15180 TTTGATAGCT
*
15190 TTTAA-TTTTATAATTTTTA-A-ATGATT-AAA
1 TTTAATTTTTATTATTTTTAGAGA-GATTAAAA
15219 TTTAATTTTTATTATTTTTAGAGAGATTAAAA
1 TTTAATTTTTATTATTTTTAGAGAGATTAAAA
*
15251 TATAATTTTATATT
1 TTTAATTTT-TATT
15265 TATTAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 5 0.13
30 13 0.33
31 5 0.13
32 12 0.31
33 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTAATTTTTATTATTTTTAGAGAGATTAAAA
Found at i:18978 original size:29 final size:28
Alignment explanation
Indices: 18919--18985 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
18909 TGGTTAAAAA
* *
18919 AATTGTATTTTATTATTTTTAATTTAAAC
1 AATTATATTTAATTATTTTTAATTT-AAC
18948 AATTATATTTAATTATTTTATAGATTT-AC
1 AATTATATTTAATTATTTT-TA-ATTTAAC
*
18977 AATTTTATT
1 AATTATATT
18986 AAGATTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 27 0.82
30 2 0.06
31 4 0.12
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
AATTATATTTAATTATTTTTAATTTAAC
Found at i:30515 original size:7 final size:7
Alignment explanation
Indices: 30503--30536 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
30493 TTTTGGCTCT
30503 GTCTCAA
1 GTCTCAA
30510 GTCTCAA
1 GTCTCAA
30517 GTCTCAA
1 GTCTCAA
*
30524 GTCCCAA
1 GTCTCAA
*
30531 CTCTCA
1 GTCTCA
30537 CGATAGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.35, G:0.12, T:0.26
Consensus pattern (7 bp):
GTCTCAA
Found at i:31418 original size:13 final size:13
Alignment explanation
Indices: 31376--31418 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
31366 CCGTGTAATT
31376 TTTTATTTGTTAA
1 TTTTATTTGTTAA
*
31389 TTTCATCTT-TTAA
1 TTTTAT-TTGTTAA
31402 TTTTATTTGTTAA
1 TTTTATTTGTTAA
31415 TTTT
1 TTTT
31419 TATATTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTTATTTGTTAA
Found at i:31430 original size:26 final size:26
Alignment explanation
Indices: 31376--31434 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
31366 CCGTGTAATT
* *
31376 TTTTATTTGTTAATTTCATCTTTTAA
1 TTTTATTTGTTAATTTCATATATTAA
*
31402 TTTTATTTGTTAATTT-TTATATTACA
1 TTTTATTTGTTAATTTCATATATTA-A
31428 -TTTATTT
1 TTTTATTT
31435 TTATTATCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTTATTTGTTAATTTCATATATTAA
Found at i:38667 original size:7 final size:7
Alignment explanation
Indices: 38657--38698 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
38647 AAAAAAATTG
38657 TTGCTTT
1 TTGCTTT
38664 TTGCTTT
1 TTGCTTT
38671 TTGCTTT
1 TTGCTTT
38678 TTGCTTT
1 TTGCTTT
38685 TTGCTTT
1 TTGCTTT
38692 TTGCTTT
1 TTGCTTT
38699 GTTTTCACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.71
Consensus pattern (7 bp):
TTGCTTT
Found at i:39168 original size:15 final size:14
Alignment explanation
Indices: 39148--39178 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
39138 GTATTAAATG
39148 TTCAATTACTTTTAT
1 TTCAATTA-TTTTAT
39163 TTCAATTATTTTAT
1 TTCAATTATTTTAT
39177 TT
1 TT
39179 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCAATTATTTTAT
Found at i:39544 original size:22 final size:20
Alignment explanation
Indices: 39512--39561 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
39502 AACTATAATA
*
39512 TTTTACATTTTAACCCCAAACAT
1 TTTTAC-TTTT-ACCCCAAA-AG
*
39535 TTTTACTTTTCCCCCAAAAG
1 TTTTACTTTTACCCCAAAAG
39555 TTTTACT
1 TTTTACT
39562 CCTTCCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 4 0.16
23 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTACTTTTACCCCAAAAG
Found at i:39567 original size:21 final size:21
Alignment explanation
Indices: 39525--39568 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39515 TACATTTTAA
* *
39525 CCCCAAACATTTTTACTTTTC
1 CCCCAAACAGTTTTACTCTTC
39546 CCCCAAA-AGTTTTACTCCTTC
1 CCCCAAACAGTTTTACT-CTTC
39567 CC
1 CC
39569 ATTTCCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.23, C:0.39, G:0.02, T:0.36
Consensus pattern (21 bp):
CCCCAAACAGTTTTACTCTTC
Found at i:41472 original size:4 final size:4
Alignment explanation
Indices: 41463--41491 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41453 GTCCGCACTA
41463 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
41492 CAGTTCAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41820 original size:63 final size:63
Alignment explanation
Indices: 41744--41868 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
41734 TTGTATAATT
41744 TGATGTGATTAAGTAACATGTGCGATTGGAATATTGTGTTCTTGTTTTGTATGTTAATGGAAC
1 TGATGTGATTAAGTAACATGTGCGATTGGAATATTGTGTTCTTGTTTTGTATGTTAATGGAAC
41807 TGATGTGATTAAGTAACATGTGCGATTGGAATATTGTGTTCTTGTTTTGTATGTTAATGGAA
1 TGATGTGATTAAGTAACATGTGCGATTGGAATATTGTGTTCTTGTTTTGTATGTTAATGGAA
41869 ATTTTTCGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (63 bp):
TGATGTGATTAAGTAACATGTGCGATTGGAATATTGTGTTCTTGTTTTGTATGTTAATGGAAC
Found at i:42939 original size:31 final size:31
Alignment explanation
Indices: 42904--42999 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
42894 AGTTTAGGTG
* *
42904 CCAAATTAAGAAAAAGTGTCAAGTTCAGGTA
1 CCAAATTAGGAAAAAGTGTCAAGTTCAAGTA
**
42935 CCAAATT-GGATAAAA---AAAAG-TCTAAGTA
1 CCAAATTAGGA-AAAAGTGTCAAGTTC-AAGTA
*
42963 CCAAATTAGGAAAAAGTGTCAAGTTTAAGTA
1 CCAAATTAGGAAAAAGTGTCAAGTTCAAGTA
42994 CCAAAT
1 CCAAAT
43000 GTTATATTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
27 2 0.04
28 18 0.35
29 3 0.06
30 2 0.04
31 25 0.49
32 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (31 bp):
CCAAATTAGGAAAAAGTGTCAAGTTCAAGTA
Found at i:42978 original size:59 final size:59
Alignment explanation
Indices: 42811--42999 Score: 188
Period size: 59 Copynumber: 3.2 Consensus size: 59
42801 TAATAAATTT
* * * * * *
42811 AGGTACCAAAATGAATCTAAAAAAACT-TAGGTACCAAATTAGAAAAA-TATGCTAAGTTA
1 AGGTACCAAATTGGATCAAAAAAAAGTCTAAGTACCAAATTAGAAAAAGTGT-C-AAGTTA
* * * * * * *
42870 AGGTATCAAATTGGGTCCAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGGATCAAAAAAAAGTCTAAGTACCAAATT-AGAAAAAGTGTCAAGTTA
42930 AGGTACCAAATTGGAT-AAAAAAAAGTCTAAGTACCAAATTAGGAAAAAGTGTCAAGTTTA
1 AGGTACCAAATTGGATCAAAAAAAAGTCTAAGTACCAAATTA-GAAAAAGTGTCAAG-TTA
42990 A-GTACCAAAT
1 AGGTACCAAAT
43000 GTTATATTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 64 0.59
60 34 0.31
61 8 0.07
62 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (59 bp):
AGGTACCAAATTGGATCAAAAAAAAGTCTAAGTACCAAATTAGAAAAAGTGTCAAGTTA
Found at i:43773 original size:96 final size:96
Alignment explanation
Indices: 43584--43775 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
43574 ATTTTTGCAA
** *
43584 AAGGATATTCGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
43649 AAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
43680 AAGGGTATTTGATTAT-TTCGATTTGAAGAAAAATTGCGCCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
* * *
43743 CGAAATTCGAA-ATAAA-AGAATATTGTCTCGATT
64 C-AAAATCGAAGATAAAGA-AACATTGCCTCGATT
43776 TTTAAAGTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 4 0.05
96 69 0.85
97 8 0.10
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:44162 original size:29 final size:29
Alignment explanation
Indices: 44129--44441 Score: 238
Period size: 29 Copynumber: 11.0 Consensus size: 29
44119 GGACATCCGG
*
44129 GGGGT-AAAATGGTAATTTTTTGAAGTTTC
1 GGGGTCAAAATGG-AATTTTTGGAAGTTTC
*
44158 GGGGTCAAAATGGGATTTTTGGAAGTTTC
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
* *
44187 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
* *
44216 GGGGTCAAAATGGGATTTTTGGAAGTTTG
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
*
44245 GGGGT-AAAATGGAGTTTTTGGAAGTTTC
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
* * *
44273 GAGGTCAAAAAT-GAGATTTGTGGAAGTTTA
1 GGGGTC-AAAATGGA-ATTTTTGGAAGTTTC
* * * *
44303 GTGGTAAAAATGGAAGTTTTGG--G-GTC
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
* * *
44329 -----AAAAATAGG-TTTTTTGGAAGTTTT
1 GGGGTCAAAAT-GGAATTTTTGGAAGTTTC
* * *
44353 GGGGTAAAAATAGAATTTTTGGAAGTTTT
1 GGGGTCAAAATGGAATTTTTGGAAGTTTC
* *
44382 GGGGTTAAAAAATGGGATTTTTGGAAG-TTC
1 GGGG-T-CAAAATGGAATTTTTGGAAGTTTC
* * *
44412 GGGGGTAAAAACGAAATTTTTGGACAGTTT
1 -GGGGTCAAAATGGAATTTTTGGA-AGTTT
44442 AGGAACCTTC
Statistics
Matches: 231, Mismatches: 33, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
21 12 0.05
22 2 0.01
23 1 0.00
24 1 0.00
26 1 0.00
27 1 0.00
28 25 0.11
29 128 0.55
30 36 0.16
31 24 0.10
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGGAATTTTTGGAAGTTTC
Found at i:44206 original size:58 final size:58
Alignment explanation
Indices: 44129--44441 Score: 326
Period size: 58 Copynumber: 5.5 Consensus size: 58
44119 GGACATCCGG
* *
44129 GGGGT-AAAATGGTAATTTTTTGAAGTTTCGGGGTCAAAATGGGATTTTTGGAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTC
*
44187 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTC
* * * * * *
44245 GGGGT-AAAATGGAGTTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTGTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTTC
* * * *
44303 GTGGT--AAA---AA----TGGAAGTTTTGGGGTCAAAAATAGGTTTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTTC
* *
44353 GGGGTAAAAATAGAATTTTTGGAAGTTTTGGGGTTAAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG-T-CAAAATGGGATTTTTGGAAGTTTC
* *
44412 GGGGGTAAAAACGAAATTTTTGGACAGTTT
1 -GGGGTAAAAATGGAATTTTTGGA-AGTTT
44442 AGGAACCTTC
Statistics
Matches: 214, Mismatches: 26, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
50 37 0.17
52 3 0.01
54 1 0.00
55 2 0.01
57 29 0.14
58 76 0.36
59 23 0.11
60 38 0.18
61 5 0.02
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTC
Found at i:44334 original size:21 final size:20
Alignment explanation
Indices: 44293--44334 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
44283 ATGAGATTTG
*
44293 TGGAAGTTTAGTGGTAAAAA
1 TGGAAGTTTAGGGGTAAAAA
*
44313 TGGAAGTTTTGGGGTCAAAAA
1 TGGAAGTTTAGGGGT-AAAAA
44334 T
1 T
44335 AGGTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (20 bp):
TGGAAGTTTAGGGGTAAAAA
Found at i:44347 original size:50 final size:50
Alignment explanation
Indices: 44263--44374 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 50
44253 ATGGAGTTTT
* * *
44263 TGGAAGTTTCGAGGTCAAAAATGAGATTTGTGGAAGTTTAGTGGTAAAAA
1 TGGAAGTTTTGGGGTCAAAAATGAGATTTGTGGAAGTTTAGGGGTAAAAA
* * *
44313 TGGAAGTTTTGGGGTCAAAAAT-AGGTTTTTTGGAAGTTTTGGGGTAAAAA
1 TGGAAGTTTTGGGGTCAAAAATGA-GATTTGTGGAAGTTTAGGGGTAAAAA
* *
44363 TAGAATTTTTGG
1 TGGAAGTTTTGG
44375 AAGTTTTGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 52 0.98
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (50 bp):
TGGAAGTTTTGGGGTCAAAAATGAGATTTGTGGAAGTTTAGGGGTAAAAA
Found at i:44417 original size:60 final size:59
Alignment explanation
Indices: 44313--44441 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 59
44303 GTGGTAAAAA
* * **
44313 TGGAAGTTTTGGGGTCAAAAATAGGTTTTTTGGAAGTTTTGGGGTAAAAATAG-AATTTT
1 TGGAAGTTTTGGGGTAAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAAA-AGAAATTTT
* *
44372 TGGAAGTTTTGGGGTTAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAACGAAATTTT
1 TGGAAGTTTTGGGG-TAAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAAAAGAAATTTT
44432 TGGACAGTTT
1 TGGA-AGTTT
44442 AGGAACCTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 15 0.25
60 41 0.67
61 5 0.08
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (59 bp):
TGGAAGTTTTGGGGTAAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAAAAGAAATTTT
Found at i:45547 original size:9 final size:9
Alignment explanation
Indices: 45521--45550 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
45511 AATCTTTTTT
45521 TTAATATTA
1 TTAATATTA
45530 TTAATTATTA
1 TTAA-TATTA
45540 TTAATATTA
1 TTAATATTA
45549 TT
1 TT
45551 CATTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTAATATTA
Found at i:57621 original size:35 final size:36
Alignment explanation
Indices: 57550--57626 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
57540 ATATTTGACC
*
57550 TTATCAACTTTATAAAAAAAAAATAATTTTAATTTT
1 TTATCAACTTCATAAAAAAAAAATAATTTTAATTTT
* * *
57586 TTATCAACTTCAT-AAAAGAAAGTCATTTTAATTTT
1 TTATCAACTTCATAAAAAAAAAATAATTTTAATTTT
*
57621 TCATCA
1 TTATCA
57627 CTTTTATTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 24 0.67
36 12 0.33
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (36 bp):
TTATCAACTTCATAAAAAAAAAATAATTTTAATTTT
Found at i:59409 original size:318 final size:318
Alignment explanation
Indices: 58832--59469 Score: 1258
Period size: 318 Copynumber: 2.0 Consensus size: 318
58822 AAAGCGGGTG
58832 TGAAAGTATTAATCAAAATCTAAGAATACATGAACTTGGTAGAGGTGTGAAACTAGGATTGCAGC
1 TGAAAGTATTAATCAAAATCTAAGAATACATGAACTTGGTAGAGGTGTGAAACTAGGATTGCAGC
58897 TTTATTAGTAGTCATTGTTATGTTTAGTCAAAGTTGAAAACCATTGACACCTACCAAGAGATGTG
66 TTTATTAGTAGTCATTGTTATGTTTAGTCAAAGTTGAAAACCATTGACACCTACCAAGAGATGTG
58962 ATGAAATGGTTAATGCTATATAAAATCTTAGGAAGAAGTCAACCCTTTTTTTGTGGTTACTATTA
131 ATGAAATGGTTAATGCTATATAAAATCTTAGGAAGAAGTCAACCCTTTTTTTGTGGTTACTATTA
59027 ATAATATTATCGATTTGTTTCCCATTAACTTGATTGAGATCCACCTAATCTTTTTTATATCAGTA
196 ATAATATTATCGATTTGTTTCCCATTAACTTGATTGAGATCCACCTAATCTTTTTTATATCAGTA
59092 GTGATCGTCCATATGATTCGTATCACATGAGTTCGCACGTGATGGGTTTGTATCATTA
261 GTGATCGTCCATATGATTCGTATCACATGAGTTCGCACGTGATGGGTTTGTATCATTA
59150 TGAAAGTATTAATCAAAATCTAAGAATACATGAACTTGGTAGAGGTGTGAAACTAGGATTGCAGC
1 TGAAAGTATTAATCAAAATCTAAGAATACATGAACTTGGTAGAGGTGTGAAACTAGGATTGCAGC
59215 TTTATTAGTAGTCATTGTTATGTTTAGTCAAAGTTGAAAACCATTGACACCTACCAAGAGATGTG
66 TTTATTAGTAGTCATTGTTATGTTTAGTCAAAGTTGAAAACCATTGACACCTACCAAGAGATGTG
59280 ATGAAATGGTTAATGCTATATAAAATCTTAGGAAGAAGTCAACCCTTTTTTTGTGGTTACTATTA
131 ATGAAATGGTTAATGCTATATAAAATCTTAGGAAGAAGTCAACCCTTTTTTTGTGGTTACTATTA
*
59345 ATAATATTATCGATTTGTTTCCCGTTAACTTGATTGAGATCCACCTAATCTTTTTTATATCAGTA
196 ATAATATTATCGATTTGTTTCCCATTAACTTGATTGAGATCCACCTAATCTTTTTTATATCAGTA
*
59410 GTGATCGTCCATATGGTTCGTATCACATGAGTTCGCACGTGATGGGTTTGTATCATTA
261 GTGATCGTCCATATGATTCGTATCACATGAGTTCGCACGTGATGGGTTTGTATCATTA
59468 TG
1 TG
59470 CAAGCAAACC
Statistics
Matches: 318, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 318 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (318 bp):
TGAAAGTATTAATCAAAATCTAAGAATACATGAACTTGGTAGAGGTGTGAAACTAGGATTGCAGC
TTTATTAGTAGTCATTGTTATGTTTAGTCAAAGTTGAAAACCATTGACACCTACCAAGAGATGTG
ATGAAATGGTTAATGCTATATAAAATCTTAGGAAGAAGTCAACCCTTTTTTTGTGGTTACTATTA
ATAATATTATCGATTTGTTTCCCATTAACTTGATTGAGATCCACCTAATCTTTTTTATATCAGTA
GTGATCGTCCATATGATTCGTATCACATGAGTTCGCACGTGATGGGTTTGTATCATTA
Found at i:90557 original size:17 final size:17
Alignment explanation
Indices: 90529--90577 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
90519 ATATATATGG
* *
90529 AAATGCAATGACAATAT
1 AAATGCAGTGACAATAA
*
90546 AAATGTAGTGACAATAA
1 AAATGCAGTGACAATAA
*
90563 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
90578 TATACTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Done.