Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008840.1 Hibiscus syriacus cultivar Beakdansim tig00112044_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: 1122218
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:10388 original size:13 final size:12
Alignment explanation
Indices: 10370--10413 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
10360 CTTTTCTTCG
10370 ATATTAAAAATAA
1 ATATT-AAAATAA
10383 ATATTAAAATAA
1 ATATTAAAATAA
*
10395 TTTATTTAAAATAA
1 -ATA-TTAAAATAA
10409 ATATT
1 ATATT
10414 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:10414 original size:13 final size:13
Alignment explanation
Indices: 10370--10415 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
10360 CTTTTCTTCG
*
10370 ATATTAAAAATAA
1 ATATTTAAAATAA
10383 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
10395 TTTATTTAAAATAA
1 -ATATTTAAAATAA
10409 ATATTTA
1 ATATTTA
10416 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:11223 original size:15 final size:15
Alignment explanation
Indices: 11203--11232 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11193 TTTAGTAGTT
11203 TTTTTTTTCTTTCTC
1 TTTTTTTTCTTTCTC
11218 TTTTTTTTCTTTCTC
1 TTTTTTTTCTTTCTC
11233 CGGTTCTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTTTCTC
Found at i:11258 original size:17 final size:17
Alignment explanation
Indices: 11236--11271 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11226 CTTTCTCCGG
11236 TTCTGTCTCTC-TTTTTT
1 TTCTGTCTC-CGTTTTTT
11253 TTCTGTCTCCGTTTTTT
1 TTCTGTCTCCGTTTTTT
11270 TT
1 TT
11272 TCAGGTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.69
Consensus pattern (17 bp):
TTCTGTCTCCGTTTTTT
Found at i:11700 original size:14 final size:15
Alignment explanation
Indices: 11681--11717 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
11671 GGTCTGTAAT
11681 TATTTATTT-ATATA
1 TATTTATTTAATATA
11695 TATTTATTTAATATA
1 TATTTATTTAATATA
11710 TATTTATT
1 TATTTATT
11718 ATTAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:11722 original size:17 final size:17
Alignment explanation
Indices: 11684--11724 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
11674 CTGTAATTAT
*
11684 TTATTTATATATATTTA
1 TTATTAATATATATTTA
11701 -T-TTAATATATATTTA
1 TTATTAATATATATTTA
11716 TTATTAATA
1 TTATTAATA
11725 ATAATAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 13 0.62
16 2 0.10
17 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAATATATATTTA
Found at i:11726 original size:3 final size:3
Alignment explanation
Indices: 11720--11770 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
11710 TATTTATTAT
*
11720 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11768 TAA
1 TAA
11771 AAAATATGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12576 original size:40 final size:40
Alignment explanation
Indices: 12458--12576 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
12448 CGCATACAAA
* * * * *
12458 GGTTAATATGACTATCGACCCTCGTTCATTACAGGTTGAT
1 GGTTAATATGACTATCGATCCTCATTCATTACAAGTTCAG
* *
12498 GGTTAATATGGCTATCGATCCTCATTCATTACATGTTCAG
1 GGTTAATATGACTATCGATCCTCATTCATTACAAGTTCAG
* * *
12538 GGTTAATATCACTATCGATCTTCATTCATTATAAGTTCA
1 GGTTAATATGACTATCGATCCTCATTCATTACAAGTTCA
12577 CGAGTCGAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (40 bp):
GGTTAATATGACTATCGATCCTCATTCATTACAAGTTCAG
Found at i:13162 original size:18 final size:18
Alignment explanation
Indices: 13139--13174 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
13129 AAAAATTATT
13139 TTATTATTT-TACTTTTAA
1 TTATTATTTGTA-TTTTAA
13157 TTATTATTTGTATTTTAA
1 TTATTATTTGTATTTTAA
13175 AAACTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTATTTGTATTTTAA
Found at i:21016 original size:14 final size:14
Alignment explanation
Indices: 20994--21030 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20984 CGCATGCATG
20994 CTCTAGTTCACTTT
1 CTCTAGTTCACTTT
* *
21008 CTCTGGTTCATTTT
1 CTCTAGTTCACTTT
21022 CTCTAGTTC
1 CTCTAGTTC
21031 GAGCTATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.11, T:0.51
Consensus pattern (14 bp):
CTCTAGTTCACTTT
Found at i:29184 original size:3 final size:3
Alignment explanation
Indices: 29176--29245 Score: 131
Period size: 3 Copynumber: 23.0 Consensus size: 3
29166 TATATTTATT
29176 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29222 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
29246 ATTAGTGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29491 original size:76 final size:76
Alignment explanation
Indices: 29392--30153 Score: 1339
Period size: 76 Copynumber: 10.0 Consensus size: 76
29382 GTCTTATGAC
* * *
29392 TGACCCTGAGGGTTTGAACACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
*
29457 GGGCTTACAGA
66 GGACTTACAGA
* ** *
29468 TGACCC-GAAGGTTTTGAAAACATCAAAAAGTTCCCTAAGGCTTTTTGGAAACATCATGCACTGA
1 TGACCCTG-AGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
29532 AGGACTTACAGA
65 AGGACTTACAGA
29544 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
29609 GGACTTACAGA
66 GGACTTACAGA
29620 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
29685 GGACTTACAGA
66 GGACTTACAGA
*
29696 TGACCCTGAGGCTTTGAAAATATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
*
29761 GGACTTACAAA
66 GGACTTACAGA
*
29772 TGACCC-GAAGGTTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 TGACCCTG-AGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
29836 AGGACTTACAGA
65 AGGACTTACAGA
* *
29848 TGACCCCGAGGCTTTGAAAATATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
29913 GGACTTACAGA
66 GGACTTACAGA
*
29924 TGACCCAGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
29989 GGACTTACAGA
66 GGACTTACAGA
*
30000 TGACCCTGAGGCTTTGAAAATATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
30065 GGACTTACAGA
66 GGACTTACAGA
* *
30076 TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
1 TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
30141 GGACTTACAGA
66 GGACTTACAGA
30152 TG
1 TG
30154 TGAGAAATAG
Statistics
Matches: 659, Mismatches: 23, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
75 2 0.00
76 655 0.99
77 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
TGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
GGACTTACAGA
Found at i:33697 original size:93 final size:93
Alignment explanation
Indices: 33535--33727 Score: 332
Period size: 93 Copynumber: 2.1 Consensus size: 93
33525 CTCCTTATTT
* * *
33535 ATACTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGAT
1 ATACTATGAGCAAATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGAT
*
33600 CAGATAACTCAAAGAACACTTCCAGAAG
66 CAGATAACTCAAAGAACACTTCCAAAAG
* *
33628 ATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGAT
1 ATACTATGAGCAAATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGAT
33693 CAGATAACTCAAAGAACACTTCCAAAAG
66 CAGATAACTCAAAGAACACTTCCAAAAG
33721 ATACTAT
1 ATACTAT
33728 TGGGTCTTCT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (93 bp):
ATACTATGAGCAAATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGAT
CAGATAACTCAAAGAACACTTCCAAAAG
Found at i:38309 original size:21 final size:21
Alignment explanation
Indices: 38285--38324 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38275 AAAAGTAAAA
38285 ATACAAAATGAAAATGCATAG
1 ATACAAAATGAAAATGCATAG
*
38306 ATACAAAATGTAAATGCAT
1 ATACAAAATGAAAATGCAT
38325 GTATGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
ATACAAAATGAAAATGCATAG
Found at i:40428 original size:24 final size:24
Alignment explanation
Indices: 40378--40427 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40368 CTTGCAATAT
40378 AAATAATATATATAAATACTATAA
1 AAATAATATATATAAATACTATAA
* *
40402 AAATAATATGTATATATA-TATAA
1 AAATAATATATATAAATACTATAA
40425 AAA
1 AAA
40428 AGAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAATATATATAAATACTATAA
Found at i:40885 original size:50 final size:49
Alignment explanation
Indices: 40813--40912 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 49
40803 ATTGGTACTT
*
40813 TTTAATTATAAATTGTCTTTATTATTAAAAATTAAAAAA-ATTCAAAATATA
1 TTTAATTATAAATTGTATTTA-T-TTAAAAATTAAAAAATATTCAAAA-ATA
* *
40864 TTTAATT-TAAATT-TATATTATTTCAAAATTAAAAAATATTTAAAAATA
1 TTTAATTATAAATTGTAT-TTATTTAAAAATTAAAAAATATTCAAAAATA
40912 T
1 T
40913 CGGAAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
48 18 0.41
49 10 0.23
50 9 0.20
51 7 0.16
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (49 bp):
TTTAATTATAAATTGTATTTATTTAAAAATTAAAAAATATTCAAAAATA
Found at i:41282 original size:11 final size:11
Alignment explanation
Indices: 41266--41329 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
41256 TATATATGAC
41266 TAAAATAATAA
1 TAAAATAATAA
41277 TAAAATAATAA
1 TAAAATAATAA
**
41288 TTAAAGCAATAA
1 -TAAAATAATAA
41300 TTAAAAT-AT-A
1 -TAAAATAATAA
*
41310 -AAAGTAATAA
1 TAAAATAATAA
41320 TAAAATAATA
1 TAAAATAATA
41330 TTGTAATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 4 0.09
9 2 0.05
10 2 0.05
11 21 0.49
12 14 0.33
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:42584 original size:3 final size:3
Alignment explanation
Indices: 42576--42633 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
42566 TATATTTATT
42576 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42622 TAA TAA TAA TAA
1 TAA TAA TAA TAA
42634 AATTAGTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43629 original size:16 final size:17
Alignment explanation
Indices: 43600--43631 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43590 CACTTTTTAA
43600 TTTTAAACTATAATAAC
1 TTTTAAACTATAATAAC
43617 TTTTAAA-TATAATAA
1 TTTTAAACTATAATAA
43632 ATAACGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAACTATAATAAC
Found at i:44361 original size:26 final size:26
Alignment explanation
Indices: 44332--44385 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
44322 TAATATATGC
* * *
44332 TTTTTTTATTTTAGTTACTTAAATTA
1 TTTTTTGATCTTAGGTACTTAAATTA
*
44358 TTTTTTGGTCTTAGGTACTTAAATTA
1 TTTTTTGATCTTAGGTACTTAAATTA
44384 TT
1 TT
44386 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (26 bp):
TTTTTTGATCTTAGGTACTTAAATTA
Found at i:46035 original size:22 final size:21
Alignment explanation
Indices: 46010--46050 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
46000 TATAAAAAAT
46010 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
46032 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
46051 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:46152 original size:17 final size:17
Alignment explanation
Indices: 46132--46169 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
46122 AACATGATCA
*
46132 GTTCGCTAACCGGTCCG
1 GTTCGCTAACCGGTCCC
46149 GTTCGCTAACCGGTCCC
1 GTTCGCTAACCGGTCCC
46166 GTTC
1 GTTC
46170 TGAAATCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.37, G:0.26, T:0.26
Consensus pattern (17 bp):
GTTCGCTAACCGGTCCC
Found at i:46526 original size:26 final size:25
Alignment explanation
Indices: 46495--46545 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
46485 CTCATAAAAT
*
46495 GATTTTCAGTATTCAGAA-ATAAAACA
1 GATTTTCAG-ACTC-GAATATAAAACA
46521 GATTTTCAGACTCGAATATAAAACA
1 GATTTTCAGACTCGAATATAAAACA
46546 AAATACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 11 0.48
26 9 0.39
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (25 bp):
GATTTTCAGACTCGAATATAAAACA
Found at i:47086 original size:31 final size:31
Alignment explanation
Indices: 47051--47139 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
47041 GGGCTTGAAA
* * *
47051 GCCTACCCAAGAAAGATTTCAGGGCCACGGG
1 GCCTACCCGAGAAAGATCTCAGGGCCACAGG
* * *
47082 GCCTACCTGAGAACACATCTCAGGGCCATAGG
1 GCCTACCCGAGAA-AGATCTCAGGGCCACAGG
*
47114 GCCTACCCGAGAATGATCTCAGGGCC
1 GCCTACCCGAGAAAGATCTCAGGGCC
47140 GTAGAGCCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
31 22 0.46
32 26 0.54
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
GCCTACCCGAGAAAGATCTCAGGGCCACAGG
Found at i:59317 original size:128 final size:121
Alignment explanation
Indices: 59086--59342 Score: 451
Period size: 128 Copynumber: 2.1 Consensus size: 121
59076 AATACCAAGC
59086 ATCAAAGACTATAATTTCATAGCATCAGCAATGCTACATATAACACACCCAAAAATAAATAAAAG
1 ATCAAAGACTATAATTTCATAGCATCAGCAATGCTACATATAACACACCCAAAAATAAATAAAAG
59151 ATGTAATGAAGTCTTAATCCTCAAATCCAATCAAGACTGAGGTGAACTGCTAGTTT
66 ATGTAATGAAGTCTTAATCCTCAAATCCAATCAAGACTGAGGTGAACTGCTAGTTT
59207 ATCAAAGACTATAATTTCATAGCATCAGCAATGCTACATATAACACACCCAAATCAACAAAATAA
1 ATCAAAGACTATAATTTCATAGCATCAGCAATGCTACATATAACACA-CC----C-A-AAAATAA
59272 ATAAAAGATGTAATGAAGTCTTAATCCTCAAATCCAATCAAGACTGAGGTGAACTGCTAGTTT
59 ATAAAAGATGTAATGAAGTCTTAATCCTCAAATCCAATCAAGACTGAGGTGAACTGCTAGTTT
59335 ATCAAAGA
1 ATCAAAGA
59343 AGGAATGAAC
Statistics
Matches: 129, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
121 47 0.36
122 2 0.02
126 1 0.01
127 1 0.01
128 78 0.60
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (121 bp):
ATCAAAGACTATAATTTCATAGCATCAGCAATGCTACATATAACACACCCAAAAATAAATAAAAG
ATGTAATGAAGTCTTAATCCTCAAATCCAATCAAGACTGAGGTGAACTGCTAGTTT
Found at i:61863 original size:78 final size:80
Alignment explanation
Indices: 61726--61872 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 80
61716 AAAAAATTGG
* * * * *
61726 ATTGAGAAAAGTCAAAAATTAGAGAAAAAAATATTCTAGCTAAAAGTTCTATCAAATCTGAAGAT
1 ATTGAGAAAAATCAAAAATCAGAGAAAAAAAAAATCTAGCTAAAAGTTCAATCAAATCTGAAGAT
61791 TACTATATGAGATAT
66 TACTATATGAGATAT
* *
61806 ATTGAGAAAAATCAAGAA-CAG-GAAAAAAAAAATCTAGCTAAAAGTTCAATCACATCTGAAGAT
1 ATTGAGAAAAATCAAAAATCAGAGAAAAAAAAAATCTAGCTAAAAGTTCAATCAAATCTGAAGAT
61869 TACT
66 TACT
61873 TTACTACATG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 42 0.70
79 2 0.03
80 16 0.27
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (80 bp):
ATTGAGAAAAATCAAAAATCAGAGAAAAAAAAAATCTAGCTAAAAGTTCAATCAAATCTGAAGAT
TACTATATGAGATAT
Found at i:73779 original size:29 final size:29
Alignment explanation
Indices: 73732--73833 Score: 127
Period size: 29 Copynumber: 3.5 Consensus size: 29
73722 GAATTTTTTG
*
73732 AATACTTTAGGTACATATTTTGACCGAAA
1 AATACTTTAGGTACATATTTTGACCAAAA
73761 AATACTTTAGGTA-ACTATTTTGACCAAAA
1 AATACTTTAGGTACA-TATTTTGACCAAAA
* * *
73790 ATATAAATTTAGATACTTATTTTGA-CAAAA
1 A-AT-ACTTTAGGTACATATTTTGACCAAAA
73820 AATACTTTAGGTAC
1 AATACTTTAGGTAC
73834 TTAATTGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
28 10 0.16
29 29 0.46
30 8 0.13
31 16 0.25
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (29 bp):
AATACTTTAGGTACATATTTTGACCAAAA
Found at i:80806 original size:31 final size:31
Alignment explanation
Indices: 80771--80830 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
80761 TTTCATTTAT
*
80771 GTCCCCCAACATTTAGTCCGTTTGCAATACA
1 GTCCCCCAACATATAGTCCGTTTGCAATACA
80802 GTCCCCCAACATATAGTCCGTTTGCAATA
1 GTCCCCCAACATATAGTCCGTTTGCAATA
80831 TGGTTACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (31 bp):
GTCCCCCAACATATAGTCCGTTTGCAATACA
Found at i:82775 original size:31 final size:31
Alignment explanation
Indices: 82740--82806 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
82730 GCCGGTTAAG
*
82740 TGGGGGACCATATTGCAAACAAACTAAATGT
1 TGGGGGACCATATTACAAACAAACTAAATGT
** ***
82771 TGGGGGACTGTATTACAAATGTACTAAATGT
1 TGGGGGACCATATTACAAACAAACTAAATGT
82802 TGGGG
1 TGGGG
82807 ACTGCACTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (31 bp):
TGGGGGACCATATTACAAACAAACTAAATGT
Found at i:84334 original size:2 final size:2
Alignment explanation
Indices: 84327--84362 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
84317 CTCTAATGTC
84327 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
84363 CACACCTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90710 original size:4 final size:4
Alignment explanation
Indices: 90696--90745 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
90686 TTTCCTTTTC
**
90696 ATTT A-TT ATTT ATTTT ATTT ATTT A-AC ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
90743 ATT
1 ATT
90746 GTCTAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:93813 original size:13 final size:13
Alignment explanation
Indices: 93803--93827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93793 GGAAAAAACA
93803 AAAGAACAAAAAG
1 AAAGAACAAAAAG
93816 AAAGAACAAAAA
1 AAAGAACAAAAA
93828 TCGAAAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAACAAAAAG
Found at i:94465 original size:22 final size:22
Alignment explanation
Indices: 94437--94492 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
94427 AACTACCCCA
*
94437 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAACATCAAATG
94459 TCAAACCTTTGAACATCAAATG
1 TCAAACCTTTGAACATCAAATG
*
94481 CCAAACCTTTGA
1 TCAAACCTTTGA
94493 CCAATCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCTTTGAACATCAAATG
Found at i:95259 original size:73 final size:69
Alignment explanation
Indices: 95182--95344 Score: 186
Period size: 70 Copynumber: 2.3 Consensus size: 69
95172 CAATATAAAT
* * *
95182 TTTGTCTCGCTTGAGACAGTTTCATTTAATGCAGATGATTATCTCACTTGAGATTA-TTTTTCTT
1 TTTGTCTCGCTTGAGACAGTTTCA-CT-A-GAAGAT-ATTATCTCACTTGAGA-TAGTTTCTCTT
95246 AAAACAAGA-
61 AAAACAA-AC
* * *
95255 TTTGTCTCGCTTGAGACCGTTTTCACTAGAAGATTTTATCTCACTTGAGATAGTTTCTCTTGAAA
1 TTTGTCTCGCTTGAGACAG-TTTCACTAGAAGATATTATCTCACTTGAGATAGTTTCTCTTAAAA
95320 CAAAC
65 CAAAC
*
95325 TTTGTCTCCCTTGAGACAGT
1 TTTGTCTCGCTTGAGACAGT
95345 CTCTCTTGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
69 4 0.05
70 45 0.57
71 5 0.06
72 1 0.01
73 19 0.24
74 5 0.06
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (69 bp):
TTTGTCTCGCTTGAGACAGTTTCACTAGAAGATATTATCTCACTTGAGATAGTTTCTCTTAAAAC
AAAC
Found at i:95486 original size:36 final size:36
Alignment explanation
Indices: 95411--95489 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
95401 GTTTTCCTTA
* ** *
95411 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
* *
95447 AAACAAATTTTGTCTCCCATGAGGCAGTTTCGCTCG
1 AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
95483 AAACAAA
1 AAACAAA
95490 ACAATGTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (36 bp):
AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
Found at i:95911 original size:65 final size:65
Alignment explanation
Indices: 95830--96052 Score: 294
Period size: 64 Copynumber: 3.5 Consensus size: 65
95820 TTGGAACTCA
* * *
95830 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTAAACAAAAACTTCCCAGTTTC
* * *
95895 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAAGTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTAAACAAAAACTTCCCAGTTTC
* *
95959 AGACAGA-ACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATT
1 AGACA-ACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTAAACAAA-AACTTCCCAGTT
96023 TC
64 TC
* * *
96025 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
96053 ATATTGGACT
Statistics
Matches: 142, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
63 21 0.15
64 58 0.41
65 50 0.35
66 13 0.09
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTAAACAAAAACTTCCCAGTTTC
Found at i:96088 original size:170 final size:172
Alignment explanation
Indices: 95895--96249 Score: 599
Period size: 171 Copynumber: 2.1 Consensus size: 172
95885 TCCCAGTATC
* * *
95895 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAGTT-CCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGATTGTCAACAAAAATTCCCCAGTTTA
95959 AGACAGAACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATTT
66 AGACAGAACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATTT
96024 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-A
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
96065 AGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGATTGTCAACAAAAATTCCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGATTGTCAACAAAAATTCCCCAGTTTA
* * *
96130 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
66 AGACAGAACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATTT
* * *
96195 CAGAGTCAATTTCAACTTCATAGCGAAGGATATTGGCCTCGA
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
*
96237 A-ACAACGCAAGTT
1 AGACAACACAAGTT
96250 GCATTGGATT
Statistics
Matches: 173, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
170 52 0.30
171 119 0.69
172 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (172 bp):
AGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGATTGTCAACAAAAATTCCCCAGTTTA
AGACAGAACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
Found at i:96116 original size:235 final size:231
Alignment explanation
Indices: 95738--96194 Score: 713
Period size: 235 Copynumber: 2.0 Consensus size: 231
95728 CGAGACAGCT
* *
95738 CAAGTTCAACTTCACAACGAAAGGGCCGCTGACTGTCAACAAACAATTTCCCAATCCAATTTCAA
1 CAAGTTCAACTTCACAACGAAAGGGCCGCTGACTGTAAACAAACAACTTCCCAATCCAATTTCAA
*
95803 CTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
66 CTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCT
* * * *
95868 GGTTGTTAACAAAAATTTCCCAGTATCAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
131 GATTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
* *
95933 GGTTGTCAAC-AA-AAGTTCCCAGTTTAAGACAGAA
196 GGCTGTCAACAAACAACTTCCCAGTTTAAGACAGAA
* *
95967 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTAAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAAGGGCCGCTGACTGTAAACAAACAACTTCCCAA--T-----CCA
96032 ATTTCAACTTCACAGCGAAGGATATTGG-ACTCAAGACAACACAAGTTCAACTTCACAAAGAAGG
59 ATTTCAACTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAAAGAAGG
* *
96096 GGCCGCTGATTGTCAACAAAAATTCCCCAGTTTAAGACAGCACAAGTTCAACTTCACAACGAAGG
124 GGCCGCTGATTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGG
96161 GGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
189 GGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
96195 CAGAGTCAAT
Statistics
Matches: 206, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
229 50 0.24
231 1 0.00
235 110 0.53
236 33 0.16
237 12 0.06
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (231 bp):
CAAGTTCAACTTCACAACGAAAGGGCCGCTGACTGTAAACAAACAACTTCCCAATCCAATTTCAA
CTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCT
GATTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
GGCTGTCAACAAACAACTTCCCAGTTTAAGACAGAA
Found at i:96144 original size:65 final size:66
Alignment explanation
Indices: 96064--96194 Score: 203
Period size: 65 Copynumber: 2.0 Consensus size: 66
96054 TATTGGACTC
*
96064 AAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGATTGTCAACAAA-AA-TTCCCCAGT
1 AAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGACTGTCAACAAACAACTT-CCCAGT
96127 TT
65 TT
* * *
96129 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
1 AAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAGTT
96194 T
66 T
96195 CAGAGTCAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 48 0.80
66 10 0.17
67 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (66 bp):
AAGACAACACAAGTTCAACTTCACAAAGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAGTT
T
Found at i:97948 original size:16 final size:17
Alignment explanation
Indices: 97909--97951 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
97899 ATGTTCTAAG
* *
97909 TTTTTTACTTTATTTTA
1 TTTTTTTCTTTATATTA
*
97926 TTATTTTCTTTA-ATTA
1 TTTTTTTCTTTATATTA
97942 TTTTTTTCTT
1 TTTTTTTCTT
97952 CTTTCTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTATATTA
Found at i:98052 original size:4 final size:4
Alignment explanation
Indices: 98038--98087 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
98028 TTTCCTTTTC
**
98038 ATTT A-TT ATTT ATTTT ATTT ATTT A-AC ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
98085 ATT
1 ATT
98088 GTCTAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:109255 original size:91 final size:91
Alignment explanation
Indices: 109087--109277 Score: 319
Period size: 91 Copynumber: 2.1 Consensus size: 91
109077 TTTTTTCGAT
* * *
109087 CTTAGATGGAAAAAATTGAATAGTTTAGGTACCTATTTTGAGTAAAAAGATGATTTTAGGTATTT
1 CTTAAATGAAAAAAATTGAATAGTTTAGGTACCTATTTTGACTAAAAAGATGATTTTAGGTATTT
109152 ATTTTGACCAAATAATACTTTAAGTA
66 ATTTTGACCAAATAATACTTTAAGTA
* *
109178 CTTAAATGAAAAAAATTGAATAGTTTAGGTTCTTATTTTGACTAAAAAGATGATTTTAGGTATTT
1 CTTAAATGAAAAAAATTGAATAGTTTAGGTACCTATTTTGACTAAAAAGATGATTTTAGGTATTT
*
109243 ATTTTGATCAAATAATACTTTAAGTA
66 ATTTTGACCAAATAATACTTTAAGTA
*
109269 TTTAAATGA
1 CTTAAATGA
109278 TAAATAAAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (91 bp):
CTTAAATGAAAAAAATTGAATAGTTTAGGTACCTATTTTGACTAAAAAGATGATTTTAGGTATTT
ATTTTGACCAAATAATACTTTAAGTA
Found at i:109304 original size:91 final size:90
Alignment explanation
Indices: 109095--109306 Score: 282
Period size: 91 Copynumber: 2.3 Consensus size: 90
109085 ATCTTAGATG
* * * * *
109095 GAAAAAATTGAATAGTTTAGGTACCTATTTTGAGTAAAAAGATGATTTTAGGTATTTATTTTGAC
1 GAAAAAAATGAATACTTTAGATACTTATTTTGACTAAAAAGATGATTTTAGGTATTTATTTTGAC
109160 CAAATAATACTTTAAGTACTTAAAT
66 CAAATAATACTTTAAGTACTTAAAT
* * *
109185 GAAAAAAATTGAATAGTTTAGGTTCTTATTTTGACTAAAAAGATGATTTTAGGTATTTATTTTGA
1 GAAAAAAA-TGAATACTTTAGATACTTATTTTGACTAAAAAGATGATTTTAGGTATTTATTTTGA
* *
109250 TCAAATAATACTTTAAGTATTTAAAT
65 CCAAATAATACTTTAAGTACTTAAAT
* *
109276 GATAAATAAA-GTATACTTTATATACTTATTT
1 GA-AAA-AAATGAATACTTTAGATACTTATTT
109307 ATGATATAAG
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
90 7 0.06
91 95 0.88
92 3 0.03
93 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (90 bp):
GAAAAAAATGAATACTTTAGATACTTATTTTGACTAAAAAGATGATTTTAGGTATTTATTTTGAC
CAAATAATACTTTAAGTACTTAAAT
Found at i:118433 original size:19 final size:20
Alignment explanation
Indices: 118404--118444 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
118394 CGAATAAAGA
118404 TAAACAAACATAAACAAACG
1 TAAACAAACATAAACAAACG
*
118424 TAAA-AAACATAAACGAACG
1 TAAACAAACATAAACAAACG
118443 TA
1 TA
118445 CATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.12
Consensus pattern (20 bp):
TAAACAAACATAAACAAACG
Found at i:118436 original size:9 final size:10
Alignment explanation
Indices: 118403--118437 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
118393 ACGAATAAAG
118403 ATAAACAAAC
1 ATAAACAAAC
118413 ATAAACAAAC
1 ATAAACAAAC
*
118423 GTAAA-AAAC
1 ATAAACAAAC
118432 ATAAAC
1 ATAAAC
118438 GAACGTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.69, C:0.17, G:0.03, T:0.11
Consensus pattern (10 bp):
ATAAACAAAC
Found at i:119461 original size:42 final size:42
Alignment explanation
Indices: 119402--119872 Score: 621
Period size: 42 Copynumber: 11.3 Consensus size: 42
119392 GGAAACTGAT
* ** *
119402 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTAGAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * * *
119444 TTGCGATAGTCCAAGTT--CTTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CG
* * *
119484 TTGCGATTTATTCTAAATT--CGTTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
119526 TTGAGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
119568 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
119610 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
119652 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
** *
119694 TTGCGATAGTCGAAGTTCGTTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * * *
119736 TTGCGATAGTCCAAGTTTGCGTTGCGATGTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * * *
119778 TTGCGATAATCCAAGTTCGCGTTGTGATTTATTTCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
119820 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
119862 TTGCGATAGTC
1 TTGCGATAGTC
119873 CAAAATCGCA
Statistics
Matches: 379, Mismatches: 42, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
38 8 0.02
40 23 0.06
42 339 0.89
44 9 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:119551 original size:63 final size:62
Alignment explanation
Indices: 119402--119847 Score: 376
Period size: 63 Copynumber: 7.1 Consensus size: 62
119392 GGAAACTGAT
** *
119402 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTAGAAATTCGTTGCGA-TAGTCCAAGTTCT
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCG
* * *
119463 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGA-TTAGTCCAAGTTCG
*
119526 TTGAGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTT--CG
* * * * * *
119589 TTGCGATTTATTCCAAGTTCG--TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 TTGCGA--TAGTCGAAGTTCGCATTGCGATTTATTCCAAATT--CGTTGCGA-TTAGTCCAAGTT
119650 CG
61 CG
* * * *
119652 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA-TAGTCGAAGTTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCG
* * * * * * *
119713 TTTTGCGATTTATTCCAAATTCG--TTGCGA--TAGTCCAAGTTTGCGTTGCGATGTATTCCAAA
1 --TTGCGA--TAGTCGAAGTTCGCATTGCGATTTATTCCAA-ATT-CGTTGCGAT-TAGTCCAAG
119774 TTCG
59 TTCG
* * * * * * *
119778 TTGCGATAATCCAAGTTCGCGTTGTGATTTATTTCAAGTTCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTT--CG
119841 TTGCGAT
1 TTGCGAT
119848 TTATTCCAAG
Statistics
Matches: 316, Mismatches: 41, Indels: 54
0.77 0.10 0.13
Matches are distributed among these distances:
61 110 0.35
62 2 0.01
63 147 0.47
64 2 0.01
65 55 0.17
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (62 bp):
TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCG
Found at i:120006 original size:21 final size:21
Alignment explanation
Indices: 119980--120046 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
119970 GACCACGTCC
119980 ACGCGAACTTGGACAATCGCA
1 ACGCGAACTTGGACAATCGCA
*
120001 ACGCGAACTTGGAATAAATCGCA
1 ACGCGAACTTGG-A-CAATCGCA
* * *
120024 ACACGAACTTAGACTATCGCA
1 ACGCGAACTTGGACAATCGCA
120045 AC
1 AC
120047 AAATTTGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 20 0.51
22 2 0.05
23 17 0.44
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
ACGCGAACTTGGACAATCGCA
Found at i:120024 original size:23 final size:21
Alignment explanation
Indices: 119980--120033 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 21
119970 GACCACGTCC
*
119980 ACGCGAACTTGGACAATCGCA
1 ACGCGAACTTGGAAAATCGCA
120001 ACGCGAACTTGGAATAAATCGCA
1 ACGCGAACTTGG-A-AAATCGCA
*
120024 ACACGAACTT
1 ACGCGAACTT
120034 AGACTATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
22 1 0.03
23 16 0.55
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (21 bp):
ACGCGAACTTGGAAAATCGCA
Found at i:121456 original size:24 final size:24
Alignment explanation
Indices: 121410--121458 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
121400 TTGATAAGAA
*
121410 AGTTTATAAAACATAAATTATTTT
1 AGTTTATAAAACATAAATAATTTT
*
121434 AGTTTATAACA-ATAATATAATTTT
1 AGTTTATAAAACATAA-ATAATTTT
121458 A
1 A
121459 ATGCATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
AGTTTATAAAACATAAATAATTTT
Found at i:121729 original size:21 final size:21
Alignment explanation
Indices: 121703--121746 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
121693 AAAATCTACA
*
121703 ATATTGATGTAATAGTTCATG
1 ATATTGATGTAATAGTACATG
* *
121724 ATATTGTTGTGATAGTACATG
1 ATATTGATGTAATAGTACATG
121745 AT
1 AT
121747 GGACGATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
ATATTGATGTAATAGTACATG
Found at i:122613 original size:2 final size:2
Alignment explanation
Indices: 122606--122631 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
122596 TAATACAATA
122606 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
122632 CATCTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122878 original size:29 final size:29
Alignment explanation
Indices: 122846--122915 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
122836 TGTTTAAATG
122846 TAATAAAATTCATTATATAAT-ATTTTTTA
1 TAATAAAATTCATTATATAATCA-TTTTTA
* * * *
122875 TAATATACTTTATTATGTAATCATTTTTA
1 TAATAAAATTCATTATATAATCATTTTTA
122904 TAAATATAAATT
1 T-AATA-AAATT
122916 AAACATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 24 0.75
30 5 0.16
31 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (29 bp):
TAATAAAATTCATTATATAATCATTTTTA
Found at i:126714 original size:3 final size:3
Alignment explanation
Indices: 126706--126757 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
126696 ATAACATTTG
**
126706 TAA TAA TAA TAA TAA TAA TAA TAA TTG TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
126753 TAA TA
1 TAA TA
126758 TATTCTCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:127047 original size:20 final size:20
Alignment explanation
Indices: 127019--127072 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
127009 AAAACATCCT
* *
127019 ACCCTGAGGTTTTATAAATG
1 ACCCGGAGGTTTTACAAATG
* *
127039 ACCCGGAGGATTTACAAATT
1 ACCCGGAGGTTTTACAAATG
127059 ACCCGGAGGTTTTA
1 ACCCGGAGGTTTTA
127073 ATTTTCTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:127166 original size:20 final size:20
Alignment explanation
Indices: 127138--127191 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
127128 AAAACATCTT
* *
127138 ACCCTGAGGTTTTATAAATG
1 ACCCGGAGGTTTTACAAATG
*
127158 ACCCGGAGGTTTTACAAATT
1 ACCCGGAGGTTTTACAAATG
*
127178 ACCTGGAGGTTTTA
1 ACCCGGAGGTTTTA
127192 ATTTTCTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:127392 original size:119 final size:119
Alignment explanation
Indices: 126890--127395 Score: 762
Period size: 119 Copynumber: 4.3 Consensus size: 119
126880 AATTAAAGTA
* * * * * * *
126890 AAAACATCATACCCGGAGGTTTTACAGATGACCCGGA-GATTTTATAAATCAACAGGAGGATTTA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGA-TTTACAAATTACCCGGAGGTTTTA
*
126954 ATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTTTCATTTTCATACG
65 ATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACG
* *
127009 AAAACATCCTACCCTGAGGTTTTATAAATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
*
127074 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTATACG
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACG
* * * * *
127128 AAAACATCTTACCCTGAGGTTTTATAAATGACCCGGAGGTTTTACAAATTACCTGGAGGTTTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
* **
127193 TTTTCTTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACG
* * *
127247 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGTAGGATTTACAAATTACCCCGAGGTTTAAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
* * *
127312 TTTTCTAGAACATTAAATGAGAAACTTTGGAAATCGCTTTCTTATTTTCATGCG
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACG
*
127366 AAAACATCCTACCCTTAGGTTTTACAGATG
1 AAAACATCCTACCCTGAGGTTTTACAGATG
127396 GCCCTAAGGA
Statistics
Matches: 355, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
119 353 0.99
120 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (119 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACG
Found at i:128779 original size:51 final size:50
Alignment explanation
Indices: 128676--128821 Score: 175
Period size: 51 Copynumber: 2.9 Consensus size: 50
128666 ATATCCCAAC
* * * * * *
128676 CTTTTTATGATGGTGTGAGCCTTCAAGATTCCTCACGTGGATTACTTCTGT
1 CTTTTTATGCTGATGTGAGCCTTCAAGATACC-CACATGGATAACTTATGT
*
128727 CTTTTTCATGCTGATGTGAGCCTTTAAGATACCCACATGGATAACTTATGT
1 CTTTTT-ATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTATGT
* * *
128778 CTTTTTTATGCTGATGTGAGCCTTCAAGATGCCCAGATAGATAA
1 C-TTTTTATGCTGATGTGAGCCTTCAAGATACCCACATGGATAA
128822 TATGGACCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 55 0.67
52 27 0.33
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (50 bp):
CTTTTTATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTATGT
Found at i:130321 original size:8 final size:8
Alignment explanation
Indices: 130308--130401 Score: 99
Period size: 8 Copynumber: 11.9 Consensus size: 8
130298 GATTCAATTT
130308 TTTTCTTC
1 TTTTCTTC
130316 TTTTCTTC
1 TTTTCTTC
130324 TTTTCTTC
1 TTTTCTTC
130332 TTTTCTT-
1 TTTTCTTC
*
130339 TTTTCTTT
1 TTTTCTTC
*
130347 TTTTTTTC
1 TTTTCTTC
130355 TTTT-TT-
1 TTTTCTTC
130361 TTTTCTTTTC
1 TTTTC--TTC
130371 TTTTCTTTTC
1 TTTTC--TTC
130381 TTTTC-TC
1 TTTTCTTC
130388 TTTTC-TC
1 TTTTCTTC
130395 TTTTCTT
1 TTTTCTT
130402 TTCTTTCTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
6 4 0.05
7 23 0.29
8 34 0.44
9 2 0.03
10 15 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTC
Found at i:130329 original size:5 final size:5
Alignment explanation
Indices: 130313--130412 Score: 95
Period size: 5 Copynumber: 20.4 Consensus size: 5
130303 AATTTTTTTC
130313 TTCTT TTCTT CTT-TT CTTCTT TTCTT TT-TT CTT-TT TT-TT TTCTTT
1 TTCTT TTCTT -TTCTT -TTCTT TTCTT TTCTT -TTCTT TTCTT TTC-TT
* * *
130358 TTTTT TTCTT TTCTT TTCTT TTCTT TTCTC TT-TT CTCTT TTCTT TTC-T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
130406 TTCTT TT
1 TTCTT TT
130413 TGTTGAAAAC
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
4 14 0.17
5 60 0.73
6 8 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:130367 original size:34 final size:35
Alignment explanation
Indices: 130308--130407 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 35
130298 GATTCAATTT
* *
130308 TTTTCTTCTTTTCTTCTTTTCTTCTTTTCTTTTTTC
1 TTTTCTT-TTTTCTTTTTTTTTTCTTTTCTTTTTTC
130344 TTTT-TTTTTTCTTTTTTTTTTCTTTTC--TTTTC
1 TTTTCTTTTTTCTTTTTTTTTTCTTTTCTTTTTTC
* *
130376 TTTTCTTTTCTCTTTTCTCTTTTCTTTTCTTT
1 TTTTCTTTTTTCTTTT-TTTTTTCTTTTCTTT
130408 CTTTTTGTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 9 0.16
33 10 0.18
34 30 0.54
35 2 0.04
36 5 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTTCTTTTTTCTTTTTTTTTTCTTTTCTTTTTTC
Found at i:130367 original size:42 final size:43
Alignment explanation
Indices: 130305--130410 Score: 142
Period size: 42 Copynumber: 2.4 Consensus size: 43
130295 CTTGATTCAA
* *
130305 TTTTTTTCTTCTTTTCTTCTTTTC-TTCTTTTCTTTTTTCTTT
1 TTTTTTTCTTTTTTTCTTCTTTTCTTTCTTTTCTTTTCTCTTT
*
130347 TTTTTTTCTTTTTTTTTTCTTTTCTTTTCTTTTCTTTTCTCTTT
1 TTTTTTTCTTTTTTTCTTCTTTTC-TTTCTTTTCTTTTCTCTTT
*
130391 TCTCTTTTCTTTTCTTTCTT
1 T-TTTTTTCTTTT-TTTCTT
130411 TTTGTTGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 22 0.40
44 18 0.33
45 10 0.18
46 5 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (43 bp):
TTTTTTTCTTTTTTTCTTCTTTTCTTTCTTTTCTTTTCTCTTT
Found at i:130372 original size:39 final size:36
Alignment explanation
Indices: 130305--130412 Score: 119
Period size: 39 Copynumber: 2.8 Consensus size: 36
130295 CTTGATTCAA
*
130305 TTTTTTTCTTCTTTTCTTCTTTTC-TTCTTTTCTTTTTTC
1 TTTTTTTTTTCTTTT-TT-TTTTCTTTCTTTTC--TTTTC
130344 TTTTTTTTTTCTTTTTTTTTTCTTTTCTTTTCTTTTC
1 TTTTTTTTTTCTTTTTTTTTTC-TTTCTTTTCTTTTC
* *
130381 TTTTCTCTTTTCTCTTTTCTTTTCTTTCTTTT
1 TTTT-TTTTTTCT-TTTTTTTTTCTTTCTTTT
130413 TGTTGAAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
37 14 0.23
38 17 0.27
39 31 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTTTTTTTTCTTTTTTTTTTCTTTCTTTTCTTTTC
Found at i:136813 original size:16 final size:15
Alignment explanation
Indices: 136791--136853 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
136781 TAACTCAACA
136791 CTTTTCTTTT-TCTTT
1 CTTTTCTTTTAT-TTT
136806 CATTTTCTTTTAATTTT
1 C-TTTTCTTTT-ATTTT
*
136823 CTTTTCTTTTCTCATTT
1 CTTTTCTTTTAT--TTT
136840 -TTTTCTTTT-TTTT
1 CTTTTCTTTTATTTT
136853 C
1 C
136854 CTGATGGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
13 3 0.07
15 3 0.07
16 27 0.66
17 7 0.17
18 1 0.02
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTCTTTTATTTT
Found at i:136965 original size:22 final size:22
Alignment explanation
Indices: 136937--136989 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
136927 TATTCTTGAC
136937 TGTATTTGATCTTCAAGAACTT
1 TGTATTTGATCTTCAAGAACTT
*
136959 TGTATTTGTTCTTCAAGAACTT
1 TGTATTTGATCTTCAAGAACTT
136981 TGTATTTGA
1 TGTATTTGA
136990 CCTACCTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (22 bp):
TGTATTTGATCTTCAAGAACTT
Found at i:140845 original size:55 final size:55
Alignment explanation
Indices: 140801--140944 Score: 261
Period size: 55 Copynumber: 2.6 Consensus size: 55
140791 CTAAGAATTG
**
140801 TGTCTGCTCTCTATTTATTCAGAGAGTATGAGACACGAACAATCTTCAATAATCT
1 TGTCTGCTCTCTATTCGTTCAGAGAGTATGAGACACGAACAATCTTCAATAATCT
140856 TGTCTGCTCTCTATTCGTTCAGAGAGTATGAGACACGAACAATCTTCAATAATCT
1 TGTCTGCTCTCTATTCGTTCAGAGAGTATGAGACACGAACAATCTTCAATAATCT
*
140911 TGTCTGCTCTCTATTCGTTCAGAGAGTATAAGAC
1 TGTCTGCTCTCTATTCGTTCAGAGAGTATGAGAC
140945 TCGGACATAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 86 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (55 bp):
TGTCTGCTCTCTATTCGTTCAGAGAGTATGAGACACGAACAATCTTCAATAATCT
Found at i:141135 original size:54 final size:54
Alignment explanation
Indices: 140965--142218 Score: 1529
Period size: 54 Copynumber: 23.7 Consensus size: 54
140955 TCTTCTTATA
* **
140965 GGTTCGCTCCTTCTTT-TTTAGGGAGTATGGAACTC-AA-A-AATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * *
141015 GGTTCGCTCCCTCTTT-TTTCAGGAAGTATAGAACTCGAACA---ACTTCAAACG
1 GGTTCGCTCCCTCTTTCTTT-AGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * *
141066 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAATATCCTCTTCAAATG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * *
141120 GGTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTT---ACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * * * * *
141171 GGTTTGCTTCTTCTTTCTTTAAGGAGTATGGATCTCGGATATTTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
** * *
141225 GGTTCGCTCATTCTTTCTTTAAGGAGTATGGAACTCGGACATCTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* *
141279 GGTTCGCTCCCTCTTT-TTTAGGGAGTATGGAACTCG-A-AT-ATCTTCACACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* *
141329 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * *
141383 GGTTCGTTCCCTCTTT-TTCTATGGAGTATGGAACTCGAATA-ATT-TTCAAACG
1 GGTTCGCTCCCTCTTTCTT-TAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * *
141435 GGTTCGTTCCCTCTTTCTCTAGGGAGTATGTAACTCGGACATCTTCTTGAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* **
141489 GGTTCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCGAA-A-AATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * *
141541 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATATT-TTTAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * **
141594 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAAAATCTTCTTCTTACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * *
141648 GGTTCGCTCCTTCTTTCTTTAAGGAGAATGGAACTCGAACATC-TCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * *
141701 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
141755 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTC-AGACATCTT-TTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGA-ACATCTTCTTCAAACG
* * *
141808 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCCAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * *
141862 GGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATC-TCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * * * *
141915 AGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAATG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
141969 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
*
142023 GGTTCGCTCCCTC--TCTTCAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
* * * * * *
142075 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCAAAAATCTTCTGCGAACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
*
142129 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTT-ATTACG
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCA-AACG
** *
142183 GGTTCGCTCATTCTTTCTTTAAGGAGTATGGAACTC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTC
142219 TAAACGCGAT
Statistics
Matches: 1042, Mismatches: 133, Indels: 54
0.85 0.11 0.04
Matches are distributed among these distances:
50 43 0.04
51 116 0.11
52 144 0.14
53 224 0.21
54 515 0.49
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (54 bp):
GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
Found at i:141679 original size:107 final size:107
Alignment explanation
Indices: 140965--142218 Score: 1521
Period size: 107 Copynumber: 11.8 Consensus size: 107
140955 TCTTCTTATA
* *
140965 GGTTCGCTCCTTCTTT-TTTAGGGAGTATGGAACTC-AAAA--ATCTTCAAACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* * *
141026 TCTTT-TTTCAGGAAGTATAGAACTCGAACAAC--TTCAAACG
66 TCTTTCTTTAAGG-AGTATGGAACTCGAACATCTTTTCAAACG
* * * * * *
141066 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAATATCCTCTTCAAATGGGTTTGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* * *
141131 TCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTT---ACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* * * * * * * * **
141171 GGTTTGCTTCTTCTTTCTTTAAGGAGTATGGATCTCGGATATTTTCTTCAAACGGGTTCGCTCAT
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
*
141236 TCTTTCTTTAAGGAGTATGGAACTCGGACATCTTCTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* *
141279 GGTTCGCTCCCTCTTT-TTTAGGGAGTATGGAACTCG--AAT-ATCTTCACACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* * *
141340 TCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* * *
141383 GGTTCGTTCCCTCTTT-TTCTATGGAGTATGGAACTCGAATAA--TT-TTCAAACGGGTTCGTTC
1 GGTTCGCTCCCTCTTTCTT-TAGGGAGTATGGAACTCGAA-AATCTTCTTCAAACGGGTTCGCTC
* * * * *
141444 CCTCTTTCTCTAGGGAGTATGTAACTCGGACATCTTCTTGAAACG
64 CCTCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* *
141489 GGTTCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCGAAAA--ATCTTCAAACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* * * * *
141552 TCTTTCTCTAGGGAGTATGGAACTCGGACATATTTTTAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTTTTCAAACG
* * ** *
141594 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCT
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* *
141659 TCTTTCTTTAAGGAGAATGGAACTCGAACATCTCTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTTTTCAAACG
* * * *
141701 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
*
141766 TCTTTCTTTAGGGAGTATGGAACTC-AGACATCTTTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGA-ACATCTTTTCAAACG
* * * *
141808 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCCAACGGGTTCACTCCT
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
*
141873 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTCTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTTTTCAAACG
* * * * * *
141915 AGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAATGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
*
141980 TCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* * *
142023 GGTTCGCTCCCTC--TCTTCAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCT
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
* * * *
142086 TCTTTCTTTAAGGAGTATGGAACTCAAAAATCTTCTGCGAACG
66 TCTTTCTTTAAGGAGTATGGAACTCGAACATCTT-TTCAAACG
* * *
142129 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTT-ATTACGGGTTCGCTCA
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCA-AACGGGTTCGCTCC
*
142193 TTCTTTCTTTAAGGAGTATGGAACTC
65 CTCTTTCTTTAAGGAGTATGGAACTC
142219 TAAACGCGAT
Statistics
Matches: 1013, Mismatches: 115, Indels: 43
0.87 0.10 0.04
Matches are distributed among these distances:
101 16 0.02
102 18 0.02
103 3 0.00
104 74 0.07
105 200 0.20
106 239 0.24
107 353 0.35
108 110 0.11
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (107 bp):
GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
TCTTTCTTTAAGGAGTATGGAACTCGAACATCTTTTCAAACG
Found at i:143980 original size:11 final size:11
Alignment explanation
Indices: 143966--143995 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
143956 TTCTTTCTTT
143966 TTTTTTTGTTC
1 TTTTTTTGTTC
143977 TTTTTTTGTTC
1 TTTTTTTGTTC
143988 TCTTTTTT
1 T-TTTTTT
143996 TATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTGTTC
Found at i:146276 original size:14 final size:14
Alignment explanation
Indices: 146259--146351 Score: 77
Period size: 14 Copynumber: 6.6 Consensus size: 14
146249 TTCCTTATTA
*
146259 TTTTTTTTCATTTC
1 TTTTTTTTCTTTTC
* *
146273 TTTTTCTCCTTTTC
1 TTTTTTTTCTTTTC
146287 TTTATTCATTTC--TTC
1 TTT-TT--TTTCTTTTC
*
146302 TTCTTCTTT-TTTTC
1 TT-TTTTTTCTTTTC
146316 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
*
146330 TTTTTTTT-TTTTT
1 TTTTTTTTCTTTTC
146343 TTTTTTTTC
1 TTTTTTTTC
146352 CCTTTTTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
13 20 0.32
14 32 0.51
15 8 0.13
16 1 0.02
17 2 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:146317 original size:17 final size:17
Alignment explanation
Indices: 146295--146328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
146285 TCTTTATTCA
146295 TTTCTTCTTCTTCTTTT
1 TTTCTTCTTCTTCTTTT
* *
146312 TTTCTTTTTTTTCTTTT
1 TTTCTTCTTCTTCTTTT
146329 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTCTTCTTCTTTT
Found at i:146324 original size:26 final size:26
Alignment explanation
Indices: 146259--146348 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 26
146249 TTCCTTATTA
* **
146259 TTTTTTTTCATTTCTTTTTCTCCTTTTC
1 TTTTTTTTC--TTCTTCTTCTTTTTTTC
146287 TTTATTCATTTCTTCTTCTTCTTTTTTTC
1 TTT-TT--TTTCTTCTTCTTCTTTTTTTC
* *
146316 TTTTTTTTCTT-TTCTTTTTTTTTTT
1 TTTTTTTTCTTCTTCTTCTTTTTTTC
146341 TTTTTTTT
1 TTTTTTTT
146349 TTCCCTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
25 20 0.37
26 6 0.11
28 5 0.09
29 19 0.35
31 4 0.07
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTTCTTCTTCTTCTTTTTTTC
Found at i:146349 original size:26 final size:26
Alignment explanation
Indices: 146259--146349 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
146249 TTCCTTATTA
*
146259 TTTTTTTTCATTTCTTTTTCTCCTTTTCTT
1 TTTTTTTTCTTTTCTTTTT-T--TTTT-TT
** * *
146289 TATTCATTTCTTCTTC-TTCTTTTTTTC
1 T-TTTTTTTCTT-TTCTTTTTTTTTTTT
146316 TTTTTTTTCTTTTCTTTTTTTTTTTT
1 TTTTTTTTCTTTTCTTTTTTTTTTTT
146342 TTTTTTTT
1 TTTTTTTT
146350 TCCCTTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
25 3 0.06
26 25 0.51
27 2 0.04
28 4 0.08
30 2 0.04
31 10 0.20
32 3 0.06
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTTCTTTTCTTTTTTTTTTTT
Found at i:146361 original size:22 final size:23
Alignment explanation
Indices: 146307--146361 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
146297 TCTTCTTCTT
146307 CTTTTTTTCTTTTTTTTCTTTT-C
1 CTTTTTTT-TTTTTTTTCTTTTCC
* *
146330 TTTTTTTTTTTTTTTTTTTTTCC
1 CTTTTTTTTTTTTTTTCTTTTCC
146353 CTTTTTTTT
1 CTTTTTTTT
146362 CGTTTTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (23 bp):
CTTTTTTTTTTTTTTTCTTTTCC
Found at i:146368 original size:1 final size:1
Alignment explanation
Indices: 146308--146350 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
146298 CTTCTTCTTC
* * *
146308 TTTTTTTCTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
146351 CCCTTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:149314 original size:21 final size:21
Alignment explanation
Indices: 149270--149406 Score: 159
Period size: 21 Copynumber: 6.6 Consensus size: 21
149260 CATGCGAAGT
* *
149270 GGTCTTCTCGTCTTTACG-AA
1 GGTCTTCTCGTCTTGATGAAA
*
149290 GGTCTTCTCGTCTTTATGAAA
1 GGTCTTCTCGTCTTGATGAAA
* *
149311 GGTCTTCTCGTCTTTATAAAA
1 GGTCTTCTCGTCTTGATGAAA
*
149332 GGTCTTCTCGTCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
* *
149353 GGCCTTCTCGTCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
* * *
149374 GGCCTTCTTGTCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
*
149395 GGCCTTCTCGTC
1 GGTCTTCTCGTC
149407 CTTGGTACGA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
20 17 0.16
21 91 0.84
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (21 bp):
GGTCTTCTCGTCTTGATGAAA
Found at i:159146 original size:3 final size:3
Alignment explanation
Indices: 159138--159233 Score: 133
Period size: 3 Copynumber: 32.7 Consensus size: 3
159128 GTAATATTTG
** * **
159138 TAA TAA TAA TAA T-A TTT TTA TAA TAA TAA TTG TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
159184 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
159232 TA
1 TA
159234 TATTCTCAGA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
2 4 0.05
3 80 0.95
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:159162 original size:17 final size:17
Alignment explanation
Indices: 159129--159185 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
159119 TCCGATTTTG
*
159129 TAATATTTGTAATAATAA
1 TAATATTT-TTATAATAA
159147 TAATATTTTTATAATAA
1 TAATATTTTTATAATAA
**
159164 TAAT-TGTAATATAATAA
1 TAATAT-TTTTATAATAA
159181 TAATA
1 TAATA
159186 ATAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.03
17 25 0.74
18 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TAATATTTTTATAATAA
Found at i:160067 original size:2 final size:2
Alignment explanation
Indices: 160060--160117 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
160050 TGAAACAAGA
160060 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
160102 AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
160118 GAAATTTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160535 original size:19 final size:19
Alignment explanation
Indices: 160508--160546 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
160498 TACCGTAAAA
160508 ATTAAAAAT-TATAATATAT
1 ATTAAAAATATATAAT-TAT
*
160527 ATTATAAATATATAATTAT
1 ATTAAAAATATATAATTAT
160546 A
1 A
160547 AAAGAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAAAATATATAATTAT
Found at i:166023 original size:75 final size:76
Alignment explanation
Indices: 165896--166103 Score: 285
Period size: 75 Copynumber: 2.8 Consensus size: 76
165886 CCGTTGTACA
* * * *
165896 AGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
**
165959 CAAAACTGTTT
66 CAAAACCATTT
* *
165970 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
166035 CAAAACCATTT
66 CAAAACCATTT
* * * *
166046 AGGGGGGATCGGTTCCTCCTATGAGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGAATCGGTTCCTCCTATG-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
166104 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 18 0.15
75 39 0.33
76 31 0.26
77 30 0.25
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.25
Consensus pattern (76 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
CAAAACCATTT
Found at i:166423 original size:13 final size:13
Alignment explanation
Indices: 166405--166431 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
166395 GAAATTACTC
166405 CCCCTTACTTTAA
1 CCCCTTACTTTAA
166418 CCCCTTACTTTAA
1 CCCCTTACTTTAA
166431 C
1 C
166432 ACTTCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (13 bp):
CCCCTTACTTTAA
Found at i:174613 original size:75 final size:76
Alignment explanation
Indices: 174506--174702 Score: 254
Period size: 75 Copynumber: 2.6 Consensus size: 76
174496 GTTGTACAAG
* * * * *
174506 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATAATGGAATTCTCGGAG-T
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAGCC
**
174569 AAAACTGTTTA
66 AAAACCATTTA
** *
174580 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAGCC
174645 AAAACCATTTA
66 AAAACCATTTA
* * *
174656 GGGGGGATCGGTTCCTCCTATGGGGGGGATTCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
174703 ATTTGTAATT
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 17 0.16
75 38 0.36
76 29 0.27
77 23 0.21
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAGCC
AAAACCATTTA
Found at i:177389 original size:127 final size:128
Alignment explanation
Indices: 177109--177617 Score: 873
Period size: 128 Copynumber: 4.0 Consensus size: 128
177099 GTACTATTCA
*
177109 CGTGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA-TATCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTA-CC
*
177173 CTATTATGTCACTTATGT--CCCCTGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
65 CTATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
* * * * *
177235 CGTGAAGGCGCTTTCCTGGGGGCGCGCCTTCCATTATTTTTTCAGAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
177300 TATTATGTCACTTATGT-CCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
*
177362 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
177427 TATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
*
177490 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
177555 TATTATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATATCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
177618 TTTAAAGCGC
Statistics
Matches: 361, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
126 74 0.20
127 119 0.33
128 168 0.47
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:177558 original size:255 final size:254
Alignment explanation
Indices: 177109--177617 Score: 896
Period size: 255 Copynumber: 2.0 Consensus size: 254
177099 GTACTATTCA
177109 CGTGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATATCCC
1 CGTGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATATCCC
*
177174 TATTATGTCACTTATGTCCCCTGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGACCGTG
66 TATTATGTCACTTATGTCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGACCGTG
* * * * *
177239 AAGGCGCTTTCCTGGGGGCGCGCCTTCCATTATTTTTTCAGAGAATATGTTATTATTGCCCTATT
131 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCTATT
177304 ATGTCACTTATGT-CCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
196 ATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
177362 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCAT-TACC
1 CGTGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATAT-CC
177426 CTATTATGTCACTTATGTCCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGACC
65 CTATTATGTCACTTATGT--CCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGACC
177491 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCT
128 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCT
*
177556 ATTATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATATCTATTATTCCTTAGGGGAC
193 ATTATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
177618 TTTAAAGCGC
Statistics
Matches: 243, Mismatches: 9, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
252 1 0.00
253 78 0.32
255 120 0.49
256 44 0.18
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (254 bp):
CGTGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATATCCC
TATTATGTCACTTATGTCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGACCGTG
AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCTATT
ATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:178085 original size:34 final size:34
Alignment explanation
Indices: 178047--178147 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
178037 GAATTTAATG
*
178047 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
178081 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
178115 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
178148 AACATTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:178698 original size:21 final size:21
Alignment explanation
Indices: 178668--178740 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
178658 TATGGTATAA
**
178668 AACCCTGCGGGCTAGGCTTGT
1 AACCCTGCGGGCTAGGAATGT
178689 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
178710 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
178731 AACACTGCGG
1 AACCCTGCGG
178741 AGATGACATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:180587 original size:31 final size:31
Alignment explanation
Indices: 180520--180620 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
180510 TAATTAGCAC
* * *
180520 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
180548 AAACAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
180579 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
180610 TAAAATATAAT
1 -AAAAAATAAT
180621 AACTATTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:180961 original size:61 final size:60
Alignment explanation
Indices: 180825--180970 Score: 188
Period size: 60 Copynumber: 2.4 Consensus size: 60
180815 TTAATGAAAG
* *
180825 GCGCGTCCCCAGGGATGCGCCTTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCAAAATAAAGGTAAA
* * * * *
180885 GCGCATCCCCGGGGATGTGCCTTTCACACGTGGCATC-CAACTCAGTGTAAAAT-CAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAA-TCA--GCAAAATAAAGGTAAA
180946 GCGCGTCCCCGGGGATGCGCCTTTC
1 GCGCGTCCCCGGGGATGCGCCTTTC
180971 GCCACCTCAG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.03
60 36 0.49
61 30 0.41
62 6 0.08
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (60 bp):
GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCAAAATAAAGGTAAA
Found at i:181793 original size:17 final size:17
Alignment explanation
Indices: 181762--181800 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
181752 AAATTATAAT
*
181762 TAATT-TAAATAATATG
1 TAATTATAAATAATATC
*
181778 TAATTATAACTAATATC
1 TAATTATAAATAATATC
181795 TAATTA
1 TAATTA
181801 ATTTGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:182451 original size:21 final size:20
Alignment explanation
Indices: 182417--182456 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
182407 CAGAGTTGTA
*
182417 AAATATAATTCGAATAACTC
1 AAATATAACTCGAATAACTC
182437 AAATAGTAACTCGAATAACT
1 AAATA-TAACTCGAATAACT
182457 TGAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (20 bp):
AAATATAACTCGAATAACTC
Found at i:183241 original size:19 final size:19
Alignment explanation
Indices: 183186--183233 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
183176 ACATGTCATG
183186 CAATCTAATAATTTTATTA
1 CAATCTAATAATTTTATTA
183205 CAATCTAATAATTTTATTA
1 CAATCTAATAATTTTATTA
183224 CAATCTAATA
1 CAATCTAATA
183234 TATGTATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (19 bp):
CAATCTAATAATTTTATTA
Found at i:190193 original size:19 final size:20
Alignment explanation
Indices: 190169--190227 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
190159 CTAGAACCCC
190169 AGGGGGTATCGATTCCCTT-
1 AGGGGGTATCGATTCCCTTA
* *
190188 AGGGGGAATCGGTTCCCATTCA
1 AGGGGGTATCGATTCCC-TT-A
190210 AGGGGGTATCGATTCCCT
1 AGGGGGTATCGATTCCCT
190228 CTTCCCTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.45
20 2 0.06
21 1 0.03
22 15 0.45
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (20 bp):
AGGGGGTATCGATTCCCTTA
Found at i:191473 original size:14 final size:14
Alignment explanation
Indices: 191443--191486 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
191433 TTTTTATATA
191443 AATAATAAGAATAAT
1 AATAATAA-AATAAT
191458 AATAA-AAAAGTAAT
1 AATAATAAAA-TAAT
191472 AATAATAAAATAAT
1 AATAATAAAATAAT
191486 A
1 A
191487 TTGCAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.07
14 16 0.59
15 9 0.33
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:192389 original size:24 final size:23
Alignment explanation
Indices: 192330--192396 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
192320 TTGCTGTTGG
** *
192330 TCTCTTCCTCTCTTCGTTTCTGTC
1 TCTCTTCCTCT-TTTTTTTTTGTC
192354 TCTCTTCCTCTTTTTATTTTTGTC
1 TCTCTTCCTCTTTTT-TTTTTGTC
192378 TCTCTTCCTCTTTTTTTTT
1 TCTCTTCCTCTTTTTTTTT
192397 GCAGGTGTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.15
24 33 0.85
ACGTcount: A:0.01, C:0.30, G:0.04, T:0.64
Consensus pattern (23 bp):
TCTCTTCCTCTTTTTTTTTTGTC
Found at i:192793 original size:3 final size:3
Alignment explanation
Indices: 192785--192840 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
192775 ATTAATTATT
* *
192785 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAT TAA -AA CAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
192829 TAA TAA TAA TAA
1 TAA TAA TAA TAA
192841 ATAAAACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:192809 original size:19 final size:20
Alignment explanation
Indices: 192785--192841 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
192775 ATTAATTATT
*
192785 TAATAATAATAATA-TAATA
1 TAATAATAATAATATTAAAA
192804 TAATAATAATAATATTAAAA
1 TAATAATAATAATATTAAAA
* *
192824 CAA-AATAATAATAATAAA
1 TAATAATAATAATATTAAA
192842 TAAAACAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 28 0.82
20 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAATAATAATATTAAAA
Found at i:192810 original size:22 final size:22
Alignment explanation
Indices: 192764--192844 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
192754 GGCCTATTTG
* *
192764 TAATAATATTAAT-TAAT-TATT
1 TAATAATAATAATATAATATA-A
192785 TAATAATAATAATATAATATAA
1 TAATAATAATAATATAATATAA
* * * *
192807 TAATAATAATATTAAAACAAAA
1 TAATAATAATAATATAATATAA
192829 TAATAATAATAA-ATAA
1 TAATAATAATAATATAA
192845 AACAAATGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 15 0.30
22 33 0.66
23 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAATAATAATATAATATAA
Found at i:192851 original size:22 final size:22
Alignment explanation
Indices: 192785--192851 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
192775 ATTAATTATT
* *
192785 TAATAATAATAATATAATA-TAA
1 TAATAATAATAA-ATAAAACAAA
*
192807 TAATAATAAT-ATTAAAACAAAA
1 TAATAATAATAAATAAAAC-AAA
192829 TAATAATAATAAATAAAACAAA
1 TAATAATAATAAATAAAACAAA
192851 T
1 T
192852 GAAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 26 0.68
23 7 0.18
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAATAAATAAAACAAA
Found at i:193277 original size:113 final size:113
Alignment explanation
Indices: 193070--193671 Score: 772
Period size: 113 Copynumber: 5.4 Consensus size: 113
193060 TGTAGTGTAG
* * * * *
193070 CAAAAAGGTTGAACAAGCTCTTCTAATTGTGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 CAAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
*
193135 ATTATGAACTTTCTCTGGAAAAGTAGATCCATCGAATGATGAATTCAAA
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* * *
193184 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
*
193249 TTATGAACTTTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* * *
193297 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-TTTCCTTCTTCAGATAAGTTCTTCTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTT-CTTCTTCAGATGAGTTCTTCTC
*
193361 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGAATTCAAA
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAA
* *** *
193410 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTC-AGAT--GACGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
193471 TTATGAACTCTACT-TGGCAATGTTGATCCATCAAATGATAAATTCAAG
66 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* * *
193519 CGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
** * * *
193584 TTATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGA
66 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAA-A
* *
193633 -GAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
193672 GGAAAAGTGT
Statistics
Matches: 430, Mismatches: 47, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
109 85 0.20
110 7 0.02
111 2 0.00
112 6 0.01
113 324 0.75
114 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
Found at i:193476 original size:19 final size:17
Alignment explanation
Indices: 193426--193479 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
193416 GTTGAACAAA
193426 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
193443 TTCTTCTTCA-GATGACGAG
1 TTCTTC-TCATTATGA--AC
193462 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
193479 T
1 T
193480 CTACTTGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
17 12 0.41
18 6 0.21
19 11 0.38
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:193588 original size:222 final size:222
Alignment explanation
Indices: 193072--193671 Score: 827
Period size: 222 Copynumber: 2.7 Consensus size: 222
193062 TAGTGTAGCA
* * *
193072 AAAAGGTTGAACAAGCTCTTCTAATTGTGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
193137 TATGAACTTTCTCTGGAAAAG-TAGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGCT-GATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
* * * *
193201 TCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCTTTATGAACTTTCTCTAG
130 TCTTCTCATTATGAA---CTTC-TTCTTCTACAGACGAGTTCTTCTCATTATGAACTTACTCTAG
* *
193266 AAAAGTTGATCCATCGAATGATGAATTCAAAC
191 AAAAGTTGATCCATCAAATGATAAATTCAAAC
* *
193298 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
193363 TATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGAATTCAAACAAAAAGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCGAA-TGATGAATTCAAACAAAAAGTTGAACAAAT
* * *
193427 TCTTCTCATTATGAACTTCTTCTTC-AGATGACGAGTTCTTCTCATTATGAACTCTACT-TGGCA
130 TCTTCTCATTATGAACTTCTTCTTCTACA-GACGAGTTCTTCTCATTATGAACT-TACTCTAGAA
* *
193490 ATGTTGATCCATCAAATGATAAATTCAAGC
193 AAGTTGATCCATCAAATGATAAATTCAAAC
* *
193520 GAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCA
1 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * *
193584 TTATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGA-GAAAAGTTGAACAA
65 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAA-ACAAAAAGTTGAACAA
* *
193647 GTTCTTCTCATTATGAACTTTTTCT
128 ATTCTTCTCATTATGAACTTCTTCT
193672 GGAAAAGTGT
Statistics
Matches: 339, Mismatches: 27, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
221 1 0.00
222 186 0.55
223 15 0.04
225 2 0.01
226 134 0.40
227 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (222 bp):
AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCTACAGACGAGTTCTTCTCATTATGAACTTACTCTAGAAAAG
TTGATCCATCAAATGATAAATTCAAAC
Found at i:193925 original size:113 final size:113
Alignment explanation
Indices: 193716--194014 Score: 474
Period size: 113 Copynumber: 2.7 Consensus size: 113
193706 TAGAGTCATA
** * *
193716 CAAAAGGTTGAACAAATTTTTCTCATTATGAACTTCTTCTT-CATCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* **
193780 ATATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAAAGATGGATTTGAG
*
193828 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** *
193893 TTATGAACTTTCTCTGGAAATTTTGATTCATCAAAAGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAAAGATGGATTTGAG
* *
193941 CAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
194006 TTATGAACT
66 TTATGAACT
194015 CTTCCAAAAA
Statistics
Matches: 172, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
112 38 0.22
113 134 0.78
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGCTGATCCATCAAAAGATGGATTTGAG
Found at i:193972 original size:309 final size:305
Alignment explanation
Indices: 193409--193975 Score: 764
Period size: 309 Copynumber: 1.8 Consensus size: 305
193399 ATGAATTCAA
* *
193409 ACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCACATGACGAGTTCTTCTCAATA
* * *
193474 TGAACTCTACTTGGCAATGTTGATCCATCAAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCT
66 TGAACTCTACTTGGAAATGCTGATCCATCAAATGATAAATTCAAGCGAAAAGTTGAACAAGCTCT
* * *
193539 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCGACCTGGTAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCGACCTGGAAA
* * *
193604 TGCTGATCCATCGAATGATGAATTCAAGAGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTT
196 TGCTGATCCATCAAAAGATGAATT-AAGAGAAAAGTTGAACAAGCTCTTCTCATTATGAACTTTT
193669 TCTGGAAAAGTGTATGCTAATCTATCTCCTTCTGTGATAGAGTCAT
260 TCTGGAAAAGTGTATGCTAATCTATCTCCTTCTGTGATAGAGTCAT
* * * *
193715 ACAAAAGGTTGAACAAATTTTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCA
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCA-CAT--GACGAGTTCTTCTCA
* * ** **
193780 ATATGAACT-TTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGC-AAAAGGTTGAACAA
63 ATATGAACTCTACT-TGGAAATGCTGATCCATCAAATGATAAATTCAAGCGAAAA-GTTGAACAA
**
193843 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTC
126 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCGAC-C
** * * * *
193907 TGGAAATTTTGATTCATCAAAAGATGGATT-TGAGCAAAAGGTTGAACAAGCTCTTCTTATTATG
190 TGGAAATGCTGATCCATCAAAAGATGAATTAAGAG-AAAA-GTTGAACAAGCTCTTCTCATTATG
193971 AACTT
253 AACTT
193976 CTTATTCCTT
Statistics
Matches: 224, Mismatches: 29, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
306 42 0.19
307 4 0.02
308 12 0.05
309 166 0.74
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (305 bp):
ACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCACATGACGAGTTCTTCTCAATA
TGAACTCTACTTGGAAATGCTGATCCATCAAATGATAAATTCAAGCGAAAAGTTGAACAAGCTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCGACCTGGAAA
TGCTGATCCATCAAAAGATGAATTAAGAGAAAAGTTGAACAAGCTCTTCTCATTATGAACTTTTT
CTGGAAAAGTGTATGCTAATCTATCTCCTTCTGTGATAGAGTCAT
Found at i:194526 original size:22 final size:22
Alignment explanation
Indices: 194449--194524 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
194439 GATAAAGCTT
*
194449 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
194471 TCATCTTTAAAAAG-GAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
194492 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
194514 TCATCTTTGAA
1 TCATCTTTGAA
194525 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.37
22 31 0.63
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:199402 original size:9 final size:9
Alignment explanation
Indices: 199388--199517 Score: 54
Period size: 9 Copynumber: 14.3 Consensus size: 9
199378 CAATTTCTCC
199388 CTTTTTTTT
1 CTTTTTTTT
199397 C--TTTTTT
1 CTTTTTTTT
**
199404 CCCTTTTTT
1 CTTTTTTTT
**
199413 CTCATTTTT
1 CTTTTTTTT
199422 C--TTTTTT
1 CTTTTTTTT
199429 CATATTTTTTT
1 C-T-TTTTTTT
*
199440 C-TTTTTTC
1 CTTTTTTTT
*
199448 CTTTTTTCT
1 CTTTTTTTT
199457 CATTTTTTTT
1 C-TTTTTTTT
*
199467 CATCTTTTTT
1 C-TTTTTTTT
* *
199477 CTTTCTTTG
1 CTTTTTTTT
**
199486 CTAGATTTTT
1 CT-TTTTTTT
* *
199496 CTTTTTGTC
1 CTTTTTTTT
199505 CTTTTTTCTT
1 CTTTTTT-TT
199515 CTT
1 CTT
199518 CAAGTATAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
7 13 0.14
8 7 0.08
9 37 0.41
10 26 0.29
11 7 0.08
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.74
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:199408 original size:18 final size:18
Alignment explanation
Indices: 199380--199474 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 18
199370 TCTTGATTCA
* *
199380 ATTTCTCCCTTTTTTTTC
1 ATTTTTCCCTTTTTTCTC
*
199398 TTTTTTCCCTTTTTTCTC
1 ATTTTTCCCTTTTTTCTC
199416 ATTTTT--CTTTTTTCAT-
1 ATTTTTCCCTTTTTTC-TC
**
199432 ATTTTTTTCTTTTTTC-C
1 ATTTTTCCCTTTTTTCTC
* * *
199449 TTTTTTCTCATTTTTTTTC
1 ATTTTTC-CCTTTTTTCTC
199468 ATCTTTT
1 AT-TTTT
199475 TTCTTTCTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
16 14 0.23
17 6 0.10
18 34 0.57
19 2 0.03
20 4 0.07
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTCCCTTTTTTCTC
Found at i:199412 original size:16 final size:16
Alignment explanation
Indices: 199391--199447 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
199381 TTTCTCCCTT
199391 TTTTTTCT-TTTTTCCC
1 TTTTTTCTATTTTT-CC
199407 TTTTTTCTCATTTTT-C
1 TTTTTTCT-ATTTTTCC
*
199423 TTTTTTCATATTTTTTTC
1 TTTTTTC-TA-TTTTTCC
199441 TTTTTTC
1 TTTTTTC
199448 CTTTTTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 17 0.47
17 6 0.17
18 13 0.36
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCTATTTTTCC
Found at i:199420 original size:25 final size:25
Alignment explanation
Indices: 199392--199474 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 25
199382 TTCTCCCTTT
* *
199392 TTTTTCTTTTTTCCCTTTTTTCTCA
1 TTTTTCTTTTTTCCATTTTTTTTCA
*
199417 TTTTTCTTTTTT-CATATTTTTTTCT
1 TTTTTCTTTTTTCCAT-TTTTTTTCA
199442 TTTTTCCTTTTTTCTCATTTTTTTTCA
1 TTTTT-CTTTTTTC-CATTTTTTTTCA
199469 TCTTTT
1 T-TTTT
199475 TTCTTTCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
24 2 0.04
25 24 0.49
26 7 0.14
27 9 0.18
28 7 0.14
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTCTTTTTTCCATTTTTTTTCA
Found at i:199476 original size:10 final size:10
Alignment explanation
Indices: 199421--199477 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
199411 TTCTCATTTT
199421 TCTTTTTTCA
1 TCTTTTTTCA
*
199431 TATTTTTT--
1 TCTTTTTTCA
*
199439 TCTTTTTTCC
1 TCTTTTTTCA
199449 T-TTTTTCTCA
1 TCTTTTT-TCA
*
199459 TTTTTTTTCA
1 TCTTTTTTCA
199469 TCTTTTTTC
1 TCTTTTTTC
199478 TTTCTTTGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.18
9 5 0.13
10 22 0.56
11 5 0.13
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (10 bp):
TCTTTTTTCA
Found at i:199481 original size:26 final size:26
Alignment explanation
Indices: 199407--199482 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
199397 CTTTTTTCCC
* *
199407 TTTTTTCTCATTTTTCTTTTTTCATAT
1 TTTTTTCTCTTTTTTC-TTTCTCATAT
* *
199434 TTTTTTCTTTTTTCCTTTTTTCTCAT-T
1 TTTTTTCTCTTTT--TTCTTTCTCATAT
199461 TTTTTTCATCTTTTTTCTTTCT
1 TTTTTTC-TCTTTTTTCTTTCT
199483 TTGCTAGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 7 0.17
27 19 0.47
28 12 0.30
29 2 0.05
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTCTCTTTTTTCTTTCTCATAT
Found at i:203111 original size:14 final size:14
Alignment explanation
Indices: 203077--203130 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
203067 CATAAAAATA
* *
203077 CAAATGCAAAGATG
1 CAAATGTAAATATG
203091 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
203106 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
203120 TAAATGTAAAT
1 CAAATGTAAAT
203131 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:204774 original size:16 final size:15
Alignment explanation
Indices: 204740--204779 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
204730 AAAATAAATA
204740 AATAACAAATAATAAT
1 AATAA-AAATAATAAT
204756 AATAAAAATAATAAGT
1 AATAAAAATAATAA-T
204772 AATAAAAA
1 AATAAAAA
204780 ATTTGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAAAAATAATAAT
Found at i:205289 original size:24 final size:25
Alignment explanation
Indices: 205256--205306 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
205246 TATTTCAAAA
205256 TTATAATTATAAA-AAAATATTAAT
1 TTATAATTATAAATAAAATATTAAT
* *
205280 TTATATTTATAAATAAAATATTTAT
1 TTATAATTATAAATAAAATATTAAT
205305 TT
1 TT
205307 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATAATTATAAATAAAATATTAAT
Found at i:205415 original size:109 final size:108
Alignment explanation
Indices: 205264--205503 Score: 272
Period size: 109 Copynumber: 2.2 Consensus size: 108
205254 AATTATAATT
* * * *
205264 ATAAAAAAATATTAATTTAT-ATTTATAAATAAAATATTTA-TT-TTTAGAAATATCAGAAAAT-
1 ATAAATAAATATTAATATATGATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATG
* * * *
205325 GACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAA
66 GACATCCAGGTGCCTTAAGACAGC-CCTTTCTT-AATATTAAAAA
**
205370 ATAAATAAATAATTAATATATGATTTAAAAAATATGATATTTATTTATTTAAAAATATCAGAAAA
1 ATAAATAAAT-ATTAATATATGATTT-AAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA
* ** * *
205435 TGGACATCCAGTTGTTTTAAGACTGCCCTTTCTTAATATTGAAAA
64 TGGACATCCAGGTGCCTTAAGACAGCCCTTTCTTAATATTAAAAA
*
205480 ATAAATAAATATTAAAATATGATT
1 ATAAATAAATATTAATATATGATT
205504 ATTAAAAGTA
Statistics
Matches: 112, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
106 9 0.08
107 9 0.08
108 4 0.04
109 26 0.23
110 21 0.19
111 25 0.22
112 18 0.16
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (108 bp):
ATAAATAAATATTAATATATGATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATG
GACATCCAGGTGCCTTAAGACAGCCCTTTCTTAATATTAAAAA
Found at i:205510 original size:111 final size:109
Alignment explanation
Indices: 205297--205503 Score: 267
Period size: 111 Copynumber: 1.9 Consensus size: 109
205287 TATAAATAAA
* * * * *
205297 ATATTTATTTTTAGAAATATCAGAAAATGACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTCGAT
1 ATATTTATTTTTAAAAATATCAGAAAATGACATCCAGGTGCCTTAAGACAGCTCCTTTCTTCAAT
*
205362 ATTAAAAAATAAATAAATAATTAATATATGATTTAAAAAATATG
66 ATTAAAAAATAAATAAATAATTAAAATATGATTTAAAAAATATG
* ** *
205406 ATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTAAGACTGC-CCTTTCTT-
1 ATATTTA-TT-TTTAAAAATATCAGAAAAT-GACATCCAGGTGCCTTAAGACAGCTCCTTTCTTC
*
205469 AATATTGAAAAATAAATAAAT-ATTAAAATATGATT
63 AATATTAAAAAATAAATAAATAATTAAAATATGATT
205504 ATTAAAAGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
109 20 0.24
110 21 0.25
111 25 0.30
112 18 0.21
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (109 bp):
ATATTTATTTTTAAAAATATCAGAAAATGACATCCAGGTGCCTTAAGACAGCTCCTTTCTTCAAT
ATTAAAAAATAAATAAATAATTAAAATATGATTTAAAAAATATG
Found at i:206496 original size:24 final size:24
Alignment explanation
Indices: 206468--206529 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
206458 TTGTTGTTGG
206468 TCTCTTCCTCTCTTCGTTTCTATC
1 TCTCTTCCTCTCTTCGTTTCTATC
* *
206492 TCTCTTCCTCTTTTCGTTTCTGTC
1 TCTCTTCCTCTCTTCGTTTCTATC
206516 TCTCTTCCTCTCTT
1 TCTCTTCCTCTCTT
206530 TTTTTGCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.02, C:0.37, G:0.05, T:0.56
Consensus pattern (24 bp):
TCTCTTCCTCTCTTCGTTTCTATC
Found at i:206932 original size:3 final size:3
Alignment explanation
Indices: 206924--206982 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
206914 ATTAATTATT
* *
206924 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAT TAA -AA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
206969 -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
206983 ATAAAACAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 8 0.16
3 42 0.84
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:206948 original size:19 final size:20
Alignment explanation
Indices: 206903--206986 Score: 84
Period size: 19 Copynumber: 4.3 Consensus size: 20
206893 GGCCTGTTTG
* * *
206903 TAATAATATTAATTAATTATT
1 TAATAATAATAA-TAATAATA
206924 TAATAATAATAAT-ATAATA
1 TAATAATAATAATAATAATA
*
206943 TAATAATAATAATAATATTA
1 TAATAATAATAATAATAATA
* *
206963 AAACAA-AATAATAATAATA
1 TAATAATAATAATAATAATA
206982 -AATAA
1 TAATAA
206987 AACAAATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
18 4 0.07
19 29 0.54
20 10 0.19
21 11 0.20
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:206949 original size:22 final size:22
Alignment explanation
Indices: 206903--206985 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
206893 GGCCTGTTTG
* *
206903 TAATAATATTAAT-TAAT-TATT
1 TAATAATAATAATATAATATA-A
206924 TAATAATAATAATATAATATAA
1 TAATAATAATAATATAATATAA
* *
206946 TAATAATAATAATATTAAAACAA
1 TAATAATAATAATA-TAATATAA
206969 -AATAATAATAATA-AATA
1 TAATAATAATAATATAATA
206986 AAACAAATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
20 3 0.06
21 12 0.22
22 31 0.57
23 8 0.15
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAATAATAATATAATATAA
Done.