Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2860
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: 77275
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:2778 original size:27 final size:27
Alignment explanation
Indices: 2747--2897 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
2737 TAAATTGTAC
2747 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2774 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2800 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2828 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2856 AGCACTAAGTGTGCGATTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2883 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2898 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2861 original size:82 final size:81
Alignment explanation
Indices: 2748--2897 Score: 230
Period size: 82 Copynumber: 1.8 Consensus size: 81
2738 AAATTGTACA
*
2748 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATAT-ATAGCACTAAGTG
2812 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** * *
2829 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATATAGCACTGAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTG
2894 TGCG
65 TGCG
2898 GACTCAATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 17 0.27
82 45 0.73
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19305 original size:21 final size:21
Alignment explanation
Indices: 19281--19320 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19271 TTTCTAGGAC
*
19281 ATGAATTGAATTAAATTGAGT
1 ATGAAATGAATTAAATTGAGT
*
19302 ATGAAATGGATTAAATTGA
1 ATGAAATGAATTAAATTGA
19321 TGCTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (21 bp):
ATGAAATGAATTAAATTGAGT
Found at i:19846 original size:25 final size:24
Alignment explanation
Indices: 19804--19856 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
19794 CACAAATGCA
*
19804 GCTCTTTATGAACGTCCTGATATAG
1 GCTCTTTATGAACGTCCTAATAT-G
* * *
19829 GCTCTTTGTGAGCTTCCTAATATG
1 GCTCTTTATGAACGTCCTAATATG
19853 GCTC
1 GCTC
19857 GCATTAACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAACGTCCTAATATG
Found at i:22034 original size:55 final size:53
Alignment explanation
Indices: 21947--22199 Score: 225
Period size: 55 Copynumber: 4.8 Consensus size: 53
21937 ATTAGGGTTT
*
21947 AAGGATACCATGTAAGACCATG-CTAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * *
22002 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * * * *
22057 AAATG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTC-TAAGGC
*
22110 AATGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTT-TAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * * *
22159 AAGGATACCACGTAAGACCATGACAAGTCATGGAAATGGTA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTA
22200 GGGTACCCGC
Statistics
Matches: 165, Mismatches: 24, Indels: 24
0.77 0.11 0.11
Matches are distributed among these distances:
48 2 0.01
49 34 0.21
52 8 0.05
53 40 0.24
54 11 0.07
55 66 0.40
56 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:22153 original size:108 final size:110
Alignment explanation
Indices: 21954--22154 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
21944 TTTAAGGATA
* *
21954 CCATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
22019 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAATGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTC
* * * *
22064 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAATGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
22126 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
22155 TTAAAAGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.09
110 25 0.30
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTC
Found at i:22414 original size:16 final size:16
Alignment explanation
Indices: 22393--22423 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22383 ATACATTTGA
22393 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
22409 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
22424 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:29344 original size:28 final size:25
Alignment explanation
Indices: 29312--29390 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 25
29302 AAAAATCAAA
29312 TATATGATATACTAAAACTATAAAACT
1 TATAT-ATATA-TAAAACTATAAAACT
*
29339 TA-ATATA-ATAAAACTTTAAAACGT
1 TATATATATATAAAACTATAAAAC-T
*
29363 TATGTAATATAATAAAACTATAAAACT
1 TATAT-ATAT-ATAAAACTATAAAACT
29390 T
1 T
29391 GACTTAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 13 0.30
24 4 0.09
25 4 0.09
26 5 0.11
27 4 0.09
28 14 0.32
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (25 bp):
TATATATATATAAAACTATAAAACT
Found at i:29398 original size:28 final size:28
Alignment explanation
Indices: 29336--29407 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
29326 AAACTATAAA
*
29336 ACTTAATATAATAAAACTTTAAAACGTT
1 ACTTAATATAATAAAACTATAAAACGTT
29364 A-TGTAATATAATAAAACTATAAAAC-TT
1 ACT-TAATATAATAAAACTATAAAACGTT
29391 GACTTAATATAATAAAA
1 -ACTTAATATAATAAAA
29408 GTTTACGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 3 0.08
28 36 0.90
29 1 0.03
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (28 bp):
ACTTAATATAATAAAACTATAAAACGTT
Found at i:29451 original size:16 final size:16
Alignment explanation
Indices: 29430--29464 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29420 TCTTAATATA
*
29430 ATAATACTAAATTAAG
1 ATAATACTAAACTAAG
*
29446 ATAATACTCAACTAAG
1 ATAATACTAAACTAAG
29462 ATA
1 ATA
29465 TTATATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAATACTAAACTAAG
Found at i:29582 original size:25 final size:27
Alignment explanation
Indices: 29549--29605 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
29539 ATCATGATAA
* *
29549 TATTCATTAA-AAAAAGTTTACCCTG-
1 TATTAATTAAGAAAAAGTTTACCATGT
*
29574 TATTAATTAAGATAAAGTTTACCATGT
1 TATTAATTAAGAAAAAGTTTACCATGT
29601 TATTA
1 TATTA
29606 TGTTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 9 0.33
26 13 0.48
27 5 0.19
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (27 bp):
TATTAATTAAGAAAAAGTTTACCATGT
Found at i:33659 original size:31 final size:31
Alignment explanation
Indices: 33624--33685 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
33614 CAGGTACATA
*
33624 ACCAATGATTTTTCATACATGAGATTTCTCT
1 ACCAATGATTTTTCATACATAAGATTTCTCT
*
33655 ACCAATGATTTTTCATACATAAGTTTTCTCT
1 ACCAATGATTTTTCATACATAAGATTTCTCT
33686 TTTGCAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (31 bp):
ACCAATGATTTTTCATACATAAGATTTCTCT
Found at i:40562 original size:18 final size:18
Alignment explanation
Indices: 40492--40569 Score: 66
Period size: 18 Copynumber: 4.0 Consensus size: 18
40482 CAGTTAAACC
*
40492 ATTTGATTGATATATTTA
1 ATTTGATTTATATATTTA
*
40510 ATTTGATTTATTTATTTATA
1 ATTTGATTTATATA-TT-TA
*
40530 ATTGAGTATTATTATATATTTA
1 ATT-TG-A-T-TTATATATTTA
*
40552 ATTTGATTTATTTATTTA
1 ATTTGATTTATATATTTA
40570 TAAATAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 22 0.46
19 3 0.06
20 6 0.12
21 2 0.04
22 6 0.12
23 3 0.06
24 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
ATTTGATTTATATATTTA
Found at i:40633 original size:22 final size:22
Alignment explanation
Indices: 40608--40649 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
40598 ATAATTTAAA
40608 ATATAAATTTATTAATATATAT
1 ATATAAATTTATTAATATATAT
*
40630 ATATAAATTTTTTAATATAT
1 ATATAAATTTATTAATATAT
40650 GTAAAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAAATTTATTAATATATAT
Found at i:40754 original size:19 final size:20
Alignment explanation
Indices: 40730--40775 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
40720 CATCCAAACA
40730 CCAGAAAAGTAAATTA-TTT
1 CCAGAAAAGTAAATTATTTT
40749 CCAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATTATTTT
40769 CCAGAAA
1 CCAGAAA
40776 TTATTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (20 bp):
CCAGAAAAGTAAATTATTTT
Found at i:40778 original size:14 final size:14
Alignment explanation
Indices: 40759--40789 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40749 CCAGAAAAGT
40759 AAATTATTTTCCAG
1 AAATTATTTTCCAG
40773 AAATTATTTTCCAG
1 AAATTATTTTCCAG
40787 AAA
1 AAA
40790 ACATTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:47099 original size:24 final size:25
Alignment explanation
Indices: 47052--47099 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
47042 TTAGGTCTCA
* * *
47052 TGAGCTTCCTGCTTAATGGTTCTTG
1 TGAGCTTCCCGCTTAATAGCTCTTG
47077 TGAGCTTCCCG-TTAATAGCTCTT
1 TGAGCTTCCCGCTTAATAGCTCTT
47100 CCAAGCACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (25 bp):
TGAGCTTCCCGCTTAATAGCTCTTG
Found at i:60090 original size:11 final size:11
Alignment explanation
Indices: 60076--60102 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60066 TTTAATTTAT
60076 ATTTGGGGAAA
1 ATTTGGGGAAA
60087 ATTTGGGGAAA
1 ATTTGGGGAAA
60098 ATTTG
1 ATTTG
60103 ATGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (11 bp):
ATTTGGGGAAA
Found at i:69300 original size:27 final size:27
Alignment explanation
Indices: 69111--69301 Score: 258
Period size: 27 Copynumber: 7.1 Consensus size: 27
69101 GGATAAGTTC
*
69111 TAGAATTA-TCGAAATACCCCTGTAAGG
1 TAGAATTACT-GAAATACCCCTGTAGGG
*
69138 TAGAATTACCGAAATACCCCTGTAGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
*
69165 TAGAATTATTGAAATACCCCTGTAGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
*
69192 TAGAATTACTGAAATACCCCTGTAGGA
1 TAGAATTACTGAAATACCCCTGTAGGG
* *
69219 TAGAATTACTGAAATACCCTTGTAGAG
1 TAGAATTACTGAAATACCCCTGTAGGG
* *
69246 TAGAAATACTGAAATACCCCTGCAGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
* * * *
69273 TAGAATTACCGAGATACCCTTGTGGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
69300 TA
1 TA
69302 AAACTACCAT
Statistics
Matches: 144, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TAGAATTACTGAAATACCCCTGTAGGG
Found at i:70005 original size:27 final size:26
Alignment explanation
Indices: 69961--70012 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
69951 CTCGTTGCAA
*
69961 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
69988 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
70013 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:75162 original size:26 final size:26
Alignment explanation
Indices: 75058--75191 Score: 136
Period size: 26 Copynumber: 5.2 Consensus size: 26
75048 ATTCAGTGAT
*
75058 ATTCTA-CCTACAAGGG--TTTCGTA
1 ATTCTACCCTACAGGGGTATTTCGTA
* *
75081 ATTCTATCCT-CA-GGATATTTCGTA
1 ATTCTACCCTACAGGGGTATTTCGTA
*
75105 ATTCTACCCTACAAGGGGTAATTTC-AA
1 ATTCTACCCTAC-AGGGGT-ATTTCGTA
75132 TATTCTACCCTACAGGGGTATTTCGTA
1 -ATTCTACCCTACAGGGGTATTTCGTA
**
75159 ATTCTACAATACAGGGGTATTTCGATA
1 ATTCTACCCTACAGGGGTATTTCG-TA
75186 ATTCTA
1 ATTCTA
75192 ACCAACTTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.02
23 8 0.09
24 19 0.20
25 1 0.01
26 28 0.30
27 19 0.20
28 17 0.18
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
ATTCTACCCTACAGGGGTATTTCGTA
Done.