Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2021
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: 23035
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:631 original size:39 final size:39
Alignment explanation
Indices: 472--634 Score: 196
Period size: 39 Copynumber: 4.3 Consensus size: 39
462 GCTACTCGTT
* *
472 CAAATGCCTTCGGGACAT-GCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
511 CAAATG-CTTCGGGACTTAACCCGGTTTAGT-AC-CGCA
1 CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
*
547 CAAATG-CTGC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
* * *
585 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
624 CAAATGCCTTC
1 CAAATGCCTTC
635 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
35 13 0.12
36 19 0.17
37 4 0.04
38 24 0.22
39 49 0.44
40 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:3802 original size:17 final size:17
Alignment explanation
Indices: 3780--3920 Score: 96
Period size: 17 Copynumber: 7.9 Consensus size: 17
3770 ATGAAAATAT
*
3780 AATCTTCAATGATATGC
1 AATCTTAAATGATATGC
*
3797 AATCTTAAAT-ATGATAC
1 AATCTTAAATGAT-ATGC
3814 AATCTTAGATATGAT-TGC
1 AATCTTA-A-ATGATATGC
3832 AATCTTAGATATGATA--C
1 AATCTTA-A-ATGATATGC
*
3849 AATCTTAGATATGATATAC
1 AATCTTA-A-ATGATATGC
3868 AATCTTAGATATGAT-TGC
1 AATCTTA-A-ATGATATGC
*
3886 AATCTTAGATATGATATAC
1 AATCTTA-A-ATGATATGC
3905 AATCTTAGAA-GATATG
1 AATCTTA-AATGATATG
3921 ATTTTGTAAT
Statistics
Matches: 110, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
16 2 0.02
17 41 0.37
18 36 0.33
19 29 0.26
20 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
AATCTTAAATGATATGC
Found at i:3834 original size:35 final size:36
Alignment explanation
Indices: 3788--3913 Score: 200
Period size: 35 Copynumber: 3.5 Consensus size: 36
3778 ATAATCTTCA
* *
3788 ATGATATGCAATCTTAAATATGATACAATCTTAGAT
1 ATGATATACAATCTTAGATATGATACAATCTTAGAT
*
3824 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATACAATCTTAGATATGATACAATCTTAGAT
*
3859 ATGATATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATACAATCTTAGATATGA-TACAATCTTAGAT
3896 ATGATATACAATCTTAGA
1 ATGATATACAATCTTAGA
3914 AGATATGATT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
35 34 0.40
36 21 0.25
37 30 0.35
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (36 bp):
ATGATATACAATCTTAGATATGATACAATCTTAGAT
Found at i:3912 original size:19 final size:19
Alignment explanation
Indices: 3788--3913 Score: 174
Period size: 19 Copynumber: 6.9 Consensus size: 19
3778 ATAATCTTCA
* *
3788 ATGATATGCAATCTTAAAT
1 ATGATATACAATCTTAGAT
3807 ATG--ATACAATCTTAGAT
1 ATGATATACAATCTTAGAT
*
3824 ATGAT-TGCAATCTTAGAT
1 ATGATATACAATCTTAGAT
3842 ATG--ATACAATCTTAGAT
1 ATGATATACAATCTTAGAT
3859 ATGATATACAATCTTAGAT
1 ATGATATACAATCTTAGAT
*
3878 ATGAT-TGCAATCTTAGAT
1 ATGATATACAATCTTAGAT
3896 ATGATATACAATCTTAGA
1 ATGATATACAATCTTAGA
3914 AGATATGATT
Statistics
Matches: 95, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
17 30 0.32
18 32 0.34
19 33 0.35
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGATATACAATCTTAGAT
Found at i:3919 original size:54 final size:54
Alignment explanation
Indices: 3788--3919 Score: 198
Period size: 54 Copynumber: 2.4 Consensus size: 54
3778 ATAATCTTCA
* *
3788 ATGATATGCAATCTTA-AATATGATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATACAATCTTAGAAGAT-ATACAATCTTAGATATGATTGCAATCTTAGAT
3842 ATG--ATACAATCTTAGATATGATATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATACAATCTTAGA-A-GATATACAATCTTAGATATGATTGCAATCTTAGAT
3896 ATGATATACAATCTTAGAAGATAT
1 ATGATATACAATCTTAGAAGATAT
3920 GATTTTGTAA
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
52 10 0.14
53 1 0.01
54 44 0.62
55 3 0.04
56 13 0.18
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (54 bp):
ATGATATACAATCTTAGAAGATATACAATCTTAGATATGATTGCAATCTTAGAT
Found at i:12175 original size:39 final size:40
Alignment explanation
Indices: 12093--12314 Score: 260
Period size: 39 Copynumber: 5.7 Consensus size: 40
12083 GCTACTCGTT
*
12093 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
**
12133 CAAATGCCTTCGGGACTTAATCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
12172 CAAATGCCTT-GGG-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
12210 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
12249 CAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
12290 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12315 CATCATTCAA
Statistics
Matches: 158, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
37 7 0.04
38 30 0.19
39 59 0.37
40 52 0.33
41 10 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12214 original size:77 final size:79
Alignment explanation
Indices: 12093--12259 Score: 234
Period size: 77 Copynumber: 2.1 Consensus size: 79
12083 GCTACTCGTT
* *
12093 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAATCC-G
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGG
*
12157 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* *
12172 CAAATGCCTT-GGG-CTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGG
*
12234 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
12249 CAAATGCCTTC
1 CAAATGCCTTC
12260 AGATCTTAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
76 6 0.08
77 58 0.73
78 5 0.06
79 10 0.13
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGA
ATTAGTAACTCGCA
Found at i:12308 original size:40 final size:40
Alignment explanation
Indices: 12074--12314 Score: 255
Period size: 40 Copynumber: 6.1 Consensus size: 40
12064 CGGAATTTAA
** *
12074 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* **
12114 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12154 CC-GATTTAGTAACTCGCACAAATGCCTT-GGG-CTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12191 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
12230 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-AGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12270 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12310 CCGGA
1 CCGGA
12315 CATCATTCAA
Statistics
Matches: 172, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
37 7 0.04
38 30 0.17
39 60 0.35
40 64 0.37
41 11 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:15485 original size:18 final size:18
Alignment explanation
Indices: 15445--15580 Score: 195
Period size: 18 Copynumber: 7.6 Consensus size: 18
15435 CAATGATATG
*
15445 CAATCTTAAATATGA-TA
1 CAATCTTAGATATGATTA
*
15462 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
*
15480 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
15498 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
15515 CAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
*
15534 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
*
15552 TAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
15571 CAATCTTAGA
1 CAATCTTAGA
15581 AGATATGATT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
17 30 0.28
18 50 0.46
19 28 0.26
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (18 bp):
CAATCTTAGATATGATTA
Found at i:15514 original size:72 final size:73
Alignment explanation
Indices: 15436--15587 Score: 224
Period size: 72 Copynumber: 2.1 Consensus size: 73
15426 TATAATCTTC
*
15436 AATGATATGCAATCTTAAATATG-ATACAATCTTAGATATGATTGCAATCTTAGATATGAT-TGC
1 AATGATATGCAATCTTAAATATGAATACAATCTTAGATATGATTGCAATCTTAGATATGATATAC
15499 AATCTTAG
66 AATCTTAG
* *
15507 ATATGATA--CAATCTTAGATATGATATACAATCTTAGATATGATTGTAATCTTAGATATGATAT
1 A-ATGATATGCAATCTTAAATATGA-ATACAATCTTAGATATGATTGCAATCTTAGATATGATAT
15570 ACAATCTTAG
64 ACAATCTTAG
15580 AA-GATATG
1 AATGATATG
15588 ATTTTGTAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
70 13 0.18
71 5 0.07
72 43 0.60
73 11 0.15
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (73 bp):
AATGATATGCAATCTTAAATATGAATACAATCTTAGATATGATTGCAATCTTAGATATGATATAC
AATCTTAG
Found at i:15586 original size:54 final size:54
Alignment explanation
Indices: 15437--15580 Score: 227
Period size: 54 Copynumber: 2.6 Consensus size: 54
15427 ATAATCTTCA
* *
15437 ATGATATGCAATCTTAAATATGATACAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGAT
15491 ATGATTGCAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGAT
*
15545 ATGATTGTAATCTTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA
15581 AGATATGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
53 34 0.40
54 37 0.44
56 13 0.15
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (54 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGAT
Found at i:15606 original size:22 final size:20
Alignment explanation
Indices: 15463--15616 Score: 87
Period size: 18 Copynumber: 8.1 Consensus size: 20
15453 AATATGATAC
*
15463 AATCTT-AGATATGA-TTGC
1 AATCTTGAGATATGATTTGT
*
15481 AATCTT-AGATATGA-TTGC
1 AATCTTGAGATATGATTTGT
**
15499 AATCTT-AGATATGA--TAC
1 AATCTTGAGATATGATTTGT
* **
15516 AATCTT-AGATATGATATAC
1 AATCTTGAGATATGATTTGT
15535 AATCTT-AGATATGA-TTGT
1 AATCTTGAGATATGATTTGT
* **
15553 AATCTT-AGATATGATATAC
1 AATCTTGAGATATGATTTGT
15572 AATCTTAGAAGATATGATTTTGT
1 AATCTT-G-AGATATGA-TTTGT
* *
15595 AATCTTGGAGATTTAATTTGT
1 AATCTT-GAGATATGATTTGT
15616 A
1 A
15617 GATATCCTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
17 16 0.14
18 47 0.41
19 24 0.21
21 6 0.05
22 14 0.12
23 9 0.08
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (20 bp):
AATCTTGAGATATGATTTGT
Found at i:22532 original size:44 final size:44
Alignment explanation
Indices: 22391--22570 Score: 204
Period size: 44 Copynumber: 4.1 Consensus size: 44
22381 CAAAGAAACA
* *
22391 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * * **
22435 AGATCTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
22480 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
22523 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
22567 AGAT
1 AGAT
22571 CTAACCTTCA
Statistics
Matches: 111, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 13 0.12
44 81 0.73
45 14 0.13
46 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:22888 original size:114 final size:118
Alignment explanation
Indices: 22562--22911 Score: 622
Period size: 114 Copynumber: 3.0 Consensus size: 118
22552 CAGATCGAAG
22562 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGG-ATTCTTGTGT
*
22627 TTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAACAT
65 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAA-AT
22682 ATAGCAGATCTAA-CTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTG-
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGG-ATTCTTGTGT
22745 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAT
65 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAT
22799 AT-GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC-A-ATGATTTGG-TTCTTGTGTT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGATTCTTGTGTT
22860 TACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAA
66 TACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAA
22912 CAGACTCTAG
Statistics
Matches: 227, Mismatches: 1, Indels: 10
0.95 0.00 0.04
Matches are distributed among these distances:
113 8 0.04
114 53 0.23
115 9 0.04
116 11 0.05
117 32 0.14
118 51 0.22
119 50 0.22
120 13 0.06
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (118 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGATTCTTGTGTT
TACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAT
Done.