Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008234.1 Hibiscus syriacus cultivar Beakdansim tig00110878_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: 105818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2668 original size:19 final size:19
Alignment explanation
Indices: 2644--2685 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2634 CATTAATTTC
*
2644 GAAATAATCTCAAAACTTT
1 GAAATAATCCCAAAACTTT
2663 GAAATAATCCCAAAACTTT
1 GAAATAATCCCAAAACTTT
2682 GAAA
1 GAAA
2686 ACCTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (19 bp):
GAAATAATCCCAAAACTTT
Found at i:3608 original size:22 final size:23
Alignment explanation
Indices: 3573--3620 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
3563 CATTTAGATT
3573 TTTAACTAATTTATAAT-TATATG
1 TTTAACTAATTTATAATATA-ATG
*
3596 TTTAA-TATTTTATAATATAATG
1 TTTAACTAATTTATAATATAATG
3618 TTT
1 TTT
3621 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAACTAATTTATAATATAATG
Found at i:8776 original size:30 final size:30
Alignment explanation
Indices: 8734--8804 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
8724 GAACAAAGCT
* *
8734 GAAGACAT-ACTGTCTTCCCGGCGATTTTTC
1 GAAGAC-TCACTGTCTTCCCGGCGACTTTCC
* *
8764 GAAGACTCACTGTGTTTCCGGCGACTTTCC
1 GAAGACTCACTGTCTTCCCGGCGACTTTCC
*
8794 GAAGACGCACT
1 GAAGACTCACT
8805 ATATTCCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (30 bp):
GAAGACTCACTGTCTTCCCGGCGACTTTCC
Found at i:10111 original size:61 final size:60
Alignment explanation
Indices: 9985--10112 Score: 132
Period size: 61 Copynumber: 2.1 Consensus size: 60
9975 TAGATTGTAC
* * * * *** * * *
9985 ATCAACTTAATCATTAAATTTTAAAATATTTCAATTTAAATATTGGATTTTAGATTTTGT
1 ATCAATTTTATCATTAAATTTAAAAATATTTCAATTTAAACATAAAACTTTAGATTTCGA
*
10045 ATCAATTTTATCATTAAACTTTAAAAATGTTTCAATTTAAACATAAAACTTTA-ATTTCGA
1 ATCAATTTTATCATTAAA-TTTAAAAATATTTCAATTTAAACATAAAACTTTAGATTTCGA
10105 ATTCAATT
1 A-TCAATT
10113 AAAAAATTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
60 22 0.40
61 33 0.60
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (60 bp):
ATCAATTTTATCATTAAATTTAAAAATATTTCAATTTAAACATAAAACTTTAGATTTCGA
Found at i:11849 original size:121 final size:119
Alignment explanation
Indices: 11709--11938 Score: 406
Period size: 121 Copynumber: 1.9 Consensus size: 119
11699 CGAGAGGTTT
11709 ACCCTTACATATACAATTCAATATTCAACATCTTTTAGTGTATAAAGATGTTGAATTAAAATTCG
1 ACCCTTACATATACAATTCAATATTCAACATCTTTTAGTGTATAAAGATGTTGAATTAAAATTCG
11774 TAATTATAGACACATACGTGTAATATATATGATGTTATTATAAAATCCATGTTTTG
66 TAATTATAGACACATACGTGT-A-ATATATGATGTTATTATAAAATCCATGTTTTG
*
11830 ACCCTTACATATACAATTCAATATTCAGCATCTTTTAGTGTATAAAGATGTTGAATTAAAATTCG
1 ACCCTTACATATACAATTCAATATTCAACATCTTTTAGTGTATAAAGATGTTGAATTAAAATTCG
* * *
11895 TAATTGTAGACACATATGTGTAATGTATGATGTTATTATAAAAT
66 TAATTATAGACACATACGTGTAATATATGATGTTATTATAAAAT
11939 ATAATATAAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
119 21 0.20
120 1 0.01
121 83 0.79
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (119 bp):
ACCCTTACATATACAATTCAATATTCAACATCTTTTAGTGTATAAAGATGTTGAATTAAAATTCG
TAATTATAGACACATACGTGTAATATATGATGTTATTATAAAATCCATGTTTTG
Found at i:18063 original size:20 final size:20
Alignment explanation
Indices: 18038--18077 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18028 TTTATATGAC
* *
18038 TTATTAATAATTTTAATTAA
1 TTATTAAAAATATTAATTAA
18058 TTATTAAAAATATTAATTAA
1 TTATTAAAAATATTAATTAA
18078 CTATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAAAATATTAATTAA
Found at i:18953 original size:35 final size:35
Alignment explanation
Indices: 18914--18984 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
18904 ATTTTAAAGC
18914 TACTTTTATTTATTTGTTTATTTATTCATACATGA
1 TACTTTTATTTATTTGTTTATTTATTCATACATGA
*
18949 TACTTTTATTTATTTGTTTATTTATTCATATATGA
1 TACTTTTATTTATTTGTTTATTTATTCATACATGA
18984 T
1 T
18985 CTGCTACCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.07, G:0.06, T:0.62
Consensus pattern (35 bp):
TACTTTTATTTATTTGTTTATTTATTCATACATGA
Found at i:20656 original size:30 final size:30
Alignment explanation
Indices: 20278--20634 Score: 525
Period size: 30 Copynumber: 11.9 Consensus size: 30
20268 TTCCCCATGC
*
20278 TGTTGTTGGGTGGCGGCATCCCTCGCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
* *
20308 CGTTGTTGGGTGGCGGCATCCCTCGCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
* * *
20338 CGTTGTTGGGTGACGGCATCCCTCGCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
* *
20368 CGTTGTTGGGTGGCGGCATCCCTCCCATGT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
20398 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
*
20428 TGTTGTTGGGTGGCGGCATGCCTCCCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
**
20458 TGTTGTTGGGTGGCGGCATCCCTCCCACGT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
** * * * *
20488 TCATGTTGGGTGGGGGCATTCCTCGCATAC
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
20518 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
* *
20548 TGTTGTTGGGTGGTGGCATTCCTCCCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
*
20578 TGTTGTTGGGTGGCGGTATCCCTCCCATAT
1 TGTTGTTGGGTGGCGGCATCCCTCCCATAT
*
20608 TGTTGTTGGGTGGGGGCATCCCTCCCA
1 TGTTGTTGGGTGGCGGCATCCCTCCCA
20635 CGTTCATGTT
Statistics
Matches: 295, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 295 1.00
ACGTcount: A:0.10, C:0.25, G:0.32, T:0.32
Consensus pattern (30 bp):
TGTTGTTGGGTGGCGGCATCCCTCCCATAT
Found at i:29401 original size:12 final size:12
Alignment explanation
Indices: 29386--29432 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
29376 CCGGTTTTTT
*
29386 AACCGGATAAAA
1 AACCGGTTAAAA
29398 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
29413 AACCGGTTAAAA
1 AACCGGTTAAAA
29425 AACCGGTT
1 AACCGGTT
29433 TTTATCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:29514 original size:11 final size:10
Alignment explanation
Indices: 29486--29513 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29476 GTTAATATAG
29486 CCGTTTTTGA
1 CCGTTTTTGA
29496 CCGTTTTTGA
1 CCGTTTTTGA
29506 CCGTTTTT
1 CCGTTTTT
29514 TTCTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.21, G:0.18, T:0.54
Consensus pattern (10 bp):
CCGTTTTTGA
Found at i:31750 original size:21 final size:21
Alignment explanation
Indices: 31726--31765 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31716 TTTATTTTAT
31726 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
31747 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
31766 AACTTGAAGT
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:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:31813 original size:33 final size:33
Alignment explanation
Indices: 31760--31858 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
31750 TTTGTTTCAA
31760 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
31792 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
31825 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
31858 T
1 T
31859 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:31887 original size:13 final size:13
Alignment explanation
Indices: 31844--31898 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
31834 TTGGAAGTAT
31844 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
31857 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
31871 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
31884 TTAAGTATTTGAA
1 TTAAGTATTTCAA
31897 TT
1 TT
31899 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:31944 original size:11 final size:11
Alignment explanation
Indices: 31922--31957 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
31912 GTTTGATGCT
31922 TTCTCT-TTGA
1 TTCTCTCTTGA
31932 TTCTCTCTTGA
1 TTCTCTCTTGA
31943 TTCTCTCTTGA
1 TTCTCTCTTGA
31954 TTCT
1 TTCT
31958 AGTTGCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:32345 original size:17 final size:18
Alignment explanation
Indices: 32325--32358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32315 TTTTTTTTAT
32325 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
32342 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
32359 CCAAAACCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:32358 original size:16 final size:16
Alignment explanation
Indices: 32307--32358 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
32297 CTGGAATATT
* *
32307 AAAATCGGTTTTTTTT
1 AAAACCGGTTTTTTTA
* *
32323 ATAACCGGTTTTTTAAA
1 AAAACCGGTTTTTT-TA
32340 AAAACCGGTTTTTTTA
1 AAAACCGGTTTTTTTA
32356 AAA
1 AAA
32359 CCAAAACCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (16 bp):
AAAACCGGTTTTTTTA
Found at i:33915 original size:15 final size:15
Alignment explanation
Indices: 33895--33923 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33885 TGTCCAGTAA
33895 TTACATAATAATAAC
1 TTACATAATAATAAC
33910 TTACATAATAATAA
1 TTACATAATAATAA
33924 GATAACTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
TTACATAATAATAAC
Found at i:34580 original size:39 final size:39
Alignment explanation
Indices: 34511--34589 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
34501 TTAAACACAA
34511 AGAATATACACACAGACGTACATCAGAATGAAGATCAAT
1 AGAATATACACACAGACGTACATCAGAATGAAGATCAAT
* * * *
34550 AGAATATACACATAGATGTACTTCATAATGAAGATCAAT
1 AGAATATACACACAGACGTACATCAGAATGAAGATCAAT
34589 A
1 A
34590 CATCAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (39 bp):
AGAATATACACACAGACGTACATCAGAATGAAGATCAAT
Found at i:37323 original size:35 final size:35
Alignment explanation
Indices: 37277--37352 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
37267 AAAACAGTCA
* *
37277 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
**
37312 TCAATTTCATTCTAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
37347 TCAATT
1 TCAATT
37353 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:37895 original size:130 final size:130
Alignment explanation
Indices: 37749--37996 Score: 442
Period size: 130 Copynumber: 1.9 Consensus size: 130
37739 TATTTATATA
*
37749 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
37814 TTAGCACATGATCATGACATGTGTCATTGGTGAAACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATGTGTCATTAGTGAAACATGTCACCACCTAATTATTTATATATGCT
37879 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
37944 TTAACACATGATCATGATATGTGTTATTAGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATGTGTCATTAGTGAAACATGTCACCACCTAATTA
37997 GAAGAAAATT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 112 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACATGTGTCATTAGTGAAACATGTCACCACCTAATTATTTATATATGCT
Found at i:38027 original size:130 final size:129
Alignment explanation
Indices: 37763--38027 Score: 327
Period size: 130 Copynumber: 2.0 Consensus size: 129
37753 ATTTGGTCCT
* *
37763 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
37828 TGACATGTGTCATTGGTGAAACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATGTGTCATTAGTGAAACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
37893 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * *
37958 TGATATGTGTTATTAGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATGTGTCATTAGTGAAACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
38022 -A
128 CA
38023 AAATT
1 AAATT
38028 TGGGTCTTGG
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
130 102 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACATGTGTCATTAGTGAAACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:38356 original size:28 final size:27
Alignment explanation
Indices: 38325--38387 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
38315 AGTTGATACA
*
38325 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
38353 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
38381 ATATTTT
1 ATATTTT
38388 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:38488 original size:16 final size:18
Alignment explanation
Indices: 38467--38500 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
38457 ATTTCTTATT
38467 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
38483 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
38501 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:38581 original size:22 final size:21
Alignment explanation
Indices: 38556--38615 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
38546 AATATACATT
* *
38556 TATATAAATATATTTTTATTCA
1 TATATAAA-ATATTTTGATTAA
*
38578 TATATTGAAATATTTTGATTAA
1 TATA-TAAAATATTTTGATTAA
*
38600 AATATAAACATATTTT
1 TATATAAA-ATATTTT
38616 AAATACTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATATAAAATATTTTGATTAA
Found at i:39467 original size:15 final size:15
Alignment explanation
Indices: 39447--39476 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39437 GGATAAAGTC
39447 GGTGCTGATGCTGGA
1 GGTGCTGATGCTGGA
39462 GGTGCTGATGCTGGA
1 GGTGCTGATGCTGGA
39477 ATCAGAAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (15 bp):
GGTGCTGATGCTGGA
Found at i:43576 original size:479 final size:477
Alignment explanation
Indices: 42681--43637 Score: 1761
Period size: 479 Copynumber: 2.0 Consensus size: 477
42671 ACAATTATTT
* *
42681 ATAAGGCTCTCTTTAAGCACATCTAGGGATGGCAAACGGGCGGGTCAGATGCGGATACCCCCTCC
1 ATAAGGCCCTCTTTAAGCACATCTAGGGATGGCAAACGGGCAGGTCAGATGCGGATACCCCCTCC
*
42746 CCATCCCCACCTAATATTTTTCAATCCACCACCCGCCCACCACCCATGATGGGTAAAAAAATTTA
66 CCATCCCCACCTAATATTTTTCAATCCACCACCCGCCCACCACCCACGATGGGTAAAAAAATTTA
42811 AATCCACACCCGCCCACACGGGTACATTCTCAAATCCATCCCCACACCCACCGAGTCGAGCTCGA
131 AATCCACACCCGCCCACACGGGTACATTCTCAAATCCATCCCCACACCCACCGAGTCGAGCTCGA
*
42876 GTATTGCTGAGCTCGACTCGAACTCGAAAACTTTAAAAGTAGGCTCGACTCGACTGAAAAACTCG
196 GTATTGCTAAGCTCGACTCGAACTCGAAAACTTTAAAAGTAGGCTCGACTCGACTGAAAAACTCG
* *
42941 CGAGCTAAAAATTATCAAGCTCAACTCGAACTTGAAATATAATATTGAAACTCGACTCGAACTCG
261 CGAGCTAAAAATTATCAAGCTCAACTCGAACTTGAAATATAATATGGAAACTCGACTCAAACTCG
*
43006 AAAAAACTCAAACTCAAAAAAATTTCAAGAGCTCAATTGAAGCTCGATTTTAAGCTCAATTCTAG
326 AAAAAACTCAAACTCAAAAAAATTTCAAGAGCTCAATTGAAGCTCGATTTTAAGCTCAATTCAAG
*
43071 CTCAAACTCACCCACTACCACAAATTATGACGTAAGCTCTCCTACAGTGGGAAGACCTTAGGCGA
391 CTCAAACTCACCCACTACCACAAATTATGACGTAAGCTCTCCAACAGTGGGAAGACCTTAGGCGA
43136 GCGCCCCTCCCAAGTGCAATGG
456 GCGCCCCTCCCAAGTGCAATGG
*
43158 ATAAGGCCCTCTTTAAGCACATCTAGGGATGGCAAACGGGCAGGTCGGATGCGGATACCCCCTCC
1 ATAAGGCCCTCTTTAAGCACATCTAGGGATGGCAAACGGGCAGGTCAGATGCGGATACCCCCT-C
*
43223 CCCATCCCCACCTAATATTTTTCAATCCACCACCCGCCCACCACCCACGATGGGTAAAAAATTTT
65 CCCATCCCCACCTAATATTTTTCAATCCACCACCCGCCCACCACCCACGATGGGTAAAAAAATTT
* *
43288 AAATCCACACCTGCCCACACGGGTACATTCTCAAATCCATCCCCACGCCCACCGAGTCGAGCTTC
130 AAATCCACACCCGCCCACACGGGTACATTCTCAAATCCATCCCCACACCCACCGAGTCGAGC-TC
43353 GAGTATTGCTAAGCTCGACTCGAACTCGAAAACTTTAAAAGTAGGCTCGACTCGACTGAAAAACT
194 GAGTATTGCTAAGCTCGACTCGAACTCGAAAACTTTAAAAGTAGGCTCGACTCGACTGAAAAACT
43418 CGCGAGCTAAAAATTATCAAGCTCAACTCGAACTTGAAATATAATATGGAAACTCGACTCAAACT
259 CGCGAGCTAAAAATTATCAAGCTCAACTCGAACTTGAAATATAATATGGAAACTCGACTCAAACT
* *
43483 TGAAAAAACTCAAACTCAAAAAAATTTCAAGAGCTCAATTGAAGCTCGATTTTAAGCTCGATTCA
324 CGAAAAAACTCAAACTCAAAAAAATTTCAAGAGCTCAATTGAAGCTCGATTTTAAGCTCAATTCA
*
43548 AGCTCAAACTCACCCACTACCACAAATTATGACGTAGGCTCTCCAACAGTGGGAAGACCTTAGGC
389 AGCTCAAACTCACCCACTACCACAAATTATGACGTAAGCTCTCCAACAGTGGGAAGACCTTAGGC
43613 GAGCGCCCCTCCCAAGTGCAATGG
454 GAGCGCCCCTCCCAAGTGCAATGG
43637 A
1 A
43638 GGTCGCTTAC
Statistics
Matches: 463, Mismatches: 15, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
477 60 0.13
478 124 0.27
479 279 0.60
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.21
Consensus pattern (477 bp):
ATAAGGCCCTCTTTAAGCACATCTAGGGATGGCAAACGGGCAGGTCAGATGCGGATACCCCCTCC
CCATCCCCACCTAATATTTTTCAATCCACCACCCGCCCACCACCCACGATGGGTAAAAAAATTTA
AATCCACACCCGCCCACACGGGTACATTCTCAAATCCATCCCCACACCCACCGAGTCGAGCTCGA
GTATTGCTAAGCTCGACTCGAACTCGAAAACTTTAAAAGTAGGCTCGACTCGACTGAAAAACTCG
CGAGCTAAAAATTATCAAGCTCAACTCGAACTTGAAATATAATATGGAAACTCGACTCAAACTCG
AAAAAACTCAAACTCAAAAAAATTTCAAGAGCTCAATTGAAGCTCGATTTTAAGCTCAATTCAAG
CTCAAACTCACCCACTACCACAAATTATGACGTAAGCTCTCCAACAGTGGGAAGACCTTAGGCGA
GCGCCCCTCCCAAGTGCAATGG
Found at i:54480 original size:14 final size:14
Alignment explanation
Indices: 54461--54516 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
54451 CGTTCGTGAA
54461 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
54475 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
54488 --TT-GTTTATGTT
1 CGTTCGATTATGTT
54499 CGTTCGATTATGTT
1 CGTTCGATTATGTT
54513 CGTT
1 CGTT
54517 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:54495 original size:24 final size:24
Alignment explanation
Indices: 54468--54537 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
54458 GAACGTTCGA
*
54468 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
54492 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
54516 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
54538 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:55277 original size:10 final size:10
Alignment explanation
Indices: 55262--55336 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
55252 GGGTCTCCAA
55262 CGTTTATGTT
1 CGTTTATGTT
55272 CGTTTATGTT
1 CGTTTATGTT
55282 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
55293 ATGTTCGTGTT
1 -CGTTTATGTT
55304 CGTTTATGTT
1 CGTTTATGTT
55314 CG----TGTT
1 CGTTTATGTT
55320 CGTTTATGTT
1 CGTTTATGTT
55330 CGTTTAT
1 CGTTTAT
55337 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:55293 original size:16 final size:16
Alignment explanation
Indices: 55268--55332 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
55258 CCAACGTTTA
55268 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
55284 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
55300 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
55316 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
55332 T
1 T
55333 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:65508 original size:5 final size:5
Alignment explanation
Indices: 65498--65526 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
65488 TTATAGGGTG
65498 TGATT TGATT TGATT TGATT TGATT TGAT
1 TGATT TGATT TGATT TGATT TGATT TGAT
65527 GTTTTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
TGATT
Found at i:72393 original size:7 final size:8
Alignment explanation
Indices: 72374--72401 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
72364 CCTGGGGGTA
72374 AAAAAATC
1 AAAAAATC
72382 AAAAAATC
1 AAAAAATC
72390 AAAAAATC
1 AAAAAATC
72398 AAAA
1 AAAA
72402 CCCAACGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATC
Found at i:76294 original size:21 final size:22
Alignment explanation
Indices: 76270--76332 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
76260 TCTAAACATA
*
76270 TAAACTTTTAATAAAT-T-ATAT
1 TAAAATTTTAA-AAATATAATAT
76291 TAAAATTTTAAAAATATAATAT
1 TAAAATTTTAAAAATATAATAT
*
76313 TACAAAATTTAAAATATATA
1 TA-AAATTTTAAAA-ATATA
76333 TAAATTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 4 0.11
21 11 0.31
22 6 0.17
23 10 0.28
24 5 0.14
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATTTTAAAAATATAATAT
Found at i:76326 original size:22 final size:22
Alignment explanation
Indices: 76287--76332 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
76277 TTAATAAATT
*
76287 ATATTAAAATTTTAAAAATATA
1 ATATTAAAAATTTAAAAATATA
76309 ATATTACAAAATTTAAAATATATA
1 ATATTA-AAAATTTAAAA-ATATA
76333 TAAATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 10 0.48
24 5 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTAAAAATTTAAAAATATA
Found at i:76371 original size:14 final size:15
Alignment explanation
Indices: 76291--76387 Score: 63
Period size: 15 Copynumber: 6.0 Consensus size: 15
76281 TAAATTATAT
76291 TAAAAT-TTTAAAAA
1 TAAAATATTTAAAAA
*
76305 TATAATA-TTACAAAA
1 TAAAATATTTA-AAAA
76320 TTTAAAATATATATAAATTAA
1 --TAAAATAT-T-TAAA--AA
*
76341 TAAAAAAATATTAAAAA
1 T-AAAATAT-TTAAAAA
* *
76358 TACAATTTTTAAAAA
1 TAAAATATTTAAAAA
76373 TAAAATATTTAAAAA
1 TAAAATATTTAAAAA
76388 ATACAATCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
14 8 0.12
15 24 0.37
16 4 0.06
17 9 0.14
19 8 0.12
20 10 0.15
21 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:76371 original size:15 final size:16
Alignment explanation
Indices: 76351--76394 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
76341 TAAAAAAATA
76351 TTAAAAATACAAT-TT
1 TTAAAAATACAATATT
*
76366 TTAAAAATAAAATATT
1 TTAAAAATACAATATT
*
76382 TAAAAAATACAAT
1 TTAAAAATACAAT
76395 CATCTCGACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAATACAATATT
Found at i:76388 original size:31 final size:29
Alignment explanation
Indices: 76337--76394 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
76327 TATATATAAA
76337 TTAATAAAAAAATATTAAAAATACAATTT
1 TTAATAAAAAAATATTAAAAATACAATTT
76366 TTAA-AAATAAAATATTTAAAAAATACAAT
1 TTAATAAA-AAAATA-TT-AAAAATACAAT
76395 CATCTCGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 3 0.12
29 10 0.38
30 2 0.08
31 11 0.42
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
TTAATAAAAAAATATTAAAAATACAATTT
Found at i:79000 original size:2 final size:2
Alignment explanation
Indices: 78993--79053 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
78983 TTTCTTAAAG
78993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79035 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
79054 AGGGACCAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89809 original size:3 final size:3
Alignment explanation
Indices: 89801--89868 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
89791 GATATTTTAA
89801 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
89849 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
89869 GGTAATGGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:90183 original size:21 final size:21
Alignment explanation
Indices: 90135--90193 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
90125 AGAGCGTTAT
* **
90135 CTAAAATATTATTTTTTTCTAC
1 CTAAAATATTA-ATTTCGCTAC
*
90157 CGAAAATATTAATTTCGCTAC
1 CTAAAATATTAATTTCGCTAC
90178 CTAAAATGATT-ATTTC
1 CTAAAAT-ATTAATTTC
90194 ATATAGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (21 bp):
CTAAAATATTAATTTCGCTAC
Found at i:100849 original size:20 final size:20
Alignment explanation
Indices: 100824--100895 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
100814 TTTTCCCAAT
100824 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
100844 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
100864 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
100885 TCGCAATGCGA
1 TCGCAATGCGA
100896 TACTGACTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:100908 original size:41 final size:41
Alignment explanation
Indices: 100881--100958 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
100871 GCGAATTGGG
* * *
100881 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
100922 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
100959 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:100909 original size:20 final size:20
Alignment explanation
Indices: 100884--100978 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
100874 AATTGGGAAA
*
100884 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
100904 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
100925 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
100945 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
100965 TTCGCAACGCGATA
1 ATCGCAACGCGATA
100979 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:101194 original size:22 final size:22
Alignment explanation
Indices: 101166--101209 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101156 CACTCTCTCA
101166 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
101188 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
101210 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:101494 original size:20 final size:20
Alignment explanation
Indices: 101469--101506 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101459 CGATTCTCTC
101469 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
101489 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
101507 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:102820 original size:18 final size:18
Alignment explanation
Indices: 102799--102837 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
102789 TCCACTTCGG
*
102799 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
102817 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
102835 GAG
1 GAG
102838 ACATTATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.44, G:0.18, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:103360 original size:20 final size:21
Alignment explanation
Indices: 103307--103353 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
103297 TAGTTTACTT
*
103307 TCGC-AACACGAAAATGACTA
1 TCGCAAACGCGAAAATGACTA
*
103327 TCGCAAACGCGAAAATGGCTA
1 TCGCAAACGCGAAAATGACTA
103348 TCGCAA
1 TCGCAA
103354 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (21 bp):
TCGCAAACGCGAAAATGACTA
Found at i:103382 original size:14 final size:14
Alignment explanation
Indices: 103363--103420 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
103353 ATGCGAAATG
103363 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
103377 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
103393 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
103409 AAAATCGCAACG
1 AAAATCGCAACG
103421 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:103405 original size:32 final size:33
Alignment explanation
Indices: 103347--103437 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
103337 GAAAATGGCT
103347 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
103380 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
103412 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
103438 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:103473 original size:14 final size:14
Alignment explanation
Indices: 103454--103510 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
103444 TTGTGTTTCG
103454 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
103468 CGTTGCAATTCATT-T
1 CGTTGCGATT--TTGT
103483 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
103499 CATTGCGATTTT
1 CGTTGCGATTTT
103511 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 5 0.14
16 4 0.11
17 7 0.20
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:103491 original size:31 final size:33
Alignment explanation
Indices: 103449--103526 Score: 115
Period size: 31 Copynumber: 2.4 Consensus size: 33
103439 GCGATTTGTG
* *
103449 TTTCGCGTTGCGATTTTGTCGTTGC-A-ATTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATATTCA
*
103480 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATATTCA
103513 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
103527 AGCCATTCCG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 23 0.55
32 1 0.02
33 18 0.43
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCATTGCGATATTCA
Found at i:103523 original size:19 final size:19
Alignment explanation
Indices: 103476--103567 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 19
103466 GTCGTTGCAA
103476 TTCATTTCGCATTGCGA-T
1 TTCATTTCGCATTGCGATT
*
103494 TT--TGT--CATTGCGATT
1 TTCATTTCGCATTGCGATT
*
103509 TTCATTTCGCATTGCGATA
1 TTCATTTCGCATTGCGATT
** * * *
103528 GCCATTCCGCGTTGCGATA
1 TTCATTTCGCATTGCGATT
* *
103547 GTCATTTCGCGTTGCGATT
1 TTCATTTCGCATTGCGATT
103566 TT
1 TT
103568 AAGTTTCGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
14 8 0.14
15 3 0.05
16 2 0.03
17 2 0.03
18 2 0.03
19 41 0.71
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCATTTCGCATTGCGATT
Found at i:105413 original size:14 final size:14
Alignment explanation
Indices: 105394--105429 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
105384 ATTGTTTAAT
105394 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
105408 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
105422 TGATTTGT
1 TGATTTGT
105430 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:105538 original size:20 final size:20
Alignment explanation
Indices: 105513--105550 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
105503 GCAAAACAGA
*
105513 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
105533 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
105551 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:105569 original size:19 final size:19
Alignment explanation
Indices: 105545--105612 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
105535 ATCGCAACGA
105545 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
105564 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
105583 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
105597 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
105613 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:105686 original size:19 final size:20
Alignment explanation
Indices: 105640--105708 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
105630 GATTTCCTCG
105640 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
105660 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
105680 G-TGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
105699 GTTGCGATAG
1 GTTGCGATAG
105709 TCAATGAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.40
20 29 0.60
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Done.