Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2333
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: 25681
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:3088 original size:13 final size:13
Alignment explanation
Indices: 3072--3097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3062 TAGAGTAGCT
3072 TTGTATCGATACA
1 TTGTATCGATACA
3085 TTGTATCGATACA
1 TTGTATCGATACA
3098 AACACTTATG
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):
TTGTATCGATACA
Found at i:4158 original size:19 final size:20
Alignment explanation
Indices: 4134--4181 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4124 CTCATTATAT
4134 TATTAAAA-TATA-ATTTTTA
1 TATTAAAATTATATA-TTTTA
4153 TATTAATAATTATATATTTTA
1 TATTAA-AATTATATATTTTA
4174 TAATTAAA
1 T-ATTAAA
4182 TTTAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 11 0.44
22 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAAATTATATATTTTA
Found at i:5788 original size:21 final size:21
Alignment explanation
Indices: 5769--5812 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5759 TTGTTTATTT
5769 TATTAAATATATTTTATATTAA
1 TATT-AATATATTTTATATTAA
*
5791 TATTTATATATTTTATAATTAA
1 TATTAATATATTTTAT-ATTAA
5813 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATATATTTTATATTAA
Found at i:5816 original size:21 final size:21
Alignment explanation
Indices: 5775--5817 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
5765 ATTTTATTAA
5775 ATATATTTTATATTAATATTT
1 ATATATTTTATATTAATATTT
5796 ATATATTTTATAATTAA-ATTT
1 ATATATTTTAT-ATTAATATTT
5817 A
1 A
5818 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTTTATATTAATATTT
Found at i:6519 original size:18 final size:17
Alignment explanation
Indices: 6472--6524 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
6462 TAATGTCTCC
6472 AAATTTATAT-AATA-T
1 AAATTTATATAAATATT
6487 AAA-TTAT-TAAGATATCT
1 AAATTTATATAA-ATAT-T
*
6504 AAATTTATATAAATATA
1 AAATTTATATAAATATT
6521 AAAT
1 AAAT
6525 ATATTAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
17 8 0.26
18 8 0.26
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAATATT
Found at i:6524 original size:17 final size:16
Alignment explanation
Indices: 6472--6522 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
6462 TAATGTCTCC
6472 AAATTTATAT-AATAT
1 AAATTTATATAAATAT
6487 AAA-TTAT-TAAGATATCT
1 AAATTTATATAA-ATA--T
6504 AAATTTATATAAATAT
1 AAATTTATATAAATAT
6520 AAA
1 AAA
6523 ATATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 6 0.20
16 4 0.13
17 4 0.13
18 7 0.23
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATTTATATAAATAT
Found at i:9394 original size:28 final size:28
Alignment explanation
Indices: 9313--9394 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
9303 TTTTGGAGAT
*
9313 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
9341 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
9369 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
9395 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:9500 original size:105 final size:104
Alignment explanation
Indices: 9372--9714 Score: 286
Period size: 105 Copynumber: 3.3 Consensus size: 104
9362 CCGATGAAAT
* * *
9372 AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
*
9437 TATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAA
66 TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * * * * *
9476 AACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGA
1 AA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
* * * * * ** *
9540 GTATCCCCTCAGAAATAACGG-G--GTTGGAGTATCCCGATGAT-T
65 GTAT-CCC-C-G-ATTAAAGGAGAAATTGGTGT-T-CTGAAAATAA
* *
9582 AACGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTG
1 AACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAGTTG
* ** * *
9647 GAGTATCCCCGATTATA-GA-AAATTAATGTTTTGAAAGTAA
63 GAGTATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * *
9687 AATCGGAGTTGGAATATCCTCGATTGTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG
9715 GAGAATTGAG
Statistics
Matches: 180, Mismatches: 43, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
104 31 0.17
105 71 0.39
106 34 0.19
107 8 0.04
108 10 0.06
109 26 0.14
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (104 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
Found at i:9537 original size:51 final size:51
Alignment explanation
Indices: 9377--9547 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
9367 GAAATAACGA
* * *
9377 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
9429 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
9482 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
9533 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
9548 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:9656 original size:55 final size:51
Alignment explanation
Indices: 9588--9719 Score: 133
Period size: 51 Copynumber: 2.5 Consensus size: 51
9578 GATTAACGGG
* **
9588 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG---TTTT-GAAAGTAAAATCGGA
*
9643 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAGTAAAATCGGA
* *
9694 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
9720 TTGAGCAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
50 4 0.06
51 31 0.47
52 2 0.03
53 4 0.06
54 7 0.11
55 18 0.27
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:12084 original size:13 final size:13
Alignment explanation
Indices: 12066--12091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12056 ACAAAGATCC
12066 ATGTATCGATACA
1 ATGTATCGATACA
12079 ATGTATCGATACA
1 ATGTATCGATACA
12092 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:12087 original size:33 final size:33
Alignment explanation
Indices: 12045--12111 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12035 AAAATTTCCA
***
12045 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
12078 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
12111 A
1 A
12112 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12155 original size:19 final size:18
Alignment explanation
Indices: 12131--12198 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
12121 CAGTAGCTAA
12131 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
12150 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
12165 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
12182 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
12199 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:12171 original size:13 final size:13
Alignment explanation
Indices: 12153--12177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12143 ACAATACTTA
12153 TGTATCGATACAT
1 TGTATCGATACAT
12166 TGTATCGATACA
1 TGTATCGATACA
12178 AAACTTATGT
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:12175 original size:32 final size:32
Alignment explanation
Indices: 12134--12196 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12124 TAGCTAATTA
*
12134 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
12166 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
12197 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:12278 original size:21 final size:21
Alignment explanation
Indices: 12254--12310 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
12244 CATTTGTAGG
12254 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
12275 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
12296 ATGTATCGATACATT
1 ATGTATCGATACATT
12311 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:12337 original size:15 final size:15
Alignment explanation
Indices: 12317--12346 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12307 CATTTAAATT
12317 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
12332 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
12347 ACACTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTTTCAA
Found at i:13023 original size:55 final size:55
Alignment explanation
Indices: 12939--13727 Score: 1154
Period size: 55 Copynumber: 14.3 Consensus size: 55
12929 ATAAATTGTA
* * * * * *
12939 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12994 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
13049 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
13104 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
13159 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTAG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT-G
13215 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
13270 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
13325 TCCTACTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
13380 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
13435 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
13490 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
13545 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
13600 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
13655 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
13710 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
13728 AAAAAGCGGA
Statistics
Matches: 685, Mismatches: 33, Indels: 32
0.91 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 12 0.02
55 608 0.89
56 61 0.09
57 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:13459 original size:26 final size:26
Alignment explanation
Indices: 13371--13460 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
13361 GTGTGGGCTT
*
13371 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
13397 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
13424 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
13452 TGAAAGGTG
1 TGAAAGGTG
13461 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:14713 original size:1 final size:1
Alignment explanation
Indices: 14709--14765 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
14699 CTTTTCTCTC
* * * * ** *
14709 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTTTGCTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14766 GAAGAGAAGG
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:14733 original size:13 final size:12
Alignment explanation
Indices: 14709--14765 Score: 62
Period size: 13 Copynumber: 4.7 Consensus size: 12
14699 CTTTTCTCTC
*
14709 TTTTTCTTTGTT
1 TTTTTTTTTGTT
14721 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
14734 TTTTTTTTT-TT
1 TTTTTTTTTGTT
* *
14745 TTTTTTTGCTCTT
1 TTTTTTT-TTGTT
14758 TTTTTTTT
1 TTTTTTTT
14766 GAAGAGAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.23
12 10 0.26
13 20 0.51
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGTT
Done.