Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2824
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: 54285
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7076 original size:27 final size:27
Alignment explanation
Indices: 7046--7246 Score: 251
Period size: 27 Copynumber: 7.4 Consensus size: 27
7036 TGAGTCCGCT
* * * *
7046 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
7073 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
7100 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
7128 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
7155 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
7182 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
7209 CACTTAGTGCTACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
7236 CACTTAGTGCT
1 CACTTAGTGCT
7247 GTACAATTTA
Statistics
Matches: 153, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 129 0.84
28 24 0.16
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:14305 original size:28 final size:27
Alignment explanation
Indices: 14265--14461 Score: 243
Period size: 27 Copynumber: 7.2 Consensus size: 27
14255 CCGCTAACTC
* * *
14265 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* *
14292 AGTGGCTACGTAATCAAATCGCACACTT
1 AGT-GCTACATAGTCAAATCGCACACTT
14320 AGTGCTACATAGTCAAACTCGCACACTT
1 AGTGCTACATAGTCAAA-TCGCACACTT
** * *
14348 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* **
14375 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAGTCAAATCGCACACTT
*
14402 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
14429 AGTGCTACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
14456 AGTGCT
1 AGTGCT
14462 GTACAATTTA
Statistics
Matches: 149, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
27 101 0.68
28 48 0.32
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (27 bp):
AGTGCTACATAGTCAAATCGCACACTT
Found at i:14859 original size:28 final size:27
Alignment explanation
Indices: 14828--15016 Score: 177
Period size: 28 Copynumber: 6.8 Consensus size: 27
14818 TAAATTGTAC
14828 AGCACTAAGTGTGCGATTTGGACTATGT
1 AGCACTAAGTGTGCGATTT-GACTATGT
14856 AGCACTAAGTGTGCGATTTGGAACTATGTT
1 AGCACTAAGTGTGCGATTT-G-ACTATG-T
* ** *
14886 GGCACTAAGTGGTGCGAAATGAATATGAT
1 AGCACTAAGT-GTGCGATTTGACTATG-T
* *
14915 GGCACTAAGTGTGCGAATTGAC-ATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
*
14940 GGCACTAAGTGTGGCGAGTTTTGACTATGT
1 AGCACTAAGTGT-GCGA--TTTGACTATGT
* *
14970 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
14997 AGGAC-AAGTGTGCGAGTTGA
1 AGCACTAAGTGTGCGATTTGA
15017 TTATATAGGC
Statistics
Matches: 140, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
25 12 0.09
26 18 0.13
27 16 0.11
28 36 0.26
29 29 0.21
30 22 0.16
31 7 0.05
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:15025 original size:26 final size:26
Alignment explanation
Indices: 14976--15025 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
14966 ATGTAGCACT
* *
14976 AAGTGTGCGATTTGATTACGTAGGAC
1 AAGTGTGCGAGTTGATTACATAGGAC
*
15002 AAGTGTGCGAGTTGATTATATAGG
1 AAGTGTGCGAGTTGATTACATAGG
15026 CAACTGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (26 bp):
AAGTGTGCGAGTTGATTACATAGGAC
Found at i:22132 original size:27 final size:27
Alignment explanation
Indices: 22102--22302 Score: 251
Period size: 27 Copynumber: 7.4 Consensus size: 27
22092 TAAATTGTAC
22102 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
22129 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
22156 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
22182 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
22210 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
22238 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
22265 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
22292 AGCACTGAGTG
1 AGCACTAAGTG
22303 AGCGGACTCA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29663 original size:10 final size:10
Alignment explanation
Indices: 29643--29682 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
29633 TAAGTATTTG
29643 AAAAAACATTC
1 AAAAAA-ATTC
29654 AAAAAAATTC
1 AAAAAAATTC
*
29664 AAAAAAATTA
1 AAAAAAATTC
29674 AAAAAAATT
1 AAAAAAATT
29683 ATTATTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:30204 original size:46 final size:46
Alignment explanation
Indices: 30152--30243 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
30142 ACAAAGAAAA
30152 GACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATG
1 GACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATG
* *
30198 GACCTCGACCCACTATCAAGGATGATAGGATCCTTGGTATATGATG
1 GACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATG
30244 AACGCCACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (46 bp):
GACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATG
Found at i:33856 original size:40 final size:40
Alignment explanation
Indices: 33808--34114 Score: 560
Period size: 40 Copynumber: 7.7 Consensus size: 40
33798 GCAAACACAT
* *
33808 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
33848 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
33888 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
33928 TTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
33968 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
34008 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
34048 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
34088 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
34115 ATCCAATGTT
Statistics
Matches: 257, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 257 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:42704 original size:40 final size:40
Alignment explanation
Indices: 42656--42966 Score: 561
Period size: 40 Copynumber: 7.8 Consensus size: 40
42646 GCAAACACAT
* *
42656 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
42696 TTGCCTTC-GGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42735 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42775 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42815 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42855 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42895 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42935 TTGCCTTCGGGTCTTAGCCCGGATATAATCAA
1 TTGCCTTCGGGTCTTAGCCCGGATAT-ATCAA
42967 TGTTCACGCA
Statistics
Matches: 261, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
39 35 0.13
40 221 0.85
41 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:46741 original size:40 final size:40
Alignment explanation
Indices: 46634--46934 Score: 465
Period size: 40 Copynumber: 7.7 Consensus size: 40
46624 AACATTGGAT
46634 TATATCCGGGCTAAGACCCGAAGGCAA-T-TGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46672 TATATCC-GGCT-AGA-CCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46709 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
46749 TATATCCGGGCTAAGACCCTGAAGGCGATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCC-GAAGGCAATTATGCGAGTTGA
* *
46790 CATATCGGGGCTAAGA--CGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
46828 TATA-CCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46867 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
46907 TATGTCCGGGTTAAGACCCGAAGGCAAT
1 TATATCCGGGCTAAGACCCGAAGGCAAT
46935 GTGTTTGCGG
Statistics
Matches: 240, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
35 10 0.04
36 4 0.02
37 30 0.12
38 34 0.14
39 28 0.12
40 100 0.42
41 34 0.14
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:46848 original size:118 final size:117
Alignment explanation
Indices: 46634--46934 Score: 448
Period size: 118 Copynumber: 2.6 Consensus size: 117
46624 AACATTGGAT
* *
46634 TATATCCGGGCTAAGACCCGAAGGCAAT-TGCGAGTTGATATATCCGGCT-AGACCGAAGGCAAT
1 TATATCCGGGCTAAGACCCGAAGGCATTATGCGAGTTGATATATCGGGCTAAGACCGAAGGCAAT
*
46697 TATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
66 TATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
*
46749 TATATCCGGGCTAAGACCCTGAAGGCGATTATGCGAGTTGACATATCGGGGCTAAGA-CGAAGGC
1 TATATCCGGGCTAAGACCC-GAAGGC-ATTATGCGAGTTGATATATC-GGGCTAAGACCGAAGGC
* *
46813 AATTATGCGAGTTGATATA-CCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
63 AATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
* *
46867 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATGTCCGGGTTAAGACCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTATGCGAGTTGATATAT-CGGGCTAAGA-CCGAAGGC
46932 AAT
63 AAT
46935 GTGTTTGCGG
Statistics
Matches: 168, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
115 19 0.11
116 6 0.04
117 33 0.20
118 67 0.40
119 40 0.24
120 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (117 bp):
TATATCCGGGCTAAGACCCGAAGGCATTATGCGAGTTGATATATCGGGCTAAGACCGAAGGCAAT
TATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
Found at i:46922 original size:158 final size:154
Alignment explanation
Indices: 46635--46931 Score: 472
Period size: 158 Copynumber: 1.9 Consensus size: 154
46625 ACATTGGATT
46635 ATATCCGGGCTAAGACCCGAAGGCAATTGCGAGTTGATATATCCGGCTAGACCGAAGGCAATTAT
1 ATATCCGGGCTAAGA-CCGAAGGCAATTGCGAGTTGATATATCCGGCTAGACCGAAGGCAATTAT
*
46700 GCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGA
65 GCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGA
46765 CCCTGAAGGCGATTATGCGAGTTGAC
130 CCC-GAAGGCGATTATGCGAGTTGAC
*
46791 ATATCGGGGCTAAGA-CGAAGGCAATTATGCGAGTTGATATA-CCGGGCTATGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCGAAGGCAA-T-TGCGAGTTGATATATCC-GGCTA-GA-CCGAAGGCAA
* * *
46854 TTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATGTCCGGGTT
61 TTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCT
46919 AAGACCCGAAGGC
126 AAGACCCGAAGGC
46932 AATGTGTTTG
Statistics
Matches: 131, Mismatches: 5, Indels: 9
0.90 0.03 0.06
Matches are distributed among these distances:
154 9 0.07
155 3 0.02
156 33 0.25
157 8 0.06
158 78 0.60
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (154 bp):
ATATCCGGGCTAAGACCGAAGGCAATTGCGAGTTGATATATCCGGCTAGACCGAAGGCAATTATG
CGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGAC
CCGAAGGCGATTATGCGAGTTGAC
Done.