Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3362
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: 52837
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1114 original size:39 final size:39
Alignment explanation
Indices: 1051--1265 Score: 328
Period size: 39 Copynumber: 5.5 Consensus size: 39
1041 TCGGATGGAA
* *
1051 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATA-T
1091 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1130 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1169 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
*
1208 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-CTATAT
*
1248 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGT-CCGAAGG
1266 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
39 130 0.77
40 38 0.23
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:1263 original size:118 final size:118
Alignment explanation
Indices: 1051--1265 Score: 330
Period size: 118 Copynumber: 1.8 Consensus size: 118
1041 TCGGATGGAA
* *
1051 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGA
*
1116 GCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
66 GCGAGTTACTATATCCGGGCTAAATCCGAAGGCATTTGTGCGAGTTACTATAT
*
1169 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAGT-CCGAAGGCATTT
1232 GAGCGAG-TAGCTATATCC-GGCTAAATCCCGAAGG
64 GAGCGAGTTA-CTATATCCGGGCTAAAT-CCGAAGG
1266 TACTTGGTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
116 2 0.02
117 43 0.48
118 44 0.49
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (118 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGA
GCGAGTTACTATATCCGGGCTAAATCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:9202 original size:39 final size:40
Alignment explanation
Indices: 9050--9262 Score: 317
Period size: 40 Copynumber: 5.4 Consensus size: 40
9040 TGGTAACCGA
* *
9050 GCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGG
*
9090 GCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
9130 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
9170 GCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* * *
9209 GCTAAGTCCCAAAGGCATTTGAGTGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
*
9248 GCTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
9263 TACTTGGTTT
Statistics
Matches: 161, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 54 0.34
40 106 0.66
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:9243 original size:79 final size:80
Alignment explanation
Indices: 9050--9262 Score: 303
Period size: 79 Copynumber: 2.7 Consensus size: 80
9040 TGGTAACCGA
*
9050 GCTAAGTCCCGAAGGCATTTGTGCT-AGT-GACTA-ATTCCGGGCTAAGTCCTGAAGGCATTTGT
1 GCTAAGTCCCGAAGGCATTTGTG-TGAGTAG-CTATA-TCCGGGCTAAGTCCCGAAGGCATTTGT
9112 GCGAGTTACTATATCCGG
63 GCGAGTTACTATATCCGG
*
9130 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGGCA-TTGTGC
1 GCTAAGTCCCGAAGGCATTTGTGTGAG-TAGCTATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
9193 GAGTTACTATATCCGG
65 GAGTTACTATATCCGG
* * *
9209 GCTAAGTCCCAAAGGCATTTGAGTGAGTAGCTATATCC-GGCTAAATCCCGAAGG
1 GCTAAGTCCCGAAGGCATTTGTGTGAGTAGCTATATCCGGGCTAAGTCCCGAAGG
9263 TACTTGGTTT
Statistics
Matches: 122, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
78 17 0.14
79 54 0.44
80 49 0.40
81 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
GCTAAGTCCCGAAGGCATTTGTGTGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCG
AGTTACTATATCCGG
Found at i:11576 original size:40 final size:40
Alignment explanation
Indices: 11497--11673 Score: 209
Period size: 40 Copynumber: 4.5 Consensus size: 40
11487 CGGATGATAA
* * * *
11497 CCGGACTAAGATCCGAAGGCATTCGTGCAAGTT-TCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGT-TATAT
* * * *
11537 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
11577 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
11617 CAGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
11657 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
11674 ATACTTGGGT
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.01
39 14 0.12
40 100 0.85
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:13143 original size:12 final size:12
Alignment explanation
Indices: 13126--13150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13116 CGATCGAGGA
13126 ATGAATCTGATG
1 ATGAATCTGATG
13138 ATGAATCTGATG
1 ATGAATCTGATG
13150 A
1 A
13151 GGAGGATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATGAATCTGATG
Found at i:17225 original size:43 final size:42
Alignment explanation
Indices: 17141--17285 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 42
17131 GTTTGTTTGA
* * * **
17141 AAAAAAG-GCCGCTAAAGATCATGACTTTTAGCGACGCTTTTT
1 AAAAAAGCGCCACTAAAGACCAGGACTTTTAGCGGTG-TTTTT
*
17183 ATAAAAA-CACCACTAAAGACCAGGACTTTTAGCGGTGTTTTTT
1 A-AAAAAGCGCCACTAAAGACCAGGACTTTTAGCGGTG-TTTTT
* * * **
17226 AAAAAAGCGCCGCGAATGACCAGGACCATTAGCGGTGTTTTT
1 AAAAAAGCGCCACTAAAGACCAGGACTTTTAGCGGTGTTTTT
17268 AGAAAAAGCGCCACTAAA
1 A-AAAAAGCGCCACTAAA
17286 AGTCATGATC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
42 12 0.14
43 71 0.86
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (42 bp):
AAAAAAGCGCCACTAAAGACCAGGACTTTTAGCGGTGTTTTT
Found at i:24291 original size:49 final size:49
Alignment explanation
Indices: 24070--24769 Score: 1108
Period size: 49 Copynumber: 14.6 Consensus size: 49
24060 CCCTTCGGGA
* * * *
24070 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
24117 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
24164 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24211 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24258 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24307 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24354 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24403 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTACGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA-GGC
*
24451 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24498 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24547 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24594 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
24643 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
24692 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
24741 CTTATCACATATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
24770 TATTCAAATA
Statistics
Matches: 620, Mismatches: 22, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 272 0.44
48 45 0.07
49 302 0.49
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:24308 original size:96 final size:96
Alignment explanation
Indices: 24070--24769 Score: 1146
Period size: 96 Copynumber: 7.3 Consensus size: 96
24060 CCCTTCGGGA
* * * * *
24070 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
24133 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24164 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
24227 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
24258 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
24323 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
24354 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
24419 ACTTTCACATTCATCACATCGGCCATTACGGC
66 ACTTTCACATTCATCACATCGGCCATTA-GGC
24451 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
* *
24514 ACACTTTCACATTCATCACATTGGCCATTCGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24547 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
24610 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
24643 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
*
24708 ACACTTTCACATTCATCACATTGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
24741 CTTATCACATATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
24770 TATTCAAATA
Statistics
Matches: 573, Mismatches: 24, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
93 1 0.00
94 91 0.16
95 47 0.08
96 275 0.48
97 45 0.08
98 114 0.20
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:24316 original size:22 final size:22
Alignment explanation
Indices: 24288--24363 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
24278 TTTCACATTC
24288 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
24310 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
24334 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
24357 ATCACAT
1 ATCACAT
24364 ATATATACAC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:27872 original size:40 final size:40
Alignment explanation
Indices: 27817--28078 Score: 411
Period size: 40 Copynumber: 6.6 Consensus size: 40
27807 TATTCGGATG
27817 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
27857 ATAACCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
27897 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
27937 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
27977 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
28017 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* *
28057 ATATCC-GGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
28079 TACTTGGTTT
Statistics
Matches: 207, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
39 17 0.08
40 190 0.92
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:32750 original size:19 final size:19
Alignment explanation
Indices: 32728--32765 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32718 ATTTAAAAAA
32728 ATTTATAGTAAAA-TTGTTG
1 ATTT-TAGTAAAATTTGTTG
*
32747 ATTTTGGTAAAATTTGTTG
1 ATTTTAGTAAAATTTGTTG
32766 TTAAGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (19 bp):
ATTTTAGTAAAATTTGTTG
Found at i:34908 original size:21 final size:21
Alignment explanation
Indices: 34871--34910 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34861 CTTGTTCGAC
*
34871 AATGATTCGACAGTGATTTGT
1 AATGATTCCACAGTGATTTGT
34892 AATGATTCCACTA-TGATTT
1 AATGATTCCAC-AGTGATTT
34911 AGTATTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
AATGATTCCACAGTGATTTGT
Found at i:35130 original size:47 final size:48
Alignment explanation
Indices: 35023--35153 Score: 174
Period size: 47 Copynumber: 2.8 Consensus size: 48
35013 GTGCGAGTTA
** * * ** *
35023 TACCTTGATTCAGCTACGGGCCATGGTATAGGTATTTTGGAGAGGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGGAGAGAAGT
* *
35071 TACCTTGATTTGGCTACAGGCCGTGGTATAGGTACTCCGG-GATAAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGGAGAGAAGT
35118 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
35154 TATCGATTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 40 0.55
48 33 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (48 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGGAGAGAAGT
Done.