Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 226 of 226
Found at i:70606123 original size:114 final size:114
Alignment explanation
Indices: 70605918--70606137 Score: 395
Period size: 114 Copynumber: 1.9 Consensus size: 114
70605908 TAAGGGATTG
*
70605918 ATGCATGGTATTTATAAGTGAAGGTCAGGGGTAAAGTTTACTAAAAATAGATTTCAAATTCCTTC
1 ATGCATGGTATTTATAAGTGAAGGTAAGGGGTAAAGTTTACTAAAAATAGATTTCAAATTCCTTC
*
70605983 TTTTCCTATCATACATGGCCGGCCATATTTCAAGGAGAAGGAGATGACT
66 TTTTCCTATCATACATGGCCGACCATATTTCAAGGAGAAGGAGATGACT
* *
70606032 ATGCATGGTATTTATAAGTGAAGGTAAGGGGTGAAGTTTGCTAAAAATAGATTTCAAATTCCTTC
1 ATGCATGGTATTTATAAGTGAAGGTAAGGGGTAAAGTTTACTAAAAATAGATTTCAAATTCCTTC
*
70606097 TTTTCCTATCATACATGGCCGACCATATTTCAATGAGAAGG
66 TTTTCCTATCATACATGGCCGACCATATTTCAAGGAGAAGG
70606138 GGATAAATTA
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
ATGCATGGTATTTATAAGTGAAGGTAAGGGGTAAAGTTTACTAAAAATAGATTTCAAATTCCTTC
TTTTCCTATCATACATGGCCGACCATATTTCAAGGAGAAGGAGATGACT
Found at i:70606851 original size:22 final size:22
Alignment explanation
Indices: 70606799--70606858 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
70606789 TTAAGTGTTG
70606799 AATGTCGCGACT-TTAGCTTCC
1 AATGTCGCGACTCTTAGCTTCC
* * **
70606820 AATATTGCGACTCTTAGCTTTT
1 AATGTCGCGACTCTTAGCTTCC
70606842 AATGTCGCGAC-CTTAGC
1 AATGTCGCGACTCTTAGC
70606859 GAAAATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (22 bp):
AATGTCGCGACTCTTAGCTTCC
Found at i:70606858 original size:21 final size:21
Alignment explanation
Indices: 70606799--70606858 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
70606789 TTAAGTGTTG
*
70606799 AATGTCGCGACTTTAGCTTCC
1 AATGTCGCGACCTTAGCTTCC
* * **
70606820 AATATTGCGACTCTTAGCTTTT
1 AATGTCGCGAC-CTTAGCTTCC
70606842 AATGTCGCGACCTTAGC
1 AATGTCGCGACCTTAGC
70606859 GAAAATTTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGTCGCGACCTTAGCTTCC
Found at i:70617256 original size:20 final size:20
Alignment explanation
Indices: 70617219--70617257 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70617209 ATAATGATAA
*
70617219 TTTATATTCTAAGTATAACT
1 TTTATATTCTAAGAATAACT
* *
70617239 TTTATTTTCTGAGAATAAC
1 TTTATATTCTAAGAATAAC
70617258 AATTCTACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTATATTCTAAGAATAACT
Found at i:70620881 original size:40 final size:40
Alignment explanation
Indices: 70620837--70620986 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 40
70620827 ATAATAAATA
* *
70620837 TTTTTATTTTTTTTATTTTAAAATAGTTTTAAAATACTTT
1 TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
* *
70620877 TTTTTAATTTTTTAAATTTTAAAATTTTTTTAAAATACTTT
1 TTTTT-ATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
*
70620918 TTAATT-TTTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TT-TTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
*
70620958 TTTTAATTTTTGTTTTAATTTTTAAAATA
1 TTTT--TATTT-TTTTAA-TTTTAAAATA
70620987 AATTTTTGGT
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.01
40 39 0.41
41 34 0.36
42 5 0.05
43 6 0.06
44 10 0.11
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
Found at i:70621997 original size:4 final size:4
Alignment explanation
Indices: 70621978--70622016 Score: 60
Period size: 4 Copynumber: 9.2 Consensus size: 4
70621968 TGCAGCAAAG
70621978 TTTA TTTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
70622017 GGGGTTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.74
5 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:70629763 original size:5 final size:5
Alignment explanation
Indices: 70629753--70629792 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
70629743 CACCAAAATT
70629753 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
70629793 AATGATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:70636436 original size:53 final size:53
Alignment explanation
Indices: 70636356--70636462 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
70636346 GCTTCCGAAG
70636356 TATTTTGGTCCTTTTAAGCTCTTAAACAAGATAGGAACAATGGCCTATTAGCT
1 TATTTTGGTCCTTTTAAGCTCTTAAACAAGATAGGAACAATGGCCTATTAGCT
70636409 TATTTTGGTCCTTTTAAGCTCTTAAACAAGATAGGAACAATGGCCTATTAGCT
1 TATTTTGGTCCTTTTAAGCTCTTAAACAAGATAGGAACAATGGCCTATTAGCT
70636462 T
1 T
70636463 GAGTCACCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (53 bp):
TATTTTGGTCCTTTTAAGCTCTTAAACAAGATAGGAACAATGGCCTATTAGCT
Found at i:70644462 original size:17 final size:17
Alignment explanation
Indices: 70644440--70644474 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
70644430 ATACCTAAAT
*
70644440 CCTGAGTGGATGGTGGA
1 CCTGAGTGGATGGCGGA
70644457 CCTGAGTGGATGGCGGA
1 CCTGAGTGGATGGCGGA
70644474 C
1 C
70644475 TATGTCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.20
Consensus pattern (17 bp):
CCTGAGTGGATGGCGGA
Found at i:70650844 original size:26 final size:23
Alignment explanation
Indices: 70650786--70650837 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
70650776 GTAAGTCTGG
70650786 TAGCCTTGAAGAAGTTTACTTTA
1 TAGCCTTGAAGAAGTTTACTTTA
70650809 TAGCCTTGAAGAAGTTTACTTTA
1 TAGCCTTGAAGAAGTTTACTTTA
70650832 TAGCCT
1 TAGCCT
70650838 CTCTGAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (23 bp):
TAGCCTTGAAGAAGTTTACTTTA
Found at i:70667393 original size:27 final size:29
Alignment explanation
Indices: 70667363--70667425 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
70667353 CAGAAACCCG
* * *
70667363 AAAACCATGACCATTATCAC-AG-CCCAA
1 AAAACCAGGACAACTATCACAAGTCCCAA
* *
70667390 AAAAACAGGACAACTATCACAAGTCGCAA
1 AAAACCAGGACAACTATCACAAGTCCCAA
70667419 AAAACCA
1 AAAACCA
70667426 ATGGCCACAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 16 0.57
28 2 0.07
29 10 0.36
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.11
Consensus pattern (29 bp):
AAAACCAGGACAACTATCACAAGTCCCAA
Found at i:70674511 original size:27 final size:29
Alignment explanation
Indices: 70674481--70674543 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
70674471 CAGAAACCCG
* * *
70674481 AAAACCATGACCATTATCAC-AG-CCCAA
1 AAAACCAGGACAACTATCACAAGTCCCAA
* *
70674508 AAAAACAGGACAACTATCACAAGTCGCAA
1 AAAACCAGGACAACTATCACAAGTCCCAA
70674537 AAAACCA
1 AAAACCA
70674544 ATGGCCACAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 16 0.57
28 2 0.07
29 10 0.36
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.11
Consensus pattern (29 bp):
AAAACCAGGACAACTATCACAAGTCCCAA
Found at i:70676646 original size:38 final size:38
Alignment explanation
Indices: 70676587--70676680 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
70676577 TGTTGCTCTG
* *
70676587 TAAAGCCTGTAGATAATCATTTTCATGGTGTCGCTTCA
1 TAAAGCCTGTAGATAACCATTTTCATGGTGTCGCTCCA
*
70676625 TAGAGCCTGTAGATAACCATTTTCATGGTGTCGCTCCA
1 TAAAGCCTGTAGATAACCATTTTCATGGTGTCGCTCCA
*
70676663 TAAAGCTTGTAGATAACC
1 TAAAGCCTGTAGATAACC
70676681 GTACCACGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (38 bp):
TAAAGCCTGTAGATAACCATTTTCATGGTGTCGCTCCA
Found at i:70677662 original size:18 final size:17
Alignment explanation
Indices: 70677638--70677672 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
70677628 ATGGAGACCT
70677638 ATTTTTTTTTTAAATTG
1 ATTTTTTTTTTAAATTG
70677655 ATTTTTTTTTTAAATTG
1 ATTTTTTTTTTAAATTG
70677672 A
1 A
70677673 AAGGCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTTTTTTTTAAATTG
Found at i:70678599 original size:18 final size:19
Alignment explanation
Indices: 70678576--70678633 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 19
70678566 AACCAACCAA
70678576 TTTAATATATATAATAT-T
1 TTTAATATATATAATATAT
* *
70678594 TTTAATTTATTTAAATATAT
1 TTTAATATATAT-AATATAT
70678614 TTATAATATATGATAA-ATAT
1 TT-TAATATAT-ATAATATAT
70678634 AATGTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.31
19 5 0.16
20 7 0.22
21 9 0.28
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTAATATATATAATATAT
Found at i:70678615 original size:21 final size:22
Alignment explanation
Indices: 70678589--70678646 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
70678579 AATATATATA
* *
70678589 ATATTTTTAATTTAT-TTAAAT
1 ATATTTTTAATATATGATAAAT
*
70678610 ATATTTATAATATATGATAAAT
1 ATATTTTTAATATATGATAAAT
70678632 ATAATGTTTTAATAT
1 AT-AT-TTTTAATAT
70678647 CATATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.43
22 7 0.23
23 2 0.07
24 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
ATATTTTTAATATATGATAAAT
Found at i:70683957 original size:39 final size:39
Alignment explanation
Indices: 70683903--70683986 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
70683893 CCTACGGCCA
** *
70683903 CCACCATTGTCGTTCACGAGTCAGGCAGTCACCAACGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
* *
70683942 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
70683981 CCACCA
1 CCACCA
70683987 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:70685888 original size:2 final size:2
Alignment explanation
Indices: 70685881--70685914 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
70685871 TTCATATGCT
*
70685881 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
70685915 GCTAGGCAGG
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:70688163 original size:21 final size:21
Alignment explanation
Indices: 70688137--70688188 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
70688127 GAAATTCCGT
70688137 TCCGGTTCAGTTGTTTTGGTG
1 TCCGGTTCAGTTGTTTTGGTG
70688158 TCCGGTTCAGTTGTTTTGGTG
1 TCCGGTTCAGTTGTTTTGGTG
70688179 TCCGGTTCAG
1 TCCGGTTCAG
70688189 ATCACTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.06, C:0.17, G:0.33, T:0.44
Consensus pattern (21 bp):
TCCGGTTCAGTTGTTTTGGTG
Found at i:70690111 original size:21 final size:20
Alignment explanation
Indices: 70690087--70690130 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
70690077 TGTTTCAATC
*
70690087 TTTGCTGATTATTTATTTAGT
1 TTTG-TGATTATTTAATTAGT
* *
70690108 TTTGTGCTTATTTAATTCGT
1 TTTGTGATTATTTAATTAGT
70690128 TTT
1 TTT
70690131 TTTTACCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.16, C:0.07, G:0.14, T:0.64
Consensus pattern (20 bp):
TTTGTGATTATTTAATTAGT
Found at i:70696795 original size:40 final size:40
Alignment explanation
Indices: 70696740--70696823 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
70696730 TTACTGCATC
70696740 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
*
70696780 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGTTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
70696820 TGTG
1 TGTG
70696824 ACGCACGTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.39
Consensus pattern (40 bp):
TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
Found at i:70697712 original size:21 final size:21
Alignment explanation
Indices: 70697688--70697728 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
70697678 GGTTTTCCCC
70697688 TGTCCGGTTCAG-TTCTTTTAG
1 TGTCCGGTTCAGATT-TTTTAG
70697709 TGTCCGGTTCAGATTTTTTA
1 TGTCCGGTTCAGATTTTTTA
70697729 TGCTGCAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (21 bp):
TGTCCGGTTCAGATTTTTTAG
Found at i:70702628 original size:4 final size:5
Alignment explanation
Indices: 70702593--70702627 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
70702583 AATATTTTGG
70702593 TTTAA TTTAA TTTAA TTTAA TTT-A TTTAA -TTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
70702628 ACCATTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Done.