Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2911
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: 21118
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Found at i:1594 original size:39 final size:39
Alignment explanation
Indices: 1532--1609 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
1522 CTCTCCCTAA
*
1532 ATCCAAATTCGGCACATTGAACAACCCAAATGCTAACCT
1 ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
* *
1571 ATCCAAGTTCGGCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
1610 CAACGTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.22
Consensus pattern (39 bp):
ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
Found at i:3614 original size:83 final size:79
Alignment explanation
Indices: 3409--3933 Score: 588
Period size: 83 Copynumber: 6.8 Consensus size: 79
3399 CCAGCATGAT
* * * *
3409 TGCT-TTCGGATTTAG-CCGGATAT-TCACTAGC-CGAATGCTCTTCGGAAATTAGCCC-GATAC
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
3469 ATCACTAGCACG-A
66 ATCACTAGCACGAA
* *
3482 -GCTCTTCGGACTTAGGCCC-GATATATCA-TAGCTCAAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGACTTA-GCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
3544 TATCACTTAGCACGAA
65 TATCAC-TAGCACGAA
3560 TGCTCTTCGGACTTAGCCCGGATCATAATCACTAGCCACGAATGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGACTTAGCCCGGAT-AT-ATCACTAG-CACGAATGCTCTTCGGGACTTAGCCCGGA
*
3625 TACATCACTAGCACGAA
63 TATATCACTAGCACGAA
* *
3642 TGC-CTTCTCGGGACTTTAGCCCGGATACATCACTAGCACGGAATGCTCTTCGGAACTTAGCCCC
1 TGCTC-T-TC-GGAC-TTAGCCCGGATATATCACTAGCAC-GAATGCTCTTCGGGACTTAG-CCC
3706 GGATATATCCACTAG---GAA
60 GGATATAT-CACTAGCACGAA
3724 TGCTCTTCGGGAACTTAGGCCCGGATATATTCACTAGCACGAATGCTCTTC--GACTTAGCCCGG
1 TGCTCTTC-GG-ACTTA-GCCCGGATATA-TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
3787 ATATA-CACTAGCACGAA
62 ATATATCACTAGCACGAA
*
3804 TGCTCTTCGGACTTAAGCCCGGATATATC-CT-GCTCGAATGCTCTTC-GG---TAGCCC-GAT-
1 TGCTCTTCGGACTT-AGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
3861 TATCACT-GCACGAA
65 TATCACTAGCACGAA
3875 TGCTC-TCGGACTTAGCCCGGATATAGT-ACTAGCAC-AATG--CTTCGGGACTTAGCCCGGAT
1 TGCTCTTCGGACTTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
3934 TATTGGTCCC
Statistics
Matches: 398, Mismatches: 15, Indels: 78
0.81 0.03 0.16
Matches are distributed among these distances:
68 4 0.01
69 14 0.04
70 15 0.04
71 17 0.04
72 16 0.04
73 18 0.05
74 10 0.03
75 40 0.10
76 12 0.03
77 15 0.04
78 20 0.05
79 30 0.08
80 19 0.05
81 13 0.03
82 49 0.12
83 74 0.19
84 15 0.04
85 17 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
ATCACTAGCACGAA
Found at i:3653 original size:41 final size:40
Alignment explanation
Indices: 3420--3933 Score: 572
Period size: 37 Copynumber: 13.3 Consensus size: 40
3410 GCTTTCGGAT
* *
3420 TTAG-CCGGATAT-TCACTAGC-CGAATGCTCTTCGGAAA
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
*
3457 TTAGCCC-GATACATCACTAGCACG-A-GCTCTTC-GGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
* *
3493 TTAGGCCC-GATATATCA-TAGCTCAAATGCTCTTCGGGAC
1 TTA-GCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
3532 TTAGCCCGGATATATCACTTAGCACGAATGCTCTTC-GGAC
1 TTAGCCCGGATATATCAC-TAGCACGAATGCTCTTCGGGAC
3572 TTAGCCCGGATCATAATCACTAGCCACGAATGCTCTTCGGGAC
1 TTAGCCCGGAT-AT-ATCACTAG-CACGAATGCTCTTCGGGAC
*
3615 TTAGCCCGGATACATCACTAGCACGAATGC-CTTCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTC-T-TCGGGAC
* *
3656 TTTAGCCCGGATACATCACTAGCACGGAATGCTCTTCGGAAC
1 -TTAGCCCGGATATATCACTAGCAC-GAATGCTCTTCGGGAC
3698 TTAGCCCCGGATATATCCACTAG---GAATGCTCTTCGGGAAC
1 TTAG-CCCGGATATAT-CACTAGCACGAATGCTCTTCGGG-AC
3738 TTAGGCCCGGATATATTCACTAGCACGAATGCTCTTC--GAC
1 TTA-GCCCGGATATA-TCACTAGCACGAATGCTCTTCGGGAC
3778 TTAGCCCGGATATA-CACTAGCACGAATGCTCTTC-GGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
*
3816 TTAAGCCCGGATATATC-CT-GCTCGAATGCTCTTC-GG--
1 TT-AGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
3852 -TAGCCC-GAT-TATCACT-GCACGAATGCTC-TC-GGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
3886 TTAGCCCGGATATAGT-ACTAGCAC-AATG--CTTCGGGAC
1 TTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGGAC
3923 TTAGCCCGGAT
1 TTAGCCCGGAT
3934 TATTGGTCCC
Statistics
Matches: 423, Mismatches: 14, Indels: 80
0.82 0.03 0.15
Matches are distributed among these distances:
32 8 0.02
33 16 0.04
34 5 0.01
35 8 0.02
36 15 0.04
37 72 0.17
38 48 0.11
39 57 0.13
40 52 0.12
41 42 0.10
42 60 0.14
43 39 0.09
44 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
Found at i:5784 original size:38 final size:37
Alignment explanation
Indices: 5704--5784 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
5694 TCTTATACGA
* *
5704 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
*
5741 AGTCTTACCCGGACAAAAT-TCCCAACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATCT-CC-ACACGAAGTCATCG
*
5779 GGTCTT
1 AGTCTT
5785 TAGAGCCGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 1 0.03
37 20 0.53
38 17 0.45
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
Found at i:6112 original size:84 final size:88
Alignment explanation
Indices: 5931--6437 Score: 414
Period size: 88 Copynumber: 5.9 Consensus size: 88
5921 CACTTTCACA
* * * * * *
5931 TCATCACATCGGCCATTAGGCCTTTATCTCACATACAC-TGCTCAACATTCATCACATTGG-CAC
1 TCATC-CATTGGCCATTCGGCC-TTATCACACATATACATGTTC-AC-TTCATCACA-TGGCCAT
* * *
5994 TCGGCCTTATCACACATACACCTTTCACAT
61 TCGGCCTTATC-CACATATACATGTC-CAT
*
6024 TCATCCATTGGCCATATCGGCCTTATCACACATACACATG-TCAC-TC-TCACATGGCCATTC-G
1 TCATCCATTGGCCAT-TCGGCCTTATCACACATATACATGTTCACTTCATCACATGGCCATTCGG
* *
6085 CCTTATCCATATATGCA-GTCCAT
65 CCTTATCCACATATACATGTCCAT
*
6108 TCATCACATTGGCCATTCGCCCTTATCACACATATACATGTTCACTTCATCACATTGGCCATTCG
1 TCATC-CATTGGCCATTCGGCCTTATCACACATATACATGTTCACTTCATCACA-TGGCCATTCG
*
6173 GCCTTATCACACATATACATGTTCACT
64 GCCTTATC-CACATATACATGTCCA-T
*
6200 TCAT-CACTTGGCCATTCGGCCTTATCACACAT-TACATGTTTACTTTCATCACAT-GCCATTCG
1 TCATCCA-TTGGCCATTCGGCCTTATCACACATATACATGTTCAC-TTCATCACATGGCCATTCG
*
6262 GCCTTATCCACATATACATGTTCACT
64 GCCTTATCCACATATACATGTCCA-T
* *
6288 TC-TACA-T-GCCATTCGG-C-TATCA-ACATACA-ATGTTCACTTTC-TCACATTGG-CA-TCG
1 TCATCCATTGGCCATTCGGCCTTATCACACATATACATGTTCAC-TTCATCACA-TGGCCATTCG
*
6343 G-CTTA-CCA-ATATA-GTGTTCCAT
64 GCCTTATCCACATATACATG-TCCAT
*
6365 TCATCACATT-GCCATTC-GCCTTAT--C-CA-ATACATGTT-ACATCATCACATGGCCA-TC-G
1 TCATC-CATTGGCCATTCGGCCTTATCACACATATACATGTTCACTTCATCACATGGCCATTCGG
* *
6421 CCCTATTCACATATACA
65 CCTTATCCACATATACA
6438 CTTCACATTT
Statistics
Matches: 356, Mismatches: 26, Indels: 76
0.78 0.06 0.17
Matches are distributed among these distances:
77 11 0.03
78 25 0.07
79 15 0.04
80 18 0.05
81 12 0.03
82 18 0.05
83 7 0.02
84 31 0.09
85 25 0.07
86 9 0.03
87 17 0.05
88 40 0.11
89 26 0.07
90 21 0.06
91 39 0.11
92 30 0.08
93 12 0.03
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (88 bp):
TCATCCATTGGCCATTCGGCCTTATCACACATATACATGTTCACTTCATCACATGGCCATTCGGC
CTTATCCACATATACATGTCCAT
Found at i:6157 original size:130 final size:130
Alignment explanation
Indices: 5976--6389 Score: 443
Period size: 130 Copynumber: 3.2 Consensus size: 130
5966 CACTGCTCAA
* * * *
5976 CATTCATCACATTGGCACTCGGCCTTATCACACATACACCT-TTCACATTCATCCATTGGCCATA
1 CATTCATCACATTGCCATTCGGCCTTATCACACATATACATGTTCAC-TTCATCCATTGGCCAT-
6040 TCGGCCTTATCACACATACACATG-TCAC-TCTCACATGGCCATTCGCCTTATCCATATATGCAG
64 TCGGCCTTATCACACATACACATGTTCACTTCTCACATGGCCATTCGCCTTATCCATATATGCAG
6103 TC
129 TC
*
6105 CATTCATCACATTGGCCATTCGCCCTTATCACACATATACATGTTCACTTCATCACATTGGCCAT
1 CATTCATCACATT-GCCATTCGGCCTTATCACACATATACATGTTCACTTCATC-CATTGGCCAT
* * * *
6170 TCGGCCTTATCACACATATACATGTTCACTTCATCACTTGGCCATTCGGCCTTATCACACAT-TA
64 TCGGCCTTATCACACATACACATGTTCACTTC-TCACATGGCCATTC-GCCTTATC-CATATATG
*
6234 CATGTTTA
126 CA-G--TC
* *
6242 CTTTCATCACA-TGCCATTCGGCCTTATC-CACATATACATGTTCACTTC-TACA-T-GCCATTC
1 CATTCATCACATTGCCATTCGGCCTTATCACACATATACATGTTCACTTCATCCATTGGCCATTC
*
6302 GG-C-TATCA-ACATACA-ATGTTCACTTTCTCACATTGG-CA-TCGGCTTA-CCAATATAGTG-
66 GGCCTTATCACACATACACATGTTCAC-TTCTCACA-TGGCCATTCGCCTTATCC-ATATA-TGC
*
6359 -TTC
127 AGTC
6362 CATTCATCACATTGCCATTC-GCCTTATC
1 CATTCATCACATTGCCATTCGGCCTTATC
6390 CAATACATGT
Statistics
Matches: 247, Mismatches: 21, Indels: 43
0.79 0.07 0.14
Matches are distributed among these distances:
120 19 0.08
121 8 0.03
122 1 0.00
123 4 0.02
124 5 0.02
125 3 0.01
126 14 0.06
127 12 0.05
128 5 0.02
129 14 0.06
130 61 0.25
131 20 0.08
132 4 0.02
133 14 0.06
134 31 0.13
135 20 0.08
136 1 0.00
137 11 0.04
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.33
Consensus pattern (130 bp):
CATTCATCACATTGCCATTCGGCCTTATCACACATATACATGTTCACTTCATCCATTGGCCATTC
GGCCTTATCACACATACACATGTTCACTTCTCACATGGCCATTCGCCTTATCCATATATGCAGTC
Found at i:6280 original size:44 final size:45
Alignment explanation
Indices: 5917--6437 Score: 447
Period size: 46 Copynumber: 12.1 Consensus size: 45
5907 TATCACATTT
* * *
5917 TATACACT-TTCACATCATCACATCGGCCATTAGGCCTTTATCTCACA
1 TATACA-TGTTCACTTCATCACATTGGCCATTCGGCC-TTATC-CACA
* * *
5964 TACAC-TGCTCAACATTCATCACATTGG-CACTCGGCCTTATCACACA
1 TATACATGTTC-AC-TTCATCACATTGGCCATTCGGCCTTATC-CACA
* *
6010 TACACCT-TTCACATTCATC-CATTGGCCATATCGGCCTTATCACACA
1 TATACATGTTCAC-TTCATCACATTGGCCAT-TCGGCCTTATC-CACA
* *
6056 TACACATG-TCAC-TC-TCACA-TGGCCATTC-GCCTTATCCATA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATCCACA
* * *
6096 TATGCA-GTCCA-TTCATCACATTGGCCATTCGCCCTTATCACACA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATC-CACA
6140 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATCACACA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATC-CACA
6186 TATACATGTTCACTTCATCAC-TTGGCCATTCGGCCTTATCACACA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATC-CACA
*
6231 T-TACATGTTTACTTTCATCACA-T-GCCATTCGGCCTTATCCACA
1 TATACATGTTCAC-TTCATCACATTGGCCATTCGGCCTTATCCACA
*
6274 TATACATGTTCACTTC-T-ACA-T-GCCATTCGG-C-TATCAACA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATCCACA
*
6313 TACA-ATGTTCACTTTC-TCACATTGG-CA-TCGG-CTTA-CCA-A
1 TATACATGTTCAC-TTCATCACATTGGCCATTCGGCCTTATCCACA
*
6352 TATA-GTGTTC-CATTCATCACATT-GCCATTC-GCCTTAT-C-CA
1 TATACATGTTCAC-TTCATCACATTGGCCATTCGGCCTTATCCACA
* * *
6392 -ATACATGTT-ACATCATCACA-TGGCCA-TC-GCCCTATTCACA
1 TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATCCACA
6432 TATACA
1 TATACA
6438 CTTCACATTT
Statistics
Matches: 408, Mismatches: 30, Indels: 78
0.79 0.06 0.15
Matches are distributed among these distances:
38 22 0.05
39 50 0.12
40 37 0.09
41 36 0.09
42 13 0.03
43 24 0.06
44 54 0.13
45 50 0.12
46 97 0.24
47 14 0.03
48 11 0.03
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (45 bp):
TATACATGTTCACTTCATCACATTGGCCATTCGGCCTTATCCACA
Found at i:6372 original size:39 final size:38
Alignment explanation
Indices: 6329--6422 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 38
6319 GTTCACTTTC
* * *
6329 TCACATTGGCATCGGCTTA-CCAATATAGTGTTCCATTCA
1 TCACATTGGCATCGCCTTATCCAATACA-TGTTACA-TCA
*
6368 TCACATTGCCATTCGCCTTATCCAATACATGTTACATCA
1 TCACATTGGCA-TCGCCTTATCCAATACATGTTACATCA
6407 TCACA-TGGCCATCGCC
1 TCACATTGG-CATCGCC
6423 CTATTCACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
38 7 0.15
39 20 0.43
40 13 0.28
41 7 0.15
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (38 bp):
TCACATTGGCATCGCCTTATCCAATACATGTTACATCA
Found at i:8224 original size:37 final size:39
Alignment explanation
Indices: 8163--8238 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 39
8153 CTCTCCCTAA
*
8163 ATCCAAATTCGGCACATTGAACAACCCAAATG-TAACCT
1 ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
* *
8201 ATCCAAGTTC-GCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
8239 CAACGTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.22
Consensus pattern (39 bp):
ATCCAAATTCGGCACATTCAACAACCCAAATGCTAACCT
Found at i:11893 original size:27 final size:27
Alignment explanation
Indices: 11558--11889 Score: 339
Period size: 27 Copynumber: 12.3 Consensus size: 27
11548 TATCCTATAG
*
11558 GGGTATTTCGGTCATTTTACCTTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
11585 GGGTATTTCGATCATTTTATCCTTCAA
1 GGGTATTTCGGTCATTTTACCCTTCGA
** * *
11612 GATTATTTCGGTCATTTTATCCTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
11639 GGGTATTTAGGTTATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
*
11666 GGGTATTTCAGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* *
11693 AGGTATTTCGGTCATTTTACCCTT-TA
1 GGGTATTTCGGTCATTTTACCCTTCGA
*
11719 GGGGTATTTTGGTCATTTTACCCTTC-A
1 -GGGTATTTCGGTCATTTTACCCTTCGA
*
11746 GGGGTATTTCGGTCATTTTACCCTTCAA
1 -GGGTATTTCGGTCATTTTACCCTTCGA
* * * *
11774 GGGTATTTCAGTTATTTAACCC-TCCA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * * *
11800 GGGGTATTTCAGTTA-TTTACCATTCGG
1 -GGGTATTTCGGTCATTTTACCCTTCGA
* * * *
11827 GGGTATTTTGATTATTTTACCCTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCGA
**
11854 GGGTATTTCAATCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
11881 GGGTATTTC
1 GGGTATTTC
11890 AATCCTTTGC
Statistics
Matches: 257, Mismatches: 42, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
26 20 0.08
27 236 0.92
28 1 0.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTCGA
Found at i:16620 original size:43 final size:43
Alignment explanation
Indices: 16519--16670 Score: 135
Period size: 43 Copynumber: 3.4 Consensus size: 43
16509 ATAAACAATG
* ** *
16519 TTCTCATTCTTTTCCCTGATGACACTTAATTCTTCACAATTTCCTTT
1 TTCTC-TTCTTTT-TCTGATGAC-CTTTCTTCTTCCCAATTTCC-TT
* **
16566 TTCTTCTTTCTTTTTCTGGTGATGTTTCTTCTTCCCAATTTCCTT
1 TTC-TC-TTCTTTTTCTGATGACCTTTCTTCTTCCCAATTTCCTT
* * *
16611 TTCTCTTCTTTTTCTCTATGACCTTTCTTCTT-CAAATTTCGTT
1 TTCTCTTCTTTTTCT-GATGACCTTTCTTCTTCCCAATTTCCTT
16654 TTCTCTTCTTTTCTCTG
1 TTCTCTTCTTTT-TCTG
16671 CTAAAAACAT
Statistics
Matches: 87, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 31 0.36
44 17 0.20
45 5 0.06
46 16 0.18
47 9 0.10
48 9 0.10
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (43 bp):
TTCTCTTCTTTTTCTGATGACCTTTCTTCTTCCCAATTTCCTT
Done.