Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006672.1 Hibiscus syriacus cultivar Beakdansim tig00016533_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: 72057
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1082 original size:22 final size:22
Alignment explanation
Indices: 1041--1082 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1031 AATCGAACCG
***
1041 ACCGAACCGAACCGTTAAAAAA
1 ACCGAACCGAACCAAAAAAAAA
1063 ACCGAACCGAACCAAAAAAA
1 ACCGAACCGAACCAAAAAAA
1083 CCGGTTTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.29, G:0.12, T:0.05
Consensus pattern (22 bp):
ACCGAACCGAACCAAAAAAAAA
Found at i:5726 original size:66 final size:67
Alignment explanation
Indices: 5620--5751 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 67
5610 TCAGTCAAAC
* *
5620 GTTAACTGCTTACATGGATGAATTGACTGCAATGTTAGAAAATAATTGAAAT-CCTTTGACCGGT
1 GTTAACTGCTTACATGGATGAATTGACTACAACGTTAGAAAATAATTGAAATCCCTTTGACCGGT
5684 GT
66 GT
* * *
5686 GTTAACTGCTTACGTGGATGGATTGACTACCACGTTAGAAAATAATTGAAATCCCTTTGACCGGT
1 GTTAACTGCTTACATGGATGAATTGACTACAACGTTAGAAAATAATTGAAATCCCTTTGACCGGT
5751 G
66 G
5752 CTTGAATATT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
66 47 0.78
67 13 0.22
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (67 bp):
GTTAACTGCTTACATGGATGAATTGACTACAACGTTAGAAAATAATTGAAATCCCTTTGACCGGT
GT
Found at i:6921 original size:3 final size:3
Alignment explanation
Indices: 6913--7288 Score: 119
Period size: 3 Copynumber: 115.0 Consensus size: 3
6903 CCTTTAGTTA
* *
6913 TTC TTC TTC TT- TTC TTC TTC TTTC ATATA GTC TTC TTC TTC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC -T-TC TTC TTC TTC TTC TTC -TTC
* * * * * *
6961 ATATA GTC TTT TTC TTT TTC TTC TTC TTC TTC TTTC ATATA GTC TTC
1 -T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -T-TC TTC TTC
* * * *
7008 TTC TTC TTC TTTC TTC TTC TTTC ATA GTA TTC TTC TTC TTC TTC TTTC
1 TTC TTC TTC -TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC -TTC
* * * * * *
7056 ATATA GTC GTC TTC TTC TTC TTC TTTC ATATA GTC GTC TTC TTC TTC
1 -T-TC TTC TTC TTC TTC TTC TTC -TTC -T-TC TTC TTC TTC TTC TTC
* * * * *
7103 TTC TTTC ATATA GTC GTC TTC TTC TTC TTC TTC TTC TTTC ATAC AGTC
1 TTC -TTC -T-TC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC -TTC
* * * *
7151 GTC TTC TTC TTC TT- TTC ATATA GTC TTC TTC TT- TTC TTC TTTC ATATA
1 TTC TTC TTC TTC TTC TTC -T-TC TTC TTC TTC TTC TTC TTC -TTC -T-TC
* * *
7199 GTC TTC TTC TTTC TTC TTC TTTC ATATA GTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC -TTC TTC TTC -TTC -T-TC TTC TTC TTC TTC -TTC TTC
* * * *
7246 TTC TTTC ATA GTC TTC TTC TTC TTC TTC CTC TTC TTC TTC TTC
1 TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
7289 AACGTCATAT
Statistics
Matches: 281, Mismatches: 65, Indels: 54
0.70 0.16 0.14
Matches are distributed among these distances:
2 6 0.02
3 211 0.75
4 55 0.20
5 9 0.03
ACGTcount: A:0.09, C:0.26, G:0.04, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:6956 original size:24 final size:24
Alignment explanation
Indices: 6920--7131 Score: 186
Period size: 24 Copynumber: 8.7 Consensus size: 24
6910 TTATTCTTCT
6920 TCTT-TTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTTCATATAG
6943 TCTTCTTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTTCATATAG
* * **
6967 TCTTTTTCTTTTTC-TTC-T-TCT
1 TCTTCTTCTTCTTCTTTCATATAG
** **
6988 TCTTCTTTCATATAGTC-TTC-T-TCT
1 TCTTC-TTC-T-TCTTCTTTCATATAG
*
7012 TCTTCTTTCTTCTTCTTTCATAGTAT
1 TCTTC-TTCTTCTTCTTTCATA-TAG
7038 TCTTCTTCTTCTTCTTTCATATAGTCG
1 TCTTCTTCTTCTTCTTTCATATA---G
7065 TCTTCTTCTTCTTCTTTCATATAGTCG
1 TCTTCTTCTTCTTCTTTCATATA---G
7092 TCTTCTTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTTCATATAG
*
7116 TCGTCTTCTTCTTCTT
1 TCTTCTTCTTCTTCTT
7132 CTTCTTCTTT
Statistics
Matches: 166, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
21 5 0.03
22 7 0.04
23 12 0.07
24 69 0.42
25 16 0.10
26 7 0.04
27 50 0.30
ACGTcount: A:0.10, C:0.25, G:0.05, T:0.60
Consensus pattern (24 bp):
TCTTCTTCTTCTTCTTTCATATAG
Found at i:6975 original size:27 final size:27
Alignment explanation
Indices: 6917--7273 Score: 382
Period size: 27 Copynumber: 12.6 Consensus size: 27
6907 TAGTTATTCT
6917 TCTTCTT-TTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
* * **
6943 TCTTCTTCTTCTTCTTTCATATAGTCTTTTTCT
1 TCTTCTTCTTCTTC-TTC-T-T--TC-ATATAG
*
6976 TTTTCTTCTTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
*
7003 TCTTCTTCTTCTTCTTTCTTCTTCTTTCATAG
1 TCTTCTTCTTCTTC-TTC-T-TTC-AT-ATAG
*
7035 TATTCTTCTTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
*
7062 TCGTCTTCTTCTTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
*
7089 TCGTCTTCTTCTTCTTCTTTCATATAGTCG
1 TCTTCTTCTTCTTCTTCTTTCATATA---G
*
7119 TCTTCTTCTTCTTCTTCTTCTTTCATACAG
1 ---TCTTCTTCTTCTTCTTCTTTCATATAG
*
7149 TCGTCTTCTTCTTC-T-TTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
7174 TCTTCTTCTT-TTCTTCTTTCATATAG
1 TCTTCTTCTTCTTCTTCTTTCATATAG
7200 TCTTCTTCTTTCTTCTTCTTTCATATAG
1 TCTTCTTC-TTCTTCTTCTTTCATATAG
*
7228 TCTTCTTCTTCTTTCTTC-TTCTTTCATAG
1 TCTTCTTCTTC-TTCTTCTTTC-AT-ATAG
7257 TCTTCTTCTTCTTCTTC
1 TCTTCTTCTTCTTCTTC
7274 CTCTTCTTCT
Statistics
Matches: 285, Mismatches: 21, Indels: 48
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.01
25 19 0.07
26 26 0.09
27 97 0.34
28 46 0.16
29 20 0.07
30 8 0.03
31 5 0.02
32 22 0.08
33 39 0.14
ACGTcount: A:0.10, C:0.26, G:0.04, T:0.60
Consensus pattern (27 bp):
TCTTCTTCTTCTTCTTCTTTCATATAG
Found at i:6983 original size:36 final size:36
Alignment explanation
Indices: 6943--7053 Score: 172
Period size: 36 Copynumber: 3.1 Consensus size: 36
6933 TTTCATATAG
* *
6943 TCTTCTTCTTCTTCTTTCATATAGTCTTTTTCTTTT
1 TCTTCTTCTTCTTCTTTCATATAGTCTTCTTCTTCT
6979 TCTTCTTCTTCTTCTTTCATATAGTCTTCTTCTTCT
1 TCTTCTTCTTCTTCTTTCATATAGTCTTCTTCTTCT
*
7015 TC-T-TTCTTCTTCTTTCATAGTATTCTTCTTCTTCT
1 TCTTCTTCTTCTTCTTTCATA-TAGTCTTCTTCTTCT
7050 TCTT
1 TCTT
7054 TCATATAGTC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
34 16 0.23
35 17 0.24
36 37 0.53
ACGTcount: A:0.08, C:0.25, G:0.03, T:0.64
Consensus pattern (36 bp):
TCTTCTTCTTCTTCTTTCATATAGTCTTCTTCTTCT
Found at i:7854 original size:196 final size:197
Alignment explanation
Indices: 7518--7905 Score: 690
Period size: 196 Copynumber: 2.0 Consensus size: 197
7508 ATTTTTAAGT
7518 CCTTTAGTTATTTTTATTTTACTTACTTGATATTGTTTTCATTTAACAATAGAATAAAAGGGGAA
1 CCTTTAGTTATTTTTATTTTACTTACTTGATATTGTTTTCATTTAACAATAGAATAAAAGGGGAA
* *
7583 AAAAAGGAGAGGAAGTAATAAATAAGCAATATATATGACTGTGTTACACTGCCTTCTTTAAATTG
66 AAAAAGGAGAGGAAGTAATAAATAAGCAATATATATGACTGTGTTACACTGCCTGCTTTAAATTA
*
7648 CTATCCGATCAAGTCCCAAACTTTGAAAGAAAGAACATAAATTCATACAAAATCCATGGAATGGA
131 CTATCCGATCAAGTCCCAAACTTTG-AAGAAAGAACATAAATTCATACAAAATCCATGAAATGGA
7713 AGA
195 AGA
* *
7716 CCTTTAGTTATTTTTATTTTACTTACTTGATTTTGTTTTCATTTAACAATATAATAAAA-GGG-A
1 CCTTTAGTTATTTTTATTTTACTTACTTGATATTGTTTTCATTTAACAATAGAATAAAAGGGGAA
* *
7779 AAAAAGGAGAGGAAGTAATAAATAAGCAATATATATGGCTGTGTTACACTGCCTGCTTTAAGTTA
66 AAAAAGGAGAGGAAGTAATAAATAAGCAATATATATGACTGTGTTACACTGCCTGCTTTAAATTA
7844 CTATCCGATCAAGTCCCAAACTTTGAAGAAAGAACATAAATTCATACAAAATCCATGAAATG
131 CTATCCGATCAAGTCCCAAACTTTGAAGAAAGAACATAAATTCATACAAAATCCATGAAATG
7906 ATAGAACTTC
Statistics
Matches: 183, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
195 36 0.20
196 87 0.48
197 3 0.02
198 57 0.31
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (197 bp):
CCTTTAGTTATTTTTATTTTACTTACTTGATATTGTTTTCATTTAACAATAGAATAAAAGGGGAA
AAAAAGGAGAGGAAGTAATAAATAAGCAATATATATGACTGTGTTACACTGCCTGCTTTAAATTA
CTATCCGATCAAGTCCCAAACTTTGAAGAAAGAACATAAATTCATACAAAATCCATGAAATGGAA
GA
Found at i:11687 original size:2 final size:2
Alignment explanation
Indices: 11680--11704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11670 TTGATAATTA
11680 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
11705 AAGAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19335 original size:11 final size:11
Alignment explanation
Indices: 19319--19345 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19309 CGGACAGGAT
19319 ACTGTGGATCA
1 ACTGTGGATCA
19330 ACTGTGGATCA
1 ACTGTGGATCA
19341 ACTGT
1 ACTGT
19346 CCTGAGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (11 bp):
ACTGTGGATCA
Found at i:24590 original size:66 final size:63
Alignment explanation
Indices: 24483--24606 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 63
24473 TTTGTTGAAG
* *
24483 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGAACATCGAATACCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATACCATT
24548 A
63 A
* *
24549 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATA
1 GTGCATCGATGCACAAGGAGTGCATCGATGCA-CT-CATTAAAATAAAAACATCGAATA
24607 GGATTTATGC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
64 11 0.21
66 38 0.73
67 2 0.04
68 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATACCATTA
Found at i:25228 original size:22 final size:22
Alignment explanation
Indices: 25199--25290 Score: 138
Period size: 22 Copynumber: 4.4 Consensus size: 22
25189 ATATTAGTCA
25199 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
* *
25221 TTCAGGACGTATCCAGTGGTCA
1 TTCGGGACGTATCCAGTGGTCC
25243 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
25265 TTCGGGAC--AT--AGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
25283 TTCGGGAC
1 TTCGGGAC
25291 AAATATTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.24
20 2 0.03
22 48 0.73
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.27
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:25280 original size:18 final size:18
Alignment explanation
Indices: 25257--25291 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
25247 GGACGTATCC
25257 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
25275 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
25292 AATATTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:31483 original size:65 final size:62
Alignment explanation
Indices: 31377--31498 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 62
31367 TTTGTTGAAG
*
31377 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGAACATCGAATGCCATA
1 GTGCATCGATGCACATGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATGCCATA
* *
31442 GTGCATCGATGCATCA-GGAGTGCATCGATGTACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCA-CATGGAGTGCATCGATGCA-CT-CATTAAAATAAAAACATCGAAT
31499 AGGATTTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
63 10 0.20
65 36 0.71
66 4 0.08
67 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (62 bp):
GTGCATCGATGCACATGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATGCCATA
Found at i:35604 original size:17 final size:17
Alignment explanation
Indices: 35582--35615 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35572 CAACAACTTA
35582 AACCCAATCTCTACAAG
1 AACCCAATCTCTACAAG
35599 AACCCAATCTCTACAAG
1 AACCCAATCTCTACAAG
35616 TCCCATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.18
Consensus pattern (17 bp):
AACCCAATCTCTACAAG
Found at i:36611 original size:23 final size:22
Alignment explanation
Indices: 36580--36623 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
36570 CCGAAAAACT
36580 TGTCAAAAGGCAAAAGAAAATA
1 TGTCAAAAGGCAAAAGAAAATA
* *
36602 TGTCATAAAGGCATACGAAAAT
1 TGTCA-AAAGGCAAAAGAAAAT
36624 GTACTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.18
Consensus pattern (22 bp):
TGTCAAAAGGCAAAAGAAAATA
Found at i:36833 original size:20 final size:20
Alignment explanation
Indices: 36808--36986 Score: 134
Period size: 20 Copynumber: 8.8 Consensus size: 20
36798 ATGCGAAACA
*
36808 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
36828 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
36848 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
36868 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
36889 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
36910 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
36930 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* *
36951 -AAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
36970 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
36987 CCAAGAATCG
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 100 0.79
21 9 0.07
22 14 0.11
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:36946 original size:40 final size:39
Alignment explanation
Indices: 36892--36999 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 39
36882 ATCTTCCAAG
*
36892 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTC-AAGAATCGCAACGCGATTGAGAA
* *
36932 AATCGCAACGCGATTCCAGAAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCAAG-AATCGCAACGCGATTGAGAA
36972 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATT-CAAGAATCGCAA
37000 AACGGCAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 2 0.03
40 57 0.92
41 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (39 bp):
AATCGCAACGCGATTCAAGAATCGCAACGCGATTGAGAA
Found at i:36978 original size:60 final size:61
Alignment explanation
Indices: 36866--36986 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 61
36856 AACGGTCAAA
36866 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
*
36928 AGAAAATCGCAACGCGA-TTCC-AGAAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGACTTCCAAG-AATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
36987 CCAAGAATCG
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
59 2 0.04
60 35 0.62
61 2 0.04
62 17 0.30
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:37893 original size:6 final size:6
Alignment explanation
Indices: 37882--37926 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
37872 TCTCGTCTCG
37882 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
37927 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:38062 original size:20 final size:20
Alignment explanation
Indices: 38037--38348 Score: 303
Period size: 20 Copynumber: 15.4 Consensus size: 20
38027 TTTTGCCGTT
*
38037 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
**
38057 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
38077 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
38097 TTGCGATT-TTCTCAATCACG
1 TTGCGATTCTT-GGAATCGCG
38117 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
38137 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
*
38157 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
38177 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
*
38197 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
38217 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
38237 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
* *
38257 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCG
*
38279 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
* *
38299 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCG
38319 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
38341 TTGCGATT
1 TTGCGATT
38349 TTCTTTTGAT
Statistics
Matches: 247, Mismatches: 29, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
19 14 0.06
20 187 0.76
21 17 0.07
22 29 0.12
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:38084 original size:40 final size:40
Alignment explanation
Indices: 38037--38429 Score: 465
Period size: 40 Copynumber: 9.8 Consensus size: 40
38027 TTTTGCCGTT
*
38037 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
*
38077 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCACG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
38117 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
*
38157 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
*
38197 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
* * ** *
38237 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATT-TTCTCA-ATCGCG
* *** *
38279 TTGCGATTCTTGGAATCGCATTGCGATTCTT-TGGCTCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATT-TTCTCAATCGCG
* *
38319 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT--TTTGATCG
1 TTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTCAATCG--CG
**** * *
38361 TTGCGATT-TTCTTTTCAACGTTGCGATTTTCTAAATCGCG
1 TTGCGATTCTTGGAATC-GCGTTGCGATTTTCTCAATCGCG
38401 TTGCGATT-TT-GATATCGCGTTGCGATTTT
1 TTGCGATTCTTGGA-ATCGCGTTGCGATTTT
38430 GTTGGTCATT
Statistics
Matches: 312, Mismatches: 30, Indels: 23
0.85 0.08 0.06
Matches are distributed among these distances:
39 14 0.04
40 229 0.73
41 9 0.03
42 60 0.19
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
Found at i:38402 original size:20 final size:20
Alignment explanation
Indices: 38049--38429 Score: 288
Period size: 20 Copynumber: 18.9 Consensus size: 20
38039 GCGATTCTTG
*
38049 GAATCGCATTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
38069 CAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
38089 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* * *
38109 CAATCACGTTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
38129 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
38149 CAATCGCGTTGCGATTATT-G
1 GAATCGCGTTGCGATT-TTCT
38169 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
38189 CAATCGCGTTGCGATTATT-G
1 GAATCGCGTTGCGATT-TTCT
38209 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
*
38229 CAATCGCGTTGCGATTCTT-T
1 GAATCGCGTTGCGATT-TTCT
*
38249 GAATCGCATTGCGATTCTTC-
1 GAATCGCGTTGCGATT-TTCT
* *
38269 GAAGATCGCATTGCGATTCTT-G
1 G-A-ATCGCGTTGCGATT-TTCT
*
38291 GAATCGCATTGCGATTCTT-T
1 GAATCGCGTTGCGATT-TTCT
** * *
38311 GGCTCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
38331 GAAGATCGCGTTGCGATTTTCTTTT
1 G-A-ATCGCGTTGCGATTTTC---T
38356 G-AT--CGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
** *
38373 -TTTCAACGTTGCGATTTTCT
1 GAATC-GCGTTGCGATTTTCT
*
38393 AAATCGCGTTGCGA-TTT-T
1 GAATCGCGTTGCGATTTTCT
38411 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
38430 GTTGGTCATT
Statistics
Matches: 300, Mismatches: 35, Indels: 52
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.01
18 2 0.01
19 23 0.08
20 224 0.75
21 16 0.05
22 32 0.11
25 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
GAATCGCGTTGCGATTTTCT
Found at i:39825 original size:229 final size:227
Alignment explanation
Indices: 39425--39868 Score: 780
Period size: 229 Copynumber: 1.9 Consensus size: 227
39415 TTATCTATCT
* *
39425 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATA
1 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATA
**
39490 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGT
66 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
*
39555 AAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
131 AAATTAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTGAAACA
39620 TAAATTACATAACTTTCAAAAAAGTATATATTA
196 TAAATTACATAACTTT-AAAAAAGTATATATTA
* *
39653 TTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAAT
1 TTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGTTAAT
* *
39718 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAATAATCAAATAAAATTTTGTG
65 ATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
*
39783 TAAATTAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAATAAATTGAAAC
130 TAAATTAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTGAAAC
39848 ATAAATTACATAACTTTAAAA
195 ATAAATTACATAACTTTAAAA
39869 GCAGTTTTAA
Statistics
Matches: 205, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 35 0.17
229 170 0.83
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (227 bp):
TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATA
TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
AAATTAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTGAAACA
TAAATTACATAACTTTAAAAAAGTATATATTA
Found at i:39957 original size:20 final size:19
Alignment explanation
Indices: 39934--39979 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
39924 CGATATACCA
39934 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
39954 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
39974 GGTAAA
1 GGTAAA
39980 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:40122 original size:20 final size:19
Alignment explanation
Indices: 40099--40145 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
40089 CGATATAACA
40099 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
40119 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
40139 GGTAAAA
1 GGTAAAA
40146 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:40147 original size:17 final size:19
Alignment explanation
Indices: 40108--40150 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
40098 AGGTAAAAAT
40108 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
40128 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
40145 ATGATA
1 ATGATA
40151 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:42425 original size:21 final size:21
Alignment explanation
Indices: 42378--42442 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
42368 AAGACAATCA
* *
42378 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
42400 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
42420 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
42441 AG
1 AG
42443 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:42523 original size:33 final size:33
Alignment explanation
Indices: 42476--42541 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
42466 AAATAGATGG
* *
42476 AGTGGTGAATGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
42509 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
42542 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:44360 original size:19 final size:19
Alignment explanation
Indices: 44336--44384 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
44326 AATGTAGGGT
44336 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
44355 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
44374 TATTTTTGTAT
1 TAATTTTGTAT
44385 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:44844 original size:199 final size:199
Alignment explanation
Indices: 44503--44997 Score: 972
Period size: 199 Copynumber: 2.5 Consensus size: 199
44493 CAATATGGCC
44503 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
44568 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
44633 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAA
44698 TGGAA
195 TGGAA
44703 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
44768 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
44833 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
44898 GGAA
196 GGAA
44902 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
44967 CAAAAGTATAATGTAATATGTAATTTTTCAA
66 CAAAAGTATAATGTAATATGTAATTTTTCAA
44998 GAGAAAATAA
Statistics
Matches: 294, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
199 259 0.88
200 35 0.12
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
GGAA
Found at i:45281 original size:47 final size:41
Alignment explanation
Indices: 45139--45393 Score: 311
Period size: 41 Copynumber: 6.0 Consensus size: 41
45129 ATTCGCGTTG
* *
45139 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
* *
45180 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
45221 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATCGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTCGCG-T----T-GCGATTTTC
45268 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
* *
45309 CGTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTC
* *
45351 CAAATT--CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 C-ATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTC
45392 CA
1 CA
45394 AATTCGTTGT
Statistics
Matches: 199, Mismatches: 6, Indels: 19
0.89 0.03 0.08
Matches are distributed among these distances:
40 1 0.01
41 138 0.69
42 17 0.09
43 2 0.01
46 2 0.01
47 39 0.20
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
Found at i:45297 original size:88 final size:83
Alignment explanation
Indices: 45139--45393 Score: 304
Period size: 88 Copynumber: 3.0 Consensus size: 83
45129 ATTCGCGTTG
* * *
45139 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TG
1 CATTTCGCGTTGCGATAGTCT-ACAGTCGTCGTCGCGATTTTCCATTTCGCGTTGCGATAGTCT-
* *
45201 AAAATCGCGTTGCGATTTTC
64 ACAGTCGCGTTGCGATTTTC
45221 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATCGCGATTTTCCATTTCGCGTTGCGATAG
1 CATTTCGCGTTGCGATAGTCTACAGT--CG-T-CG-TCGCGATTTTCCATTTCGCGTTGCGATAG
45286 TCTACAGTCGCGTTGCGATTTTC
61 TCTACAGTCGCGTTGCGATTTTC
* * * *
45309 CGTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGTCTACAGTCGTCGTCGCGATTTTCC-ATTTCGCGTTGCGATAGTCTA
*
45372 CAGTTGTCGTTGCGATTTTC
65 CAGTCG-CGTTGCGATTTTC
45392 CA
1 CA
45394 AATTCGTTGT
Statistics
Matches: 152, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
82 42 0.28
83 26 0.17
84 7 0.05
85 1 0.01
86 1 0.01
87 2 0.01
88 72 0.47
89 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (83 bp):
CATTTCGCGTTGCGATAGTCTACAGTCGTCGTCGCGATTTTCCATTTCGCGTTGCGATAGTCTAC
AGTCGCGTTGCGATTTTC
Found at i:45297 original size:129 final size:130
Alignment explanation
Indices: 45139--45387 Score: 355
Period size: 129 Copynumber: 1.9 Consensus size: 130
45129 ATTCGCGTTG
45139 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AA
*
45203 AATCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATCGCGATT
65 AATCGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTCGTCGTTGCGATCGCGATT
45265 TTC
128 TTC
* * * *
45268 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCGTTTCGCGTTGCGATAGTCTAC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAA
* * *
45332 AGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGAT
65 AATCGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTCGTCGTTGCGAT
45388 TTTCCAAATT
Statistics
Matches: 107, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
129 79 0.74
130 25 0.23
131 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (130 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAA
ATCGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTCGTCGTTGCGATCGCGATTTTC
Found at i:45361 original size:19 final size:19
Alignment explanation
Indices: 45337--45402 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
45327 TCTACAGTTG
45337 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
45356 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
45377 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
45397 TCGTTG
1 TCGTTG
45403 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:45496 original size:6 final size:6
Alignment explanation
Indices: 45485--45529 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
45475 GACACGTATT
45485 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
45530 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:46038 original size:6 final size:6
Alignment explanation
Indices: 46022--46059 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
46012 GTCCGTCTCG
46022 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
46060 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:46184 original size:21 final size:21
Alignment explanation
Indices: 46158--46211 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
46148 AATTTGGAAA
* *
46158 ATCGCAACGCGATTTTCA-ACT
1 ATCGCAACGCGACTGT-AGACT
46179 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCGACTGTAGACT
46200 ATCGCAACGCGA
1 ATCGCAACGCGA
46212 AATGCAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGACTGTAGACT
Found at i:46271 original size:20 final size:20
Alignment explanation
Indices: 46248--46353 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
46238 AGATCGCGTT
*
46248 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
46268 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
46288 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
46309 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
46329 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
46350 GCGA
1 GCGA
46354 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:46305 original size:41 final size:41
Alignment explanation
Indices: 46255--46357 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
46245 GTTGCGATTT
*
46255 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
46296 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
46337 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
46358 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:46361 original size:21 final size:21
Alignment explanation
Indices: 46255--46361 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
46245 GTTGCGATTT
46255 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
46276 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
46296 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
46317 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
46337 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
46358 CAAC
1 CAAC
46362 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:46837 original size:198 final size:198
Alignment explanation
Indices: 46499--47379 Score: 1654
Period size: 198 Copynumber: 4.4 Consensus size: 198
46489 TTATTTTCTC
***
46499 ATTTTTCAATCTAACCGGTACAATTATACTTATTTTATGAGAGAATATGTCTAAATAATGTGTCG
1 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
46564 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
66 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
*
46629 GTGTCGATCCATATATAAGAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
131 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
46694 GTA
196 GTA
*
46697 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCG
1 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
46762 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
66 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
46827 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
131 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
46892 GTA
196 GTA
* *
46895 ATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAGAATATGTATAAATAATGTGTCG
1 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
46960 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
66 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
47025 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
131 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
47090 GTA
196 GTA
***
47093 ATTTTTCAATCTAACCGGTACAATTATACTTATTTTATGAGAGAATATGTCTAAATAATGTGTCG
1 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
47158 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
66 ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
47223 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
131 GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
47288 GTA
196 GTA
* *
47291 ATTTTTCAATATAACCGGTACAATTATACCGGTTTTAAGAGAGAATATGTCTAAATAATGTGTCG
1 ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
47356 ACACTAATATAGTTTGTGTCGATA
66 ACACTAATATAGTTTGTGTCGATA
47380 CTAATTTAAA
Statistics
Matches: 667, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 667 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (198 bp):
ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCG
ACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAA
GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
GTA
Found at i:49628 original size:2 final size:2
Alignment explanation
Indices: 49621--49670 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
49611 TATTTTGTTA
49621 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
49663 AT AT AT AT
1 AT AT AT AT
49671 GTATTTACTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51105 original size:12 final size:10
Alignment explanation
Indices: 51074--51104 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
51064 TTTATCACAC
51074 CAAATTCTCT
1 CAAATTCTCT
51084 CAAATTCTCT
1 CAAATTCTCT
*
51094 CAAATACTCT
1 CAAATTCTCT
51104 C
1 C
51105 TTTTTAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:51183 original size:17 final size:18
Alignment explanation
Indices: 51144--51184 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51134 ATATTATGTA
* *
51144 TTTAATTTATTTAAGTTT
1 TTTACTTTATTTAAGTAT
51162 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
51179 TTTACT
1 TTTACT
51185 AATATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:51440 original size:111 final size:111
Alignment explanation
Indices: 51246--51467 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
51236 TGGAAATCAT
* * *
51246 ATATCTCTATACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
51311 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
51357 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
51422 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
51468 TTTTTGTAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:55675 original size:27 final size:28
Alignment explanation
Indices: 55601--55682 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 28
55591 ATAGTTAAAA
*
55601 ATTTTAAATTATTATATATTTTATATTTTTT
1 ATTTT-AATTATTATA-AGTTTAT-TTTTTT
* *
55632 ATATTATTTATTGATAA-TTTATTTTTTT
1 ATTTTAATTATT-ATAAGTTTATTTTTTT
55660 CATTTTAATT-TTATAAGTTTATT
1 -ATTTTAATTATTATAAGTTTATT
55683 GTTCATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.09
28 14 0.32
29 12 0.27
30 7 0.16
31 7 0.16
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTTAATTATTATAAGTTTATTTTTTT
Found at i:66596 original size:14 final size:14
Alignment explanation
Indices: 66573--66608 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
66563 TTTGGAGTGC
66573 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
*
66588 AAAAGAAGAAAAGC
1 AAAAGAAGAAAAGA
66602 AAAAGAA
1 AAAAGAA
66609 AAGTGAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Done.