Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2336
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: 22148
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1862 original size:118 final size:118
Alignment explanation
Indices: 1654--1892 Score: 399
Period size: 118 Copynumber: 2.0 Consensus size: 118
1644 CCATTTAATG
*
1654 TACCTAGAGATCATTAAGAGCTACAATAATGGATGTTAATCTCATAACTTGTGAAAATGTATCAA
1 TACCTAGAGATCATTAAGAGCTACAATAATGGATGTTAATCTCATAACTTGTGAAAACGTATCAA
* *
1719 AGTAATCGATTCTTTCCTTTTGCTTGTAA-CTTTTTATAATAAATCGAGCTTTA
66 AGTAATCGAGTATTTCCTTTTGCTTGTAAGC-TTTTATAATAAATCGAGCTTTA
*
1772 TACCTAGAGATCATTAAGAGCTACAATAATGGATGTTATTCTCATAACTTGTGAAAACGTATCAA
1 TACCTAGAGATCATTAAGAGCTACAATAATGGATGTTAATCTCATAACTTGTGAAAACGTATCAA
* * *
1837 AGTAATTGAGTATTTCTTTTTGCTTGTAAGCTTTTATAATAAGTCGAGCTTTA
66 AGTAATCGAGTATTTCCTTTTGCTTGTAAGCTTTTATAATAAATCGAGCTTTA
1890 TAC
1 TAC
1893 TTTTGTATTG
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
118 112 0.99
119 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (118 bp):
TACCTAGAGATCATTAAGAGCTACAATAATGGATGTTAATCTCATAACTTGTGAAAACGTATCAA
AGTAATCGAGTATTTCCTTTTGCTTGTAAGCTTTTATAATAAATCGAGCTTTA
Found at i:2427 original size:249 final size:249
Alignment explanation
Indices: 1987--2454 Score: 776
Period size: 249 Copynumber: 1.9 Consensus size: 249
1977 AGTTTCCATG
* * *
1987 TATGATTTTGTATGATGGATTCTATTTCATTATTAATGGTCTTTTTCCAGAATGGTGCTTCTAGA
1 TATGATTTTGTATGATGGATTCTATTTCATTATTAATGGTATCTTTCCAGAATGGTGCTTCCAGA
* * * *
2052 GATGATGTACCTTCTTTAAAGGTTTGAAATTCATTTTCTAACAAATAAGTTGGAAAATTTTGATC
66 GATGATGTACCTTCTTTAAAAGTTTAAAATTCATTTTCTAACAAATAAGTTAGAAAATTTCGATC
* ** * *
2117 AAAAGTAGTTAGTACTTTAGCGTGTTTAATTCTTCGAGGTTTAACTTGTTCTGTTTTATCCATTT
131 AAAAGTAGTTAGCACTTTAGCCCGTTTAATTCTTCAAGGTTCAACTTGTTCTGTTTTATCCATTT
2182 GTGGACCACTGTTTAAGTCATCATGAGTTCACTTCACAATCTTATTTTTAGAAA
196 GTGGACCACTGTTTAAGTCATCATGAGTTCACTTCACAATCTTATTTTTAGAAA
* *
2236 TATGATTTTGTATGATGGATTCTATTTTATTATTAATGGTATCTTTCCAGAATGGTGCTTCCCGA
1 TATGATTTTGTATGATGGATTCTATTTCATTATTAATGGTATCTTTCCAGAATGGTGCTTCCAGA
*
2301 GATGATGTAGCTTCTTTAAAAGTTTAAAATTCATTTTCTAACAAATAAGTTAGAAAATTTCGATC
66 GATGATGTACCTTCTTTAAAAGTTTAAAATTCATTTTCTAACAAATAAGTTAGAAAATTTCGATC
2366 AAAAGTAGTTAGCACTTTAGCCCGTTTAATTCTTCAAGGTTCAACTTGTTCT-TTCTTATCCATT
131 AAAAGTAGTTAGCACTTTAGCCCGTTTAATTCTTCAAGGTTCAACTTGTTCTGTT-TTATCCATT
*
2430 TGTGGACCACTGTTTAAGTCCTCAT
195 TGTGGACCACTGTTTAAGTCATCAT
2455 TGTCGGAATG
Statistics
Matches: 202, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
248 2 0.01
249 200 0.99
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (249 bp):
TATGATTTTGTATGATGGATTCTATTTCATTATTAATGGTATCTTTCCAGAATGGTGCTTCCAGA
GATGATGTACCTTCTTTAAAAGTTTAAAATTCATTTTCTAACAAATAAGTTAGAAAATTTCGATC
AAAAGTAGTTAGCACTTTAGCCCGTTTAATTCTTCAAGGTTCAACTTGTTCTGTTTTATCCATTT
GTGGACCACTGTTTAAGTCATCATGAGTTCACTTCACAATCTTATTTTTAGAAA
Found at i:4658 original size:47 final size:47
Alignment explanation
Indices: 4600--4722 Score: 210
Period size: 47 Copynumber: 2.6 Consensus size: 47
4590 CGGTTTTGCT
* * *
4600 TGGTTGTTGCTTCGATTGTTGATGCTGCTGGTGTTGGTTTCGAGTGC
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
*
4647 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGT
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
4694 TGGTTGCTGCTTTGATTGTTGCTGCTGCT
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCT
4723 CCTCCTTTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.05, C:0.14, G:0.35, T:0.46
Consensus pattern (47 bp):
TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
Found at i:4905 original size:17 final size:18
Alignment explanation
Indices: 4872--4912 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
4862 TTTCAGCTTG
*
4872 TTGCTTTGCTGTTCCACT
1 TTGCTTTGCTCTTCCACT
4890 TTGCTTTG-TCTTCCACT
1 TTGCTTTGCTCTTCCACT
4907 TT-CTTT
1 TTGCTTT
4913 ATTGTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.05, C:0.27, G:0.12, T:0.56
Consensus pattern (18 bp):
TTGCTTTGCTCTTCCACT
Found at i:4919 original size:45 final size:45
Alignment explanation
Indices: 4869--5082 Score: 329
Period size: 45 Copynumber: 4.8 Consensus size: 45
4859 ATTTTTCAGC
* *
4869 TTGTTGCTTTGCTGTTCCACTTTGCTTTGTCTTCCACTTTCTTTA
1 TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* *
4914 TTGTTGGTTTGTTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
1 TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* *
4959 TTGTTGCTTTGTTATTCCACGTTGCTTTGTCTTCCACTTTCTTTC
1 TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* * * *
5004 TTGTTACTTTGCTGTTCCACGTTGCTTTATCTTCTACTTTCTTTA
1 TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
*
5049 TTATTGCTTTGCTATTCCACGTTGCTTTGTCTTC
1 TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTC
5083 ATCATTGCTG
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 153 1.00
ACGTcount: A:0.08, C:0.23, G:0.14, T:0.55
Consensus pattern (45 bp):
TTGTTGCTTTGCTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
Found at i:5255 original size:16 final size:17
Alignment explanation
Indices: 5225--5258 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5215 GTGCTGCACG
5225 TTATCTATTTATTTTAT
1 TTATCTATTTATTTTAT
*
5242 TTAT-TATTTTTTTTAT
1 TTATCTATTTATTTTAT
5258 T
1 T
5259 CCAGTACTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATCTATTTATTTTAT
Found at i:5883 original size:17 final size:17
Alignment explanation
Indices: 5832--5873 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
5822 GAAATGCATT
5832 TATGCATGAAATGAACA
1 TATGCATGAAATGAACA
5849 TATGCATGAAATGAACA
1 TATGCATGAAATGAACA
5866 TATGCATG
1 TATGCATG
5874 CATGAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (17 bp):
TATGCATGAAATGAACA
Found at i:5991 original size:15 final size:14
Alignment explanation
Indices: 5971--6021 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 14
5961 ACGTTTTCTC
*
5971 TTTTTTTCTTTGAT
1 TTTTTTTTTTTGAT
5985 TTTTTTTGTTTTGAT
1 TTTTTTT-TTTTGAT
*
6000 TTCTTTGATTTTTGAT
1 TT-TTT-TTTTTTGAT
6016 TTTTTT
1 TTTTTT
6022 AAATTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 7 0.23
15 11 0.35
16 12 0.39
17 1 0.03
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTTTGAT
Found at i:6020 original size:24 final size:24
Alignment explanation
Indices: 5975--6021 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5965 TTTCTCTTTT
*
5975 TTTCTTTGATTTTTTTTGTTTTGA
1 TTTCTTTGATTTTTATTGTTTTGA
*
5999 TTTCTTTGATTTTTGATTTTTTT
1 TTTCTTTGATTTTT-ATTGTTTT
6022 AAATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.09, C:0.04, G:0.11, T:0.77
Consensus pattern (24 bp):
TTTCTTTGATTTTTATTGTTTTGA
Found at i:9120 original size:481 final size:481
Alignment explanation
Indices: 8218--9662 Score: 2550
Period size: 481 Copynumber: 3.0 Consensus size: 481
8208 AAAAACTCAC
*
8218 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATTTAACAAGTTGTTTAGTCTATTAGGA
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
8283 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
66 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
8348 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
131 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
8413 AAGTAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
196 AAGTAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
8478 TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
261 TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
* *
8543 CCATTTGTCATACAAAAATAACATGACCAATTTAGATATATTTAAAATACTTATTTTATAAAAAT
326 CCATTTGTCATACAAAAATAACATGATCAATTTAGTTATATTTAAAATACTTATTTTATAAAAAT
8608 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAAA
391 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAAA
8673 AATATCAAAAACAAGATTTATCAAAA
456 AATATCAAAAACAAGATTTATCAAAA
8699 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
8764 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
66 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
* * *
8829 CCGTTTCTCATTCCATAAGAACTAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
131 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
* *
8894 AAATAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAGTTTCTCAGATCTCTC
196 AAGTAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
*
8959 TTCATGCATCGCATATGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
261 TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
* *
9024 CCATTTGTCATACAAAGATAACATGATCAATTTAGTTATATTTAAAATACTTATTTTATAGAAAT
326 CCATTTGTCATACAAAAATAACATGATCAATTTAGTTATATTTAAAATACTTATTTTATAAAAAT
*
9089 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCGGTGTATAATATATATTTATATACAATAAA
391 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAAA
9154 AATATCAAAAACAAGATTTATCAAAA
456 AATATCAAAAACAAGATTTATCAAAA
9180 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATT-GAG
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAG-G
9244 AATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCA
65 AATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCA
*
9309 TCTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCTATAAAAACTTGGCCAAATTCAATGTAGT
130 TCTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGT
* *
9374 CTAAGTAAAAGAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTC
195 C-AAGTAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTC
* * * * * *
9439 TCTTCATGCATCGCATGTTGAAGTAACCATGCAATAAACACACTAATATAATTAATTCTCGATTC
259 TCTTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTC
* * * * **
9504 TATCATTTGTCATACAAATATAATACGATCAATTTAGTTACGTTTAAAATACTTATTTTATAAAA
324 TACCATTTGTCATACAAAAATAACATGATCAATTTAGTTATATTTAAAATACTTATTTTATAAAA
* * * * * *
9569 ATAAGTTAACTAGCACACAATTTAAAATATATTAGTCAGTGTATAATATATATTTATATATAATA
389 ATAAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATA
* *
9634 AAAATATCAAAATCAAGATTTATTAAAA
454 AAAATATCAAAAACAAGATTTATCAAAA
9662 A
1 A
9663 GTATTGTTCC
Statistics
Matches: 919, Mismatches: 43, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
480 1 0.00
481 658 0.72
482 260 0.28
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (481 bp):
ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
AAGTAAAAAAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
CCATTTGTCATACAAAAATAACATGATCAATTTAGTTATATTTAAAATACTTATTTTATAAAAAT
AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAAA
AATATCAAAAACAAGATTTATCAAAA
Found at i:10219 original size:2 final size:2
Alignment explanation
Indices: 10212--10246 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10202 CACATTAACA
*
10212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10247 AACAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16078 original size:28 final size:28
Alignment explanation
Indices: 16038--16098 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
16028 AAAGGTCAAC
16038 AAATGAAATCTATCTTTGACGATGAGTT
1 AAATGAAATCTATCTTTGACGATGAGTT
16066 AAATGAAATCTATCTTTGACGATGAGTT
1 AAATGAAATCTATCTTTGACGATGAGTT
16094 AAATG
1 AAATG
16099 TATCTCAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (28 bp):
AAATGAAATCTATCTTTGACGATGAGTT
Found at i:21155 original size:30 final size:30
Alignment explanation
Indices: 21096--21155 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
21086 AATTTTAAAA
*
21096 TAATAAAATATAAAATATAAATTATTAATT
1 TAATAAAATATAAAATATAAATAATTAATT
21126 TAAT-AAATATAAAA-ATAATATAATATAATT
1 TAATAAAATATAAAATATAA-ATAAT-TAATT
21156 AAAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 4 0.15
29 14 0.52
30 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
TAATAAAATATAAAATATAAATAATTAATT
Found at i:21468 original size:12 final size:13
Alignment explanation
Indices: 21450--21479 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
21440 TTCTTTGGTT
21450 TATTAATTAATTA
1 TATTAATTAATTA
21463 -ATTAATTAATTA
1 TATTAATTAATTA
21475 TATTA
1 TATTA
21480 GATAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTAATTAATTA
Found at i:21766 original size:52 final size:55
Alignment explanation
Indices: 21672--21802 Score: 137
Period size: 53 Copynumber: 2.4 Consensus size: 55
21662 TTAATTTTGA
* *
21672 TAAAATTAAAAATAATAATAATAGTATATCAATAAGATTAAATAT-T-ATAATAG
1 TAAAATTAAAATTAATAACAATAGTATATCAATAAGATTAAATATATGATAATAG
** *
21725 TAAAATTAAAATTAATAACAATA-TATAT-TTTTAGATTTAAATATAATGATAATAG
1 TAAAATTAAAATTAATAACAATAGTATATCAATAAGA-TTAAATAT-ATGATAATAG
* *
21780 T-AAAGTAAATTATAATAACAATA
1 TAAAATTAAAAT-TAATAACAATA
21803 AAAAATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
51 4 0.06
52 13 0.20
53 21 0.32
54 9 0.14
55 19 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (55 bp):
TAAAATTAAAATTAATAACAATAGTATATCAATAAGATTAAATATATGATAATAG
Done.