Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:2100088 original size:3 final size:3
Alignment explanation
Indices: 2100080--2100111 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2100070 GGATACTAAA
*
2100080 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2100112 ATCTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2102499 original size:20 final size:20
Alignment explanation
Indices: 2102447--2102502 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2102437 CAATGCTGGT
*
2102447 AGTATCGATACTACCTAGTG
1 AGTATCGATACTTCCTAGTG
*
2102467 AGTATCGATACTTCTTAGTG
1 AGTATCGATACTTCCTAGTG
2102487 AGTATCGATACTTCCT
1 AGTATCGATACTTCCT
2102503 TTACCTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTTCCTAGTG
Found at i:2108396 original size:2 final size:2
Alignment explanation
Indices: 2108389--2108422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2108379 CGGTTTATGA
2108389 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
2108423 TGAATGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2122565 original size:21 final size:19
Alignment explanation
Indices: 2122527--2122572 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2122517 AATTAATCCT
2122527 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
2122547 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
2122568 A-TAAT
1 ACTAAT
2122573 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:2125731 original size:3 final size:3
Alignment explanation
Indices: 2125723--2125752 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2125713 AAATATTTAA
2125723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2125753 TTAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2127293 original size:3 final size:3
Alignment explanation
Indices: 2127279--2127329 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2127269 TATTTATTTG
* *
2127279 TAA TAA -AA TAA TAA T-A TTA TAT TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
*
2127323 GAA TAA T
1 TAA TAA T
2127330 TTTAATGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2127335 original size:19 final size:19
Alignment explanation
Indices: 2127285--2127329 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2127275 TTTGTAATAA
* *
2127285 AATAATAATATTATATTAAT
1 AATAATAATAATA-ATTAAG
2127305 AATAATAATAATAATTAAG
1 AATAATAATAATAATTAAG
2127324 AATAAT
1 AATAAT
2127330 TTTAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATAATAATAATTAAG
Found at i:2127594 original size:25 final size:24
Alignment explanation
Indices: 2127566--2127640 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 24
2127556 AAAAGTTCCC
2127566 GAAGGTTTTAAAAACATCATGCACT
1 GAAGGTTTT-AAAACATCATGCACT
** * * *
2127591 GAAGGGGTT-ACAGATGA-GC-C-
1 GAAGGTTTTAAAACATCATGCACT
2127611 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTT-AAAACATCATGCACT
2127636 GAAGG
1 GAAGG
2127641 GCTTACAAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 7 0.20
21 1 0.03
22 7 0.20
23 7 0.20
24 1 0.03
25 12 0.34
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.23
Consensus pattern (24 bp):
GAAGGTTTTAAAACATCATGCACT
Found at i:2127684 original size:25 final size:25
Alignment explanation
Indices: 2127611--2127685 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
2127601 CAGATGAGCC
*
2127611 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGAACT
** * * *
2127636 GAAGGGCTT----ACA-AATGACCC
1 GAAGGTTTTGAAAACATCATGAACT
2127656 GAAGGTTTTGAAAACATCATGAACT
1 GAAGGTTTTGAAAACATCATGAACT
2127681 GAAGG
1 GAAGG
2127686 ACTTACAGAT
Statistics
Matches: 34, Mismatches: 11, Indels: 10
0.62 0.20 0.18
Matches are distributed among these distances:
20 11 0.32
21 3 0.09
24 3 0.09
25 17 0.50
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGAACT
Found at i:2127728 original size:46 final size:46
Alignment explanation
Indices: 2127563--2128338 Score: 1237
Period size: 46 Copynumber: 17.0 Consensus size: 46
2127553 TCAAAAAGTT
* * **
2127563 CCCGAAGG-TTTTAAAAACATCATGCACTGAAGGGGTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* * * *
2127608 GCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* *
2127653 CCCGAAGG-TTTTGAAAACATCATGAACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
2127698 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
2127744 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2127790 CCCGAAGG-TTTTGAAAAACATCATGCACTGAATGG-CTTACAGATGA
1 CCCGAAGGTTTTTG-ATAACATCATGCACTGAA-GGACTTACAGATGA
*
2127836 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACCTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2127882 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* * ** *
2127928 CCCGGAGG-TTTTGAAAACAAAATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* *
2127973 CCCGAAGG-TTTTGAAAACAACATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2128018 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
2128063 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
2128109 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2128155 CTCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
2128201 CCCGAAGGTTATTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTT-TTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2128248 CCCGTAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
*
2128294 CCCGAAGGTTATTTGATAACATCATGCACCGAAGGAC-TACAGATG
1 CCCGAAGGTT-TTTGATAACATCATGCACTGAAGGACTTACAGATG
2128339 TTGGAAATAG
Statistics
Matches: 694, Mismatches: 29, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
45 225 0.32
46 392 0.56
47 77 0.11
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (46 bp):
CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2132596 original size:32 final size:32
Alignment explanation
Indices: 2132560--2132621 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2132550 GAAGAAATGA
* *
2132560 TTGTTATGTTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
2132592 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
2132622 TGTGTCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:2133075 original size:8 final size:8
Alignment explanation
Indices: 2133062--2133130 Score: 115
Period size: 8 Copynumber: 8.8 Consensus size: 8
2133052 CTTGGTTCAA
2133062 TTTTTTCC
1 TTTTTTCC
2133070 TTTTTT-C
1 TTTTTTCC
2133077 TTTTTTCCC
1 TTTTTT-CC
2133086 TTTTTT-C
1 TTTTTTCC
2133093 TTTTTTCC
1 TTTTTTCC
2133101 TTTTTTCC
1 TTTTTTCC
2133109 TTTTTTCC
1 TTTTTTCC
2133117 TTTTTTCC
1 TTTTTTCC
2133125 TTTTTT
1 TTTTTT
2133131 TTCAAGTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
7 14 0.24
8 37 0.64
9 7 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2137477 original size:28 final size:26
Alignment explanation
Indices: 2137422--2137479 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
2137412 AAACATTAAT
*
2137422 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
2137448 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
2137476 AAAA
1 AAAA
2137480 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:2139732 original size:3 final size:3
Alignment explanation
Indices: 2139718--2139785 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
2139708 TATTTATTTG
2139718 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2139765 TAA TAA TAA -AA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
2139786 TAAGTATAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2143934 original size:23 final size:22
Alignment explanation
Indices: 2143908--2143956 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
2143898 CTGACCGGTT
2143908 CGACCCGACCCATTGACCCGACC
1 CGACCCGACCCATTGA-CCGACC
*
2143931 CGACCCGACCCGTTGACCGACC
1 CGACCCGACCCATTGACCGACC
2143953 CGAC
1 CGAC
2143957 GAGACCCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.08
Consensus pattern (22 bp):
CGACCCGACCCATTGACCGACC
Found at i:2143962 original size:22 final size:23
Alignment explanation
Indices: 2143908--2143964 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2143898 CTGACCGGTT
* *
2143908 CGACCCGACCCATTGACCCGACC
1 CGACCAGACCCGTTGACCCGACC
*
2143931 CGACCCGACCCGTTGA-CCGACC
1 CGACCAGACCCGTTGACCCGACC
*
2143953 CGACGAGACCCG
1 CGACCAGACCCG
2143965 ACGAGACCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.21, C:0.49, G:0.23, T:0.07
Consensus pattern (23 bp):
CGACCAGACCCGTTGACCCGACC
Found at i:2143964 original size:10 final size:10
Alignment explanation
Indices: 2143949--2143974 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2143939 CCCGTTGACC
2143949 GACCCGACGA
1 GACCCGACGA
2143959 GACCCGACGA
1 GACCCGACGA
2143969 GACCCG
1 GACCCG
2143975 TTGACCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.42, G:0.31, T:0.00
Consensus pattern (10 bp):
GACCCGACGA
Found at i:2143965 original size:32 final size:33
Alignment explanation
Indices: 2143927--2143989 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2143917 CCATTGACCC
*
2143927 GACCCGACCCGACCCGTTGACC-GACCCGACGA
1 GACCCGACCAGACCCGTTGACCTGACCCGACGA
*
2143959 GACCCGACGAGACCCGTTGACCTGACCCGAC
1 GACCCGACCAGACCCGTTGACCTGACCCGAC
2143990 CCGGTGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.08
Consensus pattern (33 bp):
GACCCGACCAGACCCGTTGACCTGACCCGACGA
Found at i:2144075 original size:20 final size:19
Alignment explanation
Indices: 2144030--2144076 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
2144020 CAGTGACATT
2144030 CATTATTTTTAAAACGATGA
1 CATT-TTTTTAAAACGATGA
2144050 CAATTTTTTGTAAAACTG-TGA
1 C-ATTTTTT-TAAAAC-GATGA
2144071 CATTTT
1 CATTTT
2144077 GGTAATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 10 0.42
21 13 0.54
22 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
CATTTTTTTAAAACGATGA
Found at i:2151089 original size:29 final size:27
Alignment explanation
Indices: 2151030--2151165 Score: 111
Period size: 27 Copynumber: 4.9 Consensus size: 27
2151020 CCCGACCCGA
*
2151030 TGACATTTTGGGAATTTTTTTAAAA-AC
1 TGACATTTT-GGAATTTTTTTAAAATAG
2151057 TGACATTTTAGGAATTTTTTTAAAAATAG
1 TGACATTTT-GGAATTTTTTT-AAAATAG
* **
2151086 TGACA--TT--CATTATTTTTAAAACGG
1 TGACATTTTGGAATT-TTTTTAAAATAG
*
2151110 TGACAATTTGGGAATTTTTTTTTAAAATAG
1 TGAC-ATTTTGGAA--TTTTTTTAAAATAG
2151140 TGACATTTTGGTAATTATTTTTAAAA
1 TGACATTTTGG-AATT-TTTTTAAAA
2151166 AGGTGATATT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
24 12 0.14
25 6 0.07
27 23 0.26
28 6 0.07
29 22 0.25
30 16 0.18
31 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.46
Consensus pattern (27 bp):
TGACATTTTGGAATTTTTTTAAAATAG
Found at i:2151179 original size:30 final size:29
Alignment explanation
Indices: 2151030--2151184 Score: 114
Period size: 29 Copynumber: 5.6 Consensus size: 29
2151020 CCCGACCCGA
* *
2151030 TGACATTTTGGGAATT-TTTTTAAAAA-C
1 TGACATTTTGGTAATTATTTTTAAAAAGG
*
2151057 TGACATTTTAGG-AATT-TTTTTAAAAATAG
1 TGACATTTT-GGTAATTATTTTTAAAAA-GG
* *
2151086 TGACA---T--TCATTATTTTTAAAACGG
1 TGACATTTTGGTAATTATTTTTAAAAAGG
* * *
2151110 TGACAATTTGGGAATTTTTTTTTAAAATA-G
1 TGACATTTTGGTAA-TTATTTTTAAAA-AGG
2151140 TGACATTTTGGTAATTATTTTTAAAAAGG
1 TGACATTTTGGTAATTATTTTTAAAAAGG
* *
2151169 TGATATTTTTGTAATT
1 TGACATTTTGGTAATT
2151185 TTCGATGGTG
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
24 9 0.09
25 9 0.09
26 1 0.01
27 24 0.24
28 3 0.03
29 32 0.31
30 24 0.24
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (29 bp):
TGACATTTTGGTAATTATTTTTAAAAAGG
Found at i:2152114 original size:32 final size:31
Alignment explanation
Indices: 2152041--2152118 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
2152031 CTAATGTGAC
* * *
2152041 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** **
2152072 TCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
2152104 TCTTAGGTAGGCCCT
1 TCTTAGGTAGGCCCT
2152119 ACAGCCCCGA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:2152143 original size:63 final size:63
Alignment explanation
Indices: 2152041--2152164 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
2152031 CTAATGTGAC
* * * * *
2152041 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACAGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGACCCTAAGATGTGT
* * *
2152104 TCTTAGGTAGGCCCTACAGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACAGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGACCCTAAGATGT
2152165 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACAGCCCCGAAATCATTCTCGGGTAGGCCCTCAGACCCTAAGATGTGT
Found at i:2157453 original size:29 final size:29
Alignment explanation
Indices: 2157411--2157473 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
2157401 CGACCCGATG
*
2157411 ACATTTTGGGAATTGTTTTAAAAATAGTA
1 ACATTTTAGGAATTGTTTTAAAAATAGTA
* *
2157440 ACATTTTAGGAATTTTTTTAAAAATAGTG
1 ACATTTTAGGAATTGTTTTAAAAATAGTA
2157469 ACATT
1 ACATT
2157474 CATTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (29 bp):
ACATTTTAGGAATTGTTTTAAAAATAGTA
Found at i:2157556 original size:29 final size:29
Alignment explanation
Indices: 2157475--2157557 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
2157465 AGTGACATTC
*
2157475 ATTATTTTTAAAATGGTGATATTTTGGGA
1 ATTATTTTTAAAAAGGTGATATTTTGGGA
* * *
2157504 ATT-TTTTGTAAAACA-ATGACATTTTGGTA
1 ATTATTTT-TAAAA-AGGTGATATTTTGGGA
2157533 ATTATTTTTAAAAAGGTGATATTTT
1 ATTATTTTTAAAAAGGTGATATTTT
2157558 TTCAATTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.11
29 35 0.80
30 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (29 bp):
ATTATTTTTAAAAAGGTGATATTTTGGGA
Found at i:2158658 original size:25 final size:25
Alignment explanation
Indices: 2158581--2158647 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
2158571 AGGGTAACTC
2158581 TTTTATGAGATTTACTGCAATATAA
1 TTTTATGAGATTTACTGCAATATAA
*
2158606 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCAATATAA
2158631 TTTTATGAGATTTACTG
1 TTTTATGAGATTTACTG
2158648 GACTATGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCAATATAA
Found at i:2162570 original size:21 final size:19
Alignment explanation
Indices: 2162532--2162577 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2162522 AATTAATCCT
2162532 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
2162552 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
2162573 A-TAAT
1 ACTAAT
2162578 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:2166945 original size:10 final size:10
Alignment explanation
Indices: 2166930--2166959 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2166920 TAGGGAGGTG
*
2166930 ACTTGCTCTA
1 ACTTGCCCTA
2166940 ACTTGCCCTA
1 ACTTGCCCTA
2166950 ACTTGCCCTA
1 ACTTGCCCTA
2166960 GGGGTGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.37, G:0.10, T:0.33
Consensus pattern (10 bp):
ACTTGCCCTA
Found at i:2168462 original size:41 final size:41
Alignment explanation
Indices: 2168415--2168503 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
2168405 ACCTTGGTAT
* * *
2168415 CGATACTCCTATGGGGAGTATTGATACTCTACTC-TTGGCAG
1 CGATACTCCAATGGGGAGCATCGATACTCTAC-CATTGGCAG
* *
2168456 CGATACTCCAATGGGGAGCATCGATGCTCTACCATTGGTAG
1 CGATACTCCAATGGGGAGCATCGATACTCTACCATTGGCAG
2168497 CGATACT
1 CGATACT
2168504 TTCTTCGAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (41 bp):
CGATACTCCAATGGGGAGCATCGATACTCTACCATTGGCAG
Found at i:2171502 original size:112 final size:111
Alignment explanation
Indices: 2171302--2171531 Score: 381
Period size: 112 Copynumber: 2.1 Consensus size: 111
2171292 ACCGAAGTGC
* *
2171302 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCATCGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTAGCACCTTTTATGCCGAAAATGCACCGT
* *
2171367 TATGCATTAAACAAAATCAATCGATAACTT-TCATACACGAAGTTTGT
66 TATGCATTAAACAAAATCAATCGAT-A-TTATCATACACAAAGTATGT
2171414 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTAGCACCTTTTATGCCGAAAATGCACCGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTAGCACCTTTTATGCCGAAAATGCACCGT
*
2171479 TATGCATTAAACAAAATCGATCGATATTATCATACACAAAGTATGT
66 TATGCATTAAACAAAATCAATCGATATTATCATACACAAAGTATGT
*
2171525 TGAAATG
1 CGAAATG
2171532 CACCTATGAC
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
110 2 0.02
111 22 0.20
112 87 0.78
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTCATTATGAATACCATGGGTAGCACCTTTTATGCCGAAAATGCACCGT
TATGCATTAAACAAAATCAATCGATATTATCATACACAAAGTATGT
Found at i:2171627 original size:20 final size:20
Alignment explanation
Indices: 2171602--2171648 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2171592 TTTATTTATG
2171602 CAACATCGATAACCATTGAA
1 CAACATCGATAACCATTGAA
2171622 CAACATCGATAACCATTGAA
1 CAACATCGATAACCATTGAA
2171642 CAACATC
1 CAACATC
2171649 AACATTCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.28, G:0.09, T:0.19
Consensus pattern (20 bp):
CAACATCGATAACCATTGAA
Found at i:2172776 original size:15 final size:15
Alignment explanation
Indices: 2172739--2172776 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2172729 TTTGGCTGTG
2172739 GGGAGAACGGGAGAA
1 GGGAGAACGGGAGAA
2172754 TGGGAGAACGGGAAGAA
1 -GGGAGAACGGG-AGAA
2172771 -GGAGAA
1 GGGAGAA
2172777 GATAACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.50, T:0.03
Consensus pattern (15 bp):
GGGAGAACGGGAGAA
Found at i:2175281 original size:9 final size:9
Alignment explanation
Indices: 2175267--2175332 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 9
2175257 GGCTGCTGGA
2175267 AACCGGTTT
1 AACCGGTTT
2175276 AACCGGTTTT
1 AACCGG-TTT
2175286 CAACCGGTTCT
1 -AACCGGTT-T
*
2175297 GACCGGTTT
1 AACCGGTTT
*
2175306 CAACCGGTTCG
1 -AACCGGTT-T
2175317 AACCGGTTT
1 AACCGGTTT
*
2175326 GACCGGT
1 AACCGGT
2175333 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.28
10 27 0.57
11 7 0.15
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:2175292 original size:20 final size:21
Alignment explanation
Indices: 2175267--2175325 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
2175257 GGCTGCTGGA
2175267 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
2175287 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
2175307 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
2175326 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:2175304 original size:30 final size:29
Alignment explanation
Indices: 2175268--2175332 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
2175258 GCTGCTGGAA
2175268 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
2175298 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
2175327 ACCGGT
1 ACCGGT
2175333 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:2175345 original size:5 final size:5
Alignment explanation
Indices: 2175335--2175375 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2175325 TGACCGGTCT
*
2175335 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
2175376 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:2175360 original size:22 final size:22
Alignment explanation
Indices: 2175334--2175382 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2175324 TTGACCGGTC
2175334 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
2175356 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
2175378 TGACC
1 TGACC
2175383 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:2175384 original size:7 final size:7
Alignment explanation
Indices: 2175372--2175402 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2175362 GACCCGACCC
2175372 GACCGTT
1 GACCGTT
2175379 GACCGTT
1 GACCGTT
2175386 GACCGTT
1 GACCGTT
2175393 GACCGTT
1 GACCGTT
2175400 GAC
1 GAC
2175403 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2182593 original size:10 final size:10
Alignment explanation
Indices: 2182569--2182618 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
2182559 GATGCTGGAA
*
2182569 ACCGGTT-TA
1 ACCGGTTCTG
2182578 ACCGGTTCTG
1 ACCGGTTCTG
2182588 ACCGGTTC-G
1 ACCGGTTCTG
2182597 AACCGGTT-TG
1 -ACCGGTTCTG
2182607 ACCGG-TCTG
1 ACCGGTTCTG
2182616 ACC
1 ACC
2182619 CGACCCGACC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 1 0.03
9 18 0.50
10 17 0.47
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:2182636 original size:17 final size:17
Alignment explanation
Indices: 2182614--2182652 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2182604 TTGACCGGTC
2182614 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2182631 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2182648 TGACC
1 TGACC
2182653 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2185579 original size:18 final size:18
Alignment explanation
Indices: 2185539--2185580 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2185529 TTAGACATTT
* *
2185539 TTTTA-TTTTTTATTGAT
1 TTTTATTTTTTTATTAAA
2185556 TATTTATTTTTTTATTAAA
1 T-TTTATTTTTTTATTAAA
2185575 TTTTAT
1 TTTTAT
2185581 AAATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 9 0.43
19 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTATTAAA
Found at i:2199343 original size:3 final size:3
Alignment explanation
Indices: 2199335--2199441 Score: 160
Period size: 3 Copynumber: 35.7 Consensus size: 3
2199325 TTTTTATCCA
* * *
2199335 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2199383 TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2199431 TAT TAT TAT TA
1 TAT TAT TAT TA
2199442 AATATATTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2202805 original size:183 final size:183
Alignment explanation
Indices: 2202498--2202863 Score: 700
Period size: 183 Copynumber: 2.0 Consensus size: 183
2202488 AAACAAAAAA
2202498 TTGCAGTTTATCAGACTTACGGAGACATCCCATATTTGCTCTATGTTGAAGTTTGATGATGAATT
1 TTGCAGTTTATCAGACTTACGGAGACATCCCATATTTGCTCTATGTTGAAGTTTGATGATGAATT
2202563 ACTCAGAGCCCTAGTTCAATTCTGAATCCAGGGTACAATTGCTTCACTTTCAATAAGGAGGACTT
66 ACTCAGAGCCCTAGTTCAATTCTGAATCCAGGGTACAATTGCTTCACTTTCAATAAGGAGGACTT
2202628 GGTCCCTACTATTGAAGAATATAC-ACTTTGTTACATCTTGAAGGTGCTTTGG
131 GGTCCCTACTATTGAAGAATATACAACTTTGTTACATCTTGAAGGTGCTTTGG
2202680 TTGCAGTTTTATCAGACTTACGGAGACATCCCATATTTGCTCTATGTTGAAG-TTGATGATGAAT
1 TTGCAG-TTTATCAGACTTACGGAGACATCCCATATTTGCTCTATGTTGAAGTTTGATGATGAAT
2202744 TACTCAGAGCCCTAGTTCAATTCTGGAATCCAGGGTACAATTGCTTCACTTTCAATAAGGAGGAC
65 TACTCAGAGCCCTAGTTCAATTCT-GAATCCAGGGTACAATTGCTTCACTTTCAATAAGGAGGAC
2202809 TTGGTCCCTACTATTGAAGAATATACAACTTTGTTACATCTTGAAGGTGCTTTGG
129 TTGGTCCCTACTATTGAAGAATATACAACTTTGTTACATCTTGAAGGTGCTTTGG
2202864 AGAATCGAAT
Statistics
Matches: 181, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
182 42 0.23
183 111 0.61
184 28 0.15
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (183 bp):
TTGCAGTTTATCAGACTTACGGAGACATCCCATATTTGCTCTATGTTGAAGTTTGATGATGAATT
ACTCAGAGCCCTAGTTCAATTCTGAATCCAGGGTACAATTGCTTCACTTTCAATAAGGAGGACTT
GGTCCCTACTATTGAAGAATATACAACTTTGTTACATCTTGAAGGTGCTTTGG
Found at i:2212355 original size:1 final size:1
Alignment explanation
Indices: 2212349--2212394 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
2212339 ATGCTTGAAG
* * *
2212349 AAAAAAAAGAAAAAAAAAAGAAAAGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2212395 GAAAGGGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2213674 original size:83 final size:82
Alignment explanation
Indices: 2213521--2213912 Score: 596
Period size: 83 Copynumber: 4.8 Consensus size: 82
2213511 TTAATAGAAC
* * *
2213521 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACATAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGG-CAGAA
*
2213586 TCAATCATTGAAGTGGGA
65 CCAATCATTGAAGTGGGA
2213604 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGCAGAA
2213669 CCAATCATTGAAGTTGGGA
65 CCAATCATTGAAG-TGGGA
2213688 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGATTTGGCAGAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGCAGAA
* *
2213752 CCAATCATTGAATTTGG-
65 CCAATCATTGAAGTGGGA
* * *
2213769 -AA-GAAAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACATAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGG-CAGAA
*
2213832 TCAATCATTGAAGT-GGA
65 CCAATCATTGAAGTGGGA
* *
2213849 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGTTTGGTAGAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAA
2213913 ATTACAGAAC
Statistics
Matches: 286, Mismatches: 16, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
79 37 0.13
80 35 0.12
81 5 0.02
82 55 0.19
83 109 0.38
84 45 0.16
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (82 bp):
AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAAC
CAATCATTGAAGTGGGA
Found at i:2213809 original size:163 final size:162
Alignment explanation
Indices: 2213521--2213912 Score: 583
Period size: 163 Copynumber: 2.4 Consensus size: 162
2213511 TTAATAGAAC
* * *
2213521 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACATAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTT-CTTGAGTTATCTGATCTGTTTGG-CAGAA
* *
2213586 TCAATCATTGAAGTGGGAAAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64 CCAATCATTGAAGTGGG-AAATGAAAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
2213651 TGATCTGATTTGG-CAGAACCAATCATTGAAGTTGGGA
128 TGATCTG-GTTGGACAGAACCAATCATTGAAG-T-GGA
2213688 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTGAGTTATCTGATCTGATTTGGCAGAAC
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTGAGTTATCTGATCTG-TTTGGCAGAAC
* *
2213753 CAATCATTGAATTTGG-AA-GAAAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
65 CAATCATTGAAGTGGGAAATGAAAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* *
2213816 ATCTGGTTGGACATAATCAATCATTGAAGTGGA
130 ATCTGGTTGGACAGAACCAATCATTGAAGTGGA
* *
2213849 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGTTTGGTAGAA
1 AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGTTTGGCAGAA
2213913 ATTACAGAAC
Statistics
Matches: 210, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
161 48 0.23
162 21 0.10
163 65 0.31
164 2 0.01
166 35 0.17
167 39 0.19
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (162 bp):
AAATGAATATGTTCATAGCATCTTCTGGAAGTGTTCTTGAGTTATCTGATCTGTTTGGCAGAACC
AATCATTGAAGTGGGAAATGAAAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
TCTGGTTGGACAGAACCAATCATTGAAGTGGA
Found at i:2214645 original size:112 final size:113
Alignment explanation
Indices: 2214503--2215234 Score: 1164
Period size: 112 Copynumber: 6.7 Consensus size: 113
2214493 CCATCTGAAA
*
2214503 TCAT-ATGAG-AGAACTCA--TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *** * * *
2214564 CTTTTACCTGAATTCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
2214612 TC-TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG-TCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
2214675 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
2214723 TCATAATGAGAAGAA--CATCTGAAGAAGGAAG-AG-AGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * *
2214784 TTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAAGGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
2214832 TCATAATGAGAAG-ACTCATCTGAAG-A-G--GAAGAAGTTC--AATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
2214890 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
2214938 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
2215003 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAG-GAAAGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
2215050 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
2215115 TTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGT
66 TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
* *
2215163 TCATGAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT-ATGAGAA-AGCTTGTTCAA
1 TCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
*
2215226 C-CTTTGTTT
65 CTTTTTGTTT
2215235 GATATTATCT
Statistics
Matches: 585, Mismatches: 19, Indels: 36
0.91 0.03 0.06
Matches are distributed among these distances:
106 80 0.14
107 14 0.02
108 11 0.02
109 94 0.16
110 33 0.06
111 84 0.14
112 151 0.26
113 79 0.14
114 39 0.07
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
TTTTTGTTTAAATTCATCATTTGATGGATCAACTTTTCCAGAGAAAGT
Found at i:2215529 original size:3 final size:3
Alignment explanation
Indices: 2215521--2215624 Score: 149
Period size: 3 Copynumber: 35.3 Consensus size: 3
2215511 ATTTTTATCC
* *
2215521 ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
2215569 AAT ATT ATT A-T ATT -TT ATT TTT ATT ATT ATT ATT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2215615 ATT ATT ATT A
1 ATT ATT ATT A
2215625 ATATATTAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
2 4 0.04
3 85 0.96
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2223602 original size:146 final size:147
Alignment explanation
Indices: 2223337--2223606 Score: 436
Period size: 146 Copynumber: 1.8 Consensus size: 147
2223327 ATTAATGGAA
*
2223337 AATTTGGGATTTATCATAAAAATGAATTTTAAATTCATTTAAATTAGGATAAAGCCATGTGTTTA
1 AATTTGGGATTTATCATAAAAATGAATTTTAAATTCATTTAAATTAGGATAAAGCCATCTGTTTA
* *
2223402 AGTGATAATTAGGAAGAAAAAAAAATAAATTTTCAGCCTTCTTCTTCCTCAAACCGTGAACTCCA
66 AGTGATAAGTAGGAAGAAAAAAAAAGAAATTTTCAGCCTTCTTCTTCCTCAAACCGTGAACTCCA
2223467 TGGAATTGCATATATTT
131 TGGAATTGCATATATTT
* * *
2223484 AATTTGGGATTTCTCAT-AAAATGAATTTTAAATTCTTTTAAATTACGG-TTAAGCCATCTGTTT
1 AATTTGGGATTTATCATAAAAATGAATTTTAAATTCATTTAAATTA-GGATAAAGCCATCTGTTT
* * *
2223547 AAGTGTTAAGTAGGAAGGAAAAAAAAGAATTTTTCAGCCTTCTTCTTCCTCAAACCGTGA
65 AAGTGATAAGTAGGAAGAAAAAAAAAGAAATTTTCAGCCTTCTTCTTCCTCAAACCGTGA
2223607 TAAGGAAAGG
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
146 95 0.84
147 18 0.16
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (147 bp):
AATTTGGGATTTATCATAAAAATGAATTTTAAATTCATTTAAATTAGGATAAAGCCATCTGTTTA
AGTGATAAGTAGGAAGAAAAAAAAAGAAATTTTCAGCCTTCTTCTTCCTCAAACCGTGAACTCCA
TGGAATTGCATATATTT
Found at i:2229424 original size:13 final size:15
Alignment explanation
Indices: 2229406--2229439 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2229396 TGATGGTATT
2229406 ATTTTAGT-AT-GAA
1 ATTTTAGTGATGGAA
2229419 ATTTTAGTGATGGAA
1 ATTTTAGTGATGGAA
2229434 ATTTTA
1 ATTTTA
2229440 CTAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 2 0.11
15 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (15 bp):
ATTTTAGTGATGGAA
Found at i:2231720 original size:6 final size:6
Alignment explanation
Indices: 2231709--2231737 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2231699 TTAATTGCGA
2231709 AAATTG AAATTG AAATTG AAATTG AAATT
1 AAATTG AAATTG AAATTG AAATTG AAATT
2231738 TAAAAACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
AAATTG
Found at i:2231836 original size:12 final size:11
Alignment explanation
Indices: 2231817--2231922 Score: 53
Period size: 11 Copynumber: 9.7 Consensus size: 11
2231807 TTAGATTGTA
2231817 AAAT-AAAAAT
1 AAATAAAAAAT
*
2231827 AAATATAAAA-
1 AAATAAAAAAT
**
2231837 AAA-AATTAAT
1 AAATAAAAAAT
*
2231847 ATAATAATAAAT
1 A-AATAAAAAAT
2231859 AAATAAATAAAT
1 AAATAAA-AAAT
*
2231871 AAAT-AAAATT
1 AAATAAAAAAT
* *
2231881 GAGTAAAAAACT
1 AAATAAAAAA-T
*
2231893 AAA-AAATTAAT
1 AAATAAA-AAAT
2231904 AAATAATAAAA-
1 AAATAA-AAAAT
2231915 AAATAAAA
1 AAATAAAA
2231923 TAAAAAAAGT
Statistics
Matches: 72, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
9 3 0.04
10 15 0.21
11 30 0.42
12 23 0.32
13 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:2231842 original size:16 final size:16
Alignment explanation
Indices: 2231815--2231877 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2231805 TGTTAGATTG
2231815 TAAAATAAAAATAAATA
1 TAAAA-AAAAATAAATA
*
2231832 TAAAAAAAAATTAATA
1 TAAAAAAAAATAAATA
* *
2231848 TAATAATAAATAAATA
1 TAAAAAAAAATAAATA
*
2231864 -AATAAATAAATAAA
1 TAA-AAAAAAATAAA
2231878 ATTGAGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
15 2 0.05
16 33 0.82
17 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAAAAAATAAATA
Found at i:2231859 original size:4 final size:4
Alignment explanation
Indices: 2231823--2231926 Score: 65
Period size: 4 Copynumber: 25.8 Consensus size: 4
2231813 TGTAAAATAA
* *
2231823 AAAT AAAT ATAA- AAAA AAAT TAAT ATAAT -AAT AAAT AAAT AAAT AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
* * * *
2231871 AAAT AAAATT GAGT AAA- AAACT AAA- AAAT TAAT AAAT -AAT AAAA AAAT
1 AAAT -AAA-T AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2231919 AAAAT AAA
1 -AAAT AAA
2231927 AAAAGTGTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
3 14 0.18
4 47 0.60
5 16 0.21
6 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2233307 original size:3 final size:3
Alignment explanation
Indices: 2233288--2233344 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
2233278 ACCTATAAAA
*
2233288 AAT AAA AAT AA- AAT AAT AAT AAT AAT AAT AAT -AT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
2233332 -AT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT
2233345 TTTTAGACCC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2233317 original size:20 final size:21
Alignment explanation
Indices: 2233282--2233344 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
2233272 CATGGAACCT
* *
2233282 ATAAAAAATAAAAATAAAATA
1 ATAAATAATAATAATAAAATA
*
2233303 AT-AATAATAATAATAATATA
1 ATAAATAATAATAATAAAATA
2233323 ATAAATAAT-ATAATAAAATA
1 ATAAATAATAATAATAAAATA
2233343 AT
1 AT
2233345 TTTTAGACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAATAATAATAATAAAATA
Found at i:2234196 original size:15 final size:15
Alignment explanation
Indices: 2234172--2234201 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2234162 TTACCAAATG
*
2234172 CCATTGAAATATCTT
1 CCATTAAAATATCTT
2234187 CCATTAAAATATCTT
1 CCATTAAAATATCTT
2234202 ATAGTCAAAG
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:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (15 bp):
CCATTAAAATATCTT
Found at i:2234680 original size:227 final size:226
Alignment explanation
Indices: 2234263--2234702 Score: 810
Period size: 227 Copynumber: 1.9 Consensus size: 226
2234253 TTTTCGAAAA
2234263 ATGCAATTTAGTCATTTAATTTTCTCAATTTCGGCTAAATAGAGAAAATTATCTTCAACTCCACT
1 ATGCAATTTAGTCATTTAATTTTCTCAATTTCGGCTAAATAGAGAAAATTATCTTCAACTCCACT
2234328 GGTCCATGCTAAATTTCACTGTTCTAAATATGAAAATAATATTTCCAACATTTATCTAACATTCT
66 GGTCCATGCTAAATTTCACTGTTCTAAATATGAAAATAATATTTCCAACATTTATCTAACATTCT
2234393 TCAAATTTTCGTAAAATTCTGGTTCGATCGTGGCTATACTGCTTTATAGCTTTTAATACAAACCT
131 TCAAATTTTCGTAAAATTCTGGTTCGATCGTGGCTATACTGCTTTATAGCTTTTAATACAAACCT
2234458 AAATCAAAATTTTAATTCTATGCAATTTTCC
196 AAATCAAAATTTTAATTCTATGCAATTTTCC
*
2234489 ATGCAATTTAGTCATTTAATTTTCTCAATTTCGGCTAAATAGAGAAAATTATCTTCAATTCCACT
1 ATGCAATTTAGTCATTTAATTTTCTCAATTTCGGCTAAATAGAGAAAATTATCTTCAACTCCACT
* * *
2234554 GGTCCATGCTAAATTTCACTGTTCTAAAATATGGAAATAATATTTTCAACCTTTATCTAACATTC
66 GGTCCATGCTAAATTTCACTGTTCT-AAATATGAAAATAATATTTCCAACATTTATCTAACATTC
2234619 TTCAAATTTTCGTAAAATTCTGGTTCGATCCG-GGCTATACTGCTTTATAGCTTTTAATACAAAC
130 TTCAAATTTTCGTAAAATTCTGGTTCGAT-CGTGGCTATACTGCTTTATAGCTTTTAATACAAAC
*
2234683 CTGAATCAAAATTTTAATTC
194 CTAAATCAAAATTTTAATTC
2234703 CCATGAAAAT
Statistics
Matches: 207, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
226 89 0.43
227 116 0.56
228 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (226 bp):
ATGCAATTTAGTCATTTAATTTTCTCAATTTCGGCTAAATAGAGAAAATTATCTTCAACTCCACT
GGTCCATGCTAAATTTCACTGTTCTAAATATGAAAATAATATTTCCAACATTTATCTAACATTCT
TCAAATTTTCGTAAAATTCTGGTTCGATCGTGGCTATACTGCTTTATAGCTTTTAATACAAACCT
AAATCAAAATTTTAATTCTATGCAATTTTCC
Found at i:2235733 original size:15 final size:15
Alignment explanation
Indices: 2235713--2235743 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2235703 ACACAAACCA
2235713 ACAAATATACCATTC
1 ACAAATATACCATTC
2235728 ACAAATATACCATTC
1 ACAAATATACCATTC
2235743 A
1 A
2235744 AAGAACCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
ACAAATATACCATTC
Found at i:2239479 original size:27 final size:27
Alignment explanation
Indices: 2239441--2239502 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
2239431 TATATTATAG
2239441 ATTAATTAAATTTCAATCACTTACTTT
1 ATTAATTAAATTTCAATCACTTACTTT
2239468 ATTAATTAAATTTCAATCACTTACTTT
1 ATTAATTAAATTTCAATCACTTACTTT
2239495 ATTAATTA
1 ATTAATTA
2239503 TATTACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAATTAAATTTCAATCACTTACTTT
Found at i:2240143 original size:23 final size:24
Alignment explanation
Indices: 2240115--2240162 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2240105 TATATGTATA
2240115 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
2240138 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
2240162 T
1 T
2240163 TTCTTTACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:2240256 original size:14 final size:14
Alignment explanation
Indices: 2240218--2240265 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2240208 TATATTATTA
2240218 TTTTTTATCTATGTT
1 TTTTTTA-CTATGTT
2240233 TACTTATTTACTATGTT
1 T--TT-TTTACTATGTT
*
2240250 TTTTTTACTATATT
1 TTTTTTACTATGTT
2240264 TT
1 TT
2240266 CCTAACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
17 10 0.34
18 4 0.14
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTTTTACTATGTT
Found at i:2240281 original size:2 final size:2
Alignment explanation
Indices: 2240274--2240311 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2240264 TTCCTAACGT
2240274 TA TA TA TA TA TA TA TA TA TA T- 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 TA T
2240312 CTTACTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2240468 original size:23 final size:23
Alignment explanation
Indices: 2240413--2240488 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 23
2240403 CTATTTAGTA
* * *
2240413 TTTTATTATATTATACATACATT
1 TTTTATTATTTTATATATATATT
*
2240436 TTATA-T-TTTTATATATATATT
1 TTTTATTATTTTATATATATATT
*
2240457 TTTTATTATTTTATTTATACTATT
1 TTTTATTATTTTATATATA-TATT
2240481 TATTTATT
1 T-TTTATT
2240489 TTCATTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.37
22 2 0.05
23 14 0.33
24 5 0.12
25 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATTATTTTATATATATATT
Found at i:2240475 original size:21 final size:21
Alignment explanation
Indices: 2240363--2240502 Score: 63
Period size: 21 Copynumber: 6.5 Consensus size: 21
2240353 TTAGTTAATA
* *
2240363 TTATATGTATTTATT-TTTCAT
1 TTATAT-TTTTTATTATTTTAT
*
2240384 TTAT-TTATTATTATTATTACTAT
1 TTATATT-TT-TTATTATT-TTAT
* *
2240407 TTAGTATTTTATTA-TATTATAC
1 TTA-TATTTT-TTATTATTTTAT
* * * * *
2240429 ATACATTTTATATTTTTATAT
1 TTATATTTTTTATTATTTTAT
*
2240450 ATATATTTTTTATTATTTTAT
1 TTATATTTTTTATTATTTTAT
* *
2240471 TTATACTATTTATTTATTTTCA-
1 TTATATTTTTTA-TTATTTT-AT
2240493 TTATATTTTT
1 TTATATTTTT
2240503 AGTTTCTTTG
Statistics
Matches: 91, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 46 0.51
22 21 0.23
23 10 0.11
24 7 0.08
25 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (21 bp):
TTATATTTTTTATTATTTTAT
Found at i:2240499 original size:28 final size:27
Alignment explanation
Indices: 2240443--2240500 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2240433 ATTTTATATT
* *
2240443 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
2240470 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
2240498 TTT
1 TTT
2240501 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:2240615 original size:20 final size:19
Alignment explanation
Indices: 2240588--2240643 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2240578 TATTATCTTC
2240588 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
2240607 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
2240627 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
2240644 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:2241796 original size:19 final size:19
Alignment explanation
Indices: 2241772--2241808 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2241762 ACCTTACTAA
2241772 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
2241791 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
2241809 ATCATCTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:2244987 original size:17 final size:16
Alignment explanation
Indices: 2244960--2245024 Score: 78
Period size: 16 Copynumber: 4.0 Consensus size: 16
2244950 ACAAAAAGGG
*
2244960 CAAAAACAAAAAAGAA
1 CAAAAAGAAAAAAGAA
*
2244976 -AAGAAGGAAAAAAGAA
1 CAA-AAAGAAAAAAGAA
*
2244992 CAAAACAAAAAAAAGAA
1 CAAAA-AGAAAAAAGAA
2245009 CAAAAAGAAAAAAGAA
1 CAAAAAGAAAAAAGAA
2245025 AAAGGGACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 2 0.05
16 23 0.56
17 16 0.39
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (16 bp):
CAAAAAGAAAAAAGAA
Found at i:2244996 original size:9 final size:8
Alignment explanation
Indices: 2244967--2245027 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
2244957 GGGCAAAAAC
2244967 AAAAAAGA
1 AAAAAAGA
* *
2244975 AAAGAAGG
1 AAAAAAGA
2244983 AAAAAAGA
1 AAAAAAGA
2244991 ACAAAACA-A
1 A-AAAA-AGA
2245000 AAAAAAGA
1 AAAAAAGA
2245008 ACAAAAAG-
1 A-AAAAAGA
2245016 AAAAAAGA
1 AAAAAAGA
2245024 AAAA
1 AAAA
2245028 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
7 7 0.16
8 24 0.55
9 12 0.27
10 1 0.02
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2245003 original size:26 final size:25
Alignment explanation
Indices: 2244964--2245027 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
2244954 AAAGGGCAAA
*
2244964 AACAAAAAAGAAAAGAAGGA-AAAAAG
1 AACAAAAAA-AAAA-AAGAACAAAAAG
2244990 AACAAAACAAAAAAAAGAACAAAAAG
1 AACAAAA-AAAAAAAAGAACAAAAAG
*
2245016 AA-AAAAGAAAAA
1 AACAAAAAAAAAA
2245028 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.15
25 8 0.24
26 19 0.56
27 2 0.06
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (25 bp):
AACAAAAAAAAAAAAGAACAAAAAG
Found at i:2245028 original size:6 final size:7
Alignment explanation
Indices: 2244961--2245027 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
2244951 CAAAAAGGGC
*
2244961 AAAAACA
1 AAAAAGA
2244968 AAAAAGA
1 AAAAAGA
2244975 AAAGAAGGA
1 AAA-AA-GA
2244984 AAAAAGAA
1 AAAAAG-A
*
2244992 CAAAACAAA
1 -AAAA-AGA
2245001 AAAAAGAA
1 AAAAAG-A
2245009 CAAAAAGA
1 -AAAAAGA
2245017 AAAAAGA
1 AAAAAGA
2245024 AAAA
1 AAAA
2245028 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
7 22 0.44
8 11 0.22
9 16 0.32
10 1 0.02
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2245662 original size:22 final size:22
Alignment explanation
Indices: 2245631--2245685 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2245621 GCTACCCCAT
2245631 CAAACCTTTGAGCATAAAATGC
1 CAAACCTTTGAGCATAAAATGC
* *
2245653 CAAACTTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATAAAATGC
2245675 CAAACCTTTGA
1 CAAACCTTTGA
2245686 CCAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATAAAATGC
Found at i:2247916 original size:106 final size:106
Alignment explanation
Indices: 2246653--2247915 Score: 1999
Period size: 106 Copynumber: 11.9 Consensus size: 106
2246643 TGAGACATCA
* * * *
2246653 CAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
2246718 ATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2246759 CAAGTTCAACTTAACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
2246824 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2246865 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
2246930 ATTTCAATTTCTCAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2246971 CAAGTTCAACTTCATGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
2247036 ATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
2247077 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2247142 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2247183 CAAGTTCAACTTCATGATGAAGGGACCGTTGGTTGTCAACAAACAACTTCCCAATTTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2247248 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2247289 CAAGTTCAACTTCACGACGAATGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCTGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2247354 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
2247395 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2247460 ATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
2247501 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2247566 ATTTTAACTTCACAACGAAGGATATTGGACTCCACACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
2247607 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2247672 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * **
2247713 CAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
2247778 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
2247819 CAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
2247883 AATTTCAACTTCACGAA-GGAGGATATTGGACTC
65 AATTTCAACTTCAC-AACGAAGGATATTGGACTC
2247916 GGAACAATGC
Statistics
Matches: 1071, Mismatches: 84, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 1068 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:2248711 original size:37 final size:37
Alignment explanation
Indices: 2248659--2248762 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
2248649 CTTTTCGTCC
* *
2248659 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* * *
2248696 TTCTAGGATTCAAACTCTTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
2248733 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2248763 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:2249284 original size:20 final size:20
Alignment explanation
Indices: 2249245--2249296 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2249235 ATTATTTTCC
*
2249245 TATTATTATATATATATATA
1 TATTATTATTTATATATATA
* *
2249265 TATTATTATTTTTATCTATA
1 TATTATTATTTATATATATA
2249285 T-TTACTTATTTA
1 TATTA-TTATTTA
2249297 CTTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTTATATATATA
Found at i:2249377 original size:29 final size:28
Alignment explanation
Indices: 2249337--2249404 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
2249327 ATATATATTC
* * *
2249337 TTACTTTATTTTATTTTATATTCTATGA
1 TTACTTTATTTTAGTTAATATTATATGA
*
2249365 TTACTATTTTTTTAGTTAATATTATATG-
1 TTACT-TTATTTTAGTTAATATTATATGA
2249393 TATA-TTTATTTT
1 T-TACTTTATTTT
2249405 CATTATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 6 0.18
28 7 0.21
29 20 0.61
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
TTACTTTATTTTAGTTAATATTATATGA
Found at i:2249482 original size:12 final size:12
Alignment explanation
Indices: 2249465--2249508 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
2249455 ACATTTTATA
2249465 TTTTTATATATT
1 TTTTTATATATT
2249477 TTTTTAT-TATT
1 TTTTTATATATT
2249488 TTATTTATACTATT
1 TT-TTTATA-TATT
*
2249502 TATTTAT
1 TTTTTAT
2249509 TTTCATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.21
12 12 0.43
13 5 0.18
14 5 0.18
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATATATT
Found at i:2251556 original size:21 final size:20
Alignment explanation
Indices: 2251523--2251561 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2251513 TAAAAATTTA
*
2251523 AATTATTTAAGTTAATATTCG
1 AATTATTCAAGTT-ATATTCG
*
2251544 AATTATTCGAGTTATATT
1 AATTATTCAAGTTATATT
2251562 TCATAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
AATTATTCAAGTTATATTCG
Found at i:2254154 original size:3 final size:3
Alignment explanation
Indices: 2254146--2254192 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2254136 AAAATGACTC
2254146 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2254193 GTTTTAGGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2255810 original size:21 final size:21
Alignment explanation
Indices: 2255786--2255846 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2255776 AACTTTGAAA
2255786 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2255807 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
2255821 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2255842 AAATG
1 AAATG
2255847 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2255893 original size:36 final size:36
Alignment explanation
Indices: 2255778--2255886 Score: 184
Period size: 35 Copynumber: 3.0 Consensus size: 36
2255768 TGTCAACCAA
2255778 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
2255815 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
2255850 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
2255887 GTTGAAATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
35 35 0.51
36 7 0.10
37 27 0.39
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2257093 original size:15 final size:15
Alignment explanation
Indices: 2257069--2257101 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2257059 AGGCAGATCG
*
2257069 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
2257084 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
2257099 AAA
1 AAA
2257102 AAAGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.24, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:2260494 original size:36 final size:37
Alignment explanation
Indices: 2260387--2260496 Score: 174
Period size: 35 Copynumber: 3.1 Consensus size: 37
2260377 CCAACATTGA
2260387 AAAAATGGTTTTT-AAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
2260423 -AAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
* *
2260458 AAAAATGGTTTTTCAAAGTTTGGTAGATG-TTGTTTG
1 AAAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
2260494 AAA
1 AAA
2260497 TATTGTAATG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
34 4 0.06
35 30 0.43
36 16 0.23
37 19 0.28
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45
Consensus pattern (37 bp):
AAAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:2261576 original size:21 final size:21
Alignment explanation
Indices: 2261550--2261590 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261540 TCCGAGTTAC
*
2261550 CCGCGACAGCCGCAATAGCGT
1 CCGCGACAGCCACAATAGCGT
*
2261571 CCGCGACAGCTACAATAGCG
1 CCGCGACAGCCACAATAGCG
2261591 CCCACGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (21 bp):
CCGCGACAGCCACAATAGCGT
Found at i:2264801 original size:20 final size:19
Alignment explanation
Indices: 2264778--2264815 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2264768 GTGTTTTGGC
2264778 ACACAAATCTATGCAAGTAT
1 ACAC-AATCTATGCAAGTAT
*
2264798 ACACAATTTATGCAAGTA
1 ACACAATCTATGCAAGTA
2264816 ATATAGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (19 bp):
ACACAATCTATGCAAGTAT
Found at i:2271288 original size:16 final size:15
Alignment explanation
Indices: 2271252--2271301 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
2271242 AATCTTAATT
2271252 TAAAAAAT--TAAAA
1 TAAAAAATAATAAAA
**
2271265 TATCAAATAATAAAAA
1 TAAAAAATAAT-AAAA
*
2271281 TAAAAAATAGTAAAA
1 TAAAAAATAATAAAA
2271296 TAAAAA
1 TAAAAA
2271302 CAACACAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 6 0.21
15 11 0.38
16 12 0.41
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAAAAATAATAAAA
Found at i:2273943 original size:12 final size:12
Alignment explanation
Indices: 2273926--2273956 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2273916 CTCCAACCGT
2273926 CTTTCTTCAAGC
1 CTTTCTTCAAGC
2273938 CTTTCTTCAAGC
1 CTTTCTTCAAGC
2273950 CTTTCTT
1 CTTTCTT
2273957 TAGGGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.32, G:0.06, T:0.48
Consensus pattern (12 bp):
CTTTCTTCAAGC
Found at i:2282606 original size:27 final size:28
Alignment explanation
Indices: 2282571--2282629 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
2282561 GCTTTTATTT
*
2282571 TGGCTTGGCC-TAGCCTTTTTAAAAGCC
1 TGGCCTGGCCATAGCCTTTTTAAAAGCC
2282598 TGGCCTGGCCTGATAGCCTTTTTAAAAGCC
1 TGGCCTGGCC--ATAGCCTTTTTAAAAGCC
2282628 TG
1 TG
2282630 AATAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.32
30 19 0.68
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (28 bp):
TGGCCTGGCCATAGCCTTTTTAAAAGCC
Found at i:2283098 original size:40 final size:41
Alignment explanation
Indices: 2283019--2283100 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
2283009 GCTTATAAGC
* * * *
2283019 CTTTTTAATAAGCCTAAGCATGTTCTATTTAATTTAATAGG
1 CTTTTAAAAAAGCCTAAGCATGATCTATTTAATTAAATAGG
*
2283060 CTTTTAAAAAAGCCTAAGCCTGATCTATTT-ATTAAATAGG
1 CTTTTAAAAAAGCCTAAGCATGATCTATTTAATTAAATAGG
2283100 C
1 C
2283101 CAGTCCAGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 10 0.28
41 26 0.72
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (41 bp):
CTTTTAAAAAAGCCTAAGCATGATCTATTTAATTAAATAGG
Found at i:2286016 original size:3 final size:3
Alignment explanation
Indices: 2286008--2286042 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2285998 TTGTTTAAAT
2286008 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2286043 TTACTCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2289542 original size:2 final size:2
Alignment explanation
Indices: 2289535--2289574 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2289525 AAAGATGTTA
2289535 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- 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
2289575 TTAAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2291348 original size:15 final size:15
Alignment explanation
Indices: 2291328--2291358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2291318 ATAATATTAT
2291328 ATAATAAAAAATAAA
1 ATAATAAAAAATAAA
*
2291343 ATAATAATAAATAAA
1 ATAATAAAAAATAAA
2291358 A
1 A
2291359 CAAATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAATAAAAAATAAA
Found at i:2291356 original size:25 final size:24
Alignment explanation
Indices: 2291311--2291370 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
2291301 TTAATTATTT
* *
2291311 AATAATAATAATATTATATAATAAAA
1 AATAA-AATAATAATAAATAA-AAAA
*
2291337 AATAAAATAATAATAAATAAAACA
1 AATAAAATAATAATAAATAAAAAA
*
2291361 AATGAAATAA
1 AATAAAATAA
2291371 AACTAGTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.40
25 13 0.43
26 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
AATAAAATAATAATAAATAAAAAA
Found at i:2291829 original size:123 final size:123
Alignment explanation
Indices: 2291608--2292245 Score: 677
Period size: 123 Copynumber: 5.4 Consensus size: 123
2291598 CTCCTCTTTT
* * * *
2291608 TTCAGATGAGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGCTGATACTGATCTATCTCCTTCT
1 TTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGATGCTGATCTATCTCCTTCT
* *
2291672 GTGATAGAATCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTT
65 GTGATAGAGTCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
* * *
2291731 TTCATACGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTG
* *
2291796 TGATAGAGTCAAATAAAGGTTTAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TC
66 TGATAGAGTCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
* *
2291853 TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTT
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTG
*
2291918 TGATAGAGTCATGCA-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
66 TGATAGAGTCA--AATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
* * * ** **
2291977 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C-CATCGA-GTGATGAAT
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCT-TCT
** *
2292039 -T--TA-AG-C--A-AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
65 GTGATAGAGTCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
* * * * *
2292090 TTCAGATGAGTTCTTCTCATTATGAACTCT-TCTAG-AAA--TG-T--TGATCCAT-T-GTTATG
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTG
* * * * *
2292146 -GATTTGA---ACA-AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCATCTTCCTTC
66 TGA-TAGAGTCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
* ** *
2292200 TTTCAAATGAGTTCTTCTCATTATGAACACT-TCTGGAAATGTTGAT
1 -TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
2292246 CTATTGTGAT
Statistics
Matches: 451, Mismatches: 45, Indels: 46
0.83 0.08 0.08
Matches are distributed among these distances:
106 2 0.00
107 1 0.00
108 6 0.01
109 3 0.01
110 42 0.09
111 35 0.08
112 6 0.01
113 71 0.16
114 2 0.00
115 1 0.00
117 1 0.00
118 2 0.00
119 2 0.00
121 3 0.01
122 77 0.17
123 147 0.33
124 50 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (123 bp):
TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTG
TGATAGAGTCAAATAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
Found at i:2292252 original size:111 final size:111
Alignment explanation
Indices: 2291930--2292264 Score: 494
Period size: 113 Copynumber: 3.0 Consensus size: 111
2291920 ATAGAGTCAT
*
2291930 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
2291995 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTT-AA
66 ATTATGAACTCT-TCTGGAAATGTTGATCCAT--TGTGATGGATTTGAA
* *
2292043 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2292108 ATTATGAACTCTTCTAGAAATGTTGATCCATTGTTATGGATTTGAA
66 ATTATGAACTCTTCTGGAAATGTTGATCCATTGTGATGGATTTGAA
* * *
2292154 -CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCATCTTCCTTCTTTCAAATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCT
* *
2292218 CATTATGAACACTTCTGGAAATGTTGATCTATTGTGATGGATTTGAA
65 CATTATGAACTCTTCTGGAAATGTTGATCCATTGTGATGGATTTGAA
2292265 TCTTTGCTAA
Statistics
Matches: 202, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
110 51 0.25
111 61 0.30
112 17 0.08
113 73 0.36
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTCTGGAAATGTTGATCCATTGTGATGGATTTGAA
Found at i:2293660 original size:7 final size:7
Alignment explanation
Indices: 2293648--2293677 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2293638 CATCACTGAC
2293648 ATACAAA
1 ATACAAA
2293655 ATACAAA
1 ATACAAA
2293662 ATACAAA
1 ATACAAA
*
2293669 ATTCAAA
1 ATACAAA
2293676 AT
1 AT
2293678 CGAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (7 bp):
ATACAAA
Found at i:2295879 original size:430 final size:425
Alignment explanation
Indices: 2295088--2295943 Score: 1603
Period size: 430 Copynumber: 2.0 Consensus size: 425
2295078 TCCGATCAGA
2295088 TAACTCAAAGAAAACTTCCAGAAGATGCTATTGGGCCTTCTCATTTCTACTATGAGAATGTGGTA
1 TAACTCAAAGAAAACTTCCAGAAGATGCTATTGGGCCTTCTCATTTCTACTATGAGAATGTGGTA
2295153 CTTGCTGCAGTTGGTGTTTGGACCGAAATGTCACGGTACTCGAAAAGGGGCTATATTTATAATAT
66 CTTGCTGCAGTTGGTGTTTGGACCGAAATGTCACGGTACTCGAAAAGGGGCTATATTTATAATAT
2295218 GCCAATTGAGAAAATATTTTCTCTTATTATGCTTCCTCCACGCACATAATGCTTTTCCATTGACA
131 GCCAATTGAGAAAATATTTTCTCTTATTATGCTTCCTCCACGCACATAATGCTTTTCCATTGACA
2295283 AAGAAATGGTGACCTTCCTAGGATCCAAAACAAGTTGAATTGTTTACAATATGTACAGGAAGTGC
196 AAGAAATGGTGACCTTCCTAGGATCCAAAACAAGTTGAATTGTTTACAATATGTACAGGAAGTGC
2295348 CAAATTGACAGAAATGTTCAAGAACTGAATGTGATCGTTTGGAGCAATTGATGAGTAGATTTAAC
261 CAAATTGACAGAAATGTTCAAGAACTGAATGTGATCGTTTGGAGCAATTGATGAGTAGATTTAAC
2295413 GGACTCGACCTTGTTGTCGGTGACATCCAGTATAACAACCTTATTGGAAGAAAT-AA-A-CATAG
326 GGACTCGACCTTGTTGTCGGTGACATCCAGTATAACAACCTTATTGGAAGAAATAAACATCATAG
2295475 GGATGAACTAG-AGATTTTTGTTAGTGCATTTTCT
391 GGATGAACTAGAAGATTTTTGTTAGTGCATTTTCT
2295509 TAACTCAAAGAAAACTTCCAGAAGATGCTATTGGGCCTTCTCATTTCTACTATGAGAATGTGGTA
1 TAACTCAAAGAAAACTTCCAGAAGATGCTATTGGGCCTTCTCATTTCTACTATGAGAATGTGGTA
2295574 CTTGCTGCAGTTGGTGTTTGGACCGAAATGTCACGGTACTCGAAAAGGGGGCTATATTTATAATA
66 CTTGCTGCAGTTGGTGTTTGGACCGAAATGTCACGGTACTCGAAAA-GGGGCTATATTTATAATA
2295639 TGCCAATTGAGAAAATATTTTCTCTTATTATGCTTCCTCCACGCACCATACATAATGCTTTTCCA
130 TGCCAATTGAGAAAATATTTTCTCTTATTATGCTTCCTCCACG---C--ACATAATGCTTTTCCA
2295704 TTGACAAAGAAATGGTGACCTTCCTAGGATCCAAGAACAAAGTTGAATTGTTTACAAATATGTAC
190 TTGACAAAGAAATGGTGACCTTCCTAGGATCCAA-AAC-AAGTTGAATTGTTTAC-AATATGTAC
2295769 AGGAAGTGCCAAATTGACAGAAATGTTCAAGAACTGAATGTGATCGTTTGGAGCAATTGATGAGT
252 AGGAAGTGCCAAATTGACAGAAATGTTCAAGAACTGAATGTGATCGTTTGGAGCAATTGATGAGT
2295834 AGATTTAACGGACTCGACCTTGTTGTCGGTGACATCCAGTATAACAACCTTATTGGAAGAAATAA
317 AGATTTAACGGACTCGACCTTGTTGTCGGTGACATCCAGTATAACAACCTTATTGGAAGAAATAA
2295899 ACATCATAGGGATGAACTAGAAGATTTTTGTTAGTGCATTTTCT
382 ACATCATAGGGATGAACTAGAAGATTTTTGTTAGTGCATTTTCT
2295943 T
1 T
2295944 GCAATAACTG
Statistics
Matches: 422, Mismatches: 0, Indels: 13
0.97 0.00 0.03
Matches are distributed among these distances:
421 111 0.26
422 61 0.14
425 1 0.00
427 50 0.12
428 3 0.01
429 16 0.04
430 137 0.32
431 2 0.00
432 1 0.00
433 16 0.04
434 24 0.06
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (425 bp):
TAACTCAAAGAAAACTTCCAGAAGATGCTATTGGGCCTTCTCATTTCTACTATGAGAATGTGGTA
CTTGCTGCAGTTGGTGTTTGGACCGAAATGTCACGGTACTCGAAAAGGGGCTATATTTATAATAT
GCCAATTGAGAAAATATTTTCTCTTATTATGCTTCCTCCACGCACATAATGCTTTTCCATTGACA
AAGAAATGGTGACCTTCCTAGGATCCAAAACAAGTTGAATTGTTTACAATATGTACAGGAAGTGC
CAAATTGACAGAAATGTTCAAGAACTGAATGTGATCGTTTGGAGCAATTGATGAGTAGATTTAAC
GGACTCGACCTTGTTGTCGGTGACATCCAGTATAACAACCTTATTGGAAGAAATAAACATCATAG
GGATGAACTAGAAGATTTTTGTTAGTGCATTTTCT
Found at i:2297418 original size:7 final size:7
Alignment explanation
Indices: 2297406--2297461 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
2297396 TTGGTTCAAT
2297406 TTTTTTC
1 TTTTTTC
2297413 TTTTTTC
1 TTTTTTC
*
2297420 TTTTCTC
1 TTTTTTC
2297427 TTTTTTC
1 TTTTTTC
2297434 TCCTTTTT-
1 T--TTTTTC
2297442 TTCTTTT-
1 TT-TTTTC
*
2297449 TTTTTCC
1 TTTTTTC
2297456 TTTTTT
1 TTTTTT
2297462 TCTATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.10
7 31 0.76
8 1 0.02
9 5 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:2297442 original size:19 final size:18
Alignment explanation
Indices: 2297405--2297470 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
2297395 CTTGGTTCAA
2297405 TTTTTTTC-TTTTT-T-C
1 TTTTTTTCTTTTTTCTCC
*
2297420 -TTTTCTCTTTTTTCTCC
1 TTTTTTTCTTTTTTCTCC
*
2297437 TTTTTTTCTTTTTTTTTCC
1 TTTTTTTC-TTTTTTCTCC
2297456 TTTTTTTCTATTTTT
1 TTTTTTTCT-TTTTT
2297471 TTTCAAGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 1 0.02
17 1 0.02
18 7 0.17
19 22 0.52
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTCTTTTTTCTCC
Found at i:2297443 original size:11 final size:10
Alignment explanation
Indices: 2297405--2297472 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
2297395 CTTGGTTCAA
2297405 TTTTTTTCT-
1 TTTTTTTCTC
*
2297414 TTTTTCTTTTC
1 TTTTT-TTCTC
2297425 TCTTTTTTCTCC
1 T-TTTTTTCT-C
*
2297437 TTTTTTTCTT
1 TTTTTTTCTC
2297447 TTTTTTTC-C
1 TTTTTTTCTC
*
2297456 TTTTTTTCTA
1 TTTTTTTCTC
2297466 TTTTTTT
1 TTTTTTT
2297473 TCAAGCATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 13 0.27
10 18 0.37
11 12 0.24
12 6 0.12
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:2297462 original size:30 final size:32
Alignment explanation
Indices: 2297405--2297474 Score: 99
Period size: 30 Copynumber: 2.2 Consensus size: 32
2297395 CTTGGTTCAA
* *
2297405 TTTTTTTCTTTTTTCTTTTCTCTTTTTTCTCC
1 TTTTTTTCTTTTTTCTTTCCTCTTTTTTCTAC
*
2297437 TTTTTTTCTTTTTT-TTTCCT-TTTTTTCTAT
1 TTTTTTTCTTTTTTCTTTCCTCTTTTTTCTAC
2297467 TTTTTTTC
1 TTTTTTTC
2297475 AAGCATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 16 0.46
31 5 0.14
32 14 0.40
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTTTTCTTTTTTCTTTCCTCTTTTTTCTAC
Found at i:2297471 original size:19 final size:19
Alignment explanation
Indices: 2297420--2297472 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
2297410 TTCTTTTTTC
*
2297420 TTTTCTCTTTTTTCTCCTTT
1 TTTTCTATTTTTT-TCCTTT
*
2297440 TTTTCTTTTTTTTTCCTTT
1 TTTTCTATTTTTTTCCTTT
2297459 TTTTCTATTTTTTT
1 TTTTCTATTTTTTT
2297473 TCAAGCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTCTATTTTTTTCCTTT
Found at i:2297473 original size:11 final size:10
Alignment explanation
Indices: 2297405--2297474 Score: 63
Period size: 11 Copynumber: 6.8 Consensus size: 10
2297395 CTTGGTTCAA
2297405 TTTTTTTCTT
1 TTTTTTTCTT
2297415 TTTTCTTT-TCT
1 TTTT-TTTCT-T
* *
2297426 CTTTTTTCTCC
1 TTTTTTTCT-T
2297437 TTTTTTTCTT
1 TTTTTTTCTT
*
2297447 TTTTTTTC-C
1 TTTTTTTCTT
2297456 TTTTTTTCTAT
1 TTTTTTTCT-T
2297467 TTTTTTTC
1 TTTTTTTC
2297475 AAGCATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.16
10 16 0.33
11 25 0.51
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2297694 original size:78 final size:78
Alignment explanation
Indices: 2297520--2297675 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
2297510 TGGTTTCTCA
2297520 AAACTTTCCTTTCCATTTCTGCCAAAATCAATGCTCCTCCGGAAAAGGCCCTTTTTATTTTACAA
1 AAACTTTCCTTTCCATTTCTGCCAAAATCAATGCTCCTCCGGAAAAGGCCCTTTTTATTTTACAA
2297585 CATATGACCCTTC
66 CATATGACCCTTC
2297598 AAACTTTCCTTTCCATTTCTGCCAAAATCAATGCTCCTCCGGAAAAGGCCCTTTTTATTTTACAA
1 AAACTTTCCTTTCCATTTCTGCCAAAATCAATGCTCCTCCGGAAAAGGCCCTTTTTATTTTACAA
2297663 CATATGACCCTTC
66 CATATGACCCTTC
2297676 CCAATTTTGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.35
Consensus pattern (78 bp):
AAACTTTCCTTTCCATTTCTGCCAAAATCAATGCTCCTCCGGAAAAGGCCCTTTTTATTTTACAA
CATATGACCCTTC
Found at i:2300920 original size:15 final size:15
Alignment explanation
Indices: 2300900--2300935 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2300890 CATAAAAATA
2300900 CAAATGCAAAGATGC
1 CAAATGCAAAGATGC
*
2300915 CAAATGCAAATATGC
1 CAAATGCAAAGATGC
*
2300930 AAAATG
1 CAAATG
2300936 TAAAAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (15 bp):
CAAATGCAAAGATGC
Found at i:2302715 original size:23 final size:26
Alignment explanation
Indices: 2302687--2302769 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 26
2302677 ATTTAATACT
2302687 TGAAAATAAAATA-A-A-AAATATTAA
1 TGAAAATAAAATACATATAAATATT-A
*
2302711 T-AAAATAATATACATATAAATATTA
1 TGAAAATAAAATACATATAAATATTA
* * *
2302736 TGAAAATAATAAGTATATATAAAAATTT
1 TGAAAATAA-AA-TACATATAAATATTA
2302764 TGAAAA
1 TGAAAA
2302770 GAAAGAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.21
24 2 0.04
25 3 0.06
26 14 0.29
27 1 0.02
28 18 0.38
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (26 bp):
TGAAAATAAAATACATATAAATATTA
Found at i:2302753 original size:26 final size:26
Alignment explanation
Indices: 2302687--2302754 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
2302677 ATTTAATACT
*
2302687 TGAAAATAA-AATA-AAAAATATTAA
1 TGAAAATAATAATATATAAATATTAA
*
2302711 T-AAAATAATATACATATAAATATT-A
1 TGAAAATAATA-ATATATAAATATTAA
2302736 TGAAAATAATAAGTATATA
1 TGAAAATAATAA-TATATA
2302755 TAAAAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 7 0.19
24 2 0.06
25 5 0.14
26 22 0.61
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (26 bp):
TGAAAATAATAATATATAAATATTAA
Found at i:2303454 original size:24 final size:23
Alignment explanation
Indices: 2303427--2303471 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2303417 ATAGATTAAT
*
2303427 ATATATATATAATTTAAAAATAGG
1 ATATATAT-TAACTTAAAAATAGG
* *
2303451 ATATTTATTTACTTAAAAATA
1 ATATATATTAACTTAAAAATA
2303472 TAAAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
ATATATATTAACTTAAAAATAGG
Found at i:2305140 original size:3 final size:3
Alignment explanation
Indices: 2305132--2305178 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2305122 ATTAATTATT
*
2305132 TAA TAA TAA AAA T-A TAA -AA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
2305176 TAA
1 TAA
2305179 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2305156 original size:19 final size:19
Alignment explanation
Indices: 2305132--2305182 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
2305122 ATTAATTATT
2305132 TAATAATAAA-AATATAAAA
1 TAATAATAAATAATA-AAAA
*
2305151 TAATAATAAATAATAATAA
1 TAATAATAAATAATAAAAA
2305170 TAATAATAAATAA
1 TAATAATAAATAA
2305183 AACAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATAATAAATAATAAAAA
Found at i:2305158 original size:13 final size:13
Alignment explanation
Indices: 2305133--2305178 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
2305123 TTAATTATTT
*
2305133 AATAATAAAAATA
1 AATAATAATAATA
2305146 TAA-AATAATAATA
1 -AATAATAATAATA
2305159 AATAATAATAAT-
1 AATAATAATAATA
2305171 AATAATAA
1 AATAATAA
2305179 ATAAAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 10 0.33
13 18 0.60
14 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:2314837 original size:25 final size:25
Alignment explanation
Indices: 2314809--2314868 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
2314799 TAATGTACAT
* *
2314809 TATACGTATACATACGTTATAAGAA
1 TATACTTATACATACATTATAAGAA
*
2314834 TATACTTATGCATACATTATAAGAA
1 TATACTTATACATACATTATAAGAA
2314859 TATACTTATA
1 TATACTTATA
2314869 TAAGTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (25 bp):
TATACTTATACATACATTATAAGAA
Found at i:2314850 original size:42 final size:44
Alignment explanation
Indices: 2314804--2314902 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 44
2314794 ATATATAATG
*
2314804 TACATTATACGTATACATACGT-TATAAGAATATACT-TATGCA
1 TACATTATACGTATACATACGTATATAAGAATATACTATAAGCA
* * * * *
2314846 TACATTATAAG-A-ATATACTTATATAAGTATATACTATAAGTA
1 TACATTATACGTATACATACGTATATAAGAATATACTATAAGCA
*
2314888 TACATTATACTTATA
1 TACATTATACGTATA
2314903 ATATATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
40 6 0.13
41 14 0.31
42 23 0.51
43 1 0.02
44 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (44 bp):
TACATTATACGTATACATACGTATATAAGAATATACTATAAGCA
Found at i:2314910 original size:2 final size:2
Alignment explanation
Indices: 2314899--2315026 Score: 121
Period size: 2 Copynumber: 66.5 Consensus size: 2
2314889 ACATTATACT
* *
2314899 TA TA -A TA TA TA TT TA CA TA TA TA -A GTA 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
2314940 TA TA -A GTA TA TA T- TA GTA TA TA TA -A TA TA -A GTA TA TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* *
2314979 -A GA -A TA CA T- 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
2315018 TA TA TA TA T
1 TA TA TA TA T
2315027 GAATGTTATA
Statistics
Matches: 107, Mismatches: 6, Indels: 26
0.77 0.04 0.19
Matches are distributed among these distances:
1 9 0.08
2 93 0.87
3 5 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2314928 original size:10 final size:9
Alignment explanation
Indices: 2314899--2315043 Score: 85
Period size: 8 Copynumber: 16.3 Consensus size: 9
2314889 ACATTATACT
2314899 TATAATATA
1 TATAATATA
* *
2314908 TATTTACATA
1 TA-TAATATA
2314918 TATAAGTATA
1 TATAA-TATA
2314928 TAT-ATATA
1 TATAATATA
2314936 TATATATAAGTA
1 TATA-AT-A-TA
*
2314948 TATATTAGTA
1 TATAATA-TA
2314958 TAT-ATA-A
1 TATAATATA
2314965 TATAAGTATA
1 TATAA-TATA
*
2314975 TATAAGA-A
1 TATAATATA
* *
2314983 TACATTATA
1 TATAATATA
2314992 TAT-ATATA
1 TATAATATA
2315000 TAT-ATATA
1 TATAATATA
2315008 TAT-ATATA
1 TATAATATA
2315016 TAT-ATATA
1 TATAATATA
*
2315024 TATGAATGT-
1 TAT-AATATA
2315033 TATAATA-A
1 TATAATATA
2315041 TAT
1 TAT
2315044 GATGCATTTA
Statistics
Matches: 109, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
7 4 0.04
8 50 0.46
9 16 0.15
10 31 0.28
11 2 0.02
12 6 0.06
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (9 bp):
TATAATATA
Found at i:2315130 original size:13 final size:13
Alignment explanation
Indices: 2315085--2315124 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
2315075 ATGCATTCAT
2315085 TATAAGTATATACTTA
1 TATAAGTATATA---A
2315101 TATAAGTATATAA
1 TATAAGTATATAA
2315114 TATAAGTATAT
1 TATAAGTATAT
2315125 GTTATACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.50
16 12 0.50
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (13 bp):
TATAAGTATATAA
Found at i:2315696 original size:30 final size:31
Alignment explanation
Indices: 2315632--2315701 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2315622 TTATATTAAA
* * *
2315632 TTCTCATTTGCCGCTCAGTCCTCCTTATTTT
1 TTCTCATTTGCCGCTCAATCCTCCCTACTTT
**
2315663 TTCTCATTTTTCGCTCAATCCTCCCT-CTTT
1 TTCTCATTTGCCGCTCAATCCTCCCTACTTT
2315693 TTCTCATTT
1 TTCTCATTT
2315702 CCGTTGTACG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.10, C:0.33, G:0.06, T:0.51
Consensus pattern (31 bp):
TTCTCATTTGCCGCTCAATCCTCCCTACTTT
Found at i:2319506 original size:12 final size:12
Alignment explanation
Indices: 2319489--2319545 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
2319479 ACGGAGATAT
2319489 CAGAAATCA-AA
1 CAGAAATCAGAA
2319500 GCAGAAATCAGAA
1 -CAGAAATCAGAA
* *
2319513 CATAAATCAGAG
1 CAGAAATCAGAA
*
2319525 TAGAAATCAGAA
1 CAGAAATCAGAA
2319537 CAGAAATCA
1 CAGAAATCA
2319546 TAGAAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 36 0.95
13 2 0.05
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:2319529 original size:24 final size:24
Alignment explanation
Indices: 2319489--2319545 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
2319479 ACGGAGATAT
2319489 CAGAAATCAAAGCAGAAATCAGAA
1 CAGAAATCAAAGCAGAAATCAGAA
* * *
2319513 CATAAATCAGAGTAGAAATCAGAA
1 CAGAAATCAAAGCAGAAATCAGAA
2319537 CAGAAATCA
1 CAGAAATCA
2319546 TAGAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (24 bp):
CAGAAATCAAAGCAGAAATCAGAA
Done.