Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 168 of 168
Found at i:51032954 original size:13 final size:13
Alignment explanation
Indices: 51032936--51032960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51032926 GGTTCGGGGT
51032936 TTGGGGCTTGGGC
1 TTGGGGCTTGGGC
51032949 TTGGGGCTTGGG
1 TTGGGGCTTGGG
51032961 GTTTAGGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.56, T:0.32
Consensus pattern (13 bp):
TTGGGGCTTGGGC
Found at i:51036669 original size:21 final size:21
Alignment explanation
Indices: 51036643--51036684 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
51036633 TCTACTTTGG
51036643 GGATATCCCGTCATATCCTAA
1 GGATATCCCGTCATATCCTAA
51036664 GGATATCCCGTCATATCCTAA
1 GGATATCCCGTCATATCCTAA
51036685 TCGGGATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
GGATATCCCGTCATATCCTAA
Found at i:51037712 original size:16 final size:16
Alignment explanation
Indices: 51037691--51037722 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51037681 TTGGGGGAGA
51037691 TAATGTTTCGTTCTCT
1 TAATGTTTCGTTCTCT
51037707 TAATGTTTCGTTCTCT
1 TAATGTTTCGTTCTCT
51037723 CAATCCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (16 bp):
TAATGTTTCGTTCTCT
Found at i:51038560 original size:24 final size:24
Alignment explanation
Indices: 51038528--51038577 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
51038518 ATTGGAGCTG
51038528 AGCACATCATGATAGTAATATTTA
1 AGCACATCATGATAGTAATATTTA
51038552 AGCACATCATGATAGTAATATTTA
1 AGCACATCATGATAGTAATATTTA
51038576 AG
1 AG
51038578 AAATGATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (24 bp):
AGCACATCATGATAGTAATATTTA
Found at i:51039835 original size:29 final size:28
Alignment explanation
Indices: 51039802--51039861 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
51039792 AATGGCCAAC
* * *
51039802 CATGCTGCTGTTATGTTTTTGTTAAAGTG
1 CATGCTGCTATGATGATTTTGTT-AAGTG
*
51039831 CATGCTGCTATGATGATTTTGTTGAGTG
1 CATGCTGCTATGATGATTTTGTTAAGTG
51039859 CAT
1 CAT
51039862 ACAGCTCGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (28 bp):
CATGCTGCTATGATGATTTTGTTAAGTG
Found at i:51046872 original size:11 final size:11
Alignment explanation
Indices: 51046856--51046883 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
51046846 AAATACTTTA
51046856 AAATTAAAAAT
1 AAATTAAAAAT
51046867 AAATTAAAAAT
1 AAATTAAAAAT
51046878 AAATTA
1 AAATTA
51046884 CACGTGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:51047447 original size:39 final size:39
Alignment explanation
Indices: 51047393--51047476 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
51047383 CCTACGGCCA
** *
51047393 CCACCATTGTCGTTCACGAGTCAGGCAGTCACCAACGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
* *
51047432 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
51047471 CCACCA
1 CCACCA
51047477 GTCAATCGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (39 bp):
CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
Found at i:51049370 original size:2 final size:2
Alignment explanation
Indices: 51049363--51049396 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
51049353 TTCATATGCT
*
51049363 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
51049397 TAGAATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:51058883 original size:230 final size:229
Alignment explanation
Indices: 51058464--51058988 Score: 734
Period size: 230 Copynumber: 2.3 Consensus size: 229
51058454 TAGCAGAATA
*
51058464 ATTTTTGTAATATCCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
1 ATTTTTGTAATATTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
* **
51058529 TCTTGTTTTTGCTTAGCAGAGTAATTTTGGGGTTTGGTGTTTTTGAGCCTGAATCACGATTAGAT
66 TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
* *
51058594 TTTGGCTTTTCATTTATATTTTTGTCATTATAGTTACTTTTCCAATTAACATGACACTAGTT-CT
131 TTTGGCTTATCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCCT
*
51058658 ATTGCTCCCA-ACACTGAAGAAAATATCTATATTAAG
196 -TTGCTCCCAGA-ACTCAAGAAAATATCTATA-TAAG
* * *
51058694 ATTTTTTTAATATTCGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTTT
1 ATTTTTGTAATATTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
* * * * * *
51058759 TCTTGTTTTTGCTTAGTAGAATAATTTTGTGGTTTGGTTTTTTTGGGCCCAAATCAGGCTTAGAT
66 TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
*
51058824 TTTGGCTTATCATTTATATTTTTGTCATTATAGTT-CATTTTCCAAATAACATTACACTAGTTCC
131 TTTGGCTTATCATTTATATTTTTGTCATTATAGTTAC-TTTTCCAAATAACATGACACTAGTTCC
* * * * * *
51058888 TTTGCTCTCAGAACTCAGGATAGTATCTTTATAAT
195 TTTGCTCCCAGAACTCAAGAAAATATCTATATAAG
* * * *
51058923 ATTTTTGTAAT-TTCTGCTTAGCAGAATACTATTCCTCTCTGTTTTTAGTTGACATATGCTTCTT
1 ATTTTTGTAATATTC-GCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTT
51058987 TT
65 TT
51058989 TGCTAATATG
Statistics
Matches: 261, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
228 3 0.01
229 59 0.23
230 196 0.75
231 3 0.01
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (229 bp):
ATTTTTGTAATATTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
TTTGGCTTATCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCCT
TTGCTCCCAGAACTCAAGAAAATATCTATATAAG
Found at i:51062394 original size:21 final size:20
Alignment explanation
Indices: 51062370--51062409 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
51062360 GGTTTTCCCC
*
51062370 TGTCCGGTTCAGTTCTTTTAG
1 TGTCCGGTTCAATT-TTTTAG
51062391 TGTCCGGTTCAATTTTTTA
1 TGTCCGGTTCAATTTTTTA
51062410 TGCTGCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.50
Consensus pattern (20 bp):
TGTCCGGTTCAATTTTTTAG
Found at i:51062450 original size:95 final size:95
Alignment explanation
Indices: 51062327--51062518 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
51062317 AAGCTATTCT
51062327 GGGGATATCCCTTTCATATCCCATCCCGATTCAGGTTTTCCCCTGTCCGGTTCAGTTCTTTTAGT
1 GGGGATATCCCTTTCATATCCCATCCCGATTCAGGTTTTCCCCTGTCCGGTTCAGTTCTTTTAGT
51062392 GTCCGGTTCAATTTTTTATGCTGCAGGACC
66 GTCCGGTTCAATTTTTTATGCTGCAGGACC
51062422 GGGGATATCCCTTTCATATCCCATCCCGATTCAGGTTTTCCCCTGTCCGGTTCAGTTCTTTTAGT
1 GGGGATATCCCTTTCATATCCCATCCCGATTCAGGTTTTCCCCTGTCCGGTTCAGTTCTTTTAGT
51062487 GTCCGGTTCAATTTTTTATGCTGCAGGACC
66 GTCCGGTTCAATTTTTTATGCTGCAGGACC
51062517 GG
1 GG
51062519 ACTACCTGTC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (95 bp):
GGGGATATCCCTTTCATATCCCATCCCGATTCAGGTTTTCCCCTGTCCGGTTCAGTTCTTTTAGT
GTCCGGTTCAATTTTTTATGCTGCAGGACC
Found at i:51062489 original size:21 final size:20
Alignment explanation
Indices: 51062465--51062504 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
51062455 GGTTTTCCCC
*
51062465 TGTCCGGTTCAGTTCTTTTAG
1 TGTCCGGTTCAATT-TTTTAG
51062486 TGTCCGGTTCAATTTTTTA
1 TGTCCGGTTCAATTTTTTA
51062505 TGCTGCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.50
Consensus pattern (20 bp):
TGTCCGGTTCAATTTTTTAG
Found at i:51062615 original size:31 final size:32
Alignment explanation
Indices: 51062545--51062616 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
51062535 ATTCCACGAA
*
51062545 GGGATATCCCATTCTGCGTATATCCCGGGTTG
1 GGGATATCCCATTCGGCGTATATCCCGGGTTG
51062577 GGGATATCCCATTCGGCGTATATCCCGGGTT-
1 GGGATATCCCATTCGGCGTATATCCCGGGTTG
51062608 GGGATATCC
1 GGGATATCC
51062617 TAAGAAGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 9 0.23
32 30 0.77
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (32 bp):
GGGATATCCCATTCGGCGTATATCCCGGGTTG
Found at i:51064620 original size:14 final size:14
Alignment explanation
Indices: 51064603--51064636 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51064593 ATAGCAATTA
**
51064603 TAATATTATTTAAT
1 TAATATTATACAAT
51064617 TAATATTATACAAT
1 TAATATTATACAAT
51064631 TAATAT
1 TAATAT
51064637 AAAATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATACAAT
Found at i:51071083 original size:23 final size:23
Alignment explanation
Indices: 51071056--51071110 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
51071046 ATTTTCTAAC
51071056 AATAAAATTATTTATGAGTGGCT
1 AATAAAATTATTTATGAGTGGCT
* *
51071079 GATAAAATTATTTATGATTGGCT
1 AATAAAATTATTTATGAGTGGCT
51071102 AATAAAATT
1 AATAAAATT
51071111 TAAAGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (23 bp):
AATAAAATTATTTATGAGTGGCT
Found at i:51072691 original size:17 final size:17
Alignment explanation
Indices: 51072669--51072702 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51072659 TTTATCTATA
51072669 TTTATATTAAAAATAAT
1 TTTATATTAAAAATAAT
*
51072686 TTTATATTAAGAATAAT
1 TTTATATTAAAAATAAT
51072703 AAAAAAAGCC
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:0.03, T:0.47
Consensus pattern (17 bp):
TTTATATTAAAAATAAT
Found at i:51073975 original size:31 final size:31
Alignment explanation
Indices: 51073932--51074008 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
51073922 TCGAGAGATT
*
51073932 TTCCAGGGATATCCCAACGTCAATTAAGCTA
1 TTCCAGGGATATCCCAACATCAATTAAGCTA
* * *
51073963 TTCCCGGGATATCCTAACATGAATTAAGCTA
1 TTCCAGGGATATCCCAACATCAATTAAGCTA
* *
51073994 TTCTAGGAATATCCC
1 TTCCAGGGATATCCC
51074009 TGTCAAATCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (31 bp):
TTCCAGGGATATCCCAACATCAATTAAGCTA
Found at i:51074486 original size:8 final size:8
Alignment explanation
Indices: 51074456--51074515 Score: 81
Period size: 8 Copynumber: 7.9 Consensus size: 8
51074446 TCTGGGTTTT
*
51074456 GGGTTTTA
1 GGGTCTTA
51074464 GGGT-TTA
1 GGGTCTTA
51074471 GGGT-TTA
1 GGGTCTTA
51074478 GGGTCTTA
1 GGGTCTTA
*
51074486 GCGTCTTA
1 GGGTCTTA
51074494 GGGT-TTA
1 GGGTCTTA
51074501 GGGTCTTA
1 GGGTCTTA
51074509 GGGTCTT
1 GGGTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
7 21 0.44
8 27 0.56
ACGTcount: A:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (8 bp):
GGGTCTTA
Found at i:51074503 original size:7 final size:7
Alignment explanation
Indices: 51074229--51074512 Score: 143
Period size: 7 Copynumber: 39.6 Consensus size: 7
51074219 GTTTCTTTTT
*
51074229 GGGTTTG
1 GGGTTTA
51074236 GGGTTTA
1 GGGTTTA
*
51074243 GGGGTTA
1 GGGTTTA
51074250 GGGTTTA
1 GGGTTTA
*
51074257 -GGTTTT
1 GGGTTTA
*
51074263 GGGGTTA
1 GGGTTTA
*
51074270 GTGTTTTTA
1 G-G-GTTTA
51074279 GGGTTT-
1 GGGTTTA
*
51074285 GGGGTTA
1 GGGTTTA
51074292 GTGGTTT-
1 G-GGTTTA
**
51074299 GGG-GAA
1 GGGTTTA
51074305 GGGGTTTA
1 -GGGTTTA
*
51074313 GGGTTTT
1 GGGTTTA
* *
51074320 GGGGTTG
1 GGGTTTA
51074327 GGGTTT-
1 GGGTTTA
*
51074333 GGGGTT-
1 GGGTTTA
*
51074339 GGGGTTA
1 GGGTTTA
51074346 GGGTTTA
1 GGGTTTA
*
51074353 GGGGTTA
1 GGGTTTA
51074360 GGGTTTA
1 GGGTTTA
*
51074367 GGGGTTTG
1 -GGGTTTA
51074375 GGGTTGTA
1 GGGTT-TA
**
51074383 GGGCTTGG
1 GGG-TTTA
**
51074391 GGGTCTGG
1 GGGT-TTA
*
51074399 GGGTCTA
1 GGGTTTA
*
51074406 GGGGTTA
1 GGGTTTA
51074413 TGGG-TTA
1 -GGGTTTA
*
51074420 GGGGTTTG
1 -GGGTTTA
*
51074428 GGGTTTC
1 GGGTTTA
*
51074435 GGGTTTC
1 GGGTTTA
51074442 GGGTTCT-
1 GGGTT-TA
*
51074449 GGGTTTT
1 GGGTTTA
51074456 GGGTTTTA
1 GGG-TTTA
51074464 GGGTTTA
1 GGGTTTA
51074471 GGGTTTA
1 GGGTTTA
51074478 GGGTCTTA
1 GGGT-TTA
*
51074486 GCGTCTTA
1 GGGT-TTA
51074494 GGGTTTA
1 GGGTTTA
51074501 GGGTCTTA
1 GGGT-TTA
51074509 GGGT
1 GGGT
51074513 CTT
Statistics
Matches: 219, Mismatches: 38, Indels: 39
0.74 0.13 0.13
Matches are distributed among these distances:
6 24 0.11
7 130 0.59
8 59 0.27
9 6 0.03
ACGTcount: A:0.08, C:0.04, G:0.49, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:51074514 original size:23 final size:23
Alignment explanation
Indices: 51074449--51074515 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
51074439 TTCGGGTTCT
* *
51074449 GGGTTTTGGGTTTTAGGGT-TTA
1 GGGTTTAGGGTCTTAGGGTCTTA
*
51074471 GGGTTTAGGGTCTTAGCGTCTTA
1 GGGTTTAGGGTCTTAGGGTCTTA
51074494 GGGTTTAGGGTCTTAGGGTCTT
1 GGGTTTAGGGTCTTAGGGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 16 0.40
23 24 0.60
ACGTcount: A:0.10, C:0.07, G:0.39, T:0.43
Consensus pattern (23 bp):
GGGTTTAGGGTCTTAGGGTCTTA
Done.