Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002378.1 Hibiscus syriacus cultivar Beakdansim tig00004861_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: 61137
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:614 original size:21 final size:22
Alignment explanation
Indices: 566--619 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
556 AAAAAGCATA
* *
566 AAAATATAT-TACTTTATTATT
1 AAAATTTATATACTTTATTAAT
*
587 TAAATTTATATACTTT-TTAAT
1 AAAATTTATATACTTTATTAAT
608 AAAATTTATATA
1 AAAATTTATATA
620 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATTTATATACTTTATTAAT
Found at i:8106 original size:23 final size:23
Alignment explanation
Indices: 8046--8106 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
8036 ACTAAATTTT
*
8046 AATTATAATTTTAAAAAAAATAAA
1 AATTATAATATT-AAAAAAATAAA
*
8070 AATT-TAAGTATTAAAAAAATTAA
1 AATTATAA-TATTAAAAAAATAAA
*
8093 AATTATAATCTTAA
1 AATTATAATATTAA
8107 CATTATGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AATTATAATATTAAAAAAATAAA
Found at i:14933 original size:3 final size:3
Alignment explanation
Indices: 14921--14959 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
14911 TTCAAGTTTG
*
14921 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14960 TTATGGATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15412 original size:42 final size:42
Alignment explanation
Indices: 15352--15432 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
15342 ATCATTTTGT
* *
15352 TCGAAAGTCTTATAAATGGCCCGAAGGATTTACGCATCATGC
1 TCGAAAGACTTATAAATGGCCCGAAGGACTTACGCATCATGC
*
15394 TCGAAAGACTTACT-AATGGCCCGAAGGACTTACTCATCA
1 TCGAAAGACTTA-TAAATGGCCCGAAGGACTTACGCATCA
15433 AGAAACCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
TCGAAAGACTTATAAATGGCCCGAAGGACTTACGCATCATGC
Found at i:15642 original size:20 final size:21
Alignment explanation
Indices: 15590--15647 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
15580 GGTCTTATGG
15590 ATGGCCCG-AAGTTCTTATTAT
1 ATGGCCCGAAAG-TCTTATTAT
* * *
15611 CTTGCTCGAAAGTCTTA-TAT
1 ATGGCCCGAAAGTCTTATTAT
*
15631 ATGGCCCGAAAGACTTA
1 ATGGCCCGAAAGTCTTA
15648 CACATCATGC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 16 0.55
21 10 0.34
22 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGGCCCGAAAGTCTTATTAT
Found at i:15677 original size:42 final size:42
Alignment explanation
Indices: 15613--15696 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
15603 CTTATTATCT
* *
15613 TGCTCGAAAGTCTTATATATGGCCCGAAAGACTTACACATCA
1 TGCTCGAAAGACTTATAGATGGCCCGAAAGACTTACACATCA
* * *
15655 TGCTCGAAAGACTTACT-GATGGCTCGAAGGACTTACTCATCA
1 TGCTCGAAAGACTTA-TAGATGGCCCGAAAGACTTACACATCA
15697 AGAAACCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
TGCTCGAAAGACTTATAGATGGCCCGAAAGACTTACACATCA
Found at i:15788 original size:263 final size:262
Alignment explanation
Indices: 15252--16035 Score: 1079
Period size: 264 Copynumber: 3.0 Consensus size: 262
15242 TAAGTGATGC
* * *
15252 GTTGTTGATTCAACTCCATATGTGATGAATCGAGTACCAGAAATGTTGAAAACATCCTGCCAAAG
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATCATGCCAAAG
* * *
15317 GTCTTATGGATGGCCCAAAGGTCTTATCATTTTGTTCGAAAGTCTTATAAATGGCCCGAAGGATT
66 GTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGTCTTATAAATGGCCCGAAAGATT
* *
15382 TACGCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAA
131 TACACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAA
* * * * *
15447 ATCAAGCTTAGTTTCTTAGTTGTCATTCAAGGAACCCCTACATATCAAGTTGGTCCCTCGAGTGA
196 ATCAAACCTAGTTTCTTAGTTGTCA-TCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGA
15512 GGT
260 GGT
*** * * * * *
15515 GGAACTGATTCAACTCCATATGTGATAAATTGAGTATCAGAAATATTGAAAACATCATGCCCGAT
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATCATG-CCAAA
* * * * *
15580 GGTCTTATGGATGGCCCGAAGTTCTTATTATCTTGCTCGAAAGTCTTATATATGGCCCGAAAGAC
65 GGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGTCTTATAAATGGCCCGAAAGAT
*
15645 TTACACATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTACTCATCAAGAAACCCTTGAA
130 TTACACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAA
* * *
15710 GATCAAACCTAGTTTCTTAGATGTTATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGA
195 AATCAAACCTAGTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGA
15775 GGT
260 GGT
*
15778 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATC-GAAAATGTTGAAAACATCTTGTCCAA
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAG-AAATGTTGAAAACATCATG-CCAA
* * * * * * * *
15842 AGGTTTTATGGATGGCCTAAAGGACTTATCATCTTACTTCGAAAGACTTATAGATGACCCGAATG
64 AGGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGC-TCGAAAGTCTTATAAATGGCCCGAAAG
* * *
15907 ATTTA-AGCATCATACTGGAAAGACTTACTGATGGCCCGAAGGACTTTCTCATCAAGAAACCCTT
128 ATTTACA-CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTT
* * *
15971 GAAAATC-AAGCTACGTTTCTTAGTTGTCATCAAAGGACCTCTACATATCACGTTGGTCCCTTGA
192 GAAAATCAAACCTA-GTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGA
16035 G
256 G
16036 CTTAGTTTCT
Statistics
Matches: 454, Mismatches: 62, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
262 1 0.00
263 177 0.39
264 276 0.61
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (262 bp):
GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATCATGCCAAAG
GTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGTCTTATAAATGGCCCGAAAGATT
TACACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAA
ATCAAACCTAGTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGAG
GT
Found at i:16166 original size:112 final size:113
Alignment explanation
Indices: 15955--16213 Score: 372
Period size: 112 Copynumber: 2.3 Consensus size: 113
15945 AAGGACTTTC
* * * *
15955 TCATCAAGAAACCCTTGAAAATCAAGC-TACGTTTCTTAGTTGTCATCAAAGGACCTCTACATAT
1 TCATAAAGAAACCCCTGAAAATCAGGCTTA-GTTTCTTAGTTGTCATCAAAGAACCTCTACATAT
*
16019 CACGTTGGTCCCTTGAGCTTAGTTTCTTATAAAAATTCATTGAAAATCG
65 CACGTTGGTCCATTGAGCTTAGTTTCTTATAAAAATTCATTGAAAATCG
16068 TCATAAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCATC-AAGAAACC-CTACATAT
1 TCATAAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCATCAAAG-AACCTCTACATAT
*
16131 CACGTTGGT-CATTCGATCTTAGTTTCTTATAAAAATTCATTGAAAATCG
65 CACGTTGGTCCATT-GAGCTTAGTTTCTTATAAAAATTCATTGAAAATCG
16180 TCATAAA-AAA--CCT-AAAACTCAGGCTTAGTTTCTT
1 TCATAAAGAAACCCCTGAAAA-TCAGGCTTAGTTTCTT
16214 TAAAAAATCT
Statistics
Matches: 136, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
108 4 0.03
109 19 0.14
111 6 0.04
112 61 0.45
113 44 0.32
114 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (113 bp):
TCATAAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCATCAAAGAACCTCTACATATC
ACGTTGGTCCATTGAGCTTAGTTTCTTATAAAAATTCATTGAAAATCG
Found at i:18177 original size:4 final size:4
Alignment explanation
Indices: 18164--18220 Score: 57
Period size: 4 Copynumber: 14.8 Consensus size: 4
18154 ATTGGTTTTA
* * *
18164 TTTC -TTC TTTC TTTC TTTC TTTC TTTTC TTT- TCTC TATC TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC
18211 TTT- TTTC TTT
1 TTTC TTTC TTT
18221 TTTTTCTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
3 8 0.18
4 32 0.73
5 4 0.09
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:18190 original size:28 final size:29
Alignment explanation
Indices: 18159--18240 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 29
18149 ATTTGATTGG
* *
18159 TTTTATTTCT-TCTTTCTTTCTTTCTTTCT
1 TTTTTTTTCTATCTTTTTTTCTTT-TTTCT
18188 TTTCTTTTCTCTATCTTTTTTTCTTTTTTC-
1 TTT-TTTT-TCTATCTTTTTTTCTTTTTTCT
*
18218 TTTTTTTTCTGT-TTTTTTTCTTT
1 TTTTTTTTCTATCTTTTTTTCTTT
18241 ATTTTCTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 11 0.23
28 4 0.09
29 7 0.15
30 6 0.13
31 7 0.15
32 12 0.26
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.79
Consensus pattern (29 bp):
TTTTTTTTCTATCTTTTTTTCTTTTTTCT
Found at i:18191 original size:24 final size:24
Alignment explanation
Indices: 18164--18220 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
18154 ATTGGTTTTA
*
18164 TTTCTTCTTTCTTTCTTTCTTTCT
1 TTTCTTCTTTCTATCTTTCTTTCT
*
18188 TTTCTT-TTCTCTATCTTTTTTTCT
1 TTTCTTCTT-TCTATCTTTCTTTCT
18212 TTT-TTCTTT
1 TTTCTTCTTT
18221 TTTTTCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTCTTCTTTCTATCTTTCTTTCT
Found at i:18193 original size:9 final size:9
Alignment explanation
Indices: 18171--18247 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
18161 TTATTTCTTC
18171 TTTCTTTC-
1 TTTCTTTCT
18179 TTTCTTTCT
1 TTTCTTTCT
18188 TTTCTTTTCT
1 TTTC-TTTCT
*
18198 CTATCTTT-T
1 -TTTCTTTCT
18207 TTTC-TT-T
1 TTTCTTTCT
*
18214 TTTCTTTTT
1 TTTCTTTCT
*
18223 TTTCTGTTTTT
1 TTTC--TTTCT
*
18234 TTTCTTTAT
1 TTTCTTTCT
18243 TTTCT
1 TTTCT
18248 ATATTTTATG
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.12
8 13 0.22
9 19 0.32
10 8 0.14
11 12 0.20
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:18222 original size:8 final size:8
Alignment explanation
Indices: 18171--18234 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 8
18161 TTATTTCTTC
*
18171 TTTCTTTC
1 TTTCTTTT
18179 TTTCTTTCT
1 TTTCTTT-T
18188 TTTCTTTT
1 TTTCTTTT
18196 CTCTATCTTTT
1 -T-T-TCTTTT
18207 TTTC-TTT
1 TTTCTTTT
18214 TTTCTTTTT
1 TTTC-TTTT
18223 TTTCTGTTT
1 TTTCT-TTT
18232 TTT
1 TTT
18235 TTCTTTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
7 7 0.15
8 11 0.23
9 22 0.46
10 2 0.04
11 6 0.12
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:18234 original size:20 final size:21
Alignment explanation
Indices: 18211--18285 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 21
18201 TCTTTTTTTC
*
18211 TTTTTTCTTTTTTTTCTGT-T
1 TTTTTTCTTTTTTTTCTATAT
*
18231 TTTTTTCTTTATTTTCTATAT
1 TTTTTTCTTTTTTTTCTATAT
* *
18252 TTTATGTCTTTTTTTGCTATAT
1 TTT-TTTCTTTTTTTTCTATAT
18274 CTTTTCTTCTTT
1 -TTTT-TTCTTT
18286 CTCTCTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.38
21 4 0.09
22 16 0.36
23 8 0.18
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTCTATAT
Found at i:18254 original size:22 final size:21
Alignment explanation
Indices: 18211--18285 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
18201 TCTTTTTTTC
* *
18211 TTTTTTCTTTTTTT-TCTGTT
1 TTTTTTCTTTTTTTCTATATT
18231 TTTTTTCTTTATTTTCTATATT
1 TTTTTTCTTT-TTTTCTATATT
* *
18253 TTATGTCTTTTTTTGCTATATCT
1 TTTTTTCTTTTTTT-CTATAT-T
*
18276 TTTCTTCTTT
1 TTTTTTCTTT
18286 CTCTCTGTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.23
21 8 0.18
22 18 0.41
23 8 0.18
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTCTTTTTTTCTATATT
Found at i:18254 original size:29 final size:28
Alignment explanation
Indices: 18201--18266 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
18191 CTTTTCTCTA
* * *
18201 TCTTTTTTTCTTTTTTCTTTTTTTTCTG
1 TCTTTTTTTCTTTTTTCTATATTTTATG
18229 T-TTTTTTTCTTTATTTTCTATATTTTATG
1 TCTTTTTTTC-TT-TTTTCTATATTTTATG
18258 TCTTTTTTT
1 TCTTTTTTT
18267 GCTATATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.25
28 3 0.09
29 14 0.44
30 7 0.22
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (28 bp):
TCTTTTTTTCTTTTTTCTATATTTTATG
Found at i:21774 original size:147 final size:147
Alignment explanation
Indices: 21507--21800 Score: 534
Period size: 147 Copynumber: 2.0 Consensus size: 147
21497 CCATCTTTCA
* *
21507 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCGCTCTGCAACTGATGTATTTGAGCTTCTTAT
1 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
* *
21572 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGTTTTTTTCCTTGGACTCCATTGGCTT
66 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
21637 CACTTTAACTAGATGTT
131 CACTTTAACTAGATGTT
*
21654 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAGCTGATGTATTTGAGCTTCGTAT
1 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
*
21719 TTCAGCAAATGCTCTTTAATTTGGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
66 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
21784 CACTTTAACTAGATGTT
131 CACTTTAACTAGATGTT
21801 TGGTTATTGA
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (147 bp):
CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
CACTTTAACTAGATGTT
Found at i:22638 original size:17 final size:19
Alignment explanation
Indices: 22601--22639 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
22591 AGGCAAAAAG
22601 AAAACAAGTTAAGACGTATA
1 AAAACAAGTTAAGA-GTATA
22621 AAAACAAG-TAAG-GTATA
1 AAAACAAGTTAAGAGTATA
22638 AA
1 AA
22640 GGTAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAACAAGTTAAGAGTATA
Found at i:23103 original size:149 final size:149
Alignment explanation
Indices: 22832--23124 Score: 379
Period size: 149 Copynumber: 2.0 Consensus size: 149
22822 TTCAAATCTT
* * *
22832 CTACTTCATCTCCTACTTCTAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGTTTCGG
1 CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
* * *
22897 CGTTGAATCATCTCGAGTCCGACTTGTTACCTCAGCAGACAAATGTTTGGATCGTCTCCTTAGAA
66 CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
22962 GATAGACTCCCTCTAGCTC
131 GATAGACTCCCTCTAGCTC
* * ** *
22981 CTACTTTATCTCTTACTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCAG
1 CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
* * * *** * * * *
23046 TATTGAATCATCTCGAGTTCAACTTGTTACCTTAGCAGGTGAATGTCTGGCTTGTCTCTTTAGTA
66 CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
* *
23111 GGTAGACTCTCTCT
131 GATAGACTCCCTCT
23125 TGAGCTTCTC
Statistics
Matches: 121, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
149 121 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (149 bp):
CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
GATAGACTCCCTCTAGCTC
Found at i:25115 original size:22 final size:21
Alignment explanation
Indices: 25083--25128 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
25073 TGCAAAAATT
*
25083 AAAATAACAGTGGCTAAATCA
1 AAAATAACAGTGACTAAATCA
*
25104 AAAACTAACAGTGACTAAATTA
1 AAAA-TAACAGTGACTAAATCA
25126 AAA
1 AAA
25129 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (21 bp):
AAAATAACAGTGACTAAATCA
Found at i:25135 original size:22 final size:21
Alignment explanation
Indices: 25078--25132 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
25068 CAAAATGCAA
*
25078 AAATTAAAAT-AACAGTGGCT
1 AAATTAAAATAAACAGTGACT
*
25098 AAATCAAAA-ACTAACAGTGACT
1 AAATTAAAATA--AACAGTGACT
25120 AAATTAAAATAAA
1 AAATTAAAATAAA
25133 ACAAAACAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 17 0.61
23 1 0.04
ACGTcount: A:0.58, C:0.11, G:0.09, T:0.22
Consensus pattern (21 bp):
AAATTAAAATAAACAGTGACT
Found at i:25301 original size:13 final size:13
Alignment explanation
Indices: 25283--25308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25273 AATTTTGGTC
25283 TCTAAAGGGACCA
1 TCTAAAGGGACCA
25296 TCTAAAGGGACCA
1 TCTAAAGGGACCA
25309 AAATATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
TCTAAAGGGACCA
Found at i:32554 original size:18 final size:18
Alignment explanation
Indices: 32531--32566 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32521 GAACAAAAAT
32531 CACAGGCAGTAACATGAC
1 CACAGGCAGTAACATGAC
32549 CACAGGCAGTAACATGAC
1 CACAGGCAGTAACATGAC
32567 GTGCAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
CACAGGCAGTAACATGAC
Found at i:34845 original size:16 final size:16
Alignment explanation
Indices: 34824--34861 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
34814 TCAATTTTTA
*
34824 CAATAACGATTAGCAT
1 CAATAACGATGAGCAT
34840 CAATAACGATGAGCAT
1 CAATAACGATGAGCAT
*
34856 CTATAA
1 CAATAA
34862 ATTAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (16 bp):
CAATAACGATGAGCAT
Found at i:35020 original size:229 final size:229
Alignment explanation
Indices: 34611--35055 Score: 755
Period size: 229 Copynumber: 1.9 Consensus size: 229
34601 CGATGAACAC
* * * *
34611 CAATGACGATGAACATCGATAAATTAATTTGTAAAATGATAAAATTATAAGGTACTGAACGTATA
1 CAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTACTCAACGTATA
34676 ATTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCACAATATTAATTACATTGTGTT
66 ATTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCACAATATTAATTACATTGTGTT
* * *
34741 TTTAATATTTTTGGGTAAATTACAAGTTTAGTGTCTAAAGTTTCACTTTTAGTACGTTTTCGTAC
131 TTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTACGATTTAGTAC
*
34806 TTGAACTTTCAATTTTTACAATAACGATTAGCAT
196 TTAAACTTTCAATTTTTACAATAACGATTAGCAT
* *
34840 CAATAACGATGAGCATCTATAAATTAATTTATAAAACGATAAAATTATAAGGTACTCAACGTATA
1 CAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTACTCAACGTATA
* *
34905 CTTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCAGAATATTAATTACATTGTGTT
66 ATTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCACAATATTAATTACATTGTGTT
* *
34970 TTTAATATTTTTGGGTAAATTACAAGTTTTGTATCTAAAGTTTGACTTTTAGTACGATTTAGTAC
131 TTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTACGATTTAGTAC
*
35035 TTAAACTTTTAATTTTTACAA
196 TTAAACTTTCAATTTTTACAA
35056 AATTATACCT
Statistics
Matches: 201, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
229 201 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (229 bp):
CAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTACTCAACGTATA
ATTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCACAATATTAATTACATTGTGTT
TTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTACGATTTAGTAC
TTAAACTTTCAATTTTTACAATAACGATTAGCAT
Found at i:35462 original size:23 final size:24
Alignment explanation
Indices: 35436--35512 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
35426 ATTTTATATA
* *
35436 ATTATTTAGTTAAAGA-CTAAAAT
1 ATTATTTAGTTAAAAATATAAAAT
*
35459 ATTAATTTATTTAAAAATATAAAAT
1 ATT-ATTTAGTTAAAAATATAAAAT
*
35484 ATT-TTTAGTATAAACTATATAAAAT
1 ATTATTTAGT-TAAA-AATATAAAAT
35509 ATTA
1 ATTA
35513 AATCATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.18
24 15 0.34
25 21 0.48
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTATTTAGTTAAAAATATAAAAT
Found at i:35671 original size:20 final size:20
Alignment explanation
Indices: 35633--35671 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35623 AATAAAGCTG
*
35633 AAATAATTTAATTTTTAATT
1 AAATAATTTAATTTATAATT
**
35653 AAATAATTTGGTTTATAAT
1 AAATAATTTAATTTATAAT
35672 GAAAAATGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATAATTTAATTTATAATT
Found at i:39923 original size:14 final size:15
Alignment explanation
Indices: 39898--39926 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39888 AGGAAATTAC
39898 TTTTATTATTAAAAT
1 TTTTATTATTAAAAT
39913 TTTTATT-TTAAAAT
1 TTTTATTATTAAAAT
39927 GGTCGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTATTAAAAT
Found at i:45595 original size:12 final size:12
Alignment explanation
Indices: 45572--45605 Score: 50
Period size: 12 Copynumber: 2.7 Consensus size: 12
45562 TTGTTTAATA
45572 GTTGATATGGAAT
1 GTTGA-ATGGAAT
45585 GTTGAATGGAAT
1 GTTGAATGGAAT
45597 GTTGTAATG
1 GTTG-AATG
45606 ATGAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (12 bp):
GTTGAATGGAAT
Found at i:45779 original size:20 final size:21
Alignment explanation
Indices: 45734--45773 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
45724 TACTATGCTG
45734 GAATTTAGATGTTAGAATGTT
1 GAATTTAGATGTTAGAATGTT
45755 GAATTTA-ATGTTAGAATGT
1 GAATTTAGATGTTAGAATGT
45774 GAAATTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (21 bp):
GAATTTAGATGTTAGAATGTT
Found at i:46903 original size:17 final size:17
Alignment explanation
Indices: 46880--46967 Score: 79
Period size: 17 Copynumber: 5.1 Consensus size: 17
46870 AAGATATAGT
46880 ACAGTAAAAAAAAAGAA
1 ACAGTAAAAAAAAAGAA
* ** *
46897 ACGGTAAAGTAAAAGTA
1 ACAGTAAAAAAAAAGAA
46914 ACAGTATAAGAAAAAAG-A
1 ACAGTA-AA-AAAAAAGAA
*
46932 ACAGTACAAAAAAGAGAA
1 ACAGTA-AAAAAAAAGAA
* *
46950 ACAGTAGAAGAAAAGAA
1 ACAGTAAAAAAAAAGAA
46967 A
1 A
46968 ACAATATAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
17 33 0.59
18 18 0.32
19 5 0.09
ACGTcount: A:0.66, C:0.07, G:0.18, T:0.09
Consensus pattern (17 bp):
ACAGTAAAAAAAAAGAA
Found at i:46928 original size:18 final size:17
Alignment explanation
Indices: 46880--46967 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 17
46870 AAGATATAGT
*
46880 ACAGTAAAAAAAAAGAA
1 ACAGTAAAGAAAAAGAA
* * *
46897 ACGGTAAAGTAAAAGTA
1 ACAGTAAAGAAAAAGAA
46914 ACAGTATAAGAAAAA-AGA
1 ACAGTA-AAGAAAAAGA-A
46932 ACAGTACAA-AAAAGAGAA
1 ACAGTA-AAGAAAA-AGAA
46950 ACAGTAGAAG-AAAAGAA
1 ACAGTA-AAGAAAAAGAA
46967 A
1 A
46968 ACAATATAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 27 0.47
18 29 0.51
19 1 0.02
ACGTcount: A:0.66, C:0.07, G:0.18, T:0.09
Consensus pattern (17 bp):
ACAGTAAAGAAAAAGAA
Found at i:46978 original size:18 final size:18
Alignment explanation
Indices: 46913--46992 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
46903 AAGTAAAAGT
46913 AACAGTATAAGAAAA-AA
1 AACAGTATAAGAAAAGAA
*
46930 GAACAGTACAA-AAAAGAGA
1 -AACAGTATAAGAAAAGA-A
*
46949 AACAGTAGAAGAAAAGAA
1 AACAGTATAAGAAAAGAA
*
46967 AACAATATAAGAAGAA-AA
1 AACAGTATAAGAA-AAGAA
*
46985 GACAGTAT
1 AACAGTAT
46993 TGGTTTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.08
18 39 0.75
19 9 0.17
ACGTcount: A:0.65, C:0.07, G:0.17, T:0.10
Consensus pattern (18 bp):
AACAGTATAAGAAAAGAA
Found at i:46990 original size:54 final size:52
Alignment explanation
Indices: 46880--46991 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 52
46870 AAGATATAGT
* * *
46880 ACAGTAAAAAAAAAGAAACGGTAAAGTAAAAGTAACAGTATAAGAAAAAAGA
1 ACAGTAAAAAAAAAGAAACAGTAAAGTAAAAGAAACAATATAAGAAAAAAGA
*
46932 ACAGTACAAAAAAGAGAAACAGTAGAAG-AAAAGAAAACAATATAAGAAGAAAAG-
1 ACAGTA-AAAAAAAAGAAACAGTA-AAGTAAAAG-AAACAATATAAGAA-AAAAGA
46986 ACAGTA
1 ACAGTA
46992 TTGGTTTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
52 6 0.12
53 20 0.38
54 21 0.40
55 5 0.10
ACGTcount: A:0.65, C:0.07, G:0.18, T:0.10
Consensus pattern (52 bp):
ACAGTAAAAAAAAAGAAACAGTAAAGTAAAAGAAACAATATAAGAAAAAAGA
Found at i:55257 original size:15 final size:15
Alignment explanation
Indices: 55237--55287 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
55227 ACTAGAAATA
55237 TGCTGTGGCTGCTGC
1 TGCTGTGGCTGCTGC
* *
55252 TGCTGTGACAG-TGC
1 TGCTGTGGCTGCTGC
*
55266 ATGCTGTGGCTGCTGT
1 -TGCTGTGGCTGCTGC
55282 TGCTGT
1 TGCTGT
55288 TGGTTTGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.83
16 2 0.07
ACGTcount: A:0.06, C:0.22, G:0.37, T:0.35
Consensus pattern (15 bp):
TGCTGTGGCTGCTGC
Found at i:58287 original size:63 final size:64
Alignment explanation
Indices: 58182--58304 Score: 223
Period size: 63 Copynumber: 1.9 Consensus size: 64
58172 TAACATGGTG
58182 GGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAA-ACAGTAGGTA
1 GGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTC-ATTATAATACAGTAGGTA
58246 GGTTG-AAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCATTATAATACAGTA
1 GGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCATTATAATACAGTA
58305 TAATGCATGT
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
62 7 0.12
63 46 0.79
64 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (64 bp):
GGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCATTATAATACAGTAGGTA
Done.