Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold726
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: 52563
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:21970 original size:18 final size:18
Alignment explanation
Indices: 21944--21978 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21934 GAGTTAAAAG
*
21944 AATCGAGTTATTCGAATT
1 AATCAAGTTATTCGAATT
21962 AATCAAGTTATTCGAAT
1 AATCAAGTTATTCGAAT
21979 CAAGTCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (18 bp):
AATCAAGTTATTCGAATT
Found at i:22132 original size:29 final size:31
Alignment explanation
Indices: 22096--22156 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
22086 AAACCTTTTT
* *
22096 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
22126 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
22157 CTCCCCCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:22169 original size:31 final size:30
Alignment explanation
Indices: 22106--22166 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
22096 ACTTTTCCCT
**
22106 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACTCCCCCCC
22136 CAAAACTTTTACTCCTCTCCC-CTCCCCCCC
1 CAAAACTTTTACTCCT-TCCCACTCCCCCCC
22166 C
1 C
22167 CAATCTATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCTTCCCACTCCCCCCC
Found at i:22294 original size:30 final size:31
Alignment explanation
Indices: 22260--22319 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
22250 AAACCTTTTA
*
22260 TTTTCCCCCAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
22290 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
22320 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:22438 original size:16 final size:16
Alignment explanation
Indices: 22405--22434 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22395 CCTATTTACT
22405 TTCCCTCAAACTTTTA
1 TTCCCTCAAACTTTTA
22421 TTCCCT-AAACTTTT
1 TTCCCTCAAACTTTT
22435 TATTTTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCCCTCAAACTTTTA
Found at i:22460 original size:20 final size:20
Alignment explanation
Indices: 22423--22466 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
22413 AACTTTTATT
*
22423 CCCTAAACTTTTTATTTTCC
1 CCCTAAACTTTTTATTTTCA
22443 CCCTAAAC-TTTTACTTTTCA
1 CCCTAAACTTTTTA-TTTTCA
22463 CCCT
1 CCCT
22467 TTACTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.45
Consensus pattern (20 bp):
CCCTAAACTTTTTATTTTCA
Found at i:22598 original size:17 final size:17
Alignment explanation
Indices: 22578--22624 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
22568 CACATTTTAT
22578 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
22595 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
22613 A-TATTTATATTA
1 ATTATTTATATTA
22625 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:22762 original size:19 final size:19
Alignment explanation
Indices: 22718--22763 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
22708 CTTTTATTAA
22718 AAAATCATATTTTTACATTT
1 AAAAT-ATATTTTTACATTT
22738 --AATATATTTTTA-ATTCT
1 AAAATATATTTTTACATT-T
22755 AAAATATAT
1 AAAATATAT
22764 AGTGACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 3 0.13
19 7 0.30
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATATTTTTACATTT
Found at i:26036 original size:17 final size:17
Alignment explanation
Indices: 26014--26047 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
26004 ATCCACTAAT
*
26014 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
26031 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
26048 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:30666 original size:17 final size:17
Alignment explanation
Indices: 30644--30677 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30634 ATCCACTAAT
*
30644 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
30661 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
30678 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:31074 original size:13 final size:13
Alignment explanation
Indices: 31056--31082 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31046 ACAACACCCA
31056 ACTTATAACCACC
1 ACTTATAACCACC
31069 ACTTATAACCACC
1 ACTTATAACCACC
31082 A
1 A
31083 TTAAAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (13 bp):
ACTTATAACCACC
Found at i:31929 original size:25 final size:26
Alignment explanation
Indices: 31898--31949 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
31888 AACACTTAAA
*
31898 AATAATATATATCAAT-AT-AACTAAC
1 AATAATATAAAT-AATAATAAACTAAC
31923 AATAATATAAATAATAATAAACTAAC
1 AATAATATAAATAATAATAAACTAAC
31949 A
1 A
31950 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 13 0.54
26 8 0.33
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATATAAATAATAATAAACTAAC
Found at i:32821 original size:25 final size:24
Alignment explanation
Indices: 32785--32838 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
32775 TTAATTTAAC
32785 TTTTTTACTTTT-AAATTTTAATACA
1 TTTTTTACTTTTAAAATTTTAA-A-A
*
32810 TTTTTTATTTTTAAAATTTTAAAA
1 TTTTTTACTTTTAAAATTTTAAAA
32834 TTTTT
1 TTTTT
32839 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.22
25 12 0.44
26 9 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTTACTTTTAAAATTTTAAAA
Found at i:32838 original size:9 final size:9
Alignment explanation
Indices: 32816--32871 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
32806 TACATTTTTT
32816 ATTTTTAAA
1 ATTTTTAAA
32825 A-TTTTAAA
1 ATTTTTAAA
32833 ATTTTTAAA
1 ATTTTTAAA
*
32842 ATTTTTATA
1 ATTTTTAAA
* *
32851 TTTTTTATAT
1 ATTTTTA-AA
*
32861 ATTTTTTAA
1 ATTTTTAAA
32870 AT
1 AT
32872 AATATTATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 8 0.21
9 25 0.66
10 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:32853 original size:17 final size:17
Alignment explanation
Indices: 32809--32855 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
32799 ATTTTAATAC
32809 ATTTTT-TATTTTTAAA
1 ATTTTTATATTTTTAAA
* *
32825 ATTTTAAAATTTTTAAA
1 ATTTTTATATTTTTAAA
32842 ATTTTTATATTTTT
1 ATTTTTATATTTTT
32856 TATATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATATTTTTAAA
Found at i:33495 original size:123 final size:123
Alignment explanation
Indices: 33339--33583 Score: 361
Period size: 123 Copynumber: 2.0 Consensus size: 123
33329 TATTTGAATT
* * *
33339 TTAGTCTTCATAATCTTATTTTTAGAAATTTAATCAACTTCTTTTCGGATTTAAAAATTCAGGA-
1 TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
* *
33403 TCTATTATTACCACTGTTAATATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
66 TC-ATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
* * *
33462 TTAGT-TTCCATACTCTTA-TTTTAAATAATTTAATTATCTACTTTTCAGATTTAAAAATTCAGG
1 TTAGTCTT-CATAATCTTATTTTTAAA-AATTTAATCAACTACTTTTCAGATTTAAAAATTCAGG
*
33525 ACTCATTATTATCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAA
64 ACTCATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAA
33584 TTTAAAATAT
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
122 8 0.07
123 100 0.91
124 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (123 bp):
TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
TCATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
Found at i:38880 original size:38 final size:38
Alignment explanation
Indices: 38821--38926 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
38811 TATTTTTAAG
*
38821 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
38858 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
38896 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
38927 TACATATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:39269 original size:22 final size:23
Alignment explanation
Indices: 39213--39269 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
39203 AGTTTAAAAT
39213 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
39236 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
39257 AAAATATATAAAA
1 AAAATATATAAAA
39270 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:39998 original size:13 final size:13
Alignment explanation
Indices: 39980--40004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39970 AAATGCGTAG
39980 ATAAATAAATGAA
1 ATAAATAAATGAA
39993 ATAAATAAATGA
1 ATAAATAAATGA
40005 TAGATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:40505 original size:41 final size:41
Alignment explanation
Indices: 40460--40541 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
40450 TACAGCTGCT
40460 CCTCTTTGCTCATTGTCGTGTAACGAGAATGAAGCAAAGAC
1 CCTCTTTGCTCATTGTCGTGTAACGAGAATGAAGCAAAGAC
40501 CCTCTTTGCTCATTGTCGTGTAACGAGAATGAAGCAAAGAC
1 CCTCTTTGCTCATTGTCGTGTAACGAGAATGAAGCAAAGAC
40542 TTTTGACGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CCTCTTTGCTCATTGTCGTGTAACGAGAATGAAGCAAAGAC
Found at i:46982 original size:2 final size:2
Alignment explanation
Indices: 46975--47004 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46965 GTATACGTGC
46975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47005 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47751 original size:18 final size:18
Alignment explanation
Indices: 47719--47775 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
47709 TTTCAAAACG
* *
47719 AAAAGAAAGAGAAAAAAT
1 AAAAGAAAAAAAAAAAAT
47737 AAAAGAAAAATAAAATAAAT
1 AAAAGAAAAA-AAAA-AAAT
47757 AAAA-AAAACAAAAAAAAT
1 AAAAGAAAA-AAAAAAAAT
47775 A
1 A
47776 GAGAACTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 14 0.41
19 11 0.32
20 9 0.26
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAAAT
Found at i:47758 original size:9 final size:9
Alignment explanation
Indices: 47730--47775 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
47720 AAAGAAAGAG
47730 AAAAAATAAA
1 AAAAAAT-AA
47740 AGAAAAATAA
1 A-AAAAATAA
*
47750 AATAAATAA
1 AAAAAATAA
*
47759 AAAAAACAA
1 AAAAAATAA
47768 AAAAAATA
1 AAAAAATA
47776 GAGAACTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 21 0.68
10 4 0.13
11 6 0.19
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (9 bp):
AAAAAATAA
Found at i:47771 original size:20 final size:20
Alignment explanation
Indices: 47733--47775 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
47723 GAAAGAGAAA
*
47733 AAATAAAAGAAAAATAAAAT
1 AAATAAAAGAAAAAAAAAAT
*
47753 AAATAAAA-AAAACAAAAA-
1 AAATAAAAGAAAAAAAAAAT
47771 AAATA
1 AAATA
47776 GAGAACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (20 bp):
AAATAAAAGAAAAAAAAAAT
Done.