Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2689
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: 37274
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Found at i:7941 original size:22 final size:22
Alignment explanation
Indices: 7916--7961 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7906 TAATAATTTA
*
7916 AATATG-ATCATAACATAAAAAT
1 AATATGAAT-ATAAAATAAAAAT
*
7938 AATATGAATATAAAATAAATAT
1 AATATGAATATAAAATAAAAAT
7960 AA
1 AA
7962 AAAATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
AATATGAATATAAAATAAAAAT
Found at i:9416 original size:2 final size:2
Alignment explanation
Indices: 9406--9443 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
9396 ATTCTTTTTT
*
9406 TA TA T- TA TA TA -A TA TA TA CA 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
9444 GTTTCAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9519 original size:33 final size:33
Alignment explanation
Indices: 9467--9530 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
9457 ACTCTATATA
* *
9467 TATATATATATATACACACGTCAGCCTTGCAAG
1 TATATATATACACACACACGTCAGCCTTGCAAG
* * *
9500 TATATATATACACATACACGTCGGCGTTGCA
1 TATATATATACACACACACGTCAGCCTTGCA
9531 CGTGTTTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (33 bp):
TATATATATACACACACACGTCAGCCTTGCAAG
Found at i:12676 original size:1 final size:1
Alignment explanation
Indices: 12670--12699 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
12660 CATAAACTGC
12670 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12700 GAATTACACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13288 original size:23 final size:24
Alignment explanation
Indices: 13245--13292 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13235 AAGTAAATAT
* *
13245 AAAAACATCAATGCTGACATGAAA
1 AAAAAAATCAACGCTGACATGAAA
13269 AAAAAAATCAACGCTG-CATGAAA
1 AAAAAAATCAACGCTGACATGAAA
13292 A
1 A
13293 TTGTGGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (24 bp):
AAAAAAATCAACGCTGACATGAAA
Found at i:15245 original size:21 final size:21
Alignment explanation
Indices: 15219--15261 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
15209 ATAAATAAAC
*
15219 ATATATTTTTTTATAAAAATA
1 ATATATTTTTTGATAAAAATA
15240 ATATATTTTTTGATAAAAATA
1 ATATATTTTTTGATAAAAATA
15261 A
1 A
15262 CTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATTTTTTGATAAAAATA
Found at i:15260 original size:18 final size:18
Alignment explanation
Indices: 15213--15260 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
15203 ACATAAATAA
* *
15213 ATAAACATATATTTTTTT
1 ATAAAAATATATTTTTTG
15231 ATAAAAATAATATATTTTTTG
1 AT--AAA-AATATATTTTTTG
15252 ATAAAAATA
1 ATAAAAATA
15261 ACTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 3 0.12
21 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAAAAATATATTTTTTG
Found at i:15289 original size:21 final size:21
Alignment explanation
Indices: 15265--15304 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15255 AAAATAACTA
*
15265 AATAT-ATATTTTAATATTTAT
1 AATATAATATTAT-ATATTTAT
15286 AATATAATATTATATATTT
1 AATATAATATTATATATTT
15305 TTATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATAATATTATATATTTAT
Found at i:15289 original size:29 final size:28
Alignment explanation
Indices: 15257--15330 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
15247 TTTTGATAAA
15257 AATAACTAA-ATATATATTTTAATATTTAT
1 AATAA-TAATATATATATTTTAAT-TTTAT
*
15286 AAT-ATAATATTATATATTTTTATTTTAT
1 AATAATAATA-TATATATTTTAATTTTAT
15314 AATATATAATATATATA
1 AATA-ATAATATATATA
15331 AATATAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 21 0.52
30 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAATAATATATATATTTTAATTTTAT
Found at i:15512 original size:16 final size:17
Alignment explanation
Indices: 15491--15524 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
15481 ATATTAAATA
15491 AATTTTTAAAT-AATTT
1 AATTTTTAAATAAATTT
15507 AATTTTTAAATAAATTT
1 AATTTTTAAATAAATTT
15524 A
1 A
15525 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTTAAATAAATTT
Found at i:20600 original size:72 final size:72
Alignment explanation
Indices: 20483--20631 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 72
20473 TTGAGACTTA
* *
20483 ATGGAATGTTAGCATGATTTCTACAATATCTTTGCACTTTCTTTTTTAAGATTCCATTATGCTCT
1 ATGGAATGTTAGCATGATTTCTACAATATCTCTACACTTTCTTTTTTAAGATTCCATTATGCTCT
20548 GGTGCAT
66 GGTGCAT
* * *
20555 ATGGAATGTTAGCATGGTTTCTACAATATCTCTACGCTTTCTTTTTTGAGATTCCATTATGCTCT
1 ATGGAATGTTAGCATGATTTCTACAATATCTCTACACTTTCTTTTTTAAGATTCCATTATGCTCT
20620 GGTGCAT
66 GGTGCAT
20627 ATGGA
1 ATGGA
20632 GGTGTTTTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (72 bp):
ATGGAATGTTAGCATGATTTCTACAATATCTCTACACTTTCTTTTTTAAGATTCCATTATGCTCT
GGTGCAT
Found at i:22271 original size:13 final size:13
Alignment explanation
Indices: 22253--22278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22243 CAATTTTTTG
22253 TGTATCGATACAT
1 TGTATCGATACAT
22266 TGTATCGATACAT
1 TGTATCGATACAT
22279 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22402 original size:20 final size:20
Alignment explanation
Indices: 22350--22404 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
22340 CATATTTTTG
*
22350 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
22370 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
22390 ATGTATCGATACTTT
1 ATGTATCGATACTTT
22405 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:26959 original size:15 final size:15
Alignment explanation
Indices: 26939--26979 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
26929 GTTCATCGAT
26939 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
26954 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
26969 CTCAATTTGGA
1 TTC-ATTTGGA
26980 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:31071 original size:13 final size:13
Alignment explanation
Indices: 31053--31078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31043 CAATTTTTTG
31053 TGTATCGATACAT
1 TGTATCGATACAT
31066 TGTATCGATACAT
1 TGTATCGATACAT
31079 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31075 original size:33 final size:33
Alignment explanation
Indices: 31033--31097 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31023 TACAAGCCAA
* *
31033 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
31066 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
31098 AGTTTGGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:31202 original size:20 final size:20
Alignment explanation
Indices: 31150--31204 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
31140 CATATTTTTG
*
31150 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
31170 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
31190 ATGTATCGATACTTT
1 ATGTATCGATACTTT
31205 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:32778 original size:36 final size:36
Alignment explanation
Indices: 32738--32809 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
32728 TTATTATTAT
32738 TAAAACCTCATGATATCAAAATATCAAACTAAAAGA
1 TAAAACCTCATGATATCAAAATATCAAACTAAAAGA
32774 TAAAACCTCATGATATCAAAATATCAAACTAAAAGA
1 TAAAACCTCATGATATCAAAATATCAAACTAAAAGA
32810 AGTTTATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (36 bp):
TAAAACCTCATGATATCAAAATATCAAACTAAAAGA
Found at i:33864 original size:3 final size:3
Alignment explanation
Indices: 33856--33886 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
33846 TTTTGTACCC
33856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33887 TCCATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36376 original size:17 final size:17
Alignment explanation
Indices: 36354--36386 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36344 ATATATTAAG
36354 TATAAATATTAACATAT
1 TATAAATATTAACATAT
*
36371 TATAAATTTTAACATA
1 TATAAATATTAACATA
36387 ATAGTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAATATTAACATAT
Found at i:36457 original size:13 final size:14
Alignment explanation
Indices: 36420--36457 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
36410 ATCGTGTTTG
36420 TATATTTTTT-TAA
1 TATATTTTTTATAA
*
36433 TATAATTTTTATAA
1 TATATTTTTTATAA
36447 -ATATTTTTTAT
1 TATATTTTTTAT
36458 TAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATTTTTTATAA
Found at i:36486 original size:14 final size:15
Alignment explanation
Indices: 36422--36491 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 15
36412 CGTGTTTGTA
36422 TATTTTT-TTAATAT
1 TATTTTTATTAATAT
* *
36436 AATTTTTATAAATAT
1 TATTTTTATTAATAT
* *
36451 TTTTTATTAATTAAAAT
1 TATTT-TT-ATTAATAT
36468 ATATTTTTATTAA-AT
1 -TATTTTTATTAATAT
36483 TATTTTTAT
1 TATTTTTAT
36492 ATTTTCAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
14 15 0.33
15 11 0.24
16 7 0.16
17 8 0.18
18 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTTATTAATAT
Found at i:36502 original size:34 final size:33
Alignment explanation
Indices: 36431--36502 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 33
36421 ATATTTTTTT
36431 AATATAATTTTTATAAATATTTTTTATTAATTAA
1 AATATAATTTTTATAAATATTTTTTATT-ATTAA
*
36465 AATAT-ATTTTTATTAAATTATTTTTATATT-TTCA
1 AATATAATTTTTA-TAAA-TATTTTT-TATTATTAA
36499 AATA
1 AATA
36503 CATGATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 7 0.21
34 16 0.47
35 7 0.21
36 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
AATATAATTTTTATAAATATTTTTTATTATTAA
Done.