Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1251
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: 28822
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2555 original size:22 final size:22
Alignment explanation
Indices: 2504--2555 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
2494 GTGATCTATG
2504 ACAGTGATGTATCGATACATGA
1 ACAGTGATGTATCGATACATGA
2526 A-AGTGATGTATCGATACATGA
1 ACAGTGATGTATCGATACATGA
2547 ACAGTGATG
1 ACAGTGATG
2556 AATAGTGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (22 bp):
ACAGTGATGTATCGATACATGA
Found at i:2562 original size:10 final size:10
Alignment explanation
Indices: 2543--2573 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2533 GTATCGATAC
2543 ATGAACAGTG
1 ATGAACAGTG
*
2553 ATGAATAGTG
1 ATGAACAGTG
2563 ATGAACAGTG
1 ATGAACAGTG
2573 A
1 A
2574 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2671 original size:53 final size:53
Alignment explanation
Indices: 2597--2733 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
2587 CTACTTCCAA
*
2597 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGGTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
2650 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
2703 TGTATCGATACATATTTTTGTGTATCGATAC
1 TGTATCGATACATA-TTTTGTGTATCGATAC
2734 TATGCAATTG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.81
54 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:2728 original size:20 final size:20
Alignment explanation
Indices: 2703--2772 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
2693 GCCAATGTCT
*
2703 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTTATG
**
2723 TGTATCGATAC-TATGCAAT-
1 TGTATCGATACATAT-TTATG
2742 TGTATCGATACAT-TTATATG
1 TGTATCGATACATATT-TATG
2762 TGTATCGATAC
1 TGTATCGATAC
2773 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTTATG
Found at i:2838 original size:21 final size:21
Alignment explanation
Indices: 2812--2852 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2802 GTCAACCTTG
2812 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
2833 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
2853 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:7157 original size:22 final size:19
Alignment explanation
Indices: 7132--7177 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 19
7122 AATTTTCCAC
7132 AAATTTTCACTTTTTCACTTCA
1 AAATTTTCA-TTTTTCA--TCA
7154 AAATTTTTCATTTTTCATCA
1 AAA-TTTTCATTTTTCATCA
7174 AAAT
1 AAAT
7178 CATCAACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
22 10 0.43
23 6 0.26
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTTCATTTTTCATCA
Found at i:9478 original size:20 final size:19
Alignment explanation
Indices: 9432--9488 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
9422 TTGTATCCAT
9432 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
9451 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
9470 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
9489 AGATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:9560 original size:33 final size:33
Alignment explanation
Indices: 9518--9582 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
9508 CAACCACTGT
9518 TTGTATTGATACATG-GGACAATGTATCGATACA
1 TTGTATTGATACATGAGGA-AATGTATCGATACA
*
9551 TTGTATTGATACATGATGGAATTGTATCGATA
1 TTGTATTGATACATGA-GGAAATGTATCGATA
9583 ACATGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.52
34 11 0.38
35 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (33 bp):
TTGTATTGATACATGAGGAAATGTATCGATACA
Found at i:9576 original size:21 final size:21
Alignment explanation
Indices: 9550--9607 Score: 98
Period size: 22 Copynumber: 2.7 Consensus size: 21
9540 GTATCGATAC
*
9550 ATTGTATTGATACATGATGGA
1 ATTGTATCGATACATGATGGA
9571 ATTGTATCGATAACATGATGGA
1 ATTGTATCGAT-ACATGATGGA
9593 ATTGTATCGATACAT
1 ATTGTATCGATACAT
9608 TGCTTGTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
ATTGTATCGATACATGATGGA
Found at i:18103 original size:14 final size:14
Alignment explanation
Indices: 18084--18113 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18074 ATATATATAT
18084 ATTTGGAGTCATAC
1 ATTTGGAGTCATAC
18098 ATTTGGAGTCATAC
1 ATTTGGAGTCATAC
18112 AT
1 AT
18114 ATAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (14 bp):
ATTTGGAGTCATAC
Found at i:18125 original size:2 final size:2
Alignment explanation
Indices: 18112--18142 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18102 GGAGTCATAC
*
18112 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18143 ACTTAGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18709 original size:25 final size:25
Alignment explanation
Indices: 18669--18724 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
18659 ATTTGTGTTG
*
18669 TTTTTAATATATTTTTTGTGTTATGT
1 TTTTTAATATATTTTTTATGTTAT-T
18695 TATTTTAAT-TA-TTTTTATGTTATT
1 T-TTTTAATATATTTTTTATGTTATT
18719 TTTTTA
1 TTTTTA
18725 TCGTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 2 0.07
25 11 0.39
26 3 0.11
27 7 0.25
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (25 bp):
TTTTTAATATATTTTTTATGTTATT
Found at i:19232 original size:2 final size:2
Alignment explanation
Indices: 19220--19254 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
19210 AATGCTAGTG
*
19220 TA TA T- TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19255 AGGATACCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20048 original size:50 final size:50
Alignment explanation
Indices: 19973--20181 Score: 278
Period size: 50 Copynumber: 4.2 Consensus size: 50
19963 AAGTATTGTC
* *
19973 ATTGTTGACTATTCTTTACCAACCTTTAACAATCGAGAGAGGTAGCTGTA
1 ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGCCGTA
*
20023 ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGATAGGTAGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGCCGTA
* * * * **
20073 ATTGTTGACGATTCTTCACCAACCTTTGACAATTGAAAGAGGT-G-ATTA
1 ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGCCGTA
* * * *
20121 TAATGTTGACTATTCTTCACCAACCTTTAATAATAGAGAGAGGTTGCCGTA
1 -ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGCCGTA
20172 ATTGTTGACT
1 ATTGTTGACT
20182 CTAAGCAACT
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
48 2 0.01
49 38 0.28
50 95 0.69
51 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGCCGTA
Found at i:20174 original size:99 final size:100
Alignment explanation
Indices: 19973--20180 Score: 294
Period size: 99 Copynumber: 2.1 Consensus size: 100
19963 AAGTATTGTC
* * * * *
19973 ATTGTTGACTATTCTTTACCAACCTTTAACAATCGAGAGAGGTAGCTGTAATTGTTGACTATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTAACAATCGAAAGAGGTAGATGTAAATGTTGACTATTCT
* *
20038 TCACCAACCTTTAACAATCGAGATAGGTAGCCGTA
66 TCACCAACCTTTAACAATAGAGAGAGGTAGCCGTA
* *
20073 ATTGTTGACGATTCTTCACCAACCTTTGACAATTGAAAGAGGT-GAT-TATAATGTTGACTATTC
1 ATTGTTGACGATTCTTCACCAACCTTTAACAATCGAAAGAGGTAGATGTA-AATGTTGACTATTC
* *
20136 TTCACCAACCTTTAATAATAGAGAGAGGTTGCCGTA
65 TTCACCAACCTTTAACAATAGAGAGAGGTAGCCGTA
20172 ATTGTTGAC
1 ATTGTTGAC
20181 TCTAAGCAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 2 0.02
99 56 0.58
100 38 0.40
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (100 bp):
ATTGTTGACGATTCTTCACCAACCTTTAACAATCGAAAGAGGTAGATGTAAATGTTGACTATTCT
TCACCAACCTTTAACAATAGAGAGAGGTAGCCGTA
Found at i:24538 original size:50 final size:50
Alignment explanation
Indices: 24460--24704 Score: 357
Period size: 50 Copynumber: 4.9 Consensus size: 50
24450 AGGTATTGCC
* * * *
24460 ATTGTTGATTATTCTGT-ACCAACTTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCT-TCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
24510 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
*
24560 ATTGTTTACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
* * *
24610 ATTGTTGACGATTCTTCACTAACCTTTGACAATTGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
* * * * *
24660 ATTGTTGATTATTCTTCACTAACCTTTGATAATAGAGAGATGTGG
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGG
24705 GTTGTAATTG
Statistics
Matches: 180, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 1 0.01
50 179 0.99
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCATA
Found at i:25229 original size:13 final size:13
Alignment explanation
Indices: 25211--25250 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
25201 TCACTATTCA
*
25211 TGTATCGATACAT
1 TGTATCGATACAC
25224 TGTATCGATACAC
1 TGTATCGATACAC
25237 TGTATCGATACAC
1 TGTATCGATACAC
25250 T
1 T
25251 ATAAATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:27281 original size:9 final size:9
Alignment explanation
Indices: 27267--27305 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
27257 TTTTATATTT
27267 AATTTAATA
1 AATTTAATA
27276 AATTTAATA
1 AATTTAATA
*
27285 AATTATAAAA
1 AATT-TAATA
*
27295 AAATTAATA
1 AATTTAATA
27304 AA
1 AA
27306 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATTTAATA
Found at i:27938 original size:16 final size:16
Alignment explanation
Indices: 27892--27948 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
27882 TGGGTTCAAG
* *
27892 TTCATTTGGGTTTGAA
1 TTCATTCGGGTTTGGA
**
27908 TTTGTTCGGGTTTGGA
1 TTCATTCGGGTTTGGA
27924 TTCATTCGGGTTTGGA
1 TTCATTCGGGTTTGGA
27940 CTT-ATTCGG
1 -TTCATTCGG
27949 ATTCGAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 32 0.94
17 2 0.06
ACGTcount: A:0.12, C:0.11, G:0.30, T:0.47
Consensus pattern (16 bp):
TTCATTCGGGTTTGGA
Found at i:27995 original size:17 final size:17
Alignment explanation
Indices: 27954--27997 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
27944 TTCGGATTCG
27954 AATTT-TTTTAAGTTCA
1 AATTTATTTTAAGTTCA
** *
27970 AATCGATTTTAAGTTTA
1 AATTTATTTTAAGTTCA
27987 AATTTATTTTA
1 AATTTATTTTA
27998 TATTATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAGTTCA
Found at i:28151 original size:20 final size:18
Alignment explanation
Indices: 28124--28162 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
28114 TGAAATCTAT
28124 ATTTA-TATATAAAATTA
1 ATTTATTATATAAAATTA
28141 ATTTATTATATAAAATTA
1 ATTTATTATATAAAATTA
28159 ATTT
1 ATTT
28163 TTCAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTATATAAAATTA
Found at i:28171 original size:18 final size:18
Alignment explanation
Indices: 28132--28171 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
28122 ATATTTATAT
*
28132 ATAAAATTAATTTATTAT
1 ATAAAATTAATTTATTAA
28150 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTATT-AA
28168 ATAA
1 ATAA
28172 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTATTAA
Found at i:28346 original size:12 final size:11
Alignment explanation
Indices: 28308--28351 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
28298 ACATCAAATT
28308 AATATTTAAAA
1 AATATTTAAAA
28319 AA-A-TTAAAA
1 AATATTTAAAA
*
28328 TATATTTAATAA
1 AATATTTAA-AA
28340 AATATTTAAAA
1 AATATTTAAAA
28351 A
1 A
28352 CTCATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 9 0.32
12 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:28455 original size:56 final size:56
Alignment explanation
Indices: 28395--28515 Score: 165
Period size: 56 Copynumber: 2.2 Consensus size: 56
28385 AGGCAGCAGT
* * * *
28395 AGGCAACAGCAATAAAACC-AAACCCAGATTAAAGTTTAGACCGAATTAACAGCAAC
1 AGGCAACAACAAT-AAACCTAAACACAGATTAAAGCTTAGACCAAATTAACAGCAAC
* *
28451 AGGCAACAACAATAAACCTAAACACAGATTGAAGCTTAGACCAAATTAATAGCAAC
1 AGGCAACAACAATAAACCTAAACACAGATTAAAGCTTAGACCAAATTAACAGCAAC
28507 A-GCAACAAC
1 AGGCAACAAC
28516 TTAGAAAGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 13 0.22
56 45 0.78
ACGTcount: A:0.50, C:0.23, G:0.13, T:0.14
Consensus pattern (56 bp):
AGGCAACAACAATAAACCTAAACACAGATTAAAGCTTAGACCAAATTAACAGCAAC
Done.