Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2061
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: 55618
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1715 original size:27 final size:27
Alignment explanation
Indices: 1673--1736 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1663 GGCAAAAACA
*
1673 GTCA-TTTACCCTACAAGGGTATGTTG
1 GTCATTTTACACTACAAGGGTATGTTG
*
1699 GTCATTTTACACTACAAGGGTATTTTG
1 GTCATTTTACACTACAAGGGTATGTTG
* *
1726 ATAATTTTACA
1 GTCATTTTACA
1737 AATTAAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (27 bp):
GTCATTTTACACTACAAGGGTATGTTG
Found at i:1862 original size:80 final size:77
Alignment explanation
Indices: 1778--2142 Score: 212
Period size: 79 Copynumber: 4.6 Consensus size: 77
1768 GGTATTTTAT
*
1778 TAATTTTATAAATCGAGGTGTTTTCGTGGTAATTTTACAATTGAGGGTGTTTCGTATTTCACAAA
1 TAATTTTACAAATCGAGGTGTTTTC-TGGTAATTTTACAATTGAGGGTGTTTCGTATTTCACAAA
1843 TTATGGGTATTGTGG
65 TTA-GGGTATT-TGG
* ** * * * *
1858 TAATTTTACAAATCGAGGGGTATTT-TAAATAATTTCACAATCGAGGGTATTTCGATAATTCTAC
1 TAATTTTACAAATCGAGGTGT-TTTCT-GGTAATTTTACAATTGAGGGTGTTTCG-TATTTC-AC
*
1922 AAATTAGAGGTATTTCGA
62 AAATTAG-GGTATTT-GG
* ** *
1940 TAATTTTACAAATCG-GAGT-ATTTC-GGTAATTTTACAAATTCGAAAGTGTTTGGTAATTT-AC
1 TAATTTTACAAATCGAG-GTGTTTTCTGGTAATTTTAC-AATT-GAGGGTGTTTCGT-ATTTCAC
*
2001 AAATTAAGGGTGTTTTGG
62 AAATT-AGGGT-ATTTGG
* * * ** * * **
2019 TAATTTTACAAA-AGAGGT-ATTT-AGGTAATTTTACAAATCAAGGATATTTTAATAATTTCAC-
1 TAATTTTACAAATCGAGGTGTTTTCTGGTAATTTTAC-AATTGAGGGT-GTTTCGT-ATTTCACA
* *
2080 AATCAGGGTATTTCGA
63 AATTAGGGTATTT-GG
* * *
2096 TAATTTTGAC-AATCGGGGTATGTTC-GGTAATTTTACAAATTGAGGGT
1 TAATTTT-ACAAATCGAGGTGTTTTCTGGTAATTTTAC-AATTGAGGGT
2143 TTTTAGTAAT
Statistics
Matches: 222, Mismatches: 41, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
76 3 0.01
77 17 0.08
78 40 0.18
79 56 0.25
80 53 0.24
81 22 0.10
82 31 0.14
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (77 bp):
TAATTTTACAAATCGAGGTGTTTTCTGGTAATTTTACAATTGAGGGTGTTTCGTATTTCACAAAT
TAGGGTATTTGG
Found at i:1923 original size:26 final size:27
Alignment explanation
Indices: 1715--2142 Score: 241
Period size: 27 Copynumber: 16.2 Consensus size: 27
1705 TTACACTACA
* *
1715 AGGGTATTTTGATAATTTTACAAAT-T
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
1741 AAGATATTTCGATAA-GTTAAAAAT-G
1 AGGGTATTTCGATAATTTTACAAATCG
* *
1766 AGGGTATTT-TATTAATTTTATAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
1793 AGGTGT-TTTCGTGGTAATTTTAC-AATTG
1 AGG-GTATTTC--GATAATTTTACAAATCG
* * *
1821 AGGGTGTTTCG-T-ATTTCACAAAT-T
1 AGGGTATTTCGATAATTTTACAAATCG
*
1845 ATGGGTATTGT-GGTAATTTTACAAATCG
1 A-GGGTATT-TCGATAATTTTACAAATCG
** *
1873 AGGGGTATTTTAAATAATTTCAC-AATCG
1 A-GGGTA-TTTCGATAATTTTACAAATCG
* *
1901 AGGGTATTTCGATAATTCTACAAAT-T
1 AGGGTATTTCGATAATTTTACAAATCG
1927 AGAGGTATTTCGATAATTTTACAAATCG
1 AG-GGTATTTCGATAATTTTACAAATCG
* *
1955 -GAGTATTTCGGTAATTTTACAAATTCG
1 AGGGTATTTCGATAATTTTACAAA-TCG
** * * **
1982 AAAGTGTTT-GGTAA-TTTACAAATTA
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
2007 AGGGTGTTTTGGTAATTTTACAAA-AG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
2033 A-GGTATTTAGGTAATTTTACAAATCA
1 AGGGTATTTCGATAATTTTACAAATCG
* ** *
2059 AGGATATTTTAATAATTTCAC-AATC-
1 AGGGTATTTCGATAATTTTACAAATCG
2084 AGGGTATTTCGATAATTTTGAC-AATCG
1 AGGGTATTTCGATAATTTT-ACAAATCG
* *
2111 -GGGTATGTTCGGTAATTTTACAAATTG
1 AGGGTAT-TTCGATAATTTTACAAATCG
2138 AGGGT
1 AGGGT
2143 TTTTAGTAAT
Statistics
Matches: 316, Mismatches: 56, Indels: 58
0.73 0.13 0.13
Matches are distributed among these distances:
24 8 0.03
25 71 0.22
26 88 0.28
27 95 0.30
28 36 0.11
29 18 0.06
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:2091 original size:25 final size:25
Alignment explanation
Indices: 2044--2116 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
2034 GGTATTTAGG
* * *
2044 TAATTTTACAAATCAAGGATATTTTAA
1 TAATTTCAC-AATC-AGGGTATTTCAA
*
2071 TAATTTCACAATCAGGGTATTTCGA
1 TAATTTCACAATCAGGGTATTTCAA
* *
2096 TAATTTTGACAATCGGGGTAT
1 TAA-TTTCACAATCAGGGTAT
2117 GTTCGGTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
25 12 0.31
26 19 0.49
27 8 0.21
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (25 bp):
TAATTTCACAATCAGGGTATTTCAA
Found at i:2147 original size:78 final size:78
Alignment explanation
Indices: 1805--2155 Score: 270
Period size: 78 Copynumber: 4.4 Consensus size: 78
1795 GTGTTTTCGT
* * * *
1805 GGTAATTTTAC-AATTGAGGGTGTTTCGT-ATTTCACAAATTATGGGTATTGT-GGTAATTTTAC
1 GGTAATTTTACAAATTGAGGGTTTTTAGTAATTTCACAAATTAAGGGTATT-TCGATAATTTTAC
*
1867 AAATCGAGGGGTATTTTA
65 -AATC--GGGGTA-TTTC
** * * * *
1885 AATAATTTCAC-AATCGAGGGTATTTCGATAA-TTCTACAAATT-AGAGGTATTTCGATAATTTT
1 GGTAATTTTACAAATTGAGGGTTTTTAG-TAATTTC-ACAAATTAAG-GGTATTTCGATAATTTT
*
1947 ACAAATCGGAGTATTTC
63 AC-AATCGGGGTATTTC
** * * * * *
1964 GGTAATTTTACAAATTCGAAAGTGTTTGGTAATTT-ACAAATTAAGGGTGTTTTGGTAATTTTAC
1 GGTAATTTTACAAATT-GAGGGTTTTTAGTAATTTCACAAATTAAGGGTATTTCGATAATTTTAC
** * *
2028 AAAAGAGGTATTTA
65 AATCGGGGTATTTC
** * * *
2042 GGTAATTTTACAAATCAAGGATATTTTAATAATTTCAC-AA-TCAGGGTATTTCGATAATTTTGA
1 GGTAATTTTACAAATTGAGGGT-TTTTAGTAATTTCACAAATTAAGGGTATTTCGATAATTTT-A
2105 CAATCGGGGTATGTTC
64 CAATCGGGGTAT-TTC
2121 GGTAATTTTACAAATTGAGGGTTTTTAGTAATTTC
1 GGTAATTTTACAAATTGAGGGTTTTTAGTAATTTC
2156 TCTATCATGG
Statistics
Matches: 213, Mismatches: 45, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
77 19 0.09
78 57 0.27
79 57 0.27
80 35 0.16
81 16 0.08
82 29 0.14
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (78 bp):
GGTAATTTTACAAATTGAGGGTTTTTAGTAATTTCACAAATTAAGGGTATTTCGATAATTTTACA
ATCGGGGTATTTC
Found at i:2154 original size:53 final size:52
Alignment explanation
Indices: 1715--2154 Score: 233
Period size: 53 Copynumber: 8.3 Consensus size: 52
1705 TTACACTACA
* *** * * * *
1715 AGGGTATTTTGATAATTTTACAAATTAAGATATTTCGATAA-GTTA-AAAATG
1 AGGGTATTTAG-TAATTTTACAAATCGGGGTATTTCGGTAATTTTACAAATTG
* *
1766 AGGGTATTTTATTAATTTTATAAATCGAGGTGT-TTTCGTGGTAATTTTAC-AATTG
1 AGGGTA-TTTAGTAATTTTACAAATCG-GG-GTATTTC--GGTAATTTTACAAATTG
* * * ** *
1821 AGGGTGTTTCGT-ATTTCACAAATTATGGGTATTGT-GGTAATTTTACAAATCG
1 AGGGTATTTAGTAATTTTACAAA-TCGGGGTATT-TCGGTAATTTTACAAATTG
* * * *
1873 AGGGGTATTTTAAATAATTTCAC-AATCGAGGGTATTTCGATAATTCTACAAATT-
1 A-GGGTA-TTT-AGTAATTTTACAAATCG-GGGTATTTCGGTAATTTTACAAATTG
* *
1927 AGAGGTATTTCGATAATTTTACAAATCGGAGTATTTCGGTAATTTTACAAATTCG
1 AG-GGTATTTAG-TAATTTTACAAATCGGGGTATTTCGGTAATTTTACAAATT-G
** * * ** * * *
1982 AAAGTGTTTGGTAA-TTTACAAATTAAGGGTGTTTTGGTAATTTTACAAA-AG
1 AGGGTATTTAGTAATTTTACAAA-TCGGGGTATTTCGGTAATTTTACAAATTG
* * *** * *
2033 A-GGTATTTAGGTAATTTTACAAATCAAGGATATTTTAATAATTTCAC-AA-TC
1 AGGGTATTTA-GTAATTTTACAAATC-GGGGTATTTCGGTAATTTTACAAATTG
*
2084 AGGGTATTTCGATAATTTTGAC-AATCGGGGTATGTTCGGTAATTTTACAAATTG
1 AGGGTATTTAG-TAATTTT-ACAAATCGGGGTAT-TTCGGTAATTTTACAAATTG
*
2138 AGGGTTTTTAGTAATTT
1 AGGGTATTTAGTAATTT
2155 CTCTATCATG
Statistics
Matches: 294, Mismatches: 63, Indels: 62
0.70 0.15 0.15
Matches are distributed among these distances:
50 5 0.02
51 45 0.15
52 75 0.26
53 85 0.29
54 41 0.14
55 36 0.12
56 7 0.02
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (52 bp):
AGGGTATTTAGTAATTTTACAAATCGGGGTATTTCGGTAATTTTACAAATTG
Found at i:6640 original size:26 final size:26
Alignment explanation
Indices: 6609--6686 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
6599 TTACCCGAGC
*
6609 CGATTGTAAAATTATCGAAATACCCG
1 CGATTGTAAAATTATCAAAATACCCG
* *
6635 CGATTGTGAAAATTAT-AAAATATCCT
1 CGATTGT-AAAATTATCAAAATACCCG
* * *
6661 TGATTTGTAAAATTACCTAAATACCC
1 CGA-TTGTAAAATTATCAAAATACCC
6687 CTGATTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
26 23 0.55
27 19 0.45
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (26 bp):
CGATTGTAAAATTATCAAAATACCCG
Found at i:6837 original size:87 final size:86
Alignment explanation
Indices: 6638--6946 Score: 196
Period size: 87 Copynumber: 3.7 Consensus size: 86
6628 ATACCCGCGA
* * * * * *
6638 TTGTGAAAATTA-TAAAATATCCTTGATTTGTAAAATTACCTAAATACCCCTGATTTTTGCTAAA
1 TTGT-AAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTTGGCTAAA
6702 ATCCTACCAAAACACCCTTAAT
65 ATCCTACCAAAACACCCTTAAT
* *
6724 TTGTAAAATTACCAAAACACCTTCGATTTGGTAAAATTACCGAAATACCTCCCGCA-TTTGGCTA
1 TTGTAAAATTACCAAAATACCCTCGATTT-GTAAAATTACCGAAATACC-CCCG-ATTTTGGCTA
* * * *
6788 AAAT-TTATCGAAATA-CCTCTAAT
63 AAATCCTACCAAAACACCCT-TAAT
* * * * ** * *
6811 TTGTAGAATTATCGAAATACCCTCGA-TTGTGAAATTA-TTAAAAACCCTCGA-TTT-G-T-AAA
1 TTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTTGGCTAAAA
* *
6870 T--TACCAAAATACCCATAAT
66 TCCTACCAAAACACCCTTAAT
* ** * *
6889 TTGTGAATATTA-TGAAACACCCTCAATTATGTAAAATTACCGAAA-ACACCCTCGATTT
1 TTGT-AAAATTACCAAAATACCCTCGATT-TGTAAAATTACCGAAATAC-CCC-CGATTT
6947 AATAAATTAA
Statistics
Matches: 176, Mismatches: 34, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
78 27 0.15
79 12 0.07
80 12 0.07
81 6 0.03
82 7 0.04
83 5 0.03
84 6 0.03
85 15 0.09
86 21 0.12
87 50 0.28
88 14 0.08
89 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (86 bp):
TTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTTGGCTAAAA
TCCTACCAAAACACCCTTAAT
Found at i:6892 original size:78 final size:83
Alignment explanation
Indices: 6798--7009 Score: 203
Period size: 82 Copynumber: 2.6 Consensus size: 83
6788 AAATTTATCG
* * **
6798 AAATACCTCTAATTTGTAGAATTATCGAAATACCCTCGA-T-TGTGAAATTA-TTAAAA-ACCCT
1 AAATACC-CTAATTTGTAGAATTATCGAAATACCCTCAATTATGTAAAATTACCGAAAACACCCT
*
6859 CGATTT-GTAAATT-ACCA
65 CGATTTAATAAATTAACCA
*
6876 AAATACCCATAATTTGT-GAATATTAT-GAAACACCCTCAATTATGTAAAATTACCGAAAACACC
1 AAATACCC-TAATTTGTAG-A-ATTATCGAAATACCCTCAATTATGTAAAATTACCGAAAACACC
**
6939 CTCGATTTAATAAATTAATTA
63 CTCGATTTAATAAATTAACCA
* *
6960 AAATACCCTCAATTT-TA-AATTATCGAAATATCCTTAATT-TGTCAAAATTA
1 AAATACCCT-AATTTGTAGAATTATCGAAATACCCTCAATTATGT-AAAATTA
7010 TCAAAATACC
Statistics
Matches: 110, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
77 2 0.02
78 27 0.25
79 6 0.05
80 9 0.08
81 12 0.11
82 31 0.28
83 8 0.07
84 15 0.14
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (83 bp):
AAATACCCTAATTTGTAGAATTATCGAAATACCCTCAATTATGTAAAATTACCGAAAACACCCTC
GATTTAATAAATTAACCA
Found at i:7022 original size:28 final size:27
Alignment explanation
Indices: 6612--7052 Score: 193
Period size: 28 Copynumber: 15.9 Consensus size: 27
6602 CCCGAGCCGA
* **
6612 TTGTAAAATTATCGAAATACCCGCGA-
1 TTGTAAAATTATCAAAATACCCTTGAT
*
6638 TTGTGAAAATTAT-AAAATATCCTTGAT
1 TTGT-AAAATTATCAAAATACCCTTGAT
* * *
6665 TTGTAAAATTACCTAAATACCCCTGATTT
1 TTGTAAAATTATCAAAATACCCTTGA--T
* * *
6694 TTGCTAAAATCCTACCAAAACACCCTTAAT
1 TTG-TAAAAT--TATCAAAATACCCTTGAT
* *
6724 TTGTAAAATTACCAAAACA-CCTTCGAT
1 TTGTAAAATTATCAAAATACCCTT-GAT
* * **
6751 TTGGTAAAATTACCGAAATACCTCCCGCAT
1 TT-GTAAAATTATCAAAATACC-CTTG-AT
* *
6781 TTGGCTAAAATTTATCGAAATA-CCTCTAAT
1 TT-G-TAAAA-TTATCAAAATACCCT-TGAT
* * *
6811 TTGTAGAATTATCGAAATACCCTCGA-
1 TTGTAAAATTATCAAAATACCCTTGAT
* * *
6837 TTGTGAAATTATTAAAA-ACCCTCGAT
1 TTGTAAAATTATCAAAATACCCTTGAT
* * *
6863 TTGT-AAATTACCAAAATACCCATAAT
1 TTGTAAAATTATCAAAATACCCTTGAT
* * * **
6889 TTGTGAATATTAT-GAAACACCCTCAAT
1 TTGT-AAAATTATCAAAATACCCTTGAT
* * *
6916 TATGTAAAATTACCGAAAACACCCTCGAT
1 T-TGTAAAATTATC-AAAATACCCTTGAT
* * **
6945 TT-AATAAATTAATTAAAATACCCTCAAT
1 TTGTA-AAATT-ATCAAAATACCCTTGAT
* * *
6973 TT-T-AAATTATCGAAATATCCTTAAT
1 TTGTAAAATTATCAAAATACCCTTGAT
*
6998 TTGTCAAAATTATCAAAATACCCTTGTAG
1 TTGT-AAAATTATCAAAATACCCTTG-AT
* * *
7027 TTGTAAAAATGACCAACATACCCTTG
1 TTGT-AAAATTATCAAAATACCCTTG
7053 TAGCGGTAAG
Statistics
Matches: 324, Mismatches: 61, Indels: 57
0.73 0.14 0.13
Matches are distributed among these distances:
25 33 0.10
26 57 0.18
27 66 0.20
28 67 0.21
29 50 0.15
30 22 0.07
31 6 0.02
32 23 0.07
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
TTGTAAAATTATCAAAATACCCTTGAT
Found at i:13109 original size:27 final size:26
Alignment explanation
Indices: 13073--13185 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
13063 CAGCGTGGCT
* * *
13073 ACCAGAACAGATAATGTGACTGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
13099 ACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
* *
13127 ACTAGAACAGAAATATGTGGCAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* *
13154 ACCAGATCAGATAATTGTGGCATAGCC
1 ACCAGAACAGATAA-TGTGGCAGAGCC
13181 ACCAG
1 ACCAG
13186 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.70
28 15 0.20
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:13134 original size:54 final size:54
Alignment explanation
Indices: 13076--13182 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
13066 CGTGGCTACC
* * *
13076 AGAACAGATA-ATGTGACTGAGTCACCAGATACAGATAATCGTGGCAGAGCCACT
1 AGAACAGAAATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCACT
* * *
13130 AGAACAGAAATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCAC
1 AGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCAC
13183 CAGGACGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 29 0.63
55 17 0.37
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (54 bp):
AGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACT
Found at i:14631 original size:24 final size:24
Alignment explanation
Indices: 14604--14674 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
14594 CTAGATTTCC
**
14604 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
14628 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
14652 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
14675 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:19583 original size:25 final size:25
Alignment explanation
Indices: 19542--19623 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
19532 CTGGAGGCCT
* * *
19542 AGCCTCTTTTAAT-AACTGGGGTAA
1 AGCCTTTTTTGATAAACTGGGGCAA
19566 AGCCTTTTTTGATAAACTGGGGCAA
1 AGCCTTTTTTGATAAACTGGGGCAA
* * * *
19591 AGCCCTTTTCGATAAACTAGGGCAT
1 AGCCTTTTTTGATAAACTGGGGCAA
19616 AGCCTTTT
1 AGCCTTTT
19624 AGCACTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 11 0.22
25 38 0.78
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (25 bp):
AGCCTTTTTTGATAAACTGGGGCAA
Found at i:20454 original size:25 final size:28
Alignment explanation
Indices: 20417--20473 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
20407 CATACGGAAC
*
20417 ATAAGGGCATATT-C-GTCATTTTACCAT
1 ATAAGGG-ATATTACGGTCACTTTACCAT
*
20444 ATAAGGG-TATTACGGTCACTTTACCCT
1 ATAAGGGATATTACGGTCACTTTACCAT
20471 ATA
1 ATA
20474 GGGGCTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 1 0.04
27 21 0.81
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (28 bp):
ATAAGGGATATTACGGTCACTTTACCAT
Found at i:20461 original size:27 final size:26
Alignment explanation
Indices: 20431--20508 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
20421 GGGCATATTC
*
20431 GTCATTTTACCATATAAGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
*
20458 GTCACTTTACCCTATAGGGGCT-TTACG
1 GTCATTTTA-CCTATAGGGG-TATTACG
* *
20485 ATCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-TAGGGGTATT
20509 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 34 0.81
28 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:20597 original size:27 final size:27
Alignment explanation
Indices: 20549--20605 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20539 GTAAATCTAC
*
20549 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTCTAGTAATTTTGT
* *
20576 AAACCAATGGTATTCCTA-TAATTTTTT
1 AAACCAAGGGTATT-CTAGTAATTTTGT
20603 AAA
1 AAA
20606 AAAAGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTCTAGTAATTTTGT
Found at i:20655 original size:27 final size:27
Alignment explanation
Indices: 20614--20765 Score: 114
Period size: 27 Copynumber: 5.6 Consensus size: 27
20604 AAAAAAGTTA
** **
20614 AGGGTATTTCTGTAATTTTGTAAA-TC
1 AGGGTATTTAGGTAATTTTACAAATTC
*
20640 ACGGGTATTTAGGTAATTTTACAAATTG
1 A-GGGTATTTAGGTAATTTTACAAATTC
* * *
20668 AGGGTATTTTGGTAATTTCACAAA-CC
1 AGGGTATTTAGGTAATTTTACAAATTC
* * *
20694 AGTGGTATTTCGGCAATTTTACAAACT-
1 AG-GGTATTTAGGTAATTTTACAAATTC
* *
20721 AGGGGTATTTTGGTAATTTTACAAACT-
1 A-GGGTATTTAGGTAATTTTACAAATTC
*
20748 AGGAGTATTTTGGTAATT
1 AGG-GTATTTAGGTAATT
20766 CTATCCTACA
Statistics
Matches: 105, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
26 5 0.05
27 97 0.92
28 3 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
AGGGTATTTAGGTAATTTTACAAATTC
Found at i:20701 original size:54 final size:53
Alignment explanation
Indices: 20642--20807 Score: 165
Period size: 54 Copynumber: 3.1 Consensus size: 53
20632 TGTAAATCAC
*
20642 GGGTATTTAGGTAATTTTACAAA-TTGAGGGTATTTTGGTAATTTCACAAACCA
1 GGGTATTTAGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTCACAAACCA
* * * *
20695 GTGGTATTTCGGCAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTA
1 G-GGTATTTAGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAACCA
* * ** ** * *
20749 GGAGTATTTTGGTAATTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAATCGA
1 GG-GTATTTAGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTCACAAACCA
20803 GGGTA
1 GGGTA
20808 AAACGATAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 5 0.05
54 84 0.89
55 5 0.05
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (53 bp):
GGGTATTTAGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAACCA
Found at i:20784 original size:27 final size:27
Alignment explanation
Indices: 20642--20768 Score: 132
Period size: 27 Copynumber: 4.7 Consensus size: 27
20632 TGTAAATCAC
* * *
20642 GGGTATTTAGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTCTACAAACTAG
*
20668 AGGGTATTTTGGTAATT-TCACAAACCAG
1 -GGGTATTTTGGTAATTCT-ACAAACTAG
* * * *
20696 TGGTATTTCGGCAATTTTACAAACTAG
1 GGGTATTTTGGTAATTCTACAAACTAG
*
20723 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTCTACAAACTAG
*
20750 GAGTATTTTGGTAATTCTA
1 GGGTATTTTGGTAATTCTA
20769 TCCTACAGGG
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 82 0.96
28 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTACAAACTAG
Found at i:20793 original size:81 final size:81
Alignment explanation
Indices: 20615--20798 Score: 196
Period size: 81 Copynumber: 2.3 Consensus size: 81
20605 AAAAAGTTAA
* ** *
20615 GGGTATTTCTGTAATTTTGTAAATCACGGGTATTTAGGTAATTTTACAAATTGAGGGTATTTTGG
1 GGGTATTTCAGTAATTTTACAAATCACGGGTATTTAGGTAATTTTACAAACTGAGGGTATTTTGG
20680 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * * * *
20696 TGGTATTTCGGCAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACT-AGGAGTATTTT
1 GGGTATTTCAGTAATTTTACAAATC-ACGGGTATTTAGGTAATTTTACAAACTGAGG-GTATTTT
**
20759 GGTAA-TTCTATCCTA-CAG
64 GGTAATTTC-A-CAAACCAG
*
20777 GGGTATTTCAGTAATTTCACAA
1 GGGTATTTCAGTAATTTTACAA
20799 TCGAGGGTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
80 7 0.08
81 76 0.89
82 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.39
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCACGGGTATTTAGGTAATTTTACAAACTGAGGGTATTTTGG
TAATTTCACAAACCAG
Found at i:20980 original size:54 final size:54
Alignment explanation
Indices: 20797--20972 Score: 273
Period size: 54 Copynumber: 3.3 Consensus size: 54
20787 GTAATTTCAC
*
20797 AATCGAGGGTAAAACGATAATTTTGTAAA-CTAAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGATAATTTTGTAAATC-AAGGGTAAAATGGTAATTCTATA
* * *
20851 AATCAAGGGTAAAACGATAATTCTGTAAATCAATGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTAAATCAAGGGTAAAATGGTAATTCTATA
* * *
20905 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTGAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTAAATCAAGGGTAAAATGGTAATTCTATA
20959 AATCGAGGGTAAAA
1 AATCGAGGGTAAAA
20973 TGGTAATTCT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 110 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
AATCGAGGGTAAAACGATAATTTTGTAAATCAAGGGTAAAATGGTAATTCTATA
Found at i:20983 original size:27 final size:27
Alignment explanation
Indices: 20797--20982 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
20787 GTAATTTCAC
* * *
20797 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
20824 AA-CTAAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAATGGTAATTCTGTA
* * *
20851 AATCAAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
20878 AATCAATGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
20905 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
20932 AATCGAGGGTGAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
20959 AATCGAGGGTAAAATGGTAATTCT
1 AATCGAGGGTAAAATGGTAATTCT
20983 ACAAATTGAT
Statistics
Matches: 137, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 135 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:23414 original size:30 final size:31
Alignment explanation
Indices: 23305--23418 Score: 196
Period size: 31 Copynumber: 3.7 Consensus size: 31
23295 TCAGTACCGA
23305 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
23335 CATATCACTGGGCCGAAGCGTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
23366 CATATCACTGGACCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
23397 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
23419 ACTGTAAGCG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 17 0.22
31 62 0.78
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:23666 original size:25 final size:25
Alignment explanation
Indices: 23638--23707 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
23628 CTCTTTTAAT
* *
23638 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTAGGGCAAAGCCCTTTTCGATA
*
23663 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTAGGGCAAAGCCCTTTTCGATA
* *
23688 AACTCGGGCATAGCCCTTTT
1 AACTAGGGCAAAGCCCTTTT
23708 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTCGATA
Found at i:24545 original size:27 final size:27
Alignment explanation
Indices: 24515--24579 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
24505 GGGCATATTC
24515 GTCATTTTACCATAC-GAGGG-TATTACG
1 GTCATTTTACCATACAG-GGGCT-TTACG
* *
24542 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
*
24569 GTCTTTTTACC
1 GTCATTTTACC
24580 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCTTTACG
Found at i:24663 original size:27 final size:27
Alignment explanation
Indices: 24633--24743 Score: 73
Period size: 27 Copynumber: 3.9 Consensus size: 27
24623 GTAAATCTAC
24633 AAACCAAGGGTATTTTAGTAATTTTTT
1 AAACCAAGGGTATTTTAGTAATTTTTT
* * *
24660 AAACCAATGGTATTCCTA-TCATTTTTTT
1 AAACCAAGGGTATT-TTAGT-AATTTTTT
** *
24688 AAAAAAGTTAAGGGTATTTCT-GTAATTTTGT
1 ---AAA-CCAAGGGTATTT-TAGTAATTTTTT
* *
24719 AAATCAAGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTTAGTAATTTT
24744 AAAAATTGAG
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
26 1 0.02
27 33 0.51
28 12 0.18
31 9 0.14
32 10 0.15
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTTT
Found at i:24749 original size:27 final size:26
Alignment explanation
Indices: 24697--24849 Score: 155
Period size: 27 Copynumber: 5.7 Consensus size: 26
24687 TAAAAAAGTT
**
24697 AAGGGTATTTCT-GTAATTTTGTAAATC
1 AAGGGTATTT-TGGTAATTTTACAAA-C
* *
24724 AAGGGTATTTTGGTAATTTTAAAAATT
1 AAGGGTATTTTGGTAATTTTACAAA-C
* *
24751 GAGGGTATTTTGGTAATTTCACAAAC
1 AAGGGTATTTTGGTAATTTTACAAAC
* *
24777 CAGTGGTATTTCGGTAATTTTACAAAC
1 AAG-GGTATTTTGGTAATTTTACAAAC
*
24804 TAGGGATATTTTGGTAATTTTACAAAC
1 AAGGG-TATTTTGGTAATTTTACAAAC
*
24831 TAGGAGTATTTTGGTAATT
1 AAGG-GTATTTTGGTAATT
24850 CTATCCTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.05
27 104 0.95
28 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (26 bp):
AAGGGTATTTTGGTAATTTTACAAAC
Found at i:24785 original size:54 final size:53
Alignment explanation
Indices: 24725--24849 Score: 171
Period size: 54 Copynumber: 2.3 Consensus size: 53
24715 TTGTAAATCA
*
24725 AGGGTATTTTGGTAATTTTAAAAATTGAGGG-TATTTTGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTAAAAACT-AGGGATATTTTGGTAATTTCACAAACC
* * * *
24778 AGTGGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATTTTACAAACT
1 AG-GGTATTTTGGTAATTTTAAAAACTAGGGATATTTTGGTAATTTCACAAACC
24832 AGGAGTATTTTGGTAATT
1 AGG-GTATTTTGGTAATT
24850 CTATCCTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
53 7 0.11
54 56 0.89
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (53 bp):
AGGGTATTTTGGTAATTTTAAAAACTAGGGATATTTTGGTAATTTCACAAACC
Found at i:24866 original size:81 final size:81
Alignment explanation
Indices: 24699--24918 Score: 216
Period size: 81 Copynumber: 2.7 Consensus size: 81
24689 AAAAAGTTAA
* ** *
24699 GGGTATTTCTGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTTGG
1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTAAAAACTGAGGGTATTTTGG
24764 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * * *
24780 TGGTATTTCGGTAATTTTACAAA-CTAGGGATATTTTGGTAATTTTACAAACT-AGGAGTATTTT
1 GGGTATTTCAGTAATTTTACAAATCAAGGG-TATTTTGGTAATTTTAAAAACTGAGG-GTATTTT
**
24843 GGTAA-TTCTATCCTA-CAG
64 GGTAATTTC-A-CAAACCAG
* * *** **
24861 GGGTATTTCAGTAATTTCAC-AATCGAGGGTAAAATGGTAATTTTGTAAACTGAGGGTA
1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTAAAAACTGAGGGTA
24919 AAATGGTAAT
Statistics
Matches: 115, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
80 33 0.29
81 80 0.70
82 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTAAAAACTGAGGGTATTTTGG
TAATTTCACAAACCAG
Found at i:24868 original size:54 final size:54
Alignment explanation
Indices: 24727--24882 Score: 147
Period size: 54 Copynumber: 2.9 Consensus size: 54
24717 GTAAATCAAG
* * * *
24727 GGTATTTTGGTAATTTTA-AAAATTGAGGGTATTTTGGTAATTTCACAAACCAGT
1 GGTATTTCGGTAATTCTACAAACTAG-GGGTATTTTGGTAATTTCACAAACCAGT
* * * *
24781 GGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATTTTACAAACTAG-
1 GGTATTTCGGTAATTCTACAAACTAGGGGTATTTTGGTAATTTCACAAACCAGT
* ** **
24834 GAGTATTTTGGTAATTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAA
1 G-GTATTTCGGTAATTCTA-CAAACTAGGGGTATTTTGGTAATTTCACAA
24883 TCGAGGGTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
53 1 0.01
54 76 0.89
55 8 0.09
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
GGTATTTCGGTAATTCTACAAACTAGGGGTATTTTGGTAATTTCACAAACCAGT
Found at i:24915 original size:27 final size:27
Alignment explanation
Indices: 24881--25078 Score: 263
Period size: 27 Copynumber: 7.3 Consensus size: 27
24871 GTAATTTCAC
* *
24881 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTATA
* *
24908 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTCTATA
*
24935 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
**
24962 AATTAAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
* * *
24989 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTATA
* *
25016 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
*
25043 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTATA
25070 AATCGAGGG
1 AATCGAGGG
25079 CATTTCAGTA
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 150 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTATA
Found at i:24997 original size:81 final size:81
Alignment explanation
Indices: 24881--25078 Score: 308
Period size: 81 Copynumber: 2.4 Consensus size: 81
24871 GTAATTTCAC
* * * *
24881 AATCGAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCAAGGGTAAAATGGTAATTCTATAAATC-GAGGGTAAAACGGTAATTTTGTAAATCGAGGGT
24945 AAAACGGTAATTCTATA
65 AAAACGGTAATTCTATA
* *
24962 AATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTG
1 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
25027 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* *
25043 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGG
25079 CATTTCAGTA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
81 106 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (81 bp):
AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:26059 original size:15 final size:14
Alignment explanation
Indices: 26039--26068 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
26029 GAACCCCCAC
26039 TCAAGGCCCAATATT
1 TCAAGGCCCAA-ATT
26054 TCAAGGCCCAAATT
1 TCAAGGCCCAAATT
26068 T
1 T
26069 AGGGTGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (14 bp):
TCAAGGCCCAAATT
Found at i:27277 original size:10 final size:9
Alignment explanation
Indices: 27256--27291 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
27246 TTGTTTTAGT
27256 TAATTATTA
1 TAATTATTA
27265 TAATTATTTA
1 TAATTA-TTA
27275 TAATTATTA
1 TAATTATTA
27284 -AATTATTA
1 TAATTATTA
27292 GTTTTATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTATTA
Found at i:28237 original size:44 final size:43
Alignment explanation
Indices: 28166--28278 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 43
28156 GGCGTTAGAA
** *
28166 CGGCGCTTTTTTAAAAAACGCCGCTATAGACCTGTACTTTTAG
1 CGGCGCTTTTGAAAAAAACGCCGCTATAAACCTGTACTTTTAG
28209 CGGCGCTTTTAGAAAAAAACGCCGCTATAAACCTGTACTTTTAG
1 CGGCGCTTTT-GAAAAAAACGCCGCTATAAACCTGTACTTTTAG
**
28253 CGGCGCTTTTTTAAAAAACGCCGCTA
1 CGGCGCTTTTGAAAAAAACGCCGCTA
28279 ATTTGCCCAG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 24 0.38
44 40 0.62
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
CGGCGCTTTTGAAAAAAACGCCGCTATAAACCTGTACTTTTAG
Found at i:31006 original size:47 final size:47
Alignment explanation
Indices: 30955--31267 Score: 502
Period size: 47 Copynumber: 6.7 Consensus size: 47
30945 TTAGGATTCT
* * *
30955 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
31002 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31049 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31096 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
31143 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
31190 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
31237 ACGTGATGGATGTGAAAGTGTATAAATGTGA
1 ATGTGATGAATGTGAAAGTGTATATATGTGA
31268 AAGTCCGAAG
Statistics
Matches: 252, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 251 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31531 original size:37 final size:37
Alignment explanation
Indices: 31387--31524 Score: 240
Period size: 37 Copynumber: 3.7 Consensus size: 37
31377 CCGAGCTCTA
31387 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
31424 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* *
31461 AAGACCCGATGACTACGTGTGGAGATTTTGTCTGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* *
31498 AAGACCCGATAACTTCGTGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
31525 TCGTCTGAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
Found at i:32850 original size:40 final size:40
Alignment explanation
Indices: 32806--33031 Score: 326
Period size: 40 Copynumber: 5.7 Consensus size: 40
32796 GGGCTAAATC
32806 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
32846 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
32886 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
* * *
32926 CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTC
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
** * * * * * *
32966 CCGAAGAGCATTTATGCTGGTGTTATATCCGGGCTAGGTC
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
* * *
33006 CCGAAGAGCAATCATGCTGGTGATGT
1 CCGAAGAGCATTCGTGCTAGTGATGT
33032 GTATTCGGGC
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 174 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
Found at i:36920 original size:49 final size:49
Alignment explanation
Indices: 36802--37169 Score: 358
Period size: 47 Copynumber: 7.3 Consensus size: 49
36792 GTGAACATGC
*
36802 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
36851 ATAT-T-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
36898 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
** * * * *
36947 ATATATGTGATAAGTGTATATATATG-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 ATATATGTGATAAG-GCCTA-AT-GGCCGAT---G--TGAT-G--AATGT---------GAAAGT
37011 GTAT
46 GTAT
*
37015 ATATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
37062 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * *
37109 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
37158 A-A-ATGTGATAAG
1 ATATATGTGATAAG
37170 TCCCGAAGGG
Statistics
Matches: 270, Mismatches: 24, Indels: 52
0.78 0.07 0.15
Matches are distributed among these distances:
47 139 0.51
48 3 0.01
49 69 0.26
50 3 0.01
51 5 0.02
52 1 0.00
54 1 0.00
56 3 0.01
57 1 0.00
58 4 0.01
59 4 0.01
60 1 0.00
61 3 0.01
63 1 0.00
65 1 0.00
66 4 0.01
67 3 0.01
68 24 0.09
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:36967 original size:68 final size:68
Alignment explanation
Indices: 36884--37028 Score: 283
Period size: 68 Copynumber: 2.1 Consensus size: 68
36874 GATGTGATGA
36884 ATGTGA-AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 ATGTGATAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
36948 TAT
66 TAT
36951 ATGTGATAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 ATGTGATAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
37016 TAT
66 TAT
37019 ATGTGATAAG
1 ATGTGATAAG
37029 GCCTAATGGC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 6 0.08
68 71 0.92
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (68 bp):
ATGTGATAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TAT
Found at i:36970 original size:21 final size:19
Alignment explanation
Indices: 36933--36979 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
36923 GATGTGATGA
36933 ATGTGA-AAGTGTATATAT
1 ATGTGATAAGTGTATATAT
36951 ATGTGATAAGTGTATATAT
1 ATGTGATAAGTGTATATAT
36970 ATGTGATAAG
1 ATGTGATAAG
36980 GCCTAATGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (19 bp):
ATGTGATAAGTGTATATAT
Found at i:36990 original size:117 final size:113
Alignment explanation
Indices: 36837--37075 Score: 426
Period size: 117 Copynumber: 2.1 Consensus size: 113
36827 GATGTGATGA
36837 ATGTGA-AAGTGTATATATTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 ATGTGATAAGTGTATATATTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
36901 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
66 TATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTG--TATAT
36951 ATGTGATAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 ATGTGATAAGTGTATATAT-T-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
37016 TATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTGTATAT
64 TATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTGTATAT
37066 ATGTGATAAG
1 ATGTGATAAG
37076 GCCTAATGGC
Statistics
Matches: 121, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
114 6 0.05
115 27 0.22
116 1 0.01
117 87 0.72
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.32
Consensus pattern (113 bp):
ATGTGATAAGTGTATATATTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTGTATAT
Found at i:36996 original size:164 final size:164
Alignment explanation
Indices: 36802--37114 Score: 576
Period size: 164 Copynumber: 1.9 Consensus size: 164
36792 GTGAACATGC
36802 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT-T-TGATAAGGC
1 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
*
36865 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
66 CTAATGGCCGAAGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGA
36930 TGAATGTGAAAGTGTATATATATGTGATAAGTGTAT
129 TGAATGTGAAAGTGTATATATATGTGATAAGTGTAT
*
36966 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
37031 CTAATGGCCGAAGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
66 CTAATGGCCGAAGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
37096 AATGTGAAAGTGTATATAT
131 AATGTGAAAGTGTATATAT
37115 GTGACAGGGC
Statistics
Matches: 145, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
164 106 0.73
165 1 0.01
166 38 0.26
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (164 bp):
ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
CTAATGGCCGAAGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGTATATATATGTGATAAGTGTAT
Found at i:37426 original size:37 final size:37
Alignment explanation
Indices: 37288--37425 Score: 240
Period size: 37 Copynumber: 3.7 Consensus size: 37
37278 CCGAGCTCTA
*
37288 AAGACCCGATGACTACGTGTGGAGGTTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
37325 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
*
37362 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* *
37399 AAGACCCGATAACTTCGTGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
37426 TCGTCTGAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
Found at i:39108 original size:18 final size:18
Alignment explanation
Indices: 39076--39113 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39066 TACAATATAG
39076 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
39095 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
39112 TA
1 TA
39114 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:47213 original size:48 final size:48
Alignment explanation
Indices: 47137--47269 Score: 185
Period size: 48 Copynumber: 2.8 Consensus size: 48
47127 TAGGGTTATG
*
47137 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATA
1 TGTGATCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGATA
* * * *
47185 TGTGATCCCATGTAAGACCATATATGGGATATGGCATTGGCATCTATA
1 TGTGATCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGATA
** * *
47233 TGTGATTTCTTGTAAGACCATGTTTGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTATGGGACATGGCAT
47270 CGATATGAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGATA
Found at i:48412 original size:292 final size:292
Alignment explanation
Indices: 47888--48421 Score: 1023
Period size: 292 Copynumber: 1.8 Consensus size: 292
47878 TTTAGCAAGC
*
47888 GTGTTGGCTTATAATGATTTGATGATTCATTTTGTATATGGCCATGAGATATGGTTCATATTGAT
1 GTGTTGGCTTATAATGATTTGATGATTCATTTTGTATATGGCCATGAGATATGGTTCATATTGAC
* *
47953 TATTAGGTTGTAAACCTAATTATTTATGCATGCATGTGTCAAAGTCTTTATGATGATGGATGGTG
66 TATTAGGTTGTAAACCTAATTATTTATGCATGCATGTGTCAAAGTCTTGATGATAATGGATGGTG
*
48018 TTATATGGCATACAAGTATGATGAATGGATGATGACAAATTGGTATGGCTATGATCATGGTTTAA
131 TTATATGGCATACAAGTATGATGAATGGATGATGACAAATTGGTATGGCTATGATCATAGTTTAA
48083 ATGTGTGAATTGAGAGTAGATTAATAATGTTGATTGGATATGAAATTAGTAAGTAAGCTTGTTAA
196 ATGTGTGAATTGAGAGTAGATTAATAATGTTGATTGGATATGAAATTAGTAAGTAAGCTTGTTAA
48148 TTTGAGTATGTGTCATATTAATTTGGCCATGT
261 TTTGAGTATGTGTCATATTAATTTGGCCATGT
48180 GTGTTGGCTTATAATGATTTGATGATTCATTTTGTATATGGCCATGAGATATGGTTCATATTGAC
1 GTGTTGGCTTATAATGATTTGATGATTCATTTTGTATATGGCCATGAGATATGGTTCATATTGAC
*
48245 TATTGGGTTGTAAACCTAATTATTTATGCATGCATGTGTCAAAGTCTTGATGATAATGGATGGTG
66 TATTAGGTTGTAAACCTAATTATTTATGCATGCATGTGTCAAAGTCTTGATGATAATGGATGGTG
48310 TTATATGGCATACAAGTATGATGAATGGATGATGACAAATTGGTATGGCTATGATCATAGTTTAA
131 TTATATGGCATACAAGTATGATGAATGGATGATGACAAATTGGTATGGCTATGATCATAGTTTAA
48375 ATGTGTGAATTGAGAGTAGATTAATAATGTTGATTGGATATGAAATT
196 ATGTGTGAATTGAGAGTAGATTAATAATGTTGATTGGATATGAAATT
48422 GGTGTGGAGT
Statistics
Matches: 237, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
292 237 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (292 bp):
GTGTTGGCTTATAATGATTTGATGATTCATTTTGTATATGGCCATGAGATATGGTTCATATTGAC
TATTAGGTTGTAAACCTAATTATTTATGCATGCATGTGTCAAAGTCTTGATGATAATGGATGGTG
TTATATGGCATACAAGTATGATGAATGGATGATGACAAATTGGTATGGCTATGATCATAGTTTAA
ATGTGTGAATTGAGAGTAGATTAATAATGTTGATTGGATATGAAATTAGTAAGTAAGCTTGTTAA
TTTGAGTATGTGTCATATTAATTTGGCCATGT
Found at i:48677 original size:29 final size:29
Alignment explanation
Indices: 48643--48706 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
48633 GTGTGTAGGC
*
48643 CGTGTGTGACACATGGTCAGCCCCATGGG
1 CGTGTGTGACACACGGTCAGCCCCATGGG
48672 CGTGTGTGACACACGGTCAGCCCCATGGG
1 CGTGTGTGACACACGGTCAGCCCCATGGG
48701 CGTGTG
1 CGTGTG
48707 ACCTGACCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.20
Consensus pattern (29 bp):
CGTGTGTGACACACGGTCAGCCCCATGGG
Done.