Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2214
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: 53307
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:383 original size:26 final size:26
Alignment explanation
Indices: 354--460 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
344 TGGTACAAAT
354 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
380 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
406 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
432 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
457 TGAT
1 TGAT
461 GGGCATTTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 22 0.28
26 57 0.72
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:7412 original size:26 final size:26
Alignment explanation
Indices: 7383--7490 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
7373 TGGTACAAAT
7383 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
7409 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
7435 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
7461 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
7487 TGAT
1 TGAT
7491 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:10951 original size:2 final size:2
Alignment explanation
Indices: 10944--10968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10934 CTGTAATCTA
10944 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10969 AAATAGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12892 original size:19 final size:20
Alignment explanation
Indices: 12860--12900 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12850 CACATTCTTT
*
12860 TTAATTATTCATT-AATATA
1 TTAATAATTCATTAAATATA
*
12879 TTAATAATTTATTAAATATA
1 TTAATAATTCATTAAATATA
12899 TT
1 TT
12901 CTTATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATAATTCATTAAATATA
Found at i:17698 original size:21 final size:21
Alignment explanation
Indices: 17639--17703 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
17629 TAGAAGCAGT
* * *
17639 ATACGATACATAAAGTACCTGA
1 ATACGACACATATAGTGCCT-A
** *
17661 A-ACGACACACGTGGTGCCTA
1 ATACGACACATATAGTGCCTA
17681 ATACGACACATATAGTGCCTA
1 ATACGACACATATAGTGCCTA
17702 AT
1 AT
17704 TGGCAAAGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTA
Found at i:18883 original size:10 final size:10
Alignment explanation
Indices: 18856--18893 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
18846 ATATATTATA
*
18856 ATAATATAAT
1 ATAATAAAAT
18866 AT-ATAAAAT
1 ATAATAAAAT
*
18875 ATAATAAAAC
1 ATAATAAAAT
18885 ATAATAAAA
1 ATAATAAAA
18894 ATCTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:28627 original size:19 final size:21
Alignment explanation
Indices: 28605--28644 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28595 GAACTTTGTC
*
28605 CAAAAT-TTTTCTAAG-TATT
1 CAAAATATTTTATAAGATATT
28624 CAAAATATTTTATAAGATATT
1 CAAAATATTTTATAAGATATT
28645 TGAAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (21 bp):
CAAAATATTTTATAAGATATT
Found at i:33275 original size:126 final size:126
Alignment explanation
Indices: 33050--33430 Score: 753
Period size: 126 Copynumber: 3.0 Consensus size: 126
33040 GCATGTTGCA
*
33050 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCTA
1 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
33115 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
66 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
33176 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
1 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
33241 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
66 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
33302 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
1 TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
33367 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
66 AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
33428 TAA
1 TAA
33431 GGTACCTAAA
Statistics
Matches: 254, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 254 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (126 bp):
TAAAAATTGATAAGTACTGGAGGTGCTTTTCCTATCTAATTTGCTTCCTTCAAAATCTGCATCCA
AGAATGCATGTAAGCTAAAGGATGAGTCTCTAGGATACCAAATACCTAAATTAGGTATCTC
Found at i:37449 original size:26 final size:26
Alignment explanation
Indices: 37417--37521 Score: 158
Period size: 26 Copynumber: 4.0 Consensus size: 26
37407 AATGCCCATT
37417 ATGGAACATTTACCTAAACCATTATC
1 ATGGAACATTTACCTAAACCATTATC
*
37443 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAAACCATTATC
* *
37469 ATGGAATATTTACCTAATCCATTATC
1 ATGGAACATTTACCTAAACCATTATC
*
37495 ATGGAACATTTACGT-AACCAATTATC
1 ATGGAACATTTACCTAAACC-ATTATC
37521 A
1 A
37522 ATTTGTATCA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
25 3 0.04
26 69 0.96
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (26 bp):
ATGGAACATTTACCTAAACCATTATC
Found at i:37491 original size:52 final size:52
Alignment explanation
Indices: 37417--37521 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
37407 AATGCCCATT
*
37417 ATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCAATTATC
* * *
37469 ATGGAATATTTACCTAATCCATTATCATGGAACATTTACGTAACCAATTATC
1 ATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCAATTATC
37521 A
1 A
37522 ATTTGTATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (52 bp):
ATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCAATTATC
Found at i:40990 original size:17 final size:18
Alignment explanation
Indices: 40968--41002 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40958 GATATGATAC
*
40968 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
40985 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
41003 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:41157 original size:39 final size:39
Alignment explanation
Indices: 41099--41176 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41089 AGAATGTAAG
41099 AGGGAGAGAAATTTGAGTGAAAGCTCTCAAAAATTTTTA
1 AGGGAGAGAAATTTGAGTGAAAGCTCTCAAAAATTTTTA
*
41138 AGGGAGAGAAATTTTAGTGAAAGCTCTCAAAAATTTTTA
1 AGGGAGAGAAATTTGAGTGAAAGCTCTCAAAAATTTTTA
41177 TTGATTCCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (39 bp):
AGGGAGAGAAATTTGAGTGAAAGCTCTCAAAAATTTTTA
Found at i:41337 original size:23 final size:21
Alignment explanation
Indices: 41307--41350 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41297 AAATTAAATC
41307 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC--AATCATATCT
*
41330 TCTAAGATTGCAATCATATCT
1 TCTAAGATTACAATCATATCT
41351 AAGATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (21 bp):
TCTAAGATTACAATCATATCT
Found at i:41364 original size:17 final size:18
Alignment explanation
Indices: 41330--41392 Score: 101
Period size: 17 Copynumber: 3.5 Consensus size: 18
41320 AATCATATCT
*
41330 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
41348 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
41365 TCTAAGATTGCATATCATA
1 TCTAAGATTGC-TATCATA
41384 TCTAAGATT
1 TCTAAGATT
41393 TCATATCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 16 0.38
18 10 0.24
19 16 0.38
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:41382 original size:19 final size:19
Alignment explanation
Indices: 41330--41401 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
41320 AATCATATCT
41330 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
41348 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
41365 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41384 TCTAAGATTTCATATCAT
1 TCTAAGATTGCATATCAT
41402 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 16 0.32
18 10 0.20
19 24 0.48
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41805 original size:45 final size:45
Alignment explanation
Indices: 41750--41994 Score: 276
Period size: 45 Copynumber: 5.5 Consensus size: 45
41740 GAAAGGTGAT
* * *
41750 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
41795 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATATAGAGACGTCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * *
41840 ATCTGCT-TCTTCAATTTGCTCCACATCTAATACAGAGATGTCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * *
41884 ATCTGTTATCTCCAATTTGCTTCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
41929 ATCTGTTATCTCCGATTTGCTCCCTGACTAATACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
41974 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
41995 TCGATGTAAA
Statistics
Matches: 173, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 37 0.21
45 136 0.79
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:41877 original size:89 final size:88
Alignment explanation
Indices: 41767--41994 Score: 260
Period size: 89 Copynumber: 2.5 Consensus size: 88
41757 ATCTTTGATC
* *
41767 TGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATATAGA
1 TGCT-CCC-TCTAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGA
* *
41832 GACGTCAAATCTGCT-TCTTCAATT
64 GACGCCAAATCTGCTATCTCCAATT
* * * * *
41856 TGCTCCACATCTAATACAGAGATGTCAAATCTGTTATCTCCAATTTGCTTCCCGTCTAATACAGA
1 TGCTCC-C-TCTAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGA
* * *
41921 GATGCCAAATCTGTTATCTCCGATT
64 GACGCCAAATCTGCTATCTCCAATT
* * *
41946 TGCTCCCTGACTAATACAAAGATGCCAAATCTGTCATCTTGGATCTGCT
1 TGCTCCCT--CTAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCT
41995 TCGATGTAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
88 3 0.03
89 67 0.58
90 45 0.39
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (88 bp):
TGCTCCCTCTAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGA
CGCCAAATCTGCTATCTCCAATT
Found at i:42139 original size:78 final size:78
Alignment explanation
Indices: 42019--42302 Score: 381
Period size: 78 Copynumber: 3.6 Consensus size: 78
42009 TGAATGTCAG
* * * *
42019 ATCTGCCATGTCTTTGATCTGCTCCCTGTCTAATACAAAGATGCCAAATCATCTTAGATCTGCTT
1 ATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
42084 CAATGAAGGTCCA
66 CAATGAAGGTCCA
* * *
42097 ATCTGTTATGTCTTTGATCTGCTCCCCCTCTAATACAGAGATGCCAAATCATCTTGGATCTACTT
1 ATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
*
42162 CAATGAAGGTCAA
66 CAATGAAGGTCCA
* * **
42175 ATCTGCTGTGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGAAT
1 ATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
*
42240 CAATGAAAGT-CA
66 CAATGAAGGTCCA
* * * ** *
42252 GATCTGCTATGTCTTCGATCTGCTCTCCGTCAAATATGGAGATGTCAAATC
1 -ATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
42303 TGTTTCTTCA
Statistics
Matches: 180, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 1 0.01
78 179 0.99
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (78 bp):
ATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
CAATGAAGGTCCA
Found at i:50930 original size:19 final size:19
Alignment explanation
Indices: 50906--50942 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
50896 AATCATATCT
50906 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
50925 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
50943 TGAAGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:50950 original size:17 final size:19
Alignment explanation
Indices: 50909--50950 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
50899 CATATCTTCT
*
50909 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
50928 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
50945 AAGATT
1 AAGATT
50951 ATATTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:53171 original size:17 final size:16
Alignment explanation
Indices: 53129--53167 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
53119 ATATATAACT
53129 GTAATATTAA-TTAAA
1 GTAATATTAATTTAAA
53144 -TAATACTTAATTTAAA
1 GTAATA-TTAATTTAAA
53160 GTAATATT
1 GTAATATT
53168 TAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.24
15 4 0.19
16 7 0.33
17 5 0.24
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (16 bp):
GTAATATTAATTTAAA
Done.