Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 11 of 12
Found at i:2297750 original size:21 final size:19
Alignment explanation
Indices: 2297703--2297750 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
2297693 TCCGGTATCA
2297703 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2297722 TTGATACCGGGTTTTATCATAT
1 TT-TTACC-GGTTTTATCAT-T
2297744 TTTTACC
1 TTTTACC
2297751 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 4 0.17
21 15 0.62
22 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2297930 original size:20 final size:19
Alignment explanation
Indices: 2297884--2297930 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2297874 TCCGGTAACG
*
2297884 TTTTACGGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2297903 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2297924 TTTTACC
1 TTTTACC
2297931 TAGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2297974 original size:181 final size:181
Alignment explanation
Indices: 2297670--2298142 Score: 716
Period size: 181 Copynumber: 2.6 Consensus size: 181
2297660 CGTACTTACG
* *
2297670 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACC-GGTT
* *
2297735 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTAT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTAT
* *
2297800 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTTGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
2297851 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACGGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
2297916 TATCATATTTTTACCTAG-TATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTA
66 TATCATATTTTTACCT-GTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTA
** * *
2297980 TAGGATTTAAAACTGCTTCTCTTTTAAATTTACGAAGTGTCGATCCTTATATT
129 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
2298033 AAAGTACCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2298098 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2298143 AATTTGGATC
Statistics
Matches: 266, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
180 47 0.18
181 120 0.45
182 99 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2299177 original size:28 final size:28
Alignment explanation
Indices: 2299145--2299198 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2299135 ACAAAAGAAT
*
2299145 TATTTTATAAATTA-TAATAAATATTAAA
1 TATTTTATAAAATATTAATAAA-ATTAAA
*
2299173 TATTTTTTAAAATATTAATAAAATTA
1 TATTTTATAAAATATTAATAAAATTA
2299199 TTAAAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTTTATAAAATATTAATAAAATTAAA
Found at i:2299204 original size:20 final size:20
Alignment explanation
Indices: 2299179--2299249 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
2299169 TAAATATTTT
2299179 TTAAAATATTAATAAAATTA
1 TTAAAATATTAATAAAATTA
*
2299199 TTAAAA-ATCTAAATAATATTA
1 TTAAAATAT-T-AATAAAATTA
* * * *
2299220 -TAAATTTATTTACAAATTTA
1 TTAAA-ATATTAATAAAATTA
2299240 TTAAAATATT
1 TTAAAATATT
2299250 TTGAAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.05
20 21 0.54
21 14 0.36
22 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAATATTAATAAAATTA
Found at i:2317096 original size:29 final size:28
Alignment explanation
Indices: 2317053--2317112 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
2317043 ATGCAATTCT
2317053 AAATATTAATGAAACTAA-CATAAAAAATA
1 AAATATTAATGAAAC-AATC-TAAAAAATA
2317082 AAATCATTAAT-AAACAATTCTAAAAAATA
1 AAAT-ATTAATGAAACAA-TCTAAAAAATA
2317111 AA
1 AA
2317113 GTAAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 2 0.07
29 19 0.68
30 7 0.25
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATATTAATGAAACAATCTAAAAAATA
Found at i:2317803 original size:19 final size:16
Alignment explanation
Indices: 2317768--2317820 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 16
2317758 GTTATTAATT
*
2317768 ATAATTTATAATATTTTG
1 ATAA-TTATAAT-TTTTA
2317786 ATAGATATATATATTTTTA
1 ATA-AT-TATA-ATTTTTA
2317805 ATAATTATAATTTTTA
1 ATAATTATAATTTTTA
2317821 TTATTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.23
17 4 0.13
18 6 0.19
19 12 0.39
20 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
ATAATTATAATTTTTA
Found at i:2318028 original size:16 final size:16
Alignment explanation
Indices: 2318007--2318040 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2317997 AAACTTATGC
*
2318007 ATAAGTATATATATAT
1 ATAAGTATATACATAT
*
2318023 ATAAGTGTATACATAT
1 ATAAGTATATACATAT
2318039 AT
1 AT
2318041 CTAAGTGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (16 bp):
ATAAGTATATACATAT
Found at i:2318038 original size:18 final size:18
Alignment explanation
Indices: 2318011--2318062 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
2318001 TTATGCATAA
2318011 GTATATATATATATAAGT
1 GTATATATATATATAAGT
* *
2318029 GTATACATATATCTAAGT
1 GTATATATATATATAAGT
* *
2318047 GTGTGTATATATATAA
1 GTATATATATATATAA
2318063 AAAGTATGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (18 bp):
GTATATATATATATAAGT
Found at i:2318192 original size:19 final size:19
Alignment explanation
Indices: 2318154--2318192 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2318144 TACATATATT
*
2318154 TTATGCATATAAATTGATA
1 TTATGCATATAAATTAATA
* *
2318173 TTATGCCTATATATTAATA
1 TTATGCATATAAATTAATA
2318192 T
1 T
2318193 ACATATCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
TTATGCATATAAATTAATA
Found at i:2319610 original size:14 final size:15
Alignment explanation
Indices: 2319593--2319621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2319583 TACATGATAT
2319593 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
2319607 GCATAAAACATAAGA
1 GCATAAAACATAAGA
2319622 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:2319895 original size:22 final size:22
Alignment explanation
Indices: 2319863--2319942 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
2319853 GAGAGCTATA
*
2319863 GGTCCTTCGGGACATATCAAGT
1 GGTCCTACGGGACATATCAAGT
2319885 GGTCCTACGGGACATATCAAGT
1 GGTCCTACGGGACATATCAAGT
*
2319907 GGTCCTACGGGACATATCATGT
1 GGTCCTACGGGACATATCAAGT
*
2319929 GGTCCTTCGGGACA
1 GGTCCTACGGGACA
2319943 AATATCAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (22 bp):
GGTCCTACGGGACATATCAAGT
Found at i:2320900 original size:18 final size:17
Alignment explanation
Indices: 2320868--2320901 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2320858 TAAGATTAGA
2320868 GAATGATTCATGATGTT
1 GAATGATTCATGATGTT
*
2320885 GAATGATATTATGATGT
1 GAATGAT-TCATGATGT
2320902 GTTTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (17 bp):
GAATGATTCATGATGTT
Found at i:2325820 original size:14 final size:15
Alignment explanation
Indices: 2325803--2325831 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2325793 TACATGATAT
2325803 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
2325817 GCATAAAACATAAGA
1 GCATAAAACATAAGA
2325832 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:2326136 original size:22 final size:22
Alignment explanation
Indices: 2326108--2326211 Score: 181
Period size: 22 Copynumber: 4.7 Consensus size: 22
2326098 AGGGTTTCAC
2326108 GTGGTCCTTCGGGACATATCAA
1 GTGGTCCTTCGGGACATATCAA
2326130 GTGGTCCTTCGGGACATATCAA
1 GTGGTCCTTCGGGACATATCAA
*
2326152 GTGGTCCTACGGGACATATCAA
1 GTGGTCCTTCGGGACATATCAA
* *
2326174 GTGGTCCTACGGGACATATCAT
1 GTGGTCCTTCGGGACATATCAA
2326196 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
2326212 AATATCAATA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (22 bp):
GTGGTCCTTCGGGACATATCAA
Found at i:2327331 original size:13 final size:14
Alignment explanation
Indices: 2327299--2327336 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2327289 CATGTGTGTT
*
2327299 ATTTAATTTATTTAA
1 ATTTCATTT-TTTAA
2327314 ATTTCATTTTTT-A
1 ATTTCATTTTTTAA
2327327 ATTTCATTTT
1 ATTTCATTTT
2327337 GTTTAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTCATTTTTTAA
Found at i:2329804 original size:13 final size:13
Alignment explanation
Indices: 2329788--2329813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2329778 ACCCCTTGTA
2329788 ACTCAATTTCTTG
1 ACTCAATTTCTTG
2329801 ACTCAATTTCTTG
1 ACTCAATTTCTTG
2329814 CAACTCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTCAATTTCTTG
Found at i:2329819 original size:15 final size:14
Alignment explanation
Indices: 2329782--2329819 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
2329772 GTAGAAACCC
2329782 CTTGTAACTCAATTT
1 CTTG-AACTCAATTT
2329797 CTTG-ACTCAATTT
1 CTTGAACTCAATTT
2329810 CTTGCAACTC
1 CTTG-AACTC
2329820 TAAACTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 13 0.62
15 8 0.38
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (14 bp):
CTTGAACTCAATTT
Found at i:2340995 original size:19 final size:19
Alignment explanation
Indices: 2340968--2341018 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2340958 GTTGTTTTTA
2340968 AAATAAAAAAAATAAGAATT
1 AAAT-AAAAAAATAAGAATT
*
2340988 AAATAAAATAAA-AATAATT
1 AAATAAAA-AAATAAGAATT
*
2341007 AAATAAACAAAT
1 AAATAAAAAAAT
2341019 TAAAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.11
19 17 0.63
20 7 0.26
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:2341341 original size:21 final size:21
Alignment explanation
Indices: 2341317--2341363 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2341307 AAATTAGCTA
2341317 AGCATGACCAAAGTCATACTT
1 AGCATGACCAAAGTCATACTT
2341338 AGCATGACCAAAGTCATACTT
1 AGCATGACCAAAGTCATACTT
2341359 AGCAT
1 AGCAT
2341364 AATAGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
AGCATGACCAAAGTCATACTT
Found at i:2341634 original size:25 final size:24
Alignment explanation
Indices: 2341587--2341634 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2341577 AAATCCTAAT
* **
2341587 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
2341611 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
2341635 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:2341718 original size:76 final size:76
Alignment explanation
Indices: 2341505--2341730 Score: 245
Period size: 76 Copynumber: 3.1 Consensus size: 76
2341495 TAAAACATCT
* * *
2341505 TAAATCCTAATTAAAACACTTAAAAC-TATTTAAACTAAAATATCT---A-AAAA-ATAATATTT
1 TAAAACCTAATTAAAATAC-TAAAACATATTTAAACTAAAATACCTAAAATAAAATATAATATTT
*
2341564 AAAATAATATTC
65 AAAATAATATCC
* * * *
2341576 TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATA-TA
1 TAAAACCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAATAAA-ATATAATATTT
2341640 AAAATAATATCC
65 AAAATAATATCC
* * * *
2341652 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTGAAATA-C-AAAGATAAAATATAATGTTT
1 TAAAACCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAA-ATAAAATATAATATTT
*
2341715 AAAATATTATCC
65 AAAATAATATCC
2341727 TAAA
1 TAAA
2341731 CTTGAGTTTA
Statistics
Matches: 132, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
70 6 0.05
71 36 0.27
74 10 0.08
75 24 0.18
76 51 0.39
77 5 0.04
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (76 bp):
TAAAACCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAATAAAATATAATATTTA
AAATAATATCC
Found at i:2342374 original size:22 final size:22
Alignment explanation
Indices: 2342343--2342398 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2342333 TAGGGTAGGG
*
2342343 AAAATGCCGAAAAGAAAGGTTT
1 AAAATACCGAAAAGAAAGGTTT
2342365 AAAATACCGAAAAGAAAGGTTT
1 AAAATACCGAAAAGAAAGGTTT
2342387 AAAATACCGAAA
1 AAAATACCGAAA
2342399 CAAGAGATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.16
Consensus pattern (22 bp):
AAAATACCGAAAAGAAAGGTTT
Found at i:2348994 original size:19 final size:18
Alignment explanation
Indices: 2348975--2349023 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
2348965 GTTGTTTTTA
*
2348975 AAATAAAAAATAAGAATT
1 AAATAAAAAATAACAATT
*
2348993 AAATAAAAGAAAAACAATT
1 AAATAAAA-AATAACAATT
2349012 AAATAAACAAAT
1 AAATAAA-AAAT
2349024 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (18 bp):
AAATAAAAAATAACAATT
Found at i:2349656 original size:76 final size:71
Alignment explanation
Indices: 2349488--2349679 Score: 233
Period size: 76 Copynumber: 2.6 Consensus size: 71
2349478 TAAAACATCT
* * * *
2349488 TAAATCCTAATTAAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATTTAAAA
1 TAAAACCTAATT-AAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATTAAAAA
*
2349552 TAATATTA
64 TAATATCA
*
2349560 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AA-AAA-ATAAAAT-TAA
*
2349625 AAATAATATCC
61 AAATAATATCA
*
2349636 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATAC
2349680 AAAGATAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
70 5 0.05
71 26 0.25
72 12 0.11
73 2 0.02
74 3 0.03
75 6 0.06
76 29 0.27
77 23 0.22
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (71 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATTAAAAATA
ATATCA
Found at i:2349703 original size:77 final size:75
Alignment explanation
Indices: 2349488--2349703 Score: 221
Period size: 76 Copynumber: 2.9 Consensus size: 75
2349478 TAAAACATCT
* * * *
2349488 TAAATCCTAATTAAAAACACTTAAAA-CTATTTAAACTAAAATAC---CTAAAAAATAATATTT-
1 TAAAACCTAATT-AAAATAC-TAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTA
*
2349548 AAAATAATATTA
64 AAAATAATATCA
* * *
2349560 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATA-AA-ATAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
*
2349623 AAAAATAATATCC
63 AAAAATAATATCA
* *
2349636 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTA
1 TAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTA
2349701 AAA
64 AAA
2349704 TATTGTCATA
Statistics
Matches: 120, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
70 5 0.04
71 23 0.19
72 13 0.11
75 9 0.08
76 40 0.33
77 30 0.25
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
AATAATATCA
Found at i:2350797 original size:20 final size:20
Alignment explanation
Indices: 2350772--2350864 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
2350762 TTTTCCCAAT
2350772 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2350792 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2350812 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
2350833 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2350854 TCGCAATGCGA
1 TCGCAATGCGA
2350865 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2350814 original size:41 final size:41
Alignment explanation
Indices: 2350769--2350864 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2350759 CGATTTTCCC
2350769 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
2350810 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
2350851 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2350865 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:2350818 original size:21 final size:20
Alignment explanation
Indices: 2350772--2350864 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2350762 TTTTCCCAAT
*
2350772 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
2350792 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
2350812 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
2350833 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
2350854 TCGCAATGCGA
1 TCGCAATGCGA
2350865 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:2350878 original size:20 final size:20
Alignment explanation
Indices: 2350853--2350946 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2350843 AATTGGGAAA
*
2350853 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * * **
2350873 ATCGCAATGTGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2350894 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2350914 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2350934 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2350947 TTACATAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2351524 original size:19 final size:19
Alignment explanation
Indices: 2351500--2351544 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2351490 GCAACGAGAT
* *
2351500 AATCGCAACGTGAAATAAA
1 AATCGCAACGCGAAACAAA
*
2351519 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
2351538 AATCGCA
1 AATCGCA
2351545 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:2351562 original size:19 final size:19
Alignment explanation
Indices: 2351540--2351629 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
2351530 GAAACCAAAA
*
2351540 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2351559 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2351578 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2351597 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
2351617 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2351630 GTCTGGTATA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2351617 original size:39 final size:38
Alignment explanation
Indices: 2351540--2351629 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2351530 GAAACCAAAA
*
2351540 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
2351578 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
2351617 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2351630 GTCTGGTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2353689 original size:42 final size:42
Alignment explanation
Indices: 2353630--2353711 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
2353620 GCCCGACTCG
2353630 CCTATCATCCCTCAAGATTCCACTC-CTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGATTCCACTCTC-ATCGTTGAAGAGGCC
*
2353672 CCTATCATCCCTCAAGATTCCACTGTCATCGTTGAAGAGG
1 CCTATCATCCCTCAAGATTCCACTCTCATCGTTGAAGAGG
2353712 TCCTTCCCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (42 bp):
CCTATCATCCCTCAAGATTCCACTCTCATCGTTGAAGAGGCC
Found at i:2355107 original size:14 final size:14
Alignment explanation
Indices: 2355088--2355123 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2355078 ATTGTTTAAT
2355088 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2355102 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2355116 TGATTTGT
1 TGATTTGT
2355124 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2355287 original size:20 final size:19
Alignment explanation
Indices: 2355230--2355297 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
2355220 AAAGAGTACT
2355230 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2355249 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2355263 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
*
2355283 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
2355298 TAAATTCACG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2355348 original size:33 final size:32
Alignment explanation
Indices: 2355306--2355432 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
2355296 ATTAAATTCA
2355306 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
2355339 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
2355372 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2355405 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2355433 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2355395 original size:66 final size:66
Alignment explanation
Indices: 2355306--2355429 Score: 239
Period size: 66 Copynumber: 1.9 Consensus size: 66
2355296 ATTAAATTCA
2355306 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAAAATTA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAAAATTA
2355371 G
66 G
*
2355372 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2355430 GATAGTAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAAAATTA
G
Found at i:2357959 original size:24 final size:24
Alignment explanation
Indices: 2357925--2357978 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2357915 CTGAAACATC
* *
2357925 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
2357949 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
2357973 ATCAAA
1 ATCAAA
2357979 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:2359043 original size:20 final size:20
Alignment explanation
Indices: 2359018--2359095 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
2359008 ATTCATTTGA
2359018 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2359038 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2359058 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
2359078 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2359096 CGCAATGCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2359138 original size:14 final size:14
Alignment explanation
Indices: 2359119--2359172 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2359109 GAAAATTGCA
2359119 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2359133 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2359150 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2359166 TTGCGAT
1 TTGCGAT
2359173 AGACATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2359138 original size:33 final size:34
Alignment explanation
Indices: 2359101--2359171 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
2359091 AAAATCGCAA
2359101 TGCGAAATGAAAATT-GCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
* *** *
2359134 TGCG-ATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
2359167 TGCGA
1 TGCGA
2359172 TAGACATTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (34 bp):
TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
Found at i:2359172 original size:33 final size:33
Alignment explanation
Indices: 2359116--2359191 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
2359106 AATGAAAATT
***
2359116 GCATTGCGATTTTCTCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGACATTTC
2359149 GCATTGCGATTTTCTCGTTGCGATAGACATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGACATTTC
*
2359182 GCGTTGCGAT
1 GCATTGCGAT
2359192 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.42
Consensus pattern (33 bp):
GCATTGCGATTTTCTCGTTGCGATAGACATTTC
Found at i:2361204 original size:19 final size:19
Alignment explanation
Indices: 2361180--2361246 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2361170 GAAACTTAAA
2361180 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2361199 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCG-AAATGACT
* **
2361219 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2361238 ATCGCAACG
1 ATCGCAACG
2361247 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2361204 original size:39 final size:37
Alignment explanation
Indices: 2361161--2361277 Score: 100
Period size: 39 Copynumber: 3.2 Consensus size: 37
2361151 TAGTTTACTT
*
2361161 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAATGA-AA
* * *** *
2361200 TCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACACGAAACT-AAAATCGCAACGCGAAATG-AAA
2361239 TCGC-A-ACG--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
2361271 TCGCAAC
1 TCGCAAC
2361278 GACAAAATCG
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
32 7 0.11
33 16 0.26
35 1 0.02
37 2 0.03
38 2 0.03
39 32 0.52
40 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.14
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:2361254 original size:14 final size:14
Alignment explanation
Indices: 2361235--2361291 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
2361225 ATGCGAAATG
2361235 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2361249 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2361265 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2361281 AAAATCGCAAC
1 AAAATCGCAAC
2361292 TCGAAACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2361277 original size:32 final size:33
Alignment explanation
Indices: 2361219--2361297 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
2361209 GAAAATGGCT
*
2361219 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2361252 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
2361284 ATCGCAACTCGAAA
1 ATCGCAACGCGAAA
2361298 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2361326 original size:19 final size:17
Alignment explanation
Indices: 2361304--2361399 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
2361294 GAAACACAAA
2361304 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
2361323 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
2361339 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
2361355 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
2361371 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
*
2361388 TTGCATTGCGAT
1 TCGC-TTGCGAT
2361400 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 3 0.05
18 13 0.21
19 16 0.26
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:2361345 original size:14 final size:14
Alignment explanation
Indices: 2361326--2361383 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2361316 TTTCATTTCG
2361326 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2361340 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2361356 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2361372 CGTTGCGATTTT
1 CGTTGCGATTTT
2361384 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2361356 original size:32 final size:33
Alignment explanation
Indices: 2361309--2361399 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2361299 ACAAATCGCA
2361309 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
2361342 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
2361374 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
2361400 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:2361418 original size:20 final size:20
Alignment explanation
Indices: 2361393--2361438 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2361383 TCATTTTGCA
2361393 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
2361413 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
2361433 TTGCGA
1 TTGCGA
2361439 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:2361931 original size:18 final size:18
Alignment explanation
Indices: 2361905--2361949 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2361895 GTCGATCAGA
*
2361905 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2361923 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2361941 TGATGGCTC
1 TGATGGCTC
2361950 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2363293 original size:20 final size:20
Alignment explanation
Indices: 2363268--2363305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2363258 AATAGTTTCT
2363268 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2363288 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2363306 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2363593 original size:22 final size:22
Alignment explanation
Indices: 2363568--2363611 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2363558 GATTTAGATA
2363568 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2363590 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2363612 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2363892 original size:20 final size:20
Alignment explanation
Indices: 2363799--2363892 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2363789 GATTATGTAA
*
2363799 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
2363819 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2363839 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2363860 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2363880 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2363893 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2363911 original size:41 final size:41
Alignment explanation
Indices: 2363820--2363954 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2363810 AAAGTCAGTA
* * * ** *
2363820 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2363860 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
2363902 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2363943 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2363955 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2363925 original size:20 final size:20
Alignment explanation
Indices: 2363881--2363973 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2363871 ATAGTCAGTA
* **
2363881 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2363902 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2363922 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2363943 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2363963 TCGCATTGCGA
1 TCGCATTGCGA
2363974 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2363955 original size:41 final size:41
Alignment explanation
Indices: 2363881--2363976 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2363871 ATAGTCAGTA
*
2363881 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2363922 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2363963 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2363977 AGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2365471 original size:42 final size:43
Alignment explanation
Indices: 2365425--2365519 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 43
2365415 TAAAGTTTAG
*
2365425 TTTTTGTTTTA-TTTAAGTACCCCACCACTAAAAATTTTA-TTT
1 TTTTTGTTTTATTTTAA-TACCCCACCACTAAAAACTTTAGTTT
* *
2365467 TTTTTGTTTTATTTTAATATCCCACCATTAAAAACTTTAGTTT
1 TTTTTGTTTTATTTTAATACCCCACCACTAAAAACTTTAGTTT
*
2365510 TTGTT-TTTTA
1 TTTTTGTTTTA
2365520 GTACCACCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 35 0.74
43 12 0.26
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (43 bp):
TTTTTGTTTTATTTTAATACCCCACCACTAAAAACTTTAGTTT
Found at i:2375037 original size:23 final size:23
Alignment explanation
Indices: 2375011--2375056 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2375001 TAAAAAATTT
*
2375011 ATATACAATTTTTAAAAATAAAA
1 ATATACAATTTTTAAAAAGAAAA
* *
2375034 ATATATATTTTTTAAAAAGAAAA
1 ATATACAATTTTTAAAAAGAAAA
2375057 CACATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATACAATTTTTAAAAAGAAAA
Found at i:2385428 original size:12 final size:12
Alignment explanation
Indices: 2385411--2385435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2385401 TGATGATGGT
2385411 TCTCCAACGTCA
1 TCTCCAACGTCA
2385423 TCTCCAACGTCA
1 TCTCCAACGTCA
2385435 T
1 T
2385436 TTATATTTAT
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:0.24, C:0.40, G:0.08, T:0.28
Consensus pattern (12 bp):
TCTCCAACGTCA
Found at i:2396019 original size:2 final size:2
Alignment explanation
Indices: 2396012--2396058 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2396002 TAAACATGAA
2396012 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
2396054 AT AT A
1 AT AT A
2396059 AGTAATTATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2400052 original size:3 final size:3
Alignment explanation
Indices: 2400046--2400112 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2400036 TACCTTTCTT
2400046 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
2400094 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
2400113 CCTTTAAACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2402339 original size:14 final size:13
Alignment explanation
Indices: 2402316--2402350 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
2402306 AATTATTTCC
2402316 TATTTATTAGGATT
1 TATTT-TTAGGATT
2402330 TATCTTTTAGGATT
1 TAT-TTTTAGGATT
2402344 TATTTTT
1 TATTTTT
2402351 CTTGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (13 bp):
TATTTTTAGGATT
Found at i:2404869 original size:2 final size:2
Alignment explanation
Indices: 2404862--2404902 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2404852 TTTTGTTTTC
* *
2404862 AT AT AT AT AT AT AT AT AT AT AA AT AT A- AA 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
2404903 TTTCAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2404935 original size:23 final size:21
Alignment explanation
Indices: 2404909--2404967 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
2404899 ATATTTTCAA
2404909 TTTTAGTAATTTTATAAAAATAT
1 TTTTA-TAATTTT-TAAAAATAT
** *
2404932 TTTTAATAAAACTTTAAATATAT
1 TTTT-AT-AATTTTTAAAAATAT
2404955 TTTTATAATTTTT
1 TTTTATAATTTTT
2404968 CTTATTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 17 0.59
24 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTATAATTTTTAAAAATAT
Found at i:2411690 original size:45 final size:45
Alignment explanation
Indices: 2411626--2411715 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2411616 TGAACCTGAA
2411626 AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
1 AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
2411671 AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
1 AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
2411716 TGTATTGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (45 bp):
AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
Found at i:2412811 original size:23 final size:24
Alignment explanation
Indices: 2412767--2412826 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
2412757 CTTAACAGAG
*
2412767 TTTATATTATTTTTAAATTTAATT
1 TTTATATTATTTTTAAAATTAATT
*
2412791 TTTATA-T-TTTTTACAAATTAAAT
1 TTTATATTATTTTTA-AAATTAATT
* *
2412814 GTCATATTATTTT
1 TTTATATTATTTT
2412827 AATTTGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 6 0.21
23 12 0.41
24 7 0.24
25 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATATTATTTTTAAAATTAATT
Found at i:2413616 original size:16 final size:17
Alignment explanation
Indices: 2413580--2413614 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2413570 CATGAACATG
2413580 ATGTTATATATTAATAT
1 ATGTTATATATTAATAT
2413597 ATGTATATATATTAATAT
1 ATGT-TATATATTAATAT
2413615 GTGTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
ATGTTATATATTAATAT
Found at i:2422614 original size:22 final size:22
Alignment explanation
Indices: 2422589--2422651 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
2422579 TATAGCTCAC
*
2422589 AACTAAAGCCTTATTGCTAACA
1 AACTCAAGCCTTATTGCTAACA
*
2422611 AACTCAAGCCTTACTGCTAACA
1 AACTCAAGCCTTATTGCTAACA
*
2422633 AACTCAAGCCTAATTGCTA
1 AACTCAAGCCTTATTGCTA
2422652 CTAACAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (22 bp):
AACTCAAGCCTTATTGCTAACA
Found at i:2424241 original size:2 final size:2
Alignment explanation
Indices: 2424234--2424274 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2424224 AGATAATAAC
2424234 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
2424275 CAAAATTTAT
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:2426692 original size:4 final size:4
Alignment explanation
Indices: 2426679--2426711 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
2426669 CTTTATCTCA
2426679 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT
2426712 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:2426730 original size:25 final size:25
Alignment explanation
Indices: 2426670--2426730 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
2426660 ATAAGTCTTC
*
2426670 TTTATCTCA--ATTTATTTTATTTA
1 TTTATCTCATTATTTATTTTAATTA
*
2426693 TTTAT-TTATTTATTTATTTTTAATT-
1 TTTATCTCA-TTATTTA-TTTTAATTA
2426718 TTTATCTCATTAT
1 TTTATCTCATTAT
2426731 ACTTCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
22 2 0.07
23 5 0.17
25 14 0.47
26 9 0.30
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATCTCATTATTTATTTTAATTA
Found at i:2426850 original size:14 final size:14
Alignment explanation
Indices: 2426827--2426866 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2426817 TTTAAAACAA
2426827 TTTATATTTTATTAT
1 TTTAT-TTTTATTAT
*
2426842 TTTATTTTTATTTT
1 TTTATTTTTATTAT
*
2426856 TTTATCTTTAT
1 TTTATTTTTAT
2426867 CTTTATCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:2427653 original size:14 final size:15
Alignment explanation
Indices: 2427630--2427662 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2427620 AACATTGAAA
2427630 AAAAACAAGAAAAAG
1 AAAAACAAGAAAAAG
*
2427645 AAAAA-AAGAAGAAG
1 AAAAACAAGAAAAAG
2427659 AAAA
1 AAAA
2427663 GGGCATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAACAAGAAAAAG
Found at i:2429935 original size:21 final size:20
Alignment explanation
Indices: 2429906--2429962 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2429896 ACACAAATGT
*
2429906 AATTAGCGTTGTGAATTTGGAG
1 AATT-GCGTTGTGAATTT-GAA
*
2429928 AATTGCGTTGCGAATTTGAA
1 AATTGCGTTGTGAATTTGAA
* *
2429948 AACTGAGTTGTGAAT
1 AATTGCGTTGTGAAT
2429963 AGTTGTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 12 0.40
22 4 0.13
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (20 bp):
AATTGCGTTGTGAATTTGAA
Found at i:2430029 original size:20 final size:20
Alignment explanation
Indices: 2430006--2430096 Score: 103
Period size: 21 Copynumber: 4.5 Consensus size: 20
2429996 CGAAATTTGA
2430006 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
* *
2430026 GTTGGGATTTTGAAGAATCGC
1 GTTGCGAATTTGAA-AATCGC
* *
2430047 GTTGCGATTTTGGAGAATCGC
1 GTTGCGAATTT-GAAAATCGC
*
2430068 GTTGCGAATTTGAAAA-CTGA
1 GTTGCGAATTTGAAAATC-GC
2430088 GTTGCGAAT
1 GTTGCGAAT
2430097 AGTTGTGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 26 0.43
21 32 0.52
22 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:2430149 original size:20 final size:21
Alignment explanation
Indices: 2430124--2430198 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
2430114 TCGGTAATTA
*
2430124 GCGTTGCGAATTT-GATAATC
1 GCGTTGCGAATTTGGAGAATC
*
2430144 GCGTTGCGATTTTGGAGAATC
1 GCGTTGCGAATTTGGAGAATC
* ** *
2430165 GCGTTACGAAACTGGAG-TTC
1 GCGTTGCGAATTTGGAGAATC
*
2430185 GCGTTACGAATTTG
1 GCGTTGCGAATTTG
2430199 TTGGTTATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 26 0.58
21 19 0.42
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (21 bp):
GCGTTGCGAATTTGGAGAATC
Found at i:2430166 original size:21 final size:20
Alignment explanation
Indices: 2430124--2430174 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2430114 TCGGTAATTA
*
2430124 GCGTTGCGAATTTGATAATC
1 GCGTTGCGAATTTGAGAATC
*
2430144 GCGTTGCGATTTTGGAGAATC
1 GCGTTGCGAATTT-GAGAATC
*
2430165 GCGTTACGAA
1 GCGTTGCGAA
2430175 ACTGGAGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAGAATC
Found at i:2431262 original size:19 final size:18
Alignment explanation
Indices: 2431238--2431273 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2431228 CACCAAGCAA
*
2431238 TATATTTTCTTCATATTTT
1 TATATTTTATTCA-ATTTT
2431257 TATATTTTATTCAATTT
1 TATATTTTATTCAATTT
2431274 AAATTATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATTTTATTCAATTTT
Found at i:2431435 original size:16 final size:16
Alignment explanation
Indices: 2431414--2431451 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2431404 AATATCTAAT
*
2431414 CTTAATTAATATAAAC
1 CTTAATAAATATAAAC
*
2431430 CTTAATAAATATTAAC
1 CTTAATAAATATAAAC
2431446 C-TAATA
1 CTTAATA
2431452 TATTTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
CTTAATAAATATAAAC
Found at i:2436487 original size:149 final size:151
Alignment explanation
Indices: 2436208--2436507 Score: 552
Period size: 149 Copynumber: 2.0 Consensus size: 151
2436198 TCCTTCGTCG
2436208 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
2436273 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTGAGCTTTGAATTGGATATCATTCGCTATAAAGTT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTGAGCTTTGAATTGGATATCATTCGCTATAAAGTT
2436338 GAAATCCAATGTTG-TTGTGA
131 GAAATCCAATGTTGTTTGTGA
2436358 TGAAGTTG-AATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
* *
2436422 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGC-TTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAG-TGAGCTTTGAATTGGATATCATTCGCTATAAAGT
2436486 TGAAATCCAATGTTGTTTGTGA
130 TGAAATCCAATGTTGTTTGTGA
2436508 GCACGATATC
Statistics
Matches: 146, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
149 127 0.87
150 19 0.13
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (151 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTGAGCTTTGAATTGGATATCATTCGCTATAAAGTT
GAAATCCAATGTTGTTTGTGA
Found at i:2436561 original size:169 final size:169
Alignment explanation
Indices: 2436358--2436666 Score: 584
Period size: 169 Copynumber: 1.8 Consensus size: 169
2436348 GTTGTTGTGA
2436358 TGAAGTTGAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGAA
1 TGAAGTTGAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGAA
*
2436423 TGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGC-TTGAATTGGATATCCTTCGCTGTAAAGTT
66 TGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGTT
2436487 GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
*
2436526 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTG-AATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
2436591 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
65 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
2436656 TGAAATCCAAT
130 TGAAATCCAAT
2436667 CTTCAGTAAA
Statistics
Matches: 137, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
168 8 0.06
169 90 0.66
170 39 0.28
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (169 bp):
TGAAGTTGAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGAA
TGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGTT
GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
Found at i:2447643 original size:12 final size:13
Alignment explanation
Indices: 2447626--2447654 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2447616 CTTAATTACA
2447626 AAAATTAAAA-TT
1 AAAATTAAAATTT
2447638 AAAATTAAAATTT
1 AAAATTAAAATTT
2447651 AAAA
1 AAAA
2447655 ATTCGATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:2451113 original size:84 final size:84
Alignment explanation
Indices: 2450973--2451533 Score: 764
Period size: 84 Copynumber: 6.8 Consensus size: 84
2450963 ACCATGCAGT
* * * * * *
2450973 TGATATGCCTATGAGCTGAAT-TAAATCGAACTCGAAAGTC-TTTGATAACAGATAA-CCTTCTC
1 TGATATGCCTTTGAGCTGAGTGT-AATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTA
*
2451035 GCCTTGAGCTATGCTGTAAA
65 GCCTTGAGCTATGCTGCAAA
2451055 TTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCT
1 --TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCT
*
2451119 CGCCTTGAGCTATGCTGCAAA
64 AGCCTTGAGCTATGCTGCAAA
* * *
2451140 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAG
*
2451205 CCTTGAGTTATGCTGCAAA
66 CCTTGAGCTATGCTGCAAA
* * * *
2451224 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAG
*
2451289 CC-TGAGTTATGCTGCAAA
66 CCTTGAGCTATGCTGCAAA
* *
2451307 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTG--G-CAGATAACCCTTCTTG
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAG
2451368 CCTTGAGCTATGCTGCAAA
66 CCTTGAGCTATGCTGCAAA
** * * * *
2451387 TGATGCGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCATATAACTCTTCTAG
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAG
* *
2451452 CTTTGAGTTATGCTGCAAA
66 CCTTGAGCTATGCTGCAAA
*
2451471 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGAT-ACTCCTTCT
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAAC-CCTTCT
2451534 TTGAGTTAGA
Statistics
Matches: 434, Mismatches: 34, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
79 17 0.04
80 52 0.12
81 4 0.01
82 4 0.01
83 96 0.22
84 234 0.54
85 27 0.06
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (84 bp):
TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAG
CCTTGAGCTATGCTGCAAA
Found at i:2451260 original size:167 final size:167
Alignment explanation
Indices: 2450973--2451533 Score: 769
Period size: 167 Copynumber: 3.4 Consensus size: 167
2450963 ACCATGCAGT
* * * * ** *
2450973 TGATATGCCTATGAGCTGAAT-TAAATCGAACTCGAAAGTCTTTGATAACAGATAA-CCTTCTCG
1 TGATATGCCTTTGAGCTGAGTGT-AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAG
*
2451036 CCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTT
65 CCTTGAGCTATGCTGCAAA--TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT
* * *
2451100 GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAA
128 GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* *
2451140 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAG
* * * *
2451205 CCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
65 CCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
2451270 TGGCAGATAACCCTTCTAGCC-TGAGTTATGCTGCAAA
130 TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* *
2451307 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC--T-TTGGCAGATAACCCTTCTTGC
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGC
** *
2451369 CTTGAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTT
66 CTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT
* * *
2451434 GGCATATAACTCTTCTAGCTTTGAGTTATGCTGCAAA
131 GGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* *
2451471 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGAT-ACTCCTTCT
1 TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAAC-CCTTCT
2451534 TTGAGTTAGA
Statistics
Matches: 350, Mismatches: 34, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
163 94 0.27
164 55 0.16
167 127 0.36
168 50 0.14
169 24 0.07
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (167 bp):
TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGC
CTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT
GGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
Found at i:2451420 original size:247 final size:251
Alignment explanation
Indices: 2450996--2451533 Score: 847
Period size: 247 Copynumber: 2.2 Consensus size: 251
2450986 AGCTGAATTA
* * * * *
2450996 AATCGAACTCGAAAGTC-TTTGATAACAGATAA-CCTTCTCGCCTTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAA-TTG
*
2451059 ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCT
65 ATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTCGCCT
*
2451124 TGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGG
129 TGAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGG
2451189 CATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
194 CATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
* * *
2451247 AGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCC-TGAGTTATGCTGCAAA-TGA
1 AATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATTGA
*
2451310 TATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-G-CAGATAACCCTTCTTGCCTTG
66 TATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTCGCCTTG
*
2451373 AGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCA
131 AGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* * * * *
2451438 TATAACTCTTCTAGCTTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
196 TATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
2451494 AATCGAACTCGAAGGTCTTTTGTTGACAGAT-ACTCCTTCT
1 AATCGAACTCGAAGGTCTTTTGTTGACAGATAAC-CCTTCT
2451534 TTGAGTTAGA
Statistics
Matches: 265, Mismatches: 19, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
246 2 0.01
247 169 0.64
248 1 0.00
250 43 0.16
251 15 0.06
252 26 0.10
253 9 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (251 bp):
AATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATTGA
TATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTCGCCTTG
AGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
TATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
Found at i:2451828 original size:43 final size:43
Alignment explanation
Indices: 2451765--2451935 Score: 234
Period size: 43 Copynumber: 4.0 Consensus size: 43
2451755 CTTGTGTAGA
* * * *
2451765 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATTTG
1 TGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTG
* *
2451808 TGGGCACGATATTCTCCGTTGTGGAGTTGAAATCGTGGATGTG
1 TGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTG
* * *
2451851 TGGGTACGATATTCTCCGTCGTGGAGTTAAAATCGTGGATGTG
1 TGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTG
* * *
2451894 TGGGTACGATATCCTCCGTCGTGGAGTTGAAATTGTAGATGT
1 TGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGT
2451936 TTCGAGTCCA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.33
Consensus pattern (43 bp):
TGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTG
Found at i:2453482 original size:29 final size:30
Alignment explanation
Indices: 2453428--2453485 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2453418 TCTTTTCTTC
* *
2453428 TTTTTTTCTTTTTGATTCTTGTTCTTTGCT
1 TTTTTTTCTATTTGATTCTTGATCTTTGCT
2453458 TTTTTTTCTAATTTGA-T-TTGATCTTTGC
1 TTTTTTTCT-ATTTGATTCTTGATCTTTGC
2453486 ACTTGGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 10 0.40
31 5 0.20
ACGTcount: A:0.09, C:0.12, G:0.10, T:0.69
Consensus pattern (30 bp):
TTTTTTTCTATTTGATTCTTGATCTTTGCT
Found at i:2459665 original size:21 final size:21
Alignment explanation
Indices: 2459641--2459694 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2459631 GCGTTGCATT
2459641 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2459662 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2459683 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2459695 TTTCCATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2459708 original size:20 final size:20
Alignment explanation
Indices: 2459683--2459898 Score: 132
Period size: 20 Copynumber: 10.9 Consensus size: 20
2459673 TAGTTGAAAA
*
2459683 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
2459703 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
2459723 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
* *
2459745 T-GTCGTTGTGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
2459766 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
2459786 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
**
2459807 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
2459819 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
2459839 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
2459859 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
**
2459881 TATCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
2459899 AATTCGTTGT
Statistics
Matches: 154, Mismatches: 23, Indels: 38
0.72 0.11 0.18
Matches are distributed among these distances:
12 3 0.02
14 8 0.05
19 16 0.10
20 77 0.50
21 10 0.06
22 40 0.26
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:2459751 original size:22 final size:22
Alignment explanation
Indices: 2459726--2459797 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
2459716 TTCCAGTTCG
2459726 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
2459748 CGTTGTGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
2459767 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2459789 CGTTGCGAT
1 CGTTGCGAT
2459798 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2459771 original size:19 final size:19
Alignment explanation
Indices: 2459747--2459815 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
2459737 TCTACAGTTG
*
2459747 TCGTTGTGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
2459766 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
2459787 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2459807 TCGTTGCGA
1 TCGTTGCGA
2459816 AAATCGCGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 18 0.47
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2459780 original size:41 final size:41
Alignment explanation
Indices: 2459706--2459815 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
2459696 TTCCATTTCG
*
2459706 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
*
2459748 CGTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
2459789 CGTTGCGATTTTCCAAATTCGTTGCGA
1 CGTTGCGATTTTCCAAATTCGTTGCGA
2459816 AAATCGCGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
41 48 0.75
42 13 0.20
43 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:2459981 original size:6 final size:6
Alignment explanation
Indices: 2459970--2460002 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2459960 GACACGTATT
2459970 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2460003 CGAAACGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2460248 original size:2 final size:2
Alignment explanation
Indices: 2460241--2460277 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2460231 TATTTTTCAA
2460241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2460278 TAATTAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2467872 original size:21 final size:20
Alignment explanation
Indices: 2467828--2467881 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2467818 AATACAATTA
* * *
2467828 GTGCATCGATGAATCCTTCT
1 GTGCATCGATGCATCATGCT
2467848 GTGCATCGATGCATCATGGCT
1 GTGCATCGATGCATCAT-GCT
*
2467869 GTGCATCCATGCA
1 GTGCATCGATGCA
2467882 CGAAGGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCATGCT
Found at i:2467889 original size:21 final size:21
Alignment explanation
Indices: 2467846--2467889 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2467836 ATGAATCCTT
* *
2467846 CTGTGCATCGATGCATCATGG
1 CTGTGCATCCATGCATCAAGG
2467867 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCCATGCATC-AAGG
2467888 CT
1 CT
2467890 ACAACGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
CTGTGCATCCATGCATCAAGG
Found at i:2468308 original size:29 final size:30
Alignment explanation
Indices: 2468238--2468297 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2468228 TAATTTAAGG
2468238 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2468269 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2468298 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2468403 original size:21 final size:20
Alignment explanation
Indices: 2468377--2468472 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 20
2468367 AGGGTGTCAA
2468377 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
2468398 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
2468419 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
2468440 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
2468461 AGTGCATCCATG
1 AGTGCATCCATG
2468473 TACTCAAACA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 11 0.16
21 36 0.54
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:2468525 original size:20 final size:20
Alignment explanation
Indices: 2468500--2468569 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
2468490 CAATTAGTGT
* *
2468500 ATCGATGCATCCTTCTATGC
1 ATCGATGCATCCTGCTGTGC
**
2468520 ATCGATGCATCAAGGCTGTGC
1 ATCGATGCATC-CTGCTGTGC
2468541 ATCGATGCATCCTGCTGTGC
1 ATCGATGCATCCTGCTGTGC
*
2468561 ATCCATGCA
1 ATCGATGCA
2468570 CGAAGGCTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (20 bp):
ATCGATGCATCCTGCTGTGC
Found at i:2468543 original size:21 final size:21
Alignment explanation
Indices: 2468517--2468578 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2468507 CATCCTTCTA
2468517 TGCATCGATGCATCAAGGCTG
1 TGCATCGATGCATCAAGGCTG
**
2468538 TGCATCGATGCATC-CTGCTG
1 TGCATCGATGCATCAAGGCTG
*
2468558 TGCATCCATGCA-CGAAGGCTG
1 TGCATCGATGCATC-AAGGCTG
2468579 CAACGACTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 18 0.53
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCATCAAGGCTG
Found at i:2468547 original size:41 final size:41
Alignment explanation
Indices: 2468500--2468578 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
2468490 CAATTAGTGT
* *
2468500 ATCGATGCATCCTTCTATGCATCGATGCATC-AAGGCTGTGC
1 ATCGATGCATCCTGCTATGCATCCATGCA-CGAAGGCTGTGC
*
2468541 ATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCTG
1 ATCGATGCATCCTGCTATGCATCCATGCACGAAGGCTG
2468579 CAACGACTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (41 bp):
ATCGATGCATCCTGCTATGCATCCATGCACGAAGGCTGTGC
Found at i:2469867 original size:19 final size:20
Alignment explanation
Indices: 2469843--2469890 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2469833 AACGATTTTC
* *
2469843 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
2469862 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2469882 TTTTGAAAA
1 TTTTGAAAA
2469891 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2471102 original size:29 final size:31
Alignment explanation
Indices: 2471051--2471109 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
2471041 AATTTAAGGC
2471051 AAAATGGTTTCTGGACTTGAATTGAATTTAA
1 AAAATGGTTTCTGGACTTGAATTGAATTTAA
*
2471082 AAAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTTTCTGGACTTGAATTGAATTTA
2471110 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTTTCTGGACTTGAATTGAATTTAA
Found at i:2471215 original size:21 final size:20
Alignment explanation
Indices: 2471189--2471287 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
2471179 AGGGTGTCAA
*
2471189 AGTGCATCTATGCACCCATGC
1 AGTGCATCCATGCACCC-TGC
2471210 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
2471231 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
2471252 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
2471273 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2471288 TCAAACACCG
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 32 0.46
22 16 0.23
23 3 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:2471278 original size:20 final size:20
Alignment explanation
Indices: 2471189--2471400 Score: 147
Period size: 20 Copynumber: 10.7 Consensus size: 20
2471179 AGGGTGTCAA
* *
2471189 AGTGCATCTATGCACCCATGC
1 AGTGCATCGATGCATCC-TGC
*
2471210 AGTGCATCCATGCATCCCTGC
1 AGTGCATCGATGCAT-CCTGC
*
2471231 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCGATGCATCCTG--C
2471252 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCGATGCATCC-TGC
*
2471273 AGTGCATCCATGCA--CT-C
1 AGTGCATCGATGCATCCTGC
** *
2471290 A-AACACCGAATGCAAT--T--
1 AGTGCATCG-ATGC-ATCCTGC
2471307 AGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
2471327 TGTGCATCGATGCATCCTGT
1 AGTGCATCGATGCATCCTGC
*
2471347 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
2471367 TGTGCATCGATGCATCCTAC
1 AGTGCATCGATGCATCCTGC
* *
2471387 TGTGCATCCATGCA
1 AGTGCATCGATGCA
2471401 CGAAGGCTGC
Statistics
Matches: 162, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.03
17 11 0.07
18 8 0.05
19 5 0.03
20 82 0.51
21 32 0.20
22 17 0.10
23 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTGC
Found at i:2486321 original size:16 final size:16
Alignment explanation
Indices: 2486226--2486322 Score: 62
Period size: 16 Copynumber: 6.3 Consensus size: 16
2486216 ATCTATTTTA
* *
2486226 ATTACTATATTTATAT
1 ATTATTATATTTATTT
*
2486242 ATTATTAT-TTTAATT
1 ATTATTATATTTATTT
*
2486257 ATTTATTATATTTA-AT
1 A-TTATTATATTTATTT
* * * *
2486273 A-AATAATA-TTGTTA
1 ATTATTATATTTATTT
2486287 ATTATTAT-TATTA-TT
1 ATTATTATAT-TTATTT
2486302 ATTATTATATTTATTT
1 ATTATTATATTTATTT
2486318 ATTAT
1 ATTAT
2486323 ATTCATTTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
13 2 0.03
14 6 0.10
15 22 0.37
16 26 0.43
17 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:2488354 original size:13 final size:14
Alignment explanation
Indices: 2488333--2488387 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
2488323 CAACATAAAT
*
2488333 AAATCATTTAATTA
1 AAATAATTTAATTA
*
2488347 AAAT-ATTTAAAT-
1 AAATAATTTAATTA
*
2488359 ACATAATTTAATATA
1 AAATAATTTAAT-TA
2488374 ATAATAATTTAATT
1 A-AATAATTTAATT
2488388 TTTAAAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.09
13 13 0.39
14 5 0.15
15 2 0.06
16 10 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATAATTTAATTA
Found at i:2488367 original size:26 final size:29
Alignment explanation
Indices: 2488328--2488385 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 29
2488318 AAAAACAACA
*
2488328 TAAATAAATCATTTAAT-TAA-AAT-ATT
1 TAAATAAATAATTTAATATAATAATAATT
*
2488354 TAAATACATAATTTAATATAATAATAATT
1 TAAATAAATAATTTAATATAATAATAATT
2488383 TAA
1 TAA
2488386 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 15 0.56
27 3 0.11
28 3 0.11
29 6 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATAAATAATTTAATATAATAATAATT
Found at i:2496028 original size:2 final size:2
Alignment explanation
Indices: 2496012--2496350 Score: 138
Period size: 2 Copynumber: 176.0 Consensus size: 2
2496002 TTGAAACAAT
*
2496012 TA TA -A TA TA TA -A TA TA TA TA TA AA CTA TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
2496051 -A TA TG TA TA AA CTA TA TA -A TT TA TA CA TA -A TA TA TA TA CA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2496091 TA GTA -A TA TA TA AA TA TA -A CTA TA TA GTT TA TG T- TA -A TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * *
2496130 AA CTA TA TA -A TT TA TA T- TA -A TA AA CTA TA TA GT- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* *
2496169 TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA TA TA -A TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2496209 -A TA -A TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TA GT- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
2496250 -A TA TA TA TA -A TA TA TA -A AA TT TA TA TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
2496291 TA TA TT TA TA TA TA TA CTA TG TA TA -A T- TA TA AA T- 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
* *
2496331 CA CTA TA TA TA AA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA
2496351 GTTTATTGAA
Statistics
Matches: 249, Mismatches: 47, Indels: 82
0.66 0.12 0.22
Matches are distributed among these distances:
1 27 0.11
2 206 0.83
3 16 0.06
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2496101 original size:14 final size:13
Alignment explanation
Indices: 2496012--2496116 Score: 74
Period size: 13 Copynumber: 7.8 Consensus size: 13
2496002 TTGAAACAAT
2496012 TATAATATATA-A
1 TATAATATATACA
*
2496024 TATATATATAAACTA
1 TATA-ATATATAC-A
2496039 TATAATAATATA-A
1 TATAAT-ATATACA
* *
2496052 TAT-GTATAAACTA
1 TATAATATATAC-A
*
2496065 TATAATTTATACA
1 TATAATATATACA
2496078 TA-ATATATATACA
1 TATA-ATATATACA
*
2496091 TAGTAATATATAAA
1 TA-TAATATATACA
2496105 TATAACTATATA
1 TATAA-TATATA
2496117 GTTTATGTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
11 4 0.05
12 6 0.08
13 30 0.41
14 23 0.32
15 10 0.14
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (13 bp):
TATAATATATACA
Found at i:2496181 original size:44 final size:43
Alignment explanation
Indices: 2496024--2496330 Score: 208
Period size: 44 Copynumber: 7.0 Consensus size: 43
2496014 TAATATATAA
* *
2496024 TATATATATAAACTATATAATAATATAATATGTATAAACTATATAATT
1 TATATATATATA-TATAT-ATAATAT-ATAT-TATAAACTATAT-AGT
* *
2496072 TATACATAATATATATACATAGTAATATATA-AATATAACTATATAGT
1 TAT--AT-ATATATATATATA-TAATATATATTATA-AACTATATAGT
* * *
2496119 T-TATGT-TAATAAACTATATAATTTATATTAATAAACTATATAGT
1 TATATATAT-ATATA-TATATAATATATATT-ATAAACTATATAGT
*
2496163 TATATATATATATATATATATATATATAATT-TATA-TATAATA-T
1 TATATATATATATATATATA-ATATAT-ATTATAAACTAT-ATAGT
2496206 GTA-ATA-ATATATATATAT-ATATATA-TATAAACTATATAGT
1 -TATATATATATATATATATAATATATATTATAAACTATATAGT
* * *
2496246 TTTA-ATATATATAATATATAAAATTTATATATAAACTATATAGT
1 TATATATATATAT-ATATATAATATATAT-TATAAACTATATAGT
* * *
2496290 T-TATATTTATATATATACT-ATGTATAATTATAAATTATATA
1 TATATATATATATATATA-TAATATAT-ATTATAAACTATATA
2496331 CACTATATAT
Statistics
Matches: 210, Mismatches: 22, Indels: 59
0.72 0.08 0.20
Matches are distributed among these distances:
38 1 0.00
39 9 0.04
40 17 0.08
41 6 0.03
42 18 0.09
43 42 0.20
44 57 0.27
45 16 0.08
46 5 0.02
47 6 0.03
48 11 0.05
49 4 0.02
50 12 0.06
51 6 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (43 bp):
TATATATATATATATATATAATATATATTATAAACTATATAGT
Found at i:2496721 original size:22 final size:23
Alignment explanation
Indices: 2496671--2496731 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
2496661 ACTAGACTTG
* *
2496671 GTCTGAATACTAATT-GGAATTC
1 GTCTGAATGCTAATTAGAAATTC
2496693 GTCTGAATGCTAATTAGAAATT-
1 GTCTGAATGCTAATTAGAAATTC
* *
2496715 GTTTGAATGCTTATTAG
1 GTCTGAATGCTAATTAG
2496732 TTTTGGTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (23 bp):
GTCTGAATGCTAATTAGAAATTC
Found at i:2497344 original size:19 final size:19
Alignment explanation
Indices: 2497320--2497356 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2497310 AATAAATATA
*
2497320 TAAAGTCAATTTAGTAATT
1 TAAAGTAAATTTAGTAATT
2497339 TAAAGTAAATTTAGTAAT
1 TAAAGTAAATTTAGTAAT
2497357 ATAATGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (19 bp):
TAAAGTAAATTTAGTAATT
Found at i:2500610 original size:23 final size:23
Alignment explanation
Indices: 2500580--2500623 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2500570 TTTATGATGA
2500580 ATATAATAATATTCTTT-TGGTGC
1 ATATAAT-ATATTCTTTGTGGTGC
*
2500603 ATATAATATTTTCTTTGTGGT
1 ATATAATATATTCTTTGTGGT
2500624 TAATAGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (23 bp):
ATATAATATATTCTTTGTGGTGC
Found at i:2503294 original size:18 final size:19
Alignment explanation
Indices: 2503253--2503295 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2503243 GTCATCCAAT
2503253 TTTTTAAACCCAGACCGGA
1 TTTTTAAACCCAGACCGGA
2503272 TTTTTAAACCCAGACCGGA
1 TTTTTAAACCCAGACCGGA
2503291 TTTTT
1 TTTTT
2503296 TTCGGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (19 bp):
TTTTTAAACCCAGACCGGA
Found at i:2504982 original size:31 final size:31
Alignment explanation
Indices: 2504944--2505018 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2504934 ATATATACAC
* *
2504944 TTTTGGTCACTTACGTTGTTGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
*
2504975 TTTTGGTCAATTACGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
*
2505006 TTTTGGTTACTTA
1 TTTTGGTCACTTA
2505019 GAAATTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.19, C:0.09, G:0.17, T:0.55
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATCGTTTTATTAAG
Found at i:2511832 original size:43 final size:43
Alignment explanation
Indices: 2511784--2511910 Score: 254
Period size: 43 Copynumber: 3.0 Consensus size: 43
2511774 ATGGTATCCA
2511784 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATTCG
1 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATTCG
2511827 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATTCG
1 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATTCG
2511870 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATT
1 TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATT
2511911 ATTTAAGGAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (43 bp):
TAGTTTAGTATCGATACTAATAGTCTTATGTAAGATAAATTCG
Found at i:2511842 original size:22 final size:22
Alignment explanation
Indices: 2511817--2511885 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
2511807 TCTTATGTAA
2511817 GATAAATTCGTAGTTTAGTATC
1 GATAAATTCGTAGTTTAGTATC
* ** *
2511839 GAT--ACTAATAGTCTTATGTA-A
1 GATAAATTCGTAGT-TTA-GTATC
2511860 GATAAATTCGTAGTTTAGTATC
1 GATAAATTCGTAGTTTAGTATC
2511882 GATA
1 GATA
2511886 CTAATAGTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 13 0.38
23 6 0.18
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (22 bp):
GATAAATTCGTAGTTTAGTATC
Done.