Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009487.1 Corchorus capsularis cultivar CVL-1 contig09508, 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: 4586
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Found at i:106 original size:28 final size:28
Alignment explanation
Indices: 66--121 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
56 AATGCGGAGT
*
66 GTGGAATGTTCGAAATGGGAGCTGCTAC
1 GTGGAATGTTCGAAATGCGAGCTGCTAC
*
94 GTGGGATGTTCGAAATGCGAGCTGCTAC
1 GTGGAATGTTCGAAATGCGAGCTGCTAC
122 TTCGAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (28 bp):
GTGGAATGTTCGAAATGCGAGCTGCTAC
Found at i:182 original size:31 final size:31
Alignment explanation
Indices: 146--237 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
136 AGAGCACCAC
146 TGTGTCTTCTCGTGTACCTTCGTGTGTGT-T
1 TGTGTCTTCTCGTGTACCTTCGTGTGTGTCT
176 GTGTGTCTTCTCGTGTACCTT--TGTGTGTCT
1 -TGTGTCTTCTCGTGTACCTTCGTGTGTGTCT
* *
206 TGTGTCTTCTTGTTTACCTTCGTGTGTGTCT
1 TGTGTCTTCTCGTGTACCTTCGTGTGTGTCT
237 T
1 T
238 CTCATGTAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
29 25 0.45
30 1 0.02
31 30 0.54
ACGTcount: A:0.03, C:0.20, G:0.25, T:0.52
Consensus pattern (31 bp):
TGTGTCTTCTCGTGTACCTTCGTGTGTGTCT
Found at i:442 original size:54 final size:54
Alignment explanation
Indices: 232--672 Score: 710
Period size: 54 Copynumber: 8.2 Consensus size: 54
222 CCTTCGTGTG
*
232 TGTCTTCTCATGTAGC-TTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
285 TGTCTTCTCGTGTAG-TTTCGTGTCTGCTGGCCTCACCTCACTGTGGAGGCCTT
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
*
338 TGTCTTCTCGTGTAGCTTT-GTGTCTGCTGGCCTCGCCTCACTACGGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
391 TGTCTTCTCGTGTAGCTTTCGTGCCTGCTGGCCTCGCCTCACTGCGGAGGCCTT
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
445 TGTCTTCTCGTGTAGCTTTCATGTCTGCTGGCCTCGCTTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
*
499 TGTCTTCTCGTGTAGC-TTCGTGTCTGCTGGCCTCGCCTCACTACGGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
552 TGTCTTCTTGTGTAGCTTTCGTGTTTGCTGGCCTCGCCTCACTGCGGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * * *
606 TGTCTTCTCATGTAGCTTTCATGTATGCTGGCCTCGCCTCACTGCAGAGGCCTC
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
660 TGTCTTCTCGTGT
1 TGTCTTCTCGTGT
673 CTTCATGTGT
Statistics
Matches: 357, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
53 161 0.45
54 196 0.55
ACGTcount: A:0.07, C:0.32, G:0.26, T:0.35
Consensus pattern (54 bp):
TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
Found at i:524 original size:161 final size:161
Alignment explanation
Indices: 232--672 Score: 742
Period size: 161 Copynumber: 2.8 Consensus size: 161
222 CCTTCGTGTG
*
232 TGTCTTCTCATGTAGC-TTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
* * * * *
296 GTAG-TTTCGTGTCTGCTGGCCTCACCTCACTGTGGAGGCCTTTGTCTTCTCGTGTAGCTTTGTG
66 GTAGCTTTCATGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTG
360 TCTGCTGGCCTCGCCTCACTACGGAGGCCTC
131 TCTGCTGGCCTCGCCTCACTACGGAGGCCTC
* *
391 TGTCTTCTCGTGTAGCTTTCGTGCCTGCTGGCCTCGCCTCACTGCGGAGGCCTTTGTCTTCTCGT
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
*
456 GTAGCTTTCATGTCTGCTGGCCTCGCTTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTG
66 GTAGCTTTCATGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTG
521 TCTGCTGGCCTCGCCTCACTACGGAGGCCTC
131 TCTGCTGGCCTCGCCTCACTACGGAGGCCTC
* * *
552 TGTCTTCTTGTGTAGCTTTCGTGTTTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCAT
1 TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
* *
617 GTAGCTTTCATGTATGCTGGCCTCGCCTCACTGCAGAGGCCTCTGTCTTCTCGTGT
66 GTAGCTTTCATGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGT
673 CTTCATGTGT
Statistics
Matches: 263, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 15 0.06
160 50 0.19
161 198 0.75
ACGTcount: A:0.07, C:0.32, G:0.26, T:0.35
Consensus pattern (161 bp):
TGTCTTCTCGTGTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
GTAGCTTTCATGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGTAGCTTCGTG
TCTGCTGGCCTCGCCTCACTACGGAGGCCTC
Found at i:683 original size:107 final size:106
Alignment explanation
Indices: 232--672 Score: 661
Period size: 107 Copynumber: 4.1 Consensus size: 106
222 CCTTCGTGTG
* *
232 TGTCTTCTCATGTAGCTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTG
1 TGTCTTCTCGTGTA-CTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTG
* * *
297 TAG-TTTCGTGTCTGCTGGCCTCACCTCACTGTGGAGGCCTT
65 TAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
*
338 TGTCTTCTCGTGTAGCTTTGTGTCTGCTGGCCTCGCCTCACTACGGAGGCCTCTGTCTTCTCGTG
1 TGTCTTCTCGTGTA-CTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTG
* *
403 TAGCTTTCGTGCCTGCTGGCCTCGCCTCACTGCGGAGGCCTT
65 TAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* *
445 TGTCTTCTCGTGTAGCTTTCATGTCTGCTGGCCTCGCTTCACTGCGGAGGCCTCTGTCTTCTCGT
1 TGTCTTCTCGTGTA-CTTT-GTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
*
510 GTAGC-TTCGTGTCTGCTGGCCTCGCCTCACTACGGAGGCCTC
64 GTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
* * *
552 TGTCTTCTTGTGTAGCTTTCGTGTTTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCAT
1 TGTCTTCTCGTGTA-CTTT-GTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGT
* * *
617 GTAGCTTTCATGTATGCTGGCCTCGCCTCACTGCAGAGGCCTC
64 GTAGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
660 TGTCTTCTCGTGT
1 TGTCTTCTCGTGT
673 CTTCATGTGT
Statistics
Matches: 310, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
106 65 0.21
107 153 0.49
108 92 0.30
ACGTcount: A:0.07, C:0.32, G:0.26, T:0.35
Consensus pattern (106 bp):
TGTCTTCTCGTGTACTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCTCGTGT
AGCTTTCGTGTCTGCTGGCCTCGCCTCACTGCGGAGGCCTC
Found at i:1062 original size:22 final size:22
Alignment explanation
Indices: 1034--1078 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1024 CCCAAATTGT
1034 GTGTTGTTTGTGATTGGATGGA
1 GTGTTGTTTGTGATTGGATGGA
1056 GTGTTGTTTGTGATTGGATGGA
1 GTGTTGTTTGTGATTGGATGGA
1078 G
1 G
1079 ATACAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.44
Consensus pattern (22 bp):
GTGTTGTTTGTGATTGGATGGA
Found at i:3003 original size:322 final size:323
Alignment explanation
Indices: 1996--4578 Score: 3291
Period size: 323 Copynumber: 8.1 Consensus size: 323
1986 CCTTGAAAAA
* * * * *
1996 CGAAACAAATCTCAGCCATAATGGATTTAAGG-GTTGTTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* * * *
2060 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAGACGATATTGAAAGCGTGATAAACCCCT--
66 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTTAA
* *
2123 TTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCA-AAAAAAAATTT
131 TTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAATTT
*
2187 TCAGGTCAATTCTTATTCAAAATCGT-T--T-A-CATCACTGTTATTGGGCTAAAAACGCGTTTC
196 TCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTC
* *
2247 GAGGCACCGGCACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
261 GAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCAT
* * *
2310 CGAACCAAATCTCAGCCATAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* *
2375 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGACATTGGAAGCGTGAAAAATCCGTT-
66 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAA-CCCTTA
* * * ****
2439 AGTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAATTTTTT
130 ATTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAATT
* *
2504 TTCAGGTCAATTCTTAGTCGAAATCGTGTACTAATCATCACTGTTATTGGGCTAAAAACGCGTTT
195 TTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTT
*
2569 CGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
260 CGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCAT
* * * * *
2633 CGAATCAAATCTCAGCCATAATGGATTTAAGGATTTG-TTTTAACGAGCATCTGAATTATGTTTT
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTT-ACGAGCATCTGAATTTTGTTTC
* *
2697 GATTTAATTAGAAATAAATTCGGAAAGAAATGAGAAAACGATATTGGAAGCGTGAAAAATCCGTT
65 GATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAA-CCCTT
* * * * * **
2762 -ATTTTTTTTGGGTTGAATTGCATATTTTTTCGGAGTATTGAGACAAAAATTTCAG-AAAAATTT
129 AATTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAAT
* * *
2825 TTTCAGGTCAATTCTTAGTCGAAATCGTGTACAAACCATCACTGTTATTGGGCTAAAAACGTGTT
194 TTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTT
* * *
2890 TCGAGGCACCGACACAGTTTTGCATGATTTTTGACAGAGAGTCTACTTGAAATATCTCTATTCAT
259 TCGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCAT
* * *
2955 CTAACCAAATCTCAGCCACGTTGGATTTAAGGATTTGGTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* * * *
3020 ATTTAATGAGAAAAAAAATCGGAAAAAAATTGGGAAAACGATATTGGAAGCGTGAAAAACCCTTC
66 ATTTAATTAGAAATAAATTCGGAAAGAAA-TGGGAAAACGATATTGGAAGCGTGAAAAACCCTT-
* * * * *
3085 AATATTTTTTGCGTTAAATTATATA-TTTTTCTGAGTATTGT-AGC-AAGACTTCAGAAAAAAAA
129 AATTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGA-CAAAAATTTCAGAAAAAAAA
* * *
3147 ATTTCAGGTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGT
193 TTTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGT
* * *
3212 TTCGAGGCACCGGCACAATTTTGCATGATTTTTGGCAGATAGCCTCCTTGAAATATCTCTATTCA
258 TTCGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCA
3277 T
323 T
* *
3278 CAAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
** *
3343 AAATAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAATCCCTT-A
66 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTTAA
* ** * * *
3407 TTTTTTTTGGGTTGTATTACATATTTTTTCCGAGTATAGAGACAAAAATTTCAGAAAAAAATTTT
131 TTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAATTT
* * * * *
3472 TCAGGTCAATTCTTAGTCGAAATTGTGTACTAACCGTCACTGTTATTGGGCTAAGAACGCGTTTT
196 TCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTC
* * * * **
3537 GAGGCCCCGACTCAGTTTTGAATGATTTTTGGCTGAGAATCTCCTTGAAATATCTCTATTCAT
261 GAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCAT
* * *
3600 CAAACCAAATATCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* * * *
3665 ATTTAATCAGAAAAAAATTCGGAAAAAAAATGGGAAAACGATATTGGAAGCGTGAAAAAACCTTC
66 ATTTAATTAGAAATAAATTCGG-AAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTT-
* * * *
3730 AATATTTTTTTGCGTTAAATTATATA-TTTTTCCGAGTATTGTGGCAAGACTTT-AG-AAAAAAA
129 AAT-TTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAA
* * *
3792 TTTTCAGGTCAATTCTCAGCCAAAATCGTG---------T-AC-GTTATTGGGCT-AAAACGCAT
193 TTTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGT
* * * * *
3845 TTCGAGGCACTGGCACTGTTTTGCAT-ATTTTTGACAGAGAGTCTCCTTGAAATATCTCTATTCA
258 TTCGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCA
3909 T
323 T
* * *
3910 CGATCCAAATCTCAGCCACGTTGGATTTAAGGATTTGGTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* * *
3975 ATTTAATTAGAAA-AAAATCGGAAAAAAATTGGGAAAACAATATTGGAAGCGTGAAAAACCCTTC
66 ATTTAATTAGAAATAAATTCGGAAAGAAA-TGGGAAAACGATATTGGAAGCGTGAAAAACCCTT-
* * * * ** * * *
4039 AATATTTTTTGCCTTAAATTATATATTTTTGCTAAGTATTGTGGC-AAAACTTAAGAAAAAAAAT
129 AATTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAAT
* * * * *
4103 AATTTCAGGCCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTAGGCTAAAACCGCG
194 --TTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCG
* * * * **
4168 TTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTGAGAATCTCCTTGAAATATCTCTATTC
257 TTTCGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTC
4233 AT
322 AT
** * * *
4235 AAAACCAAATTTCAGCGACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
* * *
4300 ATTTAATCAGAAAAAAGAATTCGGAAA-AGAATGAGAAAACGATATTGGAAGCGT-AACAAACCC
66 ATTTAATTAG-AAATA-AATTCGGAAAGA-AATGGGAAAACGATATTGGAAGCGTGAA-AAACCC
* * * * *
4363 TTCAATATTTTTTGCGTTAAATTATATATTTTTTCCGAATATTGTGGC-AAAATTTGAGAAAAAA
127 TT-AATTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAG-AAAAA
* * * * * * *
4427 AAATTTTTAGGTCAATTCATAGCCAATATCGTGTACTAACAATCACAGTTATTGGGTTAAAAACG
190 AAATTTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACG
* * *
4492 CGTTTCGAGGCACCAACACAGTTTTGCATGATTTTTTGGCA-AAAGCCTCCTTGAAATATCTTTA
255 CGTTTCGAGGCACCGACACAGTTTTGCATGA-TTTTTGGCAGAGAGCCTCCTTGAAATATCTCTA
4556 TTCAT
319 TTCAT
*
4561 CGAACCAAATCTTAGCCA
1 CGAACCAAATCTCAGCCA
4579 TAATGGGA
Statistics
Matches: 2005, Mismatches: 215, Indels: 86
0.87 0.09 0.04
Matches are distributed among these distances:
308 31 0.02
309 61 0.03
310 115 0.06
311 26 0.01
312 39 0.02
313 2 0.00
314 32 0.02
315 85 0.04
316 3 0.00
317 52 0.03
318 31 0.02
319 1 0.00
320 19 0.01
321 16 0.01
322 472 0.24
323 598 0.30
324 50 0.02
325 126 0.06
326 138 0.07
327 88 0.04
328 20 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (323 bp):
CGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCG
ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTTAA
TTTTTTTTGCGTTAAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAAAAAATTT
TCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTC
GAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAGCCTCCTTGAAATATCTCTATTCAT
Found at i:3474 original size:645 final size:644
Alignment explanation
Indices: 1996--4584 Score: 3491
Period size: 645 Copynumber: 4.0 Consensus size: 644
1986 CCTTGAAAAA
* * *
1996 CGAAACAAATCTCAGCCATAATGGATTTAAGG-GTTGTTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACAATGGATTTAAGGATTTG-TTTTACGAGCATCTGAATTTTGTTTCG
* * *
2060 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAGACGATATTGAAAGCGTGATAAA-CCCCT-
65 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGA-AAATCCCTTA
* *
2123 TTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCA-AAAAAAAATTT
129 TTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGAGACAAAAATTTCAGAAAAAAATTTT
*
2187 TCAGGTCAATTCTTATTCAAAATCGT-T--T-A-CATCACTGTTATTGGGCTAAAAACGCGTTTC
194 TCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTC
* *
2247 GAGGCACCGGCACAGTTTTGCATGATTTTTGGCAGA-AAGCCTCCTTGAAATATCTCTATTCATC
259 GAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAA-TCTCCTTGAAATATCTCTATTCATC
* * * *
2311 GAACCAAATCTCAGCCATAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGA
323 AAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCGA
* * * * * *
2376 TTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGACATTGGAAGCGTGAAAAATCCGTT-A
388 TTTAATCAGAAAAAAAATCGGAAAAAAATGGGAAAACGATATTGGAAGCGTGAAAAA-CCCTTCA
* * * * * * *****
2440 GT-TTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGTGACAAAAATTTCAGAAAATTTTTT
452 ATATTTTTTGCGTTAAATTATATATTTTTTCCGAGTATTGTGGC-AAAACTTCAGAAAAAAAAAT
* * * *
2504 TTCAGGTCAATTCTTAGTCGAAATCGTGTACTAATCATCACTGTTATTGGGCTAAAAACGCGTTT
516 TTCAGGTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTT
2569 CGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
581 CGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
* * * *
2633 CGAATCAAATCTCAGCCATAATGGATTTAAGGATTTGTTTTAACGAGCATCTGAATTATGTTTTG
1 CGAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTT-ACGAGCATCTGAATTTTGTTTCG
* *
2698 ATTTAATTAGAAATAAATTCGGAAAGAAATGAGAAAACGATATTGGAAGCGTGAAAAATCCGTTA
65 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTG-AAAATCCCTTA
* * *
2763 TTTTTTTTGGGTTGAATTGCATATTTTTTCGGAGTATTGAGACAAAAATTTCAG-AAAAATTTTT
129 TTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGAGACAAAAATTTCAGAAAAAAATTTT
* * *
2827 TCAGGTCAATTCTTAGTCGAAATCGTGTACAAACCATCACTGTTATTGGGCTAAAAACGTGTTTC
194 TCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTC
* * * *
2892 GAGGCACCGACACAGTTTTGCATGATTTTTGACAGAGAGTCTACTTGAAATATCTCTATTCATCT
259 GAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAATCTCCTTGAAATATCTCTATTCATCA
* *
2957 AACCAAATCTCAGCCACGTTGGATTTAAGGATTTGGTTTTACGAGCATCTGAATTTTGTTTCGAT
324 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCGAT
*
3022 TTAATGAGAAAAAAAATCGGAAAAAAATTGGGAAAACGATATTGGAAGCGTGAAAAACCCTTCAA
389 TTAATCAGAAAAAAAATCGGAAAAAAA-TGGGAAAACGATATTGGAAGCGTGAAAAACCCTTCAA
* * *
3087 TATTTTTTGCGTTAAATTATATA-TTTTTCTGAGTATTGTAGCAAGACTTCAGAAAAAAAAATTT
453 TATTTTTTGCGTTAAATTATATATTTTTTCCGAGTATTGTGGCAAAACTTCAGAAAAAAAAATTT
3151 CAGGTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCG
518 CAGGTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCG
* * *
3216 AGGCACCGGCACAATTTTGCATGATTTTTGGCAGATAGCCTCCTTGAAATATCTCTATTCAT
583 AGGCACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
* * *
3278 CAAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACAATGGATTTAAGGATTTG-TTTTACGAGCATCTGAATTTTGTTTCG
**
3343 AAATAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAATCCCTTAT
65 ATTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAATCCCTTAT
* *
3408 TTTTTTTGGGTTGTATTACATATTTTTTCCGAGTATAGAGACAAAAATTTCAGAAAAAAATTTTT
130 TTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGAGACAAAAATTTCAGAAAAAAATTTTT
* * * * *
3473 CAGGTCAATTCTTAGTCGAAATTGTGTACTAACCGTCACTGTTATTGGGCTAAGAACGCGTTTTG
195 CAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCG
* * * *
3538 AGGCCCCGACTCAGTTTTGAATGATTTTTGGCTGAGAATCTCCTTGAAATATCTCTATTCATCAA
260 AGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAATCTCCTTGAAATATCTCTATTCATCAA
* *
3603 ACCAAATATCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTTCGATT
325 ACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATT
* *
3668 TAATCAGAAAAAAATTCGGAAAAAAAATGGGAAAACGATATTGGAAGCGTGAAAAAACCTTCAAT
390 TAATCAGAAAAAAAATCGG-AAAAAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTTCAAT
* * *
3733 ATTTTTTTGCGTTAAATTATATA-TTTTTCCGAGTATTGTGGCAAGACTTTAG-AAAAAAATTTT
454 A-TTTTTTGCGTTAAATTATATATTTTTTCCGAGTATTGTGGCAAAACTTCAGAAAAAAAAATTT
*
3796 CAGGTCAATTCTCAGCCAAAATCGTG---------T-AC-GTTATTGGGCT-AAAACGCATTTCG
518 CAGGTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCG
* * * * * *
3849 AGGCACTGGCACTGTTTTGCAT-ATTTTTGACAGAGAGTCTCCTTGAAATATCTCTATTCAT
583 AGGCACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
* **
3910 CGATCCAAATCTCAGCCACGTTGGATTTAAGGATTTGGTTTTACGAGCATCTGAATTTTGTTTCG
1 CGAACCAAATCTCAGCCACAATGGATTTAAGGATTT-GTTTTACGAGCATCTGAATTTTGTTTCG
* * * *
3975 ATTTAATTAGAAA-AAAATCGGAAAAAAATTGGGAAAACAATATTGGAAGCGTGAAAAACCCTTC
65 ATTTAATTAGAAATAAATTCGGAAAGAAA-TGGGAAAACGATATTGGAAGCGTGAAAATCCCTT-
* ** * * * ** * * * *
4039 AATATTTTTTGCCTTAAATTATATATTTTTGCTAAGTATTGTGGC-AAAACTTAAGAAAAAAAAT
128 -ATTTTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGAGACAAAAATTTCAG-AAAAAAAT
* * * * * *
4103 AATTTCAGGCCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTAGGCTAAAACCGCG
191 -TTTTCAGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCG
* * * *
4168 TTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTGAGAATCTCCTTGAAATATCTCTATTC
255 TTTCGAGGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAATCTCCTTGAAATATCTCTATTC
* * * *
4233 ATAAAACCAAATTTCAGCGACATTGGATTTAAGGATTTGCTTTTACGAGCATCTTAATTTTGTTT
320 ATCAAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTT
* *
4298 CGATTTAATCAGAAAAAAGAATTCGGAAAAGAATGAGAAAACGATATTGGAAGCGT-AACAAACC
385 CGATTTAATCAGAAAAAA-AA-TCGGAAAAAAATGGGAAAACGATATTGGAAGCGTGAA-AAACC
* * *
4362 CTTCAATATTTTTTGCGTTAAATTATATATTTTTTCCGAATATTGTGGCAAAATTTGAGAAAAAA
447 CTTCAATATTTTTTGCGTTAAATTATATATTTTTTCCGAGTATTGTGGCAAAACTTCAGAAAAAA
* * * * *
4427 AAATTTTTAGGTCAATTCAT-AGCCAATATCGTGTACTAACAATCACAGTTATTGGGTTAAAAAC
512 AAA-TTTCAGGTCAATTC-TCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAAC
* *
4491 GCGTTTCGAGGCACCAACACAGTTTTGCATGATTTTTTGGCA-AAAGCCTCCTTGAAATATCTTT
575 GCGTTTCGAGGCACCGACACAGTTTTGCATGA-TTTTTGGCAGAAAGCCTCCTTGAAATATCTCT
4555 ATTCAT
639 ATTCAT
* *
4561 CGAACCAAATCTTAGCCATAATGG
1 CGAACCAAATCTCAGCCACAATGG
4585 GA
Statistics
Matches: 1737, Mismatches: 169, Indels: 78
0.88 0.09 0.04
Matches are distributed among these distances:
631 13 0.01
632 138 0.08
633 40 0.02
634 51 0.03
635 221 0.13
636 67 0.04
637 46 0.03
638 102 0.06
639 5 0.00
640 82 0.05
641 1 0.00
644 61 0.04
645 691 0.40
646 105 0.06
647 19 0.01
648 2 0.00
649 10 0.01
650 30 0.02
651 45 0.03
652 8 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (644 bp):
CGAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTACGAGCATCTGAATTTTGTTTCGA
TTTAATTAGAAATAAATTCGGAAAGAAATGGGAAAACGATATTGGAAGCGTGAAAATCCCTTATT
TTTTTTGGGTTGAATTACATATTTTTTCCGAGTATTGAGACAAAAATTTCAGAAAAAAATTTTTC
AGGTCAATTCTTAGTCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCGA
GGCACCGACACAGTTTTGCATGATTTTTGGCAGAGAATCTCCTTGAAATATCTCTATTCATCAAA
CCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTT
AATCAGAAAAAAAATCGGAAAAAAATGGGAAAACGATATTGGAAGCGTGAAAAACCCTTCAATAT
TTTTTGCGTTAAATTATATATTTTTTCCGAGTATTGTGGCAAAACTTCAGAAAAAAAAATTTCAG
GTCAATTCTCAGCCAAAATCGTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCGAGG
CACCGACACAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCAT
Done.