Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 7 of 218
Found at i:2505979 original size:16 final size:18
Alignment explanation
Indices: 2505940--2505973 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2505930 TAATTTTATA
2505940 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2505957 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2505974 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2507578 original size:13 final size:13
Alignment explanation
Indices: 2507560--2507587 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2507550 TATGGCAGCA
2507560 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
2507573 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
2507586 AA
1 AA
2507588 GAAGACCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:2510541 original size:20 final size:19
Alignment explanation
Indices: 2510505--2510552 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
2510495 AAATTTTATA
**
2510505 TTTTAATTTTTTCTAATTT
1 TTTTAATTTTTAATAATTT
*
2510524 TTTTATATTTTTAATAATAT
1 TTTTA-ATTTTTAATAATTT
*
2510544 ATTTAATTT
1 TTTTAATTT
2510553 GAATTAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAATTTTTAATAATTT
Found at i:2537681 original size:20 final size:21
Alignment explanation
Indices: 2537632--2537682 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2537622 TCAATATTTG
*
2537632 GAGAAATAAAACAAAGAAAAT
1 GAGAAATAATACAAAGAAAAT
* * *
2537653 GATAAATAATATAATGAAAA-
1 GAGAAATAATACAAAGAAAAT
2537673 GAGAAATAAT
1 GAGAAATAAT
2537683 TTTTTATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.18
Consensus pattern (21 bp):
GAGAAATAATACAAAGAAAAT
Found at i:2537905 original size:23 final size:23
Alignment explanation
Indices: 2537875--2537920 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2537865 ACTTTTTATC
2537875 TTCAAGTCTCTTCACTCTTCATA
1 TTCAAGTCTCTTCACTCTTCATA
2537898 TTCAAGTCTCTTCACTCTTCATA
1 TTCAAGTCTCTTCACTCTTCATA
2537921 ACTTTTCATA
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:0.22, C:0.30, G:0.04, T:0.43
Consensus pattern (23 bp):
TTCAAGTCTCTTCACTCTTCATA
Found at i:2539681 original size:69 final size:69
Alignment explanation
Indices: 2539570--2539713 Score: 270
Period size: 69 Copynumber: 2.1 Consensus size: 69
2539560 AGCCTAGGTA
*
2539570 AAAAGTGAAGGAGTCTGTTGGCAGCAGTAAGCGCAAGGGAATCGAGTCGAATGAGGACTCACCTC
1 AAAAGCGAAGGAGTCTGTTGGCAGCAGTAAGCGCAAGGGAATCGAGTCGAATGAGGACTCACCTC
2539635 CTAG
66 CTAG
*
2539639 AAAAGCGAATGAGTCTGTTGGCAGCAGTAAGCGCAAGGGAATCGAGTCGAATGAGGACTCACCTC
1 AAAAGCGAAGGAGTCTGTTGGCAGCAGTAAGCGCAAGGGAATCGAGTCGAATGAGGACTCACCTC
2539704 CTAG
66 CTAG
2539708 AAAAGC
1 AAAAGC
2539714 TCCCACACAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (69 bp):
AAAAGCGAAGGAGTCTGTTGGCAGCAGTAAGCGCAAGGGAATCGAGTCGAATGAGGACTCACCTC
CTAG
Found at i:2540285 original size:23 final size:23
Alignment explanation
Indices: 2540255--2540300 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2540245 ACTTTTTATC
2540255 TTCAAGTCTCTTCACTCTTCATA
1 TTCAAGTCTCTTCACTCTTCATA
2540278 TTCAAGTCTCTTCACTCTTCATA
1 TTCAAGTCTCTTCACTCTTCATA
2540301 ACTTTTCATA
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:0.22, C:0.30, G:0.04, T:0.43
Consensus pattern (23 bp):
TTCAAGTCTCTTCACTCTTCATA
Found at i:2541177 original size:47 final size:48
Alignment explanation
Indices: 2541123--2541249 Score: 177
Period size: 47 Copynumber: 2.6 Consensus size: 48
2541113 GCACAATTTA
*
2541123 TTTTCTTTCTCAATCTTTTTTTTGCTTGAAACCCAAAAT-CC-TATCCC
1 TTTTCTTTCTC-ATCTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
*
2541170 TTTTCTTTCTCATACTTTTCTTTGCTTGAAACCCAAAATCCCATGTCCC
1 TTTTCTTTCTCAT-CTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
* *
2541219 TTTTCTTTCTCGGTCTTTTCGTTGCTTGAAA
1 TTTTCTTTCTC-ATCTTTTCTTTGCTTGAAA
2541250 AAAATATTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
46 2 0.03
47 35 0.49
48 2 0.03
49 32 0.44
50 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (48 bp):
TTTTCTTTCTCATCTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
Found at i:2545013 original size:21 final size:21
Alignment explanation
Indices: 2544987--2545027 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2544977 AGACGAGCAA
* *
2544987 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2545008 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2545028 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2548891 original size:22 final size:24
Alignment explanation
Indices: 2548866--2548916 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
2548856 TTATTTATAA
2548866 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
2548886 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
2548912 ATAAA
1 ATAAA
2548917 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:2556530 original size:43 final size:43
Alignment explanation
Indices: 2556417--2556532 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
2556407 ATCTGCTAAA
*
2556417 TTAGTGGCG-TTTTCCCACAAACGCCACTAAAGAACATGGACT
1 TTAGTGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGGACT
* * * * * *
2556459 TTAGCGGCGCTTTTACTAAAAACACCGCTAAAGAATAT-GACAT
1 TTAGTGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGGAC-T
2556502 TTAGTGGCGCTTTTCCCACAAACGCCGCTAA
1 TTAGTGGCGCTTTTCCCACAAACGCCGCTAA
2556533 GCCACTAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
42 11 0.18
43 49 0.82
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TTAGTGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGGACT
Found at i:2577246 original size:5 final size:5
Alignment explanation
Indices: 2577218--2577277 Score: 61
Period size: 5 Copynumber: 12.2 Consensus size: 5
2577208 TTTTTATGCT
* * * *
2577218 TTATA -TATA TTATT TTAT- TATATA TTATA TTATA TTATA TTGTA TTGTG
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
2577267 TTATA TTATA T
1 TTATA TTATA T
2577278 AAGTAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
4 5 0.11
5 41 0.87
6 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:2578102 original size:3 final size:3
Alignment explanation
Indices: 2578094--2578134 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
2578084 AATAAAAATT
* * *
2578094 TTA TTA TTA TTA TTG TTA ATA TAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2578135 TTAATGATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2578139 original size:21 final size:21
Alignment explanation
Indices: 2578091--2578150 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2578081 TTGAATAAAA
*
2578091 ATTTT-ATTATTATTATTGTT
1 ATTTTAATTATTATTATTATT
* *
2578111 AATATAATTATTATTATTATT
1 ATTTTAATTATTATTATTATT
* *
2578132 ATTTTAATGATTATAATTA
1 ATTTTAATTATTATTATTA
2578151 AAAGTGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTAATTATTATTATTATT
Found at i:2591946 original size:212 final size:211
Alignment explanation
Indices: 2591651--2592229 Score: 793
Period size: 212 Copynumber: 2.7 Consensus size: 211
2591641 CATCTCATGT
* * * *
2591651 TTTAAAATTGTTTATTGGATGCATGAGTCCACTTCACAGTAATTTTTTTATTTGTTAGCCTGTAC
1 TTTAAAATTGTTTACTGGATGCA--AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTAC
* * *
2591716 ATTGGATTTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTGAATAAAGGAGAGAAGACT
64 ATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACT
* * *
2591781 AGTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATTATTCTTTTATTTTTCAGTTATC
129 AGTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATC
* *
2591846 TCATGTTCAATCTTTTGC
194 TCATCTTCAAGCTTTTGC
* *
2591864 TTTGAAATTGTTTACTGGACGTGCAAGTCAACTTCACATTCA-TTTTTTATTTGTTAGCCTGTAT
1 TTTAAAATTGTTTACTGGA--TGCAAGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTAC
* *
2591928 ATTGTATCTGTTGCAGGTTGGGTGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGACT
64 ATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACT
** * *
2591993 AGTAAGAAAAATAAGGAATGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATC
129 AGTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATC
2592058 TCATCTTCAAGCTTTTGC
194 TCATCTTCAAGCTTTTGC
* * * *
2592076 TTTAAAATTGTTTGCTGGATGCATAACTCAACTTAACATTCATTTTTTTTTTAAAATTTATTAGC
1 TTTAAAATTGTTTACTGGATGC--AAGTCAACTTCACATTCA---TTTTTTT---ATTTGTTAGC
**
2592141 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTC-GACCCTAAATATTGGAGA
58 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAG-CCCTAAATAAAGGAGA
2592205 GAAGACTAGTAAGAAAAACCAGGAA
122 GAAGACTAGTAAGAAAAACCAGGAA
2592230 GGTAAAGCCG
Statistics
Matches: 322, Mismatches: 32, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
210 3 0.01
212 188 0.58
213 31 0.10
215 4 0.01
216 6 0.02
219 90 0.28
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (211 bp):
TTTAAAATTGTTTACTGGATGCAAGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACAT
TGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAG
TAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATCTC
ATCTTCAAGCTTTTGC
Found at i:2596938 original size:15 final size:15
Alignment explanation
Indices: 2596920--2596949 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2596910 CTCTCTGCCC
2596920 TTCTCCTCCACCTCT
1 TTCTCCTCCACCTCT
*
2596935 TTCTCCTCCCCCTCT
1 TTCTCCTCCACCTCT
2596950 CTCAGTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCTCCTCCACCTCT
Found at i:2601444 original size:4 final size:4
Alignment explanation
Indices: 2601435--2601495 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
2601425 CAATGACAAG
2601435 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2601483 ATAC ATAC ATAC A
1 ATAC ATAC ATAC A
2601496 ACCCTTTTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2607984 original size:15 final size:15
Alignment explanation
Indices: 2607964--2607993 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2607954 GATGTGTATT
*
2607964 TTATAAATTCGGATA
1 TTATAAATTCAGATA
2607979 TTATAAATTCAGATA
1 TTATAAATTCAGATA
2607994 ACATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (15 bp):
TTATAAATTCAGATA
Found at i:2613910 original size:22 final size:22
Alignment explanation
Indices: 2613882--2613925 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2613872 TTTTTTCGTG
2613882 TCAGAATCAAATATCAGTATAC
1 TCAGAATCAAATATCAGTATAC
2613904 TCAGAATCAAATATCAGTATAC
1 TCAGAATCAAATATCAGTATAC
2613926 GAAAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (22 bp):
TCAGAATCAAATATCAGTATAC
Found at i:2614107 original size:109 final size:107
Alignment explanation
Indices: 2613904--2614371 Score: 631
Period size: 109 Copynumber: 4.4 Consensus size: 107
2613894 ATCAGTATAC
* * * * *
2613904 TCAGAATCAAATATCAGTATACGAAAAAAGTAAAAAAAAAATTATGGGTGCTGGCCTGTCAATGG
1 TCAGAATCAGATATAAATATACGAAAAAA--ATAAAAAAAATT-TGGGTGCTAGCCTGTCAATGG
2613969 CCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTG
63 CCGGCACCCAGTACAAATTTAAAA-AAAA-TTCTTTTTTTTTTCGTG
*
2614016 TCAAAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGCCG
1 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGCCG
2614081 GCACCCAGTACAAATTTTAAAAAAAATTCTTTTTTTTTT-GTG
66 GCACCCAGTACAAA-TTTAAAAAAAATTCTTTTTTTTTTCGTG
*
2614123 TCAGAATCAGATATAAATATACGCAAAAAATAAAAATAAAAAATTTGGGTGCTAGCCTGTCAATG
1 TCAGAATCAGATATAAATATACG--AAAAA-AATAA-AAAAAATTTGGGTGCTAGCCTGTCAATG
2614188 GCCGGCACCCAGTACAAATTT-AAAAAAATTC-TTTTTTTTTCGTG
62 GCCGGCACCCAGTACAAATTTAAAAAAAATTCTTTTTTTTTTCGTG
* * *
2614232 TCAGAATCAGATATAAATATATGAAAAAAAT--------TTTGGGTGCTGGCCTGTCAATGGCTG
1 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGCCG
2614289 GCACCCAGTACAAATTTTTTAAAAAAAA---TTTTTTTTTTCGTG
66 GCACCCAGTACAAA---TTTAAAAAAAATTCTTTTTTTTTTCGTG
2614331 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATT
1 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATT
2614372 ATATATAAAC
Statistics
Matches: 324, Mismatches: 13, Indels: 43
0.85 0.03 0.11
Matches are distributed among these distances:
97 38 0.12
99 43 0.13
100 3 0.01
101 7 0.02
106 2 0.01
107 32 0.10
108 22 0.07
109 81 0.25
110 25 0.08
111 46 0.14
112 25 0.08
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (107 bp):
TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGCCG
GCACCCAGTACAAATTTAAAAAAAATTCTTTTTTTTTTCGTG
Found at i:2614297 original size:208 final size:211
Alignment explanation
Indices: 2613904--2614369 Score: 669
Period size: 208 Copynumber: 2.2 Consensus size: 211
2613894 ATCAGTATAC
* * * *
2613904 TCAGAATCAAATATCAGTATACGAAAAAAGT-AAAAAAAAAATTATGGGTGCTGGCCTGTCAATG
1 TCAGAATCAGATATAAATATACGAAAAAA-TAAAAAAAAAAATTATGGGTGCTAGCCTGTCAATG
2613968 GCCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTGTCAAAATCAGATATAAA
65 GCCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTGTCAAAATCAGATATAAA
2614033 TATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAA-TT
130 TATACGAAAAAAAT-------ATTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTT
*
2614097 TTAAAAAAAATTCTTTTTTTTTTGTG
188 TTAAAAAAAA-T-TTTTTTTTTCGTG
2614123 TCAGAATCAGATATAAATATACGCAAAAAATAAAAATAAAAAATT-TGGGTGCTAGCCTGTCAAT
1 TCAGAATCAGATATAAATATACG-AAAAAATAAAAA-AAAAAATTATGGGTGCTAGCCTGTCAAT
*
2614187 GGCCGGCACCCAGTACAAATTT-AAA-AAAA-TTC-TTTTTTTTTCGTGTCAGAATCAGATATAA
64 GGCCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTGTCAAAATCAGATATAA
* * *
2614248 ATATATGAAAAAAAT-TTTGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTACAAATTTTTTAAA
129 ATATACGAAAAAAATATTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAA-TTTTTAAA
2614312 AAAAATTTTTTTTTTCGTG
193 AAAAATTTTTTTTTTCGTG
2614331 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAA
1 TCAGAATCAGATATAAATATACG-AAAAAATAAAAAAAA
2614370 TTATATATAA
Statistics
Matches: 232, Mismatches: 10, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
207 3 0.01
208 85 0.37
209 1 0.00
210 12 0.05
216 42 0.18
217 3 0.01
218 4 0.02
219 24 0.10
220 50 0.22
221 8 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (211 bp):
TCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAAATTATGGGTGCTAGCCTGTCAATGG
CCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTGTCAAAATCAGATATAAAT
ATACGAAAAAAATATTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTTTAAAAAA
AATTTTTTTTTTCGTG
Found at i:2615082 original size:29 final size:28
Alignment explanation
Indices: 2615049--2615103 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
2615039 TCGTAATATT
*
2615049 TAAAAATATA-AGGACTAAATTCTTAAAAA
1 TAAAAATATACA-AACTAAATT-TTAAAAA
2615078 TAAAAATATACAAACTAAATTTTAAA
1 TAAAAATATACAAACTAAATTTTAAA
2615104 TTTACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 18 0.75
30 1 0.04
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (28 bp):
TAAAAATATACAAACTAAATTTTAAAAA
Found at i:2615112 original size:29 final size:29
Alignment explanation
Indices: 2615046--2615112 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
2615036 ACTTCGTAAT
*
2615046 ATTTAAAAATATAAGGACTAAATTCTTAA
1 ATTTAAAAATATAAGAACTAAATTCTTAA
**
2615075 AAATAAAAATATACA-AACTAAATT-TTAA
1 ATTTAAAAATATA-AGAACTAAATTCTTAA
2615103 ATTTACAAAA
1 ATTTA-AAAA
2615113 AATATATAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.31
Consensus pattern (29 bp):
ATTTAAAAATATAAGAACTAAATTCTTAA
Found at i:2615747 original size:90 final size:88
Alignment explanation
Indices: 2615647--2615868 Score: 302
Period size: 89 Copynumber: 2.5 Consensus size: 88
2615637 AAAAAAAATT
* *
2615647 TACTGGGTGCCGGCCACTGATAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
1 TACTGGGTGCCGGCCATTGACAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
2615712 TCACACAAAAAAATTTTT-AAATTTG
66 TCACAC---AAAATTTTTAAAATTTG
* * *
2615737 TACTAGGTGCCGGCCATTGACAGGCCAACACCTAATTTTTTTTTTTTGTATATTTATATCTGATT
1 TACTGGGTGCCGGCCATTGACAGGCCAGCACC-AATTTTTTTTTTTCGTATATTTATATCTGATT
* * **
2615802 CTGACACGATTTTTTTAAAATTTG
65 CTCACACAAAATTTTTAAAATTTG
*
2615826 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT
1 TACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAATTTTTTTT
2615869 ATTATTTTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
88 6 0.05
89 44 0.38
90 30 0.26
91 37 0.32
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (88 bp):
TACTGGGTGCCGGCCATTGACAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
TCACACAAAATTTTTAAAATTTG
Found at i:2615843 original size:89 final size:88
Alignment explanation
Indices: 2615647--2615977 Score: 304
Period size: 109 Copynumber: 3.5 Consensus size: 88
2615637 AAAAAAAATT
* *
2615647 TACTGGGTGCCGGCCACTGATAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
1 TACTGGGTGCCGGCCATTGACAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
2615712 TCACACAAAAAAATTTTTAAATTTG
66 TCACAC--AAAAATTTTTAAATTTG
* * *
2615737 TACTAGGTGCCGGCCATTGACAGGCCAACACCTAATTTTTTTTTTTTGTATATTTATATCTGATT
1 TACTGGGTGCCGGCCATTGACAGGCCAGCACC-AATTTTTTTTTTTCGTATATTTATATCTGATT
* * **
2615802 CTGACAC-GATTTTTTTAAAATTTG
65 CTCACACAAAAATTTTT-AAATTTG
*
2615826 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTTTTTTCTTATATTTAT
1 TACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AA-----TT-TT-TTTTTTTCGTATATTTAT
* *
2615891 ATCTGATTCTGATACGAAAAAAAAAGAATTTTTTTTTAAATTTG
57 ATCTGATTC---T-C---ACACAAA-AA----TTTTTAAATTTG
*
2615935 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT
1 TACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAATTTTTTTT
2615978 ATTATTTTTT
Statistics
Matches: 197, Mismatches: 21, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
88 6 0.03
89 35 0.18
90 32 0.16
91 37 0.19
95 2 0.01
96 2 0.01
97 25 0.13
100 1 0.01
101 4 0.02
102 2 0.01
103 1 0.01
104 2 0.01
105 1 0.01
108 2 0.01
109 40 0.20
110 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (88 bp):
TACTGGGTGCCGGCCATTGACAGGCCAGCACCAATTTTTTTTTTTCGTATATTTATATCTGATTC
TCACACAAAAATTTTTAAATTTG
Found at i:2615957 original size:109 final size:109
Alignment explanation
Indices: 2615811--2616299 Score: 663
Period size: 109 Copynumber: 4.5 Consensus size: 109
2615801 TCTGACACGA
*
2615811 TTTTTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
1 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
*
2615876 TTTTCTTATATTTATATCTGATTCTGATACGAAAAAAAAAGAAT
66 TTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAT
2615920 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
1 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
*
2615985 TTTTCTTATATTTATATCTGATTCTGATACGAAAAAAAAAGAAT
66 TTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAT
*
2616029 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTTATTTTTA
1 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-CAAA---TT-TTTTTA
*
2616094 TTTTTATTTTTTT-TGTATATTTATATTTGATTCTGACACGAAAAAAAAAAGAAT
60 ---TTATTTTTTTCT-TATATTTATATCTGATTCTGACACG-AAAAAAAAAGAAT
* *
2616148 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AATTTTTTTTTTACTT
1 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
* * * * ***
2616211 TTTTCATATACTGATATTTGATTCTGACACGAAAAAAATTCAA-
66 TTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAT
* * *
2616254 TTTTTTTT--A-CTGT--TGGGTGTCGGCCATTGACAGGCCATCACCCAAA
1 TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
2616300 AAAATTACTT
Statistics
Matches: 350, Mismatches: 16, Indels: 34
0.88 0.04 0.09
Matches are distributed among these distances:
101 25 0.07
102 2 0.01
103 5 0.01
104 1 0.00
106 8 0.02
107 9 0.03
108 32 0.09
109 153 0.44
110 2 0.01
111 8 0.02
112 2 0.01
114 2 0.01
115 8 0.02
117 2 0.01
118 33 0.09
119 58 0.17
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (109 bp):
TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTT
TTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAT
Found at i:2616205 original size:119 final size:117
Alignment explanation
Indices: 2615970--2616196 Score: 386
Period size: 119 Copynumber: 1.9 Consensus size: 117
2615960 CAGCACCCAA
*
2615970 ATTTTTTTATTATTTTTTTCTTATATTTATATCTGATTCTGATACGAAAAAAAAAGAATTTTTTT
1 ATTTTTTTATTATTTTTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAATTTTTTT
2616035 TTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTT
66 TTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTT
* *
2616087 ATTTTTATTTTTATTTTTTT-TGTATATTTATATTTGATTCTGACACGAAAAAAAAAAGAATTTT
1 ATTTTT-TTATTATTTTTTTCT-TATATTTATATCTGATTCTGACACG-AAAAAAAAAGAATTTT
2616151 TTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAA
63 TTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAA
2616197 TTTTTTTTTT
Statistics
Matches: 104, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
117 7 0.07
118 39 0.38
119 58 0.56
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (117 bp):
ATTTTTTTATTATTTTTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAATTTTTTT
TTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTT
Found at i:2616205 original size:228 final size:217
Alignment explanation
Indices: 2615810--2616301 Score: 658
Period size: 228 Copynumber: 2.2 Consensus size: 217
2615800 TTCTGACACG
* *
2615810 ATTTTTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC-CAAATTTTTTTATTAT
1 ATTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTATTAT
*
2615874 TTTTTTCTTATATTTATATCTGATTCTGATACGAAAAAAAAAGAATTTTTTTTTAAATTTGTACT
66 TTTTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTGTACT
* * * *
2615939 GGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTATTATTTTTTTCTTATATTTATATCT
131 GGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT-TTACTTTTTTCATATACTGATATCT
* *
2616004 GATTCTGATACGAAAAAAAAAGA
195 GATTCTGACACGAAAAAAAAACA
2616027 ATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTTATTTT
1 A-TTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAA---TT-TTTT
*
2616092 TATTTTTATTTTTTT-TGTATATTTATATTTGATTCTGACACGAAAAAAAAAAGAATTTTTTTTT
60 TA---TTATTTTTTTCT-TATATTTATATCTGATTCTGACACG-AAAAAAAAAGAATTTTTTTTT
*
2616156 AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAATTTTTTTTTTACTTTTTTCATAT
120 AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCATAT
* **
2616220 ACTGATATTTGATTCTGACACGAAAAAAATTCA
185 ACTGATATCTGATTCTGACACGAAAAAAAAACA
* * *
2616253 ATTTTTTTT--A-CTGT--TGGGTGTCGGCCATTGACAGGCCATCACCCAAAAA
1 ATTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAA
2616302 AATTACTTTT
Statistics
Matches: 245, Mismatches: 18, Indels: 21
0.86 0.06 0.07
Matches are distributed among these distances:
217 1 0.00
218 44 0.18
219 2 0.01
220 35 0.14
222 3 0.01
223 3 0.01
224 6 0.02
225 8 0.03
226 41 0.17
227 44 0.18
228 58 0.24
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (217 bp):
ATTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTATTAT
TTTTTTCTTATATTTATATCTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTGTACT
GGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCATATACTGATATCTG
ATTCTGACACGAAAAAAAAACA
Found at i:2622595 original size:24 final size:24
Alignment explanation
Indices: 2622563--2622618 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2622553 ATAGTTGTGT
2622563 TTATTTTAAGAAAAACAGTGATGG
1 TTATTTTAAGAAAAACAGTGATGG
2622587 TTATTTTAAGAAAAACAGTGATGG
1 TTATTTTAAGAAAAACAGTGATGG
2622611 TTATTTTA
1 TTATTTTA
2622619 TATATCTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (24 bp):
TTATTTTAAGAAAAACAGTGATGG
Found at i:2624212 original size:16 final size:16
Alignment explanation
Indices: 2624191--2624222 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2624181 AAAATTCAAA
2624191 ATATTTATAAAAAAAT
1 ATATTTATAAAAAAAT
*
2624207 ATATTTTTAAAAAAAT
1 ATATTTATAAAAAAAT
2624223 TATAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTATAAAAAAAT
Found at i:2624453 original size:22 final size:22
Alignment explanation
Indices: 2624411--2624455 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2624401 TATAACAAAA
**
2624411 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
2624433 TTTTAATTTAAC-TCGAATAATT
1 TTTTAATTTAACAT-GAATAATT
2624455 T
1 T
2624456 AACTCGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:2624455 original size:14 final size:14
Alignment explanation
Indices: 2624436--2624462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2624426 TTTAATTTTT
2624436 TAATTTAACTCGAA
1 TAATTTAACTCGAA
2624450 TAATTTAACTCGA
1 TAATTTAACTCGA
2624463 TTCGATTCAA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTTAACTCGAA
Found at i:2626011 original size:48 final size:48
Alignment explanation
Indices: 2625940--2626035 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
2625930 CGATGACACG
*
2625940 TTTCTCCGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
1 TTTCTCCGGAACAGCCTGAGCATATCCAAGAGTGGCACCAACTGACCA
*
2625988 TTTCTCTGGAACAGCCTGAGCATATCCAAGAGTGGCACCAACTGACCA
1 TTTCTCCGGAACAGCCTGAGCATATCCAAGAGTGGCACCAACTGACCA
2626036 CCCAATTGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (48 bp):
TTTCTCCGGAACAGCCTGAGCATATCCAAGAGTGGCACCAACTGACCA
Found at i:2628017 original size:16 final size:16
Alignment explanation
Indices: 2627980--2628019 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2627970 TTGATAAAAT
* * *
2627980 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
2627996 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
2628012 TAAAATTA
1 TAAAATTA
2628020 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:2628113 original size:16 final size:16
Alignment explanation
Indices: 2628084--2628127 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2628074 TTAGTAAAAT
*
2628084 TATTAAATTATTAATTG
1 TATT-AATTGTTAATTG
2628101 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
2628117 TAATAATTGTT
1 TATTAATTGTT
2628128 GTAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:2631237 original size:64 final size:64
Alignment explanation
Indices: 2631161--2631491 Score: 343
Period size: 64 Copynumber: 5.2 Consensus size: 64
2631151 GGCTACACCG
* *
2631161 AAAGCA-ATACAAACAAAGACCACTGTTGGCTTCAATGAGAAAGCAATGAAACTCTAAACACCCA
1 AAAGCATA-ACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * * * * *
2631225 AAAGCATAACAAACGAAAG-CCACTGTTGTGTGCAAGTAAAAAAG-AGT-AAACCCCAAACACTC
1 AAAGCATAACAAAC-AAAGACCACTGTTGTCTTCAA-TGAGAAAGCAATGAAACCCTAAACACCC
2631287 A
64 A
* * **
2631288 AAAGCATTACAAACAAAGACCAGTACTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
1 AAAGCATAACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * * * ** *
2631352 AAAGCATAACAAACGAAAG-CCACTGTTGTATGCAAATAAAAAAG-AGT-AAACCCCGAACACTC
1 AAAGCATAACAAAC-AAAGACCACTGTTGTCTTC-AATGAGAAAGCAATGAAACCCTAAACACCC
2631414 A
64 A
* * *
2631415 AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
1 AAAGCATAACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
*
2631479 AAAGCATTACAAA
1 AAAGCATAACAAA
2631492 TGTGATTTCT
Statistics
Matches: 213, Mismatches: 43, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
62 22 0.10
63 77 0.36
64 91 0.43
65 23 0.11
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (64 bp):
AAAGCATAACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
Found at i:2631294 original size:63 final size:61
Alignment explanation
Indices: 2631216--2631491 Score: 246
Period size: 63 Copynumber: 4.4 Consensus size: 61
2631206 ATGAAACTCT
*
2631216 AAACACCCAAAAGCATAACAAACGAAAGCCACTGTTGTGTGCAAGTAAAAAAGAGTAAACCCC
1 AAACACCCAAAAGCATAACAAAC-AAAGCCACTGTTGTATGCAA-TAAAAAAGAGTAAACCCC
* * * ** * * * * * *
2631279 AAACACTCAAAAGCATTACAAACAAAGACCAGTACTGTCTTCAATGAGAAAGCAATGAAACCCT
1 AAACACCCAAAAGCATAACAAACAAAG-CCACTGTTGTATGCAATAAAAAAG-AGT-AAACCCC
2631343 AAACACCCAAAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCC
1 AAACACCCAAAAGCATAACAAAC-AAAGCCACTGTTGTATGC-AATAAAAAAGAGTAAACCCC
* * * * * * * * * * *
2631406 GAACACTCAAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCT
1 AAACACCCAAAAGCATAACAAACAAAG-CCACTGTTGTATGCAATAAAAAAG-AGT-AAACCCC
*
2631470 AAACACCCAAAAGCATTACAAA
1 AAACACCCAAAAGCATAACAAA
2631492 TGTGATTTCT
Statistics
Matches: 170, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
62 22 0.13
63 72 0.42
64 64 0.38
65 12 0.07
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.15
Consensus pattern (61 bp):
AAACACCCAAAAGCATAACAAACAAAGCCACTGTTGTATGCAATAAAAAAGAGTAAACCCC
Found at i:2631371 original size:127 final size:127
Alignment explanation
Indices: 2631161--2631491 Score: 572
Period size: 127 Copynumber: 2.6 Consensus size: 127
2631151 GGCTACACCG
* * * * *
2631161 AAAGCAATACAAACAAAGACCACTGTTGGCTTCAATGAGAAAGCAATGAAACTCTAAACACCCAA
1 AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
* *
2631226 AAGCATAACAAACGAAAGCCACTGTTGTGTGCAAGTAAAAAAGAGTAAACCCCAAACACTCA
66 AAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTCA
*
2631288 AAAGCATTACAAACAAAGACCAGTACTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
1 AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
*
2631353 AAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCGAACACTCA
66 AAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTCA
2631415 AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
1 AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
*
2631480 AAGCATTACAAA
66 AAGCATAACAAA
2631492 TGTGATTTCT
Statistics
Matches: 193, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 193 1.00
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (127 bp):
AAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCAA
AAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTCA
Found at i:2631576 original size:16 final size:16
Alignment explanation
Indices: 2631519--2631586 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
2631509 ATATTTGCGC
*
2631519 ATTAAAAAATATAAAAA
1 ATTAAAAAATAT-ATAA
* *
2631536 ATTCAGAAATATATAA
1 ATTAAAAAATATATAA
**
2631552 CCTAAAAAATATATAA
1 ATTAAAAAATATATAA
* *
2631568 ATTATAAAATTTA-AA
1 ATTAAAAAATATATAA
2631583 ATTA
1 ATTA
2631587 CAATGAAAAG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 6 0.15
16 24 0.60
17 10 0.25
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (16 bp):
ATTAAAAAATATATAA
Found at i:2631756 original size:19 final size:18
Alignment explanation
Indices: 2631711--2631858 Score: 65
Period size: 19 Copynumber: 7.9 Consensus size: 18
2631701 AGACTTAATA
2631711 AAAATTA-TAAAAATATTT
1 AAAATTATTAAAAAT-TTT
* *
2631729 GAACA-TATTAAAGATTTAT
1 -AAAATTATTAAAAATTT-T
2631748 AAAATTATTAAAAATTTT
1 AAAATTATTAAAAATTTT
*
2631766 AAAA-AATTGAGAAAATCATTT
1 AAAATTATT-A-AAAAT--TTT
* *
2631787 AAAA-AATTAAAAATGATTA
1 AAAATTATTAAAAAT--TTT
* *
2631806 AAAAATATAAAAAATTATTT
1 AAAATTATTAAAAA-T-TTT
* *
2631826 GAAATT-TATAAGAATTTT
1 AAAATTAT-TAAAAATTTT
2631844 AAAATT-TTAAAAATT
1 AAAATTATTAAAAATT
2631859 ATAATATATT
Statistics
Matches: 103, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
17 10 0.10
18 22 0.21
19 40 0.39
20 19 0.18
21 12 0.12
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAAAATTTT
Found at i:2631761 original size:10 final size:10
Alignment explanation
Indices: 2631748--2631860 Score: 64
Period size: 10 Copynumber: 11.8 Consensus size: 10
2631738 AAAGATTTAT
2631748 AAAATTATTA
1 AAAATTATTA
2631758 AAAATT-TTA
1 AAAATTATTA
2631767 AAAA--ATTGA
1 AAAATTATT-A
*
2631776 GAAAATCATTTA
1 -AAAATTA-TTA
2631788 AAAA--ATTA
1 AAAATTATTA
*
2631796 AAAATGATTA
1 AAAATTATTA
* *
2631806 AAAAATATAA
1 AAAATTATTA
*
2631816 AAAATTATTT
1 AAAATTATTA
*
2631826 GAAATT-TATA
1 AAAATTAT-TA
*
2631836 AGAATT-TT-
1 AAAATTATTA
2631844 AAAATT-TTA
1 AAAATTATTA
2631853 AAAATTAT
1 AAAATTAT
2631861 AATATATTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
8 16 0.20
9 17 0.21
10 40 0.49
11 4 0.05
12 2 0.02
13 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (10 bp):
AAAATTATTA
Found at i:2631789 original size:21 final size:19
Alignment explanation
Indices: 2631754--2631818 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
2631744 TTATAAAATT
2631754 ATTAAAAAT--TTTAAAAA
1 ATTAAAAATCATTTAAAAA
2631771 ATTGAGAAAATCATTTAAAAA
1 ATT-A-AAAATCATTTAAAAA
*
2631792 ATTAAAAATGA-TTAAAAA
1 ATTAAAAATCATTTAAAAA
2631810 ATATAAAAA
1 AT-TAAAAA
2631819 ATTATTTGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.07
18 10 0.24
19 17 0.40
20 1 0.02
21 11 0.26
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
ATTAAAAATCATTTAAAAA
Found at i:2633731 original size:42 final size:43
Alignment explanation
Indices: 2633685--2633823 Score: 172
Period size: 43 Copynumber: 3.3 Consensus size: 43
2633675 TCGTGTTTTT
** * *
2633685 TAGCGGCGTTTAT-AAAAAAGCACCGCTAGAAGTCATGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAAGTCATGATCTA
**
2633727 TAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAAGTCATGATCTA
*** * *
2633770 TAGCTATGTTTATGGGAGAAGTGCCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAAGTCATGATCTA
2633813 TAGCGGCGTTT
1 TAGCGGCGTTT
2633824 GTTGGAGAAC
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 11 0.14
43 69 0.86
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:2636702 original size:21 final size:21
Alignment explanation
Indices: 2636678--2636812 Score: 64
Period size: 21 Copynumber: 6.6 Consensus size: 21
2636668 AAATTTATCA
2636678 TTTAAAGTTTAGGGTTTAAGT
1 TTTAAAGTTTAGGGTTTAAGT
* * *
2636699 TTTAGAGTTT-GAGTTTAGGT
1 TTTAAAGTTTAGGGTTTAAGT
* ** * * *
2636719 TTTTAACATTAGAGTTTAGGA
1 TTTAAAGTTTAGGGTTTAAGT
* * *
2636740 TTTATAGTTTAAGATTTAAGT
1 TTTAAAGTTTAGGGTTTAAGT
* * *
2636761 TTTAGAGTTTA-AG-TTGAGAT
1 TTTAAAGTTTAGGGTTTAAG-T
* *
2636781 TTTTAA--TTAAGGTTTAAGT
1 TTTAAAGTTTAGGGTTTAAGT
*
2636800 TTTAATGTTTAGG
1 TTTAAAGTTTAGG
2636813 ATATTATGAT
Statistics
Matches: 80, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
18 3 0.04
19 10 0.12
20 23 0.29
21 44 0.55
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (21 bp):
TTTAAAGTTTAGGGTTTAAGT
Found at i:2636748 original size:14 final size:13
Alignment explanation
Indices: 2636731--2636775 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
2636721 TTAACATTAG
*
2636731 AGTTTAGGATTTA
1 AGTTTAAGATTTA
2636744 TAGTTTAAGATTTA
1 -AGTTTAAGATTTA
*
2636758 AGTTTTAGAGTTTA
1 AGTTTAAGA-TTTA
2636772 AGTT
1 AGTT
2636776 GAGATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (13 bp):
AGTTTAAGATTTA
Found at i:2640631 original size:5 final size:6
Alignment explanation
Indices: 2640613--2640638 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2640603 CACCTAGTGC
2640613 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
2640639 CATACAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:2643120 original size:31 final size:31
Alignment explanation
Indices: 2643061--2643120 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2643051 AGTAGACTTT
* * **
2643061 TTTTGAAAAATTAATAGTTAAATCTAATTCC
1 TTTTAAAAAATTAAAAGAAAAATCTAATTCC
*
2643092 TTTTAAAAAATTAAAAGAAAAATTTAATT
1 TTTTAAAAAATTAAAAGAAAAATCTAATT
2643121 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTTAAAAAATTAAAAGAAAAATCTAATTCC
Found at i:2646459 original size:16 final size:18
Alignment explanation
Indices: 2646420--2646453 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2646410 TAAGTTTATA
2646420 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2646437 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2646454 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2650878 original size:4 final size:4
Alignment explanation
Indices: 2650869--2650909 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
2650859 TTTGCAGTGC
* *
2650869 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGC TTGC TTGT T
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT T
2650910 CTCATTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.05, G:0.24, T:0.71
Consensus pattern (4 bp):
TTGT
Found at i:2653879 original size:51 final size:51
Alignment explanation
Indices: 2653819--2653923 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
2653809 GAACTTTCGT
2653819 TAGATATCAATTAAACTAAGATTTAATCGATTATTGTTACTATTTTTATTA
1 TAGATATCAATTAAACTAAGATTTAATCGATTATTGTTACTATTTTTATTA
*
2653870 TAGATATCAATTAAACTAAGATTTAATGGATTATTGTTACTATTTTTATTA
1 TAGATATCAATTAAACTAAGATTTAATCGATTATTGTTACTATTTTTATTA
2653921 TAG
1 TAG
2653924 CCCACAGCTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (51 bp):
TAGATATCAATTAAACTAAGATTTAATCGATTATTGTTACTATTTTTATTA
Found at i:2657683 original size:31 final size:31
Alignment explanation
Indices: 2657638--2657696 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2657628 ATTATTAAAT
2657638 TATTCGAAAATTTTTATTTAAGTCACTGAAC
1 TATTCGAAAATTTTTATTTAAGTCACTGAAC
2657669 TATTC-AAAACTTTTTATTTAAGTCACTG
1 TATTCGAAAA-TTTTTATTTAAGTCACTG
2657697 GAAGTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
TATTCGAAAATTTTTATTTAAGTCACTGAAC
Found at i:2659892 original size:11 final size:11
Alignment explanation
Indices: 2659866--2659904 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2659856 GCTCTAAAGT
2659866 TGAAAAAATCA
1 TGAAAAAATCA
*
2659877 T--AAAAATTA
1 TGAAAAAATCA
2659886 TGAAAAAATCA
1 TGAAAAAATCA
2659897 TGAAAAAA
1 TGAAAAAA
2659905 GCCTGGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (11 bp):
TGAAAAAATCA
Found at i:2665000 original size:33 final size:32
Alignment explanation
Indices: 2664956--2665027 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 32
2664946 CTTTTTTTGT
*
2664956 AATTGTTGCTATTGATTCAAAAATGATTTAAA
1 AATTGTTGCTATTGATTCAAAAAAGATTTAAA
2664988 AACTTGTTGCTATTGATTCAAAAAAGATTTAAA
1 AA-TTGTTGCTATTGATTCAAAAAAGATTTAAA
2665021 AATTGTT
1 AATTGTT
2665028 ACCAACAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 7 0.18
33 31 0.82
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (32 bp):
AATTGTTGCTATTGATTCAAAAAAGATTTAAA
Found at i:2687112 original size:39 final size:39
Alignment explanation
Indices: 2687063--2687139 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
2687053 ACAGGTGTCA
*
2687063 TGTGACCAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
*
2687102 TGTGAACAGGCTGGGTCAAGTTTGTCTGGTTCAAATTC
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTC
2687140 ATCCAGCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (39 bp):
TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
Found at i:2691484 original size:74 final size:74
Alignment explanation
Indices: 2691397--2691540 Score: 261
Period size: 74 Copynumber: 1.9 Consensus size: 74
2691387 GCCTTGTGGT
* *
2691397 GAAGATGTCAAGTGAAGTGTCACCAAGGAAGCATAAGCCCCATCGGTTATATTCATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
*
2691462 GTGTCTACC
66 ATGTCTACC
2691471 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
2691536 ATGTC
66 ATGTC
2691541 GACCTTTCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (74 bp):
GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
ATGTCTACC
Found at i:2696884 original size:2 final size:2
Alignment explanation
Indices: 2696877--2696907 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2696867 CCAACTAGAA
*
2696877 AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2696908 CGTAGCAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2697431 original size:21 final size:21
Alignment explanation
Indices: 2697388--2697428 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2697378 TTTTTTTAAA
*
2697388 AATTAATTACCAAAAAATAAT
1 AATTAATTAACAAAAAATAAT
*
2697409 AATTAAATTAACAATAAATA
1 AATT-AATTAACAAAAAATA
2697429 TAAATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAATTAACAAAAAATAAT
Found at i:2700142 original size:25 final size:25
Alignment explanation
Indices: 2700094--2700142 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2700084 CTAGGATAAT
* *
2700094 CAGAGTTTAAGTGGGAAACTAAAAA
1 CAGAGTTTAACTGGGAAACGAAAAA
2700119 CAGAGTTTAACTGGGAGAA-GAAAA
1 CAGAGTTTAACTGGGA-AACGAAAA
2700143 CCAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (25 bp):
CAGAGTTTAACTGGGAAACGAAAAA
Found at i:2701877 original size:21 final size:21
Alignment explanation
Indices: 2701844--2701887 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2701834 AAGATGTGAC
**
2701844 TTGTATTGGATTGAATG-TAAA
1 TTGTATTAAATTG-ATGTTAAA
2701865 TTGTATTAAATTGATGTTAAA
1 TTGTATTAAATTGATGTTAAA
2701886 TT
1 TT
2701888 TACTCGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
TTGTATTAAATTGATGTTAAA
Found at i:2702394 original size:26 final size:27
Alignment explanation
Indices: 2702346--2702396 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2702336 GAGTATCCCG
* *
2702346 TTATATGGCTCTTCGTGATCTTCCCAA
1 TTATATGGCTCTTCATGAGCTTCCCAA
*
2702373 TTATA-GGCTCTTTATGAGCTTCCC
1 TTATATGGCTCTTCATGAGCTTCCC
2702397 GTTAATGCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (27 bp):
TTATATGGCTCTTCATGAGCTTCCCAA
Found at i:2702497 original size:25 final size:26
Alignment explanation
Indices: 2702341--2702499 Score: 100
Period size: 25 Copynumber: 6.4 Consensus size: 26
2702331 CTTATGAGTA
* *
2702341 TCCCGTTATATGGCTCTTCGTGATCT
1 TCCCGTTATATGGCTCTTTGTGAGCT
* *
2702367 TCCCAATTATA-GGCTCTTTATGAGCT
1 TCCC-GTTATATGGCTCTTTGTGAGCT
** *
2702393 TCCCGTTA-AT-GCTCACT-TGAACT
1 TCCCGTTATATGGCTCTTTGTGAGCT
* * * *
2702416 TCCCATTATATGGCTATTCG-GTGCT
1 TCCCGTTATATGGCTCTTTGTGAGCT
* **
2702441 TCCCGTTA-ATTGCTC-TTCAGAGCT
1 TCCCGTTATATGGCTCTTTGTGAGCT
* * *
2702465 ACCAGTTATA-AGCTCTTTGTGAGCT
1 TCCCGTTATATGGCTCTTTGTGAGCT
2702490 TCCCGTTATA
1 TCCCGTTATA
2702500 GTGCTTGAGA
Statistics
Matches: 97, Mismatches: 28, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
23 13 0.13
24 27 0.28
25 32 0.33
26 20 0.21
27 5 0.05
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (26 bp):
TCCCGTTATATGGCTCTTTGTGAGCT
Found at i:2704177 original size:21 final size:22
Alignment explanation
Indices: 2704139--2704186 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
2704129 TTAGTAGACT
*
2704139 CATCTTGGCTATTTGTCAAGTG
1 CATCTTGGCTATTTGTCAAGTA
2704161 CATCTTGGCTA-TTGTCAAGTA
1 CATCTTGGCTATTTGTCAAGTA
2704182 CATCT
1 CATCT
2704187 CGTGATAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
CATCTTGGCTATTTGTCAAGTA
Found at i:2715349 original size:18 final size:18
Alignment explanation
Indices: 2715326--2715360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2715316 TTTTATATGT
* *
2715326 TATAAATTATATAATATA
1 TATAAATAACATAATATA
2715344 TATAAATAACATAATAT
1 TATAAATAACATAATAT
2715361 GCGGAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAATAACATAATATA
Found at i:2720233 original size:27 final size:27
Alignment explanation
Indices: 2720196--2720250 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2720186 GTATAATTGC
2720196 GCGCGCAGTCCTTCCACTCTGCAGCAT
1 GCGCGCAGTCCTTCCACTCTGCAGCAT
2720223 GCGCGCAGTCCTTCCACTCTGCAGCAT
1 GCGCGCAGTCCTTCCACTCTGCAGCAT
2720250 G
1 G
2720251 TTTCAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.40, G:0.24, T:0.22
Consensus pattern (27 bp):
GCGCGCAGTCCTTCCACTCTGCAGCAT
Found at i:2722996 original size:18 final size:19
Alignment explanation
Indices: 2722953--2723001 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2722943 CATTATGTAT
2722953 AATTTTATTGCTAGCATGAA
1 AATTTTA-TGCTAGCATGAA
* *
2722973 AGTTTTATGCTA-CTTGAA
1 AATTTTATGCTAGCATGAA
2722991 AATTTTATGCT
1 AATTTTATGCT
2723002 TAATTACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.58
19 5 0.19
20 6 0.23
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (19 bp):
AATTTTATGCTAGCATGAA
Found at i:2725066 original size:19 final size:19
Alignment explanation
Indices: 2725042--2725085 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2725032 TAATTAAAAT
*
2725042 AAAAATTAATTTATATT-TA
1 AAAAATTAA-ATATATTCTA
2725061 AAAAA-TAAATATATTCTA
1 AAAAATTAAATATATTCTA
2725079 AAAAATT
1 AAAAATT
2725086 TGCGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAATATATTCTA
Found at i:2728543 original size:8 final size:7
Alignment explanation
Indices: 2728524--2728553 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2728514 ATCATGTTCA
2728524 AAATTTG
1 AAATTTG
2728531 AAATTTAG
1 AAATTT-G
2728539 AAATTTG
1 AAATTTG
2728546 AAATTTG
1 AAATTTG
2728553 A
1 A
2728554 GTTCAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (7 bp):
AAATTTG
Found at i:2737414 original size:40 final size:40
Alignment explanation
Indices: 2737359--2737452 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
2737349 CGTCAGCGCG
*
2737359 ATTTGCTGACGTGGACACAAATAGCGCCCTTTAGGACGCA
1 ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
* *
2737399 ATTTGCTGACGTGGACACAATTAGCGCCCTCTAGGACGCG
1 ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
2737439 ATTTGCTGACGTGG
1 ATTTGCTGACGTGG
2737453 CATGAACAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
Found at i:2744178 original size:24 final size:24
Alignment explanation
Indices: 2744150--2744201 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2744140 TTAGTAAGTC
* *
2744150 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2744174 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2744198 AAAT
1 AAAT
2744202 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2745474 original size:51 final size:52
Alignment explanation
Indices: 2745412--2745632 Score: 229
Period size: 51 Copynumber: 4.3 Consensus size: 52
2745402 TTCGGTGGTT
* * *
2745412 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCGATACATGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * * * * * *
2745463 TACACATAGTACTACACACGTGATCA-AG-CTTTCTGGTTCACGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * *
2745513 TGCACATAGTACTACACATGTGACCA-AGGCCATCC-AGTACACATAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGA-TACACGTAGTAGCC
* *
2745564 TGCACATAGTACTACAAATGTGACCATTATCTAT-CGATACACGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
*
2745615 TGCACTTAGTACTACACA
1 TGCACATAGTACTACACA
2745633 CGTGTTCATA
Statistics
Matches: 137, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 1 0.01
50 41 0.30
51 91 0.66
52 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (52 bp):
TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
Found at i:2745885 original size:21 final size:21
Alignment explanation
Indices: 2745860--2745921 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 21
2745850 CAAATACTAA
2745860 ATTTCTAATTGTTAAATAACT
1 ATTTCTAATTGTTAAATAACT
* *
2745881 ATTTC--A-TATTCAA-AA--
1 ATTTCTAATTGTTAAATAACT
2745896 ATTTCTAATTGTTAAATAACT
1 ATTTCTAATTGTTAAATAACT
2745917 ATTTC
1 ATTTC
2745922 ATATTCAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 5 0.16
17 3 0.10
18 10 0.32
19 3 0.10
21 10 0.32
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTTCTAATTGTTAAATAACT
Found at i:2745937 original size:36 final size:36
Alignment explanation
Indices: 2745858--2745929 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2745848 ATCAAATACT
2745858 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
1 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
2745894 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
1 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
2745930 CCATTTCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
Found at i:2748702 original size:44 final size:43
Alignment explanation
Indices: 2748639--2748755 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 43
2748629 TATGAGTTAT
2748639 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGGGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATGTT-GGA-TTA
** *
2748683 CGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATGTTTGATTA
1 CGTGTAAGACCACGTCTGGGAC-GTTGGCATCGATGTTGGATTA
* *
2748726 CATGTAAGACCACGTCTGAGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
2748756 TGTAAGAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.43
44 32 0.51
45 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATGTTGGATTA
Found at i:2748811 original size:23 final size:23
Alignment explanation
Indices: 2748785--2748835 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2748775 ATTCGAATAT
2748785 TGTAATATCC-CAAAAATTACTAC
1 TGTAATA-CCTCAAAAATTACTAC
*
2748808 TGTAATACCTTAAAAATTACTAC
1 TGTAATACCTCAAAAATTACTAC
*
2748831 AGTAA
1 TGTAA
2748836 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (23 bp):
TGTAATACCTCAAAAATTACTAC
Found at i:2749343 original size:11 final size:11
Alignment explanation
Indices: 2749318--2749344 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2749308 AAATAATATT
2749318 TTATTATTTTA
1 TTATTATTTTA
2749329 TTATTATTTTA
1 TTATTATTTTA
2749340 TTATT
1 TTATT
2749345 TTATTTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:2752034 original size:27 final size:27
Alignment explanation
Indices: 2752002--2752057 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2751992 AAATTCGATG
*
2752002 ATTGTAAGTAAGGTTATTTGTTTTGGT
1 ATTGTAAGTAAGGTCATTTGTTTTGGT
2752029 ATTGTAAGTAAGGTCATTTGTTTTGGT
1 ATTGTAAGTAAGGTCATTTGTTTTGGT
2752056 AT
1 AT
2752058 GTACATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (27 bp):
ATTGTAAGTAAGGTCATTTGTTTTGGT
Found at i:2769344 original size:3 final size:3
Alignment explanation
Indices: 2769338--2769373 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2769328 CAGCCACCAC
* *
2769338 CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2769374 GGTGGTGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2773209 original size:27 final size:27
Alignment explanation
Indices: 2773152--2773213 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
2773142 GCTATTTGAT
* * *
2773152 AGGCGCAACTAGTTGAGCCTATCTAAC
1 AGGCGCGACTAATTGAGCCTAACTAAC
* * *
2773179 AGGCGCGACTAATTGTGCCTAACTCAG
1 AGGCGCGACTAATTGAGCCTAACTAAC
2773206 AGGCGCGA
1 AGGCGCGA
2773214 ATGGTGGGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (27 bp):
AGGCGCGACTAATTGAGCCTAACTAAC
Found at i:2777634 original size:15 final size:15
Alignment explanation
Indices: 2777610--2777645 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2777600 ATCAATACGG
*
2777610 CCCAACTAGCCTAAA
1 CCCAATTAGCCTAAA
*
2777625 CCCAATTAGCCTAAG
1 CCCAATTAGCCTAAA
2777640 CCCAAT
1 CCCAAT
2777646 ACCCTAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:2779115 original size:3 final size:3
Alignment explanation
Indices: 2779107--2779143 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2779097 AAACATGCGT
* *
2779107 ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2779144 CAAAGTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2788687 original size:29 final size:30
Alignment explanation
Indices: 2788645--2788705 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
2788635 TTAACAATTA
2788645 ATCCTAATGTGGGTGGATTTGGTAA-GGAG
1 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
2788674 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
1 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
2788704 AT
1 AT
2788706 GCATAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.31
Consensus pattern (30 bp):
ATCCTAATGTGGGTGGATTTGGTAAGGGAG
Found at i:2788816 original size:2 final size:2
Alignment explanation
Indices: 2788811--2788863 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
2788801 TCTCTCTCTC
* * *
2788811 TA TA TA TA TA TA TA TA TA TA TA -A TA TG TGA TA TA TA TC TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
2788853 TA TA TT TA TA T
1 TA TA TA TA TA T
2788864 GTTGTGTCCG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2794522 original size:89 final size:89
Alignment explanation
Indices: 2794371--2794747 Score: 504
Period size: 89 Copynumber: 4.2 Consensus size: 89
2794361 GATAAGACTT
* * *
2794371 GTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCC
1 GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCC
2794436 ACCAGTATGGGAAGACAAGATCTG
66 ACCAGTATGGGAAGACAAGATCTG
* * *
2794460 GTATCTTTGATCTAGTTCACGCTAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCC
2794525 ACCAGTATGGGAAGACAAGATCTG
66 ACCAGTATGGGAAGACAAGATCTG
* * * *
2794549 TATATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGTTTTCTTCAATCTGCTTCGC
1 -GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGC
* *
2794614 CACCAGTATGGGAAGGCAATATCTG
65 CACCAGTATGGGAAGACAAGATCTG
* * * * *
2794639 TTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTACTTTTTCCTTCGATCTGCTTC
1 GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTCAATCTACTTC
* * *
2794704 GCCACCAGTATAGGAAGGCGAGATCT-
63 GCCACCAGTATGGGAAGACAAGATCTG
* * *
2794730 GTATATTCGATCCACTTC
1 GTATCTTTGATCTACTTC
2794748 GCTACCAATA
Statistics
Matches: 255, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
89 123 0.48
90 80 0.31
91 16 0.06
92 36 0.14
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (89 bp):
GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCC
ACCAGTATGGGAAGACAAGATCTG
Found at i:2794679 original size:179 final size:181
Alignment explanation
Indices: 2794372--2794770 Score: 572
Period size: 179 Copynumber: 2.2 Consensus size: 181
2794362 ATAAGACTTG
2794372 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCA
* * *
2794437 CCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAGTTCACGCTAGTACATGAAGACAAGATC
66 CCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATC
* *
2794502 TGC-TTT-CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTA
131 TACTTTTCCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTA
* * * *
2794551 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGTTTTCTTCAATCTGCTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCA
* * *
2794616 CCAGTATGGGAAGGCAATATCTGTTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATC
66 CCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATC
* * *
2794681 TACTTTTTCCTTCGATCTGCTTCGCCACCAGTATAGGAAGGCGAGATCTGTA
131 TAC-TTTTCCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTA
* * * * *
2794733 TA--TTCGATCCACTTCGCTACCAATATAGGAAGACAAGA
1 TATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGA
2794771 CCTGCTGCTT
Statistics
Matches: 194, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
179 122 0.63
180 12 0.06
181 19 0.10
182 41 0.21
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (181 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCA
CCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATC
TACTTTTCCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTA
Found at i:2802841 original size:20 final size:20
Alignment explanation
Indices: 2802816--2802855 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2802806 TAAAGGTCTT
*
2802816 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
2802836 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
2802856 ATGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:2807227 original size:21 final size:21
Alignment explanation
Indices: 2807198--2807238 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2807188 CAGTTAACAG
2807198 AAAAGAAAGAAAAAAAACTTTT
1 AAAAGAAAG-AAAAAAACTTTT
*
2807220 AAAA-AAAGTAAAAAACTTT
1 AAAAGAAAGAAAAAAACTTT
2807239 CTGGCGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAGAAAGAAAAAAACTTTT
Found at i:2813167 original size:23 final size:22
Alignment explanation
Indices: 2813120--2813165 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2813110 TATTTAATTA
* *
2813120 TTAATTTTTTCGATTTAACTAT
1 TTAATTTTTTCGAATTAAATAT
2813142 TTAA-TTTTTCGAGATTAAATAT
1 TTAATTTTTTCGA-ATTAAATAT
2813164 TT
1 TT
2813166 TAGTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAATTTTTTCGAATTAAATAT
Found at i:2813575 original size:16 final size:17
Alignment explanation
Indices: 2813554--2813585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2813544 GCACAAAGTA
2813554 AAATA-TTTAAAAAAAT
1 AAATATTTTAAAAAAAT
2813570 AAATATTTTAAAAAAA
1 AAATATTTTAAAAAAA
2813586 GAGACACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATTTTAAAAAAAT
Found at i:2813787 original size:32 final size:32
Alignment explanation
Indices: 2813751--2813821 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2813741 GCTAAATTCC
* ** *
2813751 TAATCAATTCTAATTCCTCCAAGGGTTTGTAT
1 TAATCAATCCTAATTCCTCCAAGAATTTGCAT
* *
2813783 TAATCAATCCTAATTTCTTCAAGAATTTGCAT
1 TAATCAATCCTAATTCCTCCAAGAATTTGCAT
2813815 TAATCAA
1 TAATCAA
2813822 CCTCTAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (32 bp):
TAATCAATCCTAATTCCTCCAAGAATTTGCAT
Found at i:2820989 original size:40 final size:40
Alignment explanation
Indices: 2820945--2821025 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2820935 ATCATCAAAG
* *
2820945 TGTGTTTATACATGAATGGTATGATCTTCAAATGAAACAA
1 TGTGTTTATACAAGAATGGTATGATCTTCAAAGGAAACAA
2820985 TGTGTTTATACAAGAATGGTATGATCTTCAAAGGAAACAA
1 TGTGTTTATACAAGAATGGTATGATCTTCAAAGGAAACAA
2821025 T
1 T
2821026 CCAAGCATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (40 bp):
TGTGTTTATACAAGAATGGTATGATCTTCAAAGGAAACAA
Found at i:2821384 original size:46 final size:46
Alignment explanation
Indices: 2821317--2821409 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
2821307 TAGCAAAAAG
2821317 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
1 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
*
2821363 AATTTTGAGATATGTCAAAGGTATGATAGATCAAGGTTTATTTCAT
1 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
2821409 A
1 A
2821410 CTCTCACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (46 bp):
AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
Found at i:2829789 original size:59 final size:59
Alignment explanation
Indices: 2829668--2829789 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
2829658 TTACATCCCG
** * **
2829668 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGTTTATTGCATCTTA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGACTATGGCATCGAA
* * * *
2829727 AACAAAGTGACAATCCACTTCAATTGCAATTTGTAACA-CAGATTGACTATGGCCTCGAA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGTAA-AGCAAATTGACTATGGCATCGAA
2829786 AACA
1 AACA
2829790 TTGTTCTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 52 0.98
60 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (59 bp):
AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGACTATGGCATCGAA
Found at i:2830326 original size:21 final size:22
Alignment explanation
Indices: 2830300--2830356 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
2830290 AATAGGGAAT
*
2830300 ATATATAATATTTTCCT-AAAG
1 ATATATAATATATTCCTAAAAG
2830321 ATATATAATATATTCCTAAAAG
1 ATATATAATATATTCCTAAAAG
2830343 ATATATAATATATT
1 ATATATAATATATT
2830357 TAGATATTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATATAATATATTCCTAAAAG
Found at i:2836553 original size:5 final size:5
Alignment explanation
Indices: 2836540--2836570 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2836530 GACTAACCTT
*
2836540 GAAAG GAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
2836571 GCAAGTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2841227 original size:29 final size:30
Alignment explanation
Indices: 2841164--2841242 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2841154 AATTTCAAAA
*
2841164 TATACATAAACTTTGGTTTAATATGCAATTG
1 TATACATAAACTTTGATTT-ATATGCAATTG
* *
2841195 TATACATGAACTTTGATTT-TATGCAATTT
1 TATACATAAACTTTGATTTATATGCAATTG
* *
2841224 TATATATCAAATTTTGATT
1 TATACAT-AAACTTTGATT
2841243 CAAACCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.37
30 9 0.22
31 17 0.41
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
TATACATAAACTTTGATTTATATGCAATTG
Found at i:2842747 original size:19 final size:20
Alignment explanation
Indices: 2842723--2842771 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2842713 ATTTATTATA
*
2842723 AATTAATTATAC-TAATTTT
1 AATTAATTATACATAATATT
*
2842742 AATTAAAT-TACATAATATT
1 AATTAATTATACATAATATT
*
2842761 AATTATTTATA
1 AATTAATTATA
2842772 TTTGGTCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.79
20 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATTATACATAATATT
Found at i:2856895 original size:32 final size:32
Alignment explanation
Indices: 2856851--2856911 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2856841 TAATTAGTAT
*
2856851 GAGTTATCAAATTAAATTAATTAATTTATCAC
1 GAGTTATCAAATTAAAGTAATTAATTTATCAC
* * *
2856883 GAGTTATTAAATTTAAGTAATTAGTTTAT
1 GAGTTATCAAATTAAAGTAATTAATTTAT
2856912 AAGTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
GAGTTATCAAATTAAAGTAATTAATTTATCAC
Found at i:2858192 original size:4 final size:4
Alignment explanation
Indices: 2858185--2858211 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2858175 CTATTTTGTT
2858185 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2858212 TTAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2865040 original size:4 final size:4
Alignment explanation
Indices: 2865031--2865088 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
2865021 ATCATCGTGA
2865031 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2865079 TATG TATG TA
1 TATG TATG TA
2865089 GAGTTACCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2869815 original size:18 final size:17
Alignment explanation
Indices: 2869782--2869820 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2869772 TTGTATAAAT
2869782 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2869800 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2869817 TGTG
1 TGTG
2869821 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2870100 original size:23 final size:23
Alignment explanation
Indices: 2870046--2870120 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
2870036 AGTGTTATTG
*
2870046 ATCAGTGATAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2870069 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2870091 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2870114 ATCAGTG
1 ATCAGTG
2870121 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 20 0.42
23 28 0.58
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2880872 original size:18 final size:17
Alignment explanation
Indices: 2880839--2880877 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2880829 TTGTATAAAT
2880839 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2880857 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2880874 TGTG
1 TGTG
2880878 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2881130 original size:23 final size:23
Alignment explanation
Indices: 2881104--2881177 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
2881094 GTGTTATTGA
2881104 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
2881127 TCAGTGGTAGCTTTGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACATT
* *
2881149 CCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
2881172 TCAGTG
1 TCAGTG
2881178 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:2881156 original size:22 final size:22
Alignment explanation
Indices: 2881105--2881170 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
2881095 TGTTATTGAT
*
2881105 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACA-TC
*
2881128 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
2881150 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
2881171 ATCAGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 21 0.52
23 19 0.47
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CAGTGGTAGCTTCGGCTACATC
Found at i:2885421 original size:33 final size:32
Alignment explanation
Indices: 2885349--2885425 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
2885339 TATATACATG
* * * **
2885349 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTAGGCTATGGCATACAAA
*
2885381 TGATAAGACCATAACTAGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTAGGCTATGGCA-TACAAA
2885415 TGTAAGACCAT
1 TGTAAGACCAT
2885426 GGCAGGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTAGGCTATGGCATACAAA
Found at i:2886227 original size:17 final size:17
Alignment explanation
Indices: 2886200--2886245 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
2886190 CCGATATAAT
* * *
2886200 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
2886217 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
2886234 AAATATTTTTAA
1 AAATATTTTTAA
2886246 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:2886276 original size:20 final size:20
Alignment explanation
Indices: 2886238--2886276 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2886228 ATTTTAAAAT
***
2886238 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAAATTTTA
2886258 ATTTTTAAAATAAAATTTT
1 ATTTTTAAAATAAAATTTT
2886277 GGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTAAAATAAAATTTTA
Found at i:2896815 original size:5 final size:6
Alignment explanation
Indices: 2896801--2896825 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2896791 ACTAAGCATT
2896801 AAAACA AAAACA AAAACA AAAACA A
1 AAAACA AAAACA AAAACA AAAACA A
2896826 CCCATTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:2900216 original size:26 final size:25
Alignment explanation
Indices: 2900179--2900229 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
2900169 TTAATATTGT
*
2900179 AATATATTTATA-ATGATAAAAGTTAA
1 AATATATATATATATG-TAAAA-TTAA
2900205 AATATATATATATATGTAAAATTAA
1 AATATATATATATATGTAAAATTAA
2900230 TTAAACTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 16 0.70
27 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AATATATATATATATGTAAAATTAA
Found at i:2910716 original size:32 final size:34
Alignment explanation
Indices: 2910679--2910752 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
2910669 TATTACACAT
*
2910679 TAATTTTAA-TTTAGTG-CATTAAAATATTTTAC
1 TAATTTTAATTTTAGTGAAATTAAAATATTTTAC
***
2910711 TAATTTTAATTTTAGTGAAATTTTCATATTTTAC
1 TAATTTTAATTTTAGTGAAATTAAAATATTTTAC
2910745 TAATTTTA
1 TAATTTTA
2910753 TTGTCTATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (34 bp):
TAATTTTAATTTTAGTGAAATTAAAATATTTTAC
Found at i:2910749 original size:17 final size:16
Alignment explanation
Indices: 2910702--2910753 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
2910692 GTGCATTAAA
2910702 ATATTTTACTAATTTT
1 ATATTTTACTAATTTT
*
2910718 A-ATTTTAGTGAAATTTT
1 ATATTTTACT--AATTTT
2910735 CATATTTTACTAATTTT
1 -ATATTTTACTAATTTT
2910752 AT
1 AT
2910754 TGTCTATGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 12 0.40
18 1 0.03
19 7 0.23
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (16 bp):
ATATTTTACTAATTTT
Found at i:2914613 original size:21 final size:21
Alignment explanation
Indices: 2914587--2914642 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2914577 TTTTTTATTT
*
2914587 ATTTTTATTTTAAAATTTTTA
1 ATTTTTATTTTAAAATTTTAA
*
2914608 ATTTTTATATTTCAAATTTTAA
1 ATTTTTAT-TTTAAAATTTTAA
* *
2914630 AATTTAATTTTAA
1 ATTTTTATTTTAA
2914643 TTATTAGTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATTTTAAAATTTTAA
Found at i:2935403 original size:98 final size:98
Alignment explanation
Indices: 2935225--2935421 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
2935215 GTACAATAAA
* * *
2935225 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACGATT
1 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* **
2935290 CCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
2935323 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
2935388 CCTTTAAAATTCCAAACTCAGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
2935421 A
1 A
2935422 TTATTTTAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:2936998 original size:16 final size:16
Alignment explanation
Indices: 2936964--2937003 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2936954 GAAAGAAAAG
2936964 AAAAAAACAATAGATA
1 AAAAAAACAATAGATA
*
2936980 AAATAAAACAA-ATATA
1 AAA-AAAACAATAGATA
2936996 AAAAAAAC
1 AAAAAAAC
2937004 TGTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 10 0.45
17 7 0.32
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAACAATAGATA
Found at i:2953795 original size:31 final size:31
Alignment explanation
Indices: 2953721--2953795 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
2953711 TATAAAATAG
* *
2953721 TCACTTAACTATTTGAAAGTATTCATTTAAT
1 TCACTGAACTATTCGAAAGTATTCATTTAAT
* * *
2953752 TCATTGAACTATTCGAAAGTTTTTATTTAAGT
1 TCACTGAACTATTCGAAAGTATTCATTTAA-T
*
2953784 T-ACTGAGCTATT
1 TCACTGAACTATT
2953796 AAGTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (31 bp):
TCACTGAACTATTCGAAAGTATTCATTTAAT
Found at i:2956364 original size:14 final size:14
Alignment explanation
Indices: 2956345--2956374 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2956335 ATTTTGTCGA
2956345 AACATATTAATACC
1 AACATATTAATACC
2956359 AACATATTAATACC
1 AACATATTAATACC
2956373 AA
1 AA
2956375 TACCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATATTAATACC
Found at i:2961369 original size:15 final size:15
Alignment explanation
Indices: 2961349--2961379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2961339 CACTTTCAAC
2961349 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
2961364 ATTTTATTGTATTTT
1 ATTTTATTCTATTTT
2961379 A
1 A
2961380 AAATTTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:2964250 original size:19 final size:20
Alignment explanation
Indices: 2964218--2964255 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2964208 TTCTACTAAA
2964218 TTTTATATTATTTTAATATT
1 TTTTATATTATTTTAATATT
*
2964238 TTTTTTATT-TTTTAATAT
1 TTTTATATTATTTTAATAT
2964256 CTAAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTATTTTAATATT
Found at i:2967398 original size:6 final size:6
Alignment explanation
Indices: 2967341--2967383 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
2967331 TTACTGTTAA
*
2967341 TATAGTT TATATT TATATT TACATT TATATT TATATT TATATT
1 TATA-TT TATATT TATATT TATATT TATATT TATATT TATATT
2967384 AGTCTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:2975372 original size:28 final size:28
Alignment explanation
Indices: 2975340--2975432 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
2975330 GTTCAAACAC
2975340 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
* *
2975368 ACTCAAGGTGCACTAAATAATTA--GTAAACTAA
1 ACTC-A--T--AATAAA-AATCAGGGTAAACTAA
2975400 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
2975428 ACTCA
1 ACTCA
2975433 AGGTCACTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
26 4 0.08
27 5 0.09
28 18 0.34
29 2 0.04
31 2 0.04
32 13 0.25
33 5 0.09
34 4 0.08
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.23
Consensus pattern (28 bp):
ACTCATAATAAAAATCAGGGTAAACTAA
Done.