Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_35 ID=scaffold_35-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: 55789
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.25
Warning! 14012 characters in sequence are not A, C, G, or T
Found at i:6187 original size:16 final size:16
Alignment explanation
Indices: 6166--6230 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
6156 TTCGCTGTAT
6166 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
6182 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
6198 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
6214 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
6230 T
1 T
6231 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:6481 original size:16 final size:16
Alignment explanation
Indices: 6444--6485 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6434 TTAACCATAT
*
6444 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6460 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6475 TTAAAATATAT
1 TTAAAATATAT
6486 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6492 original size:14 final size:15
Alignment explanation
Indices: 6453--6494 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6443 TTTAAACATA
*
6453 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6468 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
6482 A-TATAATTTAATA
1 ATTATAATTAAATA
6495 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6523 original size:37 final size:37
Alignment explanation
Indices: 6481--6560 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
6471 ATAATTAAAA
* *
6481 TATATAATTTAATAAAATTTTTAATAATCAATATTCT
1 TATATAATTTAATAAAATTCTTAATAACCAATATTCT
6518 TATATAATTTAATAAAATTCTTAATAACCAATATTCT
1 TATATAATTTAATAAAATTCTTAATAACCAATATTCT
6555 TA-ATAA
1 TATATAA
6561 AATATAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCTTAATAACCAATATTCT
Found at i:6716 original size:89 final size:89
Alignment explanation
Indices: 6442--6848 Score: 456
Period size: 89 Copynumber: 4.5 Consensus size: 89
6432 ATTTAACCAT
* *
6442 ATTTAAACATAATTATTATTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTTTTAA
1 ATTTAAA-ATAATTATTATTAAATATAATT-TAA-TAATAATATATAATTTCATAAAATTCTT-A
* * *
6505 TAATCAATATTCTTATATAATTTAATAAA
62 TAATAAATTTTCTTATATAATTT-ATATA
* * * * * * *
6534 ATTCTTAATAACCAA-TATTCTT-AATAAAATATAGAT-TTAATA-A-AATTT-AAAATAATTAT
1 A-T-TTAA-AA-TAATTATTATTAAATATAATTTA-ATAATAATATATAATTTCATAA-AATTCT
* *
6593 AACTAATAAATTTTCTTATAGAATTT-TATA
60 TA-TAATAAATTTTCTTATATAATTTATATA
6623 ATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTATAAT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTATAAT
*
6688 AAATTTTCTTTTATAATTTATATA
66 AAATTTTCTTATATAATTTATATA
*
6712 ATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTATAAT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTATAAT
6776 AAATTTTCTTATATGAATTTATATA
66 AAATTTTCTTATAT-AATTTATATA
* * *
6801 ATTTAAAATAATTAATATTAAATATAATTTAATACTGATATATAATTT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTT
6849 ATACATTTAA
Statistics
Matches: 272, Mismatches: 25, Indels: 38
0.81 0.07 0.11
Matches are distributed among these distances:
85 2 0.01
86 10 0.04
87 18 0.07
88 64 0.24
89 99 0.36
90 18 0.07
91 30 0.11
92 2 0.01
93 12 0.04
94 14 0.05
95 3 0.01
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (89 bp):
ATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTATAAT
AAATTTTCTTATATAATTTATATA
Found at i:10840 original size:16 final size:16
Alignment explanation
Indices: 10819--10850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10809 ATTTTGTTGG
*
10819 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
10835 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
10851 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:11048 original size:46 final size:43
Alignment explanation
Indices: 10988--11072 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
10978 CATGGTGGAT
*
10988 TCAGCACACAGCAACCACCCTTTGTAATCAATGATATCCGGTGGGA
1 TCAGCACACAGCAACCA-CC-TTATAATCAATGATA-CCGGTGGGA
* *
11034 TCAGCACATAGCAACCACCTTATAATTAATGATACCGGT
1 TCAGCACACAGCAACCACCTTATAATCAATGATACCGGT
11073 TCACATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 13 0.36
45 2 0.06
46 16 0.44
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
TCAGCACACAGCAACCACCTTATAATCAATGATACCGGTGGGA
Found at i:11170 original size:51 final size:49
Alignment explanation
Indices: 11078--11261 Score: 217
Period size: 51 Copynumber: 3.7 Consensus size: 49
11068 CCGGTTCACA
*
11078 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA--ACTATCCGATACACG
* * * * *
11129 TAGTGGCCTGCACATAGTACTACACATGTGATCGAAGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCAA-CTATCCGATACACG
* * *
11180 TAGTAGCCTGCACATAGTACTACACATGCGACCTA-TCATTCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAACT-A-TCCGATACACG
*
11230 TAGTAGCCTGCACATAGTACTACACACGTGAC
1 TAGTAGCCTGCACATAGTACTACACATGTGAC
11262 TATCACTTTC
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 40 0.35
51 69 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCAACTATCCGATACACG
Found at i:11284 original size:101 final size:102
Alignment explanation
Indices: 11068--11260 Score: 300
Period size: 102 Copynumber: 1.9 Consensus size: 102
11058 ATTAATGATA
* *
11068 CCGGTTCACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
* *
11133 GGCCTGCACATAGTACTACACATGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
* * *
11170 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGATACACGTAG
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAG
11233 TAGCCTGCACATAGTACTACACACGTGA
65 TAGCCTGCACATAGTACTACACACGTGA
11261 CTATCACTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 39 0.47
102 40 0.48
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
Found at i:13012 original size:18 final size:18
Alignment explanation
Indices: 12991--13026 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12981 CTCTCTAGAC
*
12991 ATTTGGATTTTATTTTGG
1 ATTTGGATTTTAATTTGG
13009 ATTTGGATTTTAATTTGG
1 ATTTGGATTTTAATTTGG
13027 GATATCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
ATTTGGATTTTAATTTGG
Found at i:27207 original size:30 final size:30
Alignment explanation
Indices: 27161--27225 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
27151 TACTTTATTA
27161 TTTAA-TCCTTTCCCTCCAAAATTCCGAAT
1 TTTAAGTCCTTTCCCTCCAAAATTCCGAAT
*
27190 TTTAAGTCCTCTT-CCTCCAAAATTCTGAAT
1 TTTAAGTCCT-TTCCCTCCAAAATTCCGAAT
27220 TTTAAG
1 TTTAAG
27226 GTTTATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 5 0.15
30 26 0.79
31 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (30 bp):
TTTAAGTCCTTTCCCTCCAAAATTCCGAAT
Found at i:35562 original size:274 final size:274
Alignment explanation
Indices: 35073--35627 Score: 858
Period size: 274 Copynumber: 2.0 Consensus size: 274
35063 ATATCTCAAT
* * * *
35073 CCCTCAAACCTCACACACTTATCATAATCAGATGCTACTAGAGTCCATGCATACCTACTTAGTCG
1 CCCTCAAACCTCAAACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
* * *
35138 TAAAAACTTGGCTTCATATTTGGCCACCGATCGGTTGCCCTGAACTAGGCTCATGAACTCGTATC
66 TAAAAACTCGACTTCATATTTGGCCACCGATCGGTCGCCCTGAACTAGGCTCATGAACTCGTATC
* * *
35203 GGTGAGCTTCAACATAATTTGCCCTCACATACTAACCTTGGAATGTGTTCTTGAAATAGTCCCAG
131 GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTAGAAGGTGTTCTTGAAATAGTCCCAG
* * * *
35268 TTCACCTGTTCAGGCTGAACACTTTGTTCAACTGTCAACCACCACTGATAAGCTTCGTCCCGAAA
196 TTCACCTGTTCAAGCTGAACACCTTGCTCAACTATCAACCACCACTGATAAGCTTCGTCCCGAAA
35333 TAAGGAAACAGCAC
261 TAAGGAAACAGCAC
* * * *
35347 CCCTCAAACTTTAAACACTTTTCATAATTAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
1 CCCTCAAACCTCAAACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
* *
35412 TAAAAACTCGACTTCCTATTTGGCCACCGATCGGTCGCCTTGAACTAGGCTCATGAACTCGTATC
66 TAAAAACTCGACTTCATATTTGGCCACCGATCGGTCGCCCTGAACTAGGCTCATGAACTCGTATC
* *
35477 GGTGAGCCTCAACATAATTTGCCCTCACATACTTACCTTAGAAGGTGTTCTTGAAATAGTCTCAG
131 GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTAGAAGGTGTTCTTGAAATAGTCCCAG
* * *
35542 TTCACCTGTTCAAGCTGAACACCTTGCTCAACTATCAACCACCACTGATAAGCTTTGTCCTGGAA
196 TTCACCTGTTCAAGCTGAACACCTTGCTCAACTATCAACCACCACTGATAAGCTTCGTCCCGAAA
* * *
35607 TAGGGACACAGCAT
261 TAAGGAAACAGCAC
35621 CCCTCAA
1 CCCTCAA
35628 TTTTTTGAGT
Statistics
Matches: 253, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
274 253 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (274 bp):
CCCTCAAACCTCAAACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
TAAAAACTCGACTTCATATTTGGCCACCGATCGGTCGCCCTGAACTAGGCTCATGAACTCGTATC
GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTAGAAGGTGTTCTTGAAATAGTCCCAG
TTCACCTGTTCAAGCTGAACACCTTGCTCAACTATCAACCACCACTGATAAGCTTCGTCCCGAAA
TAAGGAAACAGCAC
Found at i:38116 original size:19 final size:19
Alignment explanation
Indices: 38092--38131 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
38082 ACAGGCAACA
38092 AAGAATTCCCAATTCACGT
1 AAGAATTCCCAATTCACGT
38111 AAGAATTCCCAATTCACGT
1 AAGAATTCCCAATTCACGT
38130 AA
1 AA
38132 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (19 bp):
AAGAATTCCCAATTCACGT
Found at i:41219 original size:22 final size:22
Alignment explanation
Indices: 41194--41236 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
41184 AACTTAATTC
*
41194 ACATTTATTGATTGAATGTAAT
1 ACATTTATTAATTGAATGTAAT
41216 ACATTTATTAATTGAATGTAA
1 ACATTTATTAATTGAATGTAA
41237 AGAAGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ACATTTATTAATTGAATGTAAT
Found at i:47588 original size:28 final size:30
Alignment explanation
Indices: 47546--47602 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
47536 ACCATAGTGC
47546 CACTGTCAGTTGCATCAAAGTGCCACTTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTTT
* *
47576 CACTGT-A-TTGCATTAAAGTTCCACTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTT
47603 CCATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (30 bp):
CACTGTCAGTTGCATCAAAGTGCCACTTTT
Done.