Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023835.1 Corchorus olitorius cultivar O-4 contig23868, 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: 30229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3002 original size:327 final size:319
Alignment explanation
Indices: 2131--3686 Score: 1480
Period size: 327 Copynumber: 4.8 Consensus size: 319
2121 AACATTTTGC
* * * * * * *
2131 AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTACCGCAATACTCAGAAAAAATATATGATTC
1 AAAAACTGACCCGAAAATTTTTTTCTCAAATTTTTGCCACAATACTCA-AAAAAATATATAATTC
* * * * *
2196 AACACCAAAAAAATTG--GAG------ACGCTTCTAATATCGCTTTTCCATTTTTTTCGGAATTT
65 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTT
* * *
2253 ATTT-TAAATTAAATTGAAACAAGATTCATATGCTCGTAGAAACAAATCCTTAAATCCAATGTGG
130 ATTTCT-AATTAAATCGAAACAAGATTCAGATGCTCGTA-AAACAAATTCTTAAATCCAATGTGG
* * *
2317 CTGAGATTTGGTTAGATGAATATAAATATTTCAAGGTA-TCTTT-CTGTA-AAAAATCATGCAAA
193 CTGAGATTTGTTTAGATGAATATAGATATTTCAAGG-AGTCTTTAC--AACAAAAATCATGCAAA
* * *
2379 ACTGAGCAGGGCCCCGAAACGCGTTTTTAGACAAAAAAAACCGTGATGGTTAGTACATGATTTCG
255 ACTGAGCCGGGCCCCGAAACGCGTTTTTAG-C--AAAAAACCGTGATGATTAGTACACGATTTCG
2444 GCT
317 GCT
* * * * * * *
2447 AAAAATTAACCCG-AAATTTTTTTATGAAATTTTTGCCGCAATACTCAGAAAATTATATAATTCA
1 AAAAACTGACCCGAAAATTTTTTTCTCAAATTTTTGCCACAATACTCAAAAAAATATATAATTCA
* ** *
2511 ACGCCAAAAAGATTGACCGGCTTTTCACGCTTCTAATATCG----T---TTTTTTCCCGAATTTA
66 ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTTA
* * * * * *
2569 TTTCCAATTAATTCGAAACAAAATTCAAACGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGCT
131 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA-CAAATTCTTAAATCCAATGTGGCT
* * * *
2634 GAAATTTGGTTCGATGAATATATATATTTCAA-GATGTCTTTACAACAAAAATCATGCAAAACTG
195 GAGATTTGTTTAGATGAATATAGATATTTCAAGGA-GTCTTTACAACAAAAATCATGCAAAACTG
* * *
2698 AGCCGGGCCCCAAAACGCGTTTTTAGACAAAAAAATCGTGATGATTAGTACATGATTTCGGCT
259 AGCCGGGCCCCGAAACGCGTTTTTAG-C-AAAAAACCGTGATGATTAGTACACGATTTCGGCT
* * *
2761 AAAAACTGACCCGAAAAGTTTTTTTTTTTGAAAATTTTGCCACAATACTCACAAAAAATATATAA
1 AAAAACTGACCCGAAAA---TTTTTTTCTCAAATTTTTGCCACAATACTCA-AAAAAATATATAA
* * * *
2826 TTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTTTAATATCGTTTTTCCATTTTTTCCCCAA
62 TTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-CCCGA
* * *
2891 ATTTATTTTTAATCAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATTCTTAAATCTAATG
126 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATTCTTAAATCCAATG
* * *** * *
2956 TGGCTGAGATTTATTTAGATGAATATAGATACTTCAAGGAGTCTTTATGTCAAAAACCATACAAA
190 TGGCTGAGATTTGTTTAGATGAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAA
** *
3021 ACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-AGTTAGTACACGATTTCGG
255 ACTGAGCCG-GGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGA-TTAGTACACGATTTCGG
3085 CT
318 CT
* * *
3087 AAACACTGATCCGAAAATTTTTTTTCTCAAATTTTTGCCACAATACTCATAAAAAACATATAATT
1 AAAAACTGACCCGAAAA-TTTTTTTCTCAAATTTTTGCCACAATACTCA-AAAAAATATATAATT
** *
3152 CATTGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATCTTTTT-TCGAA
64 CAACGCC-AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTCCCGAA
* * * * * ** *
3216 ATAATTTCTGATTAAATCGAAACAAAATTCAGATGCTCGTAGAAACAAATTGTTTGATCCAATTT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAACAAATTCTTAAATCCAATGT
* * *** *
3281 GGCTGGGATTTGTTT---CG-ATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGAAAAA
191 GGCTGAGATTTGTTTAGATGAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAA
* * ** * * * *
3342 CTGAGTCGGGGCCCCGGAATACGTTTTTAGCCATAAACCGTGATGGTTAGTACACGATTGCAGCT
256 CTGAG-CCGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATTAGTACACGATTTC-G--
*
3407 AAAGTTTT
317 ---G--CT
* * * * ** * *
3415 GCAAAAACTGACCCGAAAAGTTTATCCTCAATTTTTTGCCTTATTACTCAGAAAAATATATAATT
1 --AAAAACTGACCCGAAAATTTTTTTCTCAAATTTTTGCCACAATACTCAAAAAAATATATAATT
3480 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTCTT-CCGAAT
64 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT-TTCCCGAAT
* * * *
3544 TTATTTCTAATTAAATTGAAAAAAAGATTCAGATGCTCGTAAAAAAATAAAAATTCTTAAATCGA
128 TTATTTCTAATTAAATCG-AAACAAGATTCAGATGCTCGT----AAA-ACAAATTCTTAAATCCA
* * * * *
3609 ATGTGGTTGGGATCTGGTTCA-ATGAATATAGATATTTCAAGGAGTTTTTA-AAGCAAAAATCAT
187 ATGTGGCTGAGAT-TTGTTTAGATGAATATAGATATTTCAAGGAGTCTTTACAA-CAAAAATCAT
*
3672 GTAAAACTGAGCCGG
250 GCAAAACTGAGCCGG
3687 AGCTAAAAAC
Statistics
Matches: 1033, Mismatches: 149, Indels: 97
0.81 0.12 0.08
Matches are distributed among these distances:
313 1 0.00
314 76 0.07
315 177 0.17
316 14 0.01
318 29 0.03
319 49 0.05
320 88 0.09
321 3 0.00
322 15 0.01
323 2 0.00
324 115 0.11
325 44 0.04
326 59 0.06
327 180 0.17
328 64 0.06
329 24 0.02
330 15 0.01
331 2 0.00
332 24 0.02
333 4 0.00
335 4 0.00
336 44 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
AAAAACTGACCCGAAAATTTTTTTCTCAAATTTTTGCCACAATACTCAAAAAAATATATAATTCA
ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCAATGTGGCTG
AGATTTGTTTAGATGAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAG
CCGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATTAGTACACGATTTCGGCT
Found at i:4181 original size:18 final size:19
Alignment explanation
Indices: 4144--4184 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4134 CATGATGAAT
*
4144 AAAAAAGTTGAATCATCTA
1 AAAAAAGTTAAATCATCTA
*
4163 AAAAAAGTTAAATGA-CTA
1 AAAAAAGTTAAATCATCTA
4181 AAAA
1 AAAA
4185 GAATACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (19 bp):
AAAAAAGTTAAATCATCTA
Found at i:8497 original size:22 final size:22
Alignment explanation
Indices: 8471--8513 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8461 ATTTTTTAAA
8471 GGATTTATTTTTGAAGAATATT
1 GGATTTATTTTTGAAGAATATT
*
8493 GGATTTATTTTTGAAGGATAT
1 GGATTTATTTTTGAAGAATAT
8514 ATTTTGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (22 bp):
GGATTTATTTTTGAAGAATATT
Found at i:8849 original size:25 final size:28
Alignment explanation
Indices: 8801--8851 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
8791 TTCATCTAAC
8801 TTATTATTAAGATTATTAAGTTATTATA
1 TTATTATTAAGATTATTAAGTTATTATA
*
8829 TTATTA-TAAG-TTA-TAATTTATTA
1 TTATTATTAAGATTATTAAGTTATTA
8852 AATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 3 0.14
27 4 0.18
28 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (28 bp):
TTATTATTAAGATTATTAAGTTATTATA
Found at i:8867 original size:14 final size:14
Alignment explanation
Indices: 8850--8900 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
8840 TATAATTTAT
8850 TAAATTTAAATTAC
1 TAAATTTAAATTAC
**
8864 TAAATTTTTATTA-
1 TAAATTTAAATTAC
8877 TAATATTACTAAATTAC
1 TAA-ATT--TAAATTAC
8894 TAAATTT
1 TAAATTT
8901 TTATTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
16 8 0.28
17 3 0.10
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATTTAAATTAC
Found at i:8890 original size:30 final size:30
Alignment explanation
Indices: 8856--8921 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
8846 TTATTAAATT
*
8856 TAAATTACTAAATTTTTATTA-TAATATTA
1 TAAATTACTAAATTTTTATTATTAATAATA
8885 CTAAATTACTAAATTTTTATTATTAATAATA
1 -TAAATTACTAAATTTTTATTATTAATAATA
8916 TAAATT
1 TAAATT
8922 TTTATTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 27 0.79
31 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAATTACTAAATTTTTATTATTAATAATA
Found at i:8905 original size:22 final size:21
Alignment explanation
Indices: 8880--8936 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
8870 TTTATTATAA
8880 TATTACTAA-ATTACTAAATTTT
1 TATTA-TAATATTA-TAAATTTT
*
8902 TATTATTAATAATATAAATTTT
1 TATTA-TAATATTATAAATTTT
8924 TATTATAATATTA
1 TATTATAATATTA
8937 GATATTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 21 0.68
23 3 0.10
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTATAATATTATAAATTTT
Found at i:9576 original size:107 final size:107
Alignment explanation
Indices: 9413--9625 Score: 399
Period size: 107 Copynumber: 2.0 Consensus size: 107
9403 CTCCCTCCGT
*
9413 CCCATATTATCTGTCCCTTTTGGGTCAAATTAATCTTACCTTTGACCTTTAATTATAGAAAAAAT
1 CCCATATTATCTGTCCCTTTTGGGTCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAAAT
*
9478 ATATACAATTAAATTTTTTAAAAAATTATATTTTGATTAAGC
66 ATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAGC
*
9520 CCCATATTATCTGTCCCTTTTGGGTCAAACTAATCTTATCTTTGACCTTTAATTATAGAAAAAAT
1 CCCATATTATCTGTCCCTTTTGGGTCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAAAT
9585 ATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAG
66 ATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAG
9626 TTAAGTTATT
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.42
Consensus pattern (107 bp):
CCCATATTATCTGTCCCTTTTGGGTCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAAAT
ATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAGC
Found at i:9735 original size:92 final size:94
Alignment explanation
Indices: 9561--9744 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 94
9551 AATCTTATCT
*
9561 TTGACCTTTAATTATAGAAAAAATATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAG
1 TTGACCTTTAATTATAGAAAAAATATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAA
9626 TTAAGTTATTTTGACCCAAAAGGGACAGA
66 TTAAGTTATTTTGACCCAAAAGGGACAGA
* *
9655 TTGACCTTTAATTATAGAAAACATATATACAATTAAA-TTTT-AAAGAATTATATTTTGATTAAA
1 TTGACCTTTAATTATAGAAAAAATATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAA
*
9718 TTAAGTTATTTTGACCCAAAATGGACA
66 TTAAGTTATTTTGACCCAAAAGGGACA
9745 AATAATATGG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
92 46 0.53
93 4 0.05
94 36 0.42
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (94 bp):
TTGACCTTTAATTATAGAAAAAATATATACAATTAAATTTTTAAAAAAATTATATTTTGATTAAA
TTAAGTTATTTTGACCCAAAAGGGACAGA
Found at i:15016 original size:31 final size:31
Alignment explanation
Indices: 14963--15027 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
14953 ATTAAGTTTT
* *
14963 TAATATTGTAAAATCGGGTCAAATCAGTCCC
1 TAATATTGCAAAATCGAGTCAAATCAGTCCC
* * *
14994 TAATGTTGCAAAATCGATTCAAATTAGTCCC
1 TAATATTGCAAAATCGAGTCAAATCAGTCCC
15025 TAA
1 TAA
15028 AGTCAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (31 bp):
TAATATTGCAAAATCGAGTCAAATCAGTCCC
Found at i:16374 original size:19 final size:19
Alignment explanation
Indices: 16350--16407 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
16340 CTGTTTAGCA
*
16350 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
16369 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
16390 AATGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
16408 TTAGAGCGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:18030 original size:16 final size:16
Alignment explanation
Indices: 18005--18050 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
17995 ACGTCATATT
18005 TTTTTATTAAAAAAATA
1 TTTTT-TTAAAAAAATA
*
18022 TTTTTTTAAAAATATA
1 TTTTTTTAAAAAAATA
*
18038 -TATTTTAAAAAAA
1 TTTTTTTAAAAAAA
18051 AGCTGGGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTTTAAAAAAATA
Found at i:18280 original size:34 final size:30
Alignment explanation
Indices: 18215--18290 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 30
18205 TTTCCCTCTG
18215 TTTTTTCAAAAAAAAAAAAGAAACCATTTTT
1 TTTTTTCAAAAAAAAAAAAGAAA-CATTTTT
18246 TCTTTTTCAAAAAAAGAAAGAAGAAA-ATGATTTT
1 T-TTTTTCAAAAAAA-AAA-AAGAAACAT--TTTT
*
18280 TTTTTTTAAAA
1 TTTTTTCAAAA
18291 TTTTGATACT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
31 1 0.03
32 15 0.38
33 12 0.31
34 11 0.28
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTTTCAAAAAAAAAAAAGAAACATTTTT
Found at i:18726 original size:25 final size:25
Alignment explanation
Indices: 18697--18748 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18687 TTTTATTCAT
18697 TTATTAGAAGAATCGGGCTAGTTAA
1 TTATTAGAAGAATCGGGCTAGTTAA
18722 TTATTAGAAGAATCGGGCTAGTTAA
1 TTATTAGAAGAATCGGGCTAGTTAA
18747 TT
1 TT
18749 GATAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (25 bp):
TTATTAGAAGAATCGGGCTAGTTAA
Found at i:18963 original size:1 final size:1
Alignment explanation
Indices: 18957--18981 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18947 GAGAGAAGGG
18957 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
18982 CATTTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24143 original size:332 final size:327
Alignment explanation
Indices: 23493--24554 Score: 1095
Period size: 333 Copynumber: 3.2 Consensus size: 327
23483 GACCCGAATT
* * *
23493 TTTCCTCAATTTTTGGCAAAAATACTCATAAAATATATATATATAATTCAACGCCAAAAATATT-
1 TTTCCTCAATTTTTGGCTAAAATACTCAT-AAA-A-A-ATATATAATTCAACACCAAAAAGATTG
* * * *
23557 AGAGGACTTTTCACGCTTCTAATATCGATTTTCATATTTTTTCTAAATTAATTTCTAATTAAATC
62 A-AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATC
* * * * * * *
23622 GAAATAAGATTCAGATGTACGTAAAAAAAAATCCTTAAATCCAATATGACTGAGATTTGATTATA
126 GAAACAAGATTAAGATCT-CGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTAG-TTAGA
* * * * * *
23687 TAAATAAAGATAATTCAGGGAGTCCCGGCGCCAAAAATCATGCAAAACACAGCCGTGGCACCGGA
189 TGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACACAG-CGTGGC-CCGGA
* * * *
23752 ATGCGTTTTTTTGCAAAAACCGTGATGGTTA-GTATACGATTTCGGCTAAAATTTTGCAAAAATT
252 ATG-GGTTTTTAGCAAAAA-CGTGATGGTAATGTAAACGATTTCGGCTAAAATTTTGCAAAAATT
23816 GACCCGAAAGATA
315 GACCCGAAAGATA
* * * *
23829 TTTCCTTAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATCAAAAAAATTGAAGG
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGG
* * *
23894 GCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAA
66 GCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTT-TTTCCAAATTAATTTCTAATTAAATCGAA
* * *
23959 ACAAGATTTAGATACTCGTAAAAACAAATCCTT-AATACAATGTGGCTGAGATGTAGTTAGATGA
129 ACAAGATTAAGAT-CTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGAT-TAGTTAGATGA
* * * ** * * * *
24023 ATATAGATATTTAAAGGAGTCTTGGCACCAAAAATCATGTAAAACTGAGCAGAGTCTCGAAATGG
192 ATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACACAGC-GTGGCCCGGAATGG
**** * *
24088 GTTTTTAGCAAAAAAAAAAGGGTAATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
256 GTTTTTAGCAAAAACGTGATGGTAAT-GTAAACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
24153 G-AA-ATA
320 GAAAGATA
* * * *
24159 TTATTCTCAATTTTTTTTTGGCCATAATACTCATAAAAAATATATAATTCAATACCAAAAAGATT
1 TT-TCCTCAA----TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACACCAAAAAGATT
* * * * * *
24224 GAAGGGCTTCTCATGCTTCTATTATCATTTTCCCTATTTTTT-CAAATTAATTTCTAATTACATC
61 GAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATC
* * * ** *
24288 GAAACAAGATTAAAATGCTCGTAAAAACAAATTCTTAAATCCAATTTGGCCAAGATTTGGTTAGA
126 GAAACAAGATTAAGAT-CTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGA-TTAGTTAGA
*
24353 TGAATATAGATATTTCAAGGAGTCTCGGCA-AAAAAATCATGCAAAACACAGGCGTGGCCCTGGA
189 TGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACACA-GCGTGGCCC-GGA
* * ** *
24417 ACGCGTAATTAGCCAAAAGCCGTGATGGTGAA--TAAACGATTTCGGCTAAAATTTTGCAAAAAT
252 ATGGGTTTTTAG-CAAAA-ACGTGATGGT-AATGTAAACGATTTCGGCTAAAATTTTGCAAAAAT
*
24480 TGACCC-ATAAGTTA
314 TGACCCGA-AAGATA
* *
24494 TTTTCTCAATTTTTGGCTAAAATACTCAT-AAAAATATATAATT-AGACATCAAAAAGATTGA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCA-ACACCAAAAAGATTGA
24555 CCTGGGACAC
Statistics
Matches: 604, Mismatches: 98, Indels: 55
0.80 0.13 0.07
Matches are distributed among these distances:
328 1 0.00
329 28 0.05
330 28 0.05
331 20 0.03
332 168 0.28
333 169 0.28
334 75 0.12
335 86 0.14
336 29 0.05
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (327 bp):
TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGG
GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAAC
AAGATTAAGATCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTAGTTAGATGAATAT
AGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACACAGCGTGGCCCGGAATGGGTTTT
TAGCAAAAACGTGATGGTAATGTAAACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
TA
Found at i:27782 original size:653 final size:649
Alignment explanation
Indices: 26468--28498 Score: 2667
Period size: 653 Copynumber: 3.1 Consensus size: 649
26458 TTCGCATCAT
* * *
26468 GCGTTTTTAGCCAAAAAAAC-GTGATGGTTAGTACATGATTTCGTCTAAAATTTTGCAAAAATTG
1 GCGTTTTTAGCC--AAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * *
26532 ACCTGAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATA-ATTTAACGCCA
64 ACCCGAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATATAATTCACGCCA
26596 AAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAAC-TTTTTCCGAATTAATTTCT
129 AAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCGAATTAATTTCT
*
26660 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGAGAT
194 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * *
26725 TTGGTAA-AATGAATATAGACATTTCAAGGATTCCTTGCGCCCAAAATCATGTAAAATTGAGCCA
259 TTGG-AATGATGAATATAGATATTTCAAGGAGTACTTGCGCCCAAAATCATGTAAAATTGAGTCA
* * *
26789 GGCTCCGAAACGCGTTTTTAGCCAAAAATTGTGATGGTTAGTACACAATTTCGGCTAAAAACTTA
323 GGCTCCGAAACGCGTTTTTAGCCAAAAACTGTGATGG---GTACACGATTTCGGCTAAAAACTGA
* *
26854 CCTGAAAAATTTTTTCTCAATTTTTTTGAAACAATACTA-AAAAATATATATAATTCAACGCCAA
385 CCCG-AAAATTTTTTCTCAA-TTTTTTAAAACAATACTAGAAAAA-ATATATAATTCAACGCCAA
* *
26918 GAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCCCATTTTTTT-AGAATTAATTTCTA
447 AAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCCCATTTTTTTCCGAATTAATTTCTA
*
26982 ATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGAGATT
512 ATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACTAATCCTTATATCGAATGTGGCTGAGATT
27047 TGGTTAGATGAATATGAATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGG
577 TGGTTAGATGAATATG-ATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGG
27112 CTCCGGAAC
641 CTCCGGAAC
* *
27121 TCGTTTTTAGCCAAAAACTATGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
1 GCGTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * *
27186 CCGGAAAA-TTTACCTCAATTTTTTTGACACACTACTCAGAAAAAATATATATAATTCTCTGCCA
66 CC-GAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATATAATTCAC-GCCA
27250 AAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCC-AGATTAATTTC
129 AAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCGA-ATTAATTTC
27314 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
193 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * *
27379 TTTGGAATGATGAATACAGATATTTCAAGGAGTGCTTGCGTCCAAAATCATGTAAAATTGAGTCA
258 TTTGGAATGATGAATATAGATATTTCAAGGAGTACTTGCGCCCAAAATCATGTAAAATTGAGTCA
*
27444 GGCTCCGAAACGCGTTCTTAGCCAAAAACTGTGATGGGTACACGATTTCGGCTAAAAACTGACCC
323 GGCTCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGGTACACGATTTCGGCTAAAAACTGACCC
* *
27509 GACAAATTTTTTCTCAATTTTTTAAAACAATACTCAGAAAAAATATATAATTCGACACCAAAAAG
388 GA-AAATTTTTTCTCAATTTTTTAAAACAATACT-AGAAAAAATATATAATTCAACGCCAAAAAG
*
27574 ATTGACCGGATTTTCACGCTTCTAAATATCGTTTTCCCATTTTTTTCCGAATTAATTTCTAATTA
451 ATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCCCATTTTTTTCCGAATTAATTTCTAATTA
27639 AATCGAAATAAGATTCAGTTACTCGTAAAAACTAATCCTTATATCGAATGTGGCTGAGATTTGGT
516 AATCGAAATAAGATTCAGTTACTCGTAAAAACTAATCCTTATATCGAATGTGGCTGAGATTTGGT
* * *
27704 TAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATATAAAATTGAGTCGGGCTCC
581 TAGATGAATAT-GATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCC
27769 GGAAC
645 GGAAC
* * *
27774 GCGTTTTTAGCAAAAAACTGTGATGGATAGTACACGATTTTGGCTAAAATTTTGTAAAAATTGAC
1 GCGTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* *
27839 CCGAAAATTTTTCCTCAATTTGTTTGCCACACTACTCAG-AAAAA-ATATATAATTCAACGCCAA
66 CCGAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATATAATTC-ACGCCAA
* *
27902 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAATTAATCTCTA
130 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCGAATTAATTTCTA
* * *
27967 ATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACTAATCCTTATATCCAATGTGGCTGAGATT
195 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * ** *
28032 TGG-TTCGATGAATATAGATATTTCAATGAG-ACTTTGCGCCCAAAATCATACAAAATTGA-TCC
260 TGGAAT-GATGAATATAGATATTTCAAGGAGTAC-TTGCGCCCAAAATCATGTAAAATTGAGTCA
* * * ** * *
28094 GGACTACGAAATGCGTTTTTATCCAGAAAAAAAAAGAGAAGCAATTGTTAGTACACGATTTCGGC
323 GG-CTCCGAAACGCGTTTTTAGCC------AAAAACTG-TG--A-TG--GGTACACGATTTCGGC
** * * **
28159 TAAAATTTTGCAAAAATTGCCTCGAAAAGTTTTTCTTCCATTTTTTTTGCCAA-AATACTTAGAA
375 TAAAA-ACTG-----A---CC-CGAAAATTTTTTC-T-CA-ATTTTTT-AAAACAATAC-TAGAA
* * * * *
28223 AAAATATATAATTCAACGCCAGAAAGATTAAAGGGTTTTTCACGCTTCT-AATATCGTTTTTCCA
425 AAAATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCG-TTTTCCC
* * * * * * * *
28287 ACTTTTTTCCTAATTTATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAA-TAAATT
489 ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACT-AATC
* * *
28351 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATTGATATTAT-AAGGAGTCTTTGCGCA
553 CTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATA-TGATATT-TCAAGGAGTCTTTGCGCC
* ** * *
28415 CAAAATCATGCAAAACAGAGCCGGGCTTCAGAAC
616 CAAAATCATGTAAAATTGAGCCGGGCTCCGGAAC
* * * *
28449 GCCTTTTTTTGCCAAAAA-TCGTGATGGTTAATACACGATTTCGGCTAAAA
1 G-CGTTTTTAGCCAAAAACT-GTGATGGATAGTACACGATTTCGGCTAAAA
28499 ACTGACCCAA
Statistics
Matches: 1224, Mismatches: 103, Indels: 79
0.87 0.07 0.06
Matches are distributed among these distances:
650 6 0.00
651 227 0.19
652 202 0.17
653 261 0.21
654 53 0.04
655 170 0.14
657 6 0.00
658 1 0.00
660 1 0.00
661 2 0.00
663 20 0.02
664 2 0.00
669 1 0.00
672 11 0.01
673 4 0.00
674 10 0.01
675 202 0.17
676 45 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (649 bp):
GCGTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
CCGAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATATAATTCACGCCAAA
AAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCCGAATTAATTTCTAA
TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
GGAATGATGAATATAGATATTTCAAGGAGTACTTGCGCCCAAAATCATGTAAAATTGAGTCAGGC
TCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGGTACACGATTTCGGCTAAAAACTGACCCGAA
AATTTTTTCTCAATTTTTTAAAACAATACTAGAAAAAATATATAATTCAACGCCAAAAAGATTGA
CGGGATTTTCACGCTTCTAAATATCGTTTTCCCATTTTTTTCCGAATTAATTTCTAATTAAATCG
AAATAAGATTCAGTTACTCGTAAAAACTAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGAT
GAATATGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTCCGGAAC
Found at i:27998 original size:332 final size:332
Alignment explanation
Indices: 26468--28498 Score: 2404
Period size: 321 Copynumber: 6.1 Consensus size: 332
26458 TTCGCATCAT
* *
26468 GCGTTTTTAGCCAAAAAAAC-GTGATGGTTAGTACATGATTTCGTCTAAAATTTTGCAAAAATTG
1 GCGTTTTTAGCC--AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * * * *
26532 ACCTGAAAAGTTTTCCTCAATTTTTTTGCCACACTACTCAGAAAAAATATATAATTTAACGCCAA
64 ACCCGAAAATTTTTCCTCAATTTTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAA
*
26597 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAA-CTTTTTCCGAATTAATTTCTA
129 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAATTAATTTCTA
*
26661 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGAGATT
194 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * * * * *
26726 TGGTAAAATGAATATAGACATTTCAAGGATTCCTTGCGCCCAAAATCATGTAAAATTGAGCCAGG
259 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGG
26791 CTCCGAAAC
324 CTCCGAAAC
* * *
26800 GCGTTTTTAGCCAAAAATTGTGATGGTTAGTACACAATTTCGGCT---A------AAAACTT-AC
1 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * *
26855 CTGAAAAATTTTTTCTCAATTTTTTTGAAACAATACT-A-AAAAATATATATAATTCAACGCCAA
66 CCG-AAAATTTTTCCTCAATTTTTTTGACACAATACTCAGAAAAA-ATATATAATTCAACGCCAA
* * * ** * *
26918 GAAGATTGACGGGATTTTCACGCTTCTAA-A-TATCGTTTTCCCATTTTTTT-AGAATTAATTTC
129 AAAGATTAAAGGTTTTTTCACGCTTCTAATATTAT--TTTTCCAATTTTTTTCCGAATTAATTTC
* * * * *
26980 TAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGAGA
192 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
27045 TTTGGTTAGATGAATAT-GAATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCC
257 TTTGGTTAGATGAATATAG-ATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCC
*
27109 GGGCTCCGGAAC
321 GGGCTCCGAAAC
* * *
27121 TCGTTTTTAGCCAAAAACTATGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
1 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * *
27186 CCGGAAAA-TTTACCTCAATTTTTTTGACACACTACTCAGAAAAAATATATATAATTC-TCTGCC
66 CC-GAAAATTTTTCCTCAATTTTTTTGACACAATACTCAG-AAAAA-ATATATAATTCAAC-GCC
*
27249 AAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAACTTTTTTCC-AGATTAATTT
127 AAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGA-ATTAATTT
27313 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
191 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * *
27378 ATTTGG-AATGATGAATACAGATATTTCAAGGAGTGC-TTGCGTCCAAAATCATGTAAAATTGAG
256 ATTTGGTTA-GATGAATATAGATATTTCAAGGAGT-CTTTGCGCCCAAAATCATGTAAAATTGAG
* *
27441 TCAGGCTCCGAAAC
319 CCGGGCTCCGAAAC
* *
27455 GCGTTCTTAGCCAAAAACTGTGATGG---GTACACGATTTCGGC--------T--AAAAACTGAC
1 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * *
27507 CCGACAAATTTTTTCTCAA-TTTTTTAAAACAATACTCAGAAAAAATATATAATTCGACACCAAA
66 CCGA-AAATTTTTCCTCAATTTTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAAA
** * *
27571 AAGATTGACCGG-ATTTTCACGCTTCTAA-A-TATCGTTTTCCCATTTTTTTCCGAATTAATTTC
130 AAGATT-AAAGGTTTTTTCACGCTTCTAATATTAT--TTTTCCAATTTTTTTCCGAATTAATTTC
* * * * * *
27633 TAATTAAATCGAAATAAGATTCAGTTACTCGTAAAAACTAATCCTTATATCGAATGTGGCTGAGA
192 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * *
27698 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCCAAAATCATATAAAATTGAGTCG
257 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCG
*
27763 GGCTCCGGAAC
322 GGCTCCGAAAC
* * * *
27774 GCGTTTTTAGCAAAAAACTGTGATGGATAGTACACGATTTTGGCTAAAATTTTGTAAAAATTGAC
1 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * *
27839 CCGAAAATTTTTCCTCAATTTGTTTGCCACACTACTCAGAAAAAATATATAATTCAACGCCAAAA
66 CCGAAAATTTTTCCTCAATTTTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAAAA
*
27904 AGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAATTAATCTCTAAT
131 AGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAATTAATTTCTAAT
* * *
27969 TAAATCGAAATAAGATTCAGATGCTCGTAAAAACTAATCCTTATATCCAATGTGGCTGAGATTTG
196 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
* * * ** * *
28034 GTTCGATGAATATAGATATTTCAATGAGACTTTGCGCCCAAAATCATACAAAATTGATCCGGACT
261 GTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCT
* *
28099 ACGAAAT
326 CCGAAAC
* ** * *
28106 GCGTTTTTATCCAGAAAAAAAAAGAGAAGCAATTGTTAGTACACGATTTCGGCTAAAATTTTGCA
1 GCGTTTTTAGCC------AAAAACTG-TG--ATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * * * *
28171 AAAATTG-CCTCGAAAAGTTTTTCTTCCATTTTTTTTGCCAAAATACTTAGAAAAAATATATAAT
57 AAAATTGACC-CGAAAA-TTTTTCCT-CAATTTTTTTGACACAATACTCAGAAAAAATATATAAT
* * ** * *
28235 TCAACGCCAGAAAGATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAACTTTTTTCCTAA
119 TCAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAA
* * * *
28300 TTTATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAATAAATTCTTAAATCCAATGT
184 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * *
28365 GGCTGAGATTTGGTTAGATGAATATTGATATTAT-AAGGAGTCTTTGCGCACAAAATCATGCAAA
249 GGCTGAGATTTGGTTAGATGAATATAGATATT-TCAAGGAGTCTTTGCGCCCAAAATCATGTAAA
** *
28429 ACAGAGCCGGGCTTC-AGAAC
313 ATTGAGCCGGGCTCCGA-AAC
* * *
28449 GCCTTTTTTTGCCAAAAA-TCGTGATGGTTAATACACGATTTCGGCTAAAA
1 G-CGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAA
28499 ACTGACCCAA
Statistics
Matches: 1457, Mismatches: 171, Indels: 139
0.82 0.10 0.08
Matches are distributed among these distances:
317 3 0.00
318 2 0.00
319 212 0.15
320 20 0.01
321 263 0.18
322 61 0.04
323 1 0.00
324 1 0.00
328 1 0.00
330 36 0.02
331 62 0.04
332 249 0.17
333 62 0.04
334 160 0.11
335 30 0.02
337 1 0.00
338 12 0.01
339 1 0.00
340 2 0.00
341 43 0.03
342 8 0.01
343 218 0.15
344 9 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
CCGAAAATTTTTCCTCAATTTTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAAAA
AGATTAAAGGTTTTTTCACGCTTCTAATATTATTTTTCCAATTTTTTTCCGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCT
CCGAAAC
Found at i:29627 original size:331 final size:329
Alignment explanation
Indices: 28716--29746 Score: 1195
Period size: 320 Copynumber: 3.1 Consensus size: 329
28706 CGAATCATGT
* * *
28716 GTTTTTAGCCAAAATAAC-GTGATGGTTAGTACATGATTTTGGCTAAAATTTTGCAAAAATTGAC
1 GTTTTTAGCC-AAA-AACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * *
28780 CCGAAAAGTTTACCTCAATTTCTTTGCCACACTACTCAGAAAAAATATATAATTCAACGCGAAAA
64 CCGAAAAATTTTCCTCAATTT-TTTGCCACACTACTCTGAAAAAATATATAATTCAACGCCAAAA
* * *
28845 AGATTAAAAGTTTTTTTACGCTTCTAATATTATTTTTCCTACATTTTTCTGAATTAATTTCTAAT
128 AGATTAAAAG-GTTTTTACGCTTCTAATATTGTTTTTCCAAC-TTTTTCTGAATTAATTTCTAAT
* * * *
28910 TAAATCGAAACAAGATTCGGATGCTCGTAAAACCAAATCCCTAAATCCAATGTGGCTGAGATTTG
191 TAAATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
* *
28975 G-TAGGATGAATATAGATATTTCAAGGAGT-CCTTGCGTCCAAAATCATGTAAAATTGAGCCGGG
256 GTTA-GATGAATATAGATATTTCAAGGA-TACTTTGCGCCCAAAATCATGTAAAATTGAGCCGGG
* *
29038 CTCCGAAACGC
319 CTTCGGAACGC
* * * *
29049 GTTTTTAGCCAAAAACTATGAT--A-ACTTACACGATTTCGGC--------T--AAAAACTAACC
1 GTTTTTAGCCAAAAACTGTGATGGATA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* * ** * *
29101 CGAAAATTTTTTTCTCAATTTTTTGAAACAATACTCAT-AAAAAATATATAATTCAATGCCAAAA
65 CGAAAA-ATTTTCCTCAATTTTTTGCCACACTACTC-TGAAAAAATATATAATTCAACGCCAAAA
* ** * * * ** * *
29165 AGATTGACCGTGTTTTTATGCTTCTAAATATCGTTTTCCCATTTTTTTCTGAAATAATTTCTAAA
128 AGATTAAAAG-GTTTTTACGCTTCT-AATATTGTTTTTCCAACTTTTTCTGAATTAATTTCTAAT
* * *
29230 TAAATCGAAATAAGATTCAG-TTACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTT
191 TAAATCGAAACAAGATTCAGATT-CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * *
29294 GGTTCGATTAGTATAGATATTTCAATGATACTTTGCACCCAAAATCATTTAAAATTGAGCCGGGC
255 GGTTAGATGAATATAGATATTTCAAGGATACTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGC
*
29359 TTCGGAATGC
320 TTCGGAACGC
*
29369 GTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCT
1 GTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
*
29434 GAAAAATTTTCCTCAAATTTTTTTCCACACTACTCTGAAAAAATATATAATTCAACGCCAAAAAG
66 GAAAAATTTTCCTC-AATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAACGCCAAAAAG
* * * * * *
29499 ATT-AAAGGCCTTTCACGCTTCTATTATTGTTTTTCCAACTTTCTTCCGAATTGATTTCTGATTA
130 ATTAAAAGG-TTTTTACGCTTCTAATATTGTTTTTCCAACTTT-TTCTGAATTAATTTCTAATTA
*
29563 AATCGAAACAAGATTCAGATTCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGT
193 AATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
* *
29628 TAGATGAATATAGATATTTCAAGGA-ATCTTTGCGCCCAAAATCATGCAAAATGGAGCCGGGCTT
258 TAGATGAATATAGATATTTCAAGGATA-CTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTT
29692 CGGAACGC
322 CGGAACGC
* * *
29700 ATTTTTAGCCAAAAA-TCGTGATGGTTATTACACGATTTCGGCTAAAA
1 GTTTTTAGCCAAAAACT-GTGATGGATAGTACACGATTTCGGCTAAAA
29747 ACTGACCCAA
Statistics
Matches: 580, Mismatches: 90, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
319 2 0.00
320 227 0.39
321 23 0.04
322 16 0.03
323 1 0.00
329 1 0.00
330 31 0.05
331 200 0.34
332 69 0.12
333 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (329 bp):
GTTTTTAGCCAAAAACTGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
GAAAAATTTTCCTCAATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAACGCCAAAAAGA
TTAAAAGGTTTTTACGCTTCTAATATTGTTTTTCCAACTTTTTCTGAATTAATTTCTAATTAAAT
CGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
ATGAATATAGATATTTCAAGGATACTTTGCGCCCAAAATCATGTAAAATTGAGCCGGGCTTCGGA
ACGC
Done.