Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1785
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: 17437
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Found at i:3978 original size:1 final size:1
Alignment explanation
Indices: 3967--4118 Score: 70
Period size: 1 Copynumber: 152.0 Consensus size: 1
3957 GGCGTCCTCC
* ** ** ** ** ** **
3967 AAAACAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAACGAAAAAATGAAAACCA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** ** * ** * *
4032 AAAAAAAAACAAAAATGAAAACCAAAAAAAAAAACAAAAAAAGCAAAAAAAAAAAACAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
4097 ATAAAAAAACAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
4119 GGGGGTCCGG
Statistics
Matches: 111, Mismatches: 40, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 111 1.00
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.03
Consensus pattern (1 bp):
A
Found at i:3992 original size:22 final size:21
Alignment explanation
Indices: 3967--4118 Score: 110
Period size: 21 Copynumber: 6.8 Consensus size: 21
3957 GGCGTCCTCC
* *
3967 AAAACAAAAAAAAAAAACGAA
1 AAAAAAAAAAAAAAAAACCAA
3988 AAAAATGAAAAACCAAAAAAA--AA
1 AAAAA--AAAAA--AAAAAAACCAA
* **
4011 AAAACGAAAAAATGAAAACCAA
1 AAAA-AAAAAAAAAAAAACCAA
4033 AAAAAAAACAAAAATGAAAACCAA
1 AAAAAAAA-AAAAA--AAAACCAA
* *
4057 AAAAAAAAACAAAAAAAGCAA
1 AAAAAAAAAAAAAAAAACCAA
* *
4078 AAAAAAAAAACAAAAAACAATA
1 AAAAAAAAAAAAAAAAACCA-A
4100 AAAAAACAAACAAAAAAAA
1 AAAAAA-AAA-AAAAAAAA
4119 GGGGGTCCGG
Statistics
Matches: 104, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
20 5 0.05
21 30 0.29
22 21 0.20
23 18 0.17
24 23 0.22
25 7 0.07
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAACCAA
Found at i:4007 original size:30 final size:28
Alignment explanation
Indices: 3967--4118 Score: 149
Period size: 29 Copynumber: 5.5 Consensus size: 28
3957 GGCGTCCTCC
3967 AAAACAAAAAAAAAAAACGAAAAAAATGA
1 AAAACAAAAAAAAAAAAC-AAAAAAATGA
*
3996 AAAACCAAAAAAAAAAAAACGAAAAAATG-
1 AAAA-C-AAAAAAAAAAAACAAAAAAATGA
*
4025 AAAAC-CAAAAAAAAAAC--AAAAATG-
1 AAAACAAAAAAAAAAAACAAAAAAATGA
*
4049 AAAACCAAAAAAAAAAACAAAAAAA-GCA
1 AAAACAAAAAAAAAAAACAAAAAAATG-A
*
4077 AAAAAAAAAAACAAAAAACAATAAAAA--A
1 AAAACAAAAAA-AAAAAACAA-AAAAATGA
4105 ACAAACAAAAAAAA
1 A-AAACAAAAAAAA
4119 GGGGGTCCGG
Statistics
Matches: 107, Mismatches: 6, Indels: 21
0.80 0.04 0.16
Matches are distributed among these distances:
24 12 0.11
25 11 0.10
26 12 0.11
27 5 0.05
28 14 0.13
29 26 0.24
30 14 0.13
31 13 0.12
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.03
Consensus pattern (28 bp):
AAAACAAAAAAAAAAAACAAAAAAATGA
Found at i:4010 original size:31 final size:30
Alignment explanation
Indices: 3972--4118 Score: 135
Period size: 30 Copynumber: 5.2 Consensus size: 30
3962 CCTCCAAAAC
3972 AAAAAAAAAAAACGAAAAAAATGAAAAACCA
1 AAAAAAAAAAAAC-AAAAAAATGAAAAACCA
*
4003 AAAAAAAAAAAACGAAAAAATG-AAAACC-
1 AAAAAAAAAAAACAAAAAAATGAAAAACCA
4031 --AAAAAAAAAAC--AAAAATG-AAAACC-
1 AAAAAAAAAAAACAAAAAAATGAAAAACCA
4055 -AAAAAAAAAAACAAAAAAA-GCAAAAA--A
1 AAAAAAAAAAAACAAAAAAATG-AAAAACCA
4082 AAAAAACAAAAAACAATAAAAA--AACAAA-CA
1 AAAAAA-AAAAAACAA-AAAAATGAA-AAACCA
4112 AAAAAAA
1 AAAAAAA
4119 GGGGGTCCGG
Statistics
Matches: 104, Mismatches: 1, Indels: 24
0.81 0.01 0.19
Matches are distributed among these distances:
24 13 0.12
25 11 0.11
26 12 0.12
27 5 0.05
28 11 0.11
29 19 0.18
30 20 0.19
31 13 0.12
ACGTcount: A:0.83, C:0.10, G:0.04, T:0.03
Consensus pattern (30 bp):
AAAAAAAAAAAACAAAAAAATGAAAAACCA
Found at i:4014 original size:25 final size:24
Alignment explanation
Indices: 4007--4093 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
3997 AAACCAAAAA
**
4007 AAAAAAAACGAAAAAATGAAAACC
1 AAAAAAAAAAAAAAAATGAAAACC
*
4031 AAAAAAAAAACAAAAATGAAAACC
1 AAAAAAAAAAAAAAAATGAAAACC
* * *
4055 AAAAAAAAAAACAAAA--AAAGCA
1 AAAAAAAAAAAAAAAATGAAAACC
4077 AAAAAAAAAAACAAAAA
1 AAAAAAAAAAA-AAAAA
4094 ACAATAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 15 0.28
23 4 0.07
24 35 0.65
ACGTcount: A:0.83, C:0.10, G:0.05, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAATGAAAACC
Found at i:4022 original size:24 final size:23
Alignment explanation
Indices: 3995--4117 Score: 96
Period size: 22 Copynumber: 5.2 Consensus size: 23
3985 GAAAAAAATG
3995 AAAAACCAAAAAAAAAAAAACGAAAAA
1 AAAAACCAAAAAAAAAAAAAC----AA
4022 ATGAAAACCAAAAAAAAAACAAA-AA
1 A--AAAACCAAAAAAAAAA-AAACAA
*
4047 TGAAAACC--AAAAAAAAAAACAA
1 -AAAAACCAAAAAAAAAAAAACAA
*
4069 AAAAAGC-AAAAAAAAAAAAC-A
1 AAAAACCAAAAAAAAAAAAACAA
*
4090 AAAAA-CAATAAAAAAACAAACAA
1 AAAAACCAA-AAAAAAAAAAACAA
4113 AAAAA
1 AAAAA
4118 AGGGGGTCCG
Statistics
Matches: 83, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.01
21 15 0.18
22 33 0.40
23 6 0.07
24 6 0.07
25 2 0.02
27 1 0.01
29 16 0.19
30 3 0.04
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAACCAAAAAAAAAAAAACAA
Found at i:5613 original size:30 final size:29
Alignment explanation
Indices: 5558--5985 Score: 286
Period size: 30 Copynumber: 14.7 Consensus size: 29
5548 TCACCCTTCA
* *
5558 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
*
5587 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
**
5616 GAAAGCCCACAAGTCAGTGGCA-A-CCTTC
1 -AAAGCCCACAAGTCAGTGGCATATTTTTC
* ** *
5644 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TATTTTTC
* * * *
5674 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
* * * *
5703 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TATTTTTC
* * * * *
5733 TTTTGTAAGCTCACAACTCTA-TAGCACT-CTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TATTTTTC
* ***
5767 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
5794 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATATTTTTC
**
5824 AAAAGCCCACAAGTCAGTGGCA-ACCTTT-
1 -AAAGCCCACAAGTCAGTGGCATATTTTTC
* *** *
5852 AAAG-CCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
*
5880 AAAAGCCCACAAGTCAGTGGCATATTTTTA
1 -AAAGCCCACAAGTCAGTGGCATATTTTTC
** *
5910 AAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
**
5938 AAAGCCCACAAGTCAGTGGCA-A-CCTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
* *
5965 AAAGCCCATAAATCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
5986 CCCTTTTCCG
Statistics
Matches: 328, Mismatches: 51, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
26 16 0.05
27 68 0.21
28 30 0.09
29 81 0.25
30 111 0.34
34 5 0.02
35 17 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATATTTTTC
Found at i:5660 original size:57 final size:57
Alignment explanation
Indices: 5584--5958 Score: 253
Period size: 57 Copynumber: 6.4 Consensus size: 57
5574 TGGCATTTTT
*
5584 TTCAAAGCCCACAAGTCAGTGGCATTTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAGCCCACAAGTCAGTGGCATATTTTTCGAAAGCCCACAAGTCAGTGGCAACC
* ** * * * *
5641 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG-AAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TATTTTTCGAAAGCCCACAAGTCAGTGGCAAC-C
* * * * * * * *
5699 TTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTC
1 TT-CAAAGCCCACAAGTCAGTGGCA-TATTTTTC----GAAAGCCCACAAGTC-AGTGGCAAC-C
*** * *** * **
5762 TTTTCAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAGCCCACAAGTCAGTGGCATATTTTTCGAAAGCCCACAAGTCAGTGGCA-A-CC
** * *
5821 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTTT--AAAG-CCACAAGTTAGTGGCACCC
1 TTC-AAAGCCCACAAGTCAGTGGCATATTTTTCGAAAGCCCACAAGTCAGTGGCAACC
*
5875 TGTTCAAAAGCCCACAAGTCAGTGGCATATTTTT-AAAAGCCCACAAGTCAGTGGCAACC
1 --TTC-AAAGCCCACAAGTCAGTGGCATATTTTTCGAAAGCCCACAAGTCAGTGGCAACC
*
5934 TTTAAAAGCCCACAAGTCAGTGGCA
1 -TTCAAAGCCCACAAGTCAGTGGCA
5959 ACCTTCAAAG
Statistics
Matches: 249, Mismatches: 50, Indels: 38
0.74 0.15 0.11
Matches are distributed among these distances:
56 41 0.16
57 86 0.35
58 14 0.06
59 50 0.20
60 18 0.07
61 6 0.02
62 15 0.06
63 5 0.02
64 14 0.06
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCATATTTTTCGAAAGCCCACAAGTCAGTGGCAACC
Found at i:5873 original size:86 final size:87
Alignment explanation
Indices: 5767--6020 Score: 349
Period size: 86 Copynumber: 3.0 Consensus size: 87
5757 CACTCTTTTC
5767 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
5832 ACAAGTCAGTGGCAACCTTT-AA
65 ACAAGTCAGTGGCAACCTTTAAA
5854 AG-CCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTT-AAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCT-TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
5917 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
* * * * *** **
5940 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCATAAATCAGTGGCACCCTTTTCCGAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
* *
6003 CAAATCGGTGGC-ACCTTT
66 CAAGTCAGTGGCAACCTTT
6021 TCCATCTTTA
Statistics
Matches: 152, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
84 29 0.19
85 49 0.32
86 55 0.36
87 19 0.12
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (87 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
CAAGTCAGTGGCAACCTTTAAA
Found at i:6000 original size:85 final size:85
Alignment explanation
Indices: 5767--6020 Score: 318
Period size: 85 Copynumber: 3.0 Consensus size: 85
5757 CACTCTTTTC
*
5767 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAAGCCCACAAGTCAGTGGCA-AATTTTCAAAAGCCC
5832 ACAAGTCAGTGGCAACCTTTAA
64 ACAAGTCAGTGGCAACCTTTAA
* *
5854 AG-CCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCT-TTCAAAAGCCCACAAGTCAGTGGCAAATTTTCAAAAGCCCA
5918 CAAGTCAGTGGCAACCTTTAAA
65 CAAGTCAGTGGCAACCTTT-AA
* * * * ** **
5940 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCATAAATCAGTGGCACCCTTTTCCGAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCA-AATTTTCAAAAGCCCA
* *
6003 CAAATCGGTGGC-ACCTTT
65 CAAGTCAGTGGCAACCTTT
6021 TCCATCTTTA
Statistics
Matches: 149, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
84 25 0.17
85 57 0.38
86 48 0.32
87 19 0.13
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (85 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCAAATTTTCAAAAGCCCAC
AAGTCAGTGGCAACCTTTAA
Found at i:6002 original size:30 final size:29
Alignment explanation
Indices: 5767--6023 Score: 127
Period size: 30 Copynumber: 8.9 Consensus size: 29
5757 CACTCTTTTC
* * **
5767 AGCCCACAAGTTAGTGGCACCCTTTTCAAA
1 AGCCCACAAATCAGTGGCA-CCTTTTCCGA
* ** **
5797 AGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAATCAGTGGCA-CCTTTTCCGA
* *
5827 AGCCCACAAGTCAGTGGCAACC-TTT--AA
1 AGCCCACAAATCAGTGGC-ACCTTTTCCGA
* * * **
5854 AG-CCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAATCAGTGGCA-CCTTTTCCGA
* ** ***
5883 AGCCCACAAGTCAGTGGCATATTTTTAAA
1 AGCCCACAAATCAGTGGCACCTTTTCCGA
* **
5912 AGCCCACAAGTCAGTGGCAACC-TTT-AAA
1 AGCCCACAAATCAGTGGC-ACCTTTTCCGA
* *
5940 AGCCCACAAGTCAGTGGCAACC--TT-CAA
1 AGCCCACAAATCAGTGGC-ACCTTTTCCGA
*
5967 AGCCCATAAATCAGTGGCACCCTTTTCCGA
1 AGCCCACAAATCAGTGGCA-CCTTTTCCGA
*
5997 AGCCCACAAATCGGTGGCACCTTTTCC
1 AGCCCACAAATCAGTGGCACCTTTTCC
6024 ATCTTTAAGT
Statistics
Matches: 195, Mismatches: 21, Indels: 23
0.82 0.09 0.10
Matches are distributed among these distances:
25 1 0.01
26 17 0.09
27 28 0.14
28 25 0.13
29 44 0.23
30 79 0.41
31 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (29 bp):
AGCCCACAAATCAGTGGCACCTTTTCCGA
Found at i:6094 original size:43 final size:43
Alignment explanation
Indices: 6026--6115 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
6016 CCTTTTCCAT
*
6026 CTTTAAGTCCAATGTAGTCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGTCGACCTTGAATCAGCACATTGGCAC
* *
6069 CTTTAAGTCCAATATAG-CTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGTC-GACCTTGAATCAGCACATTGGCAC
6112 CTTT
1 CTTT
6116 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGTCGACCTTGAATCAGCACATTGGCAC
Found at i:6147 original size:52 final size:55
Alignment explanation
Indices: 6069--6216 Score: 185
Period size: 52 Copynumber: 2.7 Consensus size: 55
6059 ACATTGGCAC
*
6069 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAG
* * * *
6121 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAG
* * * * *
6176 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
6217 GTCTTTATCA
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
52 38 0.48
53 2 0.03
54 5 0.06
55 34 0.43
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAG
Found at i:7071 original size:13 final size:13
Alignment explanation
Indices: 7053--7077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7043 CATAAAGTGT
7053 TGTATCGATACAA
1 TGTATCGATACAA
7066 TGTATCGATACA
1 TGTATCGATACA
7078 TATTTTTTTG
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:7075 original size:33 final size:33
Alignment explanation
Indices: 7033--7099 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7023 TTCAACGATT
7033 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
7066 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
7099 T
1 T
7100 TTAAGCTACT
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:7158 original size:13 final size:13
Alignment explanation
Indices: 7140--7164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7130 ATCACTTAAA
7140 TGTATCGATACAT
1 TGTATCGATACAT
7153 TGTATCGATACA
1 TGTATCGATACA
7165 CTGATCTTTG
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:7229 original size:52 final size:52
Alignment explanation
Indices: 7173--7301 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
7163 CACTGATCTT
*
7173 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
7225 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
7277 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
7302 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:10350 original size:256 final size:256
Alignment explanation
Indices: 9895--10406 Score: 988
Period size: 256 Copynumber: 2.0 Consensus size: 256
9885 GGATTTATTT
*
9895 TCAACACAATTCATACATTCAAAGGGGATCATATCAAAATAATAATAAATTGAAACCAATGCAAC
1 TCAACACAATTCATACATTCAAAGGGGATCATATCAAAATAATAATAAATCGAAACCAATGCAAC
9960 CAATATCGAGTCAAAACGTTGCTAGTAAGGTACCGATTTCGGGCGTCGCGAGGAGGTTCGTACCT
66 CAATATCGAGTCAAAACGTTGCTAGTAAGGTACCGATTTCGGGCGTCGCGAGGAGGTTCGTACCT
*
10025 CTTTGCGCGTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACGCAGACCACGGGATCG
131 CTTTGCGCGTAACCAACTCCCGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCG
10090 ATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCC
196 ATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCC
*
10151 TCAACACAATTCATACATTCAAAGGGGATCATATCAAAATAATGATAAATCGAAACCAATGCAAC
1 TCAACACAATTCATACATTCAAAGGGGATCATATCAAAATAATAATAAATCGAAACCAATGCAAC
*
10216 CAATATCGAGTCAAAACGTTGCTAGTAAGGTACCGATTTCGGGCGTCGTGAGGAGGTTCGTACCT
66 CAATATCGAGTCAAAACGTTGCTAGTAAGGTACCGATTTCGGGCGTCGCGAGGAGGTTCGTACCT
10281 CTTTGCGCGTAACCAACTCCCGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCG
131 CTTTGCGCGTAACCAACTCCCGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCG
10346 ATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCC
196 ATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCC
10407 GAAATGATCG
Statistics
Matches: 252, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
256 252 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (256 bp):
TCAACACAATTCATACATTCAAAGGGGATCATATCAAAATAATAATAAATCGAAACCAATGCAAC
CAATATCGAGTCAAAACGTTGCTAGTAAGGTACCGATTTCGGGCGTCGCGAGGAGGTTCGTACCT
CTTTGCGCGTAACCAACTCCCGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCG
ATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCC
Found at i:11701 original size:10 final size:10
Alignment explanation
Indices: 11686--11712 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11676 TGCTAACTAA
11686 GTTTTTGTTT
1 GTTTTTGTTT
11696 GTTTTTGTTT
1 GTTTTTGTTT
11706 GTTTTTG
1 GTTTTTG
11713 CTTGATACAT
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:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.