Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 109 of 210
Found at i:32051034 original size:17 final size:18
Alignment explanation
Indices: 32051001--32051034 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32050991 TATCTCTTAA
32051001 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
32051019 ATAATTTCAA-TATATT
1 ATAATTTAAACTATATT
32051035 TAATTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:32054814 original size:18 final size:18
Alignment explanation
Indices: 32054782--32054824 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
32054772 ATTAATTATT
32054782 ATATTTA-AAATAAAATC-
1 ATATTTATAAATAAAA-CG
*
32054799 ATATTTATATATAAAACG
1 ATATTTATAAATAAAACG
32054817 ATATTTAT
1 ATATTTAT
32054825 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATTTATAAATAAAACG
Found at i:32055024 original size:22 final size:21
Alignment explanation
Indices: 32054977--32055024 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
32054967 TCAAATTAAT
*
32054977 ATAATTTTGTATTCATTAATA
1 ATAATTTTGTATTCATCAATA
*
32054998 TTAATTTTGTTATT-ATCACATA
1 ATAATTTTG-TATTCATCA-ATA
32055020 ATAAT
1 ATAAT
32055025 ACAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (21 bp):
ATAATTTTGTATTCATCAATA
Found at i:32055473 original size:137 final size:137
Alignment explanation
Indices: 32055227--32055501 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
32055217 CTAGGTCCTT
32055227 TCCGCCATATTTAATCATCTCAAGCTTGATTTCTTCAATTTCTTTCTTAAAATGTTAGTGAAATC
1 TCCGCCATATTTAATCATCTCAAGCTTGATTTCTTCAATTTCTTTCTTAAAATGTTAGTGAAATC
* *
32055292 AATAGAATAAACTCATAGCAAGCTTAATTTCTTGTAGAATCAACTAGTTCTCGTGTTGGAGGAGA
66 AATAGAACAAACTCATAGCAAGCTTAATTTCTTGTAGAATCAACTAGTGCTCGTGTTGGAGGAGA
32055357 GAGAAAA
131 GAGAAAA
* *
32055364 TCCGCCATATTTAATCATCTCAAGTTTGATTTCTTCAATTTCTTTCTTAAAATTTTAGTGAAATC
1 TCCGCCATATTTAATCATCTCAAGCTTGATTTCTTCAATTTCTTTCTTAAAATGTTAGTGAAATC
32055429 AATAGAACAAACTCATAGCAAGCTTAATTTCTTGTAGAATCAACTAGTGCTCGTGTTGGAGGAGA
66 AATAGAACAAACTCATAGCAAGCTTAATTTCTTGTAGAATCAACTAGTGCTCGTGTTGGAGGAGA
32055494 GAGAAAA
131 GAGAAAA
32055501 T
1 T
32055502 TGAATTTAGG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (137 bp):
TCCGCCATATTTAATCATCTCAAGCTTGATTTCTTCAATTTCTTTCTTAAAATGTTAGTGAAATC
AATAGAACAAACTCATAGCAAGCTTAATTTCTTGTAGAATCAACTAGTGCTCGTGTTGGAGGAGA
GAGAAAA
Found at i:32058505 original size:18 final size:18
Alignment explanation
Indices: 32058471--32058512 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
32058461 AATTTAGCCT
*
32058471 TTTTTATTTTTACTTTAA
1 TTTTTATTTTTAATTTAA
32058489 TATTTTA-TTTTAATTTAA
1 T-TTTTATTTTTAATTTAA
32058507 TTTTTA
1 TTTTTA
32058513 CATTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 5 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTTTTAATTTAA
Found at i:32061932 original size:25 final size:25
Alignment explanation
Indices: 32061884--32061958 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
32061874 CACTTTAATT
*
32061884 TGTCTAAACAATAGACACAA-TTAAAG
1 TGTCTAAACTA-AGAC-CAATTTAAAG
* **
32061910 TGTCTGAACTAAGACCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAAAG
32061935 TGTCTAAACTAAGACCAATTTAAA
1 TGTCTAAACTAAGACCAATTTAAA
32061959 TCACTCAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 3 0.07
25 30 0.71
26 9 0.21
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (25 bp):
TGTCTAAACTAAGACCAATTTAAAG
Found at i:32062662 original size:35 final size:35
Alignment explanation
Indices: 32062616--32062685 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
32062606 ATGGAATGCA
32062616 GAAACCAATGTCAGAGTAAGAGTTATAAGTTGGTC
1 GAAACCAATGTCAGAGTAAGAGTTATAAGTTGGTC
*
32062651 GAAACCAATGTCAGAGTAGGAGTTATAAGTTGGTC
1 GAAACCAATGTCAGAGTAAGAGTTATAAGTTGGTC
32062686 TTACCTTCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (35 bp):
GAAACCAATGTCAGAGTAAGAGTTATAAGTTGGTC
Found at i:32063200 original size:23 final size:23
Alignment explanation
Indices: 32063170--32063217 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
32063160 CACTTGTAGA
32063170 TTAATTTCATTTCTGATCTTACC
1 TTAATTTCATTTCTGATCTTACC
*
32063193 TTAATTTCATTTTTGATCTTACC
1 TTAATTTCATTTCTGATCTTACC
32063216 TT
1 TT
32063218 TCTCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (23 bp):
TTAATTTCATTTCTGATCTTACC
Found at i:32063568 original size:22 final size:21
Alignment explanation
Indices: 32063543--32063583 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32063533 ATCTTTCACA
32063543 TTTTCTCTTCTTTCACTCTCCT
1 TTTTCTCTT-TTTCACTCTCCT
*
32063565 TTTTCTCTTTTTCATTCTC
1 TTTTCTCTTTTTCACTCTC
32063584 AAACTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTCTCTTTTTCACTCTCCT
Found at i:32064009 original size:54 final size:54
Alignment explanation
Indices: 32063927--32064030 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
32063917 ATTCCTTGAT
* **
32063927 GAATAGGAATCTCGATATAGATCTCTTCTCAGGAAATCATTAGACATTTGGCTC
1 GAATAGGAATCACGATATAGATCTCTTCTCAAAAAATCATTAGACATTTGGCTC
*
32063981 GAATAGGAATCACGATATGGATCTCTTCTCAAAAAATCATTAGACATTTG
1 GAATAGGAATCACGATATAGATCTCTTCTCAAAAAATCATTAGACATTTG
32064031 AATCCTTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (54 bp):
GAATAGGAATCACGATATAGATCTCTTCTCAAAAAATCATTAGACATTTGGCTC
Found at i:32066193 original size:25 final size:25
Alignment explanation
Indices: 32066145--32066219 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
32066135 CACTTTAATT
*
32066145 TGTCTAAACAATAGACACAA-TTAAAG
1 TGTCTAAACTA-AGAC-CAATTTAAAG
* * **
32066171 TGTCTGATCTAAGACCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAAAG
*
32066196 TGTCTAAAGTAAGACCAATTTAAA
1 TGTCTAAACTAAGACCAATTTAAA
32066220 TCACTCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
24 3 0.08
25 28 0.72
26 8 0.21
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (25 bp):
TGTCTAAACTAAGACCAATTTAAAG
Found at i:32069890 original size:36 final size:35
Alignment explanation
Indices: 32069850--32069919 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
32069840 CAAGATAAAC
*
32069850 ATTAAA-TTAATAAAATACTATTAAGATAAGTATTAA
1 ATTAAATTTAATAAAA-ACTATTAAAATAA-TATTAA
**
32069886 ATTAAATTTAATATTAACTATTAAAATAATATTA
1 ATTAAATTTAATAAAAACTATTAAAATAATATTA
32069920 TTTTTAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 5 0.17
36 18 0.60
37 7 0.23
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (35 bp):
ATTAAATTTAATAAAAACTATTAAAATAATATTAA
Found at i:32070370 original size:19 final size:19
Alignment explanation
Indices: 32070332--32070371 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32070322 AAAATATCAT
*
32070332 ATTAATTTAAATTGATTTG
1 ATTAATTTAAATTGACTTG
* *
32070351 ATTAATTTAATTTTACTTG
1 ATTAATTTAAATTGACTTG
32070370 AT
1 AT
32070372 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:32082070 original size:49 final size:50
Alignment explanation
Indices: 32081941--32082077 Score: 163
Period size: 49 Copynumber: 2.8 Consensus size: 50
32081931 GGGTAAAGAG
* *
32081941 ATCCCATGTAACACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
1 ATCCCATGTAACACCATATCTGGGACATGGCATTGGCA-CGACATGAGAAC
* * *
32081992 -TCCTATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACATGA-AAC
1 ATCCCATGTAACACCATATCTGGGACATGGCATTGGCACG-ACATGAGAAC
* * *
32082040 ATCCCATGTAATACCATACCTGGGACATGGCTTTGGCA
1 ATCCCATGTAACACCATATCTGGGACATGGCATTGGCA
32082078 TGTTATTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 37 0.50
50 33 0.45
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (50 bp):
ATCCCATGTAACACCATATCTGGGACATGGCATTGGCACGACATGAGAAC
Found at i:32089351 original size:50 final size:50
Alignment explanation
Indices: 32089242--32089538 Score: 348
Period size: 50 Copynumber: 5.8 Consensus size: 50
32089232 ATTTGGGTAA
*
32089242 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
*
32089298 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
32089348 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
32089398 AGAGGTCCCCA-GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
32089448 AGAACTCCTATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
32089497 AAACATCCCATGTCAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
32089539 TGTTATTATC
Statistics
Matches: 214, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
48 1 0.00
49 41 0.19
50 122 0.57
51 4 0.02
53 3 0.01
55 2 0.01
56 41 0.19
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:32093121 original size:22 final size:22
Alignment explanation
Indices: 32093089--32093142 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
32093079 CAGTCTTATC
* *
32093089 TATTGCAATATTCGAGTTTAGG
1 TATTGCGATATCCGAGTTTAGG
*
32093111 TATTGCGATATCCGTGTTTAGG
1 TATTGCGATATCCGAGTTTAGG
32093133 TATTGCGATA
1 TATTGCGATA
32093143 CCCAAGTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (22 bp):
TATTGCGATATCCGAGTTTAGG
Found at i:32099938 original size:14 final size:14
Alignment explanation
Indices: 32099919--32099950 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32099909 GAAAAGTCAC
*
32099919 TTTCCAGAAATCAT
1 TTTCCAGAAACCAT
32099933 TTTCCAGAAACCAT
1 TTTCCAGAAACCAT
32099947 TTTC
1 TTTC
32099951 AATAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (14 bp):
TTTCCAGAAACCAT
Found at i:32100027 original size:25 final size:25
Alignment explanation
Indices: 32099994--32100045 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
32099984 TTACCTGAAT
*
32099994 GTATTTAGTTCAATCAATTAATTTA
1 GTATTTAGTTCAATCAATCAATTTA
*
32100019 GTATTTAGTTCAATTAATCAATTTA
1 GTATTTAGTTCAATCAATCAATTTA
32100044 GT
1 GT
32100046 TTATACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (25 bp):
GTATTTAGTTCAATCAATCAATTTA
Found at i:32102368 original size:52 final size:52
Alignment explanation
Indices: 32102256--32102360 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
32102246 AAATAAATAA
*
32102256 AATACAATTTAACACTCTCTCAATGATACTTTTACTTCTTAGAACTAATATG
1 AATACAATTTAACACTCTCTCAATCATACTTTTACTTCTTAGAACTAATATG
32102308 AATACAATTTAACACTCTCTCAATCATACTTTTACTTCTTAGAACTAATATG
1 AATACAATTTAACACTCTCTCAATCATACTTTTACTTCTTAGAACTAATATG
32102360 A
1 A
32102361 GTTCAATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (52 bp):
AATACAATTTAACACTCTCTCAATCATACTTTTACTTCTTAGAACTAATATG
Found at i:32108056 original size:9 final size:9
Alignment explanation
Indices: 32108042--32108081 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
32108032 CCAAAACAAA
*
32108042 CACCTCTGC
1 CACCTCTAC
32108051 CACCTCTAC
1 CACCTCTAC
*
32108060 CACCTCCAC
1 CACCTCTAC
*
32108069 CACCACTAC
1 CACCTCTAC
32108078 CACC
1 CACC
32108082 CTCCCTTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.23, C:0.60, G:0.03, T:0.15
Consensus pattern (9 bp):
CACCTCTAC
Found at i:32116437 original size:43 final size:43
Alignment explanation
Indices: 32116350--32116447 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
32116340 ATGGCCTAAG
* * *
32116350 ACACGGGTGTGTCCCTTGGCCATGTGAACCACACAGTTTGACC
1 ACACGGGCGTGTCCCTTGGCCATGTGAACCACACAGTCTAACC
* *
32116393 ACGCGGGCGTGTCCCTTGGCCATGTGAACCACACGGTCTAACC
1 ACACGGGCGTGTCCCTTGGCCATGTGAACCACACAGTCTAACC
*
32116436 ACACAGGCGTGT
1 ACACGGGCGTGT
32116448 GACCCCTGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.20
Consensus pattern (43 bp):
ACACGGGCGTGTCCCTTGGCCATGTGAACCACACAGTCTAACC
Found at i:32116753 original size:11 final size:11
Alignment explanation
Indices: 32116737--32116762 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32116727 GTTAGAATAA
32116737 TTTAAAATTAT
1 TTTAAAATTAT
32116748 TTTAAAATTAT
1 TTTAAAATTAT
32116759 TTTA
1 TTTA
32116763 TTATATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAAAATTAT
Found at i:32118474 original size:54 final size:54
Alignment explanation
Indices: 32118332--32118475 Score: 146
Period size: 54 Copynumber: 2.7 Consensus size: 54
32118322 TGCCCCAGAC
* *
32118332 CGTGTAACTTTC-GAATTTGGGACACACGACCATGTCCCAACCTATGTCTCTACT
1 CGTGTAACTTACTG-ATTTGGGACACACGACCGTGTCCCAACCTATGTCTCTACT
* ** * * ** * * * *
32118386 CGTGTAACTCACTGGCTTGAGACACATGGTCGTGTCCCAGCTTATGTCTTTGCT
1 CGTGTAACTTACTGATTTGGGACACACGACCGTGTCCCAACCTATGTCTCTACT
*
32118440 CGTGTAACTTACTGATTTGGGTCACACGACCGTGTC
1 CGTGTAACTTACTGATTTGGGACACACGACCGTGTC
32118476 TCAGGCCGTG
Statistics
Matches: 68, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
54 67 0.99
55 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (54 bp):
CGTGTAACTTACTGATTTGGGACACACGACCGTGTCCCAACCTATGTCTCTACT
Found at i:32119704 original size:3 final size:3
Alignment explanation
Indices: 32119688--32119765 Score: 61
Period size: 3 Copynumber: 25.3 Consensus size: 3
32119678 TAATGAATAC
* * *
32119688 AAT AAT AAGA AAT AAT AAT AAA AAT AAT AA- AAT ATT CAATT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT
* *
32119735 ACT ATAT AAT AAT GAT AAT AAT AA- AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
32119766 TAAAAAAGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
2 4 0.07
3 47 0.80
4 7 0.12
5 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32120243 original size:15 final size:15
Alignment explanation
Indices: 32120225--32120283 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
32120215 GCACAAGAAT
32120225 AAAATAAAAAGGATA
1 AAAATAAAAAGGATA
*
32120240 AAAATAAAATA-AATA
1 AAAATAAAA-AGGATA
* *
32120255 AAAATGAAATAGGATG
1 AAAAT-AAAAAGGATA
*
32120271 AAATTAAAAAGGA
1 AAAATAAAAAGGA
32120284 GCAAAAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 25 0.71
16 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
AAAATAAAAAGGATA
Found at i:32124055 original size:20 final size:20
Alignment explanation
Indices: 32124030--32124071 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
32124020 CCCAGTGTCT
32124030 CAGTGCCTCAAATTGGCACC
1 CAGTGCCTCAAATTGGCACC
32124050 CAGTGCCTCAAATTGGCACC
1 CAGTGCCTCAAATTGGCACC
32124070 CA
1 CA
32124072 ATGCTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (20 bp):
CAGTGCCTCAAATTGGCACC
Found at i:32126610 original size:35 final size:35
Alignment explanation
Indices: 32126568--32126671 Score: 136
Period size: 35 Copynumber: 3.0 Consensus size: 35
32126558 CACACTAGAT
* *
32126568 GCTCATAAGAGCCAGTCCATCCGAAACACACCAAC
1 GCTCATAAGAGCTAATCCATCCGAAACACACCAAC
* * * *
32126603 GCTCATAAGAGCTAATCCCTCCAAAAAACACCAAT
1 GCTCATAAGAGCTAATCCATCCGAAACACACCAAC
* *
32126638 GCTCATAAGAGCTAATACAACCGAAACACACCAA
1 GCTCATAAGAGCTAATCCATCCGAAACACACCAA
32126672 AATATAGAGT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.13
Consensus pattern (35 bp):
GCTCATAAGAGCTAATCCATCCGAAACACACCAAC
Found at i:32128201 original size:33 final size:33
Alignment explanation
Indices: 32128154--32128383 Score: 120
Period size: 33 Copynumber: 6.4 Consensus size: 33
32128144 CGGTGGATTC
* *
32128154 AACATTTAGCAACCACCAGTGATTCGAGGAATA
1 AACACTTAGCAACCACCAATGATTCGAGGAATA
* *
32128187 AACACTTAGCAACCACCAATGATTCGGGGAATC
1 AACACTTAGCAACCACCAATGATTCGAGGAATA
* * * * *
32128220 AGCACTTAGCAACCCCGTTCACATTCAAGATACGGTGGAATC
1 AACACTTAGCAACCAC---CA-A-T---GATTC-GAGGAATA
* * *
32128262 AGCACTTAGCAACCACCAATGATTCGGGGAATT
1 AACACTTAGCAACCACCAATGATTCGAGGAATA
* * * *
32128295 AGCACTTAGCAACCCCTTTCATATTCAAGTTACG-GTCGAATC
1 AACACTTAGCAACCAC---CA-A-T-GA-TT-CGAG--GAATA
* *
32128337 AACACTTAGCAACCACCAATGATTCGGGGAATC
1 AACACTTAGCAACCACCAATGATTCGAGGAATA
32128370 AACACTTAGCAACC
1 AACACTTAGCAACC
32128384 CCTTGGGGAA
Statistics
Matches: 159, Mismatches: 18, Indels: 40
0.73 0.08 0.18
Matches are distributed among these distances:
33 83 0.52
34 6 0.04
35 3 0.02
36 5 0.03
37 4 0.03
38 4 0.03
39 5 0.03
40 3 0.02
41 6 0.04
42 40 0.25
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (33 bp):
AACACTTAGCAACCACCAATGATTCGAGGAATA
Found at i:32128273 original size:42 final size:40
Alignment explanation
Indices: 32128214--32128350 Score: 135
Period size: 42 Copynumber: 3.5 Consensus size: 40
32128204 AATGATTCGG
32128214 GGAATCAGCACTTAGCAACCCCGTTCACATTCAAGATACGGT
1 GGAATCAGCACTTAGCAACCCC-TTCA-ATTCAAGATACGGT
* *
32128256 GGAATCAGCACTTAGCAACCAC--CAA-T---GATTCGG-
1 GGAATCAGCACTTAGCAACCCCTTCAATTCAAGATACGGT
* *
32128289 GGAATTAGCACTTAGCAACCCCTTTCATATTCAAGTTACGGT
1 GGAATCAGCACTTAGCAACCCC-TTCA-ATTCAAGATACGGT
* *
32128331 CGAATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
32128351 ACCAATGATT
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 20 0.26
34 6 0.08
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
41 5 0.06
42 38 0.49
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCTTCAATTCAAGATACGGT
Found at i:32128386 original size:75 final size:75
Alignment explanation
Indices: 32128182--32128387 Score: 340
Period size: 75 Copynumber: 2.7 Consensus size: 75
32128172 GTGATTCGAG
* *
32128182 GAATAAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCGTTCACATTCA
1 GAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCA
*
32128247 AGATACGGTG
66 AGATACGGTC
* * *
32128257 GAATCAGCACTTAGCAACCACCAATGATTCGGGGAATTAGCACTTAGCAACCCCTTTCATATTCA
1 GAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCA
*
32128322 AGTTACGGTC
66 AGATACGGTC
*
32128332 GAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTT
1 GAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
32128388 GGGGAAATCA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 121 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (75 bp):
GAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCA
AGATACGGTC
Found at i:32128391 original size:26 final size:27
Alignment explanation
Indices: 32128362--32128412 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
32128352 CCAATGATTC
32128362 GGGG-AATCAACACTTAGCAACCCCTT
1 GGGGAAATCAACACTTAGCAACCCCTT
*
32128388 GGGGAAATCAGCACTTAGCAACCCC
1 GGGGAAATCAACACTTAGCAACCCC
32128413 CTTTATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (27 bp):
GGGGAAATCAACACTTAGCAACCCCTT
Found at i:32128779 original size:31 final size:30
Alignment explanation
Indices: 32128744--32128805 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
32128734 TCCTTGACTC
32128744 AACTTTTTACAAAATTACGA-TTTTGTCCCCA
1 AACTTTTT-CAAAATTAC-ACTTTTGTCCCCA
* *
32128775 AACTTTTTCATATTTACACTTTTGTCCCCA
1 AACTTTTTCAAAATTACACTTTTGTCCCCA
32128805 A
1 A
32128806 GCTCGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 19 0.68
31 8 0.29
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (30 bp):
AACTTTTTCAAAATTACACTTTTGTCCCCA
Found at i:32135869 original size:75 final size:74
Alignment explanation
Indices: 32135678--32135961 Score: 406
Period size: 75 Copynumber: 3.8 Consensus size: 74
32135668 CGTTACTCGA
* * *
32135678 TGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAACAATTAGCAACCCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGATTC-GGGAATCAACACTTAGCAACCCCTTTCACATT
32135743 CAAAGATACGG
65 C-AAGATACGG
* * *
32135754 TAGAATCAGAACTTAGCAACCACCAATGATTCGGCGAATCAACACTTAGCAACGCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGATTCGG-GAATCAACACTTAGCAACCCCTTTCACATT
32135819 CAAGATACGG
65 CAAGATACGG
* * * *
32135829 TGGAATCAGCACTAAGCAGCCACCAATGATTCGGGAAATCAGCACTTAGCAAACCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGATTCGGG-AATCAACACTTAGCAACCCCTTTCACATT
* *
32135894 CAAGTTGCGG
65 CAAGATACGG
*
32135904 TGGAATCAGCACTTAGCAACCACCAATGATTCAGGGAATCAGCACTTAGCAACCCCTT
1 TGGAATCAGCACTTAGCAACCACCAATGATTC-GGGAATCAACACTTAGCAACCCCTT
32135962 GGGGGAATCA
Statistics
Matches: 187, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
74 1 0.01
75 126 0.67
76 60 0.32
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (74 bp):
TGGAATCAGCACTTAGCAACCACCAATGATTCGGGAATCAACACTTAGCAACCCCTTTCACATTC
AAGATACGG
Found at i:32138961 original size:43 final size:44
Alignment explanation
Indices: 32138889--32138975 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
32138879 TTTTATACTA
* *
32138889 GAAAAAAGAATTTTAAAAAAAGGAAAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTTTAAAAAAAGGAAAAGATAAACATGGGTTGTT
*
32138933 GAAAAAAGAA-TTTAAAAACA-GAAGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTTTAAAAAAAGGAA-AAGATAAACATGGGTTGTT
32138976 TGATTTACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 3 0.08
43 26 0.67
44 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.24
Consensus pattern (44 bp):
GAAAAAAGAATTTTAAAAAAAGGAAAAGATAAACATGGGTTGTT
Found at i:32142465 original size:38 final size:38
Alignment explanation
Indices: 32142373--32142466 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 38
32142363 AGATTGTAAA
** * *
32142373 CTAGCACATAAAGTGCATACTGGCACACGAAGTGCATC
1 CTAGCACACGAAGTGTATACTGACACACGAAGTGCATC
32142411 CTAGCACACGAAGTGTATACTGACACACGAAGTGCATC
1 CTAGCACACGAAGTGTATACTGACACACGAAGTGCATC
* * *
32142449 CTGGCACATGAGGTGTAT
1 CTAGCACACGAAGTGTAT
32142467 CCGAGCGCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (38 bp):
CTAGCACACGAAGTGTATACTGACACACGAAGTGCATC
Found at i:32142468 original size:19 final size:19
Alignment explanation
Indices: 32142383--32142456 Score: 103
Period size: 19 Copynumber: 3.9 Consensus size: 19
32142373 CTAGCACATA
*
32142383 AAGTGCATACTGGCACACG
1 AAGTGCATCCTGGCACACG
*
32142402 AAGTGCATCCTAGCACACG
1 AAGTGCATCCTGGCACACG
* * *
32142421 AAGTGTATACTGACACACG
1 AAGTGCATCCTGGCACACG
32142440 AAGTGCATCCTGGCACA
1 AAGTGCATCCTGGCACA
32142457 TGAGGTGTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (19 bp):
AAGTGCATCCTGGCACACG
Found at i:32142865 original size:19 final size:19
Alignment explanation
Indices: 32142843--32142880 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32142833 AATAAATTTT
32142843 AAAA-TTCAAAATATTTATA
1 AAAATTTCAAAAT-TTTATA
*
32142862 AAAATTTCAACATTTTATA
1 AAAATTTCAAAATTTTATA
32142881 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTTCAAAATTTTATA
Found at i:32146014 original size:31 final size:31
Alignment explanation
Indices: 32145978--32146042 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
32145968 TTAAACATAT
32145978 AAAATGTTAAATATCATGTTATATATGATAA
1 AAAATGTTAAATATCATGTTATATATGATAA
32146009 AAAATGTTAAATATCATGTTATATATGATAA
1 AAAATGTTAAATATCATGTTATATATGATAA
32146040 AAA
1 AAA
32146043 GTTAAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (31 bp):
AAAATGTTAAATATCATGTTATATATGATAA
Found at i:32146046 original size:29 final size:29
Alignment explanation
Indices: 32145976--32146048 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 29
32145966 ATTTAAACAT
*
32145976 ATAAAATGTTAAATATCATGTTATATATG
1 ATAAAAAGTTAAATATCATGTTATATATG
32146005 ATAAAAAATGTTAAATATCATGTTATATATG
1 AT-AAAAA-GTTAAATATCATGTTATATATG
32146036 ATAAAAAGTTAAA
1 ATAAAAAGTTAAA
32146049 CAATTTTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 8 0.20
30 9 0.22
31 24 0.59
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (29 bp):
ATAAAAAGTTAAATATCATGTTATATATG
Found at i:32147015 original size:31 final size:32
Alignment explanation
Indices: 32146960--32147024 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
32146950 TTAAGTATTA
*
32146960 TTAAGTATTTATTGGTTTTCGCTT-GTAATTT
1 TTAAGTATTTATTGGTTTTCGCTTGGTAACTT
* *
32146991 TTAATTATTT-TTGGTTTGTGGCTTGGTAACTT
1 TTAAGTATTTATTGGTTT-TCGCTTGGTAACTT
32147023 TT
1 TT
32147025 CTTTTGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.24
31 14 0.48
32 8 0.28
ACGTcount: A:0.17, C:0.06, G:0.18, T:0.58
Consensus pattern (32 bp):
TTAAGTATTTATTGGTTTTCGCTTGGTAACTT
Found at i:32147786 original size:10 final size:10
Alignment explanation
Indices: 32147771--32147807 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
32147761 TACAATGCAT
32147771 AAGTAAATTA
1 AAGTAAATTA
*
32147781 AAGTAAAGTA
1 AAGTAAATTA
32147791 AAGTAAATTA
1 AAGTAAATTA
32147801 AAGTAAA
1 AAGTAAA
32147808 GCTTTAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (10 bp):
AAGTAAATTA
Found at i:32147787 original size:5 final size:5
Alignment explanation
Indices: 32147771--32147808 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
32147761 TACAATGCAT
* *
32147771 AAGTA AATTA AAGTA AAGTA AAGTA AATTA AAGTA AAG
1 AAGTA AAGTA AAGTA AAGTA AAGTA AAGTA AAGTA AAG
32147809 CTTTAGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (5 bp):
AAGTA
Found at i:32148742 original size:14 final size:13
Alignment explanation
Indices: 32148714--32148751 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
32148704 ACAATAAAAG
32148714 AAGAAGAGAGAAA
1 AAGAAGAGAGAAA
32148727 AAGAAGAGACGAAA
1 AAGAAGAGA-GAAA
32148741 AAGAAGA-AGAA
1 AAGAAGAGAGAA
32148752 GAATTGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 11 0.46
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (13 bp):
AAGAAGAGAGAAA
Found at i:32151674 original size:12 final size:12
Alignment explanation
Indices: 32151653--32151683 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
32151643 TCACTGAGTT
*
32151653 ACACGACCTAGC
1 ACACGGCCTAGC
32151665 ACACGGCCTAGC
1 ACACGGCCTAGC
32151677 ACACGGC
1 ACACGGC
32151684 GTGTGGGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.42, G:0.23, T:0.06
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:32154399 original size:20 final size:20
Alignment explanation
Indices: 32154355--32154399 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
32154345 TTTAATAAAC
32154355 TCCC-CCCAATCCCTTAACT
1 TCCCTCCCAATCCCTTAACT
*
32154374 T-TCTCCCATATCCC-TAACT
1 TCCCTCCCA-ATCCCTTAACT
32154393 TCCCTCC
1 TCCCTCC
32154400 TAAAAACTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.18, C:0.51, G:0.00, T:0.31
Consensus pattern (20 bp):
TCCCTCCCAATCCCTTAACT
Found at i:32161916 original size:18 final size:18
Alignment explanation
Indices: 32161890--32161925 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32161880 CATGTCAATC
*
32161890 TAATGTTTTTAAATTTTT
1 TAATATTTTTAAATTTTT
32161908 TAATATTTTTAAATTTTT
1 TAATATTTTTAAATTTTT
32161926 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATATTTTTAAATTTTT
Found at i:32161923 original size:8 final size:8
Alignment explanation
Indices: 32161895--32161928 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
32161885 CAATCTAATG
32161895 TTTTTAAA
1 TTTTTAAA
32161903 TTTTTTAATA
1 -TTTTTAA-A
32161913 TTTTTAAA
1 TTTTTAAA
32161921 TTTTTAAA
1 TTTTTAAA
32161929 AAATTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 9 0.38
9 14 0.58
10 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTTAAA
Found at i:32163770 original size:20 final size:20
Alignment explanation
Indices: 32163738--32163776 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
32163728 TTTTAAATTT
*
32163738 ATAATTATAAATATTTAAAA
1 ATAATTATAAATATATAAAA
32163758 ATAA-TATATAATATATAAA
1 ATAATTATA-AATATATAAA
32163777 TAACAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATTATAAATATATAAAA
Found at i:32167537 original size:43 final size:41
Alignment explanation
Indices: 32167466--32167623 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 41
32167456 ACAATACCAA
* * *
32167466 TGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCAC
1 TGTCCCAGAAG-GGTCTTACACGAAATCAAAT-ACGATGCCAC
* * * * *
32167509 TGTCCTAGATAGGGTCTTACACGAAATCATATACAATGCTAA
1 TGTCCCAGA-AGGGTCTTACACGAAATCAAATACGATGCCAC
* *
32167551 TGTCCCAAACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAAC
1 TGTCCCAGA-AGGGTCTTACACG-AAA--TCAAATACGATGCC-AC
*
32167596 -GTCCCAGACGTGGTCTTACACGAAATCA
1 TGTCCCAGAAG-GGTCTTACACGAAATCA
32167624 TATATCGGAA
Statistics
Matches: 90, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
41 3 0.03
42 26 0.29
43 31 0.34
44 24 0.27
45 6 0.07
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
TGTCCCAGAAGGGTCTTACACGAAATCAAATACGATGCCAC
Found at i:32167568 original size:42 final size:43
Alignment explanation
Indices: 32167521--32167629 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 43
32167511 TCCTAGATAG
* *
32167521 GGTCTTACACGAAATCATATA-CAATGCTAATGTCCCAAACAT
1 GGTCTTACACGAAATCATATATCAATGCCAACGTCCCAAACAT
* * * *
32167563 GGTCTTACACGTAAATC-TCAAATCGATGCCAACGTCCCAGACGT
1 GGTCTTACACG-AAATCAT-ATATCAATGCCAACGTCCCAAACAT
32167607 GGTCTTACACGAAATCATATATC
1 GGTCTTACACGAAATCATATATC
32167630 GGAATCCTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
42 12 0.21
43 16 0.29
44 28 0.50
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCATATATCAATGCCAACGTCCCAAACAT
Found at i:32172709 original size:20 final size:18
Alignment explanation
Indices: 32172684--32172725 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
32172674 ATGTTTAAGT
*
32172684 TTAATTAATTAAGGATTATA
1 TTAATTAATAAAGG-TTA-A
32172704 TTAATTAATAAAGGTTAA
1 TTAATTAATAAAGGTTAA
32172722 TTAA
1 TTAA
32172726 GTTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (18 bp):
TTAATTAATAAAGGTTAA
Found at i:32177968 original size:45 final size:45
Alignment explanation
Indices: 32177874--32177982 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
32177864 CTAAAATGAG
* * *
32177874 TAAGACCGTAGCTGAAAGATGCTATGAAATCATGATATAAATGAG
1 TAAGACCATAGCTGAAAGATGCTATGAAATCATGATATAAAGGAC
* * *
32177919 TAAGACCAT-GCCTGAAAGATGCTATGACATCTTGTTA-AACAGGAC
1 TAAGACCATAG-CTGAAAGATGCTATGAAATCATGATATAA-AGGAC
*
32177964 TAAGACTATAGCTGAAAGA
1 TAAGACCATAGCTGAAAGA
32177983 CGTTATGGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
44 3 0.06
45 50 0.93
46 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGATGCTATGAAATCATGATATAAAGGAC
Found at i:32189795 original size:26 final size:25
Alignment explanation
Indices: 32189766--32189820 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
32189756 CTAGTAAAGT
*
32189766 TTTTAACAATTTTACCCTCGTTAAAA
1 TTTTAACAATTTTACCC-CGGTAAAA
32189792 TTTTAACAATTTTACCCCGGTAAAA
1 TTTTAACAATTTTACCCCGGTAAAA
32189817 TTTT
1 TTTT
32189821 GAGAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (25 bp):
TTTTAACAATTTTACCCCGGTAAAA
Found at i:32189831 original size:26 final size:26
Alignment explanation
Indices: 32189746--32189820 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
32189736 TTTTGCATCC
* *
32189746 CAAATTTACCCT-AGTAAAGTTTTTAA
1 CAAATTTACCCTCGGTAAA-ATTTTAA
* *
32189772 CAATTTTACCCTCGTTAAAATTTTAA
1 CAAATTTACCCTCGGTAAAATTTTAA
*
32189798 CAATTTTACCC-CGGTAAAATTTT
1 CAAATTTACCCTCGGTAAAATTTT
32189821 GAGAAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.26
26 28 0.65
27 4 0.09
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (26 bp):
CAAATTTACCCTCGGTAAAATTTTAA
Found at i:32196716 original size:51 final size:50
Alignment explanation
Indices: 32196637--32196778 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
32196627 CGTCTATAAA
* * * * * *
32196637 CACGTGTGTTGCACTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAG-TTTGAT
* *
32196688 CACGTGTGTAGTACTATGTGCAGCCTACTACGTGAACCGAAAAGTTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAGTTTGAT
* *
32196738 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
32196779 TGATAATAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 42 0.53
51 37 0.47
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAGTTTGAT
Found at i:32213638 original size:12 final size:12
Alignment explanation
Indices: 32213621--32213645 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32213611 AAAATCTAAT
32213621 TTCAATGTGTAA
1 TTCAATGTGTAA
32213633 TTCAATGTGTAA
1 TTCAATGTGTAA
32213645 T
1 T
32213646 GTGTATAAGG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:32216165 original size:6 final size:6
Alignment explanation
Indices: 32216136--32216178 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
32216126 ATATTAACAT
* *
32216136 ATAAAA ATTAAA TTAAAA AT--AA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
32216179 GCTAAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
ATAAAA
Found at i:32216184 original size:22 final size:22
Alignment explanation
Indices: 32216136--32216178 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
32216126 ATATTAACAT
* *
32216136 ATAAAAATTAAATTAAAAATAA
1 ATAAAAATAAAAATAAAAATAA
32216158 ATAAAAATAAAAATAAAAATA
1 ATAAAAATAAAAATAAAAATA
32216179 GCTAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAAAATAAAAATAAAAATAA
Found at i:32217284 original size:27 final size:28
Alignment explanation
Indices: 32217254--32217308 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 28
32217244 AACGATCTGG
32217254 CACATGGCCATGTG-AGCCCGTGTGGCT
1 CACATGGCCATGTGCAGCCCGTGTGGCT
32217281 CACATGGCCATGTGTCCAGCCCGTGTGG
1 CACATGGCCATGTG--CAGCCCGTGTGG
32217309 GAAGGCCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.56
30 11 0.44
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.22
Consensus pattern (28 bp):
CACATGGCCATGTGCAGCCCGTGTGGCT
Found at i:32221690 original size:23 final size:24
Alignment explanation
Indices: 32221636--32221691 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
32221626 AGGGCACGCC
*
32221636 ACAACGACAGATGAAAAACATGTG
1 ACAAAGACAGATGAAAAACATGTG
* * *
32221660 ACAGAGACAGAT-AGAAACGTGTG
1 ACAAAGACAGATGAAAAACATGTG
*
32221683 AGAAAGACA
1 ACAAAGACA
32221692 AACTGTAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.50, C:0.14, G:0.25, T:0.11
Consensus pattern (24 bp):
ACAAAGACAGATGAAAAACATGTG
Found at i:32223801 original size:114 final size:114
Alignment explanation
Indices: 32223633--32224327 Score: 948
Period size: 114 Copynumber: 6.1 Consensus size: 114
32223623 AAAATAAGCA
* * *
32223633 TTAGCGGCGTTTTCGA-AAACGCGCCGC-AAAATACCTAAGCCCAACGACGCCGTTTT-TCGAGC
1 TTAGCGGCGTTTTTGATAAA-GCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGC
*
32223695 TTTCGGGGATTTAGCGGCGTTTTTAA-TAAAGCGCCACTAATGCTCAGGGCT
64 TTTCGGGGATTTAGCGGCGTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
* * *
32223746 TTAGCAGCGTTTTTGATAAAGCGCCACAAACAAACCTAAGCCCAACGACGACGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
32223811 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGACGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
32223860 TTAGCGACGTTTTT--T--A-TGCCACAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGATAAAGCGCCAC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
32223920 TTCGGGGATTTAGCAGCGTTTTTAA-TAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
* * * *
32223970 TTAGCGGCGTTTTTTATAAAGCGACACAAAAAAACCTAAGTCCAACGACGCCGTTTTCTTAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
32224035 TTGGGGATTTAGCGGCGTTTTCAAGTAAGCGCCGCTAGTGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * *
32224084 TTAGTGGCGTTTTTGATAAAGGGCCACAAAAAAACATAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
32224149 TCGAGGATTTAGCGGCGTTTTTAAGTACGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * *
32224198 TTAGCGGCATTTTTGGA-AAAGCGCCGC-AAAAAACCTAAGCCCAATGACGCCGTTTTCTTAGCT
1 TTAGCGGCGTTTTT-GATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
32224261 TTCGGGGATTTAGTGGCGTTTTTTAA-TAAAGCGCCGCTAATGCTCAGTGCA
65 TTCGGGGATTTAGCGGCG-TTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
32224312 TTAGCGGCGTTTTTGA
1 TTAGCGGCGTTTTTGA
32224328 GGATGCGCCG
Statistics
Matches: 518, Mismatches: 49, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
109 6 0.01
110 95 0.18
112 2 0.00
113 73 0.14
114 333 0.64
115 9 0.02
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:32224055 original size:224 final size:226
Alignment explanation
Indices: 32223660--32224325 Score: 961
Period size: 224 Copynumber: 2.9 Consensus size: 226
32223650 AACGCGCCGC
*
32223660 AAAATACCTAAGCCCAACGACGCCGTTTT-TCGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGCTTTCGGGGATTTAGCGGCGTTTTTAATAA
* * *
32223724 AGCGCCACTAATGCTCAGGGCTTTAGCAGCGTTTTTGATAAAGCGCCACAAACAAACCTAAGCCC
65 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCC
* * *
32223789 AACGACGACGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGACGCTAATGCTC
130 AACGACGCCGTTTTCTTAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTC
* *
32223854 AGGGCTTTAGCGACGTTTTT-T-A-TGCCACAA
195 AGGGCTTTAGCGGCGTTTTTATAAGGGCCAC-A
*
32223884 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCAGCGTTTTTAATAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAA
* * *
32223949 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTTATAAAGCGACACAAAAAAACCTAAGTCCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCA
* * *
32224014 ACGACGCCGTTTTCTTAGCTTTTGGGGATTTAGCGGCGTTTTCAAGTAAGCGCCGCTAGTGCTCA
131 ACGACGCCGTTTTCTTAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCA
*
32224079 GGGCTTTAGTGGCGTTTTTGATAAAGGGCCACA
196 GGGCTTTAGCGGCGTTTTT-AT-AAGGGCCACA
* * *
32224112 AAAAAACATAAGCCCAATGACGCCGTTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTAAGT-A
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAA-TAA
* * *
32224176 CGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGGA-AAAGCGCCGC-AAAAAACCTAAGCC
65 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT-GATAAAGCGCCACAAAAAAACCTAAGCC
* *
32224239 CAATGACGCCGTTTTCTTAGCTTTCGGGGATTTAGTGGCGTTTTTTAA-TAAAGCGCCGCTAATG
129 CAACGACGCCGTTTTCTTAGCTTTCGGGGATTTAGCGGCG-TTTTTAAGT-AAGCGCCGCTAATG
* *
32224303 CTCAGTGCATTAGCGGCGTTTTT
192 CTCAGGGCTTTAGCGGCGTTTTT
32224326 GAGGATGCGC
Statistics
Matches: 397, Mismatches: 35, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
224 196 0.49
225 1 0.00
226 1 0.00
227 51 0.13
228 141 0.36
229 7 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (226 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAA
GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCA
ACGACGCCGTTTTCTTAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCA
GGGCTTTAGCGGCGTTTTTATAAGGGCCACA
Found at i:32224981 original size:15 final size:15
Alignment explanation
Indices: 32224961--32224999 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
32224951 AGGGGTTAGG
32224961 TTAGGGATTTAAGGT
1 TTAGGGATTTAAGGT
*
32224976 TTAGGGATTTATGGT
1 TTAGGGATTTAAGGT
32224991 TTAGGGATT
1 TTAGGGATT
32225000 CGATGTCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (15 bp):
TTAGGGATTTAAGGT
Found at i:32225165 original size:88 final size:86
Alignment explanation
Indices: 32224991--32225326 Score: 328
Period size: 95 Copynumber: 3.8 Consensus size: 86
32224981 GATTTATGGT
* * * * *
32224991 TTAGGGATTCGATGTCAGGTTAGAGTTTAGGGTTTAGATTAATTAGTATGTTTTAA-TTATATAT
1 TTAGGGATTC-AGGTCGGGTTAGGGTTTAGGATTTAGATTAATTAGTGT-TTTTAATTTATATAT
*
32225055 TAAATAATGTTTAAGGGATAGGGGTTAAGGG
64 TAAATAAAG-TT------TAGGGGTT-AGGG
* *
32225086 TTAGGGATTCAGGATCGGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTAATTTATATATT
1 TTAGGGATTCAGG-TCGGGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTAATTTATATATT
*
32225151 AACTAAAGTTTAGGGGTTAGGG
65 AAATAAAGTTTAGGGGTTAGGG
* *
32225173 -TAGGGATTCCAGGTCAGGCTCAGGGTTTAGGATTTAGATTAATTAGTGTTTGTTAATTTATATA
1 TTAGGGATT-CAGGTC-GGGTTAGGGTTTAGGATTTAGATTAATTAGTGTTT-TTAATTTATATA
32225237 TTAAATAAAGTTTA--GG-T---G
63 TTAAATAAAGTTTAGGGGTTAGGG
** * * *
32225255 TTAGGGATTTGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAGTACTTTTTAATTTATATAT
1 TTAGGGA-TTCAGGTCGGGTTAGGGTTTAGGATTTAGATTAATTAGT-GTTTTTAATTTATATAT
32225320 TAAATAA
64 TAAATAA
32225327 GTTCTTTATA
Statistics
Matches: 214, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
82 48 0.22
83 13 0.06
84 2 0.01
85 1 0.00
86 12 0.06
87 39 0.18
88 33 0.15
94 10 0.05
95 56 0.26
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42
Consensus pattern (86 bp):
TTAGGGATTCAGGTCGGGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTAATTTATATATTA
AATAAAGTTTAGGGGTTAGGG
Found at i:32225838 original size:84 final size:85
Alignment explanation
Indices: 32225750--32225964 Score: 267
Period size: 84 Copynumber: 2.6 Consensus size: 85
32225740 GATTTTAATA
* **
32225750 AAAACGCTGCAAGGA-TTTATTAAAATTTGCCAA-AGCGGCGCCGTTTCTCTACTAGAATAAAAT
1 AAAACGCCGCAAGGAGTGAATTAAAATTTGCCAATA-CGGCGCCGTTTCTCTACTAGAATAAAAT
* *
32225813 CTTATAGTGGCGTTTTTTAGG
65 CTTATAGTGGCATTTTTTAAG
** *
32225834 AAAACGCCGCAA-GAGTGAATTAATGTTTGCCAATACGGCGTCGTTTCTCTACTAGAATAAAATC
1 AAAACGCCGCAAGGAGTGAATTAAAATTTGCCAATACGGCGCCGTTTCTCTACTAGAATAAAATC
32225898 TTATAGTGGCATTTTTTAAG
66 TTATAGTGGCATTTTTTAAG
* ** * * *
32225918 CAAACGCCGCAA-GAGTGAATTAATGTTTGTCAATGCGGCACCGTTTC
1 AAAACGCCGCAAGGAGTGAATTAAAATTTGCCAATACGGCGCCGTTTC
32225965 GCTTCATGAA
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
83 2 0.02
84 113 0.97
85 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (85 bp):
AAAACGCCGCAAGGAGTGAATTAAAATTTGCCAATACGGCGCCGTTTCTCTACTAGAATAAAATC
TTATAGTGGCATTTTTTAAG
Found at i:32227450 original size:12 final size:12
Alignment explanation
Indices: 32227433--32227461 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
32227423 ATACTTACAT
32227433 AACTTATATATA
1 AACTTATATATA
32227445 AACTTATATATA
1 AACTTATATATA
32227457 AACTT
1 AACTT
32227462 GCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:32227475 original size:9 final size:9
Alignment explanation
Indices: 32227457--32227840 Score: 126
Period size: 9 Copynumber: 44.4 Consensus size: 9
32227447 CTTATATATA
*
32227457 AACTTGCAT
1 AACTTACAT
32227466 AACTTACAT
1 AACTTACAT
*
32227475 AA-TAACATAAT
1 AACTTAC---AT
32227486 AACTTACAT
1 AACTTACAT
*
32227495 AA--TACAC
1 AACTTACAT
32227502 AACTTACAT
1 AACTTACAT
*
32227511 AACTTAAAT
1 AACTTACAT
32227520 AACTTACAT
1 AACTTACAT
* *
32227529 -A-GTACGT
1 AACTTACAT
**
32227536 AACTTTGAT
1 AACTTACAT
*
32227545 AACTAACAT
1 AACTTACAT
* *
32227554 TA--TACAC
1 AACTTACAT
32227561 AACTTACAT
1 AACTTACAT
32227570 AA--TACAT
1 AACTTACAT
**
32227577 TTCTTACAT
1 AACTTACAT
*
32227586 AACTTACAC
1 AACTTACAT
*
32227595 AA--TACAC
1 AACTTACAT
32227602 AACTTA-ATT
1 AACTTACA-T
*
32227611 AATATTATACAT
1 -A-ACT-TACAT
*
32227623 AACATACAT
1 AACTTACAT
*
32227632 AA--TACAC
1 AACTTACAT
32227639 AACTTA-ATT
1 AACTTACA-T
*
32227648 AATATTATACAT
1 -A-ACT-TACAT
* *
32227660 GACATACAT
1 AACTTACAT
32227669 AA--TACAT
1 AACTTACAT
32227676 AA--TACATAT
1 AACTTAC--AT
32227685 AACTTACAT
1 AACTTACAT
*
32227694 -A-GTACAT
1 AACTTACAT
* *
32227701 AACTAATAT
1 AACTTACAT
*
32227710 AA--TACAC
1 AACTTACAT
32227717 AACTTACAT
1 AACTTACAT
*
32227726 AACTTAAAT
1 AACTTACAT
32227735 AACTTACAT
1 AACTTACAT
*
32227744 AGCTTACAT
1 AACTTACAT
32227753 AA--TACAT
1 AACTTACAT
32227760 AACTTACAT
1 AACTTACAT
*
32227769 AACTTATAT
1 AACTTACAT
32227778 AA--TACAT
1 AACTTACAT
32227785 AACTTACAT
1 AACTTACAT
* *
32227794 AATTTACCT
1 AACTTACAT
32227803 AA--TACAT
1 AACTTACAT
* *
32227810 AA-ATATAT
1 AACTTACAT
* *
32227818 ATCATATCAT
1 AACTTA-CAT
32227828 AACTTACAT
1 AACTTACAT
32227837 AACT
1 AACT
32227841 CATTTATAGT
Statistics
Matches: 275, Mismatches: 59, Indels: 82
0.66 0.14 0.20
Matches are distributed among these distances:
7 70 0.25
8 14 0.05
9 158 0.57
10 10 0.04
11 12 0.04
12 9 0.03
13 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:32227514 original size:25 final size:25
Alignment explanation
Indices: 32227457--32227607 Score: 86
Period size: 25 Copynumber: 6.2 Consensus size: 25
32227447 CTTATATATA
*
32227457 AACTTGCATAACTTACATAATA-AC
1 AACTTACATAACTTACATAATACAC
32227481 -A--TA-ATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
32227502 AACTTACATAACTTAAATAACTTACA-
1 AACTTACATAACTTACATAA--TACAC
* * * **
32227528 TA-GTACGTAACTTTGATAACTA-AC
1 AACTTACATAACTTACATAA-TACAC
* * *
32227552 -ATTATACACAACTTACATAATACAT
1 AACT-TACATAACTTACATAATACAC
** *
32227577 TTCTTACATAACTTACACAATACAC
1 AACTTACATAACTTACATAATACAC
32227602 AACTTA
1 AACTTA
32227608 ATTAATATTA
Statistics
Matches: 94, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
20 15 0.16
21 3 0.03
22 1 0.01
23 3 0.03
24 6 0.06
25 60 0.64
26 2 0.02
27 4 0.04
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:32227636 original size:37 final size:37
Alignment explanation
Indices: 32227581--32227674 Score: 161
Period size: 37 Copynumber: 2.5 Consensus size: 37
32227571 ATACATTTCT
* *
32227581 TACATAACTTACACAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACACAACTTAATTAATATTA
32227618 TACATAACATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACACAACTTAATTAATATTA
*
32227655 TACATGACATACATAATACA
1 TACATAACATACATAATACA
32227675 TAATACATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (37 bp):
TACATAACATACATAATACACAACTTAATTAATATTA
Found at i:32227692 original size:25 final size:25
Alignment explanation
Indices: 32227664--32227808 Score: 108
Period size: 25 Copynumber: 5.8 Consensus size: 25
32227654 ATACATGACA
32227664 TACATAA-TACATAATACATATAACT
1 TACATAATTACATAATACA-ATAACT
*
32227689 TACAT-AGTACATAACTA-ATATAA--
1 TACATAATTACATAA-TACA-ATAACT
*
32227712 TACACAACTTACATAACTTA-AATAACT
1 TACATAA-TTACATAA--TACAATAACT
*
32227739 TACATAGCTTACATAATAC-ATAACT
1 TACATA-ATTACATAATACAATAACT
*
32227764 TACATAACTTATATAATAC-ATAACT
1 TACATAA-TTACATAATACAATAACT
*
32227789 TACATAATTTACCTAATACA
1 TACATAA-TTACATAATACA
32227809 TAAATATATA
Statistics
Matches: 99, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 75 0.76
26 5 0.05
27 13 0.13
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.32
Consensus pattern (25 bp):
TACATAATTACATAATACAATAACT
Found at i:32227702 original size:16 final size:16
Alignment explanation
Indices: 32227617--32227796 Score: 108
Period size: 16 Copynumber: 11.1 Consensus size: 16
32227607 AATTAATATT
*
32227617 ATACATAACATACATA
1 ATACATAACTTACATA
*
32227633 ATACACAACTTA-AT-
1 ATACATAACTTACATA
*
32227647 -TA-AT-ATTATACATGA
1 ATACATAACT-TACAT-A
32227662 CATACATAA--TACATA
1 -ATACATAACTTACATA
32227677 ATACATATAACTTACATA
1 ATAC--ATAACTTACATA
* * *
32227695 GTACATAACTAATATA
1 ATACATAACTTACATA
*
32227711 ATACACAACTTACATA
1 ATACATAACTTACATA
*
32227727 ACTTAAATAACTTACATA
1 A--TACATAACTTACATA
*
32227745 GCTTACATAA--TACATA
1 --ATACATAACTTACATA
*
32227761 ACTTACATAACTTATATA
1 A--TACATAACTTACATA
32227779 ATACATAACTTACATA
1 ATACATAACTTACATA
32227795 AT
1 AT
32227797 TTACCTAATA
Statistics
Matches: 126, Mismatches: 18, Indels: 40
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.02
12 3 0.02
13 4 0.03
14 4 0.03
15 3 0.02
16 71 0.56
17 2 0.02
18 36 0.29
19 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:32227743 original size:43 final size:41
Alignment explanation
Indices: 32227543--32227796 Score: 144
Period size: 41 Copynumber: 6.3 Consensus size: 41
32227533 CGTAACTTTG
* * **
32227543 ATAACTAACATTATACACAACTTACATAA--TACATTTCTTAC
1 ATAACTAACATAATACACAACTTACATAACTTA-A-ATAATAC
* * *
32227584 ATAACTTACACAATACACAAC-T---TAA-TTAATATTATAC
1 ATAACTAACATAATACACAACTTACATAACTTAA-ATAATAC
*
32227621 ATAAC-ATACATAATACACAAC-T---TAA-TTAATATTATAC
1 ATAACTA-ACATAATACACAACTTACATAACTTAA-ATAATAC
* * * *
32227658 ATGAC-ATACATAATACATAA--TACATATAACTTACATAGTAC
1 ATAACTA-ACATAATACACAACTTAC--ATAACTTAAATAATAC
*
32227699 ATAACTAATATAATACACAACTTACATAACTTAAATAACTTAC
1 ATAACTAACATAATACACAACTTACATAACTTAAATAA--TAC
* * * *
32227742 ATAGCTTACATAATACATAACTTACATAACTTATATAATAC
1 ATAACTAACATAATACACAACTTACATAACTTAAATAATAC
*
32227783 ATAACTTACATAAT
1 ATAACTAACATAAT
32227797 TTACCTAATA
Statistics
Matches: 176, Mismatches: 24, Indels: 26
0.78 0.11 0.12
Matches are distributed among these distances:
36 1 0.01
37 61 0.35
38 2 0.01
40 1 0.01
41 68 0.39
42 4 0.02
43 39 0.22
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.32
Consensus pattern (41 bp):
ATAACTAACATAATACACAACTTACATAACTTAAATAATAC
Found at i:32227809 original size:25 final size:25
Alignment explanation
Indices: 32227721--32227840 Score: 63
Period size: 25 Copynumber: 4.7 Consensus size: 25
32227711 ATACACAACT
* *
32227721 TACATAACTTAAATAACTTACATAGCT
1 TACATAACTTACATAACTTACATA--A
32227748 TACATAA--TACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
*
32227771 CTTATATAA--TACATAACTTACATAA
1 --TACATAACTTACATAACTTACATAA
* * * *
32227796 TTTACCTAA--TACATAAATATATATCA
1 --TACATAACTTACATAACT-TACATAA
32227822 TATCATAACTTACATAACT
1 TA-CATAACTTACATAACT
32227841 CATTTATAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
24 2 0.03
25 54 0.71
26 5 0.07
27 15 0.20
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:32228007 original size:17 final size:17
Alignment explanation
Indices: 32227985--32228056 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
32227975 ATAACTCACA
32227985 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
32228002 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
32228019 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
32228035 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
32228053 TAAT
1 TAAT
32228057 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:32228029 original size:25 final size:26
Alignment explanation
Indices: 32227993--32228056 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
32227983 CATAATAACT
*
32227993 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
32228018 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
32228044 TACATAACTTAAT
1 TACATAACTTAAT
32228057 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:32228182 original size:26 final size:28
Alignment explanation
Indices: 32228128--32228183 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
32228118 ATACATAACT
*
32228128 TTTCAACTATTTTATATATGCTGTTTTA
1 TTTCAACTATCTTATATATGCTGTTTTA
32228156 TTTCAACTA-CTT-TATATG-TGTTGTTA
1 TTTCAACTATCTTATATATGCTGTT-TTA
32228182 TT
1 TT
32228184 GTTGTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 11 0.42
27 2 0.08
28 9 0.35
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (28 bp):
TTTCAACTATCTTATATATGCTGTTTTA
Found at i:32230225 original size:43 final size:43
Alignment explanation
Indices: 32230169--32230376 Score: 265
Period size: 43 Copynumber: 4.8 Consensus size: 43
32230159 CATCAGACAA
** * *
32230169 TAGCGGCGTTTGTGAGGGAAGCGCCGCTAAAGAACATGAACTT
1 TAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGAACATGACCTT
* *
32230212 TAGCGGCGTTTGTGAGAAAAGCGTCATTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGAACATGACCTT
* * * *
32230255 TAGCAGCGTTTGTGA-AAGAGGTGCCATTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAA-AAGCGCCACTAAAGAACATGACCTT
* * *
32230298 TAGCGGCGTTTGTGAGAAATGCGCCGCTAAAGAACATGACCAT
1 TAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGAACATGACCTT
* *
32230341 TAGCGGCGTTTGTGAGAAAAGTGTCACTAAAGAACA
1 TAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGAACA
32230377 CATTATTTAG
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 2 0.01
43 139 0.97
44 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGAACATGACCTT
Found at i:32235147 original size:20 final size:20
Alignment explanation
Indices: 32235099--32235139 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
32235089 CGAGCCATTT
32235099 TAAGTTTATAATACTTTATA
1 TAAGTTTATAATACTTTATA
32235119 TAAGTTTATAATACTTTATA
1 TAAGTTTATAATACTTTATA
32235139 T
1 T
32235140 TATGTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TAAGTTTATAATACTTTATA
Found at i:32235774 original size:175 final size:175
Alignment explanation
Indices: 32235471--32235813 Score: 614
Period size: 175 Copynumber: 2.0 Consensus size: 175
32235461 GCTCAAACCC
* *
32235471 GGCCCGACCCGGCCATGAGCACCTCTAATCACCACAGATTCCCGTTAATTATTTAAAGCACTTCA
1 GGCCCGACCCGACCATGAGCACCTCTAATCACCACAGATTCCCGTTAATTATTCAAAGCACTTCA
* *
32235536 AATAACAACCGTGCTAGCAAAGGTGTGGGGACTTTAGCATGCAATAAGCCTCAAGTCTGCTAAAG
66 AATAACAACCATACTAGCAAAGGTGTGGGGACTTTAGCATGCAATAAGCCTCAAGTCTGCTAAAG
32235601 TAAATATCCAGAAAAGATCAAAGAGATCCATGTTTGTTCAAACTT
131 TAAATATCCAGAAAAGATCAAAGAGATCCATGTTTGTTCAAACTT
* * *
32235646 GGCCTGACCCGACCATGAGTACCTCTAATCACCACAGATTCCCGTTAATTATTCAAATCACTTCA
1 GGCCCGACCCGACCATGAGCACCTCTAATCACCACAGATTCCCGTTAATTATTCAAAGCACTTCA
32235711 AATAACAACCATACTAGCAAAGGTGTGGGGACTTTAGCATGCAATAAGCCTCAAGTCTGCTAAAG
66 AATAACAACCATACTAGCAAAGGTGTGGGGACTTTAGCATGCAATAAGCCTCAAGTCTGCTAAAG
*
32235776 TAAATATCTAGAAAAGATCAAAGAGATCCATGTTTGTT
131 TAAATATCCAGAAAAGATCAAAGAGATCCATGTTTGTT
32235814 GTTAGGGCAT
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
175 160 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (175 bp):
GGCCCGACCCGACCATGAGCACCTCTAATCACCACAGATTCCCGTTAATTATTCAAAGCACTTCA
AATAACAACCATACTAGCAAAGGTGTGGGGACTTTAGCATGCAATAAGCCTCAAGTCTGCTAAAG
TAAATATCCAGAAAAGATCAAAGAGATCCATGTTTGTTCAAACTT
Found at i:32237032 original size:31 final size:31
Alignment explanation
Indices: 32236994--32237064 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
32236984 ATTTAGTTAT
**
32236994 TGAACTATTTGAAAGTTTTTATTTAAGCCAG-
1 TGAACTATTCAAAAGTTTTTATTTAAGCC-GC
*
32237025 TGAACTATTCAAAAGTTTTTATTTAAGTCGC
1 TGAACTATTCAAAAGTTTTTATTTAAGCCGC
32237056 TGAACTATT
1 TGAACTATT
32237065 ATCTTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTTATTTAAGCCGC
Found at i:32247528 original size:14 final size:15
Alignment explanation
Indices: 32247509--32247541 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
32247499 TAATAAGTAT
32247509 TTTTC-TTTTCATTC
1 TTTTCTTTTTCATTC
32247523 TTTTCTTTTTCATTC
1 TTTTCTTTTTCATTC
32247538 TTTT
1 TTTT
32247542 TTACTCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTCATTC
Found at i:32279841 original size:12 final size:12
Alignment explanation
Indices: 32279824--32279848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32279814 TTCTTGTTGC
32279824 CTCTTCTTCCAT
1 CTCTTCTTCCAT
32279836 CTCTTCTTCCAT
1 CTCTTCTTCCAT
32279848 C
1 C
32279849 ATATCCCTCA
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:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTCTTCCAT
Found at i:32281544 original size:132 final size:131
Alignment explanation
Indices: 32281308--32281570 Score: 481
Period size: 132 Copynumber: 2.0 Consensus size: 131
32281298 GTCATATGAC
32281308 CATGTGGCAGGCCGTGTCAATTTCACAAATTTGGACCCAAACAGTGGAAAGACATGATTTTTAGG
1 CATGTGGCAGGCCGTGTCAATTTCACAAATTTGGACCCAAACAGTGGAAAGACATGATTTTTAGG
*
32281373 TTTTTCAGACATTCTAAGACATATATATGTCAAAAAAAGAAGATAGGAGTGAGCCATCATAGGAT
66 TTTTTCAGACATTCTAAGACATATATATGTCAAAAAAAGAAGATAGGAGCGAGCCATCATAGGAT
32281438 A
131 A
* *
32281439 CATGTGGCAGGCTGTGTCAATTTCACAAATTTGGACCCCAAACAGTGGAAAGACGTGATTTTTAG
1 CATGTGGCAGGCCGTGTCAATTTCACAAATTTGGA-CCCAAACAGTGGAAAGACATGATTTTTAG
*
32281504 GTTTTTCAGACATTCTAAGACATATATATGTCAAACAAAGAAGATAGGAGCGAGCCATCATAGGA
65 GTTTTTCAGACATTCTAAGACATATATATGTCAAAAAAAGAAGATAGGAGCGAGCCATCATAGGA
32281569 TA
130 TA
32281571 GTTAAGAAAA
Statistics
Matches: 127, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
131 34 0.27
132 93 0.73
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (131 bp):
CATGTGGCAGGCCGTGTCAATTTCACAAATTTGGACCCAAACAGTGGAAAGACATGATTTTTAGG
TTTTTCAGACATTCTAAGACATATATATGTCAAAAAAAGAAGATAGGAGCGAGCCATCATAGGAT
A
Found at i:32282542 original size:13 final size:14
Alignment explanation
Indices: 32282523--32282561 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
32282513 TTTAGCTATT
*
32282523 TTTTAATTTTTTTA
1 TTTTAATTTTTTCA
*
32282537 -TTTAATTTTTACA
1 TTTTAATTTTTTCA
32282550 TTTTAATTTTTT
1 TTTTAATTTTTT
32282562 GTTTGTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTAATTTTTTCA
Found at i:32287686 original size:20 final size:20
Alignment explanation
Indices: 32287656--32287709 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
32287646 GATATCACCC
*
32287656 TATCACTCTAGGCCATGTGA
1 TATCACCCTAGGCCATGTGA
* **
32287676 TGTCACCCTAGGCTGTGTGA
1 TATCACCCTAGGCCATGTGA
32287696 TATCACCCTAGGCC
1 TATCACCCTAGGCC
32287710 GTCTTTTCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (20 bp):
TATCACCCTAGGCCATGTGA
Found at i:32297253 original size:11 final size:10
Alignment explanation
Indices: 32297226--32297367 Score: 88
Period size: 9 Copynumber: 14.4 Consensus size: 10
32297216 GGCCTTTCCC
32297226 TATTTATTAT
1 TATTTATTAT
*
32297236 AATTTATATAT
1 TATTTAT-TAT
32297247 TATTTATTACT
1 TATTTATTA-T
* *
32297258 CTAATTATGAT
1 -TATTTATTAT
*
32297269 T-TTTGGTTCAT
1 TATTT-ATT-AT
32297280 TA-TTATTTAT
1 TATTTA-TTAT
*
32297290 TA-TTAGTAT
1 TATTTATTAT
32297299 TA-TT-TTAT
1 TATTTATTAT
*
32297307 TACTGTTACTAT
1 TA-T-TTATTAT
32297319 TA-TTATTAT
1 TATTTATTAT
32297328 TA-TTATTAT
1 TATTTATTAT
32297337 TA-TTATTAT
1 TATTTATTAT
32297346 TA-TTATTAT
1 TATTTATTAT
32297355 TA-TTATTAT
1 TATTTATTAT
32297364 TATT
1 TATT
32297368 AGTAGTAGTA
Statistics
Matches: 108, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
8 5 0.05
9 53 0.49
10 18 0.17
11 20 0.19
12 12 0.11
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (10 bp):
TATTTATTAT
Found at i:32297286 original size:3 final size:3
Alignment explanation
Indices: 32297278--32297368 Score: 130
Period size: 3 Copynumber: 30.3 Consensus size: 3
32297268 TTTTTGGTTC
* * * *
32297278 ATT ATT ATTT ATT ATT AGT ATT ATT -TT ATT ACT GTT ACT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32297323 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
32297369 GTAGTAGTAG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
3 73 0.94
4 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:32297301 original size:9 final size:9
Alignment explanation
Indices: 32297287--32297427 Score: 86
Period size: 9 Copynumber: 15.1 Consensus size: 9
32297277 CATTATTATT
32297287 TATTATTAG
1 TATTATTAG
*
32297296 TATTATT-T
1 TATTATTAG
*
32297304 TATTACTGTTAC
1 TATTA---TTAG
*
32297316 TATTATTAT
1 TATTATTAG
*
32297325 TATTATTAT
1 TATTATTAG
*
32297334 TATTATTAT
1 TATTATTAG
*
32297343 TATTATTAT
1 TATTATTAG
*
32297352 TATTATTAT
1 TATTATTAG
32297361 TATTATTAG
1 TATTATTAG
*
32297370 TAGTAGTAGTAG
1 TA-T--TATTAG
* *
32297382 TAGTAGTAG
1 TATTATTAG
* *
32297391 TAGTAGTAG
1 TATTATTAG
* *
32297400 TAGTAGTAG
1 TATTATTAG
*
32297409 TAGTATTAG
1 TATTATTAG
32297418 TATTATTAG
1 TATTATTAG
32297427 T
1 T
32297428 TGAACTACTG
Statistics
Matches: 117, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.04
9 97 0.83
10 1 0.01
11 2 0.02
12 12 0.10
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (9 bp):
TATTATTAG
Found at i:32297373 original size:3 final size:3
Alignment explanation
Indices: 32297367--32297419 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
32297357 TTATTATTAT
*
32297367 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAT
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
32297415 TAG TA
1 TAG TA
32297420 TTATTAGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:32297420 original size:6 final size:6
Alignment explanation
Indices: 32297316--32297422 Score: 79
Period size: 6 Copynumber: 17.8 Consensus size: 6
32297306 TTACTGTTAC
* * * * * * * *
32297316 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
* * * * * * *
32297364 TATTAG TAGTAG TAGTAG TAGTAG TAGTAG TAGTAG TAGTAG TAGTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
32297412 TATTAG TATTA
1 TATTAG TATTA
32297423 TTAGTTGAAC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:32309349 original size:15 final size:14
Alignment explanation
Indices: 32309331--32309368 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
32309321 ACGAATATGA
32309331 TAATATATTTCAATT
1 TAATATATTT-AATT
*
32309346 TAATAAATTTAATT
1 TAATATATTTAATT
32309360 TAAT-TATTT
1 TAATATATTT
32309369 TATAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
15 9 0.43
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATATATTTAATT
Found at i:32313679 original size:26 final size:26
Alignment explanation
Indices: 32313630--32313679 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
32313620 CTCTTTTTCA
*
32313630 TTTAAAAAATAATAATGGGGATCGAC
1 TTTAAAAAATAATAATGGGAATCGAC
*
32313656 TTTAAAAAATCAA-AATTGGAATCG
1 TTTAAAAAAT-AATAATGGGAATCG
32313680 CCACCGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (26 bp):
TTTAAAAAATAATAATGGGAATCGAC
Found at i:32316653 original size:58 final size:60
Alignment explanation
Indices: 32316591--32316704 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 60
32316581 ATCACTTTAA
*
32316591 TATTAAATTAATATAATACTTA-T-CAAGAAAAATATTAAATTAAATTAAATATTTAATC
1 TATTAAATTAATAGAATACTTACTACAAGAAAAATATTAAATTAAATTAAATATTTAATC
* * *
32316649 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTTAATTTAATATT
1 TATTAAATTAATAGAATACTTA-CTACAAGAAAAATATTAAATTAAATTAAATATT
32316705 AAGATAATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 21 0.43
60 1 0.02
61 27 0.55
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTACAAGAAAAATATTAAATTAAATTAAATATTTAATC
Found at i:32317058 original size:19 final size:19
Alignment explanation
Indices: 32317026--32317062 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
32317016 AATTTTGGGT
32317026 TCTCGGTCTCAATTTTCAA
1 TCTCGGTCTCAATTTTCAA
32317045 TCTCAGGTCT-AATTTTCA
1 TCTC-GGTCTCAATTTTCA
32317063 CTCATTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (19 bp):
TCTCGGTCTCAATTTTCAA
Found at i:32317200 original size:14 final size:15
Alignment explanation
Indices: 32317181--32317209 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
32317171 AATAACTAAG
32317181 ATTTTTCAA-AAATA
1 ATTTTTCAAGAAATA
32317195 ATTTTTCAAGAAATA
1 ATTTTTCAAGAAATA
32317210 TCTTTAATCA
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:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
ATTTTTCAAGAAATA
Found at i:32322209 original size:21 final size:20
Alignment explanation
Indices: 32322170--32322209 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
32322160 AGTCTCTTGC
* *
32322170 TGAGTTGGGTAGCCTGTTGT
1 TGAGTTGGGTAACCAGTTGT
32322190 TGAGTTTGGGTAACCAGTTG
1 TGAG-TTGGGTAACCAGTTG
32322210 GTTATGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (20 bp):
TGAGTTGGGTAACCAGTTGT
Found at i:32327274 original size:15 final size:15
Alignment explanation
Indices: 32327248--32327286 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
32327238 AATCCTATTG
32327248 GACACATCACTAACA
1 GACACATCACTAACA
* * *
32327263 GATACATGACTATCA
1 GACACATCACTAACA
32327278 GACACATCA
1 GACACATCA
32327287 AAACTAGACA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (15 bp):
GACACATCACTAACA
Found at i:32333802 original size:20 final size:20
Alignment explanation
Indices: 32333777--32333815 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
32333767 TACTTTCTTC
32333777 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
32333797 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
32333816 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:32356897 original size:26 final size:26
Alignment explanation
Indices: 32356863--32356943 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
32356853 AACACACCAA
*
32356863 TATCACAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
32356889 TATCGCAGCGAAGCTACCAGT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
* *
32356915 TATCGCAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
32356941 TAT
1 TAT
32356944 ATGTGGCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 2 0.04
26 43 0.93
27 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:32357182 original size:25 final size:25
Alignment explanation
Indices: 32357148--32357206 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
32357138 GGCCCGGCCC
* * *
32357148 ATTTTTAAAATAAACATTAAAAATT
1 ATTTTAAAAATAAAAATAAAAAATT
32357173 ATTTTAAAAATAAAAATAAAAAATT
1 ATTTTAAAAATAAAAATAAAAAATT
32357198 ATTTTAAAA
1 ATTTTAAAA
32357207 GTACTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTTTAAAAATAAAAATAAAAAATT
Found at i:32357580 original size:28 final size:27
Alignment explanation
Indices: 32357549--32357612 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
32357539 AACCTACCTC
* *
32357549 TAGGGGTATAATGGTCATTCCTATCTAT
1 TAGGGGTATAATAGTCATT-CTACCTAT
* * *
32357577 TAGGGGTAAAATAGTCATTTTACCTTT
1 TAGGGGTATAATAGTCATTCTACCTAT
32357604 TAGGGGTAT
1 TAGGGGTAT
32357613 TTTGGTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (27 bp):
TAGGGGTATAATAGTCATTCTACCTAT
Found at i:32357908 original size:20 final size:20
Alignment explanation
Indices: 32357874--32357919 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
32357864 CGAGCCCATT
32357874 GGCCC-ACACGGCCCATCT-C
1 GGCCCAACACGGCCCAT-TAC
*
32357893 GGCCCAACATGGCCCATTAC
1 GGCCCAACACGGCCCATTAC
32357913 GGCCCAA
1 GGCCCAA
32357920 GCCCATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.22, C:0.46, G:0.22, T:0.11
Consensus pattern (20 bp):
GGCCCAACACGGCCCATTAC
Found at i:32360510 original size:82 final size:82
Alignment explanation
Indices: 32360367--32360537 Score: 324
Period size: 82 Copynumber: 2.1 Consensus size: 82
32360357 GGCAACCTTG
*
32360367 AATTCGTCAAATTGATCAATGAGGTAAATAATGATGTAGGAATCCCAACTTTAGCAGGAAGAATT
1 AATT-GTCAAATTGATCAATGAGGTAAATAATGATGTAGGAATCCCAACTTTAGCAAGAAGAATT
32360432 GAGTCCTTGTGCTCAAGA
65 GAGTCCTTGTGCTCAAGA
32360450 AATTGTCAAATTGATCAATGAGGTAAATAATGATGTAGGAATCCCAACTTTAGCAAGAAGAATTG
1 AATTGTCAAATTGATCAATGAGGTAAATAATGATGTAGGAATCCCAACTTTAGCAAGAAGAATTG
32360515 AGTCCTTGTGCTCAAGA
66 AGTCCTTGTGCTCAAGA
32360532 AATTGT
1 AATTGT
32360538 GAGGACAAAT
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 83 0.95
83 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (82 bp):
AATTGTCAAATTGATCAATGAGGTAAATAATGATGTAGGAATCCCAACTTTAGCAAGAAGAATTG
AGTCCTTGTGCTCAAGA
Found at i:32363055 original size:5 final size:6
Alignment explanation
Indices: 32363027--32363058 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
32363017 CTGATATCAA
32363027 TATATT TATATT TATA-T TATATT T-TATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
32363059 ATAACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:32367091 original size:6 final size:6
Alignment explanation
Indices: 32367080--32367118 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
32367070 GGATTGCAAG
* * *
32367080 TTTCCA TTTCCA TTTTCA TTTTCG TTTCCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
32367119 TTAAAAACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.59
Consensus pattern (6 bp):
TTTCCA
Found at i:32373857 original size:11 final size:10
Alignment explanation
Indices: 32373829--32373858 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
32373819 CTTACCCTTG
32373829 GTAAAATATT
1 GTAAAATATT
32373839 GTAAAATATT
1 GTAAAATATT
32373849 GTGAAAATAT
1 GT-AAAATAT
32373859 GTTCAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (10 bp):
GTAAAATATT
Found at i:32376358 original size:27 final size:27
Alignment explanation
Indices: 32376320--32376446 Score: 141
Period size: 27 Copynumber: 4.7 Consensus size: 27
32376310 CACACCAAAA
*
32376320 AAATGGAAGCCTTTGTGGCAATTTGTG
1 AAATGGAAGCCTTTGTGGCAATTTATG
*
32376347 AAATGGAAGCCTTTGTGAC-ATTCTATG
1 AAATGGAAGCCTTTGTGGCAATT-TATG
* *
32376374 AAATGGAAGCCTTCGTGGCAATCTATG
1 AAATGGAAGCCTTTGTGGCAATTTATG
* * *
32376401 AAATGGAAGGCTTTGTGGCGATCTATGG
1 AAATGGAAGCCTTTGTGGCAATTTAT-G
*
32376429 AAA-GGAACTCCTTTGTGG
1 AAATGGAA-GCCTTTGTGG
32376447 TGCATTCTAG
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.03
27 69 0.80
28 14 0.16
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAATTTATG
Found at i:32376426 original size:54 final size:55
Alignment explanation
Indices: 32376320--32376435 Score: 157
Period size: 54 Copynumber: 2.1 Consensus size: 55
32376310 CACACCAAAA
* * *
32376320 AAATGGAAGCCTTTGTGGCAATTTGTGAAATGGAAGCCTTTGTGACATTCTAT-G
1 AAATGGAAGCCTTCGTGGCAATCTATGAAATGGAAGCCTTTGTGACATTCTATGG
* *
32376374 AAATGGAAGCCTTCGTGGCAATCTATGAAATGGAAGGCTTTGTGGCGA-TCTATGG
1 AAATGGAAGCCTTCGTGGCAATCTATGAAATGGAAGCCTTTGTGAC-ATTCTATGG
32376429 AAA-GGAA
1 AAATGGAA
32376436 CTCCTTTGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 50 0.91
55 5 0.09
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (55 bp):
AAATGGAAGCCTTCGTGGCAATCTATGAAATGGAAGCCTTTGTGACATTCTATGG
Found at i:32376585 original size:27 final size:27
Alignment explanation
Indices: 32376527--32376591 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
32376517 AGAGTGGTAA
*
32376527 ATATGTCGAACTCTGAAAGAATAGTAC
1 ATATGGCGAACTCTGAAAGAATAGTAC
* *
32376554 ATATGGTGAACTCTG-AAGAAATAGTGC
1 ATATGGCGAACTCTGAAAG-AATAGTAC
*
32376581 GTATGGCGAAC
1 ATATGGCGAAC
32376592 ATTGAGAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (27 bp):
ATATGGCGAACTCTGAAAGAATAGTAC
Found at i:32388143 original size:45 final size:45
Alignment explanation
Indices: 32388079--32388239 Score: 189
Period size: 45 Copynumber: 3.6 Consensus size: 45
32388069 ACTACGTTAT
* *
32388079 CGGGTACCATTGATTATAAATGTGGTTGTTGTGTGCTGATTCCAC
1 CGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCAC
*
32388124 CGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGGTTCCAC
1 CGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCAC
* * * * * **
32388169 CGGGTA-CTACTAATTATGAAGGTGGTTGCTATGTTTTGATTCCAC
1 CGGGTATC-ATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCAC
* * *
32388214 CGAGTATCATTGACTATAAGGGTGGT
1 CGGGTATCATTGATTATAAAGGTGGT
32388240 GCTATGTGGT
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
44 1 0.01
45 95 0.98
46 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (45 bp):
CGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCAC
Found at i:32405647 original size:17 final size:17
Alignment explanation
Indices: 32405625--32405662 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
32405615 TAAGTTGTCT
*
32405625 TTCTGGCAATGTAAACG
1 TTCTGGCAATGTAAACA
32405642 TTCTGGCAATGTAAACA
1 TTCTGGCAATGTAAACA
32405659 TTCT
1 TTCT
32405663 TACAATGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (17 bp):
TTCTGGCAATGTAAACA
Found at i:32405668 original size:17 final size:17
Alignment explanation
Indices: 32405625--32405669 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
32405615 TAAGTTGTCT
* *
32405625 TTCTGGCAATGTAAACG
1 TTCTGACAATGTAAACA
*
32405642 TTCTGGCAATGTAAACA
1 TTCTGACAATGTAAACA
*
32405659 TTCTTACAATG
1 TTCTGACAATG
32405670 CCACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (17 bp):
TTCTGACAATGTAAACA
Found at i:32405817 original size:29 final size:29
Alignment explanation
Indices: 32405784--32405844 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
32405774 GATAGTGAAA
32405784 TGTGAAATTAACTTTATTTATTTATTCAT
1 TGTGAAATTAACTTTATTTATTTATTCAT
32405813 TGTGAAATTAACTTTATTTATTTATTCAT
1 TGTGAAATTAACTTTATTTATTTATTCAT
32405842 TGT
1 TGT
32405845 TTAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.56
Consensus pattern (29 bp):
TGTGAAATTAACTTTATTTATTTATTCAT
Found at i:32412599 original size:12 final size:11
Alignment explanation
Indices: 32412574--32412611 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
32412564 GAACATGATG
32412574 AATTTTA-ATT
1 AATTTTATATT
32412584 AATTTTATAGTT
1 AATTTTATA-TT
32412596 AATTTT-TATT
1 AATTTTATATT
32412606 AATTTT
1 AATTTT
32412612 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:32422535 original size:25 final size:25
Alignment explanation
Indices: 32422507--32422555 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
32422497 CCCCCAAACA
32422507 TCCACTTATGATTTCAAACCAATCG
1 TCCACTTATGATTTCAAACCAATCG
32422532 TCCACTTATGATTTCAAACCAATC
1 TCCACTTATGATTTCAAACCAATC
32422556 ATTGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (25 bp):
TCCACTTATGATTTCAAACCAATCG
Found at i:32424246 original size:17 final size:16
Alignment explanation
Indices: 32424226--32424281 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
32424216 TGGTTTATCA
32424226 ATTTATTTCGTTTATTT
1 ATTTATTTC-TTTATTT
32424243 A-TT-TTTCTTTATTT
1 ATTTATTTCTTTATTT
* *
32424257 ATTTCTTTTCTTTAGTT
1 ATTT-ATTTCTTTATTT
32424274 ATTTATTT
1 ATTTATTT
32424282 GTATTCCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 5 0.15
17 15 0.44
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (16 bp):
ATTTATTTCTTTATTT
Found at i:32424255 original size:14 final size:15
Alignment explanation
Indices: 32424231--32424260 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
32424221 TATCAATTTA
32424231 TTTCGTTTATTTATT
1 TTTCGTTTATTTATT
32424246 TTTC-TTTATTTATT
1 TTTCGTTTATTTATT
32424260 T
1 T
32424261 CTTTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCGTTTATTTATT
Found at i:32427935 original size:17 final size:18
Alignment explanation
Indices: 32427903--32427961 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
32427893 AGAAGTTGAG
32427903 ATAATTATATATTTAAAA
1 ATAATTATATATTTAAAA
32427921 ATAATTATA-ATTTAATCAGA
1 ATAATTATATATTTAA--A-A
* *
32427941 ATTATTACATATTTAAAA
1 ATAATTATATATTTAAAA
32427959 ATA
1 ATA
32427962 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 6 0.18
18 12 0.35
19 2 0.06
20 8 0.24
21 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAATTATATATTTAAAA
Found at i:32427963 original size:17 final size:17
Alignment explanation
Indices: 32427906--32427999 Score: 59
Period size: 17 Copynumber: 5.3 Consensus size: 17
32427896 AGTTGAGATA
32427906 ATTATATATTTAAAAAT
1 ATTATATATTTAAAAAT
32427923 AATTATA-ATTTAATCAGAATT
1 -ATTATATATTTAA--A-AA-T
*
32427944 ATTACATATTTAAAAAT
1 ATTATATATTTAAAAAT
* **
32427961 ATTA-AAATTTAATTTAT
1 ATTATATATTTAA-AAAT
*
32427978 ACTTAT-TAGTTAAAAAT
1 A-TTATATATTTAAAAAT
32427995 ATTAT
1 ATTAT
32428000 TCTAATTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
16 11 0.18
17 17 0.28
18 16 0.27
19 2 0.03
20 7 0.12
21 7 0.12
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (17 bp):
ATTATATATTTAAAAAT
Found at i:32428461 original size:19 final size:18
Alignment explanation
Indices: 32428437--32428473 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
32428427 TCTTTAGGAT
32428437 TTTTTTAAAAAAATCATAA
1 TTTTTTAAAAAAAT-ATAA
*
32428456 TTTTTTGAAAAAATATAA
1 TTTTTTAAAAAAATATAA
32428474 AATTTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTTTTAAAAAAATATAA
Done.