Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1835
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: 27296
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:175 original size:5 final size:5
Alignment explanation
Indices: 130--157 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
120 TAATAACTAA
130 ATTGT ATTGT ATTGT ATTGT ATTGT ATT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATT
158 TTCTGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (5 bp):
ATTGT
Found at i:10909 original size:51 final size:51
Alignment explanation
Indices: 10838--11135 Score: 298
Period size: 51 Copynumber: 5.9 Consensus size: 51
10828 CAATGATGTT
* * * *
10838 CGGTTCACATAGTAGTCTGCACATAGTACTACACAGGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
* * * * **
10889 CGATACACGTAGTAGCCTGCACATAGTGCTACACACGTGATCGA-AATTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTACCATC
* ** * * *
10940 TGGTATGCATAGTAGCCTGCACATAGTACTACACATGTTACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
* * * * *
10991 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTACCATC
** * * * *
11042 CGGTATGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATTA--TTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATTACCATC
11092 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
11136 CACTTTCACT
Statistics
Matches: 194, Mismatches: 48, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.01
50 42 0.22
51 145 0.75
52 5 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
Found at i:10983 original size:102 final size:102
Alignment explanation
Indices: 10845--11131 Score: 461
Period size: 102 Copynumber: 2.8 Consensus size: 102
10835 GTTCGGTTCA
* *
10845 CATAGTAGTCTGCACATAGTACTACACAGGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
* * *
10910 CATAGTGCTACACACGTGATCGAAATTATCTGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* *
10947 CATAGTAGCCTGCACATAGTACTACACATGTTACCATTACCATCCGATACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
11012 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* * *
11049 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATTA--TTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATTACCATCCGATACACGTAGTAGCCTGC
11112 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
11132 CCATCACTTT
Statistics
Matches: 172, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 40 0.23
102 128 0.74
103 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:16727 original size:37 final size:36
Alignment explanation
Indices: 16676--16783 Score: 105
Period size: 37 Copynumber: 2.9 Consensus size: 36
16666 ATTCCAAAAA
*
16676 TAATA-TTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATACTTATCTTAATA-TTTAATATT-AATTTAATAT
**
16712 TAATACTTATCTTAATATTATTTTATTAATTTAATAT
1 TAATACTTATCTTAATATT-TAATATTAATTTAATAT
* *
16749 TAAAACGATTATCTTAATATTAAAT-TTAATTTAAT
1 TAATAC--TTATCTTAATATTTAATATTAATTTAAT
16784 GTTTATCTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
36 15 0.25
37 31 0.52
38 1 0.02
39 13 0.22
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (36 bp):
TAATACTTATCTTAATATTTAATATTAATTTAATAT
Found at i:16749 original size:11 final size:11
Alignment explanation
Indices: 16676--16751 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
16666 ATTCCAAAAA
*
16676 TAATATTATTT
1 TAATATTAATT
16687 TAATAGTTTAATAT
1 TAATA--TTAAT-T
16701 TAA-ATTTAATT
1 TAATA-TTAATT
16712 TAATACTT-ATCT
1 TAATA-TTAAT-T
16724 TAATATT-ATT
1 TAATATTAATT
16734 T--TATTAATT
1 TAATATTAATT
16743 TAATATTAA
1 TAATATTAA
16752 AACGATTATC
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 2 0.04
11 21 0.38
12 15 0.27
13 5 0.09
14 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:16765 original size:39 final size:37
Alignment explanation
Indices: 16698--16770 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
16688 AATAGTTTAA
*
16698 TATTAAATTTAATTTAATACTTATCTTAATATTATTT
1 TATTAAATTTAATTTAAAACTTATCTTAATATTATTT
16735 TATT-AATTTAATATTAAAACGATTATCTTAATATTA
1 TATTAAATTTAAT-TTAAAAC--TTATCTTAATATTA
16771 AATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 8 0.25
37 10 0.31
39 14 0.44
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.52
Consensus pattern (37 bp):
TATTAAATTTAATTTAAAACTTATCTTAATATTATTT
Found at i:16831 original size:62 final size:60
Alignment explanation
Indices: 16762--16879 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
16752 AACGATTATC
* * * * *
16762 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAAATTAATCTAATATTTATCTTG-A-ATAAACATTATATTAATTTAATAAGAT
*
16824 TTAATATTAAAATTAATCTAATATTTATCTTGAATAAATATTATATTAATTTAATA
1 TTAATATTAAAATTAATCTAATATTTATCTTGAATAAACATTATATTAATTTAATA
16880 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (60 bp):
TTAATATTAAAATTAATCTAATATTTATCTTGAATAAACATTATATTAATTTAATAAGAT
Found at i:23049 original size:39 final size:38
Alignment explanation
Indices: 22992--23066 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 38
22982 ACATAATAAA
22992 AAAATTATTGGATAAAAAATGGTTTTGAAAAAATAAAAT
1 AAAATTATTGGATAAAAAATGGTTTTG-AAAAATAAAAT
23031 AAAATTATTGGGAT-AAAAATGGTTTTGAAAAATAAA
1 AAAATTATT-GGATAAAAAATGGTTTTGAAAAATAAA
23067 TGAGATGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
38 9 0.26
39 22 0.63
40 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.31
Consensus pattern (38 bp):
AAAATTATTGGATAAAAAATGGTTTTGAAAAATAAAAT
Found at i:23946 original size:114 final size:114
Alignment explanation
Indices: 23719--24032 Score: 358
Period size: 112 Copynumber: 2.8 Consensus size: 114
23709 AAGAACATCA
* * *
23719 TTAGCGGCG-TTTACAACCACGCGCCGCAAA-ATCTCCTATCCAAAACGCAAT-G-TTTTCGTCT
1 TTAGCGGCGTTTTACAACCACGCGCCG-AAATATCTCCTAACCAAAACGC-ATCGTTTTTAGTGT
* * * * * *
23780 TTATGTATGCAAGAATTAGTGGCGCTTCAAAAAACATGCCGCTAAAGTGTC
64 TGATGTATCCTAGAATTAGTGGCGCTTCAAAAAACACGCCGCGAAAGCGTC
* *
23831 TTAGCGGCGTTTTAC-ACCAACGCGCCGTAATTTCTCCTAACCAAAACGCATCGTTTTTAGTGTT
1 TTAGCGGCGTTTTACAACC-ACGCGCCGAAATATCTCCTAACCAAAACGCATCGTTTTTAGTGTT
23895 GATGTATCCTAGAATTAGTGGCGCTTCTAAAAAA-ACGCCGCGAAAGCGTC
65 GATGTATCCTAGAATTAGTGGCGCTTC-AAAAAACACGCCGCGAAAGCGTC
* * * * * *
23945 TTAGCGGCGTATTGCGA-TATGCGCCGCAAATATCT--TAACCAAAACGCATCGTTTTTGGTGTT
1 TTAGCGGCGTTTTACAACCACGCGCCG-AAATATCTCCTAACCAAAACGCATCGTTTTTAGTGTT
*
24007 GATGTATCCTAGATTTAGTGGCGCTT
65 GATGTATCCTAGAATTAGTGGCGCTT
24033 TGTGATATGC
Statistics
Matches: 175, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
112 67 0.38
113 37 0.21
114 64 0.37
115 7 0.04
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (114 bp):
TTAGCGGCGTTTTACAACCACGCGCCGAAATATCTCCTAACCAAAACGCATCGTTTTTAGTGTTG
ATGTATCCTAGAATTAGTGGCGCTTCAAAAAACACGCCGCGAAAGCGTC
Found at i:24508 original size:233 final size:245
Alignment explanation
Indices: 24134--24836 Score: 960
Period size: 233 Copynumber: 2.9 Consensus size: 245
24124 TGTATACTTA
24134 TATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGC
1 TATTAGT-GCGCTTACTAGAAAACGCCGTT-AAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGC
24199 CGCAACGTATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTAGTGCGCTTATAGG
64 CGCAACGTATCTTAACAAAACGCAGTG-TTGGTCTTAAGCTATGTTACATTAG-GCGCTTATAGG
24264 AAACGCCGCAAAAATCTGAACC-AAACGCATCGTTTTGGTCTCGATGTATACTTCAATTAGT-G-
127 AAACGCCGCAAAAATCTGAACCAAAACGCA-CGTTTTGGTCTCGATGTATACTTCAATTAGTGGC
* * *
24326 GCTGACGTTAAAACGCCGCAAAAAATTCTAA-CTAAACGCGTAGTT-TTT-T-TTGAT
191 GCTGACGTTAAAACGCCGCAAAAAACT-TAACCAAAACGCGT-GTTATTTATGTT-AC
24380 TATTAGTGCGC-TACTAGAAAACGCCG-TAAGAATAGC-TT-GCGGCGCTTGAGCC-AAGCGCCG
1 TATTAGTGCGCTTACTAGAAAACGCCGTTAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCG
*
24440 CAACGTAAC-TAACAAAACGCA-TG-TGGTCTTAAGC-ATGTTACATTAGGCGCTTATAGGAAAC
66 CAACGTATCTTAACAAAACGCAGTGTTGGTCTTAAGCTATGTTACATTAGGCGCTTATAGGAAAC
* *
24501 GCCGC-AAAATATGAACCAAAACGCAC-CTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGA
131 GCCGCAAAAATCTGAACCAAAACGCACGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGA
* *
24564 CGTTAAAA-GTCGCAAAATACTTAACCAAAACGCGTGTTAATTTGATGTTAC
196 CGTTAAAACGCCGCAAAAAACTTAACCAAAACGCGTGTT-ATTT-ATGTTAC
* * * *
24615 TATATAGTGCGCTTACTAGAAAACG-CGTTAAGAATAGCTTTAGCAGCACTTGATCCAAAGTGCC
1 TAT-TAGTGCGCTTACTAGAAAACGCCGTTAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCC
* *
24679 GCAACGTATCTTAACAAAACGTAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAG
65 GCAACGTATCTTAACAAAACGCAGTG-TTGGTCTTAAGCTATGTTACA-TTA--GGCGCTTATAG
* *
24744 GAAAACGCTGCAAAATATCTGAACCAAAACGCACCGTTTTAGTCTCGATGTATACTTCAATTAGT
126 G-AAACGCCGCAAAA-ATCTGAACCAAAACGCA-CGTTTTGGTCTCGATGTATACTTCAATTAGT
24809 GGCGCTGACGTTAAAACGCCGCAAAAAA
188 GGCGCTGACGTTAAAACGCCGCAAAAAA
24837 GCAAAATACC
Statistics
Matches: 407, Mismatches: 21, Indels: 50
0.85 0.04 0.10
Matches are distributed among these distances:
231 34 0.08
232 32 0.08
233 43 0.11
234 12 0.03
235 16 0.04
236 12 0.03
237 24 0.06
238 14 0.03
239 27 0.07
240 29 0.07
241 13 0.03
242 11 0.03
243 1 0.00
244 25 0.06
245 12 0.03
246 10 0.02
248 12 0.03
249 8 0.02
250 3 0.01
251 16 0.04
252 1 0.00
253 43 0.11
254 9 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (245 bp):
TATTAGTGCGCTTACTAGAAAACGCCGTTAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCG
CAACGTATCTTAACAAAACGCAGTGTTGGTCTTAAGCTATGTTACATTAGGCGCTTATAGGAAAC
GCCGCAAAAATCTGAACCAAAACGCACGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGA
CGTTAAAACGCCGCAAAAAACTTAACCAAAACGCGTGTTATTTATGTTAC
Found at i:25995 original size:8 final size:9
Alignment explanation
Indices: 25968--25999 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
25958 TTCCCCATTT
25968 AATTCCCTA
1 AATTCCCTA
25977 AA-TCCCTA
1 AATTCCCTA
25985 AATTCCC-A
1 AATTCCCTA
25993 AATTCCC
1 AATTCCC
26000 CTGTCATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (9 bp):
AATTCCCTA
Found at i:26919 original size:17 final size:16
Alignment explanation
Indices: 26898--26947 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
26888 TAATAATTAA
26898 AATATTGTTTTAATAT
1 AATATTGTTTTAATAT
* *
26914 CTATATTAGTATT-ATA-
1 -AATATT-GTTTTAATAT
26930 AATATTGTTTTAATAT
1 AATATTGTTTTAATAT
26946 AA
1 AA
26948 CCTATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 8 0.31
18 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (16 bp):
AATATTGTTTTAATAT
Found at i:27233 original size:9 final size:8
Alignment explanation
Indices: 27188--27275 Score: 72
Period size: 9 Copynumber: 10.4 Consensus size: 8
27178 CTACATAATA
27188 AATTACAT
1 AATTACAT
27196 AATAATACAT
1 AAT--TACAT
*
27206 ACTTACAT
1 AATTACAT
*
27214 AAATTAAAT
1 -AATTACAT
27223 AAGTTACAT
1 AA-TTACAT
*
27232 AA-TACACA
1 AATTACA-T
27240 AATTACAT
1 AATTACAT
27248 AACTTACAT
1 AA-TTACAT
27257 AA-TACAT
1 AATTACAT
27264 AATTTACAT
1 AA-TTACAT
27273 AAT
1 AAT
27276 ACACAACTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
7 11 0.17
8 15 0.23
9 32 0.49
10 7 0.11
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (8 bp):
AATTACAT
Found at i:27243 original size:25 final size:25
Alignment explanation
Indices: 27209--27262 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
27199 AATACATACT
* *
27209 TACATAAATTAAATAAGTTACATAA
1 TACACAAATTAAATAACTTACATAA
*
27234 TACACAAATTACATAACTTACATAA
1 TACACAAATTAAATAACTTACATAA
27259 TACA
1 TACA
27263 TAATTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.30
Consensus pattern (25 bp):
TACACAAATTAAATAACTTACATAA
Found at i:27262 original size:16 final size:16
Alignment explanation
Indices: 27243--27290 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
27233 ATACACAAAT
27243 TACATAACTTACATAA
1 TACATAACTTACATAA
*
27259 TACATAATTTACATAA
1 TACATAACTTACATAA
* *
27275 TACACAACTGACATAA
1 TACATAACTTACATAA
27291 CTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (16 bp):
TACATAACTTACATAA
Done.