Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_979 ID=scaffold_979-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: 1753
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Found at i:242 original size:132 final size:132
Alignment explanation
Indices: 1--1753 Score: 2670
Period size: 132 Copynumber: 13.2 Consensus size: 132
* *
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCGACTACTAC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
*
66 TTTGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
131 TC
131 TC
* * * **
133 TTCTATCTGCTCCACTACTGCTTAGGGTGACAGAATTTGCAATCTTCAACCTACTTAACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * *
198 TTAAGGTGATAGGACTAATGGCTTAAATCTGTTTCTCCACTGTATTAGGAAGATAAGATT-AGCC
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA-CC
262 ATC
130 ATC
* * *
265 TTTGATCTGCTCCACAACTGATTAGTGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
330 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
395 TC
131 TC
* * * * * * *
397 TTCGATCTCCTCCACTA-TTACTT-GGTTGATAGAATCTTCAATCCTCAACGTACTCCACTACTG
1 TTCGATCTGCTCCACTACTGA-TTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
**
460 CTTAGGGTGATAGGTGTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
65 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
525 ATC
130 ATC
* * * *
528 GTCGATCTGCTCCACCACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
*
593 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAACA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
658 TC
131 TC
* * * * * * * *
660 TTCGATCTCCTCCACTA-TTACTTAGGTTGATAGCATCTTCAATCCTCAACGTACTCCACTACTG
1 TTCGATCTGCTCCACTACTGA-TTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
* **
724 CTTAGGGTGATAAGTTTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
65 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
789 ATC
130 ATC
* * *
792 TTCGATCTGCTCCACTACCT-CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAGTACTT
1 TTCGATCTGCTCCACTA-CTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
* * * * *
856 CTTAGGGTGATAGGAATAATGGCTTAAATTTCCTTCTCCATTGTATTGGGAAGATAAGATTCATC
65 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
*
921 ATA
130 ATC
* * * *
924 TTCGATCTGCTCCACTACTGTTTAAGGTGACAGAATCTGCTATCTTCAACCTACTACACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* *
989 TTAGGGAGATAGGTCTAATGGCTTTAAAATCTGCTTCTCCCACTGTATTGGGAAGATAAGATTCA
66 TTAGGGTGATAGGACTAATGGC-TT-AAATCTGCTTCT-CCACTGTATTGGGAAGATAAGATTCA
1054 CCATC
128 CCATC
* *
1059 TTCGATCTACTCCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
1 TTCGATCTGCT-CCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
* * * * *
1124 CTTAGGGAGATTGGACATAATGGCTTAAATATGTTTCTCCACTGTATTGGGAAGATAAGATTCAT
65 CTTAGGGTGATAGGAC-TAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* *
1189 CGTA
129 CATC
1193 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * *
1258 TTAGGGTGATAGGACTAACGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTAACCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
1323 TC
131 TC
** *
1325 TTTAATCTGCTCCACTACTGATTAGGGTGACAAAATCTGCAATCTTCAACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
1390 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
1455 TC
131 TC
1457 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * *
1522 TTAGGGTCATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
1587 TC
131 TC
* * *
1589 TTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTAATCCACTACTAC
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * *
1654 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTCGGAAGATAAGATTAAGCA
66 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
*
1719 TA
131 TC
*
1721 TTTGATCTGCTCCACTACTGATTAGGGTGACAG
1 TTCGATCTGCTCCACTACTGATTAGGGTGACAG
Statistics
Matches: 1469, Mismatches: 138, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
131 122 0.08
132 1109 0.75
133 69 0.05
134 49 0.03
135 48 0.03
136 65 0.04
137 7 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (132 bp):
TTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
TC
Found at i:1265 original size:44 final size:44
Alignment explanation
Indices: 1197--1662 Score: 199
Period size: 44 Copynumber: 10.6 Consensus size: 44
1187 ATCGTATTCG
*
1197 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCA
* * * * * ** *
1241 ACCTACTCCACTACTGCTTAGGGTGATAGGA-CTAACGGT-TTAA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCT-ACAATCTTCA
* * * * * * *
1284 ATCTGCTTCTCCACTGTATT-GGGAAGATA-AGAT-TAACCATCTTTA
1 ATCTGCTCCACTACTG-ATTAGGG-TGACAGA-ATCT-ACAATCTTCA
* *
1329 ATCTGCTCCACTACTGATTAGGGTGACAAAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCA
* * * * * *
1373 ACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAAT--CTTCA
* * * * * * * *
1416 ATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTC-ACCATCTTCG
1 ATCTGCTCCACTACTG-ATTAGGG-TGA-CAGAATCTACAATCTTCA
*
1461 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCA
* * * * * * *
1505 ACCTACTCCACTACTGCTTAGGGTCATAGGA-CT--AATGGCTTAA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAAT--CTTCA
* * * ** * * **
1548 ATCTGCTTCTCCACTGTATTAGGAAGATA-AGAT-TAACCATCTTTG
1 ATCTGCTCCACTACTG-ATTAGGGTGACAGA-ATCT-ACAATCTTCA
*
1593 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCA
* **
1637 ACCTAATCCACTACT-ACTTAGGGTGA
1 ATCTGCTCCACTACTGA-TTAGGGTGA
1663 TAGGACTAAT
Statistics
Matches: 302, Mismatches: 90, Indels: 60
0.67 0.20 0.13
Matches are distributed among these distances:
41 6 0.02
43 62 0.21
44 169 0.56
45 60 0.20
46 1 0.00
47 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCA
Found at i:1429 original size:665 final size:659
Alignment explanation
Indices: 5--1753 Score: 2689
Period size: 665 Copynumber: 2.6 Consensus size: 659
1 TTCG
* * *
5 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCGACTACTACTTTG
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
70 GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTT
66 GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTT
* * **
135 CTATCTGCTCCACTACTGCTTAGGGTGACAGAATTTGCAATCTTCAACCTACTTAACTACTGCTT
131 CGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
* *
200 AAGGTGATAGGACTAATGGCTTAAATCTGTTTCTCCACTGTATTAGGAAGATAAGATTAGCCATC
196 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTA-CCATC
*
265 TTTGATCTGCTCCACAACTGATT-AGTGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
260 TTTGATCTGCTCCACTACTGATTAAG-GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
329 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
324 CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
* * * * * * *
394 ATCTTCGATCTCCTCCACTATTACTT-GGTTGATAGAATCTTCAATCCTCAACGTACTCCACTAC
389 ATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCCTCAACCTACTCCACTAC
* ** *
458 TGCTTAGGGTGATAGGTGTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA
454 TGCTTAGGGAGATAGGCATAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCA
* *
523 CCATCGTCGATCTGCTCCACCACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
519 CCATAGTCGATCTGCTCCACCACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
*
588 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT
584 ACTGCTTAGGGTGATAGGACTAACGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT
*
653 CAACATCTTCG
649 CAACATCTTCA
* * * * * * * *
664 ATCTCCTCCACTA-TTACTTAGGTTGATAGCATCTTCAATCCTCAACGTACTCCACTACTGCTTA
1 ATCTGCTCCACTACTGA-TTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
* **
728 GGGTGATAAGTTTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
65 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT
* *
793 TCGATCTGCTCCACTACCT-CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAGTACTTC
130 TCGATCTGCTCCACTA-CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * * * * *
857 TTAGGGTGATAGGAATAATGGCTTAAATTTCCTTCTCCATTGTATTGGGAAGATAAGATTCATCA
194 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATT-ACCA
* * * * *
922 TATTCGATCTGCTCCACTACTGTTTAAGGTGACAGAATCTGCTATCTTCAACCTACTACACTACT
258 TCTTTGATCTGCTCCACTACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
* *
987 GCTTAGGGAGATAGGTCTAATGGCTTTAAAATCTGCTTCTCCCACTGTATTGGGAAGATAAGATT
323 GCTTAGGGTGATAGGACTAATGGC-TT-AAATCTGCTTCT-CCACTGTATTGGGAAGATAAGATT
*
1052 CACCATCTTCGATCTACTCCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCC
385 CACCATCTTCGATCTACT-CCACTACTGCTTAGGGTGACAGAATCTGCAATCCTCAACCTACTCC
* *
1117 ACTACTGCTTAGGGAGATTGGACATAATGGCTTAAATATGTTTCTCCACTGTATTGGGAAGATAA
449 ACTACTGCTTAGGGAGATAGG-CATAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAA
* * * * *
1182 GATTCATCGTATTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTAC
513 GATTCACCATAGTCGATCTGCTCCACCACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTAC
*
1247 TCCACTACTGCTTAGGGTGATAGGACTAACGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGAT
578 TCCACTACTGCTTAGGGTGATAGGACTAACGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAT
*
1312 AAGATT-AACCATCTTTA
643 AAGATTCAA-CATCTTCA
*
1329 ATCTGCTCCACTACTGATTAGGGTGACAAAATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
1394 GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTT
66 GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTT
*
1459 CGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
131 CGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
*
1524 AGGGTCATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATC
196 AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATT-ACCATC
* * *
1589 TTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTAATCCACTACTAC
260 TTTGATCTGCTCCACTACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGC
* * *
1654 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTCGGAAGATAAGATTAAGCA
325 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* * * *
1719 TATTTGATCTGCTCCACTACTGATTAGGGTGACAG
390 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAG
Statistics
Matches: 976, Mismatches: 101, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
658 2 0.00
659 300 0.31
660 7 0.01
661 33 0.03
662 77 0.08
663 22 0.02
664 53 0.05
665 480 0.49
666 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (659 bp):
ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTT
CGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
AGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTACCATCT
TTGATCTGCTCCACTACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
CTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCCTCAACCTACTCCACTACTG
CTTAGGGAGATAGGCATAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCACC
ATAGTCGATCTGCTCCACCACTGATTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAC
TGCTTAGGGTGATAGGACTAACGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA
ACATCTTCA
Done.