Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1727
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: 39440
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:4797 original size:16 final size:16
Alignment explanation
Indices: 4776--4808 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4766 ATTTCTAAAG
4776 GTGGTTACAGATATCT
1 GTGGTTACAGATATCT
4792 GTGGTTACAGATATCT
1 GTGGTTACAGATATCT
4808 G
1 G
4809 CTTACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.36
Consensus pattern (16 bp):
GTGGTTACAGATATCT
Found at i:7409 original size:20 final size:20
Alignment explanation
Indices: 7384--7433 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
7374 TGGCTTAAAA
7384 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
7404 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
7421 GTGGTAGTGGATT
1 TTGGTAGTGGATT
7434 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:11107 original size:178 final size:178
Alignment explanation
Indices: 10802--11682 Score: 1345
Period size: 178 Copynumber: 5.0 Consensus size: 178
10792 TTTTTCAAGC
* **
10802 TGCTATTATCTGTTTTACGACTTTTTACCGGGTAAAGCTGAGTTCTTCCAGCAATGGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
* *
10867 ATGAATGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
10932 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
10980 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
*
11045 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
11110 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
11158 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
*
11223 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
*
11288 CTTTGCCTTAGCCATGATTACAATATAATCTCTAATGAGCTGCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
* * *
11336 TGCTATTATCTGTTTTATGACTTTTTTCCGGGTAAAGCTTAGTTCTTCCAGCAAAGGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
*
11401 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
* *
11466 CTTTGCCTTAGCTATGATTACAATATAATCTTTAATGAGCTTCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
* * * * * * * ** *
11514 T-C--TT-TC----TAACGACGTTTTTCCGGCTGAATGTTCAAGATT-TAT-AAATAAATGTTTG
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGT-AAAGCT-GAG-TTCT-TCCAGCAAAAGTTTG
* *
11569 G-TTTTCGAGTGTTGTTTTGTAG-TAGTTGCAGCGATGATTAAAATGAGGTTTAGGGTTGTAATG
62 GATTAT-GAGTGTTGTTTTGTAGCAAG-TGCAGCGATGATTAAAATGAGGTTTAGGG-T-TAATG
* * *
11632 AGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCTCTAATGAGCTGC
123 AGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGC
11683 CGTATCTTTT
Statistics
Matches: 662, Mismatches: 33, Indels: 20
0.93 0.05 0.03
Matches are distributed among these distances:
170 15 0.02
171 9 0.01
172 58 0.09
173 4 0.01
174 53 0.08
175 2 0.00
177 1 0.00
178 520 0.79
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (178 bp):
TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
ATGAGTGTTGTTTTGTAGCAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGCTGCTTTTA
Found at i:11963 original size:180 final size:175
Alignment explanation
Indices: 11387--11964 Score: 530
Period size: 173 Copynumber: 3.3 Consensus size: 175
11377 GTTCTTCCAG
* * * * * *
11387 CAAAGGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATT--AAAATGAGGTTTAG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
* * * * ** * **
11450 GG-T-TAATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTTTAATGAGCTTCTTTT
66 GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGC-CGT
* * * * ** * *
11513 ATCTTTCTAACGACGTTTTTCCGGCTGAATGTTCAAGATTTAT-AAA
130 ATCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTT-TCAAA
* * * * *
11559 TAAATGTTTGGTTTTCGAGTGTTGTTTTGTAGTAGTTGCAGCGATGATT--AAAATGAGGTTTAG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
* * *
11622 GGTTGTAATGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCTCTAATGAGCTGCCGTA
66 GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGCCGTA
* * *
11687 TCTTTTTTACAACGTTTTTCCGACCGAATGTTCAAAATTTTTAAA
131 TCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTTTCAAA
*
11732 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTGGTAATTGCAGCGATGATTAAAGTAAATTAAGGTG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAA--AAA-TAAGGTG
* * * * * *
11797 TAGGGTTATAACGATCGAA-GTTTGTGCCTAAGCTATGTTTACAATATATTCGCTAATTAGGTGC
63 TAGGGTTATAACGAGCCAAGGTTT-TGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGC
** ** **
11861 CGTAAAGTC-TTTTTACGGCGTTCTTCCAATTGGAA-GTTCAAGGTTTTCAAA
127 CGT--A-TCTTTTTTACAACGTTCTTCCAA-CCGAATGTTCAAAATTTTCAAA
* * *
11912 CAATTGTTCT-GTTTTTGAGTGTTGTCTTGTAGTAATCGCAGCGATGATTAAAA
1 CAAATGTT-TGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAA
11965 TAAGGTTTAC
Statistics
Matches: 344, Mismatches: 48, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
172 59 0.17
173 85 0.25
174 51 0.15
175 1 0.00
177 7 0.02
178 59 0.17
180 76 0.22
181 6 0.02
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (175 bp):
CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGCCGTA
TCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTTTCAAA
Found at i:13568 original size:21 final size:21
Alignment explanation
Indices: 13542--13609 Score: 55
Period size: 28 Copynumber: 2.9 Consensus size: 21
13532 TTTTTTTACT
* *
13542 AAAATATTATAAAAAAAAATC
1 AAAATAATACAAAAAAAAATC
13563 AAAATAATACATAAAAAAATTATTTAC
1 AAAATAATACA-AAAAAAA--A--T-C
13590 TAAAATAATACAAAAAAAAA
1 -AAAATAATACAAAAAAAAA
13610 AAAACGGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 9 0.24
22 7 0.18
24 1 0.03
25 1 0.03
26 1 0.03
27 8 0.21
28 11 0.29
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATAATACAAAAAAAAATC
Found at i:14108 original size:152 final size:153
Alignment explanation
Indices: 13852--14765 Score: 1042
Period size: 152 Copynumber: 6.0 Consensus size: 153
13842 AAAAATAGTT
* * * * * *
13852 GAAATAAGGGTTTTTTTAAAAATTT-ATTT---AAGCACACTAAATGAAAATATTTTAAATATAA
1 GAAATAAGGGTTTTTTT-TAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAA
* * *
13913 TGTATTAAAATAATGTAAAATAATAAGATTAGAAAATATTATATTTTTTAAAAGTAATAAAATTC
65 TGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTT-AAAGTAATAAAATTC
* *
13978 GGGAAAAAAATATGAATAAAGGGCC
129 GGGAAAAAAATACGAACAAAGGGCC
** ** * * *
14003 GAAATAATAGTTTTTTAAAAATTT-ATTTAAAAAACACAGTAAATTAATACATTTCAAATATAAT
1 GAAATAAGGGTTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAAT
* * **
14067 GTATTAAAATAATAT-AAATAATAAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTTAG
66 GTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTCGG
* * *
14131 AAAAAAAATACGAATAAAGAGCC
131 GAAAAAAATACGAACAAAGGGCC
* * * *
14154 GAAATAA-GG-ATTTTTTAAATTT-ATTT-AAAAACACAATAAATTAATGCATTTCAAACATAAT
1 GAAATAAGGGTTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAAT
* *
14215 GTACTAAAATAATGTAAAATAATAAAATACAAAAAATAATATATTTTTATTGAAAGTAATAAAA-
66 GTACTAAAATAATGTAAAATAATAAAAT-TAGAAAATAATATA-TTTT-TT-AAAGTAATAAAAT
** *
14279 TC-TAAAAAAAATACGAACAAATGGCC
127 TCGGGAAAAAAATACGAACAAAGGGCC
* * *
14305 GAAATAATGGTTTTTTTT-AATTTCA-ATAAAAAACACACTAAACGAATACATTTCAAACATAAT
1 GAAATAAGGGTTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAAT
* * ** *
14368 GTACTAAAATAATTTAAAATAATAAAACTAGAAAATGGTAT-TTTTTTAAAGTAATAAAATCCGG
66 GTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTCGG
***
14432 G-AAAAAATACGAACAATTTGCC
131 GAAAAAAATACGAACAAAGGGCC
* * *
14454 GAAATAAGGGTTTTTTTTTAAATTTCAATAAAAAAATACACTAAATGAATACATTTCAAACATAA
1 GAAATAAGGG-TTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAA
* *
14519 TGTATTAAAATAATGTAAAATAATAAAACTAGAAAAT-ATAATATTTTTTAAAAGTAATAAAATT
65 TGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAAT-ATATTTTTT-AAAGTAATAAAATT
* * *
14583 CGGGGAAAAAATACGAATAAAGGGCT
128 CGGGAAAAAAATACGAACAAAGGGCC
* * *
14609 GAAATGAGGGTTTTTTTTTAAATTTCAATAAAAAAACACACTAAATGAATACATTTCAAACATAA
1 GAAATAAGGG-TTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAA
* *
14674 TGTACTAAAATAATGTAAAATAATAAAAATAGAAAATAGTAT-TTTTTT-AAGTAATAAAA-TCA
65 TGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTC-
* *
14736 GCG-AAAAAATACGAACAAAGGGCT
129 GGGAAAAAAATACGAACAAAGGGCC
14760 GAAATA
1 GAAATA
14766 GGAACATGTT
Statistics
Matches: 668, Mismatches: 72, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
148 57 0.09
149 57 0.09
150 36 0.05
151 122 0.18
152 133 0.20
153 123 0.18
154 23 0.03
155 116 0.17
156 1 0.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (153 bp):
GAAATAAGGGTTTTTTTTAAATTTCATTTAAAAAACACACTAAATGAATACATTTCAAACATAAT
GTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTCGG
GAAAAAAATACGAACAAAGGGCC
Found at i:21211 original size:22 final size:22
Alignment explanation
Indices: 21186--21228 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21176 ATTTTAAAAA
21186 ATATTTTTAT-ATTAACATTTAT
1 ATATTTTTATAATTAA-ATTTAT
21208 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
21229 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Done.