Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004793.1 Hibiscus syriacus cultivar Beakdansim tig00010803_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: 125248
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:134 original size:19 final size:18
Alignment explanation
Indices: 110--205 Score: 84
Period size: 17 Copynumber: 5.7 Consensus size: 18
100 TCGCAACGAG
110 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
128 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
143 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
162 AATCGCAA--CGAGA-G-
1 AATCGCAACGCGAGATGA
*
176 AATCGC-ACGCGAAATGA
1 AATCGCAACGCGAGATGA
*
193 AATCGCAATGCGA
1 AATCGCAACGCGA
206 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
13 1 0.02
14 14 0.22
15 4 0.06
16 7 0.11
17 16 0.25
18 5 0.08
19 16 0.25
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:148 original size:14 final size:14
Alignment explanation
Indices: 98--182 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
88 TTGAAATGAA
98 AATCGCAAC--GAG
1 AATCGCAACGAGAG
110 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
127 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
143 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
162 AATCGCAACGAGAG
1 AATCGCAACGAGAG
176 AATCGCA
1 AATCGCA
183 CGCGAAATGA
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.14
14 18 0.31
15 1 0.02
16 5 0.08
17 8 0.14
18 1 0.02
19 18 0.31
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:149 original size:33 final size:33
Alignment explanation
Indices: 90--200 Score: 176
Period size: 33 Copynumber: 3.5 Consensus size: 33
80 TCTTTTGGTT
90 GAAATGAAAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
121 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
154 GAAATGAAAATCGCAACGAGAGAATCGC-ACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
186 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
201 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 24 0.32
32 10 0.14
33 40 0.54
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:236 original size:14 final size:14
Alignment explanation
Indices: 217--271 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
207 TTTGGTTTCG
217 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
231 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
250 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
264 CGTTGCGA
1 CGTTGCGA
272 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:433 original size:33 final size:33
Alignment explanation
Indices: 391--461 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
381 AATACTAACT
*
391 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
424 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
457 TGAAA
1 TGAAA
462 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:865 original size:20 final size:20
Alignment explanation
Indices: 840--1012 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
830 CTTTAAATAT
840 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
860 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
882 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
901 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
921 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
941 CGCGTTGCGATTTACGGAT-
1 CGCGTTGCGATTTACGGATA
*
960 CCCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
980 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1000 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1013 TTTATTCGCG
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
19 20 0.15
20 93 0.72
21 15 0.12
22 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1008 original size:79 final size:81
Alignment explanation
Indices: 839--1012 Score: 228
Period size: 79 Copynumber: 2.2 Consensus size: 81
829 GCTTTAAATA
** * * *
839 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACCCATACGCGTTGCGATTTTACGGATTACCGTTGCGATTTACGGATACGC
904 GTTGCGATATACGGAT
66 GTTGCGATATACGGAT
* * *
920 ACGCATTGCGATTTACCCATACGCGTTGCGA-TTTACGGA-TCCCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACCCATACGCGTTGCGATTTTACGGATTACCGTTGCGATTTACGGATACGC
* *
983 GTTGCGATTTATGTG-T
66 GTTGCGATATACG-GAT
999 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1013 TTTATTCGCG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
79 46 0.57
80 7 0.09
81 27 0.34
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.35
Consensus pattern (81 bp):
TCGCGTTGCGATTTACCCATACGCGTTGCGATTTTACGGATTACCGTTGCGATTTACGGATACGC
GTTGCGATATACGGAT
Found at i:1022 original size:19 final size:19
Alignment explanation
Indices: 980--1033 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
970 TTTACGGATA
*
980 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TGTATT
*
1000 CGCGTTGCGATTTTTTATT
1 CGCGTTGCGATTTTGTATT
1019 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
1034 GAAAATCGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
CGCGTTGCGATTTTGTATT
Found at i:1025 original size:59 final size:60
Alignment explanation
Indices: 839--1031 Score: 237
Period size: 59 Copynumber: 3.2 Consensus size: 60
829 GCTTTAAATA
**
839 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGAT
* * * *** *
900 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGA-
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGAT
* * ***
959 TCCCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT-TTTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGAT
1018 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1032 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.01
59 58 0.53
60 22 0.20
61 28 0.26
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGAT
Found at i:1048 original size:21 final size:20
Alignment explanation
Indices: 1024--1100 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1014 TTATTCGCGT
1024 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1045 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1065 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1087 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1101 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1111 original size:20 final size:20
Alignment explanation
Indices: 1086--1137 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1076 AAGAATCGCG
*
1086 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1106 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1126 TTGCGATTCTGG
1 TTGCGATTCTGG
1138 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:6938 original size:43 final size:43
Alignment explanation
Indices: 6781--7004 Score: 258
Period size: 43 Copynumber: 5.2 Consensus size: 43
6771 GGCTTCAATT
* * * *
6781 TTTTTTCATTCTCACTTTTTACCTTTATAATTAAGACCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
* * * * *
6824 TTTTGTTCAGTCTCACT-TTCTACCTTTCTAATTGATGCAT-TAG
1 TTTT-TTCAATCTCACTCTT-TACCTTTATAATTGAGGCCTCTAA
* * *
6867 TTTTTTTAATCTCACTTTTTACC-TTATAAATGAGGCCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
*
6909 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGTCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
* *
6952 TTTTTTCAATCTCAC-CTTTTACCTTTATAATTGAGGCCCCCAA
1 TTTTTTCAATCTCACTC-TTTACCTTTATAATTGAGGCCTCTAA
6995 TTTTTTCAAT
1 TTTTTTCAAT
7005 TCCATAAAAT
Statistics
Matches: 154, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
41 11 0.07
42 38 0.25
43 79 0.51
44 26 0.17
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
Found at i:6957 original size:86 final size:84
Alignment explanation
Indices: 6757--7004 Score: 286
Period size: 85 Copynumber: 2.9 Consensus size: 84
6747 CATTGTGAAA
* * *
6757 ACCTTCTAT-ATTGAGGCTTCAATTTTTTTTCATTCTCACTTTTTACCTTTATAATTAAGACCTC
1 ACCTT-TATAATTGAGGCTT-AA-TTTTTTT-AATCTCACTTTTTACCTTTATAATTGAGGCCTC
*
6821 TAATTTTGTTCAGTCTCACTTTCT
62 TAATTTT-TTCAATCTCACTTTCT
* * * *
6845 ACCTTTCTAATTGATGCATTAGTTTTTTTAATCTCACTTTTTACC-TTATAAATGAGGCCTCTAA
1 ACCTTTATAATTGAGGC-TTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCTCTAA
6909 TTTTTTCAATCTCACTCTT-T
65 TTTTTTCAATCTCACT-TTCT
* * * *
6929 ACCTTTATAATTGAGGTCTCTAATTTTTTCAATCTCACCTTTTACCTTTATAATTGAGGCCCCCA
1 ACCTTTATAATTGAGG-CT-TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCTCTA
6994 ATTTTTTCAAT
64 ATTTTTTCAAT
7005 TCCATAAAAT
Statistics
Matches: 138, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
84 27 0.20
85 46 0.33
86 41 0.30
87 9 0.07
88 13 0.09
89 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.48
Consensus pattern (84 bp):
ACCTTTATAATTGAGGCTTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCTCTAAT
TTTTTCAATCTCACTTTCT
Found at i:10268 original size:63 final size:64
Alignment explanation
Indices: 10201--10346 Score: 192
Period size: 65 Copynumber: 2.3 Consensus size: 64
10191 TATCCTTTGC
*
10201 TGTGAAGTTGAA-AT-TGAC-TCTGAAACT-GGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTC
1 TGTGAAGTTGAACATGTG-CGTCTGAAACTGGGGAA-TT-TTTGTTGACAACCAGCGGCCCCTTC
10262 GT
63 GT
* *
10264 TGTGAAGTTGAACCTGTGCTGTCTTAAACTGGGGAATTTTTGTTGACAACCAGCGGCCCCTTCGT
1 TGTGAAGTTGAACATGTGC-GTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCCCCTTCGT
*
10329 TGTGAAGTTGAACTTGTG
1 TGTGAAGTTGAACATGTG
10347 TTGTCTTGAG
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
63 12 0.16
64 2 0.03
65 45 0.61
66 10 0.14
67 5 0.07
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (64 bp):
TGTGAAGTTGAACATGTGCGTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCCCCTTCGT
Found at i:10317 original size:65 final size:66
Alignment explanation
Indices: 10223--10353 Score: 212
Period size: 65 Copynumber: 2.0 Consensus size: 66
10213 ATTGACTCTG
*
10223 AAACTGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACCTGTGCTGTCT
1 AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACCTGTGCTGTCT
10288 T
66 T
* *
10289 AAACTGGGGAA-TT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAACT-GGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACCTGTGCTGTC
10352 TT
65 TT
10354 GAGTCCAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
65 49 0.80
66 7 0.11
67 5 0.08
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (66 bp):
AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACCTGTGCTGTCT
T
Found at i:10575 original size:65 final size:65
Alignment explanation
Indices: 10365--10587 Score: 319
Period size: 64 Copynumber: 3.5 Consensus size: 65
10355 AGTCCAATAT
* * * * * *
10365 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATT-TTTGTTGACAACCAGCGGC
10427 C
65 C
* *
10428 CCTTCGTTGTGAAGTTGAACTTGTGATGTCTTAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
* *
10492 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
10557 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
10588 TGAATTCCAA
Statistics
Matches: 145, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
63 21 0.14
64 60 0.41
65 52 0.36
66 12 0.08
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
Found at i:11562 original size:18 final size:18
Alignment explanation
Indices: 11535--11570 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11525 TGTTGAATCC
* *
11535 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
11553 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
11571 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:12012 original size:22 final size:22
Alignment explanation
Indices: 11986--12034 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
11976 TTGTGTTTGG
* *
11986 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
12008 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
12030 TCAAA
1 TCAAA
12035 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:12041 original size:22 final size:22
Alignment explanation
Indices: 11998--12041 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11988 AAAGGTTTGG
* * *
11998 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
12020 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
12042 TGGGTAGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:12705 original size:16 final size:14
Alignment explanation
Indices: 12659--12708 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
12649 TTCTTTTTGA
12659 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
* *
12673 ATTTTGTTTCCTTCT
1 TTTTTG-TTCTTTCT
12688 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
12704 TTTTT
1 TTTTT
12709 TGATTTTTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 5 0.17
15 15 0.52
16 9 0.31
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:13924 original size:8 final size:7
Alignment explanation
Indices: 13893--13926 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
13883 TGAAATGTAT
13893 ATGCAAA
1 ATGCAAA
13900 ATGCAAA
1 ATGCAAA
*
13907 ATGTAAA
1 ATGCAAA
13914 ATGCAAAA
1 ATGC-AAA
13922 ATGCA
1 ATGCA
13927 TGAAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.18
Consensus pattern (7 bp):
ATGCAAA
Found at i:29829 original size:2 final size:2
Alignment explanation
Indices: 29822--29852 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29812 TTATTCCGTG
29822 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 T
29853 GTTTTTACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36576 original size:13 final size:13
Alignment explanation
Indices: 36558--36585 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36548 GGGGAGCCGT
36558 CTGATTTGATAAA
1 CTGATTTGATAAA
36571 CTGATTTGATAAA
1 CTGATTTGATAAA
36584 CT
1 CT
36586 TTTACCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (13 bp):
CTGATTTGATAAA
Found at i:37486 original size:2 final size:2
Alignment explanation
Indices: 37481--37569 Score: 162
Period size: 2 Copynumber: 45.0 Consensus size: 2
37471 CTCATTTTTT
*
37481 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37523 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37564 TA TA TA
1 TA TA TA
37570 GTTTTGAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 83 0.99
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37768 original size:36 final size:35
Alignment explanation
Indices: 37555--38009 Score: 197
Period size: 35 Copynumber: 12.9 Consensus size: 35
37545 ATATATATAT
37555 ATATATATATATATAGTTTTGAAAACATATTTAAAA
1 ATATATATATATATAGTTTTGAAAACAT-TTTAAAA
* * *
37591 CAT-T-TATATATATAGTTTTTAAAACACTTTGAAA
1 -ATATATATATATATAGTTTTGAAAACATTTTAAAA
* * *
37625 ATAAATATAATATATAGTTTTTAAAACGTTTTTAAAA
1 ATATATAT-ATATATAGTTTTGAAAAC-ATTTTAAAA
* ** * *
37662 AAATATAT-TATACGGTTTTAAAAAACATTTTTAAA
1 ATATATATATATATAGTTTT-GAAAACATTTTAAAA
*
37697 ATA-A-ATATA-AT--TTTTAAAAAGAAACATTTTGAAAA
1 ATATATATATATATAGTTTT---GA-AAACATTTT-AAAA
*
37732 CATATATATATATATAGTTTTGAAATCATTTTAAAA
1 -ATATATATATATATAGTTTTGAAAACATTTTAAAA
* * **
37768 CT-TATA-ATATATAGTTTTAAAAAAACATTTT--TG
1 ATATATATATATATAGTTTT--GAAAACATTTTAAAA
* *
37801 A-A-A-CTATATA-A-TTTTGAAAACGTTTTTAAAAA
1 ATATATATATATATAGTTTTGAAAAC-ATTTT-AAAA
* *
37833 ATATATATAATATATAATTTT-AAAATACTTTTGAAAA
1 ATATATAT-ATATATAGTTTTGAAAACA-TTTT-AAAA
* **
37870 TATATAATATAATATATAGTTTTAAAAAAACATTTT-TGA
1 -ATAT-ATAT-ATATATAGTTTT--GAAAACATTTTAAAA
* *
37909 A-A-A-CTATATA-A-TTTTGAAAACGTTTTTAAAAA
1 ATATATATATATATAGTTTTGAAAAC-ATTTT-AAAA
* * *
37941 ATATATATAATATATAATTTT-AAAATACTTTTGAAA
1 ATATATAT-ATATATAGTTTTGAAAACA-TTTTAAAA
*
37977 ATATATAT-TATATAGTTTGTAGAAAATATTTTA
1 ATATATATATATATAGTTT-T-GAAAACATTTTA
38010 TATTATTATT
Statistics
Matches: 320, Mismatches: 49, Indels: 99
0.68 0.10 0.21
Matches are distributed among these distances:
28 5 0.02
29 9 0.03
30 8 0.03
31 9 0.03
32 10 0.03
33 27 0.08
34 34 0.11
35 59 0.18
36 56 0.17
37 52 0.16
38 19 0.06
39 19 0.06
41 8 0.03
42 5 0.02
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (35 bp):
ATATATATATATATAGTTTTGAAAACATTTTAAAA
Found at i:37853 original size:38 final size:37
Alignment explanation
Indices: 37805--37984 Score: 144
Period size: 38 Copynumber: 4.9 Consensus size: 37
37795 TTTTTGAAAC
*
37805 TATATAATTTTGAAAACGTTTTTAAAAAATATATATAA
1 TATATAATTTTAAAAAC-TTTTTAAAAAATATATATAA
* *
37843 TATATAATTTTAAAATACTTTTGAAAATATATAATATAA
1 TATATAATTTTAAAA-ACTTTTTAAAAAATAT-ATATAA
* * *
37882 TATATAGTTTTAAAAAAACATTTTT------GA-A-A-AC
1 TATATAATTTT--AAAAAC-TTTTTAAAAAATATATATAA
*
37913 TATATAATTTTGAAAACGTTTTTAAAAAATATATATAA
1 TATATAATTTTAAAAAC-TTTTTAAAAAATATATATAA
* *
37951 TATATAATTTTAAAATACTTTTGAAAATATATAT
1 TATATAATTTTAAAA-ACTTTTTAAAAAATATAT
37985 TATATAGTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
29 10 0.09
31 11 0.10
32 1 0.01
33 1 0.01
35 2 0.02
36 1 0.01
37 1 0.01
38 55 0.49
39 20 0.18
40 2 0.02
41 8 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATAATTTTAAAAACTTTTTAAAAAATATATATAA
Found at i:37896 original size:107 final size:108
Alignment explanation
Indices: 37770--37988 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 108
37760 TTTTAAAACT
37770 TATAATATATAGTTTTAAAAAAACATTTTTG-AAACTATATAATTTTGAAAACGTTTTTAAAAAA
1 TATAATATATAGTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAACGTTTTTAAAAAA
37834 TATATATAATATATAATTTTAAAATACTTTTGAAAATATATAA
66 TATATATAATATATAATTTTAAAATACTTTTGAAAATATATAA
37877 TATAATATATAGTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAACGTTTTTAAAAAA
1 TATAATATATAGTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAACGTTTTTAAAAAA
*
37942 TATATATAATATATAATTTTAAAATACTTTTGAAAATATATAT
66 TATATATAATATATAATTTTAAAATACTTTTGAAAATATATAA
37985 TATA
1 TATA
37989 TAGTTTGTAG
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 31 0.28
108 79 0.72
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (108 bp):
TATAATATATAGTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAACGTTTTTAAAAAA
TATATATAATATATAATTTTAAAATACTTTTGAAAATATATAA
Found at i:38046 original size:14 final size:14
Alignment explanation
Indices: 38027--38071 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
38017 ATTATCGTTG
38027 TTATTTATTTTTAT
1 TTATTTATTTTTAT
38041 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
38055 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
38070 TT
1 TT
38072 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:41212 original size:19 final size:19
Alignment explanation
Indices: 41188--41233 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
41178 ATTTAGACAT
41188 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
41207 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
41226 TTTGCATT
1 TTTGCATT
41234 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:44758 original size:84 final size:84
Alignment explanation
Indices: 44615--45234 Score: 695
Period size: 84 Copynumber: 7.5 Consensus size: 84
44605 TTTTAAATAA
* *
44615 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
*
44680 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * *
44699 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
*
44764 ACGCTCAGCT-CAACGACAC
66 ACGCTCAGCTCCAA-GGCAC
* * * ** *
44783 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT-GC--C-AAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
* * *
44844 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* *
44864 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
*
44929 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * * *
44948 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAATAAAAGACCTTTGACTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
45013 ACGCTCAGCT-CAACGGCAC
66 ACGCTCAGCTCCAA-GGCAC
* * * ** * *
45032 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT-GC--C-AAAGACCCCCGAGTTTGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
* * *
45093 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* * * * * * *
45113 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTG-ACCAAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-GCAACAAAAGACCTTCGAGTTCGAC
45177 TACGCTCAGCTCCAAGGCAC
65 TACGCTCAGCTCCAAGGCAC
* * *
45197 ATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
45235 TCCAAAGGCT
Statistics
Matches: 437, Mismatches: 84, Indels: 30
0.79 0.15 0.05
Matches are distributed among these distances:
80 45 0.10
81 77 0.18
82 3 0.01
83 11 0.03
84 253 0.58
85 48 0.11
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:44915 original size:165 final size:164
Alignment explanation
Indices: 44615--45239 Score: 639
Period size: 165 Copynumber: 3.8 Consensus size: 164
44605 TTTTAAATAA
44615 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCTTCGAGTTCGACT
* * * * * *
44680 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
62 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
*
44745 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACAC
127 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GACAC
* * * ** * *
44783 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGC
* * *
44848 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGC-TCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* *
44913 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
130 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACAC
* * * * * * *
44948 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAATAAAAGACCTTTGACTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GC---CAAAGACCTTCGAGTTCGACT
* * * *
45013 ACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-A
62 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
** * * * * * *
45074 AAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCAC
127 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGACAC
* * * * * *
45113 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA--TCTG-CC-AAAGACCTTCGAGTTCGACT
* * * * *
45178 ACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTCCAA
62 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
45240 AGGCTCCCGA
Statistics
Matches: 384, Mismatches: 59, Indels: 28
0.82 0.13 0.06
Matches are distributed among these distances:
164 51 0.13
165 220 0.57
166 7 0.02
167 4 0.01
168 80 0.21
169 22 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA
CCTTCGAGTTCGACTACGCTCAGCTCCAAGACAC
Found at i:45053 original size:249 final size:249
Alignment explanation
Indices: 44615--45228 Score: 1050
Period size: 249 Copynumber: 2.5 Consensus size: 249
44605 TTTTAAATAA
44615 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
44680 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
* *
44745 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAG
131 AAGACCTTTGACTTCAACTACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAG
44810 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
196 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
44864 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
44929 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAATAA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
*
44994 AAGACCTTTGACTTCAACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
131 AAGACCTTTGACTTCAACTACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAG
*
45059 AAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCAC
196 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * ** *
45113 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTG-TGACCAAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
* * * * *
45177 TACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGG
65 TACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGG
45229 CTATCTTCCA
Statistics
Matches: 346, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
248 3 0.01
249 343 0.99
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (249 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
AAGACCTTTGACTTCAACTACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:45309 original size:165 final size:165
Alignment explanation
Indices: 44859--45317 Score: 483
Period size: 165 Copynumber: 2.8 Consensus size: 165
44849 CAGCTTCGAG
* * * **
44859 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTT
* * * * * * * * * * *** * * *
44924 CGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTG-
62 CGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGCTATTTGT
**
44987 GCAATAAAAGACCTTTGACTTCAACTACGCTCAGCTCAAC
127 G-ACCAAAAGACCTTTGACTTCAACTACGCTCAGCTCAAC
* * *
45027 GGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGAT
1 GGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
* * ** *
45092 TACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACC
66 TACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGCTATTTGTGACC
* *
45157 AAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-
131 AAAAGACCTTTGACTTCAACTACGCTCAGCT-CAAC
* * *
45192 GGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTCCAAAGGCTCCCGAGTTCGAT
1 GGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
* * * *
45257 TACACTCAACTTCGAGGTCATATCATTTACAACATAGCTCATGGAAAGAAGGGCTATTTGT
66 TACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGCTATTTGT
45318 CAATAAAATT
Statistics
Matches: 252, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
164 26 0.10
165 181 0.72
166 4 0.02
168 41 0.16
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
GGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
TACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGCTATTTGTGACC
AAAAGACCTTTGACTTCAACTACGCTCAGCTCAAC
Found at i:45879 original size:2 final size:2
Alignment explanation
Indices: 45872--45912 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
45862 CGTCTCATTT
45872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45913 GTTTTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:45986 original size:36 final size:36
Alignment explanation
Indices: 45899--46053 Score: 127
Period size: 36 Copynumber: 4.2 Consensus size: 36
45889 ATATATATAT
* **
45899 ATATATATAATATAGTTTTGAAAACA-TATTTAAAACATTT
1 ATATA-AT-ATATAGTTTTTAAAACACT-TTT-AAA-ATAA
* *
45939 ATATATTATATAGTTTTTAAAACACTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACACTTTTAAAATAA
*
45975 ATATAATATATAGTTTTTAAAAC-GTTTTAAAA-AA
1 ATATAATATATAGTTTTTAAAACACTTTTAAAATAA
* ** * *
46009 TATATATTATACGGTTTTAAAAAACATTTTTAAAATAA
1 -ATATAATATATAGTTTT-TAAAACACTTTTAAAATAA
46047 ATATAAT
1 ATATAAT
46054 TTTTAAAAAG
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
34 2 0.02
35 21 0.22
36 29 0.30
37 17 0.18
38 20 0.21
39 2 0.02
40 5 0.05
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACACTTTTAAAATAA
Found at i:46026 original size:35 final size:37
Alignment explanation
Indices: 45899--46051 Score: 127
Period size: 38 Copynumber: 4.2 Consensus size: 37
45889 ATATATATAT
* * * *
45899 ATATATATAATATAGTTTTGAAAACA-TATTTAAAACA
1 ATATATATTATATAGTTTTTAAAACACT-TTGAAAATA
*
45936 TTTATATATTATATAGTTTTTAAAACACTTTGAAAATA
1 -ATATATATTATATAGTTTTTAAAACACTTTGAAAATA
* * *
45974 A-ATATAATATATAGTTTTTAAAAC-GTTTTAAAA-A
1 ATATATATTATATAGTTTTTAAAACACTTTGAAAATA
** * * *
46008 ATATATATTATACGGTTTTAAAAAACATTTTTAAAATA
1 ATATATATTATATAGTTTT-TAAAACACTTTGAAAATA
46046 A-ATATA
1 ATATATA
46052 ATTTTTAAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
34 2 0.02
35 21 0.22
36 27 0.28
37 13 0.14
38 32 0.33
39 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (37 bp):
ATATATATTATATAGTTTTTAAAACACTTTGAAAATA
Found at i:46044 original size:72 final size:75
Alignment explanation
Indices: 45899--46053 Score: 192
Period size: 72 Copynumber: 2.1 Consensus size: 75
45889 ATATATATAT
* * *
45899 ATATATATAATATAGTTTTGAAAACATATTTAAAACATTTATATATTATATAGTTTTTAAAACAC
1 ATATA-ATAATATAGTTTTGAAAACATATTTAAAACATATATATATTATACAGTTTTAAAAACAC
45964 TTTGAAAATAA
65 TTTGAAAATAA
* * * *
45975 ATATAAT-ATATAGTTTTTAAAACGT-TTTAAAA-A-ATATATATTATACGGTTTTAAAAAACAT
1 ATATAATAATATAGTTTTGAAAACATATTTAAAACATATATATATTATACAGTTTT-AAAAACAC
*
46036 TTTTAAAATAA
65 TTTGAAAATAA
46047 ATATAAT
1 ATATAAT
46054 TTTTAAAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
71 16 0.23
72 24 0.34
73 7 0.10
74 16 0.23
75 2 0.03
76 5 0.07
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (75 bp):
ATATAATAATATAGTTTTGAAAACATATTTAAAACATATATATATTATACAGTTTTAAAAACACT
TTGAAAATAA
Found at i:46099 original size:108 final size:106
Alignment explanation
Indices: 45958--46169 Score: 259
Period size: 108 Copynumber: 2.0 Consensus size: 106
45948 ATAGTTTTTA
* * * *
45958 AAACACTTTGAAAATAAATATAATATATAGTTTTTAAAACGTTTTAAAAAATATATATTATACGG
1 AAACACTTTGAAAATAAATATAATATATAGTTTTGAAAACATTTTAAAAAAT-TATAATATACAG
*
46023 TTTT-AAAAAACATTTTT-AAAA-TAAATATAATTTTTAAAAAG
65 TTTTAAAAAAACATTTTTGAAAACT--ATATAATTTTGAAAAAG
* * * * * *
46064 AAACATTTTGAAAACATATATATATTATATAGTTTTGAAATCATTTTAAAAACTTATAATATATA
1 AAACACTTTG-AAA-ATAAATATAATATATAGTTTTGAAAACATTTTAAAAAATTATAATATACA
46129 GTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAA
64 GTTTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAA
46170 CGTTTTTAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
106 9 0.10
107 16 0.18
108 60 0.67
109 4 0.04
110 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (106 bp):
AAACACTTTGAAAATAAATATAATATATAGTTTTGAAAACATTTTAAAAAATTATAATATACAGT
TTTAAAAAAACATTTTTGAAAACTATATAATTTTGAAAAAG
Found at i:46109 original size:38 final size:35
Alignment explanation
Indices: 45898--46161 Score: 120
Period size: 36 Copynumber: 7.2 Consensus size: 35
45888 TATATATATA
45898 TATATATATAATATAGTTTT-GAAAACATATTT-AAAAC
1 TATATA-AT-ATATAGTTTTAG-AAACAT-TTTGAAAAC
* *
45935 ATTTATATATTATATAGTTTTTA-AAACACTTTGAAAA-
1 ---TATATAATATATAG-TTTTAGAAACATTTTGAAAAC
* * *
45972 TAAATATAATATATAGTTTTTA-AAACGTTTTAAAAAA
1 T--ATATAATATATAG-TTTTAGAAACATTTTGAAAAC
* ** * *
46009 TATATATTATACGGTTTTAAAAAACATTTT-TAAA-
1 TATATAATATATAGTTTT-AGAAACATTTTGAAAAC
*
46043 -ATA-AATATA-ATTTTTAAAAAGAAACATTTTGAAAAC
1 TATATAATATATAGTTTT----AGAAACATTTTGAAAAC
*
46079 ATATATATATTATATAGTTTT-GAAATCATTTTAAAAAC
1 -TATATA-A-TATATAGTTTTAGAAA-CATTTTGAAAAC
*
46117 T-TATAATATATAGTTTTAAAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTT--AGAAACA-TTTTGAAAAC
46154 TATATAAT
1 TATATAAT
46162 TTTGAAAACG
Statistics
Matches: 179, Mismatches: 20, Indels: 52
0.71 0.08 0.21
Matches are distributed among these distances:
31 4 0.02
32 5 0.03
33 3 0.02
34 27 0.15
35 18 0.10
36 43 0.24
37 22 0.12
38 35 0.20
39 6 0.03
40 7 0.04
41 4 0.02
42 5 0.03
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (35 bp):
TATATAATATATAGTTTTAGAAACATTTTGAAAAC
Found at i:46287 original size:14 final size:14
Alignment explanation
Indices: 46268--46312 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
46258 ATTATCGTTG
46268 TTATTTATTTTTAT
1 TTATTTATTTTTAT
46282 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
46296 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
46311 TT
1 TT
46313 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:48155 original size:23 final size:24
Alignment explanation
Indices: 48129--48213 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 24
48119 GTGTTTGTGT
48129 TGTTCGTTTAT-TGT-ATTCGTTTA
1 TGTTCGTTTATGT-TCATTCGTTTA
*
48152 TGTTCGCTTATGTTCATT--TATTA
1 TGTTCGTTTATGTTCATTCGT-TTA
* *
48175 TGTTCGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCATTCGTTTA
48199 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
48214 GTTTATCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 1 0.02
23 30 0.57
24 21 0.40
25 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.59
Consensus pattern (24 bp):
TGTTCGTTTATGTTCATTCGTTTA
Found at i:48185 original size:10 final size:10
Alignment explanation
Indices: 48129--48219 Score: 65
Period size: 10 Copynumber: 8.1 Consensus size: 10
48119 GTGTTTGTGT
48129 TGTTCGTTTA
1 TGTTCGTTTA
48139 TTGTATTCGTTTA
1 -TG--TTCGTTTA
*
48152 TGTTCGCTTA
1 TGTTCGTTTA
*
48162 TGTTCATTTATTA
1 TGTTC--GT-TTA
48175 TGTTCGTTTA
1 TGTTCGTTTA
*
48185 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
48199 TGTTCGTTTA
1 TGTTCGTTTA
48209 TGTTCGTTTA
1 TGTTCGTTTA
48219 T
1 T
48220 CATTTAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
10 34 0.52
11 4 0.06
12 2 0.03
13 17 0.26
14 8 0.12
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:48195 original size:14 final size:14
Alignment explanation
Indices: 48176--48216 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
48166 CATTTATTAT
48176 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
48190 GTTCG-TT-TG-T-
1 GTTCGTTTATGTTC
48200 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
48214 GTT
1 GTT
48217 TATCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 5 0.22
11 3 0.13
12 4 0.17
13 3 0.13
14 8 0.35
ACGTcount: A:0.05, C:0.12, G:0.24, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:48206 original size:24 final size:24
Alignment explanation
Indices: 48144--48216 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
48134 GTTTATTGTA
* *
48144 TTCGTTTATGTTCGCTTATGTTCA
1 TTCGTTTATGTTCGTTTATGTTCG
48168 TT--TATTATGTTCGTTTATGTTCG
1 TTCGT-TTATGTTCGTTTATGTTCG
*
48191 TTCGTTTGTGTTCGTTTATGTTCG
1 TTCGTTTATGTTCGTTTATGTTCG
48215 TT
1 TT
48217 TATCATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 19 0.44
24 22 0.51
25 1 0.02
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (24 bp):
TTCGTTTATGTTCGTTTATGTTCG
Found at i:48673 original size:23 final size:21
Alignment explanation
Indices: 48640--48682 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
48630 TTTGATGTAC
48640 TTATTATTAAT-ATA-TATATA
1 TTATTATTAATAATATTA-ATA
48660 TTATTATTAATAATATTAATA
1 TTATTATTAATAATATTAATA
48681 TT
1 TT
48683 TATATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 8 0.38
22 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTAATAATATTAATA
Found at i:48716 original size:15 final size:14
Alignment explanation
Indices: 48681--48712 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
48671 AATATTAATA
48681 TTTATATGTTATTT
1 TTTATATGTTATTT
48695 TTTATATGTTATTT
1 TTTATATGTTATTT
48709 TTTA
1 TTTA
48713 ATATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTATATGTTATTT
Found at i:49399 original size:15 final size:15
Alignment explanation
Indices: 49379--49423 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
49369 TTGATGTACT
49379 TATTATTAATATATA
1 TATTATTAATATATA
49394 TATTATT-AT-TA-A
1 TATTATTAATATATA
* *
49406 TAATATTAATATTTA
1 TATTATTAATATATA
49421 TAT
1 TAT
49424 GTTATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 3 0.12
15 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTAATATATA
Found at i:49401 original size:18 final size:17
Alignment explanation
Indices: 49378--49411 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
49368 TTTGATGTAC
49378 TTATTATTAATATATATA
1 TTATTATTAATA-ATATA
49396 TTATTATTAATAATAT
1 TTATTATTAATAATAT
49412 TAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTATTAATAATATA
Found at i:49699 original size:20 final size:20
Alignment explanation
Indices: 49671--49715 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
49661 ATTCGAACTT
49671 AAAAATCATGT-AATTTTTA
1 AAAAATCATGTAAATTTTTA
49690 AAAAATTCATGTAAATTTTTA
1 AAAAA-TCATGTAAATTTTTA
49711 AAAAA
1 AAAAA
49716 ATTACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAATCATGTAAATTTTTA
Found at i:50646 original size:3 final size:3
Alignment explanation
Indices: 50638--50709 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
50628 TTTTGTTTTT
50638 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50686 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
50710 GTTGAAAACA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:58461 original size:17 final size:19
Alignment explanation
Indices: 58439--58484 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
58429 CTTTCACATA
58439 AATTAAATG-ATGAA-TTG
1 AATTAAATGAATGAAGTTG
58456 AATT-AATGAATGAAGTTG
1 AATTAAATGAATGAAGTTG
*
58474 -ATTAATTGAAT
1 AATTAAATGAAT
58485 TAGTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (19 bp):
AATTAAATGAATGAAGTTG
Found at i:65838 original size:10 final size:10
Alignment explanation
Indices: 65823--65853 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
65813 GACCAGGGAT
65823 GGACGGGAGG
1 GGACGGGAGG
65833 GGACGGGAGG
1 GGACGGGAGG
65843 GGACGGGAGG
1 GGACGGGAGG
65853 G
1 G
65854 AACAGTAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.71, T:0.00
Consensus pattern (10 bp):
GGACGGGAGG
Found at i:72081 original size:30 final size:30
Alignment explanation
Indices: 71840--72064 Score: 387
Period size: 30 Copynumber: 7.4 Consensus size: 30
71830 TCCGAAGGAC
* *
71840 CTATCCAGAGGTCATAAAAAAATCCTCGATAA
1 CTATCCAGAGGTCAT--AAAGATCCTCGGTAA
* *
71872 CTATCCAGAGGTCATACAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71902 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71932 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71962 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71992 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
72022 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
72052 CTATCCATAGGTC
1 CTATCCAGAGGTC
72065 CCGAAGAACC
Statistics
Matches: 186, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
30 171 0.92
32 15 0.08
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:72104 original size:31 final size:31
Alignment explanation
Indices: 72050--72126 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
72040 GATCCTCGGT
* *
72050 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
72081 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* *
72112 TACTGTCCATATGTC
1 AACTATCCATATGTC
72127 TCAAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:72592 original size:2 final size:2
Alignment explanation
Indices: 72580--72657 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
72570 TACACAACTC
72580 AT AT A- 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
72621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72658 CTGTAACATG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73252 original size:21 final size:21
Alignment explanation
Indices: 73228--73270 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
73218 TCATATTCGT
* *
73228 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
73249 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
73270 T
1 T
73271 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:74912 original size:24 final size:20
Alignment explanation
Indices: 74863--74920 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
74853 TTCCCATTGA
*
74863 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
74883 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
74906 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
74921 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:77572 original size:22 final size:22
Alignment explanation
Indices: 77547--77595 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
77537 GATCGTGGCC
77547 GCGGGCGCTATTGGACGCCATT
1 GCGGGCGCTATTGGACGCCATT
*
77569 GCGGGCGCTATTGGACGCTATT
1 GCGGGCGCTATTGGACGCCATT
77591 GCGGG
1 GCGGG
77596 TGTAGTGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.41, T:0.22
Consensus pattern (22 bp):
GCGGGCGCTATTGGACGCCATT
Found at i:78746 original size:20 final size:20
Alignment explanation
Indices: 78710--78747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
78700 AGAAGTTGCA
*
78710 TATAGATGGAAACATTAATG
1 TATAGATGGAAAAATTAATG
78730 TATAGAT-GATAAAATTAA
1 TATAGATGGA-AAAATTAA
78748 AATTGTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.32
Consensus pattern (20 bp):
TATAGATGGAAAAATTAATG
Found at i:81309 original size:27 final size:27
Alignment explanation
Indices: 81279--81332 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
81269 TTATATTCTA
*
81279 TTTTGAAATTATTAATAAACATATTTT
1 TTTTCAAATTATTAATAAACATATTTT
* *
81306 TTTTCAAATTTTTAATAAATATATTTT
1 TTTTCAAATTATTAATAAACATATTTT
81333 AAATATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTCAAATTATTAATAAACATATTTT
Found at i:81379 original size:19 final size:21
Alignment explanation
Indices: 81331--81392 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 21
81321 TAAATATATT
81331 TTAAATATATTAACAATTAATA
1 TTAAA-ATATTAACAATTAATA
*
81353 -T-AATTATTAA-AA-TAATA
1 TTAAAATATTAACAATTAATA
81370 TTAAAATATT-AC--TTAATA
1 TTAAAATATTAACAATTAATA
81388 TTAAA
1 TTAAA
81393 TACATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
19 12 0.35
20 2 0.06
21 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATATTAACAATTAATA
Found at i:86296 original size:93 final size:93
Alignment explanation
Indices: 86137--86327 Score: 382
Period size: 93 Copynumber: 2.1 Consensus size: 93
86127 AAAGTTGGAT
86137 GATGAGGTAATGAAAAAGGATAACTCTGGTGGTTACACTGCTGCAGATGTATGTAAGAAAGAAGG
1 GATGAGGTAATGAAAAAGGATAACTCTGGTGGTTACACTGCTGCAGATGTATGTAAGAAAGAAGG
86202 CGAACAGAAAGCAAATGCCCCTCCTGAA
66 CGAACAGAAAGCAAATGCCCCTCCTGAA
86230 GATGAGGTAATGAAAAAGGATAACTCTGGTGGTTACACTGCTGCAGATGTATGTAAGAAAGAAGG
1 GATGAGGTAATGAAAAAGGATAACTCTGGTGGTTACACTGCTGCAGATGTATGTAAGAAAGAAGG
86295 CGAACAGAAAGCAAATGCCCCTCCTGAA
66 CGAACAGAAAGCAAATGCCCCTCCTGAA
86323 GATGA
1 GATGA
86328 TGTCCTGATC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (93 bp):
GATGAGGTAATGAAAAAGGATAACTCTGGTGGTTACACTGCTGCAGATGTATGTAAGAAAGAAGG
CGAACAGAAAGCAAATGCCCCTCCTGAA
Found at i:89622 original size:24 final size:24
Alignment explanation
Indices: 89595--89650 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
89585 TGAACATTCG
*
89595 GTTATGTTCGTTTATATGCGTTTA
1 GTTATGTTCGTTTATATGCGTTCA
*
89619 GTTATGTTCGTTTATGTGCGTTCA
1 GTTATGTTCGTTTATATGCGTTCA
*
89643 TTTATGTT
1 GTTATGTT
89651 TAACCTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.09, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATATGCGTTCA
Found at i:91184 original size:16 final size:16
Alignment explanation
Indices: 91163--91229 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
91153 GTCTCCAACG
91163 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
91179 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
91195 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
91211 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
91225 TTTAT
1 TTTAT
91230 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:91202 original size:32 final size:32
Alignment explanation
Indices: 91161--91221 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
91151 GGGTCTCCAA
91161 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
* *
91193 CGTTTATGTTTGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
91222 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:91312 original size:16 final size:16
Alignment explanation
Indices: 91291--91322 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
91281 AAAAAAAATT
91291 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
91307 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
91323 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:98089 original size:28 final size:31
Alignment explanation
Indices: 98032--98089 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 31
98022 TATGTTTACT
*
98032 TAAACTATTACTTTTGTTTCATTTTGATACC
1 TAAACTATTACTTTTGTTTCATATTGATACC
98063 TAAACT-TTA-TTTT-TTTCAATATT-ATAC
1 TAAACTATTACTTTTGTTTC-ATATTGATAC
98090 ATATCATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 8 0.32
29 8 0.32
30 3 0.12
31 6 0.24
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.53
Consensus pattern (31 bp):
TAAACTATTACTTTTGTTTCATATTGATACC
Found at i:98606 original size:23 final size:25
Alignment explanation
Indices: 98557--98606 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
98547 ATTAGCGTTT
*
98557 GATATTTCTTCATTTTCTTTAAATAGA
1 GATATTTCTTCATTTTCATT--ATAGA
98584 GATATTTCTTCATTTT-ATT-TAGA
1 GATATTTCTTCATTTTCATTATAGA
98607 ATTAATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
26 2 0.09
27 16 0.73
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
GATATTTCTTCATTTTCATTATAGA
Found at i:100803 original size:22 final size:21
Alignment explanation
Indices: 100776--100836 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
100766 GGTTAACTAG
100776 TTTTAGGAAAATATTATTATT
1 TTTTAGGAAAATATTATTATT
*
100797 ATTTTAGAAAAATATGTATTATT
1 -TTTTAGGAAAATAT-TATTATT
*
100820 TTATTAGGGAAATATTA
1 TT-TTAGGAAAATATTA
100837 AAGACAGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (21 bp):
TTTTAGGAAAATATTATTATT
Found at i:101779 original size:18 final size:18
Alignment explanation
Indices: 101756--101796 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
101746 AACTAGCAGC
101756 AAACCAAGAAACTATTCT
1 AAACCAAGAAACTATTCT
101774 AAACCAAGAAACTATTCT
1 AAACCAAGAAACTATTCT
101792 AAACC
1 AAACC
101797 GAGCAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (18 bp):
AAACCAAGAAACTATTCT
Found at i:112638 original size:22 final size:22
Alignment explanation
Indices: 112610--112652 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
112600 TAAAAAACTC
*
112610 AAAAAAAAATCAAATCTTTAAA
1 AAAAAAAAATCAAAACTTTAAA
**
112632 AAAAAAATCTCAAAACTTTAA
1 AAAAAAAAATCAAAACTTTAA
112653 TAATCCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAAAAATCAAAACTTTAAA
Found at i:113465 original size:14 final size:14
Alignment explanation
Indices: 113448--113479 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
113438 AAAATTAAAA
113448 TAAAAAAATACAAT
1 TAAAAAAATACAAT
*
113462 TAAAGAAATACAAT
1 TAAAAAAATACAAT
113476 TAAA
1 TAAA
113480 TTTAGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (14 bp):
TAAAAAAATACAAT
Found at i:116453 original size:21 final size:21
Alignment explanation
Indices: 116424--116477 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
116414 AAATACTTTA
116424 TTATTTCTTTCTCTTCTTCAT
1 TTATTTCTTTCTCTTCTTCAT
* *
116445 TTCTTTC-TTCTTCTTCTTCCT
1 TTATTTCTTTC-TCTTCTTCAT
116466 TTATTT-TTTCTC
1 TTATTTCTTTCTC
116478 CTTTTCTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTCTTTCTCTTCTTCAT
Found at i:116458 original size:18 final size:17
Alignment explanation
Indices: 116426--116460 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
116416 ATACTTTATT
116426 ATTTCTTTCTCTTCTTC
1 ATTTCTTTCTCTTCTTC
116443 ATTTCTTTCTTCTTCTTC
1 ATTTCTTTC-TCTTCTTC
116461 TTCCTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTCTTTCTCTTCTTC
Found at i:116490 original size:21 final size:22
Alignment explanation
Indices: 116430--116492 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
116420 TTTATTATTT
*
116430 CTTTCTCTTCTTCATTTCTTTCTT
1 CTTT-TCTTCTT-ATTTCTTTCTC
116454 CTTCTTCTTCCTTTATTT-TTTCTC
1 CTT-TTCTT-C-TTATTTCTTTCTC
116478 CTTTTCTTCTTATTT
1 CTTTTCTTCTTATTT
116493 ACCCCCAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 6 0.17
22 1 0.03
23 5 0.14
24 15 0.43
25 6 0.17
26 2 0.06
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (22 bp):
CTTTTCTTCTTATTTCTTTCTC
Found at i:117486 original size:7 final size:7
Alignment explanation
Indices: 117469--117509 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
117459 TGAAGAACAT
117469 TTTCTCCG
1 TTTC-CCG
117477 TTTCCCG
1 TTTCCCG
117484 TTTCCCG
1 TTTCCCG
117491 TTTCCCG
1 TTTCCCG
117498 TTTCCCG
1 TTTCCCG
117505 TTTCC
1 TTTCC
117510 GTTAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.00, C:0.41, G:0.12, T:0.46
Consensus pattern (7 bp):
TTTCCCG
Found at i:120760 original size:19 final size:19
Alignment explanation
Indices: 120738--120776 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
120728 TACGTATAAT
120738 TTTAAATAAAAAAATAAAA
1 TTTAAATAAAAAAATAAAA
* **
120757 TTTAGATACTAAAATAAAA
1 TTTAAATAAAAAAATAAAA
120776 T
1 T
120777 AAAAGTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
TTTAAATAAAAAAATAAAA
Done.