Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01123.P2
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: 87036
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2778 original size:32 final size:32
Alignment explanation
Indices: 2737--2798 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2727 CATCTATTTT
2737 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
2769 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
2799 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
Found at i:10110 original size:13 final size:13
Alignment explanation
Indices: 10092--10119 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10082 TGAAAATTCG
10092 TTAATGGTACATT
1 TTAATGGTACATT
10105 TTAATGGTACATT
1 TTAATGGTACATT
10118 TT
1 TT
10120 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:20049 original size:21 final size:21
Alignment explanation
Indices: 20025--20068 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20015 GAATCTTTAG
*
20025 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
20046 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
20067 TA
1 TA
20069 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:22327 original size:22 final size:22
Alignment explanation
Indices: 22300--22343 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
22290 CTCTCGATTT
22300 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
22322 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
22344 AAAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTATTGCTCCTTTTCAATCA
Found at i:26498 original size:32 final size:32
Alignment explanation
Indices: 26462--26523 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
26452 AGCTTTTGGT
26462 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
26494 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
26524 AAAATAGATG
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:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:34710 original size:6 final size:6
Alignment explanation
Indices: 34699--34777 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
34689 GGGATCACTA
34699 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
* *
34742 A-GAAT A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
34778 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:34721 original size:20 final size:21
Alignment explanation
Indices: 34695--34740 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
34685 AGCCGGGATC
34695 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
34716 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
34736 ACTAA
1 ACTAA
34741 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:34765 original size:11 final size:11
Alignment explanation
Indices: 34695--34741 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
34685 AGCCGGGATC
34695 ACTAA-CTAAT
1 ACTAATCTAAT
34705 ACTAATCTAAT
1 ACTAATCTAAT
34716 -CTAA-CTAAT
1 ACTAATCTAAT
34725 ACTAATCTAAT
1 ACTAATCTAAT
34736 ACTAAT
1 ACTAAT
34742 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:34791 original size:14 final size:14
Alignment explanation
Indices: 34774--34801 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34764 CTCTAATACT
34774 AATAGAATAGAAAA
1 AATAGAATAGAAAA
34788 AATAGAATAGAAAA
1 AATAGAATAGAAAA
34802 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:42591 original size:18 final size:18
Alignment explanation
Indices: 42512--42605 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
42502 CAAGGTCACG
*
42512 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
42530 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
42548 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
42566 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
42584 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
42599 ATCAATA
1 ATCAATA
42606 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:42592 original size:9 final size:9
Alignment explanation
Indices: 42512--42592 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
42502 CAAGGTCACG
*
42512 ATCAATAGC
1 ATCAATATC
* *
42521 GTCACTATC
1 ATCAATATC
*
42530 ATCAATAGC
1 ATCAATATC
* * *
42539 GTCACTAGC
1 ATCAATATC
42548 ATCAATATC
1 ATCAATATC
* * *
42557 GTCACTAGC
1 ATCAATATC
42566 ATCAATATC
1 ATCAATATC
* *
42575 GTCACTATC
1 ATCAATATC
42584 ATCAATATC
1 ATCAATATC
42593 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:45001 original size:21 final size:21
Alignment explanation
Indices: 44971--45059 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
44961 CTCACAAAGA
* *
44971 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
44991 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
45012 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
45033 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
45057 AAA
1 AAA
45060 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:45052 original size:24 final size:21
Alignment explanation
Indices: 44971--45039 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
44961 CTCACAAAGA
* * *
44971 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
44991 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
45012 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
45033 AAAAAGA
1 AAAAAGA
45040 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:49225 original size:14 final size:14
Alignment explanation
Indices: 49206--49234 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49196 TACAATATAT
49206 ATAAGAATTATACG
1 ATAAGAATTATACG
49220 ATAAGAATTATACG
1 ATAAGAATTATACG
49234 A
1 A
49235 ATCCATCTGT
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:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:54946 original size:16 final size:16
Alignment explanation
Indices: 54921--54953 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54911 ACGGTATTCT
*
54921 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
54937 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
54953 A
1 A
54954 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:55452 original size:15 final size:15
Alignment explanation
Indices: 55419--55452 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55409 AGTTATGTCT
*
55419 ATGTATGGAATTATA
1 ATGTATGGAATTAGA
*
55434 ATGTATGGAATTAGC
1 ATGTATGGAATTAGA
55449 ATGT
1 ATGT
55453 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:56475 original size:19 final size:19
Alignment explanation
Indices: 56453--56492 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56443 TTAAACTTTT
* *
56453 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
56472 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
56491 AT
1 AT
56493 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:58198 original size:14 final size:14
Alignment explanation
Indices: 58179--58207 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58169 CTTTTTACTT
58179 TGTTATATAGATTA
1 TGTTATATAGATTA
58193 TGTTATATAGATTA
1 TGTTATATAGATTA
58207 T
1 T
58208 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:58356 original size:21 final size:21
Alignment explanation
Indices: 58332--58371 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58322 TTTATCAGTA
*
58332 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
58353 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
58372 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:58971 original size:11 final size:11
Alignment explanation
Indices: 58955--58979 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58945 CTTTATATTT
58955 ATATACAATAA
1 ATATACAATAA
58966 ATATACAATAA
1 ATATACAATAA
58977 ATA
1 ATA
58980 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:59674 original size:14 final size:15
Alignment explanation
Indices: 59643--59682 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
59633 TATCTTTATC
59643 TTATTTATATTCTATT
1 TTATTTAT-TTCTATT
59659 TTATTTATTTCT-TT
1 TTATTTATTTCTATT
*
59673 TTTTTTATTT
1 TTATTTATTT
59683 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:63562 original size:23 final size:23
Alignment explanation
Indices: 63532--63577 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
63522 TATATTTTGA
63532 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
63555 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
63578 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:64138 original size:14 final size:14
Alignment explanation
Indices: 64119--64146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64109 TCAAGATAAA
64119 GATAATATTGATCG
1 GATAATATTGATCG
64133 GATAATATTGATCG
1 GATAATATTGATCG
64147 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:65347 original size:29 final size:29
Alignment explanation
Indices: 65305--65362 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
65295 TATTAACCGA
65305 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
65334 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
65363 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:81434 original size:15 final size:15
Alignment explanation
Indices: 81414--81456 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
81404 TATTAGAAAT
81414 AAATAGATATTATAA
1 AAATAGATATTATAA
81429 AAATAGA-A--AT--
1 AAATAGATATTATAA
81439 AAATAGATATTATAA
1 AAATAGATATTATAA
81454 AAA
1 AAA
81457 GAAACTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 7 0.30
11 1 0.04
12 2 0.09
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAGATATTATAA
Found at i:81435 original size:25 final size:25
Alignment explanation
Indices: 81407--81456 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
81397 AAATATTTAT
81407 TAGAAATAAATAGATATTATAAAAA
1 TAGAAATAAATAGATATTATAAAAA
81432 TAGAAATAAATAGATATTATAAAAA
1 TAGAAATAAATAGATATTATAAAAA
81457 GAAACTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (25 bp):
TAGAAATAAATAGATATTATAAAAA
Done.