Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3324
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: 29921
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4498 original size:30 final size:30
Alignment explanation
Indices: 4462--4522 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
4452 GTGGATCCTG
4462 ATCGTT-GTGAATTCTTGACCGAAGTTCCAT
1 ATCGTTGGTGAATTCTTGACCG-AGTTCCAT
4492 ATCGTTGGTGAATTCTTGACCGAGTTCCAT
1 ATCGTTGGTGAATTCTTGACCGAGTTCCAT
4522 A
1 A
4523 ACATCGGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (30 bp):
ATCGTTGGTGAATTCTTGACCGAGTTCCAT
Found at i:4855 original size:12 final size:12
Alignment explanation
Indices: 4835--4870 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
4825 TGGGATATGC
*
4835 AATGTATGAATG
1 AATGCATGAATG
4847 AATGCATGAATG
1 AATGCATGAATG
4859 AATGCATGAATG
1 AATGCATGAATG
4871 TCAGTCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:6447 original size:16 final size:15
Alignment explanation
Indices: 6426--6473 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
6416 GATGGGAATA
6426 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
6442 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
6457 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
6473 A
1 A
6474 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:6456 original size:8 final size:8
Alignment explanation
Indices: 6422--6473 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
6412 CAATGATGGG
*
6422 AATAATAA
1 AATATTAA
6430 AATATATAA
1 AATAT-TAA
6439 AATA-TAA
1 AATATTAA
6446 AATATTAA
1 AATATTAA
*
6454 AATATCAA
1 AATATTAA
*
6462 AATATTAG
1 AATATTAA
6470 AATA
1 AATA
6474 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:6473 original size:24 final size:24
Alignment explanation
Indices: 6421--6477 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
6411 ACAATGATGG
*
6421 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
6445 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
6469 GAATAATAA
1 GAATAATAA
6478 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:6637 original size:23 final size:19
Alignment explanation
Indices: 6586--6644 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 19
6576 ATACTACATC
6586 AATATGTACATATATAAAA
1 AATATGTACATATATAAAA
**
6605 AATAAATACATGATAATATTAAA
1 AATATGTACAT-AT-ATA--AAA
6628 AATATGTACATAATATA
1 AATATGTACAT-ATATA
6645 GTGTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.29
20 2 0.06
21 3 0.10
22 3 0.10
23 14 0.45
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
AATATGTACATATATAAAA
Found at i:6655 original size:24 final size:22
Alignment explanation
Indices: 6603--6686 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
6593 ACATATATAA
* *
6603 AAAATAAATACATGATAATA-TT
1 AAAATATATACATAAT-ATAGTT
*
6625 AAAAATATGTACATAATATAGTGTT
1 -AAAATATATACATAATATA--GTT
*
6650 AAAATACATACATAATATAGTT
1 AAAATATATACATAATATAGTT
*
6672 AAGATATATACATAA
1 AAAATATATACATAA
6687 GATAACATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
22 19 0.37
23 13 0.25
24 17 0.33
25 2 0.04
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAATATATACATAATATAGTT
Found at i:6682 original size:22 final size:23
Alignment explanation
Indices: 6626--6686 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
6616 GATAATATTA
*
6626 AAAATATGTACATAATATAGTGTT
1 AAAATATATACATAATATAG-GTT
*
6650 AAAATACATACATAATATA-GTT
1 AAAATATATACATAATATAGGTT
*
6672 AAGATATATACATAA
1 AAAATATATACATAA
6687 GATAACATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.48
24 17 0.52
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAATATATACATAATATAGGTT
Found at i:6741 original size:25 final size:24
Alignment explanation
Indices: 6707--6838 Score: 98
Period size: 25 Copynumber: 5.6 Consensus size: 24
6697 AGAAAAAAAT
6707 ATATATAAATAATATAATATTAAA
1 ATATATAAATAATATAATATTAAA
* *
6731 GATATATAAATAAAATAGTA-TAAA
1 -ATATATAAATAATATAATATTAAA
* * *
6755 ATATATATACGTAATATAAAATTTAA
1 ATATATA-A-ATAATATAATATTAAA
**
6781 A-ATATACCT-A-AT-ATATTAAA
1 ATATATAAATAATATAATATTAAA
*
6801 ATAATATATATAATATAATATTAAGA
1 AT-ATATAAATAATATAATATTAA-A
6827 A-ATAT-AATAATA
1 ATATATAAATAATA
6839 AGAAAAAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
20 7 0.08
21 2 0.02
22 7 0.08
23 15 0.18
24 11 0.13
25 36 0.43
26 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (24 bp):
ATATATAAATAATATAATATTAAA
Found at i:6759 original size:50 final size:46
Alignment explanation
Indices: 6702--6833 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 46
6692 CATGTAGAAA
6702 AAAATATATATAAATAATATAATATTAAAGATATATAAATAAAATAGTAT
1 AAAATATATATAAATAATATAATATT-AAGA-ATATAAATAAAATA-T-T
** * ** *
6752 AAAATATATATACGTAATATAAAATTTAA-AATATACCTAATATATT
1 AAAATATATATAAATAATATAATA-TTAAGAATATAAATAAAATATT
*
6798 AAAATA-ATATATATAATATAATATTAAGAAATATAA
1 AAAATATATATAAATAATATAATATTAAG-AATATAA
6834 TAATAAGAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
44 4 0.06
45 14 0.20
46 13 0.19
47 1 0.01
48 11 0.16
49 1 0.01
50 23 0.33
51 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (46 bp):
AAAATATATATAAATAATATAATATTAAGAATATAAATAAAATATT
Found at i:6830 original size:15 final size:15
Alignment explanation
Indices: 6812--6843 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6802 TAATATATAT
*
6812 AATATAATATTAAGA
1 AATATAATAATAAGA
6827 AATATAATAATAAGA
1 AATATAATAATAAGA
6842 AA
1 AA
6844 AAAAAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AATATAATAATAAGA
Found at i:7349 original size:30 final size:30
Alignment explanation
Indices: 7313--7415 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
7303 TAGGTACAAG
*
7313 TGATGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGATGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
7343 TGATGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGATGGTGGAAAAGGTGTGGCTAGTGGAGT
*
7373 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGATGGTGGAAAAGGTGTGGCTAGTGGAGT
*
7403 TGGTGGTGGAAAA
1 TGATGGTGGAAAA
7416 AAAGTGGCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.24, C:0.03, G:0.48, T:0.25
Consensus pattern (30 bp):
TGATGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:7423 original size:30 final size:30
Alignment explanation
Indices: 7329--7427 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
7319 TGGAGAAGGT
*
7329 GTGGCTAGTGGAGTTGATGGTGGAAAAAGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
* *
7359 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGT
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
*
7389 GTGGCTAGTGGAGTTGGTGGTGGAAAAAAA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
7419 GTGGCTAGT
1 GTGGCTAGT
7428 TGAGAAAAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.25, C:0.04, G:0.45, T:0.25
Consensus pattern (30 bp):
GTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
Found at i:9122 original size:18 final size:18
Alignment explanation
Indices: 9101--9154 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
9091 CCACCACTAA
9101 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
9119 CTCCACTA-CC-TA--T-
1 CTCCACTAGCCACACTTG
9132 -TCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
9149 CTCCAC
1 CTCCAC
9155 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
14 2 0.07
16 2 0.07
17 2 0.07
18 13 0.46
ACGTcount: A:0.22, C:0.46, G:0.07, T:0.24
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:9748 original size:27 final size:26
Alignment explanation
Indices: 9708--9779 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
9698 ATTCTAAATT
*
9708 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
* *
9733 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
*
9758 CTATATTATTTATATATATATT
1 CTATATTATGTATATATATATT
9780 TTTTACATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.05
25 35 0.90
26 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:9777 original size:29 final size:28
Alignment explanation
Indices: 9737--9844 Score: 104
Period size: 27 Copynumber: 4.0 Consensus size: 28
9727 ATTATACTAT
9737 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* * *
9766 TTTATATATATATTTT-TTAC-ATGTTA
1 TTTATGTATATATTTTAATACTATATTA
9792 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* *
9819 TGTATGTAT-T-TTTT-ACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
9844 T
1 T
9845 GTACATATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 9 0.14
26 13 0.20
27 23 0.35
28 4 0.06
29 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:9819 original size:22 final size:22
Alignment explanation
Indices: 9789--9896 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
9779 TTTTTACATG
*
9789 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
9811 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
9836 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
9859 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
9879 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
9897 ATGTAGTATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:9845 original size:25 final size:24
Alignment explanation
Indices: 9795--9881 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
9785 CATGTTATCT
*
9795 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
9821 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
** * *
9846 TACATA-TTTTTAA-TATTATCACG
1 TATGTATTTTTTAACTA-TATTATG
*
9869 TATTTATTTTTTA
1 TATGTATTTTTTA
9882 TATATGTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 10 0.20
24 17 0.33
25 15 0.29
26 7 0.14
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:9853 original size:47 final size:49
Alignment explanation
Indices: 9762--9881 Score: 122
Period size: 48 Copynumber: 2.5 Consensus size: 49
9752 TTAATACTAT
* * * *
9762 ATTAT-TTATATATATATTTTTTACATGTTATCTTATGTATATA-TTTTA
1 ATTATATTATGTATATATTTTTTACA-GCTATATTATGTACATATTTTTA
*
9810 ATTATATTATGTATGTATTTTTTACA-CTATATTATGTACATATTTTTA
1 ATTATATTATGTATATATTTTTTACAGCTATATTATGTACATATTTTTA
* * *
9858 A-TATTATCACGTATTTATTTTTTA
1 ATTA-TATTATGTATATATTTTTTA
9882 TATATGTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 15 0.25
48 28 0.46
49 18 0.30
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (49 bp):
ATTATATTATGTATATATTTTTTACAGCTATATTATGTACATATTTTTA
Found at i:9863 original size:20 final size:20
Alignment explanation
Indices: 9838--9896 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
9828 TTTTTACACT
9838 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
9858 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
9881 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
9897 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:10035 original size:16 final size:15
Alignment explanation
Indices: 10011--10045 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
10001 TAATTATTAT
10011 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
10027 TATTTTAATATTTTA
1 TATTCTAATATTTTA
10042 TATT
1 TATT
10046 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:12974 original size:18 final size:20
Alignment explanation
Indices: 12951--12988 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
12941 ACGTGACAGT
12951 CCAACTAG-ATTT-TAAATG
1 CCAACTAGAATTTCTAAATG
*
12969 CCAACTTGAATTTCTAAATG
1 CCAACTAGAATTTCTAAATG
12989 GGATGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
CCAACTAGAATTTCTAAATG
Found at i:13025 original size:17 final size:17
Alignment explanation
Indices: 13005--13038 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12995 AAATAGATTT
13005 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
13022 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
13039 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:22232 original size:3 final size:3
Alignment explanation
Indices: 22224--22248 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22214 CTAGACTATT
22224 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
22249 CGATCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:22988 original size:7 final size:7
Alignment explanation
Indices: 22978--23007 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
22968 CCTTAAATTT
22978 TAAAATA
1 TAAAATA
22985 TAAAATA
1 TAAAATA
22992 TAAAAT-
1 TAAAATA
22998 TAAAATA
1 TAAAATA
23005 TAA
1 TAA
23008 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAATA
Found at i:23003 original size:13 final size:14
Alignment explanation
Indices: 22978--23007 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22968 CCTTAAATTT
22978 TAAAATATAAAATA
1 TAAAATATAAAATA
22992 TAAAAT-TAAAATA
1 TAAAATATAAAATA
23005 TAA
1 TAA
23008 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATATAAAATA
Found at i:24400 original size:21 final size:21
Alignment explanation
Indices: 24376--24437 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
24366 AATCCAATGC
24376 AGAATGCCCTCCTAATTTCTG
1 AGAATGCCCTCCTAATTTCTG
** *
24397 AGAAT--AATCC-AA-TGC--
1 AGAATGCCCTCCTAATTTCTG
24412 AGAATGCCCTCCTAATTTCTG
1 AGAATGCCCTCCTAATTTCTG
24433 AGAAT
1 AGAAT
24438 AATCCAATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 5 0.17
17 5 0.17
18 4 0.14
19 5 0.17
21 10 0.34
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
AGAATGCCCTCCTAATTTCTG
Found at i:24408 original size:36 final size:36
Alignment explanation
Indices: 24361--24473 Score: 219
Period size: 36 Copynumber: 3.2 Consensus size: 36
24351 TATGTATTTT
24361 AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
1 AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
24397 AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
1 AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
24433 AGAATAATCCAATGCAGAATGCCCT-CTAATTTCTG
1 AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
24468 AGAATA
1 AGAATA
24474 CCAAGCTGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 16 0.21
36 61 0.79
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (36 bp):
AGAATAATCCAATGCAGAATGCCCTCCTAATTTCTG
Found at i:27830 original size:6 final size:6
Alignment explanation
Indices: 27819--27843 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27809 TAAATATTAG
27819 GAAGCA GAAGCA GAAGCA GAAGCA G
1 GAAGCA GAAGCA GAAGCA GAAGCA G
27844 CAGACAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAGCA
Found at i:28749 original size:36 final size:34
Alignment explanation
Indices: 28708--28792 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 34
28698 ATAATTTGTT
28708 TTATTAAATTTTAATATGTTTGTAATTTTTTATTGA
1 TTATTAAATTTTAA-AT-TTTGTAATTTTTTATTGA
* *
28744 TTATTAACTTATCTAACTTTTGTAATTTTTTATTGA
1 TTATTAAATT-T-TAAATTTTGTAATTTTTTATTGA
*
28780 TTATTATATTTTA
1 TTATTAAATTTTA
28793 TTTAACTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
34 2 0.05
35 1 0.02
36 35 0.81
37 2 0.05
38 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (34 bp):
TTATTAAATTTTAAATTTTGTAATTTTTTATTGA
Done.