Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 108 of 130
Found at i:21080110 original size:19 final size:18
Alignment explanation
Indices: 21080069--21080111 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
21080059 ATAAAAACAA
*
21080069 ATATA-TATTTATTTATT
1 ATATATTATTTATTTAAT
*
21080086 AAATATTATCTTATTTAAT
1 ATATATTAT-TTATTTAAT
21080105 ATATATT
1 ATATATT
21080112 TAACAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 14 0.67
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATATTATTTATTTAAT
Found at i:21081351 original size:22 final size:23
Alignment explanation
Indices: 21081326--21081370 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
21081316 TAGAAATAAA
*
21081326 AAAATTTTAAATAT-TAAATTTT
1 AAAATTTCAAATATATAAATTTT
*
21081348 AAAATTTCAAATATATTAATTTT
1 AAAATTTCAAATATATAAATTTT
21081371 TACCTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATTTCAAATATATAAATTTT
Found at i:21082082 original size:31 final size:31
Alignment explanation
Indices: 21082024--21082119 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
21082014 TATTATAATA
* *
21082024 TTATTTATATATTATATTAATAGTATATTAT
1 TTATTAATATATTATATTAATAATATATTAT
*
21082055 TTATTAATAATATTAT-TTAGTAATATATTAT
1 TTATTAAT-ATATTATATTAATAATATATTAT
* *
21082086 AATATT-ATTTATT-TATTAAT-ATAATATTAT
1 -TTATTAATATATTATATTAATAAT-ATATTAT
21082116 TTAT
1 TTAT
21082120 AAGTAAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 6 0.11
30 15 0.28
31 22 0.41
32 11 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
TTATTAATATATTATATTAATAATATATTAT
Found at i:21082085 original size:27 final size:28
Alignment explanation
Indices: 21082021--21082114 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 28
21082011 ATTTATTATA
*
21082021 ATATTATTTAT-ATATTATATTAATAGT-AT
1 ATATTATTAATAATATT-TATT--TAGTAAT
21082050 ATTATTTATTAATAATA-TTATTTAGTAAT
1 A-TA-TTATTAATAATATTTATTTAGTAAT
* *
21082079 ATATTA-TAATATTATTTATTTATTAAT
1 ATATTATTAATAATATTTATTTAGTAAT
*
21082106 ATAATATTA
1 ATATTATTA
21082115 TTTATAAGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
26 7 0.13
27 19 0.35
28 8 0.15
29 4 0.07
30 6 0.11
31 8 0.15
32 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTATTAATAATATTTATTTAGTAAT
Found at i:21082144 original size:61 final size:65
Alignment explanation
Indices: 21082014--21082145 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 65
21082004 TAAAACTATT
* * * *
21082014 TATTATAATATTATTTATATATTATATTAATAGTATATTATTTATTAATAATATTATTTAGTAAT
1 TATTATAATATTATTTATATATTATATTAATAG-ATATTATTTATTAATAAAATTATCTAGAAAA
21082079 A
65 A
*
21082080 TATTATAATATTATTTATTTATTA-A-T-ATA-ATATTATTTA-TAAGTAAAATTATACTA-AAA
1 TATTATAATATTATTTATATATTATATTAATAGATATTATTTATTAA-TAAAATTAT-CTAGAAA
21082139 AA
64 AA
21082141 TATTA
1 TATTA
21082146 ATAAATAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
60 3 0.05
61 26 0.44
62 2 0.03
63 3 0.05
64 1 0.02
65 1 0.02
66 23 0.39
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (65 bp):
TATTATAATATTATTTATATATTATATTAATAGATATTATTTATTAATAAAATTATCTAGAAAAA
Found at i:21084911 original size:17 final size:16
Alignment explanation
Indices: 21084889--21084928 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21084879 TATTTAACAA
21084889 AAAATACAACAAAAATT
1 AAAATA-AACAAAAATT
**
21084906 AAAATAATTAAAAATT
1 AAAATAAACAAAAATT
21084922 AAAATAA
1 AAAATAA
21084929 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAAACAAAAATT
Found at i:21084920 original size:16 final size:16
Alignment explanation
Indices: 21084899--21084929 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21084889 AAAATACAAC
21084899 AAAAATTAAAATAATT
1 AAAAATTAAAATAATT
21084915 AAAAATTAAAATAAT
1 AAAAATTAAAATAAT
21084930 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAATAATT
Found at i:21087884 original size:51 final size:51
Alignment explanation
Indices: 21087772--21087871 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
21087762 TAAAAAGTAT
* *
21087772 TAAAATTAT-TTTATATCAAATAATATTTTTGTTAATAAGTTGAAAATTAG
1 TAAAATTATATTTATATCAAATAATATTTTTATTAATAAATTGAAAATTAG
* *
21087822 TAAAATTATATTTATATCAAATAATATTTTTATTATTAAATTGAGAATTA
1 TAAAATTATATTTATATCAAATAATATTTTTATTAATAAATTGAAAATTA
21087872 ATGTGTATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 9 0.20
51 36 0.80
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (51 bp):
TAAAATTATATTTATATCAAATAATATTTTTATTAATAAATTGAAAATTAG
Found at i:21089657 original size:11 final size:12
Alignment explanation
Indices: 21089646--21089676 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21089636 GTTCTTTTTT
21089646 ATTTTTTATTTA
1 ATTTTTTATTTA
*
21089658 AATTTTTATTTA
1 ATTTTTTATTTA
21089670 ATTTTTT
1 ATTTTTT
21089677 TTACTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTTATTTA
Found at i:21091296 original size:2 final size:2
Alignment explanation
Indices: 21091289--21091317 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21091279 CCATAAACAA
21091289 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21091318 AAGCCAAAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21091965 original size:33 final size:33
Alignment explanation
Indices: 21091928--21092016 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
21091918 TTGATGTTGA
* *
21091928 AATAAAACTAATAA-TTAAAAATATATAAAATAT
1 AATAAAA-TAATAAGATAAAAATATAAAAAATAT
*
21091961 AATAAAATAATAAGATAATAATATAAAAAATAT
1 AATAAAATAATAAGATAAAAATATAAAAAATAT
* *
21091994 AATGAAAATAAAAAAATAAAAAT
1 AAT-AAAATAATAAGATAAAAAT
21092017 CTCCAAGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.12
33 26 0.54
34 16 0.33
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (33 bp):
AATAAAATAATAAGATAAAAATATAAAAAATAT
Found at i:21091972 original size:8 final size:8
Alignment explanation
Indices: 21091945--21092012 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
21091935 CTAATAATTA
21091945 AAAATATAT
1 AAAATA-AT
21091954 AAAATATAAT
1 -AAA-ATAAT
21091964 AAAATAAT
1 AAAATAAT
*
21091972 AAGATAAT
1 AAAATAAT
* *
21091980 AATATAAA
1 AAAATAAT
21091988 AAATATAAT
1 AAA-ATAAT
*
21091997 GAAAATAAA
1 -AAAATAAT
21092006 AAAATAA
1 AAAATAA
21092013 AAATCTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
8 27 0.55
9 11 0.22
10 8 0.16
11 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:21092001 original size:11 final size:10
Alignment explanation
Indices: 21091945--21092011 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 10
21091935 CTAATAATTA
21091945 AAAATAT-AT
1 AAAATATAAT
21091954 AAAATATAAT
1 AAAATATAAT
21091964 AAAATAATAAGAT
1 AAAAT-AT-A-AT
21091977 AATAATATAA-
1 AA-AATATAAT
21091987 AAAATATAAT
1 AAAATATAAT
21091997 GAAAATA-AA-
1 -AAAATATAAT
21092006 AAAATA
1 AAAATA
21092012 AAAATCTCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
8 6 0.12
9 14 0.27
10 11 0.22
11 9 0.18
12 2 0.04
13 6 0.12
14 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AAAATATAAT
Found at i:21094292 original size:37 final size:37
Alignment explanation
Indices: 21094213--21094295 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
21094203 GGGAAAGAAT
* * * * * *
21094213 ATAAAATGTAAAATATTTTTATTTCATATTATTACAT
1 ATAAAATTTAAAATATATTTACTTAATATTATAACAA
*
21094250 GTAAAATTTAAAATATATTTACTTAATATTATAACAA
1 ATAAAATTTAAAATATATTTACTTAATATTATAACAA
21094287 ATAAAATTT
1 ATAAAATTT
21094296 GTTCAAGGGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (37 bp):
ATAAAATTTAAAATATATTTACTTAATATTATAACAA
Found at i:21094692 original size:33 final size:32
Alignment explanation
Indices: 21094645--21094930 Score: 252
Period size: 33 Copynumber: 8.8 Consensus size: 32
21094635 AAAAAAAAAA
** *
21094645 AAATTTAAAACCAGTTTATCTAGCCATTAATG
1 AAATTTAAGCCCAGTTTATCTGGCCATTAATG
21094677 AAACTTTAAGCCCAGTTTATCTGGCCATTAATG
1 AAA-TTTAAGCCCAGTTTATCTGGCCATTAATG
* ** * *
21094710 AAGCTTTAAGGGCAGTTTATCTGGTCATCAATG
1 AA-ATTTAAGCCCAGTTTATCTGGCCATTAATG
* * * *
21094743 ACATTTAAGCCCAGTTTATTTGGTCATTAATA
1 AAATTTAAGCCCAGTTTATCTGGCCATTAATG
* * *
21094775 AAATTTTAAGCCCAATTTATTTGGCCATCAATG
1 AAA-TTTAAGCCCAGTTTATCTGGCCATTAATG
*
21094808 AAATTTAAGCCCAGTTTATTTGGCCATTAATG
1 AAATTTAAGCCCAGTTTATCTGGCCATTAATG
* * * *
21094840 AAGTTTTAAGCCCAATTTATCTCGCC-TCAAATG
1 AA-ATTTAAGCCCAGTTTATCTGGCCAT-TAATG
** * * *
21094873 AGGTTTTAAGCTCAGTTTAGCTGGCC-TTCAATA
1 A-AATTTAAGCCCAGTTTATCTGGCCATT-AATG
* *
21094906 AAATTTAAGCCTAGTTTATTTGGCC
1 AAATTTAAGCCCAGTTTATCTGGCC
21094931 CCAAAAGAAG
Statistics
Matches: 207, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
32 77 0.37
33 130 0.63
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (32 bp):
AAATTTAAGCCCAGTTTATCTGGCCATTAATG
Found at i:21094771 original size:65 final size:65
Alignment explanation
Indices: 21094655--21094930 Score: 279
Period size: 65 Copynumber: 4.2 Consensus size: 65
21094645 AAATTTAAAA
* * * *
21094655 CCAGTTTATCTAGCCATTAATGAAACTTTAAGCCCAGTTTATCTGGCCATTAATGAAGCTTTAAG
1 CCAGTTTATCTGGCCATCAATGAAA-TTTAAGCCCAGTTTATTTGGCCATTAATGAAGTTTTAAG
*
21094720 G
65 C
* * * * * *
21094721 GCAGTTTATCTGGTCATCAATGACATTTAAGCCCAGTTTATTTGGTCATTAATAAAATTTTAAGC
1 CCAGTTTATCTGGCCATCAATGAAATTTAAGCCCAGTTTATTTGGCCATTAATGAAGTTTTAAGC
* *
21094786 CCAATTTATTTGGCCATCAATGAAATTTAAGCCCAGTTTATTTGGCCATTAATGAAGTTTTAAGC
1 CCAGTTTATCTGGCCATCAATGAAATTTAAGCCCAGTTTATTTGGCCATTAATGAAGTTTTAAGC
* * ** * ** **
21094851 CCAATTTATCTCGCC-TCAAATGAGGTTTTAAGCTCAGTTTAGCTGGCC-TTCAAT-AAAATTTA
1 CCAGTTTATCTGGCCATC-AATGA-AATTTAAGCCCAGTTTATTTGGCCATT-AATGAAGTTTTA
21094913 AGC
63 AGC
* *
21094916 CTAGTTTATTTGGCC
1 CCAGTTTATCTGGCC
21094931 CCAAAAGAAG
Statistics
Matches: 175, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
64 2 0.01
65 131 0.75
66 42 0.24
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (65 bp):
CCAGTTTATCTGGCCATCAATGAAATTTAAGCCCAGTTTATTTGGCCATTAATGAAGTTTTAAGC
Found at i:21094848 original size:98 final size:97
Alignment explanation
Indices: 21094655--21094930 Score: 270
Period size: 98 Copynumber: 2.8 Consensus size: 97
21094645 AAATTTAAAA
* * * * * *
21094655 CCAGTTTATCTAGCCATTAATGAAACTTTAAGCCCAGTTTATCTGGCCATTAATGAAGCTTTAAG
1 CCAGTTTATTTGGTCATTAATGAAATTTTAAGCCCAGTTTATCTGGCCATCAATGAA-ATTTAAG
** * *
21094720 GGCAGTTTATCTGGTCATCAATGACATTTAAGC
65 CCCAGTTTATTTGGCCATCAATGACATTTAAGC
* * *
21094753 CCAGTTTATTTGGTCATTAATAAAATTTTAAGCCCAATTTATTTGGCCATCAATGAAATTTAAGC
1 CCAGTTTATTTGGTCATTAATGAAATTTTAAGCCCAGTTTATCTGGCCATCAATGAAATTTAAGC
*
21094818 CCAGTTTATTTGGCCATTAATGA-AGTTTTAAGC
66 CCAGTTTATTTGGCCATCAATGACA--TTTAAGC
* * * ** * * * *
21094851 CCAATTTATCTCGCCTCA--AATGAGGTTTTAAGCTCAGTTTAGCTGGCCTTCAATAAAATTTAA
1 CCAGTTTAT-TTG-GTCATTAATGAAATTTTAAGCCCAGTTTATCTGGCCATCAATGAAATTTAA
*
21094914 GCCTAGTTTATTTGGCC
64 GCCCAGTTTATTTGGCC
21094931 CCAAAAGAAG
Statistics
Matches: 147, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
96 1 0.01
97 25 0.17
98 116 0.79
99 2 0.01
100 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (97 bp):
CCAGTTTATTTGGTCATTAATGAAATTTTAAGCCCAGTTTATCTGGCCATCAATGAAATTTAAGC
CCAGTTTATTTGGCCATCAATGACATTTAAGC
Found at i:21095203 original size:22 final size:22
Alignment explanation
Indices: 21095175--21095221 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
21095165 TTTGCACTTG
* *
21095175 CATAAGATATTTGCATTCGCAC
1 CATAAGAAATTCGCATTCGCAC
*
21095197 CATAAGAAATTCGCATTTGCAC
1 CATAAGAAATTCGCATTCGCAC
21095219 CAT
1 CAT
21095222 GACATCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (22 bp):
CATAAGAAATTCGCATTCGCAC
Found at i:21095570 original size:36 final size:36
Alignment explanation
Indices: 21095516--21095586 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
21095506 CATCTGGACA
21095516 TAATTTTGATTCGCGGTGTTATCCCAATCGATTCTT
1 TAATTTTGATTCGCGGTGTTATCCCAATCGATTCTT
* * *
21095552 TAATTTTGACTT-GTGGTGTTGTCCCAGTCGATTCT
1 TAATTTTGA-TTCGCGGTGTTATCCCAATCGATTCT
21095587 GTAAGACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (36 bp):
TAATTTTGATTCGCGGTGTTATCCCAATCGATTCTT
Found at i:21095605 original size:109 final size:109
Alignment explanation
Indices: 21095413--21095919 Score: 536
Period size: 109 Copynumber: 4.7 Consensus size: 109
21095403 TCATTAACTC
* ** * * * *
21095413 TGATTCGTGGTGTTATCCTGATCGATTCATT-ATTCTCGACTTGCGGTGTTGTTTCAGTCAATTC
1 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATT-TCGACTTACGGTGTTGTCTCAGTCGATTC
* *
21095477 TGTAAGACCTCC-GAGCATGATTTCTAAGACATCTG-GACATAATTT
65 TGTAAGACCTCCGGA-CATGATTTCTAAGACCTCCGAG-CATAATTT
* ** *
21095522 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATTTTGACTTGTGGTGTTGTCCCAGTCGATTCT
1 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATTTCGACTTACGGTGTTGTCTCAGTCGATTCT
*
21095587 GTAAGACCTCCGGACATGATTTCTAAGACCTCCGATCATAATTT
66 GTAAGACCTCCGGACATGATTTCTAAGACCTCCGAGCATAATTT
* * * * *
21095631 TGATTCGCGGTGTTATCCCAATCAATTCTTTAATTTCGACTTATGGTGTTGTTTCAGTTGATTTT
1 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATTTCGACTTACGGTGTTGTCTCAGTCGATTCT
** * * * * *
21095696 GTAAGACCTTTGGACATAATTTTTAAGATCTCTGGGCATAATTT
66 GTAAGACCTCCGGACATGATTTCTAAGACCTCCGAGCATAATTT
* * * * * * * *
21095740 CGATTCACGATGTTATCCCAATCAATTCATT-ATTCTCGACTTACGTTGTTATCTCAGTCAATTC
1 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATT-TCGACTTACGGTGTTGTCTCAGTCGATTC
* * * * * *
21095804 TATAAAACCTTCGGGCATGATTTTTAAGACCTCCGAGTATAATTT
65 TGTAAGACCTCCGGACATGATTTCTAAGACCTCCGAGCATAATTT
* ** * * *
21095849 CGATTCGCGGTGTTATCCTGATCGATTCTTTAATTTCGACTTACGGTGTTATCCCAATCGATTCT
1 TGATTCGCGGTGTTATCCCAATCGATTCTTTAATTTCGACTTACGGTGTTGTCTCAGTCGATTCT
21095914 GTAAGA
66 GTAAGA
21095920 TCTTCAGGCA
Statistics
Matches: 334, Mismatches: 59, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
108 3 0.01
109 323 0.97
110 8 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (109 bp):
TGATTCGCGGTGTTATCCCAATCGATTCTTTAATTTCGACTTACGGTGTTGTCTCAGTCGATTCT
GTAAGACCTCCGGACATGATTTCTAAGACCTCCGAGCATAATTT
Found at i:21095630 original size:22 final size:22
Alignment explanation
Indices: 21095588--21095630 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21095578 GTCGATTCTG
*
21095588 TAAGACCTCCGGACATGATTTC
1 TAAGACCTCCGGACATAATTTC
21095610 TAAGACCTCC-GATCATAATTT
1 TAAGACCTCCGGA-CATAATTT
21095631 TGATTCGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCGGACATAATTTC
Found at i:21095723 original size:22 final size:23
Alignment explanation
Indices: 21095691--21095739 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
21095681 GTTTCAGTTG
*
21095691 ATTTTGTAAGACCTTTGGACATA
1 ATTTTGTAAGACCTCTGGACATA
* *
21095714 ATTTT-TAAGATCTCTGGGCATA
1 ATTTTGTAAGACCTCTGGACATA
21095736 ATTT
1 ATTT
21095740 CGATTCACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (23 bp):
ATTTTGTAAGACCTCTGGACATA
Found at i:21095896 original size:36 final size:36
Alignment explanation
Indices: 21095843--21095913 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
21095833 CCTCCGAGTA
* **
21095843 TAATTTCGATTCGCGGTGTTATCCTGATCGATTCTT
1 TAATTTCGATTCACGGTGTTATCCCAATCGATTCTT
21095879 TAATTTCGACTT-ACGGTGTTATCCCAATCGATTCT
1 TAATTTCGA-TTCACGGTGTTATCCCAATCGATTCT
21095914 GTAAGATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (36 bp):
TAATTTCGATTCACGGTGTTATCCCAATCGATTCTT
Found at i:21095919 original size:218 final size:218
Alignment explanation
Indices: 21095414--21095936 Score: 599
Period size: 218 Copynumber: 2.4 Consensus size: 218
21095404 CATTAACTCT
* * * *
21095414 GATTCGTGGTGTTATCCTGATCGATTCATT-ATTCTCGACTTGCGGTGTTGTTTCAGTCAATTCT
1 GATTCGCGGTGTTATCCTGATCGATTCTTTAATT-TCGACTTACGGTGTTGTTTCAGTCGATTCT
** * * * * *
21095478 GTAAGACC-TCCGAGCATGATTTCTAAGACATCTGGACATAATTTTGATTCGCGGTGTTATCCCA
65 GTAAGACCTTAGGA-CATAATTTTTAAGACATCTGGACATAATTTCGATTCACGATGTTATCCCA
* * * ** * * * *
21095542 ATCGATTCTTTAATTTTGACTTGTGGTGTTGTCCCAGTCGATTCTGTAAGACCTCCGGACATGAT
129 ATCAATTCATTAATTTCGACTTACGGTGTTATCCCAGTCAATTCTATAAAACCTCCGGACATGAT
*
21095607 TTCTAAGACCTCCGATCATAATTTT
194 TTCTAAGACCTCCGATCATAATTTC
** * * * *
21095632 GATTCGCGGTGTTATCCCAATCAATTCTTTAATTTCGACTTATGGTGTTGTTTCAGTTGATTTTG
1 GATTCGCGGTGTTATCCTGATCGATTCTTTAATTTCGACTTACGGTGTTGTTTCAGTCGATTCTG
* *
21095697 TAAGACCTTTGGACATAATTTTTAAGATC-TCTGGGCATAATTTCGATTCACGATGTTATCCCAA
66 TAAGACCTTAGGACATAATTTTTAAGA-CATCTGGACATAATTTCGATTCACGATGTTATCCCAA
* * * *
21095761 TCAATTCATT-ATTCTCGACTTACGTTGTTATCTCAGTCAATTCTATAAAACCTTCGGGCATGAT
130 TCAATTCATTAATT-TCGACTTACGGTGTTATCCCAGTCAATTCTATAAAACCTCCGGACATGAT
*
21095825 TTTTAAGACCTCCGAGT-ATAATTTC
194 TTCTAAGACCTCCGA-TCATAATTTC
* ** *
21095850 GATTCGCGGTGTTATCCTGATCGATTCTTTAATTTCGACTTACGGTGTTATCCCAATCGATTCTG
1 GATTCGCGGTGTTATCCTGATCGATTCTTTAATTTCGACTTACGGTGTTGTTTCAGTCGATTCTG
*
21095915 TAAGATCTTCAGG-CATAATTTT
66 TAAGACCTT-AGGACATAATTTT
21095937 GATTCGCAGT
Statistics
Matches: 254, Mismatches: 45, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
217 3 0.01
218 241 0.95
219 10 0.04
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (218 bp):
GATTCGCGGTGTTATCCTGATCGATTCTTTAATTTCGACTTACGGTGTTGTTTCAGTCGATTCTG
TAAGACCTTAGGACATAATTTTTAAGACATCTGGACATAATTTCGATTCACGATGTTATCCCAAT
CAATTCATTAATTTCGACTTACGGTGTTATCCCAGTCAATTCTATAAAACCTCCGGACATGATTT
CTAAGACCTCCGATCATAATTTC
Found at i:21095977 original size:87 final size:87
Alignment explanation
Indices: 21095828--21096095 Score: 276
Period size: 87 Copynumber: 3.1 Consensus size: 87
21095818 GCATGATTTT
* * * * * *
21095828 TAAGACCTCCGAGTATAATTTCGATTCGCGGTGTTA-TCCTGATCGATTCTT-TAATTTCGACTT
1 TAAGACTTCAGAGCATAATTTCGATTCGCAGTGTTATTCC-AATCGA-TCTTCTAATTTTGACTT
*
21095891 ACGGTGTTATCCCAATCGATTCTG
64 ACGGTGTTGTCCCAATCGATTCTG
* *
21095915 TAAGATCTTCAG-GCATAATTTTGATTCGCAGTGTTATTTCAATCGATCTTCTAATTTTGACTTA
1 TAAGA-CTTCAGAGCATAATTTCGATTCGCAGTGTTATTCCAATCGATCTTCTAATTTTGACTTA
* * ** *
21095979 CGGTATTGTTCCGGTTGATTCTG
65 CGGTGTTGTCCCAATCGATTCTG
* * * *
21096002 TAAGACTTCCGAGCATAATTTCGATTCGCAGTGTTGTCCCAATCGAT-TTCATATTTTTTGACTT
1 TAAGACTTCAGAGCATAATTTCGATTCGCAGTGTTATTCCAATCGATCTTC-TA-ATTTTGACTT
*
21096066 ACGGTGTTGTCCCAATCAAATT-TG
64 ACGGTGTTGTCCCAATC-GATTCTG
21096090 TAAGAC
1 TAAGAC
21096096 CTCCGAACAT
Statistics
Matches: 148, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
86 12 0.08
87 98 0.66
88 35 0.24
89 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (87 bp):
TAAGACTTCAGAGCATAATTTCGATTCGCAGTGTTATTCCAATCGATCTTCTAATTTTGACTTAC
GGTGTTGTCCCAATCGATTCTG
Found at i:21096424 original size:15 final size:15
Alignment explanation
Indices: 21096404--21096435 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21096394 GTTTAATTAA
21096404 AATTAAAAATTAATT
1 AATTAAAAATTAATT
*
21096419 AATTAAAAATTATTT
1 AATTAAAAATTAATT
21096434 AA
1 AA
21096436 AAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTAAAAATTAATT
Found at i:21097006 original size:12 final size:12
Alignment explanation
Indices: 21096983--21097016 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21096973 GACCATCGCT
*
21096983 GGCGGTGACCCA
1 GGCGGCGACCCA
*
21096995 GGTGGCGACCCA
1 GGCGGCGACCCA
21097007 GGCGGCGACC
1 GGCGGCGACC
21097017 AGCATGACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.44, T:0.06
Consensus pattern (12 bp):
GGCGGCGACCCA
Found at i:21097465 original size:23 final size:22
Alignment explanation
Indices: 21097439--21097493 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
21097429 TTATTATTTC
* *
21097439 AAGTTTTTATATTTATGCATGAT
1 AAGTTTTTAAATTTAT-CAGGAT
* * *
21097462 AAGTTCTTAAATTTGTTAGGAT
1 AAGTTTTTAAATTTATCAGGAT
21097484 AAGTTTTTAA
1 AAGTTTTTAA
21097494 TTGTTTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.49
Consensus pattern (22 bp):
AAGTTTTTAAATTTATCAGGAT
Found at i:21097568 original size:3 final size:3
Alignment explanation
Indices: 21097560--21097604 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
21097550 AAATGCTCAA
21097560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21097605 TTTTATCATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21097837 original size:16 final size:16
Alignment explanation
Indices: 21097816--21097914 Score: 80
Period size: 16 Copynumber: 6.4 Consensus size: 16
21097806 ACACTAATTA
21097816 TAAAATTCAAAACCCC
1 TAAAATTCAAAACCCC
* * *
21097832 TAAAATCCAAAATCCT
1 TAAAATTCAAAACCCC
* *
21097848 TTAAA-TCCAAACCCC
1 TAAAATTCAAAACCCC
*
21097863 -ATAAATTCGAAACCCC
1 TA-AAATTCAAAACCCC
* *
21097879 TAAAA-TCTAAACCCT
1 TAAAATTCAAAACCCC
*
21097894 TAAAATCCAAAA-CCC
1 TAAAATTCAAAACCCC
21097909 TAAAAT
1 TAAAAT
21097915 CTGAATATTC
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
15 30 0.47
16 33 0.52
17 1 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.21
Consensus pattern (16 bp):
TAAAATTCAAAACCCC
Found at i:21097860 original size:31 final size:31
Alignment explanation
Indices: 21097816--21097915 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
21097806 ACACTAATTA
* * *
21097816 TAAAATTCAAAACCCCTAAAATCCAAAATCCT
1 TAAAA-TCCAAACCCCTAAAATCCAAAACCCC
* * *
21097848 TTAAATCCAAACCCC-ATAAATTCGAAACCCC
1 TAAAATCCAAACCCCTA-AAATCCAAAACCCC
* *
21097879 TAAAATCTAAACCCTTAAAATCCAAAA-CCC
1 TAAAATCCAAACCCCTAAAATCCAAAACCCC
21097909 TAAAATC
1 TAAAATC
21097916 TGAATATTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
30 11 0.20
31 39 0.71
32 5 0.09
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (31 bp):
TAAAATCCAAACCCCTAAAATCCAAAACCCC
Found at i:21097882 original size:15 final size:15
Alignment explanation
Indices: 21097825--21097915 Score: 92
Period size: 15 Copynumber: 5.9 Consensus size: 15
21097815 ATAAAATTCA
21097825 AAACCCCTAAAATCC
1 AAACCCCTAAAATCC
* * *
21097840 AAAATCCTTTAAATCC
1 -AAACCCCTAAAATCC
* *
21097856 AAACCCCATAAATTCG
1 AAACCCC-TAAAATCC
*
21097872 AAACCCCTAAAATCT
1 AAACCCCTAAAATCC
*
21097887 AAACCCTTAAAATCC
1 AAACCCCTAAAATCC
*
21097902 AAAACCCTAAAATC
1 AAACCCCTAAAATC
21097916 TGAATATTCA
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
15 36 0.60
16 24 0.40
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (15 bp):
AAACCCCTAAAATCC
Found at i:21099471 original size:8 final size:8
Alignment explanation
Indices: 21099455--21099511 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
21099445 TATATTAAAC
21099455 AAATAAATA
1 AAAT-AATA
21099464 AAATAATA
1 AAATAATA
*
21099472 AGATAATA
1 AAATAATA
* *
21099480 ATATAAAA
1 AAATAATA
21099488 AATATAATGA
1 AA-ATAAT-A
*
21099498 AAATAAAA
1 AAATAATA
21099506 AAATAA
1 AAATAA
21099512 AAATGAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 25 0.62
9 12 0.30
10 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (8 bp):
AAATAATA
Found at i:21099516 original size:20 final size:20
Alignment explanation
Indices: 21099455--21099521 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
21099445 TATATTAAAC
21099455 AAATAAATAAAATAATAAGAT-A
1 AAATAAA-AAAATAA-AA-ATGA
*
21099477 ATAATATAAAAAAT-ATAATGA
1 A-AATA-AAAAAATAAAAATGA
21099498 AAATAAAAAAATAAAAATGA
1 AAATAAAAAAATAAAAATGA
21099518 AAAT
1 AAAT
21099522 CTCCAAGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.18
20 16 0.41
21 3 0.08
22 2 0.05
23 9 0.23
24 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAATAAAAAAATAAAAATGA
Found at i:21101157 original size:115 final size:115
Alignment explanation
Indices: 21100952--21101187 Score: 436
Period size: 115 Copynumber: 2.1 Consensus size: 115
21100942 ACTGTATTAA
*
21100952 TAGTTACATGATTAGACATCTAACAATGATCATTTGTATTTGAATTTTTATAAATTTAAATATTT
1 TAGTTGCATGATTAGACATCTAACAATGATCATTTGTATTTGAATTTTTATAAATTTAAATATTT
*
21101017 GTTTTCAACTGATAATTTTTTAGAAAGATAATGTTTTTGAATTATAAACG
66 GTTTTCAACTGATAATTTTTCAGAAAGATAATGTTTTTGAATTATAAACG
*
21101067 TAGTTGCATGATTAGACATCTAATAATGATCATTTGTATTTGAATTTTTATAAATTTAAATATTT
1 TAGTTGCATGATTAGACATCTAACAATGATCATTTGTATTTGAATTTTTATAAATTTAAATATTT
*
21101132 GTTTTCAACTGATAATTTTTCAGAAAGATAATGTTTTTGAATTATAAATG
66 GTTTTCAACTGATAATTTTTCAGAAAGATAATGTTTTTGAATTATAAACG
21101182 TAGTTG
1 TAGTTG
21101188 AAGGATGAAT
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 117 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (115 bp):
TAGTTGCATGATTAGACATCTAACAATGATCATTTGTATTTGAATTTTTATAAATTTAAATATTT
GTTTTCAACTGATAATTTTTCAGAAAGATAATGTTTTTGAATTATAAACG
Found at i:21101919 original size:37 final size:37
Alignment explanation
Indices: 21101840--21101922 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
21101830 GGGAAAGAAT
* * * *
21101840 ATAAAATGTAAAATATTTTTATTTCATATTATTAAAT
1 ATAAAATTTAAAATATATTTATTTAATATTATTAAAA
*
21101877 GTAAAATTTAAAATATATTTATTTAATATTA-TAACAA
1 ATAAAATTTAAAATATATTTATTTAATATTATTAA-AA
21101914 ATAAAATTT
1 ATAAAATTT
21101923 GTTCAAGGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.08
37 36 0.92
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (37 bp):
ATAAAATTTAAAATATATTTATTTAATATTATTAAAA
Found at i:21102222 original size:14 final size:15
Alignment explanation
Indices: 21102198--21102226 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21102188 CTCTTTCAAT
21102198 ATCACTTTTTTTTAA
1 ATCACTTTTTTTTAA
21102213 ATCA-TTTTTTTTAA
1 ATCACTTTTTTTTAA
21102227 TTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
ATCACTTTTTTTTAA
Found at i:21105622 original size:26 final size:26
Alignment explanation
Indices: 21105586--21105638 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
21105576 TTATTCTTAC
21105586 AAAATTATGTAAAACGAAAAACCTGT
1 AAAATTATGTAAAACGAAAAACCTGT
21105612 AAAATTATGTAAAACGAAAAACCTGT
1 AAAATTATGTAAAACGAAAAACCTGT
21105638 A
1 A
21105639 TTCTTTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (26 bp):
AAAATTATGTAAAACGAAAAACCTGT
Found at i:21106117 original size:18 final size:18
Alignment explanation
Indices: 21106094--21106128 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21106084 CCCTGGTCGG
21106094 ATCGGAGAGGGGAGTGGA
1 ATCGGAGAGGGGAGTGGA
*
21106112 ATCGGAGAGGTGAGTGG
1 ATCGGAGAGGGGAGTGG
21106129 GGCGAGTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.54, T:0.14
Consensus pattern (18 bp):
ATCGGAGAGGGGAGTGGA
Found at i:21107022 original size:15 final size:14
Alignment explanation
Indices: 21107002--21107031 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21106992 AAAATCGATA
21107002 TTAAATTTAAAATTT
1 TTAAATTT-AAATTT
21107017 TTAAATTTAAATTT
1 TTAAATTTAAATTT
21107031 T
1 T
21107032 AATAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTAAATTT
Found at i:21111798 original size:13 final size:14
Alignment explanation
Indices: 21111761--21111798 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21111751 TTTAATAGAG
21111761 TAAAGTAACTTTAA
1 TAAAGTAACTTTAA
*
21111775 TGAAGTAACTTT-A
1 TAAAGTAACTTTAA
*
21111788 TAAAATAACTT
1 TAAAGTAACTT
21111799 CGATAAAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (14 bp):
TAAAGTAACTTTAA
Found at i:21112517 original size:26 final size:26
Alignment explanation
Indices: 21112462--21112518 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
21112452 CACAGTTAGG
* *
21112462 CCCATTGACGTCCGGGCCCAAGTAAG
1 CCCATTGACGTCCGAGCCCAAGTAAA
**
21112488 CCCATTGGGGTCCGAGCCC-AGTTAAA
1 CCCATTGACGTCCGAGCCCAAG-TAAA
21112514 CCCAT
1 CCCAT
21112519 CCATGCCCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (26 bp):
CCCATTGACGTCCGAGCCCAAGTAAA
Found at i:21112559 original size:3 final size:3
Alignment explanation
Indices: 21112551--21112671 Score: 56
Period size: 3 Copynumber: 41.3 Consensus size: 3
21112541 AATTTTATTG
* * *
21112551 TAT TAT TAT TAT TAT TGT TAT TTT TAT TAA TA- TACT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * ** * * * *
21112594 TAT TTT TCT TCC T-T TAG TAT TTT TGT GTA- TAT TTAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT
* *
21112639 GAT T-T TTT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21112672 CTCCTTTCCT
Statistics
Matches: 90, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
2 11 0.12
3 74 0.82
4 5 0.06
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:21118619 original size:27 final size:27
Alignment explanation
Indices: 21118580--21118641 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
21118570 ATTTTCGTGA
*
21118580 AGTATGTGAATTATCTAGCAAGTAATCT
1 AGTA-GTGAATTATCTAGCAAGCAATCT
21118608 AGTAGTGAATTATCTAGCAAGCAATCT
1 AGTAGTGAATTATCTAGCAAGCAATCT
21118635 AGTAGTG
1 AGTAGTG
21118642 CCACACCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (27 bp):
AGTAGTGAATTATCTAGCAAGCAATCT
Found at i:21121602 original size:118 final size:119
Alignment explanation
Indices: 21121392--21122096 Score: 663
Period size: 119 Copynumber: 5.9 Consensus size: 119
21121382 CATTATTCAT
* * *
21121392 TCACTTGATCTTGGCTCAGTCCAGATTATTTTTTATGATTCATGG-TTCTATTCCCGATCATTTG
1 TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTC-A-TCTCGATCATTTG
** ** * * * * *
21121456 TTCTCGACCTTGACTCGATCCTAATCACTTTATTTCAACTTGTGATATCATCTTGG
64 TTCTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATGGTTTCATCTCGA
* *
21121512 TCACTTCATCTTGGCTCAGTCCAGATCATTTCTTATGATT-TTGGTTTCATCTCGATCATTTGTT
1 TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTGTT
*
21121576 CTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTCATGGTTTCATCTC-A
66 CTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATGGTTTCATCTCGA
* * ** * * * ** *
21121629 GTCACTTGATTTTGGCTTAGTTAAGATCATTTCTTATGATTTATGG-TTCTGTTTTAATCATTTA
1 -TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTC-ATCTCGATCATTTG
* * * * * * *
21121693 TTCTCGATCTTGACTC-AGTACTGATCATTTTATTTTAAGTTATGGTTTCAT-TCCAA
64 TTCTCGACCTTGACTCGA-TCCTGGTCACTTTATTTTGACTTATGGTTTCATCT-CGA
* * * **
21121749 TCACTTGATCTTGACTCAATCCAAATCATTTCTTATGATTCATGGTTTTGTCTCGATCATTT-TT
1 TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTGTT
*
21121813 CTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATAGTTTCATCTCGA
66 CTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATGGTTTCATCTCGA
* * * * * * * * * *
21121867 TCATTTGATTTTGGCTCAATCTAGATTATTTCTTCTGATTCATGATTTTATCCCGATCATGTGTT
1 TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTGTT
* *** * ** *
21121932 -TCCGACCTTGACTCGATCCTAGTTGTTTTATTTCGACTTATGGTTTTTTCCCGA
66 CT-CGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATGGTTTCATCTCGA
* * * * *
21121986 TCACTTGATCTTGGCTCAGTGCAAATCATTTTTTATCATTCATGGTTTCATCTCGATCATTTATT
1 TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTGTT
* * * * ** *
21122051 TTCAACCTTGGCTCGA-CCTTGGTCGCTACATTTTGACTTGTGGTTT
66 CTCGACCTTGACTCGATCC-TGGTCACTTTATTTTGACTTATGGTTT
21122097 GGTTCTAGTC
Statistics
Matches: 474, Mismatches: 97, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
118 195 0.41
119 235 0.50
120 44 0.09
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (119 bp):
TCACTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTGTT
CTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTATGGTTTCATCTCGA
Found at i:21121944 original size:237 final size:237
Alignment explanation
Indices: 21121392--21122089 Score: 752
Period size: 237 Copynumber: 2.9 Consensus size: 237
21121382 CATTATTCAT
* * *
21121392 TCACTTGATCTTGGCTCAGTCCAGATTATTTTTTATGATTCATGGTTCTATTCCCGATCATT-TG
1 TCACTTGATTTTGGCTCAGTCTAGATTATTTCTTATGATTCATGGTTCTA-TCCCGATCATTGT-
* * * * * * *
21121456 TTCTCGACCTTGACTCGATCCTAATCACTTTATTTCAACTTGTGATATCA-TCTTGGTCACTTCA
64 TTCTCGACCTTGACTCGATCCT-ATCATTTTATTTCAACTTATGGTTTCATTC-CGATCACTTGA
* * *
21121520 TCTTGGCTCAGTCCAGATCATTTCTTATGATT-TTGGTTTCATCTCGATCATTTGTTCTCGACCT
127 TCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTATTCTCGACCT
* *
21121584 TGACTCGATCCTGGTCACTTTATTTTGACTCATGGTTTCATCTCAG
192 TGACTCGATCCTGGTCACTTTATTTTGACTTATAGTTTCATCTCAG
* * * * ****
21121630 TCACTTGATTTTGGCTTAGT-TAAGATCATTTCTTATGATTTATGGTTCTGTTTTAATCATT-TA
1 TCACTTGATTTTGGCTCAGTCT-AGATTATTTCTTATGATTCATGGTTCTATCCCGATCATTGT-
* * * * *
21121693 TTCTCGATCTTGACTC-AGTACTGATCATTTTATTTTAAGTTATGGTTTCATTCCAATCACTTGA
64 TTCTCGACCTTGACTCGA-TCCT-ATCATTTTATTTCAACTTATGGTTTCATTCCGATCACTTGA
* * **
21121757 TCTTGACTCAATCCAAATCATTTCTTATGATTCATGGTTTTGTCTCGATCATTT-TTCTCGACCT
127 TCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTATTCTCGACCT
21121821 TGACTCGATCCTGGTCACTTTATTTTGACTTATAGTTTCATCTC-G
192 TGACTCGATCCTGGTCACTTTATTTTGACTTATAGTTTCATCTCAG
* * * * *
21121866 ATCATTTGATTTTGGCTCAATCTAGATTATTTCTTCTGATTCATGATTTTATCCCGATCATGTGT
1 -TCACTTGATTTTGGCTCAGTCTAGATTATTTCTTATGATTCATGGTTCTATCCCGATCAT-TGT
** * *
21121931 TTC-CGACCTTGACTCGATCCTAGTTGTTTTATTTCGACTTATGGTTT-TTTCCCGATCACTTGA
64 TTCTCGACCTTGACTCGATCCTA-TCATTTTATTTCAACTTATGGTTTCATT-CCGATCACTTGA
* * * * *
21121994 TCTTGGCTCAGTGCAAATCATTTTTTATCATTCATGGTTTCATCTCGATCATTTATTTTCAACCT
127 TCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTATTCTCGACCT
* * **
21122059 TGGCTCGA-CCTTGGTCGCTACATTTTGACTT
192 TGACTCGATCC-TGGTCACTTTATTTTGACTT
21122090 GTGGTTTGGT
Statistics
Matches: 379, Mismatches: 68, Indels: 26
0.80 0.14 0.05
Matches are distributed among these distances:
236 5 0.01
237 273 0.72
238 100 0.26
239 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (237 bp):
TCACTTGATTTTGGCTCAGTCTAGATTATTTCTTATGATTCATGGTTCTATCCCGATCATTGTTT
CTCGACCTTGACTCGATCCTATCATTTTATTTCAACTTATGGTTTCATTCCGATCACTTGATCTT
GGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTCATCTCGATCATTTATTCTCGACCTTGAC
TCGATCCTGGTCACTTTATTTTGACTTATAGTTTCATCTCAG
Found at i:21122440 original size:25 final size:25
Alignment explanation
Indices: 21122407--21122468 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
21122397 TCCGGGCACG
* * **
21122407 GTTAGGCCCATAATGTTCGGGCCCAA
1 GTTAAGCCCATAAGGTTCAAGCCC-A
21122433 G-TAAGCCCATTAAGGTTCAAGCCCA
1 GTTAAGCCCA-TAAGGTTCAAGCCCA
21122458 GTTAAGCCCAT
1 GTTAAGCCCAT
21122469 CCATGCTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (25 bp):
GTTAAGCCCATAAGGTTCAAGCCCA
Found at i:21122509 original size:3 final size:3
Alignment explanation
Indices: 21122501--21122631 Score: 103
Period size: 3 Copynumber: 44.3 Consensus size: 3
21122491 AATTTTATTG
* * *
21122501 TAT TAT TAT TAT TAT TGT TAT TTT TAT TAA TA- TACT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
21122544 TAT T-T TCCT TCT T-T TAG TAT TTT TAT GTA- TATT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TAT
* *
21122589 GAT TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21122632 CTCCTTTCCT
Statistics
Matches: 105, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
2 12 0.11
3 86 0.82
4 7 0.07
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21133122 original size:16 final size:16
Alignment explanation
Indices: 21133103--21133145 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
21133093 TTTTGGAGAT
21133103 TTTTTGTTTTGTTT-TG
1 TTTTT-TTTTGTTTGTG
21133119 TTTTCATTTTTGTTTGTG
1 TTTT--TTTTTGTTTGTG
21133137 TTTTTTTTT
1 TTTTTTTTT
21133146 ACACACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.38
17 8 0.33
18 7 0.29
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTGTTTGTG
Found at i:21133128 original size:22 final size:23
Alignment explanation
Indices: 21133103--21133145 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21133093 TTTTGGAGAT
21133103 TTTTTGTTT-TGTTTTGTTTTCA
1 TTTTTGTTTGTGTTTTGTTTTCA
*
21133125 TTTTTGTTTGTGTTTTTTTTT
1 TTTTTGTTTGTGTTTTGTTTT
21133146 ACACACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.81
Consensus pattern (23 bp):
TTTTTGTTTGTGTTTTGTTTTCA
Found at i:21139765 original size:14 final size:14
Alignment explanation
Indices: 21139743--21139782 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21139733 CACATTAAGC
21139743 TTTATTAAAGTTACT
1 TTTATTAAAGTTA-T
*
21139758 TTTA-TAAAATTAT
1 TTTATTAAAGTTAT
21139771 TTTATTAAAGTT
1 TTTATTAAAGTT
21139783 GCCTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTATTAAAGTTAT
Found at i:21141611 original size:15 final size:15
Alignment explanation
Indices: 21141591--21141620 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21141581 TCATAAGCAC
21141591 TCCTTAGCCACTAGG
1 TCCTTAGCCACTAGG
21141606 TCCTTAGCCACTAGG
1 TCCTTAGCCACTAGG
21141621 CCAAGGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (15 bp):
TCCTTAGCCACTAGG
Found at i:21157218 original size:15 final size:16
Alignment explanation
Indices: 21157188--21157221 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21157178 ACATTTTGAA
*
21157188 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
21157204 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
21157219 ATT
1 ATT
21157222 TTCAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:21157961 original size:22 final size:21
Alignment explanation
Indices: 21157936--21157985 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
21157926 AATATCTTGA
*
21157936 CTTTTTCCTTAACATTTGTTTT
1 CTTTTTCCTTAA-ATTGGTTTT
* *
21157958 CTTTCTCCTTCAATTGGTTTT
1 CTTTTTCCTTAAATTGGTTTT
21157979 CTCTTTT
1 CT-TTTT
21157986 GCCAACAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.10, C:0.22, G:0.06, T:0.62
Consensus pattern (21 bp):
CTTTTTCCTTAAATTGGTTTT
Found at i:21159841 original size:27 final size:26
Alignment explanation
Indices: 21159787--21159846 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
21159777 TTTTTTGTGC
*
21159787 ATAATATTATAATAGGATAAGATAAA
1 ATAATATTATAATAGGATAAAATAAA
* *
21159813 ATGATATTATAAATAGTATGAAAAT-AA
1 ATAATATTAT-AATAGGAT-AAAATAAA
21159840 ATAATAT
1 ATAATAT
21159847 CATTATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 9 0.32
27 15 0.54
28 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (26 bp):
ATAATATTATAATAGGATAAAATAAA
Found at i:21159930 original size:17 final size:17
Alignment explanation
Indices: 21159890--21159930 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
21159880 AAGATAAGAT
21159890 AATTTATTTATTTGATAA
1 AATTTATTTATTT-ATAA
21159908 AA-TTATTTATTCT-TAA
1 AATTTATTTATT-TATAA
21159924 AATTTAT
1 AATTTAT
21159931 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTATTTATTTATAA
Found at i:21160687 original size:12 final size:13
Alignment explanation
Indices: 21160670--21160716 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
21160660 ATATATATAT
21160670 ATTATTAT-TTTA
1 ATTATTATATTTA
21160682 ATTATT-TATTTA
1 ATTATTATATTTA
21160694 ATT-TTATATTTA
1 ATTATTATATTTA
*
21160706 TATTTTTATAT
1 -ATTATTATAT
21160717 ATTTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.10
12 19 0.61
13 3 0.10
14 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATATTTA
Found at i:21160723 original size:16 final size:16
Alignment explanation
Indices: 21160663--21160725 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
21160653 CAGACTTATA
21160663 TATATATATTATTATTTT
1 TATATAT-TTA-TATTTT
*
21160681 AAT-TATTTAT-TTAATT
1 TATATATTTATATT--TT
21160697 T-TATATTTATATTTT
1 TATATATTTATATTTT
21160712 TATATATTTATATT
1 TATATATTTATATT
21160726 AAAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 2 0.05
15 5 0.13
16 24 0.63
17 5 0.13
18 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATATTTATATTTT
Found at i:21160766 original size:21 final size:20
Alignment explanation
Indices: 21160713--21160760 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
21160703 TTATATTTTT
21160713 ATATATTTATA-TTAAAAATA
1 ATAT-TTTATATTTAAAAATA
21160733 ATATTTTATATTTAAAAA-A
1 ATATTTTATATTTAAAAATA
*
21160752 TTATTTTAT
1 ATATTTTAT
21160761 TAATTTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTATATTTAAAAATA
Found at i:21161267 original size:6 final size:6
Alignment explanation
Indices: 21161256--21161289 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
21161246 TCATAGTAGG
21161256 AATGGC AATGGC AATGGC AATGGC AATGGAC AAT
1 AATGGC AATGGC AATGGC AATGGC AATGG-C AAT
21161290 TATTCTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (6 bp):
AATGGC
Found at i:21164481 original size:18 final size:18
Alignment explanation
Indices: 21164458--21164494 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
21164448 TATTAAAGTC
21164458 ACTATTTAATAGGAATGT
1 ACTATTTAATAGGAATGT
21164476 ACTATTTAATAGGAATGT
1 ACTATTTAATAGGAATGT
21164494 A
1 A
21164495 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (18 bp):
ACTATTTAATAGGAATGT
Found at i:21166280 original size:36 final size:38
Alignment explanation
Indices: 21166209--21166282 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 38
21166199 AATAAATTTG
*
21166209 ACTAAAAACCAACTTTTTCTTTTTAAATCTAATTCAAT
1 ACTAAAAACCAACTTTTTCTTTTAAAATCTAATTCAAT
*
21166247 ACTAAAAACCATC-TTTT-TTTTAAAATCTAATTCAAT
1 ACTAAAAACCAACTTTTTCTTTTAAAATCTAATTCAAT
21166283 CCAAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 18 0.53
37 4 0.12
38 12 0.35
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.42
Consensus pattern (38 bp):
ACTAAAAACCAACTTTTTCTTTTAAAATCTAATTCAAT
Found at i:21166308 original size:18 final size:19
Alignment explanation
Indices: 21166285--21166322 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21166275 AATTCAATCC
*
21166285 AAAA-TTTAATTTTTTAAA
1 AAAATTTTAATTTTATAAA
21166303 AAAATTTTAATTTTATAAA
1 AAAATTTTAATTTTATAAA
21166322 A
1 A
21166323 TTAAATCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTTTAATTTTATAAA
Found at i:21166422 original size:143 final size:141
Alignment explanation
Indices: 21166247--21166519 Score: 465
Period size: 143 Copynumber: 1.9 Consensus size: 141
21166237 CTAATTCAAT
* *
21166247 ACTAAAAACCATCTTTTTTTTAAAATCTAATTCAATCCAAAATTTAATTTTTTAAAAAAATTTTA
1 ACTAAAAACCAACTTTTTTTTAAAATCTAATTCAATCCAAAATTTAAGTTTTTAAAAAAATTTTA
*
21166312 ATTTTATAAAATTAAATCAGATCAAAATTTGAGAGATTTAAATTAGATTATCAATAATAATAGCA
66 ATTTTATAAAATTAAATCAGATCAAAATTTGAGAGATTTAAATTAGATTATCAACAATAATAGCA
21166377 GAATAAATTTG
131 GAATAAATTTG
* * *
21166388 ACTAAAAACCAACTTTTTCTTTTTAAATCTAATTCAGTCCGAAATTTAAGTTTTTAAAAAAATTT
1 ACTAAAAACCAAC-TTTT-TTTTAAAATCTAATTCAATCCAAAATTTAAGTTTTTAAAAAAATTT
*
21166453 TAATTTTGTAAAATTAAATCAGATCAAAATTTGAGAGATTTAAATTAGATTATCAACAATAATAG
64 TAATTTTATAAAATTAAATCAGATCAAAATTTGAGAGATTTAAATTAGATTATCAACAATAATAG
21166518 CA
129 CA
21166520 ACACCGTATG
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
141 12 0.10
142 4 0.03
143 107 0.87
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (141 bp):
ACTAAAAACCAACTTTTTTTTAAAATCTAATTCAATCCAAAATTTAAGTTTTTAAAAAAATTTTA
ATTTTATAAAATTAAATCAGATCAAAATTTGAGAGATTTAAATTAGATTATCAACAATAATAGCA
GAATAAATTTG
Found at i:21167454 original size:14 final size:14
Alignment explanation
Indices: 21167435--21167462 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21167425 TCATGTCTTA
21167435 TATATATTTTTATT
1 TATATATTTTTATT
21167449 TATATATTTTTATT
1 TATATATTTTTATT
21167463 AGATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATATATTTTTATT
Found at i:21167606 original size:16 final size:16
Alignment explanation
Indices: 21167587--21167645 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
21167577 AAAAAAGCTA
21167587 AAAAAATAATTTTTTT
1 AAAAAATAATTTTTTT
* **
21167603 AAAAAATAAATTTTAA
1 AAAAAATAATTTTTTT
21167619 AAAAAAGTAATTTTTTTCT
1 AAAAAA-TAA-TTTTTT-T
21167638 AAAAAATA
1 AAAAAATA
21167646 CAGATATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 19 0.56
17 3 0.09
18 6 0.18
19 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAAATAATTTTTTT
Found at i:21169037 original size:2 final size:2
Alignment explanation
Indices: 21169030--21169056 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21169020 TCTTCTATCT
21169030 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21169057 TACATTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21171315 original size:16 final size:19
Alignment explanation
Indices: 21171294--21171342 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
21171284 TTTTATGTAT
21171294 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
21171311 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
21171329 TGTATATATTTATT
1 TGTAT-TATTTATT
21171343 TATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:21172567 original size:59 final size:59
Alignment explanation
Indices: 21172504--21172786 Score: 396
Period size: 59 Copynumber: 4.7 Consensus size: 59
21172494 AAAAATTCCA
* *
21172504 AAAAAATATATTTTTAGGGAAAAGTTGAAAGCATCAATTTTCCTTAG-AAATAAATTTTC
1 AAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTTC
21172563 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATAAATTTTC
21172625 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTTC
1 -AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTTC
* * *
21172684 AAAAAAAGGGA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAAA--TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTTC
21172745 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
21172787 CTACAAAAAA
Statistics
Matches: 204, Mismatches: 7, Indels: 25
0.86 0.03 0.11
Matches are distributed among these distances:
57 36 0.18
58 13 0.06
59 50 0.25
60 34 0.17
61 16 0.08
62 12 0.06
64 43 0.21
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTTC
Found at i:21172645 original size:121 final size:116
Alignment explanation
Indices: 21172496--21172786 Score: 415
Period size: 121 Copynumber: 2.4 Consensus size: 116
21172486 TAAAAATAAA
* * *
21172496 AAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGCATCAATTTTCCTTAGAAATAAATTT
1 AAATTTCAAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
* *
21172561 TCAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT-
65 TCAAAAAA-AGATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT----G-AAAATC
21172617 AAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
1 AAA-TTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
21172682 TCAAAAAAAGGGATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
65 TCAAAAAAA--GATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
*
21172736 GAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
21172787 CTACAAAAAA
Statistics
Matches: 158, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
118 5 0.03
119 47 0.30
120 4 0.03
121 59 0.37
122 10 0.06
123 33 0.21
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (116 bp):
AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
CAAAAAAAGATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
Found at i:21177907 original size:21 final size:21
Alignment explanation
Indices: 21177883--21177922 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21177873 TTCTATTGTT
*
21177883 AAATTTTAATTTTAATAATAA
1 AAATTTAAATTTTAATAATAA
*
21177904 AAATTTAAATTTTGATAAT
1 AAATTTAAATTTTAATAAT
21177923 TTTAAATATC
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTTAAATTTTAATAATAA
Found at i:21178385 original size:18 final size:18
Alignment explanation
Indices: 21178350--21178389 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21178340 CATTTTTTCT
*
21178350 TTAAATAAAAGTTTAATA
1 TTAAATAAAAGTTAAATA
21178368 TTAAATAAAA-TTAAAATA
1 TTAAATAAAAGTT-AAATA
21178386 TTAA
1 TTAA
21178390 CAATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAATAAAAGTTAAATA
Found at i:21180249 original size:36 final size:33
Alignment explanation
Indices: 21180201--21180269 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 33
21180191 AAAATGGTTT
* *
21180201 TTATTGGTTTGGTTATTGTTGCATTGTAATGTAGTA
1 TTATTGGGTTGGTT-TTGTTG-ATTG-AATCTAGTA
21180237 TTATTGGGTTGGTTTTGTTGATTGAATCTAGTA
1 TTATTGGGTTGGTTTTGTTGATTGAATCTAGTA
21180270 CACTCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 8 0.26
34 4 0.13
35 6 0.19
36 13 0.42
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.52
Consensus pattern (33 bp):
TTATTGGGTTGGTTTTGTTGATTGAATCTAGTA
Found at i:21182752 original size:12 final size:12
Alignment explanation
Indices: 21182735--21182759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21182725 GTTACATCAC
21182735 TGTATGATAACT
1 TGTATGATAACT
21182747 TGTATGATAACT
1 TGTATGATAACT
21182759 T
1 T
21182760 TGATCAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTATGATAACT
Found at i:21185430 original size:2 final size:2
Alignment explanation
Indices: 21185423--21185475 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
21185413 AACTCATGTG
21185423 TA TA TA 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
21185465 TA TA TA T- TA TA
1 TA TA TA TA TA TA
21185476 ACATACATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21185616 original size:14 final size:13
Alignment explanation
Indices: 21185599--21185633 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
21185589 TATTTATTTT
21185599 AAATTATTTATAA
1 AAATTATTTATAA
*
21185612 AAAATATATTATAA
1 AAATTAT-TTATAA
21185626 AAATTATT
1 AAATTATT
21185634 AAATTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTATTTATAA
Found at i:21185656 original size:18 final size:17
Alignment explanation
Indices: 21185619--21185653 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21185609 TAAAAAATAT
21185619 ATTATAAAAATTATTAA
1 ATTATAAAAATTATTAA
21185636 ATTATCAAAAATT-TTAA
1 ATTAT-AAAAATTATTAA
21185653 A
1 A
21185654 ATTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTATAAAAATTATTAA
Found at i:21186058 original size:33 final size:35
Alignment explanation
Indices: 21186014--21186082 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 35
21186004 TTTATCATAA
* *
21186014 TTTTTAAAAATATTATTTA-A-TATCTTTAATTTT
1 TTTTTAAAAATAATATTTACATTATCTTTAACTTT
* *
21186047 TTTTTATAAATAATCTTTACATTATCTTTAACTTT
1 TTTTTAAAAATAATATTTACATTATCTTTAACTTT
21186082 T
1 T
21186083 AAATATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 16 0.53
34 1 0.03
35 13 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (35 bp):
TTTTTAAAAATAATATTTACATTATCTTTAACTTT
Found at i:21186966 original size:56 final size:55
Alignment explanation
Indices: 21186878--21186992 Score: 176
Period size: 56 Copynumber: 2.1 Consensus size: 55
21186868 CCCTCGATGA
* *
21186878 GAAACATATAATAGAATTTCAAATCAGGAGATTATTTTTCATTAAAAAATAAAATT
1 GAAACATATAACAGAATTTCAAATCAGAAGATTATTTTTCA-TAAAAAATAAAATT
* * *
21186934 GAAACATGTAACATAATTTTAAATCAGAAGATTATTTTTCATAAAAAATAAAATT
1 GAAACATATAACAGAATTTCAAATCAGAAGATTATTTTTCATAAAAAATAAAATT
21186989 GAAA
1 GAAA
21186993 AGAAATAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 18 0.33
56 36 0.67
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (55 bp):
GAAACATATAACAGAATTTCAAATCAGAAGATTATTTTTCATAAAAAATAAAATT
Found at i:21189281 original size:24 final size:24
Alignment explanation
Indices: 21189252--21189297 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
21189242 GAACAATTAT
*
21189252 CTATTTATATTCA-AATAATTATGA
1 CTATTTATAAT-ATAATAATTATGA
21189276 CTATTTATAATATAATAATTAT
1 CTATTTATAATATAATAATTAT
21189298 TTCTGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (24 bp):
CTATTTATAATATAATAATTATGA
Found at i:21190140 original size:226 final size:226
Alignment explanation
Indices: 21189746--21190204 Score: 846
Period size: 226 Copynumber: 2.0 Consensus size: 226
21189736 TTATATAAAT
*
21189746 AGAGTTTCTATGATATCTTCATTGCTTTAAATATTTAAATAATAAACTCCATTATAAGTATAAAA
1 AGAGTTTCTATGATATCTTCATTCCTTTAAATATTTAAATAATAAACTCCATTATAAGTATAAAA
*
21189811 ACTAATATATTTTCACATAATGGATCACACTAGATTCTAAAATTTAAATAAATTTTACTATTACT
66 ACTAATATATTTTCACATAATGGATCACACTAAATTCTAAAATTTAAATAAATTTTACTATTACT
*
21189876 TAACAAATATATAGTTTTTACTCGTTAAACTTTGTAATTAGAGGTCACTAATCTCTAATTACAAA
131 TAACAAATATATAATTTTTACTCGTTAAACTTTGTAATTAGAGGTCACTAATCTCTAATTACAAA
21189941 GTTGGGTTCATATTATTGATGTCTAATAGTA
196 GTTGGGTTCATATTATTGATGTCTAATAGTA
* *
21189972 AGAGTTTCTATGATATCTTCATTCCTTTAAATATTTAAATAATAAACTTCATTATGAGTATAAAA
1 AGAGTTTCTATGATATCTTCATTCCTTTAAATATTTAAATAATAAACTCCATTATAAGTATAAAA
* *
21190037 ACTAATCTATTTTCACGTAATGGATCACACTAAATTCTAAAATTTAAATAAATTTTACTATTACT
66 ACTAATATATTTTCACATAATGGATCACACTAAATTCTAAAATTTAAATAAATTTTACTATTACT
*
21190102 TAACAAATATATAATTTTTACTCGTTAAACTTTGTAATTATAGGTCACTAATCTCTAATTACAAA
131 TAACAAATATATAATTTTTACTCGTTAAACTTTGTAATTAGAGGTCACTAATCTCTAATTACAAA
21190167 GTTGGGTTCATATTATTGATGTCTAATAGTA
196 GTTGGGTTCATATTATTGATGTCTAATAGTA
21190198 AGAGTTT
1 AGAGTTT
21190205 AAATCCATTA
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
226 225 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (226 bp):
AGAGTTTCTATGATATCTTCATTCCTTTAAATATTTAAATAATAAACTCCATTATAAGTATAAAA
ACTAATATATTTTCACATAATGGATCACACTAAATTCTAAAATTTAAATAAATTTTACTATTACT
TAACAAATATATAATTTTTACTCGTTAAACTTTGTAATTAGAGGTCACTAATCTCTAATTACAAA
GTTGGGTTCATATTATTGATGTCTAATAGTA
Found at i:21192110 original size:15 final size:17
Alignment explanation
Indices: 21192080--21192111 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21192070 TTTGTTTATA
21192080 TTTATACAATCATAACT
1 TTTATACAATCATAACT
21192097 TTTATA-AA-CATAACT
1 TTTATACAATCATAACT
21192112 CTGTTTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATACAATCATAACT
Found at i:21192205 original size:20 final size:21
Alignment explanation
Indices: 21192176--21192224 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
21192166 GTTTGGATTG
21192176 GAAAAAATTTAC-AGTCAACA
1 GAAAAAATTTACTAGTCAACA
* *
21192196 GAAAATATTTTCTAGTCAACA
1 GAAAAAATTTACTAGTCAACA
21192217 -AAAAAATT
1 GAAAAAATT
21192225 AAAACAGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (21 bp):
GAAAAAATTTACTAGTCAACA
Found at i:21194243 original size:31 final size:30
Alignment explanation
Indices: 21194208--21194309 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
21194198 GGCAAAAATA
21194208 TTAAAAAAATTATTTA-ATTATTTTACTT-TAT
1 TTAAAAAAATTATTTATA-T-TTTTA-TTGTAT
* *
21194239 TTAAAATAAGTATTTATATTTTTATTGTAT
1 TTAAAAAAATTATTTATATTTTTATTGTAT
* *
21194269 TTAAATAAAA-T-TTTATCTTTTAATTTGTAT
1 TTAAA-AAAATTATTTATATTTTTA-TTGTAT
*
21194299 TTAAATAAATT
1 TTAAAAAAATT
21194310 CTTATTTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
29 15 0.25
30 26 0.43
31 18 0.30
32 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (30 bp):
TTAAAAAAATTATTTATATTTTTATTGTAT
Found at i:21194308 original size:29 final size:28
Alignment explanation
Indices: 21194226--21194319 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 28
21194216 ATTATTTAAT
* *
21194226 TATTTTACTT-TATTTAAAATAAGTATTTA
1 TATTTTAATTGTATTT-AAATAAAT-TTTA
*
21194255 TATTTTTATTGTATTTAAATAAAATTTTA
1 TATTTTAATTGTATTTAAAT-AAATTTTA
* *
21194284 TCTTTTAATTTGTATTTAAATAAATTCT-
1 TATTTTAA-TTGTATTTAAATAAATTTTA
21194312 TATTTTAA
1 TATTTTAA
21194320 AAAATTGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.13
29 28 0.51
30 20 0.36
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (28 bp):
TATTTTAATTGTATTTAAATAAATTTTA
Found at i:21197223 original size:7 final size:7
Alignment explanation
Indices: 21197207--21197243 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
21197197 TTTTTTTTTT
21197207 TTTTAT-
1 TTTTATA
21197213 TTTTATA
1 TTTTATA
21197220 TTTT-TA
1 TTTTATA
*
21197226 GTTTATA
1 TTTTATA
21197233 TTTTATA
1 TTTTATA
21197240 TTTT
1 TTTT
21197244 TTTCTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:21197281 original size:15 final size:15
Alignment explanation
Indices: 21197263--21197293 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21197253 TCTTTGTATC
21197263 TTATGTATTTATTAT
1 TTATGTATTTATTAT
*
21197278 TTATTTATTTATTAT
1 TTATGTATTTATTAT
21197293 T
1 T
21197294 GCTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATGTATTTATTAT
Found at i:21197374 original size:42 final size:42
Alignment explanation
Indices: 21197328--21197408 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
21197318 TTTTTTGTTA
*
21197328 ATATATATATTTGTTATTACTTAGCTATTTATATATTATTAT
1 ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
* * *
21197370 ATATATGTATTTATTATTATTTATCTATTTATATATTAT
1 ATATATATATTTATTATTACTTAGCTATTTATATATTAT
21197409 AATCTATCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (42 bp):
ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
Found at i:21197386 original size:20 final size:19
Alignment explanation
Indices: 21197361--21197425 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
21197351 GCTATTTATA
*
21197361 TATTATTATATATATGTATT
1 TATTATTATAT-TATCTATT
21197381 TATTATTAT-TTATCTATT
1 TATTATTATATTATCTATT
*
21197399 TATATATTATA--ATCTATC
1 TAT-TATTATATTATCTATT
21197417 TATTATTAT
1 TATTATTAT
21197426 TTTTATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.15
18 19 0.46
19 7 0.17
20 9 0.22
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTATTATATTATCTATT
Found at i:21197426 original size:42 final size:42
Alignment explanation
Indices: 21197341--21197487 Score: 122
Period size: 42 Copynumber: 3.5 Consensus size: 42
21197331 TATATATTTG
* * *
21197341 TTATTACTTAGCTATTTATATATTAT--TATATATATGTATTTA
1 TTATTATTTATCTATTTATATATTATAATATATCTAT-TA-TTA
*
21197383 TTATTATTTATCTATTTATATATTATAATCTATCTATTATTA
1 TTATTATTTATCTATTTATATATTATAATATATCTATTATTA
* * * * *
21197425 TTTTTATTTATCT-GTTA-ATATTTTAATTTATCTGATTATTT
1 TTATTATTTATCTATTTATATATTATAATATATCT-ATTATTA
* * *
21197466 TCTTTTAATTATCTATTAATAT
1 T-TATTATTTATCTATTTATAT
21197488 TTTTATTTGA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
40 14 0.16
41 10 0.11
42 50 0.57
43 4 0.05
44 9 0.10
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (42 bp):
TTATTATTTATCTATTTATATATTATAATATATCTATTATTA
Found at i:21197436 original size:20 final size:20
Alignment explanation
Indices: 21197380--21197495 Score: 106
Period size: 20 Copynumber: 5.6 Consensus size: 20
21197370 ATATATGTAT
*
21197380 TTATTATTATTTATCTATTTA
1 TTATTTTTATTTATCTA-TTA
* * *
21197401 TATATTATAATCTATCTATTA
1 T-TATTTTTATTTATCTATTA
*
21197422 TTATTTTTATTTATCTGTTA
1 TTATTTTTATTTATCTATTA
* *
21197442 ATATTTTAATTTATCTGATTA
1 TTATTTTTATTTATCT-ATTA
* *
21197463 TTTTCTTTTAATTATCTATTA
1 TTAT-TTTTATTTATCTATTA
*
21197484 ATATTTTTATTT
1 TTATTTTTATTT
21197496 GATTTTATTT
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
20 36 0.47
21 16 0.21
22 24 0.32
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTTTATTTATCTATTA
Found at i:21197488 original size:42 final size:40
Alignment explanation
Indices: 21197380--21197495 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 40
21197370 ATATATGTAT
* * * *
21197380 TTATTATTATTTATCTATTTATATATTATAATCTATCTATTA
1 TTATTTTTAATTATCTA-TTA-ATATTTTAATTTATCTATTA
* *
21197422 TTATTTTTATTTATCTGTTAATATTTTAATTTATCTGATTA
1 TTATTTTTAATTATCTATTAATATTTTAATTTATCT-ATTA
* *
21197463 TTTTCTTTTAATTATCTATTAATATTTTTATTT
1 TTAT-TTTTAATTATCTATTAATATTTTAATTT
21197496 GATTTTATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 14 0.22
41 10 0.16
42 40 0.62
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (40 bp):
TTATTTTTAATTATCTATTAATATTTTAATTTATCTATTA
Found at i:21198369 original size:3 final size:3
Alignment explanation
Indices: 21198361--21198399 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
21198351 TTTTATTTAT
*
21198361 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21198400 GATTAGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:21198439 original size:12 final size:12
Alignment explanation
Indices: 21198422--21198454 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21198412 TTAATATTTT
21198422 TTTTTATTTTCA
1 TTTTTATTTTCA
21198434 TTTTTATTTT-A
1 TTTTTATTTTCA
21198445 TTTTT-TTTTC
1 TTTTTATTTTC
21198455 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 6 0.30
12 10 0.50
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTCA
Found at i:21198443 original size:17 final size:16
Alignment explanation
Indices: 21198417--21198448 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
21198407 ATTGTTTAAT
21198417 ATTTTTTTTTATTTTC
1 ATTTTTTTTTATTTTC
21198433 ATTTTTATTTTATTTT
1 ATTTTT-TTTTATTTT
21198449 TTTTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTTTTTTATTTTC
Found at i:21198537 original size:59 final size:59
Alignment explanation
Indices: 21198449--21198682 Score: 298
Period size: 59 Copynumber: 4.0 Consensus size: 59
21198439 ATTTTATTTT
* * *
21198449 TTTTTCTT-TAAATAAAATTT-T-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA
1 TTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA
*
21198505 TTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA
1 TTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA
*
21198564 TTTTTCTTGAAAATAAGCTTTCTAAAAAAATATATTTTTGA-AACAAAGTTGAAAGTATCAA
1 TTTTTCTTGAAAATAAACTTTCT-AAAAAA-ATATTTTTGAGAA-AAAGTTGAAAGTATCAA
* * * * * * *
21198625 TTTTTCTTAAAAATAAATTTTC-AAAAATAGATTTTTAAGGAAAAGTTAAAAGTATCAA
1 TTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA
21198683 AGTATCAATT
Statistics
Matches: 158, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
56 8 0.05
57 10 0.06
58 25 0.16
59 61 0.39
60 8 0.05
61 46 0.29
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (59 bp):
TTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA
Found at i:21198693 original size:66 final size:66
Alignment explanation
Indices: 21198615--21198749 Score: 191
Period size: 66 Copynumber: 2.0 Consensus size: 66
21198605 AACAAAGTTG
* *
21198615 AAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAT-AGATTTTTAAGGAAAAGTTAAAAGTA
1 AAAGTATCAATTTTCCTTAAAAACAAATTTTCAAAAATGA-ATTTTTAAGGAAAAGTTAAAAGTA
21198679 TC
65 TC
* * * * *
21198681 AAAGTATCAATTTTCCTTAGAAACAAGTTTTCAAAAGTGAATTTTTGAGGAAAAGTTGAAAGTAT
1 AAAGTATCAATTTTCCTTAAAAACAAATTTTCAAAAATGAATTTTTAAGGAAAAGTTAAAAGTAT
21198746 C
66 C
21198747 AAA
1 AAA
21198750 TTTTCCTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 60 0.98
67 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (66 bp):
AAAGTATCAATTTTCCTTAAAAACAAATTTTCAAAAATGAATTTTTAAGGAAAAGTTAAAAGTAT
C
Found at i:21200313 original size:26 final size:26
Alignment explanation
Indices: 21200284--21200333 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
21200274 AAAATAGTTT
* * *
21200284 TTGATAAAATCCTTTATTTAAAAATA
1 TTGAGAAAATACTTTAGTTAAAAATA
*
21200310 TTGAGAAAATATTTTAGTTAAAAA
1 TTGAGAAAATACTTTAGTTAAAAA
21200334 ATTAACTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (26 bp):
TTGAGAAAATACTTTAGTTAAAAATA
Found at i:21201082 original size:15 final size:15
Alignment explanation
Indices: 21201061--21201102 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
21201051 GGTGTTGAGA
21201061 ATTTTGGATTTTAAGG
1 ATTTTGGATTTT-AGG
21201077 -TTTTGGATTTTAGG
1 ATTTTGGATTTTAGG
*
21201091 ATTTAGGATTTT
1 ATTTTGGATTTT
21201103 GAATTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (15 bp):
ATTTTGGATTTTAGG
Found at i:21201095 original size:22 final size:23
Alignment explanation
Indices: 21201059--21201110 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
21201049 ATGGTGTTGA
21201059 GAATTTT-GGATTTTAAGG-TTTT
1 GAATTTTAGGATTTT-AGGATTTT
*
21201081 GGATTTTAGGA-TTTAGGATTTT
1 GAATTTTAGGATTTTAGGATTTT
21201103 GAATTTTA
1 GAATTTTA
21201111 AGGTTTCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 20 0.77
23 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (23 bp):
GAATTTTAGGATTTTAGGATTTT
Found at i:21201110 original size:15 final size:14
Alignment explanation
Indices: 21201059--21201109 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
21201049 ATGGTGTTGA
21201059 GAATTTTGGATTTT
1 GAATTTTGGATTTT
21201073 -AAGGTTTTGGATTTT
1 GAA--TTTTGGATTTT
* *
21201088 AGGATTTAGGATTTT
1 -GAATTTTGGATTTT
21201103 GAATTTT
1 GAATTTT
21201110 AAGGTTTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 21 0.72
17 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (14 bp):
GAATTTTGGATTTT
Found at i:21201146 original size:14 final size:14
Alignment explanation
Indices: 21201127--21201161 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21201117 CGAGGACCTA
21201127 TGGTTTTAAGGGTT
1 TGGTTTTAAGGGTT
*
21201141 TGGTTTTAAGGTTT
1 TGGTTTTAAGGGTT
21201155 TAGGTTT
1 T-GGTTT
21201162 CGATGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (14 bp):
TGGTTTTAAGGGTT
Found at i:21201272 original size:29 final size:28
Alignment explanation
Indices: 21201200--21201324 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 28
21201190 GCTTAGATTT
**
21201200 TTTAATTTT-GGAGTTTGAGATTTTAGGG
1 TTTAATTTTAGG-GTTTGAGGGTTTAGGG
* *
21201228 TTTCAATTTAATGGTTTAGAGGGTTTAGGG
1 TTT-AATTTTAGGGTTT-GAGGGTTTAGGG
* *
21201258 TTTAATTTTAGGGTTTG-GATGTTTGGGG
1 TTTAATTTTAGGGTTTGAG-GGTTTAGGG
* * * *
21201286 TTTTGATTTTAGGGTTTGAAGTTTTAGAG
1 -TTTAATTTTAGGGTTTGAGGGTTTAGGG
21201315 TTTAGATTTT
1 TTTA-ATTTT
21201325 TTAATTTAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
27 1 0.01
28 14 0.19
29 46 0.61
30 14 0.19
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (28 bp):
TTTAATTTTAGGGTTTGAGGGTTTAGGG
Found at i:21201302 original size:58 final size:57
Alignment explanation
Indices: 21201200--21201324 Score: 128
Period size: 58 Copynumber: 2.2 Consensus size: 57
21201190 GCTTAGATTT
* * *
21201200 TTTAATTTTGGAGTTTGAGATTTTAGGGTTTCAATTTAATGGTTTAGAGGGTTTAGGG
1 TTTAATTTTGGAGTTTGAGATTTTAGGGTTTCAATTTAAGGGTTT-GAAGGTTTAGAG
* ** * *
21201258 TTTAATTTTAGG-GTTTG-GATGTTTGGGGTTTTGATTTTAGGGTTTGAAGTTTTAGAG
1 TTTAATTTT-GGAGTTTGAGAT-TTTAGGGTTTCAATTTAAGGGTTTGAAGGTTTAGAG
21201315 TTTAGATTTT
1 TTTA-ATTTT
21201325 TTAATTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
57 16 0.29
58 38 0.68
59 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (57 bp):
TTTAATTTTGGAGTTTGAGATTTTAGGGTTTCAATTTAAGGGTTTGAAGGTTTAGAG
Found at i:21201456 original size:3 final size:3
Alignment explanation
Indices: 21201450--21201501 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
21201440 TTTATGAAAT
21201450 TTA TTA TTA TTA TTA TTA TTA 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
21201498 TTA T
1 TTA T
21201502 GTTTTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21203014 original size:20 final size:20
Alignment explanation
Indices: 21202991--21203034 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21202981 ATAAAAAATT
21202991 AATATTAATATT-TTATTATC
1 AATATT-ATATTATTATTATC
* *
21203011 AATATTTTTTTATTATTATC
1 AATATTATATTATTATTATC
21203031 AATA
1 AATA
21203035 ATAGTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTATATTATTATTATC
Found at i:21203042 original size:20 final size:20
Alignment explanation
Indices: 21203003--21203048 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
21202993 TATTAATATT
* **
21203003 TTATTATCAATATTTTTTTA
1 TTATTATCAATAATAGTTTA
21203023 TTATTATCAATAATAGTTTA
1 TTATTATCAATAATAGTTTA
*
21203043 ATATTA
1 TTATTA
21203049 ATAAACAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATTATCAATAATAGTTTA
Found at i:21203323 original size:37 final size:37
Alignment explanation
Indices: 21203233--21203329 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 37
21203223 ATCACAAGTC
*
21203233 AAAGAAT-GATTGGGATAACACCGCAAGTTAGAAAAT
1 AAAGAATCGACTGGGATAACACCGCAAGTTAGAAAAT
*** ** *
21203269 AAAG-ATCGACCAAGATAACATTGTAAGTTA-AGAAAT
1 AAAGAATCGACTGGGATAACACCGCAAGTTAGA-AAAT
21203305 AAAGAATCGACTGGGATAACACCGC
1 AAAGAATCGACTGGGATAACACCGC
21203330 GAATTGAAAT
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
35 3 0.07
36 28 0.62
37 14 0.31
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (37 bp):
AAAGAATCGACTGGGATAACACCGCAAGTTAGAAAAT
Found at i:21203560 original size:88 final size:86
Alignment explanation
Indices: 21203393--21203565 Score: 222
Period size: 88 Copynumber: 2.0 Consensus size: 86
21203383 TCATACCCAA
** * *
21203393 AGGTCTTACAGAATCAACTGAGACAACATTGCAAGTTAAAAAATAAAGAATCGATCGGGATAACG
1 AGGTCTTACAGAATCAACTGAGACAACACCGCAAGTCAAAAAATAAAGAATCGACCGGGATAA--
*
21203458 CCACGAATCGAAATTATGCCTAG
64 CCACGAATCAAAATTATGCCTAG
* * *
21203481 AGGTCTTACAGAATCGACTGAGACAATACCGTAAGTCAAAAAATAAAGAATCGACCGGGATAA-C
1 AGGTCTTACAGAATCAACTGAGACAACACCGCAAGTCAAAAAATAAAGAATCGACCGGGATAACC
21203545 ATCGTAGATCAAAATTATGCC
66 A-CG-A-ATCAAAATTATGCC
21203566 CGAAAATTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
85 2 0.03
86 2 0.03
87 1 0.01
88 69 0.93
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (86 bp):
AGGTCTTACAGAATCAACTGAGACAACACCGCAAGTCAAAAAATAAAGAATCGACCGGGATAACC
ACGAATCAAAATTATGCCTAG
Found at i:21203847 original size:22 final size:22
Alignment explanation
Indices: 21203819--21203861 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21203809 CTGTGAATTG
*
21203819 AAATTATGCCCGGAGGTCTTAA
1 AAATTATGCCCGAAGGTCTTAA
*
21203841 AAATTATGCCTGAAGGTCTTA
1 AAATTATGCCCGAAGGTCTTA
21203862 GAGATCATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (22 bp):
AAATTATGCCCGAAGGTCTTAA
Found at i:21203871 original size:22 final size:22
Alignment explanation
Indices: 21203832--21203883 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
21203822 TTATGCCCGG
*
21203832 AGGTCTTAAAAATTATGCCTGA
1 AGGTCTTAAAAATCATGCCTGA
* * *
21203854 AGGTCTTAGAGATCATGCTTGA
1 AGGTCTTAAAAATCATGCCTGA
21203876 AGGTCTTA
1 AGGTCTTA
21203884 CAGAATCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (22 bp):
AGGTCTTAAAAATCATGCCTGA
Found at i:21203986 original size:21 final size:21
Alignment explanation
Indices: 21203948--21203997 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
21203938 ATATCATAAA
*
21203948 TTAAAATTATGCTTTGAGGTC
1 TTAAAATTATGCTCTGAGGTC
21203969 TTAAAGATTATGC-CTGAGGTC
1 TTAAA-ATTATGCTCTGAGGTC
21203990 TTAGAAAT
1 TTA-AAAT
21203998 CATACCTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (21 bp):
TTAAAATTATGCTCTGAGGTC
Found at i:21203991 original size:263 final size:263
Alignment explanation
Indices: 21203483--21204072 Score: 663
Period size: 263 Copynumber: 2.2 Consensus size: 263
21203473 ATGCCTAGAG
* * *
21203483 GTCTTACAGAATCGACTGAGACAATACCGTAAGTCAAAAAATAAAGAATCGACCGGGATAACA-T
1 GTCTTACAGAATCGACTGAGACAACACCGTAAGTTAAAAAATAAAGAATCGATCGGGATAACACT
* *
21203547 CGTAGATCAAAATTATGCCCGAAAATTTTAAAAATTATGTTCAGAGATCTTAGAAATCATGTACA
66 CGTAGATCAAAATTATGCCCGAAAATCTTAAAAATTATGCTCAGAGATCTTAGAAATCATGTACA
* * ** * * *
21203612 GAGATTTTACAGAATCGACTGGGACAATATTGCAAGTTAAAAAATAAAGAATTGATTGGGACAAC
131 GAGATCTTACAGAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGACAAC
* *
21203677 ACACGAATCAAAATTATGCTCGGAGGTCTTAAAGATTATACTCGAAGGTCTTAGAAATCATGTCC
196 ACACAAATCAAAATTATGCTCGGAGGTCTTAAAGATTATACTCGAAGGTCTTAGAAATCAT-ACC
21203742 AAAA
260 AAAA
* ** *
21203746 GTCTTATAGAATCGACTGAGACAACACCACAAGTTGAAAAATAAAGAATCGATCGGGATAACACT
1 GTCTTACAGAATCGACTGAGACAACACCGTAAGTTAAAAAATAAAGAATCGATCGGGATAACACT
** * ** * * *
21203811 -GT-GAATTGAAATTATGCCCGGAGGTCTTAAAAATTATGC-CTGAAGGTCTTAGAGATCATGCT
66 CGTAG-ATCAAAATTATGCCCGAAAATCTTAAAAATTATGCTCAG-AGATCTTAGAAATCATG-T
** * * *
21203873 TGA-AGGTCTTACAGAATCGATTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGAT
128 ACAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGAC
* * * ** *
21203937 AATATCATAAATTAAAATTATGCTTTGAGGTCTTAAAGATTATGC-CTG-AGGTCTTAGAAATCA
193 AACA-CACAAATCAAAATTATGCTCGGAGGTCTTAAAGATTATACTC-GAAGGTCTTAGAAATCA
* *
21204000 TACCTAGA
256 TACCAAAA
* * * * * *
21204008 GATCTTACAGAATCGACTGGGATAACACCGTAAGTTAAAAAATAAAAAATCAATCAGGACAACAC
1 G-TCTTACAGAATCGACTGAGACAACACCGTAAGTTAAAAAATAAAGAATCGATCGGGATAACAC
21204073 CATAAGTTTA
Statistics
Matches: 271, Mismatches: 49, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
262 8 0.03
263 225 0.83
264 38 0.14
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (263 bp):
GTCTTACAGAATCGACTGAGACAACACCGTAAGTTAAAAAATAAAGAATCGATCGGGATAACACT
CGTAGATCAAAATTATGCCCGAAAATCTTAAAAATTATGCTCAGAGATCTTAGAAATCATGTACA
GAGATCTTACAGAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGACAAC
ACACAAATCAAAATTATGCTCGGAGGTCTTAAAGATTATACTCGAAGGTCTTAGAAATCATACCA
AAA
Found at i:21204077 original size:131 final size:132
Alignment explanation
Indices: 21203467--21204077 Score: 563
Period size: 132 Copynumber: 4.6 Consensus size: 132
21203457 GCCACGAATC
* * * * * * *
21203467 GAAATTATGCCTAGAGGTCTTACAGAATCGACTGAGACAATACCGTAAGTCAAAAAATAAAGAAT
1 GAAATCATACCTAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGAAT
* * * * * * ** * * * *
21203532 CGACCGGGATAACATCGTAGATCAAAATTATGCCCGAAAATTTTAAAAATTATG-TTCAGAGATC
66 CGATCGGGATAACACCATAAATCAAAATTATGCTCGGAGGTCTTAAAAATTATGCCTGA-AGGTC
21203596 TTA
130 TTA
* * **
21203599 GAAATCATGTA-C-AGAGATTTTACAGAATCGACTGGGACAATATTGCAAGTTAAAAAATAAAGA
1 GAAATCA--TACCTAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGA
* * * ** * *
21203662 ATTGATTGGGACAACA-CACGAATCAAAATTATGCTCGGAGGTCTTAAAGATTAT-ACTCGAAGG
64 ATCGATCGGGATAACACCATAAATCAAAATTATGCTCGGAGGTCTTAAAAATTATGCCT-GAAGG
21203725 TCTTA
128 TCTTA
* * * * * * *
21203730 GAAATCATGTCCAAAAG-TCTTATAGAATCGACTGAGACAACACCACAAGTTGAAAAATAAAGAA
1 GAAATCAT-ACCTAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGAA
** * ** *
21203794 TCGATCGGGATAACACTGTGAATTGAAATTATGCCCGGAGGTCTTAAAAATTATGCCTGAAGGTC
65 TCGATCGGGATAACACCATAAATCAAAATTATGCTCGGAGGTCTTAAAAATTATGCCTGAAGGTC
21203859 TTA
130 TTA
* * * * * *
21203862 GAGATCAT-GCTTGAAGGTCTTACAGAATCGATTGGGACAACACCGCAAGTCAAAAAATAAAGAA
1 GAAATCATACCTAG-AGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGAA
* * * ** *
21203926 TCGATCGGGATAATATCATAAATTAAAATTATGCTTTGAGGTCTTAAAGATTATGCCTG-AGGTC
65 TCGATCGGGATAACACCATAAATCAAAATTATGCTCGGAGGTCTTAAAAATTATGCCTGAAGGTC
21203990 TTA
130 TTA
* * *
21203993 GAAATCATACCTAGAGATCTTACAGAATCGACTGGGATAACACCGTAAGTTAAAAAATAAAAAAT
1 GAAATCATACCTAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGAAT
* * *
21204058 CAATCAGGACAACACCATAA
66 CGATCGGGATAACACCATAA
21204078 GTTTAAAAAT
Statistics
Matches: 385, Mismatches: 82, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 172 0.45
132 207 0.54
133 3 0.01
134 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (132 bp):
GAAATCATACCTAGAGATCTTACAGAATCGACTGGGACAACACCGCAAGTTAAAAAATAAAGAAT
CGATCGGGATAACACCATAAATCAAAATTATGCTCGGAGGTCTTAAAAATTATGCCTGAAGGTCT
TA
Found at i:21204086 original size:37 final size:37
Alignment explanation
Indices: 21204031--21204110 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
21204021 CGACTGGGAT
*
21204031 AACACCGTAAGTTAAAAAATAAAAAATCAATCAGGAC
1 AACACCATAAGTTAAAAAATAAAAAATCAATCAGGAC
* * ** *
21204068 AACACCATAAGTTTAAAAATAAAGAATTGATCAGGAT
1 AACACCATAAGTTAAAAAATAAAAAATCAATCAGGAC
21204105 AACACC
1 AACACC
21204111 GCAAATAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (37 bp):
AACACCATAAGTTAAAAAATAAAAAATCAATCAGGAC
Found at i:21206326 original size:20 final size:20
Alignment explanation
Indices: 21206290--21206327 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21206280 TTTTTTTTGT
*
21206290 TTTTGTTTTTGTCTTTTTAC
1 TTTTGTTTTTGTATTTTTAC
21206310 TTTT-TTTTTGCTATTTTT
1 TTTTGTTTTTG-TATTTTT
21206328 TTATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTGTTTTTGTATTTTTAC
Found at i:21212997 original size:13 final size:14
Alignment explanation
Indices: 21212971--21213000 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21212961 CGAAAACCTA
21212971 TGGTTTTAAGGGTT
1 TGGTTTTAAGGGTT
21212985 TGGTTTT-AGGGTT
1 TGGTTTTAAGGGTT
21212998 TGG
1 TGG
21213001 GGGTTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (14 bp):
TGGTTTTAAGGGTT
Found at i:21213114 original size:21 final size:23
Alignment explanation
Indices: 21213082--21213141 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
21213072 TTAAAGTTTA
21213082 GTTTTAG-GATTTAGATGCTTGAG
1 GTTTTAGAG-TTTAGATGCTTGAG
* * *
21213105 GTTTT-GATTTTAG-GGTTTGAG
1 GTTTTAGAGTTTAGATGCTTGAG
21213126 GTTTTAGAGTTTAGAT
1 GTTTTAGAGTTTAGAT
21213142 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.38
22 13 0.45
23 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (23 bp):
GTTTTAGAGTTTAGATGCTTGAG
Found at i:21213137 original size:29 final size:30
Alignment explanation
Indices: 21213020--21213144 Score: 84
Period size: 29 Copynumber: 4.3 Consensus size: 30
21213010 GCTTAGATTT
* *
21213020 TTTA-ATTTTGGGGTTT-GAGATTTTA-AGG
1 TTTAGATTTTAGGGTTTAGAGGTTTTAGA-G
* * * *
21213048 TTTCA-ATTTAAGGGTTTGGAGGGTTTAAAG
1 TTT-AGATTTTAGGGTTTAGAGGTTTTAGAG
* * * *
21213078 TTTAG-TTTTAGGATTTAGATGCTTGAG-G
1 TTTAGATTTTAGGGTTTAGAGGTTTTAGAG
*
21213106 TTTTGATTTTAGGGTTT-GAGGTTTTAGAG
1 TTTAGATTTTAGGGTTTAGAGGTTTTAGAG
21213135 TTTAGATTTT
1 TTTAGATTTT
21213145 TTAATTAAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
28 15 0.20
29 47 0.64
30 11 0.15
31 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.49
Consensus pattern (30 bp):
TTTAGATTTTAGGGTTTAGAGGTTTTAGAG
Found at i:21213887 original size:20 final size:20
Alignment explanation
Indices: 21213859--21213898 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21213849 CTTTACATAA
**
21213859 AGCTAATTTTTTTTTTGTTC
1 AGCTAATTTTCCTTTTGTTC
*
21213879 AGCTTATTTTCCTTTTGTTC
1 AGCTAATTTTCCTTTTGTTC
21213899 CAGAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.62
Consensus pattern (20 bp):
AGCTAATTTTCCTTTTGTTC
Done.