Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003050.1 Hibiscus syriacus cultivar Beakdansim tig00006353_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: 135872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1274 original size:20 final size:20
Alignment explanation
Indices: 1237--1289 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1227 CGCCACCATC
1237 TGGTT-GGCTCGG-TTTGCT
1 TGGTTCGGCTCGGTTTTGCT
1255 TGGTTCGGCTCGGTTTTGCT
1 TGGTTCGGCTCGGTTTTGCT
1275 TGGTTCGGCTCGGTT
1 TGGTTCGGCTCGGTT
1290 GTAGTGGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 21 0.64
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.43
Consensus pattern (20 bp):
TGGTTCGGCTCGGTTTTGCT
Found at i:16732 original size:225 final size:227
Alignment explanation
Indices: 16326--16764 Score: 635
Period size: 225 Copynumber: 1.9 Consensus size: 227
16316 TGACATTCGG
*
16326 GTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACTCGACCGACCCGAAAATATATATAATTTTAC
1 GTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCGACCCGAAAATATATATAATTTTAC
16391 CTTATATATATTTAGGAATAATTACAATAATACCCCTCTATAGATAATTTTTTTTCAATTAAGTC
66 CTTATATATATTTAGGAATAATTACAATAATACCCCTCTATAGATAA-TTTTTTTCAATTAAGTC
* * *
16456 ACTGTTTTTATTGAATAAAGTAATTTTTTTTATTATTTCGGGTTAGGTCGGGTCGAGTTTCTAAT
130 ACTATTTTTATTGAATAAAATAATTTTTTTTATTATTTCGGGTCAGGTCGGGT----TTT-TAAT
** *
16521 TCATATATTTGGGTCAGGTCGGGTGAAACTTTATTTTA
190 TCATATATTCAGGTCAAGTCGGGTGAAACTTTATTTTA
* *
16559 GTCGGGTCGGGTTCGAGTTTAGGGTGAAAAATACCCGACCCGA-CCTAAAA-A-ATATAATTTTA
1 GTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGA-CCGACCCGAAAATATATATAATTTTA
*
16621 CC-T-TATATA-TTAGGAATAATTA-AATAATACCCCTCTATATATAA-TTTTTTCAATTAAGTC
65 CCTTATATATATTTAGGAATAATTACAATAATACCCCTCTATAGATAATTTTTTTCAATTAAGTC
* *
16681 ACTATTTTTATTGAATAAAAATAA-TTTTTTTATTATTTCTGGTCGGGTCGGGTTTTTAATTCAT
130 ACTATTTTTATTGAAT-AAAATAATTTTTTTTATTATTTCGGGTCAGGTCGGGTTTTTAATTCAT
16745 ATATTCAGGTCAAGTCGGGT
194 ATATTCAGGTCAAGTCGGGT
16765 CTCGGATGGA
Statistics
Matches: 192, Mismatches: 12, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
220 25 0.13
221 3 0.02
225 57 0.30
226 6 0.03
227 21 0.11
228 13 0.07
229 6 0.03
230 1 0.01
231 13 0.07
232 1 0.01
233 42 0.22
234 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (227 bp):
GTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCGACCCGAAAATATATATAATTTTAC
CTTATATATATTTAGGAATAATTACAATAATACCCCTCTATAGATAATTTTTTTCAATTAAGTCA
CTATTTTTATTGAATAAAATAATTTTTTTTATTATTTCGGGTCAGGTCGGGTTTTTAATTCATAT
ATTCAGGTCAAGTCGGGTGAAACTTTATTTTA
Found at i:17114 original size:39 final size:38
Alignment explanation
Indices: 17055--17134 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 38
17045 TCTGACATGT
*
17055 CTGCGAACCAAACAGAATATGGAATTGGATTCCAATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAA-TTC
*
17094 CTGCCAACCAAACAGAATATGGAATTGGATTCTAATTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
17132 CTG
1 CTG
17135 ACAGATTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 6 0.15
39 33 0.85
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (38 bp):
CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
Found at i:17147 original size:17 final size:18
Alignment explanation
Indices: 17121--17166 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
17111 TATGGAATTG
* *
17121 GATTCTAATTCC-TGACA
1 GATTCCAATTCCTTCACA
17138 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
17156 GATTCCAATTC
1 GATTCCAATTC
17167 TCTCAGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:23159 original size:28 final size:28
Alignment explanation
Indices: 23119--23189 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
23109 GTTAAGAACT
23119 TAACGGTGTTGTTGATTCAAAAAAGAAA
1 TAACGGTGTTGTTGATTCAAAAAAGAAA
*
23147 TAATGGTGTTGTTGATTCAAAAAAGAAA
1 TAACGGTGTTGTTGATTCAAAAAAGAAA
*
23175 TAACGGTGTTATTGA
1 TAACGGTGTTGTTGA
23190 CGTTTCATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (28 bp):
TAACGGTGTTGTTGATTCAAAAAAGAAA
Found at i:24215 original size:3 final size:3
Alignment explanation
Indices: 24207--24237 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
24197 ATTTTGTTCC
24207 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
24238 CATTTCCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:26064 original size:29 final size:29
Alignment explanation
Indices: 26021--26103 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
26011 CTAACCTAAC
*
26021 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
26051 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
26080 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
26104 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:30831 original size:21 final size:21
Alignment explanation
Indices: 30801--30852 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
30791 TTTAATGCAT
* *
30801 TAATAGTTGTCATTATTGATA
1 TAATACTTGTCACTATTGATA
30822 TAATACTTGTCACTATTGATA
1 TAATACTTGTCACTATTGATA
30843 TAATACTTGT
1 TAATACTTGT
30853 GCCAGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (21 bp):
TAATACTTGTCACTATTGATA
Found at i:36966 original size:17 final size:17
Alignment explanation
Indices: 36946--36978 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36936 ATATTTATTT
*
36946 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
36963 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
36979 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:39408 original size:2 final size:2
Alignment explanation
Indices: 39403--39430 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39393 GTGTGTGTGT
39403 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39431 AATATCTGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39559 original size:2 final size:2
Alignment explanation
Indices: 39552--39596 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39542 CATTACCGCA
39552 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
39594 AT A
1 AT A
39597 CATACAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39790 original size:15 final size:15
Alignment explanation
Indices: 39770--39820 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
39760 ATGGTGTAAC
*
39770 ACCCATCTCCCGTAT
1 ACCCATCTCCTGTAT
39785 ACCCATCTCCTGTAT
1 ACCCATCTCCTGTAT
39800 ACCCATCTCCTGTAT
1 ACCCATCTCCTGTAT
39815 ACCCAT
1 ACCCAT
39821 ACGTATACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.22, C:0.43, G:0.06, T:0.29
Consensus pattern (15 bp):
ACCCATCTCCTGTAT
Found at i:40443 original size:59 final size:59
Alignment explanation
Indices: 40334--40683 Score: 531
Period size: 59 Copynumber: 5.9 Consensus size: 59
40324 AAATTCATTA
* * * * * *
40334 GGAATTTCATACAATTAGTATGATTTCCGTATCATTTTAGTACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
* * *
40393 AGAAATTTATACACTTAGTATGACTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
40452 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
* * * *
40511 GGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACGCAAAGTGCCGTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
*
40570 GGAAATTCATACACTTAGTATGATTTTCTTAT-TGTTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCT-TTTTAGCACACGAAGTGCCCTATCT
* **
40629 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCT
40684 TTTTGGTAAT
Statistics
Matches: 264, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
59 264 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
Found at i:41129 original size:95 final size:95
Alignment explanation
Indices: 41044--41233 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 95
41034 ACTTCTATAT
* ** * *
41044 TATGGTACTGATACCCCCTTGGGGTATCGATACCAAAAATAGGTTCGATGTTTCCTGGTATCGAT
1 TATGGTACCGATACCCCCTACGGGTATCGATACCAAAAATAGATTCGATGTTTCATGGTATCGAT
41109 ACCCTTACCATGGTATTGATACTACCTTTC
66 ACCCTTACCATGGTATTGATACTACCTTTC
* * *
41139 TATGGTACCGATACCCCCTACTGGTATCGATACCAAAATTAGATTTGATGTTTCATGGTATCGAT
1 TATGGTACCGATACCCCCTACGGGTATCGATACCAAAAATAGATTCGATGTTTCATGGTATCGAT
* *
41204 ACCCCTTATCATGGTATCGATACTACCTTT
66 A-CCCTTACCATGGTATTGATACTACCTTT
41234 TAGGTATTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 58 0.69
96 26 0.31
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (95 bp):
TATGGTACCGATACCCCCTACGGGTATCGATACCAAAAATAGATTCGATGTTTCATGGTATCGAT
ACCCTTACCATGGTATTGATACTACCTTTC
Found at i:44279 original size:16 final size:16
Alignment explanation
Indices: 44255--44295 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
44245 AAAAGATTCA
*
44255 TTAGTCCGAGATTATG
1 TTAGCCCGAGATTATG
44271 TTAGCCCGAGATTATG
1 TTAGCCCGAGATTATG
44287 TTAGCCCGA
1 TTAGCCCGA
44296 TTTTAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (16 bp):
TTAGCCCGAGATTATG
Found at i:46411 original size:55 final size:54
Alignment explanation
Indices: 46277--46729 Score: 590
Period size: 55 Copynumber: 8.3 Consensus size: 54
46267 TTTATTAAGA
* *
46277 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCTGTGG-GT
1 TGCACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTC-GTGGATT
* **
46331 TGCACACGTAGTGCCTATATTGTTATTCATCAACTCATGATGAAATTCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATG-AATTCGTGGATT
* *
46386 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGG-GT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAA-TTCGTGGATT
*
46440 TGCACACATAGTGCCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
* * * * *
46495 TGCACACATAGTTCCTGTACGGTTATTCATCAACTCGTGATGAATTCTATGGGTT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTC-GTGGATT
** *
46550 ACACACACATAGTGTCTATACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 -TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTC-GTGGATT
* *
46606 TGTACACATAGTGCTTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
* * * *
46661 TACACATATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGT-GATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAA-TTCGTGGATT
46715 TGCACACATAGTGCC
1 TGCACACATAGTGCC
46730 AGTAGTACAC
Statistics
Matches: 351, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 108 0.31
55 191 0.54
56 50 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCGTGGATT
Found at i:46415 original size:109 final size:108
Alignment explanation
Indices: 46277--46729 Score: 624
Period size: 109 Copynumber: 4.1 Consensus size: 108
46267 TTTATTAAGA
* * *
46277 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCTGTGGGTTGCACACGTA
1 TGCACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCTGTGGGTTACACACATA
**
46341 GTGCCTATATTGTTATTCATCAACTCATGATGAAATTCGTGGATT
65 GTGCCTATACGGTTATTCATCAACTCATGATG-AATTCGTGGATT
* *
46386 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGGTTGCACACATA
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCT-GTGGGTTACACACATA
*
46450 GTGCCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
65 GTGCCTATACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
* * * *
46495 TGCACACATAGTTCCTGTACGGTTATTCATCAACTCGTGATGAATTCTATGGGTTACACACACAT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCTGTGGGTT--ACACACAT
*
46560 AGTGTCTATACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
64 AGTGCCTATACGGTTATTCATCAACTCATGATGAATTC-GTGGATT
* * * * *
46606 TGTACACATAGTGCTTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTACACATATA
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCTGTGG-GTTACACACATA
* *
46671 GTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGT-GATT
65 GTGCCTATACGGTTATTCATCAACTCATGATGAA-TTCGTGGATT
46715 TGCACACATAGTGCC
1 TGCACACATAGTGCC
46730 AGTAGTACAC
Statistics
Matches: 311, Mismatches: 24, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
108 5 0.02
109 162 0.52
110 45 0.14
111 97 0.31
112 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (108 bp):
TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTACACACATAG
TGCCTATACGGTTATTCATCAACTCATGATGAATTCGTGGATT
Found at i:46654 original size:166 final size:163
Alignment explanation
Indices: 46277--46729 Score: 590
Period size: 166 Copynumber: 2.8 Consensus size: 163
46267 TTTATTAAGA
* * * *
46277 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCTGTGG-GTTGCACACGT
1 TGCACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
* ** * ** *
46340 AGTGCCTATATTGTTATTCATCAACTCATGATGAAATTCGTGGATTTGCACACATAGTGCCTGTA
65 AGTGCCTGTACGGTTATTCATCAACTCATGATG-AATTCATGGATTCACACACATAGTGCCTATA
46405 CGGTTATTCATCAACTCATGATGAATTTCGTGGGT
129 CGGTTATTCATCAACTCATGATGAATTTCGTGGGT
*
46440 TGCACACATAGTGCCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* * * *
46505 GTTCCTGTACGGTTATTCATCAACTCGTGATGAATTCTATGGGTTACACACACATAGTGTCTATA
66 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTC-ATGGATT-CACACACATAGTGCCTATA
*
46570 CGGTTATTCATCAACTCATGATGAA-TTCTGTGGATT
129 CGGTTATTCATCAACTCATGATGAATTTC-GTGG-GT
* * * *
46606 TGTACACATAGTGCTTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTACACATATA
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* * **
46671 GTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGT-GATTTGCACACATAGTGCC
66 GTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCATGGATTCACACACATAGTGCC
46730 AGTAGTACAC
Statistics
Matches: 253, Mismatches: 30, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
163 51 0.20
164 59 0.23
165 47 0.19
166 93 0.37
167 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (163 bp):
TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCATGGATTCACACACATAGTGCCTATACG
GTTATTCATCAACTCATGATGAATTTCGTGGGT
Found at i:46717 original size:220 final size:218
Alignment explanation
Indices: 46277--46729 Score: 651
Period size: 220 Copynumber: 2.1 Consensus size: 218
46267 TTTATTAAGA
* * * *
46277 TGCACACGTAGTGCCTATACGGTAGTTCATCAACTCATGATGAATTCTGTGGGTTGCACACGTAG
1 TGCACACATAGTGCCTATACGGTAGTTCATCAACTCATGATGAATTCTATGGGTTACACACATAG
** *
46342 TGCCTATATTGTTATTCATCAACTCATGATGAAATTCGTGGATTTGCACACATAGTGCCTGTACG
66 TGCCTATACGGTTATTCATCAACTCATGATGAAATTCGTGGATTTGCACACATAGTGCCTATACG
* * * *
46407 GTTATTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTGCCTATATGGTTATTCATCA
131 GTTATTCATCAACTCATGATGAATTCCGTGGGTTACACACATAGTGCATATACGGTTATTCATCA
46472 ACTCATGATGAATTCCGTGGATT
196 ACTCATGATGAATTCCGTGGATT
* * *
46495 TGCACACATAGTTCCTGTACGGTTA-TTCATCAACTCGTGATGAATTCTATGGGTTACACACACA
1 TGCACACATAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCTATGGGTT--ACACACA
* * *
46559 TAGTGTCTATACGGTTATTCATCAACTCATGATG-AATTCTGTGGATTTGTACACATAGTGCTTA
63 TAGTGCCTATACGGTTATTCATCAACTCATGATGAAATTC-GTGGATTTGCACACATAGTGCCTA
* * *
46623 TACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTACACATATAGTGCATGTACGGTTATT
127 TACGGTTATTCATCAACTCATGATGAATTCCGTGG-GTTACACACATAGTGCATATACGGTTATT
*
46688 CATCAACTCATGATGAATTTCGT-GATT
191 CATCAACTCATGATGAATTCCGTGGATT
46715 TGCACACATAGTGCC
1 TGCACACATAGTGCC
46730 AGTAGTACAC
Statistics
Matches: 208, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
218 47 0.23
219 7 0.03
220 109 0.52
221 45 0.22
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (218 bp):
TGCACACATAGTGCCTATACGGTAGTTCATCAACTCATGATGAATTCTATGGGTTACACACATAG
TGCCTATACGGTTATTCATCAACTCATGATGAAATTCGTGGATTTGCACACATAGTGCCTATACG
GTTATTCATCAACTCATGATGAATTCCGTGGGTTACACACATAGTGCATATACGGTTATTCATCA
ACTCATGATGAATTCCGTGGATT
Found at i:47128 original size:19 final size:22
Alignment explanation
Indices: 47078--47129 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
47068 CCCCTACCAT
*
47078 GGTATCGATACTACTACACTAT
1 GGTATCGATACTACTACACTAC
47100 GGTA-CTGATACT-CTA-A-TAC
1 GGTATC-GATACTACTACACTAC
47119 GGTATCGATAC
1 GGTATCGATAC
47130 CATTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 4 0.15
22 10 0.37
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTACTACACTAC
Found at i:47196 original size:19 final size:20
Alignment explanation
Indices: 47153--47201 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
47143 TCTTATCAAT
*
47153 GGTATCGATACCTTCCTTAC
1 GGTATCGATACCTCCCTTAC
* *
47173 AGTATCGATACC-CCCTTTC
1 GGTATCGATACCTCCCTTAC
47192 GGTATCGATA
1 GGTATCGATA
47202 ATTCTTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCTCCCTTAC
Found at i:51380 original size:95 final size:94
Alignment explanation
Indices: 51268--51487 Score: 275
Period size: 95 Copynumber: 2.3 Consensus size: 94
51258 CCGACGAGGT
* *
51268 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCAAAGCTAAAATTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATAC
51333 CAGAAAGGGGTATCAGTACCATAGCAT-TA-A
66 C-GAAAGGGGTATCAGTACCATA--ATATAGA
* * * * *
51363 AGTATCGATACCATGGTAAGGGTATTGATACTAGGAAACATCGAATCTAAAATTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATAC
* *
51428 CGGAAGGGGTATCGGTACCATAATATAGA
66 CGAAAGGGGTATCAGTACCATAATATAGA
* * *
51457 AGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCATGGTAAG-GGTATCGATAC
51488 TATTGAGCTT
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
92 2 0.02
93 4 0.04
94 44 0.40
95 59 0.54
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (94 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATAC
CGAAAGGGGTATCAGTACCATAATATAGA
Found at i:52041 original size:70 final size:74
Alignment explanation
Indices: 51896--52304 Score: 416
Period size: 79 Copynumber: 5.3 Consensus size: 74
51886 CAACGAATGA
* * *
51896 ATAAAAAAATAATGCATATGGGTGCATTATTGGCATGAAAGGAGGCCATAGCTGAAATGGATATG
1 ATAAAAGAATAATGCATATGGGTG-----TTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
51961 GGTGCATTATCGAC
61 GGTGCATTATCGAC
51975 ATAAAAGAATAATGCATAT-GG-G-T-GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGC
1 ATAAAAGAATAATGCATATGGGTGTTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGC
52036 ATTATC-AGC
66 ATTATCGA-C
* * *
52045 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGAAATGCATATA
1 ATAAAAGAATAATGCATATGGGTG-----TTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
52110 GGTGCATTATCGGC
61 GGTGCATTATCGAC
*
52124 ATAAAA-AATAATGTATATGGGTGCATTATAGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTG---T-T-GGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
52188 GGTGCATTATTGGC
61 GGTGCATTATCGAC
* * * * *
52202 ATAAAAGAATAATGCACATGGGTGCATTATTGGCATGAAATGATACCATAGATGAAATGCTTATG
1 ATAAAAGAATAATGCATATGGGTG-----TTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
52267 AGTGCATTATCAAC
61 GGTGCATTATCGAC
* *
52281 ATAAAAGAATAATACATTTGGGTG
1 ATAAAAGAATAATGCATATGGGTG
52305 CATTATTGGC
Statistics
Matches: 283, Mismatches: 31, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
69 1 0.00
70 62 0.22
71 3 0.01
72 1 0.00
76 1 0.00
77 2 0.01
78 69 0.24
79 142 0.50
80 1 0.00
81 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (74 bp):
ATAAAAGAATAATGCATATGGGTGTTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGC
ATTATCGAC
Found at i:52106 original size:45 final size:45
Alignment explanation
Indices: 52055--52276 Score: 193
Period size: 45 Copynumber: 5.4 Consensus size: 45
52045 ATAAAAGAAT
52055 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
* *
52100 AATGCATATAGGTGCATTATCGGCAT-AAAA-A----ATA-ATG-
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
* * *
52137 --T--ATATGGGTGCATTATAGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
52178 AATGCATATGGGTGCATTATTGGCAT--AAA-A-G----A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
* * *
52212 AATGCACATGGGTGCATTATTGGCATGAAATGATACCATAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
* *
52257 AATGCTTATGAGTGCATTAT
1 AATGCATATGGGTGCATTAT
52277 CAACATAAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 46
0.69 0.08 0.23
Matches are distributed among these distances:
33 19 0.14
34 28 0.20
35 2 0.01
36 3 0.02
37 2 0.01
38 3 0.02
39 6 0.04
40 2 0.01
41 1 0.01
42 2 0.01
43 6 0.04
44 4 0.03
45 61 0.44
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGATGA
Found at i:52129 original size:79 final size:79
Alignment explanation
Indices: 51998--52330 Score: 497
Period size: 79 Copynumber: 4.2 Consensus size: 79
51988 GCATATGGGT
*
51998 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
1 GCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
52063 TGGGTGCATTATTG
66 TGGGTGCATTATTG
* * * *
52077 GCATGAAAAGATGCCATAGATGAAATGCATATAGGTGCATTATCGGCATAAAA-AATAATGTATA
1 GCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
*
52141 TGGGTGCATTATAG
66 TGGGTGCATTATTG
* ** *
52155 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATGCACA
1 GCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
52220 TGGGTGCATTATTG
66 TGGGTGCATTATTG
* * * * * * *
52234 GCATGAAATGATACCATAGATGAAATGCTTATGAGTGCATTATCAACATAAAAGAATAATACATT
1 GCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
52299 TGGGTGCATTATTG
66 TGGGTGCATTATTG
*
52313 GCATGATAGGATGCCATA
1 GCATGAAAGGATGCCATA
52331 AATAAAAATG
Statistics
Matches: 226, Mismatches: 27, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
78 72 0.32
79 154 0.68
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (79 bp):
GCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
TGGGTGCATTATTG
Found at i:52223 original size:157 final size:156
Alignment explanation
Indices: 51998--52330 Score: 515
Period size: 157 Copynumber: 2.1 Consensus size: 156
51988 GCATATGGGT
51998 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
*
52063 TGGGTGCATTATTGGCATGAAAAGATGCCATAGATGAAATGCATATAGGTGCATTATCGGCATAA
66 TGGGTGCATTATTGGCATGAAAAGATGCCATAGATGAAATGCATAT-GGTGCATTATCGACATAA
*
52128 AA-AATAATGTATATGGGTGCATTATAG
130 AAGAATAATGCATATGGGTGCATTAT-G
** *
52155 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATGCACA
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
* * * *
52220 TGGGTGCATTATTGGCATGAAATGATACCATAGATGAAATGCTTATGAGTGCATTATCAACATAA
66 TGGGTGCATTATTGGCATGAAAAGATGCCATAGATGAAATGCATATG-GTGCATTATCGACATAA
* *
52285 AAGAATAATACATTTGGGTGCATTATTG
130 AAGAATAATGCATATGGGTGCATTA-TG
*
52313 GCATGATAGGATGCCATA
1 GCATGAAAGGATGCCATA
52331 AATAAAAATG
Statistics
Matches: 161, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
156 1 0.01
157 122 0.76
158 37 0.23
159 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (156 bp):
GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATA
TGGGTGCATTATTGGCATGAAAAGATGCCATAGATGAAATGCATATGGTGCATTATCGACATAAA
AGAATAATGCATATGGGTGCATTATG
Found at i:53955 original size:55 final size:55
Alignment explanation
Indices: 53871--54327 Score: 582
Period size: 55 Copynumber: 8.3 Consensus size: 55
53861 TTTATTAAGA
* *
53871 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
** * * * * *
53926 TGCACACATAACGCCTCTATGGTTATTCATCAACTCATAATGAATTACGTGG-GT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
53980 TGCACACATAGTGCCTATACGATTATTCGT-ATACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCA-ACTCATGATGAATTCCGTGGATT
* *
54035 TGCACACATAGTGCCTGTACGATTATTCATCAACTCATGATGAATTCAGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
54090 TGCACACATTGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGT-G-TGT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT-T
* * * * *
54144 TGGACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCTGTAGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
54199 TGCACACATAGTGCATGTACAGTTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
54254 TGTACACATAGTGCCTGTACGGTTATTCATCAAGTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
54309 TGCGCACATAGTGTCTGTA
1 TGCACACATAGTGCCTGTA
54328 GTACACATCA
Statistics
Matches: 347, Mismatches: 48, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.01
54 89 0.26
55 252 0.73
56 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:54062 original size:109 final size:110
Alignment explanation
Indices: 53871--54321 Score: 574
Period size: 109 Copynumber: 4.1 Consensus size: 110
53861 TTTATTAAGA
* *
53871 TGCACACGTAGTGCCTATACG-GTAGTTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
1 TGCACACATAGTGCCTATACGATTA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
** * * * * *
53935 AACGCCTCTATGGTTATTCATCAACTCATAATGAATTAC-GTGG-GT
65 AGTGCCTGTACGATTATTCATCAACTCATGATGAATT-CTGTGGATT
* *
53980 TGCACACATAGTGCCTATACGATTATTCGT-ATACTCATGATGAATTTCGTGGATTTGCACACAT
1 TGCACACATAGTGCCTATACGATTATTCATCA-ACTCATGATGAATTCCGTGGATTTGCACACAT
*
54044 AGTGCCTGTACGATTATTCATCAACTCATGATGAATTCAGTGGATT
65 AGTGCCTGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * *
54090 TGCACACATTGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGT-G-TGTTGGACACAT
1 TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGAT-TTGCACACAT
* *
54153 AGTGCCTATACGATTATTCATCAACTCATGATGAATTCTGTAGATT
65 AGTGCCTGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
* * * *
54199 TGCACACATAGTGCATGTAC-AGTTATTCATCAACTCATGATGAATTCCATGGATTTGTACACAT
1 TGCACACATAGTGCCTATACGA-TTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
* *
54263 AGTGCCTGTACGGTTATTCATCAAGTCATGATGAATTCTGTGGATT
65 AGTGCCTGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
*
54309 TGCGCACATAGTG
1 TGCACACATAGTG
54322 TCTGTAGTAC
Statistics
Matches: 303, Mismatches: 30, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
108 3 0.01
109 187 0.62
110 111 0.37
111 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (110 bp):
TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
GTGCCTGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:54153 original size:164 final size:164
Alignment explanation
Indices: 53871--54321 Score: 617
Period size: 164 Copynumber: 2.7 Consensus size: 164
53861 TTTATTAAGA
* * * *
53871 TGCACACGTAGTGCCTATACG-GTAGTTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
1 TGCACACATAGTGCCTGTACGATTA-TTCATCAACTCATGATGAATTCAGTGGATTTGCACACAT
** * * *
53935 AACGCCTCTATGGTTATTCATCAACTCATAATGAATTACGTGGGTTGCACACATAGTGCCTATAC
65 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGGGTTGCACACATAGTGCCTATAC
* *
54000 GATTATTCGT-ATACTCATGATGAATT-TCGTGGATT
130 GATTATTCATCA-ACTCATGATGAATTCT-GTAGATT
*
54035 TGCACACATAGTGCCTGTACGATTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATT
1 TGCACACATAGTGCCTGTACGATTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATA
* * *
54100 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGTGTTGGACACATAGTGCCTATACG
66 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGGGTTGCACACATAGTGCCTATACG
54165 ATTATTCATCAACTCATGATGAATTCTGTAGATT
131 ATTATTCATCAACTCATGATGAATTCTGTAGATT
* *
54199 TGCACACATAGTGCATGTAC-AGTTATTCATCAACTCATGATGAATTCCA-TGGATTTGTACACA
1 TGCACACATAGTGCCTGTACGA-TTATTCATCAACTCATGATGAATT-CAGTGGATTTGCACACA
* * *
54262 TAGTGCCTGTACGGTTATTCATCAAGTCATGATGAATT-CTGTGGATTTGCGCACATAGTG
64 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTAC-GTGG-GTTGCACACATAGTG
54322 TCTGTAGTAC
Statistics
Matches: 257, Mismatches: 23, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
163 2 0.01
164 237 0.92
165 18 0.07
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (164 bp):
TGCACACATAGTGCCTGTACGATTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATA
GTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGGGTTGCACACATAGTGCCTATACG
ATTATTCATCAACTCATGATGAATTCTGTAGATT
Found at i:54699 original size:22 final size:19
Alignment explanation
Indices: 54666--54719 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
54656 TGCCCCTACC
54666 ATGGTATCGATACTACTACACT
1 ATGGTATCGATACT-CTA-A-T
54688 ATGGTA-CTGATACTCTAAT
1 ATGGTATC-GATACTCTAAT
*
54707 ATGGTATCTATAC
1 ATGGTATCGATAC
54720 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 4 0.14
22 12 0.41
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGGTATCGATACTCTAAT
Found at i:54719 original size:19 final size:22
Alignment explanation
Indices: 54666--54719 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
54656 TGCCCCTACC
*
54666 ATGGTATCGATACTACTACACT
1 ATGGTATCTATACTACTACACT
54688 ATGGTA-CTGATACT-CTA-A-T
1 ATGGTATCT-ATACTACTACACT
54707 ATGGTATCTATAC
1 ATGGTATCTATAC
54720 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 4 0.14
22 11 0.38
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (22 bp):
ATGGTATCTATACTACTACACT
Found at i:57151 original size:18 final size:18
Alignment explanation
Indices: 57124--57159 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
57114 GAGGGTTTTA
57124 GGTTGAGTAGGTATCGAT
1 GGTTGAGTAGGTATCGAT
*
57142 GGTTGGGTAGGTATCGAT
1 GGTTGAGTAGGTATCGAT
57160 ACCATGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.42, T:0.33
Consensus pattern (18 bp):
GGTTGAGTAGGTATCGAT
Found at i:57651 original size:22 final size:22
Alignment explanation
Indices: 57597--57695 Score: 87
Period size: 22 Copynumber: 4.6 Consensus size: 22
57587 TACTCCAATC
* *
57597 AGTGCTAAGGCTCTTTAGTATT
1 AGTGCTAATGCACTTTAGTATT
57619 AGTG--AATGCACTTCTA-TATT
1 AGTGCTAATGCACTT-TAGTATT
* *
57639 AGTGCTAATGCACTTTCGTATC
1 AGTGCTAATGCACTTTAGTATT
* ** *
57661 AATGCTGGTGCACTTTAGTATC
1 AGTGCTAATGCACTTTAGTATT
*
57683 AGTGCTAAAGCAC
1 AGTGCTAATGCAC
57696 CAGTTAGTCG
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
20 15 0.25
21 3 0.05
22 43 0.70
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (22 bp):
AGTGCTAATGCACTTTAGTATT
Found at i:62982 original size:90 final size:89
Alignment explanation
Indices: 62809--62986 Score: 243
Period size: 90 Copynumber: 2.0 Consensus size: 89
62799 TCGACCGATA
* *
62809 ACCATCATACACAAAGTATACCAATTACATACATAGTGTGTAGTACACAAAGTACTAATACAATA
1 ACCATCATACACAAAGTATACCAATTACATACATAATGTGTAATACACAAAGTACTAATACAATA
*
62874 CCACCTTATTTATGGTATTACAAC
66 CCACCTTATTTACGGTATTACAAC
* * * *
62898 ACCATCATACATC-AAGTATGCCAATTACATACATAATGCT-TCAATAGACAAAGTAGTACTACA
1 ACCATCATACA-CAAAGTATACCAATTACATACATAATG-TGT-AATACACAAAGTACTAATACA
*
62961 ATACCACCTTATTTCCGGTATTACAA
63 ATACCACCTTATTTACGGTATTACAA
62987 TTGAACCTAC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
89 35 0.45
90 43 0.55
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (89 bp):
ACCATCATACACAAAGTATACCAATTACATACATAATGTGTAATACACAAAGTACTAATACAATA
CCACCTTATTTACGGTATTACAAC
Found at i:68968 original size:17 final size:17
Alignment explanation
Indices: 68921--68971 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
68911 AAGATTATAC
68921 AAAATGTAAATAATG--
1 AAAATGTAAATAATGTA
* **
68936 AATAT-TAAGGAATGTA
1 AAAATGTAAATAATGTA
68952 AAAATGTAAATAATGTA
1 AAAATGTAAATAATGTA
68969 AAA
1 AAA
68972 TTGATTGCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 7 0.26
15 4 0.15
16 4 0.15
17 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (17 bp):
AAAATGTAAATAATGTA
Found at i:70346 original size:2 final size:2
Alignment explanation
Indices: 70339--70695 Score: 141
Period size: 2 Copynumber: 185.5 Consensus size: 2
70329 TCCGACCTTT
*
70339 TA TA TA TA T- TA TA TA GTA TA TA TA GTG TA TA GTA TA TA TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA
*
70380 TA TA TA TA T- TA CA -A TA TA T- TA TA TA GTA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
70418 TA CA TG T- TA TA GTT TA TA TA T- TA TA T- TA GA TA -A TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
70457 TA TA T- TA GTC T- TA TA T- TA TA GTA CTA TA CTA TA TA GTA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA -TA TA -TA TA TA -TA TA TA
*
70499 TA T- TA TA TA TA TT TA TA T- TA TA T- TA TA TA T- TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
70538 T- TA TA T- TA TA TA TT TA TA T- TA TA TA GTG TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
70577 TA TA T- TA TA -A TA -A TA GTG T- TA TA T- TG TA TG TT TA TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * **
70614 TA TA TA GTG TG TA TA TA TA TA TA TA CTA TA GGG TA T- TA TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
*
70655 TA TA TT TA TA T- TA TGA -A TA T- TA TA TA TA TCA TA CTA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA -TA TA TA
70695 T
1 T
70696 TTGTATATTA
Statistics
Matches: 273, Mismatches: 31, Indels: 102
0.67 0.08 0.25
Matches are distributed among these distances:
1 33 0.12
2 211 0.77
3 29 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70353 original size:7 final size:7
Alignment explanation
Indices: 70341--70781 Score: 152
Period size: 7 Copynumber: 63.1 Consensus size: 7
70331 CGACCTTTTA
70341 TATATAT
1 TATATAT
70348 TATATAGT
1 TATATA-T
70356 ATATATAGT
1 -TATATA-T
70365 GTATAGTA-
1 -TATA-TAT
70373 TATATAT
1 TATATAT
70380 TATATA-
1 TATATAT
*
70386 TAT-TAC
1 TATATAT
*
70392 AATATAT
1 TATATAT
*
70399 TATATAG
1 TATATAT
70406 TATTATAT
1 TA-TATAT
70414 TATATACAT
1 TATAT--AT
70423 GT-TATAGT
1 -TATATA-T
70431 T-TATA-
1 TATATAT
70436 TATTATAT
1 TA-TATAT
* *
70444 TAGATAA
1 TATATAT
70451 TATATA-
1 TATATAT
70457 TATATTAGT
1 TATA-TA-T
70466 CT-TATAT
1 -TATATAT
*
70473 TATAGTAC
1 TATA-TAT
70481 TATACTA-
1 TATA-TAT
70488 TATAGTA-
1 TATA-TAT
70495 TATATAT
1 TATATAT
70502 TATATA-
1 TATATAT
*
70508 TATTTA-
1 TATATAT
70514 TATTATAT
1 TA-TATAT
70522 TATATAT
1 TATATAT
*
70529 TATATAG
1 TATATAT
70536 TATTATAT
1 TA-TATAT
70544 TATATAT
1 TATATAT
70551 T-TATAT
1 TATATAT
*
70557 TATATAG
1 TATATAT
*
70564 TGTATA-
1 TATATAT
70570 TATATAT
1 TATATAT
70577 TATATTAT
1 TATA-TAT
*
70585 AATAATAGT
1 TAT-ATA-T
70594 GT-TATAT
1 -TATATAT
* *
70601 TGTATGT
1 TATATAT
70608 T-TATAT
1 TATATAT
*
70614 TATATAG
1 TATATAT
* *
70621 TGTGTA-
1 TATATAT
70627 TATATA-
1 TATATAT
*
70633 TATATAC
1 TATATAT
***
70640 TATAGGG
1 TATATAT
70647 TATTATAT
1 TA-TATAT
70655 TATAT-T
1 TATATAT
70661 TATATTAT
1 TATA-TAT
*
70669 GA-ATAT
1 TATATAT
70675 TATATA-
1 TATATAT
*
70681 TATCATAC
1 TAT-ATAT
70689 TATATATT
1 TATATA-T
*
70697 TGTATAT
1 TATATAT
70704 TATA-AT
1 TATATAT
70710 T-T-T-T
1 TATATAT
*
70714 TATATAA
1 TATATAT
*
70721 GAGTATA-
1 TA-TATAT
70728 TAT-TAT
1 TATATAT
70734 TA-ATAT
1 TATATAT
70740 TAT-TAT
1 TATATAT
*
70746 TATATTT
1 TATATAT
*
70753 TATACA-
1 TATATAT
70759 TAT-TATT
1 TATATA-T
70766 TATTATAT
1 TA-TATAT
70774 TATATAT
1 TATATAT
70781 T
1 T
70782 TATTTAATTA
Statistics
Matches: 335, Mismatches: 46, Indels: 106
0.69 0.09 0.22
Matches are distributed among these distances:
4 2 0.01
5 8 0.02
6 81 0.24
7 156 0.47
8 60 0.18
9 24 0.07
10 4 0.01
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (7 bp):
TATATAT
Found at i:70402 original size:5 final size:5
Alignment explanation
Indices: 70338--70778 Score: 141
Period size: 5 Copynumber: 88.2 Consensus size: 5
70328 GTCCGACCTT
*
70338 TTATA -TATA TTATA -TAGTA TATATA GTGTATA GTATA -TATA TTATA
1 TTATA TTATA TTATA TTA-TA T-TATA -T-TATA TTATA TTATA TTATA
* * * *
70384 -TATA TTACA ATATA TTATA -TAGTA TTATA TTATA TACATG TTATA GTT-TA
1 TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA T-TATA TTATA -TTATA
* * * *
70434 -TATA TTATA TTAGA TAATA -TATA -TATA TTAGTC TTATA TTATA GTACTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA TTA-TA
*
70483 -TACTA -TATA GTATA -TATA TTATA -TATA TTTATA TTATA TTATA -TATTA
1 TTA-TA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTA-TA
*
70531 TATAGTA TTATA TTATA -TAT- TTATA TTATA -TAGT- GTATA TATATA
1 T-TA-TA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA T-TATA
* * * * *
70576 TTATA TTATA --ATA ATAGTG TTATA TTGTA -TGT- TTATA TTATA -TAGTG
1 TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTA-TA
* ***
70623 TGTATA -TATA TATATA CTATA GGGTA TTATA TTATA TTTATA TTATGA
1 T-TATA TTATA T-TATA TTATA TTATA TTATA TTATA -TTATA TTAT-A
* * * *
70671 --ATA TTATA -TATA TCATA CTATA -TATT TGTATA TTATAA TT-TT TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTAT-A TTATA TTATA
* * * * *
70718 TAAGA GTATATA TTAT- TAATA TTATTA TTATA TTTTA TACATA TTATTTA
1 TTATA -T-TATA TTATA TTATA TTA-TA TTATA TTATA T-TATA TTA--TA
70768 TTATA TTATA T
1 TTATA TTATA T
70779 ATTTATTTAA
Statistics
Matches: 331, Mismatches: 50, Indels: 110
0.67 0.10 0.22
Matches are distributed among these distances:
3 5 0.02
4 71 0.21
5 177 0.53
6 57 0.17
7 21 0.06
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (5 bp):
TTATA
Found at i:70611 original size:57 final size:60
Alignment explanation
Indices: 70380--70779 Score: 116
Period size: 57 Copynumber: 6.9 Consensus size: 60
70370 GTATATATAT
* * * * *
70380 TATATATATTACAATATA--TTATATAGTATTATATTATATA--CAT-GT-TATAGTTTA
1 TATATATATTATATTATATATTATATAGTATTATATTATATATTTATATTATATAGTGTA
* * * * * *
70434 TATATTATATTAGATAATATATATATATTAGTCTTATATTATAGTA-CTATACTATATAGTATA
1 TATA-TATATTATATTATATAT-TATA-TAGTATTATATTATA-TATTTATATTATATAGTGTA
*
70497 TATAT-TATATATATT-TATATTATAT--TA-TATATTATATAGTATTATATTATATA-TTTA
1 TATATATAT-TATATTATATATTATATAGTATTATATTATATA-T-TTATATTATATAGTGTA
* * * * *
70554 TATTATATAGTGTA-TATATA-TAT-TA-TATTATAATA-ATAGTGTTATATTGTAT-GTTTA
1 TA-TATATATTATATTATATATTATATAGTATTATATTATATA-T-TTATATTATATAGTGTA
*
70611 TATTATATAGTGTGTATATATATATATACTATAGGGTATTATA-T-TATATTTATATTATGA-A-
1 TA-TATATA-T-TATAT-TATATAT-TA-TATA--GTATTATATTATATATTTATATTAT-ATAG
*
70672 TAT-
57 TGTA
* * * *
70675 TATATATATCATACTATATATT-TGTA-TATTATA--AT-T-TTT-TA-TATA-AGAGTA
1 TATATATATTATATTATATATTATATAGTATTATATTATATATTTATATTATATAGTGTA
** * *
70726 TATAT-TATTAATATTAT-TATTATATTTTATACATATTATTTA-TTATATTATATA
1 TATATATATT-ATATTATATATTATATAGTAT-TATATTATATATTTATATTATATA
70780 TTTATTTAAT
Statistics
Matches: 267, Mismatches: 32, Indels: 89
0.69 0.08 0.23
Matches are distributed among these distances:
49 2 0.01
50 11 0.04
51 15 0.06
52 6 0.02
53 4 0.01
54 12 0.04
55 15 0.06
56 13 0.05
57 46 0.17
58 34 0.13
59 23 0.09
60 13 0.05
61 18 0.07
62 7 0.03
63 20 0.07
64 3 0.01
65 12 0.04
66 2 0.01
67 4 0.01
68 7 0.03
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (60 bp):
TATATATATTATATTATATATTATATAGTATTATATTATATATTTATATTATATAGTGTA
Found at i:70771 original size:23 final size:22
Alignment explanation
Indices: 70726--70779 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
70716 TATAAGAGTA
70726 TATATTAT-TA-ATATTATTAT
1 TATATTATATACATATTATTAT
*
70746 TATATTTTATACATATTATTTAT
1 TATATTATATACATATTA-TTAT
70769 TATATTATATA
1 TATATTATATA
70780 TTTATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 6 0.21
23 14 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATATTATATACATATTATTAT
Found at i:70793 original size:28 final size:29
Alignment explanation
Indices: 70727--70784 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 29
70717 ATAAGAGTAT
70727 ATATTATTAATATTATTATTATATTTTATAC
1 ATATTATT--TATTATTATTATATTTTATAC
70758 ATATTATTTATTA-TATTATATATTTAT
1 ATATTATTTATTATTATTATAT-TTTAT
70785 TTAATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.31
29 10 0.38
31 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTATTTATTATTATTATATTTTATAC
Found at i:74824 original size:21 final size:21
Alignment explanation
Indices: 74794--74857 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
74784 CGAAAAAAGG
*
74794 AACAAACACTGGACACACCTC
1 AACAAGCACTGGACACACCTC
*
74815 AACAAGCACTGGATACACCTC
1 AACAAGCACTGGACACACCTC
*
74836 AGCAAGCACTGGACACACCTC
1 AACAAGCACTGGACACACCTC
74857 A
1 A
74858 TCCTCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.36, G:0.14, T:0.11
Consensus pattern (21 bp):
AACAAGCACTGGACACACCTC
Found at i:84105 original size:2 final size:2
Alignment explanation
Indices: 84098--84122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84088 TCTCCTCTCG
84098 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
84123 TCACCCACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88046 original size:9 final size:9
Alignment explanation
Indices: 88028--88202 Score: 68
Period size: 9 Copynumber: 19.0 Consensus size: 9
88018 GGATCATAAA
88028 ATAT-TTAT
1 ATATATTAT
88036 ATATATTAT
1 ATATATTAT
88045 ATTATATTAT
1 A-TATATTAT
*
88055 ATATAATGGAGGAT
1 ATAT-AT----TAT
*
88069 ATACATGT-T
1 ATATAT-TAT
88078 ATATATTAT
1 ATATATTAT
*
88087 AGATTATATTAC
1 --A-TATATTAT
*
88099 ATA-AATAT
1 ATATATTAT
88107 AT-TA-TAT
1 ATATATTAT
*
88114 ATAGTATTGT
1 ATA-TATTAT
88124 ATATA-T-T
1 ATATATTAT
88131 -TATATTAT
1 ATATATTAT
88139 AATATATTAT
1 -ATATATTAT
88149 -TATTATTAT
1 ATA-TATTAT
88158 -TATTATTATT
1 ATA-TATTA-T
*
88168 ATATTTTAT
1 ATATATTAT
88177 ATATATTAT
1 ATATATTAT
88186 -T-TATTAT
1 ATATATTAT
88193 ATTATATTAT
1 A-TATATTAT
88203 TTAATTATTC
Statistics
Matches: 132, Mismatches: 10, Indels: 48
0.69 0.05 0.25
Matches are distributed among these distances:
6 4 0.03
7 13 0.10
8 16 0.12
9 45 0.34
10 37 0.28
11 3 0.02
12 7 0.05
13 2 0.02
14 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (9 bp):
ATATATTAT
Found at i:88056 original size:25 final size:25
Alignment explanation
Indices: 88028--88202 Score: 71
Period size: 25 Copynumber: 6.9 Consensus size: 25
88018 GGATCATAAA
88028 ATATTTATATATATTATATTATATT
1 ATATTTATATATATTATATTATATT
* ** ** * *
88053 ATATATA-ATGGAGGATATACATGTT
1 ATATTTATATATATTATAT-TATATT
* * *
88078 ATATAT-TATAGATTATATTACATAAAT
1 ATATTTATATATATTATATT--AT-ATT
*
88105 ATATTATATATAGTATTGTA-TATATT
1 ATATT-TATATA-TATTATATTATATT
88131 -TATATTATAATATATTATTATTATTATT
1 ATAT-TTAT-ATATATTA-TATTA-TATT
*
88159 AT-TATTAT-TATATTTTA-TATA-T
1 ATAT-TTATATATATTATATTATATT
88181 ATTATTTAT-TATATTATATTAT
1 A-TATTTATATATATTATATTAT
88203 TTAATTATTC
Statistics
Matches: 113, Mismatches: 20, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
22 2 0.02
23 15 0.13
24 13 0.12
25 36 0.32
26 16 0.14
27 9 0.08
28 11 0.10
29 6 0.05
30 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (25 bp):
ATATTTATATATATTATATTATATT
Found at i:88149 original size:28 final size:27
Alignment explanation
Indices: 88104--88205 Score: 88
Period size: 28 Copynumber: 3.8 Consensus size: 27
88094 ATTACATAAA
*
88104 TATATTAT-ATATAGTATTGTATATATT
1 TATATTATAATATATTATT-TATATATT
88131 TATATTATAATATATTA-TTAT-TA-T
1 TATATTATAATATATTATTTATATATT
*
88155 TATTATTATTATTATATT-TTATATATATT
1 TA-TATTA-TAATATATTATT-TATATATT
* *
88184 ATTTATTATATTATATTATTTA
1 -TATATTATAATATATTATTTA
88206 ATTATTCAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
24 3 0.05
25 7 0.11
26 12 0.19
27 12 0.19
28 20 0.32
29 8 0.13
30 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TATATTATAATATATTATTTATATATT
Found at i:88151 original size:3 final size:3
Alignment explanation
Indices: 88133--88203 Score: 71
Period size: 3 Copynumber: 24.3 Consensus size: 3
88123 TATATATTTA
*
88133 TAT TAT AAT ATAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
88176 TAT ATAT TATT TAT TA- TAT TA- TAT TAT T
1 TAT -TAT TA-T TAT TAT TAT TAT TAT TAT T
88204 TAATTATTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
2 10 0.17
3 40 0.69
4 8 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:91255 original size:16 final size:16
Alignment explanation
Indices: 91230--91272 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
91220 TAGTGACAAC
91230 TTTT-GTAACTAAAAG
1 TTTTAGTAACTAAAAG
91245 TTTTAGTAACTAAAAG
1 TTTTAGTAACTAAAAG
91261 TTTTAGTAACTA
1 TTTTAGTAACTA
91273 TGACAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
TTTTAGTAACTAAAAG
Found at i:95751 original size:12 final size:12
Alignment explanation
Indices: 95682--95774 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
95672 ACGGAGATAT
* *
95682 CAGAAATCAAAA
1 CAGAATTCAGAA
*
95694 CAGAATTCAAAA
1 CAGAATTCAGAA
*
95706 CA-TATATCAGAA
1 CAGAAT-TCAGAA
*
95718 CAGAA-TCAAGAT
1 CAGAATTC-AGAA
*
95730 CAGAAATCAGAA
1 CAGAATTCAGAA
**
95742 CAGAATTCAGGT
1 CAGAATTCAGAA
*
95754 CATGTA-TCAGAA
1 CA-GAATTCAGAA
95766 CAGAATTCA
1 CAGAATTCA
95775 AGTCGGAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
11 6 0.10
12 51 0.82
13 5 0.08
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:95786 original size:24 final size:24
Alignment explanation
Indices: 95681--95788 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
95671 AACGGAGATA
* *
95681 TCAGAAATCAAAACAGAATTCAAA
1 TCAGAAATCAGAACAGAATTCAAG
* * *
95705 ACATATATCAGAACAGAA-TCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
95728 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
*
95753 TCATG-TATCAGAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
*
95777 TCGGAAATCAGA
1 TCAGAAATCAGA
95789 TAAAATAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
23 5 0.07
24 57 0.85
25 5 0.07
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:95787 original size:48 final size:48
Alignment explanation
Indices: 95680--95788 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
95670 AAACGGAGAT
*
95680 ATCAGAAATCAAAACAGAATTCAAAACATATATCAGAACAGAATCAAG
1 ATCAGAAATCAGAACAGAATTCAAAACATATATCAGAACAGAATCAAG
*** *
95728 ATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAAACATATATCAGAACAGAA-TCAAG
*
95777 -TCGGAAATCAGA
1 ATCAGAAATCAGA
95789 TAAAATAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 49 0.91
49 5 0.09
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAAAACATATATCAGAACAGAATCAAG
Found at i:98281 original size:18 final size:18
Alignment explanation
Indices: 98258--98323 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
98248 CAACGATCAA
*
98258 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGGGT
98276 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
98294 CAGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
98312 CGAGGGTCGGGT
1 C--GGGTCGGGT
98324 TGTGACCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 34 0.81
20 8 0.19
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:100243 original size:49 final size:45
Alignment explanation
Indices: 100171--100265 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 45
100161 CCGAGGATCC
100171 TGCGGAACTTCTTCCTTCAACAATACCCCCCATACAATTAAAACATTTT
1 TGCGGAACTTCTTCCTTCAACAATA-CCCCC---CAATTAAAACATTTT
100220 TGCGGAACTTCTTCCTTCAACAATACCCCCCAATTAAAACATTTT
1 TGCGGAACTTCTTCCTTCAACAATACCCCCCAATTAAAACATTTT
100265 T
1 T
100266 TCATCATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
45 16 0.35
48 5 0.11
49 25 0.54
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (45 bp):
TGCGGAACTTCTTCCTTCAACAATACCCCCCAATTAAAACATTTT
Found at i:100342 original size:24 final size:24
Alignment explanation
Indices: 100287--100342 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
100277 CAGAGATATA
* *
100287 AGAAATCAAAACAGAATTCAGGTC
1 AGAAATCAAAACAAAATTCAAGTC
*
100311 ATG-TATCAAAACAAAATTCAAGTC
1 A-GAAATCAAAACAAAATTCAAGTC
100335 AGAAATCA
1 AGAAATCA
100343 GATAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (24 bp):
AGAAATCAAAACAAAATTCAAGTC
Found at i:102823 original size:13 final size:13
Alignment explanation
Indices: 102805--102844 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
102795 CGGTCAACGA
102805 TCAACGGGTCAGG
1 TCAACGGGTCAGG
*
102818 TCAACGGAT-AGG
1 TCAACGGGTCAGG
*
102830 TCAACGGGTCGGG
1 TCAACGGGTCAGG
102843 TC
1 TC
102845 GGGTTGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCAGG
Found at i:102860 original size:13 final size:13
Alignment explanation
Indices: 102832--102880 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
102822 CGGATAGGTC
102832 AACGGGTCGGG-T
1 AACGGGTCGGGTT
*
102844 --CGGGTTGGGTT
1 AACGGGTCGGGTT
102855 AACGGGTCGGGTT
1 AACGGGTCGGGTT
102868 AACGGGTCGGGTT
1 AACGGGTCGGGTT
102881 GTGACCGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
13 23 0.72
ACGTcount: A:0.12, C:0.14, G:0.49, T:0.24
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:104473 original size:33 final size:32
Alignment explanation
Indices: 104435--104499 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
104425 CATCATAAAG
104435 AATTGTGACAAGTAAT-ATTCT-TTCACAATAACA
1 AATTGTGACAA--AATGATT-TATTCACAATAACA
*
104468 AATTGTTACAAAATGATTTATTCACAATAACA
1 AATTGTGACAAAATGATTTATTCACAATAACA
104500 CGTTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.14
32 15 0.52
33 10 0.34
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (32 bp):
AATTGTGACAAAATGATTTATTCACAATAACA
Found at i:104541 original size:198 final size:194
Alignment explanation
Indices: 104186--104685 Score: 689
Period size: 198 Copynumber: 2.5 Consensus size: 194
104176 TTTCGATATA
* * * * *
104186 TATTTAGTCATAATAACAATTTATAACAATTATTAATTTCTCAATATAAAAAATTATGACAAAAA
1 TATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTC-ATATAAAAAATTGTGACAAATA
* * * *
104251 ATATTATTTCATAATAACAAATTGTAACAAATTTATTTAGTTACAATAATGTAATAAATTTATTC
65 ATATT-TTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACGT-ATAAATTTAGTC
* *
104316 AAAATAAAAATTTATGTCAAATTTATTTTGTCACAATATTTTGTCAAAATAAAAAATTCTGACAA
128 AAAATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAAT-AAAAATTCTGACAA
104381 ATT
192 ATT
* * *
104384 TATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCATCATAAAGAATTGTGACAAGTA
1 TATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCAT-ATAAAAAATTGTGACAAATA
* *
104449 ATATTCTTTCACAATAACAAATTGTTACAAAATGATTTA-TTCACAATAACACGT-TAAATTTAG
65 ATATT-TTTCACAATAACAAATTGTAACAAAATTATTTAGTT-ACAAT-A-ACGTATAAATTTAG
* * * *
104512 TCAAAGTAAACAGTTATGTCAAATTTATTTCGTCTCAATATTTTGTCAAAATAAAAATTGTGACA
126 TCAAAATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAATAAAAATTCTGACA
*
104577 TATT
191 AATT
* *
104581 TATTTAATCAAAATAACAATTTGTAACAAATATTAATTTCTCATTATAAAAAAATGTGACAAATA
1 TATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCA-TATAAAAAATTGTGACAAATA
104646 ATATTTTTCACAATAACAAATTGTAACAAAATTATTTAGT
65 ATATTTTTCACAATAACAAATTGTAACAAAATTATTTAGT
104686 CATAGTAAAA
Statistics
Matches: 267, Mismatches: 29, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
196 31 0.12
197 83 0.31
198 149 0.56
199 1 0.00
200 3 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (194 bp):
TATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCATATAAAAAATTGTGACAAATAA
TATTTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACGTATAAATTTAGTCAAA
ATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAATAAAAATTCTGACAAATT
Found at i:104682 original size:31 final size:32
Alignment explanation
Indices: 104550--104682 Score: 110
Period size: 32 Copynumber: 4.2 Consensus size: 32
104540 TTCGTCTCAA
* *
104550 TATTTTGTCAAAATAA-AAATTGTGACATAT-T
1 TATTTT-TCAAAATAACAAATTGTAACAAATAT
* *
104581 TATTTAATCAAAATAACAATTTGTAACAAATAT
1 TATTT-TTCAAAATAACAAATTGTAACAAATAT
* ** * * * *
104614 TAATTTCTCATTATAAAAAAATGTGACAAATAA
1 T-ATTTTTCAAAATAACAAATTGTAACAAATAT
*
104647 TATTTTTCACAATAACAAATTGTAACAAA-AT
1 TATTTTTCAAAATAACAAATTGTAACAAATAT
104678 TATTT
1 TATTT
104683 AGTCATAGTA
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
31 20 0.25
32 33 0.42
33 22 0.28
34 4 0.05
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (32 bp):
TATTTTTCAAAATAACAAATTGTAACAAATAT
Found at i:104777 original size:17 final size:17
Alignment explanation
Indices: 104757--104791 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
104747 TTGTTGTAAT
*
104757 ATGTATTTTTTTCACGA
1 ATGTATTTTTGTCACGA
*
104774 ATGTCTTTTTGTCACGA
1 ATGTATTTTTGTCACGA
104791 A
1 A
104792 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (17 bp):
ATGTATTTTTGTCACGA
Found at i:105177 original size:23 final size:23
Alignment explanation
Indices: 105147--105191 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
105137 ATACTTTACA
105147 TGACAAGGTTGTTCTAACAAACG
1 TGACAAGGTTGTTCTAACAAACG
105170 TGACAAGGTTGTTCTAACAAAC
1 TGACAAGGTTGTTCTAACAAAC
105192 ATGGTAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (23 bp):
TGACAAGGTTGTTCTAACAAACG
Found at i:112987 original size:26 final size:26
Alignment explanation
Indices: 112951--113030 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
112941 ACTAAGTGCA
112951 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
112977 TATGGTGGGCACGACCTTATTTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
113003 TATGGTGGGAACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
113029 TA
1 TA
113031 GCACTTCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:115285 original size:21 final size:21
Alignment explanation
Indices: 115261--115313 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
115251 ATACAGGGAG
*
115261 TAGAATTTCCTACAAACCTGT
1 TAGAATTACCTACAAACCTGT
115282 TAGAATTACCTACAAACCTGT
1 TAGAATTACCTACAAACCTGT
*
115303 TATAATTACCT
1 TAGAATTACCT
115314 TTTGAGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (21 bp):
TAGAATTACCTACAAACCTGT
Found at i:120543 original size:26 final size:26
Alignment explanation
Indices: 120507--120560 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
120497 ACTAAGTGCA
*
120507 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
120533 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
120559 TA
1 TA
120561 GCACTTCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:128934 original size:22 final size:21
Alignment explanation
Indices: 128892--128931 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
128882 GAGTTTAGTT
*
128892 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
128913 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
128932 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:132635 original size:33 final size:33
Alignment explanation
Indices: 132582--132647 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
132572 TTTAAAAAAT
* * *
132582 ATATGTAATATGTACTATTTT-CAAAGCTATATA
1 ATATATAATATATACCATTTTCCAAA-CTATATA
132615 ATATATAATATATACCATTTTCCAAACTATATA
1 ATATATAATATATACCATTTTCCAAACTATATA
132648 TAATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (33 bp):
ATATATAATATATACCATTTTCCAAACTATATA
Found at i:132673 original size:12 final size:12
Alignment explanation
Indices: 132656--132680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
132646 TATAATATTT
132656 TTTTCAAAACTA
1 TTTTCAAAACTA
132668 TTTTCAAAACTA
1 TTTTCAAAACTA
132680 T
1 T
132681 ATATAATATA
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTTCAAAACTA
Found at i:132685 original size:2 final size:2
Alignment explanation
Indices: 132678--132729 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
132668 TTTTCAAAAC
* *
132678 TA TA TA TA -A TA TA TA -A TT TA T- TA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
132717 TA TA AA TA TA TA T
1 TA TA TA TA TA TA T
132730 TATTTCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.