Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022415.1 Corchorus olitorius cultivar O-4 contig22448, 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: 16322
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Found at i:1250 original size:299 final size:299
Alignment explanation
Indices: 734--1296 Score: 893
Period size: 299 Copynumber: 1.9 Consensus size: 299
724 TTAATTTCGG
* * **
734 ATTAAATCCAAACATGATTCAGATACTCGTAAAATTAAATCCTTAAATCCAATGTGGCTGAGATA
1 ATTAAATCCAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATA
**
799 TGGGATGATGAATATAGATATTTTTACGAGTCTTGGCGCCAAAAATCATGCAAAACTGATACGGG
66 TGGGATGATGAATATAGATATTTCAACGAGTCTTGGCGCCAAAAATCATGCAAAACTGATACGGG
* *
864 CCATGGAACGCGTTTTCAGCCAAAAACCGTGATGGTTGTTAGTACACGATTTCGGCAAAAATTTT
131 CCACGGAACGAGTTTTCAGCCAAAAACCGTGATGGTTGTTAGTACACGATTTCGGCAAAAATTTT
*
929 GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTTGTAAAAATATATATAA
196 GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAATATATATAA
994 TTCACGCTGCTAATATCATTTTTTCACAATTAATTTTTA
261 TTCACGCTGCTAATATCATTTTTTCACAATTAATTTTTA
* *
1033 ATTAAATCGAAA-AAGATTCAGATGA-TCATAAAAACAAATCCTTAAATCCATTGTGGCTGAGAT
1 ATTAAATCCAAACAAGATTCAGAT-ACTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * *
1096 -TCGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGT-C
65 AT-GGGATGATGAATATAGATATTTCAACGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-TAC
* *
1159 AGGGTCC-CGGAACGAGTTTTTAGCCAAAAACTGTGATGGTTGTTAGTACACGATTTCGGCAAAA
128 -GGG-CCACGGAACGAGTTTTCAGCCAAAAACCGTGATGGTTGTTAGTACACGATTTCGGCAAAA
*
1223 ATTTTGTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAATATA
191 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAATATA
1288 TATAATTCA
256 TATAATTCA
1297 ACGCCAAAAA
Statistics
Matches: 242, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
297 1 0.00
298 98 0.40
299 141 0.58
300 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (299 bp):
ATTAAATCCAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATA
TGGGATGATGAATATAGATATTTCAACGAGTCTTGGCGCCAAAAATCATGCAAAACTGATACGGG
CCACGGAACGAGTTTTCAGCCAAAAACCGTGATGGTTGTTAGTACACGATTTCGGCAAAAATTTT
GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAATATATATAA
TTCACGCTGCTAATATCATTTTTTCACAATTAATTTTTA
Found at i:2553 original size:13 final size:12
Alignment explanation
Indices: 2511--2555 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
2501 TCGTGCACCC
2511 AAAACAATTTATTT
1 AAAACAATTTA--T
*
2525 AAAACCATTTAT
1 AAAACAATTTAT
2537 AAAACAATTTGAT
1 AAAACAATTT-AT
2550 AAAACA
1 AAAACA
2556 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAACAATTTAT
Found at i:3592 original size:332 final size:333
Alignment explanation
Indices: 2963--6478 Score: 4451
Period size: 333 Copynumber: 10.6 Consensus size: 333
2953 TTTCTAGCCG
* * * * * *
2963 TTAGCCAAAAACCGTGAT-GTAACGTACACGATTTCGGCAAAAATATTACAAAAATTGACC-CGA
1 TTAGCCAAAAACCGTGATGGTTA-GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGA
* * * * * * * * *
3026 AAGATTTTTCCTCAATTTTT-AACCACAATACTCGTAAAAAAGATATAATTCAACGCCAAAAAGA
65 AAAATTTTTCCTCAATTTTTGGA-TAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGA
* * * * * * * *
3090 TTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCA-ATTTTTTCCCGAATTAATTTCTATTTA
129 TTGGAGGACTTCTCACGCTTTTAATATC-GTTTTTCATATTTTTT-CTGAATTAATTTCTAATGA
* * * * * * * **
3154 AATCGAAACAAGATTCAGATGATCGTAACAACAAATCCTTAAATCCATTGTGG-TGA-TATTTGG
192 AATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGT-TTTTA
* * * * * * *
3217 TTAGATTAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAGACTGAGCCGGGGCC
256 TTAGATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACC
*
3282 CCGGAACGCGTTT
321 CCGAAACGCGTTT
* * **
3295 TTAACCAAAAACCATGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACTTCGAA
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
*
3360 AAATATTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATT
66 AAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATT
*
3425 -GAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTATGAATTAATTTCTAATGAAATC
131 GGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAATC
*
3489 GAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTATTATTAGA
196 GAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGA
*
3554 TGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGGACCCCGAA
261 TGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAA
3619 ACGCGTTT
326 ACGCGTTT
* * * * * * * *
3627 ATAG-CAAAAACCATGATGATTAGTACACGATTTTGGCTAAAATTTTGCTAAGAACGACCGTGAT
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
* * * * *
3691 AAATATTTCCTCAGTTTTTTTGATGAAATACTCATAAAATATATATAATTTAACGCCAAAAAGAT
66 AAATTTTTCCTCA-ATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGAT
* *
3756 TGGAGGACATCTCACGCTTTTAATATCGTTTTTCATATTTTTTATGAATTAATTTCTAATGAAAT
130 TGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAAT
* *
3821 CGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAAATGTGGCTAAGTTTTTTTTA
195 CGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGC-AATGTGGCTAAGTTTTTATTA
* * **
3885 GATGAATATATATATTTCAAGGAATCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACAACG
259 GATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCG
3950 AAACGCGTTT
324 AAACGCGTTT
** * * *
3960 TTAAACAAAAACCGTGATGGTTAATACGCGATTTTGGCTAAAATTTTGCAGAAAATGACCGCG-A
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
* ** * *
4024 AAATTTTTCCT-AAATTTTGGATAAAATACTCATCGAATATATACAATGTAACGTCAAAAAGATT
66 AAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATT
* * * *
4088 GTAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTGTTATGAAATC
131 GGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAATC
* ** * *
4153 GAAACAAGATTCAAATGC-CTGGGAAAAGAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAG
196 GAAACATGATTCAAATGCTC-GTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
* * * * *
4217 ATGAATATAGATATTTCAAGAATTCCTGATGCCAAAAATCATGCAAAACTGAGACGGGACCGCGA
260 ATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGA
4282 AACGCGTTT
325 AACGCGTTT
* * *
4291 TTAGCAAAAAACCGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAAATGACTGCGA
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGC-AAAAAATGACCGCGA
* * * * * * *
4356 AAAATGTTTCCACAATTTTTTGTTAAAGTACTCATAAAAATATATATATATATAATTTAATGCCA
65 AAAATTTTTCCTCAATTTTTGGATAAAATACTCAT----A-A-A-ATATATACAATTTAACGCCA
* ** * *
4421 ACAAGAGAGGAGGACTTCTCATGCTCTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
123 AAAAGATTGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
* * *
4486 ATGAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGAAATGTGGCTAAGATT
188 ATGAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTT
* * * *
4551 TTATTAGATAAATATATAAATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGG
253 TTATTAGATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGG
*** *
4616 ATAACAAAACGCGTTT
318 ACCCCGAAACGCGTTT
* *** ** * * * **
4632 TAAAAAAAAAAAACCGTGAT-G-TCCTCCAATC-TTTTTGACGTTTTTAAAATTTTGCGGAAAAT
1 T--TAGCCAAAAACCGTGATGGTTAGTAC-A-CGATTTTG--G---CTAAAATTTTGCAAAAAAT
* * * * * ** * *
4694 TACTGC-AAAACTTTTTTCCT-AAATTTCGGAT-AAATACTCATTGAATATATACAATGTAACGT
57 GACCGCGAAAA-ATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGC
* *
4756 CAAAAAGATTGGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTC
121 CAAAAAGATTGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTC
* * * * *
4821 TAACGAAATAGAAACGTGATTCAAATGCTCGTAAAAAGAAATCCTTCAATGCAATGTGGCTAAGT
186 TAATGAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGT
* * * ** * *
4886 TATTATTAGATGAGTATAAATATTTCAATAAGTCATGACGCTAAAAATCATGCAAAACTGAGCCG
251 TTTTATTAGATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCG
* **
4951 GGGCCCCGAAATACGTTT
316 GGACCCCGAAACGCGTTT
* * * * *
4969 ATAGCCAGAAACC----------G----CGATTTTGGCTAAAATTTTGCTAAGAATGACCGTGAA
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
* * * * * * *
5020 AATTTTTTCCTCAGTTTTTTTGATGAAATAGTCAGAAAATATATATAATTTAACGCCAAAAAGAT
66 AAATTTTTCCTCA-ATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGAT
* * *
5085 TAGAGGACTTCTCACGCTTTTAATATCGTTTTTCATA-TTTTTATGAATTAATTTCTAACGAAAT
130 TGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAAT
*
5149 CGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTGTTAG
195 CGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
*
5214 ATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAATTCATGCAAAACTGAGCCGGGACCCCGA
260 ATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGA
5279 AACGCGTTT
325 AACGCGTTT
5288 TTAGCCAAAAACCGTGATGGTTTA-TACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGA
1 TTAGCCAAAAACCGTGATGG-TTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGA
* * *
5352 AAAATGTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAATGCCAAAAAGAT
65 AAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGAT
* * *
5417 TGGAGGACTTCTCATGCTCTTAATATCGTTTTTCATATTTTTGCTGAATTAATTTCTAATGAAAT
130 TGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAAT
**
5482 CGAAACATGATTGGAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
195 CGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
* *
5547 ATGAATATAGATATTTCAAGGAATCCTGACGCCAAAAATCATGCAAAACTGAGTCGGGACCCCGA
260 ATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGA
* *
5612 CACGCGATT
325 AACGCGTTT
* *
5621 TTAGCCAAAAACCGTGATAGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATTACCGCGAA
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
* * *
5686 AAATGTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAGGATT
66 AAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATT
*
5751 GGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTGCTGAATTAATTTCTAATGAAATC
131 GGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAATC
5816 GAAACATGATTCAAATGCTCG-AGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
196 GAAACATGATTCAAATGCTCGTA-AAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAG
*
5880 ATGAATATAGATATTTCAAGGAATCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGA
260 ATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGA
5945 AACGCGTTT
325 AACGCGTTT
*
5954 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAACTTTGCAAAAAAATGACCGCGA
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGC-AAAAAATGACCGCGA
* * * * * * *
6019 AAAATGTTTCCTC-GTTTTTAAGTTAAAATACTCATAAAATATATATATAATTTAATGCCGAAAA
65 AAAATTTTTCCTCAATTTTT-GGATAAAATACTCAT-AAA-ATATATACAATTTAACGCCAAAAA
* *
6083 GATTGGAGGAGTTCTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGA
127 GATTGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGA
* * *
6148 AATCAAAACATGATTCAAATGCTCGTAAAAACAAATTCTTAAATGCAATTTGGCTAAGTTTTTAT
192 AATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTAT
* *
6213 TAGATGAATATAGATATTTCAAGGAGTCCTGACGCAAAAAATTATGCAAAACTGAGCCGGGACCC
257 TAGATGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCC
**
6278 TAAAACGCGTTT
322 CGAAACGCGTTT
* * *
6290 TTAGCCAAAAACTGTGATGGTTATTACACGATTTTTGCTAAAATTTTGCAAAAAAAATGACCGCG
1 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGC--AAAAAATGACCGCG
* * * * * *
6355 ATAAATTTTTCCACAATTTTTGGATTAAATACTCTTAAAATATATACAATGTAACGTCAAAAAGA
64 AAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGA
* * * *
6420 TTGAAGGACTTTTAACGCTTTTAATATCGTTTTTCATATTTTTCCTGAGA-TAATTTCTA
129 TTGGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGA-ATTAATTTCTA
6479 TCATTATGAT
Statistics
Matches: 2777, Mismatches: 343, Indels: 125
0.86 0.11 0.04
Matches are distributed among these distances:
317 27 0.01
318 5 0.00
319 166 0.06
320 68 0.02
321 1 0.00
322 5 0.00
330 1 0.00
331 401 0.14
332 294 0.11
333 842 0.30
334 108 0.04
335 82 0.03
336 262 0.09
337 235 0.08
338 6 0.00
340 1 0.00
341 203 0.07
342 7 0.00
343 15 0.01
344 10 0.00
345 11 0.00
346 16 0.01
347 11 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (333 bp):
TTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
AAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATT
GGAGGACTTCTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATGAAATC
GAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGA
TGAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAA
ACGCGTTT
Found at i:7565 original size:23 final size:23
Alignment explanation
Indices: 7520--7566 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
7510 AACAAACAAT
*
7520 TTGGCAACTTATTGGAATTGAGA
1 TTGGCAACTTATTGGAATGGAGA
* *
7543 TTGGCAATTTATTGGAGTGGAGA
1 TTGGCAACTTATTGGAATGGAGA
7566 T
1 T
7567 GTCCCGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.36
Consensus pattern (23 bp):
TTGGCAACTTATTGGAATGGAGA
Found at i:9393 original size:20 final size:20
Alignment explanation
Indices: 9327--9603 Score: 151
Period size: 20 Copynumber: 13.8 Consensus size: 20
9317 TACGCAGCAC
*
9327 ATTCACATTTAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * **
9347 A-TCAACATTGAACTTGCCTTG
1 ATTC-ACATTCAACTTTCC-CA
*
9368 ATTCACATCCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * **
9388 ATTCACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCA
* *
9408 ATTCACATCCAAATTTCCCA
1 ATTCACATTCAACTTTCCCA
* * * **
9428 ATTGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
*
9449 ATTCACATCCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * * **
9469 ATTGACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCA
* *
9489 ATTTACATCCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * * * **
9509 AATGACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCA
* *
9529 ATTCACATCCAAATTTCCCA
1 ATTCACATTCAACTTTCCCA
* * * * **
9549 AATGACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCA
9569 ATTCACATTCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* *
9589 ATTGACATTGAACTT
1 ATTCACATTCAACTT
9604 GCCTTAATTC
Statistics
Matches: 177, Mismatches: 76, Indels: 8
0.68 0.29 0.03
Matches are distributed among these distances:
19 2 0.01
20 147 0.83
21 26 0.15
22 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (20 bp):
ATTCACATTCAACTTTCCCA
Found at i:9425 original size:40 final size:40
Alignment explanation
Indices: 9327--9616 Score: 454
Period size: 40 Copynumber: 7.2 Consensus size: 40
9317 TACGCAGCAC
** **
9327 ATTCACATTTAACTTTCCCAATCAACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
*
9367 GATTCACATCCAACTTTCCCAATTCACATTGAACTTGCCTT
1 -ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
*
9408 ATTCACATCCAAATTTCCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
9448 GATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
1 -ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
9489 ATTTACATCCAACTTTCCCAAATGACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
9529 ATTCACATCCAAATTTCCCAAATGACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
*
9569 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
9609 AATTCACA
1 -ATTCACA
9617 ATGGCCCTCA
Statistics
Matches: 233, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
40 151 0.65
41 82 0.35
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (40 bp):
ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
Found at i:9462 original size:81 final size:81
Alignment explanation
Indices: 9327--9616 Score: 465
Period size: 81 Copynumber: 3.6 Consensus size: 81
9317 TACGCAGCAC
** ** *
9327 ATTCACATTTAACTTTCCCAATCAACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTC
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTG
9392 ACATTGAACTTGCCTT
66 ACATTGAACTTGCCTT
*
9408 ATTCACATCCAAATTTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTG
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTG
9473 ACATTGAACTTGCCTT
66 ACATTGAACTTGCCTT
* * * *
9489 ATTTACATCCAACTTTCCCAAATGACATTGAACTTGCCTT-ATTCACATCCAAATTTCCCAAATG
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTG
9553 ACATTGAACTTGCCTT
66 ACATTGAACTTGCCTT
* *
9569 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTAATTCACA
1 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACA
9617 ATGGCCCTCA
Statistics
Matches: 194, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
80 75 0.39
81 119 0.61
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (81 bp):
ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACTTTCCCAATTG
ACATTGAACTTGCCTT
Found at i:11468 original size:40 final size:40
Alignment explanation
Indices: 11373--11511 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
11363 TCTTAAACGG
* * * *
11373 CTCTCGGCAGTGAAGCTACCCACACACAACGCAGAGA-GA
1 CTCTCAGCAGTAAAGCTCCCCACACAGAACGCAGAGACGA
* * *
11412 CTCTCAGTAGTGAAGCTCCCCACACAGAACACAGAGACGA
1 CTCTCAGCAGTAAAGCTCCCCACACAGAACGCAGAGACGA
* *
11452 CTCTCAGCAGTAAAGCTCCCAACACAGAACGCAAAGACGA
1 CTCTCAGCAGTAAAGCTCCCCACACAGAACGCAGAGACGA
*
11492 CTCTC-GAAAGTAAAGCTCCC
1 CTCTCAG-CAGTAAAGCTCCC
11512 AAAAAAGATT
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 33 0.38
40 54 0.62
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.12
Consensus pattern (40 bp):
CTCTCAGCAGTAAAGCTCCCCACACAGAACGCAGAGACGA
Found at i:15169 original size:331 final size:332
Alignment explanation
Indices: 13542--16322 Score: 3635
Period size: 331 Copynumber: 8.3 Consensus size: 332
13532 AATAACATCG
* * * * *
13542 ACACGATTTTCGGTAAAAATTTTGCAAAAATTTATCCGAAAGATTTTT-CTTAATTTTTAACCGC
1 ACACGA-TTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGC
*
13606 AATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTGCTAATAT
65 AATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
* * * * *
13671 CAATTTTTCAATTCTTTCCCGAATTAATTGCTAATTAAATCGAAAAAAGATTCAGATGATCATAA
130 CATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAA
* * *
13736 AAACAAATCCTTAAATCCATTGTGGCTGATATTCGG-GATGATTAATATAGATATTTCAAT-GAG
195 CAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTA-GATTAATATAGATATTTC-ATCGAG
* *
13799 TCTTGGCGCCAAAAATCTTGCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGACAAAAACCG
258 TCTTGGCGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCG
13864 TGATGGTTAGT
322 TGATGGTTAGT
* * *
13875 ACACGATTTCGGCAAAAATATTACAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCACA
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
* *
13940 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCTTCTCACGCTTCTAATATC
66 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
*
14005 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAC
131 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAC
*
14070 AACAAATCCTTAAATCCATTGTGG-TCGATATTTGGTTAGATTAATATAGATATTTCAACGAGTC
196 AACAAATCCTTAAATCCATTGTGGCT-GATATTTGGTTAGATTAATATAGATATTTCATCGAGTC
*
14134 TTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAACC--AAA-----
260 TTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTG
14192 A-----A-T
324 ATGGTTAGT
* * *
14195 ACACGATTTCGGCAAAAAATTTGCAAAAACTGAACCGAAAGATTTTTCCACAATTTTTAACCGCA
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
*
14260 ATACTCGTAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATC
66 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
* * *
14325 ATTTTTTCAA-TTTTTCTCGAATTAATTTCAATTTAAATCGAAACAAGATTCAGATGATCGTAAC
131 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAC
* * *
14389 AACAAATCCTTAAATCCATTGTGGCCGATATTTGGTTAGATTAATATAGATATTTCAACGAATCT
196 AACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCATCGAGTCT
* * * * *
14454 TGGTGCCAAAAATCATGCAAAACTGAGACGGGGCTCCGGAACGCGTTTTTAGTCAAAAACTGTGA
261 TGGCGCCAAAAATCATGCAAAACTGAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
14519 TGGTTAGT
325 TGGTTAGT
* * * *
14527 ACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTCTTCCTTAGA-TTTTAACTGC
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCA-ATTTTTAACCGC
** * * *
14591 AATACTCGTAAAATTTATATAATTCAACACCAAAAATATTGAAGGGCTTTTCATGCTTCTAATAT
65 AATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
* * *
14656 CATTTTTTCAA-TTTTTCCCGAATTAATTTCTATTTAAAACGAAAGAAGATTCAGATGATCATAA
130 CATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAA
* *
14720 CAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATAGAGATATTTCATCTAGTC
195 CAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCATCGAGTC
* *
14785 TTGGCGCCAAAAATCATGCAAAACTAAGTCGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGA
260 TTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
14849 TGGTTAGT
325 TGGTTAGT
* * *
14857 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTTAATTTATAACTGCA
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
** *
14922 ATACTCGTAAAATTTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATC
66 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
* *
14987 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAATAAGATTCCGATGATCGTAAC
131 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAC
* * *
15052 AACAAATCCTTAAATTCATTGTGGCTGATATTTGGTTAGATTAATAGAGATATTTGATCGAGTCT
196 AACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCATCGAGTCT
* *
15117 TGGTGCCAAAAATCATGCAAAACTAAGCCGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
261 TGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
15181 GGTTAGT
326 GGTTAGT
* * *
15188 ACACGATTTCGGTAAAATTTTTGCAAAATCTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
* * *
15253 ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCATGCTGCTAATATC
66 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
* * * *
15318 ATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAATTCGAAAAAAGATTCAGATGATCGTAAA
131 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAC
* * *
15383 AACAAATCCTTAAATCCATTGTGGCTGAGATTCGG-GATGATTAATATAGATATTTCAAT-GAGT
196 AACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTA-GATTAATATAGATATTTC-ATCGAGT
* * ** * *
15446 CTTGGCGCCAAAAATCTTGCAAAACTGAGCCAGAGCCTTGGAATGTGTTTTTAGCCAAAAACCGT
259 CTTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGT
15511 GA---TT--T
323 GATGGTTAGT
* * * * * *
15516 ACACGATTTCAGCAAAAATTTTGCAAAAGC-AACCCGAAACTATTTTTCCTCGATTTTTAACCGT
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAA-GATTTTTCCTCAATTTTTAACCGC
* *
15580 AATTCTCGTTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
65 AATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
*
15645 CATTTTTTCAA-TTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAA
130 CATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAA
* * *
15709 CAACAAATCCTTAAATCCATTATGGCCGATATTTGGTT-GAATTAATATAGATATTTCAACGAGT
195 CAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAG-ATTAATATAGATATTTCATCGAGT
* *
15773 CTTGGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAACCAAAAACCGT
259 CTTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGT
*
15838 GATGGTTGGT
323 GATGGTTAGT
*
15848 ACACGATTTCGGTAAAAATTTTGCAAAAATTTACACGATTTCGGTAAAAATTTTGCAAAAATTGA
1 ACACGATTTC-G----------GCAAAAA--T------TTT--GCAAAAA-----C------TGA
* * **
15913 CCCGAAAGATTTTT-CTCCATTTTTAACCGCAATACTCGTAAGAAATATATAATTCAACATCAAA
34 CCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAA
* * * *
15977 AAGATTGAAGGGCTTTTCACGCTGCTAA-ATCAATTTTTCAATTCTTTCCCGAATTAATTTCTAA
99 AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTTCCCGAATTAATTTCTAT
* * * **
16041 TTAAATCGAAAAAAGATTCTGATTG-TCGTAA-AAAAAATCCTTGAATTTATTGTGGCTGATATT
164 TTAAATCGAAAAAAGATTCAGA-TGATCGTAACAACAAATCCTTAAATCCATTGTGGCTGATATT
* * * * * * *
16104 CAGGAT-GATTAATATAGATATTTAAAT-GAGTCTTGGTGCCAAGAATCTTGCATAACTGAGCCG
228 -TGGTTAGATTAATATAGATATTT-CATCGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCG
**
16167 AGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-GACA-T
291 -GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
* * * *
16208 ACACGATTTCGGCAAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTCAATTTTTAACCACA
1 ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
* * * *
16273 ATACTCGTAAAAAATATAGAATTCAATGGCAGAAAGATTGAAGGGCTTTT
66 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTT
Statistics
Matches: 2178, Mismatches: 195, Indels: 154
0.86 0.08 0.06
Matches are distributed among these distances:
319 161 0.07
320 134 0.06
321 4 0.00
326 4 0.00
327 167 0.08
328 134 0.06
329 60 0.03
330 174 0.08
331 447 0.21
332 314 0.14
333 274 0.13
334 2 0.00
339 6 0.00
341 3 0.00
343 7 0.00
345 1 0.00
347 1 0.00
349 7 0.00
351 3 0.00
353 5 0.00
358 1 0.00
359 1 0.00
360 11 0.01
361 2 0.00
362 118 0.05
363 121 0.06
364 8 0.00
365 8 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (332 bp):
ACACGATTTCGGCAAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAC
AACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCATCGAGTCT
TGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
GGTTAGT
Found at i:15883 original size:32 final size:32
Alignment explanation
Indices: 15847--15910 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
15837 TGATGGTTGG
15847 TACACGATTTCGGTAAAAATTTTGCAAAAATT
1 TACACGATTTCGGTAAAAATTTTGCAAAAATT
15879 TACACGATTTCGGTAAAAATTTTGCAAAAATT
1 TACACGATTTCGGTAAAAATTTTGCAAAAATT
15911 GACCCGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (32 bp):
TACACGATTTCGGTAAAAATTTTGCAAAAATT
Done.