Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2417
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: 26828
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Found at i:995 original size:78 final size:79
Alignment explanation
Indices: 896--1096 Score: 235
Period size: 79 Copynumber: 2.6 Consensus size: 79
886 AATAACAGGG
* * * * *
896 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATA-ATTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATATTA
*
959 GAAAAAAAATCGGGA
65 GAAAAAAAACCGGGA
* * *
974 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATATTAG
* * * *
1039 GAACAAAGCCGGGG
66 AAAAAAAACCGGGA
* * *
1053 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1097 GAAATAACGA
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
77 6 0.06
78 46 0.44
79 52 0.50
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATATTAG
AAAAAAAACCGGGA
Found at i:1081 original size:79 final size:78
Alignment explanation
Indices: 893--1093 Score: 231
Period size: 78 Copynumber: 2.6 Consensus size: 78
883 GATAATAACA
* * * * ** * *
893 GGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATAATT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAATT
*
958 AGAAAAAAAATCG
66 AGAAAAAAAACCG
* * *
971 GGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-AT
* * * *
1036 TGGGAACAAAGCCG
65 TAGAAAAAAAACCG
* *
1050 GGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1094 GATGAAATAA
Statistics
Matches: 102, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
78 52 0.51
79 50 0.49
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAATT
AGAAAAAAAACCG
Found at i:1088 original size:28 final size:28
Alignment explanation
Indices: 1048--1119 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1038 GGAACAAAGC
** *
1048 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1076 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1104 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1120 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1177 original size:52 final size:52
Alignment explanation
Indices: 1108--1280 Score: 174
Period size: 52 Copynumber: 3.3 Consensus size: 52
1098 AAATAACGAG
* *
1108 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCGGA
** * ** *
1160 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAACC-GGA
* * * *
1213 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGTG--ATCAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAACCGGA
1264 GTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
1281 GATTAACGGG
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
51 3 0.03
52 79 0.81
53 16 0.16
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCGGA
Found at i:3739 original size:13 final size:13
Alignment explanation
Indices: 3721--3746 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3711 ACAAAGATCC
3721 ATGTATCGATACA
1 ATGTATCGATACA
3734 ATGTATCGATACA
1 ATGTATCGATACA
3747 GAAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3808 original size:19 final size:18
Alignment explanation
Indices: 3784--3851 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3774 CAGTAGCTAA
3784 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3803 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3818 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3835 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3852 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3824 original size:13 final size:13
Alignment explanation
Indices: 3806--3830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3796 ACAATACTTA
3806 TGTATCGATACAT
1 TGTATCGATACAT
3819 TGTATCGATACA
1 TGTATCGATACA
3831 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3828 original size:32 final size:32
Alignment explanation
Indices: 3787--3849 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3777 TAGCTAATTA
*
3787 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3819 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3850 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3931 original size:21 final size:21
Alignment explanation
Indices: 3907--3963 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3897 CATTTGTAGG
3907 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3928 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3949 ATGTATCGATACATT
1 ATGTATCGATACATT
3964 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3990 original size:14 final size:14
Alignment explanation
Indices: 3973--4000 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3963 TTAATTTTTT
3973 TTTTTTTTTTTTCA
1 TTTTTTTTTTTTCA
3987 TTTTTTTTTTTTCA
1 TTTTTTTTTTTTCA
4001 AACACTTTAT
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:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTCA
Found at i:6348 original size:17 final size:17
Alignment explanation
Indices: 6326--6364 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
6316 GCGTCTTTAT
6326 TCACATTATTTCCTTCA
1 TCACATTATTTCCTTCA
*
6343 TCACATTATTTCCTTTA
1 TCACATTATTTCCTTCA
6360 TCACA
1 TCACA
6365 AACGGGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (17 bp):
TCACATTATTTCCTTCA
Found at i:11540 original size:14 final size:13
Alignment explanation
Indices: 11501--11542 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11491 TTCGCGACAC
*
11501 AAAAAAAAACACA
1 AAAAAAAAACAGA
*
11514 AAAAAAAGA-AGA
1 AAAAAAAAACAGA
11526 AAAAACAAAACAGA
1 AAAAA-AAAACAGA
11540 AAA
1 AAA
11543 TCTCGGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 7 0.29
13 11 0.46
14 6 0.25
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAGA
Found at i:12268 original size:1 final size:1
Alignment explanation
Indices: 12262--12305 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
12252 AAAGTGTTTG
***
12262 AAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12306 TTTAAATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:12283 original size:19 final size:19
Alignment explanation
Indices: 12259--12296 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12249 GATAAAGTGT
12259 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
12278 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
12297 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:12334 original size:21 final size:21
Alignment explanation
Indices: 12310--12366 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
12300 AAAAAATTTA
12310 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
12331 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
12352 AATGTATCGATACAT
1 AATGTATCGATACAT
12367 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:12446 original size:19 final size:19
Alignment explanation
Indices: 12422--12489 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
12412 AATTCAACAA
12422 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
12441 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
12456 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
12473 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
12490 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:12461 original size:13 final size:13
Alignment explanation
Indices: 12443--12467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12433 ACATAAGTTT
12443 TGTATCGATACAA
1 TGTATCGATACAA
12456 TGTATCGATACA
1 TGTATCGATACA
12468 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12465 original size:32 final size:32
Alignment explanation
Indices: 12424--12486 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12414 TTCAACAATT
*
12424 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
12456 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
12487 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:12547 original size:13 final size:13
Alignment explanation
Indices: 12529--12554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12519 CATTTTTCTG
12529 TGTATCGATACAT
1 TGTATCGATACAT
12542 TGTATCGATACAT
1 TGTATCGATACAT
12555 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12551 original size:33 final size:33
Alignment explanation
Indices: 12509--12575 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12499 GCCAAGGAAA
***
12509 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
12542 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
12575 T
1 T
12576 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:15160 original size:102 final size:102
Alignment explanation
Indices: 14900--15181 Score: 349
Period size: 102 Copynumber: 2.8 Consensus size: 102
14890 CAAGTTTTCT
* * * * *
14900 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
* * *
14965 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACAC
66 CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
* **
15002 CAATTTTCCA-CAATCGGGGATACTCCAACCTCGGTTTTATTT-TCAAAACACCAATTTTCTATA
1 CAATTTTCCATC-ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACATTAATTTTCTATA
*
15065 ATCGGGGATACTCCAACTCCGATTGTATT-TCCAAAATAC
64 ATCGGGGATACTCCAACTCCGATTGTATTCT-CAAAACAC
* * *
15104 TAACTTTT-CATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATTAA-TTTCTCATA
1 CAA-TTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCT-ATA
15167 ATCGGGGATACTCCA
64 ATCGGGGATACTCCA
15182 TCCCCGTTAT
Statistics
Matches: 155, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
101 7 0.05
102 142 0.92
103 6 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
Found at i:15178 original size:153 final size:153
Alignment explanation
Indices: 14900--15181 Score: 349
Period size: 153 Copynumber: 1.8 Consensus size: 153
14890 CAAGTTTTCT
* * * *
14900 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
* *
14965 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
15030 CCTCGGTTTTATTTTCAAAACAC
131 CCTCGGTTTTATTTTCAAAACAC
* * *
15053 CAATTTT-CTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACTAACTTTT-CATC
1 CAATTTTGC-ATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAA-TTTTCCA-C
* * * ** *
15116 -ATCGGGGATACTCCAACCCCGTTTTTATT-TCTAAAATATTAA-TTTCTCATAATCGGGGATAC
63 AATCGGGGACACTCCAACCCCGATTTTATTCTC-AAAACACCAATTTTC-CACAATCGGGGATAC
15178 TCCA
126 TCCA
15182 TCCCCGTTAT
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
152 7 0.06
153 97 0.89
154 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (153 bp):
CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
CCTCGGTTTTATTTTCAAAACAC
Found at i:15189 original size:51 final size:50
Alignment explanation
Indices: 14901--15187 Score: 299
Period size: 51 Copynumber: 5.6 Consensus size: 50
14891 AAGTTTTCTC
* * *
14901 AATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATT
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * * *
14952 AATTTTCCACAATCGGGGACACTCCAACTCCGATTTTA-TTCTCAGAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
15003 AATTTTCCACAATCGGGGATACTCCAACCTCGGTTTTATTT-TCAAAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
15054 AATTTTCTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACT
1 AATTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * *
15105 AACTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATT
1 AA-TTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
*
15156 AATTTCTCATAATCGGGGATACTCCATCCCCG
1 AATTT-TCATAATCGGGGATACTCCAACCCCG
15188 TTATTTTCGG
Statistics
Matches: 201, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
50 8 0.04
51 186 0.93
52 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
AATTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
Done.