Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012853.1 Corchorus olitorius cultivar O-4 contig12886, 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: 9577
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:748 original size:15 final size:16
Alignment explanation
Indices: 723--752 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
713 AATAATTATT
723 TTTAGATTATAATATA
1 TTTAGATTATAATATA
739 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
753 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:1856 original size:332 final size:325
Alignment explanation
Indices: 1108--2108 Score: 1085
Period size: 332 Copynumber: 3.0 Consensus size: 325
1098 TCAACAAACC
**
1108 AAATCTCAGTAACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAA
1 AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAA
* * ** * *
1173 ATAGAAATTATTTTAGAAAAATTAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTT
66 TTAGAAATTAATTTAGAAAAAAAAAGAAAAACGATATTAAAAGCGTGAAAA-ACCTCCAATCTTT
* * * *
1238 TTGGTGTTATATTATATA-TTTTATAAGTGTTTTAGCCAAAAATTGAGCAAAAATTTTTCGTGTC
130 TTGGTGTTA-ATTATATATTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTTT-GTGTC
* * * *
1302 AATTTTTGA-ACAATTTTAGCTGAAATCTTGTACTAACTAACCATCACGGTTTTTTGCTGAAAAC
193 AATTTTT-ACAAAATTTTAGC-GAAATC--GT-GTAA-TAACCATCACGGTTTTTGGCT-AAAAA
* * * * * * *
1366 GCATTCCGGGGCTCTGGTTCAATTTAGCATAATTTTTGCCGCTGAGACTCCTTGAAATATCTATA
251 GCATTCC-GGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATA
1431 TTCATCTAATA
315 TTCATCTAATA
* * * * * * *
1442 AAATGTTAGCCGCATTGCATTTAAGGATTTGTTTTTACGAGCATCT-AATCGTGTTTCGATTTAA
1 AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAA
* * * *
1506 TTAGAAATTAAATTAGAAAAAAAAATGAAAAACGATATTAAAAGCATGAAAAACATTTCAATCTT
66 TTAGAAATTAATTTAGAAAAAAAAA-GAAAAACGATATTAAAAGCGTGAAAAAC-CTCCAATCTT
* * *
1571 TTTGGTGTTGAATTATATATTTTTTATGACTATTTTAGCTAAAAATTGAGGAAATATCTTTTGAG
129 TTTGGTGTT-AATTATATA-TTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAAT-TTTTGTG
* *
1636 TCAATTTTTACAAAATTTTAGTCGAAATCGTGTAATAACCATCACAGCTTTTGGCTAACAAAGCA
191 TCAATTTTTACAAAATTTTAG-CGAAATCGTGTAATAACCATCACGGTTTTTGGCTAA-AAAGCA
** * * * ** *
1701 TTCCGGGCCCCGGCTCGGTTTTGCATGATTTTTGGCACCAAGTCTCCTTGAGGTATCCATATTCA
254 TTCCGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
*
1766 TCTAATC
319 TCTAATA
* * * *
1773 ATATCTCAGCCACATTGGATTTAAAAATTTGCTTTTACGAGTATCTGAATCTTGTTTCTATTTAA
1 AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAA
* * * *
1838 TTAAAAATTAATTTAGAAAAAAATAAGAAAAACAAAATTAAAAGCGTGAAAAGTCCTCCAATCTT
66 TTAGAAATTAATTTAGAAAAAAA-AAGAAAAACGATATTAAAAGCGTGAAAA-ACCTCCAATCTT
* * * **
1903 TTTGGCGTTAAATTATATATATTTAATGAGTATTTTATCTAAAAATTGAGGAAAAAAATTTCCGT
129 TTTGGTGTT-AATTATATAT-TTTTATGAGTATTTTAGCTAAAAATTGAGG--AAAAATTTTTGT
* * * * *
1968 GTC-ATCTTTTGCAAAATTTTAGCCAAAATC-TGTACTAACCATCATGGTTTTTGGATAAAAACG
190 GTCAAT-TTTTACAAAATTTTAG-CGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAA-G
* * * *
2031 CGTTTCGCGGCCCCGACTCAATTTTGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTATAT
252 CATTCCG-GGCCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATAT
2096 TCATCTAATA
316 TCATCTAATA
2106 AAA
1 AAA
2109 GGCCTAACGT
Statistics
Matches: 551, Mismatches: 98, Indels: 37
0.80 0.14 0.05
Matches are distributed among these distances:
331 95 0.17
332 170 0.31
333 129 0.23
334 94 0.17
335 2 0.00
336 56 0.10
337 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (325 bp):
AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAA
TTAGAAATTAATTTAGAAAAAAAAAGAAAAACGATATTAAAAGCGTGAAAAACCTCCAATCTTTT
TGGTGTTAATTATATATTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTTTGTGTCAAT
TTTTACAAAATTTTAGCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAGCATTCCGGG
CCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATA
Found at i:3044 original size:332 final size:330
Alignment explanation
Indices: 2348--3052 Score: 823
Period size: 330 Copynumber: 2.1 Consensus size: 330
2338 ATATTAGTCC
* * * * * * *
2348 TCTAATAAAATGTTAGTCGCATTGCATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTC
1 TCTAATAAAATCTCAGACACATTGCATTTAAGGATTTATTTTTACGAGCATATAAATCTTATTTC
* * * * * * *
2413 GATTTATTTAGATATTAATTCAGAAAAAATATGAAAAAAGATATTAAAATCGTGAAAAACCCTTC
66 GATTTAATTACAAATTAATTCAGAAAAAATATAAAAAAAAAGATTAAAAGCGTGAAAAACCCTTC
* * * *
2478 AATCTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTGTTGCTAAAATTTGAGGAAAAGTAT
131 AATATTTTTGGCATTGAATTATATATTTTTTATAAGTATTGTTGCCAAAAATTGAGGAAAAGTAT
* * * * *
2543 TTTCGGGGCAATTTTTGTAAAATATTAGCCGAAATCGTGTACCAACACGGTTTTTTGGCTAAAAA
196 TTTCGGGGCAATTTTTGCAAAATATTAGCCGAAATCGTATAACAACACCGATTTTTGGCTAAAAA
** * *
2608 CGCGTTCCGGGGTCCCAAGCTAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATAACTAT
261 CGCGTTCCAAGCTCCCAAGCTAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATAACTAC
2673 ATTCA
326 ATTCA
* * *
2678 TCTTATAAAATCTCAGACACATTGGATTTAAGGATTTGTTTTTACGAGCATATAAATCTTATTTC
1 TCTAATAAAATCTCAGACACATTGCATTTAAGGATTTATTTTTACGAGCATATAAATCTTATTTC
* * *
2743 GATTTAATTACAAATTAATTCGGAAAAAGTA-AAAAAAACAAGATTAGAAGCGT-AAAAATCCCT
66 GATTTAATTACAAATTAATTCAGAAAAAATATAAAAAAA-AAGATTAAAAGCGTGAAAAA-CCCT
*
2806 TCAATATTTTTGGCATTGAATTATATATTTTTTATGAGTATT-TTAGCCAAAAATTGAGG-AAA-
129 TCAATATTTTTGGCATTGAATTATATATTTTTTATAAGTATTGTT-GCCAAAAATTGAGGAAAAG
* * * ** *
2868 TATCTTTTGGGTCAATTTTTGCAAAATTTTAGTTGAAATCGTATAATAATCATCACGATTTTTGG
193 TAT-TTTCGGGGCAATTTTTGCAAAATATTAGCCGAAATCGTATAACAA-CA-C-CGATTTTTGG
* * * * *
2933 CTAAAAATGCGTTCCAAAGCT-GCGAG-TCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGA
254 CTAAAAACGCGTTCC-AAGCTCCCAAGCT-AGTTTTGCATGATTTTTGGCACCAAGACTCCTTGA
* *
2996 GAT-ATTCACATTCA
317 AATAACT-ACATTCA
* *
3010 TCTAATCAAATCTCAGGCACATTGCATTTAAGGATTTATTTTT
1 TCTAATAAAATCTCAGACACATTGCATTTAAGGATTTATTTTT
3053 GTATACATTC
Statistics
Matches: 313, Mismatches: 52, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
328 3 0.01
329 52 0.17
330 148 0.47
331 4 0.01
332 104 0.33
333 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
TCTAATAAAATCTCAGACACATTGCATTTAAGGATTTATTTTTACGAGCATATAAATCTTATTTC
GATTTAATTACAAATTAATTCAGAAAAAATATAAAAAAAAAGATTAAAAGCGTGAAAAACCCTTC
AATATTTTTGGCATTGAATTATATATTTTTTATAAGTATTGTTGCCAAAAATTGAGGAAAAGTAT
TTTCGGGGCAATTTTTGCAAAATATTAGCCGAAATCGTATAACAACACCGATTTTTGGCTAAAAA
CGCGTTCCAAGCTCCCAAGCTAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATAACTAC
ATTCA
Found at i:4608 original size:335 final size:332
Alignment explanation
Indices: 3156--4803 Score: 1670
Period size: 335 Copynumber: 5.0 Consensus size: 332
3146 TTGGCGTTGT
* ** * * * *
3156 AAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTTTCTTAATAATGCGTTTCGGGGCC
1 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTCGC-TAAAAACGCGTTCCAGGGCC
**** * * * * *
3221 CCGACTCAGTTTTGCATGATTTTTGACATCGAGACTCCTCGAAATATCTATATTTATCTAATCAA
65 CCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATATTTATTCATCTAATCAA
* *
3286 ATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
130 ATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATT
* * * * ** * *
3351 ATAAATTAATTTTGAAAAAA-ATGAAAAACGATATTAAAAGTATGAAAAGTCCTCCAATCTTTTT
195 AGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATC-TTTT
* * *
3415 TCA-GTTGAATTATATATATTTTGTGAGTATTATGGCTAAAAATTGAGG-AAAA----TCGGGTC
259 TGATGTTGAATTATATAT-TTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATCTTTCGGGTC
*
3474 AA-TTTTTGT
323 AATTTTTTGC
** * *
3483 AAAATTTTAGCCGAAATCGTG---T-ACCATCACTATTTTTGGCTAAAATCGCGTTCC-GGGCCC
1 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAAACGCGTTCCAGGG-CC
** *** * *
3543 CCGGGTCAGTTTTGCATGATTTTTGGTTTTAAAACTCCTTGAAATATCA--TATTCATCTAACCA
65 CCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATAT-ATTTATTCATCTAATCA
* * * * *
3606 AATCTTAGCCACATTGGATTTAAGGATTTTTTTTTACGAGCATTTGAATCATGTTTCAATTTAAT
129 AATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
* * * * *
3671 TAGAAGTTAATTTGAAAAAAATAGGAAAAAATGATATTGGAAGCGTGAGAAGCCCTTCAATCTTT
194 TAGAAATTAATTTGGAAAAAATAGG-AAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTT
*** * * **
3736 TTGGCATTGAATTATATATATTTTTGTGAGTATTGTGGCTAAAAATT-A-GAAAAATAATTC-GG
258 TTGATGTTGAA-T-TATATATTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATCTTTCGGG
3798 --AATATTTTTGC
321 TCAAT-TTTTTGC
* * * *
3809 AAAATTTTAGCCGAAATCGTGTAC--A--ATCACGCTTTTTTGGCTAAAAACGCGTTCCA-AGAC
1 AAAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTCGCTAAAAACGCGTTCCAGGGCC
** * * * *
3869 CCGGGTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTAAAATATATCTATATTCATCTAACC
65 CCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATAT-T-TATTCATCTAATC
* * * * * * *
3934 AAATCTCAGTCACATTGTATTTAAGGATTTGGTTTTAAGAGTATCTAAATCTTATTTCAATTTAA
128 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAA
* * *
3999 TCAGCAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAG-ACTTCCAAT
193 TTAGAAATTAATTTGG-AA-AAAATAGGAAAAACGATATTAGAAGCGTG-AAAAGCCCTT-CAAT
* ** ** * * *
4063 TTTTTTGGCGTTGAATTATATATTTTTTATGAGTAAATTCGCTAGAATTTGAGGAAAAATCTTTC
254 CTTTTTGATGTTGAATTATATA-TTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATCTTTC
4128 GGGTC-A-TTTTTGC
318 GGGTCAATTTTTTGC
* * * * * * **
4141 AAAATTTTAGTCGAAATCGTATACTAACCATCACTG-ATTTCGGCTAATAACCCGTTCTGGGGCC
1 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTC-GCTAAAAACGCGTTCCAGGGCC
* * *
4205 CTG-CTCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTGAAATATATGTATTCATCTAATCAA
65 CCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATATTTATTCATCTAATCAA
* * * *
4269 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATT
130 ATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATT
* * *
4334 AGAAATTAATTCGGAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTT
195 AGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
** * * *
4399 GATGTCAAATTATATATTTTTATGAGTATTTTAGCAAAAAAAATTGAGGAAATTATCTTTCGGGT
260 GATGTTGAATTATATATTTTTATGAGTATTTTGGC--TAAAAATTGAGGAAA-AATCTTTCGGGT
4464 CAATTTTTTGC
322 CAATTTTTTGC
* *
4475 AAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTCGCTAAAAACGCGTTCCAGGGCCA
1 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAAACGCGTTCCAGGGCCC
* ** *
4540 TGACTTTGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATATTTATTCATCTAATCAAA
66 CGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATATTTATTCATCTAATCAAA
* * *
4605 TCTCAGCCACATTGCATTTAAGGATTTATTTTTACGTGCATCTGAATTTTGTTTC-ATTTAATTA
131 TCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* * * * * *
4669 GAAATTAATTCTGAAAAAAATATGAAAAACGATATTAAAAGCGTGACAAGTCCTCCAATCTTTTT
196 GAAATTAATT-TGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
*** * * * *
4734 GGCATTGAATTATATATTTTTTATGTGTATTTTTGAC-CAAAATGGAGGAAAAATCTTTCGGGTC
260 GATGTTGAATTATATA-TTTTTATGAGTA-TTTTGGCTAAAAATTGAGGAAAAATCTTTCGGGTC
4798 -ATTTTT
323 AATTTTT
4804 ACTATCATGG
Statistics
Matches: 1097, Mismatches: 174, Indels: 95
0.80 0.13 0.07
Matches are distributed among these distances:
321 90 0.08
322 58 0.05
323 52 0.05
324 29 0.03
325 8 0.01
326 75 0.07
327 44 0.04
328 1 0.00
329 101 0.09
330 71 0.06
331 72 0.07
332 59 0.05
333 98 0.09
334 95 0.09
335 219 0.20
336 20 0.02
337 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (332 bp):
AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAAACGCGTTCCAGGGCCC
CGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATATTTATTCATCTAATCAAA
TCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
GAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
ATGTTGAATTATATATTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATCTTTCGGGTCAAT
TTTTTGC
Found at i:7954 original size:25 final size:26
Alignment explanation
Indices: 7899--7954 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
7889 CTTCTAATAA
*
7899 TTATTTTTAGATTATAATATATATAT
1 TTATATTTAGATTATAATATATATAT
*
7925 ATATATTTA-ATTATAATAT-TATTAT
1 TTATATTTAGATTATAATATATA-TAT
7950 TTATA
1 TTATA
7955 GTCATGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.08
25 17 0.65
26 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTATATTTAGATTATAATATATATAT
Found at i:8927 original size:320 final size:317
Alignment explanation
Indices: 8301--9280 Score: 840
Period size: 320 Copynumber: 3.0 Consensus size: 317
8291 AAAAACATTA
* * *
8301 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAAAAATA
1 TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAATAGAAAA-A
* * * **
8366 TGATATTAAAAGCGTGAAAAGCCCTCCAATCATTTT--GAAGAATTATATATTTTTATGAGTATT
64 CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGCGTTGAATTATATATTTTTATGAGTA-T
**
8429 TTAGCCAAAAATTGAGGAGAAATCTTTCATGTCAATTTTT-CTAAAATTTTAGCCGAAATCGTGT
128 TTAG-----AA--GAGG-GAAATCTTTCGGGTCAATTTTTGC-AAAATTTTAGCCGAAATCGTG-
* * * ** ** *
8493 ACTAACTAACCATCATAGTTTTTGGCTAAAACCGCGTTGCGGGGATCTATCTCAATTTTGCATGA
183 --TAA-TAATCATCATAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGT-TCAGTTTTGCATGA
* * *** * *
8558 TTTTTGTCTCCGAGGTTACTTGAAATACCTATATTCATCTAATCAAATCTCAGCCACATTGGATT
244 TTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATT
8623 TAAGAATTTG
309 TAAG-ATTTG
* *
8633 TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTGATTCAAAAAAATATGAAAAAC
1 TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATA-GAAAAAC
8698 GATATTAAAAGCGTGAAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTAATGAGTA
65 GATATTAAAAGCGTG-AAAAGCCCTTCAATCTTTTT-GCGTTGAATTATATATTTTT-ATGAGTA
* *
8763 -TT-G-AG-GGGATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAAATCATGTAATAAT
127 TTTAGAAGAGGGAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG--AAATCGTGTAATAAT
**
8824 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGTTCAGTTTTGCATGATTTTTGGCGCC
190 CATCATAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGTTCAGTTTTGCATGATTTTTGGCGCC
*
8889 GAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG-C-C------------A-TTG
255 GAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGATTTG
* * * *
8937 TTTTTACAAGCATATGAATCA-CGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAA
1 TTTTTACGAGCATCTGAAT-ATTGTTTCGATTTAATTAGAAATTAATTC-AAAAAAATA-G-AAA
* * *
9001 AACGATATTAGAAGCGTGAAAAGCCATTCAATCTTTTTTGCGTTGAATTATATATTTTTTATTAG
62 AACGATATTAAAAGCGTGAAAAGCCCTTCAATC-TTTTTGCGTTGAATTATATA-TTTTTATGAG
* * * * ** *
9066 TACTGTGGCCAGAAATTAAGGAAAATTATTTCGGGTCAATTTTTGCAAAACATTAGCCGAAATTG
125 TA-T-T---TAG-AA--GAGGGAAA-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* ** ** ** * *
9131 TGTACCATCATGGGTTTTTTTTTTTGGCTAAAAACGCGTTCCGAGGCCCCAGG-TCGGTTTTGCA
181 TGTA--ATAAT-CATCATAGTTTTTGGCTAAAAACGCGTTCCG-GGGCCC-GGTTCAGTTTTGCA
* * *
9195 TGATTTTTGGCGTC-AAGACTCCTTGAAATATCAATATTCATCTAATCAAATCTCAACCACATTG
241 TGATTTTTGGCGCCGAA-ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG
*
9259 GATTTAAGGATTTA
305 GATTTAA-GATTTG
9273 TTTTTACG
1 TTTTTACG
9281 GGTAGAGCTG
Statistics
Matches: 532, Mismatches: 67, Indels: 94
0.77 0.10 0.14
Matches are distributed among these distances:
304 44 0.08
305 46 0.09
306 30 0.06
308 1 0.00
312 1 0.00
314 1 0.00
316 8 0.02
317 4 0.01
318 35 0.07
319 27 0.05
320 122 0.23
321 38 0.07
322 4 0.01
323 32 0.06
324 3 0.01
325 8 0.02
327 1 0.00
331 24 0.05
332 67 0.13
333 1 0.00
334 2 0.00
335 17 0.03
336 16 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (317 bp):
TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATAGAAAAACG
ATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGCGTTGAATTATATATTTTTATGAGTATTTA
GAAGAGGGAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCAT
AGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGTTCAGTTTTGCATGATTTTTGGCGCCGAAACT
CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGATTTG
Found at i:9349 original size:16 final size:16
Alignment explanation
Indices: 9318--9410 Score: 75
Period size: 16 Copynumber: 5.9 Consensus size: 16
9308 GGCGGGTTCA
9318 GGTTCGGGTA-TTTCG
1 GGTTCGGGTATTTTCG
9333 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
* * **
9349 GGCTCAGGT-TAAGTCG
1 GGTTCGGGTAT-TTTCG
* *
9365 GGTTCGTGCATTTTCG
1 GGTTCGGGTATTTTCG
* *
9381 GGCTCGGGTTATGTT-G
1 GGTTCGGG-TATTTTCG
9397 GGTTCGGGTATTTT
1 GGTTCGGGTATTTT
9411 TGAGTTCGGT
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
15 16 0.28
16 37 0.64
17 5 0.09
ACGTcount: A:0.09, C:0.14, G:0.38, T:0.40
Consensus pattern (16 bp):
GGTTCGGGTATTTTCG
Found at i:9366 original size:32 final size:32
Alignment explanation
Indices: 9330--9410 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
9320 TTCGGGTATT
9330 TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
1 TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
* * * *
9362 TCGGGTTCGTGCATTTTCGGGCTCGGGTTATG
1 TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
*
9394 TTGGGTTCGGGTATTTT
1 TCGGGTTCGGGTATTTT
9411 TGAGTTCGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.09, C:0.15, G:0.37, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
Found at i:9436 original size:17 final size:17
Alignment explanation
Indices: 9414--9458 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
9404 GTATTTTTGA
*
9414 GTTCGGTCTCGGGTAGG
1 GTTCGGGCTCGGGTAGG
*
9431 GTTCGGGCTCGGGTCGG
1 GTTCGGGCTCGGGTAGG
9448 GTTCGGGCTCG
1 GTTCGGGCTCG
9459 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.27
Consensus pattern (17 bp):
GTTCGGGCTCGGGTAGG
Done.