Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1163
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: 40650
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Found at i:1708 original size:20 final size:19
Alignment explanation
Indices: 1623--1712 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 19
1613 ACCCTAGAAA
*
1623 GTATCGATACACATCCAAAT
1 GTATCGATACACATCC-ATT
* * *
1643 GTATCGATACATTATGCTTT
1 GTATCGATACA-CATCCATT
** *
1663 GTATCGATACATGTTCATT
1 GTATCGATACACATCCATT
* *
1682 TTATCGATACACACTCAATT
1 GTATCGATACACA-TCCATT
1702 GTATCGATACA
1 GTATCGATACA
1713 TGAAATTGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.27
20 37 0.67
21 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
GTATCGATACACATCCATT
Found at i:4199 original size:17 final size:17
Alignment explanation
Indices: 4173--4206 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4163 GAATGTTATC
*
4173 ATGTACATTTATGAATT
1 ATGTAAATTTATGAATT
4190 ATGTAAATTTATGAATT
1 ATGTAAATTTATGAATT
4207 GGAATATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
ATGTAAATTTATGAATT
Found at i:4235 original size:17 final size:17
Alignment explanation
Indices: 4183--4238 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
4173 ATGTACATTT
* * *
4183 ATGAATTATGTAAATTT
1 ATGAATTATGGATATTC
*
4200 ATGAA-T-TGGAATATCC
1 ATGAATTATGG-ATATTC
4216 ATGAATTATGGATATTC
1 ATGAATTATGGATATTC
4233 ATGAAT
1 ATGAAT
4239 GTATTAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 9 0.29
17 17 0.55
18 3 0.10
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (17 bp):
ATGAATTATGGATATTC
Found at i:9688 original size:15 final size:16
Alignment explanation
Indices: 9668--9700 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9658 ATTTTTTAAT
9668 TTTTTATCTTT-ATCA
1 TTTTTATCTTTCATCA
*
9683 TTTTTATTTTTCATCA
1 TTTTTATCTTTCATCA
9699 TT
1 TT
9701 AGTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATCTTTCATCA
Found at i:9732 original size:13 final size:13
Alignment explanation
Indices: 9711--9740 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9701 AGTTTAAAAA
9711 TAAAATATATTAT
1 TAAAATATATTAT
*
9724 TAAATTATATTAT
1 TAAAATATATTAT
9737 TAAA
1 TAAA
9741 CTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAATATATTAT
Found at i:10085 original size:18 final size:19
Alignment explanation
Indices: 10054--10098 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10044 TATATTTAAA
10054 TTTAAT-TAAAAA-ATATAT
1 TTTAATATAAAAATA-ATAT
*
10072 TTTAATATAAAAATAATTT
1 TTTAATATAAAAATAATAT
10091 TTTAATAT
1 TTTAATAT
10099 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 17 0.71
20 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAATATAAAAATAATAT
Found at i:11253 original size:2 final size:2
Alignment explanation
Indices: 11246--11316 Score: 72
Period size: 2 Copynumber: 36.0 Consensus size: 2
11236 TTATATTTAC
* * * * * * *
11246 AT AT AT AT AT AT AT AT AT GT AT TT AG AT AT AT TT GT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11288 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11317 GAACATGCGA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11683 original size:12 final size:13
Alignment explanation
Indices: 11666--11706 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
11656 AAAAATAATG
11666 AAAATAA-ACATA
1 AAAATAACACATA
11678 AAAATAACACATA
1 AAAATAACACATA
* *
11691 ATAA-AACAAATA
1 AAAATAACACATA
11703 AAAA
1 AAAA
11707 ATTTCTCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAACACATA
Found at i:11938 original size:4 final size:4
Alignment explanation
Indices: 11929--11985 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
11919 AAATGAGCTT
* * * * * *
11929 TATA TATA TATA TATA TATG TATG TATG TAAA TATA TGTA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
11977 TAAA TATA T
1 TATA TATA T
11986 GTGTATGTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:11940 original size:6 final size:6
Alignment explanation
Indices: 11929--11985 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
11919 AAATGAGCTT
* * * * * *
11929 TATATA TATATA TATATA TGTATG TATGTA AATATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
11977 TAAATA TAT
1 TATATA TAT
11986 GTGTATGTAT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:11965 original size:20 final size:20
Alignment explanation
Indices: 11933--11996 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
11923 GAGCTTTATA
* *
11933 TATATATATATATATGTATG
1 TATATAAATATATGTGTATG
* *
11953 TATGTAAATATATGTATATG
1 TATATAAATATATGTGTATG
11973 TATATAAATATATGTGTATG
1 TATATAAATATATGTGTATG
11993 TATA
1 TATA
11997 AATATGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (20 bp):
TATATAAATATATGTGTATG
Found at i:12002 original size:16 final size:17
Alignment explanation
Indices: 11937--12004 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 17
11927 TTTATATATA
11937 TATATATATATGTATGTATG
1 TATA-ATATATG--TGTATG
*
11957 TA-AATATATGTATATG
1 TATAATATATGTGTATG
11973 TATATAAATATATGTGTATG
1 --TAT-AATATATGTGTATG
11993 TATAA-ATATGTG
1 TATAATATATGTG
12005 AAAAATGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 12 0.29
17 2 0.05
18 12 0.29
19 1 0.02
20 15 0.36
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
TATAATATATGTGTATG
Found at i:15337 original size:21 final size:22
Alignment explanation
Indices: 15295--15337 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
15285 AAAGTAATAT
* *
15295 ATTTAGATAAATTAAGAGTTTA
1 ATTTAGATAAATTAAAACTTTA
*
15317 ATTT-GATGAATTAAAACTTTA
1 ATTTAGATAAATTAAAACTTTA
15338 TAGAAATCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (22 bp):
ATTTAGATAAATTAAAACTTTA
Found at i:17345 original size:52 final size:52
Alignment explanation
Indices: 17275--17414 Score: 226
Period size: 52 Copynumber: 2.7 Consensus size: 52
17265 TTTGAAAAGA
*
17275 AAATGTATCGATATATTTTTTATTGTATCGATACATTCTAGGTTTTTGACCT
1 AAATGTATCGATATATTTTTTATTGTATCGATACATTCTAGGTTTTTGACCG
* * *
17327 AAATGTATCGATACATTTTTTATTATATCAATACATTCTAGGTTTTTGACCG
1 AAATGTATCGATATATTTTTTATTGTATCGATACATTCTAGGTTTTTGACCG
**
17379 AAATGTATCGATATATTTTGCATTGTATCGATACAT
1 AAATGTATCGATATATTTTTTATTGTATCGATACAT
17415 GTAGGCAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (52 bp):
AAATGTATCGATATATTTTTTATTGTATCGATACATTCTAGGTTTTTGACCG
Found at i:19793 original size:97 final size:97
Alignment explanation
Indices: 19598--19803 Score: 229
Period size: 97 Copynumber: 2.1 Consensus size: 97
19588 ACTTCTGAAA
* * *
19598 GGATACTCTAA-TCCCGTTTTTAAACTCGTCGAGATTTAAATCTTATTTTTGCTTAAATTGTCAT
1 GGATACTCCAACT-CCGTTTTTAAACTCGTCAAGATTTAAATCTTATTTTTGCCTAAATTGTCAT
* ** * **
19662 CATCGAGGATACTTCAACCCTTTTCTTCTGAGG
65 CATCGAGGACACTTCAACCCCATTCCTCCAAGG
* * *
19695 GGATACTTCAACTCCGTTTTTAAACTTGTCAAGATTTAAATTCTTA-TTTTGCCTAAATTGTTAT
1 GGATACTCCAACTCCGTTTTTAAACTCGTCAAGATTTAAA-TCTTATTTTTGCCTAAATTGTCAT
* * *
19759 CGTTGTGGACA-TTCCAACCCCATTCCTCCAAGG
65 CATCGAGGACACTT-CAACCCCATTCCTCCAAGG
19792 GGATACTCCAAC
1 GGATACTCCAAC
19804 CCTATTTTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
96 2 0.02
97 82 0.91
98 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (97 bp):
GGATACTCCAACTCCGTTTTTAAACTCGTCAAGATTTAAATCTTATTTTTGCCTAAATTGTCATC
ATCGAGGACACTTCAACCCCATTCCTCCAAGG
Found at i:22131 original size:18 final size:18
Alignment explanation
Indices: 22090--22135 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
22080 CATCTTTTTT
*
22090 ATGAAAATATGCATTTAG
1 ATGAAAAAATGCATTTAG
22108 ATGAAAAAATGCA-TTAG
1 ATGAAAAAATGCATTTAG
*
22125 TTGGAAAAAAT
1 AT-GAAAAAAT
22136 ATGTACTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (18 bp):
ATGAAAAAATGCATTTAG
Found at i:22132 original size:17 final size:18
Alignment explanation
Indices: 22092--22133 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
22082 TCTTTTTTAT
22092 GAAAATATGCATTTAGATG
1 GAAAA-ATGCATTTAGATG
* *
22111 AAAAAATGCA-TTAGTTG
1 GAAAAATGCATTTAGATG
22128 GAAAAA
1 GAAAAA
22134 ATATGTACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 4 0.20
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (18 bp):
GAAAAATGCATTTAGATG
Found at i:23584 original size:27 final size:29
Alignment explanation
Indices: 23530--23584 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
23520 TGATTTGGTG
* *
23530 TTGAGTTTGCTATTTACTTGTTATGTTGA
1 TTGAGTTTGCTATTTACTGGTTACGTTGA
*
23559 TTGATTTTG-TATTTA-TGGTTACGTTG
1 TTGAGTTTGCTATTTACTGGTTACGTTG
23585 TGATGTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 6 0.26
29 8 0.35
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.56
Consensus pattern (29 bp):
TTGAGTTTGCTATTTACTGGTTACGTTGA
Found at i:32085 original size:15 final size:16
Alignment explanation
Indices: 32065--32098 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32055 GAAATAGGGA
*
32065 AAAGGAA-AGGGAATG
1 AAAGGAAGAGGGAAGG
32080 AAAGGAAGAGGGAAGG
1 AAAGGAAGAGGGAAGG
32096 AAA
1 AAA
32099 TGCAGTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (16 bp):
AAAGGAAGAGGGAAGG
Found at i:32095 original size:21 final size:20
Alignment explanation
Indices: 32071--32115 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
32061 GGGAAAAGGA
*
32071 AAGGGAATGAAAGGAAGAGGG
1 AAGGAAATG-AAGGAAGAGGG
*
32092 AAGGAAATGCAGTGAAGAGGG
1 AAGGAAATGAAG-GAAGAGGG
32113 AAG
1 AAG
32116 ATAGGAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.47, C:0.02, G:0.44, T:0.07
Consensus pattern (20 bp):
AAGGAAATGAAGGAAGAGGG
Done.