Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01524.P17
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: 64879
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:6304 original size:6 final size:6
Alignment explanation
Indices: 6293--6371 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
6283 GGGATCACTA
6293 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
* *
6336 A-GAAT A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
6372 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:6315 original size:20 final size:21
Alignment explanation
Indices: 6289--6334 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
6279 AGCCGGGATC
6289 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
6310 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
6330 ACTAA
1 ACTAA
6335 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:6359 original size:11 final size:11
Alignment explanation
Indices: 6289--6335 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
6279 AGCCGGGATC
6289 ACTAA-CTAAT
1 ACTAATCTAAT
6299 ACTAATCTAAT
1 ACTAATCTAAT
6310 -CTAA-CTAAT
1 ACTAATCTAAT
6319 ACTAATCTAAT
1 ACTAATCTAAT
6330 ACTAAT
1 ACTAAT
6336 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:6385 original size:14 final size:14
Alignment explanation
Indices: 6368--6395 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6358 CTCTAATACT
6368 AATAGAATAGAAAA
1 AATAGAATAGAAAA
6382 AATAGAATAGAAAA
1 AATAGAATAGAAAA
6396 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:14722 original size:18 final size:18
Alignment explanation
Indices: 14643--14736 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
14633 CAAGGTCACG
*
14643 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
14661 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
14679 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
14697 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
14715 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
14730 ATCAATA
1 ATCAATA
14737 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:14723 original size:9 final size:9
Alignment explanation
Indices: 14643--14723 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
14633 CAAGGTCACG
*
14643 ATCAATAGC
1 ATCAATATC
* *
14652 GTCACTATC
1 ATCAATATC
*
14661 ATCAATAGC
1 ATCAATATC
* * *
14670 GTCACTAGC
1 ATCAATATC
14679 ATCAATATC
1 ATCAATATC
* * *
14688 GTCACTAGC
1 ATCAATATC
14697 ATCAATATC
1 ATCAATATC
* *
14706 GTCACTATC
1 ATCAATATC
14715 ATCAATATC
1 ATCAATATC
14724 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:17132 original size:21 final size:21
Alignment explanation
Indices: 17102--17190 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
17092 CTCACAAAGA
* *
17102 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
17122 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
17143 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
17164 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
17188 AAA
1 AAA
17191 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:17183 original size:24 final size:21
Alignment explanation
Indices: 17102--17170 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
17092 CTCACAAAGA
* * *
17102 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
17122 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
17143 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
17164 AAAAAGA
1 AAAAAGA
17171 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:21356 original size:14 final size:14
Alignment explanation
Indices: 21337--21365 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21327 TACAATATAT
21337 ATAAGAATTATACG
1 ATAAGAATTATACG
21351 ATAAGAATTATACG
1 ATAAGAATTATACG
21365 A
1 A
21366 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:27077 original size:16 final size:16
Alignment explanation
Indices: 27052--27084 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27042 ACGGTATTCT
*
27052 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
27068 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
27084 A
1 A
27085 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:27583 original size:15 final size:15
Alignment explanation
Indices: 27550--27583 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27540 AGTTATGTCT
*
27550 ATGTATGGAATTATA
1 ATGTATGGAATTAGA
*
27565 ATGTATGGAATTAGC
1 ATGTATGGAATTAGA
27580 ATGT
1 ATGT
27584 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:28606 original size:19 final size:19
Alignment explanation
Indices: 28584--28623 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28574 TTAAACTTTT
* *
28584 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
28603 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
28622 AT
1 AT
28624 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:30329 original size:14 final size:14
Alignment explanation
Indices: 30310--30338 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30300 CTTTTTACTT
30310 TGTTATATAGATTA
1 TGTTATATAGATTA
30324 TGTTATATAGATTA
1 TGTTATATAGATTA
30338 T
1 T
30339 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:30487 original size:21 final size:21
Alignment explanation
Indices: 30463--30502 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30453 TTTATCAGTA
*
30463 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
30484 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
30503 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:31102 original size:11 final size:11
Alignment explanation
Indices: 31086--31110 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31076 CTTTATATTT
31086 ATATACAATAA
1 ATATACAATAA
31097 ATATACAATAA
1 ATATACAATAA
31108 ATA
1 ATA
31111 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:31805 original size:14 final size:15
Alignment explanation
Indices: 31774--31813 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
31764 TATCTTTATC
31774 TTATTTATATTCTATT
1 TTATTTAT-TTCTATT
31790 TTATTTATTTCT-TT
1 TTATTTATTTCTATT
*
31804 TTTTTTATTT
1 TTATTTATTT
31814 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:35693 original size:23 final size:23
Alignment explanation
Indices: 35663--35708 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35653 TATATTTTGA
35663 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
35686 GTTCGTATATAACTAGTCAATAT
1 GTTCGTATATAACTAGTCAATAT
35709 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:36269 original size:14 final size:14
Alignment explanation
Indices: 36250--36277 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36240 TCAAGATAAA
36250 GATAATATTGATCG
1 GATAATATTGATCG
36264 GATAATATTGATCG
1 GATAATATTGATCG
36278 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:37478 original size:29 final size:29
Alignment explanation
Indices: 37436--37493 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
37426 TATTAACCGA
37436 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
37465 TTCCATAGATCTATGTAGTTCCAAAAAAG
1 TTCCATAGATCTATGTAGTTCCAAAAAAG
37494 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:56462 original size:14 final size:14
Alignment explanation
Indices: 56443--56470 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56433 TATATTAGTA
56443 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56457 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56471 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:56478 original size:6 final size:6
Alignment explanation
Indices: 56467--56545 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
56457 TTTTCTATTC
* *
56467 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
56514 -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG T
56546 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:56493 original size:11 final size:11
Alignment explanation
Indices: 56468--56549 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
56458 TTTCTATTCT
56468 ATTAGTATTAG
1 ATTAGTATTAG
56479 ---AGTATTAG
1 ATTAGTATTAG
**
56487 ATTAGTATTCT
1 ATTAGTATTAG
*
56498 ATT-CTATTAG
1 ATTAGTATTAG
56508 TATTAG-ATTAG
1 -ATTAGTATTAG
56519 TATTAGTTAGATTAG
1 -ATTAG-T--ATTAG
56534 ATTAGTATTAG
1 ATTAGTATTAG
56545 -TTAGT
1 ATTAGT
56550 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:56534 original size:20 final size:21
Alignment explanation
Indices: 56504--56549 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
56494 TTCTATTCTA
56504 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56525 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56545 TTAGT
1 TTAGT
56550 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:64755 original size:32 final size:32
Alignment explanation
Indices: 64714--64775 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
64704 CATCTATTTT
64714 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
64746 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
64776 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.