Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014495.1 Corchorus capsularis cultivar CVL-1 contig14516, 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: 11354
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:2224 original size:40 final size:42
Alignment explanation
Indices: 2180--2259 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 42
2170 TATATAAAAA
*
2180 TTAAAAGCAGAAACAG-AAAATAAAAA-T-ATTTTTTTTTATT
1 TTAAAAGCA-AAACAGAAAAAGAAAAATTAATTTTTTTTTATT
* *
2220 TTAAAAGGAAAACGGAAAAAGAAAAATTAATTTTTTTTTA
1 TTAAAAGCAAAACAGAAAAAGAAAAATTAATTTTTTTTTA
2260 AGAAAAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.15
40 17 0.50
41 1 0.03
42 11 0.32
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (42 bp):
TTAAAAGCAAAACAGAAAAAGAAAAATTAATTTTTTTTTATT
Found at i:2354 original size:40 final size:36
Alignment explanation
Indices: 2284--2362 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 36
2274 CCCTAATTTT
*
2284 AAAAACGGAAAAATATTTTTTTTTAGAAAAATCGGA
1 AAAAACGGAAAAATATTTTTTTTTAGAAAAAACGGA
*
2320 AAAAACGGAAAAAACCTTTTTTTTTTATAGAAAAAACGGA
1 AAAAACGG-AAAAA--TATTTTTTTT-TAGAAAAAACGGA
2360 AAA
1 AAA
2363 TCAAAAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 8 0.22
37 5 0.14
39 9 0.24
40 15 0.41
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.28
Consensus pattern (36 bp):
AAAAACGGAAAAATATTTTTTTTTAGAAAAAACGGA
Found at i:2661 original size:6 final size:6
Alignment explanation
Indices: 2650--2682 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2640 TAAGCAAAGC
2650 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
2683 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:4423 original size:6 final size:6
Alignment explanation
Indices: 4414--4440 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4404 AAAGCAAAGC
4414 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
4441 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:6661 original size:341 final size:332
Alignment explanation
Indices: 6036--7328 Score: 1294
Period size: 331 Copynumber: 3.9 Consensus size: 332
6026 AGCTCGATCA
* * * * * * *
6036 TTAGTACTCGATTTCAGCTAAAATTTAGTAAAAATTGACCCGA-AAGAATTATCCTCAATTTTTG
1 TTAGTACACGATTTCAGTTAAATTTTTGCAAAAATTGACCCGAGAAG-TTTCTCCTCAATTTTT-
* * * * *
6100 GCCACGATAGTCAT-AAAAAATATACAATTCAATGCCAAAGAA-ATTGAAAGACTAT-TCACGCT
64 GCCACCATAGTCATAAAAAAATATATAACTCAACGCCAAA-AAGATTGAAAGGCT-TCTCACGCT
* * * *
6162 TCTAATATCGTTTTTTTCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAA-CATGATTCATA
127 TCTAATATTGTTTTTTT-TATATTTTCCGAATTAATTTCTAATTAAATCGAAACCATGATTCAGA
* * * * * * *
6226 TGCTCGTAAAAGCAAATTCTTAAGTCCAATGTAGG-TAAGAATTGGTTAAATGAATATAGATATT
191 TGCTCGTAAAAACAAATACTTAAATCCAATGT-GGCTAAGATTTCGTTAGATAAATATAGATATT
**
6290 TCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTGGGGCTTTAGATCGCGTTTTTAGTC
255 TCAATGAGACTTTGCG-CAAAAATCATGCAAAACTGAGCTGGGGCTCCAGATCGCGTTTTTAGTC
6355 AAAAACCGTGATGG
319 AAAAACCGTGATGG
* * * * **
6369 TCAGTACACAATTTCAGTTACAGTTTTGCAAAAATTGACCCGAGAAGTTTCTCCTCAATTTCCGA
1 TTAGTACACGATTTCAGTTAAATTTTTGCAAAAATTGACCCGAGAAGTTTCTCCTCAATTTTTG-
* * *
6434 CCACCATAGTCATAAAAAAATATATAACTCAACGCCAAAAAGATTGAATGTCTTCTAACGCTTCT
65 CCACCATAGTCATAAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCT
* *
6499 AATATTGTTCTTTTTTAAAAAAATATTCTTCTGAATTAATTTCTAATTAAAGCGAAACCA-GATT
130 AATATTGTT-TTTTTT------ATATT-TTCCGAATTAATTTCTAATTAAATCGAAACCATGATT
* * * * * *
6563 AAGATGCTCGTAAAAATAAATATTTAAATCCCACGTGGCTAAGATTTCTTTAGATAAATATAGAT
187 CAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGAT
* * *
6628 ATTTCAATGAGGCTTTGTGTCAAAAATCATGCAAAACTGAGCTGGAG-TCCCAGAAT-GCGTTTT
252 ATTTCAATGAGACTTTGCG-CAAAAATCATGCAAAACTGAGCTGGGGCT-CCAG-ATCGCGTTTT
** * *
6691 TAACCAAAAACCATGATAG
314 TAGTCAAAAACCGTGATGG
* * * * *
6710 TTAGTACACGATTTCGGCTAAAATTTTTGTAGAAATTGACCCGAAATAGTTT-TCCTCAATTTTT
1 TTAGTACACGATTTCAG-TTAAATTTTTGCAAAAATTGACCCGAGA-AGTTTCTCCTCAATTTTT
* * * * * * *
6774 GCCCACAATA--C-TAAACAAAATAAATAATTCATCACCAACAAGATTGAAAGGCTTTTCACGCT
64 G-CCACCATAGTCATAAA-AAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCT
* ** * * * *
6836 TCTAAT-TCTGGTTTTCCTATTTTTTCCGAATTAATTTCTTATTAAATC-AAAACATGATTCTGA
127 TCTAATAT-TGTTTTTTTTATATTTTCCGAATTAATTTCTAATTAAATCGAAACCATGATTCAGA
* ** * * * *
6899 TGCTCGTAAAAA-AAATACTTAAATGCAATGTGATTGATATTTGGTTAGATGAATATAGATATTT
191 TGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTT
* * * * * *
6963 CAATAAAATTTTGCGACAAAAATCGTGCAAAACTGAGCCGGGGCTCCGGATCGCGTTTTTAGTCA
256 CAATGAGACTTTGCG-CAAAAATCATGCAAAACTGAGCTGGGGCTCCAGATCGCGTTTTTAGTCA
7028 AAAACCGTGATGG
320 AAAACCGTGATGG
* * * * *
7041 TTAGTATACGATTTCAGCTAAATTTTTGCAAAAATTGACCTGAGAAATTTCTCTTCAATTTTTTG
1 TTAGTACACGATTTCAGTTAAATTTTTGCAAAAATTGACCCGAGAAGTTTCTCCTCAA-TTTTTG
* *
7106 CCACCATAGTCAT-AAAAAATATATAACTCGACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCT
65 CCACCATAGTCATAAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCT
* * *
7170 AATATTGTTTTTTTGTTTCTATTTTCCGAATTAATTTCTAATTAAATTGAAACCA-GATTGAGAT
130 AATATTG--TTTTT-TTTATATTTTCCGAATTAATTTCTAATTAAATCGAAACCATGATTCAGAT
* * *
7234 G-TACGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATGTCGTTAGATAAATATAGATATTT
192 GCT-CGTAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTT
* *
7298 -AATTGAGTCTTGGCGCAGAAAATCATGCAAA
256 CAA-TGAGACTTTGCGCA-AAAATCATGCAAA
7329 GAATTTTCCT
Statistics
Matches: 774, Mismatches: 148, Indels: 74
0.78 0.15 0.07
Matches are distributed among these distances:
329 4 0.01
330 37 0.05
331 172 0.22
332 46 0.06
333 72 0.09
334 99 0.13
335 73 0.09
339 9 0.01
340 54 0.07
341 159 0.21
342 44 0.06
343 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (332 bp):
TTAGTACACGATTTCAGTTAAATTTTTGCAAAAATTGACCCGAGAAGTTTCTCCTCAATTTTTGC
CACCATAGTCATAAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
ATATTGTTTTTTTTATATTTTCCGAATTAATTTCTAATTAAATCGAAACCATGATTCAGATGCTC
GTAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATG
AGACTTTGCGCAAAAATCATGCAAAACTGAGCTGGGGCTCCAGATCGCGTTTTTAGTCAAAAACC
GTGATGG
Found at i:7526 original size:243 final size:244
Alignment explanation
Indices: 7086--7571 Score: 585
Period size: 243 Copynumber: 2.0 Consensus size: 244
7076 TGACCTGAGA
* * * *
7086 AATTTCTCTTCAATTTTTTGCCACCATAGTCATAAAAAATATATAACTCGACGCCAAAAAGATTG
1 AATTTCTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTG
* * * * *
7151 AAGGGCTTCTCACGCTTCTAATATTGTTTTTTTGTTTCTATTTTCCGAATTAATTTCTAATTAAA
66 AAAGACTTCTCACGCTTCTAATATCGTTTCTTTGTTTCTATTTTCCGAATTAATTCCTAATTAAA
* * * *
7216 TTGAAACCAGATTGAGATGTACGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATGTCGTTA
131 TCGAAACCAGATTCAGATGTACGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATGTCGTTA
*
7281 GATAAATATAGATATTT-AATTGAGTCTTGGCG-CAGAAAATCATGCAAAG
196 GATAAATATAGATATTTCAA-TGAGACTTGGCGCCA-AAAATCATGCAAAG
* *
7330 AATTT-TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAA-ATT
1 AATTTCTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAACTCAACGCCAAA-AAGATT
*
7393 GAAAGACTAT-TCACGCTTCTAATATCG-TTCTTT-TTTCTATTTTTCCTGACTTAATTCCTAAT
65 GAAAGACT-TCTCACGCTTCTAATATCGTTTCTTTGTTTCTA-TTTTCC-GAATTAATTCCTAAT
* * * * * * *
7455 TAAATCGAAA-CATGATTCATATGCT-CGTAAAAGCAAATCGTTAAGTTCAATGTGATTAAGATT
127 TAAATCGAAACCA-GATTCAGATG-TACGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATG
* * * *
7518 TGGTTAGATGAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCGTGCAAA
190 TCGTTAGATAAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAA
7572 ACTGAGCCGG
Statistics
Matches: 206, Mismatches: 28, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
241 6 0.03
242 13 0.06
243 174 0.84
244 13 0.06
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (244 bp):
AATTTCTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTG
AAAGACTTCTCACGCTTCTAATATCGTTTCTTTGTTTCTATTTTCCGAATTAATTCCTAATTAAA
TCGAAACCAGATTCAGATGTACGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATGTCGTTA
GATAAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAG
Found at i:8207 original size:335 final size:335
Alignment explanation
Indices: 7326--10074 Score: 2738
Period size: 335 Copynumber: 8.2 Consensus size: 335
7316 AAAATCATGC
*
7326 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAA-
1 AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAA-AAG
* * *
7390 ATTGAAAGACTAT-TCACGCTTCTAATATCGTTCTTTTTTCTA-TTTTTCCTGACTTAATTCCTA
65 ATTGAAAGACT-TCTCACGCTTCTAATATCGTTTTTTTTTCTATTTTTTCC-GAATTAATTTCTA
* * * * * **
7453 ATTAAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCGTTAAGTTCAATGTGATTAAGATT
128 ATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
* * * *
7518 TGGTTAGATGAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCGTGCAAAACTGAGCCGGG
193 TGGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTGAG
* * * * * *
7583 GCTCCGGATCGCGTTTTTAGTCAAAAACCGTGATGGTTAATATACGATTTCAGCTAAATTTTTGC
258 GCTCCGAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTTTGC
*
7648 AAAAATTGACCTG
323 AAAAATTGACCCG
* * *
7661 --AGAATTTTCTCTTCAATTTTTGGCCACCATAGTCATAAAAAATATATAACTCGACGCCAAAAA
1 AAAGAATTTTC-C-TCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAA
* * *
7724 GATTGAAGGGCTTCTCACGCTTCTAATA----TTTTTTTT-TATATTTTCCGAATTAATTTCTAA
64 GATTGAAAGACTTCTCACGCTTCTAATATCGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAA
* * * *
7784 TTAAATCGAAAC-TGGATTGAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATG
129 TTAAATCGAAACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
* * * * * *
7848 TCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAGC-CAG
193 TGGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTGAG
* * * *
7912 TC-CCAAAAT-GCGTTTTTAGCCTAAAAAACCATGATAGTTAGTACACGATTTCGGCTAAAATTT
258 GCTCC-GAATCGCGTTTTTAG--TCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTT
* *
7975 AGTAAAAATTGACCCG
320 TGCAAAAATTGACCCG
*
7991 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCAT-AAAAATATATAATTCAACGCCAAAGAA-
1 AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAA-AAG
* *
8054 ATTGAAAGACTAT-TCACGCTTCTAGTATCGTTCTTTTTTTCTATTTTTTCCGAATTAATTCCTA
65 ATTGAAAGACT-TCTCACGCTTCTAATATCGTT-TTTTTTTCTATTTTTTCCGAATTAATTTCTA
* * * * * *
8118 ATTAAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCGTTAAGTTCAATGTGGGTAAGATT
128 ATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
* * * * * * *
8183 TGATTAAATGAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCGTGCAAAACTGTGTTGGG
193 TGGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTGAG
* * * * * * *
8248 GCTCCTAATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGTTACAGTTTTGC
258 GCTCCGAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTTTGC
8313 AAAAATTGACCCG
323 AAAAATTGACCCG
* ** * * * * *
8326 AGA-AATTTCTCCTCAATTTCCGACCACCATAGTTATAAAAAAATATATAAATCAACGACAAAAA
1 AAAGAATTT-TCCTCAATTTTTGGCCACCATACTCAT-AAAAAATATATAATTCAACGCCAAAAA
* * * * ** *
8390 GATTG-AAGATCTTCTAACGCTTCCAACATTGTTCTTTTTTTAAAATTATTTTTCTGAATTAATT
64 GATTGAAAGA-CTTCTCACGCTTCTAATATCGTT-TTTTTTT-CTA-T-TTTTTCCGAATTAATT
* * * * ** *
8454 TCTAATTAAAGCGAAAC-CGTATTGAGATGCTCGTAAAAATAAATATTTAAATCCCATGTGGCTA
124 TCTAATTAAATCGAAACATG-ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTA
** *
8518 AGATTTCTTTAGATAAATATAGATATTTCAATGAGTCTTTGTC-CCAAAAATCATGCAAAACTGA
188 AGATTTGGTTAGATAAATATAGATATTTCAATGAGACTTTG-CGCCAAAAATCATGCAAAACTGA
* * * *
8582 GCTG-GAG-TCCGAGAAT-GTGTTTTTAGTCAAAAACCATGATAGTTAGTATATGATTTCGGCTA
252 GCTGAG-GCTCC--GAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTA
*
8644 AAATTTTGTAAAAATTGACCCG
314 AAATTTTGCAAAAATTGACCCG
* * * * * * *
8666 AAATAGTTTTCCTCAATTTTTGGCCACAATACTCATAAAAAATAAAT-ATATCATCACCAACAAG
1 AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAAT-TCAACGCCAAAAAG
* * * * *
8730 ATTGAAAGGCTTTTCACGCTTCT-A-A-C-TTTGGTTTTCCTATTTTTTCCGAATTAATTTCTAC
65 ATTGAAAGACTTCTCACGCTTCTAATATCGTTT-TTTTTTCTATTTTTTCCGAATTAATTTCTAA
* * ** * *
8791 TTAAATCGAAACATGATTCAGATGCTAGTAAAAAAAAAAAATCCTTAAATCCAATGTGATTGATA
129 TTAAATCGAAACATGATTCAGATGCTCGT---AAAAACAAATCCTTAAATCCAATGTGGCTAAGA
* * *
8856 TTTGGTTAGATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTG
191 TTTGGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTG
* * * ** * *
8921 GGGCTCCGGATCGCGTTTTTAGTAAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTT
256 AGGCTCCGAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTTT
* *
8986 CCAAAAATTGA-TC-
321 GCAAAAATTGACCCG
* ** * *
8999 TAAGAAATTTCTATTCAATTTTTGGCCACCATAGTCATAAAAAATATATAACTCAACGCCAAAAA
1 AAAG-AATTT-TCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAA
* * * * * *
9064 GATTGAAGGGCTTCTCACGCTTCTAGTA---TTTGTATTTCTA-CTTTTCCGAATTAATTTCTAA
64 GATTGAAAGACTTCTCACGCTTCTAATATCGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAA
* * ** *
9125 TTAAATCGAAACCA-GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTATCTGAGATT
129 TTAAATCGAAA-CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
* * * * *
9189 TCGTTAGACAAATATTGATATTTCAATGAGTC-TTGACGCCAAAAA-CATG-AAAACTGAGTCAG
193 TGGTTAGATAAATATAGATATTTCAATGAGACTTTG-CGCCAAAAATCATGCAAAACTGAG-CTG
** * * *
9251 AGTGC-CAAAAT-GCGTTTTTAGCCGAAAAAACATGATAGTTAGTACAGGATTTCAGCTAAAATT
256 AG-GCTCCGAATCGCGTTTTTAGTC-AAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATT
* *
9314 TTGTAAGAATTGACCCG
319 TTGCAAAAATTGACCCG
** *
9331 AAAGAATTTTCCTCAATTTTTGGCCACGGTACTCATAAAAAATATATAATTCAACGCCAGAATA-
1 AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCA-AAAAG
* * *
9395 ATTGAAAGACTAT-TCACACTTCTAATATCG---TTTTTCCTATTTTTTCCGAATTAATTCCTAA
65 ATTGAAAGACT-TCTCACGCTTCTAATATCGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAA
* * *
9456 TTGAATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTT
129 TTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTT
* * * * ** * * *
9521 GGTTAAATGAATATGGATATTTCAAGGAGACTTTGCATCAAAAATCGTG-AACAACTGAGTTGGG
194 GGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAA-AACTGAGCTGAG
* * * * * * * *
9585 GCTCCGGATCACGTTTTAAGTCAAAAACCGTGATAGTTAGTACACAATTTCAGCCACAGTTTTGC
258 GCTCCGAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTTTGC
9650 AAAAATTGACCCG
323 AAAAATTGACCCG
* ** * * * *
9663 AGA-AATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACTCAACACCAAAAAG
1 AAAGAATTT-TCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAAG
* * * * **
9727 ATTGAAGGTCTTCTAACGCTTCTAATATTGTTCTTTTCTTT-TAAAATATTTTTCTAAATTAATT
65 ATTGAAAGACTTCTCACGCTTCTAATATCGTT-TTTT-TTTCT---AT-TTTTTCCGAATTAATT
** * * * * *
9791 TCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAATAAATCTTTAAATCCCATGTTGCTAA
124 TCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAA
** * * **
9856 GATTTCTTTAGAAAAATATAGATATTTCAATGAGTCTTTGTACCAAAAATCATGCAAAACTGAGC
189 GATTTGGTTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGC
* * * * *
9921 TG-GAG-TCCCAGATTGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCGGGTAAAC
254 TGAG-GCTCCGA-ATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAA
*
9984 TTTTGTAAAAATTGACCCG
317 TTTTGCAAAAATTGACCCG
* * * * * *
10003 AAATAGTTTTCCTCAATTTTTGGCCACAATACTCATAAAAAATAAATAATTCATCGCCAATAAGA
1 AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
10068 TTGAAAG
66 TTGAAAG
10075 GCAAAGTGGT
Statistics
Matches: 1964, Mismatches: 361, Indels: 173
0.79 0.14 0.07
Matches are distributed among these distances:
328 12 0.01
329 68 0.03
330 320 0.16
331 205 0.10
332 181 0.09
333 30 0.02
334 70 0.04
335 481 0.24
336 25 0.01
337 66 0.03
338 3 0.00
339 47 0.02
340 442 0.23
341 14 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (335 bp):
AAAGAATTTTCCTCAATTTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
TTGAAAGACTTCTCACGCTTCTAATATCGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATT
AAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGG
TTAGATAAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCATGCAAAACTGAGCTGAGGCT
CCGAATCGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAA
AATTGACCCG
Found at i:8848 original size:675 final size:667
Alignment explanation
Indices: 7326--10062 Score: 3557
Period size: 665 Copynumber: 4.1 Consensus size: 667
7316 AAAATCATGC
7326 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAAA
1 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAAA
* * * *
7391 TTGAAAGACTATTCACGCTTCTAATATCGTTCTTTTTTCTA-TTTTTCCTGACTTAATTCCTAAT
66 TTGAAAGACTATTCACGCTTCT-ATATCTTTGTTTTTCCTATTTTTTCC-GAATTAATTCCTAAT
* * * * *
7455 TAAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCGTTAAGTTCAATGTGATTAAGATTTG
129 TAAATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTAAGATTTG
* * *
7520 GTTAGATGAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCGTGCAAAACTGAGCCGGGGC
194 GTTAAATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTGGGGC
* * * *
7585 TCCGGATCGCGTTTTTAGTCAAAAACCGTGATGGTTAATATACGATTTCAGCTAAATTTTTGCAA
259 TCCGGATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAGTTTTGCAA
* * * ** * *
7650 AAATTGACCTGAGAATTTTCTCTTCAATTTTTGGCCACCATAGTCATAAAAAATATATAACTCGA
324 AAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACTCAA
* * *
7715 CGCCAAAAAGATTGAAGGGCTTCTCACGCTTC--TAATATTTTTTTTTATA-TTTTCCGAATTAA
389 CGACAAAAAGATTGAAGGGCTTCTAACGCTTCAATATTATTTTTTTTTATATTTTTCCGAATTAA
* * *
7777 TTTCTAATTAAATCGAAACTGGATTGAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
454 TTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCCATGTGGCT
* * * * *
7842 GAGATGTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAA
519 AAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGTCGCCAAAAATCATGCAAAACTGA
* *
7907 GC--CAGTCCCAAAATGCGTTTTTAGCCTAAAAAACCATGATAGTTAGTACACGATTTCGGCTAA
584 GCTGGAGTCCCAAAATGCGTTTTTAG--TCAAAAACCATGATAGTTAGTACACGATTTCGGCTAA
*
7970 AATTTAGTAAAAATTGACCCG
647 AATTTTGTAAAAATTGACCCG
7991 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCAT-AAAAATATATAATTCAACGCCAAAGAAA
1 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAAA
*
8055 TTGAAAGACTATTCACGCTTCTAGTATCGTTCT-TTTTTTCTATTTTTTCCGAATTAATTCCTAA
66 TTGAAAGACTATTCACGCTTCTA-TATC-TT-TGTTTTTCCTATTTTTTCCGAATTAATTCCTAA
* * * * *
8119 TTAAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCGTTAAGTTCAATGTGGGTAAGATTT
128 TTAAATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTAAGATTT
* * * *
8184 GATTAAATGAATATAGATATTTCAATGAGACTTTGCGCCAAAAATCGTGCAAAACTGTGTTGGGG
193 GGTTAAATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTGGGG
** * *
8249 CTCCTAATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGTTACAGTTTTGCA
258 CTCCGGATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAGTTTTGCA
* *
8314 AAAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTTATAAAAAAATATATAAATC
323 AAAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCAT-AAAAAATATATAACTC
** * *
8379 AACGACAAAAAGATTGAAGATCTTCTAACGCTTCCAACATTGTTCTTTTTTTAAAATTATTTTTC
387 AACGACAAAAAGATTGAAGGGCTTCTAACGCTT-CAATATTATT-TTTTTTT---A-TATTTTTC
* * * * **
8444 TGAATTAATTTCTAATTAAAGCGAAACCGTATTGAGATGCTCGTAAAAATAAATATTTAAATCCC
446 CGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCC
*
8509 ATGTGGCTAAGATTTCTTTAGATAAATATAGATATTTCAATGAGTCTTTGTC-CCAAAAATCATG
511 ATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTC-TTGTCGCCAAAAATCATG
* * * * *
8573 CAAAACTGAGCTGGAGTCCGAGAATGTGTTTTTAGTCAAAAACCATGATAGTTAGTATATGATTT
575 CAAAACTGAGCTGGAGTCCCAAAATGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTT
8638 CGGCTAAAATTTTGTAAAAATTGACCCG
640 CGGCTAAAATTTTGTAAAAATTGACCCG
* * * * * *
8666 AAATAGTTTTCCTCAATTTTTGGCCACAATACTCATAAAAAATAAAT-ATATCATCACCAACA-A
1 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAAT-TCAACGCCAA-AGA
* * * * * *
8729 GATTGAAAGGCTTTTCACGCTTCTA-A-CTTTGGTTTTCCTATTTTTTCCGAATTAATTTCTACT
64 AATTGAAAGACTATTCACGCTTCTATATCTTTGTTTTTCCTATTTTTTCCGAATTAATTCCTAAT
* * * * * *
8792 TAAATCGAAACATGATTCAGATGCTAGTAAAAAAAAAAAATCCTTAAATCCAATGTGATTGATAT
129 TAAATCGAAACATGATTCATATGCTCGT---AAAAACAAATCCTTAAATCCAATGTGAGTAAGAT
*
8857 TTGGTTAGATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTGG
191 TTGGTTAAATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTGG
* * * * * *
8922 GGCTCCGGATCGCGTTTTTAGTAAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTC
256 GGCTCCGGATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAGTTTTG
* ** ** ** *
8987 CAAAAATTGATCTAAGAAATTTCTATTCAATTTTTGGCCACCATAGTCATAAAAAATATATAACT
321 CAAAAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACT
* * * * * * *
9052 CAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTC--TAGTATTTGTATTTCTACTTTTCCGAAT
386 CAACGACAAAAAGATTGAAGGGCTTCTAACGCTTCAATATTATTTTTTTTTATATTTTTCCGAAT
*
9115 TAATTTCTAATTAAATCGAAACCAGATTGAGATGCTCGTAAAAACAAATCCTTAAAT-CCATTGT
451 TAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCCA-TGT
** * * * *
9179 ATCTGAGATTTCGTTAGACAAATATTGATATTTCAATGAGTCTTGACGCCAAAAA-CATG-AAAA
515 GGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGTCGCCAAAAATCATGCAAAA
* * * * * *
9242 CTGAG-TCAGAGTGCCAAAATGCGTTTTTAGCCGAAAAAACATGATAGTTAGTACAGGATTTCAG
580 CTGAGCT-GGAGTCCCAAAATGCGTTTTTAGTC-AAAAACCATGATAGTTAGTACACGATTTCGG
*
9306 CTAAAATTTTGTAAGAATTGACCCG
643 CTAAAATTTTGTAAAAATTGACCCG
* *
9331 AAAGAATTTTCCTCAATTTTTGGCCACGGTACTCATAAAAAATATATAATTCAACGCCAGAA-TA
1 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCA-AAGAA
*
9395 ATTGAAAGACTATTCACACTTCTAATATC---GTTTTTCCTATTTTTTCCGAATTAATTCCTAAT
65 ATTGAAAGACTATTCACGCTTCT-ATATCTTTGTTTTTCCTATTTTTTCCGAATTAATTCCTAAT
* *
9457 TGAATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTG
129 TAAATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTAAGATTTG
* * * *
9522 GTTAAATGAATATGGATATTTCAAGGAGACTTTGCATCAAAAATCGTG-AACAACTGAGTTGGGG
194 GTTAAATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAA-AACTGAGCTGGGG
* * * * *
9586 CTCCGGATCA-CGTTTTAAGTCAAAAACCGTGATAGTTAGTACACAATTTCAGCCACAGTTTTGC
258 CTCCGGAT-AGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAGTTTTGC
9650 AAAAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACTC
322 AAAAATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACTC
* *
9715 AAC-ACCAAAAAGATTGAAGGTCTTCTAACGCTTCTAATATTGTTCTTTTCTTTTAAAATATTTT
387 AACGA-CAAAAAGATTGAAGGGCTTCTAACGCTTC-AATATT-AT-TTTT-TTTT---ATATTTT
** * *
9779 TCTAAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAATAAATCTTTAAATC
444 TCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATC
* * * *
9844 CCATGTTGCTAAGATTTCTTTAGAAAAATATAGATATTTCAATGAGTCTTTGT-ACCAAAAATCA
509 CCATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTC-TTGTCGCCAAAAATCA
* *
9908 TGCAAAACTGAGCTGGAGTCCCAGATTGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGAT
573 TGCAAAACTGAGCTGGAGTCCCAAAATGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGAT
* *
9973 TTCGGGTAAACTTTTGTAAAAATTGACCCG
638 TTCGGCTAAAATTTTGTAAAAATTGACCCG
* * * * *
10003 AAATAGTTTTCCTCAATTTTTGGCCACAATACTCATAAAAAATAAATAATTCATCGCCAA
1 AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAA
10063 TAAGATTGAA
Statistics
Matches: 1795, Mismatches: 227, Indels: 94
0.85 0.11 0.04
Matches are distributed among these distances:
661 2 0.00
662 227 0.13
663 2 0.00
664 82 0.05
665 470 0.26
666 164 0.09
667 5 0.00
668 4 0.00
669 4 0.00
670 12 0.01
671 116 0.06
672 169 0.09
673 32 0.02
674 48 0.03
675 395 0.22
676 44 0.02
677 19 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (667 bp):
AAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAGAAA
TTGAAAGACTATTCACGCTTCTATATCTTTGTTTTTCCTATTTTTTCCGAATTAATTCCTAATTA
AATCGAAACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTAAGATTTGGT
TAAATGAATATAGATATTTCAATGAGACTTTGCACCAAAAATCGTGCAAAACTGAGCTGGGGCTC
CGGATAGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAGTTTTGCAAAA
ATTGACCCGAGAAATTTCTCCTCAATTTCCGACCACCATAGTCATAAAAAATATATAACTCAACG
ACAAAAAGATTGAAGGGCTTCTAACGCTTCAATATTATTTTTTTTTATATTTTTCCGAATTAATT
TCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCCATGTGGCTAA
GATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGTCGCCAAAAATCATGCAAAACTGAGC
TGGAGTCCCAAAATGCGTTTTTAGTCAAAAACCATGATAGTTAGTACACGATTTCGGCTAAAATT
TTGTAAAAATTGACCCG
Done.