Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013373.1 Corchorus capsularis cultivar CVL-1 contig13394, 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: 54836
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:70 original size:43 final size:45
Alignment explanation
Indices: 5--99 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 45
1 CATC
* *
5 AAAATAATTGAGAATTCAAACATAACATATAACGTTCTTTAAT-A
1 AAAAAAATTGAGAATTCAAACATAACATATAACGTTCTTCAATCA
* *
49 AAAAAAATT-AGAATTCAAACATGATATATAACGTTCTTCAATCA
1 AAAAAAATTGAGAATTCAAACATAACATATAACGTTCTTCAATCA
93 AAAAAAA
1 AAAAAAA
100 AGTCCGCCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 30 0.65
44 16 0.35
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (45 bp):
AAAAAAATTGAGAATTCAAACATAACATATAACGTTCTTCAATCA
Found at i:504 original size:6 final size:6
Alignment explanation
Indices: 469--503 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
459 TTGTTGGAAT
*
469 CCTCAG CCTCAG CCTCAG CCTCAG CCTCAA CCTCA
1 CCTCAG CCTCAG CCTCAG CCTCAG CCTCAG CCTCA
504 AAGGGTGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.20, C:0.51, G:0.11, T:0.17
Consensus pattern (6 bp):
CCTCAG
Found at i:5057 original size:3 final size:3
Alignment explanation
Indices: 5049--5092 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5039 GTATAGATAT
5049 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5093 TATAGGTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5980 original size:31 final size:29
Alignment explanation
Indices: 5910--5989 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
5900 TCTCGTTTTT
* *
5910 AAAAGTTAAGGGGCCAATTTGTCGCCAAA
1 AAAAGTTAAGGGGCTAATTTATCGCCAAA
5939 AAAAGTTAAGGGGCTAATTTATC-CCAAA
1 AAAAGTTAAGGGGCTAATTTATCGCCAAA
*
5967 ATGGATAGTTAAGGGGCTAATTT
1 A---AAAGTTAAGGGGCTAATTT
5990 GGATATTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 6 0.13
29 21 0.47
31 18 0.40
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (29 bp):
AAAAGTTAAGGGGCTAATTTATCGCCAAA
Found at i:7831 original size:324 final size:317
Alignment explanation
Indices: 6991--8228 Score: 1420
Period size: 319 Copynumber: 3.9 Consensus size: 317
6981 ATGGTATACA
* * *
6991 ATTTCGTCTAAAAACTGACCCGGAATTTTTTTCCTCAATTCTTTGCCACAATACTCAGATAAAAT
1 ATTTCG-CTAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAGAAAAT
* * * * * **
7056 ATATAAGTCAACGAGCTAAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATAGTTTTTCTTTTT
65 ATATAATTCAAC--GC-CAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTC-CATT
* * *
7121 CTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCTGTAAAAAGAAATCCTTAA
126 -TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAA
*
7186 ATCCAATGTGACTGAGATTTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAA
190 ATCCAATGTGGCTGAGA-TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAA
* * * *
7251 TTATGCAAAACTGAGCCGAGGTCCTAAAACGCGTTTTTAGCTAAAAACTGTGATGGTTAGTATAC
254 TCATGCAAAACTGAGTCG-GGTCC-AAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACAC
7316 G
317 G
* * * * * *
7317 A-TTCAACTAAAAA-TCGACCTG--AATTTTTT-TTCAATT-TATTGCCACAATATTTAGAAAAA
1 ATTTC-GCTAAAAACT-GACCCGAAAATTTTTTCCTCAATTCT-TTGCCACAATACTCAGAGAAA
* * * * * * * * * * * *
7376 ATATATAACTCAATGCCAAATATATTGTACAGCTATCCACGCTTCTAATACCATTTTCCCA-TTT
63 ATATATAATTCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * ** * * *
7440 TCTGAATTAATTTTTAATTAAATCGAAGTAAGTTTCAGATACTCGTAAAAATAAATCCTTAAATC
128 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAAATC
* * * * * * *
7505 CAATATGTCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGATTGTTT-TTCCAAAAGTCAT
193 CAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
* * *
7569 ACAAAACTGAGTCGGTGTCTCGAAACGGCGTTTTTAGCTAAAAACCGTGAGGGTTAGTACACG
258 GCAAAACTGAGTCGG-GTC-CAAAAC-GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACG
** *
7632 ATTTCGGCTAAAAACTTTCCCGAAAATTTTTTCCTCAATTTTTTTGCCACAATACTC-GTAGAAA
1 ATTTC-GCTAAAAACTGACCCGAAAATTTTTTCCTCAA-TTCTTTGCCACAATACTCAG-AGAAA
*
7696 ATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
63 ATATATAATTCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCA--TT
**
7761 ATTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAA
126 -TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAA
*
7826 ATCCAATGTGGCTGAGATCTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
190 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
*
7891 CATGCAAAACTGAGTCGGGGCACCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACG
255 CATGCAAAACTGAGTC-GGG-TCCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACG
** * ** * * * * *
7956 ATTTC-CTTAAAGCCTAACCCGAATTTTTTTTTTCTCAAATCTTTGTCACAATAGTCAGATAAAA
1 ATTTCGC-TAAAAACTGACCCGAA-AATTTTTTCCTCAATTCTTTGCCACAATACTCAGAGAAAA
** * * *
8020 TATATAATTCAACGTTAAAAA-ATCGAAGAATTTTTCACGCTTCTAATATCTTTTTTCCATTTTT
64 TATATAATTCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
* * * * *
8084 CCGAAATAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCC
129 CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAAATCC
*
8149 AATGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGAGTCTTTAC-GCCAAAAATCAT
194 AATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCAT
8213 GCAAAACTGAGTCGGG
258 GCAAAACTGAGTCGGG
8229 ACCCCGAAAT
Statistics
Matches: 770, Mismatches: 117, Indels: 58
0.81 0.12 0.06
Matches are distributed among these distances:
313 1 0.00
314 29 0.04
315 70 0.09
316 81 0.11
317 2 0.00
318 11 0.01
319 168 0.22
320 71 0.09
321 2 0.00
322 71 0.09
323 58 0.08
324 158 0.21
325 44 0.06
326 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (317 bp):
ATTTCGCTAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAGAAAATA
TATAATTCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCC
GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
AAACTGAGTCGGGTCCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACG
Found at i:8170 original size:319 final size:319
Alignment explanation
Indices: 6999--8228 Score: 1412
Period size: 324 Copynumber: 3.8 Consensus size: 319
6989 CAATTTCGTC
* * *
6999 TAAAAACTGACCCGGAATTTTTTTCCTCAATTCTTTGCCACAATACTCAGATAAAATATATAAGT
1 TAAAAACTAACCC-GAATTTTTTTCCTCAAATCTTTGCCACAATACTCAGATAAAATATATAATT
* * * * ** * *
7064 CAACGAGCTAAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATAGTTTTTCTTTTTCTTTTCGA
65 CAAC--GC-CAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTC-CATTATTTCCGA
*
7129 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-CTGTAAAAAGAAATCCTTAAATCCAAT
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTC-GTAAAAAGAAATCCTTAAATCCAAT
* *
7193 GTGACTGAGATTTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATTATGCA
190 GTGGCTGAGA-TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
* * * *
7258 AAACTGAGCCGAGGTCCTAAAACGCGTTTTTAGCTAAAAACTGTGATGGTTAGTATACGA-TTCA
254 AAACTGAGTCG-GGTCCCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTC-
7322 AC-
317 ACT
* * * * * * *
7324 TAAAAA-TCGACCTGAATTTTTTT--TC-AATTTATTGCCACAATATTTAGAAAAAATATATAAC
1 TAAAAACT-AACCCGAATTTTTTTCCTCAAATCT-TTGCCACAATACTCAGATAAAATATATAAT
* * * * * * * * * * * *
7385 TCAATGCCAAATATATTGTACAGCTATCCACGCTTCTAATACCATTTTCCCA-T-TTTCTGAATT
64 TCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTATTTCCGAATT
* ** * * * *
7448 AATTTTTAATTAAATCGAAGTAAGTTTCAGATACTCGTAAAAATAAATCCTTAAATCCAATATGT
129 AATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGAAATCCTTAAATCCAATGTGG
* * * * * *
7513 CTGGGATTTGGTTCGATGAATATAGATATTTCAAGGATTGTTT-TTCCAAAAGTCATACAAAACT
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
* * * *
7577 GAGTCGGTGTCTCGAAACGGCGTTTTTAGCTAAAAACCGTGAGGGTTAGTACACGATTTCGGC-
259 GAGTCGG-GTCCCAAAAC-GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTC-ACT
** * * * *
7640 TAAAAACTTTCCCGAAAATTTTTTCCTCAATTTTTTTGCCACAATACTC-GTAGAAAATATATAA
1 TAAAAACTAACCCG-AATTTTTTTCCTCAA-ATCTTTGCCACAATACTCAG-ATAAAATATATAA
* **
7704 TTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTATTTTTGA
63 TTCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTATTTCCGA
*
7769 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAAGAAATCCTTAAATCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGAAATCCTTAAATCCAATG
*
7834 TGGCTGAGATCTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAA
191 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAA
*
7899 ACTGAGTCGGGGCACCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTC-CT
256 ACTGAGTCGGGTC-CCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCACT
** * * *
7963 TAAAGCCTAACCCGAATTTTTTTTTTCTCAAATCTTTGTCACAATAGTCAGATAAAATATATAAT
1 TAAAAACTAACCCGAA--TTTTTTTCCTCAAATCTTTGCCACAATACTCAGATAAAATATATAAT
** * * * *
8028 TCAACGTTAAAAA-ATCGAAGAATTTTTCACGCTTCTAATATCTTTTTTCCATT-TTTCCGAAAT
64 TCAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTATTTCCGAATT
* * *
8091 AATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGAAATCCTTAAATCCAATGTGG
*
8156 CTGAGATTTGGTTCGATGAATATAGATAATTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAAC
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAAC
8220 TGAGTCGGG
258 TGAGTCGGG
8229 ACCCCGAAAT
Statistics
Matches: 764, Mismatches: 117, Indels: 54
0.82 0.13 0.06
Matches are distributed among these distances:
313 1 0.00
314 29 0.04
315 69 0.09
316 81 0.11
317 11 0.01
319 169 0.22
320 70 0.09
321 6 0.01
322 69 0.09
323 49 0.06
324 170 0.22
325 40 0.05
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (319 bp):
TAAAAACTAACCCGAATTTTTTTCCTCAAATCTTTGCCACAATACTCAGATAAAATATATAATTC
AACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTATTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGA
GTCGGGTCCCAAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCACT
Found at i:8710 original size:2 final size:2
Alignment explanation
Indices: 8703--8742 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
8693 AGCAAAGTAA
8703 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8742 A
1 A
8743 ATAATAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10542 original size:340 final size:325
Alignment explanation
Indices: 9691--10561 Score: 869
Period size: 330 Copynumber: 2.6 Consensus size: 325
9681 TTCAACACCA
* * * * * **
9691 ACGATTTTGGCTAAAATTTTGCTAAAAAATAACCCGAAAAATTTTTCGTCAATTTTTTGAGAAAA
1 ACGATTTCGGCTAAAATTTTGC--AAAAATGACCCGAAAGA-TTTTC-TCAAATTTTGGCTAAAA
* * * *
9756 TACTCATAATATATATATAAGTTAACGCCAA-AAATATTGGGAAGGCTTTTCACGCTTTTAATAT
62 TACTCATAA-A-AAATATAATTTAACGCCAAGAAA-ATT-GGAGGGATTTTCACGCTTTTAATAT
* * *
9820 CGTTTTTCATATTTTTCTGAATTAGTTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAA
123 CGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* ** * *
9885 A-AAATCATAAATCCAATGTGGATGAGATTTGATTAGATAAATATGGATATCTCAAGGAGTTTTG
188 ACAAATCATAAATCAAATGTGGATGAGATTTGATTAGATAAATATAAATATCTCAAGGAGTCTCG
* * *
9949 GTGCCAAAAATCATACAAAACTGAACCAGGGCACTAGAACGCTTTTTTAGTCAAAAACTGTGATA
253 GAGCCAAAAATCATACAAAACTGAACCAGGGCACTAGAACGCGTTTTTAGTCAAAAACCGTGATA
10014 GTTATTAC
318 GTTATTAC
***
10022 ACGATTTCGGCTAAAATTTTGTGGAAATGGACCCGAAAGATATTTACTCAAATTTTGGCTAAAAT
1 ACGATTTCGGCTAAAATTTTGCAAAAAT-GACCCGAAAGAT-TTT-CTCAAATTTTGGCTAAAAT
* * * * *
10087 ACTCATAAAAAATATATATTTCAACGTC-AGAAAAATTGAAGGGTTTTTTTAC-ATTTCTAATAT
63 ACTCATAAAAAATATA-ATTT-AACGCCAAG-AAAATTGGAGGG-ATTTTCACGCTTT-TAATAT
* * *
10150 CATTTTTCCTATTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
123 CGTTTTTCATATTTTTCT-AAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * *
10215 AACAAATCCTTAAATCAAATTTGGTTGAGATTTGATTTGATGAATATAAATAT-TGCAAGTAGTC
187 AACAAAT-CATAAATCAAATGTGGATGAGATTTGATTAGATAAATATAAATATCT-CAAGGAGTC
* * * * *
10279 TCGGAGCCAAAAAAAAAATCATGCAAAATTGAGA-CAGGTC-CTTGGAACGCGTTTTTAG-CTAG
250 TCGGAGCC-----AAAAATCATACAAAACTGA-ACCAGGGCAC-TAGAACGCGTTTTTAGTC-AA
*
10341 AAACCGTGATGGTTAATTAGTAC
307 AAACCGTGATAGTT-A-T--TAC
* *
10364 ACGATTTCGGCTAAAATTTTGCAAAAACTGACACGAAAGATTTCTCTTC-AGTTTTGGCTAAAAT
1 ACGATTTCGGCTAAAATTTTGCAAAAA-TGACCCGAAAGATTT-TC-TCAAATTTTGGCTAAAAT
* * * *
10428 ACTCATAAAAACATATAATTTAATGCCAAGAAGATTGGAGGGATTTTCACGCTGTTAATATCGTA
63 ACTCATAAAAA-ATATAATTTAACGCCAAGAAAATTGGAGGGATTTTCACGCTTTTAATATCGTT
* *
10493 TTTCTTATTTTAATCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAC
127 TTTCATATTTT--TCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
10558 AAAT
190 AAAT
10562 TTTTAAATTT
Statistics
Matches: 445, Mismatches: 62, Indels: 57
0.79 0.11 0.10
Matches are distributed among these distances:
328 6 0.01
329 17 0.04
330 69 0.16
331 69 0.16
332 5 0.01
333 50 0.11
337 2 0.00
338 49 0.11
339 26 0.06
340 69 0.16
341 36 0.08
342 46 0.10
343 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (325 bp):
ACGATTTCGGCTAAAATTTTGCAAAAATGACCCGAAAGATTTTCTCAAATTTTGGCTAAAATACT
CATAAAAAATATAATTTAACGCCAAGAAAATTGGAGGGATTTTCACGCTTTTAATATCGTTTTTC
ATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCA
TAAATCAAATGTGGATGAGATTTGATTAGATAAATATAAATATCTCAAGGAGTCTCGGAGCCAAA
AATCATACAAAACTGAACCAGGGCACTAGAACGCGTTTTTAGTCAAAAACCGTGATAGTTATTAC
Found at i:11042 original size:6 final size:6
Alignment explanation
Indices: 11031--11061 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
11021 TTATTTAAAC
11031 TAAATA TAAATA TAAATA TAAATTA TAAATA
1 TAAATA TAAATA TAAATA TAAA-TA TAAATA
11062 AAAAGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:11185 original size:15 final size:16
Alignment explanation
Indices: 11167--11196 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11157 ATAAATAATC
11167 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
11182 ATATTATAATCTAAA
1 ATATTATAATCTAAA
11197 AATAATTATT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:11466 original size:2 final size:2
Alignment explanation
Indices: 11459--11491 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11449 TAGTAATAAA
11459 AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11492 ATAAGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11475 original size:12 final size:11
Alignment explanation
Indices: 11458--11494 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
11448 GTAGTAATAA
11458 AATATATATTAT
1 AATATATA-TAT
11470 AATATATATAT
1 AATATATATAT
11481 -ATATATATAT
1 AATATATATAT
11491 AATA
1 AATA
11495 AGATAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 6 0.25
12 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATATATATAT
Found at i:11476 original size:14 final size:13
Alignment explanation
Indices: 11458--11495 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
11448 GTAGTAATAA
11458 AATATATAT-TAT
1 AATATATATATAT
11470 AATATATATATAT
1 AATATATATATAT
11483 -ATATATATA-AT
1 AATATATATATAT
11494 AA
1 AA
11496 GATAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 19 0.79
13 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATATATATAT
Found at i:12007 original size:6 final size:6
Alignment explanation
Indices: 11996--12037 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
11986 TTGTTGGAAT
* * *
11996 CCTCAG CCTCAG CCTCAG CCTCAA CCTCAA CCTCAA CCTCAA
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA
12038 AGGGTGGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.26, C:0.50, G:0.07, T:0.17
Consensus pattern (6 bp):
CCTCAA
Found at i:12011 original size:12 final size:12
Alignment explanation
Indices: 11996--12036 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
11986 TTGTTGGAAT
*
11996 CCTCAGCCTCAG
1 CCTCAGCCTCAA
12008 CCTCAGCCTCAA
1 CCTCAGCCTCAA
*
12020 CCTCAACCTCAA
1 CCTCAGCCTCAA
12032 CCTCA
1 CCTCA
12037 AAGGGTGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.24, C:0.51, G:0.07, T:0.17
Consensus pattern (12 bp):
CCTCAGCCTCAA
Found at i:28738 original size:17 final size:17
Alignment explanation
Indices: 28716--28748 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28706 GTCTAATATA
28716 TTAGGATCAAATTTTAC
1 TTAGGATCAAATTTTAC
28733 TTAGGATCAAATTTTA
1 TTAGGATCAAATTTTA
28749 GTCCAGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
TTAGGATCAAATTTTAC
Found at i:46170 original size:10 final size:10
Alignment explanation
Indices: 46155--46183 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
46145 TTTACGTTAG
46155 TAAAAAAAAA
1 TAAAAAAAAA
46165 TAAAAAAAAA
1 TAAAAAAAAA
46175 -AAAAAAAAA
1 TAAAAAAAAA
46184 CAATATGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:48692 original size:7 final size:7
Alignment explanation
Indices: 48680--48708 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
48670 TCATGGTCTG
48680 ACTTTGA
1 ACTTTGA
48687 ACTTTGA
1 ACTTTGA
48694 ACTTTGA
1 ACTTTGA
48701 ACTTTGA
1 ACTTTGA
48708 A
1 A
48709 GCCTTGTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (7 bp):
ACTTTGA
Found at i:51684 original size:2 final size:2
Alignment explanation
Indices: 51679--51706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51669 TCCAAAGAAT
51679 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
51707 CCATTCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.