Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 325 of 325
Found at i:105239498 original size:22 final size:21
Alignment explanation
Indices: 105239451--105239507 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
105239441 ATTTTATGTA
* * *
105239451 TTTAAAAATATTTTTTATGATT
1 TTTAATAATA-TTTTCATAATT
105239473 TTTAATAATATTTTCATAATT
1 TTTAATAATATTTTCATAATT
*
105239494 GTTT-ATAATTTTTT
1 -TTTAATAATATTTT
105239508 ATTTTGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (21 bp):
TTTAATAATATTTTCATAATT
Found at i:105243751 original size:25 final size:25
Alignment explanation
Indices: 105243717--105243771 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
105243707 CATCAGCCCT
*
105243717 CAACGGTCAACAATAAATGCAAAAA
1 CAACAGTCAACAATAAATGCAAAAA
105243742 CAACAGTCAACAATAAATGCAAAAA
1 CAACAGTCAACAATAAATGCAAAAA
105243767 CAACA
1 CAACA
105243772 AAAACATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.58, C:0.22, G:0.09, T:0.11
Consensus pattern (25 bp):
CAACAGTCAACAATAAATGCAAAAA
Found at i:105245747 original size:23 final size:23
Alignment explanation
Indices: 105245720--105245795 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
105245710 TTTGTTCCAT
*
105245720 TAGTTTAGTATGTTTATTAAATA
1 TAGTTTAATATGTTTATTAAATA
* * **
105245743 TAGTTTTGATTTAT-TTTGTTCCAT-
1 TAG-TTT-A-ATATGTTTATTAAATA
105245767 TAGTTTAATATGTTTATTAAATA
1 TAGTTTAATATGTTTATTAAATA
105245790 TAGTTT
1 TAGTTT
105245796 TGAAGTTTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
21 3 0.08
22 8 0.20
23 12 0.30
24 6 0.15
25 8 0.20
26 3 0.08
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.57
Consensus pattern (23 bp):
TAGTTTAATATGTTTATTAAATA
Found at i:105245773 original size:47 final size:47
Alignment explanation
Indices: 105245704--105245798 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
105245694 AAGTATGTTT
*
105245704 ATTTATTTTGTTCCATTAGTTTAGTATGTTTATTAAATATAGTTTTG
1 ATTTATTTTGTTCCATTAGTTTAATATGTTTATTAAATATAGTTTTG
105245751 ATTTATTTTGTTCCATTAGTTTAATATGTTTATTAAATATAGTTTTG
1 ATTTATTTTGTTCCATTAGTTTAATATGTTTATTAAATATAGTTTTG
105245798 A
1 A
105245799 AGTTTGAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (47 bp):
ATTTATTTTGTTCCATTAGTTTAATATGTTTATTAAATATAGTTTTG
Found at i:105246875 original size:14 final size:14
Alignment explanation
Indices: 105246856--105246883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
105246846 AATTTTACAT
105246856 ATGAATAATAAATC
1 ATGAATAATAAATC
105246870 ATGAATAATAAATC
1 ATGAATAATAAATC
105246884 GACCCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
ATGAATAATAAATC
Found at i:105257498 original size:5 final size:5
Alignment explanation
Indices: 105257468--105257497 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
105257458 GTTTTGGTAG
*
105257468 ATCTC ATCTC ATCTC ATCTC ATCTC TTCTC
1 ATCTC ATCTC ATCTC ATCTC ATCTC ATCTC
105257498 TGTATTAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (5 bp):
ATCTC
Found at i:105258439 original size:6 final size:6
Alignment explanation
Indices: 105258428--105258473 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
105258418 AACGCCGTAT
*
105258428 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTT CTTTT- CTTTT- CTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
105258474 ATAAAGCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.00, C:0.17, G:0.11, T:0.72
Consensus pattern (6 bp):
CTTTTG
Found at i:105268282 original size:15 final size:15
Alignment explanation
Indices: 105268257--105268291 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
105268247 GAACGTCTCC
*
105268257 ATTCTCTTCTCTTCT
1 ATTCACTTCTCTTCT
*
105268272 CTTCACTTCTCTTCT
1 ATTCACTTCTCTTCT
105268287 ATTCA
1 ATTCA
105268292 GGGAACACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTCACTTCTCTTCT
Found at i:105280672 original size:5 final size:5
Alignment explanation
Indices: 105280662--105280688 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
105280652 TATATATATA
105280662 ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT
105280689 TCAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:105280695 original size:15 final size:14
Alignment explanation
Indices: 105280655--105280688 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
105280645 TTTCTTTTAT
105280655 ATATATAATAATATA
1 ATATA-AATAATATA
105280670 ATATAATATAATATA
1 ATATAA-ATAATATA
105280685 ATAT
1 ATAT
105280689 TCAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:105282524 original size:35 final size:35
Alignment explanation
Indices: 105282474--105282540 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
105282464 AGTGCCACGA
**
105282474 TTCACAACTTAGTATGGTTAATACCATACCTATGT
1 TTCACAACTTAGTATGGGAAATACCATACCTATGT
*
105282509 TTCACAACTTGGTATGGGAAATACCATACCTA
1 TTCACAACTTAGTATGGGAAATACCATACCTA
105282541 CATATTATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (35 bp):
TTCACAACTTAGTATGGGAAATACCATACCTATGT
Found at i:105282653 original size:35 final size:34
Alignment explanation
Indices: 105282520--105282645 Score: 171
Period size: 35 Copynumber: 3.6 Consensus size: 34
105282510 TCACAACTTG
* *
105282520 GTATGGGAAATACCATACCTACATATTATAGCTCG
1 GTAT-GGAAATACCATACCTACATATCATAGCTCA
* *
105282555 GTTTGGAGGATACCATACCTACATATCATAGCTCA
1 GTATGGA-AATACCATACCTACATATCATAGCTCA
* *
105282590 ATATGGAAATACCATACCTACATATCATATCTCA
1 GTATGGAAATACCATACCTACATATCATAGCTCA
105282624 GTATGGATAATACCATACCTAC
1 GTATGGA-AATACCATACCTAC
105282646 GTGTCATAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
34 34 0.43
35 46 0.57
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (34 bp):
GTATGGAAATACCATACCTACATATCATAGCTCA
Found at i:105282653 original size:69 final size:70
Alignment explanation
Indices: 105282484--105282656 Score: 195
Period size: 69 Copynumber: 2.5 Consensus size: 70
105282474 TTCACAACTT
* * * * *** *
105282484 AGTATGGTTAATACCATACCTATGTTTCACAACTTGGTATGGGAAATACCATACCTACATATTAT
1 AGTATGGATAATACCATACCTACGTATCATAACTCAATATGGGAAATACCATACCTACATATCAT
105282549 AGCTC
66 AGCTC
* * ** * *
105282554 GGTTTGGAGGATACCATACCTACATATCATAGCTCAATAT-GGAAATACCATACCTACATATCAT
1 AGTATGGATAATACCATACCTACGTATCATAACTCAATATGGGAAATACCATACCTACATATCAT
*
105282618 ATCTC
66 AGCTC
*
105282623 AGTATGGATAATACCATACCTACGTGTCATAACT
1 AGTATGGATAATACCATACCTACGTATCATAACT
105282657 TTTCCATGGA
Statistics
Matches: 81, Mismatches: 22, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
69 54 0.67
70 27 0.33
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (70 bp):
AGTATGGATAATACCATACCTACGTATCATAACTCAATATGGGAAATACCATACCTACATATCAT
AGCTC
Found at i:105284356 original size:23 final size:25
Alignment explanation
Indices: 105284329--105284377 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
105284319 GTTCAATAAT
105284329 AAATTAT-AC-ATATTAAAATAAAA
1 AAATTATAACAATATTAAAATAAAA
105284352 AAATTATGAACAATATTAAAATAAAA
1 AAATTAT-AACAATATTAAAATAAAA
105284378 TTTTAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.30
25 2 0.09
26 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AAATTATAACAATATTAAAATAAAA
Found at i:105290932 original size:48 final size:48
Alignment explanation
Indices: 105290876--105290972 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
105290866 TTTCAAGATG
105290876 TACATGACATCCTAATCTTATTAAGAGTTTAATTCTTGTTAAGAGACT
1 TACATGACATCCTAATCTTATTAAGAGTTTAATTCTTGTTAAGAGACT
*
105290924 TACATGACATGCTAATCTTATTAAGAGTTTAATTCTTGTTAAGAGACT
1 TACATGACATCCTAATCTTATTAAGAGTTTAATTCTTGTTAAGAGACT
105290972 T
1 T
105290973 GATGACCATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (48 bp):
TACATGACATCCTAATCTTATTAAGAGTTTAATTCTTGTTAAGAGACT
Found at i:105293734 original size:19 final size:19
Alignment explanation
Indices: 105293710--105293748 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
105293700 TTTACTTATC
105293710 ATCCAAAGTTTAAGAAATT
1 ATCCAAAGTTTAAGAAATT
105293729 ATCCAAAGTTTAAGAAATT
1 ATCCAAAGTTTAAGAAATT
105293748 A
1 A
105293749 CAGTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
ATCCAAAGTTTAAGAAATT
Found at i:105301791 original size:5 final size:5
Alignment explanation
Indices: 105301781--105301808 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
105301771 TTTATATATA
105301781 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
105301809 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:105302379 original size:22 final size:22
Alignment explanation
Indices: 105302351--105302395 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
105302341 CTAACCCTTG
105302351 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
105302373 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
105302395 T
1 T
105302396 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:105306973 original size:22 final size:22
Alignment explanation
Indices: 105306948--105306992 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
105306938 AGGGGGAGTG
105306948 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
105306970 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
105306992 T
1 T
105306993 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:105308715 original size:20 final size:18
Alignment explanation
Indices: 105308690--105308729 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
105308680 TGTTTTGGTT
*
105308690 TTATATATCATTTTGAATTA
1 TTATATA-CATGTT-AATTA
105308710 TTATATACATGTTAATTA
1 TTATATACATGTTAATTA
105308728 TT
1 TT
105308730 TTACATTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATACATGTTAATTA
Done.