Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2266
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: 51726
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6117 original size:51 final size:51
Alignment explanation
Indices: 6041--6160 Score: 186
Period size: 51 Copynumber: 2.4 Consensus size: 51
6031 AACTCAGTTA
* *
6041 TCCGGATAAAATATGAAGCTCTTGTTAAAGCTAGAGCAACAAAGTAATTAT
1 TCCGGATGAAATATGAAGCTCTTGTTAAAGCTAGAGCAACAAAGTAATAAT
* * *
6092 TCCGGATGAAATATGAAGCTCTTGTTGAAGTTAGAGCAACAAGGTAATAAT
1 TCCGGATGAAATATGAAGCTCTTGTTAAAGCTAGAGCAACAAAGTAATAAT
*
6143 TCCGGATGAAGTATGAAG
1 TCCGGATGAAATATGAAG
6161 TAAGTTTGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (51 bp):
TCCGGATGAAATATGAAGCTCTTGTTAAAGCTAGAGCAACAAAGTAATAAT
Found at i:19954 original size:17 final size:17
Alignment explanation
Indices: 19932--19966 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
19922 GCTAAGCTTT
19932 ATCACACTTTATTCGAC
1 ATCACACTTTATTCGAC
19949 ATCACACTTTATTCGAC
1 ATCACACTTTATTCGAC
19966 A
1 A
19967 GCACCAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (17 bp):
ATCACACTTTATTCGAC
Found at i:20696 original size:27 final size:28
Alignment explanation
Indices: 20636--20696 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
20626 AAATCATAAA
**
20636 TTGGTACTTAATTTTTTTTTGTCACAAG
1 TTGGTACTTAATCATTTTTTGTCACAAG
*
20664 -TAGTACTTAAATCATTTTTT-TC-CAAG
1 TTGGTACTT-AATCATTTTTTGTCACAAG
20690 TTGGTAC
1 TTGGTAC
20697 CTCTATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
26 4 0.15
27 14 0.52
28 9 0.33
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (28 bp):
TTGGTACTTAATCATTTTTTGTCACAAG
Found at i:20895 original size:19 final size:19
Alignment explanation
Indices: 20867--20903 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20857 AAGACAAAAA
*
20867 ATATTATTTTTTCTTTTAT
1 ATATTATTTTTACTTTTAT
*
20886 ATATTGTTTTTACTTTTA
1 ATATTATTTTTACTTTTA
20904 AATTTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (19 bp):
ATATTATTTTTACTTTTAT
Found at i:23073 original size:48 final size:48
Alignment explanation
Indices: 22938--23166 Score: 262
Period size: 48 Copynumber: 4.8 Consensus size: 48
22928 TCTTAAATCG
* * * *
22938 ATGCCATGTCCCAGACATGGTCTTACACGAAATCACATATCGATACCA
1 ATGCCATATCCCAGACATGGTCTTACATGAGATCACATATCGATGCCA
**
22986 ATGCCATATCCCA-ATGTGGTCTTACATGAGATCACATATCGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGAGATCACATATCGATGCCA
* * * * *
23033 ATGTCATATCCCATATATGGTCTTACATGGGATCACATATCAATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGAGATCACATATCGATGCCA
* * * * * *
23081 ATGCCATGTCTCAGACATGGTTTTACATGGGATAACACATCGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGAGATCACATATCGATGCCA
* * * *
23129 ATGTCATGTCCTAGACGTGGTCTTACATGAGATCACAT
1 ATGCCATATCCCAGACATGGTCTTACATGAGATCACAT
23167 GTAACCCTAA
Statistics
Matches: 153, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
47 41 0.27
48 112 0.73
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (48 bp):
ATGCCATATCCCAGACATGGTCTTACATGAGATCACATATCGATGCCA
Found at i:28877 original size:27 final size:27
Alignment explanation
Indices: 28846--28900 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
28836 TAAATAAGTG
28846 TTAATAAATATG-CTTTTAATCTGAACA
1 TTAATAAATATGTC-TTTAATCTGAACA
28873 TTAATAAATATGTCTTTAATCTGAACA
1 TTAATAAATATGTCTTTAATCTGAACA
28900 T
1 T
28901 GTTAATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (27 bp):
TTAATAAATATGTCTTTAATCTGAACA
Found at i:30848 original size:19 final size:18
Alignment explanation
Indices: 30817--30869 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
30807 GAAAGAATTT
*
30817 GAAAAAGAAAAAAAGAGTGA
1 GAAAAAGAAAAAGAGA-T-A
* *
30837 GAAAAAGCAAAATGAGATT
1 GAAAAAG-AAAAAGAGATA
30856 GAAAAAGAAAAAGA
1 GAAAAAGAAAAAGA
30870 ATGCGAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 8 0.29
21 7 0.25
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGATA
Found at i:32004 original size:22 final size:23
Alignment explanation
Indices: 31978--32022 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
31968 CATACTTTGT
31978 TTTGGTTAACTAC-TATTCTCTG
1 TTTGGTTAACTACATATTCTCTG
32000 TTTGGTTAACTACATTATTCTCT
1 TTTGGTTAACTACA-TATTCTCT
32023 ATCATTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTGGTTAACTACATATTCTCTG
Found at i:34663 original size:48 final size:48
Alignment explanation
Indices: 34602--34959 Score: 581
Period size: 48 Copynumber: 7.3 Consensus size: 48
34592 TGTATAAGAT
* * *
34602 AAATATATGTGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
34650 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAACGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAA----T---GGCTAGTGTG
*
34705 AAATATGTATGAGATATGTATATATGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
*
34753 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
*
34801 AAATATGTATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
*
34849 AAATATGAATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
34897 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
*
34945 AAATATGTAGGAGAT
1 AAATATGTATGAGAT
34960 GTGTGTATAT
Statistics
Matches: 291, Mismatches: 12, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
48 243 0.84
51 1 0.00
52 1 0.00
55 46 0.16
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (48 bp):
AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
Found at i:35150 original size:37 final size:37
Alignment explanation
Indices: 35100--35202 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
35090 GGAAATATAT
35100 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
35137 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
35174 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
35203 GGACTATTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:36362 original size:56 final size:58
Alignment explanation
Indices: 36302--36416 Score: 153
Period size: 56 Copynumber: 2.0 Consensus size: 58
36292 CTAATACATA
* * * *
36302 TTTTTAATGTGTCCTAGGTACAACCAAATTTAATTTGTGTTTTAG-TT-ATTACATGTT
1 TTTTTAATATGT-CTAGCTACAACCAAATTTAATTGGTGTTTTAGCTTAAATACATGTT
* *
36359 TTTTTAATATGTCTAGCTACAGCCGAATTTAATTGGTGTTTTAGCTTAAATACATGTT
1 TTTTTAATATGTCTAGCTACAACCAAATTTAATTGGTGTTTTAGCTTAAATACATGTT
36417 ACAAATATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 28 0.56
57 13 0.26
58 9 0.18
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (58 bp):
TTTTTAATATGTCTAGCTACAACCAAATTTAATTGGTGTTTTAGCTTAAATACATGTT
Found at i:37007 original size:10 final size:10
Alignment explanation
Indices: 36976--37009 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
36966 AAAAAGCAGC
36976 TTTCTGGAAT
1 TTTCTGGAAT
*
36986 TTTCTTGAAAT
1 TTTC-TGGAAT
36997 TTTCTGGAAT
1 TTTCTGGAAT
37007 TTT
1 TTT
37010 TCAGCTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.56
Consensus pattern (10 bp):
TTTCTGGAAT
Found at i:39498 original size:79 final size:81
Alignment explanation
Indices: 39389--39571 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
39379 TACTCGTTCA
* *
39389 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
39452 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
39469 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
39532 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
39548 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39572 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:39571 original size:40 final size:40
Alignment explanation
Indices: 39368--39571 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
39358 CGGAATTTAA
** *
39368 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39408 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39448 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39487 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39527 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39567 CCGGA
1 CCGGA
39572 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:47627 original size:39 final size:39
Alignment explanation
Indices: 47538--47717 Score: 165
Period size: 38 Copynumber: 4.6 Consensus size: 39
47528 GCTACTCGTT
* *
47538 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTA-ACCGGATT-TAGTAACTCGCA
47578 CAAATG-CTTCGGGACTTAACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCGGATTTAGTAACTCGCA
* * * *
47616 CCAATGCCTTCGGG-CTTAGCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCGGATTTAGTAACTCGCA
* * * * *
47654 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTA-ACCGGATTTAGTAAC-TCGCA
*
47695 CAAA-GCCTTC-GGACTTAGCCGGA
1 CAAATGCCTTCGGGACTTAACCGGA
47718 CATCATTCGA
Statistics
Matches: 119, Mismatches: 15, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
37 2 0.02
38 57 0.48
39 28 0.24
40 24 0.20
41 8 0.07
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCGGATTTAGTAACTCGCA
Found at i:47679 original size:78 final size:77
Alignment explanation
Indices: 47540--47717 Score: 184
Period size: 78 Copynumber: 2.3 Consensus size: 77
47530 TACTCGTTCA
* * *
47540 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCTTCGGGACTTAACCGGATT
1 AATGCCTTCGGG-CTTAG-CCGGAATATAGTAACTCGCACAAATGCTTCGGGACTTAACCGGATA
*
47604 TAGTAAC-TCGCACC
64 TAGTAACTTAGCA-C
* *
47618 AATGCCTTCGGGCTTAGCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGAT
1 AATGCCTTCGGGCTTAGCCGGAATATAGTAACTCGCACAAATG-CTTCGGGA-CTTA-ACCGGAT
* *
47681 ATGGTCACTTAGCAC
63 ATAGTAACTTAGCAC
* *
47696 AAAGCCTTCGGACTTAGCCGGA
1 AATGCCTTCGGGCTTAGCCGGA
47718 CATCATTCGA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
76 24 0.28
77 13 0.15
78 44 0.52
79 4 0.05
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (77 bp):
AATGCCTTCGGGCTTAGCCGGAATATAGTAACTCGCACAAATGCTTCGGGACTTAACCGGATATA
GTAACTTAGCAC
Done.