Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:4110707 original size:50 final size:50
Alignment explanation
Indices: 4110591--4110887 Score: 332
Period size: 50 Copynumber: 5.8 Consensus size: 50
4110581 GATAATAACA
* * ** * *
4110591 TGCCAAAGTCCATGTCCC-GACATGGTCTGACATGGGATGTTTCATGTAC--
1 TGCCAATG-CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** *
4110640 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
4110690 TGCCCATGCCATGTCCCAGACATGGTCTTAC-TGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCGG
* * *
4110740 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
4110790 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGTTCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA---TCTC--GG
*
4110845 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4110888 TTACCCAAAT
Statistics
Matches: 213, Mismatches: 24, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
48 9 0.04
49 30 0.14
50 126 0.59
51 1 0.00
53 4 0.02
55 2 0.01
56 41 0.19
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:4118135 original size:49 final size:50
Alignment explanation
Indices: 4118062--4118198 Score: 163
Period size: 49 Copynumber: 2.8 Consensus size: 50
4118052 GATAATAACA
* * *
4118062 TGCCAAAGCCATGTCCCAGGTATGGTATTACATGGGATGTT-TCATGTAC-
1 TGCCAATGCCATGTCCCAGATATGGTATTACATGGGATGTTCTCATAT-CG
* * *
4118111 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGA-GTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGATATGGTATTACATGGGATGTTCTCATATC-G
* *
4118161 TGCCAATGCCATGTCCCAGACATGGTGTTACATGGGAT
1 TGCCAATGCCATGTCCCAGATATGGTATTACATGGGAT
4118199 CTCTTTACCC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 37 0.50
50 33 0.45
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGATATGGTATTACATGGGATGTTCTCATATCG
Found at i:4130241 original size:18 final size:18
Alignment explanation
Indices: 4130218--4130271 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
4130208 ATTCTAAAAA
*
4130218 TAATATTATTTTAATAGT
1 TAATATTATATTAATAGT
* *
4130236 TAATATTAAATTAA-ATT
1 TAATATTATATTAATAGT
*
4130253 TAATACTTATCTTAATAGT
1 TAATA-TTATATTAATAGT
4130272 ATTTTATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 7 0.25
18 19 0.68
19 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATATTATATTAATAGT
Found at i:4133965 original size:25 final size:25
Alignment explanation
Indices: 4133919--4133966 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4133909 TTTGAGTGAT
* *
4133919 TTAAATTGGTCTTACTTTAGACAAA
1 TTAAATTGGTCTTACATCAGACAAA
*
4133944 TTAAATTGGTCTTAGATCAGACA
1 TTAAATTGGTCTTACATCAGACA
4133967 CTTTAATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTACATCAGACAAA
Found at i:4133972 original size:25 final size:25
Alignment explanation
Indices: 4133917--4133980 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
4133907 TTTTTGAGTG
* *
4133917 ATTTAAATTGGTCTTACTTTAGACA
1 ATTTAAATTGGTCTTACATCAGACA
* *
4133942 AATTAAATTGGTCTTAGATCAGACA
1 ATTTAAATTGGTCTTACATCAGACA
*
4133967 CTTT-AATTGTGTCT
1 ATTTAAATTG-GTCT
4133981 ATTGTTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAAATTGGTCTTACATCAGACA
Found at i:4136189 original size:54 final size:54
Alignment explanation
Indices: 4136107--4136210 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
4136097 GTTAAGGATT
** *
4136107 CAAATGTCTAATGATTTTTTGAGAAGAGATCCATATCGTGATTCCTATTCGAGC
1 CAAATGTCTAATGATTTCCTGAGAAGAGATCCATATCGAGATTCCTATTCGAGC
*
4136161 CAAATGTCTAATGATTTCCTGAGAAGAGATCTATATCGAGATTCCTATTC
1 CAAATGTCTAATGATTTCCTGAGAAGAGATCCATATCGAGATTCCTATTC
4136211 ATCAAGGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (54 bp):
CAAATGTCTAATGATTTCCTGAGAAGAGATCCATATCGAGATTCCTATTCGAGC
Found at i:4136533 original size:29 final size:29
Alignment explanation
Indices: 4136479--4136536 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4136469 AAAAGAAATT
**
4136479 GAAAGAAAAAGAGAGCTTGAATGAAAAGA
1 GAAAGAAAAAGAGAGCGAGAATGAAAAGA
*
4136508 GAAAGAAAAAGAGTGCGAGCAA-GAAAAGA
1 GAAAGAAAAAGAGAGCGAG-AATGAAAAGA
4136537 ACCTTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.59, C:0.05, G:0.29, T:0.07
Consensus pattern (29 bp):
GAAAGAAAAAGAGAGCGAGAATGAAAAGA
Found at i:4136578 original size:21 final size:22
Alignment explanation
Indices: 4136554--4136594 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4136544 AAAAGAGTTT
4136554 GAGAATGAAA-AAGAGAAAAAG
1 GAGAATGAAAGAAGAGAAAAAG
*
4136575 GAGAGTGAAAGAAGAGAAAA
1 GAGAATGAAAGAAGAGAAAA
4136595 TGTGAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (22 bp):
GAGAATGAAAGAAGAGAAAAAG
Found at i:4136950 original size:23 final size:23
Alignment explanation
Indices: 4136920--4136967 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
4136910 TTGATTGAGA
4136920 AAGGTAAGATCAAAAATGAAATT
1 AAGGTAAGATCAAAAATGAAATT
*
4136943 AAGGTAAGATCAGAAATGAAATT
1 AAGGTAAGATCAAAAATGAAATT
4136966 AA
1 AA
4136968 TCTACAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (23 bp):
AAGGTAAGATCAAAAATGAAATT
Found at i:4137498 original size:35 final size:35
Alignment explanation
Indices: 4137452--4137521 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4137442 GAGAAGGTAA
4137452 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
1 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
*
4137487 GACCAACTTATAACTCTTACTCTGACATTGGTTTC
1 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
4137522 TGCATTCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (35 bp):
GACCAACTTATAACTCCTACTCTGACATTGGTTTC
Found at i:4138208 original size:25 final size:25
Alignment explanation
Indices: 4138180--4138260 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
4138170 ATTGAGTGAT
4138180 TTAAATTGGTCTTAGTTTAGACAAA
1 TTAAATTGGTCTTAGTTTAGACAAA
* *
4138205 TTAAATTGGTCTTAGTTCAGAC-AC
1 TTAAATTGGTCTTAGTTTAGACAAA
* *
4138229 TTTAATTGTGTCTATTGTTTAGACAAA
1 TTAAATTG-GTCT-TAGTTTAGACAAA
4138256 TTAAA
1 TTAAA
4138261 GTGCGTCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 8 0.17
25 25 0.54
26 8 0.17
27 5 0.11
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:4141653 original size:18 final size:18
Alignment explanation
Indices: 4141625--4141666 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4141615 AATTAGAATG
*
4141625 TAAAAATTAAA-TTAAAA
1 TAAAAATTAAAGTAAAAA
4141642 TAAAATATTAAAGTAAAAA
1 TAAAA-ATTAAAGTAAAAA
4141661 TAAAAA
1 TAAAAA
4141667 AGGCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAATTAAAGTAAAAA
Found at i:4144882 original size:137 final size:137
Alignment explanation
Indices: 4144636--4144910 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
4144626 CCTAAATTCA
*
4144636 ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
1 ATTTTCTCTCTCCTCCAACACGAGAACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
*
4144701 GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAACTTGAGATGATTAAAT
66 ATTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAACTTGAGATGATTAAAT
4144766 ATGGCGG
131 ATGGCGG
4144773 ATTTTCTCTCTCCTCCAACACGAGAACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
1 ATTTTCTCTCTCCTCCAACACGAGAACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
* *
4144838 ATTCTATTGATTTCACTAACATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
66 ATTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAACTTGAGATGATTAAAT
4144903 ATGGCGG
131 ATGGCGG
4144910 A
1 A
4144911 AAGGACCTAG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (137 bp):
ATTTTCTCTCTCCTCCAACACGAGAACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
ATTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAACTTGAGATGATTAAAT
ATGGCGG
Found at i:4145336 original size:18 final size:17
Alignment explanation
Indices: 4145313--4145355 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4145303 TTTTAATTAA
4145313 ATAAATATCG-TTTTATAT
1 ATAAATAT-GATTTTAT-T
4145331 ATAAATATGATTTTATT
1 ATAAATATGATTTTATT
*
4145348 TTAAATAT
1 ATAAATAT
4145356 AATAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
ATAAATATGATTTTATT
Found at i:4149125 original size:17 final size:18
Alignment explanation
Indices: 4149103--4149136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4149093 TAATAAATTA
4149103 AATATA-TTGAAATTATC
1 AATATAGTTGAAATTATC
*
4149120 AATATAGTTTAAATTAT
1 AATATAGTTGAAATTAT
4149137 TTAAGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
AATATAGTTGAAATTATC
Found at i:4149422 original size:19 final size:18
Alignment explanation
Indices: 4149393--4149446 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
4149383 GGATCAAATT
*
4149393 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
4149411 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
4149430 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
4149447 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:4150862 original size:39 final size:39
Alignment explanation
Indices: 4150817--4150894 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
4150807 AAATGCAAAC
* *
4150817 ATGTTATGATGCATGGGCCTATGGTATAAATTCTATGAT
1 ATGTTATGATGCATAGGCCTATGGTATAAATTCAATGAT
* *
4150856 ATGTTATGATGGATAGGCCTTTGGTATAAATTCAATGAT
1 ATGTTATGATGCATAGGCCTATGGTATAAATTCAATGAT
4150895 TGCCAGTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.38
Consensus pattern (39 bp):
ATGTTATGATGCATAGGCCTATGGTATAAATTCAATGAT
Found at i:4161927 original size:46 final size:46
Alignment explanation
Indices: 4161856--4162004 Score: 271
Period size: 46 Copynumber: 3.2 Consensus size: 46
4161846 ACCACTTATC
* *
4161856 CCTACTTTTCACAACTCAGTGTGGTTTTCTTCACCGAAACACCATA
1 CCTACTTTTCATAACTCAGTATGGTTTTCTTCACCGAAACACCATA
*
4161902 CCTACTTTTCATAACTCAATATGGTTTTCTTCACCGAAACACCATA
1 CCTACTTTTCATAACTCAGTATGGTTTTCTTCACCGAAACACCATA
4161948 CCTACTTTTCATAACTCAGTATGGTTTTCTTCACCGAAACACCATA
1 CCTACTTTTCATAACTCAGTATGGTTTTCTTCACCGAAACACCATA
4161994 CCTACTTTTCA
1 CCTACTTTTCA
4162005 CACTTTGCCA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.35
Consensus pattern (46 bp):
CCTACTTTTCATAACTCAGTATGGTTTTCTTCACCGAAACACCATA
Done.