Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 95 of 196
Found at i:27705023 original size:9 final size:9
Alignment explanation
Indices: 27704963--27705022 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
27704953 TTTGCTGAGA
27704963 TTGTTGCTG
1 TTGTTGCTG
27704972 TTGTTGCTG
1 TTGTTGCTG
27704981 TTGTTGCTG
1 TTGTTGCTG
* *
27704990 CTGCTGCTG
1 TTGTTGCTG
* *
27704999 CTGTTGTTG
1 TTGTTGCTG
*
27705008 TTGTTGTTG
1 TTGTTGCTG
27705017 TTGTTG
1 TTGTTG
27705023 TCGGTGATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.00, C:0.12, G:0.33, T:0.55
Consensus pattern (9 bp):
TTGTTGCTG
Found at i:27715653 original size:26 final size:26
Alignment explanation
Indices: 27715595--27715695 Score: 116
Period size: 26 Copynumber: 3.9 Consensus size: 26
27715585 CACCAATATC
27715595 GCAGCAAAGCTGCCAGTAACA-TAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
* *
27715620 GCAACAAAGCTGCCAGTAATAGTAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
*
27715646 GCAGCAAAGCTGCCAATAACAGTATAT
1 GCAGCAAAGCTGCCAGTAACAGTA-AT
** **
27715673 GTGGCAAAGCCACCAGT-ACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
27715696 TACTTCCCCT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
25 19 0.30
26 31 0.48
27 14 0.22
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAT
Found at i:27715875 original size:27 final size:27
Alignment explanation
Indices: 27715845--27716072 Score: 264
Period size: 27 Copynumber: 8.5 Consensus size: 27
27715835 GGGTATAACA
*
27715845 GTCATTTTATCCTATCG-GGGTATTTCG
1 GTCATTTTA-CCCATCGAGGGTATTTCG
*
27715872 GTCATTTTACCCTTCG-GGGTTATTTCG
1 GTCATTTTACCCATCGAGGG-TATTTCG
* * *
27715899 ATCATTTTACCTATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * **
27715926 ATTATTTTGCCCATCGAGGGTATTTTA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
27715953 GCCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
27715980 GTTATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
27716007 GTCATTTTACCCATCGAGAGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
27716034 GTTATTTTACCCATCGAGAGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
27716061 GTTA-TTTACCCA
1 GTCATTTTACCCA
27716073 CGAATCACAA
Statistics
Matches: 176, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
26 16 0.09
27 157 0.89
28 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:27717538 original size:22 final size:23
Alignment explanation
Indices: 27717496--27717539 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
27717486 AGATCTTAAA
27717496 AAAATTATTTATTGATATAAAAG
1 AAAATTATTTATTGATATAAAAG
27717519 AAAATATATTT-TT-ATATAAAA
1 AAAAT-TATTTATTGATATAAAA
27717540 AATAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAATTATTTATTGATATAAAAG
Found at i:27726199 original size:3 final size:3
Alignment explanation
Indices: 27726187--27726225 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
27726177 GTGTGTCCAT
*
27726187 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC -TC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
27726226 TTTATAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:27734654 original size:25 final size:26
Alignment explanation
Indices: 27734626--27734679 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
27734616 TAATTAGTAT
* *
27734626 AAAATATT-AATAATTCAATA-ATTTG
1 AAAA-ATTAAATAATTAAATAGAATTG
27734651 AAAAATTAAATAATTAAATAGAATTG
1 AAAAATTAAATAATTAAATAGAATTG
27734677 AAA
1 AAA
27734680 TTTAGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 15 0.60
26 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAGAATTG
Found at i:27735349 original size:31 final size:31
Alignment explanation
Indices: 27735306--27735367 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
27735296 GAAAAAATAG
27735306 GGATTAAGGGGTTTTGTTTAGGGTTAAAAAA
1 GGATTAAGGGGTTTTGTTTAGGGTTAAAAAA
* *
27735337 GGATT-AGAGGGTTTTGTTTATGGTTTAAAAA
1 GGATTAAG-GGGTTTTGTTTAGGGTTAAAAAA
27735368 TGTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.39
Consensus pattern (31 bp):
GGATTAAGGGGTTTTGTTTAGGGTTAAAAAA
Found at i:27735534 original size:22 final size:22
Alignment explanation
Indices: 27735507--27735584 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
27735497 TTGTTTTTGT
27735507 TGTTTTTGAATTATTTGAAAAA
1 TGTTTTTGAATTATTTGAAAAA
* ***
27735529 TGTTTTTGATTTA-TTG--GGT
1 TGTTTTTGAATTATTTGAAAAA
*
27735548 TATTTTTGAATTATTT-AACAAA
1 TGTTTTTGAATTATTTGAA-AAA
*
27735570 TGTTTTTGATTTATT
1 TGTTTTTGAATTATT
27735585 GAGATTGTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 3 0.07
22 25 0.61
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (22 bp):
TGTTTTTGAATTATTTGAAAAA
Found at i:27735922 original size:27 final size:27
Alignment explanation
Indices: 27735884--27735945 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
27735874 TAAATAAGCT
*
27735884 TATTATA-TATTGT-TTAGTATTT-TTG
1 TATTATATTATTGTACTA-TATTTATTG
27735909 TATTGATATTATTGTACTATATTTATTG
1 TATT-ATATTATTGTACTATATTTATTG
27735937 TATTATATT
1 TATTATATT
27735946 TAGGTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 16 0.50
28 9 0.28
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (27 bp):
TATTATATTATTGTACTATATTTATTG
Found at i:27735923 original size:14 final size:13
Alignment explanation
Indices: 27735884--27735945 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
27735874 TAAATAAGCT
27735884 TATTATA-TATTG
1 TATTATATTATTG
*
27735896 T-TTAGTATTTTTG
1 TATTA-TATTATTG
27735909 TATTGATATTATTG
1 TATT-ATATTATTG
*
27735923 TACTATATTTATTG
1 TATTATA-TTATTG
27735937 TATTATATT
1 TATTATATT
27735946 TAGGTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.07
12 3 0.07
13 10 0.24
14 24 0.59
15 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (13 bp):
TATTATATTATTG
Found at i:27735946 original size:14 final size:14
Alignment explanation
Indices: 27735891--27735947 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
27735881 GCTTATTATA
27735891 TATTGT-TTAGTATT
1 TATTGTATTA-TATT
27735905 T-TTGTATTGATA-T
1 TATTGTATT-ATATT
*
27735918 TATTGTACTATATT
1 TATTGTATTATATT
27735932 TATTGTATTATATT
1 TATTGTATTATATT
27735946 TA
1 TA
27735948 GGTGTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.24
14 27 0.73
15 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (14 bp):
TATTGTATTATATT
Found at i:27736230 original size:43 final size:42
Alignment explanation
Indices: 27736182--27736325 Score: 184
Period size: 43 Copynumber: 3.3 Consensus size: 42
27736172 TTATTTGAAA
*** *
27736182 AAACGCCGCTAAAAATAAAGACCTTTAGCTGCGCTTTTATCAC
1 AAACGCCGC-AAAAATCTTGACCTTTAGCTGCACTTTTATCAC
27736225 AAACGCCGCAACAAATCTTGACCTTTAGC-GCCACTTTTATCAC
1 AAACGCCGCAA-AAATCTTGACCTTTAGCTG-CACTTTTATCAC
27736268 AAACGCCGCAAAAGATCTTGACCTTTAG-TGGCACTTTTATCAC
1 AAACGCCGCAAAA-ATCTTGACCTTTAGCT-GCACTTTTATCAC
27736311 AAACGCCGCTAAAAA
1 AAACGCCGC-AAAAA
27736326 CATAACCTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
42 5 0.05
43 81 0.89
44 5 0.05
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAAAAATCTTGACCTTTAGCTGCACTTTTATCAC
Found at i:27740779 original size:23 final size:23
Alignment explanation
Indices: 27740736--27740780 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27740726 TATATCAATA
* *
27740736 CTATTTTAACTTATTTATTAATT
1 CTATTTAAACTAATTTATTAATT
27740759 CTATTTAAACTAATATT-TTAAT
1 CTATTTAAACTAAT-TTATTAAT
27740781 ATATCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (23 bp):
CTATTTAAACTAATTTATTAATT
Found at i:27741234 original size:21 final size:21
Alignment explanation
Indices: 27741194--27741234 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27741184 AACCCTAAAT
* * *
27741194 CCTTAACTCTTAATCTCTAAC
1 CCTTAACCCTTAACCCCTAAC
27741215 CCTTAACCCTTAACCCCTAA
1 CCTTAACCCTTAACCCCTAA
27741235 ATCACAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (21 bp):
CCTTAACCCTTAACCCCTAAC
Found at i:27741273 original size:14 final size:15
Alignment explanation
Indices: 27741254--27741286 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
27741244 CTTAAACTAG
27741254 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
27741268 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
27741283 AATC
1 AATC
27741287 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:27741799 original size:40 final size:40
Alignment explanation
Indices: 27741723--27741799 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
27741713 CGCTTTTTCT
* *
27741723 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATG
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTTATG
*
27741763 TAAAGCGCCGCTAATGCTCGATTTTTAGCAGCGTTTT
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTT
27741800 TTGTCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTTATG
Found at i:27744359 original size:38 final size:33
Alignment explanation
Indices: 27744288--27744353 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
27744278 TAATGCAAGT
27744288 ATAACTTAAGCATGATTTTATTTAATTTAACAA
1 ATAACTTAAGCATGATTTTATTTAATTTAACAA
27744321 ATAACTTAAGCATGATTTTATTTAATTTAACAA
1 ATAACTTAAGCATGATTTTATTTAATTTAACAA
27744354 CACAAACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (33 bp):
ATAACTTAAGCATGATTTTATTTAATTTAACAA
Found at i:27744364 original size:29 final size:32
Alignment explanation
Indices: 27744288--27744369 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
27744278 TAATGCAAGT
*
27744288 ATAACTTAAGCATGATTTTATTTAATTTAACAA
1 ATAAC-TAAACATGATTTTATTTAATTTAACAA
*
27744321 ATAACTTAAGCATGATTTTATTTAATTTAAC-A
1 ATAAC-TAAACATGATTTTATTTAATTTAACAA
*
27744353 A-CAC-AAACATGATTTTA
1 ATAACTAAACATGATTTTA
27744370 ATAATTCAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
29 12 0.26
31 2 0.04
32 2 0.04
33 31 0.66
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (32 bp):
ATAACTAAACATGATTTTATTTAATTTAACAA
Found at i:27745843 original size:27 final size:27
Alignment explanation
Indices: 27745802--27745865 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
27745792 CCAAAAGTGG
* *
27745802 AAGCCTCTGTGGCAATCTT-TAAAATGA
1 AAGCCTTTGTTGCAAT-TTATAAAATGA
* *
27745829 AAGTCTTTGTTGCAATTTATGAAATGA
1 AAGCCTTTGTTGCAATTTATAAAATGA
27745856 AAGCCTTTGT
1 AAGCCTTTGT
27745866 AGCATAGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (27 bp):
AAGCCTTTGTTGCAATTTATAAAATGA
Found at i:27746526 original size:17 final size:18
Alignment explanation
Indices: 27746494--27746527 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27746484 TTCTTACCAA
27746494 AAAATATATAAAAATTTT
1 AAAATATATAAAAATTTT
*
27746512 AAAATA-ATTAAAATTT
1 AAAATATATAAAAATTT
27746528 ACTTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATATAAAAATTTT
Found at i:27756518 original size:18 final size:19
Alignment explanation
Indices: 27756490--27756526 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27756480 GCATTCACAT
27756490 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
27756509 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
27756527 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:27756811 original size:21 final size:20
Alignment explanation
Indices: 27756766--27756811 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
27756756 TTGTTGGAAT
27756766 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
27756785 GCTTGAATTTAATTCGAA-TTA
1 GGTTGAATTTAA-TC-AATTTA
27756806 GGTTGA
1 GGTTGA
27756812 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 7 0.32
21 10 0.45
22 2 0.09
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:27764659 original size:24 final size:24
Alignment explanation
Indices: 27764570--27764664 Score: 136
Period size: 24 Copynumber: 4.0 Consensus size: 24
27764560 CACGAAATAG
* * *
27764570 TGAAAAGTTTGAAAAGGTTACTAA
1 TGAAAAGGTTGAAAAGGATACCAA
* *
27764594 TGAAAAGGTTGAAAAGGTTATCAA
1 TGAAAAGGTTGAAAAGGATACCAA
*
27764618 TGAAAAGGTCGAAAAGGATACCAA
1 TGAAAAGGTTGAAAAGGATACCAA
27764642 TGAAAAGGTTGAAAAGGATACCA
1 TGAAAAGGTTGAAAAGGATACCA
27764665 TTATATTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.21
Consensus pattern (24 bp):
TGAAAAGGTTGAAAAGGATACCAA
Found at i:27769272 original size:20 final size:20
Alignment explanation
Indices: 27769226--27769291 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
27769216 TATTTATAAT
* *
27769226 GATTTA-CAAAATTTCTAAG
1 GATTTACCAAAATATCCAAG
*
27769245 G-TTATACCAAAATATCCATG
1 GATT-TACCAAAATATCCAAG
* *
27769265 GATTTACCAACATATCTAAG
1 GATTTACCAAAATATCCAAG
27769285 GATTTAC
1 GATTTAC
27769292 TAAAGTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 31 0.82
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
GATTTACCAAAATATCCAAG
Found at i:27769352 original size:20 final size:20
Alignment explanation
Indices: 27769313--27769372 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
27769303 AGGCTACTTG
*
27769313 GAAATTTTTGTAAATCCTTA
1 GAAATTTTGGTAAATCCTTA
*
27769333 GATATTTTGGTATAAT-CTTA
1 GAAATTTTGGTA-AATCCTTA
*
27769353 GAAATTTTGGTAAATTCTTA
1 GAAATTTTGGTAAATCCTTA
27769373 AGGTTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (20 bp):
GAAATTTTGGTAAATCCTTA
Found at i:27769494 original size:20 final size:19
Alignment explanation
Indices: 27769451--27769564 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 19
27769441 AGTTAAAAAC
* *
27769451 CCTTAGAAATATTGGTAACT
1 CCTTA-AAATTTTGGTAAAT
*
27769471 CCTTGGAAATTTTGGTATAA-
1 CCTT-AAAATTTTGGTA-AAT
27769491 CCTTAAGAATTTTGGTAAAT
1 CCTTAA-AATTTTGGTAAAT
27769511 CCTTAAATATTTTGGTATAA-
1 CCTTAAA-ATTTTGGTA-AAT
27769531 CC-TACTAAATTTTGGTAAAT
1 CCTTA--AAATTTTGGTAAAT
27769551 CCTTAGAAATTTTG
1 CCTTA-AAATTTTG
27769565 ATATGCCAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.10
20 64 0.81
21 7 0.09
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
CCTTAAAATTTTGGTAAAT
Found at i:27769506 original size:40 final size:38
Alignment explanation
Indices: 27769457--27769564 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
27769447 AAACCCTTAG
* *
27769457 AAATATTGGTAACTCCTTGGAAATTTTGGTATAACCTTA-
1 AAATTTTGGTAAATCCTT-GAAATTTTGGTATAACC-TAC
*
27769496 AGAATTTTGGTAAATCCTTAAATATTTTGGTATAACCTAC
1 A-AATTTTGGTAAATCCTTGAA-ATTTTGGTATAACCTAC
27769536 TAAATTTTGGTAAATCCTTAGAAATTTTG
1 -AAATTTTGGTAAATCCTT-GAAATTTTG
27769565 ATATGCCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.08
40 52 0.87
41 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (38 bp):
AAATTTTGGTAAATCCTTGAAATTTTGGTATAACCTAC
Found at i:27769632 original size:20 final size:20
Alignment explanation
Indices: 27769607--27769671 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
27769597 GGCACTAAGG
27769607 AAATCTCTAGAAATATTGGT
1 AAATCTCTAGAAATATTGGT
* * **
27769627 AAATCTTTCGAAGCATTGGT
1 AAATCTCTAGAAATATTGGT
*
27769647 AAAT-TCTTAGAAATTTTGGT
1 AAATCTC-TAGAAATATTGGT
27769667 AAATC
1 AAATC
27769672 CTTAGATATT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
AAATCTCTAGAAATATTGGT
Found at i:27769675 original size:20 final size:20
Alignment explanation
Indices: 27769614--27769677 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
27769604 AGGAAATCTC
*
27769614 TAGAAATATTGGTAAATCTT
1 TAGAAATATTGGTAAATCCT
* ** *
27769634 TCGAAGCATTGGTAAATTCT
1 TAGAAATATTGGTAAATCCT
*
27769654 TAGAAATTTTGGTAAATCCT
1 TAGAAATATTGGTAAATCCT
27769674 TAGA
1 TAGA
27769678 TATTTTGATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (20 bp):
TAGAAATATTGGTAAATCCT
Found at i:27772094 original size:43 final size:43
Alignment explanation
Indices: 27772026--27772137 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
27772016 AACTAGTACA
** * * * *
27772026 ATGCCAACGTCCCAGACGTGATCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACAAGGTCTTACACGCAAACACA-AGTCG
27772069 ATGCC-ACTGTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
1 ATGCCAAC-GTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
**
27772112 ATGCCAACGTCCCAGACGTGGTCTTA
1 ATGCCAACGTCCCAGACAAGGTCTTA
27772138 AACGATAACG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 3 0.05
43 53 0.91
44 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
Found at i:27778345 original size:43 final size:42
Alignment explanation
Indices: 27778291--27778461 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 42
27778281 ACATAAGATT
* * *
27778291 TCGATATGTGTTTTCGTGTAAGACCACATCTGGGACATTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* *
27778334 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* *
27778377 TCGTATT-TGATT-TGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGACATTGGCA
* * *
27778418 TCGATATGTGATTACATGTAAGACCACGTTTGGGACGTTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
27778461 T
1 T
27778462 TGTCCAAGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.02
41 29 0.27
42 9 0.08
43 66 0.61
44 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
TCGATTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:27778452 original size:84 final size:84
Alignment explanation
Indices: 27778306--27778461 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
27778296 ATGTGTTTTC
* * * *
27778306 GTGTAAGACCACATCTGGGACATTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACATCTGGGACAGTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGACA
27778371 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
* *
27778390 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGA-TATGTGATTACATGTAAGACCACGTTTGGGA
1 GTGTAAGACCAC-ATCTGGGACAGTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTGGGA
*
27778453 CGTTGGCAT
64 CATTGGCAT
27778462 TGTCCAAGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
83 2 0.03
84 61 0.97
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACATCTGGGACAGTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:27781876 original size:43 final size:43
Alignment explanation
Indices: 27781810--27781925 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
27781800 AACTAGTACA
* * * * *
27781810 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGCAAACACA-AGTCG
27781853 ATGCC-ACTATCCCAGACAG-GGTCTTACACGCAAACACAAGTCG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGCAAACACAAGTCG
*
27781896 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACATCCCAGACGTGGTCTTACACG
27781926 ATAACGCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 4 0.06
43 55 0.89
44 3 0.05
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGCAAACACAAGTCG
Found at i:27784614 original size:43 final size:43
Alignment explanation
Indices: 27784565--27784870 Score: 325
Period size: 43 Copynumber: 7.2 Consensus size: 43
27784555 AGAAATAAAT
* **
27784565 GCCGCTATAGATTATGACCTTTAGTAGCGCTTTTTCCACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAAC
* * * *
27784608 ACCGCTATAGATCAGGACTTTTAGCGGTGCTTTTTCCACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAAC
*
27784651 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTAT--ACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTT-TCCACAAAC
* * * * *
27784693 GCCGCTATAGCTCAAGATCTTTAGCGGTGCTTATTCCACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAAC
* * * * *
27784736 ACCGCTATAGATCATGACTTTTAACGGTGCTTTTCCCACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAAC
* *
27784779 GCCGCTATAGGTCATGA-CTTGTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCATGACCTT-TAGCGGCGCTTTTTCCACAAAC
* * **
27784822 GCCGCTATAGAACA-AACCTTTAGCGGC-AATTTTCACACAAAC
1 GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTC-CACAAAC
*
27784864 ACCGCTA
1 GCCGCTA
27784871 AAAACATATC
Statistics
Matches: 222, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
41 5 0.02
42 58 0.26
43 158 0.71
44 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
GCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAAC
Found at i:27784804 original size:128 final size:127
Alignment explanation
Indices: 27784581--27784870 Score: 386
Period size: 128 Copynumber: 2.3 Consensus size: 127
27784571 ATAGATTATG
** * *
27784581 ACCTTTAGTAGCGCTTTTTCCACAAACACCGCTATAGATCAGGACTTTTAGCGGTGCTTTTTCCA
1 ACCTTTAGCGGCGC-TTTTCCACAAACACCGCTATAGATCAGGACTTTTAACGGTGCTTTTCCCA
* **
27784646 CAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-ATACAAACGCCGCTATAGCTCAA
65 CAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAACAA
* * *
27784708 GATCTTTAGCGGTGCTTATTCCACAAACACCGCTATAGATCATGACTTTTAACGGTGCTTTTCCC
1 -ACCTTTAGCGGCGCTT-TTCCACAAACACCGCTATAGATCAGGACTTTTAACGGTGCTTTTCCC
* * *
27784773 ACAAACGCCGCTATAGGTCATGA-CTTGTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAA
64 ACAAACGCCGCTATAGATCAGGACCTT-TAGCGGCGCTTTTCACACAAACGCCGCTATAGAACAA
**
27784837 ACCTTTAGCGGCAATTTTCACACAAACACCGCTA
1 ACCTTTAGCGGCGCTTTTC-CACAAACACCGCTA
27784871 AAAACATATC
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
127 8 0.06
128 114 0.81
129 19 0.13
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (127 bp):
ACCTTTAGCGGCGCTTTTCCACAAACACCGCTATAGATCAGGACTTTTAACGGTGCTTTTCCCAC
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAACAA
Found at i:27785003 original size:35 final size:35
Alignment explanation
Indices: 27784968--27785035 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
27784958 CTACGAAAAT
*
27784968 TTTAACTTTAAAA-CTAAATATAA-AAATTAATAAA
1 TTTAAATTTAAAATCTAAA-ATAATAAATTAATAAA
*
27785002 TTTAAATTTAAAATTTAAAATAATAAATTAATAA
1 TTTAAATTTAAAATCTAAAATAATAAATTAATAA
27785036 CACAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
TTTAAATTTAAAATCTAAAATAATAAATTAATAAA
Found at i:27788067 original size:42 final size:42
Alignment explanation
Indices: 27787976--27788067 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
27787966 CTAACCCGAC
* * *
27787976 CCCTAAATCCCTAACTCTTAACCCCTATATCTAACTCCTAAA
1 CCCTAAATCCCTAACCCTTAAACCATATATCTAACTCCTAAA
* * *
27788018 CCTTAAATCCC-AACCCTTAAACCATAATCTCTAA-TCCATAAT
1 CCCTAAATCCCTAACCCTTAAACCAT-ATATCTAACTCC-TAAA
27788060 CCCTAAAT
1 CCCTAAAT
27788068 TTATACTCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (42 bp):
CCCTAAATCCCTAACCCTTAAACCATATATCTAACTCCTAAA
Found at i:27788287 original size:15 final size:15
Alignment explanation
Indices: 27788267--27788339 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
27788257 AATGTCTAAC
27788267 CCCTAAACCCTTAAA-
1 CCCTAAA-CCTTAAAT
*
27788282 CCCTAAATCTTAAAT
1 CCCTAAACCTTAAAT
*
27788297 CCCT-AATC-TATAAT
1 CCCTAAACCTTA-AAT
* *
27788311 CCCTAAACC-CATACT
1 CCCTAAACCTTA-AAT
27788326 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
27788340 ATAGTAACTC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.04
14 17 0.35
15 28 0.58
16 1 0.02
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCTAAACCTTAAAT
Found at i:27788295 original size:14 final size:14
Alignment explanation
Indices: 27788276--27788317 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
27788266 CCCCTAAACC
27788276 CTTAAACCCTAAAT
1 CTTAAACCCTAAAT
27788290 CTTAAATCCCT-AAT
1 CTTAAA-CCCTAAAT
*
27788304 CTATAATCCCTAAA
1 CT-TAAACCCTAAA
27788318 CCCATACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (14 bp):
CTTAAACCCTAAAT
Found at i:27788780 original size:82 final size:82
Alignment explanation
Indices: 27788671--27788830 Score: 248
Period size: 82 Copynumber: 2.0 Consensus size: 82
27788661 CCAATTAAGA
** * *
27788671 TAAAGCCCCCAACATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAACCCCAAGCATTAGCGGCAC
1 TAAAGCCCCCAACATTAGCGGCGCTTTTTCAAAAACACCGCTAAAACCCCAAGCATTAGCGACAC
27788736 TTTTTAGAAAACGCCGC
66 TTTTTAGAAAACGCCGC
* * * *
27788753 TAAAGCCCCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAACCCCGAGCATTATCGACAC
1 TAAAGCCCCCAACATTAGCGGCGCTTTTTCAAAAACACCGCTAAAACCCCAAGCATTAGCGACAC
27788818 TTTTTAGAAAACG
66 TTTTTAGAAAACG
27788831 ACGTCATTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (82 bp):
TAAAGCCCCCAACATTAGCGGCGCTTTTTCAAAAACACCGCTAAAACCCCAAGCATTAGCGACAC
TTTTTAGAAAACGCCGC
Found at i:27788821 original size:41 final size:41
Alignment explanation
Indices: 27788683--27788830 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
27788673 AAGCCCCCAA
* * * *
27788683 CATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAACCCCAAG
1 CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
*
27788724 CATTAGCGGCACTTTTT-AGAAAACGCCGCTAAAGCCCCGAG
1 CATTAGCGGCACTTTTTCA-AAAACGCCGCTAAAACCCCGAG
* *
27788765 CATTAGCGGCGCTTTTTCAAAAACACCGCTAAAACCCCGAG
1 CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
* *
27788806 CATTATCGACACTTTTT-AGAAAACG
1 CATTAGCGGCACTTTTTCA-AAAACG
27788831 ACGTCATTGG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.02
41 89 0.97
42 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (41 bp):
CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
Found at i:27794807 original size:51 final size:50
Alignment explanation
Indices: 27794685--27794868 Score: 217
Period size: 51 Copynumber: 3.6 Consensus size: 50
27794675 TATCATTCGA
* * * * *
27794685 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACCTTCCGG
*
27794735 TTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAA-CCTTCCGG
* * ** * *
27794786 TACACATAGTAGCCTGCACATAATACTACACATGTGACCGTTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-AAACCT-TCCGG
*
27794837 TACACGTAGTAGCCTGCACTTAGTACTACACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
27794869 CGTGTTTACA
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
50 38 0.33
51 75 0.65
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACCTTCCGG
Found at i:27796998 original size:56 final size:56
Alignment explanation
Indices: 27796938--27797053 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
27796928 CTCGAGTATC
27796938 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
1 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
27796994 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
1 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
27797050 GATA
1 GATA
27797054 GGTTTTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (56 bp):
GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
Found at i:27798803 original size:19 final size:20
Alignment explanation
Indices: 27798762--27798803 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27798752 AGTGTTACAA
*
27798762 GTAAATCTTTAAAAATGTTG
1 GTAAATCATTAAAAATGTTG
*
27798782 GTAAATCATTAGAAAT-TTG
1 GTAAATCATTAAAAATGTTG
27798801 GTA
1 GTA
27798804 TGACGGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAAATCATTAAAAATGTTG
Found at i:27798911 original size:40 final size:40
Alignment explanation
Indices: 27798843--27798962 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
27798833 GATACTCAGA
* *
27798843 AAATTTTTAGAAATTTTGAG-AAATCCTTAAAAATTTTGGT
1 AAATTCTTAGATATTTT-AGTAAATCCTTAAAAATTTTGGT
* **
27798883 -AATTCCTTAGATATTTTAGTATAA-CCTTAGAAATTTTAAT
1 AAATT-CTTAGATATTTTAGTA-AATCCTTAAAAATTTTGGT
* *
27798923 AAATTCTTAGATATTTTGGTAAATCCTTAAAAATATTGGT
1 AAATTCTTAGATATTTTAGTAAATCCTTAAAAATTTTGGT
27798963 TTCATTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
39 8 0.12
40 51 0.78
41 6 0.09
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (40 bp):
AAATTCTTAGATATTTTAGTAAATCCTTAAAAATTTTGGT
Found at i:27798961 original size:20 final size:20
Alignment explanation
Indices: 27798849--27798962 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
27798839 CAGAAAATTT
27798849 TTAGAAATTTTGAG-AAATCC
1 TTAGAAATTTTG-GTAAATCC
* *
27798869 TTAAAAATTTTGGTAATTCC
1 TTAGAAATTTTGGTAAATCC
* *
27798889 TTAGATATTTTAGTATAA-CC
1 TTAGAAATTTTGGTA-AATCC
** *
27798909 TTAGAAATTTTAATAAATTC
1 TTAGAAATTTTGGTAAATCC
*
27798929 TTAGATATTTTGGTAAATCC
1 TTAGAAATTTTGGTAAATCC
* *
27798949 TTAAAAATATTGGT
1 TTAGAAATTTTGGT
27798963 TTCATTTTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 71 0.95
21 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (20 bp):
TTAGAAATTTTGGTAAATCC
Found at i:27817485 original size:18 final size:19
Alignment explanation
Indices: 27817459--27817497 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
27817449 ATCAGGTTTT
* *
27817459 TTTTTATTTTTTTAT-ATA
1 TTTTAATTTTATTATGATA
27817477 TTTTAATTTTATTATGATA
1 TTTTAATTTTATTATGATA
27817496 TT
1 TT
27817498 GAGGTTCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTAATTTTATTATGATA
Found at i:27818419 original size:13 final size:13
Alignment explanation
Indices: 27818383--27818412 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
27818373 AGGTGATTTA
27818383 TATATATCTA-TC
1 TATATATCTATTC
27818395 TATATATCTATTC
1 TATATATCTATTC
27818408 TATAT
1 TATAT
27818413 TATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATCTATTC
Found at i:27820781 original size:20 final size:20
Alignment explanation
Indices: 27820756--27820795 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27820746 TTTTCCGGAA
27820756 ATTTCTGAAAAATGATTTAC
1 ATTTCTGAAAAATGATTTAC
*
27820776 ATTTCTGGAAAATGATTTAC
1 ATTTCTGAAAAATGATTTAC
27820796 TGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTTCTGAAAAATGATTTAC
Found at i:27820918 original size:20 final size:20
Alignment explanation
Indices: 27820893--27820931 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27820883 GTTATTACAT
27820893 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
27820913 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
27820932 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:27822085 original size:32 final size:32
Alignment explanation
Indices: 27822041--27822101 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
27822031 TGTCAATCAT
27822041 TTCAATAACTAACAAGCTTAAAACATAATAAA
1 TTCAATAACTAACAAGCTTAAAACATAATAAA
*
27822073 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATAACTAACAAGCTTAAAACATAAT
27822102 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATAACTAACAAGCTTAAAACATAATAAA
Found at i:27822108 original size:27 final size:27
Alignment explanation
Indices: 27822042--27822128 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 27
27822032 GTCAATCATT
*
27822042 TCAATAACTAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGCTTAAAAC---AT-AA
27822073 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGCTTAAAACATAA
** *
27822101 TCAATATCTAACAAATTTAAGACATAA
1 TCAATATCTAACAAGCTTAAAACATAA
27822128 T
1 T
27822129 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 25 0.49
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (27 bp):
TCAATATCTAACAAGCTTAAAACATAA
Found at i:27829210 original size:29 final size:28
Alignment explanation
Indices: 27829153--27829212 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
27829143 GGTGCCTTCG
* *
27829153 AACCAATAACTCAGTATCACTTGGTTTA
1 AACCAATAACTCAGTACCACTTGGCTTA
* *
27829181 AACCAATAGCTCGGATACCACTTGGCTTA
1 AACCAATAACTCAG-TACCACTTGGCTTA
27829210 AAC
1 AAC
27829213 TTGGCTCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (28 bp):
AACCAATAACTCAGTACCACTTGGCTTA
Found at i:27835092 original size:5 final size:5
Alignment explanation
Indices: 27835084--27835109 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27835074 TTTCATCCGA
27835084 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
27835110 GCCGATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:27838299 original size:37 final size:37
Alignment explanation
Indices: 27838258--27838339 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
27838248 AAATATTTAT
* *
27838258 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
*
27838295 TAATCAATGTTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
27838332 TAATCAAT
1 TAATCAAT
27838340 ATATTTATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
Found at i:27838420 original size:33 final size:33
Alignment explanation
Indices: 27838382--27838457 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
27838372 TTAAAACTTG
*
27838382 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
27838415 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
27838448 AATTATACAT
1 AATTATACAT
27838458 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:27840961 original size:92 final size:91
Alignment explanation
Indices: 27840797--27841005 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
27840787 TTGATTTTAG
* * * * *
27840797 TAAATCCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTTT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
27840862 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
27840889 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
27840953 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
27840981 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
27841006 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 69 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:27840968 original size:24 final size:25
Alignment explanation
Indices: 27840933--27840980 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
27840923 TTATGAAATT
27840933 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
27840957 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
27840981 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:27841134 original size:66 final size:64
Alignment explanation
Indices: 27841059--27841269 Score: 196
Period size: 66 Copynumber: 3.4 Consensus size: 64
27841049 AAATATATTT
27841059 AATATTAATTATTTCAAATTTTCATTTATAATATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTATAATATCATATATTATGATTTGAGTAAATTCATATAA
27841124 G
64 G
* * * **
27841125 AATATTAATTATTAAGAATTTTA-TTA-AAT-T-ATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTATAATATCATATATTATGATTTGAGTAAATTCATATAAG
*
27841179 AATAATAATTATGTT-AATTTATATTT-TACAGTATCATATATTATGATTTGAGTAAATTCATAT
1 AATATTAATTAT-TTAAATTT-TATTTATA-A-TATCATATATTATGATTTGAGTAAATTCATAT
27841242 AAG
62 AAG
*
27841245 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
27841270 AAATTATATA
Statistics
Matches: 114, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
53 5 0.04
54 13 0.11
55 8 0.07
56 2 0.02
57 3 0.03
58 2 0.02
59 8 0.07
60 8 0.07
61 8 0.07
62 2 0.02
63 5 0.04
64 4 0.04
65 7 0.06
66 34 0.30
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTATAATATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:27841159 original size:120 final size:120
Alignment explanation
Indices: 27841021--27841313 Score: 495
Period size: 120 Copynumber: 2.4 Consensus size: 120
27841011 AATTATTTTA
* * *
27841021 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
27841084 TTATA-A-TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TT-TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
27841141 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
27841206 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
27841261 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
27841314 TAAATATGAT
Statistics
Matches: 166, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
118 2 0.01
119 10 0.06
120 152 0.92
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:27841181 original size:15 final size:15
Alignment explanation
Indices: 27841146--27841197 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
27841136 TTAAGAATTT
*
27841146 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27841160 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27841174 TATTTAATAATAAT-
1 TATTTAATTATAATA
27841188 TATGTTAATT
1 TAT-TTAATT
27841198 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27841296 original size:16 final size:16
Alignment explanation
Indices: 27841275--27841316 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27841265 TTATTAAATT
*
27841275 ATATATTTTAATTATA
1 ATATATTTTAATAATA
27841291 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
27841306 AT-TATGTTTAA
1 ATATAT-TTTAA
27841317 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:27841301 original size:15 final size:15
Alignment explanation
Indices: 27841266--27841307 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27841256 TTAAGAATTT
*
27841266 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27841280 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27841294 TATTTAATAATAAT
1 TATTTAATTATAAT
27841308 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27841428 original size:157 final size:157
Alignment explanation
Indices: 27841250--27841566 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
27841240 ATAAGAATAT
*
27841250 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
27841315 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
27841380 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
27841407 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
27841472 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
27841537 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
27841564 TAA
1 TAA
27841567 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:27841447 original size:18 final size:17
Alignment explanation
Indices: 27841419--27841453 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27841409 ATTATTAAGA
*
27841419 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27841436 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27841454 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27841710 original size:16 final size:16
Alignment explanation
Indices: 27841689--27841740 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
27841679 GATTTGCTAT
27841689 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
27841705 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
27841721 TACACATCTAATTCAA
1 TACACCTCTAATCCAA
27841737 TACA
1 TACA
27841741 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:27843849 original size:33 final size:33
Alignment explanation
Indices: 27843812--27843896 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
27843802 TACTCTATAT
*
27843812 TTGGTGTGTTGGTTGGATTAGCTCTTA-TGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTC-GAGTGAGCA
* * *
27843845 TTGGTGTGATGGATGGATTGGCTCGAGTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
*
27843878 TCTGGTATGTTTGGTTGGA
1 T-TGGTGTG-TTGGTTGGA
27843897 CTAATGATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 1 0.02
33 28 0.67
34 6 0.14
35 7 0.17
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.39
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
Found at i:27846919 original size:11 final size:11
Alignment explanation
Indices: 27846901--27846935 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27846891 TTGCTCATAC
27846901 TAATTTTTATA
1 TAATTTTTATA
*
27846912 TTATTTTTATA
1 TAATTTTTATA
*
27846923 TAATTTTAATA
1 TAATTTTTATA
27846934 TA
1 TA
27846936 TATAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:27847168 original size:11 final size:11
Alignment explanation
Indices: 27847151--27847189 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27847141 TAATAACAAT
27847151 AAAATAATAGC
1 AAAATAATAGC
* *
27847162 AATATAATAGT
1 AAAATAATAGC
*
27847173 AAAATGATAGC
1 AAAATAATAGC
27847184 AAAATA
1 AAAATA
27847190 GGGAGAAAGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:27847168 original size:22 final size:22
Alignment explanation
Indices: 27847143--27847185 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
27847133 TATCTAAATA
27847143 ATAACAATAAAATAATAGCAAT
1 ATAACAATAAAATAATAGCAAT
* * *
27847165 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
27847186 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAT
Found at i:27851738 original size:18 final size:16
Alignment explanation
Indices: 27851705--27851737 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27851695 AATCAAAGTA
27851705 AATAAAATCTATATAT
1 AATAAAATCTATATAT
*
27851721 AATAAAATCTAAATAT
1 AATAAAATCTATATAT
27851737 A
1 A
27851738 TCTCTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATCTATATAT
Found at i:27852448 original size:36 final size:36
Alignment explanation
Indices: 27852408--27852483 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
27852398 AGCATTGATA
27852408 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
* *
27852444 GCTATCTTGAGTATCATTTGTTAAATCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
27852480 GCTA
1 GCTA
27852484 AACGATGTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (36 bp):
GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
Found at i:27852498 original size:36 final size:35
Alignment explanation
Indices: 27852415--27852498 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
27852405 ATAGCTATCT
* *
27852415 TGAGTATCATTTATTAAACCTGATGTAATGCTATC
1 TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
* * *
27852450 TTGAGTATCATTTGTTAAATCTGATGTAATGCTAAAC
1 -TGAGTACCATTTATTAAACCTGATGTAATGCT-AAC
27852487 -GATGTACCATTT
1 TGA-GTACCATTT
27852499 CACATGTGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 2 0.05
36 38 0.90
37 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (35 bp):
TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
Found at i:27858438 original size:22 final size:22
Alignment explanation
Indices: 27858406--27858457 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
27858396 CCTTTTTAGG
* *
27858406 TATTTTCTTAATAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
27858428 TATTTTTTTAACAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
27858450 TATTTTTT
1 TATTTTTT
27858458 AACTGGTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTTTAACAGTTAAAAAA
Found at i:27864346 original size:62 final size:59
Alignment explanation
Indices: 27864238--27864354 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
27864228 ATCACTTTAA
* * * *
27864238 TATTAAATTAATATAATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
27864297 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATTAA
27864355 GAAAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 1 0.02
62 29 0.58
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:27866034 original size:15 final size:15
Alignment explanation
Indices: 27866010--27866041 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27866000 TATGCATGAA
*
27866010 AAATATAAAAGACAT
1 AAATACAAAAGACAT
27866025 AAATACAAAAGACAT
1 AAATACAAAAGACAT
27866040 AA
1 AA
27866042 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:27869394 original size:24 final size:24
Alignment explanation
Indices: 27869362--27869409 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27869352 CGTATGACAC
27869362 TTGTTAAATTCCACTAAGTAAGAT
1 TTGTTAAATTCCACTAAGTAAGAT
27869386 TTGTTAAATTCCACTAAGTAAGAT
1 TTGTTAAATTCCACTAAGTAAGAT
27869410 GAATCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (24 bp):
TTGTTAAATTCCACTAAGTAAGAT
Found at i:27870534 original size:27 final size:27
Alignment explanation
Indices: 27870300--27870543 Score: 163
Period size: 27 Copynumber: 9.1 Consensus size: 27
27870290 ACACAACATC
*
27870300 AAAGAATAGCCTTTGTGGCGAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* *
27870327 AAAGAATAGTCTTTGTGG-AAAATCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * *
27870353 AAAGAATAGTCTTTGTAGCGAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * *
27870380 GAAGGATAGCCTTTGTGGCAAAGTCTC
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * * *
27870407 AAAGGATAACCTTTCTGGCATACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * ** *
27870434 AAAGAATAACCTTAGTGAAAAACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
** * * *
27870461 AAAGGAAT-GCCTCAGTGGCGAACTTTAA
1 AAA-GAATAGCCTTTGTGGCAAACTCT-G
**
27870489 AAAGAAT-GCCTCAGTGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * *
27870515 AAAGGGAT-GCCTTTGTGGCAGATTCTG
1 AAA-GAATAGCCTTTGTGGCAAACTCTG
27870542 AA
1 AA
27870544 TGGAACGATT
Statistics
Matches: 173, Mismatches: 40, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
26 26 0.15
27 140 0.81
28 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCAAACTCTG
Found at i:27878114 original size:22 final size:21
Alignment explanation
Indices: 27878063--27878114 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
27878053 ATCGCTTAAT
*
27878063 GTCTTGAGACTTATCAAGCTA
1 GTCTTGAGACTAATCAAGCTA
* *
27878084 GTCTCGAGAC-AACTCAATCTA
1 GTCTTGAGACTAA-TCAAGCTA
27878105 GGTCTTGAGA
1 -GTCTTGAGA
27878115 AAAAATGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (21 bp):
GTCTTGAGACTAATCAAGCTA
Found at i:27881976 original size:109 final size:109
Alignment explanation
Indices: 27881770--27882302 Score: 739
Period size: 109 Copynumber: 4.9 Consensus size: 109
27881760 TTTTTTTTAA
* *
27881770 AAAATGAGGCGATATTTTGCGTTTGGAAAGTCGAGAAAACGTGCCCTAATGTGTGCTGGGTTTCG
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAA--TGTGCTGGGTTTCG
* * *
27881835 ATTTTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAAAATTTC
64 ATTTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * *
27881881 AAAATAAGGCAATGTTTTGCGTCTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
* *
27881946 TTTTCTCGCTCAACCAAATAGCCAAATATCCTTTTAAAAATTTC
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * * * *
27881990 AAAATAAGGCAATGTTTTGCTTTTGGAAATTCGAGAAAATGTGCCCTAATGCGCTGGGTTTCAAT
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
*
27882055 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTA
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * *
27882099 AAAACGAGGCAATATTTTGCGTGTAGAAATTCGAGAAAATGTGCCCTAATGTGCTGGG-TTCTGA
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC-GA
* *
27882163 TTTTTCTTGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTT
65 TTTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * * * *
27882208 AAAACGAGGTAATATTTTGTGTTTGGAAACTCGAGAAAACGTGCCCTAATGCGTTGGGTTTCGA-
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
* *
27882272 TTTT-TCGTTGGACCAAATAGCCAAATATCCT
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCT
27882303 CTTATATCTT
Statistics
Matches: 383, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
107 24 0.06
108 7 0.02
109 305 0.80
110 3 0.01
111 44 0.11
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
Found at i:27884542 original size:114 final size:114
Alignment explanation
Indices: 27884279--27884947 Score: 736
Period size: 114 Copynumber: 5.9 Consensus size: 114
27884269 CTATCAAACA
* * * *
27884279 CCGCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTTATGTATATTAGAATTAGTGGCGCATA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
* * * * * *
27884344 TGAAAAAACGCTGCTAAAGTA-AGTATTAGCGGCGAT-TTGTGAAAAGCG
66 TGAGAAAACGCCGCTAACGCATAGTATTAGCGGC-ATGTCGTCAAAAGCG
* * *
27884392 CCACAAAATATATTAACCAAAACGCAGAGTTTGGTCTTGAGCTATATTAGAATTAGTGGCGCTTA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
* * * *
27884457 TGGGAAAACGCTGCTAACGGATAGTATTAGTGGCATGTCGTCAAAAGCG
66 TGAGAAAACGCCGCTAACGCATAGTATTAGCGGCATGTCGTCAAAAGCG
* * *
27884506 CCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTTTACTAGAATTAGTGGCGCTTA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
* * * *
27884571 TGGGAAAATGCCGCTAACGCATAGTATTAGTGGCGTGTCGTCAAAAGCG
66 TGAGAAAACGCCGCTAACGCATAGTATTAGCGGCATGTCGTCAAAAGCG
* **
27884620 CCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGAACTTA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
** * * * * ** **
27884685 TTCGAAAACACCGTTAATGCATAGTATTAGCGACGCGTCGTCAGGAGCG
66 TGAGAAAACGCCGCTAACGCATAGTATTAGCGGCATGTCGTCAAAAGCG
* *
27884734 CCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCTTA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
* * * *
27884799 TGAGAAAACGCCGCTAATGCATAGTATTAGCGGCGCT-TGGT-AGAAAACG
66 TGAGAAAACGCCGCTAACGCATAGTATTAGCGGC-ATGTCGTCA-AAAGCG
* * * * * * * * *
27884848 CCGCAAAATATTTTAACAAAAACGCA-ATCCTTTGGTCTTAATGTATACTAGCAGTAGTGGCACT
1 CCGCAAAATATCTTAACCAAAACGCAGA--GTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * ** *
27884912 TACGGGAAAACGCCGCGAAAACATATTATTAGCGGC
64 TATGAGAAAACGCCGCTAACGCATAGTATTAGCGGC
27884948 GCGTTTTGGG
Statistics
Matches: 480, Mismatches: 70, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
113 79 0.16
114 342 0.71
115 59 0.12
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (114 bp):
CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA
TGAGAAAACGCCGCTAACGCATAGTATTAGCGGCATGTCGTCAAAAGCG
Found at i:27884852 original size:342 final size:341
Alignment explanation
Indices: 27884279--27884927 Score: 831
Period size: 342 Copynumber: 1.9 Consensus size: 341
27884269 CTATCAAACA
* * * **
27884279 CCGCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTTATGTATATTAGAATTAGTGGCGCATA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGAACATA
* * * * *
27884344 TGAAAAAACGCTGCTAAAGTAAGTATTAGCGGCGATTTGTGAAAAGCGCCACAAAATATATTAAC
66 TGAAAAAACGCTGCTAAAGCAAGTATTAGCGACGAGTCGTCAAAAGCGCCACAAAATATATTAAC
* * *
27884409 CAAAACGCAGAGTTTGGTCTTGAGCTATATTAGAATTAGTGGCGCTTATGGGAAAACGCTGCTAA
131 CAAAACGCAGAGTTTGGTCTTAAGCTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGCTAA
* * * * * *
27884474 CGGATAGTATTAGTGGCATGTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGA-GTTT
196 CGCATAGTATTAGCGGCATGTCGTCAAAAACGCCGCAAAATATCTTAACAAAAACGCA-ACCTTT
* * * * * *
27884538 GGTCTTGAGGTTTACTAGAATTAGTGGCGCTTATGGGAAAATGCCGCTAACGCATAGTATTAGTG
260 GGTCTTAAGGTATACTAGAAGTAGTGGCACTTACGGGAAAACGCCGCTAACGCATAGTATTAGTG
27884603 GCGTGTCGTCAAAAGCG
325 GCGTGTCGTCAAAAGCG
* *
27884620 CCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGAACTTA
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGAACATA
* * * * ** *
27884685 TTCGAAAACAC-C-GTTAATGCATAGTATTAGCGACGCGTCGTCAGGAGCGCCACAAAATATCTT
66 -T-GAAAAAACGCTGCTAAAGCA-AGTATTAGCGACGAGTCGTCAAAAGCGCCACAAAATATATT
*
27884748 AACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGC
128 AACCAAAACGCAGAGTTTGGTCTTAAGCTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGC
* * * *
27884813 TAATGCATAGTATTAGCGGCGCT-TGGT-AGAAAACGCCGCAAAATATTTTAACAAAAACGCAAT
193 TAACGCATAGTATTAGCGGC-ATGTCGTCA-AAAACGCCGCAAAATATCTTAACAAAAACGCAA-
* *
27884876 CCTTTGGTCTTAATGTATACTAGCAGTAGTGGCACTTACGGGAAAACGCCGC
255 CCTTTGGTCTTAAGGTATACTAGAAGTAGTGGCACTTACGGGAAAACGCCGC
27884928 GAAAACATAT
Statistics
Matches: 260, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
341 66 0.25
342 144 0.55
343 50 0.19
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (341 bp):
CCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGAACATA
TGAAAAAACGCTGCTAAAGCAAGTATTAGCGACGAGTCGTCAAAAGCGCCACAAAATATATTAAC
CAAAACGCAGAGTTTGGTCTTAAGCTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGCTAA
CGCATAGTATTAGCGGCATGTCGTCAAAAACGCCGCAAAATATCTTAACAAAAACGCAACCTTTG
GTCTTAAGGTATACTAGAAGTAGTGGCACTTACGGGAAAACGCCGCTAACGCATAGTATTAGTGG
CGTGTCGTCAAAAGCG
Found at i:27890819 original size:21 final size:21
Alignment explanation
Indices: 27890795--27890847 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
27890785 AGGTGGTAGT
27890795 AAGGGAAGCAGAGGCTGCAGC
1 AAGGGAAGCAGAGGCTGCAGC
*
27890816 AAGGGAAGCAGAGGCTGCAGT
1 AAGGGAAGCAGAGGCTGCAGC
*
27890837 AAGAGAAGCAG
1 AAGGGAAGCAG
27890848 CGAGAGAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.42, T:0.06
Consensus pattern (21 bp):
AAGGGAAGCAGAGGCTGCAGC
Found at i:27891393 original size:41 final size:42
Alignment explanation
Indices: 27891252--27891419 Score: 171
Period size: 41 Copynumber: 3.9 Consensus size: 42
27891242 AAGAACACGA
* *
27891252 GCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTTGTT-TAAGC
1 GCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTT-TTGTAAGC
*
27891294 GCCGCTAAAGAACATGATCATTAGCGGCGTCTTTTTTTAAGCGATAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTTT----G-TAAGC
* *
27891343 GCCGCTAAAGGACATGATCTTTAGCGGCGTTTTTTTGT-AGA
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTGTAAGC
* *
27891384 GCCGGTAAAGAACATGACCTTTAGCGGCGTTTTTTT
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
27891420 CTGTAAACGC
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
41 35 0.32
42 25 0.23
43 4 0.04
44 5 0.05
47 7 0.06
49 32 0.30
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (42 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTGTAAGC
Found at i:27893570 original size:26 final size:26
Alignment explanation
Indices: 27893534--27893756 Score: 225
Period size: 26 Copynumber: 8.6 Consensus size: 26
27893524 CCTGAATAGA
*
27893534 AGGCCTTGAGCCGGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
27893560 AGGCCTTGAGCCGATGTTTGTTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
27893586 AGGCTTTGAGCCAGTGATTACTTAGT
1 AGGCTTTGAGCCGGTGTTTATTTAGC
** * *
27893612 AGGCTTTGAGCTAGTGATTACTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
27893638 AGGCTATGAGTCTGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
27893664 AGGCTTTGAGCTGATGATTATTTAAC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
*
27893690 AGGCTTTGAGCCGATGTTTA-TTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
27893715 AGACTTTGAGTCGGTGTTTATCTT-GC
1 AGGCTTTGAGCCGGTGTTTAT-TTAGC
27893741 AGGCTTTGAGCCGGTG
1 AGGCTTTGAGCCGGTG
27893757 AATGTTTATC
Statistics
Matches: 163, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
25 21 0.13
26 140 0.86
27 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (26 bp):
AGGCTTTGAGCCGGTGTTTATTTAGC
Found at i:27900040 original size:66 final size:63
Alignment explanation
Indices: 27899917--27900115 Score: 229
Period size: 70 Copynumber: 3.0 Consensus size: 63
27899907 AAGTGATAAA
* * * *
27899917 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACACTTTCATAT
1 TTCTTCATTATTTTCATTAAAAAAATTAATTTTAA-CCACATTGACTAGAGAATACTTTCATAT
27899980 TTCTTCATTATTTTCATTAAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTCGTA
1 TTCTTCATTATTTTCATT-AAAAAAATTAATTTTAAC-C-ACATTGACTAGAGAATACTTTC---
27900045 ACTTAT
60 A--TAT
* * *
27900051 TTCTTCACTATTTTCATTAAACACATTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCATTATTTTCATTAAAAAAATTAATTTTAACCA--CATTGACTAGAGAATACTTTCATAT
27900116 CTCACTTTTG
Statistics
Matches: 118, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 18 0.15
65 19 0.16
66 20 0.17
67 1 0.01
68 1 0.01
69 2 0.02
70 37 0.31
71 20 0.17
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (63 bp):
TTCTTCATTATTTTCATTAAAAAAATTAATTTTAACCACATTGACTAGAGAATACTTTCATAT
Found at i:27900071 original size:71 final size:67
Alignment explanation
Indices: 27899917--27900145 Score: 220
Period size: 70 Copynumber: 3.4 Consensus size: 67
27899907 AAGTGATAAA
* * * * *
27899917 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACACTTTC--A--
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAA-CCACATTGACTAGAGAATACTTTCTAACT
27899977 TAT
65 TAT
*
27899980 TTCTTCATTATTTTCATTAAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTCGTA
1 TTCTTCACTATTTTCATT-AAAAAAATTAATTTTAAC-C-ACATTGACTAGAGAATACTTTC-TA
27900045 ACTTAT
62 ACTTAT
* * *
27900051 TTCTTCACTATTTTCATTAAACACATTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCA--CATTGACTAGAGAATACTTTC-TAA
*
27900116 CTCACT
63 CTTA-T
*
27900122 TT-TGT-ACTATTTTTATTAAAAAAA
1 TTCT-TCACTATTTTCATTAAAAAAA
27900146 AAGTTAAATT
Statistics
Matches: 140, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
63 18 0.13
65 16 0.11
66 20 0.14
68 1 0.01
69 2 0.01
70 59 0.42
71 24 0.17
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (67 bp):
TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCACATTGACTAGAGAATACTTTCTAACTT
AT
Found at i:27904683 original size:18 final size:18
Alignment explanation
Indices: 27904660--27904696 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27904650 TAATGCTTAT
27904660 TGAGCCATCACATATCCG
1 TGAGCCATCACATATCCG
27904678 TGAGCCATCACATATCCG
1 TGAGCCATCACATATCCG
27904696 T
1 T
27904697 CCATATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (18 bp):
TGAGCCATCACATATCCG
Found at i:27910175 original size:27 final size:25
Alignment explanation
Indices: 27910117--27910169 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
27910107 GCTCATACAT
*
27910117 GCTGAATATCGATAAGCTCTCTCGA
1 GCTGAATATCGATAAGCTCTCTCAA
* *
27910142 GCTGAATATTGGTAAGCTCTCTCAA
1 GCTGAATATCGATAAGCTCTCTCAA
27910167 GCT
1 GCT
27910170 AAGAATCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (25 bp):
GCTGAATATCGATAAGCTCTCTCAA
Found at i:27911864 original size:4 final size:4
Alignment explanation
Indices: 27911855--27911882 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27911845 TATTTTTAAT
27911855 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
27911883 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:27918257 original size:138 final size:136
Alignment explanation
Indices: 27917989--27918247 Score: 320
Period size: 137 Copynumber: 1.9 Consensus size: 136
27917979 CGAGCCATAA
* * * * **
27917989 ATGGGTCTGCTAACACAAGCTGATGGTCAAAATATAGCTACATGATGTCACTTACACAAGATGGC
1 ATGGGTCTACTAACACAAGCTGATAGTCAAAATATAGCTACACGATGTCACTCACACAAGATAAC
* * * * *
27918054 GATTATCCGCAAAAAATGTCGATCTCAGCCATCGGTAGGACATTCAAGTCAAGCACCTAAAACAT
66 GAGTATCCGCAAAAAATGTAGAACTCAGCCATCAGTAGGACATTCAAGACAAGCACCTAAAACAT
27918119 GGTAAC
131 GGTAAC
* * ** *
27918125 ATGGGTCTACTCACACAAGCTGATAGTCAAAATTTAAGCTACACGATGTTGCTCACACAAGCTAA
1 ATGGGTCTACTAACACAAGCTGATAGTCAAAATAT-AGCTACACGATGTCACTCACACAAGATAA
* * * *
27918190 TGAGTATTCGCAATAAATGCTAGAACTCAGCCATCAGTAGGACATTCAAGACCAGCAC
65 CGAGTATCCGCAAAAAATG-TAGAACTCAGCCATCAGTAGGACATTCAAGACAAGCAC
27918248 TCGAAACATG
Statistics
Matches: 101, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
136 31 0.31
137 37 0.37
138 33 0.33
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (136 bp):
ATGGGTCTACTAACACAAGCTGATAGTCAAAATATAGCTACACGATGTCACTCACACAAGATAAC
GAGTATCCGCAAAAAATGTAGAACTCAGCCATCAGTAGGACATTCAAGACAAGCACCTAAAACAT
GGTAAC
Found at i:27919441 original size:17 final size:18
Alignment explanation
Indices: 27919404--27919442 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
27919394 GGAATTAATT
* *
27919404 AATTATTCATATAACATA
1 AATTATTCATATAAAAAA
27919422 AATTA-TCATATAAAAAA
1 AATTATTCATATAAAAAA
27919439 AATT
1 AATT
27919443 TTAAAACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTCATATAAAAAA
Found at i:27919973 original size:26 final size:26
Alignment explanation
Indices: 27919937--27920003 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
27919927 TACATCATTA
*
27919937 CTCACACGAGCTGTGAAATGGGCCTG
1 CTCACACGAGCTGTGAAATAGGCCTG
* *
27919963 CTCACATGAGCTATGAAATAGGCCTG
1 CTCACACGAGCTGTGAAATAGGCCTG
*
27919989 CTCACACGAGTTGTG
1 CTCACACGAGCTGTG
27920004 GAGAGTCCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (26 bp):
CTCACACGAGCTGTGAAATAGGCCTG
Found at i:27920895 original size:257 final size:259
Alignment explanation
Indices: 27920436--27920956 Score: 931
Period size: 257 Copynumber: 2.0 Consensus size: 259
27920426 AGATAATAGT
*
27920436 TTTAGGACCACAAATCTGACGAGCAAATTATTATTATTTATTATTTTAATGTTTATGAGATGTTA
1 TTTAGGACCACAAATCTGACGAGCAAA-TATTATTATTTATTAGTTTAATGTTTATGAGATGTTA
*
27920501 GTGAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAAA
65 GTAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAAA
*
27920566 AGTAGAGTTTTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATG
130 AGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATG
27920631 GTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGCG
195 GTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGCG
* *
27920696 TTTAGGACCACAAATCTGACGAG-TAA-ATTATTATTTATTAGTTTAATGTTTATGGGATGTTAG
1 TTTAGGACCACAAATCTGACGAGCAAATATTATTATTTATTAGTTTAATGTTTATGAGATGTTAG
* *
27920759 TAAGGTCGTATTGATGTTTGCATGATTAATTAAGTAAAAAGGAA-TAAATTGTAAAAGGTTCAAA
66 TAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAA-GAACTAAATCGTAAAAGGTTCAAA
27920823 AGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATG
130 AGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATG
*
27920888 GTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGCT
195 GTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGCG
27920953 TTTA
1 TTTA
27920957 AAGGTTAAAA
Statistics
Matches: 252, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
257 224 0.89
258 3 0.01
259 2 0.01
260 23 0.09
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (259 bp):
TTTAGGACCACAAATCTGACGAGCAAATATTATTATTTATTAGTTTAATGTTTATGAGATGTTAG
TAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAAAA
GTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATGG
TAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGCG
Found at i:27923011 original size:196 final size:196
Alignment explanation
Indices: 27922677--27923069 Score: 759
Period size: 196 Copynumber: 2.0 Consensus size: 196
27922667 GTATTGAGCT
27922677 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
1 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
27922742 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTACATGTAAGT
66 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTACATGTAAGT
*
27922807 TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
131 TTTGGTCATGTTTTGATGTCTTGATTATGTATACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
27922872 G
196 G
*
27922873 TGATGTTAATGATTGAAATGTGGTAACATATGCATGTTTAGGTAAGTTGTGGATGAATGCATTAG
1 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
27922938 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTACATGTAAGT
66 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTACATGTAAGT
*
27923003 TTTGGTCATGTTTTGATGTCTTGATTATGTATACAAAAGGCCTTTAGGTGTGTGCATGGTTTGGT
131 TTTGGTCATGTTTTGATGTCTTGATTATGTATACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
27923068 G
196 G
27923069 T
1 T
27923070 TTGAAATGGC
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
196 194 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (196 bp):
TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTACATGTAAGT
TTTGGTCATGTTTTGATGTCTTGATTATGTATACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
G
Found at i:27926741 original size:21 final size:21
Alignment explanation
Indices: 27926701--27926741 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27926691 TCACACTTCA
*
27926701 ATCACATACTCATATTTGTTT
1 ATCACATACTCATATCTGTTT
27926722 ATCA-ATACTCATATCCTGTT
1 ATCACATACTCATAT-CTGTT
27926742 GAACACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
ATCACATACTCATATCTGTTT
Found at i:27934630 original size:51 final size:50
Alignment explanation
Indices: 27934464--27934651 Score: 175
Period size: 51 Copynumber: 3.7 Consensus size: 50
27934454 TTATTATCAT
* * * *
27934464 TCGATACACGTAGTAGCCTTCACATAGGACTACACACGTGATCA-AACTTT
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAAC-TA
* * *
27934514 TC-AGTTCACGTAGCAGCCTGCACATAGTACTACACACGTGACCAAAGACT-
1 TCGA-TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATA-ACTA
* ** * * *
27934564 TCCGGTACATATAGTAGCCTGGACATAGTACTACACATGTGACCATTATCTA
1 T-CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TAACTA
* *
27934616 TCGATACACGTAGTAGCCTACACTTAGTACTACACA
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACA
27934652 AGTGTTTATA
Statistics
Matches: 111, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
49 1 0.01
50 38 0.34
51 68 0.61
52 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTA
Found at i:27947161 original size:16 final size:16
Alignment explanation
Indices: 27947140--27947176 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27947130 TTTGGAGAGA
27947140 TTCTTTCCACCATTAT
1 TTCTTTCCACCATTAT
* *
27947156 TTCTTTCCACCTTTTT
1 TTCTTTCCACCATTAT
27947172 TTCTT
1 TTCTT
27947177 CTTCCCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCTTTCCACCATTAT
Found at i:27956421 original size:27 final size:25
Alignment explanation
Indices: 27956342--27956423 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 25
27956332 AACGATATAT
*
27956342 AAAGAAAGCTTTTGTGACATAATAT-A
1 AAAGAAAGC-TTTGTGGCA-AATATGA
* *
27956368 AAAGAAAGCCTTTGTGGTAAAGAATGA
1 AAAGAAAG-CTTTGTGGCAAA-TATGA
27956395 AAAGAAAGCTTATGTGGCAAATCATGA
1 AAAGAAAGCTT-TGTGGCAAAT-ATGA
27956422 AA
1 AA
27956424 TAAAAGCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
25 2 0.04
26 20 0.43
27 24 0.52
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAGAAAGCTTTGTGGCAAATATGA
Found at i:27982642 original size:16 final size:14
Alignment explanation
Indices: 27982604--27982642 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
27982594 CTTAAAGATA
27982604 TCTTCCTTTTTTGT
1 TCTTCCTTTTTTGT
*
27982618 TCATCCTTTTTGTGTT
1 TCTTCCTTTTT-TG-T
27982634 TCTTCCTTT
1 TCTTCCTTT
27982643 CTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
16 9 0.43
ACGTcount: A:0.03, C:0.23, G:0.08, T:0.67
Consensus pattern (14 bp):
TCTTCCTTTTTTGT
Found at i:27992572 original size:15 final size:15
Alignment explanation
Indices: 27992554--27992583 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27992544 TAGGTAGAAA
27992554 TTAAATTAAACAAAT
1 TTAAATTAAACAAAT
*
27992569 TTAAATTAAGCAAAT
1 TTAAATTAAACAAAT
27992584 GGAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TTAAATTAAACAAAT
Found at i:28002162 original size:19 final size:19
Alignment explanation
Indices: 28002138--28002183 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28002128 TGTCAACTAT
*
28002138 ACTTGCATCGACAGTGTAC
1 ACTTGCACCGACAGTGTAC
*
28002157 ACTTGCACCGATAGTGTAC
1 ACTTGCACCGACAGTGTAC
28002176 ACTTGCAC
1 ACTTGCAC
28002184 ATTATTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (19 bp):
ACTTGCACCGACAGTGTAC
Found at i:28005200 original size:19 final size:18
Alignment explanation
Indices: 28005159--28005200 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
28005149 GTTGAGCTGA
*
28005159 AATGGGTCGTGTGGGCCC
1 AATGGGTCGTGTGGCCCC
28005177 AATGGGCTCGTG-GGCCCC
1 AATGGG-TCGTGTGGCCCC
28005195 ACATGG
1 A-ATGG
28005201 ATAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (18 bp):
AATGGGTCGTGTGGCCCC
Found at i:28012127 original size:41 final size:41
Alignment explanation
Indices: 28012065--28012212 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
28012055 GTTAATTATT
28012065 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * *
28012106 CCCTGAATTGTACATACGTGCCCCTATTTATACTTCGATAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* **
28012147 CCTTAAATTGCACATACGTGCCCCTATTTGTACTTTAGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* *
28012188 CCATGAATTGCACATACGTGCCCCT
1 CCCTAAATTGCACATACGTGCCCCT
28012213 GTTTACACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
Found at i:28012129 original size:21 final size:20
Alignment explanation
Indices: 28012065--28012212 Score: 77
Period size: 21 Copynumber: 7.2 Consensus size: 20
28012055 GTTAATTATT
*
28012065 CCCTAAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * *
28012086 CCCTATTTGTAC-TTCGGTAC
1 CCCTAATTGTACATAC-GTGC
28012106 CCCTGAATTGTACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * * *
28012127 CCCTATTTATAC-TTCGATAC
1 CCCTAATTGTACATACG-TGC
* *
28012147 CCTTAAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * *
28012168 CCCTATTTGTACTTTA-GTAC
1 CCCTAATTGTAC-ATACGTGC
* *
28012188 CCATGAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
28012209 CCCT
1 CCCT
28012213 GTTTACACTC
Statistics
Matches: 90, Mismatches: 28, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
19 5 0.06
20 38 0.42
21 42 0.47
22 5 0.06
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (20 bp):
CCCTAATTGTACATACGTGC
Found at i:28015988 original size:4 final size:4
Alignment explanation
Indices: 28015979--28016019 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
28015969 GTGTCGTTAC
28015979 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
28016020 ACCACAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:28016476 original size:18 final size:18
Alignment explanation
Indices: 28016453--28016490 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28016443 CTAGACTAGG
*
28016453 TCTTACACTATATGGTCT
1 TCTTACACTATATGGACT
*
28016471 TCTTACATTATATGGACT
1 TCTTACACTATATGGACT
28016489 TC
1 TC
28016491 CATATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (18 bp):
TCTTACACTATATGGACT
Found at i:28016614 original size:16 final size:15
Alignment explanation
Indices: 28016574--28016624 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
28016564 CATGCAACCT
*
28016574 ATGCACAGACTCATC
1 ATGCAAAGACTCATC
*
28016589 ATGCATAGACTCATTC
1 ATGCAAAGACTCA-TC
*
28016605 ATGTAAAGACTCCATC
1 ATGCAAAGACT-CATC
28016621 ATGC
1 ATGC
28016625 TTTCAAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
16 16 0.53
17 2 0.07
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (15 bp):
ATGCAAAGACTCATC
Found at i:28021301 original size:21 final size:21
Alignment explanation
Indices: 28021277--28021317 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28021267 TCATAAGCCA
28021277 ATTTCATCATCAAAT-GCATAT
1 ATTTCAT-ATCAAATGGCATAT
*
28021298 ATTTCATATCATATGGCATA
1 ATTTCATATCAAATGGCATA
28021318 CCGCATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTCATATCAAATGGCATAT
Found at i:28030013 original size:27 final size:27
Alignment explanation
Indices: 28029983--28030183 Score: 242
Period size: 27 Copynumber: 7.4 Consensus size: 27
28029973 TGAGTCCGCT
* * * *
28029983 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
28030010 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
28030037 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
28030065 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
28030092 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
* *
28030119 CATTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
28030146 CACTTAGTGCTACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
28030173 CACTTAGTGCT
1 CACTTAGTGCT
28030184 GTACAATTTA
Statistics
Matches: 151, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
27 127 0.84
28 24 0.16
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:28036488 original size:18 final size:18
Alignment explanation
Indices: 28036467--28036510 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28036457 GATAGTGCTA
*
28036467 AAGAAGAAGTTGTTCTTG
1 AAGAAGAAGTTGTTCGTG
* *
28036485 AAGAATAAGTTGTTGGTG
1 AAGAAGAAGTTGTTCGTG
28036503 AAGAAGAA
1 AAGAAGAA
28036511 AAGTTGCTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.27
Consensus pattern (18 bp):
AAGAAGAAGTTGTTCGTG
Found at i:28038108 original size:66 final size:66
Alignment explanation
Indices: 28037990--28038114 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
28037980 CTTTCTGCAC
* ** *
28037990 TAATATCGCTACATGAGTTAATTCCAGATTTCGTCATGAATTGTCGCTATAGTTGACAGATATTC
1 TAATATCGCTACATGAGTTAATTCCAAATGGCGTCATGAATTGTCGCCATAGTTGACAGATATTC
28038055 G
66 G
* * * *
28038056 TAATGTCGCTGCATGAGTTAATTCCAAATGGCATTCA-GAATTTTCGCCATAGTTGACAG
1 TAATATCGCTACATGAGTTAATTCCAAATGGC-GTCATGAATTGTCGCCATAGTTGACAG
28038115 TTGTCAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 47 0.94
67 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (66 bp):
TAATATCGCTACATGAGTTAATTCCAAATGGCGTCATGAATTGTCGCCATAGTTGACAGATATTC
G
Found at i:28046810 original size:29 final size:29
Alignment explanation
Indices: 28046775--28046851 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
28046765 CATGAGATTG
* **
28046775 GCACTAAGTGTGCGGGTTTAAATTGTATA
1 GCACTAAGTGTGCGGGTTTAAAGTACATA
*
28046804 GCACTAAGTGTGCGAGTTTAAAGTACATA
1 GCACTAAGTGTGCGGGTTTAAAGTACATA
28046833 GCACTAAGTGTGCGCGGTT
1 GCACTAAGTGTGCG-GGTT
28046852 GATTATTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 39 0.93
30 3 0.07
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTTAAAGTACATA
Found at i:28047069 original size:174 final size:174
Alignment explanation
Indices: 28046805--28047131 Score: 600
Period size: 174 Copynumber: 1.9 Consensus size: 174
28046795 AATTGTATAG
28046805 CACTAAGTGTGCGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
1 CACTAAGTGTGCGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
* * *
28046870 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGAT
66 GTACGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
28046935 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
131 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
* * *
28046979 CACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
1 CACTAAGTGTGCGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
28047044 GTACGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
66 GTACGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
28047109 TTTGGACAGCGGAAAAGGTAAGT
131 TTTGGACAGCGGAAAAGGTAAGT
28047132 ACCTTGAGTT
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
CACTAAGTGTGCGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
GTACGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
Found at i:28049375 original size:15 final size:15
Alignment explanation
Indices: 28049334--28049375 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
28049324 ATTTCAACTC
28049334 TTTGAGTTATTTCTCT
1 TTTGA-TTATTTCTCT
*
28049350 TTATGA-GATTTCTCT
1 TT-TGATTATTTCTCT
28049365 TTTGATTATTT
1 TTTGATTATTT
28049376 TAGAGGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 2 0.09
17 3 0.14
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTGATTATTTCTCT
Found at i:28064075 original size:13 final size:13
Alignment explanation
Indices: 28064057--28064081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28064047 CATGAGTATT
28064057 AAGAAAAAATTAA
1 AAGAAAAAATTAA
28064070 AAGAAAAAATTA
1 AAGAAAAAATTA
28064082 TTTTGTAATT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAGAAAAAATTAA
Found at i:28064251 original size:19 final size:20
Alignment explanation
Indices: 28064227--28064271 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28064217 CCAAATTTTT
* *
28064227 ATTTTAA-GTTATTTTGTAC
1 ATTTTAATGTTATTATGCAC
*
28064246 ATTTTAATTTTATTATGCAC
1 ATTTTAATGTTATTATGCAC
28064266 ATTTTA
1 ATTTTA
28064272 TTAACTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTAATGTTATTATGCAC
Found at i:28067972 original size:30 final size:30
Alignment explanation
Indices: 28067938--28067997 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28067928 CATTACATAG
*
28067938 CTATTATCAAATTGATGTCAAACGGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
28067968 CTATTATCAAATTGATGTCAAACAGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
28067998 GAGCATGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (30 bp):
CTATTATCAAATTGATGTCAAACAGTGTAT
Found at i:28070395 original size:20 final size:19
Alignment explanation
Indices: 28070369--28070418 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
28070359 TTGGAGTAGG
*
28070369 AATATCGATACCTTAGGAA
1 AATATCGATACCTTAAGAA
28070388 ATATATCGATACCTTAAGAA
1 A-ATATCGATACCTTAAGAA
28070408 AAGTATCGATA
1 AA-TATCGATA
28070419 GTAGATCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (19 bp):
AATATCGATACCTTAAGAA
Found at i:28077601 original size:151 final size:151
Alignment explanation
Indices: 28077327--28077627 Score: 512
Period size: 151 Copynumber: 2.0 Consensus size: 151
28077317 GAGGATCCCA
* *
28077327 AAAAAGAAGAAGAAGAAGAAGAAAGTTAAGATCCCACAGAAGGGAAGGAGACGTGGACATATTGA
1 AAAAAGAAGAAGAAGAAGAAGAAAGTGAAGATCCCACAGAAGGGAAAGAGACGTGGACATATTGA
* *
28077392 ACGGGAACGGCCATACCTAAATCATTCAACCAAGAACTAGTGATGCCAAGAGAAAAAATGTAGAT
66 ACGGGAACGACCATACCTAAATCATTCAACCAAGAACTAATGATGCCAAGAGAAAAAATGTAGAT
28077457 AAAATTTGTTTGCTTAAGAAG
131 AAAATTTGTTTGCTTAAGAAG
* *
28077478 AAAAAGAAGAAGAAGAAGAAGAAAGTGAGGATCCCACAGAAGGGAAAGAGACGTGGACGTATTGA
1 AAAAAGAAGAAGAAGAAGAAGAAAGTGAAGATCCCACAGAAGGGAAAGAGACGTGGACATATTGA
* * *
28077543 ATGGGAACGACCATACCTAAATCATTCAACCAGGAACTAATGATGCCAAGAGAAAAAATGTGGAT
66 ACGGGAACGACCATACCTAAATCATTCAACCAAGAACTAATGATGCCAAGAGAAAAAATGTAGAT
*
28077608 GAAATTTGTTTGCTTAAGAA
131 AAAATTTGTTTGCTTAAGAA
28077628 TATGGCCCAT
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
151 140 1.00
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (151 bp):
AAAAAGAAGAAGAAGAAGAAGAAAGTGAAGATCCCACAGAAGGGAAAGAGACGTGGACATATTGA
ACGGGAACGACCATACCTAAATCATTCAACCAAGAACTAATGATGCCAAGAGAAAAAATGTAGAT
AAAATTTGTTTGCTTAAGAAG
Done.