Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2369
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: 30039
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:223 original size:9 final size:9
Alignment explanation
Indices: 211--244 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
201 GCAAATCTTA
211 TTTTTTCTC
1 TTTTTTCTC
220 TTTTTTCTC
1 TTTTTTCTC
*
229 TCTTTTCTTC
1 TTTTTTC-TC
239 TTTTTT
1 TTTTTT
245 TTTCTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:244 original size:10 final size:10
Alignment explanation
Indices: 206--257 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
196 ATCTAGCAAA
*
206 TCTTATTTTT
1 TCTTCTTTTT
216 TC-TCTTTTT
1 TCTTCTTTTT
225 TCTCTCTTTTCT
1 TCT-TCTTTT-T
*
237 TCTTTTTTTT
1 TCTTCTTTTT
247 TCTTCTTTTT
1 TCTTCTTTTT
257 T
1 T
258 TTTCCTCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.22
10 13 0.36
11 11 0.31
12 4 0.11
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:244 original size:21 final size:20
Alignment explanation
Indices: 206--257 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
196 ATCTAGCAAA
*
206 TCTTATTTTTTCTC-TTTTT
1 TCTTCTTTTTTCTCTTTTTT
*
225 TCTCTCTTTTCTTCTTTTTTTT
1 TCT-TCTTTT-TTCTCTTTTTT
247 TCTTCTTTTTT
1 TCTTCTTTTTT
258 TTTCCTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 10 0.36
22 8 0.29
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTCTTTTTTCTCTTTTTT
Found at i:249 original size:13 final size:13
Alignment explanation
Indices: 231--261 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
221 TTTTTCTCTC
231 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
244 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
257 TTTTC
1 TTTTC
262 CTCTCTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTCTTTTT
Found at i:569 original size:27 final size:27
Alignment explanation
Indices: 531--589 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
521 ATTAGAAGTT
531 GAAAAATAAACTCATAAAATTTTACGA
1 GAAAAATAAACTCATAAAATTTTACGA
*
558 GAAAAATAAACTCGTAAAATTTTACGA
1 GAAAAATAAACTCATAAAATTTTACGA
585 GAAAA
1 GAAAA
590 CTCTTTGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (27 bp):
GAAAAATAAACTCATAAAATTTTACGA
Found at i:905 original size:158 final size:162
Alignment explanation
Indices: 728--1078 Score: 443
Period size: 158 Copynumber: 2.2 Consensus size: 162
718 ACTCCCCCAA
* * * * **
728 AAAATATTTATGGAATAAAAAACT-TG-ATTTTTCGAAA-ACAAAAATTTAAAAGAAAATATTCA
1 AAAACATTTATGGAGTAAAAAACTCTGTA-TTTTAGAAACAAAAAAATTT-AAAGAAAA-ATAAA
* * * *
790 AAACTTATGAAAATAAATGAATTTTTAAAA-CTGATTTAATATGAATTA-A-AATAATATTTGAT
63 AAACTCATAAAAATAAATAAATTTTTAAAACCTAATTTAATATGAATTATATAAT-ATATTTGAT
852 GAATTTTAAA-ATT-AAAACCAAG-AAAATCATCCCG
127 GAA-TTTAAAGATTAAAAACCAAGAAAAATCATCCCG
*
886 AAAACATTTATGGAGTAAAAAACTCTGTATTTTAGAAACAAAAAAATTTTAAGAAAAATAAAAAA
1 AAAACATTTATGGAGTAAAAAACTCTGTATTTTAGAAACAAAAAAATTTAAAGAAAAATAAAAAA
951 CTCATAAAAATAAATAAATTTTTAAAACCTAATTTAATATGAATTATATAATATATTTGATGAAT
66 CTCATAAAAATAAATAAATTTTTAAAACCTAATTTAATATGAATTATATAATATATTTGATGAAT
* *
1016 TTAAAGATTAAAAACTAAGAAAAATCCTCCCG
131 TTAAAGATTAAAAACCAAGAAAAATCATCCCG
* * *
1048 -AAACATTTACGGAGTAGAAAACTCCGTATTT
1 AAAACATTTATGGAGTAAAAAACTCTGTATTT
1079 CGAGAAGAAT
Statistics
Matches: 168, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
158 52 0.31
159 40 0.24
160 26 0.15
161 39 0.23
162 11 0.07
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (162 bp):
AAAACATTTATGGAGTAAAAAACTCTGTATTTTAGAAACAAAAAAATTTAAAGAAAAATAAAAAA
CTCATAAAAATAAATAAATTTTTAAAACCTAATTTAATATGAATTATATAATATATTTGATGAAT
TTAAAGATTAAAAACCAAGAAAAATCATCCCG
Found at i:6677 original size:29 final size:30
Alignment explanation
Indices: 6644--6738 Score: 86
Period size: 36 Copynumber: 3.0 Consensus size: 30
6634 CCTCACCACA
6644 CTATC-TTTCA-AGGCTAAGATAGAAACCTC
1 CTATCTTTTCACAGGCTAAGATAG-AACCTC
*
6673 CTATCTTTTCACGGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCACAGGCTAAGATAGAA---C-CT-C
* *
6708 CTATCTTTTTCAAAGACTAAGATAGAACCTC
1 CTATC-TTTTCACAGGCTAAGATAGAACCTC
6739 TCAATCACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
29 5 0.09
30 7 0.13
31 12 0.22
32 2 0.04
33 2 0.04
34 2 0.04
35 6 0.11
36 18 0.33
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (30 bp):
CTATCTTTTCACAGGCTAAGATAGAACCTC
Found at i:7204 original size:13 final size:13
Alignment explanation
Indices: 7186--7222 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
7176 ATATTTCACT
7186 ATGTATCGATACA
1 ATGTATCGATACA
7199 ATGTATCGATACA
1 ATGTATCGATACA
* *
7212 CTATATCGATA
1 ATGTATCGATA
7223 TTAAGTGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7313 original size:32 final size:33
Alignment explanation
Indices: 7272--7333 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
7262 CAATTTAGTG
*
7272 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACAAAGCAACATGTATCGATACAA
* *
7304 TGTATCGATATAAAGCAATATGTATCGATA
1 TGTATCGATACAAAGCAACATGTATCGATA
7334 AATATGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTATCGATACAA
Found at i:8194 original size:30 final size:32
Alignment explanation
Indices: 8136--8194 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
8126 TTCTTGTAAC
**
8136 TAATACCAAAAGTTTACGCAAGTTCTCCCCCT
1 TAATACCAAAAGTTTACGCAAACTCTCCCCCT
*
8168 TAATA-CAAAA-TTTATGCAAACTCTCCC
1 TAATACCAAAAGTTTACGCAAACTCTCCC
8195 TATCTCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 5 0.21
32 5 0.21
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (32 bp):
TAATACCAAAAGTTTACGCAAACTCTCCCCCT
Found at i:8329 original size:87 final size:86
Alignment explanation
Indices: 8111--8367 Score: 415
Period size: 86 Copynumber: 3.0 Consensus size: 86
8101 AAATCTATTC
* *
8111 TCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTACGCAAGTTCTCCCCCTTAATACAA
1 TCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAA
8176 AATTTATGCAAACTCTCCCTA
66 AATTTATGCAAACTCTCCCTA
* *
8197 TCTCCCTTTTTGTTATTCTTGTAACTAATACAAAAAGTTTATGCAAGCTCTCCCCCTTAATCCAA
1 TCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAA
* *
8262 AATTTATGCAAACTCTCTCTTT
66 AATTTATGCAAACTCTC-CCTA
* * *
8284 TCTCTCTTTTTATTATTCTTGTAACTATTACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAA
1 TCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAA
*
8349 AATTTATTCAAACTCTCCC
66 AATTTATGCAAACTCTCCC
8368 CCTTAATACG
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
86 79 0.50
87 78 0.50
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.39
Consensus pattern (86 bp):
TCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAA
AATTTATGCAAACTCTCCCTA
Found at i:8355 original size:30 final size:31
Alignment explanation
Indices: 8315--8376 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
8305 TAACTATTAC
*
8315 CAAAAGTTTATGCAAGCTCTCCCCCTTAATA
1 CAAAAGTTTATGCAAACTCTCCCCCTTAATA
*
8346 CAAAA-TTTATTCAAACTCTCCCCCTTAATA
1 CAAAAGTTTATGCAAACTCTCCCCCTTAATA
8376 C
1 C
8377 GTTCTCACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (31 bp):
CAAAAGTTTATGCAAACTCTCCCCCTTAATA
Found at i:9457 original size:13 final size:13
Alignment explanation
Indices: 9439--9463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9429 ATAATGCACA
9439 GTATCGATACATT
1 GTATCGATACATT
9452 GTATCGATACAT
1 GTATCGATACAT
9464 GACCACTGTA
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):
GTATCGATACATT
Found at i:9475 original size:19 final size:19
Alignment explanation
Indices: 9451--9499 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
9441 ATCGATACAT
9451 TGTATCGATACATGACCAC
1 TGTATCGATACATGACCAC
9470 TGTATCGATACATGACCAC
1 TGTATCGATACATGACCAC
9489 TGTATCGATAC
1 TGTATCGATAC
9500 TTGCAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACATGACCAC
Found at i:9589 original size:13 final size:13
Alignment explanation
Indices: 9571--9596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9561 ACATACAAGA
9571 TGTATCGATACAT
1 TGTATCGATACAT
9584 TGTATCGATACAT
1 TGTATCGATACAT
9597 GACCAAATGT
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:9592 original size:32 final size:33
Alignment explanation
Indices: 9551--9616 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 33
9541 CCTTAACTGT
9551 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
*
9583 TTGTATCGATACATGACCAAATGTGTCGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
9616 T
1 T
9617 CGGCTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 14 0.45
33 14 0.45
34 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:18319 original size:21 final size:19
Alignment explanation
Indices: 18271--18325 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
18261 GTATCGATAC
*
18271 AATTGTATCGATACATGAC
1 AATTGTATCGATACATGAA
* *
18290 AACTGTATCGATACTTGCAA
1 AATTGTATCGATACATG-AA
18310 AGATTGTATCGATACA
1 A-ATTGTATCGATACA
18326 GGTGATTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 2 0.07
21 12 0.41
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
AATTGTATCGATACATGAA
Found at i:18414 original size:34 final size:33
Alignment explanation
Indices: 18355--18424 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
18345 CCTTAACTGT
18355 TTGTATCGATACATACAAGATTGTATCAATTACA
1 TTGTATCGATACATACAAGATTGTATCAA-TACA
* *
18389 TTGTATCGATTCATGACCAA-A-TGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATTGTATCAATACA
18422 TTG
1 TTG
18425 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 7 0.22
34 20 0.62
35 2 0.06
36 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATACAAGATTGTATCAATACA
Found at i:22567 original size:33 final size:33
Alignment explanation
Indices: 22527--22595 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
22517 CTGTTACAAG
*
22527 CAATGTATCAATACAATT-TCATCATGTATC-ATA
1 CAATGTATCAATAC-ATTGTC-CCATGTATCGATA
*
22560 CAATGTATCGATACATTGTCCCATGTATCGATA
1 CAATGTATCAATACATTGTCCCATGTATCGATA
22593 CAA
1 CAA
22596 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACATTGTCCCATGTATCGATA
Found at i:22649 original size:20 final size:20
Alignment explanation
Indices: 22624--22680 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
22614 CTGCCAATTT
22624 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
* **
22644 CATGTATTGATACAA-TGAG
1 CATGTATCGATACAATTGTC
22663 CATGTATCGATAC-ATTGT
1 CATGTATCGATACAATTGT
22681 ATCGATACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.52
20 14 0.45
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:22683 original size:13 final size:13
Alignment explanation
Indices: 22665--22689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22655 ACAATGAGCA
22665 TGTATCGATACAT
1 TGTATCGATACAT
22678 TGTATCGATACA
1 TGTATCGATACA
22690 AAGCAGTATG
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:22709 original size:33 final size:32
Alignment explanation
Indices: 22646--22710 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
22636 CAATTGTCCA
* * *
22646 TGTATTGATACAATGAGCATGTATCGATACAT
1 TGTATCGATACAAAGAGCATGTATCAATACAT
*
22678 TGTATCGATACAAAGCAGTATGTATCAATACAT
1 TGTATCGATACAAAG-AGCATGTATCAATACAT
22711 CTGGAAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAAAGAGCATGTATCAATACAT
Done.