Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010939.1 Kokia drynarioides strain JFW-HI SEQ_125907, 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: 302541
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 240 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1280 original size:162 final size:162
Alignment explanation
Indices: 1013--1320 Score: 492
Period size: 162 Copynumber: 1.9 Consensus size: 162
1003 NNNNNNNNNN
*
1013 AAGTTACTGAATGCAATAATTTGAAGTATCTCTTCCCAACGTGTGTTGCTAATAGTCTTCGGCAA
1 AAGTTACTGAATGCAATAATTTGAAGTATCTCTTCCCAACATGTGTTGCTAATAGTCTTCGGCAA
*
1078 TTGAAAACTCTAAAGGTAGAGAGGTGCTATGGATTGGAAGAAATAATTCAAAACCCACCAGTGTC
66 TTGAAAACTCTAAAGATAGAGAGGTGCTATGGATTGGAAGAAATAATTCAAAACCCACCAGTGTC
1143 AAACATAAGCTTCCAAGAGCTACGGTTTGTAC
131 AAACATAAGCTTCCAAGAGCTACGGTTTGTAC
* *
1175 AAGTTACTGAATGCAATAATTTGAAGTATCTCTTCCCAACATGTGTTGCTAGTAGTCTTGGGC-A
1 AAGTTACTGAATGCAATAATTTGAAGTATCTCTTCCCAACATGTGTTGCTAATAGTCTTCGGCAA
* * * * * * **
1239 TCTGCAAATTTTGAATATAGAGAGGTGCTTTGGATTGGAAGAAATTGTTCAAAACCCACCAGTGT
66 T-TGAAAACTCTAAAGATAGAGAGGTGCTATGGATTGGAAGAAATAATTCAAAACCCACCAGTGT
1304 CAAACATAAGCTTCCAA
130 CAAACATAAGCTTCCAA
1321 TGCCTAGAGG
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
161 2 0.02
162 131 0.98
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (162 bp):
AAGTTACTGAATGCAATAATTTGAAGTATCTCTTCCCAACATGTGTTGCTAATAGTCTTCGGCAA
TTGAAAACTCTAAAGATAGAGAGGTGCTATGGATTGGAAGAAATAATTCAAAACCCACCAGTGTC
AAACATAAGCTTCCAAGAGCTACGGTTTGTAC
Found at i:3709 original size:162 final size:161
Alignment explanation
Indices: 2367--3682 Score: 1937
Period size: 162 Copynumber: 8.1 Consensus size: 161
2357 AATGCGCCCA
* * *
2367 ATCTGCGAACACTGAAGATAAAGAGGTGCTTT-GATATGGAAGAAATAATTCAAAACCCACAGGT
1 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAT-TGGAAGAAATAATTCAAAACCCACAGGT
* * * *
2431 GTCAAACATAAGCTTCCAATGCCTGAGGAAAGTAGAAGTTACTGAATGCATTAATTTGAAGTATC
65 GTCAAACATAAGCTTCCAAGGGCT-AGGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTATC
* *
2496 TCTTCCCAACGTGTGTTGCTACTAGTCTTCGGC
129 TCTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
2529 AAT-TG-AGAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGG
1 -ATCTGCA-AACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGG
*
2592 TGTCAAACATAAGCTTCCAAGGGCTATGGGTAGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
64 TGTCAAACATAAGCTTCCAAGGGCTA-GGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
2657 CTCTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
128 CTCTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
** * ** *
2691 ATCTGCAATTTTTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATTGTTCAAAACCCACAAGTG
1 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
* * * *
2756 TCAAACATAAGCTTCCAATGCCTAGAGGAAATACAAGTTACTGAATGCAATAATTTGAAGTATCT
66 TCAAACATAAGCTTCCAAGGGCTAG-GGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTATCT
*
2821 CTTCCCAACGTGTGTTGCTAATAGTCTTCGGC
130 CTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
* * * *
2853 AAT-TGAAAACTCTAAAGGTAGAGAGGTGCTATGGATTGGAAGAAATAATTCAAAACCCACMA-G
1 -ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCAC-AGG
2916 TGTCAAACATAAGCTTCCAAGGGCTATGGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
64 TGTCAAACATAAGCTTCCAAGGGCTA-GGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
* *
2981 CTCTTCCCAACGTGTGTTGCTACTAGTCTTCGGC
128 CTCTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
* * **
3015 AAT-TGGAAACTCTGAAGATAGAGAAGTGCTTTGGATTGGAAGAAATTGTTCAAAACCCACCA-G
1 -ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCA-CAGG
**
3078 TGTCAAACATAAGCTTCCAAGGGCTAGGGTTTGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
64 TGTCAAACATAAGCTTCCAAGGGCTAGGG-AAGTAGAAGTTACTGAATGCAATAATTTGAAGTAT
*
3143 CTCTTCCCAACATGTGTTGCTAATAGTCTTGGGC
128 CTCTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
* * * **
3177 ATCTGGAAATTTTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATTGTTCAAAACCCACAGGTG
1 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
* ***
3242 TCAAACATAAGCTTCCAAGAGCTATGGTTTGTAGAAGTTACTGAATGCAATAATTTGAAGTATCT
66 TCAAACATAAGCTTCCAAGGGCTA-GGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTATCT
3307 CTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
130 CTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
3339 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
1 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
** *
3404 TCAAACATAAGCTTCCAAGGGCTAGGGTTTGTAGAAGTTATTGAATGCAATAATTTGAAGTATCT
66 TCAAACATAAGCTTCCAAGGGCTAGGG-AAGTAGAAGTTACTGAATGCAATAATTTGAAGTATCT
*
3469 CTTCCCAACGTGTGTTGCTAATTGTCTTGGGC
130 CTTCCCAACGTGTGTTGCTAATAGTCTTGGGC
* *
3501 ATCTGCGAAGTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
1 ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
* * * *
3566 TCAAACATAAGCTTCCAACGCCTAGAGGAAATACAAGTTACTGAATGCAATAATTTGAAGTATCT
66 TCAAACATAAGCTTCCAAGGGCTAG-GGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTATCT
*
3631 CTTCCCAAAGTGTGTTGCTAATAGTCTTGGGCC
130 CTTCCCAACGTGTGTTGCTAATAGTCTTGGG-C
*
3664 A-CTGCCAACTCTGAAGATA
1 ATCTGCAAACTCTGAAGATA
3683 TGGAGCTGTT
Statistics
Matches: 1060, Mismatches: 76, Indels: 35
0.91 0.06 0.03
Matches are distributed among these distances:
161 13 0.01
162 1030 0.97
163 17 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (161 bp):
ATCTGCAAACTCTGAAGATAGAGAGGTGCTTTGGATTGGAAGAAATAATTCAAAACCCACAGGTG
TCAAACATAAGCTTCCAAGGGCTAGGGAAGTAGAAGTTACTGAATGCAATAATTTGAAGTATCTC
TTCCCAACGTGTGTTGCTAATAGTCTTGGGC
Found at i:20501 original size:18 final size:18
Alignment explanation
Indices: 20478--20513 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20468 ACCGTCTTCG
20478 TCCAACCCAACACACCAT
1 TCCAACCCAACACACCAT
**
20496 TCCAACCCTGCACACCAT
1 TCCAACCCAACACACCAT
20514 AAAGTGTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.50, G:0.03, T:0.14
Consensus pattern (18 bp):
TCCAACCCAACACACCAT
Found at i:21259 original size:63 final size:62
Alignment explanation
Indices: 21129--21249 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 62
21119 AATAGTATGT
* * *
21129 GCACACGGTCTGACACACGCCCATGTGCCCAGCCCGTGTGTCTCTTATACCTTGTTTACATG
1 GCACACAGTCTGACACACACCCATGTACCCAGCCCGTGTGTCTCTTATACCTTGTTTACATG
* * *
21191 GCACACAGTCTGGACACACACCCGTGTACCCAGCCCGTGTGTCTCTTGTACTTTGTTTA
1 GCACACAGTCT-GACACACACCCATGTACCCAGCCCGTGTGTCTCTTATACCTTGTTTA
21250 TAGGACACAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 10 0.19
63 42 0.81
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.28
Consensus pattern (62 bp):
GCACACAGTCTGACACACACCCATGTACCCAGCCCGTGTGTCTCTTATACCTTGTTTACATG
Found at i:22828 original size:41 final size:41
Alignment explanation
Indices: 22780--22916 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
22770 CAGGCTTTAT
* * * * * *
22780 GCCTAGCAGGCTTCGTGTCGGTGTATTGATTCAAGCTTTGT
1 GCCTAGCAGGCTTCGAGTCGGTGAATTGAATCAGGCCTTGA
* *
22821 GCCTAGCAGGCTTCGAGTCGGTGAATTGAACCAGGCCCTGA
1 GCCTAGCAGGCTTCGAGTCGGTGAATTGAATCAGGCCTTGA
*
22862 GCCTAGCAGGCTTCAAG-CTGGTGAATTGAATCAGGCCTTGA
1 GCCTAGCAGGCTTCGAGTC-GGTGAATTGAATCAGGCCTTGA
22903 GCCTAGCAGGCTTC
1 GCCTAGCAGGCTTC
22917 ATGCCGGTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 83 0.99
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (41 bp):
GCCTAGCAGGCTTCGAGTCGGTGAATTGAATCAGGCCTTGA
Found at i:22935 original size:41 final size:41
Alignment explanation
Indices: 22747--22936 Score: 174
Period size: 41 Copynumber: 4.7 Consensus size: 41
22737 GATTATATGC
*
22747 CAGGCCTT-ATGCCGGTGTATT--ATCAGG-CTTTATGCCTAG
1 CAGG-CTTCATGCCGGTGTATTGAATCAGGCCTTGA-GCCTAG
* * * * * *
22786 CAGGCTTCGTGTCGGTGTATTGATTCAAGCTTTGTGCCTAG
1 CAGGCTTCATGCCGGTGTATTGAATCAGGCCTTGAGCCTAG
* * * *
22827 CAGGCTTCGA-GTCGGTGAATTGAACCAGGCCCTGAGCCTAG
1 CAGGCTTC-ATGCCGGTGTATTGAATCAGGCCTTGAGCCTAG
* * *
22868 CAGGCTTCAAGCTGGTGAATTGAATCAGGCCTTGAGCCTAG
1 CAGGCTTCATGCCGGTGTATTGAATCAGGCCTTGAGCCTAG
* *
22909 CAGGCTTCATGCCGGTTTATTAAATCAG
1 CAGGCTTCATGCCGGTGTATTGAATCAG
22937 ATAAATTATA
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
38 3 0.02
39 15 0.12
40 1 0.01
41 100 0.83
42 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.29
Consensus pattern (41 bp):
CAGGCTTCATGCCGGTGTATTGAATCAGGCCTTGAGCCTAG
Found at i:23286 original size:17 final size:17
Alignment explanation
Indices: 23264--23304 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
23254 GGCCTAACAA
23264 AAATAAA-ATAAATAAAC
1 AAATAAATA-AAATAAAC
23281 AAATAAATAAAATAAAC
1 AAATAAATAAAATAAAC
23298 AAA-AAAT
1 AAATAAAT
23305 CCTTCATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAATAAAATAAAC
Found at i:23290 original size:21 final size:20
Alignment explanation
Indices: 23264--23304 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
23254 GGCCTAACAA
*
23264 AAATAAAATAAATAAACAAAT
1 AAATAAAATAAACAAA-AAAT
23285 AAATAAAATAAACAAAAAAT
1 AAATAAAATAAACAAAAAAT
23305 CCTTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATAAAATAAACAAAAAAT
Found at i:23898 original size:31 final size:32
Alignment explanation
Indices: 23831--23901 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
23821 CCCTCCACAT
* *
23831 TTTTATTTTTTTAAATTTCACCCATTATTTAG
1 TTTTATTTTTTTAAATTTAACCCATTAATTAG
23863 TTTTATTTTTTTAAA-TTAATCCC-TTCAATTA-
1 TTTTATTTTTTTAAATTTAA-CCCATT-AATTAG
23894 TTTTATTT
1 TTTTATTT
23902 ATTCGTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 13 0.37
32 22 0.63
ACGTcount: A:0.25, C:0.11, G:0.01, T:0.62
Consensus pattern (32 bp):
TTTTATTTTTTTAAATTTAACCCATTAATTAG
Found at i:41164 original size:23 final size:20
Alignment explanation
Indices: 41118--41158 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41108 TAGTTTGAGC
*
41118 ACAACCACCAGACGCCGACG
1 ACAACCACCAGACACCGACG
41138 ACAACCACCAGACACCGACG
1 ACAACCACCAGACACCGACG
41158 A
1 A
41159 TGACAAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.44, G:0.17, T:0.00
Consensus pattern (20 bp):
ACAACCACCAGACACCGACG
Found at i:41821 original size:16 final size:17
Alignment explanation
Indices: 41794--41825 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41784 TTTTTTTTTG
41794 TTTTGTTTAAATTTGGA
1 TTTTGTTTAAATTTGGA
41811 TTTTG-TTAAATTTGG
1 TTTTGTTTAAATTTGG
41826 GCTAGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (17 bp):
TTTTGTTTAAATTTGGA
Found at i:42615 original size:50 final size:50
Alignment explanation
Indices: 42555--42682 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 50
42545 GTCCTTACGA
* * *
42555 CTTCACTCTGCCCCTCTACAGTTTTAGGTGAATGAGATTCGCCGA-TGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTCACC-ATTGCGG
* *
42605 CTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTACCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTCACCATTGCGG
* *
42655 CTTCAAT-TCGCTCCTTTACAGCTTTAGG
1 CTTCAATCT-GCCCCTCTACAGCTTTAGG
42683 GGTATAGGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 2 0.03
50 67 0.97
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTCACCATTGCGG
Found at i:43534 original size:25 final size:23
Alignment explanation
Indices: 43500--43548 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
43490 ATGCCCCATT
43500 TTTTATACTCAAATCTCCTTTCAGG
1 TTTTATACTCAAATCT-CTTT-AGG
*
43525 TTTTCTACTCAAATCTCTTTAGG
1 TTTTATACTCAAATCTCTTTAGG
43548 T
1 T
43549 CTCGAGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 15 0.65
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (23 bp):
TTTTATACTCAAATCTCTTTAGG
Found at i:43607 original size:43 final size:42
Alignment explanation
Indices: 43558--43639 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
43548 TCTCGAGACC
* *
43558 CCTTTTACGGGTTTTCATCTCAGCCCCGCCTTTTTTTTAGCCT
1 CCTTTTACGGGTTTTCAACTCAACCCC-CCTTTTTTTTAGCCT
* *
43601 CCTTTTACGGGTTTTCAACTCAACCTCTCTTTTTTTTAG
1 CCTTTTACGGGTTTTCAACTCAACCCCCCTTTTTTTTAG
43640 GCGAAGTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 11 0.31
43 24 0.69
ACGTcount: A:0.12, C:0.29, G:0.12, T:0.46
Consensus pattern (42 bp):
CCTTTTACGGGTTTTCAACTCAACCCCCCTTTTTTTTAGCCT
Found at i:55370 original size:2 final size:2
Alignment explanation
Indices: 55358--55399 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
55348 GGAAATAGAA
55358 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55398 AT
1 AT
55400 GAAATAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55686 original size:16 final size:17
Alignment explanation
Indices: 55653--55691 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
55643 AGGGGTTGTT
*
55653 TTTGGTTTTTGTTTAAA
1 TTTGGGTTTTGTTTAAA
55670 TTTGGGTTTTG-TTAAA
1 TTTGGGTTTTGTTTAAA
55686 TTTGGG
1 TTTGGG
55692 CTAGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (17 bp):
TTTGGGTTTTGTTTAAA
Found at i:55844 original size:15 final size:16
Alignment explanation
Indices: 55824--55853 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55814 ATCAATTAAT
55824 AAATAAATA-AAAATG
1 AAATAAATAGAAAATG
55839 AAATAAATAGAAAAT
1 AAATAAATAGAAAAT
55854 TTTAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAAATAGAAAATG
Found at i:62819 original size:13 final size:13
Alignment explanation
Indices: 62787--62849 Score: 85
Period size: 12 Copynumber: 5.0 Consensus size: 13
62777 ATTAAAAGTA
62787 AATAAATTTAATT
1 AATAAATTTAATT
*
62800 -TTAAATTTAATT
1 AATAAATTTAATT
62812 AATAAATTTAATT
1 AATAAATTTAATT
*
62825 -TTAAATTTAATT
1 AATAAATTTAATT
*
62837 AATAAAATTAATT
1 AATAAATTTAATT
62850 TATCAATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
12 22 0.51
13 21 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATAAATTTAATT
Found at i:62860 original size:25 final size:25
Alignment explanation
Indices: 62787--62850 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
62777 ATTAAAAGTA
62787 AATAAATTTAATTTTAAATTTAATT
1 AATAAATTTAATTTTAAATTTAATT
62812 AATAAATTTAATTTTAAATTTAATT
1 AATAAATTTAATTTTAAATTTAATT
*
62837 AATAAAATTAATTT
1 AATAAATTTAATTT
62851 ATCAATTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATAAATTTAATTTTAAATTTAATT
Found at i:67993 original size:13 final size:15
Alignment explanation
Indices: 67963--67993 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
67953 TGACAATTAG
67963 AAAAATATATTTTAA
1 AAAAATATATTTTAA
67978 AAAAAT-TATTTTAA
1 AAAAATATATTTTAA
67992 AA
1 AA
67994 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATATATTTTAA
Found at i:71847 original size:18 final size:18
Alignment explanation
Indices: 71824--71861 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
71814 CTTTCAATTG
*
71824 TATGATATAA-ATTATTAA
1 TATGATA-AATATTATAAA
71842 TATGATAAATATTATAAA
1 TATGATAAATATTATAAA
71860 TA
1 TA
71862 ACAGTATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATGATAAATATTATAAA
Found at i:73451 original size:17 final size:17
Alignment explanation
Indices: 73424--73464 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
73414 TGTTGACAAG
*
73424 AAATAATAATATA-TAA
1 AAATAAAAATATATTAA
73440 AATATAAAAATATATTAA
1 AA-ATAAAAATATATTAA
73458 AAATAAA
1 AAATAAA
73465 TATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAATATATTAA
Found at i:75854 original size:22 final size:22
Alignment explanation
Indices: 75826--75867 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
75816 AAGATTTATT
*
75826 AAAAAAAATA-AGAAATTAAAC
1 AAAAAAAATATAAAAATTAAAC
*
75847 AAAAAAAATATAAAACTTAAA
1 AAAAAAAATATAAAAATTAAA
75868 ACAACACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAAAAAATATAAAAATTAAAC
Found at i:77652 original size:34 final size:34
Alignment explanation
Indices: 77613--77715 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 34
77603 GAACAAAGCT
77613 CACCGACTTGCCACTCCCAACACCCCAGAACACC
1 CACCGACTTGCCACTCCCAACACCCCAGAACACC
77647 CACCGACTTGCCACTCCCAACACCCCAGAACACC
1 CACCGACTTGCCACTCCCAACACCCCAGAACACC
* * *
77681 CATCGACTTGCCACTCCTAACTCCCCAGAACACC
1 CACCGACTTGCCACTCCCAACACCCCAGAACACC
77715 C
1 C
77716 TTTCACGAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.28, C:0.51, G:0.09, T:0.12
Consensus pattern (34 bp):
CACCGACTTGCCACTCCCAACACCCCAGAACACC
Found at i:88345 original size:18 final size:17
Alignment explanation
Indices: 88304--88353 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
88294 TGATTTGATA
*
88304 AAAAAATATACAAAT-TT
1 AAAAAATA-AAAAATATT
88321 AAAAAATAAAAAATATT
1 AAAAAATAAAAAATATT
*
88338 AAATAAATAATAAATA
1 AAA-AAATAAAAAATA
88354 ATTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 11 0.38
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAATAAAAAATATT
Found at i:90810 original size:15 final size:16
Alignment explanation
Indices: 90790--90821 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
90780 ATAAATAGTA
90790 TTAAAAATATT-TATT
1 TTAAAAATATTATATT
90805 TTAAAAATATTATATT
1 TTAAAAATATTATATT
90821 T
1 T
90822 ATGTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATATTATATT
Found at i:90821 original size:20 final size:23
Alignment explanation
Indices: 90796--90837 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
90786 AGTATTAAAA
90796 ATATTTAT-T-TTAAAA-ATATT
1 ATATTTATGTATTAAAATATATT
90816 ATATTTATGTATTAAAATATAT
1 ATATTTATGTATTAAAATATAT
90838 GGTTTGAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 6 0.32
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTATGTATTAAAATATATT
Found at i:95094 original size:18 final size:18
Alignment explanation
Indices: 95068--95107 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
95058 GTATAAATTA
*
95068 TTTTAATTTTTATCCTTT
1 TTTTAATTTTAATCCTTT
* *
95086 TTTTCATTTTAATTCTTT
1 TTTTAATTTTAATCCTTT
95104 TTTT
1 TTTT
95108 TTTTTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTAATTTTAATCCTTT
Found at i:97826 original size:2 final size:2
Alignment explanation
Indices: 97819--97852 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
97809 TGAAGTGTGC
97819 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
97853 TTGATGGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102813 original size:3 final size:3
Alignment explanation
Indices: 102800--102846 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
102790 TGTATGTATG
*
102800 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
102846 T
1 T
102847 TGATGATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:102853 original size:3 final size:3
Alignment explanation
Indices: 102847--102874 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
102837 TATTATTATT
102847 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
102875 AAAATATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:103697 original size:96 final size:96
Alignment explanation
Indices: 103513--103704 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
103503 TTTTTGGGAA
** * *
103513 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTCGCGCCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGAAATATTTCA
103578 GAATCGAAGATAAGAAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTGCCTCGATT
* * * * * *
103609 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTGAGTTAAGGCATAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGC-GAAATATTTC
*
103673 -GAAACTCGAA-ATAA-AAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAGAA-AACATTGCCTCGATT
103705 TTAAAGTTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 3 0.04
96 70 0.86
97 8 0.10
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGAAATATTTCA
GAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:104060 original size:59 final size:59
Alignment explanation
Indices: 103974--104477 Score: 606
Period size: 59 Copynumber: 8.7 Consensus size: 59
103964 TTTTTTTTTT
* * * * * * *
103974 AAATGGAATTTTTAGACA-TTCGGGGGTAAAAATAGAATTTTTAGAAATTTCGGGATCAA
1 AAATGGGATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* *
104033 AAATGATG-TTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAA
1 AAATG-GGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* ** * * *
104092 AAA----A-GTTT---AG---G-GGTAAAAAATAGAATTTTTGGAATTTTTGGGGTCAA
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
104139 AAATGGGATTTTTGGAAGTTC-ATGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
1 AAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * * *
104198 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAGTAGAATTTTTGGAGGTTTTGGGGTCAA
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * *
104257 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAGATGGGATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAA-ATGGAATTTTTGGAAGTTTCGGGGTCAA
* * *
104317 AAATGGGATTTTTGGAAGTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAA
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
*
104376 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * *
104435 AAATGGAATTTTTTGAAGTTCGAGGGTAAAAATAGAATTTTTG
1 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTG
104478 AATAGTTTAG
Statistics
Matches: 385, Mismatches: 42, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
47 33 0.09
48 1 0.00
51 3 0.01
52 3 0.01
54 3 0.01
55 2 0.01
58 1 0.00
59 284 0.74
60 55 0.14
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
Found at i:104088 original size:29 final size:29
Alignment explanation
Indices: 103974--104094 Score: 106
Period size: 29 Copynumber: 4.1 Consensus size: 29
103964 TTTTTTTTTT
*
103974 AAATGGAATTTTTAGACATTCGGGGGT-AA
1 AAATGGAATTTTTAGAAATTC-GGGGTCAA
* *
104003 AAATAGAATTTTTAGAAATTTCGGGATCAA
1 AAATGGAATTTTTAGAAA-TTCGGGGTCAA
* * *
104033 AAAT-GATGTTTTTGGAAGTTCGAGGGT-AA
1 AAATGGA-ATTTTTAGAAATTCG-GGGTCAA
104062 AAATGGAATTTTT-GAAAGTTTCGGGGTCAA
1 AAATGGAATTTTTAGAAA--TTCGGGGTCAA
104092 AAA
1 AAA
104095 AGTTTAGGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.04
29 41 0.55
30 31 0.41
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (29 bp):
AAATGGAATTTTTAGAAATTCGGGGTCAA
Found at i:104111 original size:16 final size:17
Alignment explanation
Indices: 104076--104111 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
104066 GGAATTTTTG
*
104076 AAAGTTTCGGGGTCAAA
1 AAAGTTTAGGGGTCAAA
104093 AAAGTTTAGGGGT-AAA
1 AAAGTTTAGGGGTCAAA
104109 AAA
1 AAA
104112 TAGAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (17 bp):
AAAGTTTAGGGGTCAAA
Found at i:104141 original size:30 final size:29
Alignment explanation
Indices: 104094--104477 Score: 427
Period size: 30 Copynumber: 13.0 Consensus size: 29
104084 GGGGTCAAAA
* *
104094 AAGTTTAGGGGTAAAAAATAGAATTTTTGG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
* * *
104124 AATTTTTGGGGTCAAAAATGGGATTTTTGG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
*
104154 AAG-TTCATGGGTAAAAATGGAATTTTTGG
1 AAGTTTC-GGGGTAAAAATGGAATTTTTGG
*
104183 AAGTTTCGGGGTCAAAAATGGGATTTTTGG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
* *
104213 AAG-TTCGAGGGTAAAAGTAGAATTTTTGG
1 AAGTTTCG-GGGTAAAAATGGAATTTTTGG
* * *
104242 AGGTTTTGGGGTCAAAAATGGGATTTTTGG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
*
104272 AAG-TTCGGGGGTAAAAGATGGGATTTTTGG
1 AAGTTTC-GGGGTAAAA-ATGGAATTTTTGG
* *
104302 AAGTTTTGGGGTCAAAAATGGGATTTTTGG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
**
104332 AAGTTAGGGGGTAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTAAAAATGGAATTTTTGG
*
104361 AAGTTTCGGGGTTAAAAATGGGATTTTTGG
1 AAGTTTCGGGG-TAAAAATGGAATTTTTGG
104391 AAG-TTCGAGGGTAAAAATGGAATTTTTGG
1 AAGTTTCG-GGGTAAAAATGGAATTTTTGG
* *
104420 AAGTTTTGGGGTCAAAAATGGAATTTTTTG
1 AAGTTTCGGGGT-AAAAATGGAATTTTTGG
*
104450 AAG-TTCGAGGGTAAAAATAGAATTTTTG
1 AAGTTTCG-GGGTAAAAATGGAATTTTTG
104478 AATAGTTTAG
Statistics
Matches: 305, Mismatches: 34, Indels: 31
0.82 0.09 0.08
Matches are distributed among these distances:
29 125 0.41
30 174 0.57
31 6 0.02
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (29 bp):
AAGTTTCGGGGTAAAAATGGAATTTTTGG
Found at i:104400 original size:178 final size:178
Alignment explanation
Indices: 104101--104477 Score: 623
Period size: 178 Copynumber: 2.1 Consensus size: 178
104091 AAAAAGTTTA
* *
104101 GGGGTAAAAAATAGAATTTTTGGAATTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCATGGGT
1 GGGGTAAAAAATAGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
*
104166 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAGT
66 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT
* *
104231 AGAATTTTTGGAGGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG
131 AGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCG
* * *
104279 GGGGTAAAAGATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT-AGGGGG
1 GGGGTAAAAAATAGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCA-GGGG
*
104343 TAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
65 TAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
* *
104408 TGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTGAAGTTCG
130 TAGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCG
*
104457 AGGGT-AAAAATAGAATTTTTG
1 GGGGTAAAAAATAGAATTTTTG
104478 AATAGTTTAG
Statistics
Matches: 183, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
177 14 0.08
178 169 0.92
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (178 bp):
GGGGTAAAAAATAGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT
AGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCG
Found at i:106374 original size:17 final size:16
Alignment explanation
Indices: 106352--106423 Score: 99
Period size: 17 Copynumber: 4.4 Consensus size: 16
106342 TTGGACTTTC
*
106352 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
*
106369 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
106385 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
106402 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
106418 TAAATT
1 TAAATT
106424 CAATTTCCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
16 22 0.45
17 27 0.55
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:106378 original size:6 final size:6
Alignment explanation
Indices: 106352--106418 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
106342 TTGGACTTTC
* *
106352 TAAATT TAATTT TATAA-- TAAATT TAAATT CAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
106397 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
106419 AAATTCAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 5 0.10
5 6 0.12
6 36 0.75
7 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:106389 original size:33 final size:33
Alignment explanation
Indices: 106352--106429 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
106342 TTGGACTTTC
* *
106352 TAAATTTAATTTTATAATAAATTTAAATTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTCAAA
* *
106385 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTCAAA
*
106418 TAAATTCAATTT
1 TAAATTTAATTT
106430 CCAATAGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTCAAA
Found at i:106435 original size:16 final size:17
Alignment explanation
Indices: 106367--106435 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 17
106357 TTAATTTTAT
*
106367 AATAAATTTAAA-TTCA
1 AATAAACTTAAATTTCA
* *
106383 AATAAATTTAAATTTAA
1 AATAAACTTAAATTTCA
106400 AATAAACTTAAATTT-A
1 AATAAACTTAAATTTCA
* *
106416 AATAAA-TTCAATTTCC
1 AATAAACTTAAATTTCA
106432 AATA
1 AATA
106436 GGCTCGGACG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.15
16 23 0.49
17 17 0.36
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAACTTAAATTTCA
Found at i:113070 original size:18 final size:18
Alignment explanation
Indices: 113036--113069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
113026 ATCCAAAATA
113036 TTAATTAAATTAATTTTC
1 TTAATTAAATTAATTTTC
*
113054 TTAATTACATT-ATTTT
1 TTAATTAAATTAATTTT
113070 TTTCTCAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTAAATTAATTTTC
Found at i:124354 original size:90 final size:90
Alignment explanation
Indices: 124233--124479 Score: 367
Period size: 90 Copynumber: 2.8 Consensus size: 90
124223 ATGGGAGGGN
* * *
124233 GGGGG-GGTGTATCTGACCAGATGCACCTTTACTAGTTGACGGCCTTGGAGGATCTTTCATCGAA
1 GGGGGTGGTGTATCTGACCAGGTGAACCTTTACTAGTTGGCGGCCTTGGAGGATCTTTCATCGAA
* *
124297 GCAATGGTCGA-CCTCGGTGGTGGTG
66 ACAATGGTCGACCCT-GGTAGTGGTG
*
124322 GGGGGCT-GTGTATCTGACCAGGTGAACCTTTACTAGTCGGCGGCCTTGGAGGATCTTTCATCGA
1 GGGGG-TGGTGTATCTGACCAGGTGAACCTTTACTAGTTGGCGGCCTTGGAGGATCTTTCATCGA
*
124386 AACAATGGTCTACCCTGGTAGTGGTG
65 AACAATGGTCGACCCTGGTAGTGGTG
* *
124412 GGGGGTGGTGTATCTGACTAGGTGAACCTTTACTAGTTGGC-GCCTTGGAGGATCTTTCATCGGA
1 GGGGGTGGTGTATCTGACCAGGTGAACCTTTACTAGTTGGCGGCCTTGGAGGATCTTTCATCGAA
124476 ACAA
66 ACAA
124480 CGCGGTCGCC
Statistics
Matches: 144, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
89 32 0.22
90 109 0.76
91 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (90 bp):
GGGGGTGGTGTATCTGACCAGGTGAACCTTTACTAGTTGGCGGCCTTGGAGGATCTTTCATCGAA
ACAATGGTCGACCCTGGTAGTGGTG
Found at i:124733 original size:22 final size:22
Alignment explanation
Indices: 124706--124757 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
124696 AATTTTTAAA
**
124706 AATATTTATATTGTTTTATTTT
1 AATATTTATATAATTTTATTTT
124728 AATATTTA-ATAATTTTATTTT
1 AATATTTATATAATTTTATTTT
124749 AAT-TTTATA
1 AATATTTATA
124758 CATAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
AATATTTATATAATTTTATTTT
Found at i:125052 original size:22 final size:21
Alignment explanation
Indices: 125012--125077 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
125002 GACTTAATTC
*
125012 AAATTAATTTAAAATATAA-ACA
1 AAATTAA-TAAAAATATAATA-A
125034 AAATTAATAAAAATAATAATAA
1 AAATTAATAAAAAT-ATAATAA
* *
125056 AAAATAAT-AATATAT-ATAA
1 AAATTAATAAAAATATAATAA
125075 AAA
1 AAA
125078 CACAAGTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.18
20 2 0.05
21 10 0.26
22 19 0.49
23 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATTAATAAAAATATAATAA
Found at i:125058 original size:13 final size:13
Alignment explanation
Indices: 125038--125067 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
125028 TAAACAAAAT
125038 TAAT-AAAAATAA
1 TAATAAAAAATAA
125050 TAATAAAAAATAA
1 TAATAAAAAATAA
125063 TAATA
1 TAATA
125068 TATATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAAAAAATAA
Found at i:125061 original size:19 final size:19
Alignment explanation
Indices: 125039--125077 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
125029 AAACAAAATT
125039 AATAAAAATA-ATAATAAAA
1 AATAAAAATATAT-ATAAAA
*
125058 AATAATAATATATATAAAA
1 AATAAAAATATATATAAAA
125077 A
1 A
125078 CACAAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAATATATATAAAA
Found at i:125692 original size:16 final size:15
Alignment explanation
Indices: 125636--125692 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 15
125626 TAATTATCAC
125636 TTAATTAATATTATTT
1 TTAATTAATATTA-TT
125652 TTAATTAATTATTATT
1 TTAATTAA-TATTATT
* *
125668 TTAAATAATGTTATT
1 TTAATTAATATTATT
125683 TTACATTAAT
1 TTA-ATTAAT
125693 TGTATAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 9 0.25
16 22 0.61
17 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTAATTAATATTATT
Found at i:127189 original size:9 final size:9
Alignment explanation
Indices: 127147--127189 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
127137 TGTCTTATAT
127147 ATATTTTTA
1 ATATTTTTA
*
127156 ATAATTTTA
1 ATATTTTTA
127165 AT-TGTTTTA
1 ATAT-TTTTA
127174 A-ATTTTTA
1 ATATTTTTA
127182 ATATTTTT
1 ATATTTTT
127190 TTGATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
ATATTTTTA
Found at i:129982 original size:30 final size:30
Alignment explanation
Indices: 129948--130297 Score: 326
Period size: 30 Copynumber: 11.8 Consensus size: 30
129938 ACTCAGGATG
* * *
129948 AAAATGAAATTTTAGAGAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* *
129978 AAAATGTGATTTT-GAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* *
130007 AAAATATGATTTTGGAAAAGTTTGAGGGGATC
1 AAAATGTAATTTTGGAAAAGTTTGA-GGG-TC
* *
130039 AAAATGTGATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * *
130069 AAAATATTATTTTGGAAAAGTTTAGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GAGGGTC
* * *
130100 AAATACG--ATGTTGGAAAAGTTT-AGGGGTT
1 AAA-ATGTAATTTTGGAAAAGTTTGA-GGGTC
130129 AAAATGTAATTTTGGAAAAGTTT-AGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGA-GGGTC
* *
130159 AAAATGTATTTTTGGAAAAGTTTG-GGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
** ** *
130188 TTAATGTAATTTCAGAAAA-TTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
130217 AAAATGTAATTTTGGAAAAGTTTGA-GGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* *
130246 AAAATGTAGTTTTGGAAAAGTTT-AGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAG-GGTC
*
130276 AAAATGGT-ATTTTTG-AAAGTTT
1 AAAAT-GTAATTTTGGAAAAGTTT
130298 AAGGACTTAC
Statistics
Matches: 270, Mismatches: 36, Indels: 29
0.81 0.11 0.09
Matches are distributed among these distances:
28 7 0.03
29 104 0.39
30 117 0.43
31 16 0.06
32 26 0.10
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTGAGGGTC
Found at i:130011 original size:59 final size:60
Alignment explanation
Indices: 129948--130301 Score: 318
Period size: 59 Copynumber: 6.0 Consensus size: 60
129938 ACTCAGGATG
* *
129948 AAAATGAAATTTTAGAGAAGTTTGAGGGTCAAAATGTGATTTT-GAAAAGTTTAAGGGTC
1 AAAATGAAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
*
130007 AAAAT-ATGATTTTGGAAAAGTTTGAGGGGATCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
1 AAAATGA-AATTTTGGAAAAGTTTGA-GGG-TCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
* * ** * * *
130069 AAAAT-ATTATTTTGGAAAAGTTTAGAGGGT-TAAATACGATGTTGGAAAAGTTTAGGGGTT
1 AAAATGA-AATTTTGGAAAAGTTT-GAGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
* * *
130129 AAAATGTAATTTTGGAAAAGTTT-AGGGGTCAAAATGT-ATTTTTGGAAAAGTTT-GGGGTT
1 AAAATGAAATTTTGGAAAAGTTTGA-GGGTCAAAATGTGA-TTTTGGAAAAGTTTAAGGGTC
** * ** * * *
130188 TTAATGTAATTTCAGAAAA-TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTGA-GGTC
1 AAAATGAAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
* * * *
130246 AAAATGTAGTTTTGGAAAAGTTT-AGAGGTTAAAATG-GTATTTTTG-AAAGTTTAAGG
1 AAAATGAAATTTTGGAAAAGTTTGAG-GGTCAAAATGTG-ATTTTGGAAAAGTTTAAGG
130302 ACTTACTAGA
Statistics
Matches: 248, Mismatches: 31, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
58 58 0.23
59 67 0.27
60 64 0.26
61 16 0.06
62 41 0.17
63 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAATGAAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
Found at i:131232 original size:20 final size:20
Alignment explanation
Indices: 131207--131254 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
131197 AAAAGGCAAA
131207 CCCAAATTTGAGTGCGAAAT
1 CCCAAATTTGAGTGCGAAAT
131227 CCCAAATTTGAGTGCGAAAT
1 CCCAAATTTGAGTGCGAAAT
131247 CCCAAATT
1 CCCAAATT
131255 CGGAACCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (20 bp):
CCCAAATTTGAGTGCGAAAT
Found at i:132224 original size:96 final size:97
Alignment explanation
Indices: 132105--132299 Score: 268
Period size: 96 Copynumber: 2.0 Consensus size: 97
132095 ACTACTGTAG
* * *
132105 TTTTAATCCAACTTCGCTGCAACTTCAGGAAGATA-AGATTTGATGTCGAAGCTTCATCTTGCTC
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGA-ATTTGACGTCGAAGCTTCATCTTGCTC
* * * *
132169 TTACTGTAA-TTCCGATAGATAAAGACTTGCTA
65 TTACTGCAACTTCAGAGAGACAAAGACTTGCTA
* * * *
132201 TTTTAATCCAACTTTACTGCAACTTCAAGATGATAGAATTTGACGTTGAAGCTTCATTTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGAATTTGACGTCGAAGCTTCATCTTGCTCT
132266 TACTGCAACTTCAGAGAGACAAAGACTTGCTA
66 TACTGCAACTTCAGAGAGACAAAGACTTGCTA
132298 TT
1 TT
132300 GTAGTTTTGA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
96 63 0.73
97 23 0.27
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (97 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGAATTTGACGTCGAAGCTTCATCTTGCTCT
TACTGCAACTTCAGAGAGACAAAGACTTGCTA
Found at i:132511 original size:49 final size:48
Alignment explanation
Indices: 132458--133061 Score: 265
Period size: 49 Copynumber: 12.3 Consensus size: 48
132448 CGGTCATAAC
* * * *
132458 CTTTCCCTTCAAATCTTCATGGTACCAGACTCGTTGTTGCGACTTCAAT
1 CTTTCCCTTCATATCTTC-TGGTACAAGATTCGTTGTTGCGACTTAAAT
* * * *
132507 CTTTCCCTTCATGT-TTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCT--GGTACAAGATTCGTTGTTGCGACTTAAAT
* * * *
132556 CTTTCCCTCCATATCTTCGTGGTACTAGATTCGCTGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTC-TGGTACAAGATTCGTTGTTGCGACTTAAAT
* * **
132605 CTTTCCCATC-TCATCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAA-
1 CTTTCCCTTCAT-ATCTTCT--GGTACAAGATTCGTTGTTGCGACTTAAAT
* * ** ** *
132654 CTTTTCCTTCCGTATCTTCGTGGTACTGGATTCGCCGTTAC-AGCTTAAAT
1 CTTTCCCTT-CATATCTTC-TGGTACAAGATTCGTTGTTGCGA-CTTAAAT
* * * * *
132704 CTTTCCCTTCAT-CCTTCTAAGGTACAAGGTTTGTCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCT--GGTACAAGATTCGTTGTTGCGACTTAAAT
* * * ** * *
132753 CTTTCCCTCCATATCTTCGTGGTACTAGAATCGCCGTTGTGGCTTAAAT
1 CTTTCCCTTCATATCTTC-TGGTACAAGATTCGTTGTTGCGACTTAAAT
* * * ** * *** *
132802 CTTTCCTTTCATGTTTTGAGGTACAAGGTTCACCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCTGGTACAAGATTCGTTGTTGCGACTTAAAT
* *** *
132850 CTTT-CCTTCCATATCTTCGTGGTACTAGATTCCCCGTTGTGACTTAAAT
1 CTTTCCCTT-CATATCTTC-TGGTACAAGATTCGTTGTTGCGACTTAAAT
* ** * * * * ** **
132899 TTTTATCATC-TCATCTTTTGAGGTATAAGGTTCACTGTTATGACTTAAA-
1 CTTTCCCTTCAT-ATCTTCT--GGTACAAGATTCGTTGTTGCGACTTAAAT
*** *** *
132948 CTTTTCCCTTCATATCTTCATGGTATTGGATTCGCCATTGCGGCTTAAAT
1 C-TTTCCCTTCATATCTTC-TGGTACAAGATTCGTTGTTGCGACTTAAAT
* * * * *
132998 ATTTCCCTTCAT-GCTTCTGAGGTACAA-AGTTCGTCGTTGTGACTTAAAC
1 CTTTCCCTTCATATCTTCT--GGTACAAGA-TTCGTTGTTGCGACTTAAAT
*
133047 CTTTCCCTCCATATC
1 CTTTCCCTTCATATC
133062 CTTGTAGTGA
Statistics
Matches: 416, Mismatches: 108, Indels: 61
0.71 0.18 0.10
Matches are distributed among these distances:
47 6 0.01
48 49 0.12
49 272 0.65
50 83 0.20
51 6 0.01
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (48 bp):
CTTTCCCTTCATATCTTCTGGTACAAGATTCGTTGTTGCGACTTAAAT
Found at i:132911 original size:294 final size:295
Alignment explanation
Indices: 132455--133061 Score: 840
Period size: 294 Copynumber: 2.1 Consensus size: 295
132445 TCGCGGTCAT
* * * ** *
132455 AACCTTTCCCTTCAAATCTTCATGGTACCAGACTCGTTGTTGCGACTTCAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCTTCATGGTACCAGAATCGCCGTTGCGACTTAAATCTTTCCCTTCATG
**
132520 TTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGA
66 TTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGA
* * * * * *
132585 TTCGCTGTTGCGGCTTAAATCTTTCCCATCTCATCTTCTGAGGTACAAGGTTCGCCGTTGCGACT
131 TTCCCCGTTGCGACTTAAATCTTTACCATCTCATCTTCTGAGGTACAAGGTTCACCGTTACGACT
* * * *
132650 TAAACTTTT-CCTTCCGTATCTTCGTGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCCTTC
196 TAAACTTTTCCCTT-CATATCTTCATGGTACTGGATTCGCCATTACAGCTTAAATATTTCCCTTC
* *
132714 ATCCTTCTAAGGTACAAGGTTTGTCGTTGCGACTTA
260 ATCCTTCTAAGGTACAAAGTTCGTCGTTGCGACTTA
* * * * *
132750 AACCTTTCCCTCCATATCTTCGTGGTACTAGAATCGCCGTTGTGGCTTAAATCTTTCCTTTCATG
1 AACCTTTCCCTCCATATCTTCATGGTACCAGAATCGCCGTTGCGACTTAAATCTTTCCCTTCATG
*
132815 TTT-TGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCTTCCATATCTTCGTGGTACTAGA
66 TTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGA
* * * * * * *
132879 TTCCCCGTTGTGACTTAAATTTTTATCATCTCATCTTTTGAGGTATAAGGTTCACTGTTATGACT
131 TTCCCCGTTGCGACTTAAATCTTTACCATCTCATCTTCTGAGGTACAAGGTTCACCGTTACGACT
* * *
132944 TAAACTTTTCCCTTCATATCTTCATGGTATTGGATTCGCCATTGCGGCTTAAATATTTCCCTTCA
196 TAAACTTTTCCCTTCATATCTTCATGGTACTGGATTCGCCATTACAGCTTAAATATTTCCCTTCA
* * *
133009 TGCTTCTGAGGTACAAAGTTCGTCGTTGTGACTTA
261 TCCTTCTAAGGTACAAAGTTCGTCGTTGCGACTTA
133044 AACCTTTCCCTCCATATC
1 AACCTTTCCCTCCATATC
133062 CTTGTAGTGA
Statistics
Matches: 272, Mismatches: 39, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
294 211 0.78
295 61 0.22
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (295 bp):
AACCTTTCCCTCCATATCTTCATGGTACCAGAATCGCCGTTGCGACTTAAATCTTTCCCTTCATG
TTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGA
TTCCCCGTTGCGACTTAAATCTTTACCATCTCATCTTCTGAGGTACAAGGTTCACCGTTACGACT
TAAACTTTTCCCTTCATATCTTCATGGTACTGGATTCGCCATTACAGCTTAAATATTTCCCTTCA
TCCTTCTAAGGTACAAAGTTCGTCGTTGCGACTTA
Found at i:139120 original size:30 final size:30
Alignment explanation
Indices: 139078--139390 Score: 314
Period size: 30 Copynumber: 10.4 Consensus size: 30
139068 ACTCGGGATG
* * *
139078 AAAATGAAATTTTAGG-GAAGTTTAAGGGTT
1 AAAATGTAATTTT-GGAAAAGTTTAAGGGTC
* * *
139108 AAAATGTGATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * *
139138 AAAATATGATTTTGGAAAAGTTTGAGTGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-A-AGGGTC
**
139170 AAAATGTGTTTTTGGAAAAGTTTAA-GGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
139199 AAATATGT--TTTTGGAAAAGTTTAGAGGGTC
1 AAA-ATGTAATTTTGGAAAAGTTTA-AGGGTC
* * * *
139229 AAAATATGATGTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
*
139259 AAAATGTAATTTTGAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * *
139289 AAAATGTAAATTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
*
139319 AAAATGTAATTTTTGAAAAGTTT-A-GGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * * *
139347 AAAATATAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
139377 AAAATAGTAATTTT
1 AAAAT-GTAATTTT
139391 TAGAAGTTTA
Statistics
Matches: 242, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
28 40 0.17
29 13 0.05
30 141 0.58
31 23 0.10
32 25 0.10
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGTC
Found at i:141020 original size:11 final size:11
Alignment explanation
Indices: 140980--141022 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
140970 AGTTAGTTGG
*
140980 GATTGGGCTTA
1 GATTGGGTTTA
*
140991 GATTTGGATTTA
1 GA-TTGGGTTTA
141003 GATTGGGTTTA
1 GATTGGGTTTA
141014 GATTGGGTT
1 GATTGGGTT
141023 ATGACTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (11 bp):
GATTGGGTTTA
Found at i:141324 original size:22 final size:23
Alignment explanation
Indices: 141298--141341 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
141288 ATTATATAAT
141298 AAATTATAATT-ATTTTCTTTTA
1 AAATTATAATTGATTTTCTTTTA
*
141320 AAATTTTAATTGATTTTCTTTT
1 AAATTATAATTGATTTTCTTTT
141342 TTTTTACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (23 bp):
AAATTATAATTGATTTTCTTTTA
Found at i:148666 original size:51 final size:51
Alignment explanation
Indices: 148590--148769 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 51
148580 TGAAAGGAAC
* *
148590 CGATGACTAAGTGTCATTGTTAGTAAATGAATCCTTTACGGATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* * * *
148641 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCGTGATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* * * * * * **
148692 CGATGAGTCAGTGTCATCCTGAGTATATGAATTCCTATACGAAACAAGAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTT
*
148745 CGATGACTATGTGTCATCGTGAGTA
1 CGATGACTAAGTGTCATCGTGAGTA
148770 TTAAATGAAA
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 72 0.69
52 8 0.08
53 25 0.24
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
Found at i:148818 original size:61 final size:60
Alignment explanation
Indices: 148718--148896 Score: 245
Period size: 61 Copynumber: 3.0 Consensus size: 60
148708 TCCTGAGTAT
* * *
148718 ATGAATTCCTATACGAAACAAGAGGTTCGATGACTATGTGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGG-TCAATGACTATGTGTCATCGTGAGTATTAAATGAA
148779 ATGAGTTCCTATACGGAACAAGAGGTCCAATGACTATGTGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGT-CAATGACTATGTGTCATCGTGAGTATTAAATGAA
* * * * *
148840 ATGAGTTCCAATGC-GAACAAG-GGTTAGATGACTTTGTGTCATCGTGAGTAATAAATG
1 ATGAGTTCCTATACGGAACAAGAGGTCA-ATGACTATGTGTCATCGTGAGTATTAAATG
148897 CGAGTGAAGA
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
58 1 0.01
59 31 0.29
60 8 0.07
61 68 0.63
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (60 bp):
ATGAGTTCCTATACGGAACAAGAGGTCAATGACTATGTGTCATCGTGAGTATTAAATGAA
Found at i:154895 original size:24 final size:24
Alignment explanation
Indices: 154858--154905 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
154848 TCAAGTGAGA
* * *
154858 CTTTATTTTTAACATTTCCATTGT
1 CTTTACTTTCAACAATTCCATTGT
*
154882 CTTTACTTTCAACAATTGCATTGT
1 CTTTACTTTCAACAATTCCATTGT
154906 TTTCATTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (24 bp):
CTTTACTTTCAACAATTCCATTGT
Found at i:156914 original size:26 final size:29
Alignment explanation
Indices: 156862--156918 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
156852 TTTATATTTG
156862 TTGCCATTATATTTATAATTAAGTTGTTAT
1 TTGCCATTATATTTAT-ATTAAGTTGTTAT
*
156892 TTGCCATTAT-TTTAT-TT-ATTTGTTAT
1 TTGCCATTATATTTATATTAAGTTGTTAT
156918 T
1 T
156919 AATTACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
27 2 0.08
29 5 0.19
30 10 0.38
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.60
Consensus pattern (29 bp):
TTGCCATTATATTTATATTAAGTTGTTAT
Found at i:157812 original size:17 final size:17
Alignment explanation
Indices: 157792--157843 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
157782 ATTGGACCCA
*
157792 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
157809 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
157826 AGTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
157843 A
1 A
157844 ATTAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:157820 original size:6 final size:6
Alignment explanation
Indices: 157794--157844 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
157784 TGGACCCAAT
* * * *
157794 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
157840 TTTAA
1 TTTAA
157845 TTAAAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:158483 original size:12 final size:13
Alignment explanation
Indices: 158455--158494 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
158445 GTATATTAAG
158455 TATAATAAATAAA
1 TATAATAAATAAA
*
158468 TATATTAAAT-AA
1 TATAATAAATAAA
158480 TATAATAAAATAAA
1 TATAAT-AAATAAA
158494 T
1 T
158495 TTATTTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 13 0.57
14 3 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TATAATAAATAAA
Found at i:158491 original size:22 final size:21
Alignment explanation
Indices: 158446--158488 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
158436 GCATTTATTG
158446 TATATTAAGTATAATAAATAAA
1 TATATTAAG-ATAATAAATAAA
158468 TATATTAA-ATAATATAATAAA
1 TATATTAAGATAATA-AATAAA
158489 ATAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATATTAAGATAATAAATAAA
Found at i:162078 original size:49 final size:49
Alignment explanation
Indices: 162004--162126 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 49
161994 ATGAATCGAT
* * * *
162004 GTACCATAAAGATATGAAGGGAAAGGTTGAGCCCGCAATGGCGAACCCA
1 GTACCATGAAGATTTGAAGGAAAAGGTTGAGCCCGCAACGGCGAACCCA
* * *
162053 GTACCATGAAGATTTGAAAGAAAAGGTTGAGGCCGCAACGGCGAACCCG
1 GTACCATGAAGATTTGAAGGAAAAGGTTGAGCCCGCAACGGCGAACCCA
*
162102 GTACCATGAAGAGTTGAAGGAAAAG
1 GTACCATGAAGATTTGAAGGAAAAG
162127 ATTTAGGTCG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (49 bp):
GTACCATGAAGATTTGAAGGAAAAGGTTGAGCCCGCAACGGCGAACCCA
Found at i:162139 original size:49 final size:49
Alignment explanation
Indices: 162025--162139 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
162015 ATATGAAGGG
* * * *
162025 AAAGGTTGAGCCCGCAATGGCGAACCCAGTACCATGAAGATTTGAAAGA
1 AAAGATTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGTTGAAAGA
* * *
162074 AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGAGTTGAAGGA
1 AAAGATTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGTTGAAAGA
* *
162123 AAAGATTTAGGTCGCAA
1 AAAGATTGAGGCCGCAA
162140 AGACGAATCT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.16
Consensus pattern (49 bp):
AAAGATTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGTTGAAAGA
Found at i:162155 original size:49 final size:49
Alignment explanation
Indices: 162025--162155 Score: 136
Period size: 49 Copynumber: 2.7 Consensus size: 49
162015 ATATGAAGGG
* * * * *
162025 AAAGGTTGAGCCCGCAATGGCGAACCCAGTACCATGAAGATTTGAAAGA
1 AAAGATTGAGGCCGCAAAGACGAACCCAGTACCATGAAGAGTTGAAAGA
* * * * *
162074 AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGAGTTGAAGGA
1 AAAGATTGAGGCCGCAAAGACGAACCCAGTACCATGAAGAGTTGAAAGA
* * * *
162123 AAAGATTTAGGTCGCAAAGACGAATCTAGTACC
1 AAAGATTGAGGCCGCAAAGACGAACCCAGTACC
162156 TTAGGATCAT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (49 bp):
AAAGATTGAGGCCGCAAAGACGAACCCAGTACCATGAAGAGTTGAAAGA
Found at i:162623 original size:116 final size:117
Alignment explanation
Indices: 162475--162808 Score: 415
Period size: 116 Copynumber: 2.9 Consensus size: 117
162465 CACAGTCATC
* ** * * * * *
162475 CGATCTTTTACCCTAAGCCTGAGGCAAATCACCATCAGTCAATCTCTTAGCTCGAGCCTGGGGCA
1 CGATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCA
* *
162540 GATTGTAATCATTCGATCTTTTACCCTGAG-CTTGAGGCA-ATTGCAACCATT
66 GATTGTAACCATTCGATCTTTTACCCTGAGCCTAG-GGCAGATTGCAACCATT
* *
162591 CGATCTCTTACCCTGAGCTT-AGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCGTGGGGC
1 CGATCTCTTACCCCGAGCTTGA-GGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGC
* * * * *
162655 AGATTGCAACCATTCGATCTCTTACCCTAAGCCTAGGGTAGATTGCAGCCATT
65 AGATTGTAACCATTCGATCTTTTACCCTGAGCCTAGGGCAGATTGCAACCATT
** *
162708 CGATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAACCAATCTCTT-CCCCGAGCTTGGGGCA
1 CGATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCA
* * *
162772 GATTGTAGCCATTTGATCTTTTACCCCGAGCCTAGGG
66 GATTGTAACCATTCGATCTTTTACCCTGAGCCTAGGG
162809 TAAATCACCA
Statistics
Matches: 189, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
115 1 0.01
116 130 0.69
117 57 0.30
118 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (117 bp):
CGATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCA
GATTGTAACCATTCGATCTTTTACCCTGAGCCTAGGGCAGATTGCAACCATT
Found at i:162675 original size:39 final size:39
Alignment explanation
Indices: 162516--162802 Score: 227
Period size: 39 Copynumber: 7.4 Consensus size: 39
162506 CCATCAGTCA
* * * * *
162516 ATCTCTTAGCTCGAGCCTGGGGCAGATTGTAATCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
* * *
162555 ATCTTTTACCCTGAGCTTGAGGCA-ATTGCAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
* * * ** * * * *
162593 ATCTCTTACCCTGAGCTTAGGGTAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
*
162632 ATCTCTTACCCCGAGCGTGGGGCAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
** * * * *
162671 ATCTCTTACCCTAAGCCTAGGGTAGATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
* * ** * * ** *
162710 ATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
* * *
162749 ATCTCTT-CCCCGAGCTTGGGGCAGATTGTAGCCATTTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
*
162787 ATCTTTTACCCCGAGC
1 ATCTCTTACCCCGAGC
162803 CTAGGGTAAA
Statistics
Matches: 186, Mismatches: 60, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
38 57 0.31
39 129 0.69
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
Found at i:162753 original size:78 final size:78
Alignment explanation
Indices: 162475--162914 Score: 297
Period size: 78 Copynumber: 5.7 Consensus size: 78
162465 CACAGTCATC
* ** * * * * * * *
162475 CGATCTTTTACCCTAAGCCTGAGGCAAATCACCATCAGTCAATCTCTTAGCTCGAGCCTGGGGCA
1 CGATCTCTTACCCCGAGCTTGAGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTA
**
162540 GATTGTAATCATT
66 GATTGTAGCCATT
* * * * * *
162553 CGATCTTTTACCCTGAGCTTGAGGCAATTGCAACCATTC-G---ATCTCTTACCCTGAGCTTAGG
1 CGATCTCTTACCCCGAGCTTGAGGTAAAT-C-ACCA-TCAGCCAATCTCTTACCCCGAGCCTAGG
*
162614 GTAGA-T-CA-CCATCAGT
63 GTAGATTGTAGCCAT---T
* * * * * ** * * ** * **
162630 CAATCTCTTACCCCGAGCGTGGGGCAGATTGCAACCATTCGATCTCTTACCCTAAGCCTAGGGTA
1 CGATCTCTTACCCCGAGCTTGAGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTA
*
162695 GATTGCAGCCATT
66 GATTGTAGCCATT
* * * * *
162708 CGATCTCTTACCCCGAGCTTGAGGTAGATCACCATCAACCAATCTCTT-CCCCGAGCTTGGGGCA
1 CGATCTCTTACCCCGAGCTTGAGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTA
162772 GATTGTAGCCATT
66 GATTGTAGCCATT
* * * *
162785 TGATCTTTTACCCCGAGCCT-AGGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGTT
1 CGATCTCTTACCCCGAGCTTGA-GGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGT
* *
162849 AAATTGTAACCATT
65 AGATTGTAGCCATT
* * * *
162863 CGATCACTTACCTCGAG-TCTGGGGCAAATCACCATCAGCCAATCTCTTACCC
1 CGATCTCTTACCCCGAGCT-TGAGGTAAATCACCATCAGCCAATCTCTTACCC
162915 NNNNNNNNNN
Statistics
Matches: 285, Mismatches: 60, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
74 4 0.01
75 3 0.01
76 2 0.01
77 107 0.38
78 154 0.54
79 2 0.01
80 7 0.02
81 6 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (78 bp):
CGATCTCTTACCCCGAGCTTGAGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTA
GATTGTAGCCATT
Found at i:162835 original size:39 final size:39
Alignment explanation
Indices: 162593--162914 Score: 122
Period size: 39 Copynumber: 8.3 Consensus size: 39
162583 CAACCATTCG
* * * *
162593 ATCTCTTACCCTGAGCTTAGGGTAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
* * * * ** * * ** *
162632 ATCTCTTACCCCGAGCGTGGGGCAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
** *
162671 ATCTCTTACCCTAAGCCTAGGGTAGATTGCAGCCATTC-G---
1 ATCTCTTACCCCGAGCCTAGGGTA-AAT-CA-CCA-TCAGCCA
* * *
162710 ATCTCTTACCCCGAG-CTTGAGGTAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTAG-GGTAAATCACCATCAGCCA
* * * * * **
162749 ATCTCTT-CCCCGAGCTTGGGGCAGATTGTAGCCATTTG---
1 ATCTCTTACCCCGAGCCTAGGGTA-AAT-CA-CCATCAGCCA
*
162787 ATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
* **** * ** *
162826 ATCTCTTACCCCGAGCCTAGGTTAAATTGTAACCATTCG
1 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
* * * * *
162865 ATCACTTACCTCGAGTCTGGGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
162904 ATCTCTTACCC
1 ATCTCTTACCC
162915 NNNNNNNNNN
Statistics
Matches: 195, Mismatches: 71, Indels: 34
0.65 0.24 0.11
Matches are distributed among these distances:
35 2 0.01
36 8 0.04
37 3 0.02
38 22 0.11
39 151 0.77
40 2 0.01
41 4 0.02
42 2 0.01
43 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
Found at i:163065 original size:78 final size:79
Alignment explanation
Indices: 162936--163297 Score: 361
Period size: 78 Copynumber: 4.6 Consensus size: 79
162926 ACCTCGAGTC
* *
162936 TGGGGCA-AATCACCATCAGCCAATCTCTTACCCCGAG-CTTGGG-GTAGATTGCAACCATTCGA
1 TGGGGCAGAA-CACCATCAACCAATCTCTTACCCCGAGCCTAGGGCG-AGATTGCAACCATTCGA
*
162998 TCATTTACCCCAAGCT
64 TCACTTACCCCAAGCT
* *
163014 TGGGGCAGAACACCATTAACCAATCTCTTACCCCGAGCCTAGGGCGA-ATTGCAACCATTTGATC
1 TGGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAGATTGCAACCATTCGATC
* *
163078 -TTTCACCCTGAA-CT
66 ACTT-ACCC-CAAGCT
* * ** *
163092 TGAGGCA-AATCACCATCAACCAATCTCTTACCCCGAGCCTAGGG-TAGATTGCAGTCATTCAAT
1 TGGGGCAGAA-CACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAGATTGCAACCATTCGAT
*
163155 CACTTACCCTAAG-T
65 CACTTACCCCAAGCT
* * * **
163169 CTAGGGCAGATCACTATCAGTCAATCTCTTACCCCGAGCCTAGGGC-AGATTG-AAGCCATTCGA
1 -TGGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAGATTGCAA-CCATTCGA
*
163232 TCACTTACCCCAAGCC
64 TCACTTACCCCAAGCT
* * * * *
163248 TGAGGTAGATCACCATCAACCAATCTTTTACCTCGAGCCTAGGGC-AGATT
1 TGGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAGATT
163298 ACCATCAGCC
Statistics
Matches: 237, Mismatches: 33, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
77 10 0.04
78 213 0.90
79 13 0.05
80 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (79 bp):
TGGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAGATTGCAACCATTCGATC
ACTTACCCCAAGCT
Found at i:163118 original size:210 final size:199
Alignment explanation
Indices: 162735--163124 Score: 428
Period size: 210 Copynumber: 1.9 Consensus size: 199
162725 CTTGAGGTAG
* * * * *
162735 ATCACCATCAACCAATCTCTTCCCCGAGCTTGGGGCAGATTGTAGCCATTTGATCTTTTACCCCG
1 ATCACCATCAACCAATCTCTTCCCCGAGCTTGGGGCAGATTGCAACCATTCGATCATTTACCCCA
* * ** *
162800 AGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGTTAAATTGTAACCATTCG
66 AGCCTAGGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGCAACCATTCG
* * *
162865 ATCACTTACCTCGAGTCTGGGGCAAATCACCATCAGCCAATCTCTTACCCNNNNNNNNNNTACCT
131 ATCACTTACCTCGACTCTGAGGCAAATCACCATCAACCAATCTCTTACCC----------TACCT
162930 CGAGTCTGGGGCAA
186 CGAGTCTGGGGCAA
* *
162944 ATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCGATCATTTACCCC
1 ATCACCATCAACCAATCTCTT-CCCCGAGCTTGGGGCAGATTGCAACCATTCGATCATTTACCCC
* * * *
163009 AAGCTTGGGGCAGAA-CACCATTAACCAATCTCTTACCCCGAGCCTAGGGCGAATTGCAACCATT
65 AAGCCTAGGGCA-AATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGCAACCATT
* *
163073 TGATC-TTTCACC-CTGAACT-TGAGGCAAATCACCATCAACCAATCTCTTACCC
129 CGATCACTT-ACCTC-G-ACTCTGAGGCAAATCACCATCAACCAATCTCTTACCC
163125 CGAGCCTAGG
Statistics
Matches: 155, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
209 23 0.15
210 128 0.83
211 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.24
Consensus pattern (199 bp):
ATCACCATCAACCAATCTCTTCCCCGAGCTTGGGGCAGATTGCAACCATTCGATCATTTACCCCA
AGCCTAGGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGCAACCATTCG
ATCACTTACCTCGACTCTGAGGCAAATCACCATCAACCAATCTCTTACCCTACCTCGAGTCTGGG
GCAA
Found at i:163173 original size:39 final size:39
Alignment explanation
Indices: 163112--163346 Score: 154
Period size: 39 Copynumber: 6.0 Consensus size: 39
163102 CACCATCAAC
* *
163112 CAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGTCATT
1 CAATCACTTACCCCGAGCCTAGGGCAGATTGCAGTCATT
** * ** *
163151 CAATCACTTACCCTAAGTCTAGGGCAGATCACTA-TCAGT
1 CAATCACTTACCCCGAGCCTAGGGCAGATTGC-AGTCATT
* * *
163190 CAATCTCTTACCCCGAGCCTAGGGCAGATTGAAGCCATT
1 CAATCACTTACCCCGAGCCTAGGGCAGATTGCAGTCATT
* * * ** **
163229 CGATCACTTACCCCAAGCCT-GAGGTAGATCACCA-TCAAC
1 CAATCACTTACCCCGAGCCTAG-GGCAGAT-TGCAGTCATT
** * * **
163268 CAATCTTTTACCTCGAGCCTAGGGCAGATTACCA-TCAGC
1 CAATCACTTACCCCGAGCCTAGGGCAGATT-GCAGTCATT
* * * *
163307 CAATCTCTTACCTCGAGCCTAGGGCAGATTACAGCCATT
1 CAATCACTTACCCCGAGCCTAGGGCAGATTGCAGTCATT
163346 C
1 C
163347 GATCTTTTAC
Statistics
Matches: 149, Mismatches: 40, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
38 4 0.03
39 142 0.95
40 3 0.02
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (39 bp):
CAATCACTTACCCCGAGCCTAGGGCAGATTGCAGTCATT
Found at i:163196 original size:288 final size:277
Alignment explanation
Indices: 162671--163202 Score: 622
Period size: 288 Copynumber: 1.9 Consensus size: 277
162661 CAACCATTCG
* * * *
162671 ATCTCTTACCCTAAGCCTAGGGTAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGAGGTAGA
1 ATCTCTTACCCCAAGCCTAGGGTAGATTGCAACCATTCGATCTCTTACCCCAAGCTTGAGGCAGA
* * * * * *
162736 TCACCATCAACCAATCTCTTCCCCGAGCTTGGGGCAGATTGTAGCCATTTGATCTTTTACCCCGA
66 ACACCATCAACCAATCTCTTCCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTCACCCCGA
* * * * * *
162801 GCCTAGGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGTTAAATTGTAACCATTCGA
131 ACCTAGGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAAATTGCAACCATTCAA
* *
162866 TCACTTACCTCGAGTCTGGGGCAAATCACCATCAGCCAATCTCTTACCCNNNNNNNNNNTACCTC
196 TCACTTACCTCAAGTCTAGGGCAAATCACCATCAGCCAATCTCTTACCC----------TACCTC
162931 GAGTCTGGGGCAAATCACCATCAGCCA
251 GAGTCTGGGGCAAATCACCATCAGCCA
* * * *
162958 ATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCGATCAT-TTACCCCAAGCTTGGGGCAG
1 ATCTCTTACCCCAAGCCTAGGGTAGATTGCAACCATTCGATC-TCTTACCCCAAGCTTGAGGCAG
*
163022 AACACCATTAACCAATCTCTTACCCCGAGCCTAGGGC-GAATTGCAACCATTTGATCTTTCACCC
65 AACACCATCAACCAATCTCTT-CCCCGAGCCTAGGGCAG-ATTGCAACCATTTGATCTTTCACCC
* * * **
163086 TGAA-CTTGAGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGTCAT
128 CGAACCTAG-GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAAATTGCAACCAT
* * *
163150 TCAATCACTTACC-CTAAGTCTAGGGCAGATCACTATCAGTCAATCTCTTACCC
192 TCAATCACTTACCTC-AAGTCTAGGGCAAATCACCATCAGCCAATCTCTTACCC
163203 CGAGCCTAGG
Statistics
Matches: 209, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
287 78 0.37
288 131 0.63
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.25
Consensus pattern (277 bp):
ATCTCTTACCCCAAGCCTAGGGTAGATTGCAACCATTCGATCTCTTACCCCAAGCTTGAGGCAGA
ACACCATCAACCAATCTCTTCCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTCACCCCGA
ACCTAGGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAAATTGCAACCATTCAA
TCACTTACCTCAAGTCTAGGGCAAATCACCATCAGCCAATCTCTTACCCTACCTCGAGTCTGGGG
CAAATCACCATCAGCCA
Found at i:163228 original size:156 final size:156
Alignment explanation
Indices: 162939--163297 Score: 431
Period size: 156 Copynumber: 2.3 Consensus size: 156
162929 TCGAGTCTGG
* * * * *
162939 GGCAAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCGATCATTT
1 GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAACCATTCAATCACTT
* *
163004 ACCCCAAGCTTGGGGCAGAACACCATTAACCAATCTCTTACCCCGAGCCTAGGGCGAATTGCAAC
66 ACCCCAAGCTTAGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAATTGCAAC
* * * *
163069 CATTTGATC-TTTCACCCTGAA-CTTGA
131 CATTCGATCACTT-ACCC-CAAGCCTGA
**
163095 GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGTCATTCAATCACTT
1 GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAACCATTCAATCACTT
* * * **
163160 ACCCTAAG-TCTAGGGCAGATCACTATCAGTCAATCTCTTACCCCGAGCCTAGGGC-AGATTG-A
66 ACCCCAAGCT-TAGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGA-ATTGCA
163222 AGCCATTCGATCACTTACCCCAAGCCTGA
129 A-CCATTCGATCACTTACCCCAAGCCTGA
* * * * *
163251 GGTAGATCACCATCAACCAATCTTTTACCTCGAGCCTAGGGCAGATT
1 GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATT
163298 ACCATCAGCC
Statistics
Matches: 175, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
155 6 0.03
156 167 0.95
157 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (156 bp):
GGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAACCATTCAATCACTT
ACCCCAAGCTTAGGGCAGAACACCATCAACCAATCTCTTACCCCGAGCCTAGGGCGAATTGCAAC
CATTCGATCACTTACCCCAAGCCTGA
Found at i:163324 original size:117 final size:117
Alignment explanation
Indices: 163169--163414 Score: 327
Period size: 117 Copynumber: 2.1 Consensus size: 117
163159 TACCCTAAGT
* * *
163169 CTAGGGCAGATCACTATCAGTCAATCTCTTACCCCGAGCCTAGGGCAGATTGA-AGCCATTCGAT
1 CTAGGGCAGATTACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT-ACAGCCATTCGAT
* *
163233 CACTTACCCCAAGCCTGAGGTAGATCACCATCAACCAATCTTTTA-CCTCGAGC
65 CACTTACCCCAAGCCTGAGATAGATCACCATCAACCAATCTCTTATCC-CGAGC
*
163286 CTAGGGCAGATTACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCAGATTACAGCCATTCGATC
1 CTAGGGCAGATTACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTCGATC
** * * * * *
163351 TTTTACCTCGAGCTTGAGATAGGTCACCATCAGCCAATCTCTTATCCCGAGC
66 ACTTACCCCAAGCCTGAGATAGATCACCATCAACCAATCTCTTATCCCGAGC
163403 C-AGGGGCAGATT
1 CTA-GGGCAGATT
163415 GTAACCATCC
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
116 2 0.02
117 109 0.96
118 2 0.02
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (117 bp):
CTAGGGCAGATTACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTCGATC
ACTTACCCCAAGCCTGAGATAGATCACCATCAACCAATCTCTTATCCCGAGC
Found at i:163338 original size:21 final size:21
Alignment explanation
Indices: 163275--163338 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
163265 AACCAATCTT
163275 TTACCTCGAGCCTAGGGCAGA
1 TTACCTCGAGCCTAGGGCAGA
** **
163296 TTACCATC-AGCC-A-ATC-TC
1 TTACC-TCGAGCCTAGGGCAGA
163314 TTACCTCGAGCCTAGGGCAGA
1 TTACCTCGAGCCTAGGGCAGA
163335 TTAC
1 TTAC
163339 AGCCATTCGA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 2 0.07
18 9 0.30
19 2 0.07
20 2 0.07
21 13 0.43
22 2 0.07
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (21 bp):
TTACCTCGAGCCTAGGGCAGA
Found at i:163352 original size:78 final size:78
Alignment explanation
Indices: 163270--163414 Score: 197
Period size: 78 Copynumber: 1.9 Consensus size: 78
163260 CCATCAACCA
* *
163270 ATCTTTTACCTCGAGCCTAG-GGCAGATTACCATCAGCCAATCTCTTA-CCTCGAGCCTA-GGGC
1 ATCTTTTACCTCGAG-CTAGAGACAGATCACCATCAGCCAATCTCTTATCC-CGAGCC-AGGGGC
163332 AGATTACAGCCATTCG
63 AGATTACAGCCATTCG
* * *
163348 ATCTTTTACCTCGAGCTTGAGATAGGTCACCATCAGCCAATCTCTTATCCCGAGCCAGGGGCAGA
1 ATCTTTTACCTCGAGCTAGAGACAGATCACCATCAGCCAATCTCTTATCCCGAGCCAGGGGCAGA
163413 TT
66 TT
163415 GTAACCATCC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
77 4 0.07
78 53 0.90
79 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (78 bp):
ATCTTTTACCTCGAGCTAGAGACAGATCACCATCAGCCAATCTCTTATCCCGAGCCAGGGGCAGA
TTACAGCCATTCG
Found at i:163915 original size:17 final size:17
Alignment explanation
Indices: 163912--163953 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
163902 ATTTAAATTT
*
163912 ATTTAAACTCATTCTAA
1 ATTTAAATTCATTCTAA
* *
163929 ATTTAAATTTATTTTAA
1 ATTTAAATTCATTCTAA
163946 ATTTAAAT
1 ATTTAAAT
163954 GTAATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAAATTCATTCTAA
Found at i:165507 original size:30 final size:30
Alignment explanation
Indices: 165458--165629 Score: 184
Period size: 30 Copynumber: 5.6 Consensus size: 30
165448 AGCCCCTGTT
* *
165458 TTCTTTAAAAATCCTATTTTGACCCTCAAAC
1 TTCTTTAAAATTTC-ATTTTGACCCTCAAAC
* *
165489 TTCTTTAAAATTGCATTTTAACCCTCAAAC
1 TTCTTTAAAATTTCATTTTGACCCTCAAAC
* * *
165519 TT-TTCCAAAATTTCATTTTTGACACTCGAAC
1 TTCTT-TAAAATTTCA-TTTTGACCCTCAAAC
* ** *
165550 TTCTCTAAAATAGCATTTTGATCCCCCAAAC
1 TTCTTTAAAATTTCATTTTGA-CCCTCAAAC
*
165581 TTCTTCAAAATTTCATTTTGACCCTCAAAC
1 TTCTTTAAAATTTCATTTTGACCCTCAAAC
*
165611 TTCTCTAAAATTTCATTTT
1 TTCTTTAAAATTTCATTTT
165630 AACTTTAAAA
Statistics
Matches: 115, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
29 2 0.02
30 56 0.49
31 56 0.49
32 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (30 bp):
TTCTTTAAAATTTCATTTTGACCCTCAAAC
Found at i:165539 original size:61 final size:60
Alignment explanation
Indices: 165473--165632 Score: 223
Period size: 61 Copynumber: 2.6 Consensus size: 60
165463 TAAAAATCCT
* *
165473 ATTTTGACCCTCAAACTTCTTTAAAATTGCATTTTAACCCTCAAACTT-TTCCAAAATTTC
1 ATTTTGACCCTCAAACTTCTCTAAAATTGCATTTTAACCCCCAAACTTCTT-CAAAATTTC
* * * *
165533 ATTTTTGACACTCGAACTTCTCTAAAATAGCATTTTGATCCCCCAAACTTCTTCAAAATTTC
1 A-TTTTGACCCTCAAACTTCTCTAAAATTGCATTTT-AACCCCCAAACTTCTTCAAAATTTC
*
165595 ATTTTGACCCTCAAACTTCTCTAAAATTTCATTTTAAC
1 ATTTTGACCCTCAAACTTCTCTAAAATTGCATTTTAAC
165633 TTTAAAATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
60 3 0.03
61 60 0.70
62 21 0.24
63 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (60 bp):
ATTTTGACCCTCAAACTTCTCTAAAATTGCATTTTAACCCCCAAACTTCTTCAAAATTTC
Found at i:165698 original size:80 final size:81
Alignment explanation
Indices: 165555--165771 Score: 210
Period size: 80 Copynumber: 2.6 Consensus size: 81
165545 CGAACTTCTC
* * *
165555 TAAAA-TAGCATTTTGATCCCCCAAACTTCTTCAAAATTTCATTTTGACCCTCAAACTTCTCTAA
1 TAAAATTA-CATTTTGA-CCCCTAAACTTCTT-AAAATTACATTTTGACCCTCAAAATTCTCTAA
*
165619 AATTTCATTT-T-AAC-TT
63 AATTACATTTCTAAACTTT
*
165635 TAAAATTACATTTTGGACCCCTAAACTTCTCTAAAATTACATTTTGACACCT-AAAATTTTCTAA
1 TAAAATTACATTTT-GACCCCTAAACTTCT-TAAAATTACATTTTGAC-CCTCAAAATTCTCTAA
165699 AATTACATTTGACCCCTAAACTTT
63 AATTACATTT-----CTAAACTTT
* *
165723 TCCAAAATTACATTTTGACCCCTTAACTTTTTTAAAATTACATTTTGAC
1 T--AAAATTACATTTTGACCCCTAAAC-TTCTTAAAATTACATTTTGAC
165772 TCCCAAACAT
Statistics
Matches: 115, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
80 57 0.50
81 8 0.07
86 1 0.01
87 3 0.03
88 3 0.03
89 27 0.23
90 16 0.14
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (81 bp):
TAAAATTACATTTTGACCCCTAAACTTCTTAAAATTACATTTTGACCCTCAAAATTCTCTAAAAT
TACATTTCTAAACTTT
Found at i:165723 original size:29 final size:30
Alignment explanation
Indices: 165635--165826 Score: 207
Period size: 30 Copynumber: 6.5 Consensus size: 30
165625 ATTTTAACTT
*
165635 TAAAATTACATTTTGGACCCCTAAACTTCTC
1 TAAAATTACATTTT-GACCCCTAAACTTTTC
* *
165666 TAAAATTACATTTTGACACCTAAAATTTTC
1 TAAAATTACATTTTGACCCCTAAACTTTTC
165696 TAAAATTACA-TTTGACCCCTAAACTTTTC
1 TAAAATTACATTTTGACCCCTAAACTTTTC
* * *
165725 CAAAATTACATTTTGACCCCTTAACTTTTT
1 TAAAATTACATTTTGACCCCTAAACTTTTC
* *
165755 TAAAATTACATTTTGACTCCC-AAAC-ATCC
1 TAAAATTACATTTTGAC-CCCTAAACTTTTC
* *
165784 CAAAATTACCATTTTG-CACCC-AAA-TTTCC
1 TAAAATTA-CATTTTGAC-CCCTAAACTTTTC
*
165813 AAAAATTACATTTT
1 TAAAATTACATTTT
165827 CAACCTCAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.04
29 51 0.36
30 66 0.47
31 17 0.12
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
TAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:165730 original size:59 final size:60
Alignment explanation
Indices: 165635--165826 Score: 223
Period size: 59 Copynumber: 3.2 Consensus size: 60
165625 ATTTTAACTT
* *
165635 TAAAATTACATTTTGGACCCCTAAACTTCTCTAAAATTACATTTTGACACCTAAAATTTTC
1 TAAAATTACATTTT-GACCCCTAAACTTTTCCAAAATTACATTTTGACACCTAAAATTTTC
* * * *
165696 TAAAATTACA-TTTGACCCCTAAACTTTTCCAAAATTACATTTTGACCCCTTAACTTTTT
1 TAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGACACCTAAAATTTTC
* * * *
165755 TAAAATTACATTTTGACTCCC-AAAC-ATCCCAAAATTACCATTTTG-CACC-CAAATTTCC
1 TAAAATTACATTTTGAC-CCCTAAACTTTTCCAAAATTA-CATTTTGACACCTAAAATTTTC
*
165813 AAAAATTACATTTT
1 TAAAATTACATTTT
165827 CAACCTCAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
58 18 0.16
59 63 0.55
60 20 0.18
61 13 0.11
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
TAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGACACCTAAAATTTTC
Found at i:165867 original size:30 final size:29
Alignment explanation
Indices: 165667--165877 Score: 105
Period size: 30 Copynumber: 7.1 Consensus size: 29
165657 AAACTTCTCT
* * *
165667 AAAATTACATTTTGACACCTAAAATTTT-CT
1 AAAATTACATTTTCA-ACC-CAAATTTTCCA
* *
165697 AAAATTACA-TTTGACCCCTAAACTTTTCC-
1 AAAATTACATTTTCAACCC-AAA-TTTTCCA
* * * **
165726 AAAATTACATTTTGACCCCTTAACTTTT-TT
1 AAAATTACATTTTCAACCC--AAATTTTCCA
* * ** *
165756 AAAATTACATTTTGACTCCCAAA-CATCCC
1 AAAATTACATTTTCA-ACCCAAATTTTCCA
165785 AAAATTACCATTTTGC-ACCCAAA-TTTCCA
1 AAAATTA-CATTTT-CAACCCAAATTTTCCA
165814 AAAATTACATTTTCAACCTCAAATTTTCCA
1 AAAATTACATTTTCAACC-CAAATTTTCCA
* *
165844 AAAGTTTCGATTTT-AATCCCAAATTTTCCA
1 AAAATTAC-ATTTTCAA-CCCAAATTTTCCA
165874 AAAA
1 AAAA
165878 ATTCAATTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.01
28 15 0.10
29 47 0.32
30 72 0.49
31 13 0.09
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTCAACCCAAATTTTCCA
Found at i:165887 original size:30 final size:30
Alignment explanation
Indices: 165801--165887 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
165791 ACCATTTTGC
165801 ACCCAAA-TTTCC-AAAAATT-ACATTTTCA
1 ACCCAAATTTTCCAAAAAATTCA-ATTTTCA
** *
165829 ACCTCAAATTTTCCAAAAGTTTCGATTTT-A
1 ACC-CAAATTTTCCAAAAAATTCAATTTTCA
165859 ATCCCAAATTTTCCAAAAAATTCAATTTT
1 A-CCCAAATTTTCCAAAAAATTCAATTTT
165888 GACCCCCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 3 0.06
29 4 0.08
30 29 0.60
31 12 0.25
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (30 bp):
ACCCAAATTTTCCAAAAAATTCAATTTTCA
Found at i:171055 original size:17 final size:18
Alignment explanation
Indices: 171027--171061 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
171017 GCTGACCATT
171027 GACCGCTCCTCTCCCCGA
1 GACCGCTCCTCTCCCCGA
*
171045 GACCG-TCCTCTGCCCGA
1 GACCGCTCCTCTCCCCGA
171062 AGCAACCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.11, C:0.51, G:0.20, T:0.17
Consensus pattern (18 bp):
GACCGCTCCTCTCCCCGA
Found at i:173132 original size:29 final size:28
Alignment explanation
Indices: 173092--173190 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 28
173082 AAACTGTCCA
*
173092 AAAATTA-TATTTTGACCTCAAAACTTTC
1 AAAATTACCATTTT-ACCTCAAAACTTTC
* *
173120 AAAATTACCATTTTACCCTCGAAACTTCTA
1 AAAATTACCATTTTA-CCTCAAAACTT-TC
* *
173150 AAAATTACCATTTTACCCCTAAACTTTC
1 AAAATTACCATTTTACCTCAAAACTTTC
173178 AAAATT-CCATTTT
1 AAAATTACCATTTT
173191 TGACCCTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 7 0.11
28 15 0.24
29 24 0.39
30 16 0.26
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAATTACCATTTTACCTCAAAACTTTC
Found at i:173156 original size:30 final size:29
Alignment explanation
Indices: 173078--173225 Score: 105
Period size: 30 Copynumber: 5.1 Consensus size: 29
173068 CCCTGGAGGT
* *
173078 CCCT-AAACTGTCCAAAAATTA-TATTTTGA
1 CCCTCAAACT-TCTAAAAATTACCATTTT-A
*
173107 -CCTCAAAACTT-TCAAAATTACCATTTTA
1 CCCTC-AAACTTCTAAAAATTACCATTTTA
173135 CCCTCGAAACTTCTAAAAATTACCATTTTA
1 CCCTC-AAACTTCTAAAAATTACCATTTTA
*
173165 CCC-CTAAACTT-TCAAAATT-CCATTTTTGA
1 CCCTC-AAACTTCTAAAAATTACCA-TTTT-A
** *
173194 CCCT-AAAAATCTCAAAAATTACCTTTTTA
1 CCCTCAAACTTCT-AAAAATTACCATTTTA
173223 CCC
1 CCC
173226 CCAGATGTCC
Statistics
Matches: 97, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.03
28 26 0.27
29 32 0.33
30 34 0.35
31 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTCAAACTTCTAAAAATTACCATTTTA
Found at i:173177 original size:58 final size:58
Alignment explanation
Indices: 173090--173226 Score: 156
Period size: 58 Copynumber: 2.4 Consensus size: 58
173080 CTAAACTGTC
* * * **
173090 CAAAAATTA-TATTTTGACCTCAAAACTTTCAAAATTACCA-TTTT-ACCCTCGAAA-CTT
1 CAAAAATTACCATTTT-ACCCCTAAACTTTCAAAATT-CCATTTTTGACCCTAAAAATC-T
173147 CTAAAAATTACCATTTTACCCCTAAACTTTCAAAATTCCATTTTTGACCCTAAAAATCT
1 C-AAAAATTACCATTTTACCCCTAAACTTTCAAAATTCCATTTTTGACCCTAAAAATCT
*
173206 CAAAAATTACCTTTTTACCCC
1 CAAAAATTACCATTTTACCCC
173227 CAGATGTCCA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
57 4 0.06
58 49 0.71
59 15 0.22
60 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCAAAATTCCATTTTTGACCCTAAAAATCT
Found at i:173196 original size:29 final size:28
Alignment explanation
Indices: 173112--173226 Score: 117
Period size: 30 Copynumber: 4.0 Consensus size: 28
173102 TTTGACCTCA
*
173112 AAACTTTCAAAATTACCATTTTACCCTCG
1 AAACTTTCAAAATTACCATTTTACCC-CT
*
173141 AAACTTCTAAAAATTACCATTTTACCCCT
1 AAACTT-TCAAAATTACCATTTTACCCCT
173170 AAACTTTCAAAATT-CCATTTTTGA-CCCT
1 AAACTTTCAAAATTACCA-TTTT-ACCCCT
* * *
173198 AAAAATCTCAAAAATTACCTTTTTACCCC
1 -AAACTTTC-AAAATTACCATTTTACCCC
173227 CAGATGTCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
27 3 0.04
28 15 0.21
29 21 0.29
30 32 0.44
31 2 0.03
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (28 bp):
AAACTTTCAAAATTACCATTTTACCCCT
Found at i:179051 original size:18 final size:18
Alignment explanation
Indices: 179016--179059 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
179006 AATAAAAATA
179016 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
179035 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
*
179053 AAAAAAT
1 AATAAAT
179060 GAAGAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:184574 original size:18 final size:19
Alignment explanation
Indices: 184539--184577 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
184529 AATAAAAATA
184539 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
184558 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
184576 AA
1 AA
184578 AAAAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:185937 original size:18 final size:18
Alignment explanation
Indices: 185914--185950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
185904 ACAATTCATA
185914 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
185932 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
185950 T
1 T
185951 TGATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:194437 original size:17 final size:16
Alignment explanation
Indices: 194406--194439 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
194396 TTTTTTTTTA
*
194406 TTTTCTTTACGATGTT
1 TTTTCATTACGATGTT
194422 TTTTCATTATCGATGTT
1 TTTTCATTA-CGATGTT
194439 T
1 T
194440 AAATTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTTCATTACGATGTT
Found at i:200035 original size:20 final size:21
Alignment explanation
Indices: 200012--200050 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
200002 TTTTTGATAA
200012 AAAAAATTAATA-ATATTTCT
1 AAAAAATTAATATATATTTCT
* *
200032 AAAATATTTATATATATTT
1 AAAAAATTAATATATATTT
200051 TTAATATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAAATTAATATATATTTCT
Found at i:200838 original size:2 final size:2
Alignment explanation
Indices: 200831--200857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
200821 ATAATACTTT
200831 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
200858 TTGATAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:204483 original size:23 final size:23
Alignment explanation
Indices: 204457--204501 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
204447 ATGATATTAA
204457 AATACAATAAGAATATGTTATAC
1 AATACAATAAGAATATGTTATAC
* * *
204480 AATATAATATGTATATGTTATA
1 AATACAATAAGAATATGTTATA
204502 GAAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (23 bp):
AATACAATAAGAATATGTTATAC
Found at i:206472 original size:62 final size:62
Alignment explanation
Indices: 206406--206542 Score: 206
Period size: 62 Copynumber: 2.2 Consensus size: 62
206396 TTAATATAAA
* *
206406 AATAATTATATTAAGA-ATGCTATTAAATTATTTATTTTTATTTTTATTAAATT-ATATTTAAT
1 AATAATTATATTAAAACATG--ATTAAATTATTTATTATTATTTTTATTAAATTAATATTTAAT
*
206468 AATAATTATACTAAAACATGATTAAATTATTTATTATTATTTTTATTAAATTAATATTTAAT
1 AATAATTATATTAAAACATGATTAAATTATTTATTATTATTTTTATTAAATTAATATTTAAT
*
206530 AATAATCATATTA
1 AATAATTATATTA
206543 TATTATAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
61 31 0.46
62 34 0.50
63 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (62 bp):
AATAATTATATTAAAACATGATTAAATTATTTATTATTATTTTTATTAAATTAATATTTAAT
Found at i:207229 original size:22 final size:20
Alignment explanation
Indices: 207219--207272 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 20
207209 TCTATAAATT
207219 ATTCAAATATTATTATTAAA
1 ATTCAAATATTATTATTAAA
*
207239 ATTCAAAT-TTA-AATTAAA
1 ATTCAAATATTATTATTAAA
207257 ATT-AAATATTATTATT
1 ATTCAAATATTATTATT
207273 TAGTAGTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.13
18 12 0.40
19 6 0.20
20 8 0.27
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTCAAATATTATTATTAAA
Found at i:209982 original size:16 final size:16
Alignment explanation
Indices: 209947--209986 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
209937 GACCCGACTC
209947 ATTTTTAT-TTATAAT
1 ATTTTTATATTATAAT
*
209962 A-TTTTATATTATATT
1 ATTTTTATATTATAAT
209977 ATTTTTATAT
1 ATTTTTATAT
209987 ATTATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATATTATAAT
Found at i:210670 original size:13 final size:14
Alignment explanation
Indices: 210647--210681 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
210637 TTAATTTTTA
210647 TTTATTAATTAAAT
1 TTTATTAATTAAAT
210661 TTTATT-ATTAAAT
1 TTTATTAATTAAAT
*
210674 TTTTTTAA
1 TTTATTAA
210682 AAAAAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTAATTAAAT
Found at i:210674 original size:18 final size:19
Alignment explanation
Indices: 210632--210674 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
210622 ATATCTTTTG
*
210632 TAAATTTAATTTTTATTTAT
1 TAAA-TTAAATTTTATTTAT
210652 T-AATTAAATTTTA-TTAT
1 TAAATTAAATTTTATTTAT
210669 TAAATT
1 TAAATT
210675 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 2 0.10
20 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATTAAATTTTATTTAT
Found at i:213325 original size:19 final size:18
Alignment explanation
Indices: 213297--213334 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
213287 TTAAGTTGTG
*
213297 TAGGGTTTAAGGTTTATTT
1 TAGGGCTTAAGGTTT-TTT
213316 TAGGGCTTAAGGTTTTTT
1 TAGGGCTTAAGGTTTTTT
213334 T
1 T
213335 GAAAGTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (18 bp):
TAGGGCTTAAGGTTTTTT
Found at i:215991 original size:21 final size:21
Alignment explanation
Indices: 215967--216010 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
215957 TGCAAGTGTG
*
215967 ATTTCTGATTTTATC-TAAGTT
1 ATTTCT-ATGTTATCTTAAGTT
*
215988 ATTTGTATGTTATCTTAAGTT
1 ATTTCTATGTTATCTTAAGTT
216009 AT
1 AT
216011 GGAATGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (21 bp):
ATTTCTATGTTATCTTAAGTT
Found at i:216815 original size:22 final size:23
Alignment explanation
Indices: 216773--216816 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
216763 TGCATGCCCA
*
216773 TTATGACTTATGTTAGCATTTTC
1 TTATGACTTATGTTAGAATTTTC
216796 TTAT-ACTTAT-TATAGAATTTT
1 TTATGACTTATGT-TAGAATTTT
216817 GAAAAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (23 bp):
TTATGACTTATGTTAGAATTTTC
Found at i:218993 original size:3 final size:3
Alignment explanation
Indices: 218985--219025 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
218975 TTTTAAGTAG
218985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
219026 CAAATATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:227909 original size:20 final size:20
Alignment explanation
Indices: 227886--227929 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
227876 GTTATATTAT
227886 TAAAAATCA-TAAAATATTTC
1 TAAAAATCATTAAAA-ATTTC
*
227906 TAAAAATTATTAAAAATTTC
1 TAAAAATCATTAAAAATTTC
227926 -AAAA
1 TAAAA
227930 TATTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATCATTAAAAATTTC
Found at i:227917 original size:30 final size:29
Alignment explanation
Indices: 227881--227956 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
227871 TCTAGGTTAT
*
227881 ATTATTAAAAATCATAAAATATTTCTAAAA
1 ATTATTAAAAAT-ATAAAATATTTCAAAAA
*
227911 ATTATTAAAAATTTCAAAATATTTCAAAAA
1 ATTATTAAAAATAT-AAAATATTTCAAAAA
*
227941 AATA-T-AAAATATAAAA
1 ATTATTAAAAATATAAAA
227957 ACCAATGTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
28 6 0.15
29 2 0.05
30 29 0.71
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTATTAAAAATATAAAATATTTCAAAAA
Found at i:228260 original size:19 final size:18
Alignment explanation
Indices: 228194--228264 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
228184 CAAACATTTT
*
228194 AAAAAGTATAAAAATATA
1 AAAAATTATAAAAATATA
* *
228212 AATAATTATTAAAAATTATTT
1 AAAAATTA-TAAAAA-TA-TA
**
228233 AAATTTTATAAAAATCATA
1 AAAAATTATAAAAAT-ATA
228252 AAAAATTATAAAA
1 AAAAATTATAAAA
228265 TAATAAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
18 6 0.15
19 19 0.47
20 9 0.22
21 6 0.15
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAAATTATAAAAATATA
Found at i:228264 original size:9 final size:9
Alignment explanation
Indices: 228193--228264 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
228183 TCAAACATTT
*
228193 TAAAAAGTA
1 TAAAAATTA
228202 TAAAAA-TA
1 TAAAAATTA
228210 TAAATAATTA
1 TAAA-AATTA
228220 TTAAAAATTA
1 -TAAAAATTA
**
228230 TTTAAATTTTA
1 --TAAAAATTA
*
228241 TAAAAATCA
1 TAAAAATTA
228250 TAAAAAATTA
1 T-AAAAATTA
228260 TAAAA
1 TAAAA
228265 TAATAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
8 6 0.12
9 19 0.37
10 15 0.29
11 12 0.23
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:228531 original size:30 final size:29
Alignment explanation
Indices: 228497--228556 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
228487 TTAAAAATTA
228497 TAAATATATAAT-TTATTAAAATAATAAAAT
1 TAAATATATAATATTA-TAAAAT-ATAAAAT
* * *
228527 TAAATTTTTATTATTATAAAATATAAAAT
1 TAAATATATAATATTATAAAATATAAAAT
228556 T
1 T
228557 TAATTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.31
30 15 0.58
31 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAATATATAATATTATAAAATATAAAAT
Found at i:228558 original size:22 final size:23
Alignment explanation
Indices: 228492--228558 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 23
228482 ATCTTTTAAA
*
228492 AATTAT-AAATATATAATTTATT
1 AATTATAAAATATAAAATTTATT
* *
228514 AAAATAATAAAAT-TAAATTTTTATT
1 --AATTATAAAATATAAA-ATTTATT
228539 -ATTATAAAATATAAAATTTA
1 AATTATAAAATATAAAATTTA
228559 ATTTCAATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
24 8 0.23
25 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTATAAAATATAAAATTTATT
Found at i:229245 original size:18 final size:18
Alignment explanation
Indices: 229219--229253 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
229209 AAATTATTAA
*
229219 GAAATTCTTTAAAATTTT
1 GAAAATCTTTAAAATTTT
*
229237 GAAAATCTTTATAATTT
1 GAAAATCTTTAAAATTT
229254 AAAATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
GAAAATCTTTAAAATTTT
Found at i:236755 original size:68 final size:68
Alignment explanation
Indices: 236677--236812 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
236667 CAGAAAGAAA
236677 AAAATATATACATGTATATCTTTGAAACTAAGCAATATCTTTCAATTATCAAAGTCGTTTATTAC
1 AAAATATATACATGTATATCTTTGAAACTAAGCAATATCTTTCAATTATCAAAGTCGTTTATTAC
236742 ATT
66 ATT
236745 AAAATATATACATGTATATCTTTGAAACTAAGCAATATCTTTCAATTATCAAAGTCGTTTATTAC
1 AAAATATATACATGTATATCTTTGAAACTAAGCAATATCTTTCAATTATCAAAGTCGTTTATTAC
236810 ATT
66 ATT
236813 TTACAAATCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (68 bp):
AAAATATATACATGTATATCTTTGAAACTAAGCAATATCTTTCAATTATCAAAGTCGTTTATTAC
ATT
Found at i:238416 original size:15 final size:16
Alignment explanation
Indices: 238393--238427 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
238383 TACGATAATT
238393 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
238409 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
238424 TTTA
1 TTTA
238428 AAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:238424 original size:18 final size:18
Alignment explanation
Indices: 238374--238424 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
238364 TGAAATTAAA
**
238374 TTATATTTTTACGATAAT
1 TTATATTTTTATAATAAT
*
238392 TTTTATTATTT-TAATAAT
1 TTATATT-TTTATAATAAT
238410 TTATATTTTTATAAT
1 TTATATTTTTATAAT
238425 TTAAAAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATTTTTATAATAAT
Done.