Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold745
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: 28510
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Found at i:616 original size:38 final size:39
Alignment explanation
Indices: 543--756 Score: 269
Period size: 39 Copynumber: 5.6 Consensus size: 39
533 CCAGCATGAT
* *
543 TGCTCTTCGGGAC-TAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
582 TGGTCTTC-GAGTTAGCACGGATATATTACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
*
620 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
* *
659 TGCTCTTCGGACTTAG-CCGGATTTATAACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
*
697 -GCTCTTCGGACTTAGCCCGGAATACATCACTAGCAC-AA
1 TGCTCTTCGGACTTAGCCCGG-ATATATCACTAGCACGAA
735 TG-TCTTCGGGACTTAGCCCGGA
1 TGCTCTTC-GGACTTAGCCCGGA
757 CATCATTCAA
Statistics
Matches: 152, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
37 17 0.11
38 60 0.39
39 75 0.49
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:756 original size:77 final size:78
Alignment explanation
Indices: 543--756 Score: 282
Period size: 77 Copynumber: 2.8 Consensus size: 78
533 CCAGCATGAT
* * *
543 TGCTCTTCGGGAC-TAGCCCGGATATA-A-CACCAGCACGAATGGTCTTC-GAGTTAGCACGGAT
1 TGCTCTTC-GGACTTAGCCCGGA-ATACATCACTAGCACGAAT-GTCTTCGGACTTAGCCCGGAT
*
604 ATATTACTAGCACGAA
63 ATATAACTAGCACGAA
*
620 TGCTCTTCGGACTTAGCCCGG-ATACATCACTAGCACGAATGCTCTTCGGACTTAG-CCGGATTT
1 TGCTCTTCGGACTTAGCCCGGAATACATCACTAGCACGAATG-TCTTCGGACTTAGCCCGGATAT
683 ATAACTAGCACGAA
65 ATAACTAGCACGAA
697 -GCTCTTCGGACTTAGCCCGGAATACATCACTAGCAC-AATGTCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGACTTAGCCCGGAATACATCACTAGCACGAATGTCTTC-GGACTTAGCCCGGA
757 CATCATTCAA
Statistics
Matches: 124, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
75 8 0.06
76 38 0.31
77 72 0.58
78 6 0.05
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (78 bp):
TGCTCTTCGGACTTAGCCCGGAATACATCACTAGCACGAATGTCTTCGGACTTAGCCCGGATATA
TAACTAGCACGAA
Found at i:1099 original size:29 final size:29
Alignment explanation
Indices: 1060--1138 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1050 CTTAATAATC
*
1060 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
1090 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
1119 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
1139 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:1181 original size:43 final size:43
Alignment explanation
Indices: 1120--1219 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
1110 TGCATTTCAA
1120 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1163 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1206 G--C-CACACTTAGTGC
1 GCCCGCACACTTAGTGC
1220 ACACTTACCC
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
40 12 0.21
41 1 0.02
43 44 0.77
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:3167 original size:37 final size:37
Alignment explanation
Indices: 3106--3184 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
3096 TTATTACGAA
* * *
3106 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
*
3143 GTCTTACCCAGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCT-CCACACGAAGTCATCGG
3180 GTCTT
1 GTCTT
3185 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
Found at i:3381 original size:47 final size:47
Alignment explanation
Indices: 3303--3936 Score: 1054
Period size: 47 Copynumber: 13.5 Consensus size: 47
3293 CCCTTCGGGA
* * * * * * *
3303 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
3350 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3397 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3444 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3491 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3538 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3585 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3632 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3679 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3728 CTTATCACATATA-ACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3774 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3821 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3868 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3915 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
3937 TTGGCTGAAT
Statistics
Matches: 559, Mismatches: 25, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
46 44 0.08
47 469 0.84
49 46 0.08
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:3382 original size:25 final size:25
Alignment explanation
Indices: 3354--3431 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
3344 CTCGGCCCTG
3354 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
3379 TCACAT-TGGCCA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
3401 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
3426 TCACAT
1 TCACAT
3432 CGGCCATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:6092 original size:85 final size:85
Alignment explanation
Indices: 5992--6170 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
5982 TATTTTATTG
*
5992 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
6057 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
6077 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
6142 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
6162 CCCATGCTC
1 CCCATGCTC
6171 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:7151 original size:34 final size:34
Alignment explanation
Indices: 7066--7160 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
7056 TTTAGTTAGG
* *
7066 GGCCTTAGCCCCTCTTTCAATAGCAGTAGCAGTCTG
1 GGCCTTAG-CCC-ATTTCAATAGCAGTAGCAGTCTA
* * *
7102 GGCCTGAGTCGATTTCAATAGCAGT-GACAGTCTA
1 GGCCTTAGCCCATTTCAATAGCAGTAG-CAGTCTA
*
7136 GGCCTTAGCCCATTTCAGTA-CAGTA
1 GGCCTTAGCCCATTTCAATAGCAGTA
7161 TGCAAACAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
33 5 0.10
34 35 0.73
35 1 0.02
36 7 0.15
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (34 bp):
GGCCTTAGCCCATTTCAATAGCAGTAGCAGTCTA
Found at i:11960 original size:51 final size:49
Alignment explanation
Indices: 11900--12039 Score: 149
Period size: 51 Copynumber: 2.8 Consensus size: 49
11890 TATTGTGAGG
*
11900 TCACGTGTGTAGTACTAAGTGCAGGCTACAATGCGTACCCGAAAACTGTGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACAATGCGTACCAGAAAA-T-TGA
* * ** *
11951 TCACGTGTGTAGTACTAAATGCAGGCTACTACAT--GTACTAGATTATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTAC-A-ATGCGTACCAGAAAATTGA
* * *
12000 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACAATGCGTACCA
12040 AATAGCTTCG
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
47 2 0.03
49 33 0.45
50 1 0.01
51 35 0.47
52 1 0.01
53 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACAATGCGTACCAGAAAATTGA
Found at i:14698 original size:27 final size:27
Alignment explanation
Indices: 14668--14845 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
14658 ATATTAAGTC
* * *
14668 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
14695 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
14723 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
14750 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
14777 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
14804 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
14831 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
14846 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:14752 original size:55 final size:54
Alignment explanation
Indices: 14668--14845 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
14658 ATATTAAGTC
* * *
14668 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
14723 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
14777 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
14831 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
14846 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:14834 original size:81 final size:82
Alignment explanation
Indices: 14689--14844 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
14679 TGCTATATAA
* *
14689 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
14754 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
14771 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
14834 ACACTTAGTGC
65 ACACTTAGTGC
14845 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:22789 original size:27 final size:27
Alignment explanation
Indices: 22759--22936 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
22749 ATATTAAGTC
* * *
22759 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
22786 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
22814 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
22841 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
22868 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
22895 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
22922 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22937 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:22843 original size:55 final size:54
Alignment explanation
Indices: 22759--22936 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
22749 ATATTAAGTC
* * *
22759 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
22814 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
22868 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
22922 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22937 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:22925 original size:81 final size:82
Alignment explanation
Indices: 22780--22935 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
22770 TGCTATATAA
* *
22780 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
22845 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
22862 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
22925 ACACTTAGTGC
65 ACACTTAGTGC
22936 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Done.