Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_977 ID=scaffold_977-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: 33164
ACGTcount: A:0.01, C:0.01, G:0.01, T:0.02
Warning! 31384 characters in sequence are not A, C, G, or T
Found at i:333 original size:132 final size:133
Alignment explanation
Indices: 1--967 Score: 1374
Period size: 132 Copynumber: 7.3 Consensus size: 133
* *
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
* *
66 ATATTCGATCTGCTCCACTAC-TGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
66 ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
130 CTG
131 CTG
133 CTTAGGGTGGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCAC
1 CTTAGGGT-GATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * * *
198 CATCTTCGATCTGCTCCAGTACAT-CTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAGT
65 CATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
262 ACTG
130 ACTG
* *
266 CTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
* * * * * *
331 ATCTTCGATCTCCTCCGCTA-TTACTTAGGCTGACAGAATCTGTAATCTTCAACTTACTCCACTA
66 ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
*
395 CTT
131 CTG
* * * * *
398 CTTAGGTTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCATC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
** * * *
463 ATAGTCGATCTGCACCACTAC-TGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACCA
66 ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
*
527 TTG
131 CTG
* *
530 CTTAGGGTGGTAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGGTAAGATTCACC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
* * * * *
595 ATCTTCGATCTGCTGCAGTACAT-CTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAGTA
66 ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
659 CTG
131 CTG
* *
662 CTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
* * * *
727 ATCATCGATCTCCTCCACTA-TTGCTTAGGCTGACAGAATCTGCAATCTTTCAGCCTACTCCACT
66 ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATC-TTCAACCTACTCCACT
791 ACTG
130 ACTG
* * *
795 CTGAGGGTGATAGGACTAATTGCTT-AATCTGCTTCTCCACTTGTATTGGGGAAGATAAGATTCA
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCAC-TGTATT-GGGAAGATAAGATTCA
* *
859 CCAACTTCGATCTCCTCCACTA-TTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
64 CCATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
*
923 TACTT
129 TACTG
* * * *
928 CTTACGATGATAGGACTAAAGGCTTAATATCTGCTTCTCC
1 CTTAGGGTGATAGGACTAATGGCTTAA-ATCTACTTCTCC
968 GCTGNNNNNN
Statistics
Matches: 743, Mismatches: 81, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
131 2 0.00
132 458 0.62
133 207 0.28
134 64 0.09
135 12 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (133 bp):
CTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCACC
ATCTTCGATCTGCTCCACTACTTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
CTG
Found at i:741 original size:396 final size:397
Alignment explanation
Indices: 1--967 Score: 1600
Period size: 396 Copynumber: 2.4 Consensus size: 397
*
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
*
66 ATATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAC
66 ATATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAT
131 TGCTTAGGGTGGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTC
131 TGCTTAGGGTGG-TAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTC
196 ACCATCTTCGATCTGCTCCAGTACATCTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAG
195 ACCATCTTCGATCTGCTCCAGTACATCTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAG
261 TACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGAT
260 TACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGAT
* * * *
326 TCACCATCTTCGATCTCCTCCGCTATTACTTAGGCTGACAGAATCTGTAATC-TTCAACTTACTC
325 TCACCATCATCGATCTCCTCCACTATTACTTAGGCTGACAGAATCTGCAATCTTTCAACCTACTC
*
390 CACTACTT
390 CACTACTG
* * * *
398 CTTAGGTTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCATC
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
* * *
463 ATAGTCGATCTGCACCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACCAT
66 ATATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAT
*
528 TGCTTAGGGTGGTAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGGTAAGATTCA
131 TGCTTAGGGTGGTAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCA
*
593 CCATCTTCGATCTGCTGCAGTACATCTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAGT
196 CCATCTTCGATCTGCTCCAGTACATCTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAGT
658 ACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATT
261 ACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATT
* *
723 CACCATCATCGATCTCCTCCACTATTGCTTAGGCTGACAGAATCTGCAATCTTTCAGCCTACTCC
326 CACCATCATCGATCTCCTCCACTATTACTTAGGCTGACAGAATCTGCAATCTTTCAACCTACTCC
788 ACTACTG
391 ACTACTG
* *
795 CTGAGGGTGATAGGACTAATTGCTT-AATCTGCTTCTCCACTTGTATTGGGGAAGATAAGATTCA
1 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC-TGTATT-GGGAAGATAAGATTCA
* * *
859 CCA-ACTTCGATCTCCTCCACTATTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
64 CCATA-TTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
* * * * *
923 TACTT-CTTACGATGATAGGACTAAAGGCTTAATATCTGCTTCTCC
128 TA-TTGCTTAGGGTGGTAGGACTAATGGCTTAA-ATCTACTTCTCC
968 GCTGNNNNNN
Statistics
Matches: 529, Mismatches: 35, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
396 242 0.46
397 178 0.34
398 96 0.18
399 13 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (397 bp):
CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
ATATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAT
TGCTTAGGGTGGTAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATTCA
CCATCTTCGATCTGCTCCAGTACATCTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCAGT
ACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGATT
CACCATCATCGATCTCCTCCACTATTACTTAGGCTGACAGAATCTGCAATCTTTCAACCTACTCC
ACTACTG
Found at i:32514 original size:88 final size:88
Alignment explanation
Indices: 32377--32563 Score: 295
Period size: 88 Copynumber: 2.1 Consensus size: 88
32367 CTTCAACCTA
* * *
32377 CTCCACTACTGTTTAGGGTGATAGGACTAATGACTTAAACCTGCTTCTCCATTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGAGATAGGACTAATGACTTAAACCTGCTTCTCCACTGTATTGGGAAGA
* *
32442 TAAGATTTACCATCTTCGATCTG
66 TAAGAATCACCATCTTCGATCTG
* *
32465 CTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGAGATAGGACTAATGACTTAAACCTGCTTCTCCACTGTATTGGGAAGA
32530 TAAGAATCACCATCTTCGATCTG
66 TAAGAATCACCATCTTCGATCTG
32553 CAT-CACTACTG
1 C-TCCACTACTG
32564 GTTAAGGTGA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 90 0.99
89 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (88 bp):
CTCCACTACTGCTTAGGGAGATAGGACTAATGACTTAAACCTGCTTCTCCACTGTATTGGGAAGA
TAAGAATCACCATCTTCGATCTG
Found at i:32705 original size:132 final size:131
Alignment explanation
Indices: 32465--33164 Score: 920
Period size: 132 Copynumber: 5.3 Consensus size: 131
32455 CTTCGATCTG
*
32465 CTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTA-GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* * * * *
32530 TAAGAATCACCATCTTCGATCTGCAT-CACTACTGGTTAAGGTGACAGAATCTGCAATATTCAAC
65 TAAGATTCACCATATTCGATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAAC
*
32594 CGA
129 CTA
* * *
32597 CTCCACTACTACTTAGGATGATAGGACTAATGGCTTAAATCTGCCTCTCCACTGTTTTGGGAAGA
1 CTCCACTACTGCTTAGG-TGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* * * *
32662 TAAGATTCACCATCTTCGATCTGCTCCACTACTCCTTAGGGTGACAAAATCTGCAAGCTTCAACC
65 TAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
32727 TA
130 TA
* * * *
32729 CTCTAGTACTGCTTAAGGTGA-ATGGACAAATGGCTTAAATCTGTTTCTCCACTGTATTGGGAAG
1 CTCCACTACTGCTT-AGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
* ** * *
32793 ATAAGATTCATCGGATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAACCTTCAAC
64 ATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAAC
32858 CTA
129 CTA
* *
32861 CTCCAGTACTGCTTAACGTGA-ATGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
1 CTCCACTACTGCTT-AGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
* * * * * *
32925 AGAAGATTCATCATATTCGATCTACTCAACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAAC
64 ATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAAC
32990 CTA
129 CTA
* * *
32993 CTCCACTACTGTTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCTCTGTATTAGGAAGA
1 CTCCACTACTGCTTA-GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* * * * * *
33058 TAAGATTAACCATTTTCGATCTGCTCCATTACTACTTAGGGTGACAGAATTTGCAATCTTGAACC
65 TAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
*
33123 GA
130 TA
*
33125 CTCCACTACTTCTTACGGTGATAGGACTAATGGCTTAAAT
1 CTCCACTACTGCTTA-GGTGATAGGACTAATGGCTTAAAT
Statistics
Matches: 503, Mismatches: 59, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
131 5 0.01
132 494 0.98
133 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (131 bp):
CTCCACTACTGCTTAGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAT
AAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCT
A
Done.