Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001074.1 Hibiscus syriacus cultivar Beakdansim tig00002128_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: 37388
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:674 original size:32 final size:31
Alignment explanation
Indices: 587--711 Score: 94
Period size: 31 Copynumber: 4.0 Consensus size: 31
577 ACCCTAATGG
*
587 AACATCTTAGGGCCTG-AGAGCCTACCCAAGA
1 AACATCTTAGGGCC-GCAGAGCCTACCTAAGA
* * * * *
618 TAGAT-TTCGGGGCCG-TGGGTCCTACCTAAGA
1 AACATCTT-AGGGCCGCAGAG-CCTACCTAAGA
* **
649 ACACATCTTAGGGCCGCAGGGCCTACCCGAGA
1 A-ACATCTTAGGGCCGCAGAGCCTACCTAAGA
**
681 ATGATCTTAGGGCCGCAGAGCCTACCTAAGA
1 AACATCTTAGGGCCGCAGAGCCTACCTAAGA
712 GTCATATTAG
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
30 5 0.07
31 43 0.60
32 19 0.26
33 5 0.07
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.18
Consensus pattern (31 bp):
AACATCTTAGGGCCGCAGAGCCTACCTAAGA
Found at i:722 original size:31 final size:31
Alignment explanation
Indices: 638--722 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
628 GGCCGTGGGT
* *
638 CCTACCTAAGAACACATCTTAGGGCCGCAGGG
1 CCTACCTAAGAA-TCATCTTAGGGCCGCAGAG
** *
670 CCTACCCGAGAATGATCTTAGGGCCGCAGAG
1 CCTACCTAAGAATCATCTTAGGGCCGCAGAG
* *
701 CCTACCTAAGAGTCATATTAGG
1 CCTACCTAAGAATCATCTTAGG
723 TCCGTAAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
31 33 0.77
32 10 0.23
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (31 bp):
CCTACCTAAGAATCATCTTAGGGCCGCAGAG
Found at i:1654 original size:29 final size:29
Alignment explanation
Indices: 1606--1698 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
1596 AAACTACCAA
* *
1606 AATGTAACATTTTTCAAAAAAAAT-CCAG
1 AATGTCACATTTTTCAAAAAAATTCCCAG
* *
1634 AATGTCACATTTTTCACAAAAATTCCCAA
1 AATGTCACATTTTTCAAAAAAATTCCCAG
* *
1663 AATGTCACCTTTTTCAAAATAATTCCCAG
1 AATGTCACATTTTTCAAAAAAATTCCCAG
1692 AATGTCA
1 AATGTCA
1699 TCGGGTCGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 21 0.38
29 35 0.62
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.31
Consensus pattern (29 bp):
AATGTCACATTTTTCAAAAAAATTCCCAG
Found at i:8028 original size:32 final size:31
Alignment explanation
Indices: 7981--8057 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
7971 CGGGGCCGTG
* * *
7981 GGGCCTACCTAAGAATACATCTTAGGGCTGCA
1 GGGCCTACCCAAGAAT-CATCTCAGGGCCGCA
* *
8013 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCCAAGAATCATCTCAGGGCCGCA
* *
8044 GAGCCTACCTAAGA
1 GGGCCTACCCAAGA
8058 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (31 bp):
GGGCCTACCCAAGAATCATCTCAGGGCCGCA
Found at i:8040 original size:63 final size:63
Alignment explanation
Indices: 7934--8057 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
7924 CCCTAAGGGA
* * * ** *
7934 ACATCTTAGGGCTTGAGAGCTTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAT
1 ACATCTTAGGGCTTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
* *
7997 ACATCTTAGGGC-TGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCTTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
8058 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (63 bp):
ACATCTTAGGGCTTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
Found at i:8991 original size:29 final size:28
Alignment explanation
Indices: 8940--9044 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 28
8930 TCTACATTCG
* *
8940 AAAATTCCCGAAATGTCA-TTTTTTAAAAA
1 AAAATT-CCAAAATGTCACATTTTT-AAAA
* * *
8969 AAAATTCCAGAATGTCACATTTTTCACA
1 AAAATTCCAAAATGTCACATTTTTAAAA
8997 AAAATTCCCAAAATGTCACATTTTTCAAAA
1 AAAATT-CCAAAATGTCACATTTTT-AAAA
* *
9027 TAATTTCCAAAATGTCAC
1 AAAATTCCAAAATGTCAC
9045 CGGGTCGGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
28 17 0.27
29 40 0.63
30 6 0.10
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAATTCCAAAATGTCACATTTTTAAAA
Found at i:9065 original size:17 final size:17
Alignment explanation
Indices: 9040--9072 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9030 TTTCCAAAAT
*
9040 GTCACCGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
9057 GTCAACGGGTCGGGTC
1 GTCAACGGGTCGGGTC
9073 AGACCGGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.27, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCG
Found at i:9098 original size:19 final size:18
Alignment explanation
Indices: 9074--9140 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
9064 GGTCGGGTCA
*
9074 GACCGGTCAACCCGGTTCG
1 GACCGGTCAA-CCGGTTTG
*
9093 GACCGGTCAGACCGGTTTA
1 GACCGGTCA-ACCGGTTTG
*
9112 GACCGATCAAACCGGTTTG
1 GACCGGTC-AACCGGTTTG
*
9131 GACCAGTCAA
1 GACCGGTCAA
9141 GTCGGTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 36 0.90
20 2 0.05
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (18 bp):
GACCGGTCAACCGGTTTG
Found at i:13996 original size:16 final size:16
Alignment explanation
Indices: 13975--14014 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
13965 GAGTCAAATG
13975 CAAGCCCAAACTCATC
1 CAAGCCCAAACTCATC
13991 CAAGCCCAAACTCATC
1 CAAGCCCAAACTCATC
14007 CAAGCCCA
1 CAAGCCCA
14015 GATCCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.45, G:0.07, T:0.10
Consensus pattern (16 bp):
CAAGCCCAAACTCATC
Found at i:14208 original size:26 final size:26
Alignment explanation
Indices: 14152--14213 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
14142 TCCTAGGGTA
* **
14152 TCATTGCCACCCTAGGTCTATTCTGG
1 TCATTGCCTCCCTAGGTCTATTCCAG
* *
14178 CCATTGCCTCCCTATGTCTATTCCAG
1 TCATTGCCTCCCTAGGTCTATTCCAG
14204 TCATTGCCTC
1 TCATTGCCTC
14214 TAGCAAATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (26 bp):
TCATTGCCTCCCTAGGTCTATTCCAG
Found at i:21098 original size:20 final size:20
Alignment explanation
Indices: 21061--21134 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
21051 TTTTCCACAA
* * *
21061 ATTTGTAAAACATGTGGTTT
1 ATTTGTAAAACCTTTGGTTC
21081 ATTTGTAAAACCTTTGGTTC
1 ATTTGTAAAACCTTTGGTTC
* * * *
21101 ATTTATAAAGCCTTCGGGTC
1 ATTTGTAAAACCTTTGGTTC
*
21121 ATTTGTAAAGCCTT
1 ATTTGTAAAACCTT
21135 CGAGTAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTTGTAAAACCTTTGGTTC
Found at i:21135 original size:20 final size:20
Alignment explanation
Indices: 21081--21149 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
21071 CATGTGGTTT
* * *
21081 ATTTGTAAAACCTTTGGTTC
1 ATTTGTAAAGCCTTCGGGTC
*
21101 ATTTATAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTC
* *
21121 ATTTGTAAAGCCTTCGAGTA
1 ATTTGTAAAGCCTTCGGGTC
21141 ATTTGTAAA
1 ATTTGTAAA
21150 TCTTTTGGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTTGTAAAGCCTTCGGGTC
Found at i:21256 original size:45 final size:44
Alignment explanation
Indices: 21206--21448 Score: 185
Period size: 45 Copynumber: 5.5 Consensus size: 44
21196 AAACAAATCG
* *
21206 AACTCCACAGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATCA
1 AACTCCACGGAAGAGTAGTGGAATGGATTTTTCAGCAAA-TATCA
* ** * *
21251 AACTCCACGGGAGAGTAGTGG-ATGGAAATTCAATCA-TAAATAT-G
1 AACTCCACGGAAGAGTAGTGGAATGG--ATT-TTTCAGCAAATATCA
*
21295 AACTCCACGAAAGAGTAGTGGAATGGATTTTTCAGCAATATATCA
1 AACTCCACGGAAGAGTAGTGGAATGGATTTTTCAGCAA-ATATCA
* * * * ** * *
21340 AACTCCATGGAAAAGTTA-TGAAAT-CA-AATTCAATCATAA-ATCTG
1 AACTCCACGGAAGAG-TAGTGGAATGGATTTTTC-AGCA-AATATC-A
*
21384 AACTCCACGGAAGAGTAGTGGAATGAATTTTTCAGCAAAGTATCA
1 AACTCCACGGAAGAGTAGTGGAATGGATTTTTCAGCAAA-TATCA
*
21429 AACTTCACGGAAGAGTAGTG
1 AACTCCACGGAAGAGTAGTG
21449 AAGCAAAAGC
Statistics
Matches: 151, Mismatches: 31, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
42 3 0.02
43 13 0.09
44 51 0.34
45 67 0.44
46 14 0.09
47 3 0.02
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (44 bp):
AACTCCACGGAAGAGTAGTGGAATGGATTTTTCAGCAAATATCA
Found at i:21339 original size:89 final size:89
Alignment explanation
Indices: 21205--21450 Score: 338
Period size: 89 Copynumber: 2.8 Consensus size: 89
21195 AAAACAAATC
* *
21205 GAACTCCAC-AGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATCAAACTCCACGGGAGAGTAG
1 GAACTCCACGA-AAGAGTAGTGGAATGGATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAG
* *
21269 TG-GATGGAAATTCAATCATAAATAT
65 TGAAAT-CAAATTCAATCATAAATAT
* *
21294 GAACTCCACGAAAGAGTAGTGGAATGGATTTTTCAGCAATA-TATCAAACTCCATGGAAAAGTTA
1 GAACTCCACGAAAGAGTAGTGGAATGGATTTTTCAGCAA-AGTATCAAACTCCACGGAAGAG-TA
*
21358 -TGAAATCAAATTCAATCATAAATCT
64 GTGAAATCAAATTCAATCATAAATAT
* * *
21383 GAACTCCACGGAAGAGTAGTGGAATGAATTTTTCAGCAAAGTATCAAACTTCACGGAAGAGTAGT
1 GAACTCCACGAAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGT
21448 GAA
66 GAA
21451 GCAAAAGCAA
Statistics
Matches: 139, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
88 3 0.02
89 130 0.94
90 6 0.04
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (89 bp):
GAACTCCACGAAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGT
GAAATCAAATTCAATCATAAATAT
Found at i:21655 original size:17 final size:18
Alignment explanation
Indices: 21625--21658 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21615 TATACGATAA
21625 TATATAATAATATTATAT
1 TATATAATAATATTATAT
*
21643 TATA-AATATTATTATA
1 TATATAATAATATTATA
21659 AAGCCCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATAATAATATTATAT
Found at i:23245 original size:2 final size:2
Alignment explanation
Indices: 23238--23274 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23228 TTTTAGTCAT
23238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23275 TTAGGTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25711 original size:56 final size:57
Alignment explanation
Indices: 25548--25796 Score: 158
Period size: 56 Copynumber: 4.4 Consensus size: 57
25538 TTGTAAAGCC
* * * * * *
25548 TTAACTTATCCAA-TCTGTTACATTCAAATAT-GAA-CGTTTAATTATTTTTGTAATGT
1 TTAACTTATCGAAGT-TGTTACATTCAAAGATGGAAGC-TTAAATAACTGTTGTAATGT
* * * * * **
25604 ATTAACTTAT-GCAGGTTATTACATTCAAAAATAGAAGTTTGGATAAC-GTTGTAATGT
1 -TTAACTTATCG-AAGTTGTTACATTCAAAGATGGAAGCTTAAATAACTGTTGTAATGT
* *
25661 TTAACTTATCGAAGTTGTTACGTTCAAAGAT-GAATGCTTAAAT-AGTGTTGTAGA-GT
1 TTAACTTATCGAAGTTGTTACATTCAAAGATGGAA-GCTTAAATAACTGTTGTA-ATGT
* * * * * *
25717 TTAACTTGT-GCAATTTGTTATATTCAAAGATGGAAGTTTGAATAACT-TTGTAATGA
1 TTAACTTATCG-AAGTTGTTACATTCAAAGATGGAAGCTTAAATAACTGTTGTAATGT
* *
25773 TTAAATTATCCAAGTTGTTACATT
1 TTAACTTATCGAAGTTGTTACATT
25797 GAAAAATGAA
Statistics
Matches: 148, Mismatches: 31, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
55 6 0.04
56 93 0.63
57 40 0.27
58 9 0.06
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (57 bp):
TTAACTTATCGAAGTTGTTACATTCAAAGATGGAAGCTTAAATAACTGTTGTAATGT
Found at i:26560 original size:171 final size:167
Alignment explanation
Indices: 26118--26654 Score: 428
Period size: 171 Copynumber: 3.2 Consensus size: 167
26108 AACTTATATG
* * * * * *
26118 AGTTTTTACATTCAAAGATGAAAGTTTGAAT---AGTGTAGTATTTACACTTGTCCAAGTTGTTA
1 AGTTGTTACATTCAAATATGGAAGTTTGAATAACATTGTAATATTTA-AC-AGTCCAAGTTGTTA
* * * ** * ** * * ** * * *
26180 CACTCAAAGATATAATTTTGAATAGTGTTGTGATGTTTAACATATTCAAGTTGCTATATTCAAAG
64 CATTCAAAGATAGAAGTTTGAATAGCATTGTAAAATTTAACTTATCCAAGTTATTACATTAAAAA
*
26245 AT-GAAAGCTT-GAA-AAACATTGTAATGTC-TAACTTAGTCA
129 ATAG-AAG-TTGGAATAAA-GTTGTAATGTCTTAACTTAG-CA
* *
26284 AGTTGTTACATTCAAATATAGAAGTTTGAATAACATTGTAATGTTTAACAGTCCAAGTTGTTACA
1 AGTTGTTACATTCAAATATGGAAGTTTGAATAACATTGTAATATTTAACAGTCCAAGTTGTTACA
* * * * * * *
26349 TTCAAATATAGAAGTTTTAATAGCGTTGTAGAGTTTAACTTATCCAAGTTGTTTCATTAAAAAAT
66 TTCAAAGATAGAAGTTTGAATAGCATTGTAAAATTTAACTTATCCAAGTTATTACATTAAAAAAT
* *
26414 GGAAGTTGGAATAATGTTGTAATGTCTTAACTTAGCGA
131 AGAAGTTGGAATAAAGTTGTAATGTCTTAACTTAGC-A
* * * * * *
26452 ACTTGTTACATTTAAAGATGGAAGTTTGAAATAGCATTTTAATATCTTGACTTA-TCCAAGTTGT
1 AGTTGTTACATTCAAATATGGAAGTTTG-AATAACATTGTAATAT-TTAAC--AGTCCAAGTTGT
* * *
26516 TACATTCAAAGAT-GAAAGTTTGAATAGCATTGTAAAATTTAACTTGTCCAGGTTATTACATTCA
62 TACATTCAAAGATAG-AAGTTTGAATAGCATTGTAAAATTTAACTTATCCAAGTTATTACATTAA
** * * * *
26580 AAGGTAGAAGTTTGAATAAAGTTATAATGT-TTACCTTATCCA
126 AAAATAGAAGTTGGAATAAAGTTGTAATGTCTTAACTTA-GCA
* * *
26622 AGTTGTTACACTGAAATATGGAAGTTCGAATAA
1 AGTTGTTACATTCAAATATGGAAGTTTGAATAA
26655 TGATATAATG
Statistics
Matches: 299, Mismatches: 58, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
166 29 0.10
167 81 0.27
168 38 0.13
169 27 0.09
170 36 0.12
171 87 0.29
172 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (167 bp):
AGTTGTTACATTCAAATATGGAAGTTTGAATAACATTGTAATATTTAACAGTCCAAGTTGTTACA
TTCAAAGATAGAAGTTTGAATAGCATTGTAAAATTTAACTTATCCAAGTTATTACATTAAAAAAT
AGAAGTTGGAATAAAGTTGTAATGTCTTAACTTAGCA
Found at i:26646 original size:56 final size:56
Alignment explanation
Indices: 25993--26654 Score: 504
Period size: 56 Copynumber: 11.8 Consensus size: 56
25983 AAACTATAGA
* *
25993 GTTTAACTTATCCAAGTTGTTACATTCGAAGATGGGAGTTTGAA-AAATGTTGTAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAA-GTTGTAAT
* * * * * * * *
26049 GTTTACCTTTTCAAAGTTGTTAC-TTCGAAGATGTAAGTTTGAATAACGATGTAGT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
* *** * * *
26104 GTTAAACTTATATGAGTTTTTACATTCAAAGATGAAAGTTTGAAT--AG-TGTAGT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
* * * ** * ** *
26157 ATTTACACTTGTCCAAGTTGTTACACTCAAAGATATAATTTTGAATAGTGTTGTGAT
1 GTTTA-ACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
* * * * * * *
26214 GTTTAACATATTCAAGTTGCTATATTCAAAGATGAAAGCTTGAA-AAACATTGTAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAA-GTTGTAAT
* * *
26270 GTCTAACTTAGT-CAAGTTGTTACATTCAAATATAGAAGTTTGAATAACA-TTGTAAT
1 GTTTAACTTA-TCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAA-AGTTGTAAT
* * * **
26326 GTTTAAC--AGTCCAAGTTGTTACATTCAAATATAGAAGTTTTAATAGCGTTGTAGA-
1 GTTTAACTTA-TCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTA-AT
* * * * *
26381 GTTTAACTTATCCAAGTTGTTTCATTAAAAAATGGAAGTTGGAATAATGTTGTAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
* * * * * *
26437 GTCTTAACTTAGCGAACTTGTTACATTTAAAGATGGAAGTTTGAA-ATAGCATTTTAAT
1 GT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAG--TTGTAAT
* * * * *
26495 ATCTTGACTTATCCAAGTTGTTACATTCAAAGATGAAAGTTTGAATAGCA-TTGTAAA
1 GT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATA-AAGTTGTAAT
* * * * * * *
26552 ATTTAACTTGTCCAGGTTATTACATTCAAAGGTAGAAGTTTGAATAAAGTTATAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
* * * * *
26608 GTTTACCTTATCCAAGTTGTTACACTGAAATATGGAAGTTCGAATAA
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAA
26655 TGATATAATG
Statistics
Matches: 476, Mismatches: 108, Indels: 44
0.76 0.17 0.07
Matches are distributed among these distances:
53 9 0.02
54 35 0.07
55 88 0.18
56 243 0.51
57 54 0.11
58 45 0.09
59 1 0.00
60 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (56 bp):
GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAGTTGTAAT
Found at i:26792 original size:149 final size:148
Alignment explanation
Indices: 26556--26845 Score: 331
Period size: 149 Copynumber: 1.9 Consensus size: 148
26546 TGTAAAATTT
* * *
26556 AACTTGTCCAGGTTATTACATTCAAAGGTAGAAGTTTGAATAAAGTTATAATGTTTACCTTATCC
1 AACTTATCCAGGTTATTACATTCAAA-GTAGAAGTTTGAATAAAGCTATAATGTTTAACTTATCC
* * * * *
26621 AAGTTGTTACACTGAAATATGGAAGT-TCGAATAATGATATAATGTCTTATCAAAACTA-TTTTA
65 AAGTTGTTACACTGAAAGATGGAA-TATCGAATAACGATATAATGCCTTAACAAAAC-ACTTTGA
26684 TGTTTATAAACTAAAGAGTTG
128 TGTTTATAAACTAAAGAGTTG
* *
26705 AACTTATCCAGGTTGTTACATTCAAA-TACGAAAGTTTGAATAGCA-CTATAATGTTTAACTTAT
1 AACTTATCCAGGTTATTACATTCAAAGTA-G-AAGTTTGAATA-AAGCTATAATGTTTAACTTAT
* * * * *
26768 CCAAGTTGTTATA-T-ACAAGGATGGAATATTGAATAGCGCTCTAATGCCTTAACAAAACACTTT
63 CCAAGTTGTTACACTGA-AA-GATGGAATATCGAATAACGATATAATGCCTTAACAAAACACTTT
26831 GATGTTTATAAACTA
126 GATGTTTATAAACTA
26846 CAAAGTTTGA
Statistics
Matches: 119, Mismatches: 15, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
147 3 0.03
148 6 0.05
149 109 0.92
150 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (148 bp):
AACTTATCCAGGTTATTACATTCAAAGTAGAAGTTTGAATAAAGCTATAATGTTTAACTTATCCA
AGTTGTTACACTGAAAGATGGAATATCGAATAACGATATAATGCCTTAACAAAACACTTTGATGT
TTATAAACTAAAGAGTTG
Found at i:27224 original size:56 final size:55
Alignment explanation
Indices: 26991--27633 Score: 360
Period size: 56 Copynumber: 11.5 Consensus size: 55
26981 ATCTATATTC
* * * ** * * *
26991 TCCAAGTTGTTAGAGTCAAATATGGAAGTTTTAATAGTGTTGTAATGTTTAAATTT
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAA-ATTTAACTTA
* * * * * *
27047 TTCATGTTTTTACATTCAAAGATGGGAAGCTTAAATAGCA-TG----CTTAACTTA
1 TCCAAGTTGTTACATTCAAAGAT-GGAAGTTTTAATAGCATTGTAAATTTAACTTA
* * * * * **
27098 TTCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACTTTGTAATGTTTAACAGA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAA-ATTTAACTTA
* * *
27154 TCCATGTTGATACATTCAATGAT-GAAGTTTTAATAGCATTGTAAGAGTTTAACTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAA-A-TTTAACTTA
* * * *
27210 TCGAAGTTGTTACATTAAAAGATGGAATTTTTAATAACA-TGTAAATTCTTAACTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAAA-T-TTAACTTA
* * * * *
27266 GT-AAAGTTGTTACATTCAAAATATGG-TGTTTGAATAGCGTTGTAATATCTTAACTTA
1 -TCCAAGTTGTTACATTC-AAAGATGGAAGTTTTAATAGCATTGTAA-AT-TTAACTTA
* ** * *
27323 TCCAAGTTGTTACATTCAAAGATGAAAGTTTGT-ATAGTGTTGTAATTTCTTAAGTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTT-TAATAGCATTGTAA-AT-TTAACTTA
* * ** * * * *
27380 TCCAAGTTGTTACAGTCAAAGATAGAAGCCTAAATAGCAATGTGATATTTAATTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGT-AAATTTAACTTA
* * ** * * *
27436 TCTAAGTTTTTACATTCAAAGATAAAAG-TCTAAAAACATTGT-AATGATTAACTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAAAT--TTAACTTA
* * ** * * * * *
27491 TCCAAGTTATTATATTCAATTATGGAAGTTTGAAGAGCGTTGTAGAGTTTTACTTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTA-AATTTAAC-TTA
* * * * * * *
27548 TCCAAGTTGTTAAATTC-AATATGGAAGTTTGATTAACTTTGTAATGTCTTAACTTA
1 TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAA-AT-TTAACTTA
*
27604 TCCAA-TATATTACATTCAAAGATGGAAGTT
1 TCCAAGT-TGTTACATTCAAAGATGGAAGTT
27634 CGAATAATGT
Statistics
Matches: 452, Mismatches: 106, Indels: 57
0.73 0.17 0.09
Matches are distributed among these distances:
50 12 0.03
51 29 0.06
53 2 0.00
55 58 0.13
56 193 0.43
57 154 0.34
58 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (55 bp):
TCCAAGTTGTTACATTCAAAGATGGAAGTTTTAATAGCATTGTAAATTTAACTTA
Found at i:27508 original size:55 final size:56
Alignment explanation
Indices: 27306--27509 Score: 160
Period size: 57 Copynumber: 3.6 Consensus size: 56
27296 TGAATAGCGT
* * ** ** ****
27306 TGTAATATCTTAACTTATCCAAGTTGTTACATTCAAAGATGAAAGTTTGTATAGTGT
1 TGTAATAT-TTAACTTATCCAAGTTATTACATTCAAAGATAAAAGCCTAAATAACAA
* * * * * *
27363 TGTAATTTCTTAAGTTATCCAAGTTGTTACAGTCAAAGATAGAAGCCTAAATAGCAA
1 TGTAATAT-TTAACTTATCCAAGTTATTACATTCAAAGATAAAAGCCTAAATAACAA
* * * * * *
27420 TGTGATATTTAATTTATCTAAGTTTTTACATTCAAAGATAAAAGTCTAAA-AACAT
1 TGTAATATTTAACTTATCCAAGTTATTACATTCAAAGATAAAAGCCTAAATAACAA
*
27475 TGTAATGA-TTAACTTATCCAAGTTATTATATTCAA
1 TGTAAT-ATTTAACTTATCCAAGTTATTACATTCAA
27510 TTATGGAAGT
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
55 31 0.26
56 37 0.31
57 51 0.43
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (56 bp):
TGTAATATTTAACTTATCCAAGTTATTACATTCAAAGATAAAAGCCTAAATAACAA
Found at i:27846 original size:92 final size:93
Alignment explanation
Indices: 27673--27917 Score: 256
Period size: 92 Copynumber: 2.6 Consensus size: 93
27663 ATATTGACAC
* *
27673 TTACAAACAAAAGAGTTTAACTCATCCAAGTTTTTACATTCAATGATGAGATTTTGAATAGCATT
1 TTACAAACAAAAGAGTTTAACTTATCCAAGTTCTTACATTCAATGATGAGATTTTGAATAGCATT
* *
27738 TAAACTTCTTAACAAAATAC-TTTGATGT
66 TAAACTTCCTAACAAAACACTTTTG-TGT
* *
27766 TTATAAA-AAAAG-GTTTTAACTTATCCAAGTTGTTACATTCAATGAT-AGAAGTTTT-AATAGC
1 TTACAAACAAAAGAG-TTTAACTTATCCAAGTTCTTACATTCAATGATGAG-A-TTTTGAATAGC
* *
27827 -TTTGTAA-TGTCCTAGCAAAACACTTTTGTGT
63 ATTT-AAACT-TCCTAACAAAACACTTTTGTGT
* * *
27858 TTACAAACTAAAGAGTTTAACTTGTCTAAGTTCTTACATTCAAAT-ATG-GATGTTTGAATA
1 TTACAAACAAAAGAGTTTAACTTATCCAAGTTCTTACATTC-AATGATGAGAT-TTTGAATA
27918 TTGTTGTAAT
Statistics
Matches: 128, Mismatches: 12, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
91 8 0.06
92 68 0.53
93 48 0.38
94 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (93 bp):
TTACAAACAAAAGAGTTTAACTTATCCAAGTTCTTACATTCAATGATGAGATTTTGAATAGCATT
TAAACTTCCTAACAAAACACTTTTGTGT
Found at i:27956 original size:56 final size:56
Alignment explanation
Indices: 27872--28005 Score: 189
Period size: 56 Copynumber: 2.4 Consensus size: 56
27862 AAACTAAAGA
* * * * * *
27872 GTTTAACTTGTCTAAGTTCTTACA-TTCAAATATGGATGTTTGAATATTGTTGTAAT
1 GTTTAACTTATCCAAGTTGTTA-AGTTCAAAGATGGAGGTTTGAATAATGTTGTAAT
*
27928 GTTTAACTTATCCAATTTGTTAAGTTCAAAGATGGAGGTTTGAATAATGTTGTAAT
1 GTTTAACTTATCCAAGTTGTTAAGTTCAAAGATGGAGGTTTGAATAATGTTGTAAT
27984 GTTTAACTTATCCAAGTTGTTA
1 GTTTAACTTATCCAAGTTGTTA
28006 CATTTAAAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 1 0.01
56 68 0.99
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (56 bp):
GTTTAACTTATCCAAGTTGTTAAGTTCAAAGATGGAGGTTTGAATAATGTTGTAAT
Found at i:28026 original size:56 final size:56
Alignment explanation
Indices: 27910--28047 Score: 170
Period size: 56 Copynumber: 2.4 Consensus size: 56
27900 AATATGGATG
* * * **
27910 TTTGAATATTGTTGTAATGTTTAACTTATCCAATTTGTTAAGTTCAAAGATGGAGG
1 TTTGAATAATGTTGTAATGTTTAACTTATCCAAGTTGTTAAGTTCAAAGATGAAAA
* *
27966 TTTGAATAATGTTGTAATGTTTAACTTATCCAAGTTGTTACA-TTTAAAGTTGAAAA
1 TTTGAATAATGTTGTAATGTTTAACTTATCCAAGTTGTTA-AGTTCAAAGATGAAAA
**
28022 TTTGAATAGCGTTGTAATGTCTTAAC
1 TTTGAATAATGTTGTAATGT-TTAAC
28048 AAAGCACTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
56 65 0.92
57 6 0.08
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (56 bp):
TTTGAATAATGTTGTAATGTTTAACTTATCCAAGTTGTTAAGTTCAAAGATGAAAA
Found at i:28186 original size:92 final size:92
Alignment explanation
Indices: 28074--28316 Score: 254
Period size: 92 Copynumber: 2.7 Consensus size: 92
28064 TAATGATTAG
28074 CTTATCCAA--GTTGTTACATTCAAAGATTGAATTTTGAATAATTTTGTAATGTTTAACTTAACA
1 CTTATCCAAGTGTTGTTACATTCAAAGATTGAATTTTGAATAATTTTGTAATGTTTAACTTAACA
28137 -TTTTGATGTTTACGAACTAAGGAGTAAAA
66 CTTTT-ATGTTTA-GAACTAAGGA-TAAAA
* * ** **
28166 CTTAT-C-AGTGTTGTTACATTCAAAGATGGAAGTTTGAATAACATTGTAATGTCTTAACAAAAC
1 CTTATCCAAGTGTTGTTACATTCAAAGATTGAATTTTGAATAATTTTGTAATGT-TTAACTTAAC
* **
28229 ACTTTTATGTTTATAACTAAGGATTTAA
65 ACTTTTATGTTTAGAACTAAGGATAAAA
* *
28257 CTTATCCAAGT-TT-CTAAATTCAAAGA-TGAAAGTTTT-AATAATGTTT-TAATGTTTAACTTA
1 CTTATCCAAGTGTTGTTACATTCAAAGATTG-AA-TTTTGAATAAT-TTTGTAATGTTTAACTTA
28317 TCCAAGTTGT
Statistics
Matches: 125, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
90 8 0.06
91 33 0.26
92 61 0.49
93 19 0.15
94 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (92 bp):
CTTATCCAAGTGTTGTTACATTCAAAGATTGAATTTTGAATAATTTTGTAATGTTTAACTTAACA
CTTTTATGTTTAGAACTAAGGATAAAA
Found at i:28363 original size:56 final size:56
Alignment explanation
Indices: 28252--28370 Score: 136
Period size: 56 Copynumber: 2.1 Consensus size: 56
28242 TAACTAAGGA
* ** *
28252 TTTAACTTATCCAAGTTTCTAAATTCAAAGATGAAAGTTTTAATAATGTTTTAATG
1 TTTAACTTATCCAAGTTTCTAAATTCAAAGATGAAAGTTTGAATAACATTGTAATG
*
28308 TTTAACTTATCCAAGTTGT-TACAA-TCAAAGATGGAAA-TTTGAATAGCATTGTAATG
1 TTTAACTTATCCAAGTT-TCTA-AATTCAAAGAT-GAAAGTTTGAATAACATTGTAATG
28364 TCTTAAC
1 T-TTAAC
28371 ATAACAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
56 42 0.78
57 12 0.22
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (56 bp):
TTTAACTTATCCAAGTTTCTAAATTCAAAGATGAAAGTTTGAATAACATTGTAATG
Found at i:28542 original size:213 final size:213
Alignment explanation
Indices: 28175--28583 Score: 506
Period size: 213 Copynumber: 1.9 Consensus size: 213
28165 ACTTATCAGT
* ** *
28175 GTTGTTACATTCAAAGATGGAAGTTTGAATAACATTGTAATGTCTTAACAAAACACTTTTATGTT
1 GTTGTTACATTAAAAGATAAAACTTTGAATAACATTGTAATGTCTTAACAAAACACTTTTATGTT
** * *
28240 TATAACTAAGGATTTAACTTATCCAAGTTTCTAAATTCAAAGATGAAAGTTTTAATAATGTTTTA
66 TATAAAAAAGGATTTAACTTATCCAAGTGTCTAAATTCAAAGATGAAAGTTTTAATAATGTTGTA
*
28305 ATGTTTAACTTATCCAAGTTGTTACAATCAA-AGATGGAAATTTGAATAGCATTGTAATGTCTTA
131 ATGTTTAACTTATCCAAGTTGTTAC-ATCAAGAGATGGAAATTTAAATAGCATTGTAATGTCTTA
28369 ACATAACAATTTGAATTAC
195 ACATAACAATTTGAATTAC
* * *
28388 GTTGTTATATTAAAAGATAAAACTTTGAATAACA-TGTAATGTGTTAGCAAAACA-TTTTGATGT
1 GTTGTTACATTAAAAGATAAAACTTTGAATAACATTGTAATGTCTTAACAAAACACTTTT-ATGT
** ** * * *
28451 TTATAAAGAAAAGTTTTTAACTTATCTGAGCTGT-TACATTCAATGATTG-AAGTTTTAATAGTG
65 TTAT-AA-AAAAGGATTTAACTTATCCAAG-TGTCTAAATTCAAAGA-TGAAAGTTTTAATAATG
* * * * *
28514 TTGTATTG-TTAACTTATCTAAGTTGTTACATTAAGAGATGGAAGTTTAAATAGTATTGTAATGT
126 TTGTAATGTTTAACTTATCCAAGTTGTTACATCAAGAGATGGAAATTTAAATAGCATTGTAATGT
28578 CTTAAC
191 CTTAAC
28584 TTATCTAATT
Statistics
Matches: 166, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
211 4 0.02
212 30 0.18
213 83 0.50
214 45 0.27
215 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (213 bp):
GTTGTTACATTAAAAGATAAAACTTTGAATAACATTGTAATGTCTTAACAAAACACTTTTATGTT
TATAAAAAAGGATTTAACTTATCCAAGTGTCTAAATTCAAAGATGAAAGTTTTAATAATGTTGTA
ATGTTTAACTTATCCAAGTTGTTACATCAAGAGATGGAAATTTAAATAGCATTGTAATGTCTTAA
CATAACAATTTGAATTAC
Found at i:28558 original size:55 final size:57
Alignment explanation
Indices: 28467--28605 Score: 167
Period size: 55 Copynumber: 2.5 Consensus size: 57
28457 AGAAAAGTTT
* * * * * * *
28467 TTAACTTATCTGAGCTGTTACATTCAATGATTGAAGTTTTAATAGTGTTGT-AT-TG
1 TTAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGTATTGTAATGTC
28522 TTAACTTATCTAAGTTGTTACATT-AAGAGATGGAAGTTTAAATAGTATTGTAATGTC
1 TTAACTTATCTAAGTTGTTACATTCAA-AGATGGAAGTTTAAATAGTATTGTAATGTC
* *
28579 TTAACTTATCTAATTTGTTGCATTCAA
1 TTAACTTATCTAAGTTGTTACATTCAA
28606 TTATGGATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
54 2 0.03
55 42 0.59
56 2 0.03
57 23 0.32
58 2 0.03
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (57 bp):
TTAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGTATTGTAATGTC
Found at i:29062 original size:149 final size:150
Alignment explanation
Indices: 28884--29178 Score: 350
Period size: 149 Copynumber: 2.0 Consensus size: 150
28874 GTTTCAATAT
* *
28884 TGTAATGTCTTCACAAAACTCATTAATGTTTACAAACT-AAG-GATTTACACTTA-TCAAAGTTG
1 TGTAATGTCTTAACAAAACACATTAATGTTTACAAACTAAAGTG-TTTA-ACTTATTC-AAGTTG
* * * * * *
28946 TTACATTCA-AAGATGATAGTTTGTATAGCGTTGTAAAGT-TTAACATATC-CAGGTTGTTACAT
63 TTACAAT-AGAAGATGAAAATTTGAATAACGTTGTAAAGTCATAACATATCTCA-GTTGTTACAT
*
29008 TCAAAGATGGAAGTTTGAATAACAA
126 TAAAAGATGGAAGTTTGAATAACAA
* * * * *
29033 TGTAATGTTTTAACAAAACACTTTGATGTTTCCAAACTAAAGTGTTTAAGTTATTCAAGTTGTTA
1 TGTAATGTCTTAACAAAACACATTAATGTTTACAAACTAAAGTGTTTAACTTATTCAAGTTGTTA
* * *
29098 CAATAGAAGATGAAAATTTGAATAACGTTGTAATGTCATAACTTATCTTAGTTGTTACATTAAAA
66 CAATAGAAGATGAAAATTTGAATAACGTTGTAAAGTCATAACATATCTCAGTTGTTACATTAAAA
29163 GATGGAAGTTTGAATA
131 GATGGAAGTTTGAATA
29179 GAATTGTAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
148 1 0.01
149 73 0.59
150 47 0.38
151 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (150 bp):
TGTAATGTCTTAACAAAACACATTAATGTTTACAAACTAAAGTGTTTAACTTATTCAAGTTGTTA
CAATAGAAGATGAAAATTTGAATAACGTTGTAAAGTCATAACATATCTCAGTTGTTACATTAAAA
GATGGAAGTTTGAATAACAA
Found at i:29220 original size:56 final size:56
Alignment explanation
Indices: 29090--29415 Score: 258
Period size: 56 Copynumber: 5.9 Consensus size: 56
29080 AAGTTATTCA
* * * *
29090 AGTTGTTACAAT-AGAAGATGAAAATTTGAATAACGTTGTAATGTCATAACTTATCTT
1 AGTTGTTACAATCA-AAGATGGAAGTTTGAATAACATTGTAATGT-TTAACTTATCTT
* * *
29147 AGTTGTTACATTAAAAGATGGAAGTTTGAATAGA-ATTGTAAAGTTTAACTTAT-TT
1 AGTTGTTACAATCAAAGATGGAAGTTTGAATA-ACATTGTAATGTTTAACTTATCTT
* * *
29202 GAGTTGTTACAATCAAAGATGGAAGTTTGAATAATATCAG-AATGTTTAACTTATCCT
1 -AGTTGTTACAATCAAAGATGGAAGTTTGAATAACAT-TGTAATGTTTAACTTATCTT
* * * * * *
29259 AGTTGTTACATTCAAAGATGTAATTTTGAATAACGTTGTGATGTTTAACTTATAC-A
1 AGTTGTTACAATCAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTAT-CTT
* * * ** * * * **
29315 AGTTGTTACATTAAAAGGTGCTAGTTTTAACAA-TTTGTAA---TTAACTTATCCA
1 AGTTGTTACAATCAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCTT
* * *
29367 AATT-TTACATTCAAAGATGGAAGTTTGAATAACGTTGTAATGTGTTAAC
1 AGTTGTTACAATCAAAGATGGAAGTTTGAATAACATTGTAATGT-TTAAC
29416 AAAACAGTTT
Statistics
Matches: 219, Mismatches: 36, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
51 23 0.11
52 19 0.09
55 9 0.04
56 128 0.58
57 38 0.17
58 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (56 bp):
AGTTGTTACAATCAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCTT
Found at i:29306 original size:112 final size:110
Alignment explanation
Indices: 29075--29415 Score: 343
Period size: 112 Copynumber: 3.1 Consensus size: 110
29065 CAAACTAAAG
* * * *
29075 TGTTTAAGTTATTCAAGTTGTTACAATAGAAGATGAAAATTTGAATAACGTTGTAATGTCATAAC
1 TGTTTAACTTATTCAAGTTGTTACAATA-AAGATGAAAGTTTGAATAA-TTTGTAATGT-TTAAC
* * *
29140 TTATCTTAGTTGTTACATTAAAAGATGGAAGTTTGAATAGA-ATTGTAA
63 TTATCCTAGTTGTTACATTCAAAGATGGAAGTTTGAATA-ACGTTGTAA
* ** * *
29188 AGTTTAACTTATTTGAGTTGTTACAATCAAAGATGGAAGTTTGAATAATATCAG-AATGTTTAAC
1 TGTTTAACTTATTCAAGTTGTTACAAT-AAAGATGAAAGTTTGAATAAT-T-TGTAATGTTTAAC
* * *
29252 TTATCCTAGTTGTTACATTCAAAGATGTAATTTTGAATAACGTTGTGA
63 TTATCCTAGTTGTTACATTCAAAGATGGAAGTTTGAATAACGTTGTAA
* * * ** * *
29300 TGTTTAACTTATACAAGTTGTTACATTAAAAGGTGCTAGTTTTAACAATTTGTAA---TTAACTT
1 TGTTTAACTTATTCAAGTTGTTACAAT-AAAGATGAAAGTTTGAATAATTTGTAATGTTTAACTT
* *
29362 ATCCAAATT-TTACATTCAAAGATGGAAGTTTGAATAACGTTGTAA
65 ATCCTAGTTGTTACATTCAAAGATGGAAGTTTGAATAACGTTGTAA
29407 TGTGTTAAC
1 TGT-TTAAC
29416 AAAACAGTTT
Statistics
Matches: 190, Mismatches: 32, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
107 36 0.19
108 19 0.10
110 1 0.01
111 4 0.02
112 82 0.43
113 46 0.24
114 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (110 bp):
TGTTTAACTTATTCAAGTTGTTACAATAAAGATGAAAGTTTGAATAATTTGTAATGTTTAACTTA
TCCTAGTTGTTACATTCAAAGATGGAAGTTTGAATAACGTTGTAA
Found at i:30890 original size:58 final size:58
Alignment explanation
Indices: 30790--31239 Score: 636
Period size: 58 Copynumber: 7.8 Consensus size: 58
30780 ATGGTATTAA
* *
30790 GTGTGCAAAAAGTTATG-AATTCATACTAAGTGTATGATTTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
30847 GTGTGTAAAAAGTTAAGAAATTCATACTAAGT-TCATGAGTTTCCGTACTT-GGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGT-ATGAATTTCCGTA-TTGGGCACTTT
* * * * * *
30905 GTGTGCAAAAAGTTAAGAAATTCATACTAAATCTATGAATTTTCTTACTAGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
30963 GAGTGCAAAAAGTTAAGAAATTCATACAAAGTGTATGAATTTCCGTATTGGGAACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
31021 GTGTACAAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGC-AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
31080 GTGTACAAAAAATTAAGAAATTCATACTAAGTGTATGAATTTACGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
31138 GTGTGCAAAAAGTCAAGAAATTCATACTGAGTGTATGAATTTTCGTATTGAGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
31196 GTGTACAAATAGTTAAGAGATTCATACTAAGTGTATGAATTTCC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCC
31240 CTATAGGAAA
Statistics
Matches: 351, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
57 17 0.05
58 275 0.78
59 59 0.17
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:31221 original size:233 final size:232
Alignment explanation
Indices: 30796--31239 Score: 669
Period size: 233 Copynumber: 1.9 Consensus size: 232
30786 TTAAGTGTGC
* * ** *
30796 AAAAAGTTATGAATTCATACTAAGTGTATGATTTTCCGTATTGGGCACTTTGTGTGTAAAAAGTT
1 AAAAAGTTAAGAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTACAAAAAATT
* * *
30861 AAGAAATTCATACTAAGTTCATGAGTTTCCGTACTTGGCACTTTGTGTGCAAAAAGTTAAGAAAT
66 AAGAAATTCATACTAAGTTCATGAATTTACGTACTTGGCACTTTGTGTGCAAAAAGTCAAGAAAT
* *
30926 TCATACTAAATCTATGAATTTTCTTACTAGGCACTTTGAGTGCAAAAAGTTAAGAAATTCATACA
131 TCATACTAAATCTATGAATTTTCGTACTAGGCACTTTGAGTACAAAAAGTTAAGAAATTCATACA
30991 AAGTGTATGAATTTCCGTATTGGGAACTTTGTGTACA
196 AAGTGTATGAATTTCCGTATTGGGAACTTTGTGTACA
31028 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTACAAAAAAT
1 AAAAAGTTAAG-AATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTACAAAAAAT
31093 TAAGAAATTCATACTAAGTGT-ATGAATTTACGTA-TTGGGCACTTTGTGTGCAAAAAGTCAAGA
65 TAAGAAATTCATACTAAGT-TCATGAATTTACGTACTT-GGCACTTTGTGTGCAAAAAGTCAAGA
* * * * * * *
31156 AATTCATACTGAGTGTATGAATTTTCGTA-TTGAGCACTTTGTGTACAAATAGTTAAGAGATTCA
128 AATTCATACTAAATCTATGAATTTTCGTACTAG-GCACTTTGAGTACAAAAAGTTAAGAAATTCA
*
31220 TACTAAGTGTATGAATTTCC
192 TACAAAGTGTATGAATTTCC
31240 CTATAGGAAA
Statistics
Matches: 190, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
232 14 0.07
233 175 0.92
234 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (232 bp):
AAAAAGTTAAGAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTACAAAAAATT
AAGAAATTCATACTAAGTTCATGAATTTACGTACTTGGCACTTTGTGTGCAAAAAGTCAAGAAAT
TCATACTAAATCTATGAATTTTCGTACTAGGCACTTTGAGTACAAAAAGTTAAGAAATTCATACA
AAGTGTATGAATTTCCGTATTGGGAACTTTGTGTACA
Found at i:37041 original size:22 final size:22
Alignment explanation
Indices: 37016--37059 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
37006 CTATTATATA
37016 TATTACTATCA-ATAATTAAAAT
1 TATTA-TATCATATAATTAAAAT
* *
37038 TATTATGTCATATTATTAAAAT
1 TATTATATCATATAATTAAAAT
37060 AAAAAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATATCATATAATTAAAAT
Done.