Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 4 of 12
Found at i:2121208 original size:94 final size:94
Alignment explanation
Indices: 2121047--2121230 Score: 368
Period size: 94 Copynumber: 2.0 Consensus size: 94
2121037 AATCTTCCGC
2121047 ATCTTGAATACTGCCTTCATCTCCTATCCAATCCAAGATGCTTGAAATCACCCTAAGGTCAGGTC
1 ATCTTGAATACTGCCTTCATCTCCTATCCAATCCAAGATGCTTGAAATCACCCTAAGGTCAGGTC
2121112 TCCACGGATCCCAAACCGAAGGGGTTATT
66 TCCACGGATCCCAAACCGAAGGGGTTATT
2121141 ATCTTGAATACTGCCTTCATCTCCTATCCAATCCAAGATGCTTGAAATCACCCTAAGGTCAGGTC
1 ATCTTGAATACTGCCTTCATCTCCTATCCAATCCAAGATGCTTGAAATCACCCTAAGGTCAGGTC
2121206 TCCACGGATCCCAAACCGAAGGGGT
66 TCCACGGATCCCAAACCGAAGGGGT
2121231 AGATAACGCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (94 bp):
ATCTTGAATACTGCCTTCATCTCCTATCCAATCCAAGATGCTTGAAATCACCCTAAGGTCAGGTC
TCCACGGATCCCAAACCGAAGGGGTTATT
Found at i:2128127 original size:29 final size:30
Alignment explanation
Indices: 2128095--2128153 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2128085 AATAAATCTC
2128095 TAATCTTTATATAT-AAAAGAATAAAAAAA
1 TAATCTTTATATATGAAAAGAATAAAAAAA
*
2128124 TAATCTTTATATGTGAAAAGAATAAAAAAA
1 TAATCTTTATATATGAAAAGAATAAAAAAA
2128154 AGGTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (30 bp):
TAATCTTTATATATGAAAAGAATAAAAAAA
Found at i:2128881 original size:62 final size:62
Alignment explanation
Indices: 2128784--2128905 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 62
2128774 GACCGATCAA
* *
2128784 CTAACAGTCTTGAATCAGAATAAAATCTATGGAAAAACCATGGGCAGGAAAACAAACGTAAC
1 CTAACAATCTTGAATCAGAATAAAATCTATGGAAAAACCATAGGCAGGAAAACAAACGTAAC
2128846 CTAACAATCTTGAATCAGAATAAAATCTATGGAAAAACCATAGGCAGGAAAACAAACGTA
1 CTAACAATCTTGAATCAGAATAAAATCTATGGAAAAACCATAGGCAGGAAAACAAACGTA
2128906 CAATGAGGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.18
Consensus pattern (62 bp):
CTAACAATCTTGAATCAGAATAAAATCTATGGAAAAACCATAGGCAGGAAAACAAACGTAAC
Found at i:2130496 original size:3 final size:3
Alignment explanation
Indices: 2130488--2130517 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2130478 CTGGTGGAGG
2130488 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2130518 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2141911 original size:19 final size:22
Alignment explanation
Indices: 2141875--2141920 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
2141865 TTTAATAAGA
2141875 TTTCTTCTCTCCTCCTAAATAC
1 TTTCTTCTCTCCTCCTAAATAC
2141897 TTTCTT-TC-CCT-CTAAATAC
1 TTTCTTCTCTCCTCCTAAATAC
2141916 TTTCT
1 TTTCT
2141921 CTTATATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.54
20 3 0.12
21 2 0.08
22 6 0.25
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTCTTCTCTCCTCCTAAATAC
Found at i:2142373 original size:52 final size:53
Alignment explanation
Indices: 2142216--2142379 Score: 206
Period size: 53 Copynumber: 3.1 Consensus size: 53
2142206 GCTATTGATG
*
2142216 AAAAACCATGAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTACTTAA-
1 AAAAAACATGAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTAC-TAAT
* * * *
2142269 AAAAACCATGAATATCCATTCCTTGAAGTGAATGTGACAAATGAGCTGCTAAT
1 AAAAAACATGAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTACTAAT
* * * * * *
2142322 AAAAAATATGAATGT-TATTCCCTGATGCGAATGTGACAAACGAGATACTAAT
1 AAAAAACATGAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTACTAAT
2142374 AAAAAA
1 AAAAAA
2142380 AATTATAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
52 39 0.40
53 58 0.60
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (53 bp):
AAAAAACATGAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTACTAAT
Found at i:2147124 original size:16 final size:18
Alignment explanation
Indices: 2147103--2147139 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2147093 ATTATTTTAA
2147103 AATA-TTAAT-ATAAAAT
1 AATATTTAATAATAAAAT
2147119 AATATTTTAATAATAAAAT
1 AATA-TTTAATAATAAAAT
2147138 AA
1 AA
2147140 ATAAATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATTTAATAATAAAAT
Found at i:2155730 original size:2 final size:2
Alignment explanation
Indices: 2155723--2155747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2155713 CGCTTGCATG
2155723 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
2155748 GTGCACGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2165140 original size:48 final size:48
Alignment explanation
Indices: 2165084--2165176 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
2165074 ACCTACAATT
*
2165084 AAACTCCAATAACAACTACCTCGAACCCTACAAACCGAAATTTTAATG
1 AAACTCCAATAACAACTACCTCCAACCCTACAAACCGAAATTTTAATG
*
2165132 AAACTCCAATAACAACTACCTCCAACCCTAGAAACCGAAATTTTA
1 AAACTCCAATAACAACTACCTCCAACCCTACAAACCGAAATTTTA
2165177 GCGTTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.44, C:0.30, G:0.05, T:0.20
Consensus pattern (48 bp):
AAACTCCAATAACAACTACCTCCAACCCTACAAACCGAAATTTTAATG
Found at i:2165988 original size:22 final size:23
Alignment explanation
Indices: 2165940--2165990 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2165930 ATTTTAAAAT
* *
2165940 TTTAAAAATTATTAATATTTAAC
1 TTTAAAAATTATAAATATTTAAA
2165963 TTTAAAAATTA-AAATA-TTAATA
1 TTTAAAAATTATAAATATTTAA-A
2165985 TTTAAA
1 TTTAAA
2165991 TTATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 10 0.40
23 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAATTATAAATATTTAAA
Found at i:2166769 original size:21 final size:20
Alignment explanation
Indices: 2166732--2166770 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2166722 TGACCCCCTC
* *
2166732 AAAAAATAAAAATAACAACA
1 AAAAAACAAAAAAAACAACA
2166752 AAAAAACAAAACAAAACAA
1 AAAAAACAAAA-AAAACAA
2166771 GATTGATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAAAACAAAAAAAACAACA
Found at i:2196828 original size:2 final size:2
Alignment explanation
Indices: 2196821--2196860 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2196811 TTTTATATTT
2196821 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
2196861 CATTAAGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2203113 original size:60 final size:60
Alignment explanation
Indices: 2203040--2203157 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
2203030 TTTTTTTCCC
2203040 TGTCGTTTCCATTCCTTCGATTCGAAGCAAACTACTTTTCGTTCTTCATATCGCCTTCTG
1 TGTCGTTTCCATTCCTTCGATTCGAAGCAAACTACTTTTCGTTCTTCATATCGCCTTCTG
*
2203100 TGTCGTTTCCATTCCTTCGATTCGAAGCAAACTACTTTTCTTTCTTCATATCGCCTTC
1 TGTCGTTTCCATTCCTTCGATTCGAAGCAAACTACTTTTCGTTCTTCATATCGCCTTC
2203158 ATTTCTATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (60 bp):
TGTCGTTTCCATTCCTTCGATTCGAAGCAAACTACTTTTCGTTCTTCATATCGCCTTCTG
Found at i:2208902 original size:2 final size:2
Alignment explanation
Indices: 2208895--2208927 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2208885 ATTTTCTCAT
2208895 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2208928 TTTGAGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2213518 original size:21 final size:21
Alignment explanation
Indices: 2213469--2213512 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2213459 ACTGCTTGTT
*
2213469 GTAGATAAAGTTTCTAGATAA
1 GTAGATAAAGTTTCAAGATAA
*
2213490 GTAGATAAAGTTTCAAGGTAA
1 GTAGATAAAGTTTCAAGATAA
2213511 GT
1 GT
2213513 TTATAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (21 bp):
GTAGATAAAGTTTCAAGATAA
Found at i:2213875 original size:23 final size:23
Alignment explanation
Indices: 2213789--2213875 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
2213779 AATATATGAT
*
2213789 TATTT-ATTTTTATTT-TTT-AA
1 TATTTAATTATTATTTATTTAAA
2213809 TATTAATAATATATTATTTATTTAAA
1 TATT--TAAT-TATTATTTATTTAAA
* *
2213835 -ATATTAATCATTAATTATTTAAA
1 TAT-TTAATTATTATTTATTTAAA
*
2213858 TATTTAATTTTTATTTAT
1 TATTTAATTATTATTTAT
2213876 AATTTAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 4 0.08
22 1 0.02
23 27 0.51
24 13 0.25
25 5 0.09
26 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTAATTATTATTTATTTAAA
Found at i:2226002 original size:21 final size:21
Alignment explanation
Indices: 2225956--2226002 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
2225946 AAATACTTGA
2225956 TTAAATAACTCAAACAATAAT
1 TTAAATAACTCAAACAATAAT
*
2225977 ATAAATAACT-AAA-AATTATAT
1 TTAAATAACTCAAACAA-TA-AT
2225998 TTAAA
1 TTAAA
2226003 AATAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
20 5 0.23
21 15 0.68
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAATAACTCAAACAATAAT
Found at i:2229953 original size:2 final size:2
Alignment explanation
Indices: 2229948--2229974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2229938 CATATATACC
2229948 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
2229975 GTTGGGCAGA
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:2236687 original size:15 final size:15
Alignment explanation
Indices: 2236653--2236693 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2236643 AATAATAAAT
2236653 ATATTAAAATTTATA
1 ATATTAAAATTTATA
2236668 A-ATTATAAATTT-TA
1 ATATTA-AAATTTATA
2236682 ATATT-AAATTTA
1 ATATTAAAATTTA
2236694 AAAAAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAAAATTTATA
Found at i:2237256 original size:17 final size:16
Alignment explanation
Indices: 2237216--2237245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2237206 ATATTAATAT
2237216 ATAAA-TTATTTTTTG
1 ATAAATTTATTTTTTG
2237231 ATAAATTTATTTTTT
1 ATAAATTTATTTTTT
2237246 ACTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
ATAAATTTATTTTTTG
Found at i:2237298 original size:52 final size:52
Alignment explanation
Indices: 2237199--2237298 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
2237189 TTGCATATAG
* * **
2237199 TATTTAAATATTAATATATAAATTATTTTTTGATAAATTTATTTTTTACTAA
1 TATTTAAATATTAATATATAAATAATTTTTTAATAAATTTAAATTTTACTAA
* *
2237251 TATTTAAATATTATTA-ATATATAATTTTTTAATAAAATTTAAATTTTA
1 TATTTAAATATTAATATATAAATAATTTTTTAAT-AAATTTAAATTTTA
2237299 ACTCCATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 14 0.34
52 27 0.66
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (52 bp):
TATTTAAATATTAATATATAAATAATTTTTTAATAAATTTAAATTTTACTAA
Found at i:2237920 original size:48 final size:48
Alignment explanation
Indices: 2237868--2237965 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
2237858 TCCTTCATGC
2237868 TGCCTGAATTGTTGTTCTGGAAATGTTAGTTTGGTGTGATCATGAATG
1 TGCCTGAATTGTTGTTCTGGAAATGTTAGTTTGGTGTGATCATGAATG
2237916 TGCCTGAATTGTTGTTCTGGAAATGTTAGTTTGGTGTGATCATGAATG
1 TGCCTGAATTGTTGTTCTGGAAATGTTAGTTTGGTGTGATCATGAATG
2237964 TG
1 TG
2237966 TTGTTTTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.20, C:0.08, G:0.30, T:0.42
Consensus pattern (48 bp):
TGCCTGAATTGTTGTTCTGGAAATGTTAGTTTGGTGTGATCATGAATG
Found at i:2240371 original size:2 final size:2
Alignment explanation
Indices: 2240366--2240417 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
2240356 TCTCTCTTTC
* * * *
2240366 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TC TT TC 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
2240408 TA TA TA TA TA
1 TA TA TA TA TA
2240418 AGGAAAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2243920 original size:58 final size:59
Alignment explanation
Indices: 2243830--2243945 Score: 175
Period size: 58 Copynumber: 2.0 Consensus size: 59
2243820 CAAGTTCCAG
2243830 TAGAATGAGATAACTAGCATAGGAAGCCCAACTGGAACA-AAAATGAATAAATAATCAA
1 TAGAATGAGATAACTAGCATAGGAAGCCCAACTGGAACAGAAAATGAATAAATAATCAA
* *
2243888 TAGAATTGAGATTAAGTAGC-T-GGAAGCCCAACTGGAACAGAAGATGAATAAATAATCA
1 TAGAA-TGAGA-TAACTAGCATAGGAAGCCCAACTGGAACAGAAAATGAATAAATAATCA
2243946 TGTAACTAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
58 23 0.43
59 23 0.43
60 7 0.13
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (59 bp):
TAGAATGAGATAACTAGCATAGGAAGCCCAACTGGAACAGAAAATGAATAAATAATCAA
Found at i:2264842 original size:2 final size:2
Alignment explanation
Indices: 2264835--2264879 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2264825 AATCAAACAA
2264835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2264877 AT A
1 AT A
2264880 CACGCGTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2265409 original size:20 final size:19
Alignment explanation
Indices: 2265384--2265424 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2265374 ATGTTATAAT
2265384 TAAAATAAATAATATTAAAA
1 TAAAATAAATAATA-TAAAA
*
2265404 TAAAATATATAATATAAAA
1 TAAAATAAATAATATAAAA
2265423 TA
1 TA
2265425 TTTTATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATAAATAATATAAAA
Found at i:2265413 original size:15 final size:15
Alignment explanation
Indices: 2265382--2265425 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
2265372 TAATGTTATA
2265382 ATTAAAAT-AAATAAT
1 ATTAAAATAAAAT-AT
2265397 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
2265412 A-TAATATAAAATAT
1 ATTAAAATAAAATAT
2265426 TTTATCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 12 0.44
15 11 0.41
16 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:2282441 original size:2 final size:2
Alignment explanation
Indices: 2282436--2282465 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2282426 TTACACACAA
2282436 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
2282466 CATTTGATTT
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:2289280 original size:15 final size:15
Alignment explanation
Indices: 2289260--2289290 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2289250 GATTGATCTA
2289260 TAGAATTATACATTG
1 TAGAATTATACATTG
2289275 TAGAATTATACATTG
1 TAGAATTATACATTG
2289290 T
1 T
2289291 TCTAAGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TAGAATTATACATTG
Found at i:2291126 original size:2 final size:2
Alignment explanation
Indices: 2291119--2291143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2291109 TTAGTTCAAA
2291119 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2291144 GTATCTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2291775 original size:24 final size:24
Alignment explanation
Indices: 2291745--2291803 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2291735 AATTTATCCA
*
2291745 CCACCCAAGCCGCCAACTTAC-TCT
1 CCACCCAAGCCGCCAAC-TACAGCT
*
2291769 CCCCCCAAGCCGCCAACTACAGCT
1 CCACCCAAGCCGCCAACTACAGCT
2291793 CCACCCAAGCC
1 CCACCCAAGCC
2291804 ACCAGTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.25, C:0.54, G:0.10, T:0.10
Consensus pattern (24 bp):
CCACCCAAGCCGCCAACTACAGCT
Found at i:2291833 original size:36 final size:36
Alignment explanation
Indices: 2291793--2291867 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
2291783 AACTACAGCT
*
2291793 CCACCCAAGCCACCAGTTCACCCACCAACTTACCCA
1 CCACCCAAGCCACCAGTTCACCCACCAACTAACCCA
* * *
2291829 CCACCCAAGCCACCGGTTCACCCTCCAACTAAGCCA
1 CCACCCAAGCCACCAGTTCACCCACCAACTAACCCA
2291865 CCA
1 CCA
2291868 ACTCAGCCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.52, G:0.08, T:0.11
Consensus pattern (36 bp):
CCACCCAAGCCACCAGTTCACCCACCAACTAACCCA
Found at i:2291870 original size:12 final size:12
Alignment explanation
Indices: 2291853--2291950 Score: 54
Period size: 12 Copynumber: 8.2 Consensus size: 12
2291843 GGTTCACCCT
2291853 CCAACTAAGCCA
1 CCAACTAAGCCA
* *
2291865 CCAACTCAGCCC
1 CCAACTAAGCCA
*
2291877 CCAACTAAGCCC
1 CCAACTAAGCCA
** * * *
2291889 CCAGTTCACCCT
1 CCAACTAAGCCA
* *
2291901 CC-AGTGAAGCCT
1 CCAACT-AAGCCA
2291913 CCAACTAAGCCA
1 CCAACTAAGCCA
* * *
2291925 CCAACTCATCCC
1 CCAACTAAGCCA
*
2291937 CCGACTAAGCCA
1 CCAACTAAGCCA
2291949 CC
1 CC
2291951 GGTTCACCCT
Statistics
Matches: 63, Mismatches: 21, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
11 1 0.02
12 60 0.95
13 2 0.03
ACGTcount: A:0.30, C:0.48, G:0.10, T:0.12
Consensus pattern (12 bp):
CCAACTAAGCCA
Found at i:2291914 original size:60 final size:60
Alignment explanation
Indices: 2291850--2291963 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
2291840 ACCGGTTCAC
*
2291850 CCTCCAACTAAGCCACCAACTCAGCCCCCAACTAAGCCCCCAGTTCACCCTCCAGTGAAG
1 CCTCCAACTAAGCCACCAACTCAGCCCCCAACTAAGCCACCAGTTCACCCTCCAGTGAAG
* * *
2291910 CCTCCAACTAAGCCACCAACTCATCCCCCGACTAAGCCACCGGTTCACCCTCCA
1 CCTCCAACTAAGCCACCAACTCAGCCCCCAACTAAGCCACCAGTTCACCCTCCA
2291964 ACATACCCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.27, C:0.48, G:0.11, T:0.14
Consensus pattern (60 bp):
CCTCCAACTAAGCCACCAACTCAGCCCCCAACTAAGCCACCAGTTCACCCTCCAGTGAAG
Found at i:2291938 original size:48 final size:48
Alignment explanation
Indices: 2291814--2291930 Score: 128
Period size: 48 Copynumber: 2.4 Consensus size: 48
2291804 ACCAGTTCAC
* * * * * *
2291814 CCACCAACTTACCCACCACCCAAGCCACCGGTTCACCCTCCAACTAAG
1 CCACCAACTAAGCCACCAACTAAGCCCCCAGTTCACCCTCCAACTAAG
* * *
2291862 CCACCAACTCAGCCCCCAACTAAGCCCCCAGTTCACCCTCC-AGTGAAG
1 CCACCAACTAAGCCACCAACTAAGCCCCCAGTTCACCCTCCAACT-AAG
*
2291910 CCTCCAACTAAGCCACCAACT
1 CCACCAACTAAGCCACCAACT
2291931 CATCCCCCGA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 2 0.04
48 55 0.96
ACGTcount: A:0.29, C:0.49, G:0.09, T:0.13
Consensus pattern (48 bp):
CCACCAACTAAGCCACCAACTAAGCCCCCAGTTCACCCTCCAACTAAG
Found at i:2291997 original size:24 final size:24
Alignment explanation
Indices: 2291910--2291998 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 24
2291900 TCCAGTGAAG
* *
2291910 CCTCCAACTAAGCCACCAACTCAT
1 CCTCCGACTAAGCCACCAGCTCAT
* * * *
2291934 CCCCCGACTAAGCCACCGGTTCAC
1 CCTCCGACTAAGCCACCAGCTCAT
* *
2291958 CCTCCAAC-ATACCCACCAGCTCAT
1 CCTCCGACTA-AGCCACCAGCTCAT
*
2291982 CCTCCGGCTAAGCCACC
1 CCTCCGACTAAGCCACC
2291999 CACTTACCCA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
23 1 0.02
24 46 0.96
25 1 0.02
ACGTcount: A:0.26, C:0.49, G:0.10, T:0.15
Consensus pattern (24 bp):
CCTCCGACTAAGCCACCAGCTCAT
Found at i:2302954 original size:12 final size:12
Alignment explanation
Indices: 2302939--2302968 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2302929 AAAAGTTGGA
2302939 AGAGAGAGAGAC
1 AGAGAGAGAGAC
*
2302951 AGAGACAGAGAC
1 AGAGAGAGAGAC
2302963 AGAGAG
1 AGAGAG
2302969 GGTTGTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAC
Found at i:2305460 original size:41 final size:41
Alignment explanation
Indices: 2305409--2305488 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
2305399 CATATTGAGT
*
2305409 TATTGGATTAAACTATTAAGATATAATATATTATAATAACC
1 TATTAGATTAAACTATTAAGATATAATATATTATAATAACC
* * * *
2305450 TATTAGATTAAATTGTTAAGATATAATATGTTATGATAA
1 TATTAGATTAAACTATTAAGATATAATATATTATAATAA
2305489 ACTTACATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (41 bp):
TATTAGATTAAACTATTAAGATATAATATATTATAATAACC
Found at i:2313765 original size:2 final size:2
Alignment explanation
Indices: 2313758--2313798 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2313748 ACATACATAC
2313758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2313799 CACACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2321045 original size:2 final size:2
Alignment explanation
Indices: 2321038--2321076 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
2321028 GTGTATATTT
2321038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
2321077 TTTGTGCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2324793 original size:26 final size:27
Alignment explanation
Indices: 2324737--2324794 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
2324727 GGTTGGTTTC
* * ***
2324737 GAAATTTTCGTTTCTTGGGTTGGACGT
1 GAAATTTTCGCTTCTTGGGTAGGAAAA
2324764 GAAATTTTC-CTTCTTGGGTAGGAAAA
1 GAAATTTTCGCTTCTTGGGTAGGAAAA
2324790 GAAAT
1 GAAAT
2324795 GTTGTGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (27 bp):
GAAATTTTCGCTTCTTGGGTAGGAAAA
Found at i:2326123 original size:18 final size:18
Alignment explanation
Indices: 2326100--2326148 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
2326090 AACACGCATG
2326100 GCAAATGATGTCAAAACT
1 GCAAATGATGTCAAAACT
*
2326118 GCAAATGAAGTCAAAACT
1 GCAAATGATGTCAAAACT
2326136 GCAAATGATGTCA
1 GCAAATGATGTCA
2326149 GAACCACCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (18 bp):
GCAAATGATGTCAAAACT
Found at i:2330076 original size:3 final size:3
Alignment explanation
Indices: 2330068--2330099 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2330058 GAGAGCCGGG
2330068 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
2330100 CATGGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:2335340 original size:2 final size:2
Alignment explanation
Indices: 2335333--2335376 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2335323 CAGTGGTAGA
2335333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2335375 AT
1 AT
2335377 TATGACTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2345183 original size:2 final size:2
Alignment explanation
Indices: 2345176--2345202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2345166 AAATTAGTTG
2345176 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2345203 GAAGTTTGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2346167 original size:4 final size:4
Alignment explanation
Indices: 2346158--2346185 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2346148 TTAGGAGTAA
2346158 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2346186 TAGTTGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:2354336 original size:9 final size:10
Alignment explanation
Indices: 2354303--2354337 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2354293 CCAAAGCCAC
*
2354303 AAAATGAAAA
1 AAAATGGAAA
2354313 ACAAATGGAAA
1 A-AAATGGAAA
2354324 AAAATGGAAA
1 AAAATGGAAA
2354334 AAAA
1 AAAA
2354338 AATAATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (10 bp):
AAAATGGAAA
Found at i:2358703 original size:30 final size:33
Alignment explanation
Indices: 2358669--2358771 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
2358659 CATTAGTTAA
*
2358669 AATAATATATATTATT-TTATATTAT-AT-AAT
1 AATAATATATATTATTAATATATTATAATAAAT
*
2358699 AATAATATGATA-TATTAATATTTTATAATAAAT
1 AATAATAT-ATATTATTAATATATTATAATAAAT
* **
2358732 AATAATATATA-TAATAATAATAACATAATAACAT
1 AATAATATATATTATTAAT-ATATTATAATAA-AT
2358766 AATAAT
1 AATAAT
2358772 TTTACTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 12 0.20
31 10 0.16
32 11 0.18
33 20 0.33
34 8 0.13
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (33 bp):
AATAATATATATTATTAATATATTATAATAAAT
Found at i:2358761 original size:8 final size:8
Alignment explanation
Indices: 2358723--2358770 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
2358713 TTAATATTTT
2358723 ATAATAA-
1 ATAATAAC
*
2358730 ATAATAAT
1 ATAATAAC
*
2358738 ATATATAATA
1 ATA-ATAA-C
2358748 ATAATAAC
1 ATAATAAC
2358756 ATAATAAC
1 ATAATAAC
2358764 ATAATAA
1 ATAATAA
2358771 TTTTACTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 7 0.19
8 18 0.50
9 8 0.22
10 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATAAC
Found at i:2358904 original size:24 final size:24
Alignment explanation
Indices: 2358863--2358912 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2358853 TAATTATTAG
*
2358863 ATATAAAAAATTATTTAATAAA-AA
1 ATATAAAAAATGATTTAA-AAATAA
2358887 ATATAAAAACATGA-TTAAAAATAA
1 ATATAAAAA-ATGATTTAAAAATAA
2358911 AT
1 AT
2358913 GAAGAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 17 0.74
25 3 0.13
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
ATATAAAAAATGATTTAAAAATAA
Found at i:2372374 original size:3 final size:3
Alignment explanation
Indices: 2372366--2372404 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2372356 AAACAAGGGT
* *
2372366 ATC ATC ATC ATC ATC ATC ATC ATC ACC GTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2372405 CATACACGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:2376041 original size:7 final size:7
Alignment explanation
Indices: 2376029--2376058 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2376019 TAAAATATTG
2376029 AAATGTA
1 AAATGTA
2376036 AAATGTA
1 AAATGTA
2376043 AAATGTA
1 AAATGTA
2376050 AAAT-TA
1 AAATGTA
2376056 AAA
1 AAA
2376059 AAAAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (7 bp):
AAATGTA
Found at i:2377065 original size:2 final size:2
Alignment explanation
Indices: 2377060--2377089 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2377050 CACACACACA
*
2377060 CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2377090 TAAAAGCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2383426 original size:6 final size:7
Alignment explanation
Indices: 2383410--2383434 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2383400 AAAGACATTC
2383410 AAAAATA
1 AAAAATA
2383417 AAAAATA
1 AAAAATA
2383424 AAAAATA
1 AAAAATA
2383431 AAAA
1 AAAA
2383435 GAAAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2394125 original size:10 final size:10
Alignment explanation
Indices: 2394098--2394135 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2394088 TTATATCTAT
2394098 TAAAAATAAA
1 TAAAAATAAA
2394108 T--AAATAAA
1 TAAAAATAAA
*
2394116 TAAAATTAAA
1 TAAAAATAAA
2394126 TAAAAATAAA
1 TAAAAATAAA
2394136 AATAATCACG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:2395832 original size:30 final size:30
Alignment explanation
Indices: 2395758--2395856 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 30
2395748 ATGTGAACGT
*
2395758 AAATATAAATTA-ATAAATTATATTTTAATATA
1 AAATA-AAATTATAAAAATT-TA-TTTAATATA
*
2395790 TAATAATTAATTATAAAAATTTATTTAATATA
1 AAATAA--AATTATAAAAATTTATTTAATATA
*
2395822 AAATAAAATTATAAAAATTTAATTAAATATA
1 AAATAAAATTATAAAAATTT-ATTTAATATA
2395853 AAAT
1 AAAT
2395857 CATATATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
30 14 0.24
31 14 0.24
32 18 0.31
33 7 0.12
34 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATAAAATTATAAAAATTTATTTAATATA
Found at i:2395845 original size:14 final size:14
Alignment explanation
Indices: 2395781--2395846 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
2395771 TAAATTATAT
*
2395781 TTTAATATATAATAA
1 TTTAAT-TATAAAAA
2395796 -TTAATTATAAAAA
1 TTTAATTATAAAAA
*
2395809 TTTATTTAATATAAAA
1 TTTAATT-ATA-AAAA
**
2395825 TAAAATTATAAAAA
1 TTTAATTATAAAAA
2395839 TTTAATTA
1 TTTAATTA
2395847 AATATAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
13 7 0.17
14 20 0.49
15 6 0.15
16 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAATTATAAAAA
Found at i:2413923 original size:24 final size:24
Alignment explanation
Indices: 2413891--2413941 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2413881 CGACGACAGG
*
2413891 ACAGCAGCAAGGA-CAAGAACAAGA
1 ACAGCAGC-AGCAGCAAGAACAAGA
*
2413915 ACAGCAGCAGCAGCAAGGACAAGA
1 ACAGCAGCAGCAGCAAGAACAAGA
2413939 ACA
1 ACA
2413942 AATTAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.51, C:0.24, G:0.25, T:0.00
Consensus pattern (24 bp):
ACAGCAGCAGCAGCAAGAACAAGA
Found at i:2416943 original size:24 final size:24
Alignment explanation
Indices: 2416916--2416962 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2416906 CATAATCCTC
*
2416916 CGGCGGTAATACTGGTTCATCAAA
1 CGGCGGTAATACGGGTTCATCAAA
2416940 CGGCGGTAATACGGGTTCATCAA
1 CGGCGGTAATACGGGTTCATCAA
2416963 CCGGTGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
CGGCGGTAATACGGGTTCATCAAA
Found at i:2417115 original size:24 final size:24
Alignment explanation
Indices: 2416957--2417113 Score: 226
Period size: 24 Copynumber: 6.5 Consensus size: 24
2416947 AATACGGGTT
2416957 CATCAACCGGTGGGGATGCTGGTG
1 CATCAACCGGTGGGGATGCTGGTG
*
2416981 CGTCAACCGGTGGGGATGCTGGTG
1 CATCAACCGGTGGGGATGCTGGTG
*
2417005 CAT-AGACCGGTGGGAATGCTGGTG
1 CATCA-ACCGGTGGGGATGCTGGTG
* *
2417029 CATCGACCTGTGGGGATGCTGGTG
1 CATCAACCGGTGGGGATGCTGGTG
* *
2417053 CATCGACCGGTGGTGATGCTGGTG
1 CATCAACCGGTGGGGATGCTGGTG
* *
2417077 CATCGACCGGTGGTGATGCTGGTG
1 CATCAACCGGTGGGGATGCTGGTG
2417101 CATCAACCGGTGG
1 CATCAACCGGTGG
2417114 TGTGCTTGAT
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.01
24 121 0.99
ACGTcount: A:0.15, C:0.21, G:0.41, T:0.22
Consensus pattern (24 bp):
CATCAACCGGTGGGGATGCTGGTG
Found at i:2435940 original size:2 final size:2
Alignment explanation
Indices: 2435933--2435966 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2435923 AAATGGAACC
2435933 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
2435967 CATCCAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2448737 original size:34 final size:34
Alignment explanation
Indices: 2448694--2448762 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2448684 TTTAACTATT
2448694 TAGACTACTAATAGGTCACATCAAAATATACTCA
1 TAGACTACTAATAGGTCACATCAAAATATACTCA
*
2448728 TAGACTACTAATAGGTCACGTCAAAATATACTCA
1 TAGACTACTAATAGGTCACATCAAAATATACTCA
2448762 T
1 T
2448763 GTGGTAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (34 bp):
TAGACTACTAATAGGTCACATCAAAATATACTCA
Found at i:2456449 original size:1 final size:1
Alignment explanation
Indices: 2456443--2456467 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2456433 CAAATTAAGA
2456443 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2456468 AAGACAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2471686 original size:20 final size:20
Alignment explanation
Indices: 2471661--2471702 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2471651 TATATAAGAG
2471661 TTATAAGTTTAAAACTATTT
1 TTATAAGTTTAAAACTATTT
* * *
2471681 TTATAATTTTATAATTATTT
1 TTATAAGTTTAAAACTATTT
2471701 TT
1 TT
2471703 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTAAAACTATTT
Found at i:2480729 original size:3 final size:3
Alignment explanation
Indices: 2480721--2480748 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2480711 CTGTAATGTA
2480721 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
2480749 ATGGCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:2497035 original size:16 final size:15
Alignment explanation
Indices: 2497003--2497041 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2496993 TTTGCTTTAC
2497003 TTATTTTAATTATTT
1 TTATTTTAATTATTT
* *
2497018 TTATTTTTATTTTATT
1 TTATTTTAATTAT-TT
2497034 TTATTTTA
1 TTATTTTA
2497042 TCCATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTAATTATTT
Found at i:2509605 original size:20 final size:21
Alignment explanation
Indices: 2509567--2509640 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
2509557 TTTCATAGTA
* *
2509567 ATATAGATTTATAAATAAATAT
1 ATATA-ATTAATATATAAATAT
2509589 ATATAATTAATAT-TAAAT-T
1 ATATAATTAATATATAAATAT
*
2509608 ATTATAATTATAATTTATAAAGTAT
1 A-TATAA-T-TAATATATAAA-TAT
2509633 ATATAATT
1 ATATAATT
2509641 TCTTAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.05
20 10 0.23
21 7 0.16
22 11 0.26
23 5 0.12
24 6 0.14
25 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
ATATAATTAATATATAAATAT
Found at i:2509672 original size:26 final size:25
Alignment explanation
Indices: 2509582--2509672 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 25
2509572 GATTTATAAA
2509582 TAAATATA-TA-TAATTAAT-A--T
1 TAAATATATTATTAATTAATAATTT
2509602 TAAAT-TATTA-TAATT-ATAATTT
1 TAAATATATTATTAATTAATAATTT
**
2509624 ATAAAGTATATATAATTTCTTAATATATTT
1 -TAAA-TATAT-T-ATTAATTAATA-ATTT
2509654 TAAATATATTATTAATTAA
1 TAAATATATTATTAATTAA
2509673 GTTTACTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
19 4 0.07
20 13 0.24
22 1 0.02
23 4 0.07
24 1 0.02
25 3 0.05
26 8 0.15
27 2 0.04
28 8 0.15
29 7 0.13
30 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TAAATATATTATTAATTAATAATTT
Found at i:2512868 original size:15 final size:15
Alignment explanation
Indices: 2512844--2512876 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2512834 TACATCATTG
2512844 TTAAATATAATA-TA
1 TTAAATATAATACTA
2512858 TTAACATATAATACTA
1 TTAA-ATATAATACTA
2512874 TTA
1 TTA
2512877 TCACCATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAATATAATACTA
Found at i:2512999 original size:28 final size:28
Alignment explanation
Indices: 2512935--2512988 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2512925 TTTGATTTAA
*
2512935 AATAAAAATATAAAATTTTATTAAATAT
1 AATAAAAATATAAAATTTTATAAAATAT
2512963 AATAAAAATATAAAATTTTA-AAAATA
1 AATAAAAATATAAAATTTTATAAAATA
2512989 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AATAAAAATATAAAATTTTATAAAATAT
Found at i:2514933 original size:28 final size:28
Alignment explanation
Indices: 2514856--2514933 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 28
2514846 GATATGTGAT
* * *
2514856 TTTTTTATTTA-AAAAATAAGATT-CAA
1 TTTTTTATTAATAAAAATAAGTTTAAAA
*
2514882 TTTTTT-TTAATTAAAAA-AATTTTAAAA
1 TTTTTTATTAA-TAAAAATAAGTTTAAAA
2514909 TTTTTTATTAATAAAAATAAGTTTA
1 TTTTTTATTAATAAAAATAAGTTTA
2514934 TTATTATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 3 0.07
26 10 0.24
27 19 0.45
28 10 0.24
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (28 bp):
TTTTTTATTAATAAAAATAAGTTTAAAA
Found at i:2535110 original size:29 final size:29
Alignment explanation
Indices: 2535052--2535127 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
2535042 AGGCATTAAA
* * *
2535052 GTGTAACAA-AAT-GTTTTTGAATATGGC
1 GTGTAACAACAATATTTTTTCAATATGAC
2535079 GTGTAACAACAATATTTTTTCAATATGAC
1 GTGTAACAACAATATTTTTTCAATATGAC
* *
2535108 GTGTAATAACAGTATTTTTT
1 GTGTAACAACAATATTTTTT
2535128 TTTTTTAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 9 0.21
28 3 0.07
29 30 0.71
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTCAATATGAC
Found at i:2535175 original size:23 final size:24
Alignment explanation
Indices: 2535149--2535199 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2535139 TACGTGTAAC
*
2535149 AACAT-TTTTT-AACTATATCGTGT
1 AACATGTTTTTGAAC-ATAGCGTGT
*
2535172 AACATGTTTTTGTACATAGCGTGT
1 AACATGTTTTTGAACATAGCGTGT
2535196 AACA
1 AACA
2535200 ACAGTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 17 0.71
25 2 0.08
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (24 bp):
AACATGTTTTTGAACATAGCGTGT
Found at i:2535182 original size:26 final size:25
Alignment explanation
Indices: 2535127--2535201 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
2535117 CAGTATTTTT
2535127 TTTTTTTAACAT-TACGTGTAACAAC
1 TTTTTTTAACATAT-CGTGTAACAAC
* **
2535152 ATTTTTTAACTATATCGTGTAACATG
1 TTTTTTTAAC-ATATCGTGTAACAAC
* *
2535178 TTTTTGT-ACATAGCGTGTAACAAC
1 TTTTTTTAACATATCGTGTAACAAC
2535202 AGTATTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
24 12 0.30
25 11 0.28
26 16 0.40
27 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (25 bp):
TTTTTTTAACATATCGTGTAACAAC
Found at i:2535264 original size:45 final size:45
Alignment explanation
Indices: 2535215--2535307 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 45
2535205 ATTTTTTTTA
* * *
2535215 ACATGGCATGTAACAATCTAA-TCATAACGTGTAACATGTTTTTGT
1 ACATGACATGCAACAACCTAACT-ATAACGTGTAACATGTTTTTGT
* * * *
2535260 ACATGACGTGCACCAACCTAACTATAGCGTGTCACATGTTTTTGT
1 ACATGACATGCAACAACCTAACTATAACGTGTAACATGTTTTTGT
2535305 ACA
1 ACA
2535308 GTGTAATATA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (45 bp):
ACATGACATGCAACAACCTAACTATAACGTGTAACATGTTTTTGT
Found at i:2535358 original size:65 final size:65
Alignment explanation
Indices: 2535243--2535372 Score: 161
Period size: 65 Copynumber: 2.0 Consensus size: 65
2535233 TAATCATAAC
* * * * * * *
2535243 GTGTAACATGTTTTTGTACATGACGTGCACCAACCTAACTATAGCGTGTCACATGTTTTTGTACA
1 GTGTAACATATTTTTGTACATGACGTACAACAACCTAACCATAACATGTCACATGTTTTTATACA
* * * *
2535308 GTGTAATATATTTTTGTGCATGACGTATAACAACTTAACCATAACATGTCACATGTTTTTATACA
1 GTGTAACATATTTTTGTACATGACGTACAACAACCTAACCATAACATGTCACATGTTTTTATACA
2535373 TGATGTGACA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (65 bp):
GTGTAACATATTTTTGTACATGACGTACAACAACCTAACCATAACATGTCACATGTTTTTATACA
Found at i:2535511 original size:17 final size:16
Alignment explanation
Indices: 2535487--2535527 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
2535477 TAAAAGAGAT
2535487 TTTTTTTTAAAAAATA
1 TTTTTTTTAAAAAATA
*
2535503 TCTTATTTTTAAAAATTA
1 T-TT-TTTTTAAAAAATA
2535521 TTTTTTT
1 TTTTTTT
2535528 AAATACTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 4 0.18
18 13 0.59
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTTTTAAAAAATA
Found at i:2544340 original size:28 final size:28
Alignment explanation
Indices: 2544303--2544439 Score: 96
Period size: 28 Copynumber: 4.9 Consensus size: 28
2544293 AATTATCTTG
*
2544303 AAAATTTAATTGTTACACGTTATATTAA
1 AAAATATAATTGTTACACGTTATATTAA
* ** * * *
2544331 AAAATATAATTGTTATATATCATGTTGA
1 AAAATATAATTGTTACACGTTATATTAA
** * *
2544359 AAAATATAGCTGTTACATGTTATATT-G
1 AAAATATAATTGTTACACGTTATATTAA
* * * *
2544386 AAAATTTTATTATTATACGTTATATTAA
1 AAAATATAATTGTTACACGTTATATTAA
* * * *
2544414 GAAATATTATTATTACACTTTATATT
1 AAAATATAATTGTTACACGTTATATT
2544440 GAAGATTTAG
Statistics
Matches: 82, Mismatches: 26, Indels: 2
0.75 0.24 0.02
Matches are distributed among these distances:
27 19 0.23
28 63 0.77
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (28 bp):
AAAATATAATTGTTACACGTTATATTAA
Found at i:2558354 original size:25 final size:27
Alignment explanation
Indices: 2558326--2558381 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
2558316 TTTGTATTTT
*
2558326 AAATAAAATAAATTTTTA-TAAT-AAA
1 AAATAAAATAAATTATTATTAATCAAA
*
2558351 AAAT--AATTAATTATTATTAATCAAA
1 AAATAAAATAAATTATTATTAATCAAA
2558376 AAATAA
1 AAATAA
2558382 CTTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATAAAATAAATTATTATTAATCAAA
Found at i:2558388 original size:25 final size:24
Alignment explanation
Indices: 2558336--2558390 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
2558326 AAATAAAATA
*
2558336 AATTTTTA-TAATAAAAAATAATT
1 AATTATTATTAATAAAAAATAATT
2558359 AATTATTATTAATCAAAAAATAACTT
1 AATTATTATTAAT-AAAAAATAA-TT
2558385 -ATTATT
1 AATTATT
2558391 TTTTATTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 4 0.14
25 15 0.54
26 2 0.07
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTATTATTAATAAAAAATAATT
Found at i:2558630 original size:19 final size:19
Alignment explanation
Indices: 2558602--2558640 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2558592 TAAAAATTAA
*
2558602 TAATTTATTTGAAATTTAT
1 TAATTAATTTGAAATTTAT
*
2558621 TAATTAATTTTAAATTTAT
1 TAATTAATTTGAAATTTAT
2558640 T
1 T
2558641 TTGTAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TAATTAATTTGAAATTTAT
Found at i:2563869 original size:3 final size:3
Alignment explanation
Indices: 2563861--2563895 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2563851 TGACGAAGCC
* *
2563861 ATG ATG ATG ATG ATG ATG ATG AAG ATG TTG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2563896 AGTGGCCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2611623 original size:27 final size:27
Alignment explanation
Indices: 2611585--2611648 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
2611575 ATGGTGCAAG
2611585 TATGGTGGATAGCTTGATGCCTGGCAC
1 TATGGTGGATAGCTTGATGCCTGGCAC
2611612 TATGGTGGATAGCTTGATGCCTGGCAC
1 TATGGTGGATAGCTTGATGCCTGGCAC
2611639 TATGGTGGAT
1 TATGGTGGAT
2611649 CTGTGAGCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (27 bp):
TATGGTGGATAGCTTGATGCCTGGCAC
Found at i:2614782 original size:32 final size:30
Alignment explanation
Indices: 2614745--2614804 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2614735 TAAAATTTTA
2614745 TTAATTAATTTACACAAAAAAAGTTAATGGTT
1 TTAATTAATTTACA-AAAAAAAG-TAATGGTT
* * *
2614777 TTAATTATTTTGCAGAAAAAAGTAATGG
1 TTAATTAATTTACAAAAAAAAGTAATGG
2614805 AAATCAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 7 0.28
32 12 0.48
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (30 bp):
TTAATTAATTTACAAAAAAAAGTAATGGTT
Found at i:2616150 original size:38 final size:38
Alignment explanation
Indices: 2616099--2616176 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
2616089 AATCCGTCAG
2616099 ATAGACTGCCCTATCATCTTTTAAAAACCAGAGCCCTC
1 ATAGACTGCCCTATCATCTTTTAAAAACCAGAGCCCTC
* *
2616137 ATAGACTGTCCTATCATCTTTTAAGAACCAGAGCCCTC
1 ATAGACTGCCCTATCATCTTTTAAAAACCAGAGCCCTC
2616175 AT
1 AT
2616177 TACCTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (38 bp):
ATAGACTGCCCTATCATCTTTTAAAAACCAGAGCCCTC
Found at i:2655253 original size:2 final size:2
Alignment explanation
Indices: 2655246--2655274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2655236 TAAGGTTTCC
2655246 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2655275 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2664548 original size:81 final size:81
Alignment explanation
Indices: 2664450--2664645 Score: 275
Period size: 81 Copynumber: 2.4 Consensus size: 81
2664440 ATGTTATATA
* * *
2664450 CCATGTTGAAAAAAAATATTGTTGTTACACGTCATGTACAAAAACATATTACATGGTATGATTAA
1 CCATGTTGAAAAAAAATATTGTTGTTACACGTCATATACAAAAACATATTACACGATATGATTAA
* *
2664515 AAAAAGTTATTACTCG
66 AAAAAATTATTACACG
* * * * * *
2664531 TCATGTTGAAAAAAAATATTGTTGCTACATGTCATATACAAAAATATATTATACGATATGGTTAA
1 CCATGTTGAAAAAAAATATTGTTGTTACACGTCATATACAAAAACATATTACACGATATGATTAA
2664596 AAAAAATTATTACACG
66 AAAAAATTATTACACG
* *
2664612 CCATGTTGAAAAAAAATATTATTATTACACGTCA
1 CCATGTTGAAAAAAAATATTGTTGTTACACGTCA
2664646 AATTATAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 99 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (81 bp):
CCATGTTGAAAAAAAATATTGTTGTTACACGTCATATACAAAAACATATTACACGATATGATTAA
AAAAAATTATTACACG
Found at i:2664601 original size:28 final size:26
Alignment explanation
Indices: 2664570--2664636 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
2664560 TGTCATATAC
*
2664570 AAAAATATATTATACGATATGGTTAAA
1 AAAAATATATTATACGACAT-GTTAAA
* *
2664597 AAAAAT-TATTACACGCCATGTTGAAA
1 AAAAATATATTATACGACATGTT-AAA
2664623 AAAAATATTATTAT
1 AAAAATA-TATTAT
2664637 TACACGTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 3 0.09
26 19 0.58
27 6 0.18
28 5 0.15
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (26 bp):
AAAAATATATTATACGACATGTTAAA
Found at i:2669064 original size:19 final size:19
Alignment explanation
Indices: 2669040--2669076 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2669030 CATTTAACCT
2669040 TGCTGCCGAAATTAAGGCC
1 TGCTGCCGAAATTAAGGCC
2669059 TGCTGCCGAAATTAAGGC
1 TGCTGCCGAAATTAAGGC
2669077 TATGTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (19 bp):
TGCTGCCGAAATTAAGGCC
Found at i:2672324 original size:14 final size:15
Alignment explanation
Indices: 2672305--2672333 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2672295 GTTTTTTTAA
2672305 GTTCCTTA-TACATT
1 GTTCCTTAGTACATT
2672319 GTTCCTTAGTACATT
1 GTTCCTTAGTACATT
2672334 AAGCAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (15 bp):
GTTCCTTAGTACATT
Found at i:2673465 original size:22 final size:22
Alignment explanation
Indices: 2673439--2673482 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2673429 ATGCTGTACG
*
2673439 TAACAATAATACTAAATGTTCA
1 TAACAAAAATACTAAATGTTCA
2673461 TAACAAAAATACTAAATGTTCA
1 TAACAAAAATACTAAATGTTCA
2673483 ATTTTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
TAACAAAAATACTAAATGTTCA
Found at i:2674538 original size:34 final size:33
Alignment explanation
Indices: 2674459--2674545 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 33
2674449 TTGATTTTTA
* * *
2674459 TCAACAAACGTAATTTTTTTTTATTTTTTTATTT
1 TCAACAAACATGA-TTTTTTTTATTTTTTAATTT
2674493 TCAACAAACATGACTTTTTTTTATTTTTTAATTT
1 TCAACAAACATGA-TTTTTTTTATTTTTTAATTT
* * *
2674527 TTAATAGACATGATTTTTT
1 TCAACAAACATGATTTTTT
2674546 CTTTTATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 6 0.13
34 40 0.87
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (33 bp):
TCAACAAACATGATTTTTTTTATTTTTTAATTT
Found at i:2685498 original size:20 final size:19
Alignment explanation
Indices: 2685475--2685534 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
2685465 TTATTAAATT
2685475 ATTTAATAAATTTTATATAA
1 ATTTAATAAATTTTAT-TAA
* ** *
2685495 ATTTATTTTATTTTATTAC
1 ATTTAATAAATTTTATTAA
2685514 ATTTAATCAAA-TTTATTAA
1 ATTTAAT-AAATTTTATTAA
2685533 AT
1 AT
2685535 AAACTTATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAATAAATTTTATTAA
Found at i:2687197 original size:2 final size:2
Alignment explanation
Indices: 2687190--2687224 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2687180 AGGATTACCA
2687190 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2687225 ACTTCATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2724207 original size:3 final size:3
Alignment explanation
Indices: 2724201--2724229 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2724191 ATTACTGTTG
2724201 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2724230 TTAGTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2739996 original size:24 final size:23
Alignment explanation
Indices: 2739935--2740010 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
2739925 TGTTTTTAAA
* *
2739935 TTATAACATGTAATATGTTTTTGT
1 TTATAATATGTAATATATTTTT-T
* *
2739959 ATATAATACGTAATATATTTTTAT
1 TTATAATATGTAATATATTTTT-T
*
2739983 TTATAATATATAATAATATTATTTT
1 TTATAATATGTAAT-ATATT-TTTT
2740008 TTA
1 TTA
2740011 ACATGACGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 30 0.71
25 9 0.21
26 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (23 bp):
TTATAATATGTAATATATTTTTT
Found at i:2752448 original size:30 final size:30
Alignment explanation
Indices: 2752414--2752481 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2752404 AGTCTAATTC
* *
2752414 AACTCTAGCTA-ATTAATAATATTGTAGTAT
1 AACTCTAACTAGA-TAATAATAGTGTAGTAT
* *
2752444 AACTCTAACTAGATAATAGTAGTGTATTAT
1 AACTCTAACTAGATAATAATAGTGTAGTAT
2752474 AACTCTAA
1 AACTCTAA
2752482 TTAAATAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (30 bp):
AACTCTAACTAGATAATAATAGTGTAGTAT
Found at i:2752488 original size:27 final size:27
Alignment explanation
Indices: 2752422--2752489 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 27
2752412 TCAACTCTAG
*
2752422 CTAATT-AATAATATTGTAGTATAACT
1 CTAATTAAATAATAGTGTAGTATAACT
* * *
2752448 CTAACTAGATAATAGTAGTGTATTATAACT
1 CTAA-T-TA-AATAATAGTGTAGTATAACT
2752478 CTAATTAAATAA
1 CTAATTAAATAA
2752490 GTTGTATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
26 4 0.12
27 5 0.16
28 1 0.03
29 1 0.03
30 21 0.66
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (27 bp):
CTAATTAAATAATAGTGTAGTATAACT
Found at i:2761628 original size:80 final size:80
Alignment explanation
Indices: 2761535--2761747 Score: 275
Period size: 80 Copynumber: 2.6 Consensus size: 80
2761525 CCTTGAGATT
* *
2761535 ATTTAGAGATAATATTTA-AATTAGATCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTC
1 ATTTAGAGATAATATTTATAATTAGACCAATC-AAAAATTAGTTATTGGTCATCCAATTTATCCC
2761599 TAAATAAATCAAAATA
65 TAAATAAATCAAAATA
* * *
2761615 ATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGTTATTGGTCATCCAATTTATCCCT
1 ATTTAGAGATAATATTTATAATTAGACCAATCAAAAATTAGTTATTGGTCATCCAATTTATCCCT
*
2761680 AAATAAATTAAAATA
66 AAATAAATCAAAATA
* * * * * * * *
2761695 ATTTGGAGATAATCTTCATATTTTTGACCAATCAAAATTTAATTATTGATCAT
1 ATTTAGAGATAATATTTATA-ATTAGACCAATCAAAAATTAGTTATTGGTCAT
2761748 TTAATTATCT
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 80 0.68
81 38 0.32
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (80 bp):
ATTTAGAGATAATATTTATAATTAGACCAATCAAAAATTAGTTATTGGTCATCCAATTTATCCCT
AAATAAATCAAAATA
Found at i:2762261 original size:80 final size:80
Alignment explanation
Indices: 2762087--2762337 Score: 321
Period size: 80 Copynumber: 3.1 Consensus size: 80
2762077 AATTTGATTT
* * * * * *
2762087 TTATCTCTAAATTAATAT-AATTA-TTAGAGATAATTTAAATGACCAATAATTAA-ATTTTGATT
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAATA-TTTGATT
* *
2762149 GGTCAAAAATATGAAGA
65 GGTC-AAAATATAAATA
2762166 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAATATTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAATATTTGATTG
2762231 GTCAAAATATAAATA
66 GTCAAAATATAAATA
* *
2762246 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTTGATT
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAA-TATTTGATT
* * *
2762311 GATC-CAATTTAAATA
65 GGTCAAAATATAAATA
*
2762326 TTATCTCCAAAT
1 TTATCTCTAAAT
2762338 AATCTCAAGG
Statistics
Matches: 154, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
79 16 0.10
80 88 0.57
81 49 0.32
82 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (80 bp):
TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAATATTTGATTG
GTCAAAATATAAATA
Found at i:2781152 original size:30 final size:30
Alignment explanation
Indices: 2781107--2781164 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2781097 GTAAACGAGT
*
2781107 TTATTTAATTCAAAATAAAAATATAAAAAA
1 TTATTCAATTCAAAATAAAAATATAAAAAA
*
2781137 TTATTCAATTTAAAATAAAAATATAAAA
1 TTATTCAATTCAAAATAAAAATATAAAA
2781165 TTGATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
TTATTCAATTCAAAATAAAAATATAAAAAA
Found at i:2781193 original size:30 final size:29
Alignment explanation
Indices: 2781120--2781193 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
2781110 TTTAATTCAA
* *
2781120 AATAAAAATATAA-AAAATTATTCAATTT
1 AATAAAAAAATAATAAAATTATTCAATGT
*
2781148 AA-AATAAAAAT-ATAAAATTGATTGAATGT
1 AATAA-AAAAATAATAAAATT-ATTCAATGT
2781177 AATAAAAAAATAATAAA
1 AATAAAAAAATAATAAA
2781194 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 3 0.08
28 13 0.34
29 15 0.39
30 7 0.18
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
AATAAAAAAATAATAAAATTATTCAATGT
Found at i:2781230 original size:21 final size:22
Alignment explanation
Indices: 2781192--2781236 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2781182 AAAAATAATA
* *
2781192 AATTTAATTAATTTTTTTTGAAT
1 AATTTAA-TAATTCTTTTTAAAT
2781215 AATTTAA-AATTCTTTTTAAAT
1 AATTTAATAATTCTTTTTAAAT
2781236 A
1 A
2781237 TTACACCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTTAATAATTCTTTTTAAAT
Found at i:2789403 original size:24 final size:24
Alignment explanation
Indices: 2789375--2789422 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2789365 CGAAGATAAA
2789375 CCAAAATGTACATCATCAACAGAT
1 CCAAAATGTACATCATCAACAGAT
*
2789399 CCAAAATGTACGTCATCAACAGAT
1 CCAAAATGTACATCATCAACAGAT
2789423 TGAACAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (24 bp):
CCAAAATGTACATCATCAACAGAT
Found at i:2797657 original size:23 final size:23
Alignment explanation
Indices: 2797627--2797672 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2797617 CTTAGTGTAC
2797627 CACTTAGGCTAATCACCAATATT
1 CACTTAGGCTAATCACCAATATT
2797650 CACTTAGGCTAATCACCAATATT
1 CACTTAGGCTAATCACCAATATT
2797673 GACCTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (23 bp):
CACTTAGGCTAATCACCAATATT
Found at i:2799770 original size:104 final size:104
Alignment explanation
Indices: 2799590--2799796 Score: 324
Period size: 104 Copynumber: 2.0 Consensus size: 104
2799580 ACATGTTGAC
* * *
2799590 AGTCTCACTCAATCAAGACAAAATTCAAAGCTTTGCTTGGGAATCAAGAGTTGTTTCTGAGGTTA
1 AGTCTCACTCAATCAAGACAAAATCCAAAGCTTTGCTCGGGAATCAAGAGTTGTTTCTGAGGCTA
2799655 GAAACTCATGTGTTCATGGTTGATGACGAGATGAAAGAG
66 GAAACTCATGTGTTCATGGTTGATGACGAGATGAAAGAG
* * * **
2799694 AGTCTGACTCAATCAAGACAAAATCCAAAGTTTTGCTCGTGAATTGAGAGTTGTTTCTGAGGCTA
1 AGTCTCACTCAATCAAGACAAAATCCAAAGCTTTGCTCGGGAATCAAGAGTTGTTTCTGAGGCTA
* *
2799759 GAAACTCATGTGTTCATGGTTGATGATGAGATGCAAGA
66 GAAACTCATGTGTTCATGGTTGATGACGAGATGAAAGA
2799797 ATCGGGAAGA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (104 bp):
AGTCTCACTCAATCAAGACAAAATCCAAAGCTTTGCTCGGGAATCAAGAGTTGTTTCTGAGGCTA
GAAACTCATGTGTTCATGGTTGATGACGAGATGAAAGAG
Found at i:2830164 original size:2 final size:2
Alignment explanation
Indices: 2830157--2830201 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2830147 ACGGTTAGAA
2830157 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2830199 CT C
1 CT C
2830202 CTGGTGTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2831667 original size:30 final size:30
Alignment explanation
Indices: 2831605--2831667 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2831595 AGTTTTTGTG
** *
2831605 TTTTTATCTTTAAATAAATAAATATTTTTA
1 TTTTTATCTTTAAATAAATAAATACATATA
*
2831635 TTTTTAT-TTTAAAGTAAATAAATCCATATA
1 TTTTTATCTTTAAA-TAAATAAATACATATA
2831665 TTT
1 TTT
2831668 AATATTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTTATCTTTAAATAAATAAATACATATA
Found at i:2846022 original size:23 final size:23
Alignment explanation
Indices: 2845996--2846040 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2845986 AATGTAAAAA
2845996 ATTATAAA-ATTAAAATAAATATT
1 ATTA-AAATATTAAAATAAATATT
*
2846019 ATTAAAATATTAACATAAATAT
1 ATTAAAATATTAAAATAAATAT
2846041 AAGAGTTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAAATATTAAAATAAATATT
Found at i:2866639 original size:2 final size:2
Alignment explanation
Indices: 2866632--2866660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2866622 AGAAATCCTT
2866632 TA 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 TA T
2866661 GTATGTAGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2882140 original size:15 final size:15
Alignment explanation
Indices: 2882120--2882151 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2882110 TCCTTCTCCT
*
2882120 TCGCTTTCCTCCGCC
1 TCGCTTTCCTCCCCC
2882135 TCGCTTTCCTCCCCC
1 TCGCTTTCCTCCCCC
2882150 TC
1 TC
2882152 TTCCTCATCA
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:0.00, C:0.56, G:0.09, T:0.34
Consensus pattern (15 bp):
TCGCTTTCCTCCCCC
Found at i:2886765 original size:2 final size:2
Alignment explanation
Indices: 2886760--2886807 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2886750 TAATATATAT
*
2886760 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA -A GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2886801 GA GA GA G
1 GA GA GA G
2886808 CTCATGTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2889945 original size:6 final size:6
Alignment explanation
Indices: 2889925--2889970 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2889915 CGTTGCCGCC
* * * *
2889925 GTTGCT GTTTCT GTTGTT GTTGTT GTTGCT GCTGCT GTTGCT GTTG
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTG
2889971 TCAAGACTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.13, G:0.33, T:0.54
Consensus pattern (6 bp):
GTTGCT
Found at i:2897541 original size:2 final size:2
Alignment explanation
Indices: 2897534--2897559 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2897524 ACACCTCCAA
2897534 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
2897560 GCCTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2911070 original size:18 final size:18
Alignment explanation
Indices: 2911031--2911085 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
2911021 TGATTGGGTC
*
2911031 AATT-TTTTAAAAAAAT-
1 AATTATTTTAAAAAATTA
2911047 AA-TATTTTAAAAAATTA
1 AATTATTTTAAAAAATTA
2911064 AATTA-TTTAAATAAATTTA
1 AATTATTTTAAA-AAA-TTA
2911083 AAT
1 AAT
2911086 AAATATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.39
17 8 0.24
18 5 0.15
19 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTTTAAAAAATTA
Found at i:2930290 original size:23 final size:21
Alignment explanation
Indices: 2930260--2930308 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
2930250 CACCCTGTGA
2930260 TTTTGTTTTGCATTTGTTTTTTG
1 TTTTGTTTTG-ATTT-TTTTTTG
* *
2930283 TTTTGTTTTGGTTTTTTTTTT
1 TTTTGTTTTGATTTTTTTTTG
2930304 TTTTG
1 TTTTG
2930309 AAAATTACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 3 0.12
23 10 0.42
ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80
Consensus pattern (21 bp):
TTTTGTTTTGATTTTTTTTTG
Found at i:2930296 original size:18 final size:18
Alignment explanation
Indices: 2930260--2930308 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2930250 CACCCTGTGA
*
2930260 TTTTGTTTTGCATTT-GTT
1 TTTTGTTTTG-TTTTGGTT
2930278 TTTTGTTTTGTTTTGGTT
1 TTTTGTTTTGTTTTGGTT
2930296 TTTT-TTTT-TTTTG
1 TTTTGTTTTGTTTTG
2930309 AAAATTACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 17 0.59
ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80
Consensus pattern (18 bp):
TTTTGTTTTGTTTTGGTT
Found at i:2933918 original size:3 final size:3
Alignment explanation
Indices: 2933910--2933945 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2933900 ACTGAAACAA
2933910 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2933946 GAATAAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2960677 original size:14 final size:14
Alignment explanation
Indices: 2960658--2960684 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2960648 ATGCTTACAG
2960658 GTAAAAAAAAAAAT
1 GTAAAAAAAAAAAT
2960672 GTAAAAAAAAAAA
1 GTAAAAAAAAAAA
2960685 ACAATATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
GTAAAAAAAAAAAT
Found at i:2972075 original size:2 final size:2
Alignment explanation
Indices: 2972068--2972101 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2972058 TGGCAGACAC
*
2972068 AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2972102 GCATAAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Done.