Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1090
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: 25391
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:1392 original size:28 final size:28
Alignment explanation
Indices: 1360--1419 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
1350 TGTTATTTTT
1360 ATGCCGTCAACTGGTAGTCCTAGTTGAA
1 ATGCCGTCAACTGGTAGTCCTAGTTGAA
1388 ATGCCGTCAACTGGTAGTCCTAGTTGAA
1 ATGCCGTCAACTGGTAGTCCTAGTTGAA
1416 ATGC
1 ATGC
1420 AACATCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (28 bp):
ATGCCGTCAACTGGTAGTCCTAGTTGAA
Found at i:2640 original size:15 final size:15
Alignment explanation
Indices: 2617--2682 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 15
2607 CATCTTTTCC
*
2617 TCTTT-TTTTTTTTT
1 TCTTTCTTTTTTCTT
2631 TCTTTC-TTTTTCTCT
1 TCTTTCTTTTTTCT-T
* * *
2646 CCTTCCTTTTTT-TG
1 TCTTTCTTTTTTCTT
*
2660 TCTTTCTTTTTCCTT
1 TCTTTCTTTTTTCTT
2675 TCTTTCTT
1 TCTTTCTT
2683 CTCTTTTCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 20 0.50
15 15 0.38
16 5 0.12
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.76
Consensus pattern (15 bp):
TCTTTCTTTTTTCTT
Found at i:2689 original size:19 final size:19
Alignment explanation
Indices: 2627--2692 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
2617 TCTTTTTTTT
*
2627 TTTTTCTTTCTTT-TTCTC
1 TTTTCCTTTCTTTCTTCTC
* *
2645 TCCTTCCTTTTTTTGTCTT-TC
1 T-TTTCC-TTTCTT-TCTTCTC
2666 TTTTTCCTTTCTTTCTTCTC
1 -TTTTCCTTTCTTTCTTCTC
2686 TTTTCCT
1 TTTTCCT
2693 CCCTCCTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.03
19 14 0.38
20 12 0.32
21 7 0.19
22 3 0.08
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTCCTTTCTTTCTTCTC
Found at i:3067 original size:25 final size:25
Alignment explanation
Indices: 2994--3068 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
2984 TTAATTTGAC
* *
2994 AAATAAAAATAACTTATAC-CTTA-
1 AAATAAAAATAAATTAAACTCTTAT
* *
3017 AAAT-AAAATAAATTTAAATTTTTAT
1 AAATAAAAATAAA-TTAAACTCTTAT
*
3042 AAATAAAAATAAATTAAACTCGTAT
1 AAATAAAAATAAATTAAACTCTTAT
3067 AA
1 AA
3069 TTATATCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 7 0.17
23 8 0.20
24 3 0.07
25 15 0.37
26 8 0.20
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (25 bp):
AAATAAAAATAAATTAAACTCTTAT
Found at i:3411 original size:14 final size:13
Alignment explanation
Indices: 3392--3421 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3382 TAATAATTTG
3392 ATTTTTTAATATAA
1 ATTTTTTAAT-TAA
3406 ATTTTTTAATTAA
1 ATTTTTTAATTAA
3419 ATT
1 ATT
3422 AAATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTTAATTAA
Found at i:3504 original size:75 final size:74
Alignment explanation
Indices: 3354--3497 Score: 193
Period size: 75 Copynumber: 2.0 Consensus size: 74
3344 GTAATTTAAA
* * *
3354 ATTTTTTATTTGATTAAAAATTAATAATTAATAATTTGATTTTTTAATATAAATTTTTTAATTAA
1 ATTTTGTATTTGATTAAAAATTAATAATTAATAAGTTGA-TTTTTAACATAAATTTTTTAATTAA
3419 ATTAAATTTT
65 ATTAAATTTT
* * * * *
3429 ATTTTGTATTTTATTAAAAATTAATAATTTATACGTTGA-TTTTAACAT-GATTTTTTAATTTAA
1 ATTTTGTATTTGATTAAAAATTAATAATTAATAAGTTGATTTTTAACATAAATTTTTTAATTAAA
3492 TTAAAT
66 TTAAAT
3498 GTTTTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
72 19 0.31
73 8 0.13
75 34 0.56
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (74 bp):
ATTTTGTATTTGATTAAAAATTAATAATTAATAAGTTGATTTTTAACATAAATTTTTTAATTAAA
TTAAATTTT
Found at i:3620 original size:14 final size:14
Alignment explanation
Indices: 3596--3648 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3586 TTCTGAATAG
3596 ATTTGTAAAAAAAAT
1 ATTT-TAAAAAAAAT
*
3611 ATTTTAAAAAATAT
1 ATTTTAAAAAAAAT
*
3625 -TTTTCAAAAAACAT
1 ATTTT-AAAAAAAAT
*
3639 AATTTAAAAA
1 ATTTTAAAAA
3649 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 22 0.67
15 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (14 bp):
ATTTTAAAAAAAAT
Found at i:5452 original size:7 final size:7
Alignment explanation
Indices: 5440--5471 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5430 ACATGAGCTA
5440 AATTGGG
1 AATTGGG
5447 AATTGGG
1 AATTGGG
5454 AATTGGG
1 AATTGGG
*
5461 AATTGAG
1 AATTGGG
5468 AATT
1 AATT
5472 TAGGTTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (7 bp):
AATTGGG
Found at i:8490 original size:2 final size:2
Alignment explanation
Indices: 8485--8521 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
8475 GCAATGTAAA
8485 AG AG AG AG AG CA- AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG A
8522 TGGGTGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9151 original size:20 final size:21
Alignment explanation
Indices: 9125--9179 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
9115 AATACTATAG
9125 GTTTATTAAACATGTATT-GT
1 GTTTATTAAACATGTATTCGT
* * *
9145 TTTTATTACAC-TGTTTTCGT
1 GTTTATTAAACATGTATTCGT
9165 GTTTATTAAACATGT
1 GTTTATTAAACATGT
9180 CATGTTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.18
20 20 0.71
21 3 0.11
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (21 bp):
GTTTATTAAACATGTATTCGT
Found at i:11118 original size:27 final size:28
Alignment explanation
Indices: 11076--11136 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
11066 GAGGCCAAAT
11076 GAGG-TACCGTTAAAAAGGTGACTCGAC
1 GAGGATACCGTTAAAAAGGTGACTCGAC
11103 GAGGATACCGTTAAAAAGGTGACTCGAC
1 GAGGATACCGTTAAAAAGGTGACTCGAC
11131 GAGGAT
1 GAGGAT
11137 GGATTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.18
Consensus pattern (28 bp):
GAGGATACCGTTAAAAAGGTGACTCGAC
Found at i:13061 original size:20 final size:20
Alignment explanation
Indices: 13032--13106 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
13022 AAAAAGACAT
*
13032 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTAAAG
* * *
13052 AATATATCGATACATTCATG
1 AATGTATCGATACATTAAAG
* * *
13072 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTAAAG
13092 AATGTATCGATACAT
1 AATGTATCGATACAT
13107 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAG
Found at i:13357 original size:20 final size:20
Alignment explanation
Indices: 13332--13382 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
13322 ATTTTAACTA
13332 GATGTATCGATACATTATTC
1 GATGTATCGATACATTATTC
13352 GATGTATCGATACATTATTC
1 GATGTATCGATACATTATTC
*
13372 AATGTATCGAT
1 GATGTATCGAT
13383 GCATCTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
GATGTATCGATACATTATTC
Found at i:13432 original size:20 final size:20
Alignment explanation
Indices: 13403--13477 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
13393 AAAAAGACAT
*
13403 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTAAAG
* * *
13423 AATATATCGATACATTCATG
1 AATGTATCGATACATTAAAG
* * *
13443 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTAAAG
13463 AATGTATCGATACAT
1 AATGTATCGATACAT
13478 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAG
Found at i:16114 original size:32 final size:32
Alignment explanation
Indices: 16073--16136 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
16063 TAAAAAAAGA
16073 AAGAACTTTCACAGAAGAAAATGATGTAGGTT
1 AAGAACTTTCACAGAAGAAAATGATGTAGGTT
16105 AAGAACTTTCACAGAAGAAAATGATGTAGGTT
1 AAGAACTTTCACAGAAGAAAATGATGTAGGTT
16137 CCATATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (32 bp):
AAGAACTTTCACAGAAGAAAATGATGTAGGTT
Found at i:20392 original size:83 final size:80
Alignment explanation
Indices: 20255--20505 Score: 281
Period size: 83 Copynumber: 3.1 Consensus size: 80
20245 CCGCTAAAGG
* * * * * *
20255 TCTTCATCACTACCATGTTATCATAACGCCGAAAATACAAGGTTAGAGGCAATTATTTCCTTGTT
1 TCTTCATCACTACGATGTTACCATAAC-CCCAAAATACAAGGCTAGAGCCAATTATTTCCTTGTC
* *
20320 GACGTCACGACTAATA
65 GACGTCACCACTAAGA
* * *
20336 TCTTCGTCACTATGATGTTTACCCATAACCTCCAAAATACAAGGCTAG-GTCCAATTATTTCCTC
1 TCTTCATCACTACGATG-TTA-CCATAACC-CCAAAATACAAGGCTAGAG-CCAATTATTTCCTT
*
20400 ATCGAC-TCACCACTAAAGA
62 GTCGACGTCACCACT-AAGA
* * * *
20419 TCTTCATCACTACGATGTTATCATAACCCCGAAATACAAGGGTAGAGCCAATCATTTCCTTGTCG
1 TCTTCATCACTACGATGTTACCATAACCCCAAAATACAAGGCTAGAGCCAATTATTTCCTTGTCG
*
20484 ACGTCGCCACTAAGA
66 ACGTCACCACTAAGA
20499 TCTTCAT
1 TCTTCAT
20506 TGGTTTCCAT
Statistics
Matches: 142, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
80 43 0.30
81 29 0.20
82 15 0.11
83 55 0.39
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (80 bp):
TCTTCATCACTACGATGTTACCATAACCCCAAAATACAAGGCTAGAGCCAATTATTTCCTTGTCG
ACGTCACCACTAAGA
Found at i:22396 original size:20 final size:19
Alignment explanation
Indices: 22348--22396 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
22338 TATAAATTTA
22348 ATATATTTATATATTTATT
1 ATATATTTATATATTTATT
*
22367 GTATAGTTTATATTATTT-TT
1 ATATA-TTTATA-TATTTATT
22387 ATAATATTTA
1 AT-ATATTTA
22397 AATTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
ATATATTTATATATTTATT
Found at i:24050 original size:18 final size:18
Alignment explanation
Indices: 24018--24052 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24008 GTTGATAATT
24018 TTTTAAGTTTTTTTTTTA
1 TTTTAAGTTTTTTTTTTA
24036 TTTT-AGTTTTATTTTTT
1 TTTTAAGTTTT-TTTTTT
24053 TAAGATCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTAAGTTTTTTTTTTA
Found at i:24325 original size:16 final size:17
Alignment explanation
Indices: 24285--24340 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 17
24275 AATTTAAAAA
24285 ATAATAAAT-AATTA-T
1 ATAATAAATAAATTATT
*
24300 ATAAT-AA-AATTTATT
1 ATAATAAATAAATTATT
24315 -TAA-AAATAAATTATT
1 ATAATAAATAAATTATT
24330 ATAATAAATAA
1 ATAATAAATAA
24341 TAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 13 0.39
16 3 0.09
17 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAAATAAATTATT
Found at i:24342 original size:20 final size:20
Alignment explanation
Indices: 24315--24361 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24305 AAAATTTATT
* *
24315 TAAA-AATAAATTATTATAA
1 TAAATAATAAATAATTAAAA
24334 TAAATAATAAATAATTAAAA
1 TAAATAATAAATAATTAAAA
24354 TAATATAA
1 TAA-ATAA
24362 AACCTAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAATAAATAATTAAAA
Found at i:24675 original size:12 final size:12
Alignment explanation
Indices: 24660--24692 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
24650 TTTTTTTTAC
24660 TTATTATTTTTT
1 TTATTATTTTTT
24672 TTATT-TTTTTT
1 TTATTATTTTTT
24683 TTATCTATTT
1 TTAT-TATTT
24693 AATCTTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 6 0.32
13 3 0.16
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTATTTTTT
Done.