Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2625
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: 32934
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1109 original size:17 final size:18
Alignment explanation
Indices: 1089--1122 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1079 TTAAAGATGC
*
1089 AATTGTATT-TTTATTTT
1 AATTATATTATTTATTTT
1106 AATTATATTATTTATTT
1 AATTATATTATTTATTT
1123 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3182 original size:21 final size:21
Alignment explanation
Indices: 3158--3198 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3148 TTTATTATAT
3158 TTATAAATATAATAAATATTA
1 TTATAAATATAATAAATATTA
* * *
3179 TTATAATTATTATAATTATT
1 TTATAAATATAATAAATATT
3199 GTAATTGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAATATAATAAATATTA
Found at i:3203 original size:9 final size:9
Alignment explanation
Indices: 3175--3204 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3165 TATAATAAAT
3175 ATTATTATA
1 ATTATTATA
3184 ATTATTATA
1 ATTATTATA
*
3193 ATTATTGTA
1 ATTATTATA
3202 ATT
1 ATT
3205 GTGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTATTATA
Found at i:3341 original size:23 final size:21
Alignment explanation
Indices: 3309--3350 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3299 TATTTTTATT
*
3309 ATAAATTTATTTATTATTTAAAG
1 ATAAAATTATTT-TT-TTTAAAG
3332 ATAAAATTATTTTTTTTAA
1 ATAAAATTATTTTTTTTAA
3351 TTTCAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATAAAATTATTTTTTTTAAAG
Found at i:11788 original size:48 final size:48
Alignment explanation
Indices: 11732--11829 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
11722 TTGCACCTGA
*
11732 CCAGATATTTGTTATGTAGTTAGTATTTTAAGTTGATATTAGTCAAAC
1 CCAGATATTTGTTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
11780 CCAGATATTTGTTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
1 CCAGATATTTGTTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
11828 CC
1 CC
11830 TAGTAACAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (48 bp):
CCAGATATTTGTTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
Found at i:19349 original size:15 final size:15
Alignment explanation
Indices: 19334--19362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19324 AAAAAAATTA
19334 AATTC-AAAATGTTT
1 AATTCAAAAATGTTT
19348 AATTCAAAAATGTTT
1 AATTCAAAAATGTTT
19363 GAGGGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
AATTCAAAAATGTTT
Found at i:25556 original size:50 final size:51
Alignment explanation
Indices: 25442--25569 Score: 195
Period size: 50 Copynumber: 2.5 Consensus size: 51
25432 AAGTTTCTCA
* *
25442 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
* * *
25493 ATTCTCCATAATCGGGGATACTCCAACTCCGA-TTTATTTCCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
*
25543 ATTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
25570 CCCGTTATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 40 0.58
51 29 0.42
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
Found at i:25756 original size:28 final size:28
Alignment explanation
Indices: 25715--25785 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
25705 TCCACAATCA
* *
25715 GGGATACTCTAACCCCGTTATTTCAT-CG
1 GGGATACTCCAACCCCGTTATTTC-TGAG
25743 GGGATACTCCAACCCCGTTATTTCTGAG
1 GGGATACTCCAACCCCGTTATTTCTGAG
*
25771 GGGATACTTCAACCC
1 GGGATACTCCAACCC
25786 TGATTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCTGAG
Found at i:25757 original size:79 final size:77
Alignment explanation
Indices: 25504--25759 Score: 318
Period size: 79 Copynumber: 3.3 Consensus size: 77
25494 TTCTCCATAA
* * * *
25504 TCGGGGATACTCCAACTCC-GATTTATTTCCAAAACACCGATTTTTCACAATCGGGGATACTCCA
1 TCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACC-AATTTTCACAATCGGGGATACTCCA
25568 ACCCCGTTATTTC
65 ACCCCGTTATTTC
* * * * *
25581 TGAGGGGATACTCTAACCACGGTTTTATTTCTAAAACATCAAATTTTCATAATCGGGGATACTCC
1 T-CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA-CCAATTTTCACAATCGGGGATACTCC
25646 AACCCCGTTATTT-
64 AACCCCGTTATTTC
* * *
25659 TCGAGGGGATACTCAAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTC
1 TC--GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATT-TTCACAATCGGGGATACTC
*
25724 TAACCCCGTTATTTC
63 CAACCCCGTTATTTC
25739 ATCGGGGATACTCCAACCCCG
1 -TCGGGGATACTCCAACCCCG
25760 TTATTTCTGA
Statistics
Matches: 153, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 20 0.13
79 129 0.84
80 1 0.01
81 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (77 bp):
TCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTC
Found at i:25818 original size:107 final size:107
Alignment explanation
Indices: 25632--25837 Score: 269
Period size: 107 Copynumber: 1.9 Consensus size: 107
25622 AATTTTCATA
*
25632 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGATTTTATTTCTAAAAC
25697 ACCAATTCTCCACAATCAGGGATACTCT-AACCCCGTTATTTC
66 ACCAATTCTCCACAATCAGGGATACT-TAAACCCCGTTATTTC
*
25739 ATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTTC-AACCCTGATTTTATTT-TCAA
1 ATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATAC-TCAAACCCCGATTTTATTTCT-AA
* *** *
25801 AATATTGATT-TCTCACAATCGGGGATACTTAAACCCC
63 AACACCAATTCTC-CACAATCAGGGATACTTAAACCCC
25838 TACCTTATTT
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
106 8 0.09
107 77 0.89
108 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (107 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGATTTTATTTCTAAAAC
ACCAATTCTCCACAATCAGGGATACTTAAACCCCGTTATTTC
Found at i:25903 original size:79 final size:79
Alignment explanation
Indices: 25820--25967 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 79
25810 TTCTCACAAT
* * * * *
25820 CGGGGATACTTAAACCCCTACCTTATTTCTAAAATATTG-GTTTCTCATAATCGGGGATACTCCA
1 CGGGGATACTCAAACCCCGACCTTATTTCTAAAACATCGATTTTCT-ATAATCGGGGATACTCCA
25884 ACCCCATTACTTTCA
65 ACCCCATTACTTTCA
* * ** * *
25899 CGGGGATGCTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCTATAATCGGGGATACTCCAT
1 CGGGGATACTCAAACCCCGACCTTATTTCTAAAACATCGATTTTCTATAATCGGGGATACTCCAA
25964 CCCC
66 CCCC
25968 GTTGTTATCT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 52 0.91
80 5 0.09
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
CGGGGATACTCAAACCCCGACCTTATTTCTAAAACATCGATTTTCTATAATCGGGGATACTCCAA
CCCCATTACTTTCA
Found at i:25984 original size:130 final size:129
Alignment explanation
Indices: 25739--25987 Score: 297
Period size: 130 Copynumber: 1.9 Consensus size: 129
25729 CCGTTATTTC
* * * *
25739 ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTTCAACCCTGATTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTC-GAGGGGATACTCCAACCCCGATTTTATTTTCAAAAC
* * * *
25804 ATTGATTTCTCACAATCGGGGATACTTAAACCCCTACCTTATTTCTAAAATATTGGTTTCTCATA
65 ATCGATTTCTCACAATCGGGGATACTCAAACCCCTACCTTATCTCCAAAATATTGGTTTCTCATA
* *
25869 ATCGGGGATACTCCAACCCCATTACTTTC-ACGGGGATGCTCCAACCCCGATTTTATTTTTAAAA
1 ATCGGGGATACTCCAACCCCATTA-TTTCGA-GGGGATACTCCAACCCCGATTTTATTTTCAAAA
* * * **
25933 CATCGATTT-TCTATAATCGGGGATACTCCATCCCCGT-TGTTATCTCCAAAATATT
64 CATCGATTTCTC-ACAATCGGGGATACTCAAACCCC-TACCTTATCTCCAAAATATT
25988 AGATTTTTCA
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
129 3 0.03
130 92 0.92
131 5 0.05
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (129 bp):
ATCGGGGATACTCCAACCCCATTATTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACA
TCGATTTCTCACAATCGGGGATACTCAAACCCCTACCTTATCTCCAAAATATTGGTTTCTCATA
Found at i:28720 original size:21 final size:20
Alignment explanation
Indices: 28692--28735 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
28682 TAAAGTTTAT
*
28692 AAAAAAAT-TATTAAACATAA
1 AAAAAAATAAATTAAA-ATAA
28712 AAAATAAATAAATTAAAATAA
1 AAAA-AAATAAATTAAAATAA
28733 AAA
1 AAA
28736 TTTTATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAATTAAAATAA
Found at i:30792 original size:17 final size:18
Alignment explanation
Indices: 30772--30805 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30762 TTAAAGATGC
*
30772 AATTGTATT-TTTATTTT
1 AATTATATTATTTATTTT
30789 AATTATATTATTTATTT
1 AATTATATTATTTATTT
30806 ATTTATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Done.