Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001976.1 Hibiscus syriacus cultivar Beakdansim tig00004004_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 915387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:8407 original size:25 final size:25
Alignment explanation
Indices: 8373--8466 Score: 172
Period size: 25 Copynumber: 3.8 Consensus size: 25
8363 GAGTAGGGGA
8373 TTAGGGTTTGAAACCCT-AATCTGTT
1 TTAGGGTTTGAAACCCTAAAT-TGTT
8398 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
8423 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
8448 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
8467 TCTGACGGGT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 65 0.96
26 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGTT
Found at i:8558 original size:37 final size:37
Alignment explanation
Indices: 8508--8584 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
8498 CAATTCTGAG
*
8508 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
1 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCCT
8545 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCCT
1 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCCT
8582 TTG
1 TTG
8585 TAATCTGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.03, C:0.19, G:0.43, T:0.35
Consensus pattern (37 bp):
TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCCT
Found at i:8633 original size:3 final size:3
Alignment explanation
Indices: 8625--8688 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
8615 GCAAAAATTG
* **
8625 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8669 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
8689 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:8680 original size:32 final size:32
Alignment explanation
Indices: 8627--8690 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
8617 AAAAATTGTA
*
8627 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
8659 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
8691 GAAAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:13812 original size:29 final size:29
Alignment explanation
Indices: 13770--13841 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
13760 TTTGGTATCG
*
13770 ATACCAAATAGATAGTTTAAGGATTTAGT
1 ATACCAAATTGATAGTTTAAGGATTTAGT
13799 ATACCAAATTGATAGTTTAAGGATTTAGT
1 ATACCAAATTGATAGTTTAAGGATTTAGT
13828 ATACCAAATTGATA
1 ATACCAAATTGATA
13842 TCAATGTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (29 bp):
ATACCAAATTGATAGTTTAAGGATTTAGT
Found at i:14311 original size:31 final size:31
Alignment explanation
Indices: 14273--14334 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
14263 GAGGAAAGGG
14273 AAAGCTTAATGTAGGGGCCAGCATGATAGTT
1 AAAGCTTAATGTAGGGGCCAGCATGATAGTT
*
14304 AAAGCTTAATGTAGGGGCCGGCATGATAGTT
1 AAAGCTTAATGTAGGGGCCAGCATGATAGTT
14335 TAACTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (31 bp):
AAAGCTTAATGTAGGGGCCAGCATGATAGTT
Found at i:14774 original size:28 final size:30
Alignment explanation
Indices: 14743--14798 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
14733 AAATTATCAA
14743 AATAATATTATTTTA-TAT-A-TTTAATATT
1 AATAATA-TATTTTAGTATCATTTTAATATT
*
14771 AATACTATATTTTAGTATCATTTTAATA
1 AATAATATATTTTAGTATCATTTTAATA
14799 AAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.29
28 9 0.38
29 1 0.04
30 7 0.29
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (30 bp):
AATAATATATTTTAGTATCATTTTAATATT
Found at i:14895 original size:23 final size:23
Alignment explanation
Indices: 14848--14898 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
14838 AATATTTTTA
* *
14848 ATATTATAATAATATACTCAGTT
1 ATATTATAATAATATACTAAATT
14871 ATATTATAATAATATA-TAATATT
1 ATATTATAATAATATACTAA-ATT
14894 ATATT
1 ATATT
14899 CTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTATAATAATATACTAAATT
Found at i:15786 original size:22 final size:25
Alignment explanation
Indices: 15761--15805 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
15751 TTCTATCAAG
15761 TGACAGAG-TC-AAA-ATTAAATAT
1 TGACAGAGATCGAAATATTAAATAT
15783 TGACAGAGATCGAAATATTAAAT
1 TGACAGAGATCGAAATATTAAAT
15806 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 3 0.15
25 7 0.35
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.27
Consensus pattern (25 bp):
TGACAGAGATCGAAATATTAAATAT
Found at i:16950 original size:16 final size:16
Alignment explanation
Indices: 16908--16950 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
16898 CTTGACTCTA
*
16908 AAGTTTACATTATTTG
1 AAGTTTAAATTATTTG
* * *
16924 AAATTTTAATTATTTT
1 AAGTTTAAATTATTTG
16940 AAGTTTAAATT
1 AAGTTTAAATT
16951 GAATAAGTCC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (16 bp):
AAGTTTAAATTATTTG
Found at i:25798 original size:12 final size:12
Alignment explanation
Indices: 25773--25842 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
25763 ACGAAGATAT
* *
25773 CAGAAATCAAAA
1 CAGAATTCAGAA
25785 CAGAATTCAGAA
1 CAGAATTCAGAA
25797 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
25809 CAGAATCCAGAT
1 CAGAATTCAGAA
*
25821 CAGAAATCAGAA
1 CAGAATTCAGAA
25833 CAGAATTCAG
1 CAGAATTCAG
25843 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:25842 original size:48 final size:47
Alignment explanation
Indices: 25771--25879 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
25761 AAACGAAGAT
*
25771 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
25818 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
25866 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
25880 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:25877 original size:24 final size:25
Alignment explanation
Indices: 25771--25879 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
25761 AAACGAAGAT
*
25771 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
25795 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
25819 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
25843 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
25868 -TCGGAAATCAGA
1 ATCAGAAATCAGA
25880 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:38194 original size:28 final size:28
Alignment explanation
Indices: 38162--38245 Score: 168
Period size: 28 Copynumber: 3.0 Consensus size: 28
38152 TTCTCTCACT
38162 AAACCAATTAAAGTTTGTAATTTGATGA
1 AAACCAATTAAAGTTTGTAATTTGATGA
38190 AAACCAATTAAAGTTTGTAATTTGATGA
1 AAACCAATTAAAGTTTGTAATTTGATGA
38218 AAACCAATTAAAGTTTGTAATTTGATGA
1 AAACCAATTAAAGTTTGTAATTTGATGA
38246 CAACGGTACC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (28 bp):
AAACCAATTAAAGTTTGTAATTTGATGA
Found at i:43893 original size:21 final size:20
Alignment explanation
Indices: 43869--43925 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
43859 ATAATAATTA
43869 AAATAAAATAAAATAGAAATG
1 AAATAAAATAAAAT-GAAATG
* *
43890 AAATTACTAA-AAAATTAAATG
1 AAA-TA-AAATAAAATGAAATG
*
43911 AAATAAAATGAAATG
1 AAATAAAATAAAATG
43926 GTTTGCCTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
19 2 0.07
20 6 0.21
21 11 0.39
22 7 0.25
23 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAAATGAAATG
Found at i:46550 original size:21 final size:21
Alignment explanation
Indices: 46494--46574 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 21
46484 GATAGAACTT
* *
46494 TATCTCTTCATGTTAACAGCTA
1 TATCT-TTCATGTTAACATCAA
*
46516 -ACCTTTCATGTTAACATC-A
1 TATCTTTCATGTTAACATCAA
* *
46535 TATTTCTTCATTTTAACA-CAA
1 TATCT-TTCATGTTAACATCAA
46556 TATCTTTCATGTTAACATC
1 TATCTTTCATGTTAACATC
46575 CATCGATATG
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.56
21 20 0.42
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (21 bp):
TATCTTTCATGTTAACATCAA
Found at i:49659 original size:65 final size:62
Alignment explanation
Indices: 49566--49693 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 62
49556 GTTTTCTCTT
49566 TATTTATTTTATTTTTAGTTTTGTGTGGACATAATCCCT-AAACTCTCTTTGATTGGTTGCA
1 TATTTATTTTATTTTTAGTTTTGTGTGGACATAATCCCTAAAACTCTCTTTGATTGGTTGCA
*
49627 TATTTATTTTATATTTTAGTTTTTGTGTGTGGACATAATCCCTAAAATTCTCTTTGATTGGTTGC
1 TATTTATTTTAT-TTTTAG--TTT-TGTGTGGACATAATCCCTAAAACTCTCTTTGATTGGTTGC
49692 A
62 A
49693 T
1 T
49694 TATTAAGATC
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
61 12 0.20
62 6 0.10
64 3 0.05
65 18 0.30
66 22 0.36
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.52
Consensus pattern (62 bp):
TATTTATTTTATTTTTAGTTTTGTGTGGACATAATCCCTAAAACTCTCTTTGATTGGTTGCA
Found at i:49716 original size:65 final size:64
Alignment explanation
Indices: 49587--49717 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 64
49577 TTTTTAGTTT
* ** * * *
49587 TGTGTGGACATAATCCCTAAACTCTCTTTGATTGGTTGCATATTTATTTTATATTTTAGTTTTTG
1 TGTGTGGACATAATCCCTAAACTCTCTTTGATTGGTTGCATATTAAGATCATATCTTA-CTTTTG
* *
49652 TGTGTGGACATAATCCCTAAAATTCTCTTTGATTGGTTGCATTATTAAGATCCTATCTT-CTTTT
1 TGTGTGGACATAATCCCT-AAACTCTCTTTGATTGGTTGCA-TATTAAGATCATATCTTACTTTT
49716 G
64 G
49717 T
1 T
49718 TTTAATAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 24 0.43
66 21 0.38
67 11 0.20
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (64 bp):
TGTGTGGACATAATCCCTAAACTCTCTTTGATTGGTTGCATATTAAGATCATATCTTACTTTTG
Found at i:54144 original size:29 final size:30
Alignment explanation
Indices: 54090--54148 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
54080 ATTCATCATA
*
54090 TCAATTATTGATGGAAACAAATAGATTATG
1 TCAATTATTGATCGAAACAAATAGATTATG
*
54120 TCAATTGTTGATCG-AACAAATAGATTATG
1 TCAATTATTGATCGAAACAAATAGATTATG
54149 ATGGCGGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (30 bp):
TCAATTATTGATCGAAACAAATAGATTATG
Found at i:55792 original size:2 final size:2
Alignment explanation
Indices: 55785--55838 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
55775 AATCAAAGCA
55785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55827 AT AT AT AT AT AT
1 AT AT AT AT AT AT
55839 TTTGAAAGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59596 original size:29 final size:29
Alignment explanation
Indices: 59502--59635 Score: 101
Period size: 29 Copynumber: 4.6 Consensus size: 29
59492 TTCGGTTTTA
* * *
59502 GTGCTATTCTGGAAATT-ATTCGAAATAT-
1 GTGCTATTTTGGGAATTAATCCGAAA-ATG
* ** * *
59530 GTGCTATTTTGGTAATTTTGTTCGAAAAAG
1 GTGCTATTTTGGGAA-TTAATCCGAAAATG
* * *
59560 GTGATATTATGGGAATTAATCCGAAATTG
1 GTGCTATTTTGGGAATTAATCCGAAAATG
** *
59589 GTGCTATTTTGGGAATTAATTTGAAAATA
1 GTGCTATTTTGGGAATTAATCCGAAAATG
*
59618 GTGCTATTTTGGTAATTA
1 GTGCTATTTTGGGAATTA
59636 TTTAAAAAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
28 13 0.15
29 52 0.62
30 19 0.23
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATCCGAAAATG
Found at i:59654 original size:30 final size:30
Alignment explanation
Indices: 59588--59656 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
59578 ATCCGAAATT
* *
59588 GGTGCTATTTTGGGAATTAATTTGAAAATA
1 GGTGCTATTTTGGGAATTAATTTAAAAAAA
*
59618 -GTGCTATTTTGGTAATT-ATTTAAAAAAAA
1 GGTGCTATTTTGGGAATTAATTT-AAAAAAA
59647 GGTGCTATTT
1 GGTGCTATTT
59657 ATGTAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.12
29 21 0.62
30 9 0.26
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.42
Consensus pattern (30 bp):
GGTGCTATTTTGGGAATTAATTTAAAAAAA
Found at i:60568 original size:42 final size:41
Alignment explanation
Indices: 60509--60796 Score: 450
Period size: 42 Copynumber: 6.9 Consensus size: 41
60499 GGAAGTATAT
60509 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* *
60551 CAGGTCACTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
60593 CAGGTCTCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
60635 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
60677 CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
* *
60718 CAGGTCCCTTTTGCTGTATGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
60761 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACA
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACA
60797 ATTTTCCTAG
Statistics
Matches: 229, Mismatches: 11, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
41 32 0.14
42 169 0.74
43 28 0.12
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.31
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:60650 original size:84 final size:83
Alignment explanation
Indices: 60509--60796 Score: 504
Period size: 84 Copynumber: 3.4 Consensus size: 83
60499 GGAAGTATAT
*
60509 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCACTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
60574 GGTAAGCCTTACAGTTTCC
65 GGTAAGCCTTACAGTTTCC
*
60593 CAGGTCTCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
60658 GGTAAGCCTTACAGTTTCC
65 GGTAAGCCTTACAGTTTCC
*
60677 CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTATGCAAG
1 CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAAG
60742 GGTAAGCCTTACAGTTTCC
65 GGTAAGCCTTACAGTTTCC
*
60761 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACA
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACA
60797 ATTTTCCTAG
Statistics
Matches: 197, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
83 29 0.15
84 158 0.80
85 10 0.05
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.31
Consensus pattern (83 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAGG
GTAAGCCTTACAGTTTCC
Found at i:62202 original size:7 final size:7
Alignment explanation
Indices: 62190--62214 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62180 CCAAAATCAA
62190 CCATCTT
1 CCATCTT
62197 CCATCTT
1 CCATCTT
62204 CCATCTT
1 CCATCTT
62211 CCAT
1 CCAT
62215 AAAGCTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (7 bp):
CCATCTT
Found at i:77309 original size:19 final size:19
Alignment explanation
Indices: 77271--77309 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
77261 AAAAAATAGG
*
77271 TTTTTATATAATTTAGATA
1 TTTTTATATAATTAAGATA
* *
77290 TTTTTTTATAATTAATATA
1 TTTTTATATAATTAAGATA
77309 T
1 T
77310 AATATGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATATAATTAAGATA
Found at i:80624 original size:45 final size:45
Alignment explanation
Indices: 80568--80672 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 45
80558 TGCACCAATC
80568 CATGCATCGATGCACCATGA-ATTAAATTG-A-ACATCGAATGCATTT
1 CATGCATCGATGCA-C-TGAGATTAAA-TGAACACATCGAATGCATTT
**
80613 CATGCATCGATGCACTGAGGATTTTATGAACACATCGAATGCATTT
1 CATGCATCGATGCACTGA-GATTAAATGAACACATCGAATGCATTT
*
80659 GATGCATCGATGCA
1 CATGCATCGATGCA
80673 TTAGCCATGC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 19 0.36
46 28 0.53
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (45 bp):
CATGCATCGATGCACTGAGATTAAATGAACACATCGAATGCATTT
Found at i:87203 original size:23 final size:23
Alignment explanation
Indices: 87158--87203 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
87148 CATTATTATA
*
87158 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
87181 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
87204 AGCTATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:89679 original size:16 final size:16
Alignment explanation
Indices: 89658--89700 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
89648 GGTAATTAAA
89658 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
89674 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
89691 GAGTGATAAG
1 GATTGATAAG
89701 TACTGATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:91856 original size:36 final size:37
Alignment explanation
Indices: 91809--91881 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
91799 TATGTGCAGG
91809 GGGGAACAGATTCCCCCT-AGAGGGTATCGATTCCCC
1 GGGGAACAGATTCCCCCTGAGAGGGTATCGATTCCCC
* *
91845 GGGGAACAGATTCCCCCTGGGTGGGTATCGATTCCCC
1 GGGGAACAGATTCCCCCTGAGAGGGTATCGATTCCCC
91882 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (37 bp):
GGGGAACAGATTCCCCCTGAGAGGGTATCGATTCCCC
Found at i:92485 original size:31 final size:31
Alignment explanation
Indices: 92447--92586 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
92437 AGGGTCGAGG
92447 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
92478 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
**
92509 GTTTACCTATGTTCTTCGGGACATATAAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
92540 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
92571 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
92587 TGGAATCTAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:93235 original size:14 final size:14
Alignment explanation
Indices: 93213--93246 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
93203 TTAACATTTG
*
93213 GGTACTGTTCATAC
1 GGTATTGTTCATAC
93227 GGTATTGTTCATAC
1 GGTATTGTTCATAC
*
93241 CGTATT
1 GGTATT
93247 TTACTGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (14 bp):
GGTATTGTTCATAC
Found at i:94537 original size:23 final size:22
Alignment explanation
Indices: 94469--94537 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
94459 CATTATTATA
94469 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTC-GTGCATTTCTACG
* * *
94492 TGGTACTACGATGCAATTCTACG
1 TGGCACTTCG-TGCATTTCTACG
*
94515 TGGCACTTCAGTGCATTTATACG
1 TGGCACTTC-GTGCATTTCTACG
94538 AGCTGTGGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (22 bp):
TGGCACTTCGTGCATTTCTACG
Found at i:96896 original size:21 final size:22
Alignment explanation
Indices: 96851--96922 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
96841 CACCTAACAA
* * *
96851 TGCATCGATGCATCATTGAATG
1 TGCATCGATACACCATTGAAGG
96873 TGCATCGATACACCA-TGAAGG
1 TGCATCGATACACCATTGAAGG
* * * *
96894 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATACAC-CATTGAAGG
96917 TGCATC
1 TGCATC
96923 AATGCACAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 16 0.40
22 14 0.35
23 10 0.25
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (22 bp):
TGCATCGATACACCATTGAAGG
Found at i:96919 original size:23 final size:23
Alignment explanation
Indices: 96851--96930 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
96841 CACCTAACAA
96851 TGCATCGATGCATCA--TTGAATG
1 TGCATCGATGCA-CACCTTGAATG
* *
96873 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
96894 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
*
96917 TGCATCAATGCACA
1 TGCATCGATGCACA
96931 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 13 0.29
22 9 0.20
23 20 0.44
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:98867 original size:14 final size:15
Alignment explanation
Indices: 98842--98870 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
98832 TTGTTTTTTA
98842 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
98857 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
98871 AAATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:98929 original size:2 final size:2
Alignment explanation
Indices: 98917--99000 Score: 126
Period size: 2 Copynumber: 45.0 Consensus size: 2
98907 TTTGAACTTA
98917 AT AT A- AT AT AT AT -T AT AT AT AT AT AT -T AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98954 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98995 AT AT AT
1 AT AT AT
99001 TTGGTTGGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 6 0.08
2 70 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:100677 original size:29 final size:29
Alignment explanation
Indices: 100575--100681 Score: 76
Period size: 29 Copynumber: 3.6 Consensus size: 29
100565 TATTGTACGA
*
100575 ATAACCGTTCATTTCATTTTGAAAATTTATT
1 ATAACTGTTCATTT--TTTTGAAAATTTATT
* * * *
100606 ATAACTGTTCATTTCTTTGCAGAATTCA-A
1 ATAACTGTTCATTTTTTTG-AAAATTTATT
* * *
100635 ATTGA-T-TATAATTTTTTTGGAAATTTATT
1 A-TAACTGT-TCATTTTTTTGAAAATTTATT
100664 ATAACTGTTCATTTTTTT
1 ATAACTGTTCATTTTTTT
100682 TCAACTTTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
28 8 0.14
29 26 0.46
30 9 0.16
31 13 0.23
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (29 bp):
ATAACTGTTCATTTTTTTGAAAATTTATT
Found at i:100932 original size:21 final size:23
Alignment explanation
Indices: 100908--100964 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
100898 AATGAAAGTG
100908 TTTTTCT-AT-GTTAAAGATTAT
1 TTTTTCTCATAGTTAAAGATTAT
*
100929 TTTTTCTCATAAGTTAGAGATTATT
1 TTTTTCTCAT-AGTTAAAGATTA-T
100954 TTTTTCTCATA
1 TTTTTCTCATA
100965 ATAAATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 7 0.23
22 2 0.06
24 11 0.35
25 11 0.35
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTTCTCATAGTTAAAGATTAT
Found at i:100949 original size:24 final size:25
Alignment explanation
Indices: 100917--100965 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
100907 GTTTTTCTAT
100917 GTTAAAGATTA-TTTTTTCTCATAA
1 GTTAAAGATTATTTTTTTCTCATAA
*
100941 GTTAGAGATTATTTTTTTCTCATAA
1 GTTAAAGATTATTTTTTTCTCATAA
100966 TAAATTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (25 bp):
GTTAAAGATTATTTTTTTCTCATAA
Found at i:101648 original size:23 final size:22
Alignment explanation
Indices: 101608--101670 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
101598 AATTATACCG
101608 TTATGACATGTTTTTTTTG-TCT
1 TTATGACATGTTTTTTTTGCT-T
*
101630 TTATGATATGATTTTTTTTGCTT
1 TTATGACATG-TTTTTTTTGCTT
*
101653 TTATGACACGTTTTTTTT
1 TTATGACATGTTTTTTTT
101671 TTGTTATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 17 0.47
23 18 0.50
24 1 0.03
ACGTcount: A:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (22 bp):
TTATGACATGTTTTTTTTGCTT
Found at i:101653 original size:22 final size:23
Alignment explanation
Indices: 101608--101670 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
101598 AATTATACCG
101608 TTATGACATGTTTTTTTTGTC-T
1 TTATGACATGTTTTTTTTGTCTT
*
101630 TTATGATATGATTTTTTTTG-CTT
1 TTATGACATG-TTTTTTTTGTCTT
*
101653 TTATGACACGTTTTTTTT
1 TTATGACATGTTTTTTTT
101671 TTGTTATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (23 bp):
TTATGACATGTTTTTTTTGTCTT
Found at i:103840 original size:69 final size:71
Alignment explanation
Indices: 103728--103870 Score: 272
Period size: 70 Copynumber: 2.0 Consensus size: 71
103718 TTAATTTACT
103728 TCACTTGTTTGTTGTCTGCTTCTTCCTTGAAACAGTCATTCATTA-GATATCTTTTGTCTTTGTA
1 TCACTTGTTTGTTGTCTGCTTCTTCCTTGAAACAGTCATTCATTATGATATCTTTTGTCTTTGTA
103792 CGCCTC
66 CGCCTC
103798 TCACTTGTTTGTTGTCT-CTTCTTCCTTGAAACAGTCATTCATTATGATATCTTTTGTCTTTGTA
1 TCACTTGTTTGTTGTCTGCTTCTTCCTTGAAACAGTCATTCATTATGATATCTTTTGTCTTTGTA
103862 CGCCTC
66 CGCCTC
103868 TCA
1 TCA
103871 TGTGGCCTCG
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 27 0.38
70 45 0.62
ACGTcount: A:0.16, C:0.23, G:0.13, T:0.48
Consensus pattern (71 bp):
TCACTTGTTTGTTGTCTGCTTCTTCCTTGAAACAGTCATTCATTATGATATCTTTTGTCTTTGTA
CGCCTC
Found at i:103991 original size:2 final size:2
Alignment explanation
Indices: 103978--104011 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
103968 CTTTGTACGC
*
103978 CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
104012 TTTGGGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:105799 original size:18 final size:19
Alignment explanation
Indices: 105776--105817 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
105766 TTCAATAGAA
*
105776 ATTAATAATAGA-TAATAT
1 ATTAATAACAGATTAATAT
105794 ATTAATAACAGATTAATAT
1 ATTAATAACAGATTAATAT
105813 -TTAAT
1 ATTAAT
105818 GAGAGAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
ATTAATAACAGATTAATAT
Found at i:110333 original size:12 final size:12
Alignment explanation
Indices: 110316--110340 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110306 TCATTAAATA
110316 TATATATATTAC
1 TATATATATTAC
110328 TATATATATTAC
1 TATATATATTAC
110340 T
1 T
110341 GGTAGTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATTAC
Found at i:119259 original size:18 final size:19
Alignment explanation
Indices: 119236--119271 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
119226 TTAAACTGAA
119236 TCAAATAG-GTCGAGTTTG
1 TCAAATAGAGTCGAGTTTG
*
119254 TCAAATCGAGTCGAGTTT
1 TCAAATAGAGTCGAGTTT
119272 AAATCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (19 bp):
TCAAATAGAGTCGAGTTTG
Found at i:123830 original size:30 final size:30
Alignment explanation
Indices: 123794--123857 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
123784 GAAGGACCTG
* *
123794 TCCAGAGGTTATAAAGAACCCCGGTAACTA
1 TCCAGAGGTCATAAAGAACCCCGGCAACTA
* *
123824 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCATAAAGAACCCCGGCAACTA
123854 TCCA
1 TCCA
123858 TATGTTCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGAACCCCGGCAACTA
Found at i:124644 original size:64 final size:64
Alignment explanation
Indices: 124531--124696 Score: 194
Period size: 64 Copynumber: 2.6 Consensus size: 64
124521 TCTTTCAATG
* * * *
124531 AATGTATGCATCGATGCACTACTTGTGTATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* * *
124593 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
124657 TA
63 TA
* * *
124659 AATTCATGCATCGATGCACTGCATGTGCATCGATGCAT
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCAT
124697 CTTAAACAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:125744 original size:25 final size:25
Alignment explanation
Indices: 125710--125759 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
125700 TATTATTTTC
*
125710 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
125735 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
125760 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:128450 original size:24 final size:24
Alignment explanation
Indices: 128423--128476 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
128413 TTGAAACATC
*
128423 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
128447 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
128471 ATCAAA
1 ATCAAA
128477 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:128490 original size:24 final size:24
Alignment explanation
Indices: 128439--128490 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
128429 ATCTGAGTAT
** *
128439 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
128463 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
128487 TGAC
1 TGAC
128491 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:129254 original size:14 final size:16
Alignment explanation
Indices: 129218--129255 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
129208 GAAATCATTG
129218 TAAAATTATATAGAAA
1 TAAAATTATATAGAAA
*
129234 TAAAATTATGTA-AAA
1 TAAAATTATATAGAAA
129249 -AAAATTA
1 TAAAATTA
129256 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 3 0.14
16 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAAAATTATATAGAAA
Found at i:129306 original size:22 final size:21
Alignment explanation
Indices: 129263--129306 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
129253 TTAGAGATGG
** *
129263 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGAGATA
129284 GGAACGGATGTCGCCGGAGATA
1 GGAA-GGATGTCGCCGGAGATA
129306 G
1 G
129307 TGATAGATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.11, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGAGATA
Found at i:129436 original size:20 final size:19
Alignment explanation
Indices: 129391--129439 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
129381 CCAAAATATT
*
129391 TGTGTTACGAAAATAAAAC
1 TGTGTTGCGAAAATAAAAC
*
129410 T-TGTTGCGAAATTAAAAC
1 TGTGTTGCGAAAATAAAAC
129428 TCGTGTTGCGAA
1 T-GTGTTGCGAA
129440 TTCGAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 9 0.35
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (19 bp):
TGTGTTGCGAAAATAAAAC
Found at i:129481 original size:41 final size:40
Alignment explanation
Indices: 129412--129491 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 40
129402 AATAAAACTT
*
129412 GTTGCGAAATTAAAACTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAACTCGTGTTACGAATTCGAAAATCGA
* * * * *
129452 GTTGCGAATTTGAAATTCAGTGTTACGAATTTGTAAATCG
1 GTTGCGAAATTAAAACTC-GTGTTACGAATTCGAAAATCG
129492 TAACGCGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (40 bp):
GTTGCGAAATTAAAACTCGTGTTACGAATTCGAAAATCGA
Found at i:129519 original size:20 final size:20
Alignment explanation
Indices: 129432--129544 Score: 81
Period size: 20 Copynumber: 5.6 Consensus size: 20
129422 TAAAACTCGT
* *
129432 GTTGCGAATTCGAAAATCGA-
1 GTTGCGAATTTGGAAATC-AC
*
129452 GTTGCGAATTT-GAAATTCAGT
1 GTTGCGAATTTGGAAA-TCA-C
* *
129473 GTTACGAATTTGTAAAT--C
1 GTTGCGAATTTGGAAATCAC
*
129491 GTAACGCGAATTTGGAAATCAC
1 GT--TGCGAATTTGGAAATCAC
*
129513 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCAC
*
129533 ATTGCGAATTTG
1 GTTGCGAATTTG
129545 ACTTCTGTGT
Statistics
Matches: 74, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.03
19 4 0.05
20 51 0.69
21 11 0.15
22 6 0.08
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCAC
Found at i:129557 original size:40 final size:38
Alignment explanation
Indices: 129428--129559 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 38
129418 AAATTAAAAC
*
129428 TCGTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAAT
1 TCGTGTTGCGAATTTGAAAATCGA-TTGCGAATTTG-AAT
* * ** *
129468 TCAGTGTTACGAATTTGTAAATCGTAACGCGAATTTGGAAA
1 TC-GTGTTGCGAATTTGAAAATCG-ATTGCGAATTT-GAAT
** * *
129509 TCACGTTGCGAATTTGGAAATCGCATTGCGAATTTGACT
1 TCGTGTTGCGAATTTGAAAATCG-ATTGCGAATTTGAAT
129548 TCTGTGTTGCGA
1 TC-GTGTTGCGA
129560 TTTACAGATT
Statistics
Matches: 71, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
39 4 0.06
40 35 0.49
41 30 0.42
42 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (38 bp):
TCGTGTTGCGAATTTGAAAATCGATTGCGAATTTGAAT
Found at i:129576 original size:20 final size:20
Alignment explanation
Indices: 129553--129599 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
129543 TGACTTCTGT
129553 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
129573 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
*
129593 ATTGCGA
1 GTTGCGA
129600 ATTTGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:129576 original size:60 final size:61
Alignment explanation
Indices: 129512--129644 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 61
129502 TTGGAAATCA
* *** * *
129512 CGTTGCGAATTTGGA-AATCGCATTGCGAATTTGACTTCTGTGTTGCG-ATTTACAGATTCG
1 CGTTGCGAATTTGCATAATCGCATTGCGAATTTGAAAACTGAGTTGCGAAATTACAG-TTCG
* * *
129572 CGTTGCG-ATTTACATATTCGCATTGCGAATTTGAAAACTGAGTTGCGAAATTAGAGTTCG
1 CGTTGCGAATTTGCATAATCGCATTGCGAATTTGAAAACTGAGTTGCGAAATTACAGTTCG
129632 CGTTGCGAATTTG
1 CGTTGCGAATTTG
129645 TTGATCATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 5 0.08
60 45 0.75
61 10 0.17
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (61 bp):
CGTTGCGAATTTGCATAATCGCATTGCGAATTTGAAAACTGAGTTGCGAAATTACAGTTCG
Found at i:154806 original size:3 final size:3
Alignment explanation
Indices: 154798--154897 Score: 103
Period size: 3 Copynumber: 32.7 Consensus size: 3
154788 TTCATTTAAA
* * *
154798 TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
154846 TAT AAT TACT AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT
154893 TAT TA
1 TAT TA
154898 CAAACGGGCC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 70 0.88
4 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:154819 original size:15 final size:15
Alignment explanation
Indices: 154799--154897 Score: 116
Period size: 15 Copynumber: 6.7 Consensus size: 15
154789 TCATTTAAAT
154799 ATTATTATTATTATA
1 ATTATTATTATTATA
154814 ATTATTATTATTATA
1 ATTATTATTATTATA
154829 ATTATTATTATTATA
1 ATTATTATTATTATA
154844 ATTA-TA--ATTACTA
1 ATTATTATTATTA-TA
*
154857 ATT-TTATTATTTATT
1 ATTATTATTA-TTATA
* *
154872 ACTAATATTATTATTA
1 ATTATTATTATTA-TA
154888 ATTATTATTA
1 ATTATTATTA
154898 CAAACGGGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.06
13 7 0.10
14 2 0.03
15 41 0.58
16 17 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:157323 original size:19 final size:19
Alignment explanation
Indices: 157277--157329 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
157267 TATATTAGTT
*
157277 TAATATTTAAATTATATTG
1 TAATATTTAAATTATAATG
*
157296 TGTATATTTAAA-TAGTAATG
1 T-AATATTTAAATTA-TAATG
157316 TAATATTTATAATT
1 TAATATTTA-AATT
157330 TTCTAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TAATATTTAAATTATAATG
Found at i:158283 original size:2 final size:2
Alignment explanation
Indices: 158276--158312 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
158266 GATATGATAC
158276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
158313 TTGTCACTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166489 original size:40 final size:42
Alignment explanation
Indices: 166431--166609 Score: 298
Period size: 41 Copynumber: 4.4 Consensus size: 42
166421 CTTTGCTTAC
166431 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGG-AAG
1 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAG
166472 CCTTACAG-TTCCCAGGTCCCTTTGCTT-TGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTG-TTGTGTGCAAGGGTAAG
166513 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAA-GGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAG
*
166554 CCTTACAGTTTCCCAGGTCCCTTTG-CGTGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAG
166595 CC-TACAGTTTCCCAG
1 CCTTACAGTTTCCCAG
166610 ACTCTTTGCT
Statistics
Matches: 132, Mismatches: 1, Indels: 11
0.92 0.01 0.08
Matches are distributed among these distances:
40 47 0.36
41 62 0.47
42 23 0.17
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (42 bp):
CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAG
Found at i:166514 original size:41 final size:42
Alignment explanation
Indices: 166431--166639 Score: 290
Period size: 41 Copynumber: 5.1 Consensus size: 42
166421 CTTTGCTTAC
166431 CCTTACAGTTTCCCAGGTCCCTTTG-TTGTGTGCAAGGG-AAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTT-TGTGCAAGGGTAAG
166472 CCTTACAG-TTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
166513 CCTTACAGTTTCCCAGGTCCCTTTG-TTGTGTGCAA-GGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTT-TGTGCAAGGGTAAG
*
166554 CCTTACAGTTTCCCAGGTCCCTTTGC-GTGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
* * * *
166595 CC-TACAGTTTCCCA-GACTCTTTGCTATGTGCAAGGATAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
*
166635 ACTTA
1 CCTTA
166640 TCATTTTGCA
Statistics
Matches: 154, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
39 8 0.05
40 59 0.38
41 64 0.42
42 23 0.15
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (42 bp):
CCTTACAGTTTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
Found at i:166625 original size:40 final size:42
Alignment explanation
Indices: 166431--166639 Score: 304
Period size: 40 Copynumber: 5.1 Consensus size: 42
166421 CTTTGCTTAC
*
166431 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGG-AAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
*
166472 CCTTACAG-TTCCCAGGTCCCTTTGCTTTGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
*
166513 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAA-GGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
166554 CCTTACAGTTTCCCAGGTCCCTTTGC-GTGTGCAAGGGTAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
* * * *
166595 CC-TACAGTTTCCCA-GACTCTTTGCTATGTGCAAGGATAAG
1 CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
*
166635 ACTTA
1 CCTTA
166640 TCATTTTGCA
Statistics
Matches: 153, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
39 8 0.05
40 61 0.40
41 60 0.39
42 24 0.16
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (42 bp):
CCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
Found at i:166667 original size:82 final size:83
Alignment explanation
Indices: 166431--166675 Score: 259
Period size: 82 Copynumber: 3.0 Consensus size: 83
166421 CTTTGCTTAC
* * * * * * *
166431 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGGAAGCCTTACAG-TTCCCAGGTCCCTTT
1 CCTTACAGTTTCCCAGGACCCTTTGCTATGTGCAAGGTAAGACTTACAGTTTCCCAGCTCCCTCT
166495 GCTTTGTGCAAGGGTAAG
66 GCTTTGTGCAAGGGTAAG
* * * * * *
166513 CCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTT
1 CCTTACAGTTTCCCAGGACCCTTTGCTATGTGCAAGGTAAGACTTACAGTTTCCCAGCTCCCTCT
*
166578 GC-GTGTGCAAGGGTAAG
66 GCTTTGTGCAAGGGTAAG
* **
166595 CC-TACAGTTTCCCA-GACTCTTTGCTATGTGCAAGGATAAGACTTATCA-TTTTGCATGCT-CC
1 CCTTACAGTTTCCCAGGACCCTTTGCTATGTGCAAGG-TAAGACTTA-CAGTTTCCCA-GCTCCC
*
166656 TCTGCTTTGTGCACGGGTAA
63 TCTGCTTTGTGCAAGGGTAA
166676 ATGTTTTAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
80 17 0.12
81 31 0.21
82 80 0.55
83 17 0.12
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (83 bp):
CCTTACAGTTTCCCAGGACCCTTTGCTATGTGCAAGGTAAGACTTACAGTTTCCCAGCTCCCTCT
GCTTTGTGCAAGGGTAAG
Found at i:167474 original size:56 final size:56
Alignment explanation
Indices: 167407--167518 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
167397 ACAAAGAGGA
167407 AAATCAGAGACATGGAAATTAGCCGTGGTCGAATGGTGCTGAAATCATCAACTTTC
1 AAATCAGAGACATGGAAATTAGCCGTGGTCGAATGGTGCTGAAATCATCAACTTTC
167463 AAATCAGAGACATGGAAATTAGCCGTGGTCGAATGGTGCTGAAATCATCAACTTTC
1 AAATCAGAGACATGGAAATTAGCCGTGGTCGAATGGTGCTGAAATCATCAACTTTC
167519 GCCATGTAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (56 bp):
AAATCAGAGACATGGAAATTAGCCGTGGTCGAATGGTGCTGAAATCATCAACTTTC
Found at i:169442 original size:20 final size:19
Alignment explanation
Indices: 169417--169456 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
169407 ATTCTGGGCA
* *
169417 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCC-TTC
169437 AGGGGAACCGATACCCTTC
1 AGGGGAACCGATACCCTTC
169456 A
1 A
169457 AACGAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATACCCTTC
Found at i:171158 original size:22 final size:21
Alignment explanation
Indices: 171125--171189 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 21
171115 TATGGACATC
*
171125 ATTCTAGGGCACTACGGTGCA
1 ATTCTAGGGCACTTCGGTGCA
171146 ATTCTACGGGCACTTCGGTGCA
1 ATTCTA-GGGCACTTCGGTGCA
171168 ATTCTATGGGCACTTCGGTGCA
1 ATTCTA-GGGCACTTCGGTGCA
171190 TTTATACGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 6 0.15
22 35 0.85
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (21 bp):
ATTCTAGGGCACTTCGGTGCA
Found at i:174267 original size:21 final size:21
Alignment explanation
Indices: 174234--174274 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
174224 TTCTGGGCAA
* *
174234 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
174255 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
174275 CGAACAAGAA
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:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:174900 original size:59 final size:57
Alignment explanation
Indices: 174804--174917 Score: 185
Period size: 59 Copynumber: 2.0 Consensus size: 57
174794 AGCAAAGTAT
*
174804 GATATAAACTATGTGATCATAGTAAAATAATTATATTATTATATGATAAGTGAAATAGA
1 GATATAAACTATGTGATCATAGTAAAATAAATATATTA-T-TATGATAAGTGAAATAGA
174863 GATATAAACTATGTGATCATAGTAAAATATAAT-TATTATTATGATAAGTGAAATA
1 GATATAAACTATGTGATCATAGTAAAATA-AATATATTATTATGATAAGTGAAATA
174918 AGCTGGATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
57 16 0.30
58 1 0.02
59 34 0.64
60 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (57 bp):
GATATAAACTATGTGATCATAGTAAAATAAATATATTATTATGATAAGTGAAATAGA
Found at i:176009 original size:21 final size:21
Alignment explanation
Indices: 175983--176051 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
175973 TTATGGACAT
*
175983 CATTCTACGGGCACTACGGTG
1 CATTCTACGGGCACTTCGGTG
176004 CATTCTACGGGCACTTCGGTG
1 CATTCTACGGGCACTTCGGTG
*
176025 CAATTCTATGGGGCACTTCGGTG
1 C-ATTCTA-CGGGCACTTCGGTG
176048 CATT
1 CATT
176052 TATACGAGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 21 0.48
22 9 0.20
23 14 0.32
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (21 bp):
CATTCTACGGGCACTTCGGTG
Found at i:179266 original size:692 final size:686
Alignment explanation
Indices: 177947--179325 Score: 2615
Period size: 692 Copynumber: 2.0 Consensus size: 686
177937 ACATAAAGAT
177947 GAGTATAAGTAATAAGACAAGAGTATGTGAACATGAAAGGAAATATATGATTAATGTATAAGGAA
1 GAGTATAAGTAATAAGACAAGAGTATGTGAACATGAAAGGAAATATATGATTAATGTATAAGGAA
178012 TAAGGATAAAGAAATGAAAAAGGGATGATTTAAAGGATCATACGATAAATATGGAAGTACAGAGG
66 TAAGGATAAAGAAATG-AAAAGGGATGATTTAAAGGATCATACGATAAATATGGAAGTACAGAGG
178077 ACAATTTTTGATATGGAATAAGACCAGTGTGCAAGGTGATGTGAAAATATTGTTTGACTCCTTAA
130 ACAATTTTTGATATGGAATAAGACCAGTGTGCAAGGTGATGTGAAAATATTGTTTGACTCCTTAA
178142 AGTATATGTTTAATCACATTGAAGAGATTTAAAGTTGAGTTTTGGTCAAATGATGACGAAATACA
195 AGTATATGTTTAATCACATTGAAGAGATTTAAAGTTGAGTTTTGGTCAAATGATGACGAAATACA
178207 AGTTTGGTATGGTTATAAGGTAATTAAAGATTGATAAAGAATTTGATTGATTAAGGATTTTGAGT
260 AGTTTGGTATGGTTATAAGGTAATTAAAGATTGATAAAGAATTTGATTGATTAAGGATTTTGAGT
178272 GATAAGAACTGATGCTATGGTTATATGATAAGTAACATGATAAGGATGTATAAAGGAAAAAGGTA
325 GATAAGAACTGATGCTATGGTTATATGATAAGTAACATGATAAGGATGTATAAAGGAAAAAGGTA
178337 GTGAAGAACTAAGAGAAAGAAGGATTAAGTAAAAGAAGTAACATAAGAACATTAGAAGATATGTT
390 GTGAAGAACTAAGAGAAAGAAGGATTAAGTAAAAGAAGTAACATAAGAACATTAGAAGATATGTT
178402 CTTACTAAGTTATTTAGTGAAAAATTCGAGGACGAATTTTTTTTAAAGGAGGGAGATTTGTAACA
455 CTTACTAAGTTATTTAGTGAAAAATTCGAGGACGAATTTTTTTTAAAGGAGGGAGATTTGTAACA
178467 TCCGCAATACCGGGTTAGTGACCAAATTGTAAAAGTTTCAGAATTTGGTGACTAAAGTAGAAGAA
520 TCCGCAATACCGGGTTAGTGACCAAATTGTAAAAGTTTCAGAATTTGGTGACTAAAGTAGAAGAA
178532 TGAAAGAATTCAATGATTATTTGATATATATTGAAGGGTATTTGGTAATTATTAAAGGAAATTAA
585 TGAAAGAATTCAATGATTATTTGATATATATTGAAGGGTATTTGGTAATTATT-AAGGAAATTAA
178597 GGGTATTATGGTCATTTGACCAGAAAGATTTTTTATAA
649 GGGTATTATGGTCATTTGACCAGAAAGATTTTTTATAA
178635 GAGTATAAGTAATAAGACAAGAGTATGTGAACATGAAAGG-AATATATGATTAATGTATAAGGAA
1 GAGTATAAGTAATAAGACAAGAGTATGTGAACATGAAAGGAAATATATGATTAATGTATAAGGAA
178699 TAAGGAATAAAGAAATG-AAAGGGATTGATTTAAAGGATCATATACGATAAATATGGAAGTAC-G
66 TAAGG-ATAAAGAAATGAAAAGGGA-TGATTTAAAGGATC--ATACGATAAATATGGAAGTACAG
178762 AGGACAATTTTTGATATGGAAATAAGACCAGTGTGCAAGGTGATGTGAAAATATTGTTTGACTCC
127 AGGACAATTTTTGATATGG-AATAAGACCAGTGTGCAAGGTGATGTGAAAATATTGTTTGACTCC
178827 TTAAAGTATATGTTTAATCACATTGAAGAAGATTTAAAGTTGAGTTTTGGTCAAATGATGACGAA
191 TTAAAGTATATGTTTAATCACATTGAAG-AGATTTAAAGTTGAGTTTTGGTCAAATGATGACGAA
178892 ATACAAGTTTTGGTATGGTTATAAGGTAATTAAAGATTGATAAAGAATTTGATTGATTAAGGATT
255 ATACAAG-TTTGGTATGGTTATAAGGTAATTAAAGATTGATAAAGAATTTGATTGATTAAGGATT
178957 TTGAGTGATAAGAACTGATGCTATTGGTTATATGATAAGTAACATGATAAGGATGTATAAAGG-A
319 TTGAGTGATAAGAACTGATGCTA-TGGTTATATGATAAGTAACATGATAAGGATGTATAAAGGAA
179021 AAAGGTAGTTGAAGAACTAAGAGAAAGAAGGATTAAGTAAAAGAAGTAACATAAGAACATTAGAA
383 AAAGGTAG-TGAAGAACTAAGAGAAAGAAGGATTAAGTAAAAGAAGTAACATAAGAACATTAGAA
179086 GATATGTTCTTACTAAGTTATTTAGTGAAAAATTCGAGGACGAATTTTTTTTAAAGGAGGGAGAT
447 GATATGTTCTTACTAAGTTATTTAGTGAAAAATTCGAGGACGAATTTTTTTTAAAGGAGGGAGAT
179151 TTGTAACATCCGCAATACCGGGTTAGTGACCAAATTGT-AAAGTTTCAGAATTTGGTGACTAAAG
512 TTGTAACATCCGCAATACCGGGTTAGTGACCAAATTGTAAAAGTTTCAGAATTTGGTGACTAAAG
179215 TAGAAGAATGAAAGAATTCAATGATTATTTGAATATATATTGAAGGGTATTTGGTAATTATTAAG
577 TAGAAGAATGAAAGAATTCAATGATTATTTG-ATATATATTGAAGGGTATTTGGTAATTATTAAG
179280 GAAATTAAGGGTATTATGGTCATTTGACCAGAAAGATTTTTTATAA
641 GAAATTAAGGGTATTATGGTCATTTGACCAGAAAGATTTTTTATAA
179326 TTTTTTTAAG
Statistics
Matches: 681, Mismatches: 0, Indels: 17
0.98 0.00 0.02
Matches are distributed among these distances:
686 7 0.01
687 43 0.06
688 71 0.10
689 94 0.14
690 43 0.06
691 195 0.29
692 228 0.33
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (686 bp):
GAGTATAAGTAATAAGACAAGAGTATGTGAACATGAAAGGAAATATATGATTAATGTATAAGGAA
TAAGGATAAAGAAATGAAAAGGGATGATTTAAAGGATCATACGATAAATATGGAAGTACAGAGGA
CAATTTTTGATATGGAATAAGACCAGTGTGCAAGGTGATGTGAAAATATTGTTTGACTCCTTAAA
GTATATGTTTAATCACATTGAAGAGATTTAAAGTTGAGTTTTGGTCAAATGATGACGAAATACAA
GTTTGGTATGGTTATAAGGTAATTAAAGATTGATAAAGAATTTGATTGATTAAGGATTTTGAGTG
ATAAGAACTGATGCTATGGTTATATGATAAGTAACATGATAAGGATGTATAAAGGAAAAAGGTAG
TGAAGAACTAAGAGAAAGAAGGATTAAGTAAAAGAAGTAACATAAGAACATTAGAAGATATGTTC
TTACTAAGTTATTTAGTGAAAAATTCGAGGACGAATTTTTTTTAAAGGAGGGAGATTTGTAACAT
CCGCAATACCGGGTTAGTGACCAAATTGTAAAAGTTTCAGAATTTGGTGACTAAAGTAGAAGAAT
GAAAGAATTCAATGATTATTTGATATATATTGAAGGGTATTTGGTAATTATTAAGGAAATTAAGG
GTATTATGGTCATTTGACCAGAAAGATTTTTTATAA
Found at i:179856 original size:21 final size:20
Alignment explanation
Indices: 179830--179873 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
179820 GATTTCTGGG
* *
179830 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
179851 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
179871 CAA
1 CAA
179874 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:181608 original size:23 final size:22
Alignment explanation
Indices: 181549--181615 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
181539 TATGGACATC
*
181549 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
181571 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
181593 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
181616 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:182713 original size:122 final size:121
Alignment explanation
Indices: 182547--182775 Score: 300
Period size: 122 Copynumber: 1.9 Consensus size: 121
182537 CATATAAGTA
* * * * * * ** *
182547 CTTTAGTGGCGTTTTTAAATAATCTGCAATAGGGTATATATATTGTGGCATTTTTAGACAAGTGT
1 CTTTAGTGGCGTTTTTAAACAAGCCGAAATAGGGTACATATATTGTGACATTTTTAGACAAACGC
182612 CGCTAAAACCCAGTACTTTAGTGGCG-TTTCTAAACAAACGCTACAAAAGAATGATT
66 CGCTAAAACCCAGTACTTTAGTGG-GTTTTCTAAACAAACGCTACAAAAGAATGATT
*
182668 CTTTAGTGGCGTTTTTTAAACAACGCCGAAATA-GGTACATATATTGTGACATTTTTAGATAAAC
1 CTTTAGTGGCG-TTTTTAAACAA-GCCGAAATAGGGTACATATATTGTGACATTTTTAGACAAAC
* * *
182732 GCCGCTAAAATCTAGTACTTTAGTGGGTTTTTTAAACAAACGCT
64 GCCGCTAAAACCCAGTACTTTAGTGGGTTTTCTAAACAAACGCT
182776 GTAATAGGGT
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
121 12 0.13
122 74 0.80
123 6 0.07
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (121 bp):
CTTTAGTGGCGTTTTTAAACAAGCCGAAATAGGGTACATATATTGTGACATTTTTAGACAAACGC
CGCTAAAACCCAGTACTTTAGTGGGTTTTCTAAACAAACGCTACAAAAGAATGATT
Found at i:182753 original size:81 final size:83
Alignment explanation
Indices: 182668--182839 Score: 246
Period size: 82 Copynumber: 2.1 Consensus size: 83
182658 AAGAATGATT
*
182668 CTTTAGTGGCGTTTTTTAAAC-AACGCCGAAATA-GGTACATATATTGT-GACATTTTTAGATAA
1 CTTTAGTGGCGTTTTTTAAACAAACGCCGAAATAGGGTACATATATTGTAG-CATTTTTAGACAA
*
182730 ACGCCGCTAAAATCTAGTA
65 ACGCCGCTAAAACCTAGTA
* * *
182749 CTTTAGTGG-GTTTTTTAAACAAACGCTGTAATAGGGTACATATATTGTAGCGTTTTTAGACAAA
1 CTTTAGTGGCGTTTTTTAAACAAACGCCGAAATAGGGTACATATATTGTAGCATTTTTAGACAAA
*
182813 CGCTGCTAAAACCTAGTA
66 CGCCGCTAAAACCTAGTA
182831 C-TTAGTGGC
1 CTTTAGTGGC
182840 ATTTCTAACA
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
80 11 0.14
81 26 0.32
82 43 0.53
83 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (83 bp):
CTTTAGTGGCGTTTTTTAAACAAACGCCGAAATAGGGTACATATATTGTAGCATTTTTAGACAAA
CGCCGCTAAAACCTAGTA
Found at i:182943 original size:41 final size:42
Alignment explanation
Indices: 182872--182967 Score: 133
Period size: 41 Copynumber: 2.3 Consensus size: 42
182862 GAATCATTCT
*
182872 TTAGTGGCGTTTTTGAAACAAATGCCGCAATA-GTTCGAAACA
1 TTAGTGGCGTTTTTGAAAAAAATGCCGCAATATGTT-GAAACA
* * *
182914 TTTGTGGCGTTTTT-AAAAAAATGCCGCAATATGTTGAACCG
1 TTAGTGGCGTTTTTGAAAAAAATGCCGCAATATGTTGAAACA
182955 TTAGTGGCGTTTT
1 TTAGTGGCGTTTT
182968 GTTTGAAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 32 0.67
42 16 0.33
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (42 bp):
TTAGTGGCGTTTTTGAAAAAAATGCCGCAATATGTTGAAACA
Found at i:185585 original size:29 final size:29
Alignment explanation
Indices: 185516--185599 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 29
185506 TTATGTATTG
*
185516 TTTAGTCCTTTAAAATTTTGTTTTTACTAT
1 TTTAGTCCTTT-AAATTTTGTTTTCACTAT
*
185546 TTTAGTCCTTTAAATTTATGTTTTCACTGT
1 TTTAGTCCTTTAAATTT-TGTTTTCACTAT
* *
185576 TTTAGTCTTTTAAGTTTCTGTTTT
1 TTTAGTCCTTTAAATTT-TGTTTT
185600 TTGTCATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 6 0.12
30 42 0.88
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.61
Consensus pattern (29 bp):
TTTAGTCCTTTAAATTTTGTTTTCACTAT
Found at i:185901 original size:16 final size:17
Alignment explanation
Indices: 185864--185901 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
185854 GCATACCAAC
185864 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
185881 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
185897 TTTTT
1 TTTTT
185902 AAAAGACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:186818 original size:17 final size:16
Alignment explanation
Indices: 186789--186822 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
186779 AAATTTCTTG
*
186789 AAAAATCATTGTGGGT
1 AAAAAGCATTGTGGGT
186805 AAAAAGCATGTGTGGGT
1 AAAAAGCAT-TGTGGGT
186822 A
1 A
186823 GGATTACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAAGCATTGTGGGT
Found at i:188974 original size:19 final size:18
Alignment explanation
Indices: 188928--188975 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
188918 ATCCAATCAG
*
188928 AACAAAGAGCAAAAAAAA
1 AACAAAAAGCAAAAAAAA
*
188946 AATAAAAAGCAAAGAAAAA
1 AACAAAAAGCAAA-AAAAA
*
188965 AACAATAAGCA
1 AACAAAAAGCA
188976 CATGTAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.75, C:0.10, G:0.10, T:0.04
Consensus pattern (18 bp):
AACAAAAAGCAAAAAAAA
Found at i:191008 original size:22 final size:22
Alignment explanation
Indices: 190973--191042 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
190963 CACCACAGCT
* *
190973 CATATA-AATGCACCGAAGTGC
1 CATATAGATTGCACCGTAGTGC
190994 CATATAGATTGCACCGTAGTG-
1 CATATAGATTGCACCGTAGTGC
* *
191015 CGTGTAGAGTTGCA-CGTAGTGC
1 CATATAGA-TTGCACCGTAGTGC
191037 CATATA
1 CATATA
191043 ATAATGTCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 19 0.47
22 21 0.52
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (22 bp):
CATATAGATTGCACCGTAGTGC
Found at i:191227 original size:103 final size:102
Alignment explanation
Indices: 191054--191269 Score: 407
Period size: 103 Copynumber: 2.1 Consensus size: 102
191044 TAATGTCCAT
191054 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
191119 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGT-CCG
191157 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
191222 AACTTCACACATGTTCCAAAGAATACATATATGTCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCG
191259 AAGGA-CACATA
1 AAGGACCACATA
191270 GACCTCGAAT
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
101 6 0.05
102 8 0.07
103 98 0.88
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCG
Found at i:194017 original size:124 final size:122
Alignment explanation
Indices: 193725--194067 Score: 451
Period size: 121 Copynumber: 2.8 Consensus size: 122
193715 AACTTGCACA
* *
193725 AGATTGGATTTCAACTTCAC-AAAGAAGGATATCCAATTCAAGGCTCAACTTCACGACAAATGGG
1 AGATTGGATTTCAACTTCACGACA-AAGGATATCCAATTCAAGGCTCAACTTCACGACAAAGGGG
* * * *
193789 TCATCCACGATTTTAACTTCACGACGATGAATATCGTGCTCACAAGCAGCAATGCAAC
65 TCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAACAATGCAAC
* * * *
193847 -CATTGGACTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTTACAACAAAGGGGT
1 AGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACGACAAAGGGGT
* * *
193911 CATCCACGATTTCAACTTCACGACGAAGGATATCGTG-TCCACCAGCAAC-ATTCATC
66 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCT-CACAAGCAACAATGCAAC
* * * * *
193967 TTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCGATGCTCAAATTCACGACGAAGA
1 ---AGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACGACAAAGG
194032 GGTCATCCACGATTTCAACTTCACGACGAAGGATAT
63 GGTCATCCACGATTTCAACTTCACGACGAAGGATAT
194068 TCAATTTAAA
Statistics
Matches: 193, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
120 6 0.03
121 97 0.50
122 2 0.01
124 88 0.46
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (122 bp):
AGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACGACAAAGGGGT
CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAACAATGCAAC
Found at i:194058 original size:32 final size:34
Alignment explanation
Indices: 193976--194062 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 34
193966 CTTTAGATTG
193976 GATTTCAACTTCACGAC-AA-AGGATATCCAATTC
1 GATTTCAACTTCACGACGAAGAGGATATCCAA-TC
* *
194009 GATGCTCAAATTCACGACGAAGAGG-TCATCC-A-C
1 GAT-TTCAACTTCACGACGAAGAGGAT-ATCCAATC
194042 GATTTCAACTTCACGACGAAG
1 GATTTCAACTTCACGACGAAG
194063 GATATTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 12 0.26
35 4 0.09
36 7 0.15
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (34 bp):
GATTTCAACTTCACGACGAAGAGGATATCCAATC
Found at i:194345 original size:43 final size:44
Alignment explanation
Indices: 194150--194394 Score: 153
Period size: 43 Copynumber: 5.6 Consensus size: 44
194140 TGACCTGATC
*** * *
194150 TCCTCATCACGTAGGAGTTGTGTCAACCAT-AGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCCTCAGATAACCAGTCG
* * * *****
194193 TCCTCATCACGTAGGAATCGTGTTATCATCCCTAATGATGGTTTGTCG
1 TCCTCATCACGTAGGAACCGTG---TCAACCCTCA-GATAACCAGTCG
* * *
194241 TCCTCATCACGTAGGAACTGTGTCATCCCTC-G---ACCAAATC-
1 TCCTCATCACGTAGGAACCGTGTCAACCCTCAGATAACC-AGTCG
** *
194281 TCCTCATCACGTAGGCGCCGTGTCAACCC-CAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCCTCAGATAACCAGTCG
* * * *
194324 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCTGTCG
1 TCCTCATCACGTAGGAACCGTGTCA--ACCCTCAGATAACCAGTCG
* *
194370 TCCTCATCGCGTAGGAATCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
194395 TCACCCGACC
Statistics
Matches: 154, Mismatches: 34, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
39 1 0.01
40 26 0.17
41 2 0.01
42 2 0.01
43 46 0.30
45 12 0.08
46 38 0.25
47 1 0.01
48 26 0.17
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (44 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCTCAGATAACCAGTCG
Found at i:194430 original size:129 final size:131
Alignment explanation
Indices: 194141--194438 Score: 424
Period size: 131 Copynumber: 2.3 Consensus size: 131
194131 TATCCAACCT
** **
194141 GACCTGATCTCCTCATCACGTAGGAGTTGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCTGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTA
* ***
194206 GGAATCGTGTTATCATCCCTAATGATGGTTTGTCGTCCTCATCACGTAGGAACTGTGTCATCCCT
66 GGAACCGTGTTATCATCCCTAATGATGACCTGTCGTCCTCATCACGTAGGAACTGTGTCATCCCT
194271 C
131 C
** *
194272 GACCAAATCTCCTCATCACGTAGGCGCCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTA
1 GACCTGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTA
* *
194337 GGAACCGTGTTATCA-CCCTTA-GATGACCTGTCGTCCTCATCGCGTAGGAA-TCGTGTCATCAC
66 GGAACCGTGTTATCATCCCTAATGATGACCTGTCGTCCTCATCACGTAGGAACT-GTGTCATC-C
194399 C-C
129 CTC
*
194401 GACCTGATTTCCTCATCACGTAGGAGCCGTGTCAACCC
1 GACCTGATCTCCTCATCACGTAGGAGCCGTGTCAACCC
194439 TTAGACGACC
Statistics
Matches: 148, Mismatches: 17, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
128 1 0.01
129 68 0.46
130 7 0.05
131 72 0.49
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (131 bp):
GACCTGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTA
GGAACCGTGTTATCATCCCTAATGATGACCTGTCGTCCTCATCACGTAGGAACTGTGTCATCCCT
C
Found at i:195583 original size:29 final size:29
Alignment explanation
Indices: 195513--195580 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
195503 TTATGTATTG
*
195513 TTTAGTCCTTTAAAATTTGTTTTTACTAT
1 TTTAGTCCTTTAAAATTTGTTTTCACTAT
*
195542 TTTAGTCCTTTAAATTTATGTTTTCACTA-
1 TTTAGTCCTTTAAAATT-TGTTTTCACTAT
195571 TTTAG-CCTTT
1 TTTAGTCCTTT
195581 TAAGTTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 10 0.28
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTAGTCCTTTAAAATTTGTTTTCACTAT
Found at i:198578 original size:28 final size:27
Alignment explanation
Indices: 198523--198578 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
198513 AATATTGTTC
* * *
198523 ATTTTTTTGAAACTATTAAATGGTTTT
1 ATTTTTTTGAAAATATCAAATGGCTTT
*
198550 ATTTTTTTGAAAGATATCAAGTGGCTTT
1 ATTTTTTTGAAA-ATATCAAATGGCTTT
198578 A
1 A
198579 GTAGTAAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.50
Consensus pattern (27 bp):
ATTTTTTTGAAAATATCAAATGGCTTT
Found at i:205380 original size:2 final size:2
Alignment explanation
Indices: 205373--205427 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
205363 AGGTTTTGAT
205373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
205415 TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA
205428 CTAGAATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:207154 original size:23 final size:25
Alignment explanation
Indices: 207128--207174 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
207118 AAATTATATA
*
207128 AAAAAATTAG-G-ATGTAAAATTAT
1 AAAAAATTAGAGAACGTAAAATTAT
*
207151 AAAATATTAGAGAACGTAAAATTA
1 AAAAAATTAGAGAACGTAAAATTA
207175 AATCATCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.28
Consensus pattern (25 bp):
AAAAAATTAGAGAACGTAAAATTAT
Found at i:213784 original size:30 final size:28
Alignment explanation
Indices: 213748--213820 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
213738 GACATAACAT
213748 ATGAATATCATTTTATCTCTAAACTTTAA
1 ATGAATATCATTTTATCT-TAAACTTTAA
* ** *
213777 ATAGAATAATAATTAGATCTTAAACTTTAT
1 AT-GAAT-ATCATTTTATCTTAAACTTTAA
213807 ATGAATATCATTTT
1 ATGAATATCATTTT
213821 GACCATATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 5 0.14
29 6 0.17
30 15 0.43
31 9 0.26
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (28 bp):
ATGAATATCATTTTATCTTAAACTTTAA
Found at i:217910 original size:125 final size:125
Alignment explanation
Indices: 217767--218032 Score: 489
Period size: 125 Copynumber: 2.1 Consensus size: 125
217757 AAAAAGAAAG
* *
217767 AATG-AAATACGAATAAAATTTACAAGGAAAAATACGAAGATTCAAATAAAGAAAAAAAAGAATA
1 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAGAATA
217831 AAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
66 AAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
217891 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAGAATA
1 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAGAATA
217956 AAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
66 AAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
*
218016 AATGAAAAAAACAAATA
1 AATG-AAAATACAAATA
218033 TGAGTAATAT
Statistics
Matches: 137, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
124 4 0.03
125 122 0.89
126 11 0.08
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.18
Consensus pattern (125 bp):
AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAGAATA
AAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
Found at i:220069 original size:43 final size:43
Alignment explanation
Indices: 220008--220359 Score: 155
Period size: 43 Copynumber: 7.4 Consensus size: 43
219998 ACCAGCGGTC
220008 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
220051 CCTTCGTTGTGAAGTTGAAATTGAGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
*
220101 CCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** *
220145 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGTGAT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCAAT-AT
*
220199 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
220243 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT
220297 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
220341 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
220360 ATTGGCCCTG
Statistics
Matches: 220, Mismatches: 57, Indels: 64
0.65 0.17 0.19
Matches are distributed among these distances:
43 79 0.36
44 6 0.03
45 10 0.05
46 17 0.08
47 1 0.00
48 13 0.06
49 3 0.01
50 7 0.03
51 22 0.10
52 10 0.05
53 7 0.03
54 5 0.02
55 40 0.18
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:220237 original size:98 final size:98
Alignment explanation
Indices: 219985--220573 Score: 963
Period size: 98 Copynumber: 6.0 Consensus size: 98
219975 AATTGGGAAG
219985 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
220050 TCCTTCGTTGTGAAGTTGAAATT-G---AGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
*
220079 TTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
220144 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
* * *
220177 TTGTTTATTGACAACCAGTGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
220242 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
220275 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
220340 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
*
220373 TTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
220438 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
* * *
220471 TTGAGAAATGTCTGTTGA-ACACCAGCGGTCCCTTCGCCATGAAGTTGAACTTGCGTTGTCTGGA
1 TT--G---T-T-TATTGACA-ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
220535 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGA
58 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
220574 GTAAAACCTG
Statistics
Matches: 466, Mismatches: 17, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
94 87 0.19
95 1 0.00
98 290 0.62
103 1 0.00
104 2 0.00
105 85 0.18
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
Found at i:220310 original size:55 final size:55
Alignment explanation
Indices: 220243--220414 Score: 161
Period size: 55 Copynumber: 3.3 Consensus size: 55
220233 AGTCCAATAT
*
220243 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
* * * ** ***
220298 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT-
1 CCTTCGTCGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
* *
220341 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTATTTATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
220396 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
220415 CTTGCGTTGT
Statistics
Matches: 85, Mismatches: 20, Indels: 24
0.66 0.16 0.19
Matches are distributed among these distances:
43 20 0.24
44 2 0.02
45 3 0.04
46 5 0.06
47 1 0.01
48 3 0.04
50 2 0.02
51 1 0.01
52 5 0.06
53 3 0.04
54 2 0.02
55 38 0.45
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (55 bp):
CCTTCGTCGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
Found at i:221421 original size:47 final size:47
Alignment explanation
Indices: 221350--221440 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
221340 TGTTTTTCTA
* *
221350 TTTTTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTTTTTCCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
* *
221397 TTTTTTTTTCCAATTTAGGGCGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTTTTCCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAA
221441 GCGAAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (47 bp):
TTTTTTTTTCCAATTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:231907 original size:125 final size:126
Alignment explanation
Indices: 231764--232030 Score: 484
Period size: 126 Copynumber: 2.1 Consensus size: 126
231754 AAAAAGAAAG
* *
231764 AATG-AAATACGAATAAAATTTACAAGGAAAAATACGAAGATTCAAATAAAG-AAAAAAAAGAAT
1 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAAGAAT
231827 AAAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
66 AAAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
231888 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAAGAAT
1 AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAAGAAT
231953 AAAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
66 AAAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
*
232014 AATGAAAAAAACAAATA
1 AATG-AAAATACAAATA
232031 TGAGTAATAT
Statistics
Matches: 137, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
124 4 0.03
125 45 0.33
126 77 0.56
127 11 0.08
ACGTcount: A:0.68, C:0.04, G:0.10, T:0.18
Consensus pattern (126 bp):
AATGAAAATACAAATAAAATTTACAAGGAAAAATAAGAAGATTCAAATAAAGAAAAAAAAAGAAT
AAAAATATAAATAGATAGGTAAATAAAAATATACATGAATAAAAAATATAAAAACAAAGAA
Found at i:242203 original size:17 final size:18
Alignment explanation
Indices: 242171--242204 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
242161 ATCAAAAAAT
242171 AAAATAGTAATATAATAA
1 AAAATAGTAATATAATAA
*
242189 AAAATATTAAT-TAATA
1 AAAATAGTAATATAATA
242205 TTAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAATAGTAATATAATAA
Found at i:244585 original size:16 final size:16
Alignment explanation
Indices: 244564--244596 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
244554 TAACAAATAA
244564 ATGAACATAAACGAAC
1 ATGAACATAAACGAAC
244580 ATGAACATAAACGAAC
1 ATGAACATAAACGAAC
244596 A
1 A
244597 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (16 bp):
ATGAACATAAACGAAC
Found at i:244686 original size:16 final size:16
Alignment explanation
Indices: 244662--244720 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
244652 CATTTAATAA
244662 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
244678 ATAAGCGAACACGAAC
1 ATAAACGAACACGAAC
*
244694 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
244710 ATAAACGAACA
1 ATAAACGAACA
244721 TAAACGTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.56, C:0.22, G:0.14, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:244974 original size:19 final size:19
Alignment explanation
Indices: 244950--244994 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
244940 TGAACAATCA
*
244950 TTTTCAGCTATTACATTCT
1 TTTTCAGCTATTACACTCT
244969 TTTTCAGCTATTACACTCT
1 TTTTCAGCTATTACACTCT
244988 TTTTCAG
1 TTTTCAG
244995 AAATTGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTCAGCTATTACACTCT
Found at i:245499 original size:24 final size:25
Alignment explanation
Indices: 245472--245533 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
245462 TATTGGGTTA
*
245472 AACATAAAT-GAATGAACATAAACG
1 AACATAAATCGAACGAACATAAACG
245496 AACAT-AATCGAACGAACATAAACG
1 AACATAAATCGAACGAACATAAACG
245520 AACAT-AATCGAACG
1 AACATAAATCGAACG
245534 TTCGCGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.15
Consensus pattern (25 bp):
AACATAAATCGAACGAACATAAACG
Found at i:245500 original size:10 final size:10
Alignment explanation
Indices: 245485--245532 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
245475 ATAAATGAAT
245485 GAACATAAAC
1 GAACATAAAC
245495 GAACATAATCGAAC
1 GAACAT-A---AAC
245509 GAACATAAAC
1 GAACATAAAC
*
245519 GAACATAATC
1 GAACATAAAC
245529 GAAC
1 GAAC
245533 GTTCGCGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:245509 original size:14 final size:14
Alignment explanation
Indices: 245492--245533 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
245482 AATGAACATA
245492 AACGAACATAATCG
1 AACGAACATAATCG
245506 AACGAACAT-A---
1 AACGAACATAATCG
245516 AACGAACATAATCG
1 AACGAACATAATCG
245530 AACG
1 AACG
245534 TTCGCGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:246714 original size:6 final size:6
Alignment explanation
Indices: 246703--246734 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
246693 TCGTCTCGTC
246703 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
246735 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:247434 original size:60 final size:60
Alignment explanation
Indices: 247360--247509 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
247350 GCATCACAAG
* * * * * *
247360 TCCTTGAACTATGACCTTCATTTTAAATTGGTCCTTAAACTTTTAAA-AGCTTCAGTTTCA
1 TCCTTAAACTATGACCTTCATTCTAAATTAGTCCTCAAACGTTTAAACA-CTTCAATTTCA
*
247420 TCCTTAAACTATGA-CTATCATTCTAAATTAGTCCTCAAACGTTTAAACATTTCAATTTCA
1 TCCTTAAACTATGACCT-TCATTCTAAATTAGTCCTCAAACGTTTAAACACTTCAATTTCA
** * *
247480 TCCCCAAACCATGACTTTCATTCTAAATTA
1 TCCTTAAACTATGACCTTCATTCTAAATTA
247510 ATCCCCAATA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 72 0.95
61 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (60 bp):
TCCTTAAACTATGACCTTCATTCTAAATTAGTCCTCAAACGTTTAAACACTTCAATTTCA
Found at i:247545 original size:60 final size:60
Alignment explanation
Indices: 247415--247548 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
247405 AAAGCTTCAG
** * * * *
247415 TTTCATCCTTAAACTATGACTATCATTCTAAATTAGTCCTCAAACGTTTAAACATTTCAA
1 TTTCATCCCCAAACCATGACTATCATTCTAAATTAATCCCCAAACGTTTAAACATTCCAA
* ** *
247475 TTTCATCCCCAAACCATGACTTTCATTCTAAATTAATCCCCAATATTTTTTAACATTCCAA
1 TTTCATCCCCAAACCATGACTATCATTCTAAATTAATCCCCAA-ACGTTTAAACATTCCAA
247536 TATT-A-CCCCAAAC
1 T-TTCATCCCCAAAC
247549 TATATGTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 45 0.73
61 15 0.24
62 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (60 bp):
TTTCATCCCCAAACCATGACTATCATTCTAAATTAATCCCCAAACGTTTAAACATTCCAA
Found at i:247760 original size:60 final size:60
Alignment explanation
Indices: 247679--247799 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
247669 TATGAATTTG
*** *
247679 GGGATGAAATTGGAAGATTTAAAAGTTTGGGGA-TAAATTTAAAAAGAGGGTTATAGTTTA
1 GGGATGAAATTGGAAGATTTAAAAGTTTAAAGACT-AATTTAAAAAGAGAGTTATAGTTTA
* * *
247739 GGGATGAGATTTGAATG-TTTAAAAGTTTAAAGACTAATTTAAAATGAGAGTTATAGTTTA
1 GGGATGAAATTGGAA-GATTTAAAAGTTTAAAGACTAATTTAAAAAGAGAGTTATAGTTTA
247799 G
1 G
247800 AAACATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTGGAAGATTTAAAAGTTTAAAGACTAATTTAAAAAGAGAGTTATAGTTTA
Found at i:258174 original size:18 final size:19
Alignment explanation
Indices: 258151--258195 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
258141 CACAGTAATC
*
258151 TTATTCT-CTGATAATCTT
1 TTATTCTACTGATAATATT
258169 TTATTCTTACTGATAATATT
1 TTATTC-TACTGATAATATT
*
258189 ATATTCT
1 TTATTCT
258196 GTTAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (19 bp):
TTATTCTACTGATAATATT
Found at i:258183 original size:20 final size:20
Alignment explanation
Indices: 258158--258195 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
258148 ATCTTATTCT
* *
258158 CTGATAATCTTTTATTCTTA
1 CTGATAATATTATATTCTTA
258178 CTGATAATATTATATTCT
1 CTGATAATATTATATTCT
258196 GTTAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (20 bp):
CTGATAATATTATATTCTTA
Found at i:261786 original size:20 final size:20
Alignment explanation
Indices: 261744--261816 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
261734 GAATATGTAA
* *
261744 ATCGCAACGCGA-TTCTGACT
1 ATCGCAACGCGATTTC-CAGT
261764 ATCGCAACGCGATTTCCAGT
1 ATCGCAACGCGATTTCCAGT
**
261784 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAACGCGA-TTTCCAGT
261803 ATTCGCAACGCGAT
1 A-TCGCAACGCGAT
261817 AATACAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
20 37 0.86
21 4 0.09
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTTCCAGT
Found at i:261856 original size:19 final size:20
Alignment explanation
Indices: 261832--261879 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
261822 AAAATTGCAA
261832 TGCGATTTTCCAAATT-CGT
1 TGCGATTTTCCAAATTACGT
** *
261851 TGCGATAATCCAAGTTCACGT
1 TGCGATTTTCCAAATT-ACGT
261872 TGCGATTT
1 TGCGATTT
261880 CTTAAGAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
TGCGATTTTCCAAATTACGT
Found at i:262288 original size:19 final size:19
Alignment explanation
Indices: 262264--262300 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
262254 TTATTTTGGA
262264 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
262283 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
262301 ACACGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:262676 original size:21 final size:20
Alignment explanation
Indices: 262655--262763 Score: 94
Period size: 20 Copynumber: 5.3 Consensus size: 20
262645 TCAAAATACA
*
262655 GAATTTGGAATTCGCAACAC
1 GAATTTGAAATTCGCAACAC
* * * *
262675 AGAA-GTCAAATTCCCAACGC
1 -GAATTTGAAATTCGCAACAC
*
262695 GAATTTGAAATTCGCAAAAC
1 GAATTTGAAATTCGCAACAC
* *
262715 ATAATTTGAAATTCGCAACTC
1 -GAATTTGAAATTCGCAACAC
*
262736 GATTTTGACAATTTCGCAACAC
1 GAATTTGA-AA-TTCGCAACAC
262758 GAATTT
1 GAATTT
262764 CTTTTTCGCA
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
19 3 0.04
20 28 0.42
21 22 0.33
22 14 0.21
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
GAATTTGAAATTCGCAACAC
Found at i:262709 original size:40 final size:41
Alignment explanation
Indices: 262655--262761 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 41
262645 TCAAAATACA
*
262655 GAATTTGGAATTCGCAACACAGAA-GTCAAATTCCCAACGC
1 GAATTTGAAATTCGCAACACAGAATGTCAAATTCCCAACGC
* * * * * *
262695 GAATTTGAAATTCGCAAAACATAATTTGAAATTCGCAACTC
1 GAATTTGAAATTCGCAACACAGAATGTCAAATTCCCAACGC
*
262736 GATTTTGACAATTTCGCAACAC-GAAT
1 GAATTTGA-AA-TTCGCAACACAGAAT
262762 TTCTTTTTCG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 21 0.39
41 19 0.35
42 5 0.09
43 9 0.17
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (41 bp):
GAATTTGAAATTCGCAACACAGAATGTCAAATTCCCAACGC
Found at i:262788 original size:19 final size:20
Alignment explanation
Indices: 262747--262796 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
262737 ATTTTGACAA
262747 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
*
262767 TTTCGCAACTC-AATTTTCTT
1 TTTCGCAACACGAA-TTTCTT
262787 TTTCGCAACA
1 TTTCGCAACA
262797 TGATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCTT
Done.