Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001587.1 Hibiscus syriacus cultivar Beakdansim tig00003166_pilon, 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: 107487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1709 original size:12 final size:12
Alignment explanation
Indices: 1681--1726 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1671 CATGGTAAAT
*
1681 TTTTTTGTTT-C
1 TTTTTTCTTTAC
* *
1692 TGTTTTGTTTAC
1 TTTTTTCTTTAC
1704 TTTTTTCTTTAC
1 TTTTTTCTTTAC
1716 TTTTTTCTTTA
1 TTTTTTCTTTA
1727 TTTACTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTCTTTAC
Found at i:4391 original size:322 final size:319
Alignment explanation
Indices: 3806--4446 Score: 1176
Period size: 322 Copynumber: 2.0 Consensus size: 319
3796 ATGAATATTA
3806 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
*
3871 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTTGTTCACTATTTTAACCT
66 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
* *
3936 TTCGCCTTTACACTATAAGAGCTTCGAGATTTGCATGGTGCCTAGGCGAAACATTTCTTGACCTT
131 TTCGCCTTGACACTATAAGAGCTTCGAGAATTGCATGGTGCCTAGGCGAAACATTTCTTGACCTT
4001 GTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGAT
196 GTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGAT
4066 AGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
261 AGATCTACATGAGCAATGGAATAGATCC--GATGGTGAT-TTCTAACCTGCCTGCCTTAGAG
4128 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
* * *
4193 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
66 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
*
4258 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
131 TTCGCCTTGACACTATAAGAGCTTCGAGA-ATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
4323 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTC-AGAGATTTAAGA
195 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
4387 TAGATCTACATGAGCAATGGAATAGATCCGATGGTGATTTCTAACCTGCCTGCCTTAGAG
260 TAGATCTACATGAGCAATGGAATAGATCCGATGGTGATTTCTAACCTGCCTGCCTTAGAG
4447 ATAAGGAGGA
Statistics
Matches: 311, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
319 22 0.07
320 9 0.03
322 194 0.62
323 86 0.28
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (319 bp):
TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
TTCGCCTTGACACTATAAGAGCTTCGAGAATTGCATGGTGCCTAGGCGAAACATTTCTTGACCTT
GTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGAT
AGATCTACATGAGCAATGGAATAGATCCGATGGTGATTTCTAACCTGCCTGCCTTAGAG
Found at i:7373 original size:5 final size:5
Alignment explanation
Indices: 7363--7387 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7353 AAAGGATCCC
7363 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
7388 CGAACTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:11118 original size:111 final size:110
Alignment explanation
Indices: 10984--11369 Score: 513
Period size: 106 Copynumber: 3.5 Consensus size: 110
10974 TTACTTTACA
* *
10984 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAACTCTTTACCGGTTTATCATAATGAAA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTTTGTCATAATGAAA
*
11049 CTGGTTTTTGTCATA-TTTTACTTGTTATATTGTAAAGAATCGATAC
66 CTGG-TTTTGTCATATTTTTACATGTTATATTGTAAAG-ATCGATAC
* * * *
11095 ATTTTTATAAAGTATCGATACTTTCAACATATCTGGTATCTCTTTACCGATTTTGTCATAATAAA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCG-GTTTGTCATAATGAA
11160 ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCGATAC
65 ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAG-ATCGATAC
* *
11207 A----T-T-AAGTATCGATACTTTCAACATATCCGGTAGCACTTTACCAGTTTTGTCATAATGAA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACC-GGTTTGTCATAATGAA
*
11266 ATTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGATCGATA-
65 ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGATCGATAC
* ** *
11311 ATGTACA-AGAAGTATCGATACTTTTAACATATCC-GTAGCTCTTTACCGGTTTTGTCATA
1 ATTTTTATA-AAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGG-TTTGTCATA
11370 TTTTTACCTG
Statistics
Matches: 248, Mismatches: 16, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
104 1 0.00
105 7 0.03
106 87 0.35
107 2 0.01
108 2 0.01
109 21 0.08
110 24 0.10
111 57 0.23
112 47 0.19
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (110 bp):
ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTTTGTCATAATGAAA
CTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGATCGATAC
Found at i:11619 original size:73 final size:73
Alignment explanation
Indices: 11513--11742 Score: 367
Period size: 73 Copynumber: 3.2 Consensus size: 73
11503 CGGTAAGTAG
11513 TTAATGTAATA-GTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAACC
1 TTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAGCAACCTT-AAAAAAACC
11577 GGTAGGTATT
64 GGTAGGTATT
*
11587 TTAATGTAATAGGTAGCG-CTATTTTTTTTACCGTTTTCATTATTAGCAACCTTAAAAAAAACCG
1 TTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT-AAAAAAACCG
11651 GTAGGTATT
65 GTAGGTATT
* * * *
11660 TTAATGTAATAGGTAGTGCCTA-TTTTTTTACCGTTTATATTATTAACAACCTTAAAAAAACCAG
1 TTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCGG
11724 TAGGTATT
66 TAGGTATT
11732 TTAATGTAATA
1 TTAATGTAATA
11743 AATTTTGTTA
Statistics
Matches: 147, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
72 29 0.20
73 95 0.65
74 17 0.12
75 6 0.04
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (73 bp):
TTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCGG
TAGGTATT
Found at i:12055 original size:23 final size:23
Alignment explanation
Indices: 12007--12056 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
11997 ACATATTTTA
* *
12007 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCCAATACG
* *
12030 TTATATAAGTGCTACCCAATATG
1 TTATATAAGCGCTACCCAATACG
12053 TTAT
1 TTAT
12057 TATACTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCCAATACG
Found at i:12152 original size:158 final size:158
Alignment explanation
Indices: 11862--12648 Score: 1185
Period size: 158 Copynumber: 5.0 Consensus size: 158
11852 ATAATACACA
* * * * *
11862 ACCTATTACGTTACATAAGTGCTACCAAATATGTTATTATACTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
* * * ** *
11927 TCGATTATGTTATCATTGACAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAGGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
11992 AATTAACATATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
* * * * * *
12020 ACCTATTACGTTATATAAGTGCTACCCAATATGTTATTATACTTTATAATGTTTCTAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
12085 TCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
*
12150 AATTAACATATTTTA-T-TATAAGTGCT
131 AATTAACATATTTTATTATATAAGCGCT
*
12176 A--TATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
12239 CCGGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
12304 AATTAACATA--TT-TTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
* *
12329 ACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
12394 CCGGTTATGTTATTCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
** *
12459 TTTTAACCTATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
* * * *
12487 ACCAATTACATTATTTAAGCGCTACCTAATATGTTATTGTGCTTGATATTGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
* * * * *
12552 CTGGTTGTGCTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAAAAAATT-AGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
*
12616 AATTAACCTATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
12644 ACCTA
1 ACCTA
12649 ATATGTGCTT
Statistics
Matches: 581, Mismatches: 41, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
152 3 0.01
153 10 0.02
154 128 0.22
155 129 0.22
156 10 0.02
157 36 0.06
158 265 0.46
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (158 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
AATTAACATATTTTATTATATAAGCGCT
Found at i:12365 original size:23 final size:23
Alignment explanation
Indices: 12311--12365 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
12301 AGTAATTAAC
*
12311 ATATTTTATATAAGCGCTACCTA
1 ATATATTATATAAGCGCTACCTA
* *
12334 TTACATTATATAAGCGCTACCTA
1 ATATATTATATAAGCGCTACCTA
*
12357 ATATGTTAT
1 ATATATTAT
12366 TGTGCTTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (23 bp):
ATATATTATATAAGCGCTACCTA
Found at i:12447 original size:309 final size:313
Alignment explanation
Indices: 11864--12648 Score: 1184
Period size: 309 Copynumber: 2.5 Consensus size: 313
11854 AATACACAAC
* * * * * *
11864 CTATTACGTTACATAAGTGCTACCAAATATGTTATTATACTTGATAATGTTTCCAGTAATTAATC
1 CTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACC
* * ** * *
11929 GATTATGTTATCATTGACAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAGGTAA
66 GGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGTAA
* *
11994 TTAACATATTTTATTATATAAGCGCTACCTATTACGTTATATAAGTGCTACCCAATATGTTATTA
131 TTAACATA--TTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCCAATATGTTATTA
* *
12059 TACTTTATAATGTTTCTAGTAATTAATCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACC
194 TACTTGATAATGTTTCTAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACC
*
12124 TAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTA-T-TATAAGTGCTA
259 TAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTATTATATAAGCGCTA
*
12177 -TATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACC
1 CTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACC
12241 GGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGTAA
66 GGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGTAA
* * *
12306 TTAACATATT-TTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTG
131 TTAACATATTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCCAATATGTTATTATA
*
12370 CTTGATAATGTTTCTAGTAATTAACCGGTTATGTTATTCTTGGTAACATTTTAGGCGTTTACCTA
196 CTTGATAATGTTTCTAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTA
** *
12435 ATATGTTGTAATAACAAATTAAGTTTTTAACCTATTTTATTATATAAGCGCTA
261 ATATGTTGTAATAACAAATTAAGTAATTAACATATTTTATTATATAAGCGCTA
* * * *
12488 CCAATTACATTATTTAAGCGCTACCTAATATGTTATTGTGCTTGATATTGTTTCCAGTAATTAAC
1 -CTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAAC
* * * *
12553 TGGTTGTGCTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAAAAAATT-AGTA
65 CGGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGTA
*
12617 ATTAACCTATTTTATTATATAAGCGCTACCTA
130 ATTAA-C-ATATTATTATATAAGCGCTACCTA
12649 ATATGTGCTT
Statistics
Matches: 430, Mismatches: 35, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
309 147 0.34
310 3 0.01
311 10 0.02
312 133 0.31
313 115 0.27
314 4 0.01
315 18 0.04
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (313 bp):
CTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACC
GGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGTAA
TTAACATATTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCCAATATGTTATTATA
CTTGATAATGTTTCTAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTA
ATATGTTGTAATAACAAATTAAGTAATTAACATATTTTATTATATAAGCGCTA
Found at i:12730 original size:128 final size:129
Alignment explanation
Indices: 12524--12777 Score: 411
Period size: 128 Copynumber: 2.0 Consensus size: 129
12514 AATATGTTAT
* ** * *
12524 TGTGCTTGATATTGTTTCCAGTAATTAACTGGTTGTGCTATCCTTGGTAACATTTTAGACGTTTA
1 TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGCTATCCTCGGTAACATTTTAGACGTTTA
*
12589 CCTAATATGTTGTAATAAAAAATT-AGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
66 CCTAATAAGTTGTAATAAAAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
* * *
12652 TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGTTATCCTCGGTAACATTTTAGGCGTTTT
1 TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGCTATCCTCGGTAACATTTTAGACGTTTA
*
12717 CCTAATAAGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTA
66 CCTAATAAGTTGTAATAAAAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTA
12778 TTATATTATA
Statistics
Matches: 115, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 79 0.69
129 36 0.31
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (129 bp):
TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGCTATCCTCGGTAACATTTTAGACGTTTA
CCTAATAAGTTGTAATAAAAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
Found at i:12776 original size:23 final size:23
Alignment explanation
Indices: 12750--12809 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
12740 TAAGTAATTA
*
12750 ACCTATTTTATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
12773 ACCTATTATATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
* *
12796 ACCTAATATGTTAT
1 ACCTATTATATTAT
12810 TGTATTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (23 bp):
ACCTATTATATTATATAAGCGCT
Found at i:22416 original size:18 final size:18
Alignment explanation
Indices: 22393--22428 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22383 TTCTTTAGAT
22393 GATACTTAAGCTTAAAGA
1 GATACTTAAGCTTAAAGA
22411 GATACTTAAGCTTAAAGA
1 GATACTTAAGCTTAAAGA
22429 AAGCTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GATACTTAAGCTTAAAGA
Found at i:23695 original size:21 final size:21
Alignment explanation
Indices: 23665--23704 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23655 TTCTATATGG
23665 TCCTTCGGAACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
23686 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
23705 GGTACCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:23714 original size:21 final size:20
Alignment explanation
Indices: 23662--23737 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
23652 GGATTCTATA
23662 TGGTCCTTCGGAACATATATG
1 TGGTCCTT-GGAACATATATG
**
23683 TAATCCTTTGGAACATATATG
1 TGGTCC-TTGGAACATATATG
* *
23704 TGGTACCTTGGTACACT-TATT
1 TGGT-CCTTGGAACA-TATATG
23725 TGGTCCATTGGAA
1 TGGTCC-TTGGAA
23738 TATGTATATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 37 0.84
22 5 0.11
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (20 bp):
TGGTCCTTGGAACATATATG
Found at i:30505 original size:21 final size:21
Alignment explanation
Indices: 30467--30507 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30457 GTCCTTAGGG
* *
30467 ACATATATGTAATCCTTTGGA
1 ACATATATGCAATACTTTGGA
*
30488 ACATATATGCAGTACTTTGG
1 ACATATATGCAATACTTTGG
30508 TACACTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
ACATATATGCAATACTTTGGA
Found at i:40567 original size:32 final size:31
Alignment explanation
Indices: 40531--40607 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
40521 TGGGGCCATG
* *
40531 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
* * **
40563 GGGCCTACTTGAGAATGATCTCAGGGCCACA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
40594 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
40608 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:48383 original size:29 final size:28
Alignment explanation
Indices: 48344--48420 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 28
48334 TCCACATTCG
*
48344 AAAATTACCAAAATGTCACCTTTTTCAAA
1 AAAATT-CCAAAATGTCACCTATTTCAAA
*
48373 AAAATTCCCAAAATGTCACCTATTTCACA
1 AAAATT-CCAAAATGTCACCTATTTCAAA
48402 AAAATTCCAAGAATGTCAC
1 AAAATTCCAA-AATGTCAC
48421 TGGGTCGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 4 0.09
29 40 0.91
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAATTCCAAAATGTCACCTATTTCAAA
Found at i:55248 original size:40 final size:41
Alignment explanation
Indices: 55193--55269 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
55183 ACAATGGAAA
55193 AAAAATACAGATCCAGTAAATCCTACTCAAAG-AAAAGTAC
1 AAAAATACAGATCCAGTAAATCCTACTCAAAGCAAAAGTAC
* *
55233 AAAAATATAGATCCAGTAGATCCTACTCAAAGCAAAA
1 AAAAATACAGATCCAGTAAATCCTACTCAAAGCAAAA
55270 CTGACAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.18
Consensus pattern (41 bp):
AAAAATACAGATCCAGTAAATCCTACTCAAAGCAAAAGTAC
Found at i:59302 original size:2 final size:2
Alignment explanation
Indices: 59295--59324 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
59285 AGCGAAAATG
59295 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59325 GTTTAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59466 original size:12 final size:13
Alignment explanation
Indices: 59439--59471 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59429 TAATATATCC
*
59439 TTTAAAATTCTAT
1 TTTAAAAATCTAT
59452 TTTAAAAAT-TAT
1 TTTAAAAATCTAT
59464 TTTAAAAA
1 TTTAAAAA
59472 AATAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATCTAT
Found at i:61043 original size:3 final size:3
Alignment explanation
Indices: 61035--61083 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
61025 CGGGTCTTTT
* *
61035 TTA TTA TTA TT- TATA TAA ATA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
61081 TTA
1 TTA
61084 CATATTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 34 0.87
4 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:67535 original size:20 final size:20
Alignment explanation
Indices: 67488--67536 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
67478 CCAGCTCCCC
67488 ACAGCAGCACCAAATCCGCG
1 ACAGCAGCACCAAATCCGCG
*
67508 ACAACAGCACCAAATCCGCG
1 ACAGCAGCACCAAATCCGCG
*
67528 GCAGCAGCA
1 ACAGCAGCA
67537 GCCCTAGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.39, G:0.20, T:0.04
Consensus pattern (20 bp):
ACAGCAGCACCAAATCCGCG
Found at i:75437 original size:60 final size:60
Alignment explanation
Indices: 75365--75496 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
75355 TAGTCGGGTC
* * ** * *
75365 ACCATTTCGTAATTTTTAATAGTC-AAGAGACTCAATAATGTAGCACCCTATAGTTGAGGG
1 ACCATTTTGTAATTTTTAATAGTCAAAG-GACTCAACAATACAACACCCTATAGTCGAGGG
*
75425 ACTATTTTGTAATTTTTAATAGTCAAAGGACTCAACAATACAACACCCTATAGTCGAGGG
1 ACCATTTTGTAATTTTTAATAGTCAAAGGACTCAACAATACAACACCCTATAGTCGAGGG
75485 ACCATTTGTGTA
1 ACCATTT-TGTA
75497 CTTTACCCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
60 55 0.89
61 7 0.11
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (60 bp):
ACCATTTTGTAATTTTTAATAGTCAAAGGACTCAACAATACAACACCCTATAGTCGAGGG
Found at i:77770 original size:90 final size:89
Alignment explanation
Indices: 77617--77791 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
77607 CCTAACACAC
* * *
77617 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
77682 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* *
77707 CCTTTTATATCCGAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
77772 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
77792 ATATTCGGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:88690 original size:60 final size:60
Alignment explanation
Indices: 88626--88758 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 60
88616 ATAGTCAAGT
* *
88626 GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACGCCCTATAGTTGA-G
1 GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCCTATAGTCGATG
* *
88685 AGACCATTTTGTAACTTTTAATAGTCAAATGACTCAACAAAGTAACACCCTATAGTCGATG
1 -GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCCTATAGTCGATG
88746 GACCATTTGTGTA
1 GACCATTT-TGTA
88759 CTTCATCCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
60 62 0.93
61 5 0.07
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCCTATAGTCGATG
Found at i:89468 original size:43 final size:41
Alignment explanation
Indices: 89381--89483 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 41
89371 GGGGTTTTTG
89381 TATT-AAAATAATAATTATTAATTAATAATATTTTATTATT
1 TATTAAAAATAATAATTATTAATTAATAATATTTTATTATT
* *
89421 TATTAAAAATAATAGATTAGTTAACTT-ATTATTTTTTATTATT
1 TATTAAAAATAATA-ATTA-TTAA-TTAATAATATTTTATTATT
89464 TATTAATAAATTAATAATTA
1 TATTAA-AAA-TAATAATTA
89484 CTATTTAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
40 4 0.07
41 9 0.16
42 4 0.07
43 24 0.44
44 9 0.16
45 5 0.09
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
TATTAAAAATAATAATTATTAATTAATAATATTTTATTATT
Found at i:90606 original size:24 final size:24
Alignment explanation
Indices: 90579--90653 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
90569 TACTTTGAAC
90579 AATTAATTTAATAGTACATAAATA
1 AATTAATTTAATAGTACATAAATA
* * * *
90603 AATTAATTTCAT--TACTTTGAA-C
1 AATTAATTTAATAGTAC-ATAAATA
90625 AATTAATTTAATAGTACATAAATA
1 AATTAATTTAATAGTACATAAATA
90649 AATTA
1 AATTA
90654 TAGAAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
22 14 0.36
23 6 0.15
24 19 0.49
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (24 bp):
AATTAATTTAATAGTACATAAATA
Found at i:90629 original size:46 final size:46
Alignment explanation
Indices: 90562--90653 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
90552 ATTGTTATAT
90562 ATTTCATTACTTTGAACAATTAATTTAATAGTACATAAATAAATTA
1 ATTTCATTACTTTGAACAATTAATTTAATAGTACATAAATAAATTA
90608 ATTTCATTACTTTGAACAATTAATTTAATAGTACATAAATAAATTA
1 ATTTCATTACTTTGAACAATTAATTTAATAGTACATAAATAAATTA
90654 TAGAAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (46 bp):
ATTTCATTACTTTGAACAATTAATTTAATAGTACATAAATAAATTA
Found at i:90631 original size:22 final size:22
Alignment explanation
Indices: 90562--90633 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
90552 ATTGTTATAT
90562 ATTTCATTACTTTGAACAATTA
1 ATTTCATTACTTTGAACAATTA
* * * *
90584 ATTTAATAGTAC-ATAAATAAATTA
1 ATTTCAT--TACTTTGAA-CAATTA
90608 ATTTCATTACTTTGAACAATTA
1 ATTTCATTACTTTGAACAATTA
90630 ATTT
1 ATTT
90634 AATAGTACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 18 0.47
23 6 0.16
24 14 0.37
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTCATTACTTTGAACAATTA
Found at i:91011 original size:29 final size:29
Alignment explanation
Indices: 90976--91040 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
90966 ATGAAATTAT
*
90976 AAAAATTGGGAACCT-TAACTATAAATATA
1 AAAAATT-GAAACCTCTAACTATAAATATA
* *
91005 AAAAATTGAAAGCTCTAATTATAAATATA
1 AAAAATTGAAACCTCTAACTATAAATATA
91034 AAAAATT
1 AAAAATT
91041 TGGGGGCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (29 bp):
AAAAATTGAAACCTCTAACTATAAATATA
Found at i:92209 original size:36 final size:36
Alignment explanation
Indices: 92169--92237 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
92159 ACTAAACAAA
*
92169 AAGAATATTGACCTT-AAATTATTAATATTTTTTATG
1 AAGAATATTGAACTTAAAATTATTAAT-TTTTTTATG
* *
92205 AAGAATATTGAATTTAAAATTTTTAATTTTTTT
1 AAGAATATTGAACTTAAAATTATTAATTTTTTT
92238 GAACAATTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (36 bp):
AAGAATATTGAACTTAAAATTATTAATTTTTTTATG
Found at i:94423 original size:17 final size:17
Alignment explanation
Indices: 94401--94435 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
94391 TATCAATAGT
94401 AAATATAAAATAAATTA
1 AAATATAAAATAAATTA
* *
94418 AAATATATAATAATTTA
1 AAATATAAAATAAATTA
94435 A
1 A
94436 TATTTTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAAATAAATTA
Found at i:96699 original size:29 final size:30
Alignment explanation
Indices: 96614--96699 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 30
96604 ATTAGTTCTT
*
96614 AAACTTTTGAA-CATTCCAATTTCATCCTC
1 AAACTTTTGAATCATTCCAATTTCATCCCC
* * * * **
96643 AAA-TTGTGACTCATTCTAAATTGGTCCCC
1 AAACTTTTGAATCATTCCAATTTCATCCCC
*
96672 AAACTTTTGAATC-TTCCAATTTTATCCC
1 AAACTTTTGAATCATTCCAATTTCATCCC
96700 TAAATTCATC
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
28 5 0.12
29 30 0.71
30 7 0.17
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTTGAATCATTCCAATTTCATCCCC
Found at i:96865 original size:60 final size:60
Alignment explanation
Indices: 96739--96870 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
96729 TTAGTATAAT
* * * *
96739 GATCATATTTTGGGGATGAAACTGAAATGTTAAAGACTTTAAGGACTAATTTAAAATAATA
1 GATCATAATTTAGGGATGAAACTAAAATGTTAAAGAATTTAAGGACTAATTTAAAAT-ATA
*
96800 G-TCATAATTTAGGGATGAAATTAAAATGTTTAAA-AATTT-AGAGACTAATTTAAAAT-TA
1 GATCATAATTTAGGGATGAAACTAAAATG-TTAAAGAATTTAAG-GACTAATTTAAAATATA
96858 GGATCATAATTTA
1 -GATCATAATTTA
96871 AGAAAGTGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
58 2 0.03
59 3 0.05
60 51 0.82
61 6 0.10
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (60 bp):
GATCATAATTTAGGGATGAAACTAAAATGTTAAAGAATTTAAGGACTAATTTAAAATATA
Found at i:97658 original size:15 final size:16
Alignment explanation
Indices: 97638--97675 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
97628 ATATTTATAC
97638 ATTATAAA-TAAAATA
1 ATTATAAATTAAAATA
*
97653 ATTATAAATTAAATTA
1 ATTATAAATTAAAATA
97669 A-TATAAA
1 ATTATAAA
97676 ACTTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTATAAATTAAAATA
Found at i:102142 original size:33 final size:33
Alignment explanation
Indices: 102100--102164 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
102090 TATAACATCG
102100 GATGTTTATATTATGTTCATTATCGCCACTAAT
1 GATGTTTATATTATGTTCATTATCGCCACTAAT
102133 GATGTTTATATTATGTTCATTATCGCCACTAA
1 GATGTTTATATTATGTTCATTATCGCCACTAA
102165 GGTCACATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (33 bp):
GATGTTTATATTATGTTCATTATCGCCACTAAT
Found at i:103131 original size:54 final size:54
Alignment explanation
Indices: 103070--103561 Score: 505
Period size: 54 Copynumber: 9.1 Consensus size: 54
103060 AATTCACCCG
* * * *
103070 TAGTGCCGATACGGTCATTCATAAACATA-TATGAATTCCGTGGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGT-GAAATGCACACT
* * * *
103124 TAATGCCG-AATGGTTATTCATCCACATAGGATGAATTCCTTGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
** * * *
103177 TAGTGCCGAAACAATTATTCATCTACGTAGGATGAATTCCGTGAAATACACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
* * * * * *
103231 TAGTGCCGAAACGGTTGTTCATCCACGTTGGATGAATTTCATGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
* * * **
103285 TAGT-CTGAAACGGTTGTTCATCCACATAGGATGAATTCTATGAAATGCACACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATG--CACACT
* * * **
103340 TAGTGCC-AAACGGTTGTTCATCCATATAGGATGAATTCTATGAAATGTACACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATG--CACACT
* * * * *
103395 TAGTG-C-AAACGATTGTTCATCAGCATAGAATGAATTTCGTGAAATGCACACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATG--CACACT
* *
103449 TAGTGCCGAAACGGTTGTTCATCCACATAGGATGAATTCCGTGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
* * * *
103503 TAGTGTCGAAACGGTTATTCATCCACGTAGG-TGAATTCCCTG-AATGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
103555 TAGTGCC
1 TAGTGCC
103562 AATTTGGTAA
Statistics
Matches: 380, Mismatches: 51, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
52 16 0.04
53 82 0.22
54 184 0.48
55 62 0.16
56 36 0.09
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (54 bp):
TAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACT
Found at i:104028 original size:20 final size:19
Alignment explanation
Indices: 103976--104032 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
103966 CTATTTTGAA
*
103976 TGGTATCGATACCTTACCTT
1 TGGTATCGATA-CTCACCTT
*
103996 TGGTATCGATACTCCCCTT
1 TGGTATCGATACTCACCTT
104015 TCGGTATCGATACT-ACCT
1 T-GGTATCGATACTCACCT
104033 AGTAGATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (19 bp):
TGGTATCGATACTCACCTT
Found at i:104082 original size:18 final size:17
Alignment explanation
Indices: 104055--104088 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
104045 CCAATTTAGC
*
104055 CTATAGTATCGGTACTT
1 CTATAGTATCGATACTT
104072 CTATCAGTATCGATACT
1 CTAT-AGTATCGATACT
104089 CGTGCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (17 bp):
CTATAGTATCGATACTT
Done.