Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1616
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: 28636
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Found at i:1028 original size:10 final size:10
Alignment explanation
Indices: 1013--1039 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1003 ATGTATCAAG
1013 CAAAAACAAA
1 CAAAAACAAA
1023 CAAAAACAAA
1 CAAAAACAAA
1033 CAAAAAC
1 CAAAAAC
1040 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:5261 original size:52 final size:51
Alignment explanation
Indices: 5176--5299 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
5166 ATATGAAAAG
* *
5176 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
5227 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
5279 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
5300 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:5312 original size:51 final size:51
Alignment explanation
Indices: 5176--5319 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
5166 ATATGAAAAG
*
5176 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
5228 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
5279 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
5320 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:5326 original size:13 final size:13
Alignment explanation
Indices: 5308--5332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5298 CAAAGATCAG
5308 TGTATCGATACAA
1 TGTATCGATACAA
5321 TGTATCGATACA
1 TGTATCGATACA
5333 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5410 original size:33 final size:33
Alignment explanation
Indices: 5373--5439 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5363 AGTAGCTTAA
5373 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5406 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5439 A
1 A
5440 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5413 original size:13 final size:13
Alignment explanation
Indices: 5395--5419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5385 CAAAAAAATA
5395 TGTATCGATACAT
1 TGTATCGATACAT
5408 TGTATCGATACA
1 TGTATCGATACA
5420 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6561 original size:47 final size:49
Alignment explanation
Indices: 6438--6756 Score: 380
Period size: 47 Copynumber: 6.7 Consensus size: 49
6428 AAAATGATGT
* *
6438 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
* *
6490 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6539 CAATGTGC-GAGTCAA-GCCAGCTACATT-GACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
6585 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
6627 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6676 CAAT-AGCTGATTCAAGGCCAGC-ATATGGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
6723 CAATAG-G-TGATTCAA-GCCAGCTATATTGGGCTTA
1 CAAT-GTGCTGATTCAAGGCCAGCTATATTGGACTTA
6757 GAAGGGTTGC
Statistics
Matches: 234, Mismatches: 20, Indels: 31
0.82 0.07 0.11
Matches are distributed among these distances:
42 31 0.13
43 7 0.03
45 3 0.01
46 33 0.14
47 62 0.26
48 38 0.16
49 22 0.09
51 1 0.00
52 37 0.16
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:6734 original size:137 final size:136
Alignment explanation
Indices: 6485--6748 Score: 399
Period size: 137 Copynumber: 1.9 Consensus size: 136
6475 AGATGGAAAA
* *
6485 GGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCGAG
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGAGCGAG
*
6550 TCAAGCCAGCTACATTGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATGG
66 TCAAGCCAGCTACATGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA-GCCAGCTATATGG
6615 ACTTAAT
130 ACTTAAT
* *
6622 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAAT-AGCTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGAGC-GA
* * *
6686 TTCAAGGCCAGC-ATATGGGACTTAAAGATAAAGGTGCCAATA-GGTGATTCAAGCCAGCTATAT
65 GTCAA-GCCAGCTACAT-GGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGCCAGCTATAT
6749 TGGGCTTAGA
Statistics
Matches: 116, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
136 13 0.11
137 73 0.63
138 30 0.26
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (136 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGAGCGAG
TCAAGCCAGCTACATGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGCCAGCTATATGGA
CTTAAT
Found at i:6851 original size:57 final size:57
Alignment explanation
Indices: 6763--6952 Score: 197
Period size: 57 Copynumber: 3.3 Consensus size: 57
6753 CTTAGAAGGG
* * *
6763 TTGCCACCGACTGTGTGGGC-TTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGA
1 TTGCCACTGACT-TGT-GGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGA
* * * *
6820 TTGCCACTGACTTGTGGCTTTTTGAACAGGGTGCCACTAACTTGT-GGCTTTTAAAGG
1 TTGCCACTGACTTGTGGC-TTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGA
*** *
6877 TTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAA
1 TTGCCACTGACTTGT-GGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGA
* *
6935 GGTGCCACTAACTTGTGG
1 -TTGCCACTGACTTGTGG
6953 GCTGAAAAGA
Statistics
Matches: 110, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
55 3 0.03
56 6 0.05
57 74 0.67
58 14 0.13
59 13 0.12
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (57 bp):
TTGCCACTGACTTGTGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGA
Found at i:6856 original size:30 final size:28
Alignment explanation
Indices: 6764--7168 Score: 188
Period size: 30 Copynumber: 13.9 Consensus size: 28
6754 TTAGAAGGGT
* *
6764 TGCCACCGACTGTGTGGGC-TTGGAAAAGGG
1 TGCCACTGACT-TGT-GGCTTTTGAAAA-GG
* * *
6794 TGCCACTGATTTGTGGGC-TTTGAAGA-T
1 TGCCACTGACTTGT-GGCTTTTGAAAAGG
*
6821 TGCCACTGACTTGTGGCTTTTTGAACAGGG
1 TGCCACTGACTTGTGGC-TTTTGAA-AAGG
*
6851 TGCCACTAACTTGTGGCTTTT--AAAGG
1 TGCCACTGACTTGTGGCTTTTGAAAAGG
**
6877 TTGCCACTGACTTGTGGGCTTTTGAAAAATA
1 -TGCCACTGACTTGT-GGCTTTTG-AAAAGG
6908 TGCCACTGACTTGTGGGCTTTTGAAAAGG
1 TGCCACTGACTTGT-GGCTTTTGAAAAGG
*
6937 TGCCACTAACTTGTGGGC---TGAAAAGAG
1 TGCCACTGACTTGT-GGCTTTTGAAAAG-G
* * **
6964 TGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGAG
1 TGCCACT-GACTTGTG-GCTT----TTG-AAAAG-G
* * * *
6999 TGCCACGGAGTTGTGGACTTTGGAAAAGA
1 TGCCACTGACTTGTGG-CTTTTGAAAAGG
* * **
7028 TGCCGCCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGT-GGCTTTTGAAAA-GG
*
7058 TGCCACTGATTTGTGGGC-TTTG--AAGG
1 TGCCACTGACTTGT-GGCTTTTGAAAAGG
* **
7084 TTGCCACTGACTTGTGGGCTTTCGAAAAAAA
1 -TGCCACTGACTTGT-GGCTTTTG-AAAAGG
* **
7115 TGCCACCGACTTGTGGGC-TTTGAAAAAAA
1 TGCCACTGACTTGT-GGCTTTTG-AAAAGG
7144 TGCCACTGACTTGTGGACTTTTGAA
1 TGCCACTGACTTGTGG-CTTTTGAA
7169 GGGTGATGAA
Statistics
Matches: 301, Mismatches: 43, Indels: 63
0.74 0.11 0.15
Matches are distributed among these distances:
26 17 0.06
27 58 0.19
28 18 0.06
29 86 0.29
30 92 0.31
31 6 0.02
34 2 0.01
35 22 0.07
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGCTTTTGAAAAGG
Found at i:6978 original size:86 final size:85
Alignment explanation
Indices: 6780--6961 Score: 237
Period size: 86 Copynumber: 2.1 Consensus size: 85
6770 CGACTGTGTG
* * *
6780 GGCTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGATTGCCACTGACTTGTGGCTTTTTG
1 GGCTT-GAAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAATTGCCACTGACTTGTGGCTTTTTG
*
6844 AACAGGGTGCCACTAACTTGT
65 AACAAGGTGCCACTAACTTGT
**
6865 GGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGC-TTT
1 GGCTTGAAAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAT-TGCCACTGACTTGT-GGCTTTT
6929 TGAA-AAGGTGCCACTAACTTGT
63 TGAACAAGGTGCCACTAACTTGT
6951 GGGC-TGAAAAG
1 -GGCTTGAAAAG
6962 AGTGCTATAG
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
84 22 0.26
85 9 0.11
86 26 0.31
87 24 0.29
88 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (85 bp):
GGCTTGAAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAATTGCCACTGACTTGTGGCTTTTTGA
ACAAGGTGCCACTAACTTGT
Found at i:7041 original size:29 final size:29
Alignment explanation
Indices: 6992--7164 Score: 161
Period size: 29 Copynumber: 5.9 Consensus size: 29
6982 TTACAAAAGA
* * *
6992 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* * *
7022 AAAAGATGCCGCCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
7051 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
7080 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
7109 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
7138 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
7165 TGAAGGGTGA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.18
28 2 0.02
29 50 0.42
30 46 0.39
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:7099 original size:121 final size:121
Alignment explanation
Indices: 6878--7159 Score: 267
Period size: 121 Copynumber: 2.4 Consensus size: 121
6868 TTTTAAAGGT
* * * * **
6878 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCAC
1 TGCCACGGACTTGTGGACTTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGTGCCAC
* *
6943 TAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAG
66 TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAAGAAAAAGAG
* * *
6999 TGCCACGGAGTTGTGGAC-TTTGGAAAAGATGCCGCCGACTTGTGGGCTTCGGAAAAGGGTGCCA
1 TGCCACGGACTTGTGGACTTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAA-GGTGCCA
* * *** * * *
7063 CTGATTTGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTC----GAAAAA-AA
65 CTAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACAAAAGAAAAAGAG
* * * *
7115 TGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACGGACTTGTGGACTTTTGAAAAAGATGCCACCGACTTGTGG
7160 ACTTTTGAAG
Statistics
Matches: 132, Mismatches: 26, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
116 39 0.30
117 6 0.05
120 33 0.25
121 53 0.40
122 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (121 bp):
TGCCACGGACTTGTGGACTTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAAGAAAAAGAG
Found at i:8608 original size:1 final size:1
Alignment explanation
Indices: 8604--8727 Score: 86
Period size: 1 Copynumber: 124.0 Consensus size: 1
8594 CCGGACCCCC
* * * * * * * * *
8604 TTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTTCTTTTGTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * ** * *
8669 TTTTTTTTTCATTCATTTTTTTTGTTTTTTTCATTTTTTTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8728 GGAGGACGCC
Statistics
Matches: 90, Mismatches: 33, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:8625 original size:18 final size:17
Alignment explanation
Indices: 8604--8728 Score: 117
Period size: 17 Copynumber: 6.9 Consensus size: 17
8594 CCGGACCCCC
*
8604 TTTTTGTTTTTGTTTGTT
1 TTTTTATTTTT-TTTGTT
*
8622 TTTTTATTGTTTTTGTT
1 TTTTTATTTTTTTTGTT
*
8639 TTTTTTTTTTCTTTTGTTT
1 TTTTTATTTT-TTTTG-TT
* *
8658 TTTTTGTTTTTTTTTTT
1 TTTTTATTTTTTTTGTT
8675 TTTCATTCATTTTTTTTGTT
1 TTT--TT-ATTTTTTTTGTT
8695 TTTTTCATTTTTTTTTGTT
1 TTTTT-A-TTTTTTTTGTT
8714 TTTGTT-TTTTTTTTG
1 TTT-TTATTTTTTTTG
8729 GAGGACGCCG
Statistics
Matches: 92, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
17 28 0.30
18 22 0.24
19 27 0.29
20 15 0.16
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTTATTTTTTTTGTT
Found at i:18437 original size:10 final size:10
Alignment explanation
Indices: 18422--18448 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18412 ATGTATCAAG
18422 CAAAAACAAA
1 CAAAAACAAA
18432 CAAAAACAAA
1 CAAAAACAAA
18442 CAAAAAC
1 CAAAAAC
18449 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:22672 original size:52 final size:51
Alignment explanation
Indices: 22587--22710 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
22577 ATATGAAAAG
* *
22587 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
22638 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
22690 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
22711 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:22723 original size:51 final size:51
Alignment explanation
Indices: 22587--22730 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
22577 ATATGAAAAG
*
22587 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
22639 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
22690 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
22731 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:22737 original size:13 final size:13
Alignment explanation
Indices: 22719--22743 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22709 CAAAGATCAG
22719 TGTATCGATACAA
1 TGTATCGATACAA
22732 TGTATCGATACA
1 TGTATCGATACA
22744 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:22821 original size:33 final size:33
Alignment explanation
Indices: 22784--22850 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22774 AGTAGCTTAA
22784 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
22817 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
22850 A
1 A
22851 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:22824 original size:13 final size:13
Alignment explanation
Indices: 22806--22830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22796 CAAAAAAATA
22806 TGTATCGATACAT
1 TGTATCGATACAT
22819 TGTATCGATACA
1 TGTATCGATACA
22831 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:27951 original size:19 final size:20
Alignment explanation
Indices: 27903--27963 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
27893 GGGCAAAAAA
* *
27903 AACCCAGAATGTATCGATAA
1 AACCTAGAATGTATCGATAC
*
27923 AATCCTAGAATGTATCAATAC
1 AA-CCTAGAATGTATCGATAC
27944 AA-CTAGAATGTATCGATAC
1 AACCTAGAATGTATCGATAC
27963 A
1 A
27964 GTTACTTGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.47
20 2 0.06
21 17 0.47
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (20 bp):
AACCTAGAATGTATCGATAC
Done.