Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1731
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: 1961
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Found at i:362 original size:24 final size:24
Alignment explanation
Indices: 330--379 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
320 ATTGATTCTT
330 ATAACAATCTCCACTCTTTTCGAG
1 ATAACAATCTCCACTCTTTTCGAG
354 ATAACAATCTCCACTCTTTTCGAG
1 ATAACAATCTCCACTCTTTTCGAG
378 AT
1 AT
380 TGGGAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (24 bp):
ATAACAATCTCCACTCTTTTCGAG
Found at i:1241 original size:474 final size:474
Alignment explanation
Indices: 3--1961 Score: 3037
Period size: 474 Copynumber: 4.0 Consensus size: 474
1 AG
* * *
3 AAAACATGAATAGACGCAC--ATCCGCA-TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCT
1 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
65 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
66 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
* * * *
130 AAGTCTAGGTTTGTGCCTCAAATGTGCCAAACATGGATTGTAGTAGTGATCTACTTCACGTTGTG
131 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
195 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
196 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
260 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
261 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTG-
325 TTCTTATAACAATCTCCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
325 -----------A--T----TC---TC---ATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
* *
390 AAACACAGTCCTTTCAGTAGGACACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
367 AAACACAGTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
* *
455 TGAACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGA
432 TCAACCATTTTCGACAGAATCAAAGTTTATCTCTTAAATAAGA
* *
498 AAAACATGAATGGACATACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
1 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
563 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
66 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
628 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
131 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
693 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
196 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
* * *
758 AAATCTTTTCTGTGCCCTATTTTCCTTAAAGTGAAAGTTCCTTCCTTAAATAAGGCAAGCTTTGA
261 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
* * * * *
823 TTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCATTCCTTTCAATAGGATA
326 TTCTCATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGGATA
* * *
888 CACGACATTGACGCTTTAATGTCGCAAGAAAACCATTTCTTTCAACCGTTTTTGACAGAATCAAA
391 CACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCATTTTCGACAGAATCAAA
*
953 GTTTGTCTCTTAAATAAGA
456 GTTTATCTCTTAAATAAGA
*
972 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGGTTAGGCACCATAAACTTAGTCTCCT
1 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
*
1037 CATAAGCGTACATGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
66 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
1102 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
131 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
* * * * * *
1167 ATTAGGCAGTATAAACTTATTTTCCTCCTTAGGATAAATGATATGGATGATTTTCTATTGCCTGA
196 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
1232 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGG-AAGCATTGA
261 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTG-
1296 TTCTCATAACAATCTTCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
325 -----------A---T---TC---TC---ATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
*
1361 AAACACTGTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
367 AAACACAGTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
* *
1426 TGAACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGA
432 TCAACCATTTTCGACAGAATCAAAGTTTATCTCTTAAATAAGA
*
1469 AAAACATGAATAGACATACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
1 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
1534 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
66 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
1599 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
131 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
1664 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
196 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
*
1729 AAATCTTTTCTTTGCCCTATTTTCCTTAAAATCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
261 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
*
1794 TTCTCATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGAATA
326 TTCTCATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGGATA
* * ** *
1859 CGCGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCGTTTTTAACAAAATCAAA
391 CACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCATTTTCGACAGAATCAAA
* *
1924 GTTTGTCTCTTAAATAAGG
456 GTTTATCTCTTAAATAAGA
1943 AAAACATGAATAGAC-CACA
1 AAAACATGAATAGACACACA
Statistics
Matches: 1364, Mismatches: 72, Indels: 78
0.90 0.05 0.05
Matches are distributed among these distances:
473 10 0.01
474 582 0.43
477 4 0.00
480 4 0.00
483 1 0.00
484 1 0.00
485 1 0.00
486 2 0.00
488 1 0.00
491 2 0.00
494 2 0.00
495 16 0.01
497 443 0.32
498 295 0.22
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (474 bp):
AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGG
AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
TTCTCATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGGATA
CACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCATTTTCGACAGAATCAAA
GTTTATCTCTTAAATAAGA
Found at i:1333 original size:24 final size:24
Alignment explanation
Indices: 1301--1350 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1291 ATTGATTCTC
*
1301 ATAACAATCTTCACTCTTTTCGAG
1 ATAACAATCTCCACTCTTTTCGAG
1325 ATAACAATCTCCACTCTTTTCGAG
1 ATAACAATCTCCACTCTTTTCGAG
1349 AT
1 AT
1351 TGGGAACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (24 bp):
ATAACAATCTCCACTCTTTTCGAG
Found at i:1911 original size:971 final size:969
Alignment explanation
Indices: 3--1961 Score: 3553
Period size: 971 Copynumber: 2.0 Consensus size: 969
1 AG
*
3 AAAACATGAATAGACGCAC-ATCCGCATCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCA
1 AAAACATGAATAGAC-CACAATCCGCATCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCA
67 TAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAA
65 TAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAA
* * *
132 GTCTAGGTTTGTGCCTCAAATGTGCCAAACATGGATTGTAGTAGTGATCTACTTCACGTTGTGAT
130 GTCTAGGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGAT
* * *
197 TAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAA
195 TAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGATTTTCTATTGCATGAAA
262 ATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATT
260 ATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATT
*
327 CTTATAACAATCTCCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAA
325 CTCATAACAATCTCCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAA
*
392 ACACAGTCCTTTCAGTAGGACACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTG
390 ACACAGTCCTTTCAATAGGACACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTG
*
457 AACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGAAAAACATGAATGGACATACAAATC
455 AACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGAAAAACATGAATAGACATACAAATC
522 CTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGATGG
520 CTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGATGG
587 TTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATG
585 TTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATG
652 TGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTC
650 TGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTC
717 CTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTGTGCCCTATTTTC
715 CTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTGTGCCCTATTTTC
* * * *
782 CTTAAAGTGAAAGTTCCTTCCTTAAATAAGGCAAGCTTTGATTCTCATAACAATCTTCACTCTTT
780 CTTAAAATCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATTCTCATAACAATCTCCACTCTTT
* * * * *
847 TTGAGTTTGGGAACCAAAAACGCATTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCG
845 TCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGAATACACGACATTGACGCTTTAATGTCG
* *
912 CAAGAAAACCATTTCTTTCAACCGTTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGA
910 CAAGAAAACCATTTCTTTCAACCGTTTTTAACAAAATCAAAGTTTGTCTCTTAAATAAGA
* *
972 AAAACATGAATAGACACACAAATCCTCATTCTTTTTTAGGTTAGGCACCATAAACTTAGTCTCCT
1 AAAACATGAATAGAC-CAC-AATCCGCA-TCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCT
*
1037 CATAAGCGTACATGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
63 CATAAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTA
*
1102 AAGTCTATGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
128 AAGTCTAGGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTG
* * *
1167 ATTAGGCAGTATAAACTTATTTTCCTCCTTAGGATAAATGATATGGATGATTTTCTATTGCCTGA
193 ATTAGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGATTTTCTATTGCATGA
1232 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGG-AAGCATTGA
258 AAATCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGA
*
1296 TTCTCATAACAATCTTCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
323 TTCTCATAACAATCTCCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAA
* *
1361 AAACACTGTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
388 AAACACAGTCCTTTCAATAGGACACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTT
1426 TGAACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGAAAAACATGAATAGACATACAAA
453 TGAACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGAAAAACATGAATAGACATACAAA
1491 TCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGAT
518 TCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGAT
1556 GGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAA
583 GGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAA
1621 TGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTC
648 TGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTC
*
1686 TCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTT
713 TCCTCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTGTGCCCTATTT
1751 TCCTTAAAATCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATTCTCATAACAATCTCCACTCT
778 TCCTTAAAATCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATTCTCATAACAATCTCCACTCT
*
1816 TTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGAATACGCGACATTGACGCTTTAATGT
843 TTTCGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGAATACACGACATTGACGCTTTAATGT
* *
1881 CGCAAGAAAAGCATTTCTTTCAACCGTTTTTAACAAAATCAAAGTTTGTCTCTTAAATAAGG
908 CGCAAGAAAACCATTTCTTTCAACCGTTTTTAACAAAATCAAAGTTTGTCTCTTAAATAAGA
1943 AAAACATGAATAGACCACA
1 AAAACATGAATAGACCACA
Statistics
Matches: 951, Mismatches: 36, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
969 19 0.02
970 3 0.00
971 656 0.69
972 273 0.29
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (969 bp):
AAAACATGAATAGACCACAATCCGCATCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCAT
AAGCGTACACGATATTGATGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAG
TCTAGGTTCGTGCCTCAAATGTGCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATT
AGGCAGTATAAACTTATTCTCCTCCTTAGGATAAAGGATATGGATGATTTTCTATTGCATGAAAA
TCTTTTCTTTGCCCTATTTTCCTTAAAGTCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATTC
TCATAACAATCTCCACTCTTTTCGAGATAACAATCTCCACTCTTTTCGAGATTGGGAACCAAAAA
CACAGTCCTTTCAATAGGACACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTGA
ACCATTTTCGATAGAATCAAAGTTTATCTCTTAAATAAGAAAAACATGAATAGACATACAAATCC
TCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGATGGT
TAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGT
GCCAAACATGGATTCTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCC
TCCTTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTGTGCCCTATTTTCC
TTAAAATCAAAGTTCCTTCCTTAAATAAGGCAAGCATTGATTCTCATAACAATCTCCACTCTTTT
CGAGATTGGGAACCAAAAACACAGTCCTTTCAATAGAATACACGACATTGACGCTTTAATGTCGC
AAGAAAACCATTTCTTTCAACCGTTTTTAACAAAATCAAAGTTTGTCTCTTAAATAAGA
Done.