Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2816
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: 45482
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:6668 original size:6 final size:5
Alignment explanation
Indices: 6644--6698 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
6634 AAGAGAAAAT
*
6644 AAAGA AAAGA AAAGAA AAAGCA AAAG- -AAGA AAAGA AAATG- AAATA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AAAGA
6689 AAAGA AAAGA
1 AAAGA AAAGA
6699 GAGCAAGAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
3 3 0.07
5 28 0.67
6 11 0.26
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:6693 original size:20 final size:19
Alignment explanation
Indices: 6637--6698 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
6627 TCTTGTAAAG
6637 AGAAAAT-AAAGAAAAGAAA
1 AGAAAATGAAA-AAAAGAAA
* *
6656 AGAAAAAGCAAAAGAAGAAA
1 AGAAAATG-AAAAAAAGAAA
6676 AGAAAATGAAATAAAAGAAA
1 AGAAAATGAAA-AAAAGAAA
6696 AGA
1 AGA
6699 GAGCAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.25
20 24 0.67
21 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.05
Consensus pattern (19 bp):
AGAAAATGAAAAAAAGAAA
Found at i:6783 original size:11 final size:12
Alignment explanation
Indices: 6751--6781 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6741 TTGAGAGAAC
6751 TTGAAAAAGCCT
1 TTGAAAAAGCCT
6763 TTGAAAAAGCCT
1 TTGAAAAAGCCT
6775 TTGAAAA
1 TTGAAAA
6782 GCAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:6816 original size:29 final size:31
Alignment explanation
Indices: 6784--6863 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 31
6774 TTTGAAAAGC
*
6784 AAAAGAAAATGAAAAAGAAA-ATGAGATTG-
1 AAAAGAAAATGAAAAAGAAATATGAGAGTGA
* * *
6813 AAAAGAGAACG-AAAAGAAATTTGAGAGTGA
1 AAAAGAAAATGAAAAAGAAATATGAGAGTGA
*
6843 AAAAGAAGATGAAAAAGAAAT
1 AAAAGAAAATGAAAAAGAAAT
6864 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 8 0.20
31 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.23, T:0.12
Consensus pattern (31 bp):
AAAAGAAAATGAAAAAGAAATATGAGAGTGA
Found at i:6849 original size:28 final size:28
Alignment explanation
Indices: 6796--6849 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6786 AAGAAAATGA
*
6796 AAAAGAAAATGAGATTGAAAAGAGAACG
1 AAAAGAAAATGAGAGTGAAAAGAGAACG
*
6824 AAAAGAAATTTGAGAGTGAAAA-AGAA
1 AAAAGAAA-ATGAGAGTGAAAAGAGAA
6850 GATGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAAATGAGAGTGAAAAGAGAACG
Found at i:9100 original size:20 final size:20
Alignment explanation
Indices: 9054--9100 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9044 AGCTCGTTTC
*
9054 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
9074 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
9094 CAGCTCA
1 CAGCTCA
9101 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:10548 original size:30 final size:30
Alignment explanation
Indices: 10453--10549 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
10443 AGCTCACTCC
* * *
10453 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
10483 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
10513 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
10543 TAGCTCA
1 TAGCTCA
10550 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:11220 original size:24 final size:24
Alignment explanation
Indices: 11192--11239 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11182 AATTTACTAG
11192 GTTCATGCTGCCATTTATGAACCT
1 GTTCATGCTGCCATTTATGAACCT
*
11216 GTTCATGCTGCTATTTATGAACCT
1 GTTCATGCTGCCATTTATGAACCT
11240 ACATGCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (24 bp):
GTTCATGCTGCCATTTATGAACCT
Found at i:11462 original size:22 final size:20
Alignment explanation
Indices: 11430--11478 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
11420 GCCGAATTTA
11430 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
11453 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
11473 TGAACA
1 TGAACA
11479 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:15702 original size:20 final size:21
Alignment explanation
Indices: 15655--15702 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
15645 ATTTTGTCCA
*
15655 AATTA-GTTAAGTTGTTATTT
1 AATTATGTTAAGTTGCTATTT
*
15675 AAGT-TGTT-AGTTGCTATTT
1 AATTATGTTAAGTTGCTATTT
15694 AATTATGTT
1 AATTATGTT
15703 TAAATGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (21 bp):
AATTATGTTAAGTTGCTATTT
Found at i:19183 original size:42 final size:43
Alignment explanation
Indices: 19106--19207 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
19096 TCTCGGACGT
* * ** *
19106 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCTAAACAA
1 GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAAACAA
* *
19149 GGTCTTACACG-AAATCAGATAT-GATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAAATCA-ATATCGATGCCGATGTCCCAAACAA
*
19191 GGTCTTATACGTAAATC
1 GGTCTTACACGTAAATC
19208 TCAATCGAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 30 0.61
43 19 0.39
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAAACAA
Found at i:22219 original size:55 final size:55
Alignment explanation
Indices: 22153--22259 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
22143 ACCCGGTCTG
22153 GTTAAATCTCAAAATCTTGCTCCTCATCTTCCCTAAAGGTATTCTGATGTCTCCT
1 GTTAAATCTCAAAATCTTGCTCCTCATCTTCCCTAAAGGTATTCTGATGTCTCCT
22208 GTTAAATCTCAAAATCTTGCTCCTCATCTTCCCTAAAGGTATTCTGATGTCT
1 GTTAAATCTCAAAATCTTGCTCCTCATCTTCCCTAAAGGTATTCTGATGTCT
22260 TCAGGAGTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.38
Consensus pattern (55 bp):
GTTAAATCTCAAAATCTTGCTCCTCATCTTCCCTAAAGGTATTCTGATGTCTCCT
Found at i:22366 original size:44 final size:44
Alignment explanation
Indices: 22316--22750 Score: 602
Period size: 44 Copynumber: 10.1 Consensus size: 44
22306 AGGAACACCG
* *
22316 ATCTGTTATCTTCGATCTGCTCTCCACTGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
22360 ATCTGTTATCTTCGATCTGTTCTCCGCC-CTTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGC-TACAGAGACGCCAA
*
22404 ATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
22444 ATCTGTTATCTTCGATCTACTCTCCGTCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
22488 ATCTGTTATCTTCGATCTGCTCT-CGCCGCTATAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * * *
22531 ATCTATTATCTTCGATCTGCTTTCCACCGCTACAAAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
22575 ATCTATTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
22619 ATCTGCTATCTTTGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
22663 ATCTGTTATCTTCGATCTGCTCTTCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
22707 ATC----ATCTTCGATCTACTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
22747 ATCT
1 ATCT
22751 ATTGTCTGTT
Statistics
Matches: 350, Mismatches: 33, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
40 74 0.21
41 1 0.00
43 39 0.11
44 236 0.67
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (44 bp):
ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
Found at i:27869 original size:30 final size:30
Alignment explanation
Indices: 27774--27870 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
27764 AGCTCACTCC
*
27774 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
27804 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
27834 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
27864 TAGCTCA
1 TAGCTCA
27871 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:30051 original size:14 final size:13
Alignment explanation
Indices: 30028--30082 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
30018 GTAGAAAGAG
*
30028 GGGTACGAACATAA
1 GGGTAGGAACA-AA
*
30042 TGGTAGGAACGAAA
1 GGGTAGGAAC-AAA
30056 GGGTAGGAACAAA
1 GGGTAGGAACAAA
*
30069 GGGATATGAACAAA
1 GGG-TAGGAACAAA
30083 TTGGTCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 6 0.17
14 28 0.80
15 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.33, T:0.13
Consensus pattern (13 bp):
GGGTAGGAACAAA
Found at i:32831 original size:37 final size:37
Alignment explanation
Indices: 32781--32859 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
32771 TTATTATGAA
* *
32781 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
32818 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
32855 GTCTT
1 GTCTT
32860 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:33128 original size:47 final size:47
Alignment explanation
Indices: 32979--33451 Score: 768
Period size: 47 Copynumber: 10.1 Consensus size: 47
32969 CCTTCGGGAA
* * * * * * *
32979 TTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
33026 CTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
33072 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
33119 TTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
33166 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* * *
33213 TTATCACACATATACATTTTCACATTCATCACATCGGCTATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
33260 TTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
33307 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
33354 TTATCACACATAATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGCC
33402 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
33449 TTA
1 TTA
33452 CTATCATTTC
Statistics
Matches: 401, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
46 40 0.10
47 316 0.79
48 45 0.11
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:35174 original size:14 final size:13
Alignment explanation
Indices: 35139--35163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35129 CGTAGCTTCG
35139 AAAAAAAAAGTTA
1 AAAAAAAAAGTTA
35152 AAAAAAAAAGTT
1 AAAAAAAAAGTT
35164 TTGAAAAAAA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAGTTA
Found at i:38522 original size:40 final size:40
Alignment explanation
Indices: 38429--38653 Score: 226
Period size: 40 Copynumber: 5.7 Consensus size: 40
38419 GCTCCTCGTT
* * *
38429 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAA-TC-CA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38467 CACAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CA-AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
38508 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
38548 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
38588 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
38629 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
38654 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 106 0.68
41 17 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:38662 original size:41 final size:41
Alignment explanation
Indices: 38585--38662 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38575 CTTGTATCTC
* * *
38585 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38626 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38663 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.