Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015816.1 Corchorus olitorius cultivar O-4 contig15849, 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: 57324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:492 original size:17 final size:18
Alignment explanation
Indices: 461--495 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
451 ATATATATAT
461 ATATATAATTTTTATGTA
1 ATATATAATTTTTATGTA
479 ATATATAA-TTTTATGTA
1 ATATATAATTTTTATGTA
496 TAAAATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
ATATATAATTTTTATGTA
Found at i:3517 original size:22 final size:22
Alignment explanation
Indices: 3480--3523 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3470 CGTGTTGCGT
* *
3480 CGGCACGTGAGTCGTGCTGTGC
1 CGGCACGTGAGCCGTGCCGTGC
*
3502 CGGCACGTGGGCCGTGCCGTGC
1 CGGCACGTGAGCCGTGCCGTGC
3524 TAGCCCATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.32, G:0.43, T:0.18
Consensus pattern (22 bp):
CGGCACGTGAGCCGTGCCGTGC
Found at i:3691 original size:12 final size:12
Alignment explanation
Indices: 3674--3698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3664 CCATTCTACC
3674 ATCTCTAATTAT
1 ATCTCTAATTAT
3686 ATCTCTAATTAT
1 ATCTCTAATTAT
3698 A
1 A
3699 AAGTTCACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ATCTCTAATTAT
Found at i:22781 original size:34 final size:35
Alignment explanation
Indices: 22738--22808 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
22728 AAACTATATT
*
22738 ATAAATAAACTAC-A-AACTAAACTCACATTTCGTG
1 ATAAATAAACTACTACAACCAAA-TCACATTTCGTG
22772 ATAAATAAACTACTTACAACCAAATCACATTTCGTG
1 ATAAATAAACTAC-TACAACCAAATCACATTTCGTG
22808 A
1 A
22809 GAGTTGAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 13 0.39
36 14 0.42
37 6 0.18
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (35 bp):
ATAAATAAACTACTACAACCAAATCACATTTCGTG
Found at i:27977 original size:18 final size:18
Alignment explanation
Indices: 27954--27990 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27944 AATTTTGCAA
27954 ACTTAAGTAACCAAATCG
1 ACTTAAGTAACCAAATCG
27972 ACTTAAGTAACCAAATCG
1 ACTTAAGTAACCAAATCG
27990 A
1 A
27991 TACTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ACTTAAGTAACCAAATCG
Found at i:28708 original size:12 final size:12
Alignment explanation
Indices: 28691--28741 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
28681 GGAGCAAAAC
28691 AGAAAAAACTAA
1 AGAAAAAACTAA
28703 AGAAAAAA--AA
1 AGAAAAAACTAA
*
28713 AGAGAAAACT--
1 AGAAAAAACTAA
28723 -GAAAAAACTAA
1 AGAAAAAACTAA
28734 AGAAAAAA
1 AGAAAAAA
28742 AAACTAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
9 8 0.25
10 9 0.28
12 15 0.47
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (12 bp):
AGAAAAAACTAA
Found at i:28713 original size:15 final size:15
Alignment explanation
Indices: 28693--28754 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
28683 AGCAAAACAG
28693 AAAAAACTAAAGAAA
1 AAAAAACTAAAGAAA
* *
28708 AAAAAA-GAGAA-AACTG
1 AAAAAACTA-AAGAA--A
28724 AAAAAACTAAAGAAA
1 AAAAAACTAAAGAAA
*
28739 AAAAAACTAGAGAAA
1 AAAAAACTAAAGAAA
28754 A
1 A
28755 GTGTTCTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.08
15 23 0.62
16 8 0.22
17 3 0.08
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.06
Consensus pattern (15 bp):
AAAAAACTAAAGAAA
Found at i:28721 original size:31 final size:31
Alignment explanation
Indices: 28686--28744 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
28676 GGAGAGGAGC
28686 AAAACAGAAAAAACTAAAGAAAAAAAAAGAG
1 AAAACAGAAAAAACTAAAGAAAAAAAAAGAG
*
28717 AAAACTGAAAAAACTAAAGAAAAAAAAA
1 AAAACAGAAAAAACTAAAGAAAAAAAAA
28745 CTAGAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (31 bp):
AAAACAGAAAAAACTAAAGAAAAAAAAAGAG
Found at i:29762 original size:50 final size:50
Alignment explanation
Indices: 29699--29806 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
29689 TCAATTATCA
* * * * *
29699 ATATATATCTAGAAATATTGAATCTCGACAAATTCGAAATTAATCGAGTT
1 ATATATATCTAGAAACATTGAATCCCGACAAATTCAAAATTAATCCAGCT
*
29749 ATATATATTTAGAAACATTGAATCCCGACAAATTCAAAATTAATCCAGCT
1 ATATATATCTAGAAACATTGAATCCCGACAAATTCAAAATTAATCCAGCT
29799 ATATATAT
1 ATATATAT
29807 ATATATGACA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (50 bp):
ATATATATCTAGAAACATTGAATCCCGACAAATTCAAAATTAATCCAGCT
Found at i:32364 original size:29 final size:30
Alignment explanation
Indices: 32314--32370 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
32304 GAAAAAAGAG
* * *
32314 TCCAAAATTGAGAGTTTAAGGGGTAAAATA
1 TCCAAAATTGAAAGTTCAAGGGGCAAAATA
32344 TCCAAAATT-AAAGTTCAAGGGGCAAAA
1 TCCAAAATTGAAAGTTCAAGGGGCAAAA
32371 CGTCTAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.23
Consensus pattern (30 bp):
TCCAAAATTGAAAGTTCAAGGGGCAAAATA
Found at i:34402 original size:65 final size:65
Alignment explanation
Indices: 34321--34450 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
34311 CCATTGACCC
34321 AGTAACCCGAGACCTCCATCGGGTCAATCTCCGATCCTATTCTAATAACTATGGATAATAGTACT
1 AGTAACCCGAGACCTCCATCGGGTCAATCTCCGATCCTATTCTAATAACTATGGATAATAGTACT
* *
34386 AGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATATTAGTACT
1 AGTAACCCGAGACCTCCATCGGGTCAATCTCCGATCCTATTCTAATAACTATGGATAATAGTACT
34451 TCTATAATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AGTAACCCGAGACCTCCATCGGGTCAATCTCCGATCCTATTCTAATAACTATGGATAATAGTACT
Found at i:34557 original size:100 final size:100
Alignment explanation
Indices: 34379--34678 Score: 512
Period size: 100 Copynumber: 3.0 Consensus size: 100
34369 CTATGGATAA
*
34379 TAGTACTAGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATAT
1 TAGTACTAGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATAA
34444 TAGTACTTCTATAATTAAATTAAATACCTATTAGG
66 TAGTACTTCTATAATTAAATTAAATACCTATTAGG
* ** *
34479 TAGTACTAGTAACCCGAGACCTCTATCGGGTCAATCTCCGACCCTATTCTAATAACTATGGCTAA
1 TAGTACTAGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATAA
* *
34544 TAGTACTTTTATAATCAAATTAAATACCTATTAGG
66 TAGTACTTCTATAATTAAATTAAATACCTATTAGG
* *
34579 TAATACTAGTAA-CCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCAAATAACTATGGATAA
1 TAGTACTAGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATAA
34643 TAGTACTTCTATAATTAAATTAAATACCTATTAGG
66 TAGTACTTCTATAATTAAATTAAATACCTATTAGG
34678 T
1 T
34679 TATAAATTCT
Statistics
Matches: 185, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
99 81 0.44
100 104 0.56
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (100 bp):
TAGTACTAGTAACCCGAGACCTCCATCGGGTCAATCTCCGGTCCTATTCTAATAACTATGGATAA
TAGTACTTCTATAATTAAATTAAATACCTATTAGG
Found at i:47410 original size:27 final size:27
Alignment explanation
Indices: 47355--47411 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
47345 TTTTATATAG
* *
47355 AAACATTCATGATTTTTTTTTTGTTCA
1 AAACATTCATGATTTTTTTCTTGTACA
47382 AAACATTCATGATTTTCTTTCTTG-ACA
1 AAACATTCATGATTTT-TTTCTTGTACA
47409 AAA
1 AAA
47412 GTGTGTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (27 bp):
AAACATTCATGATTTTTTTCTTGTACA
Found at i:51016 original size:15 final size:16
Alignment explanation
Indices: 50991--51020 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50981 AATAATTATT
50991 TTTAGATTATAATATA
1 TTTAGATTATAATATA
51007 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
51021 TATTATTTAT
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:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:53340 original size:334 final size:332
Alignment explanation
Indices: 51371--54689 Score: 3118
Period size: 334 Copynumber: 10.0 Consensus size: 332
51361 AATGCATCAA
** ** * *
51371 CTAACCAAATCTCAGTAACATTGGATTTAAAAATTTGTTTTTACGAACATCTGAATCTTGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * * *
51436 ATTTAATTAGAAATTAATTTA-CAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCC
66 ATTTAATTAGAAATTAATTCAGAAAAAAAT-TGAAAAACGATATTAAAAGCCTGAAAAACCCTTC
* * * * * * * * *
51500 AATCTTTTTAG-CGTTGAATTATATA-TTTTTATAAGTATTTTAGCCAAAAATTGAGCATAAATC
130 AATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATT
* * **
51563 TTTCGTG-TCAATTTTTGCACAATTTTAGCCGAAATCGTGTACTAACTAACCATCACGGTTTTTG
195 TTTCG-GATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT---T-TCCATCACGGTTTTAA
* * * * * *
51627 GCTGAAAAACGCATTCCGGGGCCCTTG-CTCAATTTAGCATAATTTTTGGCGCTG-AGACTCCTT
255 GCT-AAAAACGCGTTTCGGGGCCC--GACTCAGTTTTGCATGATTTTTGGCAC-GAAGACTCCTT
51690 GAAATATCTATATTCAT
316 GAAATATCTATATTCAT
** * * * * * * *
51707 CTAATAAAATGTTAGCCGC--TGCATTTAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * *
51770 ATTTAATTAGAAATTAAATCAG-AAAAAA-TGAAAAACGATATTAAAAGCGTGAAAAACACTTCA
66 ATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAACGATATTAAAAGCCTGAAAAACCCTTCA
* * ** * * * **
51833 ATCTTTTTGGT-GTTGAATTATATATTTTTTATGACTATT-TCAGCTAAAAATTGAGGAAATACC
131 ATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGT-GGCCAAAAATTGAGGAAAAATT
* * * * ** ** *
51896 TTTC-GAGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTAATAACCATCACAACTTTT-GGCT
195 TTTCGGA-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCAC-GGTTTTAAGCT
* * * * * * *
51959 AACAAA-GCGTTGCAGGGCCCCGACTCAGTTTTGCATGATTTTTGTCCCCAAGCCTCCTTGAGAT
258 AA-AAACGCGTTTC-GGGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAAT
*
52023 ATCCATATTCAT
321 ATCTATATTCAT
* * * ** * * * *
52035 CTAATCAAATCTCAGTCAAATTGGATTTAAAAATTTGTTTTAACGAGTATCTGAATCTTGTTTCC
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * ** *
52100 ATTTAATTAAAAATTAAATT-AGAAAAAAATAAGAAAAAAGAAATTAAAAGCGTGAAAAGTCCTC
66 ATTTAATTAGAAATT-AATTCAGAAAAAAAT-TGAAAAACGATATTAAAAGCCTGAAAAACCCTT
* * * * * * * * ** *
52164 CAATCTTTTTGGT-GTTAAATTAATATATATCTAATAAGAATTTTATCCAAAAATTAACGGAAAA
129 CAATCTTTTTTGTCTTTGAATT-ATATATTTTTTATGAGAATTGTGGCCAAAAATTGA-GG-AAA
* * ** * *
52228 AATTTTTCGTG-TC-ATCTATTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTT
191 AATTTTTCG-GATCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTA
* * * *
52291 GGATAAAAACACCTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACTG-AGACTCCTT-
254 AGCTAAAAACGCGTTTCGGGG-CCCGACTCAGTTTTGCATGATTTTTGGCAC-GAAGACTCCTTG
52354 AAATATCTATATTCAT
317 AAATATCTATATTCAT
** * * * * * *
52370 CTAATAAAATGTTAGCCGCATTGCATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * * *
52435 ATTTATTTAGATATTAGTTCA-AAAAAAATATAAAAAACGATATTAAAATCGTGAAAAGCCCTTC
66 ATTTAATTAGAAATTAATTCAGAAAAAAAT-TGAAAAACGATATTAAAAGCCTGAAAAACCCTTC
* * * ** * * * * *
52499 AAT-ATTTTTGGCGTTGAATTGCATATTTTTTATGAGTATTGTGGCTAAAATTTGAGGAAATATC
130 AATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATT
* * * * *
52563 TTTCGGGTCAAGTTTTGCAAAATTTAAGCCGAAATAGTGTAATAATCATTTTCCATCACAGTTTT
195 TTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-A-C--TTTCCATCACGGTTTT
* * * ** *
52628 AAGCTAAAAAAGCGTTTTGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAAAAAGACTTCTTGA
253 AAGCTAAAAACGCGTTTCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGA
* *
52693 AATATTTATATTTAT
318 AATATCTATATTCAT
* * *
52708 CTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTATGACCATCTGAATCATGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
52773 ATTTTATTTGAAATTAATTCAG-AAAAAATTGGAAAATGATATTAAAAGCCTGAAAAACCTTTCA
66 ATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAACGATATTAAAAGCCTGAAAAACCCTTCA
* * *
52837 AGC-TTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGACCAAAAATTGAGGAAAAA-TT
131 ATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTT
* * * * *
52900 TTCGAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTATCCATCACGATTTTAAGTTAA
196 TTCG-GATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAA
*** * *
52965 AAACGCGTTTCGAGATACCGACTCAGTTTTGCATGATTTTTGGCACGAAGTCTCCTTGAACTATC
260 AAACGCGTTTCG-GGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATC
53030 TATATTCAT
324 TATATTCAT
* * * * * *
53039 CTGACCAAATCTCAGCCACTTTGTATTTAATGATTTGTATTTACGAGCATCTGAATCATGTTTCT
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * *
53104 ATTTAATTCGAAATTAATTCAGAAAAAAAATTGTAAAAACGGTATTAGAAA-CCTGGAAACCCCT
66 ATTTAATTAGAAATTAATTCAG-AAAAAAATTG-AAAAACGATATTA-AAAGCCTGAAAAACCCT
* * *
53168 TCAATCTTTTTTGTCTTTGAATTCTATTTTTTTTATAAGAATTGTGGCCAAAAATTGAGGAAAAA
128 TCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAA
* * * * *
53233 TTTTTCGCATCAA-TTTAGCAAAATTGTAGCCGAAATCGTGTACTTTCTATCACAGTTTTAAGCT
193 TTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCT
* * *
53297 AAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTTCAAATA
258 AAAAACGCGTTTCGGGGC-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* *
53362 TTTATATTTAT
322 TCTATATTCAT
** * * *
53373 CTAAGAAAATCTCAGTCACATTGGATTTAAGGATTTATTTTTACGACCATCTGAATCATGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * *
53438 ATTTTATTTGAAATTAATTCAG-AAAAAATTGGAAAAACGATATTATAAA-CGTGAAAAACCCTT
66 ATTTAATTAGAAATTAATTCAGAAAAAAATT-GAAAAACGATATTA-AAAGCCTGAAAAACCCTT
* * * * *
53501 CAATC-ATTTTGACTTTGAATTATATATATTTTATGAGATTTGTGGCCAAAACTTGAGGAAAAAT
129 CAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAAT
* * * * * * *
53565 TTTCCGTATCAATTTTTGCAAAATTTTAACAGAAATCGTATACTTTCCATCACGGCTTTAAGATA
194 TTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCTA
* * * * * * *
53630 AAAACACGTTTTGGGACACCGACGT-AGTTTTGCATGATTTTTTGCACAAAGATTCCTTGAAATT
259 AAAACGCGTTTCGGGGC-CCGAC-TCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* *
53694 TTTATATTTAT
322 TCTATATTCAT
* * * * * *
53705 CTGACCAAATCTCAGCCACTTTGGATATAAGGATTTG-TTTTACGAGCATTTGTATCATGTTTCT
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * *
53769 ATTTAATTCA-AAATTAATTAAGAAAAAAATTGGAAAAAACGATATCAAAAGTCTGAAAAACCTT
66 ATTTAATT-AGAAATTAATTCAGAAAAAAATT-G-AAAAACGATATTAAAAGCCTGAAAAACCCT
* * *
53833 TCAAAC-TTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAAATGGAGGAAAAA
128 TCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAA
* * *
53897 TTTTTCGGATCAATTTTTGCAAAATTTTAGGCGAAATCGTGTACTATATCCAGCACTGTTTTAAG
193 TTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-T-TCCATCACGGTTTTAAG
* *
53962 CTAAAAACGCGTTTCGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTCAAA
256 CTAAAAACGCGTTTCGGGGCCC-GACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTT-GAA
54027 ATATCTATATTCAT
319 ATATCTATATTCAT
* * * * * * * * *
54041 TTGACCAAATTTAAGCCACTTTTGTTTTAAGGATTCCG-TTTTACGAGCATCTGAATCAGGTTTC
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATT-TGTTTTTACGAGCATCTGAATCATGTTTC
* * * *** * * * * *
54105 TATTTAATTCGAAATTAATTTAGAAAAAAGGGGAAAAACGATATTAGAAGCCTTAATAGCCTTTC
65 GATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAACGATATTAAAAGCCTGAAAAACCCTTC
* * *
54170 AATC-TTTTTATCTTTGAATTATATA-TTTTTATGAGAATTTTGGCCAAAAAGTGAGGAAAAATT
130 AATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATT
* * *
54233 TTCCGAATCAATTTTTGCAAAATTTT---C-----C--G-A------ATCACGGTTTTAAGCTTA
195 TTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAA
* * * * * *
54281 AAACGCGTTTTGGGACACTGACTCAGTTTTGCATGATTTTTTGCACGAAGAATCCTTGAACTATC
260 AAACGCGTTTCGGGGC-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATC
54346 TATATTCAT
324 TATATTCAT
* * * * * *
54355 CTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTATGAGCATTTGTATCATGTTTCT
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* *
54420 AATTAATTCA-AATTTAATTCA-AAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAAACCCTT
66 ATTTAATT-AGAAATTAATTCAGAAAAAAATT-GAAAAACGATATTAAAAGCCTGAAAAACCCTT
* * **
54483 CAAGCTTTTTTTTCTTTGAATTATATATTTTCCATGAGAATTGTGGCCAAAAATTGAGGAAAAA-
129 CAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAAT
* * * *
54547 TTTTCAGGAACAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTTAAGCT
194 TTTTC-GGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCT
* * ** * *
54612 AAAAACACATTTCAAGGCCTCGACTCAATTTTGCATGATTTATGGCACGAAGACTCCTTGAAATA
258 AAAAACGCGTTTCGGGGCC-CGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
54677 TCTATATTCAT
322 TCTATATTCAT
54688 CT
1 CT
54690 GACTGAATTT
Statistics
Matches: 2449, Mismatches: 443, Indels: 185
0.80 0.14 0.06
Matches are distributed among these distances:
313 7 0.00
314 115 0.05
315 88 0.04
316 53 0.02
319 1 0.00
323 1 0.00
324 2 0.00
326 2 0.00
327 2 0.00
328 63 0.03
329 21 0.01
330 88 0.04
331 276 0.11
332 245 0.10
333 345 0.14
334 404 0.16
335 267 0.11
336 157 0.06
337 193 0.08
338 119 0.05
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (332 bp):
CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
ATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAACGATATTAAAAGCCTGAAAAACCCTTCA
ATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTT
TTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAA
AACGCGTTTCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTA
TATTCAT
Found at i:53395 original size:665 final size:663
Alignment explanation
Indices: 51371--54689 Score: 3234
Period size: 665 Copynumber: 5.0 Consensus size: 663
51361 AATGCATCAA
* ** * *
51371 CTAACCAAATCTCAGTAACATTGGATTTAAAAATTTGTTTTTACGAACATCTGAATCTTGTTTCG
1 CTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCATGTTTCG
* * * * *
51436 ATTTAATTAGAAATTAATTTACAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAGGAAA-ACGATATTAAAAGCGTGAAAAACCCTTCA
* * * * * *
51501 ATCTTTTTAG-CGTTGAATTATATATTTTTATAAGTATTTTAGCCAAAAATTGAGCATAAATCTT
130 ATCTTTTT-GTCTTTGAATTATATATTTTTATGAGAATTTGA-CCAAAAATTGAGGAAAAAT-TT
* * * **
51565 TCGTG-TCAATTTTTGCACAATTTTAGCCGAAATCGTGTACTAACTAACCATCACGGTTTTTGGC
192 TCGAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTG--C--ACTAACCATCACGGTTTTAAG-
* * * * * * * *
51629 TGAAAAACGCATTCCGGGGC-CCTTG-CTCAATTTAGCATAATTTTTGGCGCTG-AGACTCCTTG
252 TTAAAAACGCGTTTCGGGACACC--GACTCAGTTTTGCATGATTTTTGGCAC-GAAGACTCCTTG
* ** * * * *
51691 AAATATCTATATTCATCTAATAAAATGTTAGCCGC--TGCATTTAAGGATTTGTTTTTACGAGTA
314 AAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGCA
* * * * *
51754 TCTAAATCTTGTTTCGATTTAATTAGAAATTAAATCAG--AAAAAA-TG-AAAAACGATATTAAA
379 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAAATTGAAAAAACGATATTAAA
* * * * ** * *
51815 AGCGTGAAAAACACTTCAATCTTTTTGGT-GTTGAATTATATATTTTTTATGACTATT-TCAGCT
444 AGCCTGAAAAACCCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGT-GGCC
* ** * * * * **
51878 AAAAATTGAGGAAATACCTTTC-GAGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTAATAAC
508 AAAAATTGAGGAAAAATTTTTCGGA-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTC
* * * *
51942 CATCACAACTTTT-GGCTAACAAA-GCGTTGCAGGGCCCCGACTCAGTTTTGCATGATTTTTGTC
572 CATCAC-AGTTTTAAGCTAA-AAACGCGTTTCAGGG-CCCGACTCAGTTTTGCATGATTTTTGGC
* * * * *
52005 CCCAAGCCTCCTTGAGATATCCATATTCAT
634 ACGAAGACTCCTTGAAATATCTATATTCAT
* * ** * ** * *
52035 CTAATCAAATCTCAGTCAAATTGGATTTAAAAATTTGTTTTAACGAGTATCTGAATCTTGTTTCC
1 CTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCATGTTTCG
* * * * ** *
52100 ATTTAATTAAAAATTAAATT-AGAAAAAAATAAGAAAAAAGAAATTAAAAGCGTGAAAAGTCCTC
66 ATTTAATTAGAAATT-AATTCAG-AAAAAAT-AGGAAAACGATATTAAAAGCGTGAAAAACCCTT
* * * * * * *
52164 CAATCTTTTTGGT-GTTAAATTAATATATATCTAATAAGAATTTTATCCAAAAATTAACGGAAAA
128 CAATCTTTTT-GTCTTTGAATT-ATATAT-TTTTATGAGAATTTGA-CCAAAAATTGA-GG-AAA
* * * *
52228 AATTTTTCGTG-TC-ATCTATTGCAAAATTTTAGCCA-AAATCGTGTACTAACCATCATGGTTTT
187 AA-TTTTCGAGATCAAT-TTTTGCAAAATTTTAG-CAGAAATCGTGCACTAACCATCACGGTTTT
** * * * * *
52290 TGGATAAAAACACCTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACTG-AGACTCCTT
249 AAGTTAAAAACGCGTTTCGGGACACCGACTCAGTTTTGCATGATTTTTGGCAC-GAAGACTCCTT
* ** * * * * *
52354 -AAATATCTATATTCATCTAATAAAATGTTAGCCGCATTGCATTTAAGGATTTATTTTTACGAGC
313 GAAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGC
* * * * * *
52418 ATCTGAATCTTGTTTCGATTTATTTAGATATTAGTTC--AAAAAAAATAT-AAAAAACGATATTA
378 ATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAAAT-TGAAAAAACGATATTA
* * * * * * ** *
52480 AAATCGTGAAAAGCCCTTCAAT-ATTTTTGGCGTTGAATTGCATATTTTTTATGAGTATTGTGGC
442 AAAGCCTGAAAAACCCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGC
* * * * * * * *
52544 TAAAATTTGAGGAAATATCTTTCGGGTCAAGTTTTGCAAAATTTAAGCCGAAATAGTGTAATAAT
507 CAAAAATTGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-A-
* *
52609 CATTTTCCATCACAGTTTTAAGCTAAAAAAGCGTTT-TGGGCCCCGACTCAGTTTTGCATGATTT
567 C--TTTCCATCACAGTTTTAAGCTAAAAACGCGTTTCAGGG-CCCGACTCAGTTTTGCATGATTT
** * * *
52673 TTGGCAAAAAGACTTCTTGAAATATTTATATTTAT
629 TTGGCACGAAGACTCCTTGAAATATCTATATTCAT
* * *
52708 CTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTATGACCATCTGAATCATGTTTCG
1 CTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCATGTTTCG
* * * * * *
52773 ATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAATGATATTAAAAGCCTGAAAAACCTTTCAA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAACGATATTAAAAGCGTGAAAAACCCTTCAA
*
52838 GCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGACCAAAAATTGAGGAAAAATTTTC
131 TCTTTTTGTCTTTGAATTATATATTTT-TATGAGAATT-TGACCAAAAATTGAGGAAAAATTTTC
* *
52903 GAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTATCCATCACGATTTTAAGTTAAAAA
194 GAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTAACCATCACGGTTTTAAGTTAAAAA
* * * *
52968 CGCGTTTCGAGATACCGACTCAGTTTTGCATGATTTTTGGCACGAAGTCTCCTTGAACTATCTAT
259 CGCGTTTCGGGACACCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTAT
* * *
53033 ATTCATCTGACCAAATCTCAGCCACTTTGTATTTAATGATTTGTATTTACGAGCATCTGAATCAT
324 ATTCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCAT
* * *
53098 GTTTCTATTTAATTCGAAATTAATTCAGAAAAAAAATTGTAAAAACGGTATTAGAAA-CCTGGAA
389 GTTTCTATTTAATTCGAAATTAATTCAGAAAAAAAATTGAAAAAACGATATTA-AAAGCCTGAAA
* * * *
53162 ACCCCTTCAATCTTTTTTGTCTTTGAATTCTATTTTTTTTATAAGAATTGTGGCCAAAAATTGAG
453 AACCCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAG
* * * *
53227 GAAAAATTTTTCGCATCAA-TTTAGCAAAATTGTAGCCGAAATCGTGTACTTTCTATCACAGTTT
518 GAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACAGTTT
* * *
53291 TAAGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTT
583 TAAGCTAAAAACGCGTTTCAGGGC-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTT
* * *
53356 CAAATATTTATATTTAT
647 GAAATATCTATATTCAT
** *
53373 CTAAGAAAATCTCAGTCACATTGGATTTAAGGATTTATTTTTACGACCATCTGAATCATGTTTCG
1 CTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCATGTTTCG
* * *
53438 ATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAAACGATATTATAAA-CGTGAAAAACCCTTC
66 ATTTAATTAGAAATTAATTCAGAAAAAATAGG-AAAACGATATTA-AAAGCGTGAAAAACCCTTC
* * * * *
53502 AATCATTTTGACTTTGAATTATATATATTTTATGAGATTTGTGGCCAAAACTTGAGGAAAAATTT
129 AATCTTTTTGTCTTTGAATTATATAT-TTTTATGAGAATT-TGACCAAAAATTGAGGAAAAATTT
* * ** ** * *
53567 TCCG-TATCAATTTTTGCAAAATTTTAACAGAAATCGTATACTTTCCATCACGGCTTTAAGATAA
192 T-CGAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTAACCATCACGGTTTTAAGTTAA
* * * * * *
53631 AAACACGTTTTGGGACACCGACGT-AGTTTTGCATGATTTTTTGCACAAAGATTCCTTGAAATTT
256 AAACGCGTTTCGGGACACCGAC-TCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATAT
* * * * * *
53695 TTATATTTATCTGACCAAATCTCAGCCACTTTGGATATAAGGATTTG-TTTTACGAGCATTTGTA
320 CTATATTCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * * *
53759 TCATGTTTCTATTTAATTCAAAATTAATTAAG-AAAAAAATTGGAAAAAACGATATCAAAAGTCT
385 TCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAAATT-GAAAAAACGATATTAAAAGCCT
* * *
53823 GAAAAACCTTTCAAAC-TTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAAAT
449 GAAAAACCCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAAT
* * *
53887 GGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGGCGAAATCGTGTACTATATCCAGCA
514 TGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-T-TCCATCA
*
53952 CTGTTTTAAGCTAAAAACGCGTTTC-GAGGCCCTGACTCAGTTTTGCATGATTTTTGGCACGAAG
577 CAGTTTTAAGCTAAAAACGCGTTTCAG-GGCCC-GACTCAGTTTTGCATGATTTTTGGCACGAAG
*
54016 ACTCCTTCAAAATATCTATATTCAT
640 ACTCCTT-GAAATATCTATATTCAT
* * * * * * * * * * *
54041 TTGACCAAATTTAAGCCACTTTTGTTTTAAGGATTCCG-TTTTACGAGCATCTGAATCAGGTTTC
1 CTAACCAAATCTCAGTCACATTGGATTTAAGGATT-TGTTTTTACGACCATCTGAATCATGTTTC
* * * ** * * * * * *
54105 TATTTAATTCGAAATTAATTTAGAAAAAAGGGGAAAAACGATATTAGAAGCCTTAATAGCCTTTC
65 GATTTAATTAGAAATTAATTCAGAAAAAATAGG-AAAACGATATTAAAAGCGTGAAAAACCCTTC
* * *
54170 AATCTTTTTATCTTTGAATTATATATTTTTATGAGAATTTTGGCCAAAAAGTGAGGAAAAATTTT
129 AATCTTTTTGTCTTTGAATTATATATTTTTATGAGAA-TTTGACCAAAAATTGAGGAAAAATTTT
54235 CCGA-ATCAATTTTTGCAAAATTTT--C------C--G-----A--ATCACGGTTTTAAGCTT-A
193 -CGAGATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTAACCATCACGGTTTTAAG-TTAA
* * * * *
54281 AAACGCGTTTTGGGACACTGACTCAGTTTTGCATGATTTTTTGCACGAAGAATCCTTGAACTATC
256 AAACGCGTTTCGGGACACCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATC
* * * *
54346 TATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTATGAGCATTTGTAT
321 TATATTCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
54411 CATGTTTCTAATTAATTC-AAATTTAATTC--AAAAAAAATTGGAAAAACGATATTAAAAGCCTG
386 CATGTTTCTATTTAATTCGAAA-TTAATTCAGAAAAAAAATTGAAAAAACGATATTAAAAGCCTG
* * **
54473 AAAAACCCTTCAAGCTTTTTTTTCTTTGAATTATATATTTTCCATGAGAATTGTGGCCAAAAATT
450 AAAAACCCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATT
* * *
54538 GAGGAAAAA-TTTTCAGGAACAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCAC-
515 GAGGAAAAATTTTTC-GGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACA
* * * * *
54601 GATTTTAAGCTAAAAACACATTTCAAGGCCTCGACTCAATTTTGCATGATTTATGGCACGAAGAC
579 G-TTTTAAGCTAAAAACGCGTTTCAGGGCC-CGACTCAGTTTTGCATGATTTTTGGCACGAAGAC
54666 TCCTTGAAATATCTATATTCAT
642 TCCTTGAAATATCTATATTCAT
54688 CT
1 CT
54690 GACTGAATTT
Statistics
Matches: 2270, Mismatches: 310, Indels: 167
0.83 0.11 0.06
Matches are distributed among these distances:
647 18 0.01
648 67 0.03
649 40 0.02
650 217 0.10
651 41 0.02
659 1 0.00
663 36 0.02
664 229 0.10
665 386 0.17
666 246 0.11
667 276 0.12
668 241 0.11
669 124 0.05
670 30 0.01
671 101 0.04
672 72 0.03
673 127 0.06
674 18 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (663 bp):
CTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCATGTTTCG
ATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAACGATATTAAAAGCGTGAAAAACCCTTCAA
TCTTTTTGTCTTTGAATTATATATTTTTATGAGAATTTGACCAAAAATTGAGGAAAAATTTTCGA
GATCAATTTTTGCAAAATTTTAGCAGAAATCGTGCACTAACCATCACGGTTTTAAGTTAAAAACG
CGTTTCGGGACACCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATAT
TCATCTGACCAAATCTCAGCCACTTTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGT
TTCTATTTAATTCGAAATTAATTCAGAAAAAAAATTGAAAAAACGATATTAAAAGCCTGAAAAAC
CCTTCAATCTTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAA
AAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACAGTTTTAA
GCTAAAAACGCGTTTCAGGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAA
TATCTATATTCAT
Found at i:55750 original size:334 final size:330
Alignment explanation
Indices: 55194--56154 Score: 1378
Period size: 334 Copynumber: 2.9 Consensus size: 330
55184 AAGACCCCTT
* *
55194 AATCTTTCGGATCAATTTAGGAAAATTTTAGCCGAAATCATGTACTTTCCATAACAGTTTTAAGC
1 AATCTTTCGGATCAATTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATAACA-TTTTAAGC
* *
55259 TAAAAAAGCGTTTCGGGTCCCCGACTCAGTTTTGCATGA-TTTTTTGCAAGAAGACTTCTTGAAA
65 TAAAAAA-CGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTTTACAA-AAGACTTCTTGAAA
55323 TATTTATATTTATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGACCATCT
128 TATTTATATTTATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGACCATCT
55388 GAATCATGTATCGATTTAATTTGAAATTAATTCAGAAAAATTTTGGAAAACGATATTAGAAGGTT
193 GAATCATGTATCGATTTAATTTGAAATTAATTCAGAAAAATTTTGGAAAACGATATTAGAAGGTT
* * *
55453 GAAAAACCCTTCAATCTTTTTGGCTTTAAATTATATATATTTTTATGAGAGTTGTGGCCAAAACT
258 GAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTTATGAGAATTGTGGCCAAAAAT
55518 TGAGGAAA
323 TGAGGAAA
* ** * * *
55526 AAT-TTTCCGGATCAATTTTTGCAAAATTTTAGAAGAAATCGTATACTTTCCATTACGACTTTAA
1 AATCTTT-CGGATCAA-TTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATAAC-ATTTTAA
* *
55590 GCTAAAAACACGTTTCGGGACACCGACTCAGTTTTGCATGATTTTTTTACACAAAGACTCCTTGA
63 GCTAAAAA-ACGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTTTACA-AAAGACTTCTTGA
* * * * * **
55655 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGGTTTGTTTTTACGAGTAT
126 AATATTTATATTTATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGACCAT
* * * * * **
55720 ATGAATCATGTTTCTATTTAATTCGAAATTAATTTAGAAAAAAATTGGAAAAACGATATTAGAAG
191 CTGAATCATGTATCGATTTAATTTGAAATTAATTCAGAAAAATTTTGG-AAAACGATATTAGAAG
** * * *
55785 CCTGAAAAACCCTTCAATCTTTTTGTCTTTGAA-T-TATAT-TTTTTATGCGAATTGTGGCGAAA
255 GTTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTTATGAGAATTGTGGCCAAA
55847 AATTGAGGAAA
320 AATTGAGGAAA
* * *
55858 AATCTTTCGAATCAGTTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATGACAATTTTAAGC
1 AATCTTTCGGATCAATTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATAAC-ATTTTAAGC
* * ** *
55923 TAAACAAGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGGA-AGAAGACTTCTTGAAA
65 TAAA-AAACGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTT-TTACAAAAGACTTCTTGAAA
*
55987 TATTTATATTTATCTAACCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGACCATCT
128 TATTTATATTTATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGACCATCT
56052 GAATCATGTATCGATTTAATTTGAAATTAATTCAG-AAAATTTTGGAAAACGATATTAGAAGGTT
193 GAATCATGTATCGATTTAATTTGAAATTAATTCAGAAAAATTTTGGAAAACGATATTAGAAGGTT
56116 GAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATA
258 GAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATA
56155 CTTTCCATTA
Statistics
Matches: 548, Mismatches: 68, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
328 46 0.08
329 9 0.02
330 105 0.19
331 85 0.16
332 53 0.10
333 83 0.15
334 121 0.22
335 46 0.08
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
AATCTTTCGGATCAATTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATAACATTTTAAGCT
AAAAAACGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTTTACAAAAGACTTCTTGAAATAT
TTATATTTATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAA
TCATGTATCGATTTAATTTGAAATTAATTCAGAAAAATTTTGGAAAACGATATTAGAAGGTTGAA
AAACCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTTATGAGAATTGTGGCCAAAAATTGA
GGAAA
Done.