Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1520
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: 48550
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:102 original size:47 final size:47
Alignment explanation
Indices: 48--540 Score: 766
Period size: 47 Copynumber: 10.6 Consensus size: 47
38 TATTTGAATA
* *
48 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
95 AATGTGAAAGTGTATATATATTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATAT-GTGATAAGGCCTAATGGCCGATGTGATG
*
143 AATGTGAAAGTGTATATATGTGATAAGGCC-GATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
188 AATGTGAAAG-GTATATATATGAT-AGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
233 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT-G
* *
281 AATGTG-AAGTGTA-ATATGTGAT-AGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
325 AATGTGAAAGTGTTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
373 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
420 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
467 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
514 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
541 TCCCGAAGGG
Statistics
Matches: 412, Mismatches: 24, Indels: 20
0.90 0.05 0.04
Matches are distributed among these distances:
43 5 0.01
44 25 0.06
45 60 0.15
46 29 0.07
47 210 0.51
48 83 0.20
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:11524 original size:20 final size:20
Alignment explanation
Indices: 11501--11561 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
11491 ATTTTTTATA
11501 TTTTA-AATTTATTATAATTT
1 TTTTACAATTT-TTATAATTT
*
11521 TTTTACAATTTTTATAAATT
1 TTTTACAATTTTTATAATTT
*
11541 TTTAACAATTTTT-TAATTT
1 TTTTACAATTTTTATAATTT
11560 TT
1 TT
11562 AAACAACTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.19
20 25 0.68
21 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTACAATTTTTATAATTT
Found at i:11532 original size:10 final size:9
Alignment explanation
Indices: 11501--11666 Score: 63
Period size: 10 Copynumber: 17.6 Consensus size: 9
11491 ATTTTTTATA
11501 TTTTAAATT
1 TTTTAAATT
*
11510 TATTATAATTT
1 T-TT-TAAATT
11521 TTTTACAATT
1 TTTTA-AATT
11531 TTTATAAATT
1 TTT-TAAATT
*
11541 TTTAACAATT
1 TTTTA-AATT
11551 TTTT-AA-T
1 TTTTAAATT
**
11558 TTTTAAACA
1 TTTTAAATT
**
11567 ACTTAAATT
1 TTTTAAATT
*
11576 TTTTATATAT
1 TTTTAAAT-T
*
11586 TTTTAAATAAA
1 TTTTAAAT--T
11597 TTTTAAATT
1 TTTTAAATT
*
11606 TTCTAAATAAT
1 TTTTAAAT--T
*
11617 TTTGGAAATT
1 TTT-TAAATT
*
11627 TTAT-AA-T
1 TTTTAAATT
11634 TTTTACAATT
1 TTTTA-AATT
**
11644 TTTTTCA-T
1 TTTTAAATT
11652 TTTTAAATAT
1 TTTTAAAT-T
11662 TTTTA
1 TTTTA
11667 TGATTTTCGA
Statistics
Matches: 115, Mismatches: 25, Indels: 33
0.66 0.14 0.19
Matches are distributed among these distances:
7 9 0.08
8 12 0.10
9 24 0.21
10 46 0.40
11 20 0.17
12 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTAAATT
Found at i:11566 original size:19 final size:19
Alignment explanation
Indices: 11506--11673 Score: 77
Period size: 20 Copynumber: 8.8 Consensus size: 19
11496 TTATATTTTA
*
11506 AATTTATTATAATTTTTTTAC
1 AATTT-TTATAA-TTTTTAAC
11527 AATTTTTATAAATTTTTAAC
1 AATTTTTAT-AATTTTTAAC
11547 AATTTTT-TAATTTTTAAAC
1 AATTTTTATAATTTTT-AAC
* * *
11566 AA--CTTA-AATTTTTTAT
1 AATTTTTATAATTTTTAAC
*
11582 ATATTTTTAAATAAATTTT-A-
1 A-ATTTTT--ATAATTTTTAAC
**
11602 AATTTTCTAAATAATTTTGGA-
1 AATTTT-T--ATAATTTTTAAC
11623 AA-TTTTATAATTTTT-AC
1 AATTTTTATAATTTTTAAC
* *
11640 AATTTTTTTCATTTTTAA-
1 AATTTTTATAATTTTTAAC
*
11658 ATATTTTTATGATTTT
1 A-ATTTTTATAATTTT
11674 CGAATGATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 32
0.73 0.08 0.20
Matches are distributed among these distances:
16 3 0.03
17 20 0.17
18 19 0.16
19 27 0.23
20 32 0.27
21 12 0.10
22 6 0.05
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTTATAATTTTTAAC
Found at i:18397 original size:15 final size:15
Alignment explanation
Indices: 18377--18406 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18367 AACCTTCAAC
18377 ATCTCTATACTCCCT
1 ATCTCTATACTCCCT
18392 ATCTCTATACTCCCT
1 ATCTCTATACTCCCT
18407 CAAGCTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCTCTATACTCCCT
Found at i:19210 original size:3 final size:3
Alignment explanation
Indices: 19202--19249 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
19192 AATTGAGCAT
19202 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19250 AACCTTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30948 original size:33 final size:33
Alignment explanation
Indices: 30875--30952 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
30865 ATATGTATAT
* * *
30875 GTGTAAGACCATAGCTGGGCTATGGCATCCTGA
1 GTGTAAGACCATAACTAGGCTATGGCATACTGA
*
30908 -TGATAAGACCATAACTAGGTTATGGCATTAC-GA
1 GTG-TAAGACCATAACTAGGCTATGGCA-TACTGA
30941 GTGTAAGACCAT
1 GTGTAAGACCAT
30953 GTCAGCGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 32 0.84
34 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (33 bp):
GTGTAAGACCATAACTAGGCTATGGCATACTGA
Found at i:32732 original size:18 final size:18
Alignment explanation
Indices: 32711--32774 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
32701 TAGCAATTGG
*
32711 TTATTCAGTAACGGTCAA
1 TTATTCAGTAACAGTCAA
*
32729 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAA
*
32747 TCT-TTCAGTAATAGTCAA
1 T-TATTCAGTAACAGTCAA
32765 TTATTCAGTA
1 TTATTCAGTA
32775 CATTTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
17 1 0.03
18 38 0.95
19 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:32897 original size:6 final size:6
Alignment explanation
Indices: 32886--32920 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
32876 TACACTGTAT
*
32886 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAG CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
32921 CACAAAGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:33006 original size:51 final size:53
Alignment explanation
Indices: 32896--33011 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 53
32886 CAGTAACAGT
* *
32896 AACAGTAACAGTAACAGTAGCAGTACACAAAGTACCTCATCGGGACAAATTCGG
1 AACAGTAACAGTAACAGTAG-AGTACACAAAGTACCTCATCGGAACAAATCCGG
* * * *
32950 AACAGTAACAGTAACAGTA-AGGTATA-GAA-TACCTCTTCGGAACGAATCCGG
1 AACAGTAACAGTAACAGTAGA-GTACACAAAGTACCTCATCGGAACAAATCCGG
33001 AACAGTAACAG
1 AACAGTAACAG
33012 GAAGGCGACA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 29 0.53
52 3 0.05
53 4 0.07
54 19 0.35
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAGAGTACACAAAGTACCTCATCGGAACAAATCCGG
Found at i:33191 original size:18 final size:19
Alignment explanation
Indices: 33168--33204 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33158 TAAGCTAATC
*
33168 ATATATAT-TTTCAGTTCA
1 ATATATATATTTCAATTCA
33186 ATATATATATTTCAATTCA
1 ATATATATATTTCAATTCA
33205 CTTTACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATATATATTTCAATTCA
Found at i:35647 original size:50 final size:51
Alignment explanation
Indices: 35570--35698 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
35560 GACCATGGCA
* *
35570 ACAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
35621 A-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
35671 ACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
35699 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 46 0.66
51 24 0.34
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:35712 original size:31 final size:31
Alignment explanation
Indices: 35674--35822 Score: 253
Period size: 31 Copynumber: 4.8 Consensus size: 31
35664 ACAAATGACA
35674 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
35705 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
35736 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
35767 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
35798 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
35823 AAGTGACAAG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:35993 original size:48 final size:48
Alignment explanation
Indices: 35922--36052 Score: 159
Period size: 42 Copynumber: 2.9 Consensus size: 48
35912 GCATCAGTGA
*
35922 GATATGTGATTCGTGTAAAACCATAGCT-GACTATGGCATCGATATGT
1 GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
* *
35969 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
* *
36018 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATC
36053 ATTATGTGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
42 29 0.37
44 1 0.01
45 1 0.01
46 1 0.01
47 11 0.14
48 17 0.22
49 19 0.24
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
Found at i:36090 original size:42 final size:42
Alignment explanation
Indices: 35982--36079 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
35972 ATGTGATTAC
*
35982 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAT
*
36024 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAAGAT
36066 GTGTAAGACCATAG
1 GTGTAAGACCATAG
36080 TTGAACTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAT
Found at i:37381 original size:20 final size:18
Alignment explanation
Indices: 37345--37389 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
37335 AAACATTCAA
37345 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
37363 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
37383 -TTTCCCT
1 TTTTCCCT
37390 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:39682 original size:26 final size:26
Alignment explanation
Indices: 39653--39762 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
39643 TGGTACAAAT
*
39653 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTCCA
39679 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
39705 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
39731 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
39757 TGATAA
1 TGATAA
39763 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:41444 original size:28 final size:27
Alignment explanation
Indices: 41378--41463 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
41368 GAGGAAGCGT
* *
41378 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
41405 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
* *
41433 TCTGGTGACTCTGTCACATTATCTGT-
1 TCTGGTGGCTCTGCCACATTATCTGTA
41459 TCTGG
1 TCTGG
41464 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.09
27 32 0.60
28 16 0.30
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACATTATCTGTA
Found at i:43705 original size:26 final size:25
Alignment explanation
Indices: 43676--43727 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
43666 TCAAACATGC
43676 ATTTAAGTCAATTTAACCCTAGGGGT
1 ATTTAAGT-AATTTAACCCTAGGGGT
** * *
43702 ATTTCGGTAATTTATCTCTAGGGGT
1 ATTTAAGTAATTTAACCCTAGGGGT
43727 A
1 A
43728 AAACTGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (25 bp):
ATTTAAGTAATTTAACCCTAGGGGT
Found at i:45236 original size:26 final size:26
Alignment explanation
Indices: 45205--45286 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
45195 TGAAATGCCC
*
45205 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
45231 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
45257 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
45283 ATCA
1 ATCA
45287 ATTTGTACCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Done.