Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 71 of 230
Found at i:19388740 original size:14 final size:14
Alignment explanation
Indices: 19388721--19388747 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19388711 ATGCATAATA
19388721 TTATATATATTAAG
1 TTATATATATTAAG
19388735 TTATATATATTAA
1 TTATATATATTAA
19388748 TTTTTTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TTATATATATTAAG
Found at i:19388952 original size:16 final size:18
Alignment explanation
Indices: 19388931--19388965 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
19388921 TATTCAAAAA
19388931 TAAAAATT-AAT-ATATT
1 TAAAAATTCAATAATATT
19388947 TAAAAATTCAATAATATT
1 TAAAAATTCAATAATATT
19388965 T
1 T
19388966 TTTTAGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAATTCAATAATATT
Found at i:19389096 original size:30 final size:30
Alignment explanation
Indices: 19389013--19389089 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 30
19389003 TTATTTAAGG
*
19389013 TTTAAAAATTATGTGTTACATTTTTATTATA
1 TTTAAAAA-TATGTATTACATTTTTATTATA
*
19389044 ATTAAAAATACT-TATTACATTTTTA-TA-A
1 TTTAAAAATA-TGTATTACATTTTTATTATA
19389072 TTTAAAAATATGTATTAC
1 TTTAAAAATATGTATTAC
19389090 CAATTTTAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 1 0.02
28 16 0.39
29 2 0.05
30 14 0.34
31 8 0.20
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTAAAAATATGTATTACATTTTTATTATA
Found at i:19389097 original size:29 final size:27
Alignment explanation
Indices: 19389039--19389097 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
19389029 TACATTTTTA
*
19389039 TTATAATTAAAAATACTTATTACATTT
1 TTATAATTAAAAATACTTATTACAATT
19389066 TTATAATTTAAAAATA-TGTATTACCAATT
1 TTATAA-TTAAAAATACT-TATTA-CAATT
19389095 TTA
1 TTA
19389098 GAAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
28 14 0.50
29 7 0.25
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATAATTAAAAATACTTATTACAATT
Found at i:19391838 original size:7 final size:7
Alignment explanation
Indices: 19391826--19391855 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
19391816 TGCCAACACA
19391826 CAATCTT
1 CAATCTT
19391833 CAATCTT
1 CAATCTT
19391840 CAATCTT
1 CAATCTT
19391847 CAATCTT
1 CAATCTT
19391854 CA
1 CA
19391856 TCCAAAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (7 bp):
CAATCTT
Found at i:19402534 original size:42 final size:42
Alignment explanation
Indices: 19402458--19402551 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
19402448 TCCTAGACGA
* * *
19402458 GGTCTTACATGTAATCAAATACCGATCCACTGTCCCAAACAG
1 GGTCTTACACGAAATCAAATACCGATCCAATGTCCCAAACAG
* * *
19402500 GGTCTTACACGAAATCATATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATACCGAT-CCAATGTCCCAAACAG
19402542 GGTCTTACAC
1 GGTCTTACAC
19402552 ATAATCTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACCGATCCAATGTCCCAAACAG
Found at i:19403887 original size:43 final size:42
Alignment explanation
Indices: 19403811--19403936 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 42
19403801 CTGTTACATA
* * * * *
19403811 TATCACATA-CAATGCCAAATCCCAGATATGGTCTTACATGT
1 TATCACATATCGATGCCATATCCCAGAAAGGGTCTTACACGT
19403852 TATCACATATCGATGCCACTATCCCAGAAAGGGTCTTACACGT
1 TATCACATATCGATGCCA-TATCCCAGAAAGGGTCTTACACGT
* * * * *
19403895 AAT-ATCATATCGATGCCAATGTCCCAGACATGATCTTACACG
1 TATCA-CATATCGATGCC-ATATCCCAGAAAGGGTCTTACACG
19403937 AAATCACACC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 9 0.13
42 8 0.11
43 53 0.75
44 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (42 bp):
TATCACATATCGATGCCATATCCCAGAAAGGGTCTTACACGT
Found at i:19405241 original size:23 final size:23
Alignment explanation
Indices: 19405215--19405392 Score: 95
Period size: 24 Copynumber: 7.7 Consensus size: 23
19405205 ATGTTTAAAC
19405215 TTATTATTAATTTATCAT-TAATA
1 TTATT-TTAATTTATCATGTAATA
*
19405238 TTA-TCTAAGTTTAT--TGTATATTA
1 TTATTTTAA-TTTATCATGTA-A-TA
**
19405261 TTATTTTAGATTTATCATGTTTTA
1 TTATTTTA-ATTTATCATGTAATA
* * *
19405285 TTATTTGCAATTTATCA-ATATTA
1 TTATTT-TAATTTATCATGTAATA
*
19405308 TTATTTTAAATTTATCCTGT-ATA
1 TTATTTT-AATTTATCATGTAATA
*
19405331 TTTATTTAAAATTTATCAT-TAATA
1 -TTATTT-TAATTTATCATGTAATA
* * *
19405355 -T-TTTAAATTTATTATGTACTA
1 TTATTTTAATTTATCATGTAATA
*
19405376 TTATTTTGGATTTATCA
1 TTATTTT-AATTTATCA
19405393 CGTATGATTA
Statistics
Matches: 119, Mismatches: 18, Indels: 35
0.69 0.10 0.20
Matches are distributed among these distances:
20 11 0.09
21 12 0.10
22 9 0.08
23 32 0.27
24 50 0.42
25 2 0.02
26 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.57
Consensus pattern (23 bp):
TTATTTTAATTTATCATGTAATA
Found at i:19405285 original size:24 final size:24
Alignment explanation
Indices: 19405256--19405458 Score: 140
Period size: 24 Copynumber: 8.8 Consensus size: 24
19405246 GTTTATTGTA
*
19405256 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* ** *
19405280 TTTTATTATTTGCAATTTATCA-A
1 TATTATTATTTTAAATTTATCATG
*
19405303 TATTATTATTTTAAATTTATCCTG
1 TATTATTATTTTAAATTTATCATG
*
19405327 TA-TATTTATTTAAAATTTATCAT-
1 TATTA-TTATTTTAAATTTATCATG
*
19405350 TA--A-TATTTTAAATTTATTATG
1 TATTATTATTTTAAATTTATCATG
* ** *
19405371 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
19405395 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
19405418 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
*
19405440 TATTATTATTTCAAATTTA
1 TATTATTATTTTAAATTTA
19405459 ATATATATGG
Statistics
Matches: 135, Mismatches: 32, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
20 17 0.13
21 8 0.06
22 8 0.06
23 30 0.22
24 71 0.53
25 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:19405380 original size:44 final size:44
Alignment explanation
Indices: 19405257--19405381 Score: 135
Period size: 47 Copynumber: 2.8 Consensus size: 44
19405247 TTTATTGTAT
* * **
19405257 ATTATTATTTTAGATTTATCATGTTTTATTATTTGCAATTTATCAA
1 ATTATTATTTTAAATTTATCATG-TATATTATTTAAAATTTATC-A
*
19405303 TATTATTATTTTAAATTTATCCTGTATATTTATTTAAAATTTATC-
1 -ATTATTATTTTAAATTTATCATGTATA-TTATTTAAAATTTATCA
* *
19405348 ATTAATATTTTAAATTTATTATGTACTATTATTT
1 ATTATTATTTTAAATTTATCATGTA-TATTATTT
19405382 TGGATTTATC
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 28 0.41
45 2 0.03
46 3 0.04
47 35 0.51
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (44 bp):
ATTATTATTTTAAATTTATCATGTATATTATTTAAAATTTATCA
Found at i:19410759 original size:190 final size:190
Alignment explanation
Indices: 19410426--19410796 Score: 555
Period size: 190 Copynumber: 2.0 Consensus size: 190
19410416 AGATAATCAG
* *
19410426 ATTTCAGCACTATACAACACAAACGAATTCGAATAAACAATTTCTTATGCTTCTCAACTGCAAGT
1 ATTTCAGCACTATACAACACAAACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAGT
* *
19410491 ACACCCATATTCAACACTAATAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
66 ACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
* *
19410556 TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTATAGATCTAATTATAATAAA
131 TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAATTATAATAAA
* * * * *
19410616 ATTTTAGCATTATACAACACAGAA-GAATTCAAATAAACAATTTTTTATGTTTCTCAACTACGAG
1 ATTTCAGCACTATACAACACA-AACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAG
* * * * * * *
19410680 TACGCCCATATTTAACACCAACAGATTAACATGAATGATACCCTTCTTAGCATTTAGATATACAC
65 TACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACAC
*
19410745 TTCTCTTTAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAAT
130 TTCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAAT
19410797 ATCTTCAAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
190 159 0.99
191 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (190 bp):
ATTTCAGCACTATACAACACAAACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAGT
ACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAATTATAATAAA
Found at i:19415468 original size:39 final size:40
Alignment explanation
Indices: 19415369--19415628 Score: 329
Period size: 39 Copynumber: 6.6 Consensus size: 40
19415359 TCCTCGTTCG
* * *
19415369 AATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACA
19415409 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
19415449 AATG-CTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
19415487 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
* * *
19415527 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
** * *
19415566 AATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCACA
*
19415606 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
19415629 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 12, Indels: 17
0.87 0.05 0.07
Matches are distributed among these distances:
38 6 0.03
39 117 0.58
40 68 0.34
41 9 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
Found at i:19415575 original size:118 final size:120
Alignment explanation
Indices: 19415369--19415628 Score: 354
Period size: 118 Copynumber: 2.2 Consensus size: 120
19415359 TCCTCGTTCG
* *
19415369 AATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
19415433 TTTAGTAACTCGCACAAATGCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCAC
66 ATTAGTAACTCGCACAAATGCTTC-GGATCTTAACCCGGATATT-GTAACTTAGCAC
* *
19415487 AATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* ** *
19415550 ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC
66 ATTAGTAACTCGCACAAATG-CTTCGGATCTTAACCCGGATATTGTAACTTAGCAC
19415606 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
19415629 CAGCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
117 31 0.25
118 84 0.67
119 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCACAAATGCTTCGGATCTTAACCCGGATATTGTAACTTAGCAC
Found at i:19430377 original size:10 final size:10
Alignment explanation
Indices: 19430359--19430406 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19430349 AAGGAACTTC
19430359 AAAATTTATA
1 AAAATTTATA
* *
19430369 AAAAGTTATT
1 AAAATTTATA
*
19430379 AAAATTTTTAA
1 AAAATTTAT-A
*
19430390 AAAATATATA
1 AAAATTTATA
19430400 AAAATTT
1 AAAATTT
19430407 CAAATGTGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
AAAATTTATA
Found at i:19430384 original size:20 final size:21
Alignment explanation
Indices: 19430359--19430406 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
19430349 AAGGAACTTC
* *
19430359 AAAATTTATAAAAAGT-TATT
1 AAAATTTATAAAAAATATATA
*
19430379 AAAATTTTTAAAAAATATATA
1 AAAATTTATAAAAAATATATA
19430400 AAAATTT
1 AAAATTT
19430407 CAAATGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTTATAAAAAATATATA
Found at i:19430827 original size:15 final size:15
Alignment explanation
Indices: 19430807--19430839 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
19430797 AAAAATATGA
19430807 AATTTATAATTAGTT
1 AATTTATAATTAGTT
19430822 AATTTATAATTAGTT
1 AATTTATAATTAGTT
19430837 AAT
1 AAT
19430840 ACTGATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AATTTATAATTAGTT
Found at i:19445451 original size:17 final size:17
Alignment explanation
Indices: 19445431--19445466 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19445421 CTCCTTTTAT
* *
19445431 CTTCTCTCTCTACTTCC
1 CTTCTCTATCTACATCC
19445448 CTTCTCTATCTACATCC
1 CTTCTCTATCTACATCC
19445465 CT
1 CT
19445467 AGTAATGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (17 bp):
CTTCTCTATCTACATCC
Found at i:19457297 original size:53 final size:53
Alignment explanation
Indices: 19457236--19457417 Score: 174
Period size: 53 Copynumber: 3.3 Consensus size: 53
19457226 TATATAATTG
19457236 ATAATTGAGTTTTGGGGAGGTCATACTTAAGGTCAACTTGAACTTTAATATAT
1 ATAATTGAGTTTTGGGGAGGTCATACTTAAGGTCAACTTGAACTTTAATATAT
** * * * *
19457289 ATAATTGAGTTTTGGGCTCCTTGTTGACTGCCT-AGGTCTAACAATTGAACTTTAATATAT
1 ATAATTGAGTTTTGGG----GAGGTCA-TACTTAAGGTC-AAC--TTGAACTTTAATATAT
*
19457349 AATGATAATGAG--TT-GGGAGGTCATACTTAAGGTCAACTTGAACTTTAATATAT
1 -AT-A-ATTGAGTTTTGGGGAGGTCATACTTAAGGTCAACTTGAACTTTAATATAT
19457402 ATAATTGAGTTTTGGG
1 ATAATTGAGTTTTGGG
19457418 CTCCTTGTTG
Statistics
Matches: 100, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
50 5 0.05
51 1 0.01
52 4 0.04
53 34 0.34
55 6 0.06
56 8 0.08
57 8 0.08
58 6 0.06
60 18 0.18
61 4 0.04
62 1 0.01
63 5 0.05
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (53 bp):
ATAATTGAGTTTTGGGGAGGTCATACTTAAGGTCAACTTGAACTTTAATATAT
Found at i:19457379 original size:113 final size:119
Alignment explanation
Indices: 19457213--19457428 Score: 381
Period size: 113 Copynumber: 1.9 Consensus size: 119
19457203 TAACATCAAC
19457213 TTGAACTTTAATATATATAATTGATAATTGAGTTTTGGGGAGGTCATACTTAAGGTCAACTTGAA
1 TTGAACTTTAATATATATAATTGATAATTGAG-TTTGGGGAGGTCATACTTAAGGTCAACTTGAA
19457278 CTTTAATATATATAATTGAGTTTTGGGCTCCTTGTTGACTGCCTAGGTCTAACAA
65 CTTTAATATATATAATTGAGTTTTGGGCTCCTTGTTGACTGCCTAGGTCTAACAA
19457333 TTGAACTTT-A-ATATATAA-TGATAA-TGAG-TT-GGGAGGTCATACTTAAGGTCAACTTGAAC
1 TTGAACTTTAATATATATAATTGATAATTGAGTTTGGGGAGGTCATACTTAAGGTCAACTTGAAC
19457392 TTTAATATATATAATTGAGTTTTGGGCTCCTTGTTGA
66 TTTAATATATATAATTGAGTTTTGGGCTCCTTGTTGA
19457429 TGCTGCTAAC
Statistics
Matches: 96, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
113 66 0.69
114 2 0.02
116 4 0.04
117 6 0.06
118 8 0.08
119 1 0.01
120 9 0.09
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (119 bp):
TTGAACTTTAATATATATAATTGATAATTGAGTTTGGGGAGGTCATACTTAAGGTCAACTTGAAC
TTTAATATATATAATTGAGTTTTGGGCTCCTTGTTGACTGCCTAGGTCTAACAA
Found at i:19461096 original size:42 final size:43
Alignment explanation
Indices: 19460987--19461151 Score: 140
Period size: 43 Copynumber: 3.8 Consensus size: 43
19460977 AGCTCGTACA
* * * *
19460987 ATGCCAACGTCCTAGACGA-GGTCTTACATGTAATCAAATACCG
1 ATGCCAACGTCCCAGAC-ATGGTCTTACACGAAATCATATACCG
* * *
19461030 AT-CCCACTGTCCCAAACAGGGTCTTACACGAAATCATATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCATATACCG
* * * *
19461072 ATGCCAATGTCCCAGACATGGTCTTACACATAAATC-TCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACAC-GAAATCAT-ATACCG
* * *
19461116 ATGTCAACGTCCCAGACGTGGTCTTACATGAAATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCA
19461152 CATATCAGAA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
42 29 0.30
43 42 0.43
44 27 0.28
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCATATACCG
Found at i:19462442 original size:43 final size:42
Alignment explanation
Indices: 19462366--19462491 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 42
19462356 CTGTTACATA
* * * * *
19462366 TATCACATA-CAATGCCAAATCCCAGATATGGTCTTACATGT
1 TATCACATATCGATGCCATATCCCAGAAAGGGTCTTACACGT
19462407 TATCACATATCGATGCCACTATCCCAGAAAGGGTCTTACACGT
1 TATCACATATCGATGCCA-TATCCCAGAAAGGGTCTTACACGT
* * * * *
19462450 AAT-ATCATATCGATGCCAATGTCCCAGACATGATCTTACACG
1 TATCA-CATATCGATGCC-ATATCCCAGAAAGGGTCTTACACG
19462492 AAATCACACC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 9 0.13
42 8 0.11
43 53 0.75
44 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (42 bp):
TATCACATATCGATGCCATATCCCAGAAAGGGTCTTACACGT
Found at i:19463800 original size:24 final size:24
Alignment explanation
Indices: 19463773--19464017 Score: 126
Period size: 24 Copynumber: 10.6 Consensus size: 24
19463763 ATGTTTAAAC
19463773 TTATTATTAAATTTATCAT-TAATA
1 TTATT-TTAAATTTATCATGTAATA
* *
19463797 TTA-TCTAAGTTTAT--TGTATATTA
1 TTATTTTAAATTTATCATGTA-A-TA
* **
19463820 TTATTTTAGATTTATCATGTTTTA
1 TTATTTTAAATTTATCATGTAATA
** * *
19463844 TTATTTGCAATTTATCA-ATATTA
1 TTATTTTAAATTTATCATGTAATA
*
19463867 TTATTTTAAATTTATCCTGT-ATA
1 TTATTTTAAATTTATCATGTAATA
*
19463890 TTTATTTAAAATTTATCAT-T-A-A
1 -TTATTTTAAATTTATCATGTAATA
* *
19463912 -TATTTTAAATTTATTATGTACTA
1 TTATTTTAAATTTATCATGTAATA
** *
19463935 TTATTTTGGATTTATCACGT-ATGA
1 TTATTTTAAATTTATCATGTAAT-A
* *
19463959 TTATTCTAGAA-TTATCAT-CAA-A
1 TTATTTTA-AATTTATCATGTAATA
* *
19463981 AT-TTTTAAATTTTAT-ATGTATTA
1 TTATTTTAAA-TTTATCATGTAATA
*
19464004 TTATTTCAAATTTA
1 TTATTTTAAATTTA
19464018 ATATATATGG
Statistics
Matches: 163, Mismatches: 38, Indels: 41
0.67 0.16 0.17
Matches are distributed among these distances:
20 18 0.11
21 9 0.06
22 17 0.10
23 36 0.22
24 79 0.48
25 1 0.01
26 3 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (24 bp):
TTATTTTAAATTTATCATGTAATA
Found at i:19463866 original size:44 final size:47
Alignment explanation
Indices: 19463773--19463940 Score: 143
Period size: 47 Copynumber: 3.6 Consensus size: 47
19463763 ATGTTTAAAC
* * * **
19463773 TTATTATTAAATTTATCAT-TAATATTATCT-AAGTTTATTGTATATTA
1 TTATT-TTAAATTTATCATGTTATATTATTTAAAATTTA-TCAATATTA
* * **
19463820 TTATTTTAGATTTATCATGTTTTATTATTTGCAATTTATCAATATTA
1 TTATTTTAAATTTATCATGTTATATTATTTAAAATTTATCAATATTA
*
19463867 TTATTTTAAATTTATCCTG-TATATTTATTTAAAATTTATC---ATTA
1 TTATTTTAAATTTATCATGTTATA-TTATTTAAAATTTATCAATATTA
* *
19463911 ATATTTTAAATTTATTATG-TACTATTATTT
1 TTATTTTAAATTTATCATGTTA-TATTATTT
19463941 TGGATTTATC
Statistics
Matches: 101, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
44 28 0.28
45 2 0.02
46 15 0.15
47 51 0.50
48 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (47 bp):
TTATTTTAAATTTATCATGTTATATTATTTAAAATTTATCAATATTA
Found at i:19469342 original size:190 final size:190
Alignment explanation
Indices: 19469009--19469379 Score: 555
Period size: 190 Copynumber: 2.0 Consensus size: 190
19468999 AGATAATCAG
* *
19469009 ATTTCAGCACTATACAACACAAACGAATTCGAATAAACAATTTCTTATGCTTCTCAACTGCAAGT
1 ATTTCAGCACTATACAACACAAACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAGT
* *
19469074 ACACCCATATTCAACACTAATAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
66 ACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
* *
19469139 TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTATAGATCTAATTATAATAAA
131 TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAATTATAATAAA
* * * * *
19469199 ATTTTAGCATTATACAACACAGAA-GAATTCAAATAAACAATTTTTTATGTTTCTCAACTACGAG
1 ATTTCAGCACTATACAACACA-AACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAG
* * * * * * *
19469263 TACGCCCATATTTAACACCAACAGATTAACATGAATGATACCCTTCTTAGCATTTAGATATACAC
65 TACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACAC
*
19469328 TTCTCTTTAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAAT
130 TTCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAAT
19469380 ATCTTCAAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
190 159 0.99
191 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (190 bp):
ATTTCAGCACTATACAACACAAACGAATTCAAATAAACAATTTCTTATGCTTCTCAACTACAAGT
ACACCCATATTCAACACCAACAGATTAACATGAAGGATACCCTTATTAGCATTCAGACACACACT
TCTCTTAAAGAACTTCCTTAAAAACTTATCCAATTACTTTACAAATCTAATTATAATAAA
Found at i:19474007 original size:40 final size:40
Alignment explanation
Indices: 19473963--19474224 Score: 356
Period size: 40 Copynumber: 6.6 Consensus size: 40
19473953 TCCTCGTTCG
* *
19473963 AATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACA
*
19474003 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
*
19474043 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
*
19474083 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* *
19474123 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* * *
19474162 AATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCACA
19474202 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
19474225 CAGCATTCAA
Statistics
Matches: 204, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 144 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
Found at i:19480844 original size:12 final size:12
Alignment explanation
Indices: 19480827--19480851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19480817 AAACACTAGA
19480827 AGGGTAAACACT
1 AGGGTAAACACT
19480839 AGGGTAAACACT
1 AGGGTAAACACT
19480851 A
1 A
19480852 TGATGGAATA
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:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AGGGTAAACACT
Found at i:19485825 original size:24 final size:25
Alignment explanation
Indices: 19485781--19485872 Score: 75
Period size: 25 Copynumber: 3.6 Consensus size: 25
19485771 TACCACTTAA
*
19485781 TATATAAA-AAATAATTTAAAATAAT
1 TATATAAATAAATAA-TCAAAATAAT
*
19485806 TAT-TAAATAAATAATCAAAATATT
1 TATATAAATAAATAATCAAAATAAT
*
19485830 TATATAATATAATATAAT-ATAAT-AT
1 TATATAA-ATAA-ATAATCAAAATAAT
*
19485855 AATATAATATAATATAAT
1 TATATAA-ATAA-ATAAT
19485873 ATAATATAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 15 0.26
25 30 0.52
26 8 0.14
27 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
TATATAAATAAATAATCAAAATAAT
Found at i:19485841 original size:5 final size:5
Alignment explanation
Indices: 19485831--19485888 Score: 116
Period size: 5 Copynumber: 11.6 Consensus size: 5
19485821 CAAAATATTT
19485831 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
19485881 ATATA ATA
1 ATATA ATA
19485889 ATTATAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:19485969 original size:23 final size:23
Alignment explanation
Indices: 19485913--19485976 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
19485903 ACATCTATTG
*
19485913 CATAATGATTATATAAGTTTTTTAT
1 CATAATGA--ATATAATTTTTTTAT
* *
19485938 -TTAA-AAATATAATTTTTTTAT
1 CATAATGAATATAATTTTTTTAT
*
19485959 CATAATGAATATTATTTT
1 CATAATGAATATAATTTT
19485977 AATTTTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 11 0.35
24 3 0.10
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (23 bp):
CATAATGAATATAATTTTTTTAT
Found at i:19486096 original size:23 final size:24
Alignment explanation
Indices: 19486070--19486115 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
19486060 TTAACAAAAA
* *
19486070 ATAATTATATTTT-ATTATTTAAT
1 ATAAATATATTTTAACTATTTAAT
*
19486093 ATAAATGTATTTTAACTATTTAA
1 ATAAATATATTTTAACTATTTAA
19486116 CTATCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATAAATATATTTTAACTATTTAAT
Found at i:19491326 original size:13 final size:13
Alignment explanation
Indices: 19491308--19491333 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19491298 CTGGAAGTAT
19491308 TATGATATTATGC
1 TATGATATTATGC
19491321 TATGATATTATGC
1 TATGATATTATGC
19491334 ATAAGCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TATGATATTATGC
Found at i:19497759 original size:12 final size:11
Alignment explanation
Indices: 19497744--19497773 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
19497734 AAAAAAATTA
19497744 AAAAAGTATTTT
1 AAAAA-TATTTT
19497756 AAAAATATTTT
1 AAAAATATTTT
19497767 AAAAATA
1 AAAAATA
19497774 ACAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:19497819 original size:26 final size:26
Alignment explanation
Indices: 19497756--19497816 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
19497746 AAAGTATTTT
19497756 AAAAATATTTTAAAAATAACAAAATA
1 AAAAATATTTTAAAAATAACAAAATA
19497782 AAAAATATTTTAAAAATAA-AAAAT-
1 AAAAATATTTTAAAAATAACAAAATA
*
19497806 AAATATATTTT
1 AAAAATATTTT
19497817 TTATATTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 10 0.29
25 5 0.15
26 19 0.56
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAATATTTTAAAAATAACAAAATA
Found at i:19502293 original size:10 final size:11
Alignment explanation
Indices: 19502253--19502291 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
19502243 AATCTGTCAA
*
19502253 AAAATTTAATC
1 AAAATTTAATT
19502264 AAAATTTAATAT
1 AAAATTTAAT-T
19502276 AAAA-TTAATT
1 AAAATTTAATT
19502286 AAAATT
1 AAAATT
19502292 AAACATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 5 0.20
11 16 0.64
12 4 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTTAATT
Found at i:19502536 original size:69 final size:69
Alignment explanation
Indices: 19502425--19502574 Score: 214
Period size: 69 Copynumber: 2.2 Consensus size: 69
19502415 CGTGTTTCCA
* *
19502425 ACAGTAAACACGAGGAATATAAAGTGTAAGACCATAGTTGGACTATGGCAATCC-AGGTAGTCTG
1 ACAGTAAACACAAGGAATATAAAGTGTAAGACCATAGTTGGACTATGGCAA-CCTAGGTAGTCCG
*
19502489 TCGGG
65 TAGGG
* * *
19502494 ACAGTAAACACAAGGGATATAAGGTGTAAGATCATAGTTGGACTATGGCAACCTAGGTAGTCCGT
1 ACAGTAAACACAAGGAATATAAAGTGTAAGACCATAGTTGGACTATGGCAACCTAGGTAGTCCGT
19502559 AGGG
66 AGGG
19502563 AC-GATAAACACA
1 ACAG-TAAACACA
19502575 GGTGATACTG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
68 3 0.04
69 70 0.96
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.21
Consensus pattern (69 bp):
ACAGTAAACACAAGGAATATAAAGTGTAAGACCATAGTTGGACTATGGCAACCTAGGTAGTCCGT
AGGG
Found at i:19504431 original size:17 final size:18
Alignment explanation
Indices: 19504366--19504432 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 18
19504356 ACAACTTATG
19504366 CAAAATAATAGTTCATAT
1 CAAAATAATAGTTCATAT
*
19504384 -GAAAT-ATCAGTTCATAT
1 CAAAATAAT-AGTTCATAT
* * *
19504401 C-GAATAACAATTCAT-T
1 CAAAATAATAGTTCATAT
19504417 CAAAATAATAGTTCAT
1 CAAAATAATAGTTCAT
19504433 GCTCCATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.11
17 33 0.87
18 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
CAAAATAATAGTTCATAT
Found at i:19504529 original size:23 final size:22
Alignment explanation
Indices: 19504495--19504538 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
19504485 TTATGAAACA
19504495 TATAAGGGACTCTATCACCACC
1 TATAAGGGACTCTATCACCACC
19504517 TATAAGTGGACTCTATCACCAC
1 TATAAG-GGACTCTATCACCAC
19504539 ACATTGGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (22 bp):
TATAAGGGACTCTATCACCACC
Found at i:19505088 original size:18 final size:18
Alignment explanation
Indices: 19505065--19505125 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
19505055 AATTTGGAAA
19505065 ATTAATACAGTTCGCCAT
1 ATTAATACAGTTCGCCAT
* * *
19505083 ATTAATACAGATCACCAA
1 ATTAATACAGTTCGCCAT
*
19505101 ATTAACACAGTTCGCCAT
1 ATTAATACAGTTCGCCAT
*
19505119 AATAATA
1 ATTAATA
19505126 TAATTCACCA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (18 bp):
ATTAATACAGTTCGCCAT
Found at i:19505134 original size:36 final size:36
Alignment explanation
Indices: 19505063--19505143 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
19505053 ACAATTTGGA
* *
19505063 AAATTAATACAGTTCGCCATATTAATACAGATCACC
1 AAATTAACACAGTTCGCCATAATAATACAGATCACC
*
19505099 AAATTAACACAGTTCGCCATAATAATATA-ATTCACC
1 AAATTAACACAGTTCGCCATAATAATACAGA-TCACC
*
19505135 AAGTTAACA
1 AAATTAACA
19505144 TGGTTCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (36 bp):
AAATTAACACAGTTCGCCATAATAATACAGATCACC
Found at i:19506892 original size:32 final size:31
Alignment explanation
Indices: 19506846--19506912 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
19506836 ACTTAAAATT
* * *
19506846 ATTAATTCTAATTATTCTAA-TATTTTATTTA
1 ATTAATTATAATTATT-TAATTATATAATTTA
19506877 ATTAATTTATAATTATTTAATTATATAATTTA
1 ATTAA-TTATAATTATTTAATTATATAATTTA
19506909 ATTA
1 ATTA
19506913 CGGTTTCTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTATAATTATTTAATTATATAATTTA
Found at i:19510969 original size:41 final size:41
Alignment explanation
Indices: 19510896--19510975 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
19510886 ACGCCTAAAG
* * **** *
19510896 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCGTCATGAT
1 ATGAATAAGACCATAACTGAAAGACACCATGGCATCATGAT
19510937 ATGAATAAGACCATAACTGAAAGACACCATGGCATCATG
1 ATGAATAAGACCATAACTGAAAGACACCATGGCATCATG
19510976 GAATAGGACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (41 bp):
ATGAATAAGACCATAACTGAAAGACACCATGGCATCATGAT
Found at i:19518492 original size:3 final size:3
Alignment explanation
Indices: 19518484--19518509 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19518474 TTATACTGTT
19518484 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
19518510 TTATAGCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:19518931 original size:27 final size:26
Alignment explanation
Indices: 19518913--19518963 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
19518903 TATTAGTATT
19518913 AATC-TTATATTTTAATTTAAATATG
1 AATCGTTATATTTTAATTTAAATATG
19518938 AATCTGTTATATTTTAATTGTAAATA
1 AATC-GTTATATTTTAATT-TAAATA
19518964 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
27 13 0.57
28 6 0.26
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
AATCGTTATATTTTAATTTAAATATG
Found at i:19527307 original size:16 final size:16
Alignment explanation
Indices: 19527254--19527309 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
19527244 TTATATCCTT
*
19527254 TTTATAATATGTAAAC
1 TTTATAATATATAAAC
* *
19527270 TAATATATATATATAAAA
1 T-TTATA-ATATATAAAC
*
19527288 TTTATAATATATAACC
1 TTTATAATATATAAAC
19527304 TTTATA
1 TTTATA
19527310 GAAAAAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 15 0.47
17 8 0.25
18 9 0.28
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTATAATATATAAAC
Found at i:19530457 original size:27 final size:27
Alignment explanation
Indices: 19530426--19530603 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
19530416 TAAATTGTAC
19530426 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19530453 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19530479 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19530507 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
19530535 AGCACTAAGTGTGCGATTTGA-TTTCGT
1 AGCACTAAGTGTGCGATTTGACTAT-GT
* * *
19530562 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
**
19530589 AGCACTGTGTGTGCG
1 AGCACTAAGTGTGCG
19530604 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.02
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19537031 original size:14 final size:14
Alignment explanation
Indices: 19537012--19537039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19537002 GAAACAATAC
19537012 TAGTTATGTATTTT
1 TAGTTATGTATTTT
19537026 TAGTTATGTATTTT
1 TAGTTATGTATTTT
19537040 AATAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (14 bp):
TAGTTATGTATTTT
Found at i:19546110 original size:26 final size:27
Alignment explanation
Indices: 19546027--19546121 Score: 147
Period size: 27 Copynumber: 3.6 Consensus size: 27
19546017 AGACCCTAAA
* *
19546027 ATAGGGTAAAATAACTGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
19546054 ATAGGGTAAAATGACCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
* *
19546081 ATAGGATAAAATGACCG-AATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCT
19546107 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
19546122 TGTTATACCC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
26 22 0.35
27 41 0.65
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCT
Found at i:19546129 original size:27 final size:27
Alignment explanation
Indices: 19546027--19546132 Score: 133
Period size: 27 Copynumber: 4.0 Consensus size: 27
19546017 AGACCCTAAA
* *
19546027 ATAGGGTAAAATAACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
* *
19546054 ATAGGGTAAAATGACCGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
* *
19546081 ATAGGATAAAATGACCG-AATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
**
19546107 ATAGGGTAAAATGACTGTTATACCCC
1 ATAGGGTAAAATGACTGAAATACCCC
19546133 TAGGTGATGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
26 23 0.32
27 48 0.68
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:19546734 original size:37 final size:37
Alignment explanation
Indices: 19546693--19546773 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
19546683 CCAATCATTT
* *
19546693 ACTGTTACGGGAA-GGGCTTAGGCCCACACTGAACTGG
1 ACTGTTACGGGAATGGGCTAAGGCCCA-ACTGAACTGA
****
19546730 ACTGTTATTTTAATGGGCTAAGGCCCAACTGAACTGA
1 ACTGTTACGGGAATGGGCTAAGGCCCAACTGAACTGA
19546767 ACTGTTA
1 ACTGTTA
19546774 TTAAATTGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
37 25 0.68
38 12 0.32
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (37 bp):
ACTGTTACGGGAATGGGCTAAGGCCCAACTGAACTGA
Found at i:19546784 original size:37 final size:37
Alignment explanation
Indices: 19546706--19546794 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
19546696 GTTACGGGAA
* * *
19546706 GGGCTTAGGCCCACACTGAACTGGACTGTTATTTTAAT
1 GGGCTAAGGCCCA-ACTGAACTGAACTGTTATTTAAAT
19546744 GGGCTAAGGCCCAACTGAACTGAACTGTTA-TTAAATT
1 GGGCTAAGGCCCAACTGAACTGAACTGTTATTTAAA-T
19546781 GGGCTTAA-GCCCAA
1 GGGC-TAAGGCCCAA
19546795 ACTGTAAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
36 4 0.09
37 27 0.59
38 15 0.33
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (37 bp):
GGGCTAAGGCCCAACTGAACTGAACTGTTATTTAAAT
Found at i:19547101 original size:17 final size:17
Alignment explanation
Indices: 19547079--19547141 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
19547069 ATTGAATCAC
19547079 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
19547096 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
19547116 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
19547133 TACATAATT
1 TACATAATT
19547142 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:19547116 original size:37 final size:37
Alignment explanation
Indices: 19547070--19547144 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
19547060 ATTACCCGAA
*
19547070 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
19547107 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
19547144 T
1 T
19547145 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:19547319 original size:38 final size:39
Alignment explanation
Indices: 19547275--19547352 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
19547265 ACTTAAGAGT
*
19547275 TAGACTTTACTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTACTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
19547313 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTACTTTTAGTTTTATTGGGTTGGGTAATTGGG
19547352 T
1 T
19547353 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTACTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:19547351 original size:13 final size:13
Alignment explanation
Indices: 19547333--19547357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19547323 TTTTAGTTTT
19547333 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
19547346 ATTGGGTTGGGT
1 ATTGGGTTGGGT
19547358 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:19549019 original size:17 final size:18
Alignment explanation
Indices: 19548987--19549020 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19548977 AATTTCTTTT
19548987 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
19549005 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
19549021 AACTGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:19549477 original size:28 final size:29
Alignment explanation
Indices: 19549459--19549515 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
19549449 AAAATCTTAT
19549459 AATATCT-TTTACTTAATAATAAATAATA
1 AATATCTATTTACTTAATAATAAATAATA
*
19549487 AATATCTATTTACTTAAATAATAAGTAAT
1 AATATCTATTTACTT-AATAATAAATAAT
19549516 TTAAATCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
29 7 0.27
30 12 0.46
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (29 bp):
AATATCTATTTACTTAATAATAAATAATA
Found at i:19573172 original size:13 final size:12
Alignment explanation
Indices: 19573146--19573187 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
19573136 TCTTTTTCTA
19573146 TAAAAT-TCCAT
1 TAAAATATCCAT
19573157 TAAAATATCTCAT
1 TAAAATATC-CAT
19573170 TAAAATAATCC-T
1 TAAAAT-ATCCAT
19573182 TAAAAT
1 TAAAAT
19573188 GCTAATTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 9 0.32
13 10 0.36
14 3 0.11
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATATCCAT
Found at i:19574331 original size:32 final size:32
Alignment explanation
Indices: 19574295--19574366 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
19574285 TTTAAAAGAT
* *
19574295 ACATAATTATTCAACTAATATCTCTTGATTAA
1 ACATAATTATTCAAATAATATCTCTTGAATAA
* * *
19574327 ACATAACTATTCAAATAATATTTTTTGAATAA
1 ACATAATTATTCAAATAATATCTCTTGAATAA
*
19574359 TCATAATT
1 ACATAATT
19574367 CTTTGTCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (32 bp):
ACATAATTATTCAAATAATATCTCTTGAATAA
Found at i:19576183 original size:26 final size:26
Alignment explanation
Indices: 19576153--19576254 Score: 120
Period size: 26 Copynumber: 3.9 Consensus size: 26
19576143 TATCATCCCT
19576153 ATTTTACCCCTTA-TAAAATTTTGACG
1 ATTTT-CCCCTTAGTAAAATTTTGACG
* *
19576179 ATTTTGCCCTTAGTAAAATTTTGACA
1 ATTTTCCCCTTAGTAAAATTTTGACG
*
19576205 ATTTTGCCCC-TAGTAAAATTTTGATG
1 ATTTT-CCCCTTAGTAAAATTTTGACG
*
19576231 ATTTCTCCCC-TGGTAAAATTTTGA
1 ATTT-TCCCCTTAGTAAAATTTTGA
19576255 GAAAATTTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.09
26 57 0.85
27 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTCCCCTTAGTAAAATTTTGACG
Found at i:19576215 original size:52 final size:52
Alignment explanation
Indices: 19576153--19576254 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
19576143 TATCATCCCT
*
19576153 ATTTTACCCCTTA-TAAAATTTTGACGATTT-TGCCCTTAGTAAAATTTTGACA
1 ATTTTACCCC-TAGTAAAATTTTGACGATTTCT-CCCCTAGTAAAATTTTGACA
* * *
19576205 ATTTTGCCCCTAGTAAAATTTTGATGATTTCTCCCCTGGTAAAATTTTGA
1 ATTTTACCCCTAGTAAAATTTTGACGATTTCTCCCCTAGTAAAATTTTGA
19576255 GAAAATTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 2 0.05
52 41 0.93
53 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (52 bp):
ATTTTACCCCTAGTAAAATTTTGACGATTTCTCCCCTAGTAAAATTTTGACA
Found at i:19579120 original size:21 final size:21
Alignment explanation
Indices: 19579096--19579165 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
19579086 CACTATAACA
19579096 GAAATGAATAAGACCATAGTT
1 GAAATGAATAAGACCATAGTT
* * * * *
19579117 GAAA-GACTCTATGGCACTATACTG
1 GAAATGA--ATA-AG-ACCATAGTT
19579141 GAAATGAATAAGACCATAGTT
1 GAAATGAATAAGACCATAGTT
19579162 GAAA
1 GAAA
19579166 GAAACTATGG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 3 0.09
23 3 0.09
24 10 0.29
25 2 0.06
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (21 bp):
GAAATGAATAAGACCATAGTT
Found at i:19579205 original size:90 final size:90
Alignment explanation
Indices: 19579052--19579218 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 90
19579042 TTGGCTTGAA
* *
19579052 AAATGAATAAGACCATAGGTGAAAGACACTATGGCACTATAACAGAAATGAATAAGACCATAGTT
1 AAATGAATAAGACCATAGGTGAAAGAAACTATGGCACTATAACAGAAATAAATAAGACCATAGTT
*
19579117 GAAAGACTCTATGGCACTATACTGG
66 GAAAGACACTATGGCACTATACTGG
* *
19579142 AAATGAATAAGACCATAGTTGAAAGAAACTATGGCAAC-ATGAA-TGAAATAAATAAGACCATAG
1 AAATGAATAAGACCATAGGTGAAAGAAACTATGGC-ACTAT-AACAGAAATAAATAAGACCATAG
19579205 TTGAAAGACACTAT
64 TTGAAAGACACTAT
19579219 AGCATCATGT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
90 66 0.94
91 4 0.06
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (90 bp):
AAATGAATAAGACCATAGGTGAAAGAAACTATGGCACTATAACAGAAATAAATAAGACCATAGTT
GAAAGACACTATGGCACTATACTGG
Found at i:19579210 original size:21 final size:21
Alignment explanation
Indices: 19579141--19579210 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
19579131 CACTATACTG
*
19579141 GAAATGAATAAGACCATAGTT
1 GAAATAAATAAGACCATAGTT
* * * *
19579162 GAAAGAAACTATGGCAACAT-GAAT
1 GAAATAAA-TA-AG-ACCATAG-TT
19579186 GAAATAAATAAGACCATAGTT
1 GAAATAAATAAGACCATAGTT
19579207 GAAA
1 GAAA
19579211 GACACTATAG
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
21 15 0.43
22 4 0.11
23 4 0.11
24 12 0.34
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (21 bp):
GAAATAAATAAGACCATAGTT
Found at i:19579235 original size:45 final size:45
Alignment explanation
Indices: 19579052--19579243 Score: 232
Period size: 45 Copynumber: 4.3 Consensus size: 45
19579042 TTGGCTTGAA
* *
19579052 AAATGAATAAGACCATAGGTGAAAGACACTATGGCACTATAACAG
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATGACAG
* *
19579097 AAATGAATAAGACCATAGTTGAAAGACTCTATGGCACTAT-ACTGG
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATGAC-AG
*
19579142 AAATGAATAAGACCATAGTTGAAAGAAACTATGGCAAC-ATGA-ATG
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGC-ACTATGACA-G
* * *
19579187 AAATAAATAAGACCATAGTTGAAAGACACTATAGCA-TCATGTCAG
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCACT-ATGACAG
19579232 AAATCG-ATAAGA
1 AAAT-GAATAAGA
19579244 TCGTAGCTAA
Statistics
Matches: 128, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
44 3 0.02
45 121 0.95
46 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (45 bp):
AAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATGACAG
Found at i:19590629 original size:26 final size:26
Alignment explanation
Indices: 19590600--19590681 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
19590590 CCCTAGCAAT
* *
19590600 ATTTTGACGATTTTACCTCTGGTAAA
1 ATTTTGACGATTTTGCCCCTGGTAAA
* *
19590626 ATTTTGACAATATTGCCCCTGGTAAA
1 ATTTTGACGATTTTGCCCCTGGTAAA
* *
19590652 TTTTTGATGATTTTGCCCCTGGT-AA
1 ATTTTGACGATTTTGCCCCTGGTAAA
19590677 ATTTT
1 ATTTT
19590682 CAAGAAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 6 0.13
26 41 0.87
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTTTGACGATTTTGCCCCTGGTAAA
Found at i:19595133 original size:16 final size:15
Alignment explanation
Indices: 19595112--19595141 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19595102 ACTGCTTCCC
19595112 AAAAGAAGAAAAAAGA
1 AAAAGAA-AAAAAAGA
19595128 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
19595142 CAAACAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:19597992 original size:9 final size:9
Alignment explanation
Indices: 19597968--19598020 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
19597958 GAGTTAAACG
*
19597968 AATCAAGTT
1 AATCGAGTT
*
19597977 ATTCGAGTT
1 AATCGAGTT
*
19597986 AAACGAGTT
1 AATCGAGTT
*
19597995 ATTCGAGTT
1 AATCGAGTT
19598004 AATCGAGTT
1 AATCGAGTT
*
19598013 ATTCGAGT
1 AATCGAGT
19598021 CAACTTGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:19597996 original size:18 final size:18
Alignment explanation
Indices: 19597973--19598020 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
19597963 AAACGAATCA
19597973 AGTTATTCGAGTTAAACG
1 AGTTATTCGAGTTAAACG
*
19597991 AGTTATTCGAGTTAATCG
1 AGTTATTCGAGTTAAACG
19598009 AGTTATTCGAGT
1 AGTTATTCGAGT
19598021 CAACTTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (18 bp):
AGTTATTCGAGTTAAACG
Found at i:19598413 original size:17 final size:17
Alignment explanation
Indices: 19598357--19598415 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
19598347 TAATATCTAC
*
19598357 TATTTATATTATTAAAT
1 TATTTATATTATTGAAT
* *
19598374 TAAATTTCATA-TATTGTAC
1 T--ATTT-ATATTATTGAAT
19598393 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
19598410 TATTTA
1 TATTTA
19598416 ATCATATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.09
17 17 0.52
19 10 0.30
20 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:19604585 original size:42 final size:42
Alignment explanation
Indices: 19604539--19604630 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
19604529 GTCCCAATGT
19604539 GCTCAAGCAAGTCCCTAG-TGACCCTCTAGTCAG-CCTCCATAG
1 GCTCAAGCAAGT-CCTAGATGACCCTCTAGTCAGTCCT-CATAG
* * * *
19604581 GCTCAGGCAAGTTCTTGATGACCCTCTAGTCAGTCCTTATAG
1 GCTCAAGCAAGTCCTAGATGACCCTCTAGTCAGTCCTCATAG
19604623 GCTCAAGC
1 GCTCAAGC
19604631 TAGCTTTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.86
43 3 0.07
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (42 bp):
GCTCAAGCAAGTCCTAGATGACCCTCTAGTCAGTCCTCATAG
Found at i:19604757 original size:25 final size:26
Alignment explanation
Indices: 19604724--19604812 Score: 126
Period size: 26 Copynumber: 3.4 Consensus size: 26
19604714 ACAAATTTTC
*
19604724 TCAAAAATTTACCATGGGTAAAATCT
1 TCAAAATTTTACCATGGGTAAAATCT
*
19604750 TCAAAATTTTACCATAGGTAAAATCT
1 TCAAAATTTTACCATGGGTAAAATCT
* *
19604776 TCAAAATTTTACTAAGGGTAAAAT-T
1 TCAAAATTTTACCATGGGTAAAATCT
19604801 GTCAAAATTTTA
1 -TCAAAATTTTA
19604813 TTAAGGGTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
25 1 0.02
26 56 0.98
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (26 bp):
TCAAAATTTTACCATGGGTAAAATCT
Found at i:19604817 original size:26 final size:26
Alignment explanation
Indices: 19604724--19604825 Score: 118
Period size: 26 Copynumber: 3.9 Consensus size: 26
19604714 ACAAATTTTC
* * *
19604724 TCAAAAATTTACCATGGGTAAAATCT
1 TCAAAATTTTACTAAGGGTAAAATCT
*
19604750 TCAAAATTTTACCATA-GGTAAAATCT
1 TCAAAATTTTACTA-AGGGTAAAATCT
19604776 TCAAAATTTTACTAAGGGTAAAAT-T
1 TCAAAATTTTACTAAGGGTAAAATCT
* *
19604801 GTCAAAATTTTATTAAGGGTGAAAT
1 -TCAAAATTTTACTAAGGGTAAAAT
19604826 TTGGATGAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
25 2 0.03
26 66 0.97
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTAAGGGTAAAATCT
Found at i:19617096 original size:10 final size:10
Alignment explanation
Indices: 19617078--19617125 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19617068 AAGGAACTTC
19617078 AAAATTTATA
1 AAAATTTATA
* *
19617088 AAAAGTTATT
1 AAAATTTATA
*
19617098 AAAATTTTTAA
1 AAAATTTAT-A
*
19617109 AAAATATATA
1 AAAATTTATA
19617119 AAAATTT
1 AAAATTT
19617126 CAAATGTGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
AAAATTTATA
Found at i:19617103 original size:20 final size:21
Alignment explanation
Indices: 19617078--19617125 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
19617068 AAGGAACTTC
* *
19617078 AAAATTTATAAAAAGT-TATT
1 AAAATTTATAAAAAATATATA
*
19617098 AAAATTTTTAAAAAATATATA
1 AAAATTTATAAAAAATATATA
19617119 AAAATTT
1 AAAATTT
19617126 CAAATGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTTATAAAAAATATATA
Found at i:19617545 original size:15 final size:15
Alignment explanation
Indices: 19617525--19617557 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
19617515 AAAAATATGA
19617525 AATTTATAATTAGTT
1 AATTTATAATTAGTT
19617540 AATTTATAATTAGTT
1 AATTTATAATTAGTT
19617555 AAT
1 AAT
19617558 ACTGATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AATTTATAATTAGTT
Found at i:19631993 original size:5 final size:5
Alignment explanation
Indices: 19631983--19632008 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19631973 CTAATCTTGG
19631983 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
19632009 TATCTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:19632493 original size:17 final size:17
Alignment explanation
Indices: 19632471--19632506 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19632461 TCCTTTTTAT
* *
19632471 CTTCTCTCTCTACTTCC
1 CTTCTCTATCTACATCC
19632488 CTTCTCTATCTACATCC
1 CTTCTCTATCTACATCC
19632505 CT
1 CT
19632507 AGTAATGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (17 bp):
CTTCTCTATCTACATCC
Found at i:19637192 original size:21 final size:20
Alignment explanation
Indices: 19637163--19637206 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19637153 TTCAGACTAA
19637163 TAAAAATTTAAAAATAATATT
1 TAAAAATTTAAAAATAA-ATT
* * *
19637184 TAAATATTTTAGAATAAATT
1 TAAAAATTTAAAAATAAATT
19637204 TAA
1 TAA
19637207 GTAATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAAATTTAAAAATAAATT
Found at i:19637576 original size:3 final size:3
Alignment explanation
Indices: 19637564--19637594 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19637554 AATTAAAAAC
19637564 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19637595 GTCAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19638261 original size:21 final size:20
Alignment explanation
Indices: 19638209--19638263 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
19638199 ATTATTATTC
*
19638209 TAGAATTTTTTTTTATTTTT
1 TAGAATTTTTTTATATTTTT
* *
19638229 TA-ACTTTCTTTATATATTTT
1 TAGAATTTTTTTATAT-TTTT
19638249 TAGAATTTTTTTATA
1 TAGAATTTTTTTATA
19638264 AAATATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 10 0.36
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TAGAATTTTTTTATATTTTT
Found at i:19643634 original size:3 final size:3
Alignment explanation
Indices: 19643626--19643678 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
19643616 ATTGAGGAGT
19643626 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19643674 ATA AT
1 ATA AT
19643679 TAAGAAGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19650229 original size:10 final size:8
Alignment explanation
Indices: 19650200--19650227 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
19650190 CATGTATCAC
19650200 ATATTAAT
1 ATATTAAT
19650208 ATATTAAT
1 ATATTAAT
19650216 ATATTAAT
1 ATATTAAT
19650224 ATAT
1 ATAT
19650228 ATACATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTAAT
Found at i:19650440 original size:42 final size:42
Alignment explanation
Indices: 19650361--19650489 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
19650351 CCTGAAGGCT
** * * * *
19650361 AAATAGAAGCTCATGAGAGCTAAACGGAAATCCATAAGGGTTG
1 AAAT-GAAGCTCAAAAGAGCTGAACGAAAACCCATAAGGGTTA
* ** * *
19650404 AACTGAAGCTCGTAAGAGTTGAACGAAAACCTATAAGGGTTA
1 AAATGAAGCTCAAAAGAGCTGAACGAAAACCCATAAGGGTTA
*
19650446 AAATGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AAATGAAGCTCAAAAGAGCTGAACGAAAACCCATAAGGGTTA
19650488 AA
1 AA
19650490 CAAAAAATTA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 68 0.96
43 3 0.04
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (42 bp):
AAATGAAGCTCAAAAGAGCTGAACGAAAACCCATAAGGGTTA
Found at i:19656566 original size:83 final size:81
Alignment explanation
Indices: 19656457--19656717 Score: 292
Period size: 84 Copynumber: 3.1 Consensus size: 81
19656447 TTACAAGATT
*
19656457 TTATTTAATTCAATTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCAGGA
1 TTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGC-GGA
19656522 ATAAATTCTGAAACAGAA
65 ATAAATTCTGAAACA-AA
* * *** * * * *
19656540 TTATTTGATT-ACGTCTTTGTTTGGAAACAAAACAACATCAAATAAAATCTTGTTAAACGGCGGG
1 TTATTTAATTCAAGTC-AAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGC-GG
* *
19656604 AATAAATCCCGAAACAAA
64 AATAAATTCTGAAACAAA
* *
19656622 TTTTATTTAATTCAATTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAAATGGCGA
1 --TTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCG-
19656687 GAATAAA-TCTCGAAACAAA
63 GAATAAATTCT-GAAACAAA
19656706 TTTTATTTAATT
1 --TTATTTAATT
19656718 TAATTTCTCG
Statistics
Matches: 146, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
82 5 0.03
83 65 0.45
84 73 0.50
85 3 0.02
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (81 bp):
TTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGGAA
TAAATTCTGAAACAAA
Found at i:19656680 original size:84 final size:85
Alignment explanation
Indices: 19656449--19656886 Score: 359
Period size: 87 Copynumber: 5.2 Consensus size: 85
19656439 TTGGGTTGTT
*
19656449 ACAAGATTTTATTTAATTCAATTC-AAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAA
1 ACAA-ATTTTATTTAATTCAATTCTAAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAA
* * * *
19656513 ATGGCAGGAATAAATTCTGAA
65 ACGGCGGGAATAAATCCCGAA
* ** *** * * * *
19656534 ACAGAA--TTATTTGATT-ACGTCTTTGTTTGGAAACAAAACAACATCAAATAAAATCTTGTTAA
1 ACA-AATTTTATTTAATTCAATTCTAAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAA
19656596 ACGGCGGGAATAAATCCCGAA
65 ACGGCGGGAATAAATCCCGAA
19656617 ACAAATTTTATTTAATTCAATTC-AAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAAA
1 ACAAATTTTATTTAATTCAATTCTAAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAAA
* * *
19656681 TGGCGAGAATAAATCTCGAA
66 CGGCGGGAATAAATCCCGAA
* *** * * * * *
19656701 ACAAATTTTATTTAATTTAATTTCTCGTTTGTGGCAACAAAATCAAATCAAATAAATTTTTATTA
1 ACAAATTTTATTTAATTCAA-TTCTAAATT-AGGAAACAAAATAAAATCAAATAAAATCTTATTA
** *
19656766 AACGTTGGGAATAAATCCCAAA
64 AACGGCGGGAATAAATCCCGAA
* * * ** * * ** **
19656788 ATAGATTTTATTTAATTTAATTTCTCATTTTTGGCAACAAAATTAAAATGTAAT-AAATC-CGTT
1 ACAAATTTTATTTAATTCAA-TTCT-AAATTAGGAAACAAAA-TAAAATCAAATAAAATCTTATT
* * *
19656851 GAACGGCGGGAATGAATCTCGAA
63 AAACGGCGGGAATAAATCCCGAA
*
19656874 ACATATTTTATTT
1 ACAAATTTTATTT
19656887 TACTCGTTTT
Statistics
Matches: 283, Mismatches: 60, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
82 5 0.02
83 63 0.22
84 79 0.28
85 10 0.04
86 33 0.12
87 82 0.29
88 11 0.04
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (85 bp):
ACAAATTTTATTTAATTCAATTCTAAATTAGGAAACAAAATAAAATCAAATAAAATCTTATTAAA
CGGCGGGAATAAATCCCGAA
Found at i:19657037 original size:79 final size:75
Alignment explanation
Indices: 19656842--19657040 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 75
19656832 AAAATGTAAT
* * *
19656842 AAATCCGTTGAACGGCGGGAATGAATCTCGAAACATATTTTATTTTACTCGTTTTTGGAAATAAA
1 AAAT-CGTTGAACGGCGGGAATCAATCCCGAAACAGATTTTATTTTACTCGTTTTTGGAAATAAA
*
19656907 AAATTGGAATA
65 AAATTAGAATA
* * *
19656918 AAATCGTTGAACGGCGGGAATCAAACCTGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAA
1 AAATCGTTGAACGGCGGGAATCAATCCCGAAACAGATTTTATTTTACTCGTTTTTGGAAAT--AA
19656983 CAAAATTTAGAATA
64 -AAAA-TTAGAATA
* * *
19656997 AAATCGTTAAACGTCGGGAATCAATCCCGAAATAGATTTTATTT
1 AAATCGTTGAACGGCGGGAATCAATCCCGAAACAGATTTTATTT
19657041 ACCTTTAATT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
75 51 0.48
76 4 0.04
77 2 0.02
78 4 0.04
79 45 0.42
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (75 bp):
AAATCGTTGAACGGCGGGAATCAATCCCGAAACAGATTTTATTTTACTCGTTTTTGGAAATAAAA
AATTAGAATA
Found at i:19657082 original size:88 final size:88
Alignment explanation
Indices: 19656969--19657140 Score: 222
Period size: 89 Copynumber: 2.0 Consensus size: 88
19656959 TTTTACTCGT
* * * * *
19656969 TTTTGGAAATAAAACAAAATTTAGAATAAAA-TCGTTAAACGTCGGGAATCAATCCCGAAATAGA
1 TTTTGGAAATAAAACAAAATATAGAATAAAATTCGTTAAACGGCGAGAATAAATCCCGAAACAGA
19657033 TTTTATTTACCTTTAATTTCCCG
66 TTTTATTTACCTTTAATTTCCCG
** * *
19657056 TTTT-GAAATAAAATCAAAATAATAGAATAAAATTCGTTGTACGGCGAGAATAAATCCTGAAACG
1 TTTTGGAAATAAAA-CAAAAT-ATAGAATAAAATTCGTTAAACGGCGAGAATAAATCCCGAAACA
*
19657120 GATTTTATTTACTTTTAATTT
64 GATTTTATTTACCTTTAATTT
19657141 TGGAAAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
86 9 0.12
87 10 0.14
88 10 0.14
89 43 0.60
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (88 bp):
TTTTGGAAATAAAACAAAATATAGAATAAAATTCGTTAAACGGCGAGAATAAATCCCGAAACAGA
TTTTATTTACCTTTAATTTCCCG
Found at i:19663184 original size:19 final size:19
Alignment explanation
Indices: 19663160--19663196 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19663150 TTTTAATTTC
*
19663160 AAAATAAAATAAAGATAAT
1 AAAATAAAATAAAAATAAT
*
19663179 AAAATAAGATAAAAATAA
1 AAAATAAAATAAAAATAA
19663197 AATACAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAAAAATAAT
Found at i:19671389 original size:39 final size:39
Alignment explanation
Indices: 19671345--19671427 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
19671335 ATAAATAAGC
* *
19671345 ATTTTAGTTAGTAGAATTCAATAATGATTAATTTTTACG
1 ATTTTAGTTAGTAGAATTCAATAACGATTAACTTTTACG
** *
19671384 ATTTTAGTTAGTAGAATTTGATAGCGATTAACTTTTACG
1 ATTTTAGTTAGTAGAATTCAATAACGATTAACTTTTACG
19671423 ATTTT
1 ATTTT
19671428 TACGATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (39 bp):
ATTTTAGTTAGTAGAATTCAATAACGATTAACTTTTACG
Found at i:19676583 original size:817 final size:812
Alignment explanation
Indices: 19674702--19676584 Score: 2857
Period size: 817 Copynumber: 2.3 Consensus size: 812
19674692 TTATATTTAA
19674702 ATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
1 ATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
*
19674767 ATGTCATAACAATTATCAAAATAAAAAAATCTACTAAAAAGCATTAAACTTATAAATAAAGACAA
66 ATGTCATAACAATTATC---A-AAAAAAATCTACTAAAAATCATTAAACTTATAAATAAAGACAA
19674832 ATAAAATAAATTAAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGTGG
127 ATAAAATAAATTAAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGTGG
* ** ** *
19674897 CGTTTATTGCAAAAACGCCGCAAAATGTGTAATCGAAAGGACTTCGTTTTTATACTGTTTATTGG
192 CGTTTATTGCAAAAACGCCGCAAAACGTGTAATCGAAA-GACTTCG-TTTT-T--TGTAAAACGC
* ** * ** * * ** * * *
19674962 TATTACCGGCGTTTTTTGTAAAAATGCCGCAAATGAAAGTTATGTATTTTAGGGTTTTGGGATTA
252 CACAAACGAAGTTGTGTCAAAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGAATTA
19675027 ATATTTAAGTTTTGTTGTATACGGTTTGGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTA
317 ATATTTAAGTTTTGTTGTATACGGTTTGGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTA
*
19675092 GGATTACAATTTTATGTTTAGGGTTTTGGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGT
382 GGATTACAATTTTATGTTTAGGGTTTTGGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGAT
* *
19675157 TTGAGTTTACGTGTTAGTTTTAATGCGAGGTTTACGGCTTATAAGATATATTAATGATCAAATTT
447 TTGAGTTTACATGTTAGTTTTAATGCGAGGTTTACGGCTTATAAGA-ATAGTAATGATCAAATTT
* * *
19675222 ATTGTTTTACGGCTTGATGTTTATGGTTTATGGTTTACCCTTATTGATTTGAATGTTACAATGCT
511 ACTGTTTTACGGCTTAATGTTTATGGTTTATGGTTCACCCTTATTGATTTGAATGTTACAATGCT
* * *
19675287 TGGTTTTTGTGTTCGGATTTGCATGAAGAATATGAGTTAGCTAGGGTTTAGCTTTTAATTTTAAT
576 TGGTTTTTGCGTTCGGATTTGCATGAAGAATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAAT
19675352 GTTTACGGGTTATAGGGATTAATAGCTTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAA
641 GTTTACGGGTTATAGGGATTAATAGCTTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAA
*
19675417 TTCTTTCTGCTTTTTACTTCTTATTATGTCACTAGTATATAGGATTATAAGAGACAGGGTTATAT
706 TTCTTTCTACTTTTTACTTCTTATTATGTCACTAGTATATAGGATTATAAGAGACAGGGTTATAT
19675482 ATATAATATGCCACGATATATATCTATGCATATATGTTATAT
771 ATATAATATGCCACGATATATATCTATGCATATATGTTATAT
*
19675524 ATTATACATATTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
1 ATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
*
19675589 ATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTATAAATAAAGACAAA
66 ATGTCATAACAATTATC--AA-AAAAAATCTACTAAAAATCATTAAACTTATAAATAAAGACAAA
** **
19675654 TAAAATAAATTAAAAAATTAGCGGCATTTATACAGAAAACGCCGCTATAGAACAAGATTTGTAAC
128 TAAAATAAATTAAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGT-GG
** * *** ***** * * * * * **
19675719 CG---A-AACGACTTCGTTTTTATACTGTTTATTGGTATTAG-CGGCGTTTTTTGTAAAAACGCC
192 CGTTTATTGCAAAAACGCCGCAAAAC-GTGTAATCG-A-AAGACTTCGTTTTTTGT-AAAACGCC
*
19675779 ACAAATGAAAGTTGTGTCAAAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGAATTA
253 ACAAACG-AAGTTGTGTCAAAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGAATTA
* *
19675844 ATATTTAAGTTTTGTTGTATGCGGTTTGGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTA
317 ATATTTAAGTTTTGTTGTATACGGTTTGGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTA
* *
19675909 GGATTATAATTTTATGTTTAGGGTTTTGGGTTTAGGTTTACGGTTTGAGGAATGGGGTTTAGGAT
382 GGATTACAATTTTATGTTTAGGGTTTTGGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGAT
19675974 TTGAGTTTACATGTTAGTTTTAATGCGAGGTTTACGGCTTATAAG-AT-GTAATGATCAAATTTA
447 TTGAGTTTACATGTTAGTTTTAATGCGAGGTTTACGGCTTATAAGAATAGTAATGATCAAATTTA
19676037 CTGTTTTACGGCTTAATGTTTATGGTTTATGGTTCACCCTTATTGATTTGAATGTTACAATGCTT
512 CTGTTTTACGGCTTAATGTTTATGGTTTATGGTTCACCCTTATTGATTTGAATGTTACAATGCTT
19676102 GGTTTTTGCGTTCGGATTTGCATGAAGAATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATG
577 GGTTTTTGCGTTCGGATTTGCATGAAGAATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATG
19676167 TTTACGGGTTATAGGGATTAATAGCTTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAAATTAAAA
642 TTTACGGGTTATAGGGATTAATAGCTTCGGGTTTTAGGGTACAAAAGC-AAAAAAAAAATTAAAA
* *
19676232 TTCTTTCTACTTTTTACTTCTTATTATTTCACTAGTATATATATAGGATTATAAGTGACAGGGTT
706 TTCTTTCTACTTTTTACTTCTTATTATGTCACTAG----TATATAGGATTATAAGAGACAGGGTT
*
19676297 ATATATA-ATATATGTCACGATATATATCTATGCATATATGTTATAT
767 ATATATATA-ATATGCCACGATATATATCTATGCATATATGTTATAT
* *
19676343 ATTATATATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATGTATCAATTTAAAATA
1 ATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
* *
19676408 ATATCATAACAATTATC-AAAAAAATCTATTAAAAATCATTAAACTTATAAATAAAGACAAATAA
66 ATGTCATAACAATTATCAAAAAAAATCTACTAAAAATCATTAAACTTATAAATAAAGACAAATAA
*
19676472 AATAAATTGAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGTGGCGTT
131 AATAAATTAAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGTGGCGTT
*
19676537 TATTGCAAAAACGCCGCAAAACGTGTAACCGAAACGACTTCGTTTTTT
196 TATTGCAAAAACGCCGCAAAACGTGTAATCGAAA-GACTTCGTTTTTT
19676585 ATACTGTTTA
Statistics
Matches: 950, Mismatches: 92, Indels: 43
0.88 0.08 0.04
Matches are distributed among these distances:
814 189 0.20
815 155 0.16
816 8 0.01
817 233 0.25
818 18 0.02
819 156 0.16
820 3 0.00
821 105 0.11
822 83 0.09
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (812 bp):
ATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTATCAATTTAAAATA
ATGTCATAACAATTATCAAAAAAAATCTACTAAAAATCATTAAACTTATAAATAAAGACAAATAA
AATAAATTAAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACAAGATTTGTGGCGTT
TATTGCAAAAACGCCGCAAAACGTGTAATCGAAAGACTTCGTTTTTTGTAAAACGCCACAAACGA
AGTTGTGTCAAAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGAATTAATATTTAAG
TTTTGTTGTATACGGTTTGGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAA
TTTTATGTTTAGGGTTTTGGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGATTTGAGTTTA
CATGTTAGTTTTAATGCGAGGTTTACGGCTTATAAGAATAGTAATGATCAAATTTACTGTTTTAC
GGCTTAATGTTTATGGTTTATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGC
GTTCGGATTTGCATGAAGAATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGT
TATAGGGATTAATAGCTTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTAC
TTTTTACTTCTTATTATGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATG
CCACGATATATATCTATGCATATATGTTATAT
Found at i:19676964 original size:16 final size:16
Alignment explanation
Indices: 19676943--19676973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19676933 ATTTTTTCTC
*
19676943 TTCTAAAATTCCTAAG
1 TTCTAAAATCCCTAAG
19676959 TTCTAAAATCCCTAA
1 TTCTAAAATCCCTAA
19676974 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:19684347 original size:87 final size:87
Alignment explanation
Indices: 19684194--19684382 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
19684184 ACACAACTTA
* * *
19684194 AAGCGGAGGCAACATCGAGAGAAGCTGAAGTTCAAAAAAGATATGAAGAACTCCAACTACAACTT
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAAGTTCAAAAAAGATATGAACAACTCCAACTACAACTT
* *
19684259 AAAGTAGATGCGGCAGTAAGAG
66 AAAGCAGATGCGGCAGCAAGAG
* * * * *
19684281 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAACAACTCTAGC-AGCAGC
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAAGTTCAA-AAAAGATATGAACAACTCCAACTA-CAAC
*
19684344 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGGCAGCAAGAG
* *
19684368 AAGCAAAGGCTACAG
1 AAGCAGAGGCAACAG
19684383 AAAGGGAAGT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 1 0.01
87 80 0.93
88 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.28, T:0.13
Consensus pattern (87 bp):
AAGCAGAGGCAACAGCGAGAGAAGCTGAAGTTCAAAAAAGATATGAACAACTCCAACTACAACTT
AAAGCAGATGCGGCAGCAAGAG
Found at i:19684781 original size:43 final size:43
Alignment explanation
Indices: 19684732--19685240 Score: 743
Period size: 43 Copynumber: 11.8 Consensus size: 43
19684722 GTTTTTCTAA
* * *
19684732 AAGCGCCGCTAAAAACCATGAG-CTATAGCGGCGTTTGTTGGTT
1 AAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTTGATGGAT
*
19684775 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTTGTATGG-T
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTG-ATGGAT
* * * *
19684818 AAGCGCCGCTAAAGACCAAGATCTATAGCGGCGTTTTATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
* * * * *
19684861 AAGCACCGCTAAAGGCCATGGGCTATAGCAGCGTTTGATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
* *
19684904 TAGCGCCGCTAAAGACCATGATCTATAGCGGCGTTTGATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
*
19684947 AAGCGCCGCTAAAGACCATGGTTTATAGCGGCGTTTGATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
*
19684990 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAA
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
*
19685033 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAA
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
*
19685076 AAGTGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
** *
19685119 AAGTACCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
* *
19685162 AAGCGCCGCTAAAGACCATGGTCTATAGTGGCATTTGATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
* * *
19685205 AAACGCCGCAAAAGACCCTGGTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTT
19685241 ATTATAAAAA
Statistics
Matches: 423, Mismatches: 40, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
42 5 0.01
43 415 0.98
44 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAT
Found at i:19685568 original size:25 final size:26
Alignment explanation
Indices: 19685528--19685576 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
19685518 GTAAAATTAT
19685528 AATAAAATTTTGAT-AAAATAATAAG
1 AATAAAATTTTGATAAAAATAATAAG
19685553 AATAAAATTATT-ATAAAAATAATA
1 AATAAAATT-TTGATAAAAATAATA
19685577 TTTCAGTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATAAAATTTTGATAAAAATAATAAG
Found at i:19685778 original size:20 final size:18
Alignment explanation
Indices: 19685753--19685812 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 18
19685743 TCATTAAAAT
19685753 AAATTAAATAAATTATTAAA
1 AAATTAAA-AAA-TATTAAA
*
19685773 AAATTAAAAAAATATT-TA
1 AAATT-AAAAAATATTAAA
19685791 AAA-TAAAAAATATTTAAA
1 AAATTAAAAAATA-TTAAA
19685809 AAAT
1 AAAT
19685813 AAAGAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 8 0.24
19 4 0.12
20 8 0.24
21 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTAAAAAATATTAAA
Found at i:19685798 original size:16 final size:16
Alignment explanation
Indices: 19685779--19685809 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19685769 TAAAAAATTA
19685779 AAAAAATATTTAAAAT
1 AAAAAATATTTAAAAT
19685795 AAAAAATATTTAAAA
1 AAAAAATATTTAAAA
19685810 AATAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATATTTAAAAT
Found at i:19685811 original size:18 final size:18
Alignment explanation
Indices: 19685768--19685815 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
19685758 AAATAAATTA
19685768 TTAAAAAATTAAAAAAATAT
1 TTAAAAAA-T-AAAAAATAT
19685788 TT--AAAATAAAAAATAT
1 TTAAAAAATAAAAAATAT
19685804 TTAAAAAATAAA
1 TTAAAAAATAAA
19685816 GAAAATCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 12 0.46
20 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAAATAAAAAATAT
Found at i:19686484 original size:22 final size:21
Alignment explanation
Indices: 19686454--19686503 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19686444 GATATTATTA
19686454 TTTTT-ATAAAAATTTTATAAC
1 TTTTTAATAAAAATTTTAT-AC
** *
19686475 TTTTTAATAAATTTTTTATAG
1 TTTTTAATAAAAATTTTATAC
19686496 TTTTTAAT
1 TTTTTAAT
19686504 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTAATAAAAATTTTATAC
Found at i:19686490 original size:21 final size:21
Alignment explanation
Indices: 19686466--19686510 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19686456 TTTATAAAAA
19686466 TTTTATAACTTTTTAATAAATT
1 TTTTAT-ACTTTTTAATAAATT
* *
19686488 TTTTATAGTTTTTAATTAATT
1 TTTTATACTTTTTAATAAATT
19686509 TT
1 TT
19686511 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATACTTTTTAATAAATT
Found at i:19686683 original size:52 final size:52
Alignment explanation
Indices: 19686619--19686724 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
19686609 GTAAATATTT
19686619 TCAATAAAGAACCTAAATGCTATCAAAAGCATAGGCAGTTTTATACCTTTCA
1 TCAATAAAGAACCTAAATGCTATCAAAAGCATAGGCAGTTTTATACCTTTCA
*
19686671 TCAATAAAGAACCTAAATGCTATCTAAAGCATAGGCAGTTTTATACCTTTCA
1 TCAATAAAGAACCTAAATGCTATCAAAAGCATAGGCAGTTTTATACCTTTCA
19686723 TC
1 TC
19686725 CGAAGTCCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (52 bp):
TCAATAAAGAACCTAAATGCTATCAAAAGCATAGGCAGTTTTATACCTTTCA
Found at i:19688290 original size:125 final size:124
Alignment explanation
Indices: 19688068--19688325 Score: 381
Period size: 125 Copynumber: 2.1 Consensus size: 124
19688058 AAATAGTGGG
** * * * *
19688068 AAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTAGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTCTGAAATAGCGCCCTCGTAGACGCGATT
19688133 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACGTTTTCTGAGCAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACG-TTTCTGAGCAAATAGTATA
* * *
19688193 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTCTGAAATTGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTCTGAAATAGCGCCCTCGTAGACGCGATT
* * *
19688258 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAG-TGGTCATGTAAGAAATAA-TTTTTTTTTGACGTTTCTGAGCAAATAGTATA
19688319 AAATCGC
1 AAATCGC
19688326 ACCCTCGTGG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
125 65 0.55
126 41 0.34
127 13 0.11
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTCTGAAATAGCGCCCTCGTAGACGCGATT
TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:19690391 original size:23 final size:23
Alignment explanation
Indices: 19690361--19690603 Score: 258
Period size: 23 Copynumber: 10.1 Consensus size: 23
19690351 TGTTGCTTCG
*
19690361 ATTAGGTTAAGGTTTTTAATTAA
1 ATTAGGTTAGGGTTTTTAATTAA
*
19690384 ATTAGGTTAAGGTTTTTAATT-A
1 ATTAGGTTAGGGTTTTTAATTAA
*
19690406 AGTAGGGTTAGGGTTTTTAATTAA
1 ATTA-GGTTAGGGTTTTTAATTAA
* *
19690430 GTTATGTTAGGGTTTTTAATTTAATTA
1 ATTAGGTTAGGGTTTTTAA-TT-A--A
19690457 AGTTAGGTTA-GGTTTTATAATTAA
1 A-TTAGGTTAGGGTTTT-TAATTAA
* *
19690481 GTTATGTTAGGGTTTTTAATTAA
1 ATTAGGTTAGGGTTTTTAATTAA
19690504 ATTAGGTTAGGGTTTTTAATTAAA
1 ATTAGGTTAGGGTTTTTAATT-AA
19690528 TTAGGTTAGGGTTAGGGTTTTTAATT-A
1 --A--TTA-GGTTAGGGTTTTTAATTAA
*
19690555 AGTAGGGTTAGGGTTTTTAATTAA
1 ATTA-GGTTAGGGTTTTTAATTAA
*
19690579 ATTAGGTTAGGGTTTTTAATCAA
1 ATTAGGTTAGGGTTTTTAATTAA
19690602 AT
1 AT
19690604 AATGTCAAAA
Statistics
Matches: 190, Mismatches: 14, Indels: 32
0.81 0.06 0.14
Matches are distributed among these distances:
22 4 0.02
23 124 0.65
24 18 0.09
25 2 0.01
26 2 0.01
27 10 0.05
28 13 0.07
29 17 0.09
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (23 bp):
ATTAGGTTAGGGTTTTTAATTAA
Found at i:19690490 original size:74 final size:73
Alignment explanation
Indices: 19690375--19690598 Score: 342
Period size: 74 Copynumber: 3.0 Consensus size: 73
19690365 GGTTAAGGTT
* * *
19690375 TTTAATTAAATTAGGTTAAGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAATTAAGTTATGTTAG
1 TTTAATTAAGTTAGGTT-AGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
19690440 GGTTTTTAA
65 GGTTTTTAA
*
19690449 TTTAATTAAGTTAGGTTAGGTTTTATAATTAAGTTA-TGTTAGGGTTTTTAATTAAATTAGGTTA
1 TTTAATTAAGTTAGGTTAGGTTTT-TAATTAAG-TAGGGTTAGGGTTTTTAATTAAATTAGGTTA
19690513 GGGTTTTTAA
64 GGGTTTTTAA
* *
19690523 TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 TTTAATTAAGTTA-GGTTA-GGTTTTTAATTAAGTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
19690588 GGGTTTTTAA
64 GGGTTTTTAA
19690598 T
1 T
19690599 CAAATAATGT
Statistics
Matches: 138, Mismatches: 7, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
73 7 0.05
74 72 0.52
75 53 0.38
76 6 0.04
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (73 bp):
TTTAATTAAGTTAGGTTAGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
GTTTTTAA
Found at i:19692754 original size:14 final size:15
Alignment explanation
Indices: 19692737--19692770 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19692727 AATAAATATC
19692737 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
19692751 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
19692766 TAAAA
1 TAAAA
19692771 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:19692998 original size:22 final size:22
Alignment explanation
Indices: 19692968--19693009 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19692958 ATTTGGAGAT
*
19692968 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
19692990 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
19693010 TTTGAGAGAA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:19693017 original size:30 final size:30
Alignment explanation
Indices: 19692981--19693039 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19692971 TTGAAGGAAA
* * *
19692981 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTAGAAGGAAATTGAGAGT
19693011 TTGAGAGAATTTTAGAAGGAAATTGAGAG
1 TTGAGAGAATTTTAGAAGGAAATTGAGAG
19693040 AAATTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTAGAAGGAAATTGAGAGT
Found at i:19693030 original size:52 final size:51
Alignment explanation
Indices: 19692959--19693061 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
19692949 TTAATATGGA
* * *
19692959 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTAGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
19693010 TTTGAGAGAATTTTAGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTAGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
19693062 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTAGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:19693039 original size:22 final size:22
Alignment explanation
Indices: 19693011--19693102 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
19693001 ATTTGAGAGT
*
19693011 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
* *
19693033 TTGAGAGAAATTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
19693055 TTGAGAGAATTTTTGAAAGG-AA
1 TTGAGAGAATTTTTG-AAGGAAA
*
19693077 TTGAGCGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
19693099 TTGA
1 TTGA
19693103 TATTGAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
21 4 0.06
22 55 0.87
23 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.28, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:19701341 original size:6 final size:6
Alignment explanation
Indices: 19701330--19701357 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19701320 TTATGCTGGA
19701330 AATGGC AATGGC AATGGC AATGGC AATG
1 AATGGC AATGGC AATGGC AATGGC AATG
19701358 ACAAGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (6 bp):
AATGGC
Found at i:19701369 original size:18 final size:18
Alignment explanation
Indices: 19701326--19701366 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19701316 CTAATTATGC
*
19701326 TGGAAATGGCAATGGCAA
1 TGGAAATGGCAATGACAA
*
19701344 TGGCAATGGCAATGACAA
1 TGGAAATGGCAATGACAA
19701362 -GGAAA
1 TGGAAA
19701367 ATGTTGCTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.41, C:0.12, G:0.32, T:0.15
Consensus pattern (18 bp):
TGGAAATGGCAATGACAA
Found at i:19703407 original size:11 final size:11
Alignment explanation
Indices: 19703391--19703427 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
19703381 TTAATCAAAT
19703391 ATATATATTTA
1 ATATATATTTA
**
19703402 ATATATATAAA
1 ATATATATTTA
19703413 ATATATATTTA
1 ATATATATTTA
19703424 ATAT
1 ATAT
19703428 GGGCCAGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATATTTA
Found at i:19703414 original size:24 final size:23
Alignment explanation
Indices: 19703355--19703427 Score: 78
Period size: 22 Copynumber: 3.1 Consensus size: 23
19703345 TAGCCGAAAT
*
19703355 TATATATTAAATATATAT-TTTTA
1 TATATA-TAAATATATATATTTAA
* *
19703378 TTTTTAATCAAATATATATATTTAA
1 TATAT-AT-AAATATATATATTTAA
19703403 TATATATAAA-ATATATATTTAA
1 TATATATAAATATATATATTTAA
19703425 TAT
1 TAT
19703428 GGGCCAGGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 15 0.36
23 7 0.17
24 13 0.31
25 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATATAAATATATATATTTAA
Found at i:19704859 original size:10 final size:10
Alignment explanation
Indices: 19704841--19704877 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
19704831 CTCCACCTTT
19704841 CCTAGCCGAG
1 CCTAGCCGAG
*
19704851 CCGAGCCGAG
1 CCTAGCCGAG
*
19704861 CCTAGCCTAG
1 CCTAGCCGAG
19704871 CCTAGCC
1 CCTAGCC
19704878 AGGCGTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.11
Consensus pattern (10 bp):
CCTAGCCGAG
Found at i:19711426 original size:31 final size:31
Alignment explanation
Indices: 19711391--19711457 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
19711381 AACCAAAAAA
* *
19711391 AAGTTCAAACTCCAATGTGAGAACAATTACC
1 AAGTTCAAACTCCAATATAAGAACAATTACC
* ** *
19711422 AAGTTCAAGCTTTAATATAAGAACAATTATC
1 AAGTTCAAACTCCAATATAAGAACAATTACC
19711453 AAGTT
1 AAGTT
19711458 TAGGGATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (31 bp):
AAGTTCAAACTCCAATATAAGAACAATTACC
Found at i:19711446 original size:91 final size:90
Alignment explanation
Indices: 19711316--19711485 Score: 198
Period size: 91 Copynumber: 1.9 Consensus size: 90
19711306 AGGCCTCAAA
* * ** * * *
19711316 GTGAGAACAACTATCAAGTTCAAGTCTCAATTTGGGAACAATTGTCAAATTCAGGGGTTAATTTG
1 GTGAGAACAACTACCAAGTTCAAGTCTCAATATAAGAACAATTATCAAATTCAGGGATTAACTTG
19711381 AACCAAAAAAAAGTTCAAACTCCAAT
66 AA-CAAAAAAAAGTTCAAACTCCAAT
* * * *
19711407 GTGAGAACAATTACCAAGTTCAAG-CTTTAATATAAGAACAATTATCAAGTTTAGGGATTAACTT
1 GTGAGAACAACTACCAAGTTCAAGTC-TCAATATAAGAACAATTATCAAATTCAGGGATTAACTT
* *
19711471 GGATAAAAAAAAGTT
65 GAACAAAAAAAAGTT
19711486 TCAACCCCTA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
90 12 0.18
91 53 0.82
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (90 bp):
GTGAGAACAACTACCAAGTTCAAGTCTCAATATAAGAACAATTATCAAATTCAGGGATTAACTTG
AACAAAAAAAAGTTCAAACTCCAAT
Found at i:19711574 original size:17 final size:18
Alignment explanation
Indices: 19711554--19711595 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
19711544 AAATAAACAA
19711554 TTAAAAAT-CATAAAATT
1 TTAAAAATACATAAAATT
*
19711571 TTAAAAATATATAAAATT
1 TTAAAAATACATAAAATT
19711589 TATAAAA
1 T-TAAAA
19711596 CTGGTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAATACATAAAATT
Found at i:19713310 original size:76 final size:76
Alignment explanation
Indices: 19713214--19713355 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
19713204 TGCATGATTT
19713214 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAGACCT-TTACCAAAATCTGCTCCTTCAG
1 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAA-ACCTCTT-CCAAAATCTGCTCCTTCAG
19713278 CTACCATAGCGTG
64 CTACCATAGCGTG
* * * * * *
19713291 TTGAAGTT-AAAAGCGTTGATGTTGTGCAGATGTAAAACCTCTTTCGAATTCTGCTCCTTCAGCT
1 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAACCTCTTCCAAAATCTGCTCCTTCAGCT
19713355 A
66 A
19713356 TACCGGTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
75 23 0.40
76 28 0.48
77 7 0.12
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (76 bp):
TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAACCTCTTCCAAAATCTGCTCCTTCAGCT
ACCATAGCGTG
Found at i:19726660 original size:24 final size:24
Alignment explanation
Indices: 19726633--19726685 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
19726623 TATTAATTGA
*
19726633 AGAAAGGATTAAATTGTAAAAGTG
1 AGAAAGGATTAAATTGCAAAAGTG
*
19726657 AGAAATGATTAAATTGCAAAAGTG
1 AGAAAGGATTAAATTGCAAAAGTG
19726681 AGAAA
1 AGAAA
19726686 AATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.23
Consensus pattern (24 bp):
AGAAAGGATTAAATTGCAAAAGTG
Found at i:19729682 original size:16 final size:15
Alignment explanation
Indices: 19729656--19729685 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19729646 TATTATTTCA
19729656 TTATTTATTCTTTTG
1 TTATTTATTCTTTTG
19729671 TTATTCTATTCTTTT
1 TTATT-TATTCTTTT
19729686 CATGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTATTCTTTTG
Found at i:19735023 original size:17 final size:18
Alignment explanation
Indices: 19734998--19735038 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
19734988 TTGTTTTCTT
*
19734998 TTTACTCTTTTA-GTTTC
1 TTTACTCTTTTATGTTTA
*
19735015 TTTATTCTTTTATGTTTA
1 TTTACTCTTTTATGTTTA
19735033 TTTACT
1 TTTACT
19735039 TTATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTACTCTTTTATGTTTA
Done.