Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01524.P1
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: 65009
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:5571 original size:6 final size:6
Alignment explanation
Indices: 5560--5638 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
5550 GGGATCACTA
5560 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
* *
5603 A-GAAT A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
5639 GAATAGAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
4 3 0.05
5 27 0.43
6 27 0.43
8 6 0.10
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:5582 original size:20 final size:21
Alignment explanation
Indices: 5556--5601 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
5546 AGCCGGGATC
5556 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
5577 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
5597 ACTAA
1 ACTAA
5602 TAGAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:5626 original size:11 final size:11
Alignment explanation
Indices: 5556--5602 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
5546 AGCCGGGATC
5556 ACTAA-CTAAT
1 ACTAATCTAAT
5566 ACTAATCTAAT
1 ACTAATCTAAT
5577 -CTAA-CTAAT
1 ACTAATCTAAT
5586 ACTAATCTAAT
1 ACTAATCTAAT
5597 ACTAAT
1 ACTAAT
5603 AGAATAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:5652 original size:14 final size:14
Alignment explanation
Indices: 5635--5662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5625 CTCTAATACT
5635 AATAGAATAGAAAA
1 AATAGAATAGAAAA
5649 AATAGAATAGAAAA
1 AATAGAATAGAAAA
5663 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:13989 original size:18 final size:18
Alignment explanation
Indices: 13910--14003 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
13900 CAAGGTCACG
*
13910 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
13928 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
13946 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
13964 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
13982 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
13997 ATCAATA
1 ATCAATA
14004 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:13990 original size:9 final size:9
Alignment explanation
Indices: 13910--13990 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
13900 CAAGGTCACG
*
13910 ATCAATAGC
1 ATCAATATC
* *
13919 GTCACTATC
1 ATCAATATC
*
13928 ATCAATAGC
1 ATCAATATC
* * *
13937 GTCACTAGC
1 ATCAATATC
13946 ATCAATATC
1 ATCAATATC
* * *
13955 GTCACTAGC
1 ATCAATATC
13964 ATCAATATC
1 ATCAATATC
* *
13973 GTCACTATC
1 ATCAATATC
13982 ATCAATATC
1 ATCAATATC
13991 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:16399 original size:21 final size:21
Alignment explanation
Indices: 16369--16457 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
16359 CTCACAAAGA
* *
16369 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
16389 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
16410 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
16431 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
16455 AAA
1 AAA
16458 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:16450 original size:24 final size:21
Alignment explanation
Indices: 16369--16437 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
16359 CTCACAAAGA
* * *
16369 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
16389 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
16410 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
16431 AAAAAGA
1 AAAAAGA
16438 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:25651 original size:16 final size:16
Alignment explanation
Indices: 25626--25658 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25616 ACGGTATTCT
*
25626 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
25642 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
25658 A
1 A
25659 AGGAATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:26157 original size:15 final size:15
Alignment explanation
Indices: 26124--26157 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26114 AGTTATGTCT
*
26124 ATGTATGGAATTATA
1 ATGTATGGAATTAGA
*
26139 ATGTATGGAATTAGC
1 ATGTATGGAATTAGA
26154 ATGT
1 ATGT
26158 CAAAAAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTATGGAATTAGA
Found at i:27180 original size:19 final size:19
Alignment explanation
Indices: 27158--27197 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27148 TTAAACTTTT
* *
27158 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
27177 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
27196 AT
1 AT
27198 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTAAACTTTTCGATTCTA
Found at i:28903 original size:14 final size:14
Alignment explanation
Indices: 28884--28912 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28874 CTTTTTACTT
28884 TGTTATATAGATTA
1 TGTTATATAGATTA
28898 TGTTATATAGATTA
1 TGTTATATAGATTA
28912 T
1 T
28913 TATTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTATATAGATTA
Found at i:29061 original size:21 final size:21
Alignment explanation
Indices: 29037--29076 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29027 TTTATCAGTA
*
29037 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
29058 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
29077 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:29676 original size:11 final size:11
Alignment explanation
Indices: 29660--29684 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29650 CTTTATATTT
29660 ATATACAATAA
1 ATATACAATAA
29671 ATATACAATAA
1 ATATACAATAA
29682 ATA
1 ATA
29685 CAATAATCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATACAATAA
Found at i:30379 original size:14 final size:15
Alignment explanation
Indices: 30348--30387 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
30338 TATCTTTATC
30348 TTATTTATATTCTATT
1 TTATTTAT-TTCTATT
30364 TTATTTATTTCT-TT
1 TTATTTATTTCTATT
*
30378 TTTTTTATTT
1 TTATTTATTT
30388 ATCCATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 4 0.17
16 8 0.35
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTATTTCTATT
Found at i:35072 original size:23 final size:23
Alignment explanation
Indices: 35042--35087 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35032 TATATTTTGA
35042 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
35065 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
35088 CTAATATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
GTTCGTATATAACTAGTCAATAT
Found at i:35648 original size:14 final size:14
Alignment explanation
Indices: 35629--35656 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35619 TCAAGATAAA
35629 GATAATATTGATCG
1 GATAATATTGATCG
35643 GATAATATTGATCG
1 GATAATATTGATCG
35657 AAGGTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GATAATATTGATCG
Found at i:36857 original size:29 final size:29
Alignment explanation
Indices: 36815--36872 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
36805 TATTAACCGA
36815 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
36844 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
36873 AATTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (29 bp):
TTCCATAGATCTATGTAGTTCCAAAAAAG
Found at i:56592 original size:14 final size:14
Alignment explanation
Indices: 56573--56600 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56563 TATATTAGTA
56573 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56587 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56601 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:56608 original size:6 final size:6
Alignment explanation
Indices: 56597--56675 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
56587 TTTTCTATTC
* *
56597 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
56644 -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG T
56676 TAGTGATCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.06
5 28 0.44
6 26 0.41
8 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:56623 original size:11 final size:11
Alignment explanation
Indices: 56598--56679 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
56588 TTTCTATTCT
56598 ATTAGTATTAG
1 ATTAGTATTAG
56609 ---AGTATTAG
1 ATTAGTATTAG
**
56617 ATTAGTATTCT
1 ATTAGTATTAG
*
56628 ATT-CTATTAG
1 ATTAGTATTAG
56638 TATTAG-ATTAG
1 -ATTAGTATTAG
56649 TATTAGTTAGATTAG
1 -ATTAG-T--ATTAG
56664 ATTAGTATTAG
1 ATTAGTATTAG
56675 -TTAGT
1 ATTAGT
56680 GATCCCGGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 19
0.69 0.07 0.23
Matches are distributed among these distances:
8 8 0.14
10 9 0.16
11 28 0.50
13 1 0.02
14 5 0.09
15 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:56664 original size:20 final size:21
Alignment explanation
Indices: 56634--56679 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
56624 TTCTATTCTA
56634 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56655 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56675 TTAGT
1 TTAGT
56680 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:64885 original size:32 final size:32
Alignment explanation
Indices: 64844--64905 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
64834 CATCTATTTT
64844 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
64876 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
64906 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Done.