Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2873
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: 21328
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:7190 original size:17 final size:17
Alignment explanation
Indices: 7164--7324 Score: 137
Period size: 17 Copynumber: 9.2 Consensus size: 17
7154 ACGAGATTTT
7164 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
7182 TTTTCAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
* **
7199 TTTTTGAAAACAAGAGGA
1 TTTTT-AAAACACGAAAA
* *
7217 TTTTTGAAATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
7235 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
7252 TTTTTGAAACACGGAAA
1 TTTTTAAAACACGAAAA
*
7269 TTTTTGAAA-ACGAAAA
1 TTTTTAAAACACGAAAA
* *
7285 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
*
7302 TTTTTAGAAGACACTAAAA
1 TTTTTA-AA-ACACGAAAA
7321 TTTT
1 TTTT
7325 GGAAAATGGA
Statistics
Matches: 116, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
16 15 0.13
17 57 0.49
18 32 0.28
19 12 0.10
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:7203 original size:35 final size:35
Alignment explanation
Indices: 7164--7329 Score: 176
Period size: 35 Copynumber: 4.8 Consensus size: 35
7154 ACGAGATTTT
**
7164 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
7199 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
7234 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
**
7269 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * *
7302 TTTTTAGAAGACACTAAAATTTTGGAAA
1 TTTTT-GAAAACACGAAAATTTTTGAAA
7330 ATGGATTTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
33 27 0.25
34 6 0.06
35 60 0.56
36 15 0.14
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:7325 original size:51 final size:51
Alignment explanation
Indices: 7165--7330 Score: 142
Period size: 53 Copynumber: 3.2 Consensus size: 51
7155 CGAGATTTTT
* ** * * *
7165 TTTTGAAAAC-ACGAAAATTTTCAAAACACCGAAATTTTTGAAA-ACAAGAGGAT
1 TTTTGAAAACGA--AAAATTTTGAAAACACAAAAATTTTTGAAACAC-GGA-AAA
* *
7218 TTTTGAAATACGAAAAATTTTGAAAACACGAAAATTTTTGAAACACGGAAAT
1 TTTTGAAA-ACGAAAAATTTTGAAAACACAAAAATTTTTGAAACACGGAAAA
* *
7270 TTTTGAAAACGAAAATTTTTG-AAACACAAAAATTTTTAGAAGACAC-TAAAA
1 TTTTGAAAACGAAAAATTTTGAAAACACAAAAATTTTT-GAA-ACACGGAAAA
7321 TTTTGGAAAA
1 TTTT-GAAAA
7331 TGGATTTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
50 15 0.15
51 22 0.22
52 19 0.19
53 37 0.38
54 4 0.04
55 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (51 bp):
TTTTGAAAACGAAAAATTTTGAAAACACAAAAATTTTTGAAACACGGAAAA
Found at i:7530 original size:20 final size:18
Alignment explanation
Indices: 7498--7543 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
7488 CGAATATATT
7498 TTTTTGAAACACGAGAAAA
1 TTTTTGAAACACGA-AAAA
*
7517 TTTTTGAAGGCACGAAAAA
1 TTTTTGAA-ACACGAAAAA
7536 -TTTTGAAA
1 TTTTTGAAA
7544 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 12 0.50
20 5 0.21
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (18 bp):
TTTTTGAAACACGAAAAA
Found at i:7911 original size:8 final size:8
Alignment explanation
Indices: 7898--7951 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
7888 TTGAAACTCT
7898 TTTTTTTC
1 TTTTTTTC
7906 TTTTTTTC
1 TTTTTTTC
*
7914 -TTCTTTC
1 TTTTTTTC
7921 TTTTTTTC
1 TTTTTTTC
*
7929 -TTTCTTC
1 TTTTTTTC
*
7936 TTTTCTTC
1 TTTTTTTC
7944 TTTTTTTC
1 TTTTTTTC
7952 CTGGCCTGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 12 0.30
8 28 0.70
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:7922 original size:15 final size:14
Alignment explanation
Indices: 7900--7948 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 14
7890 GAAACTCTTT
7900 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
7914 TTCTTTCTTTTTTTC
1 TT-TTTCTTTTTTTC
*
7929 TTTCTTCTTTTCTTC
1 TTT-TTCTTTTTTTC
7944 TTTTT
1 TTTTT
7949 TTCCTGGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:7928 original size:23 final size:23
Alignment explanation
Indices: 7898--7951 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
7888 TTGAAACTCT
7898 TTTTTTTCTTT-TT-TTCTTCTTTC
1 TTTTTTTCTTTCTTCTT-TTC-TTC
7921 TTTTTTTCTTTCTTCTTTTCTTC
1 TTTTTTTCTTTCTTCTTTTCTTC
7944 TTTTTTTC
1 TTTTTTTC
7952 CTGGCCTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 22 0.76
24 5 0.17
25 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTCTTTCTTCTTTTCTTC
Found at i:7933 original size:27 final size:25
Alignment explanation
Indices: 7897--7950 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
7887 ATTGAAACTC
*
7897 TTTTTTTTCTTTTTTTCTTCTTTCTT
1 TTTTTTTTCTTCTTTTCTTCTTT-TT
7923 TTTTTCTTTCTTCTTTTCTTCTTTTT
1 TTTTT-TTTCTTCTTTTCTTCTTTTT
7949 TT
1 TT
7951 CCTGGCCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTTTTCTTCTTTTCTTCTTTTT
Found at i:8069 original size:15 final size:16
Alignment explanation
Indices: 8051--8090 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
8041 GGCTGTTTTT
8051 TTTTTTTTTTGGGC-C
1 TTTTTTTTTTGGGCGC
*
8066 TTTTCTTTTTGGGCTGC
1 TTTTTTTTTTGGGC-GC
8083 TTTTTTTT
1 TTTTTTTT
8091 GCTTTGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.00, C:0.12, G:0.17, T:0.70
Consensus pattern (16 bp):
TTTTTTTTTTGGGCGC
Found at i:8125 original size:29 final size:31
Alignment explanation
Indices: 8071--8136 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
8061 GGGCCTTTTC
* *
8071 TTTTTGGGCTGCTTTTTTTTGCTTTG-GTT-
1 TTTTTTGGCTGATTTTTTTTGCTTTGTGTTG
*
8100 TTTTTTGGCTGATTTGTTTTT-TTTTGTGTTG
1 TTTTTTGGCTGATTT-TTTTTGCTTTGTGTTG
8131 TTTTTT
1 TTTTTT
8137 TAATTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 17 0.55
30 8 0.26
31 6 0.19
ACGTcount: A:0.02, C:0.06, G:0.21, T:0.71
Consensus pattern (31 bp):
TTTTTTGGCTGATTTTTTTTGCTTTGTGTTG
Found at i:8257 original size:3 final size:3
Alignment explanation
Indices: 8251--8285 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
8241 TTTTTTTTCT
8251 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC T
8286 CCTCCTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:8262 original size:19 final size:19
Alignment explanation
Indices: 8238--8285 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
8228 TTAAATTTTT
*
8238 TTCTTT-TTTTTCTTTCTTC
1 TTCTTTCTTCTTC-TTCTTC
8257 TTCTTTCTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTCTTC
8276 TTC-TTCTTCT
1 TTCTTTCTTCT
8286 CCTCCTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTCTTTCTTCTTCTTCTTC
Found at i:8671 original size:29 final size:29
Alignment explanation
Indices: 8638--8754 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
8628 TGTAATTTTT
*
8638 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
8667 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
8697 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
8726 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
8755 TTTTTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:8693 original size:30 final size:30
Alignment explanation
Indices: 8653--8754 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
8643 ATTTAGGATT
*
8653 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
8683 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
8713 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
8743 AAAATGCAATTT
1 AAAATGAAATTT
8755 TTTTTTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:8821 original size:12 final size:12
Alignment explanation
Indices: 8806--8839 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
8796 ATTTTTCAAA
8806 TTTTTTTGTTTTT
1 TTTTTTTG-TTTT
8819 TTTTTTTGTTTT
1 TTTTTTTGTTTT
8831 TTTTTTTGT
1 TTTTTTTGT
8840 AAATTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:8824 original size:13 final size:13
Alignment explanation
Indices: 8806--8837 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
8796 ATTTTTCAAA
8806 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
8819 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
8832 TTTTTT
1 TTTTTT
8838 GTAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:8857 original size:61 final size:58
Alignment explanation
Indices: 8752--8894 Score: 171
Period size: 57 Copynumber: 2.4 Consensus size: 58
8742 CAAAATGCAA
*** *
8752 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTCAATTTTTATATTTTTCAAATTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTCAAAAATTATA----CCAAATTTTTTTG
* * * *
8814 TTTTTTTTTTTTGTTTTTTTTTTTG-TAAATTTTGAAAAATTATACCATATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTCAAAAATTATACCAAATTTTTTTG
8871 TTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
8895 TTTTTTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 33 0.46
61 15 0.21
62 24 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.78
Consensus pattern (58 bp):
TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTCAAAAATTATACCAAATTTTTTTG
Found at i:8867 original size:1 final size:1
Alignment explanation
Indices: 8863--8918 Score: 112
Period size: 1 Copynumber: 56.0 Consensus size: 1
8853 TTATACCATA
8863 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8919 AATCAAAACC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8895 original size:61 final size:59
Alignment explanation
Indices: 8752--8900 Score: 165
Period size: 63 Copynumber: 2.4 Consensus size: 59
8742 CAAAATGCAA
* **
8752 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTCAATTTTTATATTTTTCAAATTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTAAATTTCCATATTTTT---ATTTTTTTG
* * *
8814 TTTTTTTTTTTTGTTTTTTTTTTTG-TAAATTTTGAAAAATTATACCATATTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTT---AAATT-T-CCATATTTTTATTTTTTTG
8877 TTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
8901 TTTTTTTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
61 8 0.11
62 24 0.32
63 30 0.40
64 4 0.05
65 1 0.01
66 8 0.11
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (59 bp):
TTTTTTTTTTTTTTTTTTTTTTTTGTTAAATTTTAAATTTCCATATTTTTATTTTTTTG
Found at i:9608 original size:17 final size:16
Alignment explanation
Indices: 9576--9628 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 16
9566 ATATTTAAAA
9576 AATTTAGAAAAAATAT
1 AATTTAGAAAAAATAT
9592 AATTTAGAAAAACATAT
1 AATTTAGAAAAA-ATAT
*
9609 AATTATAAAAAAAATTAT
1 AATT-TAGAAAAAA-TAT
9627 AA
1 AA
9629 GAATAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 12 0.36
17 9 0.27
18 12 0.36
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (16 bp):
AATTTAGAAAAAATAT
Found at i:10773 original size:23 final size:24
Alignment explanation
Indices: 10747--10813 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
10737 ATTAATTTAA
10747 TTTAAATTTTTGGGTTTTTAT-TT
1 TTTAAATTTTTGGGTTTTTATGTT
* *
10770 TTT-AATTTTTGGAGGTTTTCTGTT
1 TTTAAATTTTTGG-GTTTTTATGTT
* *
10794 TTTAAATTTCTAGGTTTTTA
1 TTTAAATTTTTGGGTTTTTA
10814 GGTGTTCGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 9 0.26
23 9 0.26
24 10 0.29
25 7 0.20
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTAAATTTTTGGGTTTTTATGTT
Found at i:10795 original size:24 final size:22
Alignment explanation
Indices: 10751--10798 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
10741 ATTTAATTTA
*
10751 AATTTTTGGGTTTTTATTTTTT
1 AATTTTTGGGGTTTTATTTTTT
*
10773 AATTTTTGGAGGTTTTCTGTTTTT
1 AATTTTTGG-GGTTTTAT-TTTTT
10797 AA
1 AA
10799 ATTTCTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.65
Consensus pattern (22 bp):
AATTTTTGGGGTTTTATTTTTT
Found at i:12509 original size:5 final size:5
Alignment explanation
Indices: 12483--12540 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
12473 ATGTGTTAAA
* *
12483 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
12532 ATATT ATAT
1 ATATT ATAT
12541 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:12519 original size:10 final size:9
Alignment explanation
Indices: 12484--12541 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
12474 TGTGTTAAAA
12484 TATATATAT
1 TATATATAT
*
12493 TAAAT-TAT
1 TATATATAT
12501 TAT-TATAT
1 TATATATAT
12509 TATAGTATAT
1 TATA-TATAT
12519 TATAT-TA-
1 TATATATAT
12526 TATATTATAT
1 TATA-TATAT
12536 TATATA
1 TATATA
12542 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:12531 original size:12 final size:12
Alignment explanation
Indices: 12486--12541 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
12476 TGTTAAAATA
*
12486 TATATATTAAAT
1 TATATATTATAT
12498 TAT-TATTATATT
1 TATATATTATA-T
12510 ATAGTATATTATAT
1 -TA-TATATTATAT
12524 TATATATTATAT
1 TATATATTATAT
12536 TATATA
1 TATATA
12542 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:14258 original size:18 final size:19
Alignment explanation
Indices: 14237--14277 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
14227 AATGAAATGA
14237 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
14255 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
14274 GAAA
1 GAAA
14278 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:18497 original size:49 final size:50
Alignment explanation
Indices: 18353--18516 Score: 233
Period size: 49 Copynumber: 3.3 Consensus size: 50
18343 ACTTCTGATC
* *
18353 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
18404 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
18454 AGTG-TAAGTGA-AAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
*
18503 AGTGAAAATGTGAT
1 AGTGACAA-GTGAT
18517 TAATGTAAGA
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
48 10 0.10
49 35 0.35
50 31 0.31
51 25 0.25
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Done.