Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 101 of 444
Found at i:24801329 original size:81 final size:81
Alignment explanation
Indices: 24801055--24801346 Score: 280
Period size: 81 Copynumber: 3.6 Consensus size: 81
24801045 GGGTATTTCT
** * * * * * *
24801055 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACGGTAATTTTATA
1 GTAATTTTACAAATCGAAGGTAAAACAGTAATTATATAAATCGAGGGTAAAACAGTAATTCTGTA
*
24801120 AATCGAGGGTAAAACA
66 AATCGAGGGTAAAACG
* ** * * *
24801136 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTA
1 GTAATTTTACAAATCGAAGGTAAAACAGTAATTATATAAATCGAGGGTAAAACAGTAATTCTGTA
24801201 AATCGAGGGTAAAACG
66 AATCGAGGGTAAAACG
** * * * *
24801217 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCGGGGGTAAAAC-GATAATTCTGT
1 GTAATTTTACAAATCGAAGGTAAAACAGTAATTATATAAATCGAGGGTAAAACAG-TAATTCTGT
* ****
24801281 AAATCGGGGGTACTTTG
65 AAATCGAGGGTAAAACG
* *** * *
24801298 GTAATTTTACAAGTCGAAGGTATTTCAGTAATTTTACAAATCGAGGGTA
1 GTAATTTTACAAATCGAAGGTAAAACAGTAATTATATAAATCGAGGGTA
24801347 TTTCAGTATT
Statistics
Matches: 181, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
80 1 0.01
81 180 0.99
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (81 bp):
GTAATTTTACAAATCGAAGGTAAAACAGTAATTATATAAATCGAGGGTAAAACAGTAATTCTGTA
AATCGAGGGTAAAACG
Found at i:24801339 original size:54 final size:54
Alignment explanation
Indices: 24801281--24801387 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
24801271 ATAATTCTGT
* * *
24801281 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCAGTAATTTTAC
* * *
24801335 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTTTA
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTA
24801388 GTAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.13
54 39 0.87
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTAC
Found at i:24801401 original size:27 final size:27
Alignment explanation
Indices: 24801298--24801402 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
24801288 GGGTACTTTG
* *
24801298 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
24801325 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
24801352 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
24801379 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
24801403 CTAAACATGG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.03
27 55 0.85
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:24809406 original size:31 final size:31
Alignment explanation
Indices: 24809368--24809430 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
24809358 TGATGATTTT
24809368 AGCATATTGAAATGGCATGTTTTGGTTATGG
1 AGCATATTGAAATGGCATGTTTTGGTTATGG
*
24809399 AGCATATTGAAATTGCATGTTTTGGTTATGG
1 AGCATATTGAAATGGCATGTTTTGGTTATGG
24809430 A
1 A
24809431 ATTGAGTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (31 bp):
AGCATATTGAAATGGCATGTTTTGGTTATGG
Found at i:24811191 original size:30 final size:32
Alignment explanation
Indices: 24811130--24811194 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
24811120 TTCAATCTCA
24811130 ACATATACTGGGCCGAAGCCTCTTCATAATTC
1 ACATATACTGGGCCGAAGCCTCTTCATAATTC
*
24811162 ACAT-TACTGGGCCGAAGCCT-TTTATAATTC
1 ACATATACTGGGCCGAAGCCTCTTCATAATTC
24811192 ACA
1 ACA
24811195 ACTCATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 12 0.38
31 16 0.50
32 4 0.12
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (32 bp):
ACATATACTGGGCCGAAGCCTCTTCATAATTC
Found at i:24811473 original size:26 final size:26
Alignment explanation
Indices: 24811440--24811510 Score: 117
Period size: 25 Copynumber: 2.8 Consensus size: 26
24811430 CTCTTTTAAT
* *
24811440 AACTGGGGCAAAGCCCTTTTTTGTTA
1 AACTGGGGCAAAGCCCTTTTTCGGTA
24811466 AACTGGGGCAAAGCCC-TTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTTCGGTA
24811491 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
24811511 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTTCGGTA
Found at i:24811583 original size:20 final size:21
Alignment explanation
Indices: 24811558--24811605 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
24811548 AAATGAATAC
*
24811558 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
24811578 ATCATGTGCATATCATATCAA
1 ATCATGTGCATATCATATCAA
24811599 ATCATGT
1 ATCATGT
24811606 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:24817067 original size:43 final size:43
Alignment explanation
Indices: 24817011--24817181 Score: 149
Period size: 43 Copynumber: 4.0 Consensus size: 43
24817001 ATATCGTACA
* *
24817011 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCATATCTCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
* *
24817054 ATGCCACTATCCCAGACAG-GGTCTTACACG-AATCAAATAT-G
1 ATGCCACTGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
* * * * * *
24817095 ATGTCGA-TGTCCCAGACATGGTTTTACATGTAATTACATATCA
1 ATG-CCACTGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
*
24817138 ATGCCAAC-GTCCCAGACGTGGTCTTACATG-AATACACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACATGTAAT-CAAATATCG
24817181 A
1 A
24817182 AAATCCTATG
Statistics
Matches: 102, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
41 22 0.22
42 24 0.24
43 55 0.54
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
Found at i:24825772 original size:15 final size:15
Alignment explanation
Indices: 24825752--24825780 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24825742 CAAAAATTCC
24825752 AATCCAAAACATATT
1 AATCCAAAACATATT
24825767 AATCCAAAACATAT
1 AATCCAAAACATAT
24825781 CTAACATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
AATCCAAAACATATT
Found at i:24830509 original size:40 final size:39
Alignment explanation
Indices: 24830454--24830555 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 39
24830444 TATTCGGATG
*
24830454 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 ATAACC-GGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
24830494 ATAACCAGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT
1 ATAACC-GGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT
* * *
24830534 ATATCCGGCTAAATCCCAAAGG
1 ATAACCGGCTAAGTCCCGAAGG
24830556 TACTTGGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 16 0.29
40 40 0.71
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (39 bp):
ATAACCGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT
Found at i:24836993 original size:42 final size:44
Alignment explanation
Indices: 24836883--24837007 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 44
24836873 AGACATCATG
* * * * **
24836883 TAAGACCGTGTCTAAGACACAGGCCTCGAT-TGAGATTTACGTA
1 TAAGACCATGTCTGAGACAGAGGCATCGATATCTGATTTACGTA
* ** *
24836926 TAAGACCATGTCTGGGACATTGGCATC-ATATCTGATTT-CGTG
1 TAAGACCATGTCTGAGACAGAGGCATCGATATCTGATTTACGTA
* *
24836968 TAAGATCATGTCTGAGACAGAGGCATCGATAT-TGAATTAC
1 TAAGACCATGTCTGAGACAGAGGCATCGATATCTGATTTAC
24837008 ATGTAATACC
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
42 33 0.51
43 32 0.49
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
TAAGACCATGTCTGAGACAGAGGCATCGATATCTGATTTACGTA
Found at i:24840512 original size:40 final size:40
Alignment explanation
Indices: 24840448--24840523 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
24840438 CTATGTTTGG
*
24840448 CACTTAGTGTGTGATTCGAGATAGCTTCAGCTATATAAAA
1 CACTTAGTGTGCGATTCGAGATAGCTTCAGCTATATAAAA
* **
24840488 CACTTAGTGTGCGAATTGGA-ATAGCTTTGGCTATAT
1 CACTTAGTGTGCG-ATTCGAGATAGCTTCAGCTATAT
24840524 GTGGCACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 26 0.84
41 5 0.16
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (40 bp):
CACTTAGTGTGCGATTCGAGATAGCTTCAGCTATATAAAA
Found at i:24843114 original size:50 final size:50
Alignment explanation
Indices: 24842990--24843185 Score: 243
Period size: 49 Copynumber: 4.0 Consensus size: 50
24842980 GTAGACAAGG
** * *
24842990 TTATCTGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AA
1 TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
* * *
24843039 TTATCTGGTACATGTAGTAGCCTGCACCTAGTACTACACACGTGACCTAA
1 TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
** * ** *
24843089 CCATCTGATACACGTAAAAGCCTGCACTTAGTACTACACATGCGA-CTAA
1 TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
* *
24843138 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCT
24843186 CACAATAGAT
Statistics
Matches: 121, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 81 0.67
50 40 0.33
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
Found at i:24843461 original size:27 final size:27
Alignment explanation
Indices: 24843431--24843484 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24843421 TCATACAACC
* *
24843431 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
24843458 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
24843485 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:24849940 original size:18 final size:18
Alignment explanation
Indices: 24849914--24849954 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
24849904 TACCATCTTA
*
24849914 TATTTCATACTATATTTT
1 TATTACATACTATATTTT
24849932 TATTACATACTATATTTT
1 TATTACATACTATATTTT
24849950 TATTA
1 TATTA
24849955 TTCAATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTACATACTATATTTT
Found at i:24850084 original size:21 final size:22
Alignment explanation
Indices: 24850058--24850118 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
24850048 GCAAGATACT
24850058 TATTATATTT-TTATTATTTTA
1 TATTATATTTCTTATTATTTTA
24850079 TATTATATTTCCTTA-TATTTTA
1 TATTATATTT-CTTATTATTTTA
* *
24850101 T-TCATATTATATTATTAT
1 TATTATATT-TCTTATTAT
24850119 ACATAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 19 0.56
22 12 0.35
23 3 0.09
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATATTTCTTATTATTTTA
Found at i:24855291 original size:28 final size:27
Alignment explanation
Indices: 24855215--24855292 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 27
24855205 GCAATAAGCC
* *
24855215 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTT-ATAATCAAACT
24855243 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCT-TATAATCAAACT
*
24855271 TGCACACTTAGTGCTGTATAAT
1 CGCACACTTAGTGCT-TATAAT
24855293 TTGAATCCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 44 0.98
29 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATCAAACT
Found at i:24866930 original size:68 final size:68
Alignment explanation
Indices: 24866858--24867054 Score: 254
Period size: 70 Copynumber: 2.8 Consensus size: 68
24866848 ACACCCTATA
* * * * *
24866858 GTAGCTAGGTCACATGTGTGATACGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAGA
1 GTAGCTAGGTCGCATGCGTGATACAAG-TGAAGACACCATGTAGACAA-AGAGCTACGTGAAAGA
24866921 TAAAT
64 TAAAT
*
24866926 GTAGCTAGGTCGCATGCGTGACTCCAAGTGAAGGACACCATGTAGACAAAGAGCTACGTGAAAGA
1 GTAGCTAGGTCGCATGCGTGA-TACAAGTGAA-GACACCATGTAGACAAAGAGCTACGTGAAAGA
24866991 TAAAT
64 TAAAT
*
24866996 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGA-TACAAGTGAA-GACACCATGTAGACAA-AGAGCTACG
24867055 AGACAAATCG
Statistics
Matches: 117, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
68 22 0.19
69 4 0.03
70 70 0.60
71 21 0.18
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (68 bp):
GTAGCTAGGTCGCATGCGTGATACAAGTGAAGACACCATGTAGACAAAGAGCTACGTGAAAGATA
AAT
Found at i:24866986 original size:70 final size:71
Alignment explanation
Indices: 24866892--24867054 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
24866882 GAGATGTATC
24866892 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGACTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGACTCCAAGTGA
24866957 AGGACA
66 AGGACA
*
24866963 CCATGTAGACAA-AGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGACTCCAAGTGA
24867027 AGGACA
66 AGGACA
24867033 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
24867055 AGACAAATCG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
70 69 0.77
71 21 0.23
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGACTCCAAGTGA
AGGACA
Found at i:24869215 original size:28 final size:27
Alignment explanation
Indices: 24869152--24869221 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
24869142 ATAGTGAGTC
24869152 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
24869179 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
24869207 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24869222 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:24872118 original size:24 final size:24
Alignment explanation
Indices: 24872091--24872137 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
24872081 CTAGATTTCC
**
24872091 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
24872115 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
24872138 CTCCTCACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:24874862 original size:30 final size:31
Alignment explanation
Indices: 24874819--24874876 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
24874809 TATAATTGCA
*
24874819 TTTTACTTATATTTTAATTTAGC-CCTAATT
1 TTTTACTTATATTTCAATTTAGCTCCTAATT
24874849 TTTTACATT-TATTTCAATTTAGCTCCTA
1 TTTTAC-TTATATTTCAATTTAGCTCCTA
24874877 TGGCTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTACTTATATTTCAATTTAGCTCCTAATT
Found at i:24875206 original size:25 final size:24
Alignment explanation
Indices: 24875124--24875253 Score: 71
Period size: 25 Copynumber: 5.5 Consensus size: 24
24875114 TATTATATAA
* *
24875124 ATATTTATAAATTT-TATTATACGTT
1 ATATTTATATATTTATATTTTA--TT
*
24875149 ATATTT-T-TA-TTATATATTATT
1 ATATTTATATATTTATATTTTATT
24875170 -TATTCTATTATATTTATATTTTATT
1 ATATT-TA-TATATTTATATTTTATT
*
24875195 ATATGTTATATAATTT-T-TTTTACT
1 ATAT-TTATAT-ATTTATATTTTATT
* *
24875219 ATA--TATATATTATTTATTTTACT
1 ATATTTATATATT-TATATTTTATT
*
24875242 ATATTTTTATAT
1 ATATTTATATAT
24875254 GTAAAATTAC
Statistics
Matches: 85, Mismatches: 6, Indels: 28
0.71 0.05 0.24
Matches are distributed among these distances:
20 7 0.08
21 9 0.11
22 3 0.04
23 17 0.20
24 12 0.14
25 27 0.32
26 9 0.11
27 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (24 bp):
ATATTTATATATTTATATTTTATT
Found at i:24875214 original size:23 final size:24
Alignment explanation
Indices: 24875181--24875245 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
24875171 ATTCTATTAT
* *
24875181 ATTTATATTTTATTATATGTTATATA
1 ATTT-TATTTTACTATAT-ATATATA
*
24875207 ATTTT-TTTTACTATATATATATT
1 ATTTTATTTTACTATATATATATA
24875230 A-TTTATTTTACTATAT
1 ATTTTATTTTACTATAT
24875246 TTTTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 3 0.09
23 17 0.49
24 10 0.29
25 1 0.03
26 4 0.11
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTATTTTACTATATATATATA
Found at i:24875225 original size:21 final size:22
Alignment explanation
Indices: 24875159--24875245 Score: 76
Period size: 21 Copynumber: 4.1 Consensus size: 22
24875149 ATATTTTTAT
* *
24875159 TATATAT-TATTTATTCTATTA
1 TATATATATATTTATTTTACTA
* * *
24875180 TATTTATAT-TTTATTATA-TG
1 TATATATATATTTATTTTACTA
*
24875200 T-TATATA-ATTTTTTTTACTA
1 TATATATATATTTATTTTACTA
24875220 TATATATATTATTTATTTTACTA
1 TATATATA-TATTTATTTTACTA
24875243 TAT
1 TAT
24875246 TTTTATATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 12 0.23
20 4 0.08
21 20 0.38
22 1 0.02
23 15 0.29
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (22 bp):
TATATATATATTTATTTTACTA
Found at i:24878181 original size:124 final size:123
Alignment explanation
Indices: 24877960--24878183 Score: 315
Period size: 124 Copynumber: 1.8 Consensus size: 123
24877950 GAATTATGTG
* * * * * * *
24877960 AAATGAAATATGGATGTGTATTGATTATTGATTATGTGTGTATGAGTATTTGAATGATACCCGGG
1 AAATGAAATATGAATGTCTAATGATTATTGATCATGTGTGCATGAGCAATTGAATGATACCCGGG
* * **
24878025 CTAAGTCCCGAAGGCGATTATGCTTGTGATTATATTTGCGTTTGAGCCTTAGTAACGA
66 CTAAGTCCCGAAGACGATTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
*
24878083 AAATGAAATATGAATGTCTAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGAT-CATGTGTGCATGAGCAATTGAATGATACCCGG
24878148 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
65 GCTAAGTCCCGAAGACGATTA-TGCTGGAAATTATAT
24878184 CCGGGTTAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
123 32 0.37
124 55 0.63
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGAATGTCTAATGATTATTGATCATGTGTGCATGAGCAATTGAATGATACCCGGG
CTAAGTCCCGAAGACGATTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
Found at i:24878305 original size:40 final size:40
Alignment explanation
Indices: 24878178--24878307 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
24878168 TTGCTGGAAA
* *
24878178 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
24878218 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
24878258 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
24878298 TTATATCCGG
1 TTATATCCGG
24878308 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:24892282 original size:44 final size:44
Alignment explanation
Indices: 24892232--24892637 Score: 634
Period size: 44 Copynumber: 9.2 Consensus size: 44
24892222 TCACCGGTGA
*
24892232 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
24892276 CAGATTTGACATCTCTGTATTGTCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
24892320 CAGATTTGGCGTTTCTATATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
24892364 CAGATTTGGCATGTTTGTATTG-CTAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTC-AGAGAGCAGATCGAAGATAG
24892408 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
24892452 CAGATTTGGCGTATCTATATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
*
24892496 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
24892540 CGGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
24892584 CAGATTTGGCATCTCTGTATTGTTAGAGAGCAGATCAAAGATAA
1 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
*
24892628 CAGATCTGGC
1 CAGATTTGGC
24892638 GTTCCTGAGT
Statistics
Matches: 330, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
43 1 0.00
44 328 0.99
45 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (44 bp):
CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
Found at i:24894298 original size:23 final size:20
Alignment explanation
Indices: 24894266--24894366 Score: 79
Period size: 18 Copynumber: 5.0 Consensus size: 20
24894256 ATGCTGTATT
24894266 TTTATTATATATATATTATTTA
1 TTTATTATATATATA-T-TTTA
*
24894288 TTCTATTATATTTATATTTTA
1 TT-TATTATATATATATTTTA
24894309 TTATATGT-TATATA-ATTTT-
1 TT-TAT-TATATATATATTTTA
*
24894328 TTTACTATATATATA--TTA
1 TTTATTATATATATATTTTA
*
24894346 TTTATTTTACTATAT-TTTTA
1 TTTATTATA-TATATATTTTA
24894366 T
1 T
24894367 ATGTAAAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.05
18 15 0.23
19 8 0.12
20 9 0.14
21 14 0.22
22 4 0.06
23 12 0.18
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTATTATATATATATTTTA
Found at i:24894337 original size:39 final size:39
Alignment explanation
Indices: 24894265--24894344 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
24894255 TATGCTGTAT
* * *
24894265 TTTTATTATATATATATTATTTATTCTATTATATTTATA
1 TTTTATTATATATATATAATTTATTCTACTATATATATA
* *
24894304 TTTTATTATATGTTATATAATTT-TTTTACTATATATATA
1 TTTTATTATAT-ATATATAATTTATTCTACTATATATATA
24894343 TT
1 TT
24894345 ATTTATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 26 0.74
40 9 0.26
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (39 bp):
TTTTATTATATATATATAATTTATTCTACTATATATATA
Found at i:24894338 original size:25 final size:25
Alignment explanation
Indices: 24894302--24894368 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 25
24894292 ATTATATTTA
24894302 TATTTTA-T-TATATGTTATATAATT
1 TATTTTACTATATAT-TTATATAATT
*
24894326 T-TTTTACTATATA--TATATTATT
1 TATTTTACTATATATTTATATAATT
*
24894348 TATTTTACTATATTTTTATAT
1 TATTTTACTATATATTTATAT
24894369 GTAAAATTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 9 0.25
23 16 0.44
24 2 0.06
25 9 0.25
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (25 bp):
TATTTTACTATATATTTATATAATT
Found at i:24894470 original size:41 final size:40
Alignment explanation
Indices: 24894381--24894470 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
24894371 AAAATTACTT
*
24894381 TTTATATTATTTTATTATTTTATATATTACTTATCATATTG
1 TTTATATTATTTTATTATTTTATAAATTA-TTATCATATTG
* * *
24894422 TTCATATTATTATATATTTTGTTTATAAATT-TTATTATA-TG
1 TTTATATTATT-T-TATTAT-TTTATAAATTATTATCATATTG
24894463 TTTATATT
1 TTTATATT
24894471 TTTCCACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
41 19 0.46
42 8 0.20
43 5 0.12
44 9 0.22
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (40 bp):
TTTATATTATTTTATTATTTTATAAATTATTATCATATTG
Found at i:24900954 original size:28 final size:28
Alignment explanation
Indices: 24900918--24900999 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
24900908 GCAATCAAAT
24900918 ATGGCACTTAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
24900946 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* * *
24900974 ATGACACTTAGTGTACAAAATTTTGA
1 ATGGCACTTAGTGTACGAAATATTGA
24901000 ATGATTCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:24901872 original size:30 final size:31
Alignment explanation
Indices: 24901838--24901899 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
24901828 TTAAAAGCTT
24901838 ACTCTGTGTTTTC-TTTTCTTATGTTTATAG
1 ACTCTGTGTTTTCTTTTTCTTATGTTTATAG
24901868 ACTCTGTGTTTTCTTTTTCTTATGTTTATAG
1 ACTCTGTGTTTTCTTTTTCTTATGTTTATAG
24901899 A
1 A
24901900 TTTTCGGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.60
Consensus pattern (31 bp):
ACTCTGTGTTTTCTTTTTCTTATGTTTATAG
Found at i:24904389 original size:40 final size:40
Alignment explanation
Indices: 24904352--24904536 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
24904342 GCTACTCGTT
*
24904352 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
24904392 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
24904432 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
24904471 CAAATGACTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
24904512 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
24904537 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 77 0.63
41 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:24904496 original size:79 final size:80
Alignment explanation
Indices: 24904354--24904534 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
24904344 TACTCGTTCA
* ** *
24904354 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGACTTCGGGACTTAACCCGGAT
* *
24904419 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
**
24904434 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTCGCACAAATGACTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGACTTCGGGA-CTTAACCCGG
* *
24904496 ATATGGTCACTTAGCAC
64 ATATAGTAACTTAGCAC
*
24904513 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
24904535 GACATCATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.66
80 26 0.30
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGACTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:24911928 original size:40 final size:40
Alignment explanation
Indices: 24911879--24912027 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 40
24911869 AGTGATTCGT
* * *
24911879 ACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGC
1 ACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGC
* * * *
24911919 ACGAATGCCTTCAGGACTTAACCCGGTTTTGGTAACTCGC
1 ACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGC
* *
24911959 ACAAATGCCTTCGGGACTTAACCC-GATTTTAGTCACTTAGC
1 ACAAATGCCTTCGGGACTTAACCCGGA-TTTAGTAAC-TCGC
* *
24912000 ACAAAAGCCTTCGGGACTTAGCCCGGAT
1 ACAAATGCCTTCGGGACTTAACCCGGAT
24912028 ACCATTCGAA
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.68
41 26 0.29
42 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
ACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGC
Found at i:24912741 original size:2 final size:2
Alignment explanation
Indices: 24912734--24912763 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24912724 ATGTGCAAAC
24912734 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
24912764 GCTAGAGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24919905 original size:30 final size:29
Alignment explanation
Indices: 24919811--24919912 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
24919801 TATAGTGAAT
* * *
24919811 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
24919840 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
24919868 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
24919898 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
24919913 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:24923109 original size:40 final size:40
Alignment explanation
Indices: 24923060--24923242 Score: 153
Period size: 40 Copynumber: 4.6 Consensus size: 40
24923050 GACTAGCTCG
* * *
24923060 ATTGTCTTCGGGACATT-GCCCGATTATAGTGATTCGCACA
1 ATTGCCTTCGGGACATTAGCCCGATT-TAGTAACTCGCACA
24923100 ATTGCCTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACGA
1 ATTGCCTTCGGGACATTAGCCC-GATTTAGTAACTCGCAC-A
* * *
24923141 A-TGCCTTCGGGAC-TTAACCCGGTTTTGGTAACTCGCACA
1 ATTGCCTTCGGGACATTAGCCC-GATTTAGTAACTCGCACA
* * * * *
24923180 AATGCCTTCGGGAC-TTAACCCAGTTTTAGTCACTTAGCACA
1 ATTGCCTTCGGGACATTAGCCC-GATTTAGTAAC-TCGCACA
**
24923221 AAAGCCTTCGGGAC-TTAGCCCG
1 ATTGCCTTCGGGACATTAGCCCG
24923243 GATACCATTC
Statistics
Matches: 125, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 5 0.04
40 89 0.71
41 31 0.25
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
ATTGCCTTCGGGACATTAGCCCGATTTAGTAACTCGCACA
Found at i:24923232 original size:41 final size:40
Alignment explanation
Indices: 24923093--24923243 Score: 194
Period size: 40 Copynumber: 3.8 Consensus size: 40
24923083 TTATAGTGAT
* * * *
24923093 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTAGTAAC
* *
24923133 TCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTAGTAAC
* *
24923173 TCGCACAAATGCCTTCGGGACTTAACCCAGTTTTAGTCAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTAGTAAC
* * *
24923213 TTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 -TCGCACAAATGCCTTCGGGACTTAACCCGG
24923244 ATACCATTCG
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 70 0.73
41 26 0.27
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTAGTAAC
Found at i:24923959 original size:2 final size:2
Alignment explanation
Indices: 24923952--24923983 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24923942 ATGTGCAAAC
24923952 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
24923984 GCTAGAGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24930521 original size:6 final size:6
Alignment explanation
Indices: 24930510--24930536 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24930500 GGTTTTAAGT
24930510 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
24930537 GTTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:24935671 original size:34 final size:33
Alignment explanation
Indices: 24935628--24935721 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
24935618 GTTAGGCCCT
* *
24935628 AGCCCATTTCAGAATCAGAAATAGTATGGGCCTG
1 AGCCCATTTCAGAATCAG-TATAGTATGGGCCTA
*
24935662 AGCCCATTTCAGTAA-CAGTATCAGT-GGGGCCTA
1 AGCCCATTTCAG-AATCAGTAT-AGTATGGGCCTA
*
24935695 AGCCCATTACAGAATCAGTATAGTATG
1 AGCCCATTTCAGAATCAGTATAGTATG
24935722 CAATTAGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 5 0.10
33 26 0.51
34 18 0.35
35 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (33 bp):
AGCCCATTTCAGAATCAGTATAGTATGGGCCTA
Found at i:24936080 original size:27 final size:27
Alignment explanation
Indices: 24936050--24936237 Score: 207
Period size: 27 Copynumber: 7.0 Consensus size: 27
24936040 GTAGGCAAAT
24936050 CAGTCATTTTA-CCTCACAGGGGTATTA
1 CAGTCATTTTACCCT-ACAGGGGTATTA
* *
24936077 CAGTCATTTTACCCTAAAAGGGTATTA
1 CAGTCATTTTACCCTACAGGGGTATTA
* * * *
24936104 TAGTCATGTTACCCTACAGGGCTTTTA
1 CAGTCATTTTACCCTACAGGGGTATTA
* *
24936131 TAGTCATTTTACCCTACAGGGGTGTTA
1 CAGTCATTTTACCCTACAGGGGTATTA
* * * * * *
24936158 AAGTCATGTTACCTTATAAGGGTATTT
1 CAGTCATTTTACCCTACAGGGGTATTA
* *
24936185 CAGTCATTTTACCCTACAAGGGTATTT
1 CAGTCATTTTACCCTACAGGGGTATTA
*
24936212 CAGTCATTTTACCCTATAGGGGTATT
1 CAGTCATTTTACCCTACAGGGGTATT
24936238 TCGGATATTA
Statistics
Matches: 136, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
27 133 0.98
28 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
CAGTCATTTTACCCTACAGGGGTATTA
Found at i:24936190 original size:81 final size:81
Alignment explanation
Indices: 24936049--24936237 Score: 242
Period size: 81 Copynumber: 2.3 Consensus size: 81
24936039 CGTAGGCAAA
* *
24936049 TCAGTCATTTTA-CCTCACAGGGGTATTACAGTCATTTTACCCTAAAAGGGTATTATAGTCATGT
1 TCAGTCATTTTACCCT-ACAGGGGTATTAAAGTCATGTTACCCTAAAAGGGTATTATAGTCATGT
24936113 TACCCTAC-AGGGCT-TT
65 TACCCTACAAGGG-TATT
* * * * *
24936129 TATAGTCATTTTACCCTACAGGGGTGTTAAAGTCATGTTACCTTATAAGGGTATT-TCAGTCATT
1 T-CAGTCATTTTACCCTACAGGGGTATTAAAGTCATGTTACCCTAAAAGGGTATTAT-AGTCATG
24936193 TTACCCTACAAGGGTATT
64 TTACCCTACAAGGGTATT
*
24936211 TCAGTCATTTTACCCTATAGGGGTATT
1 TCAGTCATTTTACCCTACAGGGGTATT
24936238 TCGGATATTA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
80 2 0.02
81 82 0.87
82 10 0.11
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (81 bp):
TCAGTCATTTTACCCTACAGGGGTATTAAAGTCATGTTACCCTAAAAGGGTATTATAGTCATGTT
ACCCTACAAGGGTATT
Found at i:24939635 original size:13 final size:14
Alignment explanation
Indices: 24939617--24939646 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
24939607 GCTCTAATGA
24939617 TTTGAACTGAA-CT
1 TTTGAACTGAATCT
24939630 TTTGAACTGAATCT
1 TTTGAACTGAATCT
24939644 TTT
1 TTT
24939647 TGAGTTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (14 bp):
TTTGAACTGAATCT
Found at i:24940878 original size:21 final size:19
Alignment explanation
Indices: 24940844--24940905 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
24940834 TAAGTTATGT
24940844 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
24940866 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
24940888 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
24940906 GTATCTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:24940976 original size:29 final size:29
Alignment explanation
Indices: 24940931--24940987 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
24940921 AAATATGGTA
*
24940931 AAATAATTAGTATTAAAAAAATAAATAAT
1 AAATAATTAGTAATAAAAAAATAAATAAT
* *
24940960 AAATAATATA-TAATAAAAATATATATAA
1 AAATAAT-TAGTAATAAAAAAATAAATAA
24940988 GAAAGATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAATAATTAGTAATAAAAAAATAAATAAT
Found at i:24941040 original size:18 final size:18
Alignment explanation
Indices: 24941017--24941057 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
24941007 GAATATTGAA
24941017 TAATAAAAATATAGTATG
1 TAATAAAAATATAGTATG
24941035 TAATAAAAATATAGTATG
1 TAATAAAAATATAGTATG
*
24941053 AAATA
1 TAATA
24941058 TAATATGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (18 bp):
TAATAAAAATATAGTATG
Found at i:24941430 original size:14 final size:14
Alignment explanation
Indices: 24941400--24941474 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
24941390 ACAATTTTAA
24941400 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
24941412 GAAATATATAAAAT
1 AAAATATATAAAAT
*
24941426 AAAATATATAATAT
1 AAAATATATAAAAT
* * *
24941440 AATATAATTTATAGAT
1 AAAAT-ATATA-AAAT
24941456 AAAATATATAATAAT
1 AAAATATATAA-AAT
24941471 AAAA
1 AAAA
24941475 AATAATGGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.16
13 3 0.06
14 17 0.35
15 14 0.29
16 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:24941443 original size:26 final size:30
Alignment explanation
Indices: 24941400--24941468 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 30
24941390 ACAATTTTAA
24941400 AAAATATATAA-AGAAATAT-A-TA-AAAT
1 AAAATATATAATAGAAATATAATTATAAAT
* *
24941426 AAAATATATAATA-TAATATAATTTATAGAT
1 AAAATATATAATAGAAATATAA-TTATAAAT
24941456 AAAATATATAATA
1 AAAATATATAATA
24941469 ATAAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 16 0.44
27 2 0.06
29 2 0.06
30 16 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATATATAATAGAAATATAATTATAAAT
Found at i:24941469 original size:12 final size:12
Alignment explanation
Indices: 24941380--24941469 Score: 53
Period size: 12 Copynumber: 7.1 Consensus size: 12
24941370 CAAATTTAGT
24941380 AAATA-ATAATA
1 AAATATATAATA
* *
24941391 CAAT-TTTAA-A
1 AAATATATAATA
24941401 AAATATATAA-A
1 AAATATATAATA
24941412 GAAATATATAAAATA
1 -AAATATAT--AATA
24941427 AAATATATAATA
1 AAATATATAATA
24941439 TAATATAATTTATAGATA
1 -AA-AT-A--TATA-ATA
24941457 AAATATATAATA
1 AAATATATAATA
24941469 A
1 A
24941470 TAAAAAATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.06
11 11 0.17
12 16 0.25
13 6 0.10
14 12 0.19
15 3 0.05
16 2 0.03
17 6 0.10
18 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (12 bp):
AAATATATAATA
Found at i:24941509 original size:11 final size:10
Alignment explanation
Indices: 24941424--24941522 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
24941414 AATATATAAA
24941424 ATAA-AATAT
1 ATAATAATAT
24941433 ATAAT-ATAAT
1 ATAATAAT-AT
* *
24941443 ATAATTTATAG
1 ATAA-TAATAT
24941454 ATAA-AATAT
1 ATAATAATAT
24941463 ATAATAATA-
1 ATAATAATAT
24941472 A-AA-AATA-
1 ATAATAATAT
*
24941479 ATGGATAATA-
1 AT-AATAATAT
*
24941489 ATAGTAATAT
1 ATAATAATAT
24941499 ATAACTAATAT
1 ATAA-TAATAT
* *
24941510 TTAAAAATAT
1 ATAATAATAT
24941520 ATA
1 ATA
24941523 TAAAGTATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 20 0.29
10 26 0.37
11 15 0.21
12 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (10 bp):
ATAATAATAT
Found at i:24943504 original size:206 final size:206
Alignment explanation
Indices: 24943136--24943885 Score: 1182
Period size: 206 Copynumber: 3.6 Consensus size: 206
24943126 TCGATTTGTC
* * **
24943136 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCAAAAGCCAAA
1 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCATAAGCACGTGAAAGCCAAA
* * * *
24943201 TCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACGAGGATACCAAACCATCTTAGATCTGCTTCA
66 TCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGCTTCA
* * ** *
24943266 GTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATGGAGACTCCAAAC
131 GTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGACTCCAAAC
24943331 TTTGATTTATT
196 TTTGATTTATT
* *
24943342 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGT-GTAAGCACGTGAAAGCTAA
1 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-TCATAAGCACGTGAAAGCCAA
* * *
24943406 ATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATTTTGGATCTGCTT
65 ATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGCTT
*
24943470 CAGTATAAACATCTGAAGGCCAGATCTTCTATGTGTCTGCTCTCCGTCGAATATGGAGA-TGCCA
129 CAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGACT-CCA
*
24943534 AACTTCGATTTATT
193 AACTTTGATTTATT
* * *
24943548 CTCTGATAATACAGATATGCCAAATCATCTTAGATTTCCTTCATCATAAGCACGTGAAAGCCAAA
1 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCATAAGCACGTGAAAGCCAAA
* *
24943613 TCAGCTATGTCTTCGATTTGTTCCTTGTGAGCACAAGGATGCCAAATCATCTTGGATCTGCTTCA
66 TCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGCTTCA
* *
24943678 GTATAAACATCTGAAGGCCAAATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGACGCCAAAC
131 GTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGACTCCAAAC
*
24943743 TTTGATTTGTT
196 TTTGATTTATT
*
24943754 CTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCATCATAAGCACGTGAAAGCCAAA
1 CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCATAAGCACGTGAAAGCCAAA
24943819 TCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCCTGCTTC
66 TCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT-CTGCTTC
24943884 AG
130 AG
24943886 CCAGATCTGC
Statistics
Matches: 500, Mismatches: 37, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
205 3 0.01
206 487 0.97
207 10 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (206 bp):
CTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCATAAGCACGTGAAAGCCAAA
TCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGCTTCA
GTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGACTCCAAAC
TTTGATTTATT
Found at i:24947033 original size:46 final size:45
Alignment explanation
Indices: 24946983--24947155 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
24946973 TGGTTGAGCA
24946983 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA-G
* * *
24947029 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A-G
** *
24947074 CATCCGAACTTATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAAG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AAAG
* * *
24947122 CCCGAGCTCGTTGACTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
24947156 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 57 0.55
47 27 0.26
48 3 0.03
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAG
Found at i:24947141 original size:93 final size:93
Alignment explanation
Indices: 24946980--24947150 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
24946970 GGATGGTTGA
* * *
24946980 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGACT
24947045 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
24947073 GCATCCGAACTTATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAA-GCCCGAGCTCGTTGAC
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGC-AAATGCCCGAACTCGTTGAC
24947137 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
24947151 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 68 0.96
94 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGACT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:24947417 original size:19 final size:20
Alignment explanation
Indices: 24947380--24947417 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
24947370 ATAAGGTGGT
24947380 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
24947400 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
24947418 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:24956433 original size:28 final size:27
Alignment explanation
Indices: 24956357--24956434 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 27
24956347 GCAATAAGCC
* *
24956357 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTT-ATAATCAAACT
24956385 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCT-TATAATCAAACT
*
24956413 TGCACACTTAGTGCTGTATAAT
1 CGCACACTTAGTGCT-TATAAT
24956435 TTGAATCCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 44 0.98
29 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATCAAACT
Found at i:24968218 original size:27 final size:27
Alignment explanation
Indices: 24968178--24968289 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
24968168 AGGAAGAGTC
*
24968178 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
24968205 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
24968232 CTGGTGGCTCTGCCACGATTATCTATAT
1 CTGGTGGCTCTGCCACAATTATCT-GAT
* * *
24968260 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
24968286 CTGG
1 CTGG
24968290 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 47 0.64
28 18 0.25
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:24968284 original size:54 final size:54
Alignment explanation
Indices: 24968178--24968289 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
24968168 AGGAAGAGTC
* *
24968178 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
24968232 CTGGTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCT-GATCTGGTGACTCTGCCACATATATCTGTT
24968286 CTGG
1 CTGG
24968290 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:24969485 original size:28 final size:28
Alignment explanation
Indices: 24969454--24969547 Score: 152
Period size: 28 Copynumber: 3.4 Consensus size: 28
24969444 GATATTTTGC
24969454 ACACTAAGTGTCATTCTCAATATCTCGT
1 ACACTAAGTGTCATTCTCAATATCTCGT
*
24969482 ACACTAAGTGTCATTCTCAATATCTCGC
1 ACACTAAGTGTCATTCTCAATATCTCGT
* *
24969510 ACACTAAGTGCCATTCTCAATATTTCGT
1 ACACTAAGTGTCATTCTCAATATCTCGT
*
24969538 ACACTGAGTG
1 ACACTAAGTG
24969548 CCATATTTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (28 bp):
ACACTAAGTGTCATTCTCAATATCTCGT
Found at i:24971171 original size:41 final size:41
Alignment explanation
Indices: 24971126--24971243 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
24971116 TGAAAGATAA
24971126 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
24971167 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24971197 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24971238 ATGTAG
1 ATGTAG
24971244 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:24971182 original size:71 final size:71
Alignment explanation
Indices: 24971094--24971257 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
24971084 GAGATGTATC
24971094 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24971159 AGGACA
66 AGGACA
24971165 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24971230 AGGACA
66 AGGACA
24971236 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
24971258 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:24978748 original size:41 final size:41
Alignment explanation
Indices: 24978703--24978820 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
24978693 TGAAAGATAA
24978703 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
24978744 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24978774 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24978815 ATGTAG
1 ATGTAG
24978821 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:24978759 original size:71 final size:71
Alignment explanation
Indices: 24978671--24978834 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
24978661 GAGATGTATC
24978671 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24978736 AGGACA
66 AGGACA
24978742 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24978807 AGGACA
66 AGGACA
24978813 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
24978835 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:24989614 original size:24 final size:24
Alignment explanation
Indices: 24989582--24989631 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
24989572 CTAGGAAGAT
* *
24989582 AGAGAACTAAGATAGTATTTATAA
1 AGAGAACTAAGACAATATTTATAA
*
24989606 AGAGAACTAAGACAATGTTTATAA
1 AGAGAACTAAGACAATATTTATAA
24989630 AG
1 AG
24989632 TTGAACTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (24 bp):
AGAGAACTAAGACAATATTTATAA
Found at i:24993747 original size:29 final size:29
Alignment explanation
Indices: 24993713--24993783 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
24993703 TACTCAATCA
* *
24993713 CGCACACTTAGTGCCATAT-GATTCAAGCC
1 CGCACACTTAGTGCCATATAG-TCCAAACC
* *
24993742 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATAGTCCAAACC
24993771 CGCACACTTAGTG
1 CGCACACTTAGTG
24993784 TCGTACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATAGTCCAAACC
Found at i:25006360 original size:21 final size:20
Alignment explanation
Indices: 25006325--25006374 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
25006315 ACTTAGAGCG
25006325 GAGGCAGC-AGAGAGAGGCA
1 GAGGCAGCAAGAGAGAGGCA
*
25006344 GCGGCAGCAACGAGAGAGGCA
1 GAGGCAGCAA-GAGAGAGGCA
25006365 GAGGCAGCAA
1 GAGGCAGCAA
25006375 TGATGGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.26
20 1 0.04
21 19 0.70
ACGTcount: A:0.36, C:0.20, G:0.44, T:0.00
Consensus pattern (20 bp):
GAGGCAGCAAGAGAGAGGCA
Found at i:25006649 original size:33 final size:33
Alignment explanation
Indices: 25006607--25006687 Score: 112
Period size: 31 Copynumber: 2.5 Consensus size: 33
25006597 TTAGAATTAA
*
25006607 TGTTTTTGGTTGTATTTTTTATGCTAAATTTGC
1 TGTTTTTGGTTGCATTTTTTATGCTAAATTTGC
* *
25006640 TGTTTTTGGTTGCA--TTTTATGCTATATTTGT
1 TGTTTTTGGTTGCATTTTTTATGCTAAATTTGC
*
25006671 TGTTTTTGGTTGGATTT
1 TGTTTTTGGTTGCATTT
25006688 AATGCAGGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 28 0.67
33 14 0.33
ACGTcount: A:0.12, C:0.05, G:0.21, T:0.62
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTTATGCTAAATTTGC
Found at i:25009075 original size:31 final size:32
Alignment explanation
Indices: 25009037--25009108 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
25009027 TAGGTTGTAT
* *
25009037 TATATATAATACATGTGTGTGGGTT-TT-TTTA
1 TATATATAATACATATGTGT-GGTTCTTGATTA
*
25009068 TATATATAATATATATGTGTGGTTCTTGATTA
1 TATATATAATACATATGTGTGGTTCTTGATTA
25009100 TATATATAA
1 TATATATAA
25009109 CGTATATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 20 0.56
32 12 0.33
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (32 bp):
TATATATAATACATATGTGTGGTTCTTGATTA
Found at i:25011256 original size:5 final size:5
Alignment explanation
Indices: 25011246--25011270 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25011236 CTAACCTGGG
25011246 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
25011271 GAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:25012425 original size:9 final size:9
Alignment explanation
Indices: 25012406--25012436 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
25012396 TTATGTGTTC
25012406 TTTATTTTTA
1 TTTA-TTTTA
25012416 TTTATTTTA
1 TTTATTTTA
25012425 TTTATTTTA
1 TTTATTTTA
25012434 TTT
1 TTT
25012437 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:25019208 original size:17 final size:17
Alignment explanation
Indices: 25019188--25019245 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
25019178 ATATTTAATG
25019188 ATATAATATATAAAAAT
1 ATATAATATATAAAAAT
*
25019205 ATAT--T-TATAAGAAT
1 ATATAATATATAAAAAT
25019219 A-ATAATTATATAAAAAT
1 ATATAA-TATATAAAAAT
*
25019236 ATAAAATATA
1 ATATAATATA
25019246 ATGGTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 1 0.03
16 1 0.03
17 17 0.52
18 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATAATATATAAAAAT
Found at i:25019556 original size:23 final size:23
Alignment explanation
Indices: 25019542--25019715 Score: 79
Period size: 26 Copynumber: 6.8 Consensus size: 23
25019532 AAATGACATA
25019542 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
*
25019565 ATAATATAAAAGTATATATGTGAA-A-
1 ATAATATAAAA-TA-A-ATAT-AATAT
*
25019590 ATAATATATAATATATATAAATAATAT
1 ATAATATA-AA-ATA-A-ATATAATAT
25019617 GAGTAATATATAAAATAATTATATAATAT
1 -A-TAATAT--AAAATAA--ATATAATAT
* *
25019646 ATAATATAAAAATAAAAATAA-AG
1 ATAATAT-AAAATAAATATAATAT
25019669 A-AA-ATAACAATAAAATTTTATATATAT
1 ATAATATAA-AAT-AAA---TATA-ATAT
25019696 ATAATAATAAAATAAATATA
1 ATAAT-ATAAAATAAATATA
25019716 TAGGGTTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 44
0.69 0.05 0.26
Matches are distributed among these distances:
20 2 0.02
21 5 0.04
22 5 0.04
23 13 0.11
24 7 0.06
25 18 0.15
26 22 0.18
27 11 0.09
28 8 0.07
29 21 0.18
30 6 0.05
31 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:25019566 original size:7 final size:7
Alignment explanation
Indices: 25019539--25019653 Score: 81
Period size: 7 Copynumber: 17.1 Consensus size: 7
25019529 ATAAAATGAC
25019539 ATAATAAT
1 ATAAT-AT
25019547 ATAA-A-
1 ATAATAT
25019552 ATAA-AT
1 ATAATAT
25019558 ATAATAT
1 ATAATAT
25019565 ATAATAT
1 ATAATAT
25019572 A-AA-AGT
1 ATAATA-T
25019578 AT-ATAT
1 ATAATAT
*
25019584 GTGAA-A-
1 AT-AATAT
25019590 ATAATAT
1 ATAATAT
25019597 ATAATAT
1 ATAATAT
*
25019604 AT-ATAA
1 ATAATAT
25019610 ATAATAT
1 ATAATAT
25019617 GAGTAATAT
1 -A-TAATAT
25019626 ATAA-A-
1 ATAATAT
25019631 ATAATTAT
1 ATAA-TAT
25019639 ATAATAT
1 ATAATAT
25019646 ATAATAT
1 ATAATAT
25019653 A
1 A
25019654 AAAATAAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
5 12 0.14
6 20 0.23
7 39 0.44
8 11 0.12
9 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:25019603 original size:20 final size:19
Alignment explanation
Indices: 25019539--25019654 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 19
25019529 ATAAAATGAC
25019539 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
* *
25019558 ATAATATATAATATAAAAGT
1 ATAATATATAAAATAATA-T
*
25019578 AT-ATATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
25019597 ATAATATATATAAATAATAT
1 ATAATATATA-AAATAATAT
25019617 GAGTAATATATAAAATAATTAT
1 -A-TAATATATAAAATAA-TAT
*
25019639 ATAATATATAATATAA
1 ATAATATATAAAATAA
25019655 AAATAAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.12
19 15 0.18
20 38 0.46
21 8 0.10
22 12 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:25021786 original size:205 final size:205
Alignment explanation
Indices: 25021320--25021872 Score: 867
Period size: 205 Copynumber: 2.7 Consensus size: 205
25021310 AAATTTGCTT
* *
25021320 CTTCGATTTGTTCTCTGACAATACAGAAATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * * * *
25021385 GTGAAAGCCAAATCGGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGTCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* ** * * * *
25021450 GGATCTTGTTTCAGTGAAATTATCTAAAGGTGAGATCTGTTATGTGTCTGCTCTCCGTTGAAATA
131 GGATC-TGCTTCAGTGAAAACATCTAAAGGTGAGATCTGCTATGTGTCTGCCCTCCATCGAAATA
25021515 GAGATGCCAGA
195 GAGATGCCAGA
*
25021526 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTATATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
*
25021591 GTGAAAGCCAAATTAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * * * *
25021656 GGATCTACTTCAGT-ATAAACATCTGAAGGTTG-GATTTGCTATGTGTTTGCCCTCTATCGAAGT
131 GGATCTGCTTCAGTGA-AAACATCTAAAGG-TGAGATCTGCTATGTGTCTGCCCTCCATCGAAAT
25021719 AGAGATGCCAGA
194 AGAGATGCCAGA
25021731 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
25021796 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
25021861 GGATCTGCTTCA
131 GGATCTGCTTCA
25021873 ACCAGATCTG
Statistics
Matches: 320, Mismatches: 25, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
204 1 0.00
205 191 0.60
206 128 0.40
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTGAAAACATCTAAAGGTGAGATCTGCTATGTGTCTGCCCTCCATCGAAATAG
AGATGCCAGA
Found at i:25030035 original size:14 final size:14
Alignment explanation
Indices: 25030012--25030041 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25030002 ATCTCGATTC
25030012 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
25030026 AACTTTATTTAGAA
1 AACTTCATTTAGAA
25030040 AA
1 AA
25030042 AGAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:25033256 original size:17 final size:17
Alignment explanation
Indices: 25033236--25033293 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
25033226 ATATTTAATG
25033236 ATATAATATATAAAAAT
1 ATATAATATATAAAAAT
*
25033253 ATAT--T-TATAAGAAT
1 ATATAATATATAAAAAT
25033267 A-ATAATTATATAAAAAT
1 ATATAA-TATATAAAAAT
*
25033284 ATAAAATATA
1 ATATAATATA
25033294 ATGGTTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 1 0.03
16 1 0.03
17 17 0.52
18 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATAATATATAAAAAT
Found at i:25033600 original size:23 final size:23
Alignment explanation
Indices: 25033586--25033710 Score: 74
Period size: 29 Copynumber: 4.9 Consensus size: 23
25033576 AAATGACATA
25033586 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
*
25033609 ATAATATAAAAGTATATATGTGAA-A-
1 ATAATATAAAA-TA-A-ATAT-AATAT
*
25033634 ATAATATATAATATATATAAATAATAT
1 ATAATATA-AA-ATA-A-ATATAATAT
25033661 GAGTAATATATAAAATAATTATATAATAT
1 -A-TAATAT--AAAATAA--ATATAATAT
*
25033690 ATAATATAAAAGTAAAAATAA
1 ATAATATAAAA-TAAATATAA
25033711 AGCAAATAAC
Statistics
Matches: 83, Mismatches: 5, Indels: 27
0.72 0.04 0.23
Matches are distributed among these distances:
23 11 0.13
24 7 0.08
25 15 0.18
26 17 0.20
27 9 0.11
28 3 0.04
29 18 0.22
30 2 0.02
31 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:25033610 original size:7 final size:7
Alignment explanation
Indices: 25033583--25033697 Score: 81
Period size: 7 Copynumber: 17.1 Consensus size: 7
25033573 ATAAAATGAC
25033583 ATAATAAT
1 ATAAT-AT
25033591 ATAA-A-
1 ATAATAT
25033596 ATAA-AT
1 ATAATAT
25033602 ATAATAT
1 ATAATAT
25033609 ATAATAT
1 ATAATAT
25033616 A-AA-AGT
1 ATAATA-T
25033622 AT-ATAT
1 ATAATAT
*
25033628 GTGAA-A-
1 AT-AATAT
25033634 ATAATAT
1 ATAATAT
25033641 ATAATAT
1 ATAATAT
*
25033648 AT-ATAA
1 ATAATAT
25033654 ATAATAT
1 ATAATAT
25033661 GAGTAATAT
1 -A-TAATAT
25033670 ATAA-A-
1 ATAATAT
25033675 ATAATTAT
1 ATAA-TAT
25033683 ATAATAT
1 ATAATAT
25033690 ATAATAT
1 ATAATAT
25033697 A
1 A
25033698 AAAGTAAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
5 12 0.14
6 20 0.23
7 39 0.44
8 11 0.12
9 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:25033647 original size:20 final size:19
Alignment explanation
Indices: 25033583--25033698 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 19
25033573 ATAAAATGAC
25033583 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
* *
25033602 ATAATATATAATATAAAAGT
1 ATAATATATAAAATAATA-T
*
25033622 AT-ATATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
25033641 ATAATATATATAAATAATAT
1 ATAATATATA-AAATAATAT
25033661 GAGTAATATATAAAATAATTAT
1 -A-TAATATATAAAATAA-TAT
*
25033683 ATAATATATAATATAA
1 ATAATATATAAAATAA
25033699 AAGTAAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.12
19 15 0.18
20 38 0.46
21 8 0.10
22 12 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:25033686 original size:29 final size:27
Alignment explanation
Indices: 25033583--25033697 Score: 89
Period size: 29 Copynumber: 4.3 Consensus size: 27
25033573 ATAAAATGAC
*
25033583 ATAATAATATAAAATA-A-ATATAATAT
1 ATAAT-ATATAAAATATATAAATAATAT
* **
25033609 ATAATATA-AAAGTATATATGTGAA-A-
1 ATAATATATAAAATATATAAAT-AATAT
*
25033634 ATAATATATAATATATATAAATAATAT
1 ATAATATATAAAATATATAAATAATAT
*
25033661 GAGTAATATATAAAATA-ATTATATAATAT
1 -A-TAATATATAAAATATA-TAAATAATAT
25033690 ATAATATA
1 ATAATATA
25033698 AAAGTAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
24 5 0.07
25 14 0.19
26 19 0.26
27 9 0.12
28 3 0.04
29 22 0.31
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATAATATATAAAATATATAAATAATAT
Found at i:25042522 original size:27 final size:27
Alignment explanation
Indices: 25042291--25042596 Score: 244
Period size: 27 Copynumber: 11.4 Consensus size: 27
25042281 TTTGGTTTAC
*
25042291 AAAATTACCAAAATACCCT-GCTTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * * *
25042317 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
*
25042344 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
*
25042371 AAAATTACCAAAATACCCT-TAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
* *
25042398 AAAATTATCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
*
25042425 AAAATTACCAAAATACCC-CTAATTTGT
1 AAAATTACCAAAATACCCTC-GATTTGT
* ** * **
25042452 GAAATTACTGAAATAACCTCGACCTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*** *
25042479 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* *
25042506 AAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
* ****
25042533 AGAATTACCGTTTTACCCTCGATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
**** *
25042560 AAAATTACCGTTTTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
*
25042587 AGAATTACCA
1 AAAATTACCA
25042597 TTTTACCCTC
Statistics
Matches: 236, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
26 18 0.08
27 216 0.92
28 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:25042600 original size:27 final size:27
Alignment explanation
Indices: 25042519--25042839 Score: 414
Period size: 27 Copynumber: 11.9 Consensus size: 27
25042509 ATTACCAAAG
*
25042519 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
25042546 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25042573 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
25042600 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
25042627 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25042654 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
25042681 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
25042708 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
25042735 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25042762 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25042789 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
25042816 TACCCTCGATTTACAAAATTACCG
1 TACCCTCGATTTACAGAATTACCG
25042840 AAATACCCTC
Statistics
Matches: 262, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.01
27 258 0.98
28 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:25042846 original size:27 final size:27
Alignment explanation
Indices: 25042708--25042956 Score: 95
Period size: 27 Copynumber: 9.1 Consensus size: 27
25042698 ATTATCGTTT
* * * ***
25042708 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCGAAA
* * * ***
25042735 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCGAAA
* * ***
25042762 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACCGAAA
* * * * ***
25042789 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACCGAAA
*
25042816 TACCCTCGATTTACAAAATTACCGAAA
1 TACCCTCGATTTATAAAATTACCGAAA
* * *
25042843 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCGAAA
* * *
25042870 TACCC-CTGATTTACAAAGTTACAGAAA
1 TACCCTC-GATTTATAAAATTACCGAAA
* * ** *
25042897 TACCCTTGACTTTTTAAAAATTATAGAAG
1 TACCCTCGA-TTTAT-AAAATTACCGAAA
* * * * *
25042926 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTATAAAATTACCGAAA
25042953 TACC
1 TACC
25042957 TTTGGTTTGT
Statistics
Matches: 182, Mismatches: 36, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 158 0.87
28 6 0.03
29 17 0.09
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCGAAA
Found at i:25042847 original size:81 final size:81
Alignment explanation
Indices: 25042492--25042864 Score: 387
Period size: 81 Copynumber: 4.6 Consensus size: 81
25042482 ATTATTGAAA
* ** * ** *
25042492 TACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCGATTTACCCTCGATTTATAGAATTACTGTTTTACCCTCGATT
** *
25042557 TGTAAAATTACCGTTT
66 TACAGAATTACCGTTT
* * * *
25042573 TACCCTCGATTTATAGAATTACC-ATTTTACCCTC-AGTTTACAGAATTACTATTTTACCCTCGA
1 TACCCTCGATTTACAAAATTACCGA-TTTACCCTCGA-TTTATAGAATTACTGTTTTACCCTCGA
*
25042636 TTTATAGAATTACCGTTT
64 TTTACAGAATTACCGTTT
* * * * *
25042654 TACCC-CTAATTTACATAATTACCGTTTTACCC-CTGATTTACATAATTA-TCGTTTTACCCTCG
1 TACCCTC-GATTTACAAAATTACCGATTTACCCTC-GATTTATAGAATTACT-GTTTTACCCTCG
*
25042716 ACTTACAGAATTACCGTTT
63 ATTTACAGAATTACCGTTT
* * * *
25042735 TACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACCGATTTACCCTCGATTTATAGAATTACTGTTTTACCCTCGATT
*
25042800 TACAGAATTACTGTTT
66 TACAGAATTACCGTTT
** * * *
25042816 TACCCTCGATTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTAC
1 TACCCTCGATTTACAAAATTACCGATTTACCCTCGATTTATAGAATTAC
25042865 CAAAATACCC
Statistics
Matches: 250, Mismatches: 32, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
80 5 0.02
81 241 0.96
82 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCGATTTACCCTCGATTTATAGAATTACTGTTTTACCCTCGATT
TACAGAATTACCGTTT
Found at i:25042961 original size:27 final size:26
Alignment explanation
Indices: 25042909--25042964 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
25042899 CCCTTGACTT
*
25042909 TTTAAAAATTATAGAAGTACCATTGG
1 TTTAAAAATTATAGAAATACCATTGG
*
25042935 TTTACAAAATTACT-GAAATACCTTTGG
1 TTTA-AAAATTA-TAGAAATACCATTGG
25042962 TTT
1 TTT
25042965 GTTGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACCATTGG
Found at i:25043082 original size:27 final size:27
Alignment explanation
Indices: 25043018--25043082 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
25043008 ACCCCTAAAA
*
25043018 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
25043045 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
25043072 GGTAAAATGAC
1 GGTAAAATGAC
25043083 GAATATGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:25044269 original size:25 final size:25
Alignment explanation
Indices: 25044240--25044287 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25044230 TTATAATATG
* * *
25044240 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
25044265 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
25044288 GTTTATGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:25044356 original size:20 final size:20
Alignment explanation
Indices: 25044331--25044389 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
25044321 TAAATATGGT
25044331 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
25044351 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
25044371 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
25044390 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:25044467 original size:24 final size:24
Alignment explanation
Indices: 25044440--25044582 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
25044430 GAGGAAGTGA
25044440 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
25044464 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
25044488 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
25044511 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
25044535 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
25044559 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
25044583 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:25044533 original size:47 final size:47
Alignment explanation
Indices: 25044440--25044582 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
25044430 GAGGAAGTGA
25044440 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
25044488 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
25044535 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
25044583 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:25044556 original size:71 final size:72
Alignment explanation
Indices: 25044440--25044583 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
25044430 GAGGAAGTGA
*
25044440 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
25044503 CCAGTTAT
65 CCAGTTAT
** * *
25044511 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
25044576 CAGTTAT
66 CAGTTAT
25044583 A
1 A
25044584 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:25044809 original size:31 final size:31
Alignment explanation
Indices: 25044774--25044868 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
25044764 CGTTTACAGT
*
25044774 AAAGGCTTCGGCCCAGTAATATGAAATCTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
25044805 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
25044836 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
25044867 AA
1 AA
25044869 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:25048174 original size:11 final size:10
Alignment explanation
Indices: 25048160--25048230 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
25048150 GAACCCCCTC
25048160 TCTTTCTC-T
1 TCTTTCTCTT
25048169 TCTCTTC-CTT
1 TCT-TTCTCTT
25048179 T-TTT-TCTT
1 TCTTTCTCTT
25048187 TCTTTCTCTCT
1 TCTTTCTCT-T
25048198 TC-TT-TCTT
1 TCTTTCTCTT
*
25048206 TCTTTCCTCAT
1 TCTTT-CTCTT
*
25048217 TCTTTCCCTT
1 TCTTTCTCTT
25048227 TCTT
1 TCTT
25048231 CTTCCCTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
8 9 0.18
9 13 0.26
10 17 0.34
11 11 0.22
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (10 bp):
TCTTTCTCTT
Found at i:25048190 original size:4 final size:4
Alignment explanation
Indices: 25048160--25048211 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
25048150 GAACCCCCTC
* *
25048160 TCTT TCTCT TCTCT TCCTT TTTT TCTT TCTT TCTC TC-T TCTT TCTT TCTT
1 TCTT TCT-T TCT-T T-CTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
25048210 TC
1 TC
25048212 CTCATTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 28 0.68
5 9 0.22
6 2 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:25048201 original size:27 final size:27
Alignment explanation
Indices: 25048160--25048211 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
25048150 GAACCCCCTC
*
25048160 TCTTTCTCTTCTCTTCCTTTTTTTCTT
1 TCTTTCTCTTCTCTTCCTTTCTTTCTT
*
25048187 TCTTTCTC-TCTTCTTTCTTTCTTTC
1 TCTTTCTCTTC-TCTTCCTTTCTTTC
25048212 CTCATTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTTCTCTTCTCTTCCTTTCTTTCTT
Found at i:25048202 original size:15 final size:15
Alignment explanation
Indices: 25048182--25048222 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25048172 CTTCCTTTTT
25048182 TTCTTTCTTTCTCTC
1 TTCTTTCTTTCTCTC
*
25048197 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTCTC
* *
25048212 CTCATTCTTTC
1 TTCTTTCTTTC
25048223 CCTTTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTTTCTTTCTCTC
Found at i:25048202 original size:23 final size:23
Alignment explanation
Indices: 25048160--25048230 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
25048150 GAACCCCCTC
*
25048160 TCTTTCTCTTCTCTTCCTTTTTT
1 TCTTTCTCTTCTCTTCCTTTCTT
*
25048183 TCTTTCT-TTCTCTCTTCTTTCTT
1 TCTTTCTCTTCTCT-TCCTTTCTT
25048206 TCTTTCCTCATTCT-TTCCCTTTCTT
1 TCTTT-CTC-TTCTCTT-CCTTTCTT
25048231 CTTCCCTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 6 0.15
23 19 0.47
24 3 0.08
25 8 0.20
26 4 0.10
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (23 bp):
TCTTTCTCTTCTCTTCCTTTCTT
Found at i:25048203 original size:19 final size:18
Alignment explanation
Indices: 25048156--25048222 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 18
25048146 GTTCGAACCC
25048156 CCTC-TCTTTCTCTTCTCTT
1 CCTCTTCTTTCT-TTCT-TT
*
25048175 CCT-TTTTTTCTTTCTTT
1 CCTCTTCTTTCTTTCTTT
25048192 CTCTCTTCTTTCTTTCTTT
1 C-CTCTTCTTTCTTTCTTT
25048211 CCTCATTCTTTC
1 CCTC-TTCTTTC
25048223 CCTTTCTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.07
18 9 0.21
19 30 0.71
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.64
Consensus pattern (18 bp):
CCTCTTCTTTCTTTCTTT
Found at i:25048238 original size:24 final size:25
Alignment explanation
Indices: 25048199--25048248 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
25048189 TTTCTCTCTT
*
25048199 CTTTCTTTCTTTCCTCATTCTTTCC
1 CTTTCTTTCTTCCCTCATTCTTTCC
* *
25048224 CTTTC-TTCTTCCCTCTTTTTTTCC
1 CTTTCTTTCTTCCCTCATTCTTTCC
25048248 C
1 C
25048249 CCATTTCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (25 bp):
CTTTCTTTCTTCCCTCATTCTTTCC
Found at i:25048471 original size:21 final size:21
Alignment explanation
Indices: 25048431--25048471 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25048421 ACTGTACTCA
*
25048431 GAGGTTCGACAGTCTTGATGC
1 GAGGTTCGACAGTCTCGATGC
25048452 GAGGTTCGACAG-CATCGATG
1 GAGGTTCGACAGTC-TCGATG
25048472 AGACTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (21 bp):
GAGGTTCGACAGTCTCGATGC
Found at i:25051872 original size:389 final size:388
Alignment explanation
Indices: 25051148--25051913 Score: 1108
Period size: 389 Copynumber: 2.0 Consensus size: 388
25051138 AAGAGATTTT
* *
25051148 AATTAACCAACCTAAAGTTAGTTGTTCTTAGTCTCGAGAGAGATATTAACATAAATTAGGGATTT
1 AATTAACCAACCTAAAGTCAGTTGTTCTTAGTCTCGAGAGAGATATTAACATAAATCAGGGATTT
* * *
25051213 TTACGAATTAAGTTAAGTGAATAAATTGTCTAATTCAGAAGTACTAAGTGAAGTCTAGGTGAATT
66 ATACGAATTAAGTCAAGTGAATAAATCGTCTAATTCAGAAGTACTAAGTGAAGTCTAGGTGAATT
* * ** * * * *
25051278 TTTCCTTGGGTATTGTCTTCTCCATCTGTTTCTCCCAAAGTATTTTCCAAACTTCATCTTTGTTG
131 GTTCCTTGGGTATTGTCTTCTCCATCGGTTTCTCAAAAAGTATTTTCCAAACTTAATCTCTATCG
* *
25051343 TAATATTAGTAAATTAGATAAATATTTTTAGTTTAAAAACACACTTTAATTCTTAGGCTAGATAA
196 TAATATTAGTAAATTAGATAAATAGTCTTAGTTTAAAAACACACTTTAATTCTTAGGCTAGATAA
* * * *
25051408 TAAAAAGATAGTAATTACTAGTACTTTTACTTCTCATGGATACGATATTTTCGGTCTCACCATAA
261 TAAAAAGATAGTAATTACTAGTACGTTTACTCCTCATGGATACGATATTTCCGGTCTAACCATAA
*
25051473 CTATACTACTGTTCGATAGGTGCGCTTGCCTTAAGTCAAATTTTTAGTTAGTTACACGATCATC
326 CTATACTACTGTTCGATAGGTGAGCTTGCCTT-AGTCAAATTTTTAGTTAGTTACACGATCATC
* * *
25051537 AATTAATCAACCTAGAGTCAGTTGTTTTTAGTCTCGAGAGAGATATTAACATAAATCAGGGATTT
1 AATTAACCAACCTAAAGTCAGTTGTTCTTAGTCTCGAGAGAGATATTAACATAAATCAGGGATTT
* * *
25051602 ATACGGATTAAGTCAAGTGAATAAATCGTCTAATTCAGAAGTGA-TAAGTGAAGTCTATGTGGAT
66 ATACGAATTAAGTCAAGTGAATAAATCGTCTAATTCAGAAGT-ACTAAGTGAAGTCTAGGTGAAT
*
25051666 TGTTCCTTGGGTATTGTCTTTTCCATCGGTTT-TCTAAAAAGTATTTTCC-AACTTTAATCTCTA
130 TGTTCCTTGGGTATTGTCTTCTCCATCGGTTTCTC-AAAAAGTATTTTCCAAAC-TTAATCTCTA
* * * * ** *
25051729 TCGTAATTTTAGTTAATTAGATAATTAGTCTTA-TTTTAAAACATTCTCTTAATTGTTAGGCTAG
193 TCGTAATATTAGTAAATTAGATAAATAGTCTTAGTTTAAAAACACACT-TTAATTCTTAGGCTAG
* **
25051793 ATAATAAAAAGATAGTAATTACTAGTACGTTTAGTCCTTGTGGATACGATATTTCCGGTCTAACC
257 ATAATAAAAAGATAGTAATTACTAGTACGTTTACTCCTCATGGATACGATATTTCCGGTCTAACC
* *
25051858 ATAACTATACTACTGTTCGATAGGTGATCTTGCCTTAGTCGAATTTTTAGTTAGTT
322 ATAACTATACTACTGTTCGATAGGTGAGCTTGCCTTAGTCAAATTTTTAGTTAGTT
25051914 TAGCGACCAT
Statistics
Matches: 334, Mismatches: 39, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
388 35 0.10
389 298 0.89
390 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (388 bp):
AATTAACCAACCTAAAGTCAGTTGTTCTTAGTCTCGAGAGAGATATTAACATAAATCAGGGATTT
ATACGAATTAAGTCAAGTGAATAAATCGTCTAATTCAGAAGTACTAAGTGAAGTCTAGGTGAATT
GTTCCTTGGGTATTGTCTTCTCCATCGGTTTCTCAAAAAGTATTTTCCAAACTTAATCTCTATCG
TAATATTAGTAAATTAGATAAATAGTCTTAGTTTAAAAACACACTTTAATTCTTAGGCTAGATAA
TAAAAAGATAGTAATTACTAGTACGTTTACTCCTCATGGATACGATATTTCCGGTCTAACCATAA
CTATACTACTGTTCGATAGGTGAGCTTGCCTTAGTCAAATTTTTAGTTAGTTACACGATCATC
Found at i:25055409 original size:10 final size:10
Alignment explanation
Indices: 25055385--25055454 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
25055375 CTTGCTCTCC
25055385 TTCTCTTCTTCT
1 TTCT-TTCTT-T
25055397 TTCTTTCTTT
1 TTCTTTCTTT
*
25055407 TTCTTTCCTT
1 TTCTTTCTTT
**
25055417 CCCTTTC-TT
1 TTCTTTCTTT
*
25055426 TTCTTTCCTTC
1 TTCTTT-CTTT
*
25055437 CTCTTTCTTT
1 TTCTTTCTTT
*
25055447 TCCTTTCT
1 TTCTTTCT
25055455 CCCCTCTTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 6 0.13
10 25 0.54
11 11 0.24
12 4 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:25055422 original size:20 final size:20
Alignment explanation
Indices: 25055399--25055471 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
25055389 CTTCTTCTTT
25055399 CTTTCTTTTTCTTTCCTTCC
1 CTTTCTTTTTCTTTCCTTCC
25055419 CTTTC-TTTTCTTTCCTTCC
1 CTTTCTTTTTCTTTCCTTCC
* *
25055438 TCTTTCTTTTCCTTT-CTCCC
1 -CTTTCTTTTTCTTTCCTTCC
*
25055458 CTCTTCTCTTTCTT
1 CT-TTCTTTTTCTT
25055472 CCTCATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.35
20 23 0.50
21 7 0.15
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
CTTTCTTTTTCTTTCCTTCC
Found at i:25055474 original size:40 final size:39
Alignment explanation
Indices: 25055384--25055474 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
25055374 CCTTGCTCTC
* *
25055384 CTTCTC-TTCTT-CTTTCTTTCTTTTTCTTTCCTTCCCT
1 CTTCTCTTTCTTCCTTTCTTTCTTTTCCTTTCCTCCCCT
25055421 -TTCT-TTTCTTTCCTTCCTCTTTCTTTTCCTTT-CTCCCCT
1 CTTCTCTTTC-TTCCTT--TCTTTCTTTTCCTTTCCTCCCCT
25055460 CTTCTCTTTCTTCCT
1 CTTCTCTTTCTTCCT
25055475 CATTTTTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
36 7 0.16
37 2 0.04
38 3 0.07
39 6 0.13
40 23 0.51
41 4 0.09
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (39 bp):
CTTCTCTTTCTTCCTTTCTTTCTTTTCCTTTCCTCCCCT
Found at i:25055691 original size:10 final size:10
Alignment explanation
Indices: 25055676--25055725 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
25055666 CCTTTTACCC
25055676 TTTATTTTTA
1 TTTATTTTTA
25055686 TTTA--TTTA
1 TTTATTTTTA
25055694 TTTATTTTTA
1 TTTATTTTTA
* * *
25055704 ATTATTATTC
1 TTTATTTTTA
*
25055714 TTTATTATTA
1 TTTATTTTTA
25055724 TT
1 TT
25055726 ATTACTGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:25055695 original size:14 final size:15
Alignment explanation
Indices: 25055676--25055728 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 15
25055666 CCTTTTACCC
25055676 TTTATTT-TTATTTA
1 TTTATTTATTATTTA
25055690 TTTATTTATT-TTTA
1 TTTATTTATTATTTA
* *
25055704 ATTA-TTATTCTTTA
1 TTTATTTATTATTTA
25055718 -TTA-TTATTATT
1 TTTATTTATTATT
25055729 ACTGTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 15 0.43
14 18 0.51
15 2 0.06
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:25055712 original size:3 final size:3
Alignment explanation
Indices: 25055704--25055784 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
25055694 TTTATTTTTA
* * *
25055704 ATT ATT ATT CTTT ATT ATT ATT ATT ACT GTT ATT ATT CATT A-T ATTT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT A-TT
* *
25055751 GTT ATT AATT ATT ATT ATT ATT ATG ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
25055785 CCTTTATTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.03
3 52 0.83
4 9 0.14
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:25055737 original size:38 final size:38
Alignment explanation
Indices: 25055695--25055767 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
25055685 ATTTATTTAT
*
25055695 TTATTTTTAATTATTATTCT-TTATT-ATTATTATTACTG
1 TTATTATTAATTA-TATT-TGTTATTAATTATTATTACTG
*
25055733 TTATTATTCATTATATTTGTTATTAATTATTATTA
1 TTATTATTAATTATATTTGTTATTAATTATTATTA
25055768 TTATTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 9 0.29
38 21 0.68
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (38 bp):
TTATTATTAATTATATTTGTTATTAATTATTATTACTG
Found at i:25072097 original size:13 final size:13
Alignment explanation
Indices: 25072079--25072105 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25072069 TAATGTTTCA
25072079 AGTAAAAGGATCG
1 AGTAAAAGGATCG
25072092 AGTAAAAGGATCG
1 AGTAAAAGGATCG
25072105 A
1 A
25072106 CTAGTCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.30, T:0.15
Consensus pattern (13 bp):
AGTAAAAGGATCG
Found at i:25082315 original size:45 final size:45
Alignment explanation
Indices: 25082266--25082363 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
25082256 TATGCCATAG
* * *
25082266 TCTTACTCAT-TTATTTCATGATGCCATAACATCTTAT-AGCTATGA
1 TCTTACTCATCTT-TATCATAATACCATAACATCTT-TCAGCTATGA
* * *
25082311 TCTTACTCATCTTTATCATAATACCATAGCATCTTTCAGTTATGG
1 TCTTACTCATCTTTATCATAATACCATAACATCTTTCAGCTATGA
25082356 TCTTACTC
1 TCTTACTC
25082364 GTTTTAGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.02
45 42 0.93
46 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (45 bp):
TCTTACTCATCTTTATCATAATACCATAACATCTTTCAGCTATGA
Found at i:25084796 original size:28 final size:28
Alignment explanation
Indices: 25084751--25084819 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
25084741 CTTAAAACCC
*
25084751 TAGGGGT-ATATCGGTAATTTTACTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
*
25084778 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
25084806 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
25084820 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTACTCTT
Found at i:25086672 original size:19 final size:18
Alignment explanation
Indices: 25086635--25086678 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25086625 ATACATACAG
25086635 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
25086652 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
25086671 TACTAATT
1 TAATAATT
25086679 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:25088588 original size:19 final size:18
Alignment explanation
Indices: 25088551--25088594 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25088541 ATACATACAG
25088551 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
25088568 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
25088587 TACTAATT
1 TAATAATT
25088595 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:25090507 original size:19 final size:18
Alignment explanation
Indices: 25090470--25090513 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25090460 ATACATACAG
25090470 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
25090487 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
25090506 TACTAATT
1 TAATAATT
25090514 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:25092922 original size:28 final size:28
Alignment explanation
Indices: 25092877--25092945 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
25092867 CTTAAAACCC
* *
25092877 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
25092904 TAGGGGTAATTTCGGTAATTTTACTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
25092932 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
25092946 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTACTCTT
Found at i:25094801 original size:19 final size:18
Alignment explanation
Indices: 25094764--25094807 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25094754 ATACATACAG
25094764 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
25094781 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
25094800 TACTAATT
1 TAATAATT
25094808 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Done.