Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_986
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: 39421
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9030 original size:27 final size:27
Alignment explanation
Indices: 8993--9053 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
8983 TTGGTGCAGA
**
8993 ATCATCATCATTTTCAACAACAGCAAC
1 ATCATCATCATCATCAACAACAGCAAC
**
9020 ATCATCATCATCATCTGCAACAGCAAC
1 ATCATCATCATCATCAACAACAGCAAC
*
9047 AACATCA
1 ATCATCA
9054 ACAGCAGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (27 bp):
ATCATCATCATCATCAACAACAGCAAC
Found at i:10612 original size:16 final size:17
Alignment explanation
Indices: 10583--10617 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
10573 CCTTTTGCTG
10583 TAATTTGAAATATGAGT
1 TAATTTGAAATATGAGT
10600 TAATTTG-AATATGAGT
1 TAATTTGAAATATGAGT
10616 TA
1 TA
10618 TATTAGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (17 bp):
TAATTTGAAATATGAGT
Found at i:11701 original size:86 final size:88
Alignment explanation
Indices: 11584--11746 Score: 269
Period size: 86 Copynumber: 1.9 Consensus size: 88
11574 TTAAATGTAT
* *
11584 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA-TCATAATA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTAAAATTATACAAATTCAT-ATA
11648 AAAAAATTTATTATCAAGAATTAA
65 AAAAAATTTATTATCAAGAATTAA
11672 AAATTAT-TATCATTATT-AATTATATTTAATATTAATTATTTAAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTAAAATTATACAAATTCATATAA
*
11735 GAAAATTTATTA
66 AAAAATTTATTA
11747 GGTATAATTA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
86 50 0.70
87 14 0.20
88 7 0.10
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (88 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTAAAATTATACAAATTCATATAA
AAAAATTTATTATCAAGAATTAA
Found at i:11895 original size:13 final size:14
Alignment explanation
Indices: 11879--11910 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
11869 AGATATTTTA
11879 TTAATTATATAT-T
1 TTAATTATATATAT
11892 TTAATTATATATAT
1 TTAATTATATATAT
11906 TTAAT
1 TTAAT
11911 AATAATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTATATATAT
Found at i:11904 original size:15 final size:16
Alignment explanation
Indices: 11871--11907 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
11861 TATTATTAAG
11871 ATATTTTATTAATTAT
1 ATATTTTATTAATTAT
11887 ATATTTTAATT-A-TAT
1 ATATTTT-ATTAATTAT
11902 ATATTT
1 ATATTT
11908 AATAATAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 8 0.40
17 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTTTATTAATTAT
Found at i:12098 original size:14 final size:14
Alignment explanation
Indices: 12050--12113 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
12040 CATATAAGGA
*
12050 ATATTT-ATTAGAT
1 ATATTTAATTATAT
* *
12063 TTATTAAATTATAT
1 ATATTTAATTATAT
12077 AT-TTTAATTATAT
1 ATATTTAATTATAT
*
12090 ATATTTAATAATA-
1 ATATTTAATTATAT
12103 ATATGTTAATT
1 ATAT-TTAATT
12114 TTTTTATTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
13 20 0.49
14 21 0.51
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTTAATTATAT
Found at i:12220 original size:107 final size:109
Alignment explanation
Indices: 12087--12302 Score: 313
Period size: 107 Copynumber: 2.0 Consensus size: 109
12077 ATTTTAATTA
12087 TATATATTTAATAATAATATGTTAATTT-T-TTTATTAGTATCATATATTATGATTTGGAGT-AA
1 TATATATTTAATAAT-ATATGTTAATTTATATTTA-T-GTATCATATA-TATGATTT-GAGTAAA
12149 -TTCA-TATAAGAATA-TGATTATTAAGAATTTTATTAA-TTATTATTTAT
61 TTTCATTA-AAGAATATTGATTATTAAGAATTTTATTAATTTATT-TTTAT
12196 TATATATTTAATAAT-TATGTTAATTTATATTTATGTATCATATATATGATTTGAGTAAATTTCA
1 TATATATTTAATAATATATGTTAATTTATATTTATGTATCATATATATGATTTGAGTAAATTTCA
12260 TTAAAGAATATTGATTATTAAGAATTTTATTAATTTATTTTTA
66 TTAAAGAATATTGATTATTAAGAATTTTATTAATTTATTTTTA
12303 ATTAAAATAT
Statistics
Matches: 100, Mismatches: 0, Indels: 15
0.87 0.00 0.13
Matches are distributed among these distances:
105 4 0.04
106 10 0.10
107 32 0.32
108 30 0.30
109 24 0.24
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (109 bp):
TATATATTTAATAATATATGTTAATTTATATTTATGTATCATATATATGATTTGAGTAAATTTCA
TTAAAGAATATTGATTATTAAGAATTTTATTAATTTATTTTTAT
Found at i:12387 original size:16 final size:18
Alignment explanation
Indices: 12353--12389 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12343 TAATTTATTT
12353 TATTATTGATAATAATAAA
1 TATTATTGATAAT-ATAAA
12372 TATTATT-ATAAT-TAAA
1 TATTATTGATAATATAAA
12388 TA
1 TA
12390 ACTAATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTATTGATAATATAAA
Found at i:17638 original size:16 final size:17
Alignment explanation
Indices: 17602--17639 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17592 TGGCGAATCA
*
17602 TTTATTTTATTTTTGTC
1 TTTATTTTATATTTGTC
*
17619 TTTATTTTA-ATTTGTT
1 TTTATTTTATATTTGTC
17635 TTTAT
1 TTTAT
17640 GAAGGTACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTATTTTATATTTGTC
Found at i:17753 original size:19 final size:20
Alignment explanation
Indices: 17718--17755 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17708 AATGAAGGAC
17718 TTGTTCCGTTGGAGCGAAAT
1 TTGTTCCGTTGGAGCGAAAT
*
17738 TTGTTTCGTT-GAGCGAAA
1 TTGTTCCGTTGGAGCGAAA
17756 CTAGGCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (20 bp):
TTGTTCCGTTGGAGCGAAAT
Found at i:30544 original size:20 final size:20
Alignment explanation
Indices: 30486--30544 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
30476 CAGTAGCCTT
*
30486 TTTTATATTTTTAATATAAA
1 TTTTATATTTTTAATTTAAA
*
30506 TTTTATATTTTATTAATTTATA
1 TTTTATA-TTT-TTAATTTAAA
30528 -TTTATATTTTCTAATTT
1 TTTTATATTTT-TAATTT
30545 TTCTAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
21 9 0.26
22 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATATTTTTAATTTAAA
Found at i:30841 original size:14 final size:15
Alignment explanation
Indices: 30816--30859 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
30806 CATTTTATTA
30816 AATAAA-ATAAAATT
1 AATAAATATAAAATT
30830 -ATAAATATAAAATT
1 AATAAATATAAAATT
30844 AATAGAATATAAAATT
1 AATA-AATATAAAATT
30860 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 3 0.11
16 11 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATAAATATAAAATT
Found at i:30964 original size:3 final size:3
Alignment explanation
Indices: 30956--30990 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30946 TTTAAAATTC
30956 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30991 AAATATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31302 original size:15 final size:15
Alignment explanation
Indices: 31272--31313 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
31262 GGAATCAATT
*
31272 ATATTAATATTATTTA
1 ATATTAA-AATATTTA
31288 AT-TTATAAATATTTA
1 ATATTA-AAATATTTA
31303 ATATTAAAATA
1 ATATTAAAATA
31314 ATACAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAAAATATTTA
Found at i:32140 original size:45 final size:46
Alignment explanation
Indices: 32069--32328 Score: 195
Period size: 46 Copynumber: 5.6 Consensus size: 46
32059 TACGTATGAT
*
32069 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
32112 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * * *
32158 CACTTATCACTTTATCACCACTTATCACTTGTTCACGATCAGATAAATGTAGCTAAAGCTAC
1 CACTTATCAC----T------TTGTCACTTGATCA-GATAAG-T--G--TAGCTAAAGCTAC
*
32220 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--A---A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
32256 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGTTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
32302 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
32329 AGTACTCAAA
Statistics
Matches: 174, Mismatches: 14, Indels: 55
0.72 0.06 0.23
Matches are distributed among these distances:
36 28 0.16
37 1 0.01
38 2 0.01
39 1 0.01
40 2 0.01
42 2 0.01
43 11 0.06
44 6 0.03
45 22 0.13
46 41 0.24
50 1 0.01
51 4 0.02
52 11 0.06
56 12 0.07
57 5 0.03
58 2 0.01
62 23 0.13
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:32209 original size:62 final size:63
Alignment explanation
Indices: 32110--32232 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 63
32100 TAGCTAGGCT
*
32110 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
1 ACCACTTATCACTTTGTCAC-TGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTATC
32174 ACCACTTATCAC-TTGTTCAC-GATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTT
1 ACCACTTATCACTTTG-TCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTT
32233 GTCTCTTGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
62 38 0.67
63 3 0.05
64 16 0.28
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (63 bp):
ACCACTTATCACTTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTATC
Found at i:32260 original size:36 final size:36
Alignment explanation
Indices: 32220--32290 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
32210 CTAAAGCTAC
*
32220 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAA
*
32256 CACTTATCACTTTTTCACTTGATCAGATAAGTGTA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTA
32291 GTTAAAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAA
Found at i:32311 original size:82 final size:80
Alignment explanation
Indices: 32176--32328 Score: 252
Period size: 82 Copynumber: 1.9 Consensus size: 80
32166 ACTTTATCAC
*
32176 CACTTATCACTTGTTCACGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
1 CACTTATCACTTGTTCACGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTATCTCTTG
32241 ATCAGATAAGTGTAA
66 ATCAGATAAGTGTAA
* * *
32256 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGTTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTGTTCAC--GATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTATCTCT
32321 TGATCAGA
64 TGATCAGA
32329 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 17 0.25
82 50 0.75
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (80 bp):
CACTTATCACTTGTTCACGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTATCTCTTG
ATCAGATAAGTGTAA
Found at i:35146 original size:15 final size:15
Alignment explanation
Indices: 35121--35159 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
35111 TTGATCAACT
* *
35121 TTAACTTTTTTTCTCA
1 TTAA-TTTTTTTATAA
35137 TTAATTTTTTTATAA
1 TTAATTTTTTTATAA
35152 TTAATTTT
1 TTAATTTT
35160 AGTATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTTTTTTATAA
Done.