Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1330
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: 35921
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:4049 original size:104 final size:103
Alignment explanation
Indices: 3870--4058 Score: 256
Period size: 104 Copynumber: 1.8 Consensus size: 103
3860 CATTTTGAGC
* * * * *
3870 CATTTTTAACCTTTGCTTATTGACCTAATATCTGGTTTGAACATGTTTTGTTATAGCAAAATTCA
1 CATTTTCAACCTTTGCTCATTGACCTAATATCTAGTTTGAACATGTTTTGTTACACCAAAATTCA
*
3935 TGTCAAATTCACACTAGAATGCTTTAGATATTTCGACT
66 TGTCAAATTCACACCAGAATGCTTTAGATATTTCGACT
* *
3973 CATTTTCAGCCTTTGCTCATTGACCTAATGTTCTAGTTTGAACATGTTTT-TTCACACCAAAATT
1 CATTTTCAACCTTTGCTCATTGACCTAAT-ATCTAGTTTGAACATGTTTTGTT-ACACCAAAATT
*
4037 CATG-CTAGATTCACACCAGAAT
64 CATGTC-AAATTCACACCAGAAT
4059 ACATTTAGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
103 29 0.39
104 45 0.61
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (103 bp):
CATTTTCAACCTTTGCTCATTGACCTAATATCTAGTTTGAACATGTTTTGTTACACCAAAATTCA
TGTCAAATTCACACCAGAATGCTTTAGATATTTCGACT
Found at i:13113 original size:22 final size:22
Alignment explanation
Indices: 13059--13117 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
13049 TTCTAGCATT
13059 ATTTTGGCCTTAAAACAATCTTC
1 ATTTTGGCC-TAAAACAATCTTC
*
13082 A-TTTGAGCCTCAAACAATCTT-
1 ATTTTG-GCCTAAAACAATCTTC
13103 AGTTTTGGCCTAAAA
1 A-TTTTGGCCTAAAA
13118 TTTCTAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
22 22 0.71
23 8 0.26
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTTTGGCCTAAAACAATCTTC
Found at i:17278 original size:78 final size:78
Alignment explanation
Indices: 17170--17342 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 78
17160 GATACTTGCC
* ** *
17170 GAAAGTATGCTTTAGAGATAAGTCTGTCATTTCAGATCATTACTAAGTCTTTTAAGGTCATCGAG
1 GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
17235 ATACTTTCATGTT
66 ATACTTTCATGTT
* * * * * *
17248 GAAGGTATGCTTTAGGGATAGGTCCATCATTTTATATCATTACTAAGCCTTTTAAGGTTATTGAG
1 GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
17313 ATACTTTCATGTT
66 ATACTTTCATGTT
* *
17326 GAAAGTATACCTTAGGG
1 GAAAGTATGCTTTAGGG
17343 GATATTTTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (78 bp):
GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
ATACTTTCATGTT
Found at i:17395 original size:79 final size:79
Alignment explanation
Indices: 17304--17461 Score: 246
Period size: 79 Copynumber: 2.0 Consensus size: 79
17294 GCCTTTTAAG
** * *
17304 GTTATTGAGATACTTTCATGTTGAAAGTATACCTTA-GGGGATATTTTAATAATTTCATCTCAAA
1 GTTATTGAGATACTTTCACATCGAAAGTATACCTTAGGGGGAT-TTTCAATAATTTCATCTCAAA
17368 ACTAAGTCTATTAGA
65 ACTAAGTCTATTAGA
*
17383 GTTATTGAGATACTTTCACATCGAAAGTATACCTTAGGGGGCTTTTCAATAATTTCATCTCAAAA
1 GTTATTGAGATACTTTCACATCGAAAGTATACCTTAGGGGGATTTTCAATAATTTCATCTCAAAA
*
17448 CTAATTCTATTAGA
66 CTAAGTCTATTAGA
17462 ATTGTTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 67 0.93
80 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (79 bp):
GTTATTGAGATACTTTCACATCGAAAGTATACCTTAGGGGGATTTTCAATAATTTCATCTCAAAA
CTAAGTCTATTAGA
Found at i:18298 original size:20 final size:19
Alignment explanation
Indices: 18272--18344 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
18262 CTGCCAGTTT
*
18272 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
18292 TATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
18311 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
18332 -ATGTATCGATACA
1 CATGTATCGATACA
18345 TCTGGATGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.38
20 27 0.60
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:18317 original size:19 final size:20
Alignment explanation
Indices: 18272--18325 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
18262 CTGCCAGTTT
*
18272 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
18292 TATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
18311 CATGTATCGATACAA
1 CATGTATCGATACAA
18326 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:18923 original size:17 final size:17
Alignment explanation
Indices: 18903--18936 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18893 TATTTAAAAC
18903 TTTATAAAACAAATTTA
1 TTTATAAAACAAATTTA
18920 TTTATAAAACAAATTTA
1 TTTATAAAACAAATTTA
18937 ACAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAAACAAATTTA
Found at i:18942 original size:26 final size:26
Alignment explanation
Indices: 18910--18962 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18900 AACTTTATAA
18910 AACAAATTTATTTATAAAACAAATTT
1 AACAAATTTATTTATAAAACAAATTT
*
18936 AACAAATTTATTTATAAAATAAATTT
1 AACAAATTTATTTATAAAACAAATTT
18962 A
1 A
18963 TTTAAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AACAAATTTATTTATAAAACAAATTT
Found at i:20816 original size:13 final size:13
Alignment explanation
Indices: 20797--20836 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
20787 ATAGTAACCC
20797 ATGTATCGATACA
1 ATGTATCGATACA
* *
20810 TTGTATCGATATA
1 ATGTATCGATACA
*
20823 ATGTATTGATACA
1 ATGTATCGATACA
20836 A
1 A
20837 AGATCCTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21273 original size:13 final size:13
Alignment explanation
Indices: 21255--21279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21245 ATAATGCATA
21255 GTATCGATACATT
1 GTATCGATACATT
21268 GTATCGATACAT
1 GTATCGATACAT
21280 GACTAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:21292 original size:20 final size:21
Alignment explanation
Indices: 21267--21319 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
21257 ATCGATACAT
**
21267 TGTATCGATACATG-ACTAAA
1 TGTATCGATACATGCAAAAAA
* *
21287 TGTATCAATACTTGCAAAAAA
1 TGTATCGATACATGCAAAAAA
21308 TGTATCGATACA
1 TGTATCGATACA
21320 GGTGATTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGCAAAAAA
Found at i:28526 original size:52 final size:52
Alignment explanation
Indices: 28378--28506 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
28368 TGAAATATGA
*
28378 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
28430 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
28482 AAATTTGTCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
28507 AAGATTAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:28533 original size:13 final size:13
Alignment explanation
Indices: 28515--28573 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
28505 CAAAGATTAG
28515 TGTATCGATACAA
1 TGTATCGATACAA
28528 TGTATCGATAC-A
1 TGTATCGATACAA
28540 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
28549 TGTATCGATACAA
1 TGTATCGATACAA
28562 TGTATCGATACA
1 TGTATCGATACA
28574 TTTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:28558 original size:34 final size:34
Alignment explanation
Indices: 28515--28594 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
28505 CAAAGATTAG
28515 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
28549 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
28583 TGTATCGATACA
1 TGTATCGATACA
28595 TTTTCTTGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:28655 original size:19 final size:19
Alignment explanation
Indices: 28628--28690 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
28618 CGATACATTA
*
28628 TATCCATACAAAACTTATG
1 TATCGATACAAAACTTATG
28647 TATCGATAC---A--T-TG
1 TATCGATACAAAACTTATG
* *
28660 TGTCGATACAACACTTATG
1 TATCGATACAAAACTTATG
28679 TATCGATACAAA
1 TATCGATACAAA
28691 TTGTTGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
16 2 0.06
18 1 0.03
19 20 0.59
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (19 bp):
TATCGATACAAAACTTATG
Found at i:28669 original size:32 final size:32
Alignment explanation
Indices: 28618--28688 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
28608 AGCTTCGTAG
28618 CGATACATTATATCCATACAAAACTTATGTAT
1 CGATACATTATATCCATACAAAACTTATGTAT
* * * *
28650 CGATACATTGTGTCGATACAACACTTATGTAT
1 CGATACATTATATCCATACAAAACTTATGTAT
28682 CGATACA
1 CGATACA
28689 AATTGTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTATATCCATACAAAACTTATGTAT
Found at i:30068 original size:33 final size:33
Alignment explanation
Indices: 30026--30116 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
30016 TTAGGGATAA
*
30026 TGTATCGATACAAT-T-CTTCATGTATCGATACAC
1 TGTATCGATACAATGTGC--CATGTATCAATACAC
*
30059 TGTATCGATATAATGTGCCATGTATCAATACAC
1 TGTATCGATACAATGTGCCATGTATCAATACAC
* *
30092 TGTATCGATATAATATGCCATGTAT
1 TGTATCGATACAATGTGCCATGTAT
30117 TGATACAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 51 0.96
34 1 0.02
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCAATACAC
Found at i:30123 original size:33 final size:33
Alignment explanation
Indices: 30044--30123 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
30034 TACAATTCTT
*
30044 CATGTATCGATACACTGTATCGATATAATGTGC
1 CATGTATCGATACACTGTATCGATATAATATGC
*
30077 CATGTATCAATACACTGTATCGATATAATATGC
1 CATGTATCGATACACTGTATCGATATAATATGC
*
30110 CATGTATTGATACA
1 CATGTATCGATACA
30124 AATAGTGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (33 bp):
CATGTATCGATACACTGTATCGATATAATATGC
Found at i:30184 original size:20 final size:20
Alignment explanation
Indices: 30156--30207 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
30146 CCAGTTTCAT
*
30156 GTATCGATACAATTAAACAC
1 GTATTGATACAATTAAACAC
* *
30176 GTATTGATACAA-TGAACAT
1 GTATTGATACAATTAAACAC
*
30195 ATATTGATACAAT
1 GTATTGATACAAT
30208 GTATCGATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATTGATACAATTAAACAC
Found at i:31737 original size:8 final size:8
Alignment explanation
Indices: 31726--31795 Score: 70
Period size: 8 Copynumber: 8.5 Consensus size: 8
31716 AAATACATTT
*
31726 TAAACAAA
1 TAAAAAAA
31734 TAAAAAAA
1 TAAAAAAA
31742 TAAAAAAA
1 TAAAAAAA
31750 TTAGAAAAAA
1 -TA-AAAAAA
**
31760 GGAAAAAA
1 TAAAAAAA
*
31768 T-ATAAAA
1 TAAAAAAA
31775 TATAAAAAA
1 TA-AAAAAA
31784 TAAAAAAA
1 TAAAAAAA
31792 TAAA
1 TAAA
31796 TGTAAGTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.12
8 31 0.60
9 9 0.17
10 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:31835 original size:14 final size:13
Alignment explanation
Indices: 31816--31847 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31806 AGAAAATAGG
*
31816 TTAAAAATTTGGT
1 TTAAAAAATTGGT
31829 TTAAAAAATTGGT
1 TTAAAAAATTGGT
31842 TTAAAA
1 TTAAAA
31848 GAAAATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
TTAAAAAATTGGT
Found at i:34115 original size:11 final size:11
Alignment explanation
Indices: 34099--34137 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
34089 TAAGGTGGTT
34099 TTTTTCACTTG
1 TTTTTCACTTG
34110 TTTTTCACTTG
1 TTTTTCACTTG
34121 -TTTTCTACTTTG
1 TTTTTC-AC-TTG
34133 TTTTT
1 TTTTT
34138 GCTCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 13 0.52
12 3 0.12
13 4 0.16
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTCACTTG
Found at i:34471 original size:17 final size:18
Alignment explanation
Indices: 34449--34484 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
34439 TTCATGCATT
34449 TTATGACATTT-TGTGCA
1 TTATGACATTTCTGTGCA
34466 TTATGACATTTCTGTGCA
1 TTATGACATTTCTGTGCA
34484 T
1 T
34485 AGTTGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (18 bp):
TTATGACATTTCTGTGCA
Found at i:34893 original size:58 final size:60
Alignment explanation
Indices: 34779--35046 Score: 225
Period size: 59 Copynumber: 4.5 Consensus size: 60
34769 ACATCTTAGG
* ** *
34779 ACCATTTTAGGT-ATTTTTCATGTTTTAAGAACTTTTTATGCT-ATTTCATACATTTTAGAC
1 ACCATTTTA-GTCATTTTTCATGATTTAAG-GGTTTTTATGCTAATTTCATGCATTTTAGAC
* *
34839 -CCATTTTAGTCATTTTTAATGATTTAAGGGTTTTTATG-TAATTTCATGTATTTTAG-C
1 ACCATTTTAGTCATTTTTCATGATTTAAGGGTTTTTATGCTAATTTCATGCATTTTAGAC
* * * *
34896 ATCATTTTAAG-CATTTTTCATGATTT-AGGGATTTTTGTGCTAGTTT-ATTGCATTTCAGA-
1 ACCATTTT-AGTCATTTTTCATGATTTAAGGG-TTTTTATGCTAATTTCA-TGCATTTTAGAC
* ** * *
34955 ATCATTTTAGTCATTTTTTTCATGATTTAAGCATTATTATG-TAATTTCATGCACTTTA-AC
1 ACCATTTTAGTCA--TTTTTCATGATTTAAGGGTTTTTATGCTAATTTCATGCATTTTAGAC
* *
35015 ACTATTTTAGTACATTTTTCATGGTTTTAAGG
1 ACCATTTTAGT-CATTTTTCAT-GATTTAAGG
35047 ATCAATATGC
Statistics
Matches: 169, Mismatches: 23, Indels: 32
0.75 0.10 0.14
Matches are distributed among these distances:
57 6 0.04
58 54 0.32
59 57 0.34
60 28 0.17
61 22 0.13
62 2 0.01
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (60 bp):
ACCATTTTAGTCATTTTTCATGATTTAAGGGTTTTTATGCTAATTTCATGCATTTTAGAC
Done.