Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold370
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: 857924
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:842691 original size:12 final size:12
Alignment explanation
Indices: 842661--842719 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
842651 TATGTGGTGG
842661 AAAAGAAAG-AA
1 AAAAGAAAGAAA
*
842672 AGAAGAAAGAAA
1 AAAAGAAAGAAA
842684 AAAAGAAAGAAA
1 AAAAGAAAGAAA
*
842696 GAAAGAAAG-AA
1 AAAAGAAAGAAA
*
842707 AGAAGAAA-AAA
1 AAAAGAAAGAAA
842718 AA
1 AA
842720 TTATAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 19 0.47
12 21 0.52
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:843117 original size:11 final size:10
Alignment explanation
Indices: 843088--843118 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
843078 CATGTTCGTC
843088 CCTTTTTCTT
1 CCTTTTTCTT
843098 CCTTTTTCTT
1 CCTTTTTCTT
843108 CCTTTCTTCTT
1 CCTTT-TTCTT
843119 TCTTGTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CCTTTTTCTT
Found at i:845519 original size:5 final size:5
Alignment explanation
Indices: 845502--845554 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
845492 TTTTTTCTTC
* * *
845502 TTTC- TTTCC TTTCT TTTC- TTTCT TTT-T TTT-T TTTTT TTTTT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
845548 TTTCT TT
1 TTTCT TT
845555 ACTCTTACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 16 0.36
5 28 0.64
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:845527 original size:9 final size:9
Alignment explanation
Indices: 845499--845569 Score: 69
Period size: 9 Copynumber: 8.1 Consensus size: 9
845489 ATTTTTTTTC
845499 TTCTTTCTT
1 TTCTTTCTT
*
845508 TCCTTTCTT
1 TTCTTTCTT
845517 TTCTTTCTT
1 TTCTTTCTT
845526 TT-TTT-TT
1 TTCTTTCTT
845533 TT-TTT-TT
1 TTCTTTCTT
*
845540 TTTTTTCTT
1 TTCTTTCTT
845549 TTCTTTACTCT
1 TTCTTT-CT-T
*
845560 TACTTTCTT
1 TTCTTTCTT
845569 T
1 T
845570 CTTATTCCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
7 11 0.20
8 6 0.11
9 27 0.50
10 4 0.07
11 6 0.11
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:845591 original size:4 final size:4
Alignment explanation
Indices: 845495--845572 Score: 52
Period size: 4 Copynumber: 18.5 Consensus size: 4
845485 CTCCATTTTT
* * * *
845495 TTTC -TTC TTTC TTTCC TTTC TTTTC TTTC TTT- TTTT TTTT TTTT TTTT
1 TTTC TTTC TTTC TTT-C TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC
845543 TTTC TTTTC TTTAC TCTTAC TTTC TTTC TT
1 TTTC -TTTC TTT-C T-TT-C TTTC TTTC TT
845573 ATTCCACTGT
Statistics
Matches: 66, Mismatches: 1, Indels: 14
0.81 0.01 0.17
Matches are distributed among these distances:
3 6 0.09
4 39 0.59
5 16 0.24
6 5 0.08
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:848472 original size:21 final size:21
Alignment explanation
Indices: 848448--848514 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
848438 AATTCGCTGG
848448 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* *
848469 CCTTTAA--ACCAATATCGCTGG--
1 CCTTGAATCAGC-ATAT---TGGCA
848490 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
848511 CCTT
1 CCTT
848515 TAAAGCAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 16 0.47
22 4 0.12
23 5 0.15
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:848488 original size:42 final size:43
Alignment explanation
Indices: 848433--848700 Score: 263
Period size: 42 Copynumber: 6.0 Consensus size: 43
848423 ACATGTGTGG
*
848433 AGACGAAT-TCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
848475 A-ACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * *
848517 A-AGCAATGTTGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTA
*
848565 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * * *
848608 AGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGTATCTTCATCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGG------CACCTTTA
* * * * *
848657 AGTCCGATATCGTTGGCCTTGAATCAGCATATTGACATCTTTA
1 AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
848700 A
1 A
848701 CATTCCTAAG
Statistics
Matches: 192, Mismatches: 20, Indels: 27
0.80 0.08 0.11
Matches are distributed among these distances:
41 5 0.03
42 67 0.35
43 46 0.24
45 1 0.01
46 1 0.01
48 6 0.03
49 66 0.34
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
AGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
Found at i:848583 original size:49 final size:49
Alignment explanation
Indices: 848527--848821 Score: 264
Period size: 49 Copynumber: 6.1 Consensus size: 49
848517 AAGCAATGTT
848527 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* *
848576 GCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* * *
848619 GCCGGCCTTGAATCAGCACATTGGTATCTTCATCTTTAAGTCCGATATC
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* * * * * * * *
848668 GTTGGCCTTGAATCAGCATATTGACATCTTTAACATTCCTAAGCCCAATGTT
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATC-TT--TAAGTCCAATATC
** * * * *
848720 GCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* ** * *
848767 GCTGGCCATGAATCAGCACATTATCATTCTTCGCATCTTCAAGCCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCA-TCTT--CATCTTTAAGTCCAATATC
848819 GCT
1 GCT
848822 AGCCGCATAT
Statistics
Matches: 193, Mismatches: 39, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
43 38 0.20
45 1 0.01
47 31 0.16
49 68 0.35
50 7 0.04
52 48 0.25
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
Found at i:848657 original size:92 final size:90
Alignment explanation
Indices: 848477--848700 Score: 358
Period size: 92 Copynumber: 2.5 Consensus size: 90
848467 CACCTTTAAA
* *
848477 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAAGCAATGTTGCTGGCCTTGAATCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-AAGCAATGTCGCCGGCCTTGAATCA
848542 GCACATTGGCATCTTCATCTTTAAGT
65 GCACATTGGCATCTTCATCTTTAAGT
848568 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGCCGGCCTTGAATC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAG--CAATGTCGCCGGCCTTGAATC
*
848633 AGCACATTGGTATCTTCATCTTTAAGT
64 AGCACATTGGCATCTTCATCTTTAAGT
* * * *
848660 CCGATATCGTTGGCCTTGAATCAGCATATTGACATCTTTAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAA
848701 CATTCCTAAG
Statistics
Matches: 124, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
90 3 0.02
91 39 0.31
92 82 0.66
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (90 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGCAATGTCGCCGGCCTTGAATCAG
CACATTGGCATCTTCATCTTTAAGT
Found at i:849457 original size:19 final size:18
Alignment explanation
Indices: 849433--849515 Score: 86
Period size: 19 Copynumber: 4.7 Consensus size: 18
849423 AAACAGTAAC
849433 TGTATCGATACATAAGTGT
1 TGTATCGATACA-AAGTGT
849452 TGTATCGATAC-AA----
1 TGTATCGATACAAAGTGT
*
849465 TGTATCGATACAACACTGT
1 TGTATCGATACAA-AGTGT
*
849484 TGTATCGGTACATAAGTGT
1 TGTATCGATACA-AAGTGT
849503 TGTATCGATACAA
1 TGTATCGATACAA
849516 TGTATCGCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
15 1 0.02
17 2 0.04
18 1 0.02
19 37 0.69
20 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAAGTGT
Found at i:849470 original size:13 final size:13
Alignment explanation
Indices: 849452--849477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
849442 ACATAAGTGT
849452 TGTATCGATACAA
1 TGTATCGATACAA
849465 TGTATCGATACAA
1 TGTATCGATACAA
849478 CACTGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:849474 original size:32 final size:32
Alignment explanation
Indices: 849433--849495 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
849423 AAACAGTAAC
*
849433 TGTATCGATACATA-AGTGTTGTATCGATACAA
1 TGTATCGATACA-ACACTGTTGTATCGATACAA
*
849465 TGTATCGATACAACACTGTTGTATCGGTACA
1 TGTATCGATACAACACTGTTGTATCGATACA
849496 TAAGTGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTGTTGTATCGATACAA
Found at i:849585 original size:13 final size:13
Alignment explanation
Indices: 849567--849594 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
849557 ATTACTTAAA
849567 TGTATCGATACAT
1 TGTATCGATACAT
849580 TGTATCGATACAT
1 TGTATCGATACAT
849593 TG
1 TG
849595 ATCTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:850401 original size:19 final size:19
Alignment explanation
Indices: 850342--850438 Score: 92
Period size: 19 Copynumber: 5.7 Consensus size: 19
850332 TTTCAATGAT
850342 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
850362 TTGTATCGATAC--AA--G
1 TTGTATCGATACATAAGTG
850377 --GTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
850394 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
850408 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
850426 TTGTATCGATACA
1 TTGTATCGATACA
850439 ATTTAAGCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
13 21 0.32
15 5 0.08
17 5 0.08
19 22 0.34
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:850440 original size:32 final size:32
Alignment explanation
Indices: 850343--850440 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
850333 TTCAATGATT
850343 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
850376 GGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
850408 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
850440 T
1 T
850441 TTAAGCTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 50 0.81
33 12 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:850499 original size:13 final size:13
Alignment explanation
Indices: 850481--850505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
850471 ATTACTCAAA
850481 TGTATCGATACAT
1 TGTATCGATACAT
850494 TGTATCGATACA
1 TGTATCGATACA
850506 CTGATCTTTT
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):
TGTATCGATACAT
Found at i:850556 original size:52 final size:53
Alignment explanation
Indices: 850494--850638 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 53
850484 ATCGATACAT
*** *
850494 TGTATCGATACACTGAT-CTTTTTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
850546 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
850598 TGTATCGATACACT-ATTAAATGTATTGATATATGCAGGCAA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAA
850639 CTTTTCATAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 3 0.04
52 79 0.95
53 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Done.