Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4641.1
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: 50009
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.30
Warning! 1160 characters in sequence are not A, C, G, or T
Found at i:9976 original size:119 final size:120
Alignment explanation
Indices: 9794--10016 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
9784 TCCTCGTTCA
* *
9794 AATGTCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
*
9859 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTCGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
9914 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
9976 ATATGGTCACTTCGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTCGCACAAAGCCTTCGGGACTTAACCCGGA
10017 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTCGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:10016 original size:40 final size:40
Alignment explanation
Indices: 9792--10016 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
9782 GCTCCTCGTT
* * *
9792 CAAATGTCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9832 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9872 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9912 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * *
9951 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
9992 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
10017 CATCATTCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 118 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:17347 original size:26 final size:26
Alignment explanation
Indices: 17287--17350 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
17277 TACATCGTTT
* * *
17287 CTCACACAAGCTATGAAATGAGTCTA
1 CTCACACGAGCTATGAAATGAGCCAA
* *
17313 CTTACACGAGCTATGAAATGGGCCAA
1 CTCACACGAGCTATGAAATGAGCCAA
*
17339 CTCATACGAGCT
1 CTCACACGAGCT
17351 GTGGGTCAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (26 bp):
CTCACACGAGCTATGAAATGAGCCAA
Found at i:20321 original size:49 final size:49
Alignment explanation
Indices: 20244--20488 Score: 276
Period size: 49 Copynumber: 4.9 Consensus size: 49
20234 TAGCCGAAGC
* * *
20244 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * *
20293 TATAC-GGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAAC
1 TAT-CTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * *
20343 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* * * * *
20394 TTTCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * *
20443 TATCTAGTACACGTAGTAGCCTACACTTAGTATTACACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
20489 TCACAATAGC
Statistics
Matches: 162, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
49 78 0.48
50 47 0.29
51 37 0.23
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:20481 original size:100 final size:101
Alignment explanation
Indices: 20257--20486 Score: 281
Period size: 100 Copynumber: 2.3 Consensus size: 101
20247 CTGGTACGCA
* * * * * * *
20257 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTAT-ACGGTACACGTAGTAGCCTACAC
1 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTTTCA-GGTACGCATAGTAGCCTACAC
*
20319 TTAGTACTACACACGTGACCTAACCATCTGATACACG
65 TTAGTACTACACACGCGACCTAACCATCTGATACACG
* *
20356 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTTTCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTTTCAGGTACGCATAGTAGCCTACACT
* **
20421 TAGTACTACACATGCGACC-AATTATCT-AGTACACG
66 TAGTACTACACACGCGACCTAACCATCTGA-TACACG
*
20456 TAGTAGCCTACACTTAGTATTACACACGTGA
1 TAGTAGCCTACACTTAGTACTACACACGTGA
20487 CCTCACAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
99 30 0.26
100 44 0.39
101 39 0.34
102 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTTTCAGGTACGCATAGTAGCCTACACT
TAGTACTACACACGCGACCTAACCATCTGATACACG
Found at i:26218 original size:27 final size:27
Alignment explanation
Indices: 26188--26239 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
26178 GGAAGGCCCT
26188 CATTCCTGCTTCAGCCACTTATGACAC
1 CATTCCTGCTTCAGCCACTTATGACAC
26215 CATTCCTGCTTCAGCCACTTATGAC
1 CATTCCTGCTTCAGCCACTTATGAC
26240 CCCAGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.37, G:0.12, T:0.31
Consensus pattern (27 bp):
CATTCCTGCTTCAGCCACTTATGACAC
Found at i:33483 original size:52 final size:52
Alignment explanation
Indices: 33423--33527 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
33413 TCTTTCATTC
*
33423 ATGGTCTTACTCATCATACTTAGCTACCCTAACATCTTTCATCTATGGTTTT
1 ATGGTCTTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
*
33475 ATGGTCTTACTCATCATACTTGGCTACCATAACATCTTTCATCTATGGTTTT
1 ATGGTCTTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
33527 A
1 A
33528 CACCGACTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (52 bp):
ATGGTCTTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
Found at i:37136 original size:50 final size:50
Alignment explanation
Indices: 36922--37199 Score: 349
Period size: 48 Copynumber: 5.7 Consensus size: 50
36912 TGAGATTCCA
* * *
36922 TGTAAGACCATGTCTAGGACATGGCATTGGC-AT-CTGA-GTATGTGCCTA-
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATAAT-ATGTATGTGCC-AG
*
36970 TGTAAGACCATGTCTGGGACATGGCATCGGTGATAATATGTA--TGCCTA-
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATGTATGTGCC-AG
* * *
37018 TGTAAGACCATGTTTGGGACATGGCATCAGCGATAATATGTA--TGCCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATGTATGTGCCAG
* * *
37066 TGTAAGACCATGTCTAGGACATGGCATTGGCGATAATATATATGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATGTATGTGCCAG
* *
37116 TGTAAGACCATGTCTGGGACATGGCATCGGTGATAATATATATGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATGTATGTGCCAG
*
37166 TGTAAGATCATGTCTGGGACATGGCATCGGCGAT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGAT
37200 GATGTGTGGA
Statistics
Matches: 205, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
48 114 0.56
49 3 0.01
50 88 0.43
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATGTATGTGCCAG
Found at i:41126 original size:39 final size:38
Alignment explanation
Indices: 41074--41149 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
41064 ATGCCAACGT
* * *
41074 CCCAGACATGGTCTTACATGTAATCAAATATCGATGCCG
1 CCCAGACAGGGTCTTACACGAAATCAAATAT-GATGCCG
* *
41113 CCCAGATAGGGTCTTACACGAAATCATATATGATGCC
1 CCCAGACAGGGTCTTACACGAAATCAAATATGATGCC
41150 AATGTCCCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (38 bp):
CCCAGACAGGGTCTTACACGAAATCAAATATGATGCCG
Found at i:41201 original size:44 final size:41
Alignment explanation
Indices: 41072--41218 Score: 149
Period size: 44 Copynumber: 3.5 Consensus size: 41
41062 CAATGCCAAC
* *
41072 GTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCC--
1 GTCCCAGACATGGTCTTACACGTAATCATA-ATCGATGCCAT
* * *
41112 G-CCCAGATAGGGTCTTACACGAAATCATATAT-GATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAATCATA-ATCGATGCC-AT
*
41153 GTCCCAGACATGGTTTTACACGTGAATCATAAGTCGATGCCGAT
1 GTCCCAGACATGGTCTTACACGT-AATCATAA-TCGATGCC-AT
*
41197 GTCCCAGACGTGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
41219 ATATCACACC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
38 6 0.07
39 26 0.30
40 1 0.01
41 1 0.01
42 18 0.20
43 8 0.09
44 28 0.32
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACACGTAATCATAATCGATGCCAT
Found at i:43103 original size:37 final size:36
Alignment explanation
Indices: 43052--43159 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
43042 ATTCCAAAAA
*
43052 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATAT
*
43088 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATAT
*
43125 TAACCTAATTATCTTAA-ATTTTAAT-TTAATTTAAT
1 TAA--T-ATTATCTTAATAGTTTAATATTAATTTAAT
43160 GTTTAAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 13 0.21
37 32 0.52
38 5 0.08
39 10 0.16
40 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATAT
Done.