Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1010 ID=scaffold_1010-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, 912
Length: 1521
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Found at i:249 original size:132 final size:132
Alignment explanation
Indices: 1--1521 Score: 1947
Period size: 132 Copynumber: 11.5 Consensus size: 132
* * * * *
1 GATCTGCTCCACTACTGCTTAGTGTGACAGAATCTCCAATCTTCAACTTACTCTAGTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* * * * *
66 GGGTGATAGGATTAATGGCTTAAATTTGCTTCTCCATTGTATTGGGAAGATAAGATTCATCATAT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
131 TC
131 TC
* * * * *
133 GATCTGCTCAACTACTGTTTAAGGTGACAGAATCTGTAATATTCAACCTACTCCACTACTGCTCT
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT-T
** ** * * * *
198 -GGGAAATAGGTTTGATGGCTTAAATCTGCTTCTCTACTGTAATGGGTAGATAAGATTCACCATC
65 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATC
262 TTC
130 TTC
* * * *
265 GATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAACCCTCAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* * * * * * * * * *
330 GGGAGATTGGACTAATGGCTTACATTTACTTCTCCACTATCTTGAGAAGA-AATAATTCAACATC
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA-GATTCACCATC
394 TTC
130 TTC
* *
397 GATCCGCTGCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
*
462 GGGTGATAGGACTAATGACTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
527 TC
131 TC
* * * *
529 GATCTACTCCACTGCTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
*
594 GGATGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGGGAAGATAAGATTCACCATC
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTA-TTGGGAAGATAAGATTCACCATC
659 TTC
130 TTC
* * * *
662 GATCTGCAT-CACTACTGGTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACGACTTCTT
1 GATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
* * ** *
726 AGGGTCATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATTATA
65 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATC
791 TTC
130 TTC
* * * * * *
794 GATCTGCTCCACTACTGTTTAGGGCGACAAAATCTGTAATCTTTAACCTACTCCACTACTGCTGA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
** * * *
859 GGGTGATAATACTAATGGCTTAAATCTGCTTCTCCTCTGTATTAGGAAGATAAGATTAACCATCT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
924 TC
131 TC
* * * * * *
926 GATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCGGTAAACCGACTCCACCACTTCTT
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATC-TTCAACCTACTCCACTACTGCTT
* * *
991 AGGTTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGACTCACCATC
65 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATC
1056 TTC
130 TTC
* ** * *
1059 GATCTACTCCTGTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* * * * * *
1124 GGATGATAGGACTAATTGCTTAAGTCTGCTTCTCCACTGTATTGGAAAAATAAGATTCACCATAT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
1189 TC
131 TC
* * * *
1191 GATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCAACTCCACTA-TGGTTT
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTT
* * * *
1255 AGGGAGATAGGATTATTGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATA
65 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATC
1320 TTC
130 TTC
* * * * *
1323 GATCT-CATCCACTATTACATAGGGTGACAGAATGTGTAATCTTCAACCTACT-CATCTACTGCT
1 GATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCA-CTACTGCT
* * * * *
1386 TAGGGTGATTGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGAAAAGATATGACTCACCA
64 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG-GAAGATAAGATTCACCA
1451 TCTTC
128 TCTTC
* * * *
1456 GATCTGTTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTTCAACTTACTCTAGTACTGCTT
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATC-TTCAACCTACTCCACTACTGCTT
1521 A
65 A
Statistics
Matches: 1194, Mismatches: 179, Indels: 30
0.85 0.13 0.02
Matches are distributed among these distances:
131 8 0.01
132 875 0.73
133 290 0.24
134 20 0.02
135 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
TC
Found at i:455 original size:44 final size:44
Alignment explanation
Indices: 406--595 Score: 129
Period size: 44 Copynumber: 4.3 Consensus size: 44
396 CGATCCGCTG
406 CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
1 CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
* * * * * *
450 CACTACTGCTTAGGGTGATAGGA-CT--AATGACTTAAATCTGCTT
1 CACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAACCTACTC
* * * * * * * * * *
493 CTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTACTC
1 CACTACTGCT-TAGGG-TGA-CAGAATCTGCAATCTTCAACCTACTC
* * *
538 CACTGCTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTC
1 CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
582 CACTACTGCTTAGG
1 CACTACTGCTTAGG
596 ATGATAGGAC
Statistics
Matches: 102, Mismatches: 34, Indels: 20
0.65 0.22 0.13
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 26 0.25
44 50 0.49
45 19 0.19
46 1 0.01
47 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (44 bp):
CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
Found at i:850 original size:397 final size:396
Alignment explanation
Indices: 1--1509 Score: 1943
Period size: 397 Copynumber: 3.8 Consensus size: 396
* * * * *
1 GATCTGCTCCACTACTGCTTAGTGTGACAGAATCTCCAATCTTCAACTTACTCTAGTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* * * *
66 GGGTGATAGGATTAATGGCTTAAATTTGCTTCTCCATTGTATTGGGAAGATAAGATTCATCATAT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATAT
* *** * *
131 TCGATCTGCTCAACTACTGTTTAAGGTGACAGAATCTGTAATATTCAACCTACTCCACTACTGCT
131 TCGATCTGCTCCACTACTACATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
* * ** * * * * * *
196 CTGGGA-AATAGGTTTGATGGCTTAAATCTGCTTCTCTACTGTAATGGGTAGATAAGATTCACCA
196 -TAGGATGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGACTCACCA
* * *
260 TCTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAACCCTCAACCTACTCCACTACT
260 TCTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACCACT
* * * * * * * *
325 GCTTAGGGAGAT-TGGACTAATGGCTTACATTTACTTCTCCACTATCTTGAGAAGA-AATAATTC
325 GCTTAGGGTGATAT-GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA-GATTC
*
388 AACATCTTC
388 AACATATTC
* *
397 GATCCGCTGCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* *
462 GGGTGATAGGACTAATGACTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATAT
* * *
527 TCGATCTACTCCACTGCTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
131 TCGATCTGCTCCACTACTACATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
* *
592 TAGGATGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGGGAAGATAAGATTCACCA
196 TAGGATGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTA-TTGGGAAGATAAGACTCACCA
* * *
657 TCTTCGATCTGCAT-CACTACTGGTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACGAC
260 TCTTCGATCTAC-TCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACCAC
* *
721 TTCTTAGGGTCATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA
324 TGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA
**
786 TTATATTC
389 ACATATTC
* * * * * *
794 GATCTGCTCCACTACTGTTTAGGGCGACAAAATCTGTAATCTTTAACCTACTCCACTACTGCTGA
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
** * * * *
859 GGGTGATAATACTAATGGCTTAAATCTGCTTCTCCTCTGTATTAGGAAGATAAGATTAACCATCT
66 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATAT
* * * * * * *
924 TCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCGGTAAACCGACTCCACCACTTC
131 TCGATCTGCTCCACTACTACATAAGGTGACAGAATCTGCAATC-TTCAACCTACTCCACTACTGC
*
989 TTAGGTTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGACTCACCA
195 TTAGGATGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGACTCACCA
** * *
1054 TCTTCGATCTACTCCTGTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACCACT
260 TCTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACCACT
* * * * * * *
1119 GCTTAGGATGATAGGACTAATTGCTTAAGTCTGCTTCTCCACTGTATTGGAAAAATAAGATTCAC
325 GCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAA
1184 CATATTC
390 CATATTC
* * * *
1191 GATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCAACTCCACTA-TGGTTT
1 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTT
* * *
1255 AGGGAGATAGGATTATTGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATA
65 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATA
* * * *
1320 TTCGATCT-CATCCACTATTACATAGGGTGACAGAATGTGTAATCTTCAACCTACT-CATCTACT
130 TTCGATCTGC-TCCACTACTACATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCA-CTACT
* * * *
1383 GCTTAGGGTGATTGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGAAAAGATATGACTCA
193 GCTTAGGATGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGG-GAAGATAAGACTCA
** * *
1448 CCATCTTCGATCTGTTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTTCAACTTACTC
257 CCATCTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAATC-TTCAACCTACTC
1510 TAGTACTGCT
Statistics
Matches: 975, Mismatches: 126, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
395 6 0.01
396 269 0.28
397 627 0.64
398 73 0.07
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (396 bp):
GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATAT
TCGATCTGCTCCACTACTACATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
TAGGATGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGATAAGACTCACCAT
CTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACCACTG
CTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAAC
ATATTC
Done.