Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1319
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: 52798
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6768 original size:20 final size:19
Alignment explanation
Indices: 6739--6813 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
6729 AAAAAGACAT
6739 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
6758 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
6779 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
6799 AATGTATCGATACAT
1 AATGTATCGATACAT
6814 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:6796 original size:40 final size:39
Alignment explanation
Indices: 6736--6813 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
6726 GGTAAAAAGA
*
6736 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
6775 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
6814 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:7326 original size:22 final size:22
Alignment explanation
Indices: 7301--7346 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
7291 GTTGATTCAA
7301 TGCTAGTGATGTCAGACAGTGG
1 TGCTAGTGATGTCAGACAGTGG
7323 TGCTAGTGATGTCAGACAGTGG
1 TGCTAGTGATGTCAGACAGTGG
7345 TG
1 TG
7347 ATTTGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (22 bp):
TGCTAGTGATGTCAGACAGTGG
Found at i:7594 original size:29 final size:29
Alignment explanation
Indices: 7434--8512 Score: 1236
Period size: 29 Copynumber: 37.0 Consensus size: 29
7424 CGAAAAAAGT
* * *
7434 TGCCACTGACAGTGTGGGCTTTGAAAAGAG
1 TGCCACTGAC-TTGTGGGCTTTGAAAGGGG
** *
7464 TGTTACTGACTTGCGTGGGCTTT-AAAAGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGGG
* **
7494 TACCACTGACTTGCGTGGGCTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGGG
* * *
7524 TGCCACTGACTCGTGAGCTTTGAAA-GGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* *
7552 TGCCACTGACTTGTGAGCTTCGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* *
7581 TGCCACT-ATCTTGTGGGCTTTGAAAAGAG
1 TGCCACTGA-CTTGTGGGCTTTGAAAGGGG
7610 TGCCACTGACTTGCGTGGGCTTTGAAAGGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGGG
*
7641 TGCCACTAACTTGTGGGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
7670 TGCCACTGACTTGTGGGCTTTGAAA-GGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* * *
7698 TGCCATTGACTTGTGGGCTTTGAAAAGAGT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGG
* * **
7728 TGCCACCGACTCGTGTGGGCTTTGAAAAGAA
1 TGCCACTGACT--TGTGGGCTTTGAAAGGGG
* * *
7759 TGCCACTGACTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
7788 TGCCACTGACTTGTGAGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* * *
7817 TGCCACTGTCTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
**
7846 TGCCACTGACTTGTGGGCTTT-AAAATGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
7874 TGCCACTGACTTGCGTGGGCTTTGAAAGGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGGG
* *
7905 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
7934 TGCCACTGACTTGTGGGCTTT-AAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
7962 TGCCACTAACTTGTGGGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* * *
7991 TGCCACTGTCTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* *
8020 TGCCACTAACTTGTGGGCTTT-AAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
8048 TGCCACTGACTTGCGTGGGCTTTGAAAGGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGGG
8079 TGCCACTGACTTGTGGGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
8108 TGCCACTGACTTGTGGGCTTTGAAA-GGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* * *
8136 TGCCACTGACTTATGGGCTTTGAAAAGAGT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGG
* * * *
8166 TGCCACCGACTCGTATGGGCTTTGAAAAGAG
1 TGCCACTGACT--TGTGGGCTTTGAAAGGGG
8197 TGCCACTGACTTGTGGGCTTTGAAA-GGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
8225 TGCCACTGACTTGTGGGCTTTGAAAGAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* * *
8254 TGCCACTGTCTTGTGGGCTCTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
8282 TGCCACTGACTTGTGGGCTTTGAAA-GGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
* **
8310 TGCCACTAACTTGTGGGCTTTGAAA-AAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
**
8338 TGCCACTGACTTGTGGGC-TTGAAA-AAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
*
8365 TGCCACTGACTTGCGTGGGCTTTGAAAAGAGG
1 TGCCACTGACTT--GTGGGCTTTG-AAAGGGG
** ***
8397 TGCCACCAACTCGTGTGGGCTTTGAAAAAAG
1 TGCCACTGACT--TGTGGGCTTTGAAAGGGG
8428 TGCCACTGACTTGTGGGCTTTGAAA-GGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
8456 TGCCACTGACTTGTGGGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGG
**
8485 TGCCACTGACTTGTGAACTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
8513 TTTGAACGTT
Statistics
Matches: 920, Mismatches: 97, Indels: 65
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.02
28 267 0.29
29 384 0.42
30 88 0.10
31 116 0.13
32 43 0.05
34 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGGG
Found at i:7710 original size:146 final size:144
Alignment explanation
Indices: 7446--8513 Score: 1282
Period size: 146 Copynumber: 7.3 Consensus size: 144
7436 CCACTGACAG
** *
7446 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTT-AAAAGGGTACCACTGACTTGCGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGGGTGCCACTGACTT--GT
** * * * * *
7510 GGGCTTTGAAA-GAATGCCACTGACTCGTGAGCTTTGAAAGGATGCCACTGACTTGTGAGCTTCG
62 GGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
7574 AAAGGGGTGCCACTATCT
127 AAAGGGGTGCCACTATCT
* *
7592 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
*
7657 GCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAA
64 GCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-A
* * * *
7722 AAGAGTTGCCACCGACTCG
128 AAGGGGTGCCA-CTA-TCT
* * * *
7741 TGTGGGCTTTGAAAAGAATGCCACTGACTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGAGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC
* *
7806 TTTGAAAGGGGTGCCACTGTCTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT-AAA
66 TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
**
7870 ATGGTGCCACTGA-CT
130 GGGGTGCCACT-ATCT
* * *
7885 TGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
* * *
7950 GCTTT-AAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGTCTTGTGGGCTTTGA
64 GCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGA
* * *
8014 AAAGAGTGCCACTAACT
128 AAGGGGTGCCACTATCT
* *
8031 TGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
*
8095 GCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAA
64 GCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-A
* * * *
8160 AAGAGTTGCCACCGACTCG
128 AAGGGGTGCCA-CTA-TCT
*
8179 TATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC
* * * *
8243 TTTGAAAGAGGTGCCACTGTCTTGTGGGCTCTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAA-
66 TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
* *
8307 GGATGCCACTAACT
131 GGGTGCCACTATCT
*
8321 TGTGGGCTTTGAAAA-AGTGCCACTGACTTGTGGGC-TTGAAAA-AGTGCCACTGACTTGCGTGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGG
* ** **
8383 GCTTTGAAAAGAGGTGCCACCAACTCGTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTT
64 GCTTTG-AAAGGGGTGCCACTGACT--TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
8448 TGAAA-GGGTGCCACTGA-CT
125 TGAAAGGGGTGCCACT-ATCT
* * **
8467 TGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGAACTTTG-AAAGGGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGT
8514 TTGAACGTTC
Statistics
Matches: 809, Mismatches: 83, Indels: 58
0.85 0.09 0.06
Matches are distributed among these distances:
140 16 0.02
141 23 0.03
142 25 0.03
143 35 0.04
144 20 0.02
145 135 0.17
146 343 0.42
147 121 0.15
148 42 0.05
149 49 0.06
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (144 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
GGGTGCCACTATCT
Found at i:9766 original size:10 final size:10
Alignment explanation
Indices: 9731--9793 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 10
9721 CCCTTTTCTC
9731 TTTTTTTGCTAT
1 TTTTTTTG-T-T
9743 TTTTTCTTGGTTT
1 TTTTT-TT-G-TT
*
9756 TTTTGTTTTTT
1 TTTT-TTTGTT
9767 TTTGTTTTGTT
1 TTT-TTTTGTT
9778 TTTTTTTGTT
1 TTTTTTTGTT
9788 TTTTTT
1 TTTTTT
9794 GTGTAAAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 13 0.30
11 13 0.30
12 6 0.14
13 9 0.20
14 3 0.07
ACGTcount: A:0.02, C:0.03, G:0.11, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:9776 original size:15 final size:15
Alignment explanation
Indices: 9756--9793 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
9746 TTCTTGGTTT
9756 TTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTG
9771 TTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTG
9786 TTTT-TTTT
1 TTTTGTTTT
9794 GTGTAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTGTTTTTTTTTG
Found at i:23654 original size:20 final size:19
Alignment explanation
Indices: 23625--23699 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
23615 AAAAAGACAT
23625 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
23644 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
23665 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
23685 AATGTATCGATACAT
1 AATGTATCGATACAT
23700 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:23682 original size:40 final size:39
Alignment explanation
Indices: 23622--23699 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
23612 GGTAAAAAGA
*
23622 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
23661 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
23700 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:25099 original size:40 final size:40
Alignment explanation
Indices: 25054--25141 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
25044 CATGCCGGGA
25054 CTGGATGCTGATATAGTGGTTCATAAGCTTCCCATCAAGC
1 CTGGATGCTGATATAGTGGTTCATAAGCTTCCCATCAAGC
*
25094 TTGGATGCTGATATAGTGGTTCATAAGCTTCCCATCAAGC
1 CTGGATGCTGATATAGTGGTTCATAAGCTTCCCATCAAGC
25134 CTGGATGC
1 CTGGATGC
25142 AAACCAATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (40 bp):
CTGGATGCTGATATAGTGGTTCATAAGCTTCCCATCAAGC
Found at i:27884 original size:8 final size:8
Alignment explanation
Indices: 27871--27943 Score: 62
Period size: 8 Copynumber: 9.2 Consensus size: 8
27861 TCCTCGGCAA
27871 AAAAAAAC
1 AAAAAAAC
27879 AAAAAAAC
1 AAAAAAAC
27887 AAACAAAA-
1 AAA-AAAAC
27895 AAAGAAAA-
1 AAA-AAAAC
*
27903 AAAACAA-
1 AAAAAAAC
*
27910 AACAAAAC
1 AAAAAAAC
*
27918 AAAAAAAT
1 AAAAAAAC
* *
27926 AGACAAAC
1 AAAAAAAC
27934 AAAAAAAC
1 AAAAAAAC
27942 AA
1 AA
27944 CAACAAAAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
7 8 0.15
8 40 0.77
9 4 0.08
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:27890 original size:12 final size:12
Alignment explanation
Indices: 27869--27952 Score: 67
Period size: 11 Copynumber: 7.5 Consensus size: 12
27859 CGTCCTCGGC
27869 AAAAAA-AAACA
1 AAAAAACAAACA
27880 AAAAAACAAAC-
1 AAAAAACAAACA
*
27891 AAAAAA-AGA-A
1 AAAAAACAAACA
27901 AAAAAAC-AA-A
1 AAAAAACAAACA
*
27911 ACAAAACAAA-A
1 AAAAAACAAACA
*
27922 AAATAGACAAACA
1 AAA-AAACAAACA
27935 AAAAAAC-AACA
1 AAAAAACAAACA
27946 ACAAAAA
1 A-AAAAA
27953 GGGTCTGGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 16 0.27
11 22 0.37
12 18 0.30
13 4 0.07
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.01
Consensus pattern (12 bp):
AAAAAACAAACA
Found at i:27894 original size:21 final size:20
Alignment explanation
Indices: 27870--27940 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 20
27860 GTCCTCGGCA
27870 AAAAAAAACAAAAAAACAAAC
1 AAAAAAAA-AAAAAAACAAAC
27891 AAAAAAAGAAAAAAAACAAAAC
1 AAAAAAA-AAAAAAAAC-AAAC
* *
27913 AAAACAAAAAAATAGACAAAC
1 AAAA-AAAAAAAAAAACAAAC
27934 AAAAAAA
1 AAAAAAA
27941 CAACAACAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.07
21 23 0.51
22 16 0.36
23 3 0.07
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAAAAAAACAAAC
Found at i:27902 original size:27 final size:27
Alignment explanation
Indices: 27872--27953 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
27862 CCTCGGCAAA
27872 AAAAAACAAAAAAACAAACAAAAAAAG
1 AAAAAACAAAAAAACAAACAAAAAAAG
* *
27899 AAAAAA-AACAAAACAAAACAAAAAAAT
1 AAAAAACAAAAAAAC-AAACAAAAAAAG
*
27926 AGACAAACAAAAAAAC-AACAACAAAAAG
1 A-AAAAACAAAAAAACAAACAA-AAAAAG
27954 GGTCTGGATG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.15
27 23 0.50
28 9 0.20
29 7 0.15
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (27 bp):
AAAAAACAAAAAAACAAACAAAAAAAG
Found at i:27911 original size:39 final size:40
Alignment explanation
Indices: 27868--27952 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 40
27858 GCGTCCTCGG
27868 CAAAAAAAAACAAAAAAACAAACAAA-AAAAGAAA-AAAAA
1 CAAAAAAAAACAAAAAAACAAACAAACAAAA-AAACAAAAA
* * * *
27907 CAAAACAAAACAAAAAAATAGACAAACAAAAAAACAACAA
1 CAAAAAAAAACAAAAAAACAAACAAACAAAAAAACAAAAA
27947 CAAAAA
1 CAAAAA
27953 GGGTCTGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 26 0.67
40 13 0.33
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.01
Consensus pattern (40 bp):
CAAAAAAAAACAAAAAAACAAACAAACAAAAAAACAAAAA
Found at i:29423 original size:30 final size:28
Alignment explanation
Indices: 29379--29611 Score: 312
Period size: 28 Copynumber: 8.2 Consensus size: 28
29369 GACATTCTTT
29379 ACCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
29407 ATCCTTTTCAAAAGCCCACAAGTCAGTGGC
1 A-CCTTTTC-AAAGCCCACAAGTCAGTGGC
*
29437 ATCCTTTTCAAAAGCCCACAAGTCAGTAGC
1 A-CCTTTTC-AAAGCCCACAAGTCAGTGGC
29467 AACC--TTCAGAAGCCCACAAGTCAGTGGC
1 -ACCTTTTCA-AAGCCCACAAGTCAGTGGC
29495 ACCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
29523 ACTTTTTCAAAGCCCACAAGTCAGTGAC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
*
29551 ACCTTTTCAAAGCCCACAAGTCAATGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
29579 AACC--TTCAAAGCCCATAAGACAGTGGC
1 -ACCTTTTCAAAGCCCACAAGTCAGTGGC
29606 AACCTT
1 -ACCTT
29612 CAAAAGCACA
Statistics
Matches: 186, Mismatches: 10, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
27 28 0.15
28 92 0.49
29 14 0.08
30 51 0.27
31 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (28 bp):
ACCTTTTCAAAGCCCACAAGTCAGTGGC
Found at i:29837 original size:52 final size:49
Alignment explanation
Indices: 29674--29994 Score: 280
Period size: 49 Copynumber: 6.6 Consensus size: 49
29664 CATCTTCTAC
29674 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
29717 TAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
29766 TAAGTCCACTATGGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T--TCATCTT
** *
29818 TAAAACCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * * *
29867 TAAGTCCGATATTGTTGGCCTTCAATCAGCATATTGGCATCTTTAATATTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTCAT-CTT
* * ** * *
29918 CTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTT
1 -TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
29966 CAAGTCTAAATGTCGCTGGCCATGAATCA
1 TAAGTC-CAATATCGCTGGCCTTGAATCA
29995 ACACATTGTC
Statistics
Matches: 221, Mismatches: 44, Indels: 21
0.77 0.15 0.07
Matches are distributed among these distances:
43 35 0.16
47 5 0.02
48 20 0.09
49 80 0.36
50 6 0.03
51 3 0.01
52 72 0.33
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:29928 original size:101 final size:100
Alignment explanation
Indices: 29732--29954 Score: 270
Period size: 101 Copynumber: 2.2 Consensus size: 100
29722 CCAATGTTGT
* *
29732 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCACTATGGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCACTATGGCTGGCCTTCAATCAGCA
* *
29797 TATTGGCGCCTTCGTCATCTTTAAAACCAATATCGC
66 TATTGGCACCTTC-TAATCTTTAAAACCAATATCGC
* * *
29833 TGGCCTTGAATCAGCATATTGACACCTTCATCTTTAAGTCCGA-TATTGTTGGCCTTCAATCAGC
1 TGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCC-ACTATGGCTGGCCTTCAATCAGC
* * ** *
29897 ATATTGGCATCTT-TAATATTTCTAAGCCCAATGTCGC
65 ATATTGGCACCTTCTAAT-CTT-TAAAACCAATATCGC
**
29934 TGGCCTTGTCTCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
29955 GCATTCTTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
99 3 0.03
100 2 0.02
101 98 0.94
102 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (100 bp):
TGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCACTATGGCTGGCCTTCAATCAGCA
TATTGGCACCTTCTAATCTTTAAAACCAATATCGC
Found at i:34537 original size:9 final size:9
Alignment explanation
Indices: 34523--34552 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
34513 ATATCTTATT
34523 TTATATTTA
1 TTATATTTA
34532 TTATATTTA
1 TTATATTTA
34541 TTATATTTA
1 TTATATTTA
34550 TTA
1 TTA
34553 AATATATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:35017 original size:34 final size:34
Alignment explanation
Indices: 34967--35059 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
34957 TCTTACATTC
*
34967 TAAAAAA-TAATATAATAAATATGGTATATCTAA
1 TAAAAAATTAATATAATAAATATGATATATCTAA
* * * * *
35000 TAAAAAATTAATGTAATAAGTATCATATTTTTAA
1 TAAAAAATTAATATAATAAATATGATATATCTAA
*
35034 TAAAAAAATTAGTATAATAAATATGA
1 T-AAAAAATTAATATAATAAATATGA
35060 CACAATATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 7 0.15
34 21 0.44
35 20 0.42
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (34 bp):
TAAAAAATTAATATAATAAATATGATATATCTAA
Found at i:36933 original size:21 final size:22
Alignment explanation
Indices: 36890--36931 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
36880 ATAAATAGTA
36890 AAAAAATTTATAATAGTAATTT
1 AAAAAATTTATAATAGTAATTT
*
36912 AAAAATTTTATAA-A-TAATTT
1 AAAAAATTTATAATAGTAATTT
36932 TATTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAATTTATAATAGTAATTT
Found at i:39061 original size:11 final size:12
Alignment explanation
Indices: 39042--39080 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
39032 CACTTTAAAC
39042 ATAT-AAAAATA
1 ATATGAAAAATA
*
39053 ATATGAAAACAAA
1 ATATGAAAA-ATA
39066 ATATGAAAAATA
1 ATATGAAAAATA
39078 ATA
1 ATA
39081 CAAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (12 bp):
ATATGAAAAATA
Found at i:40107 original size:17 final size:16
Alignment explanation
Indices: 40087--40123 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
40077 TTAATCGTAT
*
40087 TTATATTATTTTTTATA
1 TTATATTATATTTTA-A
40104 TTATATTATATTTTAA
1 TTATATTATATTTTAA
40120 TTAT
1 TTAT
40124 TTTCTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:43116 original size:20 final size:21
Alignment explanation
Indices: 43065--43116 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
43055 ACTATTGATC
* *
43065 ATTGATTTTGGTCGATTGACT
1 ATTGATTTTGATCGACTGACT
*
43086 -TTGATCGTTGATCG-CTGACT
1 ATTGAT-TTTGATCGACTGACT
43106 ATTGATTTTGA
1 ATTGATTTTGA
43117 CTTCGAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (21 bp):
ATTGATTTTGATCGACTGACT
Found at i:46444 original size:88 final size:88
Alignment explanation
Indices: 46295--46472 Score: 338
Period size: 88 Copynumber: 2.0 Consensus size: 88
46285 TCTATAGGCT
* *
46295 TAAACAAGCGTCTCATCAATGGTATTACAAATTTCACAAAGTTATTGCCTCATTCAATTTTGAGA
1 TAAACAAGCGTCTCATCAATAGTATTACAAATTTCACAAAGTTATTGCCCCATTCAATTTTGAGA
46360 TGAATCTGGTTGAGGATTGTATA
66 TGAATCTGGTTGAGGATTGTATA
46383 TAAACAAGCGTCTCATCAATAGTATTACAAATTTCACAAAGTTATTGCCCCATTCAATTTTGAGA
1 TAAACAAGCGTCTCATCAATAGTATTACAAATTTCACAAAGTTATTGCCCCATTCAATTTTGAGA
46448 TGAATCTGGTTGAGGATTGTATA
66 TGAATCTGGTTGAGGATTGTATA
46471 TA
1 TA
46473 CCACAAGTTC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (88 bp):
TAAACAAGCGTCTCATCAATAGTATTACAAATTTCACAAAGTTATTGCCCCATTCAATTTTGAGA
TGAATCTGGTTGAGGATTGTATA
Found at i:47425 original size:28 final size:27
Alignment explanation
Indices: 47394--47463 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
47384 GAGTTTATAA
47394 TTTTAGATTTTTTTTG-TTATAGATACAT
1 TTTTAGATTTTTTTTGTTTATAGAT--AT
* *
47422 TTTTA-ATTATTTTAGTTTATAGATAT
1 TTTTAGATTTTTTTTGTTTATAGATAT
*
47448 TTTAAGATTATTTTTT
1 TTTTAGATT-TTTTTT
47464 TGCAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 6 0.18
27 11 0.32
28 17 0.50
ACGTcount: A:0.27, C:0.01, G:0.09, T:0.63
Consensus pattern (27 bp):
TTTTAGATTTTTTTTGTTTATAGATAT
Found at i:49373 original size:13 final size:13
Alignment explanation
Indices: 49355--49379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49345 CATAAAGTGT
49355 TGTATCGATATAA
1 TGTATCGATATAA
49368 TGTATCGATATA
1 TGTATCGATATA
49380 TAAGTATTGT
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:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:49395 original size:32 final size:32
Alignment explanation
Indices: 49335--49431 Score: 149
Period size: 32 Copynumber: 3.0 Consensus size: 32
49325 TTCAACGATT
* *
49335 TGTATCGATACATAAAGTGTTGTATCGATATAA
1 TGTATCGATACAT-AAGTATTGTATCGATACAA
*
49368 TGTATCGATATATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
49400 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
49432 AGTAGGCTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 47 0.80
33 12 0.20
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:49405 original size:13 final size:13
Alignment explanation
Indices: 49387--49411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49377 ATATAAGTAT
49387 TGTATCGATACAA
1 TGTATCGATACAA
49400 TGTATCGATACA
1 TGTATCGATACA
49412 TAAGTTTTGT
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:49424 original size:19 final size:18
Alignment explanation
Indices: 49333--49434 Score: 82
Period size: 19 Copynumber: 6.1 Consensus size: 18
49323 ATTTCAACGA
49333 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
49352 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
*
49368 --TGTATCGATATATAAG
1 TTTGTATCGATACATAAG
49384 TATTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
49400 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
49416 TTTTGTATCGATACA-AAG
1 -TTTGTATCGATACATAAG
49434 T
1 T
49435 AGGCTACTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 28
0.70 0.01 0.29
Matches are distributed among these distances:
13 20 0.29
15 6 0.09
17 5 0.07
18 5 0.07
19 23 0.33
20 10 0.14
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:49491 original size:13 final size:13
Alignment explanation
Indices: 49473--49497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49463 ATTACTCAAA
49473 TGTATCGATACAT
1 TGTATCGATACAT
49486 TGTATCGATACA
1 TGTATCGATACA
49498 CTGATTTTTG
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:49548 original size:52 final size:52
Alignment explanation
Indices: 49506--49634 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
49496 CACTGATTTT
* * *
49506 TGTATCGATACATGCAAGTAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
49558 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
49610 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
49635 TTATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:51786 original size:24 final size:26
Alignment explanation
Indices: 51759--51809 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
51749 CAAAAAATTT
51759 ATTCAT-C-GGAGACACTCCAACCCC
1 ATTCATCCAGGAGACACTCCAACCCC
* *
51783 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGAGACACTCCAACCCC
51810 GTTTTCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 1 0.05
27 16 0.73
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.18
Consensus pattern (26 bp):
ATTCATCCAGGAGACACTCCAACCCC
Done.