Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1522
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: 32840
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Found at i:5780 original size:32 final size:32
Alignment explanation
Indices: 5741--5802 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
5731 ATTATGTATT
5741 CTTTATTGTTCTTAATGCTTCTAATTTTAACA
1 CTTTATTGTTCTTAATGCTTCTAATTTTAACA
*
5773 CTTTATTGTTCTTACTGCTTCTAATTTTAA
1 CTTTATTGTTCTTAATGCTTCTAATTTTAA
5803 TGCTTCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (32 bp):
CTTTATTGTTCTTAATGCTTCTAATTTTAACA
Found at i:6641 original size:20 final size:21
Alignment explanation
Indices: 6597--6650 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
6587 GTTTACAATT
* *
6597 TGTATCGATATAAACAGTAAA
1 TGTATCGATACATACAGTAAA
*
6618 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
*
6638 TGTATCAATACAT
1 TGTATCGATACAT
6651 GCCTGAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:6764 original size:42 final size:42
Alignment explanation
Indices: 6694--6773 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
6684 TTTTTGAAAG
*
6694 AAATTGTATCGATACATAAATGAATGTATCAATACATTACTT
1 AAATTGTATCGATACATAAATCAATGTATCAATACATTACTT
* * * *
6736 AAATTGTATCGATACATTATTCATTGTATCGATACATT
1 AAATTGTATCGATACATAAATCAATGTATCAATACATT
6774 CTGGGTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (42 bp):
AAATTGTATCGATACATAAATCAATGTATCAATACATTACTT
Found at i:6773 original size:20 final size:20
Alignment explanation
Indices: 6695--6773 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
6685 TTTTGAAAGA
* *
6695 AATTGTATCGATACATAAATG
1 AATTGTATCGATACAT-TATT
*
6716 AA-TGTATCAATACATTACTT
1 AATTGTATCGATACATTA-TT
6736 AAATTGTATCGATACATTATT
1 -AATTGTATCGATACATTATT
*
6757 CATTGTATCGATACATT
1 AATTGTATCGATACATT
6774 CTGGGTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.02
20 29 0.58
21 6 0.12
22 14 0.28
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (20 bp):
AATTGTATCGATACATTATT
Found at i:13131 original size:19 final size:17
Alignment explanation
Indices: 13095--13133 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
13085 AAATTGTAGT
13095 AATCATTACAAAACTCA
1 AATCATTACAAAACTCA
*
13112 AATCGATTACTAAAATTCA
1 AATC-ATTAC-AAAACTCA
13131 AAT
1 AAT
13134 TAATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (17 bp):
AATCATTACAAAACTCA
Found at i:15353 original size:14 final size:14
Alignment explanation
Indices: 15334--15361 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15324 TTATCATCTC
15334 TACTCCAAATTAGG
1 TACTCCAAATTAGG
15348 TACTCCAAATTAGG
1 TACTCCAAATTAGG
15362 ATTGATTTAA
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:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TACTCCAAATTAGG
Found at i:15906 original size:108 final size:103
Alignment explanation
Indices: 15740--15966 Score: 258
Period size: 108 Copynumber: 2.2 Consensus size: 103
15730 CTATCTACCA
* * * *
15740 AATTATTATATGGTAAATTAATTGTAACATATCACTAAGATACATGATATGTACGTAATCGTAAC
1 AATTATTATTTGGTAAATTAAGTGTAACATAGCACTAAGATACATGACATGTACGTAATCGTAAC
* *
15805 ATCTTTTAATTTCATCAAATATTGATAAAATTTCTTCCTATCC
66 ATCTTTCAATTTCATCAAATA-TGA-AAAA---CTACCTATCC
* * * * *
15848 AATTATTATTTGGTAAATTAAGTGTAACGTGGCAC-AAGCATATATGACATTTATGTAATCGTAA
1 AATTATTATTTGGTAAATTAAGTGTAACATAGCACTAAG-ATACATGACATGTACGTAATCGTAA
* * *
15912 TATCTTTCAATTTCATTAAATATGAAAAACTAGCTATCC
65 CATCTTTCAATTTCATCAAATATGAAAAACTACCTATCC
*
15951 AATTATTATTTTGTAA
1 AATTATTATTTGGTAA
15967 CTAAGTATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
103 23 0.22
106 4 0.04
107 6 0.06
108 70 0.68
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (103 bp):
AATTATTATTTGGTAAATTAAGTGTAACATAGCACTAAGATACATGACATGTACGTAATCGTAAC
ATCTTTCAATTTCATCAAATATGAAAAACTACCTATCC
Found at i:16021 original size:103 final size:103
Alignment explanation
Indices: 15842--16043 Score: 252
Period size: 103 Copynumber: 2.0 Consensus size: 103
15832 AAATTTCTTC
* * * *
15842 CTATCCAATTATTATTTGGTAAATTAAGTGTAACGTGGCACAAGCATATATGACATTTATGTAAT
1 CTATCCAATTATTATTTGGTAAACTAAGTATAACGTGGCACAAGCATACATGACATTTATATAAT
*
15907 CGTAATATCTTTC-AATTTCATTAAATATGAAAAACTAG
66 CATAATATCTTTCAAATTT-ATTAAATATGAAAAACTAG
* *
15945 CTATCCAATTATTATTTTGT-AACTAAGTATAA-GATGTTGC-C-AGCATACATTACATTTTATA
1 CTATCCAATTATTATTTGGTAAACTAAGTATAACG-TG--GCACAAGCATACATGACA-TTTATA
*
16006 TAATCATAATGTCTTTCAAATTTATTAAATATGAAAAA
62 TAATCATAATATCTTTCAAATTTATTAAATATGAAAAA
16044 GTCCACCAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
101 1 0.01
102 23 0.27
103 55 0.64
104 7 0.08
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (103 bp):
CTATCCAATTATTATTTGGTAAACTAAGTATAACGTGGCACAAGCATACATGACATTTATATAAT
CATAATATCTTTCAAATTTATTAAATATGAAAAACTAG
Found at i:16297 original size:107 final size:105
Alignment explanation
Indices: 16165--16815 Score: 670
Period size: 107 Copynumber: 6.1 Consensus size: 105
16155 CAATTACAAA
* *
16165 TTCATTAAATATTGAAAAAAGTCTACCGCTCCAATTATTATATGGTAAATTAAGTGTAACGTGTT
1 TTCATTAAATATTGAAAAAAATCTA-C-CTCCAATTATTATATGGTAAATTAAGTGTAACGTCTT
* * * * * ** *
16230 GCCAATAAACATTACATTTATATAAGCATAACATCTTTCAAT
64 GCCAACATATATAACATTTATGTAAGTGTAACGTCTTTCAAT
*
16272 TTCATTAAATATTGAAAAAAATCTACCTACCTAATCATTATATGGTAAATTAAGTGTAACGTCTT
1 TTCATTAAATATTGAAAAAAATCTACCT-CC-AATTATTATATGGTAAATTAAGTGTAACGTCTT
*
16337 GCCAACATATATAACATTTATGT-AGTTGTAACGTTTTTCAAT
64 GCCAACATATATAACATTTATGTAAG-TGTAACGTCTTTCAAT
* * **
16379 TTCATTAAATATT-AAAAAAATCTACCTTCATAATCATTATATGGTAAATTAAGTGTAACACCTT
1 TTCATTAAATATTGAAAAAAATCTACC-TC-CAATTATTATATGGTAAATTAAGTGTAACGTCTT
* *
16443 GGCAACATATATAACATTTATGTAATTGTAACGTCTTTCAAT
64 GCCAACATATATAACATTTATGTAAGTGTAACGTCTTTCAAT
* * * * *
16485 TTCATTAAATATTGAAAAATATCTACTTTCCCAATTATTATATAGTAAATTATGTGTAACGCCTT
1 TTCATTAAATATTGAAAAAAATCTAC-CT-CCAATTATTATATGGTAAATTAAGTGTAACGTCTT
* * * *
16550 GCCAGCATATATAATATTTATGTAATTGTAATGTCTTTCAAT
64 GCCAACATATATAACATTTATGTAAGTGTAACGTCTTTCAAT
* * *
16592 TTCATTAAATATTGAAAAATATCTACCTTCTCAATTATTATATGGTAAATTCAGTATAACG-CTT
1 TTCATTAAATATTGAAAAAAATCTACC-TC-CAATTATTATATGGTAAATTAAGTGTAACGTCTT
* * * * *
16656 CACCAACATACATAACATTTATGTAACCT-TAAAGTCTTTCGAT
64 -GCCAACATATATAACATTTATGTAA-GTGTAACGTCTTTCAAT
* * *
16699 TTCATTAAATA-TAAAAAAAATCTACCT--ACTTATTTATATGGTAAATTAAATGTAACG-CTTC
1 TTCATTAAATATTGAAAAAAATCTACCTCCAATTA-TTATATGGTAAATTAAGTGTAACGTCTT-
* * * * * * ** * *
16760 ACCAGCCTACATGACTTTTATGTAAACGTTACGTCTTTTAAT
64 GCCAACATATATAACATTTATGTAAGTGTAACGTCTTTCAAT
*
16802 TTTATTAAATATTG
1 TTCATTAAATATTG
16816 CATATTCACA
Statistics
Matches: 469, Mismatches: 59, Indels: 35
0.83 0.10 0.06
Matches are distributed among these distances:
102 4 0.01
103 66 0.14
104 1 0.00
105 3 0.01
106 117 0.25
107 276 0.59
108 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (105 bp):
TTCATTAAATATTGAAAAAAATCTACCTCCAATTATTATATGGTAAATTAAGTGTAACGTCTTGC
CAACATATATAACATTTATGTAAGTGTAACGTCTTTCAAT
Found at i:16571 original size:213 final size:211
Alignment explanation
Indices: 16165--16815 Score: 711
Period size: 213 Copynumber: 3.1 Consensus size: 211
16155 CAATTACAAA
* * * **
16165 TTCATTAAATATTGAAAAAAGTCTACCGCTCCAATTATTATATGGTAAATTAAGTGTAACGTGTT
1 TTCATTAAATATTGAAAAAAATCTACC-TTCTAATTATTATATGGTAAATTAAGTGTAAC-CCTT
* * * * * *
16230 GCCAATAAACATTACATTTATATAAGCATAACATCTTTCAATTTCATTAAATATTGAAAAAAATC
64 GCCAACATACATAACATTTATGTAA-CTTAACGTCTTTCAATTTCATTAAATATTGAAAAAAATC
* * *
16295 TACCTACCTAATCATTATATGGTAAATTAAGTGTAACGTCTTGCCAACATATATAACATTTATGT
128 TACCTACCCAATCATTATATAGTAAATTAAGTGTAACGCCTTGCCAACATATATAACATTTATGT
* *
16360 AGTTGTAACGTTTTTCAAT
193 AATTGTAACGTCTTTCAAT
*
16379 TTCATTAAATATT-AAAAAAATCTACCTTCATAATCATTATATGGTAAATTAAGTGTAACACCTT
1 TTCATTAAATATTGAAAAAAATCTACCTTC-TAATTATTATATGGTAAATTAAGTGTAAC-CCTT
* * * *
16443 GGCAACATATATAACATTTATGTAATTGTAACGTCTTTCAATTTCATTAAATATTGAAAAATATC
64 GCCAACATACATAACATTTATGTAACT-TAACGTCTTTCAATTTCATTAAATATTGAAAAAAATC
* * * * * *
16508 TACTTTCCCAATTATTATATAGTAAATTATGTGTAACGCCTTGCCAGCATATATAATATTTATGT
128 TACCTACCCAATCATTATATAGTAAATTAAGTGTAACGCCTTGCCAACATATATAACATTTATGT
*
16573 AATTGTAATGTCTTTCAAT
193 AATTGTAACGTCTTTCAAT
* * * *
16592 TTCATTAAATATTGAAAAATATCTACCTTCTCAATTATTATATGGTAAATTCAGTATAACGCTTC
1 TTCATTAAATATTGAAAAAAATCTACCTTCT-AATTATTATATGGTAAATTAAGTGTAACCCTT-
* * * *
16657 ACCAACATACATAACATTTATGTAACCTTAAAGTCTTTCGATTTCATTAAATA-TAAAAAAAATC
64 GCCAACATACATAACATTTATGTAA-CTTAACGTCTTTCAATTTCATTAAATATTGAAAAAAATC
** * * * * * * * *
16721 TACCTA-CTTAT--TTATATGGTAAATTAAATGTAACG-CTTCACCAGCCTACATGACTTTTATG
128 TACCTACCCAATCATTATATAGTAAATTAAGTGTAACGCCTT-GCCAACATATATAACATTTATG
** * *
16782 TAAACGTTACGTCTTTTAAT
192 TAATTGTAACGTCTTTCAAT
*
16802 TTTATTAAATATTG
1 TTCATTAAATATTG
16816 CATATTCACA
Statistics
Matches: 369, Mismatches: 61, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
209 3 0.01
210 65 0.18
212 5 0.01
213 197 0.53
214 98 0.27
215 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (211 bp):
TTCATTAAATATTGAAAAAAATCTACCTTCTAATTATTATATGGTAAATTAAGTGTAACCCTTGC
CAACATACATAACATTTATGTAACTTAACGTCTTTCAATTTCATTAAATATTGAAAAAAATCTAC
CTACCCAATCATTATATAGTAAATTAAGTGTAACGCCTTGCCAACATATATAACATTTATGTAAT
TGTAACGTCTTTCAAT
Found at i:17104 original size:31 final size:31
Alignment explanation
Indices: 17066--17137 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
17056 TGATCTTTGC
17066 ATCGATACATCTAGAAATTTTACCCAGATGT
1 ATCGATACATCTAGAAATTTTACCCAGATGT
*
17097 ATCGATACATCTAGAAATTTTACCTAGATGT
1 ATCGATACATCTAGAAATTTTACCCAGATGT
17128 ATCGATACAT
1 ATCGATACAT
17138 TATTCAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (31 bp):
ATCGATACATCTAGAAATTTTACCCAGATGT
Found at i:21061 original size:75 final size:75
Alignment explanation
Indices: 20938--21088 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
20928 ATGTTGACAT
20938 ATATGAAAAAAATTGATAAATCTTAACAATACATGTAGTTTAGTTGAGTAATAAGGTCCTCTAAG
1 ATATGAAAAAAATTGATAAATCTTAACAATACATGTAGTTTAGTTGAGTAATAAGGTCCTCTAAG
21003 TAAATCATTA
66 TAAATCATTA
* *
21013 ATATGAAAAAAATTGATAAATCTTAACAATGCATGTAGTTTAGTTGAGTAATAAGGTCTTCTAAG
1 ATATGAAAAAAATTGATAAATCTTAACAATACATGTAGTTTAGTTGAGTAATAAGGTCCTCTAAG
21078 TAAATCATTA
66 TAAATCATTA
21088 A
1 A
21089 AAGCAAAGTA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.34
Consensus pattern (75 bp):
ATATGAAAAAAATTGATAAATCTTAACAATACATGTAGTTTAGTTGAGTAATAAGGTCCTCTAAG
TAAATCATTA
Found at i:29199 original size:20 final size:20
Alignment explanation
Indices: 29174--29221 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
29164 TTCTACAATT
* *
29174 TGTATCGATATATAAGTTAA
1 TGTATCGATACATAAGTGAA
*
29194 TGTATCGCTACATAAGTGAA
1 TGTATCGATACATAAGTGAA
29214 TGTATCGA
1 TGTATCGA
29222 GACTAGACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:30765 original size:21 final size:21
Alignment explanation
Indices: 30739--30790 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
30729 TTTTACAATT
*
30739 TGTATCGATATGA-ACAGTAAA
1 TGTATCGATATCATA-AGTAAA
*
30760 TGTATCGATA-CATAAGTGAA
1 TGTATCGATATCATAAGTAAA
30780 TGTATCGATAT
1 TGTATCGATAT
30791 ATTTTCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTATCGATATCATAAGTAAA
Found at i:31425 original size:13 final size:13
Alignment explanation
Indices: 31407--31431 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31397 ATAAAGTGTT
31407 TGTATCGATACAA
1 TGTATCGATACAA
31420 TGTATCGATACA
1 TGTATCGATACA
31432 TGTTTTTTTG
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:31513 original size:13 final size:13
Alignment explanation
Indices: 31495--31519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31485 ATCACTTAAA
31495 TGTATCGATACAT
1 TGTATCGATACAT
31508 TGTATCGATACA
1 TGTATCGATACA
31520 CTGATCTTTG
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:31572 original size:52 final size:52
Alignment explanation
Indices: 31528--31708 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
31518 CACTGATCTT
31528 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
31580 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
31632 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
31684 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
31709 TCATATTTCG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.