Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012443.1 Corchorus capsularis cultivar CVL-1 contig12464, whole genome shotgun sequence
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: 27946
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:904 original size:335 final size:331
Alignment explanation
Indices: 1--2356 Score: 2899
Period size: 335 Copynumber: 7.1 Consensus size: 331
* * **
1 ATGAATACAAAAATTTCTAGGAGTTTCTGCGTAAAAAATCATGAAAAACTTAGCCGGGGCCCCAT
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AAAACTTAGCCGGGG-CCCGG
* *
66 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTT-CAAAAAAC
64 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAAAT
* * * *
130 TGA-CCTGAAAGA-TTTTTCCTCAATTAATGGAAAAAATAATCATAAAGAATATATAATTCAATG
128 TGATCC-GAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATG
* * *
193 CCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCG----T--TTTTTTTTTCGAATTAGTTT
192 CCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTT
** * * * * * *
252 TTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAA-GCCAATGTGGTTGA
257 CAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATG-CAATGTGGCTGA
316 GATTTGGATAG
321 GATTTGGATAG
* *
327 ATGAATACAAAAATTTCTAGGAGCCT-TGGCGCAAAAAATCATGCAAAACTGT-GCCGGGACCTC
1 ATGAATACAAAAATTTCTAGGAGTCTCT-GCGCAAAAAATCATG-AAAACT-TAGCCGGGGCC-C
* *** * * * *
390 GGAACGCGATTTTAGTAAAAAGTTGTAATAATTAGTACACGATTTCGACTGAAATTTTGCAAAAA
62 GGAACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
* * *
455 TTGATCCGAAAGATTTTTTGATCAATTTGTGGCAAAAATAATCATAAAAAATATATAATTTAATG
127 TTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATG
* *
520 CCAAAAAGATTGAAGGACTTATCACGCTTCTAATACCGTTTTTCCTTTTTTTTTCAAATTAATTT
192 CCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTT
* *
585 CAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAAATCCTTAAATGCAATTTGACTG
257 CAAATCAAAACGAAACAAGATTTAGATGTTTGT--AAAAAAAAATCCTTAAATGCAATGTGGCTG
***
650 AGATTCATATAG
320 AGATTTGGATAG
* * * *
662 ATTAGTACAGAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGATAAACTAAGCCGGGGCCCGGA
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGA-AAACTTAGCCGGGGCCCGGA
* * *
727 ACGCGATTTTAGCAAAAAACAGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAGTTG
65 ACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * * *
792 ATCCGAAATATTTTTTGCTCAATTTATGGCAAAAATAGTCATAAAAAATTATATAATTCTACGCC
130 ATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAA-TATATAATTCAATGCC
* * * * ** *
857 AAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGTTTTCCCTTTTTTTCCCGAATTAATTTCA
194 AAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCA
* * * *
922 AATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAGAAATCCTTAAATCCAAAGTGTCTGAGAT
259 AATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATGTGGCTGAGAT
987 TTGGATAG
324 TTGGATAG
* * *
995 ACGAATTACAAAAATTTTTGAGGAGTTTCTGCGCAAAAAATCATGAAAAACTTAGCCGGGGCTCC
1 ATGAA-TACAAAAATTTCT-AGGAGTCTCTGCGCAAAAAATCATG-AAAACTTAGCCGGGGC-CC
1060 GGAACGCGATTTTAGTC-AAAAACCGTGATAG-TATGTACACGATTTCGGCTAAAATTTTGCAAA
62 GGAACGCGATTTTAG-CAAAAAACCGTGATAGTTA-GTACACGATTTCGGCTAAAATTTTGCAAA
* *
1123 AATTGATCCGAAATATTTTTTGCTCAATTTATGGAAAAAATAATCATAAAAAATATATAATTCAA
125 AATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAA
* * * ** *
1188 TGCCAAAAAGATTGTAGGGCTTTTCACGCTTCTAATATCG-TTTTACTTTTTTTCCCAAATTCAT
190 TGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAAT
* * * *
1252 TTCAAAT-AAAATCGAAACAAGATTTAGATGTTTGTAGAAACAAATCGTTAAATCCAATGTGGCT
255 TTCAAATCAAAA-CGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATGTGGCT
*
1316 GAGATTTGGATGG
319 GAGATTTGGATAG
* * * ** * *
1329 ATGCATACAAAAATTTCTAGGAGTCTCGGTGCAAAAAATCATGCAAGAA-AGAGTCGGGGCCCTA
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AA-AACTTAGCCGGGGCCC-G
* ** *
1393 GAACGCGATTTTAGCCAAAAAAAACCGTGATAGTTACTACATTATTTTGGCTAAAATTTTGCAAA
63 GAACGCGATTTTAG-C--AAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * *
1458 AATTGACCCGGAAGATTTTTTCCTCAACTTATGGCAAAAATAATCATAAAAAATATATAATTCAA
125 AATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAA
* * * * *
1523 TTCCAAAAAGATTGAAGGGCTTTTCAAGCTTCTAATATAGTTTATTCC--TTTTTTTCGAATTAA
190 TGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTT-TTCCTTTTTTTTTCAAATTAA
** ** * * * *
1586 TTTTTAATTTAATCGAAACAAGATTTAGATGTTCGTAAAAAAGAATTCTTAAA-GCCAATGTGGC
254 TTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATG-CAATGTGGC
*
1650 TGAGATTTTGATAG
318 TGAGATTTGGATAG
* ** * * *
1664 ATGAATACAAAAATTTCTAGGAGCCTAGGCGCAAAAAATCATGCAAAACTGAGACGGGACCCCGG
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AAAACTTAGCCGGG-GCCCGG
* ** * * * *
1729 AACGCGATTTTAGTAAAAAAATTGTAATAGTTAGTACACGATTTCCGTTGAAATTTTGCAAAAAT
64 AACGCGATTTTAG-CAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
1794 TGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAA-ATATCATAAAAAATATATAATTCAATG
128 TGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATA-ATCATAAAAAATATATAATTCAATG
* * *
1858 CCAAAAATATTGAAGAGCTTATCACGCTTCTAATATCGTTTTTCTTTTTTTTTTTTTCAAATTAA
192 CCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTC---CTTTTTTTTTCAAATTAA
* * * * *
1923 TTTCAAATCAAAACGAAACAAGATTTAGACGATTGTAAAAACAAATCCTTAAATCCAAAGTGGCT
254 TTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATGTGGCT
*
1988 GAGATTTGGATAA
319 GAGATTTGGATAG
* * * *
2001 ACGAATACAAAAATTTCTAGGAGTCTCTGTGCAAACAATCATGAAAAACTTAGTCGGGGCCCCGG
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AAAACTTAGCCGGGG-CCCGG
* *
2066 AACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATT
64 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * *
2131 GACCCGAAAGA-TTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCC
129 GATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATGCC
*
2195 AAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCC-TTTTTTTTCAAATTAATTTCA
194 AAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCA
* *
2259 AATCAAAACGAAACAAGATTTAGATGTTTGT-AAAAAAAATCCTTAAATGCAATTTGACTGAGAT
259 AATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATGTGGCTGAGAT
**
2323 TCAGATAG
324 TTGGATAG
2331 AT-AAGTACAAAAATTTCTAGGAGTCT
1 ATGAA-TACAAAAATTTCTAGGAGTCT
2357 GATCGAGCTC
Statistics
Matches: 1745, Mismatches: 237, Indels: 92
0.84 0.11 0.04
Matches are distributed among these distances:
325 3 0.00
326 112 0.06
327 83 0.05
329 2 0.00
330 55 0.03
331 53 0.03
332 51 0.03
333 232 0.13
334 206 0.12
335 627 0.36
336 174 0.10
337 147 0.08
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (331 bp):
ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTTAGCCGGGGCCCGGAA
CGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
TCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAA
AAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAA
TCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATGTGGCTGAGATTT
GGATAG
Found at i:1845 original size:668 final size:662
Alignment explanation
Indices: 1--2353 Score: 3124
Period size: 668 Copynumber: 3.5 Consensus size: 662
* * *
1 ATGAATACAAAAATTTCTAGGAGTTTCTGCGTAAAAAATCATGAAAAACTTAGCCGGGGCCCCAT
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAAC-TAGCCGGGGCCCCAG
*
66 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTT-CAAAAAAC
65 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGC-AAAAAT
* * *
130 TGACCTGAAAGATTTTTCCTCAATTAATGGAAAAAATAATCATAAAGAATATATAATTCAATGCC
129 TGACCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCC
* * * ** *
195 AAAAAGATTGAATGGCTTATCACGCTTCTAATATCG--TTT--TTTTTTTCGAATTAGTTTTTAC
194 AAAAAGATTGAAGGGCTTATCAAGCTTCTAATATCGTTTTTCCTTTTTTTCGAATTAATTTCAAA
* * *
256 TTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGTTGAGATTT
259 TCAAAACGAAACAAGATTTAGATGTTCGTAAAAA-AAATCCTTAAAGCCAATGTGGCTGAGATTT
* *
321 GGATAGATGAA-TACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATCATGCAAAACTGTGCCGGG
323 GGATAGATGAAGTACAAAAATTTCTAGGAGCCTAGGCGCAAAAAATCATGCAAAACTGAGCCGGG
* * *
385 ACCTCGGAACGCGATTTTAGTAAAAAGTTGTAATAATTAGTACACGATTT-CGACTGAAATTTTG
388 ACCCCGGAACGCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCCG-CTGAAATTTTG
* *
449 CAAAAATTGATCCGAAAGATTTTTTGATCAATTTGTGGC-AAAAATAATCATAAAAAATATATAA
452 CAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAAATAATCATAAAAAATATATAA
* * * *
513 TTTAATGCCAAAAAGATTGAAGGACTTATCACGCTTCTAATACCGTTTTTCCTTTTTTTTTCAAA
517 TTCAATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCG-TTTTACTTTTTTTTTCAAA
* *
578 TTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAAATCCTTAAATGCAAT
581 TTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTTGT--AAAAACAAATCCTTAAATCCAAT
* * ***
643 TTGACTGAGATTCATATAG
644 GTGGCTGAGATTTGGATAG
* * * * *
662 ATTAGTACAGAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGATAAACTAAGCCGGGG-CCCGG
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACT-AGCCGGGGCCCCAG
* * * *
726 AACGCGATTTTAGCAAAAAACAGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAGTT
65 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATT
* * * * * * *
791 GATCCGAAATATTTTTTGCTCAATTTATGGCAAAAATAGTCATAAAAAATTATATAATTCTACGC
130 GACCCGAAAGA-TTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAA-TATATAATTCAATGC
* * *
856 CAAAAAGATTGAAGGG-TTTTTAACGCTTCTAATATCGTTTTCCCTTTTTTTCCCGAATTAATTT
193 CAAAAAGATTGAAGGGCTTATCAA-GCTTCTAATATCGTTTTTCCTTTTTTT--CGAATTAATTT
* * * *
920 CAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAGAAATCCTTAAATCCAAAGTGTCTGAG
255 CAAATCAAAACGAAACAAGATTTAGATGTTCGTAAAAA-AAATCCTTAAAGCCAATGTGGCTGAG
* * * ** ** * *
985 ATTTGGATAGACGAATTACAAAAATTTTTGAGGAGTTTCTGCGCAAAAAATCATGAAAAACTTAG
319 ATTTGGATAGATGAAGTACAAAAATTTCT-AGGAGCCTAGGCGCAAAAAATCATGCAAAACTGAG
* * * ** * * *
1050 CCGGGGCTCCGGAACGCGATTTTAGTCAAAAACCGTGATAG-TATGTACACGATTTCGGCTAAAA
383 CCGGGACCCCGGAACGCGATTTTAGTAAAAAATTGTAATAGTTA-GTACACGATTTCCGCTGAAA
*
1114 TTTTGCAAAAATTGATCCGAAATATTTTTTGCTCAATTTATGG-AAAAAATAATCATAAAAAATA
447 TTTTGCAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAAATAATCATAAAAAATA
* * **
1178 TATAATTCAATGCCAAAAAGATTGTAGGGCTTTTCACGCTTCTAATATCGTTTTACTTTTTTTCC
512 TATAATTCAATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTACTTTTTTTTT
* * *
1243 CAAATTCATTTCAAAT-AAAATCGAAACAAGATTTAGATGTTTGTAGAAACAAATCGTTAAATCC
577 CAAATTAATTTCAAATCAAAA-CGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATCC
*
1307 AATGTGGCTGAGATTTGGATGG
641 AATGTGGCTGAGATTTGGATAG
* * * * * *
1329 ATGCATACAAAAATTTCTAGGAGTCTCGGTGCAAAAAATCATGCAAGAAA-GAGTCGGGGCCCTA
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AA-AAACTAGCCGGGGCCCCA
* ** *
1393 GAACGCGATTTTAGCCAAAAAAAACCGTGATAGTTACTACATTATTTTGGCTAAAATTTTGCAAA
64 GAACGCGATTTTAG-C--AAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAA
*
1458 AATTGACCCGGAAGATTTTTTCCTCAACTT-ATGGCAAAAATAATCATAAAAAATATATAATTCA
126 AATTGACCCGAAAGA-TTTTTCCTCAA-TTAATGGCAAAAATAATCATAAAAAATATATAATTCA
* * *
1522 ATTCCAAAAAGATTGAAGGGCTTTTCAAGCTTCTAATATAGTTTATTCCTTTTTTTCGAATTAAT
189 ATGCCAAAAAGATTGAAGGGCTTATCAAGCTTCTAATATCGTTT-TTCCTTTTTTTCGAATTAAT
** ** * *
1587 TTTTAATTTAATCGAAACAAGATTTAGATGTTCGTAAAAAAGAATTCTTAAAGCCAATGTGGCTG
253 TTCAAATCAAAACGAAACAAGATTTAGATGTTCGTAAAAAA-AATCCTTAAAGCCAATGTGGCTG
*
1652 AGATTTTGATAGATGAA-TACAAAAATTTCTAGGAGCCTAGGCGCAAAAAATCATGCAAAACTGA
317 AGATTTGGATAGATGAAGTACAAAAATTTCTAGGAGCCTAGGCGCAAAAAATCATGCAAAACTGA
* *
1716 GACGGGACCCCGGAACGCGATTTTAGTAAAAAAATTGTAATAGTTAGTACACGATTTCCGTTGAA
382 GCCGGGACCCCGGAACGCGATTTTAGT-AAAAAATTGTAATAGTTAGTACACGATTTCCGCTGAA
1781 ATTTTGCAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAAAT-ATCATAAAAAAT
446 ATTTTGCAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAAATAATCATAAAAAAT
* * *
1845 ATATAATTCAATGCCAAAAATATTGAAGAGCTTATCACGCTTCTAATATCGTTTTTCTTTTTTTT
511 ATATAATTCAATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTAC----TTTT
* *
1910 TTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGACGATTGTAAAAACAAATCCTTAA
572 TTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAA
* *
1975 ATCCAAAGTGGCTGAGATTTGGATAA
637 ATCCAATGTGGCTGAGATTTGGATAG
* * * * *
2001 ACGAATACAAAAATTTCTAGGAGTCTCTGTGCAAACAATCATGAAAAACTTAGTCGGGGCCCCGG
1 ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAAC-TAGCCGGGGCCCCAG
*
2066 AACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATT
65 AACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATT
2131 GACCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCA
130 GACCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCA
* * *
2196 AAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATTAATTTCAAA
195 AAAAGATTGAAGGGCTTATCAAGCTTCTAATATCGTTTTTCC-TTTTTTTCGAATTAATTTCAAA
* * * *
2261 TCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAATCCTTAAATG-CAATTTGACTGAGATTC
259 TCAAAACGAAACAAGATTTAGATGTTCGTAAAAAAAATCCTTAAA-GCCAATGTGGCTGAGATTT
*
2325 AGATAGAT-AAGTACAAAAATTTCTAGGAG
323 GGATAGATGAAGTACAAAAATTTCTAGGAG
2354 TCTGATCGAG
Statistics
Matches: 1465, Mismatches: 186, Indels: 76
0.85 0.11 0.04
Matches are distributed among these distances:
660 70 0.05
661 88 0.06
662 41 0.03
664 2 0.00
666 9 0.01
667 182 0.12
668 381 0.26
669 210 0.14
670 227 0.15
671 105 0.07
672 146 0.10
673 4 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (662 bp):
ATGAATACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTAGCCGGGGCCCCAGA
ACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTG
ACCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAA
AAAGATTGAAGGGCTTATCAAGCTTCTAATATCGTTTTTCCTTTTTTTCGAATTAATTTCAAATC
AAAACGAAACAAGATTTAGATGTTCGTAAAAAAAATCCTTAAAGCCAATGTGGCTGAGATTTGGA
TAGATGAAGTACAAAAATTTCTAGGAGCCTAGGCGCAAAAAATCATGCAAAACTGAGCCGGGACC
CCGGAACGCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCCGCTGAAATTTTGCAAA
AATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAAATAATCATAAAAAATATATAATTCA
ATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTACTTTTTTTTTCAAATTAAT
TTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATCCAATGTGGCTG
AGATTTGGATAG
Found at i:2995 original size:10 final size:10
Alignment explanation
Indices: 2980--3004 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2970 GTTGCTGCTC
2980 AATTCCAGAA
1 AATTCCAGAA
2990 AATTCCAGAA
1 AATTCCAGAA
3000 AATTC
1 AATTC
3005 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:6120 original size:312 final size:311
Alignment explanation
Indices: 5083--6342 Score: 1278
Period size: 312 Copynumber: 4.0 Consensus size: 311
5073 TTCGTAAAAC
* * * * *
5083 CAAATCCTGAAAGCTAATGTGGCTGAGATTTGGATAGATGAATACAAAAATTTCTAGGAGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAATACAAAAATTTCTAGGAGTCTTT
* * * * * *
5148 GCGCAAAATATTATGTAAAACTGAGCCGGCGCACCGAAACGCGATTTTAGTCAAAAAAACCGTGA
66 GCGCAAAAAATCATGCAAAACTGAGCCGGGGCACCGGAACGCGATTTTAG-C-CAAAAACCGTGA
* * * * * *
5213 TA-TAACGTATACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAATATTTTTTGCTCAATT
129 TAGTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAGTTTTTCCTCAATT
* * *
5277 TATGGCAAAAATAGTCATAAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACG
193 TATGGCAAAAATAATCATAAAAAA-TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACG
*
5342 CTTCTAATATCGTTTTCCCTTTTTTTTCCCGAATTAATTTCAAATCAAAACGAAACAAGATTTAG
257 CTTCTAATATCGTTTTTCCTTTTTTTTCCCGAATTAATTTCAAATC---A--AAAC---------
5407 ATGTTTGTAAAAA
308 ------G---AAA
* * *
5420 CAAATCCTTAAATCCAAAGTGGCTGAGATTTGGATAGACGAATACAAAAATTTCTAGGAGT-TTC
1 CAAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAATACAAAAATTTCTAGGAGTCTT-
* * * **
5484 TGCGCAAAAAATCATGAAAAACTTAGCCGGGGCTCCGGAACGCGATTTTAGTTAAAAACC--G-T
65 TGCGCAAAAAATCATGCAAAACTGAGCCGGGGCACCGGAACGCGATTTTAGCCAAAAACCGTGAT
*
5546 -G--A-T-----A-----G-T-AAATTTTGCAAAAATTGACCCGAAA-AGTTTTTCCTCAATTTG
130 AGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAGTTTTTCCTCAATTTA
* * *
5594 TGGCAAAAATAATCTTAAAAAATATATAATTCAATGCCAAAGAGATTAAAGGGCTTTTCACGCTT
195 TGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTT
* * *
5659 CTAATATCATTTTTCCTTTTTGTTT-TCAAATTAATTTCAAATCAAAACGAAA
260 CTAATATCGTTTTTCCTTTTT-TTTCCCGAATTAATTTCAAATCAAAACGAAA
* *
5711 CAAGATTTAGATGTTTGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTCAGATAGATGAG
1 C-----------------------AAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAA
* * **
5776 TACAAAAATTTCTAGGAGCCTATGTACAAAAAATCATGCAAAACTGAGCCGGGGTC-CCGGAACG
43 TACAAAAATTTCTAGGAGTCTTTGCGCAAAAAATCATGCAAAACTGAGCCGGGG-CACCGGAACG
5840 CGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
107 CGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
*
5905 CGAAAGA-TTTATTCCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATGCTAAA
172 CGAAAGAGTTT-TTCCTCAATTTATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAA
*
5969 AAGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCCCGAATTAATTTCAA
236 AAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTT-CCCGAATTAATTTCAA
6034 ATCAAAACGAAA
300 ATCAAAACGAAA
* *
6046 CAAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAGTACAAAAATTTCTTGGAGTCTTT
1 CAAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAATACAAAAATTTCTAGGAGTCTTT
* * * *
6111 GCGCAAAAAATCATGCAAAACTGTGTCGGGGTC-CCGGAATGTGATTTTAGCCAAAAACCGTGAT
66 GCGCAAAAAATCATGCAAAACTGAGCCGGGG-CACCGGAACGCGATTTTAGCCAAAAACCGTGAT
* *
6175 AGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCAGAAAGAGTTTTTCCTCAATTTA
130 AGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAGTTTTTCCTCAATTTA
* * * * **
6240 TGGCAAAAATAATCTTAAAAAATATATAATTCAATGCAAAAAATATTGAAAGGCTTTTCAAAC-T
195 TGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTT
*
6304 CTTAACATCGTTTTTCCTTTTTTTTCCCCGAATTAATTT
260 C-TAATATCGTTTTTCCTTTTTTTT-CCCGAATTAATTT
6343 GTAATTCAAT
Statistics
Matches: 799, Mismatches: 71, Indels: 131
0.80 0.07 0.13
Matches are distributed among these distances:
291 4 0.01
294 1 0.00
309 4 0.01
311 3 0.00
312 269 0.34
313 3 0.00
314 180 0.23
315 39 0.05
316 25 0.03
317 2 0.00
318 2 0.00
320 1 0.00
321 1 0.00
323 1 0.00
326 1 0.00
328 1 0.00
330 1 0.00
331 1 0.00
332 2 0.00
333 32 0.04
334 92 0.12
335 33 0.04
336 2 0.00
337 99 0.12
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (311 bp):
CAAATCCTTAAATCCAATGTGGCTGAGATTCGGATAGATGAATACAAAAATTTCTAGGAGTCTTT
GCGCAAAAAATCATGCAAAACTGAGCCGGGGCACCGGAACGCGATTTTAGCCAAAAACCGTGATA
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAGTTTTTCCTCAATTTAT
GGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
TAATATCGTTTTTCCTTTTTTTTCCCGAATTAATTTCAAATCAAAACGAAA
Found at i:6586 original size:29 final size:28
Alignment explanation
Indices: 6522--6597 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
6512 TTTCCAATAT
* * *
6522 AAAATTTGTAAAG-TATGTTGCAAAAAT
1 AAAATTTGTAAAGTTTTGTGGCAAAAAG
*
6549 AAAATTTGTAAAGTTTTGTGGCCGAAAAG
1 AAAATTTGTAAAGTTTTGTGG-CAAAAAG
*
6578 AAAATTTGTATAGTGTTTGT
1 AAAATTTGTAAAGT-TTTGT
6598 CACATTCTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.32
28 5 0.12
29 18 0.44
30 5 0.12
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (28 bp):
AAAATTTGTAAAGTTTTGTGGCAAAAAG
Found at i:6687 original size:3 final size:3
Alignment explanation
Indices: 6679--6707 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6669 GGAATAAATA
6679 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6708 AAAGTCAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12145 original size:13 final size:13
Alignment explanation
Indices: 12127--12158 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12117 ACTTCCTTCT
*
12127 AAAAAGGAAAAAG
1 AAAAAGGAAAAAA
12140 AAAAAGGAAAAAA
1 AAAAAGGAAAAAA
12153 AAAAAG
1 AAAAAG
12159 AGTTGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAA
Found at i:13942 original size:40 final size:40
Alignment explanation
Indices: 13882--13966 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
13872 TTTTTTCATA
* *
13882 ATCAAGACTCAAAGCTGAATTTTATTTAAGGGGAACAAAT
1 ATCAAGACTCAAAGCTGAATTTTATTTAAAGAGAACAAAT
* *
13922 ATCAAGACTCGAAG-TCGAATTTTGTTTAAAGAGAACAAAT
1 ATCAAGACTCAAAGCT-GAATTTTATTTAAAGAGAACAAAT
13962 ATCAA
1 ATCAA
13967 ACCACTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (40 bp):
ATCAAGACTCAAAGCTGAATTTTATTTAAAGAGAACAAAT
Found at i:21460 original size:42 final size:42
Alignment explanation
Indices: 21401--21487 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
21391 AGCATGTTAG
*
21401 TACCTGACCTAAAATGCTCCTAGAAAGGCCATGAGAAAGGAA
1 TACCTCACCTAAAATGCTCCTAGAAAGGCCATGAGAAAGGAA
* * *
21443 TACCTCACCTAAAATGCTCCTTGAAAGGCCATGAGATAGGCA
1 TACCTCACCTAAAATGCTCCTAGAAAGGCCATGAGAAAGGAA
21485 TAC
1 TAC
21488 TCTGACAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
TACCTCACCTAAAATGCTCCTAGAAAGGCCATGAGAAAGGAA
Found at i:23747 original size:16 final size:16
Alignment explanation
Indices: 23728--23761 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23718 TCCATACATC
*
23728 ATATTGTCGTATTCTA
1 ATATTGTCGTATTATA
23744 ATATTGTCGTATTATA
1 ATATTGTCGTATTATA
23760 AT
1 AT
23762 TAGAGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (16 bp):
ATATTGTCGTATTATA
Done.