Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 8 of 103
Found at i:3177196 original size:6 final size:6
Alignment explanation
Indices: 3177128--3177198 Score: 52
Period size: 6 Copynumber: 11.0 Consensus size: 6
3177118 TAATTTAATT
* * * *
3177128 TTTAAG TTTAAA TATTAAA TATTAAA TATTATAA TTTATA TTAAAA TTTTAA
1 TTTAAA TTTAAA T-TTAAA T-TTAAA T-TTA-AA TTTAAA TTTAAA TTTAAA
*
3177180 TTTAATT TTTAAA TTTAAA
1 TTTAA-A TTTAAA TTTAAA
3177199 ATATTAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 25 0.47
7 25 0.47
8 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:3177238 original size:53 final size:53
Alignment explanation
Indices: 3177134--3177240 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 53
3177124 AATTTTTAAG
* *
3177134 TTTAAATATTAAATATTAAATATTATAATTTATATTAAAATTTTAATTTAATT
1 TTTAAATATTAAATATTAAATATTATAACTTATATTAAAATTTTAACTTAATT
* *
3177187 TTTAAAT-TTAAAATATT-AATTTTCATAACTTATATTCAAAA-TTTAGCTTAATT
1 TTTAAATATT-AAATATTAAATATT-ATAACTTATATT-AAAATTTTAACTTAATT
3177240 T
1 T
3177241 ATAGAGAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
52 7 0.15
53 36 0.77
54 4 0.09
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (53 bp):
TTTAAATATTAAATATTAAATATTATAACTTATATTAAAATTTTAACTTAATT
Found at i:3192472 original size:1 final size:1
Alignment explanation
Indices: 3192431--3192461 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3192421 AAGGGTGGGT
*
3192431 GGGGNGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3192462 CACCTTGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:3204926 original size:125 final size:124
Alignment explanation
Indices: 3204788--3205045 Score: 290
Period size: 125 Copynumber: 2.1 Consensus size: 124
3204778 CAGAAAACTC
* * **
3204788 AAAAAAATATGTTATTAAACGTTATGTT-GAAAAAAATGATTACATGCCATATTTAAGGCATTTA
1 AAAAAAATATG---TTAAACGTCATGTTAAAAAAAAATGATTACACACCATATTTAAGGCATTTA
* *
3204852 AC-TCTAAGAGTTTATTTCTTAGTGAAATACAAAAATAAAGACCAAGTTACATGCCATG-TTGA
63 ACTTC-AAGAGTTTATGTCCTAGTGAAATACAAAAATAAAGACCAAGTTACATGCCA-GATTGA
* * * **
3204914 AAAAAAAT-TGTTACACGTCATGTTAAAAAAAAAAATTATTACACACCATGTTTAAGGTGTTTAA
1 AAAAAAATATGTTAAACGTCATGTT--AAAAAAAAATGATTACACACCATATTTAAGGCATTTAA
* * * *
3204978 CTTCAAGAGTTTATGTCCTAGTGAAATACAAAGATAGAGACTAAGTTACATGTCAGATTGA
64 CTTCAAGAGTTTATGTCCTAGTGAAATACAAAAATAAAGACCAAGTTACATGCCAGATTGA
3205039 AAAAAAA
1 AAAAAAA
3205046 ATTATTACAC
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
122 12 0.11
124 1 0.01
125 89 0.79
126 10 0.09
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (124 bp):
AAAAAAATATGTTAAACGTCATGTTAAAAAAAAATGATTACACACCATATTTAAGGCATTTAACT
TCAAGAGTTTATGTCCTAGTGAAATACAAAAATAAAGACCAAGTTACATGCCAGATTGA
Found at i:3204935 original size:26 final size:26
Alignment explanation
Indices: 3204897--3204965 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 26
3204887 TAAAGACCAA
* *
3204897 GTTACATGCCATGTTGAAAAAAAATT
1 GTTACACGCCATGTTAAAAAAAAATT
*
3204923 GTTACACGTCATGTTAAAAAAAAAAATT
1 GTTACACGCCATGTT--AAAAAAAAATT
* *
3204951 ATTACACACCATGTT
1 GTTACACGCCATGTT
3204966 TAAGGTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 13 0.37
28 22 0.63
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (26 bp):
GTTACACGCCATGTTAAAAAAAAATT
Found at i:3205052 original size:98 final size:98
Alignment explanation
Indices: 3204940--3205250 Score: 348
Period size: 98 Copynumber: 3.2 Consensus size: 98
3204930 GTCATGTTAA
*
3204940 AAAAAAAAATTATTACACACCATGTTTAAGGTGTTTAACTTCAAGAGTTTATGTCCTAGTGAAAT
1 AAAAAAAAATTATTACACACCAAGTTTAAGGTGTTTAACTTCAAGAGTTTATGTCCTAGTGAAAT
3205005 ACAAAGATAGAGACTAAGTTACATGTCAGATTG
66 ACAAAGATAGAGACTAAGTTACATGTCAGATTG
* * * *
3205038 AAAAAAAAATTATTACACACCAAGTTTACGATGTTTAA-TTCTAACGA-TATATATCCTAGTGAA
1 AAAAAAAAATTATTACACACCAAGTTTAAGGTGTTTAACTTC-AA-GAGTTTATGTCCTAGTGAA
* * **
3205101 ATACAAAAATAGAGA-TCAAGTTGCATACCATG-TTG
64 ATACAAAGATAGAGACT-AAGTTACATGTCA-GATTG
** * * **
3205136 AAAAAAAAA-TATTACATGCCACA-TTTAAGGTGTTTAACTCCAACAGTTTATGTTTTAGTGAAA
1 AAAAAAAAATTATTACACACCA-AGTTTAAGGTGTTTAACTTCAAGAGTTTATGTCCTAGTGAAA
* * *
3205199 TACAAAGATGGAGACCAAGTTACATGTCACATTG
65 TACAAAGATAGAGACTAAGTTACATGTCAGATTG
* *
3205233 -AACAAAAATTGTTACACA
1 AAAAAAAAATTATTACACA
3205251 TTATGTTGAA
Statistics
Matches: 173, Mismatches: 30, Indels: 21
0.77 0.13 0.09
Matches are distributed among these distances:
96 8 0.05
97 72 0.42
98 90 0.52
99 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (98 bp):
AAAAAAAAATTATTACACACCAAGTTTAAGGTGTTTAACTTCAAGAGTTTATGTCCTAGTGAAAT
ACAAAGATAGAGACTAAGTTACATGTCAGATTG
Found at i:3205281 original size:25 final size:25
Alignment explanation
Indices: 3205230--3205287 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
3205220 ACATGTCACA
* **
3205230 TTGAACAAAAATTGTTACACATTATG
1 TTGAA-AAAAATTATTACACACCATG
*
3205256 TTGAAAAAAATTATTACACGCCATG
1 TTGAAAAAAATTATTACACACCATG
*
3205281 TTTAAAA
1 TTGAAAA
3205288 TGTATAACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (25 bp):
TTGAAAAAAATTATTACACACCATG
Found at i:3205951 original size:2 final size:2
Alignment explanation
Indices: 3205946--3206014 Score: 81
Period size: 2 Copynumber: 35.5 Consensus size: 2
3205936 GAAATCTAAT
* * *
3205946 TA TA TA TA TA TA TA TA TA TA TA TA TA TN TC GA -A TA CTA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
3205986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3206015 TTGCTAAACC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
1 3 0.05
2 54 0.92
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3215923 original size:79 final size:79
Alignment explanation
Indices: 3215788--3215946 Score: 228
Period size: 79 Copynumber: 2.0 Consensus size: 79
3215778 TAGACTTGAC
* *
3215788 AATGGAACAAAGTTTACCTTAGCTGAGTTTAAAGATTTCATCACCAAAAATAGAGTGAAACATCA
1 AATGGAACAAAGTTTACATTAGATGAGTTTAAAGATTTCATCACCAAAAATAGAGTGAAACATCA
3215853 ACTAACCATAACAT
66 ACTAACCATAACAT
* * * ** *
3215867 AATGGAACAGAGTTTACATTAGATGAGTTTGAAGATTTCTTTGCCAAAAATGGAGTGAAACATCA
1 AATGGAACAAAGTTTACATTAGATGAGTTTAAAGATTTCATCACCAAAAATAGAGTGAAACATCA
* *
3215932 ATTAATCATAACAT
66 ACTAACCATAACAT
3215946 A
1 A
3215947 CAACCCTCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (79 bp):
AATGGAACAAAGTTTACATTAGATGAGTTTAAAGATTTCATCACCAAAAATAGAGTGAAACATCA
ACTAACCATAACAT
Found at i:3216127 original size:18 final size:20
Alignment explanation
Indices: 3216106--3216142 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
3216096 CTAATGATTT
*
3216106 TAAGTTAAT-TAAT-TTAGG
1 TAAGCTAATCTAATCTTAGG
3216124 TAAGCTAATCTAATCTTAG
1 TAAGCTAATCTAATCTTAG
3216143 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (20 bp):
TAAGCTAATCTAATCTTAGG
Found at i:3226529 original size:35 final size:35
Alignment explanation
Indices: 3226474--3226601 Score: 184
Period size: 35 Copynumber: 3.7 Consensus size: 35
3226464 TATTATATAG
* * *
3226474 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAATAACTAGAACAAGTGAAGTGTTACTTTACGC
* * *
3226509 ATAATAACTAGAACAAGTGAAGTGCTACTTTACGT
1 AGAATAACTAGAACAAGTGAAGTGTTACTTTACGC
3226544 AGAATAACTAGAACAAGTGAAGTGTTACTTTACGC
1 AGAATAACTAGAACAAGTGAAGTGTTACTTTACGC
* *
3226579 AGAATAATTAAAACAAGTGAAGT
1 AGAATAACTAGAACAAGTGAAGT
3226602 ACTATTTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 82 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (35 bp):
AGAATAACTAGAACAAGTGAAGTGTTACTTTACGC
Found at i:3226623 original size:35 final size:35
Alignment explanation
Indices: 3226485--3226642 Score: 140
Period size: 35 Copynumber: 4.5 Consensus size: 35
3226475 GAACAACCAG
** * * * *
3226485 AACAAGTGAAGTGTTACTTCACGCATAATAACTAG
1 AACAAGTGAAGTACTACTTTACGCAGAATAATTAA
* * * *
3226520 AACAAGTGAAGTGCTACTTTACGTAGAATAACTAG
1 AACAAGTGAAGTACTACTTTACGCAGAATAATTAA
**
3226555 AACAAGTGAAGTGTTACTTTACGCAGAATAATTAA
1 AACAAGTGAAGTACTACTTTACGCAGAATAATTAA
* *
3226590 AACAAGTGAAGTACTA-TTTAAAGCAGAACAATTAGA
1 AACAAGTGAAGTACTACTTT-ACGCAGAATAATTA-A
* *
3226626 AA-AAGTAAAGTATTACT
1 AACAAGTGAAGTACTACT
3226643 CCATATAGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
34 3 0.03
35 99 0.93
36 4 0.04
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (35 bp):
AACAAGTGAAGTACTACTTTACGCAGAATAATTAA
Found at i:3226626 original size:70 final size:70
Alignment explanation
Indices: 3226474--3226666 Score: 208
Period size: 70 Copynumber: 2.8 Consensus size: 70
3226464 TATTATATAG
* * * *
3226474 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGCATAATAACTAGAACAAGTGAAGTGCTACTT
1 AGAACAACTAGAACAAGTGAAGTGTTACTTCACGCAGAATAACTAAAACAAGTGAAGTACTACTT
* *
3226539 TACGT
66 TAAGC
* * *
3226544 AGAATAACTAGAACAAGTGAAGTGTTACTTTACGCAGAATAATTAAAACAAGTGAAGTACTA-TT
1 AGAACAACTAGAACAAGTGAAGTGTTACTTCACGCAGAATAACTAAAACAAGTGAAGTACTACTT
3226608 TAAAGC
66 T-AAGC
* * * * * *** *
3226614 AGAACAATTAGAAAAAGTAAAGTATTACTCCATATAGAATAACTAATACAAGT
1 AGAACAACTAGAACAAGTGAAGTGTTACTTCACGCAGAATAACTAAAACAAGT
3226667 AGAACAACCA
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
69 3 0.03
70 98 0.97
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (70 bp):
AGAACAACTAGAACAAGTGAAGTGTTACTTCACGCAGAATAACTAAAACAAGTGAAGTACTACTT
TAAGC
Found at i:3226910 original size:29 final size:29
Alignment explanation
Indices: 3226886--3226941 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3226876 CTTATTCATG
3226886 TACAGCTTATTCTCTTGTACCTATTCTCA
1 TACAGCTTATTCTCTTGTACCTATTCTCA
*
3226915 TACAGCTTCTTCTCTTGTACCTATTCT
1 TACAGCTTATTCTCTTGTACCTATTCT
3226942 TGTTCACCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.07, T:0.46
Consensus pattern (29 bp):
TACAGCTTATTCTCTTGTACCTATTCTCA
Found at i:3227187 original size:13 final size:13
Alignment explanation
Indices: 3227169--3227193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3227159 ACTTGAGAGC
3227169 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
3227182 TTCTCTCTCTAA
1 TTCTCTCTCTAA
3227194 TTATCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:3227259 original size:22 final size:21
Alignment explanation
Indices: 3227233--3227275 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3227223 TCTTTTCTTA
3227233 TTGTCTTCCACCCGTCACAGC
1 TTGTCTTCCACCCGTCACAGC
*
3227254 NTTGTCTTCCACCTGTCACAGC
1 -TTGTCTTCCACCCGTCACAGC
3227276 ACTTAGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.40, G:0.14, T:0.30
Consensus pattern (21 bp):
TTGTCTTCCACCCGTCACAGC
Found at i:3231340 original size:2 final size:2
Alignment explanation
Indices: 3231335--3231363 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3231325 CAGATATATA
3231335 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3231364 ATATGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3241055 original size:16 final size:17
Alignment explanation
Indices: 3241034--3241066 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3241024 AATTAACAGA
*
3241034 ACAAAA-TATAAATTTT
1 ACAAAATTACAAATTTT
3241050 ACAAAATTACAAATTTT
1 ACAAAATTACAAATTTT
3241067 GATGGTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTACAAATTTT
Found at i:3243754 original size:26 final size:26
Alignment explanation
Indices: 3243725--3243777 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3243715 ATCTTCACGA
*
3243725 TGAATATTCTAGTCCAGATAATGTTT
1 TGAATATTCTAGTCCAGAAAATGTTT
3243751 TGAATATTCTAGTCCAGAAAATGTTT
1 TGAATATTCTAGTCCAGAAAATGTTT
3243777 T
1 T
3243778 TGCAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (26 bp):
TGAATATTCTAGTCCAGAAAATGTTT
Found at i:3251477 original size:15 final size:15
Alignment explanation
Indices: 3251457--3251485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3251447 ACTGTATTTG
3251457 CAAAGGTTGGTGCCA
1 CAAAGGTTGGTGCCA
3251472 CAAAGGTTGGTGCC
1 CAAAGGTTGGTGCC
3251486 CTAGAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (15 bp):
CAAAGGTTGGTGCCA
Found at i:3253760 original size:2 final size:2
Alignment explanation
Indices: 3253706--3253748 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3253696 CTATAGAAGA
*
3253706 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3253748 A
1 A
3253749 AAGAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3255786 original size:16 final size:16
Alignment explanation
Indices: 3255765--3255796 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3255755 TGAACTTAAA
*
3255765 GTTTATTCTCTTGATC
1 GTTTATTCCCTTGATC
3255781 GTTTATTCCCTTGATC
1 GTTTATTCCCTTGATC
3255797 AATTATGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (16 bp):
GTTTATTCCCTTGATC
Found at i:3257545 original size:18 final size:18
Alignment explanation
Indices: 3257524--3257566 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3257514 TCACCACCGC
3257524 CACCACCTTCTTTCTTCT
1 CACCACCTTCTTTCTTCT
* *
3257542 CACCGCCTTCTTTTTTCT
1 CACCACCTTCTTTCTTCT
*
3257560 CTCCACC
1 CACCACC
3257567 GCCTTCCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.09, C:0.47, G:0.02, T:0.42
Consensus pattern (18 bp):
CACCACCTTCTTTCTTCT
Found at i:3257566 original size:21 final size:21
Alignment explanation
Indices: 3257529--3257602 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
3257519 ACCGCCACCA
3257529 CCTTCTT-TCTTCTCACCGCCTT
1 CCTTCTTCTC-TC-CACCGCCTT
* *
3257551 CTTTTTTCTCTCCACCGCCTT
1 CCTTCTTCTCTCCACCGCCTT
*
3257572 CCTTCTTCTCTCCGCCGCCTT
1 CCTTCTTCTCTCCACCGCCTT
3257593 CCTTCTTCTC
1 CCTTCTTCTC
3257603 GCCGCCGGCG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 37 0.80
22 7 0.15
23 2 0.04
ACGTcount: A:0.03, C:0.47, G:0.05, T:0.45
Consensus pattern (21 bp):
CCTTCTTCTCTCCACCGCCTT
Found at i:3257607 original size:21 final size:21
Alignment explanation
Indices: 3257544--3257609 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3257534 TTTCTTCTCA
* * *
3257544 CCGCCTTCTTTTTTCTCTCCA
1 CCGCCTTCCTTCTTCTCTCCG
3257565 CCGCCTTCCTTCTTCTCTCCG
1 CCGCCTTCCTTCTTCTCTCCG
*
3257586 CCGCCTTCCTTCTTCTCGCCG
1 CCGCCTTCCTTCTTCTCTCCG
3257607 CCG
1 CCG
3257610 GCGGCATCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.02, C:0.50, G:0.11, T:0.38
Consensus pattern (21 bp):
CCGCCTTCCTTCTTCTCTCCG
Found at i:3257656 original size:21 final size:21
Alignment explanation
Indices: 3257630--3257677 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
3257620 CTTTTCCTTT
3257630 GTCTTTGTTCTCACCTCCGGC
1 GTCTTTGTTCTCACCTCCGGC
*
3257651 GTCTTTTTTCTCACCTCCGGC
1 GTCTTTGTTCTCACCTCCGGC
3257672 GTCTTT
1 GTCTTT
3257678 CTTAGGGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.35, G:0.17, T:0.44
Consensus pattern (21 bp):
GTCTTTGTTCTCACCTCCGGC
Found at i:3261357 original size:28 final size:28
Alignment explanation
Indices: 3261326--3261414 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
3261316 AACAACAACA
3261326 TTTTAAATATTAAAGTGTAACAA-AATAT
1 TTTTAAATA-TAAAGTGTAACAATAATAT
* * *
3261354 TTTTGAATATGACGTGTAACAATAATATT
1 TTTTAAATATAAAGTGTAACAATAATA-T
* * * * *
3261383 TTTTTAATATGATGTATAAGAATAATAT
1 TTTTAAATATAAAGTGTAACAATAATAT
3261411 TTTT
1 TTTT
3261415 TTTTTCAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 11 0.21
28 17 0.33
29 24 0.46
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (28 bp):
TTTTAAATATAAAGTGTAACAATAATAT
Found at i:3261406 original size:29 final size:29
Alignment explanation
Indices: 3261343--3261416 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
3261333 TATTAAAGTG
* *
3261343 TAACAA-AATA-TTTTTGAATATGACGTG
1 TAACAATAATATTTTTTTAATATGACGTA
*
3261370 TAACAATAATATTTTTTTAATATGATGTA
1 TAACAATAATATTTTTTTAATATGACGTA
*
3261399 TAAGAATAATATTTTTTT
1 TAACAATAATATTTTTTT
3261417 TTTCAATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 6 0.15
28 4 0.10
29 31 0.76
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (29 bp):
TAACAATAATATTTTTTTAATATGACGTA
Found at i:3261464 original size:45 final size:44
Alignment explanation
Indices: 3261415--3261524 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
3261405 TAATATTTTT
* * * * *
3261415 TTTTTCAATATGACGTGTAATAACCTAATCATGATGTGTCATATG
1 TTTTT-AATATGACGTGTAATAACCTAACCATAACGTATCACATG
* * * *
3261460 TTTTTGTACATGACGTATAATAATCTAACCATAACGTATCACATG
1 TTTTT-AATATGACGTGTAATAACCTAACCATAACGTATCACATG
3261505 TTTTTATATATGACGTGTAA
1 TTTTTA-ATATGACGTGTAA
3261525 CAATTGAATT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (44 bp):
TTTTTAATATGACGTGTAATAACCTAACCATAACGTATCACATG
Found at i:3261605 original size:45 final size:45
Alignment explanation
Indices: 3261498--3261584 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3261488 CCATAACGTA
*
3261498 TCACATGTTTTTATATATGACGTGTAACAATTGAATTATGACGAG
1 TCACATGTTTTTATATATGACATGTAACAATTGAATTATGACGAG
* * *
3261543 TCACATATTTTTATATATGGCATGTAACAATTTAATTATGAC
1 TCACATGTTTTTATATATGACATGTAACAATTGAATTATGAC
3261585 ATGTTATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (45 bp):
TCACATGTTTTTATATATGACATGTAACAATTGAATTATGACGAG
Found at i:3266740 original size:2 final size:2
Alignment explanation
Indices: 3266733--3266764 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3266723 TTCGACAGAA
3266733 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3266765 ACACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3280870 original size:74 final size:74
Alignment explanation
Indices: 3280744--3280898 Score: 292
Period size: 74 Copynumber: 2.1 Consensus size: 74
3280734 TCTTGGATGG
* *
3280744 TTTTCTCCTCATTTATGATCGTTTAAAACCCTTTAAATACTTAGAGGACAGTTTCTAACCCTTAC
1 TTTTGTCCTCATTTATAATCGTTTAAAACCCTTTAAATACTTAGAGGACAGTTTCTAACCCTTAC
3280809 TAGCCATTA
66 TAGCCATTA
3280818 TTTTGTCCTCATTTATAATCGTTTAAAACCCTTTAAATACTTAGAGGACAGTTTCTAACCCTTAC
1 TTTTGTCCTCATTTATAATCGTTTAAAACCCTTTAAATACTTAGAGGACAGTTTCTAACCCTTAC
3280883 TAGCCATTA
66 TAGCCATTA
3280892 TTTTGTC
1 TTTTGTC
3280899 TTCTAGTGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTTGTCCTCATTTATAATCGTTTAAAACCCTTTAAATACTTAGAGGACAGTTTCTAACCCTTAC
TAGCCATTA
Found at i:3295282 original size:28 final size:28
Alignment explanation
Indices: 3295251--3295306 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3295241 CTCTGAAAGA
3295251 GAGTTCTGCAACTTAGATTAGCTGATGG
1 GAGTTCTGCAACTTAGATTAGCTGATGG
*
3295279 GAGTTCTGCAACTTAGATTAGTTGATGG
1 GAGTTCTGCAACTTAGATTAGCTGATGG
3295307 CTGACTGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
GAGTTCTGCAACTTAGATTAGCTGATGG
Found at i:3317088 original size:18 final size:17
Alignment explanation
Indices: 3317055--3317113 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
3317045 TGTCTCTTAT
3317055 ACAAATATAACTTTTGA
1 ACAAATATAACTTTTGA
*
3317072 ACAAATATATCCTTTTGA
1 ACAAATATA-ACTTTTGA
* *
3317090 AAAAATATAATTATTTGA
1 ACAAATATAACT-TTTGA
3317108 ACAAAT
1 ACAAAT
3317114 TCGTATTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 10 0.29
18 25 0.71
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (17 bp):
ACAAATATAACTTTTGA
Found at i:3320518 original size:31 final size:30
Alignment explanation
Indices: 3320480--3320562 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
3320470 TGGAAGGCAC
* *
3320480 CAGGGGAGCATCGATATGGTGC-TCCTCAAGT
1 CAGGGGAGCATCGATCTGGTGCTTCCT--AGG
* *
3320511 CAGGGGAGCA-CAATCTAGTGCTTCCTAGG
1 CAGGGGAGCATCGATCTGGTGCTTCCTAGG
3320540 CTAGGGGAGCATCGATCTGGTGC
1 C-AGGGGAGCATCGATCTGGTGC
3320563 CTCTTTAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.07
30 17 0.40
31 23 0.53
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.22
Consensus pattern (30 bp):
CAGGGGAGCATCGATCTGGTGCTTCCTAGG
Found at i:3324005 original size:29 final size:30
Alignment explanation
Indices: 3323963--3324032 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
3323953 AATTAAAGAC
* * *
3323963 CAAACAAAATAAAG-AAAAAAACACCTAAA
1 CAAACAAAAAAAAGAAAAAAAAAAACTAAA
3323992 CAAACAAAAAAAAGCTAAAAAAAAAAACTAAA
1 CAAACAAAAAAAAG--AAAAAAAAAAACTAAA
3324024 -AAACAAAAA
1 CAAACAAAAA
3324033 GAGTTGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.37
31 9 0.26
32 13 0.37
ACGTcount: A:0.77, C:0.14, G:0.03, T:0.06
Consensus pattern (30 bp):
CAAACAAAAAAAAGAAAAAAAAAAACTAAA
Found at i:3324009 original size:19 final size:18
Alignment explanation
Indices: 3323977--3324018 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
3323967 CAAAATAAAG
3323977 AAAAAAACACCTAAACAAA
1 AAAAAAACACCTAAA-AAA
*
3323996 CAAAAAAA-AGCTAAAAAA
1 -AAAAAAACACCTAAAAAA
3324014 AAAAA
1 AAAAA
3324019 CTAAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 6 0.29
20 7 0.33
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAAAAACACCTAAAAAA
Found at i:3324015 original size:13 final size:13
Alignment explanation
Indices: 3323997--3324032 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
3323987 CTAAACAAAC
*
3323997 AAAAAAAAGCTAA
1 AAAAAAAAACTAA
3324010 AAAAAAAAACTAA
1 AAAAAAAAACTAA
3324023 AAAACAAAAA
1 AAAA-AAAAA
3324033 GAGTTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.83, C:0.08, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAAAACTAA
Found at i:3324016 original size:14 final size:14
Alignment explanation
Indices: 3323997--3324033 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3323987 CTAAACAAAC
3323997 AAAAAAAAGCTAAA
1 AAAAAAAAGCTAAA
3324011 AAAAAAAA-CTAAA
1 AAAAAAAAGCTAAA
3324024 AAACAAAAAG
1 AAA-AAAAAG
3324034 AGTTGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.81, C:0.08, G:0.05, T:0.05
Consensus pattern (14 bp):
AAAAAAAAGCTAAA
Found at i:3325388 original size:18 final size:18
Alignment explanation
Indices: 3325365--3325446 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 18
3325355 AATTATATTA
*
3325365 TTTATTATTATTTTTCAT
1 TTTATTATTATTTTTTAT
**
3325383 TTTATTATTA-TCATTAT
1 TTTATTATTATTTTTTAT
*
3325400 TTT-TTATTTTTATTTTAT
1 TTTATTATTATT-TTTTAT
3325418 TTTA-TA-TATTTTTTAT
1 TTTATTATTATTTTTTAT
3325434 TTT-TTATT-TTTTT
1 TTTATTATTATTTTT
3325447 ATCTAAAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
16 21 0.40
17 12 0.23
18 19 0.37
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTATTATTTTTTAT
Found at i:3325390 original size:30 final size:29
Alignment explanation
Indices: 3325356--3325448 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
3325346 TTTTCTCCCA
3325356 ATTATATTATTTATTATTATTTTTCATTTT
1 ATTATATTATTTATTATTATTTTT-ATTTT
* *
3325386 ATTATTATCA-TTATTTTTTATTTTTATTTT
1 ATTA-TATTATTTA-TTATTATTTTTATTTT
* *
3325416 ATTTTATATATTTTTTA-T-TTTTTATTTT
1 ATTATAT-TATTTATTATTATTTTTATTTT
*
3325444 TTTAT
1 ATTAT
3325449 CTAAAAGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 13 0.25
29 4 0.08
30 18 0.35
31 16 0.31
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (29 bp):
ATTATATTATTTATTATTATTTTTATTTT
Found at i:3325398 original size:24 final size:25
Alignment explanation
Indices: 3325360--3325417 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
3325350 CTCCCAATTA
*
3325360 TATTATTTATTATTATTTTTCA-TTT
1 TATTA-TTATCATTATTTTTCATTTT
*
3325385 TATTATTATCATTATTTTTTATTTT
1 TATTATTATCATTATTTTTCATTTT
3325410 TATT-TTAT
1 TATTATTAT
3325418 TTTATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTATTATCATTATTTTTCATTTT
Found at i:3325407 original size:34 final size:33
Alignment explanation
Indices: 3325356--3325446 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 33
3325346 TTTTCTCCCA
*
3325356 ATTATATTATTTATTATTATTTTTCATTTTAT-T
1 ATTATATTATTTTTTATT-TTTTTCATTTTATAT
*
3325389 ATTATCATTATTTTTTATTTTTATTTTATTTTATAT
1 ATTAT-ATTATTTTTTA-TTTT-TTTCATTTTATAT
*
3325425 ATT-TTTTATTTTTTATTTTTTT
1 ATTATATTATTTTTTATTTTTTT
3325447 ATCTAAAAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
32 3 0.06
33 9 0.18
34 22 0.43
35 13 0.25
36 4 0.08
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (33 bp):
ATTATATTATTTTTTATTTTTTTCATTTTATAT
Found at i:3325443 original size:7 final size:7
Alignment explanation
Indices: 3325372--3325445 Score: 64
Period size: 7 Copynumber: 10.3 Consensus size: 7
3325362 TTATTTATTA
3325372 TTATTTT
1 TTATTTT
*
3325379 TCATTTT
1 TTATTTT
*
3325386 ATTATTATCA
1 -TTATT-T-T
3325396 TTATTTT
1 TTATTTT
3325403 TTA-TTT
1 TTATTTT
3325409 TTA--TT
1 TTATTTT
3325414 TTATTTT
1 TTATTTT
3325421 ATATATTTT
1 -T-TATTTT
3325430 TTATTTT
1 TTATTTT
3325437 TTATTTT
1 TTATTTT
3325444 TT
1 TT
3325446 TATCTAAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.09
6 6 0.11
7 26 0.46
8 7 0.12
9 12 0.21
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (7 bp):
TTATTTT
Found at i:3325505 original size:3 final size:3
Alignment explanation
Indices: 3325492--3325558 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
3325482 TGCATCATGA
* * *
3325492 ATT ACT ATT ATT ATT ATT ATT -TT TTT ATT -TT TTT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3325537 ATC ATT ATT -TT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
3325559 TTTTTGATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 10 0.19
3 44 0.81
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (3 bp):
ATT
Found at i:3325529 original size:16 final size:16
Alignment explanation
Indices: 3325499--3325569 Score: 67
Period size: 16 Copynumber: 4.4 Consensus size: 16
3325489 TGAATTACTA
3325499 TTATTATTATTATTTTT
1 TTATT-TTATTATTTTT
* *
3325516 TTATTTTTTTATTTTA
1 TTATTTTATTATTTTT
*
3325532 TTATTATCATTA-TTTT
1 TTATT-TTATTATTTTT
3325548 TTA--TTATTATTTTT
1 TTATTTTATTATTTTT
3325562 TTGATTTT
1 TT-ATTTT
3325570 TAATATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 1 0.02
16 20 0.47
17 11 0.26
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (16 bp):
TTATTTTATTATTTTT
Found at i:3325532 original size:13 final size:12
Alignment explanation
Indices: 3325499--3325562 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
3325489 TGAATTACTA
*
3325499 TTATTATTATTAT
1 TTATT-TTATTTT
3325512 TT-TTTTATTTTT
1 TTATTTTA-TTTT
*
3325524 TTATTTTA-TTA
1 TTATTTTATTTT
*
3325535 TTATCATTATTTT
1 TTAT-TTTATTTT
3325548 TTATTATTATTTT
1 TTATT-TTATTTT
3325561 TT
1 TT
3325563 TGATTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 9 0.22
12 10 0.24
13 22 0.54
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:3325538 original size:19 final size:19
Alignment explanation
Indices: 3325516--3325569 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3325506 TATTATTTTT
3325516 TTATTTTTTTATTTTATTA
1 TTATTTTTTTATTTTATTA
* *
3325535 TTATCATTATT-TTTTATTA
1 TTAT-TTTTTTATTTTATTA
3325554 TTATTTTTTTGATTTT
1 TTATTTTTTT-ATTTT
3325570 TAATATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTTTATTTTATTA
Found at i:3325544 original size:39 final size:39
Alignment explanation
Indices: 3325492--3325569 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
3325482 TGCATCATGA
* *
3325492 ATTACTATTATTATTATTATT-TTTTTATTTTTTT-ATTTT
1 ATTACTATCATTATT-TT-TTATTATTATTTTTTTGATTTT
*
3325531 ATTATTATCATTATTTTTTATTATTATTTTTTTGATTTT
1 ATTACTATCATTATTTTTTATTATTATTTTTTTGATTTT
3325570 TAATATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 2 0.06
38 14 0.41
39 18 0.53
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (39 bp):
ATTACTATCATTATTTTTTATTATTATTTTTTTGATTTT
Found at i:3325558 original size:30 final size:32
Alignment explanation
Indices: 3325497--3325560 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
3325487 CATGAATTAC
* *
3325497 TATTATTATTATTATTTTTTTATTTTTTTATTT
1 TATTATTATCATTATTTTTTTA-TTTATTATTT
3325530 TATTATTATCATTA-TTTTTTA-TTATTATTT
1 TATTATTATCATTATTTTTTTATTTATTATTT
3325560 T
1 T
3325561 TTTGATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.31
32 7 0.24
33 13 0.45
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (32 bp):
TATTATTATCATTATTTTTTTATTTATTATTT
Found at i:3326624 original size:10 final size:10
Alignment explanation
Indices: 3326605--3326647 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
3326595 CCATCCCGAT
*
3326605 TTTTTTTTTA
1 TTTTTATTTA
3326615 TTTTTATTTA
1 TTTTTATTTA
3326625 -TTTTATTTTA
1 TTTTTA-TTTA
*
3326635 TTTATATTTA
1 TTTTTATTTA
3326645 TTT
1 TTT
3326648 ATTTAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 5 0.17
10 20 0.69
11 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:3326633 original size:20 final size:20
Alignment explanation
Indices: 3326605--3326651 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3326595 CCATCCCGAT
* *
3326605 TTTTTTTTTATTTTTATTTA
1 TTTTATTTTATTTATATTTA
3326625 TTTTATTTTATTTATATTTA
1 TTTTATTTTATTTATATTTA
3326645 -TTTATTT
1 TTTTATTT
3326652 AAGTGTCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTATTTTATTTATATTTA
Found at i:3326635 original size:14 final size:14
Alignment explanation
Indices: 3326610--3326652 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
3326600 CCGATTTTTT
3326610 TTTTATTTTTATTTA
1 TTTTA-TTTTATTTA
3326625 TTTTATTTTATTTA
1 TTTTATTTTATTTA
3326639 TATTTA-TTTATTTA
1 T-TTTATTTTATTTA
3326653 AGTGTCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:3326638 original size:24 final size:24
Alignment explanation
Indices: 3326606--3326651 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3326596 CATCCCGATT
* *
3326606 TTTTTTTTATTTTTATTTATTTTA
1 TTTTATTTATATTTATTTATTTTA
3326630 TTTTATTTATATTTATTTATTT
1 TTTTATTTATATTTATTTATTT
3326652 AAGTGTCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTATTTATATTTATTTATTTTA
Found at i:3326648 original size:10 final size:10
Alignment explanation
Indices: 3326611--3326649 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3326601 CGATTTTTTT
*
3326611 TTTATTTTTA
1 TTTATTTATA
3326621 TTTATTT-TA
1 TTTATTTATA
3326630 TTTTATTTATA
1 -TTTATTTATA
3326641 TTTATTTAT
1 TTTATTTAT
3326650 TTAAGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTATA
Found at i:3328124 original size:17 final size:18
Alignment explanation
Indices: 3328083--3328125 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3328073 GAATTTTCAC
3328083 AAAAAATTTATTTTTGTT
1 AAAAAATTTATTTTTGTT
*
3328101 AATAAATTT-TTTCTT-TT
1 AAAAAATTTATTT-TTGTT
3328118 AAAAAATT
1 AAAAAATT
3328126 GTCAATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
AAAAAATTTATTTTTGTT
Found at i:3328978 original size:22 final size:23
Alignment explanation
Indices: 3328950--3329008 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
3328940 GTGACATGAT
3328950 AATATGTACAT-ATTATT-TCTAA
1 AATATGTA-ATAATTATTATCTAA
*
3328972 AATATGTATTAATTATTATCTAA
1 AATATGTAATAATTATTATCTAA
* *
3328995 AATACGTATTAATT
1 AATATGTAATAATT
3329009 TTAACTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 14 0.42
23 18 0.55
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (23 bp):
AATATGTAATAATTATTATCTAA
Found at i:3328997 original size:23 final size:22
Alignment explanation
Indices: 3328961--3329008 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
3328951 ATATGTACAT
*
3328961 ATTATTTCTAAAATATGTATTA
1 ATTATTTCTAAAATACGTATTA
3328983 ATTATTATCTAAAATACGTATTA
1 ATTATT-TCTAAAATACGTATTA
3329006 ATT
1 ATT
3329009 TTAACTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
ATTATTTCTAAAATACGTATTA
Found at i:3343964 original size:80 final size:80
Alignment explanation
Indices: 3343861--3344036 Score: 311
Period size: 80 Copynumber: 2.2 Consensus size: 80
3343851 TGTTATATAT
3343861 ATATATATATTATATTTACAAGTATCTAAATATATTTATACTATAAATATTTTCTTCTTTTTAAA
1 ATATATATATTATATTTACAAGTATCTAAATATATTTATACTATAAATATTTTCTTCTTTTTAAA
3343926 CATTTCTTTTTTTAC
66 CATTTCTTTTTTTAC
3343941 NATATATATATTATA-TTACAAGTATCTAAATATATTTATACTATAAATATTTTCTTCTTTTTAA
1 -ATATATATATTATATTTACAAGTATCTAAATATATTTATACTATAAATATTTTCTTCTTTTTAA
3344005 ACATTTCTTTTTTTAC
65 ACATTTCTTTTTTTAC
* *
3344021 -TATTTATACTATATTT
1 ATATATATATTATATTT
3344037 TAAAATATTA
Statistics
Matches: 92, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
78 11 0.12
79 2 0.02
80 65 0.71
81 14 0.15
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (80 bp):
ATATATATATTATATTTACAAGTATCTAAATATATTTATACTATAAATATTTTCTTCTTTTTAAA
CATTTCTTTTTTTAC
Found at i:3344022 original size:39 final size:39
Alignment explanation
Indices: 3343899--3344023 Score: 96
Period size: 39 Copynumber: 3.2 Consensus size: 39
3343889 AATATATTTA
3343899 TACTATAAATATTTTCTTCTTTTTAAACATTTCTTTTTT
1 TACTATAAATATTTTCTTCTTTTTAAACATTTCTTTTTT
* * * * * * * *
3343938 TACNATATATATATTATATTACAAGTATCT-AA-A--TATATTTA
1 TAC--TATAAATATTTTCTT-C---TTTTTAAACATTTCTTTTTT
3343979 TACTATAAATATTTTCTTCTTTTTAAACATTTCTTTTTT
1 TACTATAAATATTTTCTTCTTTTTAAACATTTCTTTTTT
3344018 TACTAT
1 TACTAT
3344024 TTATACTATA
Statistics
Matches: 60, Mismatches: 16, Indels: 20
0.62 0.17 0.21
Matches are distributed among these distances:
35 3 0.05
36 2 0.03
37 1 0.02
38 1 0.02
39 26 0.43
41 20 0.33
42 1 0.02
43 1 0.02
44 2 0.03
45 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.01, T:0.55
Consensus pattern (39 bp):
TACTATAAATATTTTCTTCTTTTTAAACATTTCTTTTTT
Found at i:3344420 original size:4 final size:4
Alignment explanation
Indices: 3344391--3344448 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
3344381 TCCCCCCTTA
* *
3344391 TTCT CTCT TTC- TT-T TTCT TT-T CTCT TTC- TTCT TTCT TTC- -TCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
3344433 TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT
3344449 CTCCTAGCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 2 0.05
3 9 0.20
4 33 0.75
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:3344423 original size:79 final size:78
Alignment explanation
Indices: 3344317--3344468 Score: 211
Period size: 79 Copynumber: 1.9 Consensus size: 78
3344307 CGTTTGCCTT
* *
3344317 TCTTTCTCTTTTTTTTCTTTTTGTTCTTTTTCTTTCTC-TCTTTCTTTCTTTCTCT-CTCAACCG
1 TCTTTCTCTTTTTTTTCTCTTTCTTC--TTTCTTTCTCTTCTTTCTTTCTTTCTCTCCT-AACCG
3344380 TTCCCCCCTTATTCTC
63 TTCCCCCCTTATTCTC
*
3344396 TCTTTCT-TTTTCTTTTCTCTTTCTTCTTTCTTTCTCTTTCTTTCTTTCTTTCTCTCCTAGCCGT
1 TCTTTCTCTTTT-TTTTCTCTTTCTTCTTTCTTTCTC-TTCTTTCTTTCTTTCTCTCCTAACCGT
3344460 TCCCCCCTT
64 TCCCCCCTT
3344469 TCTTCTCGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
77 10 0.15
78 4 0.06
79 50 0.76
80 2 0.03
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (78 bp):
TCTTTCTCTTTTTTTTCTCTTTCTTCTTTCTTTCTCTTCTTTCTTTCTTTCTCTCCTAACCGTTC
CCCCCTTATTCTC
Found at i:3344427 original size:18 final size:17
Alignment explanation
Indices: 3344394--3344450 Score: 89
Period size: 17 Copynumber: 3.3 Consensus size: 17
3344384 CCCCTTATTC
3344394 TCTCTTTCTT-TTTCTTT
1 TCTCTTTCTTCTTTC-TT
3344411 TCTCTTTCTTCTTTCTT
1 TCTCTTTCTTCTTTCTT
3344428 TCTCTTTCTTTCTTTCTT
1 TCTCTTTC-TTCTTTCTT
3344446 TCTCT
1 TCTCT
3344451 CCTAGCCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 20 0.53
18 18 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTCTTTCTTCTTTCTT
Found at i:3344427 original size:83 final size:79
Alignment explanation
Indices: 3344314--3344468 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 79
3344304 TGCCGTTTGC
* *
3344314 CTTTCTTTCTCTTTTTTTTCTTTTTGTTCTTTTTCTTTCTCTCTTTCTTTCTTTCTCTCTCAACC
1 CTTTCTTTCTCTTTTTTTTCTTTCTGTTCTTTCTCTTTCTCTCTTTCTTTC--TCTC-CT-AACC
3344379 GTTCCCCCCTTATTCTCT
62 GTTCCCCCCTTATTCTCT
* * *
3344397 CTTTCTTTTTCTTTTCTCTTTC-TTCT-TTCTTTCTCTTTCTTTCTTTCTTTCTCTCCTAGCCGT
1 CTTTCTTTCTCTTTT-T-TTTCTTTCTGTTCTTTCTCTTTCTCTCTTTCTTTCTCTCCTAACCGT
3344460 TCCCCCCTT
64 TCCCCCCTT
3344469 TCTTCTCGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
79 14 0.22
80 2 0.03
81 4 0.06
83 37 0.57
84 4 0.06
85 4 0.06
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (79 bp):
CTTTCTTTCTCTTTTTTTTCTTTCTGTTCTTTCTCTTTCTCTCTTTCTTTCTCTCCTAACCGTTC
CCCCCTTATTCTCT
Found at i:3345004 original size:32 final size:30
Alignment explanation
Indices: 3344959--3345017 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
3344949 TTCTTCTTTT
3344959 TTTATTTTATTTTATTTTTTATTCTTATTAGA
1 TTTATTTTATTTTA-TTTTT-TTCTTATTAGA
3344991 TTTATTTGT-TTTTATTTTTTTCTTATT
1 TTTATTT-TATTTTATTTTTTTCTTATT
3345018 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 8 0.31
31 5 0.19
32 12 0.46
33 1 0.04
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTATTTTATTTTATTTTTTTCTTATTAGA
Found at i:3345675 original size:74 final size:75
Alignment explanation
Indices: 3345519--3345678 Score: 223
Period size: 75 Copynumber: 2.1 Consensus size: 75
3345509 TGAATTTTTT
** *
3345519 AAATTAAAATACTATCCTTAATTTTAAAAATTTCTTTTTAAGTAGGAAACAATTTCCTATTTTAT
1 AAATTAAAATACTATCCTTAATTTTAAAAATGGCTTTTAAAGTAGGAAACAATTTCCTATTTTAT
3345584 GAATCACCCA
66 GAATCACCCA
* ** * *
3345594 AAATTAAAATTCTATCCTTAATTTTAGGAATGGCTTTTAAAGTAGGAAACAATTT-TTTTTTTAT
1 AAATTAAAATACTATCCTTAATTTTAAAAATGGCTTTTAAAGTAGGAAACAATTTCCTATTTTAT
* *
3345658 GGATCACTCA
66 GAATCACCCA
3345668 AAATTAAAATA
1 AAATTAAAATA
3345679 GATGGTATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 25 0.34
75 49 0.66
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (75 bp):
AAATTAAAATACTATCCTTAATTTTAAAAATGGCTTTTAAAGTAGGAAACAATTTCCTATTTTAT
GAATCACCCA
Found at i:3361754 original size:7 final size:7
Alignment explanation
Indices: 3361742--3361825 Score: 54
Period size: 7 Copynumber: 12.1 Consensus size: 7
3361732 CTTCCAATTA
3361742 TATTATT
1 TATTATT
3361749 TATTA-T
1 TATTATT
3361755 TATTATT
1 TATTATT
3361762 TATTTATT
1 TA-TTATT
3361770 T-TTCATTT
1 TATT-A-TT
3361778 TATTA-T
1 TATTATT
*
3361784 TATCATT
1 TATTATT
3361791 TAATT-TT
1 T-ATTATT
3361798 TA-TATT
1 TATTATT
*
3361804 T-TATATA
1 TAT-TATT
*
3361811 TATTTTT
1 TATTATT
3361818 TATTATT
1 TATTATT
3361825 T
1 T
3361826 TTTTATCTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
5 1 0.02
6 17 0.28
7 27 0.45
8 13 0.22
9 2 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTATT
Found at i:3361779 original size:29 final size:27
Alignment explanation
Indices: 3361747--3361827 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
3361737 AATTATATTA
3361747 TTTATTATTATTATTTATTTATTTTTCAT
1 TTTATTATTATTATTTA-TTATTTTT-AT
* *
3361776 TTTATTATTATCATTTAATT-TTTATAT
1 TTTATTATTATTATTT-ATTATTTTTAT
*
3361803 TTTA-TATATATTTTTTATTATTTTT
1 TTTATTAT-TATTATTTATTATTTTT
3361828 TTATCTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.14
27 16 0.36
28 4 0.09
29 17 0.39
30 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTATTATTATTATTTATTATTTTTAT
Found at i:3361798 original size:20 final size:19
Alignment explanation
Indices: 3361775--3361824 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
3361765 TTATTTTTCA
*
3361775 TTTTATTATTATCATTTAAT
1 TTTTATTATTAT-ATATAAT
* *
3361795 TTTTATATTTTATATATATT
1 TTTTAT-TATTATATATAAT
3361815 TTTTATTATT
1 TTTTATTATT
3361825 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 17 0.68
21 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTATTATATATAAT
Found at i:3362421 original size:23 final size:24
Alignment explanation
Indices: 3362379--3362426 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
3362369 TCTTAGCCGG
*
3362379 CGAATCGCTTCGCCTTCCGTTGGC
1 CGAATCGCTTCGCCTTCCGTCGGC
3362403 CGAATC-CTTC-CCTTCCCGTCGGC
1 CGAATCGCTTCGCCTT-CCGTCGGC
3362426 C
1 C
3362427 CCTCTCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.08, C:0.44, G:0.21, T:0.27
Consensus pattern (24 bp):
CGAATCGCTTCGCCTTCCGTCGGC
Found at i:3373455 original size:14 final size:14
Alignment explanation
Indices: 3373409--3373456 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
3373399 AGAGAAAATC
*
3373409 AAAAAAATCAAAAA
1 AAAAAAATTAAAAA
*
3373423 ACAAAAATCATAAACAA
1 AAAAAAAT--TAAA-AA
3373440 AAAAAAATTAAAAA
1 AAAAAAATTAAAAA
3373454 AAA
1 AAA
3373457 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 3 0.11
17 9 0.32
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAATTAAAAA
Found at i:3374752 original size:17 final size:17
Alignment explanation
Indices: 3374730--3374768 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3374720 GAGAATATAG
*
3374730 AAATAATAAAGAATAA-A
1 AAATAAAAAAG-ATAATA
3374747 AAATAAAAAAGATAATA
1 AAATAAAAAAGATAATA
3374764 AAATA
1 AAATA
3374769 TTCTTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAATAAAAAAGATAATA
Found at i:3375008 original size:3 final size:3
Alignment explanation
Indices: 3375000--3375038 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3374990 AAAAATAGAA
3375000 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3375039 TCATGACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3375245 original size:15 final size:15
Alignment explanation
Indices: 3375227--3375337 Score: 65
Period size: 15 Copynumber: 7.5 Consensus size: 15
3375217 AAAATCATTC
3375227 AATAAATAATAAATA
1 AATAAATAATAAATA
* *
3375242 AATAAATAATAGATG
1 AATAAATAATAAATA
* *
3375257 AA-AAAGAAGAATATA
1 AATAAATAATAA-ATA
3375272 AA-AAATAAT-AAT-
1 AATAAATAATAAATA
3375284 AATAAGA-AATAAAATA
1 AATAA-ATAAT-AAATA
* *
3375300 AAGGATATAAT-AATA
1 AA-TAAATAATAAATA
*
3375315 AA-AAATAATAAAGA
1 AATAAATAATAAATA
3375329 AATATAATA
1 AATA-AATA
3375338 TACAAAATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.03
13 13 0.18
14 13 0.18
15 34 0.47
16 7 0.10
17 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (15 bp):
AATAAATAATAAATA
Found at i:3375323 original size:10 final size:10
Alignment explanation
Indices: 3375308--3375363 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 10
3375298 TAAAGGATAT
3375308 AATAATAAAA
1 AATAATAAAA
3375318 AATAATAAAGAA
1 AATAAT-AA-AA
3375330 ATATAATATACAA
1 A-ATAATA-A-AA
3375343 AATAAT-AAA
1 AATAATAAAA
*
3375352 AATAGTAAAA
1 AATAATAAAA
3375362 AA
1 AA
3375364 ATGATGAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 7 0.18
10 12 0.31
11 2 0.05
12 9 0.23
13 9 0.23
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (10 bp):
AATAATAAAA
Found at i:3375344 original size:25 final size:25
Alignment explanation
Indices: 3375269--3375355 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 25
3375259 AAAGAAGAAT
* *
3375269 ATAAAAAATAATAATAATAAGAAATAAA
1 ATAAAGAAT-ATAATAATAA-AAA-ATA
*
3375297 ATAAAGGATATAATAATAAAAAATA
1 ATAAAGAATATAATAATAAAAAATA
*
3375322 ATAAAGAAATATAAT-ATACAAAATA
1 ATAAAG-AATATAATAATAAAAAATA
3375347 ATAAA-AATA
1 ATAAAGAATA
3375356 GTAAAAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 4 0.08
25 22 0.42
26 10 0.19
27 10 0.19
28 7 0.13
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (25 bp):
ATAAAGAATATAATAATAAAAAATA
Found at i:3375497 original size:18 final size:18
Alignment explanation
Indices: 3375467--3375506 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3375457 GATAAGAAAA
*
3375467 AAATATAATAATAATAAT
1 AAATATAATAATAAGAAT
3375485 AAATAATAA-AATAAGAAT
1 AAAT-ATAATAATAAGAAT
3375503 AAAT
1 AAAT
3375507 TTCAATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATATAATAATAAGAAT
Found at i:3381902 original size:21 final size:20
Alignment explanation
Indices: 3381877--3381936 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3381867 AGATGTCTAA
*
3381877 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
3381898 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
3381918 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
3381936 A
1 A
3381937 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:3384139 original size:19 final size:19
Alignment explanation
Indices: 3384115--3384152 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3384105 ACTTCTAAAC
3384115 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
3384134 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
3384153 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:3385780 original size:106 final size:106
Alignment explanation
Indices: 3385607--3385806 Score: 364
Period size: 106 Copynumber: 1.9 Consensus size: 106
3385597 CATACTGATA
*
3385607 TTTAAGCCTATCTCTGTTAAAATAGCCTTCTGCAATATTAAGCCTGTAATAGCTAGTCTTGACAT
1 TTTAAGCCTATCTCTGTCAAAATAGCCTTCTGCAATATTAAGCCTGTAATAGCTAGTCTTGACAT
3385672 TTATCATCTTGCCACACATCATGAGGCTTTCCATATTGAAT
66 TTATCATCTTGCCACACATCATGAGGCTTTCCATATTGAAT
* * *
3385713 TTTAAGCCTATCTCTGTCAAAATAGCCTTTTGCAATATTAAGCCTGTAATAGTTGGTCTTGACAT
1 TTTAAGCCTATCTCTGTCAAAATAGCCTTCTGCAATATTAAGCCTGTAATAGCTAGTCTTGACAT
3385778 TTATCATCTTGCCACACATCATGAGGCTT
66 TTATCATCTTGCCACACATCATGAGGCTT
3385807 AGAAGGTGTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (106 bp):
TTTAAGCCTATCTCTGTCAAAATAGCCTTCTGCAATATTAAGCCTGTAATAGCTAGTCTTGACAT
TTATCATCTTGCCACACATCATGAGGCTTTCCATATTGAAT
Found at i:3386934 original size:22 final size:21
Alignment explanation
Indices: 3386908--3386999 Score: 62
Period size: 22 Copynumber: 4.0 Consensus size: 21
3386898 TCGAGGAGCC
3386908 ACATTTCCTAAATCCTCCGAGT
1 ACATTT-CTAAATCCTCCGAGT
3386930 ACA-TTCTGAAGA-CCTCCGAGCAT
1 ACATTTCT-AA-ATCCTCCGAG--T
*
3386953 ATTATTCTCTTAAATCCTCCGAGT
1 A-CATT-TC-TAAATCCTCCGAGT
* *
3386977 GCATCTTCTAAAACCTCCGAGT
1 ACAT-TTCTAAATCCTCCGAGT
3386999 A
1 A
3387000 ATTAGCGTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
20 2 0.04
21 12 0.22
22 17 0.31
23 6 0.11
24 3 0.05
25 2 0.04
26 12 0.22
27 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.30
Consensus pattern (21 bp):
ACATTTCTAAATCCTCCGAGT
Found at i:3386979 original size:141 final size:142
Alignment explanation
Indices: 3386715--3387106 Score: 572
Period size: 141 Copynumber: 2.8 Consensus size: 142
3386705 ACATTTCAGA
* *
3386715 TAATTAGTGTTAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAAGAGCCACATTTCCTAAAT
1 TAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAAT
* * * *
3386780 CCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCTTTCGGGTGCATCTTCT
66 CCTCCGAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGAGTGCATCTTCT
* *
3386845 AAAACGTTCGAG
131 AAAACCTCCGAG
* * * * **
3386857 TAATTAGTATCAAGATTTTTTAAAATTAGGTTGCCTTA-AATTCGAGGAGCCACATTTCCTAAAT
1 TAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAAT
* *
3386921 CCTCCGAGTACATTCTGAAGACCTCCGAGCATATTATTCTCTTAAATCCTCCGAGTGCATCTTCT
66 CCTCCGAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGAGTGCATCTTCT
3386986 AAAACCTCCGAG
131 AAAACCTCCGAG
* *
3386998 TAATTAGCGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTTGAGGAGCCACATTTCCTAAAT
1 TAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAAT
* * *
3387063 -CTTCTAGATATATTCTGAAGACCTCCGGGCACATTATTCTCTTA
66 CCTCCGAG-TACATTCTGAAGACCTCCGGGCACATTATTCTCTTA
3387107 TAACCTCTAG
Statistics
Matches: 219, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
141 130 0.59
142 89 0.41
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (142 bp):
TAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAAT
CCTCCGAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGAGTGCATCTTCT
AAAACCTCCGAG
Found at i:3387265 original size:11 final size:11
Alignment explanation
Indices: 3387249--3387291 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3387239 TTTAAACGAT
*
3387249 AAAAAAAAATC
1 AAAAAAAAAAC
3387260 AAAAAAAAAAC
1 AAAAAAAAAAC
* **
3387271 CAAAAAAAAGG
1 AAAAAAAAAAC
3387282 AAAAAAAAAA
1 AAAAAAAAAA
3387292 AGCTTTGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:3387266 original size:12 final size:12
Alignment explanation
Indices: 3387249--3387279 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3387239 TTTAAACGAT
*
3387249 AAAAAAAAATCA
1 AAAAAAAAACCA
3387261 AAAAAAAAACCA
1 AAAAAAAAACCA
3387273 AAAAAAA
1 AAAAAAA
3387280 GGAAAAAAAA
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:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAAAAACCA
Found at i:3387275 original size:22 final size:22
Alignment explanation
Indices: 3387250--3387291 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3387240 TTAAACGATA
*
3387250 AAAAAAAATCAAAAAAAAAACC
1 AAAAAAAAGCAAAAAAAAAACC
*
3387272 AAAAAAAAGGAAAAAAAAAA
1 AAAAAAAAGCAAAAAAAAAA
3387292 AGCTTTGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGCAAAAAAAAAACC
Found at i:3387454 original size:14 final size:13
Alignment explanation
Indices: 3387437--3387469 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3387427 GAGAAAATAA
3387437 AAAAATCATAAAAC
1 AAAAATCAT-AAAC
3387451 AAAAATCATAAAC
1 AAAAATCATAAAC
3387464 AAAAAT
1 AAAAAT
3387470 GAATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCATAAAC
Found at i:3388868 original size:15 final size:16
Alignment explanation
Indices: 3388848--3388880 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3388838 TATAAAGAAA
3388848 AATAAAAAAAATA-AT
1 AATAAAAAAAATATAT
*
3388863 AATAAAAATAATATAT
1 AATAAAAAAAATATAT
3388879 AA
1 AA
3388881 ATGAATTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAAAAAATATAT
Found at i:3388880 original size:13 final size:12
Alignment explanation
Indices: 3388848--3388881 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3388838 TATAAAGAAA
*
3388848 AATAAAAAAAAT
1 AATAATAAAAAT
3388860 AATAATAAAAAT
1 AATAATAAAAAT
3388872 AATATATAAA
1 AATA-ATAAA
3388882 TGAATTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:3389245 original size:15 final size:15
Alignment explanation
Indices: 3389225--3389327 Score: 58
Period size: 15 Copynumber: 7.1 Consensus size: 15
3389215 ATCATTCAAG
3389225 AAATAATAAATAAAT
1 AAATAATAAATAAAT
* *
3389240 AAATAATAGATGAA-
1 AAATAATAAATAAAT
* *
3389254 AAAGAAGAATATAAA-
1 AAATAATAA-ATAAAT
3389269 AAATAAT-AAT-AAT
1 AAATAATAAATAAAT
*
3389282 AAGA-AATAAAATAAAG
1 AA-ATAAT-AAATAAAT
*
3389298 ATAA-AAT-AATAAAA
1 A-AATAATAAATAAAT
*
3389312 AAATAATAAAGAAAT
1 AAATAATAAATAAAT
3389327 A
1 A
3389328 TAAAATATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
12 2 0.03
13 9 0.13
14 18 0.27
15 30 0.45
16 7 0.10
17 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:3389294 original size:21 final size:19
Alignment explanation
Indices: 3389268--3389360 Score: 70
Period size: 19 Copynumber: 5.0 Consensus size: 19
3389258 AAGAATATAA
3389268 AAAATAATAATAATAAGAAAT
1 AAAATAATAATAA-AA-AAAT
*
3389289 AAAATAA-AGATAAAATAAT
1 AAAATAATA-ATAAAAAAAT
* *
3389308 AAAAAAATAATAAAGAAAT
1 AAAATAATAATAAAAAAAT
* *
3389327 ATAA-AAT-ATAAAATAAT
1 AAAATAATAATAAAAAAAT
*
3389344 -AAA-AATAGTAAAAAAAT
1 AAAATAATAATAAAAAAAT
3389361 GATGAGATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
16 5 0.08
17 16 0.27
18 3 0.05
19 20 0.34
20 4 0.07
21 11 0.19
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAATAATAATAAAAAAAT
Found at i:3389345 original size:36 final size:35
Alignment explanation
Indices: 3389233--3389348 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 35
3389223 AGAAATAATA
* * *
3389233 AATAAATAAATAATAGATGAAAAAGAAGAATATAAAA-
1 AATAAAAAAATAATA-AAG-AAAATAA-AATATAAAAT
* * * *
3389270 AATAATAATAATAAGAAATAAAAT-AAAGATAAAAT
1 AATAA-AAAAATAATAAAGAAAATAAAATATAAAAT
3389305 AATAAAAAAATAATAAAGAAATATAAAATATAAAAT
1 AATAAAAAAATAATAAAGAAA-ATAAAATATAAAAT
3389341 AATAAAAA
1 AATAAAAA
3389349 TAGTAAAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
34 21 0.33
35 8 0.12
36 22 0.34
37 6 0.09
38 7 0.11
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (35 bp):
AATAAAAAAATAATAAAGAAAATAAAATATAAAAT
Found at i:3389349 original size:34 final size:36
Alignment explanation
Indices: 3389261--3389360 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 36
3389251 GAAAAAGAAG
*
3389261 AATATAAAA-AATAATAATAAT-AAGAAATAAAATA
1 AATATAAAATAATAAAAATAATAAAGAAATAAAATA
* *
3389295 AAGATAAAATAATAAAAAAATAATAAAGAAAT-ATA-A
1 AATATAAAATAAT--AAAAATAATAAAGAAATAAAATA
* *
3389331 AATATAAAATAATAAAAATAGTAAAAAAAT
1 AATATAAAATAATAAAAATAATAAAGAAAT
3389361 GATGAGATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
34 23 0.41
35 3 0.05
36 13 0.23
37 10 0.18
38 7 0.12
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (36 bp):
AATATAAAATAATAAAAATAATAAAGAAATAAAATA
Found at i:3389357 original size:25 final size:24
Alignment explanation
Indices: 3389225--3389358 Score: 82
Period size: 26 Copynumber: 5.5 Consensus size: 24
3389215 ATCATTCAAG
3389225 AAATAATAAATAAAT-AAATAATAGA
1 AAATAATAAA-AAATAAAATAATA-A
* *
3389250 TGAAA-AAGAAGAATATAAAA-AATAA
1 --AAATAATAA-AAAATAAAATAATAA
* * *
3389275 TAATAATAAGAAATAAAATAAAGATA
1 AAATAATAAAAAATAAAAT-AATA-A
* *
3389301 AAATAATAAAAAA-ATAATAA-AG
1 AAATAATAAAAAATAAAATAATAA
*
3389323 AAAT-ATAAAATATAAAATAATAA
1 AAATAATAAAAAATAAAATAATAA
*
3389346 AAATAGTAAAAAA
1 AAATAATAAAAAA
3389359 ATGATGAGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
21 7 0.09
22 10 0.12
23 15 0.18
24 12 0.15
25 8 0.10
26 23 0.28
27 7 0.09
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (24 bp):
AAATAATAAAAAATAAAATAATAA
Found at i:3389360 original size:11 final size:11
Alignment explanation
Indices: 3389261--3389360 Score: 66
Period size: 11 Copynumber: 9.0 Consensus size: 11
3389251 GAAAAAGAAG
3389261 AATATAAAAAAT
1 AATA-AAAAAAT
*
3389273 AAT--AATAAT
1 AATAAAAAAAT
*
3389282 AAGAAATAAAAT
1 AATAAA-AAAAT
*
3389294 AA-AGATAAAAT
1 AATA-AAAAAAT
3389305 AATAAAAAAAT
1 AATAAAAAAAT
*
3389316 AATAAAGAAAT
1 AATAAAAAAAT
3389327 -ATAAAATATAA-
1 AATAAAA-A-AAT
3389338 AATAATAAAAAT
1 AATAA-AAAAAT
*
3389350 AGTAAAAAAAT
1 AATAAAAAAAT
3389361 GATGAGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
9 7 0.10
10 5 0.07
11 34 0.49
12 22 0.31
13 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:3389483 original size:16 final size:15
Alignment explanation
Indices: 3389453--3389499 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3389443 GAAACTTCGA
*
3389453 ATAAGAAAA-AAAAT
1 ATAATAAAATAAAAT
3389467 ATAATAATAATAAAAT
1 ATAATAA-AATAAAAT
3389483 ATAATAAAATAAGAAT
1 ATAATAAAATAA-AAT
3389499 A
1 A
3389500 AATTTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 7 0.24
16 16 0.55
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
ATAATAAAATAAAAT
Found at i:3399605 original size:16 final size:16
Alignment explanation
Indices: 3399581--3399615 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3399571 ATAAAACTCA
* *
3399581 AAAGTTAGGTTGGAGT
1 AAAGGTAGGGTGGAGT
3399597 AAAGGTAGGGTGGAGT
1 AAAGGTAGGGTGGAGT
3399613 AAA
1 AAA
3399616 CAGTTATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (16 bp):
AAAGGTAGGGTGGAGT
Found at i:3412622 original size:52 final size:52
Alignment explanation
Indices: 3412561--3412661 Score: 202
Period size: 52 Copynumber: 1.9 Consensus size: 52
3412551 TAAGGTCCGC
3412561 ATATATATATTTATATGTATAAAGGGTGAACTTCTTCCCCATGACCATATAT
1 ATATATATATTTATATGTATAAAGGGTGAACTTCTTCCCCATGACCATATAT
3412613 ATATATATATTTATATGTATAAAGGGTGAACTTCTTCCCCATGACCATA
1 ATATATATATTTATATGTATAAAGGGTGAACTTCTTCCCCATGACCATA
3412662 ACAATCCTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (52 bp):
ATATATATATTTATATGTATAAAGGGTGAACTTCTTCCCCATGACCATATAT
Found at i:3415642 original size:33 final size:33
Alignment explanation
Indices: 3415605--3415667 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
3415595 TTTTAATGTC
** *
3415605 ATATATTTTATTTTTATTTCTTATTATAATCTT
1 ATATATTTTATTTACATTTCTTAATATAATCTT
3415638 ATATATTTTATTTACATTTCTTAATATAAT
1 ATATATTTTATTTACATTTCTTAATATAAT
3415668 TACCAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (33 bp):
ATATATTTTATTTACATTTCTTAATATAATCTT
Found at i:3417597 original size:7 final size:7
Alignment explanation
Indices: 3417585--3417617 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3417575 AATTAAATTA
3417585 AATAAAT
1 AATAAAT
3417592 AATAAAT
1 AATAAAT
3417599 AAT-AAT
1 AATAAAT
*
3417605 AAAAAAT
1 AATAAAT
3417612 AATAAA
1 AATAAA
3417618 AAAAAATTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:3417611 original size:13 final size:13
Alignment explanation
Indices: 3417589--3417624 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3417579 AAATTAAATA
*
3417589 AATAATAAATAAT
1 AATAAAAAATAAT
3417602 AATAAAAAATAAT
1 AATAAAAAATAAT
*
3417615 AAAAAAAAAT
1 AATAAAAAAT
3417625 TGGGGATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAAAATAAT
Found at i:3417618 original size:10 final size:10
Alignment explanation
Indices: 3417583--3417620 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
3417573 TAAATTAAAT
3417583 TAAATAAATAA
1 TAAA-AAATAA
*
3417594 TAAATAATAA
1 TAAAAAATAA
3417604 TAAAAAATAA
1 TAAAAAATAA
3417614 TAAAAAA
1 TAAAAAA
3417621 AAATTGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:3426183 original size:22 final size:22
Alignment explanation
Indices: 3426129--3426173 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3426119 TAGTCCTAGG
3426129 TTACTGTTATTCATTTACTCAA
1 TTACTGTTATTCATTTACTCAA
3426151 TTACTGTTATTCATTTACTCAA
1 TTACTGTTATTCATTTACTCAA
3426173 T
1 T
3426174 ATGATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (22 bp):
TTACTGTTATTCATTTACTCAA
Found at i:3428754 original size:16 final size:16
Alignment explanation
Indices: 3428735--3428768 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3428725 CCCAAATGCT
3428735 CCAAACCCAAAATAAC
1 CCAAACCCAAAATAAC
*
3428751 CCAAACTCAAAATAAC
1 CCAAACCCAAAATAAC
3428767 CC
1 CC
3428769 GACACTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.38, G:0.00, T:0.09
Consensus pattern (16 bp):
CCAAACCCAAAATAAC
Found at i:3439525 original size:27 final size:27
Alignment explanation
Indices: 3439495--3439557 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3439485 TCAAACAATT
* *
3439495 TGATTGGCCGACGATGTTTCCTTACGC
1 TGATTGGCCGACGACGTTCCCTTACGC
** *
3439522 TGATCAGCCGACGACGTTCCCTTATGC
1 TGATTGGCCGACGACGTTCCCTTACGC
*
3439549 TAATTGGCC
1 TGATTGGCC
3439558 ACCCCATGGC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (27 bp):
TGATTGGCCGACGACGTTCCCTTACGC
Found at i:3440583 original size:2 final size:2
Alignment explanation
Indices: 3440576--3440601 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3440566 ATATGATGCA
3440576 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
3440602 GCTATGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3440671 original size:5 final size:6
Alignment explanation
Indices: 3440656--3440710 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
3440646 TTAATTATAT
* * *
3440656 TTTTTA TTTTTA TTTTTA TTTTCTA -TTTTA TTTCTAA TTATTA TTATT-
1 TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTT-TTA TTTTTA TTTTTA
3440704 TTTTTA T
1 TTTTTA T
3440711 ACTTTACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 6 0.15
6 29 0.71
7 6 0.15
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:3440824 original size:10 final size:11
Alignment explanation
Indices: 3440801--3440868 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 11
3440791 AGTGACAAAA
3440801 ATTTTATATTT
1 ATTTTATATTT
3440812 ATTTTAT-TTT
1 ATTTTATATTT
3440822 ATTTTATATTT
1 ATTTTATATTT
* *
3440833 -TTATATTTTGT
1 ATTTTATATT-T
*
3440844 ATATATATATATAT
1 AT-T-T-TATATTT
3440858 ATTTTATATTT
1 ATTTTATATTT
3440869 CTATATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 17 0.38
11 17 0.38
12 2 0.04
13 2 0.04
14 3 0.07
15 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:3440825 original size:21 final size:20
Alignment explanation
Indices: 3440801--3440880 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
3440791 AGTGACAAAA
*
3440801 ATTTTATATTTATTTTATTTT
1 ATTTTATATTT-TTATATTTT
3440822 ATTTTATATTTTTATATTTT
1 ATTTTATATTTTTATATTTT
* * * *
3440842 GTATATATATATATATATTTTAT
1 AT-TTTATATTTTTATA-TTT-T
3440865 ATTTCTATATTTTTAT
1 ATTT-TATATTTTTAT
3440881 TATTATTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 9 0.20
21 22 0.48
22 4 0.09
23 11 0.24
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (20 bp):
ATTTTATATTTTTATATTTT
Found at i:3440836 original size:8 final size:8
Alignment explanation
Indices: 3440823--3440895 Score: 74
Period size: 8 Copynumber: 8.5 Consensus size: 8
3440813 TTTTATTTTA
3440823 TTTTATAT
1 TTTTATAT
3440831 TTTTATAT
1 TTTTATAT
3440839 TTTGTATAT
1 TTT-TATAT
*
3440848 ATATATATAT
1 -T-TTTATAT
3440858 ATTTTATAT
1 -TTTTATAT
*
3440867 TTCTATAT
1 TTTTATAT
3440875 TTTTATTAT
1 TTTTA-TAT
*
3440884 TATTATAT
1 TTTTATAT
3440892 TTTT
1 TTTT
3440896 TCGTAAACAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
8 28 0.51
9 18 0.33
10 8 0.15
11 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (8 bp):
TTTTATAT
Found at i:3440841 original size:36 final size:36
Alignment explanation
Indices: 3440801--3440891 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
3440791 AGTGACAAAA
* *
3440801 ATTTTATATTTATTTTAT-TTTATTTTATATTTTTAT
1 ATTTT-TATTTATTTTATATATATTTTATATTTCTAT
* *
3440837 ATTTTGTATATA-TATATATATATTTTATATTTCTAT
1 ATTTT-TATTTATTTTATATATATTTTATATTTCTAT
3440873 ATTTTTA-TTATTATTATAT
1 ATTTTTATTTATT-TTATAT
3440892 TTTTTCGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
34 2 0.04
35 7 0.16
36 36 0.80
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (36 bp):
ATTTTTATTTATTTTATATATATTTTATATTTCTAT
Found at i:3440846 original size:17 final size:16
Alignment explanation
Indices: 3440823--3440895 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 16
3440813 TTTTATTTTA
3440823 TTTTATATTTTTATAT
1 TTTTATATTTTTATAT
*
3440839 TTTGTATATATATATATAT
1 TTT-TATAT-T-TTTATAT
*
3440858 ATTTTATATTTCTATAT
1 -TTTTATATTTTTATAT
*
3440875 TTTTATTATTATTATAT
1 TTTTA-TATTTTTATAT
3440892 TTTT
1 TTTT
3440896 TCGTAAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
16 8 0.17
17 24 0.50
18 2 0.04
19 11 0.23
20 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (16 bp):
TTTTATATTTTTATAT
Found at i:3442071 original size:24 final size:22
Alignment explanation
Indices: 3442044--3442106 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
3442034 AACAAAAATC
3442044 ATAAACAAAAAATGAATTAAAAAA
1 ATAAA-AAAAAATGAATT-AAAAA
*
3442068 ATAAAAATAATAA-AAATTAAAAA
1 ATAAAAA-AA-AATGAATTAAAAA
3442091 ATAAAGAAAAAATGAA
1 ATAAA-AAAAAATGAA
3442107 AAAAAGGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 2 0.06
23 16 0.48
24 13 0.39
25 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (22 bp):
ATAAAAAAAAATGAATTAAAAA
Found at i:3442614 original size:28 final size:28
Alignment explanation
Indices: 3442574--3442635 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
3442564 GGGATTTGGG
**
3442574 GAGAAGCTGCCGGTAGGTGAGAGAGAAA
1 GAGAAGCAACCGGTAGGTGAGAGAGAAA
3442602 GAGAAGCAACCGGTAGGTGAGAGAGAAA
1 GAGAAGCAACCGGTAGGTGAGAGAGAAA
3442630 GAGAAG
1 GAGAAG
3442636 GACGTCGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.42, T:0.08
Consensus pattern (28 bp):
GAGAAGCAACCGGTAGGTGAGAGAGAAA
Found at i:3443581 original size:15 final size:15
Alignment explanation
Indices: 3443551--3443592 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3443541 AATCTTCAAA
*
3443551 AAATAA-TAATAAAT
1 AAATAATTAAAAAAT
3443565 AAATAATTAAAAAAT
1 AAATAATTAAAAAAT
*
3443580 AACTAATTTAAAA
1 AAATAA-TTAAAA
3443593 TTAAGTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.25
15 12 0.50
16 6 0.25
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATTAAAAAAT
Found at i:3443749 original size:17 final size:17
Alignment explanation
Indices: 3443729--3443815 Score: 69
Period size: 15 Copynumber: 5.2 Consensus size: 17
3443719 TTGTTTACGA
3443729 AAAAATATAATAATAAT
1 AAAAATATAATAATAAT
3443746 AAAAATATAGA-AAT-AT
1 AAAAATATA-ATAATAAT
3443762 -AAAATATATATATATATAT
1 AAAAATATA-ATA-ATA-AT
*
3443781 ACAAAATATAAAAAT-AT
1 A-AAAATATAATAATAAT
*
3443798 -AAAATAAAATAA-AAT
1 AAAAATATAATAATAAT
3443813 AAA
1 AAA
3443816 TATAAAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
15 21 0.37
16 5 0.09
17 16 0.28
18 1 0.02
19 4 0.07
20 2 0.04
21 8 0.14
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (17 bp):
AAAAATATAATAATAAT
Found at i:3443759 original size:8 final size:7
Alignment explanation
Indices: 3443730--3443823 Score: 66
Period size: 8 Copynumber: 12.7 Consensus size: 7
3443720 TGTTTACGAA
3443730 AAAATAT
1 AAAATAT
3443737 AATAATAAT
1 AA-AAT-AT
3443746 AAAAATAT
1 -AAAATAT
3443754 AGAAATAT
1 A-AAATAT
3443762 AAAATAT
1 AAAATAT
*
3443769 -ATATAT
1 AAAATAT
* *
3443775 ATATATAC
1 A-AAATAT
3443783 AAAATAT
1 AAAATAT
3443790 AAAAATAT
1 -AAAATAT
*
3443798 AAAATAA
1 AAAATAT
*
3443805 AATAAAAT
1 AA-AATAT
3443813 -AAATAT
1 AAAATAT
3443819 AAAAT
1 AAAAT
3443824 TTTTGTCACT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
6 9 0.13
7 26 0.37
8 28 0.40
9 5 0.07
10 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:3443787 original size:36 final size:32
Alignment explanation
Indices: 3443730--3443822 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 32
3443720 TGTTTACGAA
*
3443730 AAAATATAATAATAATAAAAATATAGAAATAT
1 AAAATATAATAATAATAAAAATATAAAAATAT
3443762 AAAATATATATATATATATACAAAATATAAAAATAT
1 AAAATATA-ATA-ATA-ATA-AAAATATAAAAATAT
*
3443798 AAAATAAAATAA-AAT--AAATATAAAA
1 AAAATATAATAATAATAAAAATATAAAA
3443823 TTTTTGTCAC
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
29 10 0.18
32 10 0.18
33 4 0.07
34 4 0.07
35 6 0.11
36 21 0.38
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (32 bp):
AAAATATAATAATAATAAAAATATAAAAATAT
Found at i:3443816 original size:21 final size:20
Alignment explanation
Indices: 3443728--3443823 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
3443718 ATTGTTTACG
3443728 AAAAAATAT--AATAATAATA
1 AAAAAATATAAAATAA-AATA
* *
3443747 AAAATATAGAAATATAAAATA
1 AAAAAATATAAA-ATAAAATA
* * * * *
3443768 TATATATATATATACAAAATA
1 AAAAAATATA-AAATAAAATA
*
3443789 TAAAAATATAAAATAAAATA
1 AAAAAATATAAAATAAAATA
3443809 AAATAAATATAAAAT
1 AAA-AAATATAAAAT
3443824 TTTTGTCACT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
19 7 0.12
20 10 0.17
21 38 0.63
22 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAAAATATAAAATAAAATA
Found at i:3443974 original size:28 final size:29
Alignment explanation
Indices: 3443909--3443974 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
3443899 TAAAAAAATG
*
3443909 TAAAGTATAAAAAATAATAATAATTAGAAA
1 TAAA-TATAAAAAATAACAATAATTAGAAA
3443939 TAAA-ATAAAAAATAACAATAA-TA-ATAA
1 TAAATATAAAAAATAACAATAATTAGA-AA
3443966 TAAATATAA
1 TAAATATAA
3443975 TTAAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.03
27 8 0.24
28 20 0.61
30 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (29 bp):
TAAATATAAAAAATAACAATAATTAGAAA
Found at i:3474082 original size:25 final size:25
Alignment explanation
Indices: 3474036--3474083 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3474026 TCATAAACGA
*
3474036 AAAATAAATAAAAATGATAAAAATT
1 AAAATAAAGAAAAATGATAAAAATT
3474061 AAAATAAAGAAGAAATGA-AAAAA
1 AAAATAAAGAA-AAATGATAAAAA
3474084 GAAGGGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAAAATGATAAAAATT
Done.