Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 31 of 51
Found at i:6275270 original size:3 final size:3
Alignment explanation
Indices: 6275262--6275313 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
6275252 TTTTTGTCCC
6275262 TTA TTA TTA TTA TTA TTA -TA TTA TTA TATA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
6275306 TTA TTA TT
1 TTA TTA TT
6275314 TAAATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6277053 original size:18 final size:18
Alignment explanation
Indices: 6277019--6277053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6277009 AAGATTATAA
*
6277019 ATTAAATTTATATTAATT
1 ATTAAATTTATACTAATT
*
6277037 ATTAAATTTCTACTAAT
1 ATTAAATTTATACTAAT
6277054 AGATAATCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAAATTTATACTAATT
Found at i:6280420 original size:16 final size:17
Alignment explanation
Indices: 6280396--6280428 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6280386 TAATTTTTTA
*
6280396 TAAATAAAATATGTTAT
1 TAAATAAAATATATTAT
6280413 TAAA-AAAATATATTAT
1 TAAATAAAATATATTAT
6280429 CAATACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATAAAATATATTAT
Found at i:6281106 original size:28 final size:29
Alignment explanation
Indices: 6281077--6281269 Score: 97
Period size: 30 Copynumber: 6.9 Consensus size: 29
6281067 CTTAACATTA
6281077 AAAAATATTTATT-TTATATT-ACTTATT
1 AAAAATATTTATTCTTATATTAACTTATT
* *
6281104 AAATATATTTATTCTTATTTTAAC---TT
1 AAAAATATTTATTCTTATATTAACTTATT
* *
6281130 AAAAATATTTTAGTCTT-TA-T--CTTA-A
1 AAAAATA-TTTATTCTTATATTAACTTATT
*
6281155 AAAATATATTTATTCTTATCTT-ACTTATT
1 AAAA-ATATTTATTCTTATATTAACTTATT
* * *
6281184 ACATAAAT-TATATTGTTA-ACTTAAATTATT
1 A-A-AAATATTTATTCTTATA-TTAACTTATT
* ** *
6281214 AAATATATTATATTCTTACCTTAAATTATT
1 AAAAATATT-TATTCTTATATTAACTTATT
* * *
6281244 AAATATAATTAATTCTTATTTTAACT
1 AAAAAT-ATTTATTCTTATATTAACT
6281270 GTAAACATTT
Statistics
Matches: 126, Mismatches: 21, Indels: 35
0.69 0.12 0.19
Matches are distributed among these distances:
23 1 0.01
25 13 0.10
26 13 0.10
27 21 0.17
28 13 0.10
29 15 0.12
30 45 0.36
31 5 0.04
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (29 bp):
AAAAATATTTATTCTTATATTAACTTATT
Found at i:6281153 original size:23 final size:24
Alignment explanation
Indices: 6281122--6281177 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
6281112 TTATTCTTAT
*
6281122 TTTAACTTAAAAATAT-TTTAGTC
1 TTTATCTTAAAAATATATTTAGTC
*
6281145 TTTATCTTAAAAAATATATTTATTC
1 TTTATCTT-AAAAATATATTTAGTC
6281170 -TTATCTTA
1 TTTATCTTA
6281178 CTTATTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.28
24 15 0.52
25 6 0.21
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTATCTTAAAAATATATTTAGTC
Found at i:6281173 original size:24 final size:25
Alignment explanation
Indices: 6281104--6281177 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
6281094 ATTACTTATT
*
6281104 AAATATATTTATTCTTATTTTAACTTA
1 AAATATATTTATTCTTATCTTAA--TA
*
6281131 AAA-ATATTTTAGTCTTTATCTTAA-A
1 AAATATA-TTTATTC-TTATCTTAATA
6281156 AAATATATTTATTCTTATCTTA
1 AAATATATTTATTCTTATCTTA
6281178 CTTATTACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 8 0.20
25 10 0.24
26 6 0.15
27 9 0.22
28 8 0.20
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (25 bp):
AAATATATTTATTCTTATCTTAATA
Found at i:6281224 original size:30 final size:30
Alignment explanation
Indices: 6281156--6281261 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
6281146 TTATCTTAAA
* *
6281156 AAATATATT-TATTCTTATCTT-ACTTATT
1 AAATATATTATATTCTTAACTTAAATTATT
* * *
6281184 ACATAAATTATATTGTTAACTTAAATTATT
1 AAATATATTATATTCTTAACTTAAATTATT
*
6281214 AAATATATTATATTCTTACCTTAAATTATT
1 AAATATATTATATTCTTAACTTAAATTATT
6281244 AAATATAATTA-ATTCTTA
1 AAATAT-ATTATATTCTTA
6281262 TTTTAACTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.11
29 10 0.15
30 45 0.68
31 4 0.06
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATATATTATATTCTTAACTTAAATTATT
Found at i:6281465 original size:30 final size:30
Alignment explanation
Indices: 6281427--6281538 Score: 99
Period size: 30 Copynumber: 3.8 Consensus size: 30
6281417 TTAATAATAG
*
6281427 AAAT-TATTTTTTAATTTAAGATAAGATTA
1 AAATATATTTTTTAAGTTAAGATAAGATTA
* * * *
6281456 AAATATATTTTTAAAATTAAAATAA-AATA
1 AAATATATTTTTTAAGTTAAGATAAGATTA
*
6281485 AAATATA-TTTTTAAGTTACA-AAAAGAATT-
1 AAATATATTTTTTAAGTTA-AGATAAG-ATTA
**
6281514 AAATATATTTAATAAGTTAAGATAA
1 AAATATATTTTTTAAGTTAAGATAA
6281539 AAAAAATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
28 12 0.18
29 23 0.35
30 31 0.47
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATATATTTTTTAAGTTAAGATAAGATTA
Found at i:6281469 original size:29 final size:29
Alignment explanation
Indices: 6281434--6281538 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
6281424 TAGAAATTAT
*
6281434 TTTTTAATTTAAGATAAGATTAAAATATA
1 TTTTTAAGTTAAGATAAGATTAAAATATA
* * *
6281463 TTTTTAAAATTAAAATAA-AATAAAATATA
1 TTTTT-AAGTTAAGATAAGATTAAAATATA
*
6281492 TTTTTAAGTTACA-AAAAGAATT-AAATATA
1 TTTTTAAGTTA-AGATAAG-ATTAAAATATA
*
6281521 TTTAATAAGTTAAGATAA
1 TTT-TTAAGTTAAGATAA
6281539 AAAAAATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
28 8 0.13
29 32 0.52
30 22 0.35
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
TTTTTAAGTTAAGATAAGATTAAAATATA
Found at i:6286372 original size:23 final size:23
Alignment explanation
Indices: 6286306--6286388 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
6286296 CTCGTATAAA
*
6286306 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
6286329 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
* *
6286352 TGCACCGAAGTGCTGCATAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
6286375 TACACC-ATAGTGCC
1 TGCACCGA-AGTGCC
6286389 ATATAAGATT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.02
23 53 0.98
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:6293344 original size:23 final size:23
Alignment explanation
Indices: 6293292--6293353 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
6293282 TCACCACAGC
6293292 TCGTATA-AA-TGCACCGAAGTG
1 TCGTATAGAATTGCACCGAAGTG
* ***
6293313 CCACGTAGAATTGCACCGAAGTG
1 TCGTATAGAATTGCACCGAAGTG
6293336 TCGTATAGAATTGCACCG
1 TCGTATAGAATTGCACCG
6293354 TAGTTCCATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 3 0.10
22 2 0.06
23 26 0.84
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (23 bp):
TCGTATAGAATTGCACCGAAGTG
Found at i:6294072 original size:63 final size:65
Alignment explanation
Indices: 6294005--6294166 Score: 192
Period size: 63 Copynumber: 2.6 Consensus size: 65
6293995 ATCCCTTGTC
* *
6294005 GGGTGCATCGATGCACTATC-TATGCATCGATACA-TAAAT-CCTATTCGATGTTTTTA-TTTAA
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATGAC-ATTCGATGTTTTTATTTTAA
*
6294066 GG
64 AG
* * *
6294068 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGACATTCGATGTTTTTATTTTAAAT
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
**
6294132 TAGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATGTGCATCGATACAC
6294167 CTTAAACAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 47 0.55
64 38 0.44
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
Found at i:6295227 original size:21 final size:21
Alignment explanation
Indices: 6295202--6295260 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
6295192 ATTATCCAAT
* *
6295202 AAACTTGACATTCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
6295223 TAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
6295244 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
6295261 TAATAAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:6298679 original size:41 final size:40
Alignment explanation
Indices: 6298625--6298936 Score: 315
Period size: 41 Copynumber: 7.6 Consensus size: 40
6298615 TTGTAAACAC
* **
6298625 AAACACCACTAAAGTACATGTCTATAGCAGTATTTGTATAA
1 AAACGCCACTAAAGTACA-GTCTATAGCAGCGTTTGTATAA
* * * * *
6298666 AATCGCCGCTAAAGTACAAGTCTATAGTACCGTTTATATAA
1 AAACGCCACTAAAGTAC-AGTCTATAGCAGCGTTTGTATAA
*
6298707 AAACGCCACTAAAGTACGAGTCTGTAGCAGCGTTTGTATAA
1 AAACGCCACTAAAGTAC-AGTCTATAGCAGCGTTTGTATAA
* *
6298748 AAACACCACTAAAGTACGAGTCTATAGCAGGGTTTGTATAA
1 AAACGCCACTAAAGTAC-AGTCTATAGCAGCGTTTGTATAA
* * * *
6298789 AAACACCACTGAAGTACAAGTCTATAGCGGCATTTGTATAA
1 AAACGCCACTAAAGTAC-AGTCTATAGCAGCGTTTGTATAA
* * * *
6298830 AAATGCCACTAAAATACGGGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTAC-AGTCTATAGCAGCGTTTGTATAA
* * *
6298871 AAACGCCACTAAAATATGAGTTTATAGC-GACGTTTGTATAA
1 AAACGCCACTAAAGTA-CAGTCTATAGCAG-CGTTTGTATAA
6298912 AATA--CCACTAAAGTACGAGTCTATA
1 AA-ACGCCACTAAAGTAC-AGTCTATA
6298937 ACGGTGAAGG
Statistics
Matches: 229, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
40 18 0.08
41 209 0.91
42 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (40 bp):
AAACGCCACTAAAGTACAGTCTATAGCAGCGTTTGTATAA
Found at i:6298770 original size:82 final size:82
Alignment explanation
Indices: 6298625--6298936 Score: 351
Period size: 82 Copynumber: 3.8 Consensus size: 82
6298615 TTGTAAACAC
* * * * *
6298625 AAACACCACTAAAGTAC-ATGTCTATAGCAGTATTTGTATAAAATCGCCGCTAAAGTACAAGTCT
1 AAACACCACTAAAGTACGA-GTCTATAGCAGCATTTGTATAAAAACACCACTAAAGTACGAGTCT
* * *
6298689 ATAGTACCGTTTATATAA
65 ATAGCAGCGTTTGTATAA
* * *
6298707 AAACGCCACTAAAGTACGAGTCTGTAGCAGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTA
1 AAACACCACTAAAGTACGAGTCTATAGCAGCATTTGTATAAAAACACCACTAAAGTACGAGTCTA
*
6298772 TAGCAGGGTTTGTATAA
66 TAGCAGCGTTTGTATAA
* * * ** * *
6298789 AAACACCACTGAAGTACAAGTCTATAGCGGCATTTGTATAAAAATGCCACTAAAATACGGGTCTA
1 AAACACCACTAAAGTACGAGTCTATAGCAGCATTTGTATAAAAACACCACTAAAGTACGAGTCTA
*
6298854 TAGCGGCGTTTGTATAA
66 TAGCAGCGTTTGTATAA
* * * * * *
6298871 AAACGCCACTAAAATATGAGTTTATAGC-GACGTTTGTAT-AAAATACCACTAAAGTACGAGTCT
1 AAACACCACTAAAGTACGAGTCTATAGCAG-CATTTGTATAAAAACACCACTAAAGTACGAGTCT
6298934 ATA
65 ATA
6298937 ACGGTGAAGG
Statistics
Matches: 194, Mismatches: 34, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
81 25 0.13
82 168 0.87
83 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (82 bp):
AAACACCACTAAAGTACGAGTCTATAGCAGCATTTGTATAAAAACACCACTAAAGTACGAGTCTA
TAGCAGCGTTTGTATAA
Found at i:6298771 original size:123 final size:122
Alignment explanation
Indices: 6298625--6298936 Score: 378
Period size: 123 Copynumber: 2.5 Consensus size: 122
6298615 TTGTAAACAC
* *
6298625 AAACACCACTAAAGTAC-ATGTCTATAGCAGTATTTGTATAAAATCGCCGCTAAAGTACAAGTCT
1 AAACACCACTAAAGTACGA-GTCTATAGCAG-ATTTGTATAAAATCACCACTAAAGTACAAGTCT
* * * *
6298689 ATAGTACCGTTTATATAAAAACGCCACTAAAGTACGAGTCTGTAGCAGCGTTTGTATAA
64 ATAGCACCATTTATATAAAAACGCCACTAAAATACGAGTCTATAGCAGCGTTTGTATAA
* * *
6298748 AAACACCACTAAAGTACGAGTCTATAGCAGGGTTTGTATAAAAACACCACTGAAGTACAAGTCTA
1 AAACACCACTAAAGTACGAGTCTATAGCA-GATTTGTATAAAATCACCACTAAAGTACAAGTCTA
** * * * *
6298813 TAGCGGCATTTGTATAAAAATGCCACTAAAATACGGGTCTATAGCGGCGTTTGTATAA
65 TAGCACCATTTATATAAAAACGCCACTAAAATACGAGTCTATAGCAGCGTTTGTATAA
* * * * *
6298871 AAACGCCACTAAAATATGAGTTTATAGC-GACGTTTGTATAAAAT-ACCACTAAAGTACGAGTCT
1 AAACACCACTAAAGTACGAGTCTATAGCAGA--TTTGTATAAAATCACCACTAAAGTACAAGTCT
6298934 ATA
64 ATA
6298937 ACGGTGAAGG
Statistics
Matches: 162, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
121 1 0.01
122 20 0.12
123 139 0.86
124 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (122 bp):
AAACACCACTAAAGTACGAGTCTATAGCAGATTTGTATAAAATCACCACTAAAGTACAAGTCTAT
AGCACCATTTATATAAAAACGCCACTAAAATACGAGTCTATAGCAGCGTTTGTATAA
Found at i:6299916 original size:31 final size:31
Alignment explanation
Indices: 6299878--6299969 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
6299868 ATATTCTTTT
6299878 TATAATATAAATATTAAAATAAAATTTTAAA
1 TATAATATAAATATTAAAATAAAATTTTAAA
* *
6299909 TATAATATAAAAATTAAAATAATTATTTT---
1 TATAATATAAATATTAAAATAA-AATTTTAAA
* *
6299938 TATTATA-AAATA-TAAAATAAATTTTTAAA
1 TATAATATAAATATTAAAATAAAATTTTAAA
6299967 TAT
1 TAT
6299970 TGTACAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.08
27 8 0.16
28 4 0.08
29 9 0.18
31 21 0.41
32 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TATAATATAAATATTAAAATAAAATTTTAAA
Found at i:6299926 original size:26 final size:27
Alignment explanation
Indices: 6299875--6299928 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
6299865 AAAATATTCT
*
6299875 TTTTATAATATAAATATTAAAATAAAA
1 TTTTATAATATAAATATAAAAATAAAA
6299902 TTTTA-AATAT-AATATAAAAATTAAAA
1 TTTTATAATATAAATATAAAAA-TAAAA
6299928 T
1 T
6299929 AATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 9 0.36
26 11 0.44
27 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TTTTATAATATAAATATAAAAATAAAA
Found at i:6299928 original size:19 final size:20
Alignment explanation
Indices: 6299886--6299929 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
6299876 TTTATAATAT
* *
6299886 AAATATTAAAATAAAATTTT
1 AAATATTAAAATAAAAATTA
*
6299906 AAATA-TAATATAAAAATTA
1 AAATATTAAAATAAAAATTA
6299925 AAATA
1 AAATA
6299930 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATTAAAATAAAAATTA
Found at i:6300372 original size:27 final size:27
Alignment explanation
Indices: 6300342--6300393 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
6300332 ATGTTGAGCA
6300342 GGAACATAGTTGACACGAACTTCACTT
1 GGAACATAGTTGACACGAACTTCACTT
6300369 GGAACATAGTTGACACGAACTTCAC
1 GGAACATAGTTGACACGAACTTCAC
6300394 CTGCTGCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (27 bp):
GGAACATAGTTGACACGAACTTCACTT
Found at i:6304171 original size:15 final size:16
Alignment explanation
Indices: 6304137--6304171 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6304127 TCTATATATT
6304137 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
*
6304153 TTTTTTGATTTCAAG-
1 TTTTTTGAGTTCAAGC
6304168 TTTT
1 TTTT
6304172 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.17, C:0.09, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:6311767 original size:15 final size:15
Alignment explanation
Indices: 6311747--6311802 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
6311737 TATATCAAAG
6311747 AAAAAATGAAAATGA
1 AAAAAATGAAAATGA
*
6311762 AAAAAATTAAAATGA
1 AAAAAATGAAAATGA
*
6311777 AAAAAA-GAAAAAGA
1 AAAAAATGAAAATGA
*
6311791 AAAAAAAGAAAA
1 AAAAAATGAAAA
6311803 AAAGAAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 12 0.32
15 25 0.68
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (15 bp):
AAAAAATGAAAATGA
Found at i:6311781 original size:8 final size:8
Alignment explanation
Indices: 6311770--6311809 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
6311760 GAAAAAAATT
*
6311770 AAAATGAA
1 AAAAAGAA
6311778 AAAAAGAA
1 AAAAAGAA
*
6311786 AAAGA-AA
1 AAAAAGAA
6311793 AAAAAGAA
1 AAAAAGAA
6311801 AAAAAGAA
1 AAAAAGAA
6311809 A
1 A
6311810 TCCAATCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:6311787 original size:21 final size:21
Alignment explanation
Indices: 6311749--6311788 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6311739 TATCAAAGAA
*
6311749 AAAATGAAAATGAAAAAAATT
1 AAAATGAAAATAAAAAAAATT
6311770 AAAATGAAAA-AAAGAAAAA
1 AAAATGAAAATAAA-AAAAA
6311789 GAAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAATGAAAATAAAAAAAATT
Found at i:6311802 original size:29 final size:29
Alignment explanation
Indices: 6311746--6311802 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
6311736 ATATATCAAA
* * **
6311746 GAAAAAATGAAAATGAAAAAAATTAAAAT
1 GAAAAAAAGAAAAAGAAAAAAAAGAAAAT
6311775 GAAAAAAAGAAAAAGAAAAAAAAGAAAA
1 GAAAAAAAGAAAAAGAAAAAAAAGAAAA
6311803 AAAGAAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (29 bp):
GAAAAAAAGAAAAAGAAAAAAAAGAAAAT
Found at i:6314108 original size:233 final size:233
Alignment explanation
Indices: 6313702--6314154 Score: 721
Period size: 233 Copynumber: 1.9 Consensus size: 233
6313692 AAGTGAAAAA
*
6313702 ATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTTCTTAC
*
6313767 CTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGC
66 CTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * *
6313832 CTAAAACCTTCGGGTTATCTGTAAACCTTTCGAGCAAGATGATAAGTCCTTC-GGTCATCCATAA
131 CTAAAACATTCGGGTCATCTGTAAACCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
*
6313896 GACCTTTGGGCAGGATGTTTTCACATGTCTATCGAAAT
196 GACCTTTGGACAGGATGTTTTCACATGTCTATCGAAAT
* * *
6313934 ATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAATTTTTTTGAAAAGTAATAAAGG-TTTCTT
1 ATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAA--ATTTTGAAAAGTAAGAAAGGTTTTCTT
*
6313998 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGAT
64 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * ** *
6314063 GCTTTAATCATTCGGGTCATCTGTAAGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCAT
129 GCCTAAAACATTCGGGTCATCTGTAAACCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCAT
6314128 AAGACCTTTGGACAGGATGTTTTCACA
194 AAGACCTTTGGACAGGATGTTTTCACA
6314155 GGTCCCTCTT
Statistics
Matches: 201, Mismatches: 17, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
232 34 0.17
233 114 0.57
234 53 0.26
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (233 bp):
ATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTTCTTAC
CTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
CTAAAACATTCGGGTCATCTGTAAACCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
GACCTTTGGACAGGATGTTTTCACATGTCTATCGAAAT
Found at i:6314444 original size:110 final size:110
Alignment explanation
Indices: 6314248--6314538 Score: 352
Period size: 110 Copynumber: 2.6 Consensus size: 110
6314238 GAATGGATCA
* *
6314248 ATCTGATATTCCCTTTCAAAGAAGCGAAACAGATCCCTCTCTTCCAAGATTTGATATTCCCTGAG
1 ATCTGATATT-CCTTTCAAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* * * ** *
6314313 TGAAAGCGGAACAAGTTTACCCCGGTTCAATGTATCAAC-TCCAAG
65 TGACAGCGAAACAAGTCTACCCCAATTCAATGGATCAACTTCCAAG
* * *
6314358 ATTTGATATTCACTTTCAAAGAAGCGGAACAGATCCCTATCTTTCAAGATTTGATATTCCCTGGG
1 ATCTGATATTC-CTTTCAAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* *
6314423 TGACGGCGAAACAAGTCTACCCCAATTCAATGGATCAACTTTCCCAG
65 TGACAGCGAAACAAGTCTACCCCAATTCAATGGATCAAC-TTCCAAG
* * ** * * *
6314470 ATCTGTTATTCCCTT-AGAAGAAATGGAACAAATCACTCTCTTTCAAGATTTGATATTCCATGAG
1 ATCTGATATTCCTTTCA-AAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
6314534 TGACA
65 TGACA
6314539 ATGGAACAAG
Statistics
Matches: 153, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
109 1 0.01
110 91 0.59
111 47 0.31
112 14 0.09
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (110 bp):
ATCTGATATTCCTTTCAAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
GACAGCGAAACAAGTCTACCCCAATTCAATGGATCAACTTCCAAG
Found at i:6318711 original size:3 final size:3
Alignment explanation
Indices: 6318687--6318771 Score: 95
Period size: 3 Copynumber: 29.0 Consensus size: 3
6318677 TTTTTCCATT
*
6318687 TTA TT- TTA TT- TTA TTA -TC TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
6318732 TTA TTA CTA TTAA TTA TTA TTG TTG TTA CTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
6318772 ACATTTTGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
2 5 0.07
3 62 0.89
4 3 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6318816 original size:18 final size:19
Alignment explanation
Indices: 6318789--6318824 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6318779 GCAGGCTCCA
*
6318789 ATCTGGAGCCC-AAGACCG
1 ATCTGAAGCCCTAAGACCG
6318807 ATCTGAAGCCCTAAGACC
1 ATCTGAAGCCCTAAGACC
6318825 ATTACCAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCTGAAGCCCTAAGACCG
Found at i:6320155 original size:37 final size:37
Alignment explanation
Indices: 6320105--6320178 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
6320095 TTTTATGTAT
*
6320105 TACATCCTTATGTCTTTTATATCTAGAATAGGCACAA
1 TACATCCTTATGTCCTTTATATCTAGAATAGGCACAA
*
6320142 TACATCCTTATGTCCTTTATATCTAGAATAGGGACAA
1 TACATCCTTATGTCCTTTATATCTAGAATAGGCACAA
6320179 GTCTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (37 bp):
TACATCCTTATGTCCTTTATATCTAGAATAGGCACAA
Found at i:6325522 original size:22 final size:22
Alignment explanation
Indices: 6325484--6325538 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
6325474 AAACCATTCA
6325484 GGGGGAATCGGTACCCCCTT-G
1 GGGGGAATCGGTACCCCCTTGG
6325505 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
6325527 GGGGGAATCGGT
1 GGGGGAATCGGT
6325539 TCCCTCTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:6325929 original size:25 final size:22
Alignment explanation
Indices: 6325878--6325939 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
6325868 ACTCCCCCTT
*
6325878 ACTTTAACACTTACT-CTTTTT
1 ACTTTAACACTTACTCCTTTTA
6325899 ACTTTAACACTTACTCCTCTTTAAA
1 ACTTTAACACTTACTCCT-TTT--A
6325924 ACTTTAACACTT-CTCC
1 ACTTTAACACTTACTCC
6325940 CCCTTTTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 3 0.08
24 4 0.11
25 12 0.33
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (22 bp):
ACTTTAACACTTACTCCTTTTA
Found at i:6326218 original size:33 final size:31
Alignment explanation
Indices: 6326181--6326245 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
6326171 AGTTCTCACC
*
6326181 ATCCATAAATCCAAACAAATT-CAAAATCAATCA
1 ATCCACAAATCCAAAC--ATTCCAAAAT-AATCA
*
6326214 ATCCACAAATTCAAACATTCCAAAATAATCA
1 ATCCACAAATCCAAACATTCCAAAATAATCA
6326245 A
1 A
6326246 AATGTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 6 0.21
33 14 0.48
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.22
Consensus pattern (31 bp):
ATCCACAAATCCAAACATTCCAAAATAATCA
Found at i:6326514 original size:12 final size:12
Alignment explanation
Indices: 6326497--6326523 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6326487 GTTGTGCTTT
6326497 CTCCTCGGGCTG
1 CTCCTCGGGCTG
6326509 CTCCTCGGGCTG
1 CTCCTCGGGCTG
6326521 CTC
1 CTC
6326524 AGGCTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.44, G:0.30, T:0.26
Consensus pattern (12 bp):
CTCCTCGGGCTG
Found at i:6328177 original size:21 final size:21
Alignment explanation
Indices: 6328151--6328190 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6328141 CAGAACCCCA
*
6328151 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
6328172 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
6328191 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:6328225 original size:20 final size:21
Alignment explanation
Indices: 6328173--6328233 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
6328163 TTCCCCTGTG
6328173 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
6328196 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
6328216 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
6328234 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:6333946 original size:20 final size:20
Alignment explanation
Indices: 6333921--6333959 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6333911 CCGTTACACA
6333921 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCTCT
*
6333941 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
6333960 CGAGCATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.41, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCTCT
Found at i:6337540 original size:538 final size:537
Alignment explanation
Indices: 6336523--6337598 Score: 2073
Period size: 538 Copynumber: 2.0 Consensus size: 537
6336513 TACTCTTTTA
6336523 TGTATTACATCCTTATGTCCTTTATATCTAGAATAGGCACAAGTCTTGGAATAATCACACTTGTA
1 TGTATTACATCCTTATGTCCTTTATATCTAGAATAGGCACAAGTCTTGGAATAATCACACTTGTA
6336588 TAGCCCATCTATTGTTTCTTGATATCTAGAGTAGACTTTAATTAACGAATAGTTTATGATATCTC
66 TAGCCCATCTATTGTTTCTTGATATCTAGAGTAGACTTTAATTAACGAATAGTTTATGATATCTC
*
6336653 ATATCAACTTATTCGAGCATGGCCATGCACTTCTAGTCTTACTCAATCAAGTGGCCTGTGATATA
131 ATATCAACTTATTCGAGCATGGCCATGCACTTCTAGTCTTACTCAATCAAGTGGCCTGTGATACA
6336718 TTTCCTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTGAGAT
196 TTTCCTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTGAGAT
6336783 ATATTCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGCTGCATCAAAACATAC
261 ATATTCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGCTGCATCAAAACATAC
*
6336848 AATAATATATGTTGGGATATTATTGATCTCAAGTTTGAGGATCATACATATAGTCATCACCATGA
326 AATAATATATGTTGGGATATTATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGA
6336913 GCAATGTTATGACTGTCACATAATAATCCAAGACATATGCTCATGGTCGGTCAATCCAATACATT
391 GCAATGTTATGACTGTCACATAATAATCCAAGACATATGCTCATGGTCGGTCAATCCAATACATT
* *
6336978 GTTCTCTAACAATAAAATCATGTATCAATTCTGACA-TCTCTATGTCAATGACAACTCATTGTCA
456 GTTCTCTAACAATAAAATCATGTATCAA-TAT-AAATTCTCTATGTCAATGACAACTCATTGTCA
6337042 TCAATCAATAACATGTTAG
519 TCAATCAATAACATGTTAG
6337061 TGTATTACATCCTTATGTCCTTTATATCTAGAATAGGCACAAGTCTTGGAATAATCACACTTGTA
1 TGTATTACATCCTTATGTCCTTTATATCTAGAATAGGCACAAGTCTTGGAATAATCACACTTGTA
6337126 TAGCCCATCTATTGTTTCTTGATATCTAGAGTAGACTTTAATTAACGAATAGTTTATGATATCTC
66 TAGCCCATCTATTGTTTCTTGATATCTAGAGTAGACTTTAATTAACGAATAGTTTATGATATCTC
*
6337191 ATATCAACTTATTCGAGCATGGCCATGCATTTCTAGTCTTACTCAATCAAGTGGCCTGTGATACA
131 ATATCAACTTATTCGAGCATGGCCATGCACTTCTAGTCTTACTCAATCAAGTGGCCTGTGATACA
6337256 TTTCCTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTGAGAT
196 TTTCCTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTGAGAT
*
6337321 ATATTCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGCTGCATCAAAACATAT
261 ATATTCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGCTGCATCAAAACATAC
6337386 AATAATATATGTTGGGATATTATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGA
326 AATAATATATGTTGGGATATTATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGA
6337451 GCAATGTTATGACTGTCACATAATAATCCAAGACATATGCTCATGGTCGGTCAATCCAATACATT
391 GCAATGTTATGACTGTCACATAATAATCCAAGACATATGCTCATGGTCGGTCAATCCAATACATT
6337516 GTTCTCTAACAATAAAATCATGTATCAATATAAATTCTCTATGTCAATGACAACTCATTGTCATC
456 GTTCTCTAACAATAAAATCATGTATCAATATAAATTCTCTATGTCAATGACAACTCATTGTCATC
6337581 AATCAATAACATGTTAG
521 AATCAATAACATGTTAG
6337598 T
1 T
6337599 CTTAAGCGTA
Statistics
Matches: 531, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
536 2 0.00
537 50 0.09
538 479 0.90
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (537 bp):
TGTATTACATCCTTATGTCCTTTATATCTAGAATAGGCACAAGTCTTGGAATAATCACACTTGTA
TAGCCCATCTATTGTTTCTTGATATCTAGAGTAGACTTTAATTAACGAATAGTTTATGATATCTC
ATATCAACTTATTCGAGCATGGCCATGCACTTCTAGTCTTACTCAATCAAGTGGCCTGTGATACA
TTTCCTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTGAGAT
ATATTCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGCTGCATCAAAACATAC
AATAATATATGTTGGGATATTATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGA
GCAATGTTATGACTGTCACATAATAATCCAAGACATATGCTCATGGTCGGTCAATCCAATACATT
GTTCTCTAACAATAAAATCATGTATCAATATAAATTCTCTATGTCAATGACAACTCATTGTCATC
AATCAATAACATGTTAG
Found at i:6340630 original size:21 final size:21
Alignment explanation
Indices: 6340597--6340636 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6340587 AGTCTAAATG
* *
6340597 TACCAAGTGTTTTACTAAACA
1 TACCAAGTCTTTTAATAAACA
*
6340618 TACCAATTCTTTTAATAAA
1 TACCAAGTCTTTTAATAAA
6340637 ATAATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (21 bp):
TACCAAGTCTTTTAATAAACA
Found at i:6341456 original size:11 final size:11
Alignment explanation
Indices: 6341437--6341471 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
6341427 TATATTTTTT
6341437 TAGTAAAATGA
1 TAGTAAAATGA
*
6341448 TAGTGAAATGA
1 TAGTAAAATGA
6341459 TAGTAAAATGA
1 TAGTAAAATGA
6341470 TA
1 TA
6341472 AACAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (11 bp):
TAGTAAAATGA
Found at i:6344632 original size:25 final size:25
Alignment explanation
Indices: 6344600--6344649 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
6344590 CCTGCAAAGC
6344600 TTATTTTT-TGGCATTATAATAAATA
1 TTATTTTTCT-GCATTATAATAAATA
*
6344625 TTATTTTTCTTCATTATAATAAATA
1 TTATTTTTCTGCATTATAATAAATA
6344650 AATTTATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (25 bp):
TTATTTTTCTGCATTATAATAAATA
Found at i:6345117 original size:38 final size:38
Alignment explanation
Indices: 6345066--6345141 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
6345056 CACCACCCAC
* *
6345066 AACCACCAACCTACCC-AGGTTATTAATGGATAATTAAT
1 AACCACCAACCTACCCGA-ATTATTAATGAATAATTAAT
6345104 AACCACCAACCTACCCGAATTATTAATGAATAATTAAT
1 AACCACCAACCTACCCGAATTATTAATGAATAATTAAT
6345142 GGTGCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (38 bp):
AACCACCAACCTACCCGAATTATTAATGAATAATTAAT
Found at i:6345466 original size:25 final size:25
Alignment explanation
Indices: 6345438--6345496 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
6345428 TAATGGTGTC
6345438 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
6345463 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
6345488 ATTATTTTT
1 ATTATTTTT
6345497 TCTACTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTATTTTTCGTCATTATAATAAAT
Found at i:6347744 original size:24 final size:24
Alignment explanation
Indices: 6347712--6347757 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6347702 TGCGGCAGAG
6347712 GCAGCAGCTACACAGGCCGTTGCA
1 GCAGCAGCTACACAGGCCGTTGCA
* * *
6347736 GCAGGAGCTGCAGAGGCCGTTG
1 GCAGCAGCTACACAGGCCGTTG
6347758 AAGGATGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.13
Consensus pattern (24 bp):
GCAGCAGCTACACAGGCCGTTGCA
Found at i:6357472 original size:3 final size:3
Alignment explanation
Indices: 6357464--6357522 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
6357454 TGTTTATAAC
* *
6357464 TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT TAT GAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
6357509 TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TA
6357523 CAAACAGATC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:6358936 original size:2 final size:2
Alignment explanation
Indices: 6358925--6358976 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
6358915 ATATCATGCT
6358925 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA 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
6358966 TA TA TA TA TA T
1 TA TA TA TA TA T
6358977 TATTTAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6358986 original size:14 final size:14
Alignment explanation
Indices: 6358925--6358993 Score: 74
Period size: 12 Copynumber: 5.1 Consensus size: 14
6358915 ATATCATGCT
6358925 TATAATATATA-TA
1 TATAATATATATTA
6358938 TAT-ATATATA-TA
1 TATAATATATATTA
6358950 TAT-ATATATATATA
1 TATAATATATAT-TA
6358964 TATATATATATATTA
1 TATA-ATATATATTA
* *
6358979 TTTAATATAAATTA
1 TATAATATATATTA
6358993 T
1 T
6358994 TTTAATCATG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
12 19 0.38
13 3 0.06
14 15 0.30
15 5 0.10
16 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATAATATATATTA
Found at i:6358986 original size:16 final size:17
Alignment explanation
Indices: 6358929--6358995 Score: 77
Period size: 18 Copynumber: 4.0 Consensus size: 17
6358919 CATGCTTATA
*
6358929 ATATATATATATATATAT
1 ATATATATATAT-TATTT
*
6358947 ATATATATATATATATAT
1 ATATATATATAT-TATTT
6358965 ATATATATATATTATTT
1 ATATATATATATTATTT
6358982 A-ATATA-A-ATTATTT
1 ATATATATATATTATTT
6358996 TAATCATGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
14 7 0.15
15 1 0.02
16 5 0.10
17 5 0.10
18 30 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATTATTT
Found at i:6359268 original size:17 final size:18
Alignment explanation
Indices: 6359248--6359283 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6359238 TTTATAAAAA
6359248 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
6359265 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
6359283 T
1 T
6359284 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:6359268 original size:25 final size:27
Alignment explanation
Indices: 6359223--6359273 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
6359213 TATTTCTAAG
6359223 TAAATAAATATCATATTTATAAAAATA
1 TAAATAAATATCATATTTATAAAAATA
6359250 TAAA-AAATAT-ATATTTATAAAAAT
1 TAAATAAATATCATATTTATAAAAAT
6359274 TAATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
26 6 0.25
27 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAATAAATATCATATTTATAAAAATA
Found at i:6360882 original size:23 final size:23
Alignment explanation
Indices: 6360848--6360898 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
6360838 GCAGCGACTA
*
6360848 GTGGCAGTAGAGGAGATGAA-AC
1 GTGGCAGCAGAGGAGATGAAGAC
6360870 GGTGGCAGCAGAGGAGATGAAGAC
1 -GTGGCAGCAGAGGAGATGAAGAC
6360894 GTGGC
1 GTGGC
6360899 CCTAGGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.31, C:0.12, G:0.45, T:0.12
Consensus pattern (23 bp):
GTGGCAGCAGAGGAGATGAAGAC
Found at i:6361141 original size:3 final size:3
Alignment explanation
Indices: 6361133--6361204 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
6361123 GACCTGTTTG
*
6361133 TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* *
6361179 TAA T-A TAT TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
6361205 AAAAATAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6362932 original size:17 final size:17
Alignment explanation
Indices: 6362910--6362968 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
6362900 AAGGTTGAAC
6362910 AACTTCTTCTCATTATG
1 AACTTCTTCTCATTATG
6362927 AACTTCTTCTTC-TTCA-G
1 AACTTCTTC-TCATT-ATG
*
6362944 ATGAGTTCTTCTCATTATG
1 A--ACTTCTTCTCATTATG
6362963 AACTTC
1 AACTTC
6362969 CTCTGGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 17 0.50
18 6 0.18
19 11 0.32
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (17 bp):
AACTTCTTCTCATTATG
Found at i:6363045 original size:120 final size:121
Alignment explanation
Indices: 6362827--6363106 Score: 400
Period size: 120 Copynumber: 2.3 Consensus size: 121
6362817 ACAATGGATA
** * * * * * *
6362827 AGTTCTTCTCATTATGAACTTTATCTGAAAATGTTGGTGTTGATCTATCTCCTTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGGTGCTGATCTATCTCCTTATGGGATAAAA
*
6362892 TCAAGCAAAAGGTTGAACAACTTCTTCTCATTATGAAC-TTCTTCTTCTTCAGATG
66 TCAAGCAAAAGGTTGAACAACTTCTTCTCATTATGAACTTTCTTCCTCTTCAGATG
*
6362947 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGGTGCTGATTTATCTCCTTATGGGATAAAA
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGGTGCTGATCTATCTCCTTATGGGATAAAA
* * * * *
6363012 TCGAGCAAAATGTTGAACAAGTTCTTCTTATTATGAACTTTTCTTCCTCTTTAGATG
66 TCAAGCAAAAGGTTGAACAACTTCTTCTCATTATGAAC-TTTCTTCCTCTTCAGATG
*
6363069 AGTTCTTCTTATTATGAACTTCCTCTGGAAATGTTGGT
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGGT
6363107 CCATCAAGTG
Statistics
Matches: 142, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
120 90 0.63
122 52 0.37
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (121 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGGTGCTGATCTATCTCCTTATGGGATAAAA
TCAAGCAAAAGGTTGAACAACTTCTTCTCATTATGAACTTTCTTCCTCTTCAGATG
Found at i:6363240 original size:73 final size:73
Alignment explanation
Indices: 6363121--6363274 Score: 245
Period size: 73 Copynumber: 2.1 Consensus size: 73
6363111 CAAGTGATGG
* * * *
6363121 AAATTTTTGTTTCTAGTGAAACTGTCTCAAGTGAGACGAATCTTGTTTTAAGAAAAACAATCTCA
1 AAATTGTTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCA
6363186 AGTGAGAT
66 AGTGAGAT
* * *
6363194 AAATTGTTGTTTCGAGTGAAACTGTCTTAAGCGAGATAAATTTTGTTTTAAGAAAAACAATCTCA
1 AAATTGTTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCA
6363259 AGTGAGAT
66 AGTGAGAT
6363267 AAATTGTT
1 AAATTGTT
6363275 ATTTGAAAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (73 bp):
AAATTGTTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCA
AGTGAGAT
Found at i:6363271 original size:36 final size:36
Alignment explanation
Indices: 6363145--6363271 Score: 146
Period size: 36 Copynumber: 3.5 Consensus size: 36
6363135 AGTGAAACTG
** *
6363145 TCTCAAGTGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
** ** **
6363181 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGATAAATT-TTGTTTTAAGAAAAACAA
* *
6363218 TCTTAAGCGAGATAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
6363254 TCTCAAGTGAGATAAATT
1 TCTCAAGTGAGATAAATT
6363272 GTTATTTGAA
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
36 43 0.61
37 28 0.39
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
Found at i:6363805 original size:12 final size:12
Alignment explanation
Indices: 6363788--6363817 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
6363778 AGTTGGTATT
6363788 TCTGATGAATCA
1 TCTGATGAATCA
6363800 TCTGATGAATCA
1 TCTGATGAATCA
6363812 TCTGAT
1 TCTGAT
6363818 CCACTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (12 bp):
TCTGATGAATCA
Found at i:6364489 original size:54 final size:54
Alignment explanation
Indices: 6364382--6364490 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
6364372 TAATTACTGG
* * *
6364382 TTCGTAAAACATTTGACAACACATTCATCTTTTCCTATGGCTTCTGCTCAGATT
1 TTCGTAAAACATTTGACAACACATTCATCATTTCCTATAGCTTCTACTCAGATT
6364436 TTCGTAAAACATTTGACAACACATTCATCATTTCCTATAGCTTCTAC-CAAGATT
1 TTCGTAAAACATTTGACAACACATTCATCATTTCCTATAGCTTCTACTC-AGATT
6364490 T
1 T
6364491 CTCATCAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (54 bp):
TTCGTAAAACATTTGACAACACATTCATCATTTCCTATAGCTTCTACTCAGATT
Found at i:6370207 original size:21 final size:21
Alignment explanation
Indices: 6370181--6370241 Score: 104
Period size: 21 Copynumber: 2.8 Consensus size: 21
6370171 GGACCTATCA
6370181 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
6370202 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
6370223 TCCCGAAGGACCTGTCATC
1 TCCCGAAGGA--TGTCATC
6370242 CCGAAGGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 31 0.82
23 7 0.18
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:6370244 original size:38 final size:38
Alignment explanation
Indices: 6370202--6370278 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
6370192 GTCATCTGTG
* * *
6370202 TCCCGAAGGATGTCATCTGTGTCCCGAAGGACCTGTCA
1 TCCCGAAGGATGTAATCTGTATCCCGAAGGACCTATCA
* *
6370240 TCCCGAAGGATGTAATCTGTATCTCGTAGGACCTATCA
1 TCCCGAAGGATGTAATCTGTATCCCGAAGGACCTATCA
6370278 T
1 T
6370279 ATGTCTCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (38 bp):
TCCCGAAGGATGTAATCTGTATCCCGAAGGACCTATCA
Found at i:6373734 original size:20 final size:20
Alignment explanation
Indices: 6373706--6373773 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
6373696 GCAAAGATGC
*
6373706 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATGAAAATGT
** *
6373726 AAATACAAACGTAAAAATGT
1 AAATACAAAAATGAAAATGT
* *
6373746 AAAGATAC-AAAATGCAAATGC
1 -AA-ATACAAAAATGAAAATGT
6373767 AAATACA
1 AAATACA
6373774 TGTATGAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
21 10 0.28
22 4 0.11
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATGAAAATGT
Found at i:6373921 original size:43 final size:44
Alignment explanation
Indices: 6373852--6373935 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
6373842 TGCATCAAAT
* *
6373852 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTCAAC
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
* * *
6373896 AAAAC-TTTACATATATGGGATAACTTTCCCTCCTAACTTC
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
6373936 TCTAAAGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 30 0.86
44 5 0.14
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (44 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
Found at i:6375286 original size:2 final size:2
Alignment explanation
Indices: 6375279--6375315 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6375269 TATTAATCAA
*
6375279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6375316 AGCATGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6375467 original size:11 final size:11
Alignment explanation
Indices: 6375453--6375477 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6375443 ATATGACTAA
6375453 AATAAAATAAT
1 AATAAAATAAT
6375464 AATAAAATAAT
1 AATAAAATAAT
6375475 AAT
1 AAT
6375478 TAGAATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:6379877 original size:38 final size:40
Alignment explanation
Indices: 6379835--6379917 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
6379825 TTTCTCTAAT
* * *
6379835 ATTTTCGATT-A-AACCTAAACTATTAGGAAGAAGGTAAC
1 ATTTTCGATTGACAACCGAAAATATTAGGAAAAAGGTAAC
* * *
6379873 ATTTTCGGTTGACAACCGAAAATGTTAGGAAAAATGTAAC
1 ATTTTCGATTGACAACCGAAAATATTAGGAAAAAGGTAAC
6379913 ATTTT
1 ATTTT
6379918 AAGTTACCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 9 0.24
39 1 0.03
40 27 0.73
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
ATTTTCGATTGACAACCGAAAATATTAGGAAAAAGGTAAC
Found at i:6380776 original size:3 final size:3
Alignment explanation
Indices: 6380724--6380761 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
6380714 TATCCCGATT
* *
6380724 TTA TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6380762 CTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:6383102 original size:16 final size:17
Alignment explanation
Indices: 6383068--6383111 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
6383058 TTTCTTTCAA
6383068 ATTTTTTATTACTTATT
1 ATTTTTTATTACTTATT
*
6383085 ATTTTTATATTATTTTATT
1 ATTTTT-TATTA-CTTATT
6383104 AATTTTTT
1 -ATTTTTT
6383112 TTATTCAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 6 0.26
20 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTACTTATT
Found at i:6383115 original size:18 final size:18
Alignment explanation
Indices: 6383069--6383116 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 18
6383059 TTCTTTCAAA
6383069 TTTTTTATTACTTATTATT
1 TTTTTTATTA-TTATTATT
6383088 TTTATATTATT-TTATTAATT
1 TTT-T-TTATTATTATT-ATT
6383108 TTTTTTATT
1 TTTTTTATT
6383117 CAGGTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 7 0.27
21 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTATTATTATTATT
Found at i:6384546 original size:8 final size:7
Alignment explanation
Indices: 6384522--6384563 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
6384512 TTTTCATACA
6384522 TGCA-TT
1 TGCATTT
6384528 TGCATTT
1 TGCATTT
6384535 TGCATCTT
1 TGCAT-TT
6384543 TGCATTT
1 TGCATTT
* *
6384550 TTCATTG
1 TGCATTT
6384557 TGCATTT
1 TGCATTT
6384564 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:6384546 original size:15 final size:14
Alignment explanation
Indices: 6384522--6384563 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
6384512 TTTTCATACA
6384522 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
6384535 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
6384550 TTCATTGTGCATTT
1 TGCATTTTGCATTT
6384564 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:6384639 original size:12 final size:12
Alignment explanation
Indices: 6384622--6384674 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
6384612 ACATTCACAT
6384622 ATTTACATTTGC
1 ATTTACATTTGC
6384634 ATTTACATTTGC
1 ATTTACATTTGC
* *
6384646 ATTTTTTACGTTTGT
1 A---TTTACATTTGC
6384661 ATTTACATTTGC
1 ATTTACATTTGC
6384673 AT
1 AT
6384675 ATTTCCATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 24 0.71
15 10 0.29
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:6384659 original size:27 final size:27
Alignment explanation
Indices: 6384623--6384674 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6384613 CATTCACATA
6384623 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* *
6384650 TTTACGTTTGTATTTACATTTGCAT
1 TTTACATTTGCATTTACATTTGCAT
6384675 ATTTCCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:6387423 original size:7 final size:7
Alignment explanation
Indices: 6387411--6387555 Score: 71
Period size: 7 Copynumber: 18.3 Consensus size: 7
6387401 TCCAGCAAAG
6387411 AAAGAAA
1 AAAGAAA
6387418 AAAGAAA
1 AAAGAAA
6387425 AATTCAGCAAA
1 AA---AG-AAA
6387436 GAAAGAAA
1 -AAAGAAA
6387444 AAA-AAA
1 AAAGAAA
6387450 AGAA-AAA
1 A-AAGAAA
*
6387457 ATATGAAAA
1 A-AAG-AAA
6387466 AAGATGAAA
1 AA-A-GAAA
6387475 AAAGAAA
1 AAAGAAA
6387482 AATGAGAAA
1 AA--AGAAA
6387491 AAAGGAAAAA
1 AAA-G--AAA
6387501 AAATGAAA
1 AAA-GAAA
*
6387509 AAGGAAA
1 AAAGAAA
6387516 AATGAGAAA
1 AA--AGAAA
6387525 AAAGAAA
1 AAAGAAA
6387532 AAAGGGAAA
1 AAA--GAAA
6387541 AAAG-AA
1 AAAGAAA
6387547 AAAGAAA
1 AAAGAAA
6387554 AA
1 AA
6387556 GGGGAGAAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 40
0.71 0.04 0.25
Matches are distributed among these distances:
6 10 0.09
7 45 0.40
8 11 0.10
9 31 0.28
10 10 0.09
11 3 0.03
12 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (7 bp):
AAAGAAA
Found at i:6387441 original size:30 final size:28
Alignment explanation
Indices: 6387407--6387510 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 28
6387397 CTCATCCAGC
6387407 AAAGAAAGAAAAAAGAAAAATTCA-GCAAA
1 AAAGAAAGAAAAAAGAAAAATT-ATG-AAA
* *
6387436 GAAAGAAAAAAAAAAGAAAAAATATGAAA
1 -AAAGAAAGAAAAAAGAAAAATTATGAAA
* *
6387465 AAAG-ATGAAAAAAGAAAAATGA-GAAA
1 AAAGAAAGAAAAAAGAAAAATTATGAAA
*
6387491 AAAGGAAA-AAAAATGAAAAA
1 AAA-GAAAGAAAAAAGAAAAA
6387511 GGAAAAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
26 7 0.11
27 26 0.41
28 5 0.08
29 4 0.06
30 21 0.33
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (28 bp):
AAAGAAAGAAAAAAGAAAAATTATGAAA
Found at i:6387482 original size:16 final size:15
Alignment explanation
Indices: 6387441--6387555 Score: 92
Period size: 16 Copynumber: 7.2 Consensus size: 15
6387431 GCAAAGAAAG
6387441 AAAAA-AAAAAGA-A
1 AAAAAGAAAAAGAGA
6387454 AAAATATGAAAAAAGATGA
1 AAAA-A-G-AAAAAGA-GA
6387473 AAAAAGAAAAATGAGA
1 AAAAAGAAAAA-GAGA
*
6387489 AAAAAGGAAAAAAAATGA
1 AAAAA-G-AAAAAGA-GA
*
6387507 AAAAGGAAAAATGAGA
1 AAAAAGAAAAA-GAGA
*
6387523 AAAAAGAAAAAAGGGA
1 AAAAAG-AAAAAGAGA
6387539 AAAAAGAAAAAGA-A
1 AAAAAGAAAAAGAGA
6387553 AAA
1 AAA
6387556 GGGGAGAAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 23
0.74 0.05 0.20
Matches are distributed among these distances:
13 4 0.05
14 5 0.06
15 6 0.07
16 33 0.39
17 19 0.23
18 12 0.14
19 5 0.06
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAAGAAAAAGAGA
Found at i:6387499 original size:34 final size:33
Alignment explanation
Indices: 6387441--6387549 Score: 136
Period size: 34 Copynumber: 3.3 Consensus size: 33
6387431 GCAAAGAAAG
6387441 AAAAA-AAAAA-GA-AAAAATATGAAAAAAGATGA
1 AAAAAGAAAAATGAGAAAAA-A-GAAAAAAGATGA
*
6387473 AAAAAGAAAAATGAGAAAAAAGGAAAAAAAATGA
1 AAAAAGAAAAATGAGAAAAAA-GAAAAAAGATGA
* *
6387507 AAAAGGAAAAATGAGAAAAAAGAAAAAAG-GGA
1 AAAAAGAAAAATGAGAAAAAAGAAAAAAGATGA
6387539 AAAAAGAAAAA
1 AAAAAGAAAAA
6387550 GAAAAAGGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
32 17 0.25
33 12 0.18
34 34 0.50
35 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (33 bp):
AAAAAGAAAAATGAGAAAAAAGAAAAAAGATGA
Found at i:6387524 original size:9 final size:9
Alignment explanation
Indices: 6387437--6387549 Score: 80
Period size: 9 Copynumber: 13.1 Consensus size: 9
6387427 TTCAGCAAAG
*
6387437 AAAGAAAAA
1 AAAGAGAAA
*
6387446 AAAAAGAAA
1 AAAGAGAAA
*
6387455 AAATATGAAA
1 AAAGA-GAAA
6387465 AAAGATG-AA
1 AAAGA-GAAA
6387474 AAA-AGAAA
1 AAAGAGAAA
*
6387482 AATGAGAAA
1 AAAGAGAAA
6387491 AAAG-GAAA
1 AAAGAGAAA
*
6387499 AAAAATG-AA
1 AAAGA-GAAA
6387508 AAAG-GAAA
1 AAAGAGAAA
*
6387516 AATGAG-AA
1 AAAGAGAAA
6387524 AAA-AGAAA
1 AAAGAGAAA
*
6387532 AAAGGGAAA
1 AAAGAGAAA
6387541 AAAGA-AAA
1 AAAGAGAAA
6387549 A
1 A
6387550 GAAAAAGGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
7 4 0.05
8 30 0.36
9 38 0.46
10 11 0.13
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (9 bp):
AAAGAGAAA
Found at i:6387527 original size:10 final size:9
Alignment explanation
Indices: 6387443--6387510 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
6387433 AAAGAAAGAA
*
6387443 AAAAAAAAG
1 AAAAAAATG
6387452 AAAAAATATG
1 AAAAAA-ATG
6387462 AAAAAAGATG
1 AAAAAA-ATG
6387472 -AAAAAA-G
1 AAAAAAATG
6387479 --AAAAATG
1 AAAAAAATG
*
6387486 AGAAAAAAGG
1 A-AAAAAATG
6387496 AAAAAAAATG
1 -AAAAAAATG
6387506 AAAAA
1 AAAAA
6387511 GGAAAAATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
6 5 0.10
7 2 0.04
8 1 0.02
9 16 0.33
10 24 0.49
11 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (9 bp):
AAAAAAATG
Found at i:6389904 original size:114 final size:114
Alignment explanation
Indices: 6389704--6389923 Score: 386
Period size: 114 Copynumber: 1.9 Consensus size: 114
6389694 CACGTTCTCG
*
6389704 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
6389769 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACACCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
*
6389818 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
6389883 GGTAGGAACACCATAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACACCAAAACCAATCATTGGAATTGAAAGATGAA
6389924 CTGGATGATC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACACCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:6390925 original size:35 final size:35
Alignment explanation
Indices: 6390874--6390940 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
6390864 TTCAACCAAA
6390874 AATAGAATATTGGGGCATT-TTGAAGGCTCATAAC
1 AATAGAATATTGGGGCATTCTTGAAGGCTCATAAC
* *
6390908 AATATGAATATTTGGGCATTCTTGGAGGCTCAT
1 AATA-GAATATTGGGGCATTCTTGAAGGCTCAT
6390941 CTCAACAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 11 0.38
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
AATAGAATATTGGGGCATTCTTGAAGGCTCATAAC
Found at i:6392517 original size:22 final size:22
Alignment explanation
Indices: 6392487--6392565 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
6392477 ACATCTACAT
*
6392487 TCTTCAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
*
6392509 TCTTTAAAGATGATAGATTCCC
1 TCTTTAAAGATGATAGATTCTC
* *
6392531 TTTTTAAAGATGACAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
6392553 T-TTTCAAAGATGA
1 TCTTT-AAAGATGA
6392566 AAGCTTTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 3 0.06
22 48 0.94
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:6393169 original size:113 final size:113
Alignment explanation
Indices: 6392984--6394107 Score: 1391
Period size: 113 Copynumber: 9.8 Consensus size: 113
6392974 CATTCAATGA
* * *
6392984 ATCAACATTT-CTGGTCGAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
6393048 AATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTTGATGG
66 AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
* *
6393096 ATCAACATTGCTAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA-
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
6393160 ATATCAGAAGAACTTGTTCAACTTTTTTCTTGAATTCATCATTTGATGG
66 A-ATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
*
6393209 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
** *
6393274 AATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGG
66 AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
* * * * *
6393322 ATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCAT
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
6393387 AATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGG
66 AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
* * *
6393435 ATCAGCAGTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
6393499 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTTGATGG
65 TAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
* * * * *
6393548 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAATAAATTCAT
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * ** *
6393613 AATGAGAAGAATTTGTTCCAACTTTTTTCTCAAATTCATCACTTGATGG
66 AATGAGAAGAACTTGTT-CAACTTTTTGCTTGAATTCATCACTCGATGG
* * * *
6393662 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAATAAATTCAT
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
6393727 AATGAGAAGAATTTGTTCCAACCTTTTGTTTGAATTCATCACTCAATGG
66 AATGAGAAGAACTTGTT-CAACTTTTTGCTTGAATTCATCACTCGATGG
* * * * *
6393776 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAATAAATTCA
1 ATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * **
6393840 TAATGAGAAGAATTTGTTCCAACCTTTTATTTGAATTCATCACTCGATGG
65 TAATGAGAAGAACTTGTT-CAACTTTTTGCTTGAATTCATCACTCGATGG
* * *
6393890 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 ATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * * **
6393954 TAATGAGAAGAGCTTGTTCAACCTTTTGCATG-ACTCTATCACAAAAGGAGATAGATCAAC
65 TAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTC-ATCAC---------TCGAT--GG
* * *
6394014 ATCAACATTTCCAAAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG-ACGAAGAAGAAGTTCA
1 ATCAACATTTCC-AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
6394077 TAATGAGAAGAACTTGTTCAAACTTTTTGCT
65 TAATGAGAAGAACTTGTTC-AACTTTTTGCT
6394108 AGATTACATC
Statistics
Matches: 917, Mismatches: 74, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
112 14 0.02
113 490 0.53
114 322 0.35
115 1 0.00
122 4 0.00
123 33 0.04
124 52 0.06
125 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGG
Found at i:6394361 original size:3 final size:3
Alignment explanation
Indices: 6394308--6394345 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
6394298 TATCCTGATT
* *
6394308 TTA TTA -TA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6394346 CTAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:6395657 original size:15 final size:15
Alignment explanation
Indices: 6395637--6395707 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
6395627 ATCCAATAGT
6395637 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
6395652 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
6395666 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
6395682 TTTTATTTTATTATTAC
1 TTTTA--ATATTATTAC
*
6395699 TTTTGATAT
1 TTTTAATAT
6395708 ATGTTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:6395747 original size:11 final size:11
Alignment explanation
Indices: 6395672--6395747 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
6395662 TTTCATTTTA
6395672 ATTATTATTATT
1 ATTATT-TTATT
6395684 -TTATTTTATT
1 ATTATTTTATT
6395694 ATTACTTTTGA-T
1 ATTA-TTTT-ATT
6395706 A-TATGTTTAAATT
1 ATTAT-TTT--ATT
* *
6395719 ATTATCTTCATG
1 ATTAT-TTTATT
6395731 ATTATTTTATT
1 ATTATTTTATT
6395742 ATTATT
1 ATTATT
6395748 ATTAAGTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.12
11 23 0.45
12 14 0.27
13 3 0.06
14 5 0.10
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:6397527 original size:2 final size:2
Alignment explanation
Indices: 6397520--6397608 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
6397510 TTTTACAAAA
6397520 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
6397562 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
6397604 -T AT AT
1 AT AT AT
6397609 CAAAATTATT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 85 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6397965 original size:13 final size:13
Alignment explanation
Indices: 6397944--6397978 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6397934 TTATTAGCCA
6397944 AAATATCCACAAT
1 AAATATCCACAAT
* *
6397957 AAGTATCCACCAT
1 AAATATCCACAAT
6397970 AAATATCCA
1 AAATATCCA
6397979 TAGTAATGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATATCCACAAT
Found at i:6401714 original size:68 final size:68
Alignment explanation
Indices: 6401634--6401771 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
6401624 TCCATCAATT
6401634 CAACGTTATATGTTATGAAATCTTTTACACAACTCTATTGTAATTTGTTTTACTCTCTCTGGGTT
1 CAACGTTATATGTTATGAAATCTTTTACACAACTCTATTGTAATTTGTTTTACTCTCTCTGGGTT
6401699 CGA
66 CGA
6401702 CAACGTTATATGTTATGAAATCTTTTACACAACTCTATTGTAATTTGTTTTACTCTCTCTGGGTT
1 CAACGTTATATGTTATGAAATCTTTTACACAACTCTATTGTAATTTGTTTTACTCTCTCTGGGTT
6401767 CGA
66 CGA
6401770 CA
1 CA
6401772 TCCGAAGCTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (68 bp):
CAACGTTATATGTTATGAAATCTTTTACACAACTCTATTGTAATTTGTTTTACTCTCTCTGGGTT
CGA
Found at i:6408627 original size:72 final size:74
Alignment explanation
Indices: 6408509--6408659 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 74
6408499 AAACTCATGT
*
6408509 TTTAGGATATTATTTTAAATATTATATTTGTTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATT
1 TTTAGGATAATATTTT-AATATTATATTTGTTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATT
6408574 TTAATTAGGA
65 TTAATTAGGA
* * *
6408584 TTTAGGATAATATTTT-ATCTTATCTTT-TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTT
1 TTTAGGATAATATTTTAATATTATATTTGTTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTT
6408647 TAATTAGGA
66 TAATTAGGA
6408656 TTTA
1 TTTA
6408660 TTTCTTTATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 48 0.67
73 9 0.12
75 15 0.21
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (74 bp):
TTTAGGATAATATTTTAATATTATATTTGTTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTT
TAATTAGGA
Found at i:6415133 original size:5 final size:6
Alignment explanation
Indices: 6415117--6415165 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
6415107 CGTTTGTTTA
* * *
6415117 ATTTTT ATTTTT ATTTTT ATTTTT CTGATTT ATTTTT GTTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT
6415166 CTTTGATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
6 32 0.89
7 4 0.11
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:6415177 original size:25 final size:25
Alignment explanation
Indices: 6415120--6415167 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
6415110 TTGTTTAATT
6415120 TTTATTTTTATTTTTATTTTTCTGA
1 TTTATTTTTATTTTTATTTTTCTGA
*
6415145 TTTATTTTTGTTTTTATTTTTCT
1 TTTATTTTTATTTTTATTTTTCT
6415168 TTGATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.79
Consensus pattern (25 bp):
TTTATTTTTATTTTTATTTTTCTGA
Found at i:6415328 original size:21 final size:23
Alignment explanation
Indices: 6415286--6415333 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
6415276 TCGTGTGGCA
**
6415286 GAAAACAAAGGAAGAATCATTT-
1 GAAAACAAAGGAAGAAGAATTTC
*
6415308 GAAAA-AAAGGAAGCAGAATTTC
1 GAAAACAAAGGAAGAAGAATTTC
6415330 GAAA
1 GAAA
6415334 TACATTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (23 bp):
GAAAACAAAGGAAGAAGAATTTC
Found at i:6421740 original size:95 final size:94
Alignment explanation
Indices: 6421538--6421758 Score: 291
Period size: 95 Copynumber: 2.3 Consensus size: 94
6421528 CCAATGAGGT
* * * *
6421538 AGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCGAATCTAAATTTGGTATCGATAC
1 AGTATCGATACCATGGT-AGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATAC
* * *
6421603 CAAAAGGGGGTATTGGTACCATAGTATTGT
65 CAAAAGGGGGTATCGGTACCATAGTATAGA
*
6421633 AGTATCAATACCATGGTAAGGGTATCGATACC-AGAAAACATCAAACCTAAATTTGATATCGATA
1 AGTATCGATACCATGGT-AGGGTATCGATACCAAG-AAACATCAAACCTAAATTTGATATCGATA
*
6421697 CCAAAAGGGGTTATCGGTACCATAGTATAGA
64 CCAAAAGGGGGTATCGGTACCATAGTATAGA
* * *
6421728 AGTATCGGTACCAGGGTAGCAGTATCGATAC
1 AGTATCGATACCATGGTAG-GGTATCGATAC
6421759 TATGGAGCCA
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
94 4 0.04
95 106 0.96
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (94 bp):
AGTATCGATACCATGGTAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATACC
AAAAGGGGGTATCGGTACCATAGTATAGA
Found at i:6422919 original size:15 final size:16
Alignment explanation
Indices: 6422899--6422939 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6422889 GTTTACTTCA
*
6422899 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
6422914 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
6422930 GAATGATTCA
1 GAATGATTCA
6422940 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:6423580 original size:21 final size:21
Alignment explanation
Indices: 6423486--6423581 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 21
6423476 TGTCCTGAAT
*
6423486 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
* * * **
6423507 AAGGACCAAATATGTGTTCTG
1 AAGGACCACATATATATTCCA
* * *
6423528 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATTCCA
** * *
6423549 AAGGATTACATATATATCCCG
1 AAGGACCACATATATATTCCA
6423570 AAGGACCACATA
1 AAGGACCACATA
6423582 GAACCCTCAA
Statistics
Matches: 54, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:6425327 original size:79 final size:78
Alignment explanation
Indices: 6425197--6425424 Score: 300
Period size: 79 Copynumber: 2.9 Consensus size: 78
6425187 TTACAAATAA
** * *
6425197 ATATGGGTGCATTATTCTCAT-AAAGGATGCCTTAGCTGAAATGCATATGGGTGCATTATCGACA
1 ATATGGGTGCATTATTGGCATAAAATGATGCCTTAGCTTAAATGCATATGGGTGCATTATC-ACA
*
6425261 TGAAAGAATAATGC
65 TAAAAGAATAATGC
* *
6425275 ATATGGGTGTATTATTGGCATAAAATGATGCCTTAGCTTAAATGAATATGGGTGCATTATCAGCA
1 ATATGGGTGCATTATTGGCATAAAATGATGCCTTAGCTTAAATGCATATGGGTGCATTATCA-CA
6425340 TAAAAGAATAATGC
65 TAAAAGAATAATGC
** *
6425354 ATATGGGTGCATTATTGGCA-AGAAATGATGCCAAAG-TTGAAATGCATATGGCTGCATTATCAA
1 ATATGGGTGCATTATTGGCATA-AAATGATGCCTTAGCTT-AAATGCATATGGGTGCATTATC-A
6425417 CATAAAAG
63 CATAAAAG
6425425 TATGCTATAA
Statistics
Matches: 133, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
78 22 0.17
79 110 0.83
80 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (78 bp):
ATATGGGTGCATTATTGGCATAAAATGATGCCTTAGCTTAAATGCATATGGGTGCATTATCACAT
AAAAGAATAATGC
Found at i:6425754 original size:29 final size:29
Alignment explanation
Indices: 6425658--6425747 Score: 153
Period size: 29 Copynumber: 3.1 Consensus size: 29
6425648 TATGCCAGTT
*
6425658 AGATGAACGGTTAAACACTGTTGAGTAAA
1 AGATGAATGGTTAAACACTGTTGAGTAAA
*
6425687 AGATGAATGGTTAAACATTGTTGAGTAAA
1 AGATGAATGGTTAAACACTGTTGAGTAAA
*
6425716 AGATGAATGGTTAAACACGGTTGAGTAAA
1 AGATGAATGGTTAAACACTGTTGAGTAAA
6425745 AGA
1 AGA
6425748 ATAATGGACT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (29 bp):
AGATGAATGGTTAAACACTGTTGAGTAAA
Found at i:6425893 original size:2 final size:2
Alignment explanation
Indices: 6425886--6425914 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6425876 AGAAGTGATG
6425886 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 A
6425915 ATGTACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6430545 original size:6 final size:6
Alignment explanation
Indices: 6430534--6430596 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
6430524 TAGTATTAAA
6430534 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
6430582 GGAAAG GGAAAG GGA
1 GGAAAG GGAAAG GGA
6430597 TAAAATCCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:6432127 original size:34 final size:34
Alignment explanation
Indices: 6432084--6432219 Score: 157
Period size: 34 Copynumber: 3.9 Consensus size: 34
6432074 TTAGTTTAAG
6432084 TGCATATGGGTGCATTATCGGCATAAAAGAATAA
1 TGCATATGGGTGCATTATCGGCATAAAAGAATAA
* *
6432118 TGCATATGGGTGCATTATTGGCATGAAAGAATGCTGAAA
1 TGCATATGGGTGCATTATCGGCATAAAAGAA---T--AA
* *
6432157 TAC-TAATGGATGCATTATCGGCATAAAAGAATAA
1 TGCAT-ATGGGTGCATTATCGGCATAAAAGAATAA
* *
6432191 TGCATATGGGTGCATTATTGGCATGAAAG
1 TGCATATGGGTGCATTATCGGCATAAAAG
6432220 GATGCCAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
34 54 0.64
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 27 0.32
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (34 bp):
TGCATATGGGTGCATTATCGGCATAAAAGAATAA
Found at i:6432204 original size:73 final size:76
Alignment explanation
Indices: 6432028--6432224 Score: 276
Period size: 73 Copynumber: 2.6 Consensus size: 76
6432018 AACAAATGAT
** * *
6432028 TAAAAGAATAATGCATATGGGTGCATTATTGAAATGAAAGGATGTCTTAGTTTAAGTGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG-CTTAG--TAAATACATATGG
*
6432093 GTGCATTATCGGCA
63 ATGCATTATCGGCA
*
6432107 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGC-T-G-AAATAC-TAATGGAT
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTTAGTAAATACAT-ATGGAT
6432168 GCATTATCGGCA
65 GCATTATCGGCA
6432180 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
6432225 CAAAAATGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
72 1 0.01
73 65 0.59
76 1 0.01
77 1 0.01
78 1 0.01
79 41 0.37
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (76 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTTAGTAAATACATATGGATG
CATTATCGGCA
Found at i:6432534 original size:29 final size:29
Alignment explanation
Indices: 6432501--6432561 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
6432491 TGAGCCAGTT
* *
6432501 AGATGAATGGTTAAACACTGTTGAGTAAA
1 AGATGAACGGTTAAACACGGTTGAGTAAA
6432530 AGATGAACGGTTAAACACGGTTGAGTAAA
1 AGATGAACGGTTAAACACGGTTGAGTAAA
6432559 AGA
1 AGA
6432562 ATAATGGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.23
Consensus pattern (29 bp):
AGATGAACGGTTAAACACGGTTGAGTAAA
Found at i:6432707 original size:2 final size:2
Alignment explanation
Indices: 6432700--6432728 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6432690 AGAAGGGATG
6432700 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 A
6432729 ATGTACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6440019 original size:25 final size:24
Alignment explanation
Indices: 6439991--6440061 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
6439981 ACTCAAAAAA
* *
6439991 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
6440016 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
6440040 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATTGAAGC
6440062 GAAAGAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 36 0.84
25 7 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:6440035 original size:24 final size:24
Alignment explanation
Indices: 6440006--6440061 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
6439996 TAGAAGTTCG
6440006 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6440030 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6440054 ATTGAAGC
1 ATTGAAGC
6440062 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:6440797 original size:15 final size:16
Alignment explanation
Indices: 6440762--6440799 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6440752 GAGCCTCTAT
*
6440762 ATCATTCAGCATTTGA
1 ATCATTCAGCACTTGA
*
6440778 ATCATTCAGCGCTT-A
1 ATCATTCAGCACTTGA
6440793 ATCATTC
1 ATCATTC
6440800 TGAAGTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (16 bp):
ATCATTCAGCACTTGA
Found at i:6443264 original size:24 final size:24
Alignment explanation
Indices: 6443236--6443287 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6443226 AATTAAAACA
*
6443236 CAAGCAATATA-ATGTTTATTAACT
1 CAAGCAATA-ACATGCTTATTAACT
* *
6443260 CAAGCGATAACCTGCTTATTAACT
1 CAAGCAATAACATGCTTATTAACT
6443284 CAAG
1 CAAG
6443288 GACTCTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (24 bp):
CAAGCAATAACATGCTTATTAACT
Found at i:6443978 original size:9 final size:8
Alignment explanation
Indices: 6443957--6443981 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6443947 AAGTCCAATT
6443957 GTTTTTTG
1 GTTTTTTG
6443965 GTTTTTTG
1 GTTTTTTG
6443973 GTTTTTTG
1 GTTTTTTG
6443981 G
1 G
6443982 AAATCCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (8 bp):
GTTTTTTG
Found at i:6455347 original size:17 final size:17
Alignment explanation
Indices: 6455325--6455367 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
6455315 CCTGGAAAAT
6455325 AATAAAAATTAAATGAA
1 AATAAAAATTAAATGAA
* *
6455342 AATAAAAA-AAAATTAA
1 AATAAAAATTAAATGAA
*
6455358 AATTAAAATT
1 AATAAAAATT
6455368 GAAAATGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAAAAATTAAATGAA
Found at i:6455350 original size:27 final size:29
Alignment explanation
Indices: 6455320--6455373 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
6455310 CGGTCCCTGG
*
6455320 AAAATAATAAAAATT-AAA-TGAAAATAA
1 AAAAAAATAAAAATTAAAATTGAAAATAA
*
6455347 AAAAAAATTAAAATTAAAATTGAAAAT
1 AAAAAAATAAAAATTAAAATTGAAAAT
6455374 GTAACGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 3 0.13
29 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (29 bp):
AAAAAAATAAAAATTAAAATTGAAAATAA
Found at i:6455372 original size:22 final size:21
Alignment explanation
Indices: 6455319--6455358 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6455309 TCGGTCCCTG
*
6455319 GAAAAT-AATAAAAATTAAAT
1 GAAAATAAAAAAAAATTAAAT
6455339 GAAAATAAAAAAAAATTAAA
1 GAAAATAAAAAAAAATTAAA
6455359 ATTAAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
GAAAATAAAAAAAAATTAAAT
Found at i:6462671 original size:36 final size:36
Alignment explanation
Indices: 6462620--6462714 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
6462610 AAACAAAGCA
*
6462620 TCGTCTCGCTAGAGACAATTTTTCTAAAAACAAATGT
1 TCGTCTCGCTTGAGACAATTTTTCTAAAAACAAAT-T
* * * *
6462657 T-GTCTCGATTGAGACAATTTCTCTCAGAACAAATT
1 TCGTCTCGCTTGAGACAATTTTTCTAAAAACAAATT
*
6462692 TCGTCTCGCTTGATAC-ATTTTTC
1 TCGTCTCGCTTGAGACAATTTTTC
6462715 CCTTTAAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 8 0.16
36 40 0.82
37 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
TCGTCTCGCTTGAGACAATTTTTCTAAAAACAAATT
Found at i:6462852 original size:66 final size:65
Alignment explanation
Indices: 6462730--6462884 Score: 163
Period size: 66 Copynumber: 2.4 Consensus size: 65
6462720 AAGTACATAA
* * * **
6462730 CTTTGAG-TCGTTTCCCTTGAAACAAGTTTTATCTCTCTTGATATAGTTTCCCTTGAAACACCTA
1 CTTTGAGATCGTTTCCCTTGAAACAAGTTTTATATCTCTTGAGACAACTTCCCTTGAAACACC-A
6462794 T
65 T
* * ** * *
6462795 CTTTGAGATCGTTTCCCTTGAAATGAA-TTTTGTATCTCTTGAGACAACTTCTTTTGAAGCATCA
1 CTTTGAGATCGTTTCCCTTGAAA-CAAGTTTTATATCTCTTGAGACAACTTCCCTTGAAACACCA
6462859 T
65 T
6462860 CTTTGAGTAT-GTTTCCCTTGAAACA
1 CTTTGAG-ATCGTTTCCCTTGAAACA
6462885 TTATCCCTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
64 1 0.01
65 29 0.39
66 43 0.57
67 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (65 bp):
CTTTGAGATCGTTTCCCTTGAAACAAGTTTTATATCTCTTGAGACAACTTCCCTTGAAACACCAT
Found at i:6463128 original size:131 final size:131
Alignment explanation
Indices: 6462890--6463150 Score: 344
Period size: 131 Copynumber: 2.0 Consensus size: 131
6462880 AAACATTATC
* * * * *
6462890 CCTAAAGATGGCCTGTTGTCCTCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTCCTCAT
1 CCTAAAGATGGCCTATCGTACTCATCACATAGGAACCGTGCCATCCCCAGACCAGACCTCCTCAT
* * * * * *
6462955 CACATAGGAGCCGTGTCAACCTTAGATAACCAACCGTCCTCATCCCGTAGGAATC-GTGTTATCA
66 CACATAGAAGCCGTGTCAACCCTAAATAACCAACCATCCTCATCACGTA-GAACCTGTGTTATCA
6463019 TA
130 TA
* *
6463021 CCTAAAGATGGCTTATCGTACTCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCAT
1 CCTAAAGATGGCCTATCGTACTCATCACATAGGAACCGTGCCATCCCCAGACCAGACCTCCTCAT
* * * * *
6463086 CACATAGAAGTCGTGTTACCCCTAAATAACCAGCCATTCTCATCACGTAGAACCTGTGTTATCAT
66 CACATAGAAGCCGTGTCAACCCTAAATAACCAACCATCCTCATCACGTAGAACCTGTGTTATCAT
6463151 CCTCTCTAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
130 4 0.04
131 107 0.96
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (131 bp):
CCTAAAGATGGCCTATCGTACTCATCACATAGGAACCGTGCCATCCCCAGACCAGACCTCCTCAT
CACATAGAAGCCGTGTCAACCCTAAATAACCAACCATCCTCATCACGTAGAACCTGTGTTATCAT
A
Found at i:6463252 original size:134 final size:131
Alignment explanation
Indices: 6462910--6463245 Score: 332
Period size: 131 Copynumber: 2.5 Consensus size: 131
6462900 GCCTGTTGTC
* * ** * * * *
6462910 CTCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTCCTCATCACATAGGAGCCGTGTCAAC
1 CTCATCACATAGGAACAGTATCATCCACAGACCAGACCTCCTCATCACATAGGAGTCGTGTCACC
* * * * * *
6462975 CTTAGATAACCAACCGTCCTCATCCCGTAGGAATCGTGTTATCATACCTAAAGATGGCTTATCGT
66 CTTAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCATACCTAAAGATGGCATACCGT
6463040 A
131 A
* * * * *
6463041 CTCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACATAGAAGTCGTGTTACC
1 CTCATCACATAGGAACAGTATCATCCACAGACCAGACCTCCTCATCACATAGGAGTCGTGTCACC
* * * * *
6463106 CCTAAATAACCAGCCATTCTCATCACGTA-GAACCTGTGTTATCATCCTCTCTAAAGATGGCATG
66 CTTAGATAACCAGCCATCCTCATCACGTAGGAACC-GTGTTATCAT--AC-CTAAAGATGGCATA
* *
6463170 CCTTC
127 CCGTA
** * * ** *
6463175 CTCATTGCGTAGGAACATTATCATCCACTTACCAGATCTCCTCATCACATAGGAGTCGTGTCACC
1 CTCATCACATAGGAACAGTATCATCCACAGACCAGACCTCCTCATCACATAGGAGTCGTGTCACC
6463240 CTTAGA
66 CTTAGA
6463246 CTACCAGAAC
Statistics
Matches: 167, Mismatches: 34, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
130 4 0.02
131 91 0.54
133 1 0.01
134 71 0.43
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (131 bp):
CTCATCACATAGGAACAGTATCATCCACAGACCAGACCTCCTCATCACATAGGAGTCGTGTCACC
CTTAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCATACCTAAAGATGGCATACCGT
A
Found at i:6468048 original size:82 final size:82
Alignment explanation
Indices: 6467944--6468303 Score: 474
Period size: 82 Copynumber: 4.4 Consensus size: 82
6467934 GATACATCAA
* * * * * * *
6467944 TGAAATGTTGCAGAAGATGATAATGTACAACTATTTCACCCATTTTCTGAAAAGTTGTTTTAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTGTCTGAAAAGTTATTTAAATT
6468009 ATGCATTGAATGACCTC
66 ATGCATTGAATGACCTC
* *
6468026 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTGACTAAAAAGTTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTGTCTGAAAAGTTATTTAAATT
*
6468091 ATGCATTGAATGACCTT
66 ATGCATTGAATGACCTC
* * * *
6468108 TGAAAAGTTGTAGAATG-TGATAATGCCCCACTATTTCACCTGTTGTCT-AAAATGTTGTTTAAA
1 TGAAAAGTTGCAGAA-GATGATAATGCACCACTATTTCACCCGTTGTCTGAAAA-GTTATTTAAA
6468171 TTATGCATTGAATGACCTC
64 TTATGCATTGAATGACCTC
* * ** *
6468190 TGAAAAGTTACAGAAGATGATAAT-AACCACTATTTCACATGTTTTCTGAAAAGTTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTGTCTGAAAAGTTATTTAAATT
*
6468254 ATGCATTGAATGGCCTC
66 ATGCATTGAATGACCTC
* **
6468271 TAAAAAGTTATAGAAGATGATAATGCACCACTA
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTA
6468304 GAGAGTTATT
Statistics
Matches: 246, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
81 73 0.30
82 172 0.70
83 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (82 bp):
TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTGTCTGAAAAGTTATTTAAATT
ATGCATTGAATGACCTC
Found at i:6481775 original size:55 final size:54
Alignment explanation
Indices: 6481714--6481945 Score: 288
Period size: 55 Copynumber: 4.2 Consensus size: 54
6481704 CAATCTTCAA
*
6481714 TATAGAACTCGAACAATCTTCATA-AAATGGGTCCGCTCTCTATTCCTTCAGAGAG
1 TATAGAACTCGAACAATCTTCA-ACAAA-CGGTCCGCTCTCTATTCCTTCAGAGAG
* * ** * * *
6481769 TATAGAAATCGAACAATCTTCAACAAACATGTATGTTCTCTATTCCTTCAAAAAG
1 TATAGAACTCGAACAATCTTCAACAAAC-GGTCCGCTCTCTATTCCTTCAGAGAG
* *
6481824 TATAGAACTCGAACAATCTTCAATAAACGAGTTCGCTCTCTATTCCTTCAGAGAG
1 TATAGAACTCGAACAATCTTCAACAAACG-GTCCGCTCTCTATTCCTTCAGAGAG
* *
6481879 TATAGAACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAG
1 TATAGAACTCGAACAATCTTCAACAAACG-GTCCGCTCTCTATTCCTTCAGAGAG
6481934 TATA-AGACTCGA
1 TATAGA-ACTCGA
6481946 TCTTCATTAA
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
54 2 0.01
55 150 0.99
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (54 bp):
TATAGAACTCGAACAATCTTCAACAAACGGTCCGCTCTCTATTCCTTCAGAGAG
Found at i:6481861 original size:110 final size:110
Alignment explanation
Indices: 6481714--6481945 Score: 342
Period size: 110 Copynumber: 2.1 Consensus size: 110
6481704 CAATCTTCAA
* *
6481714 TATAGAACTCGAACAATCTTCATAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATC
1 TATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATC
* *
6481779 GAACAATCTTCAACAAACATGTATGTTCTCTATTCCTTCAAAAAG
66 GAACAATCTTCAACAAACATGTATGCTCCCTATTCCTTCAAAAAG
* *
6481824 TATAGAACTCGAACAATCTTCA-ATAAACGAGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 TATAGAACTCGAACAATCTTCATA-AAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAAT
* * * *
6481888 CGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAG
65 CGAACAATCTTCAACAAACATGTATGCTCCCTATTCCTTCAAAAAG
6481934 TATA-AGACTCGA
1 TATAGA-ACTCGA
6481946 TCTTCATTAA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
109 2 0.02
110 108 0.98
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (110 bp):
TATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATC
GAACAATCTTCAACAAACATGTATGCTCCCTATTCCTTCAAAAAG
Found at i:6483287 original size:6 final size:6
Alignment explanation
Indices: 6483276--6483350 Score: 57
Period size: 6 Copynumber: 12.2 Consensus size: 6
6483266 CCCCCTTTTA
** *
6483276 TTTCTT TTTCTT TTTCTT TTT-TT CATCATT TTT-TCT TTTCTC TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCT-T TTTCTT TTTCTT
6483324 TTCTCTT TCTT-TT TTTCCTT TTTCTT T
1 TT-TCTT T-TTCTT TTT-CTT TTTCTT T
6483351 GTTTTTCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
5 6 0.11
6 33 0.60
7 15 0.27
8 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:6483321 original size:11 final size:11
Alignment explanation
Indices: 6483307--6483336 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6483297 TTCATCATTT
6483307 TTTCTTTTCTC
1 TTTCTTTTCTC
6483318 TTTCTTTTCTC
1 TTTCTTTTCTC
6483329 TTTCTTTT
1 TTTCTTTT
6483337 TTTCCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTCTC
Done.