Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1557
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: 75183
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:12131 original size:40 final size:39
Alignment explanation
Indices: 12076--12282 Score: 201
Period size: 40 Copynumber: 5.3 Consensus size: 39
12066 ATTTGAATGA
*
12076 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTT-TGCTAGTGATTT
*
12116 TATCCGGGCTAAG-TCCGAAGG-A-TTTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTTGCTAGTGATTT
* *
12152 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTT-TGCTAG-TGATTT
* * *
12192 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTT-TGCTAG-TGATTT
* * * * * *
12232 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGC-ATTTTGCTAGTGATTT
12272 TATCC-GGCTAA
1 TATCCGGGCTAA
12283 ATTCCGAAGA
Statistics
Matches: 147, Mismatches: 12, Indels: 17
0.84 0.07 0.10
Matches are distributed among these distances:
36 25 0.17
37 9 0.06
38 2 0.01
39 16 0.11
40 89 0.61
41 6 0.04
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTTGCTAGTGATTT
Found at i:12274 original size:80 final size:76
Alignment explanation
Indices: 12079--12282 Score: 216
Period size: 76 Copynumber: 2.6 Consensus size: 76
12069 TGAATGATAT
* * * * *
12079 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCGAAGGATTTGCT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGCCCGAAGGATTTGCT
* *
12144 AGTGATTTTAT
66 AGCGATTTTAC
* * *
12155 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAG-CCCGAAGG-ATTTG
12220 -T-GCGAGTTGCTATAC
64 CTAGCGA-TT--T-TAC
* * *
12235 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAA
12283 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
76 46 0.43
77 10 0.09
78 5 0.05
79 7 0.07
80 38 0.36
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (76 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGCCCGAAGGATTTGCT
AGCGATTTTAC
Found at i:20243 original size:40 final size:40
Alignment explanation
Indices: 20188--20398 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
20178 ATTTGAATGA
*
20188 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
20228 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
20268 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
20308 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
20348 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
20388 TATCC-GGCTAA
1 TATCCGGGCTAA
20399 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:33912 original size:20 final size:20
Alignment explanation
Indices: 33874--33921 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33864 TAAATTCTGA
* **
33874 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
33894 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
33914 AAA-ATAAA
1 AAAGATAAA
33922 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:33946 original size:27 final size:26
Alignment explanation
Indices: 33916--33978 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
33906 AGATAATTAA
33916 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
33943 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
33970 AATATAAAT
1 AATA-AAAT
33979 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:33965 original size:15 final size:15
Alignment explanation
Indices: 33945--33974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33935 ATAATCCTAA
*
33945 TAATTATCTTAATAT
1 TAATTATCCTAATAT
33960 TAATTATCCTAATAT
1 TAATTATCCTAATAT
33975 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:35537 original size:15 final size:15
Alignment explanation
Indices: 35517--35568 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
35507 TTAATATCTG
35517 AAAATAATAAATAAT
1 AAAATAATAAATAAT
35532 AAAATAATAAGATAAAAT
1 AAAATAATAA-AT--AAT
*
35550 AAATAAAATAAA-AAT
1 AAA-ATAATAAATAAT
35565 AAAA
1 AAAA
35569 ATAAAAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.50
16 2 0.06
18 7 0.22
19 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:35557 original size:22 final size:21
Alignment explanation
Indices: 35517--35573 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
35507 TTAATATCTG
35517 AAAATAATAAAT-AATAAAATA
1 AAAATAA-AAATAAATAAAATA
35538 ATAAGAT-AAAATAAATAAAATA
1 A-AA-ATAAAAATAAATAAAATA
35560 AAAATAAAAATAAA
1 AAAATAAAAATAAA
35574 AATTGGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 13 0.41
23 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAATAAAAATAAATAAAATA
Found at i:35560 original size:14 final size:14
Alignment explanation
Indices: 35529--35567 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
35519 AATAATAAAT
35529 AATAAAAT-AATAA
1 AATAAAATAAATAA
*
35542 GATAAAATAAATAA
1 AATAAAATAAATAA
35556 AATAAAAATAAA
1 AAT-AAAATAAA
35568 AATAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 7 0.32
14 7 0.32
15 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:39412 original size:104 final size:104
Alignment explanation
Indices: 39290--39513 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
39280 AATGGATATC
39290 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
39355 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
39394 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
39459 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
39498 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
39514 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:39875 original size:29 final size:29
Alignment explanation
Indices: 39842--39905 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
39832 TAATCCACCA
39842 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
39871 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
39901 CCCAA
1 CCCAA
39906 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:39879 original size:30 final size:30
Alignment explanation
Indices: 39849--39905 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39839 CCACCCAACT
39849 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
39878 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
39906 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:46962 original size:104 final size:104
Alignment explanation
Indices: 46840--47063 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
46830 AATGGATATC
46840 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
46905 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
46944 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
47009 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
47048 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
47064 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:47423 original size:29 final size:29
Alignment explanation
Indices: 47390--47453 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
47380 TAATCCACCA
47390 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
47419 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
47449 CCCAA
1 CCCAA
47454 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:47427 original size:30 final size:30
Alignment explanation
Indices: 47397--47453 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
47387 CCACCCAACT
47397 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
47426 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
47454 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:53965 original size:10 final size:11
Alignment explanation
Indices: 53946--53978 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
53936 AATAAATTAT
53946 ATAAGAATAAA
1 ATAAGAATAAA
53957 ATAAG-ATAAA
1 ATAAGAATAAA
*
53967 ATAAAAATAAA
1 ATAAGAATAAA
53978 A
1 A
53979 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
ATAAGAATAAA
Found at i:57720 original size:72 final size:72
Alignment explanation
Indices: 57634--57786 Score: 236
Period size: 72 Copynumber: 2.1 Consensus size: 72
57624 CGGGAATCAT
* **
57634 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCA-TTTCAAATTATACAAT
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCC-TTTCACATTCAAAAGATACAAT
57698 GGATATCG
65 GGATATCG
***
57706 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATACAATG
57771 GATATCG
66 GATATCG
57778 CACTTAGCA
1 CACTTAGCA
57787 CCACCAATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
71 5 0.07
72 69 0.93
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATACAATG
GATATCG
Found at i:57905 original size:102 final size:103
Alignment explanation
Indices: 57705--57925 Score: 349
Period size: 102 Copynumber: 2.2 Consensus size: 103
57695 AATGGATATC
57705 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATATGGT
* *
57770 GGATATCGCACTTAGCACCACCAATGAACCGGGAATCA
66 GGATATCGCACATAGCACCACCAATAAACCGGGAATCA
57808 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTC-AAAGATATGG
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA-TTCAAAAGATATGG
* *
57871 TGGATCA-CGCACATAGCACCACCCATAAATCGGGAATCA
65 TGGAT-ATCGCACATAGCACCACCAATAAACCGGGAATCA
**
57910 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
57926 TTTATATACA
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
102 68 0.62
103 42 0.38
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTCAAAAGATATGGT
GGATATCGCACATAGCACCACCAATAAACCGGGAATCA
Found at i:65247 original size:71 final size:72
Alignment explanation
Indices: 65107--65260 Score: 190
Period size: 71 Copynumber: 2.1 Consensus size: 72
65097 TGGGAATCAT
* *
65107 CACTTAGCAACCCCTCGGGGGAACAGGCGCACATAGCAAGCCCCCTTTTCATTTCAAATATACAA
1 CACTTAGCAACCCCTCGGGGGAACA-G-GCACATAGCAAGCCCCCTTTACATTTCAAAGATACAA
65172 TGGATATCG
64 TGGATATCG
**
65181 CACTTAGCAA-CCCTC-GGGGAATCA-GCACATAGCAA-CCCCCTTTCAACATTTCAAAGATATG
1 CACTTAGCAACCCCTCGGGGGAA-CAGGCACATAGCAAGCCCCCTTT--ACATTTCAAAGATACA
*
65242 GTGGATATCG
63 ATGGATATCG
65252 CACTTAGCA
1 CACTTAGCA
65261 CACCAATGGA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
69 8 0.11
70 11 0.15
71 30 0.42
72 6 0.08
73 7 0.10
74 10 0.14
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAACAGGCACATAGCAAGCCCCCTTTACATTTCAAAGATACAATG
GATATCG
Found at i:65388 original size:104 final size:104
Alignment explanation
Indices: 65187--65390 Score: 308
Period size: 104 Copynumber: 2.0 Consensus size: 104
65177 ATCGCACTTA
65187 GCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCAACATTTCAAAGATATGGTGGATATCG
1 GCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCAACATTTCAAAGATATGGTGGATATCG
* *
65252 CACTTAGCACACCAATGGAACCGGGGAATCAGCACTTTC
66 CACATAGCACACCAATGAAACCGGGGAATCAGCACTTTC
65291 GCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTC-ACATTTCAAAGATATGGT-GATCA
1 GCAA-CCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCAACATTTCAAAGATATGGTGGAT-A
* *
65354 -CGCACATAGCACCACCCAT-AAATCGGGGAATCAGCAC
63 TCGCACATAGCA-CACCAATGAAACCGGGGAATCAGCAC
65391 ACAGCAACCC
Statistics
Matches: 92, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
104 33 0.36
105 30 0.33
106 29 0.32
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
GCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCAACATTTCAAAGATATGGTGGATATCG
CACATAGCACACCAATGAAACCGGGGAATCAGCACTTTC
Done.