Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1881
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: 24430
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1134 original size:19 final size:18
Alignment explanation
Indices: 1102--1139 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1092 TGTTACAATT
1102 TAATTTATTAAATTTATTA
1 TAATTTATTAAATTT-TTA
1121 TAATGTTATT-AATTTTTA
1 TAAT-TTATTAAATTTTTA
1139 T
1 T
1140 TTATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TAATTTATTAAATTTTTA
Found at i:5207 original size:23 final size:23
Alignment explanation
Indices: 5181--5268 Score: 61
Period size: 23 Copynumber: 3.7 Consensus size: 23
5171 ATAATTTTAA
5181 TTATTATTTAATAATATATATTT
1 TTATTATTTAATAATATATATTT
* * **
5204 TTATAATTTAATTTAAAATATATGA
1 TTATTATTTAA--TAATATATATTT
* * *
5229 ATATTAATATAAAAATA-ATATTT
1 TTATT-ATTTAATAATATATATTT
*
5252 TATATTTTTTAATAATA
1 T-TATTATTTAATAATA
5269 AAATAAATTT
Statistics
Matches: 46, Mismatches: 15, Indels: 8
0.67 0.22 0.12
Matches are distributed among these distances:
23 22 0.48
24 7 0.15
25 12 0.26
26 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
TTATTATTTAATAATATATATTT
Found at i:5280 original size:28 final size:28
Alignment explanation
Indices: 5232--5286 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5222 TATATGAATA
*
5232 TTAATATAAAAATAATATTTTATATTTT
1 TTAATATAAAAATAATATTTTAAATTTT
5260 TTAATA-ATAAAATAA-ATTTTTAAATTT
1 TTAATATA-AAAATAATA-TTTTAAATTT
5287 AATTTTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATATAAAAATAATATTTTAAATTTT
Found at i:6049 original size:100 final size:100
Alignment explanation
Indices: 5899--6089 Score: 328
Period size: 100 Copynumber: 1.9 Consensus size: 100
5889 ATTTTTTAAG
* * *
5899 AAAAAGTTATTTTAGCTTTTTTGTCACAAAATTTGTTAATGATTTGAGGTAATAATATTTTTATA
1 AAAAAGTTATTTTAGCTTTTTTGTCACAAAATTTATTAATGATTTAAGGTAATAATATTTTTAAA
*
5964 ATATAACGAAATTTTATAAATAAGTTTATAGCTTT
66 ATATAACGAAATTTTATAAACAAGTTTATAGCTTT
*
5999 AAAAAGTTATTTTAGCTTTTTTGTCATAAAATTTATTAATGATTTAAGGTAATAATATTTTTAAA
1 AAAAAGTTATTTTAGCTTTTTTGTCACAAAATTTATTAATGATTTAAGGTAATAATATTTTTAAA
*
6064 ATATAACGAAGTTTTATAAACAAGTT
66 ATATAACGAAATTTTATAAACAAGTT
6090 CGTAGCCAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (100 bp):
AAAAAGTTATTTTAGCTTTTTTGTCACAAAATTTATTAATGATTTAAGGTAATAATATTTTTAAA
ATATAACGAAATTTTATAAACAAGTTTATAGCTTT
Found at i:6746 original size:20 final size:20
Alignment explanation
Indices: 6718--6792 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
6708 TTTTACCTAG
6718 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
6738 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
6758 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
6778 ATGTATCGATACATT
1 ATGTATCGATACATT
6793 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:6778 original size:40 final size:39
Alignment explanation
Indices: 6718--6795 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
6708 TTTTACCTAG
* *
6718 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTTCAATATATCGATACAT-TATGA
* *
6758 ATGTATCAATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCAATACATTCTTCAATATATCGATACATTATG
6796 TCTTTTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCAATACATTCTTCAATATATCGATACATTATGA
Found at i:20778 original size:12 final size:12
Alignment explanation
Indices: 20761--20815 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
20751 CATCCTTTAC
20761 AAAAAAAAAT-A
1 AAAAAAAAATAA
*
20772 AAAAAAAAACAA
1 AAAAAAAAATAA
**
20784 AAAAAAAAA-CC
1 AAAAAAAAATAA
*
20795 AAGAAAAAATAA
1 AAAAAAAAATAA
20807 CAAAAAAAA
1 -AAAAAAAA
20816 GGCGTCTAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 17 0.50
12 10 0.29
13 7 0.21
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:20791 original size:23 final size:26
Alignment explanation
Indices: 20761--20815 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
20751 CATCCTTTAC
*
20761 AAAAAAAAA-TAA-AAAAAA-AACAA
1 AAAAAAAAACCAAGAAAAAATAACAA
20784 AAAAAAAAACCAAGAAAAAATAACAA
1 AAAAAAAAACCAAGAAAAAATAACAA
20810 AAAAAA
1 AAAAAA
20816 GGCGTCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 9 0.32
24 2 0.07
25 6 0.21
26 11 0.39
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (26 bp):
AAAAAAAAACCAAGAAAAAATAACAA
Found at i:20801 original size:13 final size:11
Alignment explanation
Indices: 20761--20815 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 11
20751 CATCCTTTAC
*
20761 AAAAAAAAATA
1 AAAAAAAAACA
20772 AAAAAAAAACAA
1 AAAAAAAAAC-A
20784 AAAAAAAAACCA
1 AAAAAAAAA-CA
20796 AGAAAAAATAACA
1 A-AAAAAA-AACA
20809 AAAAAAA
1 AAAAAAA
20816 GGCGTCTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 9 0.23
12 18 0.46
13 10 0.26
14 2 0.05
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:22040 original size:29 final size:29
Alignment explanation
Indices: 21998--23178 Score: 1519
Period size: 28 Copynumber: 41.5 Consensus size: 29
21988 ATGTTCATTC
* *
21998 TTTCAAAGCACACGAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22027 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22055 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22083 TTTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22112 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22141 TTT-AAAGCCCCAAAAGTCAGTGGCACTC-
1 TTTCAAAG-CCCACAAGTCAGTGGCACTCT
* *
22169 TTTCAAAGCCGGACAACTCAGTGGCACTC-
1 TTTCAAAGCC-CACAAGTCAGTGGCACTCT
* * *
22198 TTTCAAAGCCCATAAGTCAGTAGCATTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22226 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22254 TTTC-AAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22281 TTTCAAAGCCCACAAGTCAATGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22310 TTT-AGAGCCCACAAGTCAGTGGCAC-C-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22336 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22365 TTTCAAAGCCCACAATTAAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22394 TTTCAAAGCCCACAAGTTAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
22422 TTTCAAAGCCCACAAGTTGGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22450 TTTC-AAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22477 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22505 TTTCAAAGCCCACACAAGTTAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
* *
22536 TTTCAAAGCCTACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCC--CACAAGTCAGTGGC-ACTCT
* *
22568 TTTCAAAGCCCACACGTCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22597 TTTCAAAGCCCACAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22625 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22653 TTTCAAAGCCCACAAGTCAGTGCCA-TCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22681 TTTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
** *
22712 TTT-AAAGCCCATGAGTCAGTGGCAC-AT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22739 TTTC-AAGCCCACAAGTCAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22766 TTTC-AAGCCCACAAGTCAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22793 TTTCAAAGCCCATAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22822 TTTCAAAGCCCACAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22850 TTTCAAAGCCCACAAATCAGTGCCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
22879 TTTCAAAGTCCATAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22907 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** *
22936 TTTCAAATTCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
22965 TTTC-AAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
22993 TTTCAAAGCCCACAAGTTAGTGGCA-TCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
23021 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
23049 TTTCAAAGCCCATGTAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
23079 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
23108 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
23136 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
23165 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
23179 CGAGTTGGCG
Statistics
Matches: 1025, Mismatches: 89, Indels: 76
0.86 0.07 0.06
Matches are distributed among these distances:
26 3 0.00
27 131 0.13
28 445 0.43
29 328 0.32
30 76 0.07
31 28 0.03
32 14 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:22085 original size:57 final size:57
Alignment explanation
Indices: 21997--23178 Score: 1579
Period size: 57 Copynumber: 20.8 Consensus size: 57
21987 AATGTTCATT
* * *
21997 CTTTCAAAGCACACGAGTCAGTGGCACTCTTTTCAAAGCCCACGAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
*
22054 CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCATAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
22110 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCCAAAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG-CCCACAAGTCAGTGGCACC
* * * * **
22168 CTTTCAAAGCCGGACAACTCAGTGGCACTC-TTTCAAAGCCCATAAGTCAGTAGCATT
1 CTTTCAAAGCC-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
*
22225 CTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
22280 CTTTCAAAGCCCACAAGTCAATGGCACCCTTTT-AGAGCCCACAAGTCAGTGGCA-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
22335 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAATTAAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * **
22393 TTTTCAAAGCCCACAAGTTAGTGGCACTC-TTTCAAAGCCCACAAGTTGGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
22449 TTTTC-AAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
22504 CTTTCAAAGCCCACACAAGTTAGTGGCACTCCTTTCAAAGCCTACACAAGTCGGTGGCAACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACTCTTTTCAAAGCC--CACAAGTCAGTGGC-AC-C
* * * *
22567 ATTTCAAAGCCCACACGTCGGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
22624 CTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGCCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * ** *
22680 ATTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-AAAGCCCATGAGTCAGTGGCACA
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
22738 TTTTC-AAGCCCACAAGTCAGTGGCACT-TTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
22792 TTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
22849 CTTTCAAAGCCCACAAATCAGTGCCACTCTTTTCAAAGTCCATAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* **
22906 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAATTCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
22963 CTTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
23020 ATTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCATGTAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGCACC
*
23078 CTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
*
23135 CTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCCCACA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
23179 CGAGTTGGCG
Statistics
Matches: 999, Mismatches: 95, Indels: 62
0.86 0.08 0.05
Matches are distributed among these distances:
54 28 0.03
55 162 0.16
56 153 0.15
57 404 0.40
58 164 0.16
59 38 0.04
61 38 0.04
62 3 0.00
63 9 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (57 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:23749 original size:20 final size:20
Alignment explanation
Indices: 23721--23795 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
23711 TTTTAACCAG
*
23721 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
23741 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
23761 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
23781 ATGTATCGATACATT
1 ATGTATCGATACATT
23796 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:23788 original size:40 final size:39
Alignment explanation
Indices: 23721--23798 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
23711 TTTTAACCAG
* *
23721 ATGTATCGATACATTTTTTAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
23761 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
23799 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Done.