Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_139 ID=scaffold_139-JGI_221_v2.0
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: 11294
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.31
Warning! 125 characters in sequence are not A, C, G, or T
Found at i:1014 original size:22 final size:23
Alignment explanation
Indices: 981--1039 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
971 AGAATGATAC
*
981 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
1002 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
1026 GTGATAAATTTAAA
1 ATGATAAATTTAAA
1040 CAACATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:2693 original size:50 final size:50
Alignment explanation
Indices: 2546--2707 Score: 157
Period size: 50 Copynumber: 3.2 Consensus size: 50
2536 TAACTCGTAA
* * * *
2546 CTTTAATCTGTTTAACTGAAATGTCGGGGAAGTAAGATTCGCTGTTATGG
1 CTTTAATCTGTTTAACTGCAATGTCTGGGAAGTAAGATTCGCTGTTGTAG
** ** **
2596 CTTTAATCTGTTCCACTGCACCG-CTTAAGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTAACTGCAATGTC-TGGGAAGTAAGATTCGCTGTTGTAG
* * * *
2646 CTTTAATCTTTTTAACTGCAATGTCTGGGAAGCAAGATTCACCGTTGT-G
1 CTTTAATCTGTTTAACTGCAATGTCTGGGAAGTAAGATTCGCTGTTGTAG
*
2695 ACGTTAATCTGTT
1 -CTTTAATCTGTT
2708 CCACTGTACC
Statistics
Matches: 87, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.02
50 84 0.97
51 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (50 bp):
CTTTAATCTGTTTAACTGCAATGTCTGGGAAGTAAGATTCGCTGTTGTAG
Found at i:2732 original size:100 final size:100
Alignment explanation
Indices: 2546--2738 Score: 253
Period size: 100 Copynumber: 1.9 Consensus size: 100
2536 TAACTCGTAA
* * * * *
2546 CTTTAATCTGTTTAACTGAAATGTCGGGGAAGTAAGATTCGCTGTTATGGCTTTAATCTGTTCCA
1 CTTTAATCTGTTTAACTGAAATGTCGGGGAAGCAAGATTCACCGTTATGACGTTAATCTGTTCCA
* *
2611 CTGCACCGCTTAAGAAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCTCAAGAAATAAGATTCGCTGTTGTAG
* * * *
2646 CTTTAATCTTTTTAACTGCAATGTCTGGGAAGCAAGATTCACCGTTGTGACGTTAATCTGTTCCA
1 CTTTAATCTGTTTAACTGAAATGTCGGGGAAGCAAGATTCACCGTTATGACGTTAATCTGTTCCA
* *
2711 CTGTACCGC-CAGGGAAATAAGATTCGCT
66 CTGCACCGCTCA-AGAAATAAGATTCGCT
2739 ATTCTCAGTC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 78 0.99
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (100 bp):
CTTTAATCTGTTTAACTGAAATGTCGGGGAAGCAAGATTCACCGTTATGACGTTAATCTGTTCCA
CTGCACCGCTCAAGAAATAAGATTCGCTGTTGTAG
Found at i:3273 original size:131 final size:132
Alignment explanation
Indices: 2963--3800 Score: 827
Period size: 131 Copynumber: 6.3 Consensus size: 132
2953 TCCGCCATCC
*
2963 TCGATCTGCTCCACTACTT-CTTAGGGAGATAAGATCTGTAATCTT-CAATCTATTCCACTGCTG
1 TCGATCTGCTCCACTA-TTGCTTAGGGAGATAAGATCTGTAAT-TTCCAACCTATTCCACTGCTG
* * * * * * * ** * *
3026 -CCCAGGGATATA-GAATTACTGGCTTCAATGTAC-TCCACTA-TAACCACAGGG-AGGTAA-AA
64 ACTCAGGGAGATAGGACTT-GTGGCTTAAATCTGCTTCC-CTACT--CC-TGGGGAAGATAAGAT
**
3085 TCTGCCATCT
124 TC-GCTGTCT
* * * * *
3095 TCTATCTACTCCACTACTGCTTAGGGAGATAAGATCTG-AAATCCCAACCTATTCCACTGCTGAC
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
*
3159 -CAGGGAGATAGGACTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
66 TCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
3223 CT
131 CT
* **
3225 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTGGTTTCCAACCTATTCCACTGCTG-C
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
* * * *
3289 TCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGT
66 TCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
3354 CT
131 CT
* * * * *
3356 TCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAA--TCTTCAACCTGCTCC
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCA-CTGCT-G
* ** ** * *
3419 ACTACAATCGAGGAAGGCA-AGG-CTTGTGCCTTCGATCTGCTTCGCCGT-CGAC-GCAGGAAGG
64 ACT-C-A--G-GG-A-G-ATAGGACTTGTGGCTTAAATCTGCTTC-CC-TACTCCTG-GGGAAGA
* *
3480 TGAGA-TCTGCTATCT
118 TAAGATTC-GCTGTCT
* * * *
3495 TCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTG-AAATCCCAACCTATTCCACTGCTGAC
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
* * * *
3559 -CAGGGAGATAGGACTTGCGGCTTAAATCTGCTTCCATACTCCTAGGGAAGATAAGATTCACTGT
66 TCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
3623 CT
131 CT
*
3625 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTG-C
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
* * * **
3689 TCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTATTCCTGGGGAAGATAAGATTCGCCAT
66 TCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
3754 CT
131 CT
*
3756 TCGATCTGTTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTC
1 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTC
3801 TAATCTTCAA
Statistics
Matches: 583, Mismatches: 89, Indels: 69
0.79 0.12 0.09
Matches are distributed among these distances:
129 10 0.02
130 111 0.19
131 312 0.54
132 46 0.08
133 2 0.00
134 1 0.00
135 1 0.00
136 2 0.00
137 2 0.00
138 29 0.05
139 60 0.10
140 7 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (132 bp):
TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
TCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCTGT
CT
Found at i:3559 original size:400 final size:400
Alignment explanation
Indices: 3084--3909 Score: 1418
Period size: 400 Copynumber: 2.1 Consensus size: 400
3074 GGGAGGTAAA
* * *
3084 ATCTGCCATCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAAATCCCAACCTATTC
1 ATCTGCTATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTGAAATCCCAACCTATTC
* * *
3149 CACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAG
66 CACTGCTGACCAGGGAGATAGGACTTGCGGCTTAAATCTACTTCCATACTCCTAGGGAAGATAAG
* *
3214 ATTCGCTGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTGGTTTCCAACCTATT
131 ATTCACTGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTAGTTTCCAACCTATT
3279 CCACTGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAA
196 CCACTGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAA
*
3344 GATTCGCCGTCTTCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAATCTTC
261 GATTCGCCATCTTCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAATCTTC
* * * *
3409 AACCTGCTCCACTACAATCGAGGAAGGCAAGGCTTGTGCCTTCGATCTGCTTCGCCGTCGACGCA
326 AACCTGCTCCACTACAACCGAGGAAGGCAAGACTTGTACCTTCGATCTGCTTCACCGTCGACGCA
*
3474 GGAAGGTGAG
391 GGAAGGCGAG
*
3484 ATCTGCTATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGAAATCCCAACCTATTC
1 ATCTGCTATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTGAAATCCCAACCTATTC
*
3549 CACTGCTGACCAGGGAGATAGGACTTGCGGCTTAAATCTGCTTCCATACTCCTAGGGAAGATAAG
66 CACTGCTGACCAGGGAGATAGGACTTGCGGCTTAAATCTACTTCCATACTCCTAGGGAAGATAAG
*
3614 ATTCACTGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATT
131 ATTCACTGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTAGTTTCCAACCTATT
* *
3679 CCACTGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTATTCCTGGGGAAGATAA
196 CCACTGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAA
* * * *
3744 GATTCGCCATCTTCGATCTGTTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCTAATCTTC
261 GATTCGCCATCTTCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAATCTTC
*
3809 AACCTGCTCCACTACAACCGAGGGAGGCAAGACTTGTACCTTCGATCTGCTTCACCGTCGACGCA
326 AACCTGCTCCACTACAACCGAGGAAGGCAAGACTTGTACCTTCGATCTGCTTCACCGTCGACGCA
3874 GGAAGGCGAG
391 GGAAGGCGAG
* *
3884 ATCTGCTATCTTCAACCTACTCCACT
1 ATCTGCTATCTTCGATCTACTCCACT
3910 GCAACGAGGG
Statistics
Matches: 399, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
400 399 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (400 bp):
ATCTGCTATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTGAAATCCCAACCTATTC
CACTGCTGACCAGGGAGATAGGACTTGCGGCTTAAATCTACTTCCATACTCCTAGGGAAGATAAG
ATTCACTGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTAGTTTCCAACCTATT
CCACTGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAA
GATTCGCCATCTTCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAATCTTC
AACCTGCTCCACTACAACCGAGGAAGGCAAGACTTGTACCTTCGATCTGCTTCACCGTCGACGCA
GGAAGGCGAG
Found at i:3861 original size:269 final size:262
Alignment explanation
Indices: 3092--3795 Score: 779
Period size: 269 Copynumber: 2.7 Consensus size: 262
3082 AAATCTGCCA
* * * * *
3092 TCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGATCTG-AAATCCCAACCTATTCCACTGCT
1 TCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCT
* *
3156 GAC-CAGGGAGATAGGACTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCGC
66 G-CTCAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGC
* * *
3220 TGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGACCTGTGGTT--TCCAACCTATTCCAC
130 TATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT-ATTAATCCAACCTATTCCAC
** * * *
3283 TGCTGCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATT
194 TGCAAC-CAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCATACTCCTAGGGAAGATAAGATT
*
3348 CGCCG
258 CACCG
* * *
3353 TCTTCAATATGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAA--TCTTCAACCTGC
1 TCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCA-CTGC
* * ** ** *
3416 TCCACTACAATCGAGGAAGGCA-AGG-CTTGTGCCTTCGATCTGCTTCGCCGT-CGAC-GCAGGA
65 T--GCT-C-A--G-GGAA---ATAGGACTTGTGGCTTAAATCTGCTTC-CC-TACTCCTG-GGGA
* * * *
3477 AGGTGAGA-TCTGCTATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTG-A--AATC
117 AGATAAGATTC-GCTATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTATTAAT-
* *
3538 CCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGCGGCTTAAATCTGCTTCCATACTCCTA
180 CCAACCTATTCCACTGC-AACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCATACTCCTA
*
3603 GGGAAGATAAGATTCACTG
244 GGGAAGATAAGATTCACCG
* *
3622 TCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
1 TCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCT
* * *
3687 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTATTCCTGGGGAAGATAAGATTCGCC
66 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCT
*
3752 ATCTTCGATCTGTTCCACTATTGCTTAGGGAGATAAGATCTGTA
131 ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTA
3796 ATTTCTAATC
Statistics
Matches: 362, Mismatches: 52, Indels: 57
0.77 0.11 0.12
Matches are distributed among these distances:
260 7 0.02
261 98 0.27
262 29 0.08
263 4 0.01
264 2 0.01
265 1 0.00
266 1 0.00
267 2 0.01
268 6 0.02
269 142 0.39
270 63 0.17
271 7 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (262 bp):
TCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCT
GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCT
ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTATTAATCCAACCTATTCCACTG
CAACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCATACTCCTAGGGAAGATAAGATTCAC
CG
Found at i:4005 original size:87 final size:88
Alignment explanation
Indices: 3803--4016 Score: 261
Period size: 87 Copynumber: 2.5 Consensus size: 88
3793 GTAATTTCTA
* * * * *
3803 ATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGACTTGTACCTTCGATCTGCTTCACCGTC
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTCCACCATC
* *
3868 GACGCAGGAAGGCGAGATCTGCT
66 GACGCAGGAAGGCAAGATCCGCT
* * * *
3891 ATCTTCAACCTACTCCACTGCAA-CGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTCCACTATT
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTCCACCATC
** *
3955 G-CTTAGGGAGGCAAGATCCGCT
66 GACGCAGGAAGGCAAGATCCGCT
* * *
3977 ATTTTTAATCTGCTCCACTGCAACCGAGGGAGGCAAGGCT
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCT
4017 TTGTTTTCGA
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
86 35 0.33
87 51 0.48
88 21 0.20
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (88 bp):
ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTCCACCATC
GACGCAGGAAGGCAAGATCCGCT
Found at i:5269 original size:16 final size:17
Alignment explanation
Indices: 5248--5280 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5238 TTAGCCTCTC
5248 CATTTTAC-TTTTTCAT
1 CATTTTACATTTTTCAT
*
5264 CATTTTTCATTTTTCAT
1 CATTTTACATTTTTCAT
5281 TCACTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
CATTTTACATTTTTCAT
Found at i:6298 original size:30 final size:29
Alignment explanation
Indices: 6213--6303 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
6203 CATTTTCATA
*
6213 TTTTTATTTTGACTTTGATTGATTTC-TCTT
1 TTTTTATTTTGACTTTGATT--TTTCTTTTT
**
6243 TTTTGCTTTTGACTTTGATTTTTTCTTTTGT
1 TTTTTATTTTGACTTTGA-TTTTTCTTTT-T
*
6274 TTTTTATTTTGATTTTGATTTTTCTTTTT
1 TTTTTATTTTGACTTTGATTTTTCTTTTT
6303 T
1 T
6304 GAATCTGAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
29 6 0.12
30 28 0.54
31 18 0.35
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.73
Consensus pattern (29 bp):
TTTTTATTTTGACTTTGATTTTTCTTTTT
Done.