Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 19 of 19
Found at i:2313357 original size:32 final size:33
Alignment explanation
Indices: 2313300--2313386 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
2313290 AATTTTATAT
*
2313300 TTAATATATTATATATTTAAATAAATATTAAAATA
1 TTAATATATT-TATA-TTATATAAATATTAAAATA
* * *
2313335 TTAATA-ATTTGTATTATATAAATTTTAATATA
1 TTAATATATTTATATTATATAAATATTAAAATA
*
2313367 TTTATATATTTATATTATAT
1 TTAATATATTTATATTATAT
2313387 TTTATATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 21 0.47
33 15 0.33
34 3 0.07
35 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (33 bp):
TTAATATATTTATATTATATAAATATTAAAATA
Found at i:2313392 original size:12 final size:12
Alignment explanation
Indices: 2313363--2313399 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
2313353 TAAATTTTAA
2313363 TATATTTATATATT
1 TATA-TTATAT-TT
2313377 TATATTATATTT
1 TATATTATATTT
2313389 TATATTATATT
1 TATATTATATT
2313400 ATAGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.57
13 6 0.26
14 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATATTT
Found at i:2313396 original size:17 final size:17
Alignment explanation
Indices: 2313363--2313411 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
2313353 TAAATTTTAA
2313363 TATATTTATATATTTATAT
1 TATATTT-TATA-TTATAT
2313382 TATATTTTATATTATAT
1 TATATTTTATATTATAT
*
2313399 TATAGTTTATATT
1 TATATTTTATATT
2313412 GGATCACCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 18 0.62
18 4 0.14
19 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTTTATATTATAT
Found at i:2313635 original size:11 final size:10
Alignment explanation
Indices: 2313619--2313668 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
2313609 ATATATATTT
2313619 ATATTTTATAC
1 ATATTTTAT-C
2313630 ATATTTTATC
1 ATATTTTATC
**
2313640 ATAACATTATC
1 AT-ATTTTATC
2313651 ATATTTTAT-
1 ATATTTTATC
2313660 ATATTTTAT
1 ATATTTTAT
2313669 AATACATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 9 0.26
10 8 0.24
11 17 0.50
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTTATC
Found at i:2313666 original size:30 final size:30
Alignment explanation
Indices: 2313619--2313677 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
2313609 ATATATATTT
*
2313619 ATATTTTATACATATTTTATCATAACATTATC
1 ATATTTTATA-ATATTTTATAAT-ACATTATC
2313651 ATATTTTAT-ATATTTTATAATACATTA
1 ATATTTTATAATATTTTATAATACATTA
2313678 ATAATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 11 0.42
32 9 0.35
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTTTATAATATTTTATAATACATTATC
Found at i:2313719 original size:28 final size:28
Alignment explanation
Indices: 2313630--2313721 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 28
2313620 TATTTTATAC
2313630 ATATTTTATCAT--AACATT-ATCATATTTT
1 ATATTTTAT-ATAAAACATTAAT-ATA-TTT
*
2313658 ATATATTT-TATAATACATTAATA-ATTT
1 ATAT-TTTATATAAAACATTAATATATTT
* *
2313685 ATATTTTATATAAAATATTTATATATTT
1 ATATTTTATATAAAACATTAATATATTT
2313713 ATATTTTAT
1 ATATTTTAT
2313722 TTATATTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 3 0.06
27 21 0.39
28 19 0.35
29 9 0.17
30 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTTTATATAAAACATTAATATATTT
Found at i:2313722 original size:11 final size:11
Alignment explanation
Indices: 2313708--2313755 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
2313698 AATATTTATA
2313708 TATTTATATTT
1 TATTTATATTT
*
2313719 TATTTATATTA
1 TATTTATATTT
2313730 TA-TTATATTT
1 TATTTATATTT
*
2313740 TAATTA-ATTT
1 TATTTATATTT
2313750 T-TTTAT
1 TATTTAT
2313756 CGTATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 3 0.09
10 14 0.44
11 15 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTTATATTT
Found at i:2313722 original size:19 final size:21
Alignment explanation
Indices: 2313700--2313781 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 21
2313690 TTATATAAAA
2313700 TATTTATA-TAT-TTATATTT
1 TATTTATATTATATTATATTT
2313719 TATTTATATTATATTATATTT
1 TATTTATATTATATTATATTT
* * **
2313740 TAATTA-ATT-T-TTTTATCG
1 TATTTATATTATATTATATTT
2313758 TA-TTATATTATATT-TATTAT
1 TATTTATATTATATTATATT-T
2313778 TATT
1 TATT
2313782 AAATCTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 3 0.06
18 10 0.20
19 13 0.26
20 10 0.20
21 14 0.28
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (21 bp):
TATTTATATTATATTATATTT
Found at i:2314126 original size:21 final size:21
Alignment explanation
Indices: 2314102--2314160 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 21
2314092 TAATATTTAA
2314102 TAATTAAAAATTATTTAAAT-T
1 TAATTAAAAA-TATTTAAATAT
2314123 TAATTATAAAATATTTAAATAT
1 TAATTA-AAAATATTTAAATAT
2314145 TAATATAAAAATATTT
1 TAAT-TAAAAATATTT
2314161 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.43
22 18 0.51
23 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTAAAAATATTTAAATAT
Found at i:2314147 original size:22 final size:21
Alignment explanation
Indices: 2314102--2314160 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
2314092 TAATATTTAA
2314102 TAATTA-AAAATTATTTAAATT
1 TAATTATAAAA-TATTTAAATT
2314123 TAATTATAAAATATTTAAATAT
1 TAATTATAAAATATTTAAAT-T
2314145 TAA-TATAAAAATATTT
1 TAATTAT-AAAATATTT
2314161 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTATAAAATATTTAAATT
Found at i:2314311 original size:27 final size:28
Alignment explanation
Indices: 2314281--2314358 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
2314271 ATTCATATAT
* *
2314281 ATTTTTAA-TTTATTAATAAAATATTAA
1 ATTTTTAATTTTAATAATAAAAGATTAA
*
2314308 A-TTTTAATTTTAATAATTAAAGATTAA
1 ATTTTTAATTTTAATAATAAAAGATTAA
* *
2314335 ATTATAATAATTTTAATTATAAAA
1 ATT-T-TTAATTTTAATAATAAAA
2314359 AAAAGTAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 6 0.15
27 18 0.44
28 1 0.02
29 1 0.02
30 15 0.37
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTTTTAATTTTAATAATAAAAGATTAA
Found at i:2315465 original size:11 final size:12
Alignment explanation
Indices: 2315425--2315469 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
2315415 AAAATTATTT
2315425 TATTATTTAAAA
1 TATTATTTAAAA
2315437 -A-TA-TTAAAA
1 TATTATTTAAAA
*
2315446 TATTATTTAATA
1 TATTATTTAAAA
2315458 TATT-TTTAAAA
1 TATTATTTAAAA
2315469 T
1 T
2315470 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
9 6 0.21
10 3 0.11
11 10 0.36
12 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:2316099 original size:14 final size:15
Alignment explanation
Indices: 2316073--2316102 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2316063 TAATTAATAT
2316073 AATTAATAATTTTAA
1 AATTAATAATTTTAA
2316088 AATTAA-AATTTTAA
1 AATTAATAATTTTAA
2316102 A
1 A
2316103 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAATAATTTTAA
Found at i:2318205 original size:19 final size:20
Alignment explanation
Indices: 2318169--2318208 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2318159 TTTTATTAAT
2318169 TTAATTAAAAGTATTATTTTA
1 TTAATTAAAAG-ATTATTTTA
2318190 TTAATTAAAA-ATTATTTTA
1 TTAATTAAAAGATTATTTTA
2318209 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAATTAAAAGATTATTTTA
Found at i:2318213 original size:22 final size:22
Alignment explanation
Indices: 2318164--2318213 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
2318154 TTTATTTTTA
2318164 TTAAT-TTAATTAAAAGTATTAT
1 TTAATATTAATTAAAAG-ATTAT
2318186 TT--TATTAATTAAAA-ATTATT
1 TTAATATTAATTAAAAGATTA-T
2318206 TTAATATT
1 TTAATATT
2318214 TTATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 10 0.42
22 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATATTAATTAAAAGATTAT
Found at i:2318257 original size:30 final size:29
Alignment explanation
Indices: 2318223--2318280 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2318213 TTTATTATAT
2318223 TTTAAATTATAAT-TTATTTTATTAAATCAA
1 TTTAAATT-TAATATTATTTT-TTAAATCAA
*
2318253 TTTAAATTTATTATTATTTTTTAAATCA
1 TTTAAATTTAATATTATTTTTTAAATCA
2318281 CTATCTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAAATTTAATATTATTTTTTAAATCAA
Found at i:2318491 original size:15 final size:14
Alignment explanation
Indices: 2318461--2318500 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
2318451 TGATGACAAA
*
2318461 AAATTTAATAATTT
1 AAATTTAATAAATT
2318475 AAATTTATATAAATT
1 AAATTTA-ATAAATT
2318490 AAATTTAATAA
1 AAATTTAATAA
2318501 TAATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTAATAAATT
Found at i:2318496 original size:21 final size:21
Alignment explanation
Indices: 2318470--2318540 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
2318460 AAAATTTAAT
2318470 AATTTAAATTTATATAAATTA
1 AATTTAAATTTATATAAATTA
2318491 AATTT-AA--TA-AT-AATT-
1 AATTTAAATTTATATAAATTA
* * *
2318506 AATTTAAAATTATTTATATTTA
1 AATTTAAATTTATATA-AATTA
2318528 AATTTAAATTTAT
1 AATTTAAATTTAT
2318541 TTCAATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
15 5 0.12
16 6 0.15
17 2 0.05
18 4 0.10
19 1 0.03
20 2 0.05
21 8 0.20
22 12 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAAATTTATATAAATTA
Found at i:2318509 original size:15 final size:16
Alignment explanation
Indices: 2318461--2318512 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
2318451 TGATGACAAA
2318461 AAATTTAATAAT--TT
1 AAATTTAATAATAATT
2318475 AAATTT-AT-ATAAATT
1 AAATTTAATAAT-AATT
2318490 AAATTTAATAATAATT
1 AAATTTAATAATAATT
2318506 -AATTTAA
1 AAATTTAA
2318513 AATTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 2 0.06
14 6 0.18
15 15 0.45
16 6 0.18
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTAATAATAATT
Found at i:2318531 original size:22 final size:22
Alignment explanation
Indices: 2318506--2318550 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2318496 AATAATAATT
2318506 AATTTAAAATTATTT-ATATTTA
1 AATTTAAAATTATTTCA-ATTTA
*
2318528 AATTTAAATTTATTTCAATTTA
1 AATTTAAAATTATTTCAATTTA
2318550 A
1 A
2318551 TATTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTAAAATTATTTCAATTTA
Found at i:2318541 original size:16 final size:16
Alignment explanation
Indices: 2318470--2318550 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
2318460 AAAATTTAAT
*
2318470 AATTTAAATTTATATA
1 AATTTAAATTTATTTA
*
2318486 AA-TTAAATTTA-AT-
1 AATTTAAATTTATTTA
*
2318499 AA--T-AATTAATTTA
1 AATTTAAATTTATTTA
* *
2318512 AAATT-ATTTATATTTA
1 AATTTAAATT-TATTTA
*
2318528 AATTTAAATTTATTTC
1 AATTTAAATTTATTTA
2318544 AATTTAA
1 AATTTAA
2318551 TATTAATTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
13 4 0.08
14 2 0.04
15 13 0.25
16 23 0.44
17 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:2318556 original size:22 final size:22
Alignment explanation
Indices: 2318504--2318556 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2318494 TTAATAATAA
2318504 TTAAT-TTAAAATTATTTATAT
1 TTAATATTAAAATTATTTATAT
*
2318525 TTAA-ATTTAAATTTATTTCA-AT
1 TTAATA-TTAAAATTATTT-ATAT
2318547 TTAATATTAA
1 TTAATATTAA
2318557 TTAATAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.15
22 21 0.78
23 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATATTAAAATTATTTATAT
Found at i:2320414 original size:24 final size:24
Alignment explanation
Indices: 2320362--2320414 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2320352 TTAAAATAAA
* * *
2320362 AATTTCTCACCAAAATTCATTATT
1 AATTTCTCAACAAAATCCATAATT
*
2320386 AATTTCTCAACAAAGTCCATAATT
1 AATTTCTCAACAAAATCCATAATT
*
2320410 TATTT
1 AATTT
2320415 TTCTGTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTTCTCAACAAAATCCATAATT
Found at i:2329050 original size:13 final size:13
Alignment explanation
Indices: 2329032--2329056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2329022 ACAAAACTTA
2329032 TGTATCGATACAT
1 TGTATCGATACAT
2329045 TGTATCGATACA
1 TGTATCGATACA
2329057 ACACTTTATG
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:2332799 original size:20 final size:20
Alignment explanation
Indices: 2332771--2332845 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
2332761 TTTTACCCAG
2332771 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2332791 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
2332811 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
2332831 ATGTATCGATACATT
1 ATGTATCGATACATT
2332846 ATGTCTTTTT
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:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2332816 original size:40 final size:39
Alignment explanation
Indices: 2332771--2332848 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
2332761 TTTTACCCAG
*
2332771 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
2332811 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
2332849 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:2335179 original size:10 final size:10
Alignment explanation
Indices: 2335152--2335181 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2335142 TTCAGCAGCA
*
2335152 AAAAAAAAAC
1 AAAAAAATAC
2335162 AAAAAAATAC
1 AAAAAAATAC
2335172 AAAAAAATAC
1 AAAAAAATAC
2335182 CTAGTCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATAC
Done.