Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2329
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: 46450
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2870 original size:80 final size:79
Alignment explanation
Indices: 2690--2885 Score: 266
Period size: 79 Copynumber: 2.5 Consensus size: 79
2680 CGAATACACG
* * * * * *
2690 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGC
*
2755 TTAGCACGGATATA
66 TTAGCACGGATACA
* * * * *
2769 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGG-
*
2834 CTTAGCCCGGATACA
65 CTTAGCACGGATACA
2849 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
2886 TTAGTAATCG
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 54 0.53
80 47 0.47
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGC
TTAGCACGGATACA
Found at i:2904 original size:40 final size:40
Alignment explanation
Indices: 2703--2962 Score: 280
Period size: 40 Copynumber: 6.6 Consensus size: 40
2693 CCAGCATGAT
* * * *
2703 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
2743 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
2782 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
2822 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
2862 TGCTCTTCGGGACTTAGCCCGGATTTAGT-AATCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* * *
2902 TGC-CTTC-GGTCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGACTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
2941 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
2963 CATCATTCGA
Statistics
Matches: 187, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
38 15 0.08
39 45 0.24
40 126 0.67
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:2904 original size:80 final size:78
Alignment explanation
Indices: 2690--2962 Score: 257
Period size: 79 Copynumber: 3.5 Consensus size: 78
2680 CGAATACACG
* * * * *
2690 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA-ACACCAGCACGAATGCTCTTCGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATA-ATC-GCACGAATGCTCTTCGGG
* * *
2754 TTTAGCACGGATATA
64 CTTAGCCCGGATACA
* * * * * *
2769 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAT-AATCGCACGAATGCTCTTCGGG-
2834 CTTAGCCCGGATACA
64 CTTAGCCCGGATACA
* * *
2849 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAATCGCACCAATGC-CTTCGGTC
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATA-TAATCGCACGAATGCTCTTCGGGC
* **
2913 TTAGTCCGGATATGG
65 TTAGCCCGGATA-CA
* *
2928 TCACTTAGCA-CAAAGC-CTTCGGGACTTAGCCCGGA
1 TCAC-TAGCATGAATGCTCTTCGGGACTTAGCCCGGA
2963 CATCATTCGA
Statistics
Matches: 160, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
78 31 0.19
79 64 0.40
80 63 0.39
81 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATAATCGCACGAATGCTCTTCGGGCT
TAGCCCGGATACA
Found at i:2909 original size:119 final size:119
Alignment explanation
Indices: 2690--2964 Score: 299
Period size: 119 Copynumber: 2.3 Consensus size: 119
2680 CGAATACACG
* * * * *
2690 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGC
* *
2755 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-CA
66 TTAGCACGGATATATCAATAGCACCAATGCTCTTCGG-ACTTAGCCCGGATATCA
* * * *
2809 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGG-
* * * * * **
2874 CTTAGCCCGGATTTAGT-AATCGCACCAATGC-CTTCGGTCTTAGTCCGGATATGG
65 CTTAGCACGGATATA-TCAATAGCACCAATGCTCTTCGGACTTAGCCCGGATATCA
* *
2928 TCACTTAGCA-CAAAGC-CTTCGGGACTTAGCCCGGACA
1 TCAC-TAGCATGAATGCTCTTCGGGACTTAGCCCGGACA
2965 TCATTCGAAT
Statistics
Matches: 131, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
118 32 0.24
119 70 0.53
120 28 0.21
121 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (119 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGC
TTAGCACGGATATATCAATAGCACCAATGCTCTTCGGACTTAGCCCGGATATCA
Found at i:3307 original size:29 final size:29
Alignment explanation
Indices: 3268--3346 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
3258 CTTAATAATC
*
3268 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
3298 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
3327 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3347 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:5379 original size:36 final size:37
Alignment explanation
Indices: 5303--5380 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
5293 TTATTACGAA
* *
5303 GTCTTACCCGGACATAATCTCCACACGAAGTTATCAG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
* *
5340 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
5376 GTCTT
1 GTCTT
5381 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 19 0.51
37 18 0.49
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
Found at i:5649 original size:47 final size:47
Alignment explanation
Indices: 5501--5971 Score: 728
Period size: 47 Copynumber: 10.0 Consensus size: 47
5491 CTTCGGGACC
* * * * * * * *
5501 TATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
5548 TGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
5594 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
5641 TATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
5688 TATCACATATATACACCTTCACATTCATCACATCGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
5735 TATCATATATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
5782 TATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
5829 TATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* * *
5876 TATCACACATATACACTTTCACATTCATCACATTGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
5923 TATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
5970 TA
1 TA
5972 CTATCATTTC
Statistics
Matches: 399, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
46 40 0.10
47 359 0.90
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
Found at i:16925 original size:40 final size:40
Alignment explanation
Indices: 16847--17069 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
16837 ACCCAAGTAT
* *
16847 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
16886 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
16926 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
16966 CTTCGGCACTTAGCCCGG-TATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
17008 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
17048 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17070 CATCCGAATA
Statistics
Matches: 162, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.01
39 20 0.12
40 105 0.65
41 1 0.01
42 27 0.17
43 8 0.05
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17029 original size:82 final size:80
Alignment explanation
Indices: 16847--17069 Score: 292
Period size: 82 Copynumber: 2.8 Consensus size: 80
16837 ACCCAAGTAT
* * *
16847 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
16910 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
* *
16926 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGCCTTCGGCACTTAGCCCGG-TATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
16989 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
17008 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
17070 CATCCGAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 21 0.17
80 38 0.30
81 1 0.01
82 62 0.49
83 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:17711 original size:25 final size:25
Alignment explanation
Indices: 17669--17716 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17659 ACATATATAT
**
17669 ATTATGCCATTTACTCATAAACCCC
1 ATTATGCCAAATACTCATAAACCCC
* *
17694 ATTATGCCAAATATTCATTAACC
1 ATTATGCCAAATACTCATAAACC
17717 AATAGTCACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (25 bp):
ATTATGCCAAATACTCATAAACCCC
Found at i:20217 original size:27 final size:27
Alignment explanation
Indices: 20187--20346 Score: 162
Period size: 27 Copynumber: 5.9 Consensus size: 27
20177 CTGATTGATC
*
20187 AAAATGACTGTCTTGCCCTTATGTGGT
1 AAAATGACTGTTTTGCCCTTATGTGGT
*
20214 AAAATGATTGTTTT-CCCTTTATGTGGT
1 AAAATGACTGTTTTGCCC-TTATGTGGT
* * *
20241 AAAATGACTATTTAGCCCTTATATGGT
1 AAAATGACTGTTTTGCCCTTATGTGGT
* *
20268 AAAATGATTGTTTTTG-CATTATGTGGT
1 AAAATGACTG-TTTTGCCCTTATGTGGT
* * *
20295 AAAATTACTATTTTGCCCTTATATGGT
1 AAAATGACTGTTTTGCCCTTATGTGGT
* * * *
20322 AAGAGGATTGTTTTGCCCCTATGTG
1 AAAATGACTGTTTTGCCCTTATGTG
20347 ATGTGTATAT
Statistics
Matches: 106, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
26 8 0.08
27 91 0.86
28 7 0.07
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
AAAATGACTGTTTTGCCCTTATGTGGT
Found at i:20345 original size:54 final size:54
Alignment explanation
Indices: 20187--20346 Score: 207
Period size: 54 Copynumber: 3.0 Consensus size: 54
20177 CTGATTGATC
* * *
20187 AAAATGACTGTCTTGCCCTTATGTGGTAAAATGATTGTTTT-CCCTTTATGTGGT
1 AAAATGACTATTTTGCCCTTATATGGTAAAATGATTGTTTTGCCC-TTATGTGGT
* *
20241 AAAATGACTATTTAGCCCTTATATGGTAAAATGATTGTTTTTG-CATTATGTGGT
1 AAAATGACTATTTTGCCCTTATATGGTAAAATGATTG-TTTTGCCCTTATGTGGT
* * * *
20295 AAAATTACTATTTTGCCCTTATATGGTAAGAGGATTGTTTTGCCCCTATGTG
1 AAAATGACTATTTTGCCCTTATATGGTAAAATGATTGTTTTGCCCTTATGTG
20347 ATGTGTATAT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.05
54 82 0.89
55 5 0.05
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (54 bp):
AAAATGACTATTTTGCCCTTATATGGTAAAATGATTGTTTTGCCCTTATGTGGT
Found at i:23401 original size:47 final size:47
Alignment explanation
Indices: 23279--23771 Score: 790
Period size: 47 Copynumber: 10.4 Consensus size: 47
23269 CAGCCAAGAC
* *
23279 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
23326 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
23375 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
23422 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
23471 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
23518 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
23565 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
23612 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
23659 AGTGTATATATGTGGTAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
23706 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
23753 AGTGCT-TAAATGTGATAAG
1 AGTG-TATATATGTGATAAG
23772 TCCTGAAGGG
Statistics
Matches: 421, Mismatches: 20, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
47 328 0.78
48 1 0.00
49 92 0.22
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:23946 original size:37 final size:37
Alignment explanation
Indices: 23890--23968 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
23880 CCGAGCTCTA
* * *
23890 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCAGGT
*
23927 AAGACCCGATAACTTCGTGTGGAGATTATGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
23964 AAGAC
1 AAGAC
23969 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:32648 original size:15 final size:15
Alignment explanation
Indices: 32606--32690 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 15
32596 GTATTATAAT
*
32606 TTGGATTTCCTTATC
1 TTGGATTTCTTTATC
*
32621 ATGGATTTCTTTATC
1 TTGGATTTCTTTATC
*
32636 TTGGATTTATTTAT-
1 TTGGATTTCTTTATC
** **
32650 TCTGGGCTTCTCCATC
1 T-TGGATTTCTTTATC
* *
32666 TCGGATTTCTCTATC
1 TTGGATTTCTTTATC
*
32681 TTGGTTTTCT
1 TTGGATTTCT
32691 GGTTATTTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
14 1 0.02
15 51 0.96
16 1 0.02
ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Done.