Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019688.1 Corchorus olitorius cultivar O-4 contig19721, 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: 25372
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:876 original size:315 final size:315
Alignment explanation
Indices: 302--1764 Score: 1243
Period size: 315 Copynumber: 4.6 Consensus size: 315
292 GTCTGGAGTT
* * * * *
302 CCGACTCAATTTTCAATGATTTTTGGCGCAAAGACTAC-TGAAAATATATATATTCATCGAACCA
1 CCGACTCAATTTTGAATGATTTTTGGCGTAAAGACTCCTTG-AAATATCTATATTCATCTAACCA
* * * **
366 AATCTCAGCCACATTGGA-TACAAGAATTTGTTTTTACGAGCATCCGAATCTTGTTTAAATTTAA
65 AATCTCAGCCACATTGGATTA-AAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA
* * * * * *
430 TTATAAATTAATTCGGAAAAAATGGAAAAAACGATATTGGAAGCGTGAAAAGCCCGTCAAAATTT
129 TTAGAAATTAATTCGGAAAAAAAGG-AAAAACGATATTAGAAGCGTGAAAAACCCTTC-AATTTT
* * * * * **
495 TTGGGGTTTAATTATATATTTATTCTGAATATTTTGCAAAAAAGTGA-G-AAAATTTTCTTCGTG
192 TTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGCAAAAAAGTGAGGAAAAATGAT-TT-GTG
* * * * *
558 TTAGTTTTTAGCCGAAATCATG-T-CATCATGGGTTTTGGCCAAAAATGCGTTTCGAGGCC
255 TTAGTTTTTAGCCGAAATCATGTTACATCACGGTTTTTGGCTAAAAACGTGTTTCGAGGCC
* *
617 CCGACTCAATTTTGTATGATTTTTGGCAG-AAAGACTCTTTGAAATATCTATATTCATCTAACCA
1 CCGACTCAATTTTGAATGATTTTTGGC-GTAAAGACTCCTTGAAATATCTATATTCATCTAACCA
** *
681 AATCTCAGCCTTATTGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
65 AATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAAT
* *
746 TAAAAATAAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT
130 TAGAAATTAATTCGG-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT
* *
811 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGACAAAGAATTGAGGAAAAATGATTTGTGTTA
194 GGCGTTGAATTATATATTTTTTCTGAGTATTGTG-CAAAAAAGTGAGGAAAAATGATTTGTGTTA
** * * * *
876 GTTTTT-GCAAAATTTTAGTCGAAATTGTTTACTCATCACCGTTTTTGGCTAAAAATGTGTTCCA
258 GTTTTTAGCCGAA----A-TC---A-TG-TTA--CATCACGGTTTTTGGCTAAAAACGTGTTTCG
940 AGGCC
311 AGGCC
* * ** *
945 TC-AGCTCAGTTTTGAATGATTTTTATCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCA
1 CCGA-CTCAATTTTGAATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCA
* * * * **
1009 AATCTCAGGCACATTGGATTTAACGATTTGTTTTTACGAGAATTTGAATCTTGTTTCGATTTTTT
65 AATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAAT
* * * * *
1074 TAGAAATTAATTC-GTAAAAAA--AAAGA--ATATTGGAAGCGTGAAAAACTCTTTAATCTTTTT
130 TAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT-TTTTT
* * * * * **
1134 GGGGTTGAATTATATATTTTTTATGAGTGTTGTGGCAAAAAATTGAGAAAACAAAAATTCTG-GT
194 GGCGTTGAATTATATATTTTTTCTGAGTATTGT-GCAAAAAAGTGAGGAAA-AATGATT-TGTGT
* * * * *
1198 CAGTTTGTAGCCGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGTGTTTC-AGGGC
256 TAGTTTTTAGCCGAAATCATGT--T-A-CATCACG-GTTTTTGGCTAAAAACGTGTTTCGA-GGC
1262 C
315 C
* * * * ** * *
1263 TTC-TCTTAGTTTTGTACGGA-TTTTGGCATAAAGACTCCTTGAAATATTTATATTCATCTAACC
1 -CCGACTCAATTTTG-AATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * * *
1326 AAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTAA
64 AAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA
* * * *
1391 TTAGAAATAAATTCGG-GAAAATGGAAAAACGATATTAGAAGCGT-TAAAACCCTTCAATTTTTT
129 TTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT
* *
1454 GGCTTTGAATTATATATTTTTT-TGAGTATTGTGTCAAAAAAGTGAGCAAAAACTTTTCGGGTAA
194 GGCGTTGAATTATATATTTTTTCTGAGTATTGTG-CAAAAAAGTGAGGAAAAA----T---G--A
* ** ** * * ** *
1518 GTTTTTGCAAAATTTTAGCTGAAAT--TGTGTAC-TAACCATTTTTGGCTAAAAACGTGTTCTGG
249 -TTTGTGTTAGTTTTTAGCCGAAATCATGT-TACATCACGGTTTTTGGCTAAAAACGTGTT-TCG
*
1580 A-GAC
311 AGGCC
* * * * *
1584 CCGACTTAATTTTGCATGATTTTTTGCGTAAAAACTCCTTGAATTATCTATATTCAT-TGAACCA
1 CCGACTCAATTTTGAATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCT-AACCA
* * **
1648 AATCTCAGCCACATTGGA-TATAAGGATTTGTTTTTACGAGAATCTGAATGTTATTTTAATTTAA
65 AATCTCAGCCACATTGGATTA-AAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA
* * *
1712 TTAGAATTTAATTCTGAAAAAAAAAACGGAAAAACGATTTTAGAAGCGTGAAA
129 TTAGAAATTAATTC-G--GAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAA
1765 GCGCAAAGAC
Statistics
Matches: 932, Mismatches: 152, Indels: 116
0.78 0.13 0.10
Matches are distributed among these distances:
314 40 0.04
315 173 0.19
316 18 0.02
317 14 0.02
318 148 0.16
319 31 0.03
320 36 0.04
321 144 0.15
322 43 0.05
323 53 0.06
324 19 0.02
325 12 0.01
326 30 0.03
327 7 0.01
328 164 0.18
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (315 bp):
CCGACTCAATTTTGAATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCAA
ATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATT
AGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGG
CGTTGAATTATATATTTTTTCTGAGTATTGTGCAAAAAAGTGAGGAAAAATGATTTGTGTTAGTT
TTTAGCCGAAATCATGTTACATCACGGTTTTTGGCTAAAAACGTGTTTCGAGGCC
Found at i:2205 original size:480 final size:472
Alignment explanation
Indices: 1292--2213 Score: 1076
Period size: 480 Copynumber: 1.9 Consensus size: 472
1282 ATTTTGGCAT
* * * * *
1292 AAAGACTCCTTGAAATATTTATATTCATCTAACCAAATCTTAGCTACATTGGATTTAAGGATTTG
1 AAAGACTCCTTCAAATATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAGGATTTG
*** * ** * *
1357 TTTTTACGAGTATCTGAATCTTGTTTCGTTTTAATTAGAAATAAATTCGGGAAAATGGAAAAACG
66 TTAAAACAAACATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGGAAAATGGAAAAACG
* *
1422 ATATTAGAAGCGTTAAAACCCTTCAATTTTTTGGCTTTGAATTATATATTTTTTTGAGTATTGTG
131 ATATTAGAAGCGTAAAAACCCGTCAATTTTTTGGCTTTGAATTATATATTTTTTTGAGTATTGTG
* * *
1487 TCAAAAAAGTGAGCAAAAACTTTTCGGGTAAGTTTTTGCAAAATTTTAGCTGAAATTGTGTACTA
196 GCAAAAAAGTGAGCAAAAACTTTTCGGG-AA----TTGCAAAATTTTAGCCGAAATCGTGTACTA
* * * * *
1552 ACCATTTTTGGCTAAAAACGTGTTCTGGAGACCCGACTTAATTTTGCATGATTTTTTGCGTAAAA
256 ACCATTTTTGCCTAAAAACGTGTTCTGGAGACACGACTCAATTTTCCATGATTTTTTGCATAAAA
* *
1617 ACTCCTTGAATTATCTATATTCATTGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTT
321 ACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGAATATAAGGATTTGTTTT
* * *
1682 TACGAGAATCTGAATGTTATTTTAATTTAATTAGAATTTAATTCTGAAAAAAAAAACGGAAAAAC
386 TACGAGAATCTGAATCTTATTTCAATTTAATTAGAAATTAATTCTGAAAAAAAAAACGGAAAAAC
1747 GATTTTAGAAGCGTGAAAGCGC
451 GATTTTAGAAGCGTGAAAGCGC
1769 AAAGACTCCTTCAAATATCTATATTCATCGAACCAAAT-TTCAGCCACATTGGATATAAGGATTT
1 AAAGACTCCTTCAAATATCTATATTCATCGAACCAAATCTT-AGCCACATTGGATATAAGGATTT
* *
1833 G-TAAAACAAACATCTGAATCTTATTTCGATTTAATTAGAAATTAATT-GGGAAAAAATGGAATA
65 GTTAAAACAAACATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGG--AAAATGGAAAA
*
1896 ACGATATTAGTAGCGTGAAAAACCCGTCAATCTTTTTGG-TGTTGAATTATATATATATATATTT
128 ACGATATTAGAAGCGT-AAAAACCCGTCAAT-TTTTTGGCT-TTGAATTATATAT-T-T-T-TTT
* ** * *
1960 TAGTATTGTGGCAAAAATTTGAGGAAAAACTTTTC-GG-A-T-C-AATTTTTAGCCGAAATCGTG
186 GAGTATTGTGGCAAAAAAGTGAGCAAAAACTTTTCGGGAATTGCAAAATTTTAGCCGAAATCGTG
* * * * *
2020 TACTAACCATCACGGTTTTTGCCTAAAAATGCGT-TTC-GGGGTCACGTCTCAGTTTTCCATGGT
251 TACTAA-C--CA---TTTTTGCCTAAAAA--CGTGTTCTGGAGACACGACTCAATTTTCCATGAT
* * ** * *
2083 TTTTTGGCATAAAGACTCCTTGAAATATCTTTATTCATCT-AATTAAATCTCAGTCATATTGAAT
308 TTTTT-GCATAAAAACTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGCCACATTGAAT
* * * *
2147 TTAAGGATTTGTTTTTACGTGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCTGAAAA
371 ATAAGGATTTGTTTTTACGAGAATCTGAATCTTATTTCAATTTAATTAGAAATTAATTCTGAAAA
2212 AA
436 AA
2214 TATGAAAAAC
Statistics
Matches: 374, Mismatches: 51, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
473 23 0.06
474 2 0.01
475 4 0.01
476 41 0.11
477 82 0.22
478 13 0.03
479 56 0.15
480 112 0.30
481 5 0.01
482 3 0.01
483 33 0.09
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (472 bp):
AAAGACTCCTTCAAATATCTATATTCATCGAACCAAATCTTAGCCACATTGGATATAAGGATTTG
TTAAAACAAACATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGGAAAATGGAAAAACG
ATATTAGAAGCGTAAAAACCCGTCAATTTTTTGGCTTTGAATTATATATTTTTTTGAGTATTGTG
GCAAAAAAGTGAGCAAAAACTTTTCGGGAATTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
TTTTGCCTAAAAACGTGTTCTGGAGACACGACTCAATTTTCCATGATTTTTTGCATAAAAACTCC
TTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGAATATAAGGATTTGTTTTTACGA
GAATCTGAATCTTATTTCAATTTAATTAGAAATTAATTCTGAAAAAAAAAACGGAAAAACGATTT
TAGAAGCGTGAAAGCGC
Found at i:10273 original size:12 final size:12
Alignment explanation
Indices: 10247--10289 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
10237 GCCAAGACAC
10247 AAAAACAGGG-G
1 AAAAACAGGGTG
*
10258 AAAAACAGGGTA
1 AAAAACAGGGTG
*
10270 AAAAACAGAGTG
1 AAAAACAGGGTG
10282 AAAAACAG
1 AAAAACAG
10290 AGCATGAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.60, C:0.09, G:0.26, T:0.05
Consensus pattern (12 bp):
AAAAACAGGGTG
Found at i:13094 original size:1 final size:1
Alignment explanation
Indices: 13088--13113 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13078 CTTCAAAGAG
13088 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13114 ACCTAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13192 original size:21 final size:22
Alignment explanation
Indices: 13148--13208 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
13138 TTATTTCCCA
* *
13148 TTATCTTATTATTTTATTCTATC
1 TTATCTTACTATCTTA-TCTATC
13171 TTATCTTACTATCTTA-CTATC
1 TTATCTTACTATCTTATCTATC
*
13192 TTTTCTTACTATCTTAT
1 TTATCTTACTATCTTAT
13209 AAAATCACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.59
23 14 0.41
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATCTTACTATCTTATCTATC
Found at i:13206 original size:8 final size:8
Alignment explanation
Indices: 13172--13207 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
13162 TATTCTATCT
13172 TATCTTAC
1 TATCTTAC
13180 TATCTTAC
1 TATCTTAC
13188 TATCTT--
1 TATCTTAC
13194 T-TCTTAC
1 TATCTTAC
13201 TATCTTA
1 TATCTTA
13208 TAAAATCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
5 4 0.16
6 1 0.04
7 1 0.04
8 19 0.76
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (8 bp):
TATCTTAC
Found at i:13633 original size:233 final size:235
Alignment explanation
Indices: 13180--13653 Score: 713
Period size: 241 Copynumber: 2.0 Consensus size: 235
13170 CTTATCTTAC
* * *
13180 TATCTTACTATCTTTTCTTACTATCTTATAAAATCACGAACTCAAAAATTCAAATTGGGAAATTT
1 TATCTTACCATCTTTACTTACTATCTTATAAAATCACGAACTCAAAAATTCAAATTGGAAAATTT
* *
13245 CATAAATACCCTTAATATTATAGTGTAATAATTTTTTAATAAGTATTCTTTTTAGTCATTTAACT
66 CATAAATACCCTTAATATTATAGTATAATAATTTTTTAATAAGTATTCTTTTTAGACATTTAA--
* ** *
13310 TTTTTTATTTTTTTAGATGATTAATTCAACCTTTTTATTAATAATGAAAATTTTTTGTAAATCCA
129 ----TTATTTTTTTAGATGATTAATTCAACATTTTTATTAATAATGAAAAGATATTGTAAATCCA
* *
13375 ATATTTAAATTTTTTAAATTAGGGAAAGATATTAATAATCCACTAT
190 ATATTTAAATTTTTTAAATTAGGGAAAAATATTAATAACCCACTAT
*
13421 TATCTTACCATC-TTACTATACTA-CTATATAAAATCACGAATTCAAAAATTCAAATTGGAAAAT
1 TATCTTACCATCTTTACT-TACTATCT-TATAAAATCACGAACTCAAAAATTCAAATTGGAAAAT
* *
13484 TTTATAAATACCCTTAGTATTATAGTATAATAATTTTTTAATAAGTATTCTTTTTAGACATTTAA
64 TTCATAAATACCCTTAATATTATAGTATAATAATTTTTTAATAAGTATTCTTTTTAGACATTTAA
*
13549 -T-TTTTTTTAGATGATTAATTCAACATTTTTATTAATAATGGAAAGATATTGTAAATCCAATAT
129 TTATTTTTTTAGATGATTAATTCAACATTTTTATTAATAATGAAAAGATATTGTAAATCCAATAT
13612 TTAAATTTTTTAAATTAGGGAAAAATATTAATAACCCACTAT
194 TTAAATTTTTTAAATTAGGGAAAAATATTAATAACCCACTAT
13654 AATTGTAAAT
Statistics
Matches: 216, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
233 97 0.45
234 1 0.00
240 6 0.03
241 112 0.52
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (235 bp):
TATCTTACCATCTTTACTTACTATCTTATAAAATCACGAACTCAAAAATTCAAATTGGAAAATTT
CATAAATACCCTTAATATTATAGTATAATAATTTTTTAATAAGTATTCTTTTTAGACATTTAATT
ATTTTTTTAGATGATTAATTCAACATTTTTATTAATAATGAAAAGATATTGTAAATCCAATATTT
AAATTTTTTAAATTAGGGAAAAATATTAATAACCCACTAT
Found at i:13716 original size:15 final size:15
Alignment explanation
Indices: 13696--13731 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
13686 TTATTTTTAG
13696 ATTATAATATAATTA
1 ATTATAATATAATTA
*
13711 ATTATAATATTATTA
1 ATTATAATATAATTA
*
13726 TTTATA
1 ATTATA
13732 GTCATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATAATATAATTA
Found at i:18136 original size:326 final size:329
Alignment explanation
Indices: 16557--18269 Score: 1533
Period size: 328 Copynumber: 5.2 Consensus size: 329
16547 CTTCTTAGTG
* * ** *
16557 TTGAATTATATATATTTTATGAGTATTGT-GTTTAAAAATTGAGGAATAATATTTTTGGTCATTT
1 TTGAATTATATATATTTTATGAGTATTTTAG-TTAAAAATTGAGGAA-AATCTTTCAGGTCA--A
* * * * * *** *
16621 TTTTTGCAAAATTTTAACTGAAATCGTGTACTAACCATCACAGTTTTTTTACTAAAAACGCGTTT
62 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTGATCATCAC-GGTTTTCGGCTAAAAACGCGTTC
* * * * * ** *
16686 C-GGAGTCTCGGCACAATTTTGCATGATTTTTGGCGAAGAGACTCCTTCAAATATCTATATTCAT
126 CAGG-GCCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCAT
** * * *
16750 CTAATGAAGTCTCAGCCATATTGCATTTAAGGATTTATTTTTTTTACAAGTATCTGAATCTTGTT
190 CTAACCAAATCTCAGCCAAATTG-ATTTAAGGATTTA---TTTTTACAAGCATCTGAATCTTGTT
* * **
16815 TCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTACAAGCGT-AAAATGTTC-
251 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-GCCCT
16878 TCTAATCTTTTTT-G-A
315 TC-AAT-TTTTTTGGCA
* ** * * * *
16893 GTTGAATTATATATATTTTATAAGTATTTTAGACAAAATTTGAGAAGAAATATTTCTGGTCAATT
1 -TTGAATTATATATATTTTATGAGTATTTTAGTTAAAAATTGAGGA-AAATCTTTCAGGTCAATT
* * * * *
16958 TTTGCAAAATATTAGCCGAAATTGTGTA-TGTTAGTCGAAATCACAGTTTTTGACTAAAAACGCG
64 TTTGCAAAATTTTAGCCGAAATCGTGTACTG--A-TC---ATCACGGTTTTCGGCTAAAAACGCG
* * * ** * * *
17022 CTCCTGGGCCCAGGTTC-GATGTTGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTACATT
123 TTCCAGGGCCCCGACTCAG-TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATT
* *** ** *
17086 CATCTAATCAAAAT-TCAGCCAAATTGGATTTAAGGATTT-TTAAAACAAGCAAATGAATCATGT
187 CATCTAA-CCAAATCTCAGCCAAATT-GATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGT
* * * * *
17149 TTTGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCC
250 TTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* *
17214 CTTCAATCTTTTTGGCG
313 CTTCAATTTTTTTGGCA
* * * * * **
17231 TTGAATTATATA-ATTTTTAGGATTATTGTGGTTAAAAATTGAGGAAATAACTTTC-GAGTTGAT
1 TTGAATTATATATA-TTTTATGAGTATTTTAGTTAAAAATTGAGGAAA-ATCTTTCAG-GTCAAT
** * * *
17294 TTTTGCAAAATTCCAGCCGATCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAAAACGCGT
63 TTTTGCAAAATTTTAG-C---CGAAATCGTGTACTGATCATCACGGTTTTCGGCTAAAAACGCGT
* * * * * * *
17359 TCCAAGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAGATATCCATATTCA
124 TCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
* ** * * *
17424 TTTAACCAAATCTCAGTTAAATTGGATTTAAGAATTTGTTTTTACAAGCATCTAAATCTTGTTTC
189 TCTAACCAAATCTCAGCCAAATT-GATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTTTC
*
17489 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCA
253 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
*
17554 ATTTTTTTGGCG
318 ATTTTTTTGGCA
** *
17566 TTGAATTATATATATTTTATGAGTATTTTAGCAAAAAATTGACGGAATAAT-TCTTCAGGTCATT
1 TTGAATTATATATATTTTATGAGTATTTTAGTTAAAAATTGA-GGAA-AATCT-TTCAGGTCA-A
* * *
17630 TTTTTACAAAATTTTAGCCGAAATCTTGTAC-G-T--T-ACGCTTTTCGGCTAAAAACGCGTTCC
62 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTGATCATCACGGTTTTCGGCTAAAAACGCGTTCC
* * *
17690 AGGGCCCCAACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCT
127 AGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCT
* * *
17755 AATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGAT
192 AACCAAATCTCAGCCAAATTG-ATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTTTCGAT
* ***
17820 TTAATTAGAAATTAATTCACAAAAATATGAAAAACGATATTAAAAGCGTGAACAAGGATTTCAAT
256 TTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA-AAGCCCTTCAAT
17885 TTTTTTGGCA
320 TTTTTTGGCA
* * *
17895 TTGAATTATAGT-T-TTTTATGAGTATTTTCGTTATAAATCGAGGAAAATCTTTC-GGATCAATT
1 TTGAATTATA-TATATTTTATGAGTATTTTAGTTAAAAATTGAGGAAAATCTTTCAGG-TCAATT
* *
17957 TTTAGCAAACTTTTAGCCGAAATCGTGTACTGATCATCACGGTTTTCGGCTAAAAATGCGTTCC-
64 TTT-GCAAAATTTTAGCCGAAATCGTGTACTGATCATCACGGTTTTCGGCTAAAAACGCGTTCCA
* * * * *
18021 GGGGCCCGACTCAGTTTTGCATGATTTATGGTG-C-A-A-TCTTTGAAATATCTACATTCATCTA
128 GGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTA
* * *
18082 ACCAAATCTCAGACACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTT--A--
193 ACCAAATCTCAGCCAAATT-GATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTTTCGATT
* * * *
18143 -AATT----A--AA-TCGGAAAAA-ATTGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAAT
257 TAATTAGAAATTAATTCAGAAAAATA-T-GAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
* **
18199 CTTTTTGGTG
320 TTTTTTGGCA
* * ** *
18209 TCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCA
1 TTGAATTATATATATTTTATGAGTATTTTAGTTAAAAATTGAGGAAA-ATCTTTCAGGTCA
18270 TCACGGTTTT
Statistics
Matches: 1139, Mismatches: 184, Indels: 127
0.79 0.13 0.09
Matches are distributed among these distances:
313 2 0.00
314 34 0.03
315 51 0.04
316 10 0.01
317 3 0.00
321 4 0.00
324 1 0.00
325 7 0.01
326 111 0.10
327 9 0.01
328 210 0.18
329 30 0.03
330 29 0.03
331 25 0.02
333 11 0.01
334 1 0.00
335 152 0.13
336 128 0.11
337 194 0.17
338 9 0.01
339 94 0.08
340 12 0.01
341 11 0.01
342 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (329 bp):
TTGAATTATATATATTTTATGAGTATTTTAGTTAAAAATTGAGGAAAATCTTTCAGGTCAATTTT
TGCAAAATTTTAGCCGAAATCGTGTACTGATCATCACGGTTTTCGGCTAAAAACGCGTTCCAGGG
CCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACC
AAATCTCAGCCAAATTGATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTTTCGATTTAAT
TAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATTTTTTT
GGCA
Found at i:23944 original size:16 final size:16
Alignment explanation
Indices: 23919--23954 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
23909 ATATATATTA
23919 CTCATCTTATTAGTTT
1 CTCATCTTATTAGTTT
*
23935 CTCATTTTATTAGTTT
1 CTCATCTTATTAGTTT
23951 CTCA
1 CTCA
23955 ACACCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (16 bp):
CTCATCTTATTAGTTT
Done.