Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001724.1 Hibiscus syriacus cultivar Beakdansim tig00003487_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: 146287
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1201 original size:21 final size:21
Alignment explanation
Indices: 1146--1207 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
1136 ATAGCTCGTA
*
1146 TAAATGC-CCGAAGTACCACG
1 TAAATGCACCGAAGTGCCACG
* *
1166 TAGAATTGCATCGAAGTGCCGCG
1 TA-AA-TGCACCGAAGTGCCACG
1189 TAAATGCACCGAAGTGCCA
1 TAAATGCACCGAAGTGCCA
1208 TATAAGATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.06
21 15 0.44
22 5 0.15
23 12 0.35
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (21 bp):
TAAATGCACCGAAGTGCCACG
Found at i:2336 original size:66 final size:65
Alignment explanation
Indices: 2044--2477 Score: 431
Period size: 66 Copynumber: 6.6 Consensus size: 65
2034 AAAACCTGTA
* * * *
2044 AGATTGTTTCTCTTGAAACAAGTTGTGTCTCTTTTGAGATAGTTTCTCTTGAAACGTAAGAACA-
1 AGATTGTTTC-CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-TAA-AACAT
2108 TTG
63 TTG
* * *
2111 AGATTGTTTCATTTGAAGCAAAATTTTGTCTCTCTTG-GAACATTTTTCTCTTGAAACGTAAAA-
1 AGATTGTTTC-CTTGAAAC-AAATTTTGTCTCTCTTGAG-ACA-GTTTCTCTTGAAAC-TAAAAC
2174 ATTTG
61 ATTTG
* * * * *
2179 AGTTTGTTTCCCTCGAAATAAATTTTGTCT-TGCTTGATACAATTTCTCTTGAAAC-AAAAC-TT
1 AGATTGTTT-CCTTGAAACAAATTTTGTCTCT-CTTGAGACAGTTTCTCTTGAAACTAAAACATT
2241 TG
64 TG
* *
2243 ATATTGTTTTCCTTGAAAC-AAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTTAAAACATT
1 AGATTG-TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-TAAAACATT
2307 TG
64 TG
* *
2309 AGATTGTTTCCCTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATACAAA-TTT
1 AGATTGTTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-TA-AAACATT
2373 TG
64 TG
* * * *
2375 ATATTGTTTCTCTTGAAAC-AAGTTTGTCTCCCTTTAGACAGTTTCTCTTGAAAC-ACAAACA-T
1 AGATTGTTTC-CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTA-AAACATT
2437 TG
64 TG
* * *
2439 AGATTGTTTCCCTTGAAACAAGTTTTATTTCTCTTGAGA
1 AGATTGTTT-CCTTGAAACAAATTTTGTCTCTCTTGAGA
2478 TTGTTTCCCT
Statistics
Matches: 308, Mismatches: 40, Indels: 40
0.79 0.10 0.10
Matches are distributed among these distances:
63 30 0.10
64 44 0.14
65 33 0.11
66 104 0.34
67 46 0.15
68 33 0.11
69 18 0.06
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (65 bp):
AGATTGTTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAAAACATTTG
Found at i:2455 original size:196 final size:198
Alignment explanation
Indices: 2044--2477 Score: 540
Period size: 196 Copynumber: 2.2 Consensus size: 198
2034 AAAACCTGTA
* * *
2044 AGATTGTTTCTCTTGAAACAAGTTGTGTCTCTTTTGAGATAGTTTCTCTTGAAACGTAAGAACAT
1 AGATTGTTTCCCTTGAAACAAGTT-TGTCTCTCTTGAGACAGTTTCTCTTGAAACGTAAGAACAT
** * * *
2109 TGAGATTGTTTCATTTGAAGCAAAATTTTGTCTCTCTTGGAACATTTTTCTCTTGAAACGTAAAA
65 TGAGATTGTTTCACCTGAAACAAAATTTTGTCTCTCTTGGAACATGTTTCTCTTGAAACATAAAA
* ** *
2174 ATTTGAGTTTGTTTCCCTCGAAATAAATTTTGTCTTGCTTGATACAATTTCTCTTGAAACAAAAC
130 ATTTGAGTTTGTTTCCCTCGAAATAAAGTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAAC
*
2239 TTTG
195 ATTG
* * *
2243 ATATTGTTTTCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTTAA-AACATT
1 AGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGTAAGAACA-T
2307 TGAGATTGTTTC-CCTGAAAC-AAATTTTGTCTCTCTT-GAGACA-GTTTCTCTTGAAACATACA
65 TGAGATTGTTTCACCTGAAACAAAATTTTGTCTCTCTTGGA-ACATGTTTCTCTTGAAACATA-A
* * * * * *
2368 AATTTTGA-TATTGTTTCTCTTGAAA-CAAGTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACAC
128 AAATTTGAGT-TTGTTTCCCTCGAAATAAAGTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA-
2431 AAACATTG
191 AAACATTG
* *
2439 AGATTGTTTCCCTTGAAACAAGTTTTATTTCTCTTGAGA
1 AGATTGTTTCCCTTGAAACAAG-TTTGTCTCTCTTGAGA
2478 TTGTTTCCCT
Statistics
Matches: 203, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
195 48 0.24
196 67 0.33
197 23 0.11
198 44 0.22
199 21 0.10
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (198 bp):
AGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGTAAGAACATT
GAGATTGTTTCACCTGAAACAAAATTTTGTCTCTCTTGGAACATGTTTCTCTTGAAACATAAAAA
TTTGAGTTTGTTTCCCTCGAAATAAAGTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAACA
TTG
Found at i:2498 original size:35 final size:36
Alignment explanation
Indices: 2436--2530 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 36
2426 AACACAAACA
*
2436 TTGAGATTGTTTCCCTTGAAACAAGTTTTATTTCTC
1 TTGAGATTGTTTCCCTTGAAACAAGTTTTATCTCTC
2472 TTGAGATTGTTTCCC-TGAAACAAGTTTTATCTCTC
1 TTGAGATTGTTTCCCTTGAAACAAGTTTTATCTCTC
** * *
2507 TTGAGACAGTTTCTCTTAAAACAA
1 TTGAGATTGTTTCCCTTGAAACAA
2531 ATTATCCCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
35 31 0.58
36 22 0.42
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (36 bp):
TTGAGATTGTTTCCCTTGAAACAAGTTTTATCTCTC
Found at i:2796 original size:135 final size:136
Alignment explanation
Indices: 2532--2935 Score: 465
Period size: 136 Copynumber: 3.0 Consensus size: 136
2522 TTAAAACAAA
* * * * * *
2532 TTATCCCTAAATATGGTCATCATCCTCATCACGT-GGAACCGTGTCATCCACCAACCAGATCTCA
1 TTATCCCTAAAGATGGCCAACGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCC
* * * *
2596 TCATCACATATGAG-TCGTGTCAAACTTAGATAACCAGTCATCCTCATCACGTAGGAATCGTGTT
66 TCATCACGTAGGAGCT-GTGTC-ACCTTAGATAACCAGTCGTCCTCATCACGTAGGAATCGTGTT
*
2660 ATCATCAT
129 ATCACCAT
*
2668 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAA-C-TGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCA-ACGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
* * * *
2731 CTTATCACGTAGGAGCTGCGTCACCTTAGATAACCAATCGTCCTCATCACGTAGGAATTGTGTTA
65 CTCATCACGTAGGAGCTGTGTCACCTTAGATAACCAGTCGTCCTCATCACGTAGGAATCGTGTTA
2796 TCACCAT
130 TCACCAT
** * * ** *
2803 TTATCTATAAAGATGACCAATACGTCCTCATCACGTAGGAACCGTATCATATACCGACCAGATAT
1 TTATCCCTAAAGATGGCC-A-ACGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * * * *
2868 CCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACCAGTCGTCTTCATCGCATAGGAACCATGT
64 CCTCATCACGTAGGAGCTGTGTCA-CCTTAGATAACCAGTCGTCCTCATCACGTAGGAATCGTGT
2933 TAT
128 TAT
2936 TTCTATTTAC
Statistics
Matches: 227, Mismatches: 34, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
135 60 0.26
136 73 0.32
137 16 0.07
138 42 0.19
139 36 0.16
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (136 bp):
TTATCCCTAAAGATGGCCAACGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCC
TCATCACGTAGGAGCTGTGTCACCTTAGATAACCAGTCGTCCTCATCACGTAGGAATCGTGTTAT
CACCAT
Found at i:4157 original size:29 final size:29
Alignment explanation
Indices: 4136--4199 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
4126 TATATATTTC
4136 TAACTACTAACTTTTATTTTATTACATAT
1 TAACTACTAACTTTTATTTTATTACATAT
* * * * *
4165 TAACTACTGATTTTTATTTTGTTGCATTT
1 TAACTACTAACTTTTATTTTATTACATAT
4194 TAACTA
1 TAACTA
4200 TTGTTTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (29 bp):
TAACTACTAACTTTTATTTTATTACATAT
Found at i:4458 original size:16 final size:17
Alignment explanation
Indices: 4410--4458 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
4400 ATGGCGCGGA
*
4410 CTTTTCTAACCTCTAA-
1 CTTTTCTAACCACTAAT
*
4426 CTTTTCTAACAACTAAT
1 CTTTTCTAACCACTAAT
*
4443 C-TTTCTAACCGCTAAT
1 CTTTTCTAACCACTAAT
4459 TACTAACTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.41
Consensus pattern (17 bp):
CTTTTCTAACCACTAAT
Found at i:4744 original size:15 final size:14
Alignment explanation
Indices: 4709--4747 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4699 ATTCTAATCG
*
4709 TTTATTTTTATCTC
1 TTTATTTTTATCTA
*
4723 TTTATTTTTATGTA
1 TTTATTTTTATCTA
*
4737 TTTAATTTTAT
1 TTTATTTTTAT
4748 TCGTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTATTTTTATCTA
Found at i:4754 original size:28 final size:27
Alignment explanation
Indices: 4709--4767 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
4699 ATTCTAATCG
* * *
4709 TTTATTTTTATCTCTTTATTTTTATGTA
1 TTTAATTTTATCTCTTTA-ATTAATGTA
4737 TTTAATTTTAT-TCGTTTAATTAATGTA
1 TTTAATTTTATCTC-TTTAATTAATGTA
4764 TTTA
1 TTTA
4768 TTATCCGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTAATTTTATCTCTTTAATTAATGTA
Found at i:9895 original size:20 final size:21
Alignment explanation
Indices: 9852--9895 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
9842 ATCTAATGAT
*
9852 AAAATTAAATCAATAAAATTAA
1 AAAATTAAA-CAATAAAATAAA
*
9874 AAAATTAAA-AATAATATAAA
1 AAAATTAAACAATAAAATAAA
9894 AA
1 AA
9896 TTAGCATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATTAAACAATAAAATAAA
Found at i:11240 original size:19 final size:19
Alignment explanation
Indices: 11218--11256 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11208 TAATCATTCG
*
11218 ATTATTTATTATATTTTAA
1 ATTAATTATTATATTTTAA
* *
11237 ATTAATTATTTTCTTTTAA
1 ATTAATTATTATATTTTAA
11256 A
1 A
11257 ATATAACATC
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:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAATTATTATATTTTAA
Found at i:13952 original size:12 final size:12
Alignment explanation
Indices: 13937--13967 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13927 ATTATTTAAA
13937 CGGGTATCGGGC
1 CGGGTATCGGGC
13949 CGGGTATCGGGC
1 CGGGTATCGGGC
*
13961 TGGGTAT
1 CGGGTAT
13968 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:14106 original size:36 final size:35
Alignment explanation
Indices: 14057--14132 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
14047 TAAACTCGTT
*
14057 CCCGTCTCCGTTTAACATAAACGGTTTTTCTCCGTC
1 CCCGTCTCCGTTTAACATAAACGATTTTT-TCCGTC
*
14093 CCCGTCTCTGTTTAACATAAACGATTTTTTCCGTC
1 CCCGTCTCCGTTTAACATAAACGATTTTTTCCGTC
14128 CCCGT
1 CCCGT
14133 TTAATTCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.29
36 27 0.71
ACGTcount: A:0.17, C:0.33, G:0.13, T:0.37
Consensus pattern (35 bp):
CCCGTCTCCGTTTAACATAAACGATTTTTTCCGTC
Found at i:15533 original size:10 final size:10
Alignment explanation
Indices: 15518--15546 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
15508 CTTTGAGCAT
15518 GCGTGTATGG
1 GCGTGTATGG
15528 GCGTGTATGG
1 GCGTGTATGG
15538 GCGTGTATG
1 GCGTGTATG
15547 CTCTGGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.48, T:0.31
Consensus pattern (10 bp):
GCGTGTATGG
Found at i:15582 original size:15 final size:15
Alignment explanation
Indices: 15562--15591 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15552 GGGAGTACAT
15562 GCATTTGATCTCAGG
1 GCATTTGATCTCAGG
15577 GCATTTGATCTCAGG
1 GCATTTGATCTCAGG
15592 TAAAGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
GCATTTGATCTCAGG
Found at i:16823 original size:13 final size:15
Alignment explanation
Indices: 16798--16830 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
16788 TTACATTATT
16798 TAATTTTTATTATAA
1 TAATTTTTATTATAA
16813 -AATTTTT-TTATAA
1 TAATTTTTATTATAA
16826 TAATT
1 TAATT
16831 GTGGTCGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATTTTTATTATAA
Found at i:17640 original size:185 final size:186
Alignment explanation
Indices: 17308--17667 Score: 537
Period size: 185 Copynumber: 1.9 Consensus size: 186
17298 TTCCTTTAGT
*
17308 GTGTGCACTATTCGGTTTTAACCAAACTAGTGATCAAAATAAATTAGTTTGATTAATTCAGTCGA
1 GTGTGCACTATTCGGTTTTAACCAAACTAATGATCAAAATAAATTAGTTTGATTAATTCAGTCGA
* * *
17373 TATCGAATTAGTTCAGTCGGGAAATAGTTAATAATTCTTTTAGAATTTGATTAACGATTAATTCG
66 CATCAAATTAGTTCAGTCGGGAAATAGTTAATAATTCTTTTAGAATTCGATTAACGATTAATTCG
* *
17438 ATTTAAAATCGGTTAATTCACCGAATTTACTAACATTATTAAATAGGAACATCAGG
131 ATTTAAAATCGGTTAATTCACCAAATTAACTAACATTATTAAATAGGAACATCAGG
* * * * * * * *
17494 GTGTTCACTATTCGGTTTTAACCGAATTAATGATCCAAGTGAATTAGTTTGGTTAATTCGGTCTG
1 GTGTGCACTATTCGGTTTTAACCAAACTAATGATCAAAATAAATTAGTTTGATTAATTCAGTC-G
*
17559 -CATCAAATTAGTTCAGTCGGG-AATGGTTAATAAATT-TTTTAGAATTCGATTAACGATTAATT
65 ACATCAAATTAGTTCAGTCGGGAAATAGTTAAT-AATTCTTTTAGAATTCGATTAACGATTAATT
*
17621 CGATTTAAAATCGGTTAATTCATCAAATTAACTAACATTATTAAATA
129 CGATTTAAAATCGGTTAATTCACCAAATTAACTAACATTATTAAATA
17668 TTAAATATAA
Statistics
Matches: 156, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
185 78 0.50
186 77 0.49
187 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (186 bp):
GTGTGCACTATTCGGTTTTAACCAAACTAATGATCAAAATAAATTAGTTTGATTAATTCAGTCGA
CATCAAATTAGTTCAGTCGGGAAATAGTTAATAATTCTTTTAGAATTCGATTAACGATTAATTCG
ATTTAAAATCGGTTAATTCACCAAATTAACTAACATTATTAAATAGGAACATCAGG
Found at i:22021 original size:15 final size:15
Alignment explanation
Indices: 21992--22028 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21982 GGTCAAGAAT
21992 GACAA-AAAAAGGTG
1 GACAAGAAAAAGGTG
*
22006 GACAAGAAAGAGGTG
1 GACAAGAAAAAGGTG
22021 GACAAGAA
1 GACAAGAA
22029 TCTAAGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.54, C:0.08, G:0.32, T:0.05
Consensus pattern (15 bp):
GACAAGAAAAAGGTG
Found at i:35794 original size:2 final size:2
Alignment explanation
Indices: 35787--35832 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35777 TTCGACACAA
35787 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
35829 AT AT
1 AT AT
35833 TCTTATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38222 original size:3 final size:3
Alignment explanation
Indices: 38216--38279 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
38206 AATAATTATT
*
38216 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
38261 TAA TATT TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA
38280 CAAATTTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.89
4 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:38279 original size:25 final size:25
Alignment explanation
Indices: 38205--38279 Score: 123
Period size: 25 Copynumber: 2.9 Consensus size: 25
38195 TTTGGGTTTG
38205 TAATAATTATTTAATAATAATATAATAA
1 TAATAA-TATTTAATAAT-A-ATAATAA
38233 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
38258 TAATAATATTTAATAATAATAA
1 TAATAATATTTAATAATAATAA
38280 CAAATTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
25 29 0.62
26 1 0.02
27 11 0.23
28 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:39231 original size:76 final size:76
Alignment explanation
Indices: 38409--39205 Score: 1504
Period size: 76 Copynumber: 10.5 Consensus size: 76
38399 GATGAAAATG
* * *
38409 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
38474 TCCCGAAGGCTT
65 TCCCGAAGGCTT
38486 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38551 CCCGAAGGCTT
66 CCCGAAGGCTT
38562 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38627 CCCGAAGGCTT
66 CCCGAAGGCTT
38638 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38703 CCCGAAGGCTT
66 CCCGAAGGCTT
*
38714 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38779 CCCGAAGGCTT
66 CCCGAAGGCTT
38790 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38855 CCCGAAGGCTT
66 CCCGAAGGCTT
*
38866 TTTGGAAACATCATGCACTGAATGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38931 CCCGAAGGCTT
66 CCCGAAGGCTT
38942 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39007 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
39018 TTTGGAAACATCATGCATTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39083 CCCGAAGGCTT
66 CCCGAAGGCTT
39094 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39159 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
39170 TTTGGAAACATCATGCACTGTAGGAATTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
39206 GGGAAATAGT
Statistics
Matches: 707, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
76 665 0.94
77 42 0.06
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:39906 original size:22 final size:22
Alignment explanation
Indices: 39881--39935 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
39871 CATAAAGTTT
*
39881 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
39903 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
39925 TCATCTTTGAA
1 TCATCTTTGAA
39936 GAGTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:40381 original size:54 final size:52
Alignment explanation
Indices: 40299--40417 Score: 159
Period size: 54 Copynumber: 2.3 Consensus size: 52
40289 AGAATAATAG
*** *
40299 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT-CTGTGGCTTCTGCTAAGAT
*
40353 GTTCGTAAAACATTTGACAACACATTCATTTTTTTGTGGCTTCTGCTAAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTAAGAT
*
40405 GTTC-TCAAACATT
1 GTTCGTAAAACATT
40418 GAAGCTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 8 0.14
52 21 0.36
53 4 0.07
54 26 0.44
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTAAGAT
Found at i:41376 original size:75 final size:74
Alignment explanation
Indices: 41283--41452 Score: 207
Period size: 74 Copynumber: 2.3 Consensus size: 74
41273 ATTGTGGGCC
* * *
41283 TTCAGCATGCCCCAACA-TTGGTTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATA-AA-TATTCAAAATACATCAACAGTTCTGATTCTGAT
*
41347 TGAAATGGGTT
64 TGAAAAGGGTT
* * * ** * *
41358 TTCAGCATGCCCCAACATTTTGCTGATAAATATTCAGAATATTTCAACATTTCTGATTCTGTTTG
1 TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
41423 AAAAGGGTT
66 AAAAGGGTT
*
41432 TTCAGCATGCCCCAATATTTG
1 TTCAGCATGCCCCAACATTTG
41453 CTTCTTGTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 55 0.68
75 19 0.23
76 7 0.09
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (74 bp):
TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
AAAAGGGTT
Found at i:42746 original size:114 final size:114
Alignment explanation
Indices: 42535--42760 Score: 389
Period size: 114 Copynumber: 2.0 Consensus size: 114
42525 GATCATGCAG
* *
42535 TTCACCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
42600 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
42649 TTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
42714 ACACTTCTAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
42761 CATGACACTT
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:47569 original size:21 final size:21
Alignment explanation
Indices: 47545--47584 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47535 AAAAGTAAAA
47545 ATACAAAATGAAAATGCATAG
1 ATACAAAATGAAAATGCATAG
*
47566 ATACAAAATGTAAATGCAT
1 ATACAAAATGAAAATGCAT
47585 GTATGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
ATACAAAATGAAAATGCATAG
Found at i:50376 original size:13 final size:13
Alignment explanation
Indices: 50360--50402 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
50350 GAAAAATAAA
50360 TATTAAAATAATT
1 TATTAAAATAATT
* *
50373 TATTTGAAATAA-A
1 TA-TTAAAATAATT
50386 TATTAAAATAATT
1 TATTAAAATAATT
50399 TATT
1 TATT
50403 TGAAATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTAAAATAATT
Found at i:50382 original size:14 final size:14
Alignment explanation
Indices: 50365--50410 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
50355 ATAAATATTA
50365 AAATAATTTATTTG
1 AAATAATTTATTTG
* *
50379 AAATAA-ATA-TTA
1 AAATAATTTATTTG
50391 AAATAATTTATTTG
1 AAATAATTTATTTG
50405 AAATAA
1 AAATAA
50411 ATATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
AAATAATTTATTTG
Found at i:50384 original size:26 final size:26
Alignment explanation
Indices: 50353--50415 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
50343 CGATATTGAA
50353 AAATAAATATTAAAATAATTTATTTG
1 AAATAAATATTAAAATAATTTATTTG
50379 AAATAAATATTAAAATAATTTATTTG
1 AAATAAATATTAAAATAATTTATTTG
50405 AAATAAATATT
1 AAATAAATATT
50416 TATTTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AAATAAATATTAAAATAATTTATTTG
Found at i:51824 original size:11 final size:11
Alignment explanation
Indices: 51808--51884 Score: 70
Period size: 11 Copynumber: 7.0 Consensus size: 11
51798 TTTGGGTTTG
* *
51808 TAATAATTATT
1 TAATAATAATA
51819 TAATAATAATA
1 TAATAATAATA
51830 TAATAAT-A-A
1 TAATAATAATA
*
51839 TAATATTTAATAA
1 TAATA-ATAAT-A
51852 TAATAATAATAA
1 TAATAATAAT-A
*
51864 TAATAAT-ATT
1 TAATAATAATA
51874 TAATAATAATA
1 TAATAATAATA
51885 ACAAATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
9 6 0.11
10 9 0.16
11 21 0.38
12 13 0.24
13 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATA
Found at i:51825 original size:3 final size:3
Alignment explanation
Indices: 51819--51885 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
51809 AATAATTATT
*
51819 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
51864 TAA TAA TATT TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA
51886 CAAATTTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 51 0.89
4 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:51860 original size:28 final size:28
Alignment explanation
Indices: 51808--51885 Score: 140
Period size: 28 Copynumber: 2.8 Consensus size: 28
51798 TTTGGGTTTG
51808 TAATAATTATTTAATAATAAT-ATAATAA
1 TAATAA-TATTTAATAATAATAATAATAA
51836 TAATAATATTTAATAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAATAA
51864 TAATAATATTTAATAATAATAA
1 TAATAATATTTAATAATAATAA
51886 CAAATTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.29
28 35 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TAATAATATTTAATAATAATAATAATAA
Found at i:62664 original size:31 final size:31
Alignment explanation
Indices: 62629--62696 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
62619 TAAAAATAAA
*
62629 GATAAATTTAA-GAATCATTTTTTAATAATTT
1 GATAAATTTAATG-ATCATTTTATAATAATTT
* *
62660 GATAAGTTTAATGATCATTTTATACTAATTT
1 GATAAATTTAATGATCATTTTATAATAATTT
62691 GATAAA
1 GATAAA
62697 ATTTTGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (31 bp):
GATAAATTTAATGATCATTTTATAATAATTT
Found at i:62718 original size:22 final size:23
Alignment explanation
Indices: 62685--62727 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
62675 CATTTTATAC
62685 TAATTTGATAAA-ATTTTGATTA
1 TAATTTGATAAACATTTTGATTA
62707 TAATGTTG-TAAACATTTTGAT
1 TAAT-TTGATAAACATTTTGAT
62728 AAGTATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (23 bp):
TAATTTGATAAACATTTTGATTA
Found at i:66314 original size:21 final size:20
Alignment explanation
Indices: 66262--66315 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
66252 GTCAGCATAA
66262 TGAACCATCACGTCAACATG
1 TGAACCATCACGTCAACATG
** *
66282 TGAAATATCACGTCATCATCG
1 TGAACCATCACGTCAACAT-G
*
66303 TGAACCAACACGT
1 TGAACCATCACGT
66316 GAAATGCCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (20 bp):
TGAACCATCACGTCAACATG
Found at i:67745 original size:20 final size:20
Alignment explanation
Indices: 67722--67768 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
67712 GTTTCCAAAT
67722 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
67742 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
67762 TCACAAC
1 TCGCAAC
67769 ACATAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:67786 original size:40 final size:40
Alignment explanation
Indices: 67742--67952 Score: 161
Period size: 40 Copynumber: 5.3 Consensus size: 40
67732 AATCTGTAAA
*
67742 TCGCAACGCGAATTTGTAAATCACAACACATAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACACATAAGTCAAAT
* *
67782 TCGCAACACAGAA---GTCAAATTCGCAACGCGAT-AGTCAAAT
1 TCGCAACGC-GAATTTGT-AAA-TCGCAACAC-ATAAGTCAAAT
* *
67822 TCGCAACGC-CA-TAGTCAAATTCGCAACAC-TGAAGTCAAAT
1 TCGCAACGCGAATTTGT-AAA-TCGCAACACAT-AAGTCAAAT
* * * * **
67862 TCGTAATGCGAATCTGTAAATCGCAACGCGAATCTGT-AAA-
1 TCGCAACGCGAATTTGTAAATCGCAACAC--ATAAGTCAAAT
* *
67902 TCGTAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACACATAAGTCAAAT
67942 TCGCAACGCGA
1 TCGCAACGCGA
67953 TAGTCAAATT
Statistics
Matches: 135, Mismatches: 21, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
38 7 0.05
39 6 0.04
40 105 0.78
41 12 0.09
42 4 0.03
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGAATTTGTAAATCGCAACACATAAGTCAAAT
Found at i:67790 original size:20 final size:20
Alignment explanation
Indices: 67765--68048 Score: 146
Period size: 20 Copynumber: 14.2 Consensus size: 20
67755 TTGTAAATCA
67765 CAACACATAAGTCAAATTCG
1 CAACACATAAGTCAAATTCG
*
67785 CAACACAGAAGTCAAATTCG
1 CAACACATAAGTCAAATTCG
*
67805 CAACGCGAT-AGTCAAATTCG
1 CAACAC-ATAAGTCAAATTCG
*
67825 CAACGCCAT-AGTCAAATTCG
1 CAAC-ACATAAGTCAAATTCG
67845 CAACAC-TGAAGTCAAATTCG
1 CAACACAT-AAGTCAAATTCG
* **
67865 TAATGCGA-ATCTGT-AAA-TCG
1 CAA--C-ACATAAGTCAAATTCG
* **
67885 CAACGCGAATCTGT-AAA-TCG
1 CAACAC--ATAAGTCAAATTCG
* * **
67905 TAACGCGAATTTGT-AAA-TCG
1 CAACAC--ATAAGTCAAATTCG
*
67925 CAACACAGAAGTCAAATTCG
1 CAACACATAAGTCAAATTCG
*
67945 CAACGCGAT-AGTCAAATTCG
1 CAACAC-ATAAGTCAAATTCG
* *
67965 CAACA-TTGAATTTCAAATTCG
1 CAACACAT-AA-GTCAAATTCG
* *
67986 TAACACAAAAGTCAAATTCG
1 CAACACATAAGTCAAATTCG
68006 CAACACGAT-AGTCAAATTCG
1 CAACAC-ATAAGTCAAATTCG
* *
68026 CAACGCGA-AATTCAAATTCG
1 CAACAC-ATAAGTCAAATTCG
68046 CAA
1 CAA
68049 AGCGCGTTTA
Statistics
Matches: 214, Mismatches: 30, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.03
19 4 0.02
20 177 0.83
21 22 0.10
22 3 0.01
23 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
CAACACATAAGTCAAATTCG
Found at i:67890 original size:60 final size:60
Alignment explanation
Indices: 67742--67890 Score: 187
Period size: 60 Copynumber: 2.5 Consensus size: 60
67732 AATCTGTAAA
* *
67742 TCGCAACGCGAATTTGTAAATCACAAC-ACATAAGTCAAATTCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TTGTAAATCGCAACGCCATAAGTCAAATTCGCAACACAGAAGTCAAAT
* *
67802 TCGCAACGCG-ATAGTCAAATTCGCAACGCCAT-AGTCAAATTCGCAACACTGAAGTCAAAT
1 TCGCAACGCGAATTGT-AAA-TCGCAACGCCATAAGTCAAATTCGCAACACAGAAGTCAAAT
* *
67862 TCGTAATGCGAATCTGTAAATCGCAACGC
1 TCGCAACGCGAAT-TGTAAATCGCAACGC
67891 GAATCTGTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
58 3 0.04
59 4 0.05
60 60 0.78
61 8 0.10
62 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGAATTGTAAATCGCAACGCCATAAGTCAAATTCGCAACACAGAAGTCAAAT
Found at i:67929 original size:140 final size:140
Alignment explanation
Indices: 67717--67968 Score: 400
Period size: 140 Copynumber: 1.8 Consensus size: 140
67707 ACCCAGTTTC
*
67717 CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCACAACACATAAGTCAAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCACAACACATAAGTCAAAT
67782 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCCATAGTCAAATTCGCA
66 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCCATAGTCAAATTCGCA
67847 ACACTGAAGT
131 ACACTGAAGT
* * ** * **
67857 CAAATTCGTAATGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCGTAACGCGAATTTGT-AA
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCACAACAC--ATAAGTCAA
67921 A-TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
64 ATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
67969 ATTGAATTTC
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
140 95 0.93
141 3 0.03
142 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (140 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCACAACACATAAGTCAAAT
TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCCATAGTCAAATTCGCA
ACACTGAAGT
Found at i:67966 original size:40 final size:39
Alignment explanation
Indices: 67773--68048 Score: 224
Period size: 40 Copynumber: 6.9 Consensus size: 39
67763 CACAACACAT
* *
67773 AAGTCAAATTCGCAACACAGA-AGTCAAATTCGCAACGCG
1 AAGTCAAATTCGCAACGC-GATAGTCAAATTCGCAACACG
*
67812 ATAGTCAAATTCGCAACGCCATAGTCAAATTCGCAACACTG
1 A-AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACAC-G
* * * *
67853 AAGTCAAATTCGTAATGCGAATCTGT-AAA-TCGCAACGCG
1 AAGTCAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACG
* *
67892 AA-TCTGTAAA-TCGTAACGCGAATTTGT-AAA-TCGCAACACAG
1 AAGTC---AAATTCGCAACGCG-A-TAGTCAAATTCGCAACAC-G
*
67933 AAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACATTG
1 AAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACA-CG
* * * * *
67973 AATTTCAAATTCGTAACACAAAAGTCAAATTCGCAACACG
1 AA-GTCAAATTCGCAACGCGATAGTCAAATTCGCAACACG
* *
68013 ATAGTCAAATTCGCAACGCGAAATTCAAATTCGCAA
1 A-AGTCAAATTCGCAACGCGATAGTCAAATTCGCAA
68049 AGCGCGTTTA
Statistics
Matches: 196, Mismatches: 24, Indels: 33
0.77 0.09 0.13
Matches are distributed among these distances:
38 5 0.03
39 12 0.06
40 130 0.66
41 45 0.23
42 4 0.02
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (39 bp):
AAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACG
Found at i:68203 original size:57 final size:57
Alignment explanation
Indices: 68115--68327 Score: 365
Period size: 57 Copynumber: 3.8 Consensus size: 57
68105 AACGTTGCGA
* * *
68115 ATTTAC-AATTCGCAACGCTAATTACCAATATAGCTAAACAGTACTATCGCAACGCG
1 ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
*
68171 ATTTACAAATTCGTAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
1 ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
68228 ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
1 ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
* *
68285 ATTTACAAATTCGTAATGCTAATTACCGATATAGGTAAACAGT
1 ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
68328 GTTGCGAAAA
Statistics
Matches: 149, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
56 6 0.04
57 143 0.96
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (57 bp):
ATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGTG
Found at i:68391 original size:20 final size:20
Alignment explanation
Indices: 68368--68412 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
68358 ACTTTCGCGA
68368 TGCGAATTTGACTTCAATGT
1 TGCGAATTTGACTTCAATGT
**
68388 TGCGAATTTGACTTCTGTGT
1 TGCGAATTTGACTTCAATGT
68408 TGCGA
1 TGCGA
68413 TTTACAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (20 bp):
TGCGAATTTGACTTCAATGT
Found at i:80292 original size:31 final size:29
Alignment explanation
Indices: 80247--80305 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
80237 ACTTTTACTC
* *
80247 AATTTACTTTTGTCAGTCAAATCACTTAAT
1 AATTTAATTTTGTCAATCAAATCA-TTAAT
*
80277 AATTTAATTATTGTCAATTAAATCATTAA
1 AATTTAATT-TTGTCAATCAAATCATTAA
80306 CTGTTAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (29 bp):
AATTTAATTTTGTCAATCAAATCATTAAT
Found at i:82816 original size:12 final size:12
Alignment explanation
Indices: 82799--82823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82789 ATATTTCTTA
82799 TTTTTTTTGTTT
1 TTTTTTTTGTTT
82811 TTTTTTTTGTTT
1 TTTTTTTTGTTT
82823 T
1 T
82824 CGAATCACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:103866 original size:2 final size:2
Alignment explanation
Indices: 103859--103886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
103849 TTTATTTTGA
103859 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
103887 TTCTGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104752 original size:44 final size:44
Alignment explanation
Indices: 104689--104795 Score: 205
Period size: 44 Copynumber: 2.4 Consensus size: 44
104679 GTGGCCGCAA
104689 CAGTGTAATTATCGCATTGGAACATCATTGGAACATTTTAAAGG
1 CAGTGTAATTATCGCATTGGAACATCATTGGAACATTTTAAAGG
104733 CAGTGTAATTATCGCATTGGAACATCATTGGAACATTTTAAAGG
1 CAGTGTAATTATCGCATTGGAACATCATTGGAACATTTTAAAGG
*
104777 CAGTGTAATTATTGCATTG
1 CAGTGTAATTATCGCATTG
104796 TAACGTTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.34
Consensus pattern (44 bp):
CAGTGTAATTATCGCATTGGAACATCATTGGAACATTTTAAAGG
Found at i:121984 original size:27 final size:27
Alignment explanation
Indices: 121946--122012 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
121936 GATAATGATT
*
121946 CTGAATTATTCAAAATGTACTTCTGTG
1 CTGAATTATTCAAAATGTACTTCTATG
* *
121973 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATTATTCAAAATGTACTTCTATG
122000 CTGAATTATTCAA
1 CTGAATTATTCAA
122013 CACTATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (27 bp):
CTGAATTATTCAAAATGTACTTCTATG
Found at i:122100 original size:29 final size:29
Alignment explanation
Indices: 122066--122162 Score: 185
Period size: 29 Copynumber: 3.3 Consensus size: 29
122056 CGAAACAAAC
*
122066 GCGCTGAATGTTGAATGATTTAACATTCA
1 GCGCTGAATGTTGAACGATTTAACATTCA
122095 GCGCTGAATGTTGAACGATTTAACATTCA
1 GCGCTGAATGTTGAACGATTTAACATTCA
122124 GCGCTGAATGTTGAACGATTTAACATTCA
1 GCGCTGAATGTTGAACGATTTAACATTCA
122153 GCGCTGAATG
1 GCGCTGAATG
122163 ATTCCAAAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (29 bp):
GCGCTGAATGTTGAACGATTTAACATTCA
Found at i:127552 original size:20 final size:20
Alignment explanation
Indices: 127527--127577 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
127517 CCATACAATG
127527 GGTATCGATACT-GTAGGTGA
1 GGTATCGATACTCGTAGG-GA
*
127547 GGTATCGATACTCGTAGGGT
1 GGTATCGATACTCGTAGGGA
127567 GGTATCGATAC
1 GGTATCGATAC
127578 CAAGTTCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (20 bp):
GGTATCGATACTCGTAGGGA
Found at i:129807 original size:19 final size:19
Alignment explanation
Indices: 129785--129823 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
129775 AAATATGAAC
129785 TCTATTTAAAAATTCCCTT
1 TCTATTTAAAAATTCCCTT
129804 TCTATTTAAAAATTCCCTT
1 TCTATTTAAAAATTCCCTT
129823 T
1 T
129824 AAGAACTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (19 bp):
TCTATTTAAAAATTCCCTT
Found at i:135654 original size:18 final size:20
Alignment explanation
Indices: 135601--135665 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
135591 CACTGAATAT
135601 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* **
135621 TTGTTCCGAATAACCACT-A
1 TTGTCCCGAAGGACCACTGA
135640 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
*
135659 TTATCCC
1 TTGTCCC
135666 TCGACTCTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 14 0.39
19 2 0.06
20 20 0.56
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:140109 original size:29 final size:29
Alignment explanation
Indices: 140068--140141 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
140058 AGTATTTAAT
140068 TTTTTTTATCAAAATAGAAA-CTTAAAGTA
1 TTTTTTTATCAAAATAGAAATC-TAAAGTA
** *
140097 TTTTTTTATCAAAATAGGTATCTAGAGTA
1 TTTTTTTATCAAAATAGAAATCTAAAGTA
*
140126 TTTTTTGATCAAAATA
1 TTTTTTTATCAAAATA
140142 AGAATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTTTTTATCAAAATAGAAATCTAAAGTA
Found at i:140214 original size:34 final size:30
Alignment explanation
Indices: 140176--140244 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
140166 TCGATATAAC
*
140176 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
140210 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
140239 AATTTA
1 AATTTA
140245 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:140252 original size:31 final size:31
Alignment explanation
Indices: 140185--140244 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
140175 CAATTTAAGG
*
140185 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
140216 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
140245 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:140397 original size:21 final size:21
Alignment explanation
Indices: 140371--140412 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
140361 ATTTGAATAT
*
140371 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
140392 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
140413 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:140473 original size:21 final size:21
Alignment explanation
Indices: 140440--140479 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
140430 TTTTTGCAGA
*
140440 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
140462 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
140480 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:142244 original size:60 final size:60
Alignment explanation
Indices: 142180--142297 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
142170 TAGGGACCAA
* * **
142180 TTTAGAATGAGATTCATAGTTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTGG
1 TTTAGAATAAGAGTCATAGTTTGAAGATGAAATTAGAATATTCAAAAGTTTAAGGACTGG
* * * *
142240 TTTAGAATAAGAGTCATAGTTTGAAGATGTAATTGGAATGTTTAAAAGTTTAAGGACT
1 TTTAGAATAAGAGTCATAGTTTGAAGATGAAATTAGAATATTCAAAAGTTTAAGGACT
142298 AATTAAATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (60 bp):
TTTAGAATAAGAGTCATAGTTTGAAGATGAAATTAGAATATTCAAAAGTTTAAGGACTGG
Found at i:142598 original size:15 final size:15
Alignment explanation
Indices: 142580--142608 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
142570 GCGACACCGG
142580 CCGCTCCGACGACAC
1 CCGCTCCGACGACAC
142595 CCGCTCCGACGACA
1 CCGCTCCGACGACA
142609 ACCCTCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (15 bp):
CCGCTCCGACGACAC
Done.