Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold300
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: 363256
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:330733 original size:15 final size:15
Alignment explanation
Indices: 330713--330749 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
330703 TATTCTTTAA
330713 AATATATATAATGTT
1 AATATATATAATGTT
*
330728 -A-ATATATAATTTT
1 AATATATATAATGTT
330741 AATATATAT
1 AATATATAT
330750 CTAATATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.58
14 2 0.11
15 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATATATATAATGTT
Found at i:330734 original size:13 final size:13
Alignment explanation
Indices: 330716--330748 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
330706 TCTTTAAAAT
330716 ATATATAATGTTA
1 ATATATAATGTTA
*
330729 ATATATAATTTTA
1 ATATATAATGTTA
330742 ATATATA
1 ATATATA
330749 TCTAATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
ATATATAATGTTA
Found at i:331558 original size:18 final size:19
Alignment explanation
Indices: 331537--331579 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
331527 TTAAAATGTT
*
331537 ATTTTTTAATTTTTATT-A
1 ATTTTGTAATTTTTATTAA
*
331555 ATTTTGTATTTTTTATTAA
1 ATTTTGTAATTTTTATTAA
331574 ATTTTG
1 ATTTTG
331580 ACTTATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTGTAATTTTTATTAA
Found at i:331866 original size:18 final size:17
Alignment explanation
Indices: 331837--331907 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
331827 GATCTAAAAT
331837 TAAATTTA-TTTTTAAA
1 TAAATTTATTTTTTAAA
**
331853 TAAATTTTATTTTTTATT
1 TAAA-TTTATTTTTTAAA
*
331871 TAAATTTATTTTTATAAT
1 TAAATTTATTTTT-TAAA
* *
331889 TTAATATTATTATTTAAA
1 TAAAT-TTATTTTTTAAA
331907 T
1 T
331908 TATATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.09
17 13 0.29
18 21 0.47
19 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAAATTTATTTTTTAAA
Found at i:331898 original size:19 final size:18
Alignment explanation
Indices: 331833--331908 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 18
331823 GTTAGATCTA
*
331833 AAATTAAAT-TTATTTTT
1 AAATTTAATATTATTTTT
* *
331850 AAA-TAAATTTTATTTTT
1 AAATTTAATATTATTTTT
*
331867 -TATTTAA-ATTTATTTTT
1 AAATTTAATA-TTATTTTT
331884 ATAATTTAATATTATTATTT
1 A-AATTTAATATTATT-TTT
331904 AAATT
1 AAATT
331909 ATATAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.12
17 22 0.46
19 15 0.31
20 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAATTTAATATTATTTTT
Found at i:333072 original size:25 final size:24
Alignment explanation
Indices: 333054--333101 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
333044 AAAATAAAAC
*
333054 TATAATTATTCTTATAAAAAATATA
1 TATAATTA-TATTATAAAAAATATA
333079 TATAATTATATTAT-AAAAATATA
1 TATAATTATATTATAAAAAATATA
333102 AATTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 5 0.23
25 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAATTATATTATAAAAAATATA
Found at i:333448 original size:14 final size:14
Alignment explanation
Indices: 333429--333476 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
333419 TATATATTTT
333429 TATAAATTTTAATA
1 TATAAATTTTAATA
*
333443 TATAAATAATTTATTTA
1 TATAAAT--TTTA-ATA
*
333460 TATAAATTTTAGTA
1 TATAAATTTTAATA
333474 TAT
1 TAT
333477 TTATATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.41
15 4 0.14
16 4 0.14
17 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TATAAATTTTAATA
Found at i:333608 original size:2 final size:2
Alignment explanation
Indices: 333603--333639 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
333593 AAATGAGTAT
333603 AG AG AG AG AG AG 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
333640 AATGGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:337798 original size:2 final size:2
Alignment explanation
Indices: 337791--337817 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
337781 ATTTAATGGC
337791 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
337818 TGTTTTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:337992 original size:14 final size:15
Alignment explanation
Indices: 337968--337998 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
337958 CACACACCTC
337968 TTCATTTTTTTCTTA
1 TTCATTTTTTTCTTA
337983 TTCATTTTTTT-TTA
1 TTCATTTTTTTCTTA
337997 TT
1 TT
337999 TTTTCGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCATTTTTTTCTTA
Found at i:338087 original size:19 final size:18
Alignment explanation
Indices: 338058--338118 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
338048 ATAATAATTT
*
338058 ATTTTATAAATTA-AAATA
1 ATTTT-TAAAATATAAATA
*
338076 ATTTTTACAAATATAATTA
1 ATTTTTA-AAATATAAATA
*
338095 ATTTATAAAAATATAAATA
1 ATTT-TTAAAATATAAATA
338114 ATTTT
1 ATTTT
338119 GTTTACTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 10 0.28
19 22 0.61
20 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTAAAATATAAATA
Found at i:344960 original size:2 final size:2
Alignment explanation
Indices: 344944--344979 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
344934 AACAATTATG
*
344944 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
344980 TCACATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:346564 original size:16 final size:16
Alignment explanation
Indices: 346543--346573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
346533 TATATCTTTA
*
346543 TTATATGTAAATATAT
1 TTATATATAAATATAT
346559 TTATATATAAATATA
1 TTATATATAAATATA
346574 AGTTCTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATATATAAATATAT
Found at i:348502 original size:29 final size:29
Alignment explanation
Indices: 348435--348503 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
348425 AAAAAATTAA
* *
348435 TAATATATTTTTTAGTTTTTTAAATTTATT
1 TAATA-ATTTTTTAATTTATTAAATTTATT
* *
348465 TATAAAATTTTTTAATTTATT-AATTTCTAT
1 TA-ATAATTTTTTAATTTATTAAATTTAT-T
348495 TAATAATTT
1 TAATAATTT
348504 ATATCATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 12 0.38
30 18 0.56
31 2 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TAATAATTTTTTAATTTATTAAATTTATT
Found at i:351294 original size:2 final size:2
Alignment explanation
Indices: 351276--351332 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
351266 TATACAAGTC
* *
351276 TA TA TA CA TA TA CA TA TA TA TA TA TA 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 TA TA TA
351318 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
351333 TTCTATTAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:352834 original size:2 final size:2
Alignment explanation
Indices: 352827--352885 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
352817 AAATTTCAAA
352827 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
352869 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
352886 AGACTCAACC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:354100 original size:22 final size:22
Alignment explanation
Indices: 354059--354100 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
354049 AATAATAATT
*
354059 TAATTTTAACACTAATTAAAAA
1 TAATTTTAACACTAACTAAAAA
* *
354081 TAATTTTAAGATTAACTAAA
1 TAATTTTAACACTAACTAAA
354101 TCTAATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATTTTAACACTAACTAAAAA
Found at i:355778 original size:3 final size:3
Alignment explanation
Indices: 355767--355811 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
355757 ATGATGATGC
*
355767 TAA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
355812 AGCAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:360884 original size:4 final size:4
Alignment explanation
Indices: 360875--360902 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
360865 TCTTTTTAAA
360875 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
360903 TTGATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:361130 original size:20 final size:20
Alignment explanation
Indices: 361105--361155 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
361095 CTACAAATAC
361105 AATATATTTAATATAAAAAT
1 AATATATTTAATATAAAAAT
* * * *
361125 AATATAATAAATATTAATAT
1 AATATATTTAATATAAAAAT
*
361145 AATACATTTAA
1 AATATATTTAA
361156 ATACGATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATATTTAATATAAAAAT
Found at i:361337 original size:24 final size:25
Alignment explanation
Indices: 361294--361356 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
361284 TTAAGCATAA
*
361294 ATATTATATGTATA-TTAAATATGTC
1 ATATTATAT-TATATTTAAATATATC
361319 ATATTA-ATTATATTTAAATATATC
1 ATATTATATTATATTTAAATATATC
361343 ATATTATATT-TATT
1 ATATTATATTATATT
361357 ATATTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 4 0.11
24 22 0.63
25 9 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
ATATTATATTATATTTAAATATATC
Found at i:361362 original size:14 final size:14
Alignment explanation
Indices: 361295--361369 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
361285 TAAGCATAAA
361295 TATTATATGTATATT
1 TATTATAT-TATATT
* * * *
361310 AAATATGTCATATT
1 TATTATATTATATT
* * *
361324 AATTATATTTAAATA
1 TATTATA-TTATATT
*
361339 TATCATATTATATT
1 TATTATATTATATT
*
361353 TATTATATTATTTT
1 TATTATATTATATT
361367 TAT
1 TAT
361370 ATTTATTAAG
Statistics
Matches: 44, Mismatches: 15, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
14 30 0.68
15 14 0.32
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:361799 original size:16 final size:15
Alignment explanation
Indices: 361748--361801 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
361738 ATAAATATTT
361748 TAAAATTTATATGATA
1 TAAAATTTATAT-ATA
*
361764 TAAATTATTA-ATATA
1 TAAAAT-TTATATATA
361779 TTAAAATTTATATAATA
1 -TAAAATTTATAT-ATA
361796 TAAAAT
1 TAAAAT
361802 AAATATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.19
16 20 0.62
17 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATTTATATATA
Found at i:362081 original size:23 final size:23
Alignment explanation
Indices: 362055--362119 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
362045 ATCAAATAAA
*
362055 TATTATTTAAA-ATATTAATTATT
1 TATTATATAAATA-ATTAATTATT
*
362078 TATTATATAAATAATTAATTTTT
1 TATTATATAAATAATTAATTATT
* * *
362101 TAATATATAATTAAATAAT
1 TATTATATAAATAATTAAT
362120 AGTTTAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATATAAATAATTAATTATT
Found at i:362092 original size:19 final size:19
Alignment explanation
Indices: 362040--362113 Score: 55
Period size: 19 Copynumber: 3.8 Consensus size: 19
362030 TATCATTTAA
*
362040 ATTATATCAAATAAATA-TT
1 ATTATAT-AAATAATTATTT
*
362059 ATT-TAAAATATTAATTATTT
1 ATTATATAA-A-TAATTATTT
362079 ATTATATAAATAATTAATTT
1 ATTATATAAATAATT-ATTT
* *
362099 TTTA-ATATATAATTA
1 ATTATATAAATAATTA
362114 AATAATAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 2 0.04
18 4 0.09
19 22 0.49
20 13 0.29
21 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATATAAATAATTATTT
Found at i:362114 original size:19 final size:19
Alignment explanation
Indices: 362065--362114 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
362055 TATTATTTAA
362065 AATAT-TAATT-ATTTATT
1 AATATATAATTAATTTATT
* *
362082 ATATAAATAATTAATTTTTT
1 A-ATATATAATTAATTTATT
362102 AATATATAATTAA
1 AATATATAATTAA
362115 ATAATAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 3 0.11
19 16 0.59
20 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATATAATTAATTTATT
Found at i:362125 original size:23 final size:23
Alignment explanation
Indices: 362076--362134 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
362066 ATATTAATTA
* * **
362076 TTTATTATATAAATAATTAATTT
1 TTTAATATATAAATAAATAATAG
*
362099 TTTAATATATAATTAAATAATAG
1 TTTAATATATAAATAAATAATAG
*
362122 TTTAA-ATAAAAAT
1 TTTAATATATAAAT
362135 TTATATAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAATATATAAATAAATAATAG
Found at i:362589 original size:25 final size:25
Alignment explanation
Indices: 362535--362581 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
362525 TTAGTTTAAA
*
362535 TTTAAATTTAATTTTAATATAATAT
1 TTTAAATTTAATTTTAATAAAATAT
362560 TTTAAATTTAATTTT-ATAAAAT
1 TTTAAATTTAATTTTAATAAAAT
362582 TTTATTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAAATTTAATTTTAATAAAATAT
Found at i:363166 original size:27 final size:27
Alignment explanation
Indices: 363114--363166 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
363104 ATATGATATA
* *
363114 TTTATATAAATTTTGATTAATGATTTT
1 TTTATATAAATTTTAATTAATCATTTT
*
363141 TTTATAT-AATTTTAATATATTCATTT
1 TTTATATAAATTTTAAT-TAATCATTT
363167 ATTAAGTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTATATAAATTTTAATTAATCATTTT
Found at i:363231 original size:18 final size:18
Alignment explanation
Indices: 363199--363241 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
363189 TTATGTATTA
* *
363199 TTATATTTTAATTATTTT
1 TTATATTGTAATTATGTT
*
363217 TTATATTGTATTTATGTT
1 TTATATTGTAATTATGTT
*
363235 ATATATT
1 TTATATT
363242 ATGTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATATTGTAATTATGTT
Done.