Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 651366
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 3
Found at i:2921 original size:62 final size:61
Alignment explanation
Indices: 2818--3084 Score: 225
Period size: 62 Copynumber: 4.3 Consensus size: 61
2808 ATGTTACATG
** ** * *
2818 TAAATAAATTATGGACTTGCAGAGGTTCGGTGGATGAGTACAAGAATCAGAATTGAAAATCGA
1 TAAATAAATTATGG-CTTTAAGAAATTTGGTGGATGAGTAC-AGAATCAAAATTGAAAATCGA
* * *
2881 TAAATAAATTATGGCTTT-TGAAATTTTGGTGGATGAGTACAGTAATCAAAATT-TAAATCAA
1 TAAATAAATTATGGCTTTAAGAAA-TTTGGTGGATGAGTACAG-AATCAAAATTGAAAATCGA
* * * * * * *
2942 TGAATAAATTATGGCTTTACAGAGATTTGGTGTACG-TTACGGAGATCAAAATTGAAAATTGA
1 TAAATAAATTATGGCTTTA-AGAAATTTGGTGGATGAGTACAGA-ATCAAAATTGAAAATCGA
** * * * * *
3004 TAAATAAATTATGGCTTTGCGAAGGTTTGGTGGATGAATACAGGAATCAAAACTAAAAATTGA
1 TAAATAAATTATGGCTTTAAGAA-ATTTGGTGGATGAGTACA-GAATCAAAATTGAAAATCGA
*
3067 TAAATAAATCATGGCTTT
1 TAAATAAATTATGGCTTT
3085 GTAGAGGCTC
Statistics
Matches: 165, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
60 1 0.01
61 42 0.25
62 67 0.41
63 53 0.32
64 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (61 bp):
TAAATAAATTATGGCTTTAAGAAATTTGGTGGATGAGTACAGAATCAAAATTGAAAATCGA
Found at i:3113 original size:63 final size:63
Alignment explanation
Indices: 2986--3106 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
2976 CGTTACGGAG
* * * * * ***
2986 ATCAAAATTGAAAATTGATAAATAAATTATGGCTTTGCGAAGGTTTGGTGGATGAATACAGGA
1 ATCAAAACTAAAAATTGATAAATAAATCATGGCTTTGAGAAGGCTCAATGGATGAATACAGGA
3049 ATCAAAACTAAAAATTGATAAATAAATCATGGCTTTGTAG-AGGCTCAATGGATGAATA
1 ATCAAAACTAAAAATTGATAAATAAATCATGGCTTTG-AGAAGGCTCAATGGATGAATA
3107 TGGGAATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 48 0.98
64 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (63 bp):
ATCAAAACTAAAAATTGATAAATAAATCATGGCTTTGAGAAGGCTCAATGGATGAATACAGGA
Found at i:8385 original size:37 final size:37
Alignment explanation
Indices: 8309--8414 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 37
8299 AGCTCAGACG
* * *
8309 AAATCTCCACAC-AAGTTATC--GTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
8343 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
8380 TAATCTCCACACGTAGTCATCGGGTCTTACTCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
8415 ATATATTTCC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 12 0.19
35 6 0.09
37 46 0.72
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:8686 original size:48 final size:48
Alignment explanation
Indices: 8560--8744 Score: 264
Period size: 48 Copynumber: 3.8 Consensus size: 48
8550 GCACATCGCC
*
8560 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTC--A
* *
8610 TATATATTTCACATT-GACCATTCAGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCAGCTTTACCACATATACATATCTCA
* * *
8658 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATTTATCA
1 TACATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCA
* *
8706 TACATTTTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCAGCTTTACCACATATA
8745 TGCATGTTCA
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
48 80 0.65
49 2 0.02
50 42 0.34
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCA
Found at i:8749 original size:98 final size:98
Alignment explanation
Indices: 8560--8743 Score: 284
Period size: 98 Copynumber: 1.9 Consensus size: 98
8550 GCACATCGCC
* *
8560 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATATCATACATATATTTCACATT
8625 GACCATTCAGCTTTACCACATATGCATATCTCA
66 GACCATTCAGCTTTACCACATATGCATATCTCA
* * *
8658 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATTTATCATACAT-T-TTTCACATT
1 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATATCATACATATATTTCACATT
*
8721 -AGCCATTCGGCTTTACCACATAT
66 GA-CCATTCAGCTTTACCACATAT
8744 ATGCATGTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 1 0.01
96 29 0.37
97 1 0.01
98 48 0.61
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (98 bp):
TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATATCATACATATATTTCACATT
GACCATTCAGCTTTACCACATATGCATATCTCA
Found at i:8793 original size:47 final size:47
Alignment explanation
Indices: 8666--8907 Score: 281
Period size: 47 Copynumber: 5.1 Consensus size: 47
8656 CATACATATT
* * * * **
8666 TCACATTAGCCATTCGGCTTTACCACATATA--CATTTATCATACATTTT
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGT-TC--ACATTCA
* * * *
8714 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * * *
8761 CCATATTGGCCATTCGGCCTTATCACACATATGCGTGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
8808 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* **
8855 TCACATTGGCCATTCGGCCTTATCTCATATATGCACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
8902 TCACAT
1 TCACAT
8908 AAAATCCTAA
Statistics
Matches: 171, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
47 134 0.78
48 31 0.18
49 2 0.01
50 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:8834 original size:22 final size:22
Alignment explanation
Indices: 8807--8878 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
8797 GCTCACATTC
8807 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
8829 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
8853 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
8876 ATC
1 ATC
8879 TCATATATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:8908 original size:25 final size:25
Alignment explanation
Indices: 8829--8908 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
8819 ATTCGGCCTT
**
8829 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCACATTCACATTC
* * *
8854 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACATTC-ACATTC
*
8876 ATCTCATATATGCACATTCACATTC
1 ATCACATATATGCACATTCACATTC
8901 ATCACATA
1 ATCACATA
8909 AAATCCTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 6 0.15
25 19 0.47
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACATTCACATTC
Found at i:12848 original size:25 final size:26
Alignment explanation
Indices: 12806--12857 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
12796 AAGGAATTCG
12806 CACACACACAGTGCCTC-TAATCATT
1 CACACACACAGTGCCTCTTAATCATT
* *
12831 CACACACATATGTG-CTCTTATTCATT
1 CACACACACA-GTGCCTCTTAATCATT
12857 C
1 C
12858 GTTATTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.31
Consensus pattern (26 bp):
CACACACACAGTGCCTCTTAATCATT
Found at i:13496 original size:40 final size:40
Alignment explanation
Indices: 13018--13489 Score: 692
Period size: 40 Copynumber: 12.0 Consensus size: 40
13008 GCCCGAATAC
* * * * *
13018 ACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
*** * *** *
13058 ATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
** *
13098 ATATCACTAGCACGAATGCTCTTTGGAACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13138 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13178 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13218 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13258 AC-TCACTAGCACGAATGCTCTTC-GAACTTAG-CCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13295 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCC-GAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
*
13334 ACGTCACTAGCACGAA-GCTCTTCGG-ACTTATCCCGG-T
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
*
13371 ACATCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
*
13410 ACGTCACTAGCACGAATGCTC-TCGGGACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
* *
13449 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
13489 A
1 A
13490 TATCACTCTC
Statistics
Matches: 398, Mismatches: 25, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
37 33 0.08
38 58 0.15
39 103 0.26
40 204 0.51
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
ACGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
Found at i:14826 original size:37 final size:37
Alignment explanation
Indices: 14767--14875 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
14757 AGCTCAGACG
* *
14767 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
14804 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
14841 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
14876 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:15137 original size:99 final size:95
Alignment explanation
Indices: 15020--15201 Score: 285
Period size: 99 Copynumber: 1.9 Consensus size: 95
15010 GCACATCGCC
15020 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATATTCACAT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT-TCTCATA-A-AT-TATTCACAT
15085 T-GACCATTCAGCTTTACCACATATGCATATCTCA
62 TAG-CCATTCAGCTTTACCACATATGCATATCTCA
* *
15119 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATTCTCATAAATTTTTCACATTAGC
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATTCTCATAAATTATTCACATTAGC
*
15184 CATTCGGCTTTACCACAT
66 CATTCAGCTTTACCACAT
15202 TATATGCATG
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
95 27 0.34
96 3 0.04
97 1 0.01
98 7 0.09
99 41 0.52
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (95 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATTCTCATAAATTATTCACATTAGC
CATTCAGCTTTACCACATATGCATATCTCA
Found at i:15183 original size:47 final size:48
Alignment explanation
Indices: 15026--15201 Score: 248
Period size: 47 Copynumber: 3.6 Consensus size: 48
15016 CGCCTACATA
*
15026 TTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATAT
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA-A-AT-T
* * * * *
15077 ATTCACATT-GACCATTCAGCTTTACCACATATGCATATCTCATACATA
1 TTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCATAAATT
15125 TTTCACATTAGCCATTCGGCTTTACCACATATACAT-TCTCATAAATT
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAAATT
15172 TTTCACATTAGCCATTCGGCTTTACCACAT
1 TTTCACATTAGCCATTCGGCTTTACCACAT
15202 TATATGCATG
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
47 39 0.35
48 31 0.28
49 3 0.03
50 1 0.01
51 38 0.34
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAAATT
Found at i:15234 original size:95 final size:93
Alignment explanation
Indices: 15036--15333 Score: 284
Period size: 95 Copynumber: 3.1 Consensus size: 93
15026 TTTCACACTA
*
15036 GCCATTCGGCTTTACCACATATACATATCTCATATATATATATTCACATTGACCATTCAGCTTTA
1 GCCATTCGGCTTTACCACATATACAT-TCTCATA-A-AT-TATTCACATTG-CCATTCGGCTTTA
* * *
15101 CCAC--ATATGCATATCTCATACATAT-TTCACATTA
61 CCACATATATGCATGT-TCAT--AT-TCATCACATTG
*
15135 GCCATTCGGCTTTACCACATATACATTCTCATAAATTTTTCACATTAGCCATTCGGCTTTACCAC
1 GCCATTCGGCTTTACCACATATACATTCTCATAAATTATTCACATT-GCCATTCGGCTTTACCAC
*
15200 ATTATATGCATGTTCATATTCACCACATTG
65 A-TATATGCATGTTCATATTCATCACATTG
* * * * * * * *
15230 GCCATTCGGCCTTATCACACATATGCGTGCTC--ACATTCA-TCACATTGGCCATTCGACCTTAT
1 GCCATTCGGCTTTA-C-CACATATACATTCTCATAAATT-ATTCACATT-GCCATTCGGCTTTAC
*
15292 CACATATATGCATGTTCACATTCATCACATTG
62 CACATATATGCATGTTCATATTCATCACATTG
15324 GCCATTCGGC
1 GCCATTCGGC
15334 CTTATCTCAT
Statistics
Matches: 173, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
94 37 0.21
95 73 0.42
96 4 0.02
97 17 0.10
98 16 0.09
99 26 0.15
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (93 bp):
GCCATTCGGCTTTACCACATATACATTCTCATAAATTATTCACATTGCCATTCGGCTTTACCACA
TATATGCATGTTCATATTCATCACATTG
Found at i:15274 original size:47 final size:47
Alignment explanation
Indices: 15174--15366 Score: 269
Period size: 47 Copynumber: 4.1 Consensus size: 47
15164 CATAAATTTT
* * * *
15174 TCACATTAGCCATTCGGCTTTACCACATTATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACA-TATATGCATGTTCACATTCA
* * * *
15222 CCACATTGGCCATTCGGCCTTATCACACATATGCGTGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
15269 TCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* **
15316 TCACATTGGCCATTCGGCCTTATCTCATATATGCACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
15363 TCAC
1 TCAC
15367 CATAAAATCC
Statistics
Matches: 128, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
47 105 0.82
48 23 0.18
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:15295 original size:22 final size:22
Alignment explanation
Indices: 15268--15339 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
15258 GCTCACATTC
15268 ATCACATTGGCCATTCGACCTT
1 ATCACATTGGCCATTCGACCTT
* *
15290 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
*
15314 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
15337 ATC
1 ATC
15340 TCATATATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
22 13 0.34
23 7 0.18
24 8 0.21
25 10 0.26
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:19755 original size:93 final size:93
Alignment explanation
Indices: 19643--19814 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
19633 CGCCCATAAG
*
19643 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
19707 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
19736 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19801 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19815 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19809 original size:46 final size:46
Alignment explanation
Indices: 19636--19811 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
19626 TGTAACCCGC
* *
19636 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
19682 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
19732 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19775 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19812 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43715 original size:28 final size:28
Alignment explanation
Indices: 43652--43774 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
43642 ATATTAAGTC
43652 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
43679 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
43707 CACACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
43735 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
43764 CGCACACTTAG
1 CGCACACTTAG
43775 CGCCAATCTC
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 22 0.26
28 46 0.55
29 16 0.19
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:47630 original size:46 final size:46
Alignment explanation
Indices: 47576--47794 Score: 203
Period size: 46 Copynumber: 4.7 Consensus size: 46
47566 ATTGTAGGCT
* *
47576 AGTGTAAGACATGTCTGGGACATGCATTGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGAGAGCC
* * * * *
47622 TGTGTAAGACCATGTCTAGGACATCGCATCGG-CATCGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGAGATGAGAGCC
* *
47670 AGTGTAAGACATGTAC-GGGACATGCATCGGCCTCGAGAAGTA-AGCC
1 AGTGTAAGACATGT-CTGGGACATGCATCGGCCACGAGATG-AGAGCC
* * * * *
47716 AGTGTAAGACATGTCTGGGACATCCATTGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGCC
*
47762 AGTGTAAGACCATGTCTGGGATATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
47795 ATCCTACTTC
Statistics
Matches: 140, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
45 2 0.01
46 68 0.49
47 41 0.29
48 28 0.20
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGCC
Found at i:51735 original size:22 final size:22
Alignment explanation
Indices: 51707--51749 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
51697 TTGGGATAGC
51707 TGAAGCCTCATGAGAAAAACTT
1 TGAAGCCTCATGAGAAAAACTT
51729 TGAAGCCTCATGAGAAAAACT
1 TGAAGCCTCATGAGAAAAACT
51750 ACCCGATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (22 bp):
TGAAGCCTCATGAGAAAAACTT
Found at i:54876 original size:46 final size:46
Alignment explanation
Indices: 54723--54972 Score: 220
Period size: 46 Copynumber: 5.4 Consensus size: 46
54713 GTTATTGTGG
* ** * **
54723 GCTAGTGTAAAACATGTCTGGGACATGCATCGGCC-ACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGA-GATGTTA
* * * * * * * *
54769 GCTTGTGTAAGACCATGTCTAGGACATGGCATTGGCATCGAAACGAGT-
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGAGATG-TTA
**
54817 GCTAGTGTAAGACATGTCCAGGACATGCATCGGCCTTGAGATGTTA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGTTA
* *
54863 GCTAGTGTAAGACATGTCTGGGAAATGCATCGGCCTTGAGACGTTA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGTTA
* * *
54909 GCTAGTGTAAGACATGTATGGGACATGCATCGG-CTACGAGATGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-TGAGATGTTA
54955 G-TCAGTGTAAGACCATGT
1 GCT-AGTGTAAGA-CATGT
54973 TTAGGATATG
Statistics
Matches: 168, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
45 4 0.02
46 112 0.67
47 31 0.18
48 20 0.12
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGTTA
Found at i:54935 original size:92 final size:94
Alignment explanation
Indices: 54723--54991 Score: 280
Period size: 92 Copynumber: 2.9 Consensus size: 94
54713 GTTATTGTGG
* * * * *
54723 GCTAGTGTAAAACATGTCTGGGACATGCATCGGCC-ACATTATGAGAGCTTGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGA-GATGATAGCTAGTGTAAGACCATGT
* *
54787 CTAGGACATGGCATTGGCATCGAAACGAGT
65 CTAGGAAATGGCATCGGCATCGAAACGAGT
** * *
54817 GCTAGTGTAAGACATGTCCAGGACATGCATCGGCCTTGAGATGTTAGCTAGTGTAAGA-CATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGATAGCTAGTGTAAGACCATGTC
* * * * *
54881 TGGGAAAT-GCATCGGCCTTGAGACG-TT
66 TAGGAAATGGCATCGGCATCGAAACGAGT
*
54908 AGCTAGTGTAAGACATGTATGGGACATGCATCGG-CTACGAGATGATAG-TCAGTGTAAGACCAT
1 -GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTA-GAGATGATAGCT-AGTGTAAGACCAT
* * *
54971 GTTTAGGATATGGCATTGGCA
63 GTCTAGGAAATGGCATCGGCA
54992 CCCTACCTCA
Statistics
Matches: 143, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
91 4 0.03
92 61 0.43
93 23 0.16
94 54 0.38
95 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGATAGCTAGTGTAAGACCATGTC
TAGGAAATGGCATCGGCATCGAAACGAGT
Found at i:57622 original size:29 final size:29
Alignment explanation
Indices: 57583--57639 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
57573 TAAGTTAGAG
*
57583 AAAATACATAATGTTTTTTATGTATCAAA
1 AAAATACATAATGTGTTTTATGTATCAAA
57612 AAAATACATAATGTGTTTTATGTATCAA
1 AAAATACATAATGTGTTTTATGTATCAA
57640 TGCTTCGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (29 bp):
AAAATACATAATGTGTTTTATGTATCAAA
Found at i:60901 original size:30 final size:30
Alignment explanation
Indices: 60867--60924 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
60857 TTTTCGAGCA
* * *
60867 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATAGTCATTTTACCAAAGTC
60897 TAGGGGCAAAATAGTCATTTTACCAAAG
1 TAGGGGCAAAATAGTCATTTTACCAAAG
60925 GTGTGAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATAGTCATTTTACCAAAGTC
Found at i:61423 original size:45 final size:47
Alignment explanation
Indices: 61261--61481 Score: 174
Period size: 50 Copynumber: 4.7 Consensus size: 47
61251 GCTATTGTGA
*
61261 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGTGACATTATG-AGA--
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GT-AC-TGA-GAAGAGT
* *
61307 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGTATTGAGAAGAGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGTACTGAGAAGAGT
* **
61354 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCG-ACT-ACGAATTGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGTACTGA-GAAGAGT
* * * * * *
61398 GTTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACAT-ATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GTAC-TGAGA--AGAGT
*
61448 GCTAGTGTAAGACCATGTCCGGGACATGGCATCG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG
61482 GCCTCAATGA
Statistics
Matches: 143, Mismatches: 19, Indels: 23
0.77 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 19 0.13
45 23 0.16
46 30 0.21
47 28 0.20
48 8 0.06
49 3 0.02
50 31 0.22
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGTACTGAGAAGAGT
Found at i:61460 original size:50 final size:50
Alignment explanation
Indices: 61259--61528 Score: 190
Period size: 46 Copynumber: 5.7 Consensus size: 50
61249 AGGCTATTGT
61259 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGTG-ACAT-TA--TGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-G-GCACATATATGTGA
* *
61305 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-G----TAT-TGAGAA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATATATGTG-A
* *
61350 GAGTGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGACTACGA-AT-TGT--
1 GA--GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-AC-ATATATGTGA
* *
61398 --GTTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACATATATGTGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATATATGTGA
* *
61446 GAGCTAGTGTAAGACCATGTCCGGGACATGGCATCGGC-C-TCA-ATGATAA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAT-ATATG-TGA
* * * *
61495 TAGCCAGTGTAAGACCATGTTTAGGACATGGCAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
61529 TGGGAACTAG
Statistics
Matches: 180, Mismatches: 19, Indels: 47
0.73 0.08 0.19
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 13 0.07
45 25 0.14
46 36 0.20
47 25 0.14
48 9 0.05
49 33 0.18
50 33 0.18
51 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (50 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATATATGTGA
Found at i:61522 original size:49 final size:50
Alignment explanation
Indices: 61401--61528 Score: 163
Period size: 49 Copynumber: 2.6 Consensus size: 50
61391 GAATTGTGTT
* *
61401 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACATATATGTGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACATATATGTAAGAGCC
** *
61451 AGTGTAAGACCATGTCCGGGACATGGCATCGGC-C-TCA-ATGATAATAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAT-ATATG-TAAGAGCC
*
61500 AGTGTAAGACCATGTTTAGGACATGGCAT
1 AGTGTAAGACCATGTTTGGGACATGGCAT
61529 TGGGAACTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 4 0.06
49 33 0.49
50 31 0.46
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCACATATATGTAAGAGCC
Found at i:68532 original size:39 final size:39
Alignment explanation
Indices: 68489--68602 Score: 174
Period size: 39 Copynumber: 2.9 Consensus size: 39
68479 CCGAACATAT
** * * *
68489 TTCCAGCATGTAGCTTGCGGACCTTAAGTCTGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
*
68528 TTCCAGGACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
68567 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
68603 CACATCAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:76153 original size:43 final size:41
Alignment explanation
Indices: 76052--76154 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
76042 AATCTAAACT
* *
76052 TGTTGAGTGGTCCAAGTTCATGATATATGAGGCATCCGAGC
1 TGTTGAGTGGTCCGAGTTCATGATAGATGAGGCATCCGAGC
** * * *
76093 TGTTGAGTGGTTTGAGTTCATTATGGATGCGAGCATCCGAGC
1 TGTTGAGTGGTCCGAGTTCATGATAGATGAG-GCATCCGAGC
76135 TCGTTGAGTGGTCCGAGTTC
1 T-GTTGAGTGGTCCGAGTTC
76155 GTAATGGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 24 0.47
42 11 0.22
43 16 0.31
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (41 bp):
TGTTGAGTGGTCCGAGTTCATGATAGATGAGGCATCCGAGC
Found at i:76162 original size:43 final size:42
Alignment explanation
Indices: 76052--76167 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 42
76042 AATCTAAACT
* * ** * *
76052 TGTTGAGTGGTCCAAGTTCATGATATATGAG-GCATCCGAGC
1 TGTTGAGTGGTCCGAGTTCATAATGGAAGCGAGCATCCGAGC
** * *
76093 TGTTGAGTGGTTTGAGTTCATTATGGATGCGAGCATCCGAGC
1 TGTTGAGTGGTCCGAGTTCATAATGGAAGCGAGCATCCGAGC
*
76135 TCGTTGAGTGGTCCGAGTTCGTAATGGAAGCGA
1 T-GTTGAGTGGTCCGAGTTCATAATGGAAGCGA
76168 TATATGTAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 24 0.39
42 11 0.18
43 26 0.43
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.30
Consensus pattern (42 bp):
TGTTGAGTGGTCCGAGTTCATAATGGAAGCGAGCATCCGAGC
Found at i:79962 original size:15 final size:16
Alignment explanation
Indices: 79942--79982 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
79932 GTATCGTATA
79942 TTGGATTTCTTC-ATC
1 TTGGATTTCTTCTATC
*
79957 TTGGATTT-TTCTGTC
1 TTGGATTTCTTCTATC
79972 TTGGATTTCTT
1 TTGGATTTCTT
79983 TATTTTGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 18 0.78
16 2 0.09
ACGTcount: A:0.10, C:0.15, G:0.17, T:0.59
Consensus pattern (16 bp):
TTGGATTTCTTCTATC
Found at i:79990 original size:15 final size:15
Alignment explanation
Indices: 79942--79990 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
79932 GTATCGTATA
*
79942 TTGGATTTCTTCATC
1 TTGGATTTCTTTATC
*
79957 TTGGATTT-TTCTGTC
1 TTGGATTTCTT-TATC
*
79972 TTGGATTTCTTTATT
1 TTGGATTTCTTTATC
79987 TTGG
1 TTGG
79991 TCTTCTTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.10, C:0.12, G:0.18, T:0.59
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:89128 original size:40 final size:40
Alignment explanation
Indices: 89044--89228 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
89034 TCGAATGATG
* *
89044 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
89083 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
89124 TCCGGGCTAAG-CCCGAAGGCATTGGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
89163 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
89202 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
89229 AAGGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:89180 original size:79 final size:81
Alignment explanation
Indices: 89044--89226 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
89034 TCGAATGATG
* *
89044 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
89108 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
89123 TTCCGGGCTAAG-CCCGAAGGCATTGGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
*
89185 TTTGTGCGAGTTGCTATA
64 TTTGTGCGAGTTACTATA
* *
89203 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
89227 TGAAGGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.67
80 29 0.32
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:89250 original size:79 final size:77
Alignment explanation
Indices: 89045--89261 Score: 199
Period size: 79 Copynumber: 2.7 Consensus size: 77
89035 CGAATGATGT
* * * * *
89045 CCGGGCTAAGTCCCGAAGGCTTTG-TGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTGAAG-TGAGTTACTATATCCGG-TTAAG-TCCGAAGGCATTT
*
89109 GTGCGAGTTACTAATT
62 GTGCGAGTTACTAATA
** *
89125 CCGGGCTAAGCCCGAAGGCATTGGTGTGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTGAAGTGAGTTACTATATCC-GGTTAAGT-CCGAAGGCATTTGT
*
89190 GCGAGTTGCT-ATAA
64 GCGAGTTACTAAT-A
* *
89204 CCGGGCTATGTCCCGAAGGCATTTGAAG-GAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCA-TTGAAGTGAGTTA-CTATATCCGGTT-AAGTCCGAAGG
89262 TACGGGATTC
Statistics
Matches: 117, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
78 3 0.03
79 73 0.62
80 37 0.32
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (77 bp):
CCGGGCTAAGCCCGAAGGCATTGAAGTGAGTTACTATATCCGGTTAAGTCCGAAGGCATTTGTGC
GAGTTACTAATA
Found at i:94642 original size:39 final size:40
Alignment explanation
Indices: 94597--94821 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
94587 GCTCCTCGTT
* * * *
94597 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
94637 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
94676 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
94716 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
94756 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
94797 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
94822 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:94690 original size:40 final size:38
Alignment explanation
Indices: 94564--94821 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 38
94554 AAATCACGTA
* * *
94564 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG
* * * *
94603 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG
*
94642 CCTTCGGGACTTAACCCGGATTTAATGACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG
*
94682 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG
* *
94722 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG
** * * * *
94762 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG
*
94802 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
94822 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.01
39 50 0.28
40 116 0.64
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (38 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG
Found at i:94830 original size:41 final size:41
Alignment explanation
Indices: 94753--94830 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
94743 CTTGTATCTC
* * *
94753 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
94794 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
94831 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:102666 original size:40 final size:39
Alignment explanation
Indices: 102506--102762 Score: 227
Period size: 40 Copynumber: 6.5 Consensus size: 39
102496 AAATCACGTA
* * * **
102506 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
102545 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
102584 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
102623 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
* *
102663 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCACAAATG
** * * *
102703 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
102743 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
102763 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 28, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
38 7 0.04
39 72 0.40
40 86 0.48
41 15 0.08
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:102771 original size:41 final size:41
Alignment explanation
Indices: 102694--102771 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
102684 CTTGTATCTC
* * *
102694 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
102735 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
102772 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:107734 original size:42 final size:43
Alignment explanation
Indices: 107688--107769 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
107678 GAATGGTCCA
*
107688 AGTTCATGATATATGAG-GCATCCAAGCTCATTGAGTGGTTCG
1 AGTTCATGATAGATGAGAGCATCCAAGCTCATTGAGTGGTTCG
* * ** *
107730 AGTTCATTATGGATGAGAGCATCGGAGCTCGTTGAGTGGT
1 AGTTCATGATAGATGAGAGCATCCAAGCTCATTGAGTGGT
107770 CTAAGTTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 14 0.42
43 19 0.58
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (43 bp):
AGTTCATGATAGATGAGAGCATCCAAGCTCATTGAGTGGTTCG
Found at i:107830 original size:51 final size:51
Alignment explanation
Indices: 107749--107848 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
107739 TGGATGAGAG
* *
107749 CATCGGAGCTCGTTGAGTGGTCTAAGTTCATAATGGATGCGATACATGTAA
1 CATCCGAGCTCGTTGAGAGGTCTAAGTTCATAATGGATGCGATACATGTAA
* * * *
107800 CATCCGAGCTCGTTGAGAGGTCTGAGTTCATTATGGATGTGTTACATGT
1 CATCCGAGCTCGTTGAGAGGTCTAAGTTCATAATGGATGCGATACATGT
107849 TATAAGGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGAGGTCTAAGTTCATAATGGATGCGATACATGTAA
Found at i:108096 original size:6 final size:6
Alignment explanation
Indices: 108085--108116 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
108075 AGGTATATTC
*
108085 ATGTAT ATGTAT ATGTAT ATGTAT ATGAAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
108117 TTGATTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (6 bp):
ATGTAT
Found at i:113908 original size:48 final size:48
Alignment explanation
Indices: 113846--114270 Score: 787
Period size: 48 Copynumber: 8.9 Consensus size: 48
113836 TATATATGTG
* * *
113846 TGTGGTAAATCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
113894 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
113942 TGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
113990 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
114038 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
114086 TGTGGTAAAGGCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
114134 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
114182 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
114230 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
114271 GTGTGTATAT
Statistics
Matches: 367, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 367 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:114461 original size:37 final size:37
Alignment explanation
Indices: 114411--114513 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
114401 GTAAATATAT
*
114411 TCCGGGCAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
114448 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
114485 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
114514 GGACTATTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:119261 original size:47 final size:44
Alignment explanation
Indices: 119192--119450 Score: 207
Period size: 47 Copynumber: 5.5 Consensus size: 44
119182 GATTTGTGCT
*
119192 CCAGTGTAAGACATGTCTGGGACATGCTTCGGTCACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GTCACA-TATGAGAG
* * *
119238 CCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CATCCAAACGAGGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATC-GTCA--CATATGAGAG
* ** * *
119286 CTAGTGTAAGACATGTCTAAGACATGCATCATCCACACTATGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGT-CACA-TATGAGAG
* * *
119332 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGTCACAGAGATGAGTG
1 CCAGTGTAA-GACATGTCTGGGACAT-GCATCGTCAC--ATATGAGAG
* * *
119380 CCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGATA-GAGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GTCAC-ATATGAG--AG
*
119427 CCAGTGTAAGACGTGTCTGGGACA
1 CCAGTGTAAGACATGTCTGGGACA
119451 CACATCAGCA
Statistics
Matches: 170, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
45 5 0.03
46 36 0.21
47 86 0.51
48 40 0.24
49 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (44 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGTCACATATGAGAG
Found at i:119355 original size:94 final size:94
Alignment explanation
Indices: 119192--119410 Score: 284
Period size: 94 Copynumber: 2.3 Consensus size: 94
119182 GATTTGTGCT
* * * *
119192 CCAGTGTAAGACATGTCTGGGACATGCTTCGGTCACATTATGAGAGCCAGTGTAAGACCATGTCT
1 CCAGTGTAAGACATGTCTAGGACATGCATCGATCACACTATGAGAGCCAGTGTAAGACCATGTCT
119257 GGGACATGGCATCAG-CATCCA-A-ACGAGGG
66 GGGACATGGCATC-GTCA--CAGAGACGAGGG
* * * *
119286 CTAGTGTAAGACATGTCTAAGACATGCATC-ATCCACACTATGATAGCCAGTGTAAGGCCATGTC
1 CCAGTGTAAGACATGTCTAGGACATGCATCGAT-CACACTATGAGAGCCAGTGTAAGACCATGTC
* *
119350 TGGGACATGGCATCGTCACAGAGATGAGTG
65 TGGGACATGGCATCGTCACAGAGACGAGGG
119380 CCAGTGTAAGACATGTCTAGGACATGCATCG
1 CCAGTGTAAGACATGTCTAGGACATGCATCG
119411 GCCTCGATAG
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
92 2 0.02
93 3 0.03
94 103 0.95
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (94 bp):
CCAGTGTAAGACATGTCTAGGACATGCATCGATCACACTATGAGAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGTCACAGAGACGAGGG
Found at i:119444 original size:94 final size:93
Alignment explanation
Indices: 119192--119450 Score: 278
Period size: 94 Copynumber: 2.8 Consensus size: 93
119182 GATTTGTGCT
* * * *
119192 CCAGTGTAAGACATGTCTGGGACATGCTTCGGTCACATTATGAG--AGCCAGTGTAAGACCATGT
1 CCAGTGTAAGACATGTCTAGGACATGCATCGGCCACACTA-GAGATAGCCAGTGTAAGA-CATGT
119255 CTGGGACATGGCATCAGCATCCAAACGAGGG
64 CTGGGACATGGCATCAGCA-CCAAACGAGGG
* * ** * *
119286 CTAGTGTAAGACATGTCTAAGACATGCATCATCCACACTA-TGATAGCCAGTGTAAGGCCATGTC
1 CCAGTGTAAGACATGTCTAGGACATGCATCGGCCACACTAGAGATAGCCAGTGTAA-GACATGTC
* *
119350 TGGGACATGGCATC-GTCA-CAGAGATGAGTG
65 TGGGACATGGCATCAG-CACCA-A-ACGAGGG
* *
119380 CCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-TAGAGATAGCCAGTGTAAGACGTGTC
1 CCAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ACTAGAGATAGCCAGTGTAAGACATGTC
119444 TGGGACA
65 TGGGACA
119451 CACATCAGCA
Statistics
Matches: 137, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
92 3 0.02
93 2 0.01
94 116 0.85
95 16 0.12
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (93 bp):
CCAGTGTAAGACATGTCTAGGACATGCATCGGCCACACTAGAGATAGCCAGTGTAAGACATGTCT
GGGACATGGCATCAGCACCAAACGAGGG
Found at i:119457 original size:141 final size:141
Alignment explanation
Indices: 119192--119507 Score: 311
Period size: 141 Copynumber: 2.2 Consensus size: 141
119182 GATTTGTGCT
* * **
119192 CCAGTGTAA-GACATGTCTGGGACAT-GCTTCGGTCACATTATGAGAGCCAGTGTAAGACCATGT
1 CCAGTGTAAGGCCATGTCTGGGACATGGCATC-GTCACAAGATGAGAGCCAGTGTAAGACCATGT
* * * **
119255 CTGGGACATGGCATCAGCATCCAAACGAGGGCTAGTGTAAGACATGTCTAAGACATGCATCATCC
65 CTAGGACATGGCATCAGCATCCAAACGAGAGCCAGTGTAAGACATGTCTAAGACACACATCA-CC
*
119320 ACAC-TATGATAG
129 ACACATATGAGAG
*
119332 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGTCACAGAGATGAGTGCCAGTGTAAGA-CATGT
1 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGTCACA-AGATGAGAGCCAGTGTAAGACCATGT
* * * * * ** *
119396 CTAGGACAT-GCATCGGCCTCGATAGA-GATAGCCAGTGTAAGACGTGTCTGGGACACACATCAG
65 CTAGGACATGGCATCAGCATCCA-A-ACGAGAGCCAGTGTAAGACATGTCTAAGACACACATCAC
*
119459 CACGCGTATATGAGAG
128 CACAC--ATATGAGAG
** * *
119475 CCAAAGTAAGACCATGTCTGGGATATGGCATCG
1 CCAGTGTAAGGCCATGTCTGGGACATGGCATCG
119508 ACAATATATC
Statistics
Matches: 144, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
140 23 0.16
141 63 0.44
142 22 0.15
143 36 0.25
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (141 bp):
CCAGTGTAAGGCCATGTCTGGGACATGGCATCGTCACAAGATGAGAGCCAGTGTAAGACCATGTC
TAGGACATGGCATCAGCATCCAAACGAGAGCCAGTGTAAGACATGTCTAAGACACACATCACCAC
ACATATGAGAG
Found at i:123369 original size:46 final size:46
Alignment explanation
Indices: 123302--123430 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
123292 TGTAACCCGC
* * * *
123302 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
123348 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
123394 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
123431 TGCCCAAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:123973 original size:23 final size:23
Alignment explanation
Indices: 123943--123989 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
123933 TAACAAAGAA
123943 ATTCATTATAATATTTCTCACTT
1 ATTCATTATAATATTTCTCACTT
123966 ATTCATTATAATATTTCTCACTT
1 ATTCATTATAATATTTCTCACTT
123989 A
1 A
123990 CTAATACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTCATTATAATATTTCTCACTT
Found at i:124302 original size:19 final size:19
Alignment explanation
Indices: 124278--124366 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
124268 GAATAAATTA
*
124278 CTCATCTTAGTTAATTGAG
1 CTCATCTTAGTTAATTAAG
124297 CTCATCTTAGTTAATTAAG
1 CTCATCTTAGTTAATTAAG
* * *
124316 -T--TGCTGGAATAAATT-A-
1 CTCAT-CT-TAGTTAATTAAG
124332 CTCATCTTAGTTAATTAAG
1 CTCATCTTAGTTAATTAAG
*
124351 TTCATCTTAGTTAATT
1 CTCATCTTAGTTAATT
124367 TGGTTGCTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
16 1 0.02
17 10 0.18
18 10 0.18
19 34 0.62
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (19 bp):
CTCATCTTAGTTAATTAAG
Found at i:124315 original size:54 final size:54
Alignment explanation
Indices: 124253--124381 Score: 222
Period size: 54 Copynumber: 2.4 Consensus size: 54
124243 TGTAGTTTAA
*
124253 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGCTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGCTCATCTTAG
*
124307 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGCTCATCTTAG
**
124361 TTAATTTGGTTGCTGGAATAA
1 TTAATTAAGTTGCTGGAATAA
124382 CTTAGTGTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (54 bp):
TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGCTCATCTTAG
Found at i:132565 original size:50 final size:50
Alignment explanation
Indices: 132495--132596 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
132485 TGTTACATAT
* * *
132495 ATGGTTGTTACTAAGTGATTAATGAAGCTATTCAAGTTGGGATTGGTTAC
1 ATGGCTGTTACAAAGTGATTAATGAAGCTACTCAAGTTGGGATTGGTTAC
* *
132545 ATGGCTGTTACAAAGTGATTAATGTAGCTACTCATGTTGGGATTGGTTAC
1 ATGGCTGTTACAAAGTGATTAATGAAGCTACTCAAGTTGGGATTGGTTAC
132595 AT
1 AT
132597 ACAAGGGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (50 bp):
ATGGCTGTTACAAAGTGATTAATGAAGCTACTCAAGTTGGGATTGGTTAC
Found at i:133462 original size:53 final size:54
Alignment explanation
Indices: 133395--133696 Score: 328
Period size: 55 Copynumber: 5.6 Consensus size: 54
133385 TTACCATTTT
* *
133395 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCA-CTAATGC
1 CATGACTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATC-AATGC
* * *
133448 CATGACTTGGCATGGTCTTACATGGGA-CCTTTGTCTTATAGTAACTCATCAATGC
1 CATGACTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AACTCATCAATGC
* *
133503 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGC
1 CATGACTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAATGC
* * *
133556 CATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAATGC
1 CATGACTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AACTCATCAATGC
* * * * * *
133611 CAT-ATCTTGAAATGGTCTTAAATGATTTCCTTGCCTTATAGAATTTATCAATGC
1 CATGA-CTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAATGC
* * * *
133665 TATGCCTTGGCATGGTCTTACATGATATCCTT
1 CATGACTTGACATGGTCTTACATGGTATCCTT
133697 ATCTTACCAA
Statistics
Matches: 209, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.02
53 76 0.36
54 39 0.19
55 85 0.41
56 5 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (54 bp):
CATGACTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAATGC
Found at i:133584 original size:108 final size:108
Alignment explanation
Indices: 133395--133688 Score: 462
Period size: 108 Copynumber: 2.7 Consensus size: 108
133385 TTACCATTTT
* * *
133395 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACTAATGCCATGACTTGGCA
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
*
133460 TGGTCTTACATGGGACCTTTGTCTTATAGTAACTCATCAATGC
66 TGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGC
133503 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
133568 TGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGC
66 TGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGC
* * * * * * * * *
133611 CATATCTTGAAATGGTCTTAAATGATTTCCTTGCCTTATAGAATTTATCAATGCTATGCCTTGGC
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTTGGC
133676 ATGGTCTTACATG
65 ATGGTCTTACATG
133689 ATATCCTTAT
Statistics
Matches: 172, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 138 0.80
109 34 0.20
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (108 bp):
CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
TGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGC
Found at i:137941 original size:33 final size:33
Alignment explanation
Indices: 137899--137984 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
137889 GACTACTTTG
137899 TAGGGCTTAGGCCCAGACTGC-TCTATTACTGTA
1 TAGGGCTTAGGCCCAGACTGCAT-TATTACTGTA
*
137932 TAGGGCTTAGGCCCAGACTGCATTGTTACTGTA
1 TAGGGCTTAGGCCCAGACTGCATTATTACTGTA
*
137965 TAGGGCTAAGGCCCAGACTG
1 TAGGGCTTAGGCCCAGACTG
137985 TCTTTGTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (33 bp):
TAGGGCTTAGGCCCAGACTGCATTATTACTGTA
Found at i:137997 original size:33 final size:33
Alignment explanation
Indices: 137899--137999 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
137889 GACTACTTTG
* *
137899 TAGGGCTTAGGCCCAGACTGCTCTAT-TACTGTA
1 TAGGGCTTAGGCCCAGACTG-TCTTTGTTCTGTA
*
137932 TAGGGCTTAGGCCCAGACTG-CATTGTTACTGTA
1 TAGGGCTTAGGCCCAGACTGTCTTTGTT-CTGTA
*
137965 TAGGGCTAAGGCCCAGACTGTCTTTGTTCTGTA
1 TAGGGCTTAGGCCCAGACTGTCTTTGTTCTGTA
137998 TA
1 TA
138000 TTGACTGTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
31 2 0.03
32 1 0.02
33 51 0.85
34 6 0.10
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.32
Consensus pattern (33 bp):
TAGGGCTTAGGCCCAGACTGTCTTTGTTCTGTA
Found at i:144847 original size:40 final size:40
Alignment explanation
Indices: 144646--144847 Score: 175
Period size: 40 Copynumber: 5.1 Consensus size: 40
144636 CGGAATTTAA
** * *
144646 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
144686 CCGGTTATAGTAACTCGCACAAATGCCTTCGAGAC--AAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * * * *
144724 CCAGATTTAGTGACTTGCACCAATGCCTTCAGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
144763 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
144803 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
144843 CCGGA
1 CCGGA
144848 CATTATTCGA
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
37 1 0.01
38 29 0.22
39 27 0.21
40 60 0.47
41 12 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:155126 original size:33 final size:33
Alignment explanation
Indices: 155075--155160 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
155065 GACTACTGTG
* ** *
155075 TAGGGCTTAAGCTTAGACTGC-TCTGTTTCTATA
1 TAGGGCTTAGGCCCAGACTGCAT-TGTTACTATA
*
155108 TAGGGCTTAGGCCCAGACTGCATTGTTACTGTA
1 TAGGGCTTAGGCCCAGACTGCATTGTTACTATA
*
155141 TAGGGCTAAGGCCCAGACTG
1 TAGGGCTTAGGCCCAGACTG
155161 TCTATGTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (33 bp):
TAGGGCTTAGGCCCAGACTGCATTGTTACTATA
Found at i:155173 original size:33 final size:32
Alignment explanation
Indices: 155101--155175 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
155091 ACTGCTCTGT
* *
155101 TTCTATATAGGGCTTAGGCCCAGACTGCATTG
1 TTCTGTATAGGGCTAAGGCCCAGACTGCATTG
155133 TTACTGTATAGGGCTAAGGCCCAGACTGTC-TATG
1 TT-CTGTATAGGGCTAAGGCCCAGACTG-CAT-TG
155167 TTCTGTATA
1 TTCTGTATA
155176 TTGATTGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 2 0.05
33 31 0.82
34 5 0.13
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (32 bp):
TTCTGTATAGGGCTAAGGCCCAGACTGCATTG
Found at i:156488 original size:53 final size:54
Alignment explanation
Indices: 156404--156530 Score: 184
Period size: 53 Copynumber: 2.4 Consensus size: 54
156394 GTAGTTTAAT
*
156404 TAATTAAGTTGCTGGAATAAATTACTCATCTTAGACAATTGAGTTCATCTTAGA
1 TAATTAAGTTGCTGGAATAAATTACTCATCTTAGACAATTAAGTTCATCTTAGA
* ** * *
156458 TAA-TAAGTTGCTAGAATAAATTACTCATCTTAGTTAATTAATTTCATCTTAGT
1 TAATTAAGTTGCTGGAATAAATTACTCATCTTAGACAATTAAGTTCATCTTAGA
*
156511 TAATTTAGTTGCTGGAATAA
1 TAATTAAGTTGCTGGAATAA
156531 CTTAGTGTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 47 0.73
54 17 0.27
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (54 bp):
TAATTAAGTTGCTGGAATAAATTACTCATCTTAGACAATTAAGTTCATCTTAGA
Found at i:157804 original size:20 final size:21
Alignment explanation
Indices: 157781--157831 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
157771 GAGGCACCGT
157781 AGTGTAAACAGAA-ACACTGA
1 AGTGTAAACAGAAGACACTGA
*
157801 AGTGT-AACA-AAGCCACTGA
1 AGTGTAAACAGAAGACACTGA
*
157820 AGTGCAAACAGA
1 AGTGTAAACAGA
157832 GGCATTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 9 0.35
21 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (21 bp):
AGTGTAAACAGAAGACACTGA
Found at i:159969 original size:13 final size:13
Alignment explanation
Indices: 159951--159975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
159941 TAATAATTTT
159951 CATTCAATTAAAC
1 CATTCAATTAAAC
159964 CATTCAATTAAA
1 CATTCAATTAAA
159976 TTAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
CATTCAATTAAAC
Found at i:160245 original size:14 final size:14
Alignment explanation
Indices: 160228--160259 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
160218 CAAAAATCAC
160228 TTAACAAAATGAGT
1 TTAACAAAATGAGT
160242 TTAACAAAATGAGT
1 TTAACAAAATGAGT
160256 TTAA
1 TTAA
160260 AATTCTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (14 bp):
TTAACAAAATGAGT
Found at i:167790 original size:26 final size:26
Alignment explanation
Indices: 167761--167812 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
167751 ACCAATGAAA
*
167761 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
*
167787 TCGGGGAATCAGCACATAGCATCCCC
1 TCGGGGAATCAGCACATAGCAACCCC
167813 CTTTCACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:167793 original size:104 final size:103
Alignment explanation
Indices: 167521--167890 Score: 573
Period size: 103 Copynumber: 3.6 Consensus size: 103
167511 TAGCCGTTAT
** * *
167521 TGGTGGATCCCGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
167586 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
*
167624 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGTACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
167689 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
167728 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
* *
167792 GAATCAGCACATAGCATCCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
167832 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
167891 TTTATATACA
Statistics
Matches: 249, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
103 111 0.45
104 108 0.43
105 30 0.12
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:168657 original size:27 final size:27
Alignment explanation
Indices: 168627--168718 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
168617 GGGCTGTTAC
168627 ATGACTGTTTTGCCCTTATGTGGTAAA
1 ATGACTGTTTTGCCCTTATGTGGTAAA
* * *
168654 ATGATTGTTTTGCCCATATGTAGTAAA
1 ATGACTGTTTTGCCCTTATGTGGTAAA
* ** *
168681 ATGACTATTTTGCCCTTAAATGGTAAG
1 ATGACTGTTTTGCCCTTATGTGGTAAA
168708 ATGACTGTTTT
1 ATGACTGTTTT
168719 AACCCTATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (27 bp):
ATGACTGTTTTGCCCTTATGTGGTAAA
Found at i:176414 original size:27 final size:27
Alignment explanation
Indices: 176362--176419 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
176352 AAATTTTTCT
* *
176362 CTAAACTAGACACATTTAATTGATGTC
1 CTAAACTAGACACATTTAACTGATGTA
176389 CTAAACTAGACACATTTAAGCT-ATGTA
1 CTAAACTAGACACATTTAA-CTGATGTA
176416 CTAA
1 CTAA
176420 TATAAGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
CTAAACTAGACACATTTAACTGATGTA
Found at i:181716 original size:11 final size:10
Alignment explanation
Indices: 181700--181740 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
181690 TCCAATCACT
181700 TTTTTATTTTA
1 TTTTT-TTTTA
181711 TTTTTATTTTA
1 TTTTT-TTTTA
*
181722 TTTTTTTTGA
1 TTTTTTTTTA
181732 TTTTTTTTT
1 TTTTTTTTT
181741 CAACTTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 12 0.43
11 16 0.57
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:182531 original size:22 final size:20
Alignment explanation
Indices: 182492--182531 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
182482 GCTAGAACCA
182492 TCCTTGAAGATTCTTGAACG
1 TCCTTGAAGATTCTTGAACG
*
182512 TCCTTGGAAGCTTCCTTGAA
1 TCCTT-GAAGATT-CTTGAA
182532 GTTTTCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (20 bp):
TCCTTGAAGATTCTTGAACG
Found at i:183147 original size:27 final size:26
Alignment explanation
Indices: 183100--183155 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
183090 ACTGTAACTA
*
183100 ATTAAATTTGTCTCTAAACTAGATAC
1 ATTAAATTTGTCTCTAAACTAGACAC
183126 ATTAAATTGATGTC-CTAAACTAGACAC
1 ATTAAATT--TGTCTCTAAACTAGACAC
183153 ATT
1 ATT
183156 TAAGCTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (26 bp):
ATTAAATTTGTCTCTAAACTAGACAC
Found at i:183170 original size:27 final size:27
Alignment explanation
Indices: 183113--183170 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
183103 AAATTTGTCT
* * *
183113 CTAAACTAGATACATTAAATTGATGTC
1 CTAAACTAGACACATTAAACTGATGTA
*
183140 CTAAACTAGACACATTTAAGCT-ATGTA
1 CTAAACTAGACACA-TTAAACTGATGTA
183167 CTAA
1 CTAA
183171 TATAATACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (27 bp):
CTAAACTAGACACATTAAACTGATGTA
Found at i:184785 original size:19 final size:20
Alignment explanation
Indices: 184763--184810 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
184753 AGTTATATTG
*
184763 AATTGAAAAAAATAT-AGTT
1 AATTGAAAAAAATATGAATT
*
184782 AATT-AATTAAAATATGAATT
1 AATTGAA-AAAAATATGAATT
184802 AATTGAAAA
1 AATTGAAAA
184811 CTGGAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTGAAAAAAATATGAATT
Found at i:185050 original size:47 final size:47
Alignment explanation
Indices: 184989--185094 Score: 167
Period size: 47 Copynumber: 2.3 Consensus size: 47
184979 TATTATCATT
* * *
184989 ACTGTTACTATTTCGAATTTGTTCCGATGATGTACTCTGTGTACTGC
1 ACTGTTACTGTTTCGAATTTGTTCCGATGAGGTACTCTGTGTACCGC
* *
185036 ACTGTTACTGTTTCGGATTTGTTCCGATGAGGTACTCTGTGTACCGT
1 ACTGTTACTGTTTCGAATTTGTTCCGATGAGGTACTCTGTGTACCGC
185083 ACTGTTACTGTT
1 ACTGTTACTGTT
185095 ACTGTTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (47 bp):
ACTGTTACTGTTTCGAATTTGTTCCGATGAGGTACTCTGTGTACCGC
Found at i:186322 original size:98 final size:98
Alignment explanation
Indices: 186153--186386 Score: 362
Period size: 98 Copynumber: 2.4 Consensus size: 98
186143 CACAAAGCAT
* *
186153 TTGATAACGGGTCTATAATCGGCACGAAGCCCACAATATCGATACGAAGCCCACAATAACGGCAC
1 TTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCAAAATAACGGCAC
* **
186218 ACAGCCTTCGATAACATGAT-CGACACTTGGCCA
66 ACAGCCTTCGATAACATGATAAG-CACTCAGCCA
*
186251 TTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCAAAATAACGGTAC
1 TTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCAAAATAACGGCAC
* *
186316 ACAGCCTTTGGTAACATGATAAGCACTCAGCCA
66 ACAGCCTTCGATAACATGATAAGCACTCAGCCA
* *
186349 TTGATAATGGGTCTATAATCGGCACGAAGCCTATAATA
1 TTGATAACGGGTCTATAATCGGCACGAAGCCTACAATA
186387 ACGACACACA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
98 124 0.99
99 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (98 bp):
TTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCAAAATAACGGCAC
ACAGCCTTCGATAACATGATAAGCACTCAGCCA
Found at i:186429 original size:28 final size:28
Alignment explanation
Indices: 186390--186447 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
186380 TATAATAACG
186390 ACACACAACCTTCGGTAACATGATCGGC
1 ACACACAACCTTCGGTAACATGATCGGC
186418 ACACACAACCTTCGGTAACATGATCGGC
1 ACACACAACCTTCGGTAACATGATCGGC
186446 AC
1 AC
186448 TCAACCATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (28 bp):
ACACACAACCTTCGGTAACATGATCGGC
Found at i:186801 original size:27 final size:27
Alignment explanation
Indices: 186771--186919 Score: 156
Period size: 27 Copynumber: 5.5 Consensus size: 27
186761 GGGGTAAAAT
* * *
186771 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
186798 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* * *
186825 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
186852 GGT-ATTTCTACCCTACAAGGGTATTTT
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
186879 AGTAATTTTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
186906 AGTAATTCTACCCT
1 GGTAATTTTACCCT
186920 GTAACACCCC
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.03
27 97 0.93
28 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAGGGGTATTTC
Found at i:186818 original size:54 final size:54
Alignment explanation
Indices: 186772--186919 Score: 215
Period size: 54 Copynumber: 2.7 Consensus size: 54
186762 GGGTAAAATG
* * *
186772 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTA
* * * *
186826 GTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTA
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTA
**
186880 GTAATTTTACCCTACAGGGGTATTTTAGTAATTCTACCCT
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCT
186920 GTAACACCCC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (54 bp):
GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTA
Found at i:187869 original size:27 final size:27
Alignment explanation
Indices: 187839--187943 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
187829 GGCTGATAGA
** * *
187839 ACAGATAATGTGATAGAGTCACAAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
187866 ACAGATAATCGTGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
187893 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
187921 -CAGATAATTGTGGCATAGCCACC
1 ACAGATAA-TGTGGCAGAGCCACC
187944 TGGACGCTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.77
28 15 0.22
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:187925 original size:54 final size:54
Alignment explanation
Indices: 187836--187943 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
187826 CATGGCTGAT
* *
187836 AGAACAGATAATGTGATAGAGTCACAAGATACAGATAATCGTGGCAGAGCCACC
1 AGAACAGATAATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCACC
* * * *
187890 AGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACC
1 AGAACAGATA-ATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCACC
187944 TGGACGCTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 31 0.66
55 16 0.34
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (54 bp):
AGAACAGATAATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCACC
Found at i:194802 original size:27 final size:27
Alignment explanation
Indices: 194772--195067 Score: 382
Period size: 27 Copynumber: 11.0 Consensus size: 27
194762 GGGTGTTACA
* ** *
194772 TACCCTACGGGGGTATTTTGGTATTTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* **
194799 TACCCTATAGCAGTATTTC-GATAATTC
1 TACCCTACAGGGGTATTTCAG-TAATTC
* *
194826 TACCCTATAGGGGTATCTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
194853 TACCCTACAGGGGTATTTC-GATAATTC
1 TACCCTACAGGGGTATTTCAG-TAATTC
*
194880 TACCTTACAGGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* *
194907 TACCCTACAGGGCTATTTTAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
194934 TACCTTACAGGGGTATTTC-GATAATTC
1 TACCCTACAGGGGTATTTCAG-TAATTC
*
194961 TACCTTACAGGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
194988 TACCCTACAGGGCTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* *
195015 TACCCTACAGGGGTATTTCTGTATTTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
195042 TACCCTACAAGGGTATTTCAGTAATT
1 TACCCTACAGGGGTATTTCAGTAATT
195068 TTACAAATCA
Statistics
Matches: 237, Mismatches: 26, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
26 3 0.01
27 231 0.97
28 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCAGTAATTC
Found at i:195083 original size:27 final size:27
Alignment explanation
Indices: 195049--195230 Score: 210
Period size: 27 Copynumber: 6.8 Consensus size: 27
195039 TTCTACCCTA
195049 CAAGGGTATTTCAGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
195076 CAAAGGTATTTCAGTAACTTTAC-AAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* * * *
195102 CAACGGTATTTCGGTAATTTTATAAAC
1 CAAGGGTATTTCAGTAATTTTACAAAT
* * *
195129 CAGGGGTACTTT-GGTAATTTTACAAGT
1 CAAGGGTA-TTTCAGTAATTTTACAAAT
195156 -AGAGGGTATTTCAGTAATTTTACAAAT
1 CA-AGGGTATTTCAGTAATTTTACAAAT
*
195183 CGAGGGTATTTCAGTAATTTTAC-AAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
195209 CAACGGTATTTCGGTAATTTTA
1 CAAGGGTATTTCAGTAATTTTA
195231 TAACTGGGGG
Statistics
Matches: 131, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
26 48 0.37
27 80 0.61
28 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTACAAAT
Found at i:195084 original size:54 final size:54
Alignment explanation
Indices: 194971--195230 Score: 228
Period size: 54 Copynumber: 4.9 Consensus size: 54
194961 TACCTTACAG
* ** * ** *
194971 GGGTATTTCAGTAATTCTACCCTAC-AGGGCTATTTCAGTAATTCTAC-CCTACAG
1 GGGTATTTCAGTAATTTTACAATACAAGGG-TATTTCAGTAATTTTACAAAT-CAA
* **
195025 GGGTATTTCTGT-ATTTCTACCCTACAAGGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTCAGTAATTT-TACAATACAAGGGTATTTCAGTAATTTTACAAATCAA
* * * * * * *
195079 AGGTATTTCAGTAACTTTACAAT-CAACGGTATTTCGGTAATTTTATAAACCAG
1 GGGTATTTCAGTAATTTTACAATACAAGGGTATTTCAGTAATTTTACAAATCAA
* * *
195132 GGGTACTTT-GGTAATTTTACAAGTA-GAGGGTATTTCAGTAATTTTACAAATCGA
1 GGGTA-TTTCAGTAATTTTACAA-TACAAGGGTATTTCAGTAATTTTACAAATCAA
* *
195186 GGGTATTTCAGTAATTTTACAAT-CAACGGTATTTCGGTAATTTTA
1 GGGTATTTCAGTAATTTTACAATACAAGGGTATTTCAGTAATTTTA
195231 TAACTGGGGG
Statistics
Matches: 167, Mismatches: 30, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
53 65 0.39
54 94 0.56
55 8 0.05
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAATACAAGGGTATTTCAGTAATTTTACAAATCAA
Found at i:195121 original size:53 final size:53
Alignment explanation
Indices: 195053--195230 Score: 225
Period size: 53 Copynumber: 3.3 Consensus size: 53
195043 ACCCTACAAG
* *
195053 GGTATTTCAGTAATTTTACAAATCAAAGGTATTTCAGTAACTTTACAATCAAC
1 GGTATTTCAGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAATCAAC
* * * * * *
195106 GGTATTTCGGTAATTTTATAAACCAGGGGTACTTT-GGTAATTTTACAAGT-AGAG
1 GGTATTTCAGTAATTTTACAAATCAAGGGTA-TTTCAGTAATTTTACAA-TCA-AC
*
195160 GGTATTTCAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAATCAAC
1 GGTATTTCAGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAATCAAC
*
195213 GGTATTTCGGTAATTTTA
1 GGTATTTCAGTAATTTTA
195231 TAACTGGGGG
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
53 60 0.58
54 44 0.42
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (53 bp):
GGTATTTCAGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAATCAAC
Found at i:195242 original size:26 final size:27
Alignment explanation
Indices: 194971--195254 Score: 178
Period size: 27 Copynumber: 10.6 Consensus size: 27
194961 TACCTTACAG
* *
194971 GGGTATTTCAGTAATTCTAC-CCTAC-A
1 GGGTATTTCAGTAATTTTACAACT-CGA
* *
194997 GGGCTATTTCAGTAATTCTAC-CCTAC-A
1 GGG-TATTTCAGTAATTTTACAACT-CGA
* * *
195024 GGGGTATTTCTGT-ATTTCTAC-CCTACAA
1 -GGGTATTTCAGTAATTT-TACAACT-CGA
* *
195052 GGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTCAGTAATTTTACAACTCGA
* * *
195079 AGGTATTTCAGTAACTTTACAA-TCAA
1 GGGTATTTCAGTAATTTTACAACTCGA
* * *
195105 CGGTATTTCGGTAATTTTATAAAC-C-A
1 GGGTATTTCAGTAATTTTA-CAACTCGA
* * *
195131 GGGGTACTTT-GGTAATTTTACAAGTAGA
1 -GGGTA-TTTCAGTAATTTTACAACTCGA
*
195159 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAACTCGA
*
195186 GGGTATTTCAGTAATTTTACAA-TCAA
1 GGGTATTTCAGTAATTTTACAACTCGA
* * * *
195212 CGGTATTTCGGTAATTTTATAACT-GG
1 GGGTATTTCAGTAATTTTACAACTCGA
*
195238 GGGTATTTTAGTAATTT
1 GGGTATTTCAGTAATTT
195255 GGTAAACTGA
Statistics
Matches: 217, Mismatches: 27, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
26 68 0.31
27 136 0.63
28 13 0.06
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACAACTCGA
Found at i:196181 original size:19 final size:18
Alignment explanation
Indices: 196157--196224 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
196147 AAACATAGAC
*
196157 TGTTACTAAATACTTGAAT
1 TGTTACTAAATAATTG-AT
* *
196176 TGTTACTATATATTTGAT
1 TGTTACTAAATAATTGAT
* *
196194 TTTTAC-AGAATAATTGAC
1 TGTTACTA-AATAATTGAT
196212 TGTTACTAAATAA
1 TGTTACTAAATAA
196225 CCGATCAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 1 0.03
18 24 0.60
19 15 0.38
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (18 bp):
TGTTACTAAATAATTGAT
Found at i:201269 original size:18 final size:18
Alignment explanation
Indices: 201248--201285 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
201238 GAGTAGCATC
201248 AATATGATTAAAAAGCTG
1 AATATGATTAAAAAGCTG
201266 AATATGATTAAAAAGCTG
1 AATATGATTAAAAAGCTG
201284 AA
1 AA
201286 AACACTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (18 bp):
AATATGATTAAAAAGCTG
Found at i:209766 original size:27 final size:27
Alignment explanation
Indices: 209736--209789 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
209726 ATGACCAAAA
209736 TACCCCTATAGGCTAAAATGACT-ATTT
1 TACCCCTATAGGCT-AAATGACTGATTT
* *
209763 TACCCCTCTAGGGTAAATGACTGATTT
1 TACCCCTATAGGCTAAATGACTGATTT
209790 GTGCTCTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (27 bp):
TACCCCTATAGGCTAAATGACTGATTT
Found at i:209994 original size:26 final size:26
Alignment explanation
Indices: 209958--210023 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
209948 TTAGGCCTGA
209958 TACTGGCAGCTTTGTTGCGTTACTGT
1 TACTGGCAGCTTTGTTGCGTTACTGT
209984 TACTGGCAGCTTTGTTGCGTTACTGT
1 TACTGGCAGCTTTGTTGCGTTACTGT
210010 TACTGGCAGCTTTG
1 TACTGGCAGCTTTG
210024 CTGTAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.41
Consensus pattern (26 bp):
TACTGGCAGCTTTGTTGCGTTACTGT
Found at i:211449 original size:12 final size:12
Alignment explanation
Indices: 211432--211457 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
211422 AGTTTGGCAC
211432 AGCCTAGCACAT
1 AGCCTAGCACAT
211444 AGCCTAGCACAT
1 AGCCTAGCACAT
211456 AG
1 AG
211458 GCGTGTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (12 bp):
AGCCTAGCACAT
Found at i:215644 original size:40 final size:40
Alignment explanation
Indices: 215568--215789 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
215558 CCAAGTATCA
* * **
215568 TCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCT
1 TCGGGACTTAGCCCGGATATAGTC-ACTAGCATGAATGCCT
*
215607 TCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGCCT
1 TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
215647 TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
1 TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
215687 TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
1 TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
** * * **
215727 TCGAAACTTAGCCTGGGTATAG-CAACTACTCGCACAAATGCCT
1 TCGGGACTTAGCCCGGATATAGTC-ACTA---GCATGAATGCCT
215770 TCGGGACTTAGCCCGGATAT
1 TCGGGACTTAGCCCGGATAT
215790 CATCCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 10 0.06
40 124 0.77
41 1 0.01
43 26 0.16
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGCCT
Found at i:215700 original size:80 final size:80
Alignment explanation
Indices: 215568--215789 Score: 313
Period size: 80 Copynumber: 2.8 Consensus size: 80
215558 CCAAGTATCA
* * *
215568 TCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCA
1 TCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCA
215632 CTAGCATGAATGCCT
66 CTAGCATGAATGCCT
**
215647 TCGGGACTTAGCCCGGATATAGTC-ACTAGCATGAATGCCTTCGGGACTTAGCCCGGATATAGTC
1 TCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTC
215711 ACTAGCATGAATGCCT
65 ACTAGCATGAATGCCT
** * *
215727 TCGAAACTTAGCCTGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 TCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGCCTTCGGGACTTAGCCCGGATAT
215790 CATCCGAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
79 11 0.09
80 84 0.67
81 1 0.01
83 30 0.24
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
TCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCA
CTAGCATGAATGCCT
Found at i:223792 original size:40 final size:40
Alignment explanation
Indices: 223679--223901 Score: 238
Period size: 40 Copynumber: 5.5 Consensus size: 40
223669 ACCCAAGTAT
* *
223679 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
223718 CTTCGGGTCTTAGCCCGGA-ATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
**
223757 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
223797 CTTCGAGAATTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * * *
223840 CTTCGGGACTTAGCCCGGATATAGTAAGTTGCACAAATAC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
223880 CTTCGAGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
223902 CATCCGAATA
Statistics
Matches: 157, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
39 45 0.29
40 81 0.52
43 31 0.20
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:228697 original size:46 final size:46
Alignment explanation
Indices: 228637--228812 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
228627 TATTTTGGCA
228637 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* * * * * * *
228683 TCCGAGTTCATTGAGTTGAGTCCGAGTTC-GTGAAATGTA-AC-TAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACGAATG
*
228728 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* * ** *
228776 CCCGAGCTTGTTGAGTTGAGTATGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
228813 GTGGGTTACA
Statistics
Matches: 103, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
45 3 0.03
46 65 0.63
47 32 0.31
48 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
Found at i:228742 original size:93 final size:93
Alignment explanation
Indices: 228633--228805 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
228623 AAGATATTTT
*
228633 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAG-TTCATTGA
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAGCTT-ATTGA
*
228697 GTTGAGTCCGAGTTCGTGAAATGTAACTA
65 GTTGAGTACGAGTTCGTGAAATGTAACTA
* *
228726 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTTGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAGCTTATTGAG
*
228791 TTGAGTATGAGTTCG
66 TTGAGTACGAGTTCG
228806 CTTATGGGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
93 72 0.97
94 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAGCTTATTGAG
TTGAGTACGAGTTCGTGAAATGTAACTA
Found at i:237798 original size:26 final size:26
Alignment explanation
Indices: 237763--237812 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
237753 AATGTGAAAG
*
237763 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
237789 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
237813 AGTTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:237895 original size:103 final size:103
Alignment explanation
Indices: 237684--237948 Score: 408
Period size: 103 Copynumber: 2.6 Consensus size: 103
237674 GTTGTACATA
** *
237684 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
237749 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
*
237787 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
237851 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATT-CCCC
* * *
237890 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
237949 AATAACGGTT
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
102 25 0.17
103 122 0.82
104 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
Found at i:245410 original size:103 final size:104
Alignment explanation
Indices: 245166--245431 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
245156 GTTGTACATA
** *
245166 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
245231 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
245270 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
245334 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
245373 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
245432 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:248605 original size:34 final size:34
Alignment explanation
Indices: 248558--248631 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
248548 GTCTGGCTTA
*
248558 AGCCCATGTCAGTAGCAATATTAGTGTGGGCCTT
1 AGCCCATGTCAGTAGCAATAATAGTGTGGGCCTT
* * *
248592 AGCCCAT-TACAGTAGTATTAATAGTGTGGGTCTT
1 AGCCCATGT-CAGTAGCAATAATAGTGTGGGCCTT
248626 AGCCCA
1 AGCCCA
248632 ACTCAGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (34 bp):
AGCCCATGTCAGTAGCAATAATAGTGTGGGCCTT
Found at i:259735 original size:12 final size:12
Alignment explanation
Indices: 259715--259744 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
259705 GTTTAAATGA
*
259715 ATTAAAATTGAT
1 ATTATAATTGAT
259727 ATTATAATTGAT
1 ATTATAATTGAT
259739 ATTATA
1 ATTATA
259745 TATATTCGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
ATTATAATTGAT
Found at i:260525 original size:94 final size:94
Alignment explanation
Indices: 260317--260645 Score: 597
Period size: 94 Copynumber: 3.5 Consensus size: 94
260307 CTAATTGAAT
* *
260317 TAAGTAAATTGCCTTATTATAATGAGTCAACATTGGCACTATGTGTACGGAATTAAATGT-ACTT
1 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAATTAAATGTCACTT
260381 TGTGTGCAGATTTTATATGCTATTCGAAG
66 TGTGTGCAGATTTTATATGCTATTCGAAG
*
260410 TAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAATTAAATGTCACTT
1 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAATTAAATGTCACTT
* *
260475 TGTGTGTAGATTTTACATGCTATTCGAAG
66 TGTGTGCAGATTTTATATGCTATTCGAAG
*
260504 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCAGAATTAAATGTCACTT
1 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAATTAAATGTCACTT
260569 TGTGTGCAGATTTTATATGCTATTCGAAG
66 TGTGTGCAGATTTTATATGCTATTCGAAG
260598 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
1 TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
260646 AGATTTGAAT
Statistics
Matches: 226, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
93 57 0.25
94 169 0.75
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.38
Consensus pattern (94 bp):
TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAATTAAATGTCACTT
TGTGTGCAGATTTTATATGCTATTCGAAG
Found at i:268243 original size:94 final size:94
Alignment explanation
Indices: 267885--268230 Score: 604
Period size: 94 Copynumber: 3.7 Consensus size: 94
267875 ACTATAACCG
* *
267885 TATATGCTAATT-GAATTAAGTAAATTGCCTTATTATAATGAGTCAACATTGGCACTATGTGTGC
1 TATATGCT-ATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
*
267949 GGAATTAAATGTCACTTTGTGTGTAGATTT
65 GGAATTAAATGTCACTTTGTGTGCAGATTT
* *
267979 TATATGCTATTCGAAGTAAGTTAATTTCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
268044 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
* *
268073 TACATGCTATTCAAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
*
268138 AAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
268167 TATATGCTATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
1 TATATGCTATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
268231 AGATTTGAAT
Statistics
Matches: 239, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 3 0.01
94 236 0.99
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (94 bp):
TATATGCTATTCGAAGTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATGTCACTTTGTGTGCAGATTT
Found at i:271149 original size:68 final size:68
Alignment explanation
Indices: 271040--271197 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 68
271030 TAGAGGGAAC
*
271040 GTAGCTAGGTCACATGTGTGATACGGGATGAATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGAATCCCATGTAGAAAAGAGAGCTACGTGAGAGATA
271105 AAT
66 AAT
*
271108 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGAAAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGAATCCCATGTAGAAAAGAGAGCTACGTGAGAGATA
271173 AAT
66 AAT
* *
271176 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
271198 TCCAAGTGAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 86 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.23
Consensus pattern (68 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGAATCCCATGTAGAAAAGAGAGCTACGTGAGAGATA
AAT
Found at i:271271 original size:66 final size:67
Alignment explanation
Indices: 271074--271271 Score: 174
Period size: 68 Copynumber: 2.9 Consensus size: 67
271064 GGGATGAATC
* * * *
271074 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATA-C--GGGA
1 CCATGTAGAAAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
* *
271136 TGTATC-
62 AGGA-CA
*
271142 CCATGTAGAAAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGAAAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
271207 AGGACA
62 AGGACA
* * *
271213 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGAAAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
271272 TTCACCATGT
Statistics
Matches: 114, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
66 24 0.21
67 9 0.08
68 54 0.47
69 1 0.01
70 1 0.01
71 25 0.22
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (67 bp):
CCATGTAGAAAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:272456 original size:677 final size:677
Alignment explanation
Indices: 271441--272797 Score: 2705
Period size: 677 Copynumber: 2.0 Consensus size: 677
271431 GAAAATGATT
271441 TGTAGTATATATATATGTAAGTTAAAATGAGGTTAGTATAAAGAATGTGTGAAAGAATGAAATTA
1 TGTAGTATATATATATGTAAGTTAAAATGAGGTTAGTATAAAGAATGTGTGAAAGAATGAAATTA
271506 GCATTAAAACTGTTTTGGACAGTAGCAGTAACGTGATTTTGAAAATTCACCAAAAATATAAGGAA
66 GCATTAAAACTGTTTTGGACAGTAGCAGTAACGTGATTTTGAAAATTCACCAAAAATATAAGGAA
271571 TTTAATTAGAGGTTGAATGAGATGTGAAATTAAAGCTTAATGAGTCTTTTTTCATATAAAAGAAA
131 TTTAATTAGAGGTTGAATGAGATGTGAAATTAAAGCTTAATGAGTCTTTTTTCATATAAAAGAAA
*
271636 CATAGCAAGCAAAGGAATTCTATATTTTGAGATATTTACAATTGTGTGAGACTTGCTCAGGATGA
196 CATAGCAAGCAAAGGAATTCTATATTTTGAGATATTTACAATTGTGTGAGACTTGCTCAAGATGA
271701 CTATGAAATCCCCTGTTTCAACTTTTAAAAATCATTAAAAATTGTAAAAAATAAATTAAGAAATA
261 CTATGAAATCCCCTGTTTCAACTTTTAAAAATCATTAAAAATTGTAAAAAATAAATTAAGAAATA
271766 TAGTTTATATTCATAAATTACTTATTGAATCTAGTTTTAAATGAAATAGGTTTCATGGTTATTTT
326 TAGTTTATATTCATAAATTACTTATTGAATCTAGTTTTAAATGAAATAGGTTTCATGGTTATTTT
271831 AATTGTGTACTGAGAGAAATTCAATTCGTAATGAATAGAGGTCATATCAATTGAGCTGTGTAACA
391 AATTGTGTACTGAGAGAAATTCAATTCGTAATGAATAGAGGTCATATCAATTGAGCTGTGTAACA
271896 GGGGAAACTTTAACTAATAAACTGTACTAATTGGCTAAACCAAAAATTCTATAAAAATATTAGTA
456 GGGGAAACTTTAACTAATAAACTGTACTAATTGGCTAAACCAAAAATTCTATAAAAATATTAGTA
271961 AGAATTTTTATGAGTCTAGATTCAGGGAAATTTTACGGATTTGAATTTTGAGTTTCGTAACTCGA
521 AGAATTTTTATGAGTCTAGATTCAGGGAAATTTTACGGATTTGAATTTTGAGTTTCGTAACTCGA
272026 GTTATGATTTATTTAGTGATCATGACGCAGGAGGGACAGCTTGATCAAATTGGAGTAAACAATAA
586 GTTATGATTTATTTAGTGATCATGACGCAGGAGGGACAGCTTGATCAAATTGGAGTAAACAATAA
272091 AATTAAAAATATGATATAATTGAGTTA
651 AATTAAAAATATGATATAATTGAGTTA
272118 TGTAGTATATATATATGTAAGTTAAAATGAGGTTAGTATAAAGAATGTGTGAAAGAATGAAATTA
1 TGTAGTATATATATATGTAAGTTAAAATGAGGTTAGTATAAAGAATGTGTGAAAGAATGAAATTA
272183 GCATTAAAACTGTTTTGGACAGTAGCAGTAACGTGATTTTGAAAATTCACCAAAAATATAAGGAA
66 GCATTAAAACTGTTTTGGACAGTAGCAGTAACGTGATTTTGAAAATTCACCAAAAATATAAGGAA
272248 TTTAATTAGAGGTTGAATGAGATGTGAAATTAAAGCTTAATGAGTCTTTTTTCATATAAAAGAAA
131 TTTAATTAGAGGTTGAATGAGATGTGAAATTAAAGCTTAATGAGTCTTTTTTCATATAAAAGAAA
272313 CATAGCAAGCAAAGGAATTCTATATTTTGAGATATTTACAATTGTGTGAGACTTGCTCAAGATGA
196 CATAGCAAGCAAAGGAATTCTATATTTTGAGATATTTACAATTGTGTGAGACTTGCTCAAGATGA
272378 CTATGAAATCCCCTGTTTCAACTTTTAAAAATCATTAAAAATTGTAAAAAATAAATTAAGAAATA
261 CTATGAAATCCCCTGTTTCAACTTTTAAAAATCATTAAAAATTGTAAAAAATAAATTAAGAAATA
272443 TAGTTTATATTCATAAATTACTTATTGAATCTAGTTTTAAATGAAATAGGTTTCATGGTTATTTT
326 TAGTTTATATTCATAAATTACTTATTGAATCTAGTTTTAAATGAAATAGGTTTCATGGTTATTTT
272508 AATTGTGTACTGAGAGAAATTCAATTCGTAATGAATAGAGGTCATATCAATTGAGCTGTGTAACA
391 AATTGTGTACTGAGAGAAATTCAATTCGTAATGAATAGAGGTCATATCAATTGAGCTGTGTAACA
272573 GGGGAAACTTTAACTAATAAACTGTACTAATTGGCTAAACCAAAAATTCTATAAAAATATTAGTA
456 GGGGAAACTTTAACTAATAAACTGTACTAATTGGCTAAACCAAAAATTCTATAAAAATATTAGTA
272638 AGAATTTTTATGAGTCTAGATTCAGGGAAATTTTACGGATTTGAATTTTGAGTTTCGTAACTCGA
521 AGAATTTTTATGAGTCTAGATTCAGGGAAATTTTACGGATTTGAATTTTGAGTTTCGTAACTCGA
272703 GTTATGATTTATTTAGTGATCATGACGCAGGAGGGACAGCTTGATCAAATTGGAGTAAACAATAA
586 GTTATGATTTATTTAGTGATCATGACGCAGGAGGGACAGCTTGATCAAATTGGAGTAAACAATAA
272768 AATTAAAAATATGATATAATTGAGTTA
651 AATTAAAAATATGATATAATTGAGTTA
272795 TGT
1 TGT
272798 TGTAAACATA
Statistics
Matches: 679, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
677 679 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (677 bp):
TGTAGTATATATATATGTAAGTTAAAATGAGGTTAGTATAAAGAATGTGTGAAAGAATGAAATTA
GCATTAAAACTGTTTTGGACAGTAGCAGTAACGTGATTTTGAAAATTCACCAAAAATATAAGGAA
TTTAATTAGAGGTTGAATGAGATGTGAAATTAAAGCTTAATGAGTCTTTTTTCATATAAAAGAAA
CATAGCAAGCAAAGGAATTCTATATTTTGAGATATTTACAATTGTGTGAGACTTGCTCAAGATGA
CTATGAAATCCCCTGTTTCAACTTTTAAAAATCATTAAAAATTGTAAAAAATAAATTAAGAAATA
TAGTTTATATTCATAAATTACTTATTGAATCTAGTTTTAAATGAAATAGGTTTCATGGTTATTTT
AATTGTGTACTGAGAGAAATTCAATTCGTAATGAATAGAGGTCATATCAATTGAGCTGTGTAACA
GGGGAAACTTTAACTAATAAACTGTACTAATTGGCTAAACCAAAAATTCTATAAAAATATTAGTA
AGAATTTTTATGAGTCTAGATTCAGGGAAATTTTACGGATTTGAATTTTGAGTTTCGTAACTCGA
GTTATGATTTATTTAGTGATCATGACGCAGGAGGGACAGCTTGATCAAATTGGAGTAAACAATAA
AATTAAAAATATGATATAATTGAGTTA
Found at i:279331 original size:68 final size:68
Alignment explanation
Indices: 279259--279430 Score: 235
Period size: 68 Copynumber: 2.5 Consensus size: 68
279249 CATCATGTGT
* *
279259 ACAAGAAG-GCTAC-GAGATACTATATAGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCA
1 ACAAGAAGTGCTACGGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCA
279322 TGTAG
64 TGTAG
279327 ACAAG-AGTGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
1 ACAAGAAGTGCTACG-GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
279391 GTAG
65 GTAG
* * *
279395 ATAAG-AGAGCTATGTGAGAGATAAATGTAGCTAGGT
1 ACAAGAAGTGCTACG-GAGAGATAAATGTAGCTAGGT
279431 TTCATGAGTG
Statistics
Matches: 96, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
67 2 0.02
68 85 0.89
69 4 0.04
70 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (68 bp):
ACAAGAAGTGCTACGGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATG
TAG
Found at i:279442 original size:68 final size:68
Alignment explanation
Indices: 279285--279430 Score: 265
Period size: 68 Copynumber: 2.1 Consensus size: 68
279275 ATACTATATA
*
279285 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGTGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
279350 AAT
66 AAT
* *
279353 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGATAAGAGAGCTATGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
279418 AAT
66 AAT
279421 GTAGCTAGGT
1 GTAGCTAGGT
279431 TTCATGAGTG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (68 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
AAT
Found at i:285154 original size:34 final size:34
Alignment explanation
Indices: 285107--285180 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
285097 GTCTGGCATA
285107 AGCCCATGTCAGTAGTAAT-ATCAGTGTGGGCCTT
1 AGCCCATGTCAGTAGTAATAAT-AGTGTGGGCCTT
* *
285141 AGCCCAT-TACAGTAGTATTAATAGTGTGGGTCTT
1 AGCCCATGT-CAGTAGTAATAATAGTGTGGGCCTT
*
285175 AACCCA
1 AGCCCA
285181 ACTCAGTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.03
34 32 0.91
35 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (34 bp):
AGCCCATGTCAGTAGTAATAATAGTGTGGGCCTT
Found at i:285188 original size:34 final size:33
Alignment explanation
Indices: 285115--285188 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
285105 TAAGCCCATG
* *
285115 TCAGTAGTAATATCAGTGTGGGCCTTAGCCCAT
1 TCAGTAGTAATATCAGTGTGGGCCTTAACCCAC
* *
285148 TACAGTAGTATTAAT-AGTGTGGGTCTTAACCCAAC
1 T-CAGTAGTAAT-ATCAGTGTGGGCCTTAACCC-AC
285183 TCAGTA
1 TCAGTA
285189 CAGTATCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 1 0.03
34 29 0.85
35 4 0.12
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (33 bp):
TCAGTAGTAATATCAGTGTGGGCCTTAACCCAC
Found at i:296342 original size:46 final size:46
Alignment explanation
Indices: 296274--296456 Score: 253
Period size: 46 Copynumber: 4.0 Consensus size: 46
296264 TATATATACA
* * *
296274 CATCTCATACATA-TCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACA-AGTTTCGCATTAGCCATTCGGCTTTACCACATATC
* * * *
296320 AATCTTATACAAGTTTCGCATTAGCCATTCGGCATTACCTCATATC
1 CATCTCATACAAGTTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
296366 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACAAGTTTCGCATTAGCCATTCGGCTTTACCACATATC
296412 CATCTCATACACA-TTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACA-AGTTTCGCATTAGCCATTCGGCTTTACCACATAT
296457 ATACACTTCC
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 121 0.99
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACAAGTTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:296559 original size:47 final size:47
Alignment explanation
Indices: 296430--296562 Score: 169
Period size: 47 Copynumber: 2.8 Consensus size: 47
296420 ACACATTTCG
* * * * * *
296430 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
** *
296477 CATTGGCCATTCTACCTTATCACATATATGGATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
296524 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCAC
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCAC
296563 TGTGACAGCC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 72 0.99
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:298170 original size:40 final size:39
Alignment explanation
Indices: 298082--298262 Score: 163
Period size: 40 Copynumber: 4.6 Consensus size: 39
298072 GAATGATGTT
* * *
298082 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATC
1 CGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAT-TC
* * * *
298122 CAGACTAAGATCCAAAGGCATTTGTGCGAGATACTAATTC
1 CGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAATTC
* *
298162 CGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAATTC
* * *
298201 CGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-ATAGC
1 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT-TC
*
298241 CGGGCTATGTCC-AAGGCATTTG
1 CGGGCTAAGTCCGAAGGCATTTG
298263 AACGAGTAGC
Statistics
Matches: 115, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 9 0.08
39 37 0.32
40 59 0.51
41 10 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAATTC
Found at i:298181 original size:39 final size:39
Alignment explanation
Indices: 298136--298262 Score: 159
Period size: 39 Copynumber: 3.3 Consensus size: 39
298126 CTAAGATCCA
*
298136 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCG
* *
298175 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAG-CCCG
* * * *
298215 AAGGCAATTGTGCGAGTTACT-ATAGCCGGGCTATGTCC-
1 AAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGCCCG
298253 AAGGCATTTG
1 AAGGCATTTG
298263 AACGAGTAGC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.12
39 35 0.46
40 32 0.42
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCG
Found at i:306022 original size:38 final size:38
Alignment explanation
Indices: 305922--306102 Score: 206
Period size: 40 Copynumber: 4.7 Consensus size: 38
305912 TTGAATGATG
* * *
305922 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTA-A
* *
305962 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAA
306001 TTCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT-AA
* *
306040 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAA
*
306079 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
306103 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
37 12 0.10
38 42 0.34
39 5 0.04
40 56 0.46
41 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:306057 original size:78 final size:79
Alignment explanation
Indices: 305922--306102 Score: 219
Period size: 78 Copynumber: 2.3 Consensus size: 79
305912 TTGAATGATG
* *
305922 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
305986 TGTGCGAGATACTAA
65 TGTGCGAGATACTAA
* * * **
306001 TTCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
306063 TTGTGCGAGTTACTAA
64 TTGTGCGAGATACTAA
*
306079 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
306103 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
76 9 0.10
77 14 0.16
78 48 0.54
79 7 0.08
80 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTAA
Found at i:307528 original size:25 final size:25
Alignment explanation
Indices: 307499--307576 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
307489 ATTCGGCCTT
307499 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
307524 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
307546 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
307571 ATCACA
1 ATCACA
307577 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 6 0.15
23 11 0.28
24 11 0.28
25 12 0.30
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:307539 original size:47 final size:47
Alignment explanation
Indices: 307468--307715 Score: 403
Period size: 47 Copynumber: 5.3 Consensus size: 47
307458 GGGTGTTACA
* *
307468 TTCACATTCATCACATTGGTCATTCGGCCTTATCACACATATGCATG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
*
307515 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
307562 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
*
307609 TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
* * **
307656 TTCACATTCATCACATT-GTCATTCGGCCTTAT--CATATATACACA
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
307700 TTCACATTCATCACAT
1 TTCACATTCATCACAT
307716 AAAATCCTAA
Statistics
Matches: 194, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
44 25 0.13
46 14 0.07
47 155 0.80
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATG
Found at i:307551 original size:22 final size:22
Alignment explanation
Indices: 307524--307642 Score: 59
Period size: 22 Copynumber: 5.1 Consensus size: 22
307514 GTTCACATTC
307524 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
307546 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
307570 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
307593 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
307617 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
307640 ATC
1 ATC
307643 TCATATATGC
Statistics
Matches: 71, Mismatches: 10, Indels: 32
0.63 0.09 0.28
Matches are distributed among these distances:
22 19 0.27
23 18 0.25
24 18 0.25
25 16 0.23
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Done.