Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014582.1 Corchorus olitorius cultivar O-4 contig14615, 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: 22048
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:612 original size:333 final size:329
Alignment explanation
Indices: 2--1812 Score: 2099
Period size: 333 Copynumber: 5.6 Consensus size: 329
1 T
* * * *
2 AAAACAAATCATTAAATCCAAAGTGGCTGAGATTTGGTCAAATGAATATAGATTTTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
* * * *
67 CTTCGTGCCAAAAATCATGCAAAACTGAGCCGGGGCCTCGACATGCGTTTTTAGCTTAAAACCGT
66 CTT-GTG-CAAAAATCATGCAAAACTAAGTCGGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGT
* * * * * *
132 GATGAAAAGTACACGATTTAGGCTAAAATTTTGCAGAAATTGATCCGGAAAATTTTCCCTCACTT
129 GATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAATT
* * *
197 TTTGGCCAAAAATCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAAGGTTTTTCAGGCT
194 TTTGGCCACAACTCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCA-GCT
* * **
262 TTTAATATCGTTTTTCCAATTTTTTTTCTTAATTAATTTTGAGTTAAATAGAAACATGATACAAA
258 TCTAATATCGTTTTTCCAA-TTTTTTTCTGAATTAATTTTGAAATAAATAGAAACATGATACAAA
327 TGCTCGTA
322 TGCTCGTA
*
335 AAAACAAATCCTTAAATCCAAAGTTGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
* * **
400 CTTTGTGCAAAAATTCATGCAATACTAAGTCGGTGTCC-CGAAACGTC-TTTTTAGCTTAAGTCC
66 C-TTGTGCAAAAA-TCATGCAAAACTAAGTCGG-GGCCTCGAAACG-CGTTTTTAGCTTAAAACC
* * *
463 ATGATGGAAAGTATACGATTTCTGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAA
127 GTGATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAA
* * * *
528 TTTTTGGCCACAACTCTCATAAAATATATATAATTTAAAGCCAAAAAGATCGAAGGGTTTTTCAC
192 TTTTTGGCCACAACTCTCATAAAA-ATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCA-
* * *
593 GCTTCTAATATCG-TTTTCCAA-TTTTTTCTGAATTAA-CTTCAAATAATATTGAAACATG----
255 GCTTCTAATATCGTTTTTCCAATTTTTTTCTGAATTAATTTTGAAATAA-ATAGAAACATGATAC
651 --AT--TCG--
319 AAATGCTCGTA
* * *
656 -AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATAAATATAAATATTTCAA-GA--
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
* * * * * *
717 ----AG-AAAAATCTTGCAAAACTGAGTCGGGGCCTCGAAGCGCTTTTTTAGCTTAAAACTGTGA
66 CTTGTGCAAAAATCATGCAAAACTAAGTCGGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGTGA
* * * *
777 TGGAAAGTACACGATTTCGGCTAAAATTTTGCTAAAATTGATTCGGAAAATTTTTCCTCACTTTT
131 TGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAATTTT
* * * * *
842 TGCCCAAAATTCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAAGGTTTTTCAGCCTTT
196 TGGCCACAACTCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCAG-CTTC
* *
907 TAATATCGTTTTTCCAATTTTTTCCTTAATTAATTTTG-AATATAATAGAAACATGATACAAATG
260 TAATATCGTTTTTCCAATTTTTTTCTGAATTAATTTTGAAATA-AATAGAAACATGATACAAATG
*
971 CTCATA
324 CTCGTA
* * * * *
977 AAAACAAATCATTAAATCCAATGTGACTGAGATTTGGTTATAT-ATATATAAATATTTCAA-GA-
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGA-ATATAAATATTTCAAGGAG
* * *
1039 -----AG-AAAAATCATGCAAAACTGAGTCGGGGCCTCGAAACGC-TTTTTAGCTTAAAACTGTG
65 TCTTGTGCAAAAATCATGCAAAACTAAGTCGGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGTG
* * * * *
1097 ATGAAAAGTACATGATTTCGGCTAAAATTTTGC-TAAATTTATCCGAAAGATTTTTCCTCAATTT
130 ATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAATTT
* * * * *
1161 TTGGCCAC-ACTTCTCATAAAAAAATATAATACAAAGAAAAAAAGATTGAAGGATTTTTCAGACT
195 TTGGCCACAAC-TCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCAG-CT
* * * * *
1225 TCTAATATCGTTTTTCCAA-TTTTTTCTGAATTAATTTCGAACTAAATGGAAACATGATTCAGAT
258 TCTAATATCGTTTTTCCAATTTTTTTCTGAATTAATTTTGAAATAAATAGAAACATGATACAAAT
1289 GCTCGTA
323 GCTCGTA
* * * * *
1296 AAAACAAATTCTTAATTCCAAAGTCGCTGAGATTTGGTCAGATGAATATAGATAGTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
* * *
1361 ATTCGTGCTAAAAATCATGCAAAACTAAGTCGGGGCCTTGAAACGCGTTTTTAGCTTAAAATCGT
66 CTT-GTGC-AAAAATCATGCAAAACTAAGTCGGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGT
* * * ** *
1426 GGTGGATAGTGCACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAATTTTTTTTCTCAATT
129 GATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAATT
* * *
1491 TTTGGCCACAATTCTCATAGACAATATATAATTCAAAGAAAAAAAGCTTGAAGGGTTTTTCAGGC
194 TTTGGCCACAACTCTCATA-AAAATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCA-GC
* * * *
1556 TT-TCAATATCGTTTTTTC-ATTTTTTTCTGAATTTATTTTGAATTAAAT-GAAAACATGATATA
257 TTCT-AATATCGTTTTTCCAATTTTTTTCTGAATTAATTTTGAAATAAATAG-AAACATGATACA
1618 AATGCTCGTA
320 AATGCTCGTA
*
1628 AAAACAAAACCTTAAATCC-AAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
* * * *
1692 CTTTGTGCAAAAAGTCATGC-AAACTAAGTCGGTG-TTCCGAAACGTGTTTTTAGCCTAAAACCG
66 C-TTGTGCAAAAA-TCATGCAAAACTAAGTCGGGGCCT-CGAAACGCGTTTTTAGCTTAAAACCG
* * * *
1755 TGATGGAAAGTATACGATTTCTGCTAAAATTTTGCAAAAATTGATTCGGAAAATTTTT
128 TGATGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTT
1813 AGGCACAACT
Statistics
Matches: 1265, Mismatches: 164, Indels: 101
0.83 0.11 0.07
Matches are distributed among these distances:
308 1 0.00
309 49 0.04
310 122 0.10
311 32 0.03
312 4 0.00
317 2 0.00
319 93 0.07
320 156 0.12
321 51 0.04
322 93 0.07
323 3 0.00
325 2 0.00
327 1 0.00
329 36 0.03
330 140 0.11
331 120 0.09
332 122 0.10
333 186 0.15
334 52 0.04
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (329 bp):
AAAACAAATCCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGT
CTTGTGCAAAAATCATGCAAAACTAAGTCGGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGTGA
TGGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAAATTTTTCCTCAATTTT
TGGCCACAACTCTCATAAAAATATATAATTCAAAGACAAAAAGCTTGAAGGGTTTTTCAGCTTCT
AATATCGTTTTTCCAATTTTTTTCTGAATTAATTTTGAAATAAATAGAAACATGATACAAATGCT
CGTA
Found at i:2338 original size:529 final size:528
Alignment explanation
Indices: 1328--2341 Score: 1371
Period size: 529 Copynumber: 1.9 Consensus size: 528
1318 GTCGCTGAGA
*
1328 TTTGGTCAGATGAATATAGATAGTTCAAGGAGTATTCGTGCTAAAAATCATGCAAAACTAAGTCG
1 TTTGGTCAGATGAATATAGATAGTTCAAGGAATATTCGTGCTAAAAATCATGCAAAACTAAGTCG
* * * * * * * *
1393 GGGCCTTGAAACGCGTTTTTAGCTTAAAATCGTGGTGGATAGTGCACGATTTCGGCTAAAATTTT
66 GGGCCTCGAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTCGACTAAAATTTT
* * * *
1458 GCAAAAATTGATCCGAAATTTTTTTTCTCAATTTTTGGCCACAATTCTCATAGACAATATATAAT
131 GCAAAAATTGATCCGAAA-TATTTTTCTCAATTTTTGCCCAAAATTCTCATAGAAAATATATAAT
* * ** * *
1523 TCAAAGAAAAAAAGCTTGAAGGGTTTTTCAGGCTTTCAATATCGTTTTTTCATTTTTTTCTGAAT
195 TCAAAGAAAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCCATTTTTTTCTGAAT
* * * *
1588 TTATTTTGAATTAAATGAAAACATGATATAAATGCTCGTAAAAACAAAACCTTAAATCCAAGTGG
260 TAATTTCGAATTAAATGAAAACATGATATAAATGCTCGTAAAAACAAAACCTTAAAACAAAGTGG
* *
1653 CTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTTGTGCAAAAAGTCATGCAAACTA
325 CTGAAATTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTCGTGCAAAAAGTCATGCAAACTA
* * * * * * * *
1718 AGTCGGTGTTCCGAAACGTGTTTTTAGCCTAAAACCGTGATGGAAAGTATACGATTTCTGCTAAA
390 AGTCGGGGCTCCGAAACGCGTTTTTAACCTAAAACCATGATGGAAAGTACACGAGTTCGGCTAAA
*
1783 ATTTTGCAAAAATTGATTCGGAAAATTTTTAGGCACAACTCTCATAAAAAATATATAATTCATAG
455 ATTTTGCAAAAATTGATTCCGAAAATTTTTAGGCACAACTCTCATAAAAAATATATAATTCATAG
1848 CCAAAAAAT
520 CCAAAAAAT
* * * * * *
1857 TTTGGTCAGATTAATATAGATATTTTAAGGAATCTTCGTG-TCAAAAGTCATGCAAAACTGAGTC
1 TTTGGTCAGATGAATATAGATAGTTCAAGGAATATTCGTGCT-AAAAATCATGCAAAACTAAGTC
1921 GGGGCCTCGAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTCGACTAAAATTT
65 GGGGCCTCGAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTCGACTAAAATTT
* *
1986 TGCAAAAATTGATTCGTAAA-ATTTTTCATCACTTTTTGCCCAAAATTCTCATA-AAAATATATA
130 TGCAAAAATTGATCCG-AAATATTTTTC-TCAATTTTTGCCCAAAATTCTCATAGAAAATATATA
*
2049 ATTCAAAGACAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCCAATTTTTTT-TG
193 ATTCAAAGAAAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCC-ATTTTTTTCTG
* * * *
2113 AATTAATTTCGAATT-AATTAGACACATGAT-TCATATGCTCGTAAAAACAAATCCTTAAAACAA
257 AATTAATTTCGAATTAAATGA-AAACATGATAT-AAATGCTCGTAAAAACAAAACCTTAAAAC-A
* * * *
2176 AATTGGTTTAAATTTGGTCAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAA-TCATG
319 AAGTGGCTGAAATTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTCGTG-CAAAAAGTCATG
* * *
2240 CAAAACTGAGTCGGGGC-CTCGAAACGCGTTTTTAACTTAAAACCATGATGGATAGTACACGAGT
383 C-AAACTAAGTCGGGGCTC-CGAAACGCGTTTTTAACCTAAAACCATGATGGAAAGTACACGAGT
*
2304 TCGGCTAAAATTTTGTAAAAATTGA-TCCGAAAATTTTT
446 TCGGCTAAAATTTTGCAAAAATTGATTCCGAAAATTTTT
2342 TCCTCAATTT
Statistics
Matches: 420, Mismatches: 55, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
527 5 0.01
528 111 0.26
529 222 0.53
530 82 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (528 bp):
TTTGGTCAGATGAATATAGATAGTTCAAGGAATATTCGTGCTAAAAATCATGCAAAACTAAGTCG
GGGCCTCGAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTCGACTAAAATTTT
GCAAAAATTGATCCGAAATATTTTTCTCAATTTTTGCCCAAAATTCTCATAGAAAATATATAATT
CAAAGAAAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCCATTTTTTTCTGAATT
AATTTCGAATTAAATGAAAACATGATATAAATGCTCGTAAAAACAAAACCTTAAAACAAAGTGGC
TGAAATTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTCGTGCAAAAAGTCATGCAAACTAA
GTCGGGGCTCCGAAACGCGTTTTTAACCTAAAACCATGATGGAAAGTACACGAGTTCGGCTAAAA
TTTTGCAAAAATTGATTCCGAAAATTTTTAGGCACAACTCTCATAAAAAATATATAATTCATAGC
CAAAAAAT
Found at i:2605 original size:332 final size:330
Alignment explanation
Indices: 1857--4203 Score: 2119
Period size: 331 Copynumber: 7.0 Consensus size: 330
1847 GCCAAAAAAT
* * * * * *
1857 TTTGGTCAGATTAATATAGATATTTTAAGGAATCTTCGTGTCAAAAGTCATGCAAAACTGAGTCG
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTC-
* * * * * * *
1922 GGGCCTCGAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTCGACTAAAATTTT
65 GGGCCCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTT
** * * * *
1987 GCAAAAATTGATTCGTAAA-ATTTTTCATCACTTTTTGCCCAAAATTCTCATAAAAATATATAAT
130 GCAAAAATTGACACG-AAAGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAAT
* ** * **
2051 TCAAAGACAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCCAATTTTTTT-TGAA
194 TCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTTCTGAA
* * * * * * *
2115 TTAATTTCGAATTAATTAGACACATGATTCATATGCTCGTAAAAACAAATCCTTAAAACAAAAT-
259 TTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC-AAATG
** * *
2179 TGGTTTAAA
322 TGACTGAGA
*
2188 TTTGGTCAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTCG
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTC-
* * * *
2253 GGGCCTCGAAACGCGTTTTTAACTTAAAACCATGATGGATAGTACACGAGTTCGGCTAAAATTTT
65 GGGCCCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTT
* * * *
2318 GTAAAAATTGATC-CGAAA-ATTTTTTCCTCAATTTTTGGCCACAATTCTCATAGAAATATATAA
130 GCAAAAATTGA-CACGAAAGA-TTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAA
* * * * * * *
2381 TTCAAAGACAAAAAGCTTGAAAGGTTTTTCAGGCCTTTAATATCGTTTTTCCAATTTTTTTCTTA
193 TTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTTCTGA
* ** * * *
2446 ATTAATTTTGAATTAAATAGAAACATTATACAAATGCTCGTAAAAACAAATCCTTAAATCAAAAG
258 ATTAATTTT-AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATG
2511 TGACTGAGA
322 TGACTGAGA
* * * * *
2520 TTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAACTAAGTCG
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTCG
* * * * *
2585 GTGTCCCGAAACGTGTTTTTAGCTTAAAGCCGTGATGAGA-AGTATACGATTTCTGCTAAAATTT
66 G-GCCCCGAAACGCGTTTTTAGCTTAAAACCGTGATG-GATAGTACACGATTTCGGCTAAAATTT
* * *
2649 TGCAAAAATTGATCAGGAAA-ATTTTTCCTCAATTTTTGGCCACAATTCTCATAAAATATATATA
129 TGCAAAAATTGA-CACGAAAGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAA-ATATATA
* * *
2713 ATTCAAAGTCAAAAAGATTGAAGGGTTTTTCACGCTTATAATTATCGTTTTTTCCAA-TTTTTTC
192 ATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA-TATCG-TTTTTCCAATTTTTTTC
* * * * * *
2777 TGAATTAATTTCAAATAAAATCGAAACATGATTCAGATGGTCATAAAAACAAATCTTTAAAT-AC
255 TGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCA-
2841 AATGTGGA-TGAGA
318 AATGT-GACTGAGA
* * * * * * *
2854 TTTGGTTAGATAAATATAAATATTTCCAGAAGTCTTCTTTCCAAAAATCATGCAAAATTGAGTCG
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTC-
* * *
2919 GGGCCCCGAAACGCTTTTTTAGCTTAAAACTGTGATGGAAAGTGATTATTACACGATTTCGGCTA
65 GGGCCCCGAAACGCGTTTTTAGCTTAAAACCGTGAT-----G-GA-TAGTACACGATTTCGGCTA
* * * * *
2984 AAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAAATTTTAGCCACAATACTCATAAAAAAT
123 AAATTTTGCAAAAATTGACACGAAAGATTTTTCCTCAATTTTTGGCCAAAATACTCAT-AAAAAT
* * *
3049 ATATAATTCAACGCCAAAAAGATT-AGAGGGCTTTTCACGATTTTAATATCGTTCTT-C-ATATT
187 ATATAATTCAAAGCCAAAAAGATTGA-AGGGCTTTTCACGCTTTTAATATCGTTTTTCCAAT-TT
* * * *
3111 TTTTCTGAATTAATGTCTAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATTCTTAA
250 TTTTCTGAATTAAT-TTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * *
3176 ATGC-AATGTGGCTAACTA
314 AT-CAAATGTGACTGA-GA
* * * * *
3194 TTT-ATTAGACGAATATAGATATTTCAAGGAGTC-TCGGCGCCAAAAATCTTGCAAAACTCAGTC
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTC-GTGCCAAAAATCATGCAAAACTGAGTC
* ** * *
3257 GGGGCCCCGAAACGCGTTTTTATCCAAAAACCATGAT-GA-ACGTACACGATTTTGGCTAAAATT
65 -GGGCCCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATA-GTACACGATTTCGGCTAAAATT
* * ** * *
3320 TTGCAATAGA-TGACACGAAATATTTTTTCCTCAATTTTTGGATAAAATGCTCATTAAATATATA
128 TTGCAA-AAATTGACACGAAAGA-TTTTTCCTCAATTTTTGGCCAAAATACTCA-TAAAAATATA
* * * * * * * * *
3384 TAATTTAACGCCAAAAAGATTGGATGACTTTTCACGCTTTTAATTTCTTTTTTCTTATTTTTTTT
190 TAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC-CA--ATTTTT
* * * **
3449 TTCTAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAATTTTTTTAAA
252 TTCTGAATTAA-TTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA-ATCCTTAAA
* *
3514 TCCAATCT-AGCTGAGA
315 TCAAATGTGA-CTGAGA
* * * * * * *
3530 TTTGATTAAATGAATATGGATATCTCAAGGA-TGCTTGGGGCCAAAAATCATGCAAAACTGAGCC
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGT-CTTCGTGCCAAAAATCATGCAAAACTGAGTC
* * * * ** ** * * * *
3594 GCGCCCTGCATCGC-TTTGTTAGCCAAAAATTGTGATGGTTATTACACGATTGT-GACTTAAATT
65 GGGCCCCGAAACGCGTTT-TTAGCTTAAAACCGTGATGGATAGTACACGATT-TCGGCTAAAATT
* * * * *
3657 TTGTAAAAATTGACTCGAAAGATATTTT-CTCAATTTTTAGCTAAAATAGTCATAAAAAATATAT
128 TTGCAAAAATTGACACGAAAGAT-TTTTCCTCAATTTTTGGCCAAAATACTCAT-AAAAATATAT
* * * *
3721 AATTCAACA-CCAAAAAGATTGAAGTGCTTTTCACGCTTTTAATATCATTTGT-C-ATTTCTTTC
191 AATTCAA-AGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTTC
* * *
3783 TGATTTAATTTCTAATTAAATAGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC-
255 TGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CA
* * * *
3847 AATGCGGCTAACA
318 AATGTGACTGAGA
** * * * * * *
3860 TTTTATTAGATAAATATAGATATTTCAAGGAGTC-TCAGCGCCAAAAATTATGCTAAATTGAGCC
1 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTC-GTGCCAAAAATCATGCAAAACTGAGTC
* * * *
3924 AGGGTCCCGGAATGCGTTTTTAGGC-AAAAACCGTGATGGTTAGTTAGTACACGATTTCGGCTAA
65 -GGGCCCCGAAACGCGTTTTTA-GCTTAAAACCGTGATGG--A--TAGTACACGATTTCGGCTAA
* * * * * *
3988 AATTGTGCAAAAATTGACACGAAAGATTTCTACTCAATTTTTGGCTAAAGTACTTATAAAAATAT
124 AATTTTGCAAAAATTGACACGAAAGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATAT
* * * * * **
4053 ATAATTTAACGCTAAAAAGATTGTAGGGCTTTTCACGCTTTTAATATCGTATTTCTTA-TTTTTT
189 ATAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTT
* * ** *
4117 GTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTTTTAAATCC
254 CTGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCA
*
4182 AATGTTACTGAGA
318 AATGTGACTGAGA
4195 TTTGGTTAG
1 TTTGGTTAG
4204 TTGATGCAAT
Statistics
Matches: 1661, Mismatches: 279, Indels: 148
0.80 0.13 0.07
Matches are distributed among these distances:
329 1 0.00
330 72 0.04
331 336 0.20
332 300 0.18
333 51 0.03
334 213 0.13
335 153 0.09
336 157 0.09
337 102 0.06
338 7 0.00
339 147 0.09
340 16 0.01
341 102 0.06
342 4 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (330 bp):
TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTCG
GGCCCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTG
CAAAAATTGACACGAAAGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAATTC
AAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTTCTGAATT
AATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTGAC
TGAGA
Found at i:3250 original size:673 final size:661
Alignment explanation
Indices: 1864--4203 Score: 2340
Period size: 673 Copynumber: 3.5 Consensus size: 661
1854 AATTTTGGTC
* * * * * * *
1864 AGATTAATATAGATATTTTAAGGAATCTTCGTGTCAAAAGTCATGCAAAACTGAGTCGGGGCCTC
1 AGATGAATATAGATATTTCAAGGAGTC-TCGCGCCAAAAATCATGCAAAACTGAGTCGGGTCC-C
* * * * *
1929 GAAACGCGTTTTTACCTTAAAATCGTGATGAAAAGTACAAGATTTC-GACTAAAATTTTGCAAAA
64 GAAACGCGTTTTTAGCTAAAAACCGTGATGAGAAGTACACGATTTCTG-CTAAAATTTTGCAAAA
** * * *
1993 ATTGATTCGTAAA-ATTTTTCATCACTTTTTGCCCAAAATTCTCATAAAAATATATAATTCAAAG
128 ATTGACACG-AAAGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAATATATAATTCAAAG
** * ** * *
2057 ACAAAAAGATTGAAGGGCTTTGAAGGCTTCCAATATCGTTTTTCCAATTTTTTTTGAATTAATTT
192 -CAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTCTAAATTAATTT
* * * * * * * * *
2122 CGAATTAATTAGACACATGATTCATATGCTCGTAAAAACAAATCCTTAAA-ACAAAAT-TGGTTT
256 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATAC--AATGTGGATG
* *
2185 AAATTTGGTCAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAG
319 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAG
* * * * * * *
2250 TCGGGGCCTCGAAACGCGTTTTTAACTTAAAAC--CATGATG-GA-TAGTACACGAGTTCGGCTA
384 TCGGGGCCCCGAAACGCTTTTTTAGCTTAAAACTTGATGAAGTGATTATTACACGATTTCGGCTA
* * * * *
2311 AAATTTTGTAAAAATTGATCCGAAA-ATTTTTTCCTCAATTTTTGGCCACAATTCTCAT-AGAAA
449 AAATTTTGTAAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTAGCCACAATACTCATAAAAAA
* * * * * * *
2374 TATATAATTCAAAGACAAAAAGCTTGAAAGGTTTTTCAGGCCTTTAATATCGTTTTTCCA-ATTT
513 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCG-TTTT-CATA-TT
* * ** * *
2438 TTTTCTTAATTAATTTTGAATTAAATAGAAACATTATACAAATGCTCGTAAAAACAAATCCTTAA
575 TTTTCTGAATTAATTCT-AATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * * * *
2503 AT-CAAAAGTGACTGAGATTTGGTC
639 ATGC-AATGTGGCTAACATTT-ATT
* * * * *
2527 AGATGAATATAAATATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAACTAAGTCGGTGTCCC
1 AGATGAATATAGATATTTCAAGGAGTC-TCGCGCCAAAAATCATGCAAAACTGAGTCGG-GTCCC
* * * *
2592 GAAACGTGTTTTTAGCTTAAAGCCGTGATGAGAAGTATACGATTTCTGCTAAAATTTTGCAAAAA
64 GAAACGCGTTTTTAGCTAAAAACCGTGATGAGAAGTACACGATTTCTGCTAAAATTTTGCAAAAA
* *
2657 TTGATCAGGAAA-ATTTTTCCTCAATTTTTGGCCACAATTCTCATAAAATATATATAATTCAAAG
129 TTGA-CACGAAAGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAA-ATATATAATTCAAAG
* * *
2721 TCAAAAAGATTGAAGGGTTTTTCACGCTTATAATTATCGTTTTTTCCAATTTTTTCTGAATTAAT
192 -CAAAAAGATTGAAGGGCTTTTCACGCTTTTAA-TATCG-TTTTTCCAATTTTTTCTAAATTAAT
* * * * *
2786 TTCAAATAAAATCGAAACATGATTCAGATGGTCATAAAAACAAATCTTTAAATACAATGTGGATG
254 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATACAATGTGGATG
* * * * * * *
2851 AGATTTGGTTAGATAAATATAAATATTTCCAGAAGTCTTCTTTCCAAAAATCATGCAAAATTGAG
319 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAG
2916 TCGGGGCCCCGAAACGCTTTTTTAGCTTAAAACTGTGATGGAAAGTGATTATTACACGATTTCGG
384 TCGGGGCCCCGAAACGCTTTTTTAGCTTAAAACT-TGAT-G-AAGTGATTATTACACGATTTCGG
* *
2981 CTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAAATTTTAGCCACAATACTCATAAAA
446 CTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCACAATACTCATAAAA
*
3046 AATATATAATTCAACGCCAAAAAGATT-AGAGGGCTTTTCACGATTTTAATATCGTTCTTCATAT
511 AATATATAATTCAACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTTTAATATCGTT-TTCATAT
* * * *
3110 TTTTTCTGAATTAATGTCTAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATTCTTA
574 TTTTTCTGAATTAAT-TCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
3175 AATGCAATGTGGCTAACTATTTATT
638 AATGCAATGTGGCTAAC-ATTTATT
* * * *
3200 AGACGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCTTGCAAAACTCAGTCGGGGCCCC
1 AGATGAATATAGATATTTCAAGGAGTCTC-GCGCCAAAAATCATGCAAAACTGAGTC-GGGTCCC
* * * *
3265 GAAACGCGTTTTTATCCAAAAACCATGATGA-ACGTACACGATTT-TGGCTAAAATTTTGCAATA
64 GAAACGCGTTTTTAGCTAAAAACCGTGATGAGAAGTACACGATTTCT-GCTAAAATTTTGCAA-A
* * ** * * *
3328 GA-TGACACGAAATATTTTTTCCTCAATTTTTGGATAAAATGCTCATTAAATATATATAATTTAA
127 AATTGACACGAAAGA-TTTTTCCTCAATTTTTGGCCAAAATTCTCA-TAAAAATATATAATTCAA
* * * * * * * *
3392 CGCCAAAAAGATTGGATGACTTTTCACGCTTTTAATTTCTTTTTTCTTATTTTTTTTTTCTAAAT
190 AG-CAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC-CA---ATTTTTTCTAAAT
* * * * * *
3457 TAATTTTTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAATTTTTTTAAATCCAATCT
250 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA-ATCTTTAAATACAATGT
* * * * * * * *
3522 AGCTGAGATTTGATTAAATGAATATGGATATCTCAAGGA-TGCTTGGGGCCAAAAATCATGCAAA
314 GGATGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-CTTCGTGCCAAAAATCATGCAAA
* * * * * * * * *
3586 ACTGAG-CCGCGCCCTGCATCGCTTTGTTAGC-CAAAAATTG-TG-A-TGGTTATTACACGATTG
378 ACTGAGTCGGGGCCCCGAAACGCTTTTTTAGCTTAAAACTTGATGAAGTGATTATTACACGATT-
* * * * * * *
3646 T-GACTTAAATTTTGTAAAAATTGACTCGAAAGATATTTTCTCAATTTTTAGCTAAAATAGTCAT
442 TCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCACAATACTCAT
* * *
3710 AAAAAATATATAATTCAACACCAAAAAGATTGAAGTGCTTTTCACGCTTTTAATATCATTTGTCA
507 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTT-TCA
* * *
3775 T-TTCTTTCTGATTTAATTTCTAATTAAATAGAAACAAGATTTAGATGCTCGTAAAAACAAATCC
571 TATTTTTTCTGAATTAA-TTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
*
3839 TTAAATGCAATGCGGCTAACATTTTATT
635 TTAAATGCAATGTGGCTAACA-TTTATT
* * * * *
3867 AGATAAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATTATGCTAAATTGAGCCAGGGTCCC
1 AGATGAATATAGATATTTCAAGGAGTCTC-GCGCCAAAAATCATGCAAAACTGAGTC-GGGTCCC
* * * * *
3932 GGAATGCGTTTTTAGGC-AAAAACCGTGATGGTTAGTTAGTACACGATTTCGGCTAAAATTGTGC
64 GAAACGCGTTTTTA-GCTAAAAACCGTGAT-G--AG-AAGTACACGATTTCTGCTAAAATTTTGC
* * * * * * *
3996 AAAAATTGACACGAAAGATTTCTACTCAATTTTTGGCTAAAGTACTTATAAAAATATATAATTTA
124 AAAAATTGACACGAAAGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAATATATAATTCA
* * * ** *
4061 ACGCTAAAAAGATTGTAGGGCTTTTCACGCTTTTAATATCGTATTTCTTATTTTTTGTAAATTAA
189 AAGC-AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTCTAAATTAA
* * *
4126 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTTTTAAATCCAATGT-TAC
253 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATACAATGTGGA-
4190 TGAGATTTGGTTAG
317 TGAGATTTGGTTAG
4204 TTGATGCAAT
Statistics
Matches: 1399, Mismatches: 227, Indels: 100
0.81 0.13 0.06
Matches are distributed among these distances:
663 146 0.10
664 46 0.03
665 35 0.03
666 214 0.15
667 159 0.11
668 130 0.09
669 7 0.01
670 57 0.04
671 42 0.03
672 74 0.05
673 284 0.20
674 68 0.05
675 71 0.05
676 66 0.05
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (661 bp):
AGATGAATATAGATATTTCAAGGAGTCTCGCGCCAAAAATCATGCAAAACTGAGTCGGGTCCCGA
AACGCGTTTTTAGCTAAAAACCGTGATGAGAAGTACACGATTTCTGCTAAAATTTTGCAAAAATT
GACACGAAAGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAATATATAATTCAAAGCAAA
AAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCAATTTTTTCTAAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATACAATGTGGATGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGTCGGGGC
CCCGAAACGCTTTTTTAGCTTAAAACTTGATGAAGTGATTATTACACGATTTCGGCTAAAATTTT
GTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAAT
TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTCATATTTTTTCTGAATT
AATTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGC
TAACATTTATT
Found at i:10372 original size:21 final size:21
Alignment explanation
Indices: 10347--10403 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
10337 AAACAGAATG
*
10347 AAACCCGACACAACAAGTAA-G
1 AAACCCGACACAACAAG-AACA
* * *
10368 TAACCGGAAACAAC-AGAACA
1 AAACCCGACACAACAAGAACA
10388 AAACCCGACACAACAA
1 AAACCCGACACAACAA
10404 TACTATTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 12 0.44
ACGTcount: A:0.54, C:0.30, G:0.12, T:0.04
Consensus pattern (21 bp):
AAACCCGACACAACAAGAACA
Found at i:11510 original size:6 final size:6
Alignment explanation
Indices: 11499--11525 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11489 GTCTGGGTTT
11499 AAATTC AAATTC AAATTC AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAA
11526 ACAACCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:17239 original size:2 final size:2
Alignment explanation
Indices: 17234--17263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17224 GTGTTGTGTG
17234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17264 GTATGCAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17393 original size:2 final size:2
Alignment explanation
Indices: 17386--17426 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
17376 TTTAGTGATC
*
17386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17427 ATTAAGGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.