Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006228.1 Hibiscus syriacus cultivar Beakdansim tig00014843_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: 79864
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4592 original size:28 final size:28
Alignment explanation
Indices: 4548--4736 Score: 188
Period size: 28 Copynumber: 6.8 Consensus size: 28
4538 CCCGTTGAAC
*
4548 TGGTGATATTTTAGTAATTATTTTAAAA
1 TGGTGATATTTTCGTAATTATTTTAAAA
* *
4576 TGGTGATATTTTGGTAATTATTTTCAAA
1 TGGTGATATTTTCGTAATTATTTTAAAA
* * *
4604 TTGTGTTA-TTTCATAATTA-TTTAAAA
1 TGGTGATATTTTCGTAATTATTTTAAAA
4630 TGGTGATATTTT-GTAATTA-TTTAAAA
1 TGGTGATATTTTCGTAATTATTTTAAAA
* * *
4656 AGATGATATTTTTGTAATTATTTTTAAAAA
1 TGGTGATATTTTCGTAATTA-TTTT-AAAA
* * * *
4686 AGGTGACAGTTTCGTAATTATTTAAAAA
1 TGGTGATATTTTCGTAATTATTTTAAAA
* * *
4714 GGGTGATATTTTTGTAAATATTT
1 TGGTGATATTTTCGTAATTATTT
4737 CTTCAAGGGT
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 35 0.26
27 19 0.14
28 54 0.40
29 6 0.04
30 20 0.15
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (28 bp):
TGGTGATATTTTCGTAATTATTTTAAAA
Found at i:5871 original size:113 final size:113
Alignment explanation
Indices: 5673--6004 Score: 452
Period size: 113 Copynumber: 2.9 Consensus size: 113
5663 GAAAATATTT
*
5673 CAGGCTCCTTTGC-TGTGCTCAGGGTAAGTCCTTATTGGAGTGCATGTGGGTGTATGGTTCTGGG
1 CAGGCTCCTTTGCTTGTGCTCAGGGTAAGTCCTTATT-GAGTGCAGGTGGGTGTATGGTTCTGGG
*
5737 GAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAATTTATTAC
65 GAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTAC
*
5786 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTG-GTGCAGGTGAGTGTATGGTTCTGGG
1 CAGGCTCCTTTGCT-TGTGCTCAGGGTAAGTCCTTATTGAGTGCAGGTGGGTGTATGGTTCTGGG
* * *
5850 GAACCTGCACATTTTAGTAATCGAAGTGATTGGATGGGGAAGTTATTAC
65 GAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTAC
** * * *
5899 CGTAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCT
1 C--AGGCTCCTTTGC-TTGTGCTCAGGGTAAGTCCTTA-TTGAGTGCAGGTGGGTGTATGGTTCT
* * * * *
5964 GGAGAACATACAAATTCTAGTAATCGGAGTGATTAGATGGA
62 GGGGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGA
6005 AATAGTGTTC
Statistics
Matches: 193, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
113 82 0.42
114 1 0.01
115 53 0.27
116 3 0.02
117 54 0.28
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (113 bp):
CAGGCTCCTTTGCTTGTGCTCAGGGTAAGTCCTTATTGAGTGCAGGTGGGTGTATGGTTCTGGGG
AACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTAC
Found at i:12762 original size:32 final size:32
Alignment explanation
Indices: 12726--12804 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
12716 TATATCCAAT
*
12726 GTGATGACGTGGTATATCTCACATCACCTAAG
1 GTGATGACGTGATATATCTCACATCACCTAAG
* * * * *
12758 GTGATGTCGTAATATATGTCGCATCACCTAAT
1 GTGATGACGTGATATATCTCACATCACCTAAG
12790 GTGATGACGTGATAT
1 GTGATGACGTGATAT
12805 GTATCACGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (32 bp):
GTGATGACGTGATATATCTCACATCACCTAAG
Found at i:13964 original size:27 final size:26
Alignment explanation
Indices: 13906--13968 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
13896 TTTTTTTCCT
* *
13906 TAAAATCTTATAAATTTATTCTCATC
1 TAAAATCTTATAAATTCATTCTAATC
* *
13932 TAAAATTTTATAAATTCGTTCCTAATC
1 TAAAATCTTATAAATTCATT-CTAATC
13959 TAAAATCTTA
1 TAAAATCTTA
13969 CTTCTACCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAATCTTATAAATTCATTCTAATC
Found at i:15729 original size:112 final size:112
Alignment explanation
Indices: 15529--15994 Score: 671
Period size: 112 Copynumber: 4.1 Consensus size: 112
15519 TTGTCGGTTT
* * * * *
15529 GTGTCGATATTTTATAAAAATATATTGATCCATAATAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
15594 GGTCTATAAATGATAAACCAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * * **
15641 ATATCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAATT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
15706 AGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
**
15753 GTGTCGATACTTTATAAAAATGTATCGATCCACCATATTAATATAACAGGTAAAAAAATGACAAA
1 GTGTCGATACTTTATAAAAATGTATCGAT---CCATAACAATATAACAGGTAAAAAAATGACAAA
**
15818 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
63 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
15868 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
15933 GGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
15980 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
15995 TATAAGTATC
Statistics
Matches: 313, Mismatches: 38, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
112 211 0.67
115 102 0.33
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:15967 original size:227 final size:224
Alignment explanation
Indices: 15529--15994 Score: 689
Period size: 227 Copynumber: 2.1 Consensus size: 224
15519 TTGTCGGTTT
* * *
15529 GTGTCGATATTTTATAAAAATATATTGATCCATAATAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACC
* * *
15594 GGTCTATAAATGATAAACCAGGTAAAACGCTACCGGATATATTGAAAATATCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTATAAA
* ** * *
15659 AATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAATTAGTTTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAA
*
15724 CAGGTAAAGCGCTACCGGATATATTGAAA
196 CAGATAAAGCGCTACCGGATATATTGAAA
* *
15753 GTGTCGATACTTTATAAAAATGTATCGATCCACCATATTAATATAACAGGTAAAAAAATGACAAA
1 GTGTCGATACTTTATAAAAATATATCGAT---CCATAATAATATAACAGGTAAAAAAATGACAAA
* * * *
15818 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAAGTGTCGATACTTTAT
63 ACCGGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTAT
* * *
15883 AAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCGGTCTATAAATAACA
128 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACA
* * *
15948 AAACAGATAAAGTGCTACCGGATATGTTGATA
193 AAACAGATAAAGCGCTACCGGATATATTGAAA
15980 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
15995 TATAAGTATC
Statistics
Matches: 215, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
224 26 0.12
227 189 0.88
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAA
CAGATAAAGCGCTACCGGATATATTGAAA
Found at i:16172 original size:182 final size:182
Alignment explanation
Indices: 15865--16321 Score: 745
Period size: 182 Copynumber: 2.5 Consensus size: 182
15855 AGATATATTG
* *
15865 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * * * *
15930 ACCGGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
** * * * *
15995 TATAAGTATCGACACTTTTGGAATTTAAAATAGAAGAAGTTGTAGCACTAAT
131 TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
16047 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
16112 ACCGGTCTCGAAATGACAAAACCGGTAAAG-GACTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTG-CTACCGGATATGTTGAAAGTGTCGATACTTTA
*
16176 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
130 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
*
16229 AAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
16294 ATCGGTCTCGAAATGACAAAACCGGTAA
66 ACCGGTCTCGAAATGACAAAACCGGTAA
16322 TAAAAAAGTG
Statistics
Matches: 257, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
181 1 0.00
182 256 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Found at i:17386 original size:2 final size:2
Alignment explanation
Indices: 17379--17409 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17369 AATTAACCAC
17379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17410 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19747 original size:2 final size:2
Alignment explanation
Indices: 19740--19806 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
19730 ACCACAATAA
* * * *
19740 AT AT AT AT AT TT AT AT GT -T GT AT -T AC 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
* * *
19780 AT AT GT AT GT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19807 AGTATTATTA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19782 original size:28 final size:30
Alignment explanation
Indices: 19736--19806 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
19726 TCTGACCACA
19736 ATAAATATATATAT-T-TATATGT-TGTAT
1 ATAAATATATATATATATATATGTATGTAT
*
19763 -TACATATATATATATATATATGTATGTAT
1 ATAAATATATATATATATATATGTATGTAT
19792 ATAAATATATATATA
1 ATAAATATATATATA
19807 AGTATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 12 0.32
27 1 0.03
28 7 0.18
29 5 0.13
30 13 0.34
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (30 bp):
ATAAATATATATATATATATATGTATGTAT
Found at i:20037 original size:18 final size:18
Alignment explanation
Indices: 20003--20036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19993 TTATACATCT
*
20003 ATTATTTTATATATTTTA
1 ATTATTTGATATATTTTA
20021 ATTATTTGAT-TATTTT
1 ATTATTTGATATATTTT
20037 TTTTATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTATTTGATATATTTTA
Found at i:20207 original size:4 final size:4
Alignment explanation
Indices: 20198--20227 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
20188 TTTATTATTG
20198 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
20228 GTATATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:20212 original size:31 final size:32
Alignment explanation
Indices: 20170--20229 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
20160 TGATGTTCAT
20170 TTTATTGTATTT-TGTTATTT-TATTATTGTTTA
1 TTTATTGTATTTAT-TTATTTAT-TTATTGTTTA
20202 TTTATT-TATTTATTTATTTATTTATTGT
1 TTTATTGTATTTATTTATTTATTTATTGT
20230 ATATAGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (32 bp):
TTTATTGTATTTATTTATTTATTTATTGTTTA
Found at i:20222 original size:27 final size:28
Alignment explanation
Indices: 20170--20231 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 28
20160 TGATGTTCAT
20170 TTTATTGTATTTTGTTATTTTATTATTG
1 TTTATTGTATTTTGTTATTTTATTATTG
*
20198 TTTATT-TATTTAT-TTA-TTTA-T-TTA
1 TTTATTGTATTT-TGTTATTTTATTATTG
20222 TTTATTGTAT
1 TTTATTGTAT
20232 ATAGATTGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 8 0.26
25 4 0.13
26 4 0.13
27 8 0.26
28 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (28 bp):
TTTATTGTATTTTGTTATTTTATTATTG
Found at i:20306 original size:21 final size:21
Alignment explanation
Indices: 20272--20321 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
20262 TATTTATTTA
20272 TTTTCTTTCT-TTC-TTTCTAT
1 TTTTCTTT-TGTTCTTTTCTAT
*
20292 TTTTACTTTTGTTCTTTTTTAT
1 TTTT-CTTTTGTTCTTTTCTAT
20314 TTTTCTTT
1 TTTTCTTT
20322 ATCTTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
22 10 0.38
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTGTTCTTTTCTAT
Found at i:20376 original size:9 final size:9
Alignment explanation
Indices: 20245--20384 Score: 63
Period size: 9 Copynumber: 14.7 Consensus size: 9
20235 GATTGTCCTC
20245 ATTTTCTTT
1 ATTTTCTTT
*
20254 ATTTTATTT
1 ATTTTCTTT
*
20263 A-TTTATTT
1 ATTTTCTTT
20271 ATTTTCTTT
1 ATTTTCTTT
*
20280 -CTTTCTTTCT
1 ATTTTC-TT-T
20290 ATTTTTACTTTT
1 A-TTTT-C-TTT
* *
20302 GTTCTTTTTT
1 ATT-TTCTTT
20312 ATTTTTCTTT
1 A-TTTTCTTT
*
20322 ATCTTT-TTC
1 AT-TTTCTTT
*
20331 ATCTTCATGTT
1 ATTTTC-T-TT
*
20342 TTTTTCTTT
1 ATTTTCTTT
20351 A-TTTCTTTT
1 ATTTTC-TTT
*
20360 GTTTTTCTTT
1 -ATTTTCTTT
20370 ATTTTCTTT
1 ATTTTCTTT
20379 ATTTTC
1 ATTTTC
20385 ATTTTTTATC
Statistics
Matches: 100, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
8 18 0.18
9 41 0.41
10 18 0.18
11 13 0.13
12 6 0.06
13 4 0.04
ACGTcount: A:0.11, C:0.12, G:0.02, T:0.75
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:24300 original size:95 final size:95
Alignment explanation
Indices: 24115--24377 Score: 314
Period size: 95 Copynumber: 2.7 Consensus size: 95
24105 GCATTATAAT
* * *
24115 ATTATATATATACAATAAAACTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCTCGGCTTTA
1 ATTATATATATACAAT-GAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTA
* **
24180 TGGATAAGATTTAACCAACCAGATAAAGGTG
65 TGGATAAAATTTAACCAACCAGATAAAGGCA
* * * *
24211 ATTATA-ATATGCAATGAAGCTTGAGTTGTCCTTCTAGAGAAATTGGTTAAACGCCACGGCTTTA
1 ATTATATATATACAATGAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTA
* * * *
24275 TGGATAAAATTTAGCTAGCCTGATAAAGGCA
65 TGGATAAAATTTAACCAACCAGATAAAGGCA
* *
24306 ATTATAATATCTATACAATGATA-TTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTTGGCT
1 ATTAT-ATA--TATACAATGA-ACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCT
24370 TTATGGAT
62 TTATGGAT
24378 TCAGCTAGCC
Statistics
Matches: 141, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
94 2 0.01
95 77 0.55
96 7 0.05
97 1 0.01
98 44 0.31
99 9 0.06
100 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (95 bp):
ATTATATATATACAATGAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTAT
GGATAAAATTTAACCAACCAGATAAAGGCA
Found at i:27360 original size:14 final size:14
Alignment explanation
Indices: 27341--27380 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
27331 AAGTTGACCA
27341 ACAGAATCTGTTTT
1 ACAGAATCTGTTTT
27355 ACAGAATCTGTTTT
1 ACAGAATCTGTTTT
27369 ACAGAATCTGTT
1 ACAGAATCTGTT
27381 GTCCGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (14 bp):
ACAGAATCTGTTTT
Found at i:28548 original size:36 final size:36
Alignment explanation
Indices: 28499--28614 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
28489 TAATTTACTC
*
28499 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
28536 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-TGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT-T
* * * *
28572 AAAACAACTTTTCTCTCT-TTGAGATAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
28607 GAAACAAA
1 AAAACAAA
28615 AACTTTGAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
35 20 0.29
36 42 0.60
37 8 0.11
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:28721 original size:36 final size:36
Alignment explanation
Indices: 28627--28924 Score: 261
Period size: 36 Copynumber: 8.4 Consensus size: 36
28617 CTTTGAATCT
* * * *
28627 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * * *
28663 GTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
28700 ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
28736 GTTTCCCTTGAATCAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
28772 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CA
* * * *
28801 GTTTTCCTTTAAACAAATTTCGTCTCTCTCGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*** * * *
28837 GTTTTTTTTGGAACTAAGTTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
28874 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
28910 ATTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
28925 CCAACCTTTG
Statistics
Matches: 209, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.00
29 20 0.10
30 3 0.01
35 3 0.01
36 126 0.60
37 56 0.27
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:28728 original size:21 final size:21
Alignment explanation
Indices: 28703--28767 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
28693 TTAGACAATT
28703 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
28724 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
*
28741 -C-CTTGAATCAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
28760 TCTCTTGA
1 TCTCTTGA
28768 GACAGTTTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 6 0.18
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.45
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:28848 original size:174 final size:172
Alignment explanation
Indices: 28505--28924 Score: 626
Period size: 174 Copynumber: 2.4 Consensus size: 172
28495 ACTCAAAACA
*
28505 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTT-CT
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCT
* *
28569 TGTAAAACAACTTTTCTCTCTTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCC
66 TG--AAACAAATTTTCTCTCTTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCC
* *
28634 TTGAAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACT
129 TTGAAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACT
* *
28678 AAGTTTTGGCTCTCTTTAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTT-CC
* * *
28743 TTGAATCAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCC
65 TTGAAACAAATTTTCTCTCT-TTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCC
* * *
28808 TTTAAACAAATTTCGTCTCTCTCGAGACAGTTTTTTTTGGAACT
129 TTGAAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACT
* * * * *
28852 AAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTC
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC-C
28917 TTGAAACA
65 TTGAAACA
28925 CCAACCTTTG
Statistics
Matches: 222, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
173 74 0.33
174 144 0.65
175 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (172 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCT
TGAAACAAATTTTCTCTCTTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTT
GAAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACT
Found at i:28887 original size:102 final size:102
Alignment explanation
Indices: 28701--28889 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
28691 CTTTAGACAA
* * *
28701 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAATCAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAATCAAATTTTATCTCTCTT
28766 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
* *** *
28803 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTTTTTTGGAA-CTAAGTTTTATCTCTC
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTT-GAATC-AAATTTTATCTCTC
28866 TTGAGACAGTTTCCCTTGAAACAA
64 TTGAGACAGTTTCCCTTGAAACAA
28890 GTTTTGTCTC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 34 0.44
102 43 0.56
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAATCAAATTTTATCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
Found at i:28910 original size:21 final size:20
Alignment explanation
Indices: 28852--28910 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
28842 TTTTGGAACT
28852 AAGTTTTATCTCTCTTGAGAC
1 AAGTTTT-TCTCTCTTGAGAC
*
28873 -AG--TTTC-C-CTTGAAAC
1 AAGTTTTTCTCTCTTGAGAC
28888 AAGTTTTGTCTCTCTTGAGAC
1 AAGTTTT-TCTCTCTTGAGAC
28909 AA
1 AA
28911 TTTCTCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 2 0.07
18 4 0.13
19 2 0.07
20 3 0.10
21 9 0.30
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (20 bp):
AAGTTTTTCTCTCTTGAGAC
Found at i:29403 original size:2 final size:2
Alignment explanation
Indices: 29398--29444 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
29388 ACCACAATAA
* * *
29398 AT AT AT AT AT TT AT AT AT -T GT AT -T AC 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
29438 AT AT AT A
1 AT AT AT A
29445 AGTATTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30803 original size:19 final size:19
Alignment explanation
Indices: 30753--30804 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
30743 TATATATATG
*
30753 TTTTCTTTTTACTTTATTTAT
1 TTTTCTTTTT-C-TAATTTAT
*
30774 TTATT-TATTTCTAATTTAT
1 TT-TTCTTTTTCTAATTTAT
30793 TTTTCTTTTTCT
1 TTTTCTTTTTCT
30805 TTTCTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 1 0.04
21 6 0.23
22 2 0.08
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTTCTAATTTAT
Found at i:30997 original size:21 final size:20
Alignment explanation
Indices: 30901--31058 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
30891 AAATGACCAA
**
30901 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
30920 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
30940 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
*
30960 CAAAATCGCAACACGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
30981 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
31002 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
31022 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
31043 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
31059 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 46 0.45
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:31109 original size:60 final size:60
Alignment explanation
Indices: 31025--31210 Score: 237
Period size: 60 Copynumber: 3.1 Consensus size: 60
31015 CGATTTTCCA
* ** * *
31025 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
31085 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
31145 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
31206 AAATC
1 AAATC
31211 ACGACGCGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 81 0.78
61 23 0.22
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:31218 original size:20 final size:20
Alignment explanation
Indices: 31025--31210 Score: 205
Period size: 20 Copynumber: 9.2 Consensus size: 20
31015 CGATTTTCCA
* ** *
31025 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
31045 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
31065 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31085 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
31105 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
31125 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31145 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
31165 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
31185 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
31206 AAATC
1 AAATC
31211 ACGACGCGAT
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 118 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:31640 original size:33 final size:33
Alignment explanation
Indices: 31601--31671 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
31591 TTCACTTAGA
*
31601 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
31634 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
31667 TTTCA
1 TTTCA
31672 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:31775 original size:21 final size:20
Alignment explanation
Indices: 31751--31856 Score: 82
Period size: 21 Copynumber: 5.5 Consensus size: 20
31741 TGCAGAAGAG
*
31751 TCGCAATGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
31772 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
31792 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
31813 TCACAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
31827 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
31846 TCGCAACGAGA
1 TCGCAACGAGA
31857 GAATCGCAAC
Statistics
Matches: 65, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.25
21 24 0.37
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:31808 original size:41 final size:38
Alignment explanation
Indices: 31744--31860 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 38
31734 TTCAATTTGC
* * *
31744 AGAAGAGTCGCAATGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
31782 AGAATGACTGTCGCAACGAGAGAAATGAAAATCACAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
31823 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
31856 AGAAT
1 AGAAT
31861 CGCAACGCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 31 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:31833 original size:14 final size:14
Alignment explanation
Indices: 31811--31867 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
31801 GAGAAATGAA
*
31811 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
31825 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
31844 AATCGCAACGAGAG
1 AATCGCAACGAGAG
31858 AATCGCAACG
1 AATCGCAACG
31868 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31843 original size:33 final size:33
Alignment explanation
Indices: 31803--31872 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
31793 CGCAACGAGA
31803 GAAATGAAAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
*
31836 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
31869 GAAA
1 GAAA
31873 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCACAACGAGAGAATCGCAACGC
Found at i:31879 original size:33 final size:33
Alignment explanation
Indices: 31809--31883 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
31799 GAGAGAAATG
* **
31809 AAAATCACAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
31842 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
31875 AAAATCGCA
1 AAAATCGCA
31884 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:31901 original size:19 final size:19
Alignment explanation
Indices: 31879--31976 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
31869 GAAACCAAAA
*
31879 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31898 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
31912 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31931 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
31945 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
31964 TCGCGTTGCGATT
1 TCGCGTTGCGATT
31977 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31920 original size:14 final size:14
Alignment explanation
Indices: 31901--31990 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
31891 TTTCATTTCG
31901 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31915 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
31934 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31948 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
31967 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
31981 CGTTGCGATT
1 CGTTGCGATT
31991 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31926 original size:33 final size:33
Alignment explanation
Indices: 31884--31998 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
31874 CAAAATCGCA
31884 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31917 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
31950 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31983 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
31999 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:34694 original size:20 final size:20
Alignment explanation
Indices: 34666--34895 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
34656 AAATTTCAGT
* * *
34666 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34686 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
34706 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34726 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
34746 GTTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34766 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
34786 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
34806 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
34826 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
34846 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
34866 GTTGCGATTGT-CATATTCGC
1 GTTGCGATT-TACGGATTCGC
34886 GTTGCGATTT
1 GTTGCGATTT
34896 TGGAAACTGA
Statistics
Matches: 180, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 177 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:35108 original size:13 final size:13
Alignment explanation
Indices: 35090--35127 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
35080 GATGTTCATT
35090 TTATTGTATTTTG
1 TTATTGTATTTTG
35103 TTATTGTATTTTG
1 TTATTGTATTTTG
*
35116 TTATTTTATTTT
1 TTATTGTATTTT
35128 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (13 bp):
TTATTGTATTTTG
Found at i:35136 original size:15 final size:15
Alignment explanation
Indices: 35088--35146 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
35078 TTGATGTTCA
*
35088 TTTTATTGTATTTTGT
1 TTTTATT-TATTTTAT
*
35104 TATTGTATTT-TGTTA-
1 T-TT-TATTTATTTTAT
35119 TTTTATTTTATTTTAT
1 TTTTA-TTTATTTTAT
35135 TTTTATTTATTT
1 TTTTATTTATTT
35147 ATTGATTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 12 0.34
16 9 0.26
17 3 0.09
18 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTATTTATTTTAT
Found at i:35199 original size:17 final size:17
Alignment explanation
Indices: 35177--35209 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35167 CTTCATTTTC
35177 TTTATTTTCTTTATTTA
1 TTTATTTTCTTTATTTA
35194 TTTATTTTCTTTATTT
1 TTTATTTTCTTTATTT
35210 CTATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTCTTTATTTA
Found at i:35222 original size:17 final size:16
Alignment explanation
Indices: 35173--35234 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
35163 TTGTCTTCAT
*
35173 TTTCTTTATTTTCTTTA
1 TTTCTTT-TTTACTTTA
* *
35190 TTTATTTATTTTCTTTA
1 TTTCTTT-TTTACTTTA
35207 TTTCTATTTTTACTTT-
1 TTTCT-TTTTTACTTTA
35223 TGTTCTTTTTTA
1 T-TTCTTTTTTA
35235 TTTTTTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 7 0.17
17 31 0.77
18 2 0.05
ACGTcount: A:0.13, C:0.10, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTCTTTTTTACTTTA
Found at i:35313 original size:9 final size:9
Alignment explanation
Indices: 35166--35305 Score: 92
Period size: 9 Copynumber: 15.2 Consensus size: 9
35156 ATATAGATTG
*
35166 TCTTCATTT
1 TCTTTATTT
35175 TCTTTATTT
1 TCTTTATTT
35184 TCTTTA-TT
1 TCTTTATTT
*
35192 TATTTATTT
1 TCTTTATTT
35201 TCTTTA-TT
1 TCTTTATTT
35209 TCTATT-TTT
1 TCT-TTATTT
* *
35218 ACTTTTGTTCT
1 TC-TTTATT-T
*
35229 TTTTTATTT
1 TCTTTATTT
*
35238 TTTTTATCTT
1 TCTTTAT-TT
* *
35248 T-TTCATCT
1 TCTTTATTT
35256 TCATGTTATTT
1 TC-T-TTATTT
35267 TCTTTA-TT
1 TCTTTATTT
*
35275 TCTTTTGTTTT
1 TC-TTT-ATTT
35286 TCTTTATTT
1 TCTTTATTT
35295 TCTTTATTT
1 TCTTTATTT
35304 TC
1 TC
35306 ATTTTTTTAT
Statistics
Matches: 105, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
8 18 0.17
9 60 0.57
10 16 0.15
11 11 0.10
ACGTcount: A:0.11, C:0.12, G:0.02, T:0.74
Consensus pattern (9 bp):
TCTTTATTT
Found at i:41497 original size:20 final size:20
Alignment explanation
Indices: 41472--41516 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41462 GTCATCCAAT
*
41472 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
*
41492 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
41512 TTTTT
1 TTTTT
41517 TTCCGGATAA
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:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:44395 original size:2 final size:2
Alignment explanation
Indices: 44390--44414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44380 CGTGTGTTCA
44390 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44415 CTTGCTGCTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46340 original size:14 final size:16
Alignment explanation
Indices: 46294--46340 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
46284 ATGATATGAT
* *
46294 TATATGTTATATAT-A
1 TATATATTATTTATAA
46309 TATATATTATTTATAA
1 TATATATTATTTATAA
46325 TATATATT-TTTA-AA
1 TATATATTATTTATAA
46339 TA
1 TA
46341 CTTTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 16 0.55
16 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATATTATTTATAA
Found at i:46370 original size:18 final size:19
Alignment explanation
Indices: 46329--46370 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
46319 TTATAATATA
*
46329 TATTTTTAAATACTTTTAT
1 TATTTTTAAATACATTTAT
*
46348 T-TTTTTTAATA-ATTTAT
1 TATTTTTAAATACATTTAT
46365 TATTTT
1 TATTTT
46371 ATAGATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 13 0.65
19 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTAAATACATTTAT
Found at i:51997 original size:3 final size:3
Alignment explanation
Indices: 51989--52014 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51979 ACGAGGTAAA
51989 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
52015 AAACAACGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53289 original size:14 final size:14
Alignment explanation
Indices: 53270--53297 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53260 AATCATTATT
53270 ATAAATTTAATTTA
1 ATAAATTTAATTTA
53284 ATAAATTTAATTTA
1 ATAAATTTAATTTA
53298 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAATTTAATTTA
Found at i:75579 original size:31 final size:31
Alignment explanation
Indices: 75540--75611 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
75530 AATATTACAA
75540 AGACTTAACTTTAATTCCAACAATCCCCATC
1 AGACTTAACTTTAATTCCAACAATCCCCATC
*
75571 AGATTTAACTTTAATTCCAACAATCCCCATC
1 AGACTTAACTTTAATTCCAACAATCCCCATC
75602 AGACTTAACT
1 AGACTTAACT
75612 AAACAAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (31 bp):
AGACTTAACTTTAATTCCAACAATCCCCATC
Found at i:76267 original size:26 final size:26
Alignment explanation
Indices: 76238--76287 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
76228 TTAGAACATA
*
76238 GATGAGAAGGAAC-CTTCTCAGAATTG
1 GATGAG-AGGAACTCTTCCCAGAATTG
*
76264 GATGAGCGGAACTCTTCCCAGAAT
1 GATGAGAGGAACTCTTCCCAGAAT
76288 CTCTTGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (26 bp):
GATGAGAGGAACTCTTCCCAGAATTG
Done.