Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold793
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: 691781
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 5
Found at i:663468 original size:8 final size:8
Alignment explanation
Indices: 663445--663484 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
663435 TATCTTACAT
663445 ATATTAAA
1 ATATTAAA
663453 ATA-T-AA
1 ATATTAAA
663459 ATATTAAA
1 ATATTAAA
663467 ATA-T-AA
1 ATATTAAA
663473 ATATTAAA
1 ATATTAAA
663481 ATAT
1 ATAT
663485 AATTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 10 0.36
7 4 0.14
8 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATTAAA
Found at i:663505 original size:14 final size:14
Alignment explanation
Indices: 663445--663502 Score: 89
Period size: 14 Copynumber: 4.1 Consensus size: 14
663435 TATCTTACAT
663445 ATATTAAAATATAA
1 ATATTAAAATATAA
663459 ATATTAAAATATAA
1 ATATTAAAATATAA
663473 ATATTAAAATATAA
1 ATATTAAAATATAA
* * *
663487 TTTTTAATATATAA
1 ATATTAAAATATAA
663501 AT
1 AT
663503 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:663537 original size:16 final size:15
Alignment explanation
Indices: 663516--663552 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
663506 TTTAAAAAAT
663516 AAAATATAATTTTTTA
1 AAAATAT-ATTTTTTA
*
663532 AAAATATTTTTTTTA
1 AAAATATATTTTTTA
663547 AAAATA
1 AAAATA
663553 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATATATTTTTTA
Found at i:663550 original size:36 final size:38
Alignment explanation
Indices: 663477--663573 Score: 128
Period size: 36 Copynumber: 2.6 Consensus size: 38
663467 ATATAAATAT
663477 TAAAATATAA-TTTTTAATATATAAATTTTTTTAAAAAA
1 TAAAATATAATTTTTTAA-ATATAAATTTTTTTAAAAAA
* *
663515 TAAAATATAATTTTTTAAA-A-ATATTTTTTTTAAAAA
1 TAAAATATAATTTTTTAAATATAAATTTTTTTAAAAAA
*
663551 TAAAATATATTTTTATTAAATAT
1 TAAAATATAATTTT-TTAAATAT
663574 CTATTTATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
36 27 0.52
37 6 0.12
38 12 0.23
39 7 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
TAAAATATAATTTTTTAAATATAAATTTTTTTAAAAAA
Found at i:663561 original size:22 final size:21
Alignment explanation
Indices: 663530--663570 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
663520 TATAATTTTT
*
663530 TAAAAATATTTTTTTTAAAAA
1 TAAAAATATTTTTATTAAAAA
663551 TAAAATATATTTTTATTAAA
1 TAAAA-ATATTTTTATTAAA
663571 TATCTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAATATTTTTATTAAAAA
Found at i:664342 original size:12 final size:12
Alignment explanation
Indices: 664325--664371 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
664315 ATTAGATATC
664325 AATATATATTTA
1 AATATATATTTA
*
664337 AATATAAATTTA
1 AATATATATTTA
664349 ATATATAATATTTTA
1 A-ATAT-ATA-TTTA
664364 AATATATA
1 AATATATA
664372 AAATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 12 0.40
13 7 0.23
14 6 0.20
15 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATATATTTA
Found at i:664377 original size:23 final size:25
Alignment explanation
Indices: 664351--664403 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
664341 TAAATTTAAT
*
664351 ATATAATATTTTAAATA-TATA-AA
1 ATATAATATTTTAAAAATTATATAA
*
664374 ATATAATTTTTTAAAAATTATATAA
1 ATATAATATTTTAAAAATTATATAA
664399 ATATA
1 ATATA
664404 TATCGAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
24 4 0.15
25 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATAATATTTTAAAAATTATATAA
Found at i:665011 original size:10 final size:10
Alignment explanation
Indices: 664960--665013 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
664950 ATTATTACAG
664960 TTATAATTTT
1 TTATAATTTT
664970 TTAATAA-TTT
1 TT-ATAATTTT
* **
664980 TTAAAATAAT
1 TTATAATTTT
*
664990 TTATAATATT
1 TTATAATTTT
665000 TTATAATTTT
1 TTATAATTTT
665010 TTAT
1 TTAT
665014 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 3 0.08
10 29 0.81
11 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATAATTTT
Found at i:665012 original size:20 final size:19
Alignment explanation
Indices: 664960--665013 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
664950 ATTATTACAG
664960 TTATAATTTTTTAATAATTT
1 TTATAATTTTTT-ATAATTT
* **
664980 TTAAAATAATTTATAATATT
1 TTATAATTTTTTATAAT-TT
665000 TTATAATTTTTTAT
1 TTATAATTTTTTAT
665014 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATTTTTTATAATTT
Found at i:665214 original size:17 final size:17
Alignment explanation
Indices: 665182--665215 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
665172 AATAAATAGT
*
665182 AAAATTAATTACTATAA
1 AAAATTAAATACTATAA
*
665199 AAAATTAAATATTATAA
1 AAAATTAAATACTATAA
665216 TTATAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTAAATACTATAA
Found at i:665225 original size:14 final size:14
Alignment explanation
Indices: 665199--665237 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
665189 ATTACTATAA
665199 AAAATTA-AATATT
1 AAAATTATAATATT
*
665212 ATAATTATAATATT
1 AAAATTATAATATT
665226 AAAATTACTAAT
1 AAAATTA-TAAT
665238 CAAAGCTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTATAATATT
Found at i:666734 original size:2 final size:2
Alignment explanation
Indices: 666727--666756 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
666717 TTGTTTTTGT
*
666727 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
666757 CAAAAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:673072 original size:3 final size:3
Alignment explanation
Indices: 673064--673096 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
673054 AAATCACGGT
673064 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
673097 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:673564 original size:72 final size:72
Alignment explanation
Indices: 673427--673821 Score: 349
Period size: 72 Copynumber: 5.5 Consensus size: 72
673417 AGCGTTACGT
* * * *
673427 GTATTATTTATCTTTGTTTGTAAAAGTTT-AATTATAGTTTTTTGATATGATTATATGA-TTTAA
1 GTATTATTTATCTTTATTTATAAAAGTTTAAATT-TA-TTTTTGGGTATGATTATATGAGTTTAA
673490 ATTTTTAGG
64 ATTTTTAGG
* * * * *
673499 GTATTATTTATCTTTATTTACAGAAGTTTAAATTTATTTTTGGGTATAATTATACGAGTTAAAAT
1 GTATTATTTATCTTTATTTATAAAAGTTTAAATTTATTTTTGGGTATGATTATATGAGTTTAAAT
673564 TTTTAGG
66 TTTTAGG
* * * * * *
673571 ATATAATTTATTTTTATTTATAAAAGTCTAAATATGT-TTTTTAGGGTATGCTTATATAAGTTTA
1 GTATTATTTATCTTTATTTATAAAAGTTTAAAT-T-TATTTTT-GGGTATGATTATATGAGTTTA
* *
673635 AATTTTGATG
63 AATTTTTAGG
* * * ** *
673645 GTATTA--T-T-TTTATTTATAAAAGTTTAAA-TGAGTTTTTTGGATATAATTATACAAGTTTAT
1 GTATTATTTATCTTTATTTATAAAAGTTTAAATTTA--TTTTTGGGTATGATTATATGAGTTTAA
*
673705 ATTTTTCATG
64 ATTTTT-AGG
* * * * * *
673715 GTATAATTTATTTTTATTTGTAAAAATTTAAATTTGTTTTTTGGGT-TGATTACATGAGTTTAAA
1 GTATTATTTATCTTTATTTATAAAAGTTTAAATTT-ATTTTTGGGTATGATTATATGAGTTTAAA
*
673779 TATTTAGG
65 TTTTTAGG
* *
673787 GTATTAGTTATCTTTATTTGTAAAAGTTTAAATTT
1 GTATTATTTATCTTTATTTATAAAAGTTTAAATTT
673822 TTGTTTAAAT
Statistics
Matches: 259, Mismatches: 49, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
68 1 0.00
69 22 0.08
70 32 0.12
71 18 0.07
72 102 0.39
73 28 0.11
74 55 0.21
75 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (72 bp):
GTATTATTTATCTTTATTTATAAAAGTTTAAATTTATTTTTGGGTATGATTATATGAGTTTAAAT
TTTTAGG
Found at i:676888 original size:21 final size:21
Alignment explanation
Indices: 676855--676899 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
676845 TTGCAAGTTG
*
676855 AAATAAGGAAGTTGGCTAATGA
1 AAATAAGGAAGTTAGCTAA-GA
*
676877 AAATAATG-AGTTAGCTAAGA
1 AAATAAGGAAGTTAGCTAAGA
676897 AAA
1 AAA
676900 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATAAGGAAGTTAGCTAAGA
Found at i:678723 original size:15 final size:15
Alignment explanation
Indices: 678703--678733 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
678693 TAAAAATGTC
*
678703 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
678718 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
678733 C
1 C
678734 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:680826 original size:20 final size:20
Alignment explanation
Indices: 680747--680826 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
680737 AATGTCCAAA
*
680747 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
680767 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
680792 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
680812 TTGTATCGATACATT
1 ATGTATCGATACATT
680827 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:680830 original size:13 final size:13
Alignment explanation
Indices: 680812--680850 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
680802 ACATTTTTCT
680812 TTGTATCGATACA
1 TTGTATCGATACA
680825 TTGTATCGATACA
1 TTGTATCGATACA
*
680838 CTGTATCGATACA
1 TTGTATCGATACA
680851 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:687157 original size:20 final size:20
Alignment explanation
Indices: 687128--687202 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
687118 AAAAAAATAG
687128 AATGTATCGATACATTGAAC
1 AATGTATCGATACATTGAAC
* * *
687148 AATATATCGATATATTCATAC
1 AATGTATCGATACATTGA-AC
* * *
687169 -ATGTATCAATATATTGAAA
1 AATGTATCGATACATTGAAC
687188 AATGTATCGATACAT
1 AATGTATCGATACAT
687203 CCAGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.93
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAC
Found at i:687247 original size:21 final size:21
Alignment explanation
Indices: 687221--687273 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
687211 AAAATAGAAT
687221 GTATCGATACATGAACTGTTC
1 GTATCGATACATGAACTGTTC
687242 GTATCGATACATGAACTGTTC
1 GTATCGATACATGAACTGTTC
*
687263 ATATCGATACA
1 GTATCGATACA
687274 AATCATGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (21 bp):
GTATCGATACATGAACTGTTC
Found at i:688265 original size:21 final size:19
Alignment explanation
Indices: 688239--688293 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
688229 TTTTACAATT
688239 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
688260 TGTATCGATACATAAGTTT
1 TGTATCGATACAAAAGTAA
688279 TGTATCGATACAAAA
1 TGTATCGATACAAAA
688294 CTCATTTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:688284 original size:19 final size:21
Alignment explanation
Indices: 688236--688292 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
688226 AATTTTTACA
688236 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
688257 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
688277 -TTTGTATCGATACAAA
1 ATTTGTATCGATACAAA
688293 ACTCATTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:688394 original size:20 final size:20
Alignment explanation
Indices: 688324--688394 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
688314 GAAATATATT
*
688324 GATACATTAATAAATGTATC
1 GATACATTTATAAATGTATC
688344 GATACATGCTT-TAAATTGTATC
1 GATACAT--TTATAAA-TGTATC
*
688366 GATACATTTATCAATGTATC
1 GATACATTTATAAATGTATC
688386 GATACATTT
1 GATACATTT
688395 GGGTTTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
20 24 0.53
21 7 0.16
22 14 0.31
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
GATACATTTATAAATGTATC
Done.