Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3501
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: 39339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2180 original size:45 final size:45
Alignment explanation
Indices: 2098--2227 Score: 134
Period size: 45 Copynumber: 2.9 Consensus size: 45
2088 ACCAGGAGTG
* * * * * *
2098 AGTAAGACCATAGCTGAAACATACTATGCCATAATGATGATAATA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * *
2143 AGTAAGACCATAGCTGAAAGATGCTACGATATCATGATAAAAATG
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * * * *
2188 AGTAAGACAATAGTTGAAAGACGCTATGGCATAATGATAA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAA
2228 GGGTGAGTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
Found at i:3276 original size:17 final size:17
Alignment explanation
Indices: 3254--3297 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3244 TCTGATACCA
* *
3254 ATGGCGGATACCTATCT
1 ATGGCGAATACCTATCC
3271 ATGGCGAATACCTATCC
1 ATGGCGAATACCTATCC
3288 ATGGCGAATA
1 ATGGCGAATA
3298 GTTTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (17 bp):
ATGGCGAATACCTATCC
Found at i:12518 original size:35 final size:35
Alignment explanation
Indices: 12472--12542 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
12462 TTTAACCTTA
*
12472 AAAAAAAACTTTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
*
12507 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
12542 A
1 A
12543 TCACCCTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.21
Consensus pattern (35 bp):
AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
Found at i:13517 original size:3 final size:3
Alignment explanation
Indices: 13506--13648 Score: 104
Period size: 3 Copynumber: 48.7 Consensus size: 3
13496 TGATGATAGC
* * *
13506 AAT AGT AAT AAT -AT AAT AAT AA- AGT AGAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * *
13550 AAT AAT AAT ACGTT AAT AAG AAT AAT AAT AGT -AT ATT AAT AAT AAC
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
13596 AAT AAT AGA- AAGT AAT GAT AA- AAT AAT AA- AA- AAT AAT AAT AAT
1 AAT AAT A-AT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13639 AAT AA- AAT AA
1 AAT AAT AAT AA
13649 AGAATAGTGC
Statistics
Matches: 110, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
2 13 0.12
3 91 0.83
4 4 0.04
5 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13568 original size:20 final size:20
Alignment explanation
Indices: 13542--13639 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
13532 GAAAATAATA
13542 ATAATAATAATAATAATACGT
1 ATAATAATAATAATAATA-GT
*
13563 -TAATAAGAATAATAATAGT
1 ATAATAATAATAATAATAGT
* * *
13582 ATATTAATAATAACAATAAT
1 ATAATAATAATAATAATAGT
* * *
13602 AGAAAGTAATGATAA-AATAAT
1 A-TAA-TAATAATAATAATAGT
*
13623 A-AAAAATAATAATAATA
1 ATAATAATAATAATAATA
13640 ATAAAATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.11
19 8 0.13
20 32 0.51
21 8 0.13
22 8 0.13
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
ATAATAATAATAATAATAGT
Found at i:13573 original size:23 final size:23
Alignment explanation
Indices: 13540--13647 Score: 91
Period size: 23 Copynumber: 4.9 Consensus size: 23
13530 TAGAAAATAA
*
13540 TAATAATAATAATAATAATACGT
1 TAATAATAATAATAATAATACAT
* * *
13563 TAATAAGAATAATAATAGTATAT
1 TAATAATAATAATAATAATACAT
* *
13586 TAATAATAACAATAATAGA-A-AG
1 TAATAATAATAATAATA-ATACAT
* * *
13608 TAATGATAA-AATAATAA-AAAA
1 TAATAATAATAATAATAATACAT
13629 TAATAATAATAATAA-AATA
1 TAATAATAATAATAATAATA
13648 AAGAATAGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.03
21 18 0.26
22 15 0.21
23 35 0.50
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (23 bp):
TAATAATAATAATAATAATACAT
Found at i:13725 original size:21 final size:21
Alignment explanation
Indices: 13669--13732 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
13659 CAACAATAAC
* *
13669 ATAAATAGTAATAG-AAAAACA
1 ATAAA-AGTAATAGTAATAATA
* * *
13690 ATAATAGAAACAGTAATAATA
1 ATAAAAGTAATAGTAATAATA
13711 ATAAAAGTAATAGTAATAATA
1 ATAAAAGTAATAGTAATAATA
13732 A
1 A
13733 ATGATTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAAAAGTAATAGTAATAATA
Found at i:18189 original size:10 final size:10
Alignment explanation
Indices: 18168--18196 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18158 GATTCTAAGG
18168 TTTTCG-TTT
1 TTTTCGTTTT
18177 TTTTCGTTTT
1 TTTTCGTTTT
18187 TTTTCGTTTT
1 TTTTCGTTTT
18197 AATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (10 bp):
TTTTCGTTTT
Found at i:21964 original size:44 final size:44
Alignment explanation
Indices: 21893--22430 Score: 343
Period size: 44 Copynumber: 11.7 Consensus size: 44
21883 TCATTCTTAC
* * *
21893 CCACTGCAACTTCAGAGG-TATAGGATTTGTCGCTTCAATCTGCT
1 CCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTCAATCTGCT
* * * * * *
21937 TCATTGCAACTTTAGAGAGATAAGATTTGTCATCTTCAATCTTCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGT-AGCTTCAATCTGCT
* *
21982 CCACTGCAACTTTAGGGAGATAAGATCTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT
* *
22026 CCACTGCAACTTCAGGGGGATAAGATTTGTAGCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT
* * *
22070 CCACTGCAACTTCAGGGAGATAAGATTTGTGACTTATAGCTTTAATCAGTT
1 CCACTGCAACTTCAGGGAGATAAGA-TT-TG-----TAGCTTCAATCTGCT
* * * * *
22121 CCACTGCAACTTCAAGGAAATAAGACTCGTTATGGTAGATTTAATCCGAC-
1 CCACTGCAACTTCAGGGAGATAAGA----TT-T-GTAGCTTCAATCTG-CT
** * * *
22171 CCACTATAACTTTAGAGG-TATAAGATTTGTCA-CTTTAATCTGCT
1 CCACTGCAACTTCAG-GGAGATAAGATTTGT-AGCTTCAATCTGCT
* * *
22215 CCACTGCAACTTCAGGGAGATTAGATTTGTAACTTGTAGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGA-TA-A---G--ATTTGTAGCTTCAATCTGCT
* * * * * * *
22266 CTACTGCAACTTTAGGAAAATAAGATTCGCTATCTTCAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCT
* * * * **
22311 CCACTACAACTTCAGGGAGATAAGTTTTGTAGCTTTAACCTTTT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT
* *
22355 CCACTGCAACTTCA--G-GATAAGATTCGCCATGGTAACTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATT-----T-GTAGCTTCAATCTGCT
22402 CCACTGCAACTTCAGGGAGATAAGATTTG
1 CCACTGCAACTTCAGGGAGATAAGATTTG
22431 CTATGGTGAC
Statistics
Matches: 388, Mismatches: 70, Indels: 72
0.73 0.13 0.14
Matches are distributed among these distances:
41 8 0.02
42 1 0.00
43 4 0.01
44 149 0.38
45 79 0.20
46 7 0.02
47 25 0.06
49 3 0.01
50 40 0.10
51 68 0.18
54 3 0.01
55 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT
Found at i:22048 original size:89 final size:88
Alignment explanation
Indices: 21893--22430 Score: 284
Period size: 89 Copynumber: 5.8 Consensus size: 88
21883 TCATTCTTAC
* * * * * * *
21893 CCACTGCAACTTCAGAGG-TATAGGATTTGTCGCTTCAATCTGCTTCATTGCAACTTTAGAGAGA
1 CCACTGCAACTTCAG-GGAGATAAGATCTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGA
* *
21957 TAAGATTTGTCATCTTCAATCTTCT
65 TAAGATTTGT-AGCTTCAATCTACT
* * *
21982 CCACTGCAACTTTAGGGAGATAAGATCTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGGGAT
1 CCACTGCAACTTCAGGGAGATAAGATCTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGAT
22047 AAGATTTGTAGCTTCAATCTACT
66 AAGATTTGTAGCTTCAATCTACT
* * * *
22070 CCACTGCAACTTCAGGGAGATAAGATTTGTGACTTATAGCTTTAATCAGTTCCACTGCAACTTCA
1 CCACTGCAACTTCAGGGAGATAAGA----T--C-TGTAGCTTCAATCTGCTCCACTGCAACTTCA
* * * *
22135 -AGGAAATAAGACTCGTTATGGTAGATTTAATCCGAC-
59 GA-GAGATAAGA----TT-T-GTAGCTTCAAT-CTACT
** * * * * *
22171 CCACTATAACTTTAGAGG-TATAAGATTTGTCA-CTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAG-GGAGATAAGATCTGT-AGCTTCAATCTGCTCCACTGCAACTTCAGAGAG
* * **
22234 ATTAGATTTGTAACTTGTAGCTTTAATCTGTT
64 A-TA-A---G--ATTTGTAGCTTCAATCTACT
* * * * * * * *
22266 CTACTGCAACTTTAGGAAAATAAGAT-TCGCTATCTTCAATCTGTTCCACTACAACTTCAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATCT-G-TAGCTTCAATCTGCTCCACTGCAACTTCAGAGAG
* * * **
22330 ATAAGTTTTGTAGCTTTAACCTTTT
64 ATAAGATTTGTAGCTTCAATCTACT
* *
22355 CCACTGCAACTTCA--G-GATAAGATTCGCCATGGTAACTTCAATCTACTCCACTGCAACTTCAG
1 CCACTGCAACTTCAGGGAGATAAGA-T---C-T-GTAGCTTCAATCTGCTCCACTGCAACTTCAG
*
22417 GGAGATAAGATTTG
60 AGAGATAAGATTTG
22431 CTATGGTGAC
Statistics
Matches: 352, Mismatches: 60, Indels: 72
0.73 0.12 0.15
Matches are distributed among these distances:
86 6 0.02
87 1 0.00
88 38 0.11
89 89 0.25
91 40 0.11
92 3 0.01
94 34 0.10
95 70 0.20
96 32 0.09
97 2 0.01
99 3 0.01
100 1 0.00
101 28 0.08
102 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (88 bp):
CCACTGCAACTTCAGGGAGATAAGATCTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGAT
AAGATTTGTAGCTTCAATCTACT
Found at i:22131 original size:51 final size:51
Alignment explanation
Indices: 22055--22430 Score: 192
Period size: 51 Copynumber: 7.9 Consensus size: 51
22045 ATAAGATTTG
* **
22055 TAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* * * * * * **
22106 TAGCTTTAATCAGTTCCACTGCAACTTCAAGGAAATAAGACTCGTTA-TGG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* * ** ** * *
22156 TAGATTTAATCCGACCCACTATAACTTTAGAGG-TATAAGATTTGT--C---
1 TAGCTTTAATCTGTTCCACTGCAACTTCAG-GGAGATAAGATTTGTGACTTA
* * * *
22202 -A-CTTTAATCTGCTCCACTGCAACTTCAGGGAGATTAGATTTGTAACTTG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* * * * *
22251 TAGCTTTAATCTGTTCTACTGCAACTTTAGGAAAATAAGA-TT-CG-C-TA
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* *
22298 T--CTTCAATCTGTTCCACTACAACTTCAGGGAGATAAG-TTT-TG-----
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* * * ** **
22340 TAGCTTTAACCTTTTCCACTGCAACTTCA--G-GATAAGATTCGCCA-TGG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
* * **
22387 TAACTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTG
22431 CTATGGTGAC
Statistics
Matches: 243, Mismatches: 60, Indels: 45
0.70 0.17 0.13
Matches are distributed among these distances:
41 6 0.02
42 4 0.02
43 2 0.01
44 52 0.21
45 34 0.14
46 1 0.00
47 26 0.11
48 1 0.00
49 1 0.00
50 45 0.19
51 71 0.29
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (51 bp):
TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTA
Done.