Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003908.1 Hibiscus syriacus cultivar Beakdansim tig00008454_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 240793
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2450 original size:35 final size:35
Alignment explanation
Indices: 2367--2494 Score: 134
Period size: 35 Copynumber: 3.6 Consensus size: 35
2357 AACAAAGTAC
*
2367 GTCTCGCTTGAGACAGTTTTCTATAAAA-AAAATTA
1 GTCTCGCTTGAGACAGTTTTCTA-AAAACAAATTTA
*
2402 GTCTCGCTTGAGACAGTTTTCTAAAAACAAATTTT
1 GTCTCGCTTGAGACAGTTTTCTAAAAACAAATTTA
* * * *
2437 GTCTTGCTAGAGACAAATTTTTCTCAAAACAAATTTCA
1 GTCTCGCTTGAGAC--AGTTTTCTAAAAACAAATTT-A
* *
2475 -TCTCTCTTGAGACATTTTTC
1 GTCTCGCTTGAGACAGTTTTC
2495 CTTTGAGGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
34 4 0.05
35 47 0.59
37 28 0.35
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (35 bp):
GTCTCGCTTGAGACAGTTTTCTAAAAACAAATTTA
Found at i:2706 original size:21 final size:21
Alignment explanation
Indices: 2680--2742 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
2670 CAACCTTTAA
2680 TTGTTTCCCTTGAAACAAGTT
1 TTGTTTCCCTTGAAACAAGTT
2701 TTGTTTCCCTTGAAACAAGTT
1 TTGTTTCCCTTGAAACAAGTT
* *
2722 TTGTCTCCCTTGAGAC-AGTT
1 TTGTTTCCCTTGAAACAAGTT
2742 T
1 T
2743 CTCCTGAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.12
21 35 0.88
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGTTTCCCTTGAAACAAGTT
Found at i:2793 original size:85 final size:84
Alignment explanation
Indices: 2616--2803 Score: 211
Period size: 85 Copynumber: 2.2 Consensus size: 84
2606 ACTTTGAAGG
* * ** *
2616 TGTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACGGTTTCCCTTGAAATGCCAACCTTTAAT
1 TGTTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACCAACATTTAAT
**
2681 TGTTTCCCTTGAAACAAGTTT
65 CATTTCCCTTGAAACAAG-TT
* *
2702 TGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCC-TGAAACACCCATATTTGAG
1 TGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTC-CCTTGAAACACCAACATTT-A-
2766 ATCATTTCCCTTGAAACGAA-TT
63 ATCATTTCCCTTGAAAC-AAGTT
*
2788 T-TTTCCCTTGAGACAA
1 TGTTTCCCTTGAAACAA
2804 TTTCTCTTGA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
85 51 0.58
86 20 0.23
87 15 0.17
88 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (84 bp):
TGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACCAACATTTAATC
ATTTCCCTTGAAACAAGTT
Found at i:2876 original size:66 final size:66
Alignment explanation
Indices: 2700--2881 Score: 246
Period size: 64 Copynumber: 2.8 Consensus size: 66
2690 TGAAACAAGT
* **
2700 TTTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCCTGAAACACCCATATTTGA
1 TTTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATATTTGA
2765 G
66 G
* ** * *
2766 ATCATTTCCCTTGAAACGAA-TTTT-T-TCCCTTGAGACAATTTCTCTTGAAACACAAATCTTTG
1 TTTGTTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATATTTG
2828 AG
65 AG
2830 TTTGTTT-CCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 TTTGTTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
2882 TAAATCCCTA
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 11 0.11
64 42 0.42
65 2 0.02
66 42 0.42
67 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (66 bp):
TTTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATATTTGA
G
Found at i:3070 original size:82 final size:80
Alignment explanation
Indices: 2984--3224 Score: 281
Period size: 82 Copynumber: 3.0 Consensus size: 80
2974 ATAATCAGTC
* * * * *
2984 GTCCTCATACA-TATGAATCATGTCATCCACTGATCAGGCCTCCTCATCACGTAGGAGATGTGTC
1 GTCCTCAT-CAGTA-GAACCATGTCATCCACCGACCAGACCTCCTCATCACGTTGGAG-TGTGTC
3048 ACCCCTAGATAACCAACT
63 ACCCCTAGATAACCAACT
* *
3066 GTCCTCATCAGTAGTAACCATGTCATCCACCGACCAGACCTCCTCATCACATTGGAGCCGTGTCA
1 GTCCTCATCAGTAG-AACCATGTCATCCACCGACCAGACCTCCTCATCACGTTGGAG-TGTGTCA
*
3131 CCCCTAGATAACCAATT
64 CCCCTAGATAACCAACT
* * * **
3148 ATCCTCATCAGTAGGAACCGTTTCATCCACCGACCAGATATCCTCATCACGTTGGAGTAGTGT--
1 GTCCTCATCAGTA-GAACCATGTCATCCACCGACCAGACCTCCTCATCACGTTGGAGT-GTGTCA
3211 CCCCTAGATAACCA
64 CCCCTAGATAACCA
3225 GTCATCCTCA
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
80 14 0.10
81 3 0.02
82 121 0.87
83 1 0.01
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (80 bp):
GTCCTCATCAGTAGAACCATGTCATCCACCGACCAGACCTCCTCATCACGTTGGAGTGTGTCACC
CCTAGATAACCAACT
Found at i:4534 original size:2 final size:2
Alignment explanation
Indices: 4527--4553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4517 CTTATGTGAT
4527 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 T
4554 TAAGTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7777 original size:17 final size:18
Alignment explanation
Indices: 7755--7798 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
7745 ATAATGTAAT
7755 TTATTTAA-AAATTATTA
1 TTATTTAATAAATTATTA
7772 TTATTTTAATTAAATTATTA
1 TTA-TTTAA-TAAATTATTA
*
7792 TTTTTTA
1 TTATTTA
7799 TCAAGTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 5 0.22
19 4 0.17
20 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTTAATAAATTATTA
Found at i:8506 original size:26 final size:26
Alignment explanation
Indices: 8460--8513 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
8450 TATATATCAC
* **
8460 TCTTTTATAAATTTATTTTTTTAAAA
1 TCTTTAATAAATTTAGATTTTTAAAA
*
8486 TCTTTAATAAATTTAGATTTTTGAAA
1 TCTTTAATAAATTTAGATTTTTAAAA
8512 TC
1 TC
8514 GAATTCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (26 bp):
TCTTTAATAAATTTAGATTTTTAAAA
Found at i:11164 original size:69 final size:69
Alignment explanation
Indices: 11049--11187 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
11039 AGATGGGAGT
* *
11049 TGAGATGTTGATTACCATTTTGAGCATTTACATGCCCTGATCTATCTCCGGATGAGAACATTGCC
1 TGAGATGTTGATTACCATTTTGAGCATTTACATGCCCTGATATATCTCCGGATGAAAACATTGCC
11114 TTGC
66 TTGC
* *
11118 TGAGATGTTGATTACCATTTTGAGCATTTACGTGCCCTG-TAATATCTCCTGATGAAAACATTGC
1 TGAGATGTTGATTACCATTTTGAGCATTTACATGCCCTGAT-ATATCTCCGGATGAAAACATTGC
11182 CTTGC
65 CTTGC
11187 T
1 T
11188 TACGACGGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (69 bp):
TGAGATGTTGATTACCATTTTGAGCATTTACATGCCCTGATATATCTCCGGATGAAAACATTGCC
TTGC
Found at i:15435 original size:13 final size:13
Alignment explanation
Indices: 15390--15437 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
15380 ACATAAATAT
15390 TTAATCAAATCAG
1 TTAATCAAATCAG
** *
15403 TTTCTCAAATTAG
1 TTAATCAAATCAG
*
15416 CTAATCAAATCAG
1 TTAATCAAATCAG
*
15429 TTGATCAAA
1 TTAATCAAA
15438 CCAGCTACTG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (13 bp):
TTAATCAAATCAG
Found at i:15443 original size:26 final size:26
Alignment explanation
Indices: 15391--15444 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
15381 CATAAATATT
** **
15391 TAATCAAATCAGTTTCTCAAATTAGC
1 TAATCAAATCAGTTGATCAAACCAGC
15417 TAATCAAATCAGTTGATCAAACCAGC
1 TAATCAAATCAGTTGATCAAACCAGC
15443 TA
1 TA
15445 CTGGAATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (26 bp):
TAATCAAATCAGTTGATCAAACCAGC
Found at i:19566 original size:13 final size:13
Alignment explanation
Indices: 19548--19572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19538 AAAAATGGCT
19548 TATAATCATATTA
1 TATAATCATATTA
19561 TATAATCATATT
1 TATAATCATATT
19573 TAAATAATTT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATCATATTA
Found at i:22157 original size:23 final size:23
Alignment explanation
Indices: 22096--22156 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
22086 GTGTTTTCAT
* *
22096 AAAAAAAACCCTAAAAGTATTTC
1 AAAAAAATCTCTAAAAGTATTTC
*
22119 AGAAAAATCTCTAAAAGTATTTC
1 AAAAAAATCTCTAAAAGTATTTC
22142 AAAAAAATCT-TAAAA
1 AAAAAAATCTCTAAAA
22157 AAAATGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (23 bp):
AAAAAAATCTCTAAAAGTATTTC
Found at i:23673 original size:16 final size:16
Alignment explanation
Indices: 23643--23674 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
23633 TAATTTTAAA
23643 AAAATTATTTAAAAAT
1 AAAATTATTTAAAAAT
23659 AAAATATATTTAAAAA
1 AAAAT-TATTTAAAAA
23675 AACTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTATTTAAAAAT
Found at i:25450 original size:19 final size:19
Alignment explanation
Indices: 25415--25452 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25405 TCGAAATTGG
*
25415 GTATCGATACTGAAGTATA
1 GTATCGATACTCAAGTATA
25434 GTATCGATAC-CATAGTATA
1 GTATCGATACTCA-AGTATA
25453 AAAGTATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (19 bp):
GTATCGATACTCAAGTATA
Found at i:25854 original size:17 final size:16
Alignment explanation
Indices: 25829--25862 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25819 CTTTGCTATG
25829 TGATATGATTTATGTGA
1 TGATATGATTT-TGTGA
*
25846 TGATGTGATTTTGTGA
1 TGATATGATTTTGTGA
25862 T
1 T
25863 ATAAGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
TGATATGATTTTGTGA
Found at i:25913 original size:18 final size:19
Alignment explanation
Indices: 25878--25915 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25868 TTATATGATT
25878 ATGAATTATGTAAATAACA
1 ATGAATTATGTAAATAACA
*
25897 ATGACTTATGT-AATAACA
1 ATGAATTATGTAAATAACA
25915 A
1 A
25916 GAGAAAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
ATGAATTATGTAAATAACA
Found at i:29223 original size:51 final size:48
Alignment explanation
Indices: 29149--29342 Score: 176
Period size: 49 Copynumber: 3.9 Consensus size: 48
29139 AATTCATACT
* *
29149 ATAAAAAATTGTAGCACTAAATACATACTTACATCGATGTAAGTGAATAAA
1 ATAAAAAA-TGTAACAGT-AATACATACTTACA-CGATGTAAGTGAATAAA
*
29200 ATAAACAAATGTAGTACA-TAATACATACTTACACTAGTGTAAGTGAATAAA
1 ATAAA-AAATGTA--ACAGTAATACATACTTACACGA-TGTAAGTGAATAAA
* * * *
29251 ACAAAAAGTGTAACAGTTAACACATAC-TACACCGGTGTAAGTGAATAAA
1 ATAAAAAATGTAACAG-TAATACATACTTACA-CGATGTAAGTGAATAAA
* * * *
29300 ATAAAAAATATAACACTTAACACATACTTATACTGATGTAAGT
1 ATAAAAAATGTAACA-GTAATACATACTTACAC-GATGTAAGT
29343 ATGTACATCT
Statistics
Matches: 120, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
48 3 0.03
49 41 0.34
50 29 0.24
51 41 0.34
52 4 0.03
53 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26
Consensus pattern (48 bp):
ATAAAAAATGTAACAGTAATACATACTTACACGATGTAAGTGAATAAA
Found at i:29294 original size:49 final size:49
Alignment explanation
Indices: 29171--29329 Score: 187
Period size: 49 Copynumber: 3.2 Consensus size: 49
29161 AGCACTAAAT
* * *
29171 ACATACTTACATCGATGTAAGTGAATAAAATAAACAAATGTAGTACA-TAAT
1 ACATACTTACACCGGTGTAAGTGAATAAAATAAA-AAATGTA--ACATTAAC
** * *
29222 ACATACTTACACTAGTGTAAGTGAATAAAACAAAAAGTGTAACAGTTAAC
1 ACATACTTACACCGGTGTAAGTGAATAAAATAAAAAATGTAACA-TTAAC
*
29272 ACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAATATAACACTTAAC
1 ACATACTTACACCGGTGTAAGTGAATAAAATAAAAAATGTAACA-TTAAC
29321 ACATACTTA
1 ACATACTTA
29330 TACTGATGTA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
48 3 0.03
49 43 0.47
50 17 0.18
51 29 0.32
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.25
Consensus pattern (49 bp):
ACATACTTACACCGGTGTAAGTGAATAAAATAAAAAATGTAACATTAAC
Found at i:31404 original size:83 final size:78
Alignment explanation
Indices: 31260--31420 Score: 243
Period size: 83 Copynumber: 2.0 Consensus size: 78
31250 TGAAACATGA
31260 TAGATTTCGTTTAAGGTTATTTATGAGCATTGGTTTTATATTTTCTTATTTTAGAATCAAACTGT
1 TAGATTTCGTTTAAGGTTATTTATGAGCATTGGTTTTATATTTTCTTATTTTAGAATCAAACTGT
31325 ACGTCTCCTTAGG
66 ACGTCTCCTTAGG
31338 TAGATTTCG-TTAAGGTTATTTATGAGCATTGGTTTTATTTTTATATTTTCTTATTTTAGAATCA
1 TAGATTTCGTTTAAGGTTATTTATGAGCATTGG------TTTTATATTTTCTTATTTTAGAATCA
* *
31402 AACTGTATGTGTCCTTAGG
60 AACTGTACGTCTCCTTAGG
31421 GCGACCGAGT
Statistics
Matches: 75, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
77 23 0.31
78 9 0.12
83 43 0.57
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (78 bp):
TAGATTTCGTTTAAGGTTATTTATGAGCATTGGTTTTATATTTTCTTATTTTAGAATCAAACTGT
ACGTCTCCTTAGG
Found at i:33343 original size:3 final size:3
Alignment explanation
Indices: 33335--33366 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33325 AGCACAAATC
33335 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33367 AATGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40537 original size:26 final size:28
Alignment explanation
Indices: 40504--40556 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
40494 TAATAATAAT
*
40504 TATTCAAA-T-AAATTTATAAAAAATCA
1 TATTCAAACTAAAATATATAAAAAATCA
40530 TATTCAAACTCAAAATATATAAAAAAT
1 TATTCAAACT-AAAATATATAAAAAAT
40557 AATAATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
29 14 0.61
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (28 bp):
TATTCAAACTAAAATATATAAAAAATCA
Found at i:42434 original size:2 final size:2
Alignment explanation
Indices: 42427--42455 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42417 ATATTGTCCC
42427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42456 GTCAATTTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47886 original size:17 final size:17
Alignment explanation
Indices: 47864--47901 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
47854 ATAAAGTCAA
*
47864 ACATATGGATACTTATC
1 ACATATGGATAATTATC
47881 ACATATGGATAATTATC
1 ACATATGGATAATTATC
47898 ACAT
1 ACAT
47902 GTATAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (17 bp):
ACATATGGATAATTATC
Found at i:54263 original size:14 final size:15
Alignment explanation
Indices: 54244--54280 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
54234 CCTTGTTGCA
*
54244 TTTGCATCTCGCA-T
1 TTTGCATCTCCCATT
54258 TTTGCA-CTCCCATT
1 TTTGCATCTCCCATT
54272 TTTGCATCT
1 TTTGCATCT
54281 TTGCATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.14, C:0.30, G:0.11, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCCCATT
Found at i:54289 original size:28 final size:29
Alignment explanation
Indices: 54244--54311 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
54234 CCTTGTTGCA
* *
54244 TTTGCATC-TCGCATTTTGCAC-TCCCATT
1 TTTGCATCTTTGCATTTTGCACGT-CCATC
*
54272 TTTGCATCTTTGCA-TTTGCACGTGCATC
1 TTTGCATCTTTGCATTTTGCACGTCCATC
54300 TTTGCATCTTTG
1 TTTGCATCTTTG
54312 TATTAGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 30 0.86
29 5 0.14
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTGCATCTTTGCATTTTGCACGTCCATC
Found at i:55223 original size:2 final size:2
Alignment explanation
Indices: 55216--55242 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55206 TATACCCAGA
55216 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
55243 CACAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56781 original size:36 final size:34
Alignment explanation
Indices: 56669--56781 Score: 91
Period size: 36 Copynumber: 3.1 Consensus size: 34
56659 TTGAAATATT
* *
56669 TAAAACAAAATTGATCTCACATGAGATAGTTTTCC
1 TAAAACAAAATTAATCTCACTTGAGATA-TTTTCC
* *** * * *
56704 TAATAACAAATTTTGCCTCAGTGGAGACAATTTTCC
1 TAA-AACAAAATTAATCTCACTTGAGA-TATTTTCC
56740 TTAAAACAAAATTAATCTCACTTGAGATTATTTTCTC
1 -TAAAACAAAATTAATCTCACTTGAGA-TATTTTC-C
56777 TAAAA
1 TAAAA
56782 AACAAATTTT
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
35 3 0.05
36 50 0.86
37 5 0.09
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (34 bp):
TAAAACAAAATTAATCTCACTTGAGATATTTTCC
Found at i:56840 original size:37 final size:36
Alignment explanation
Indices: 56781--56860 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
56771 TTTCTCTAAA
* *
56781 AAACAAATTTTGTCTCCCTTGAGACAGATTCTCTTG
1 AAACAAATTTTGTCACCCTTGAGACAGATTCCCTTG
** *
56817 AAACAAAGTTTTGTCACTTTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCACCCTTGAGACAGATTCCCTTG
56854 AAACAAA
1 AAACAAA
56861 ATCTTTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
36 7 0.18
37 31 0.82
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (36 bp):
AAACAAATTTTGTCACCCTTGAGACAGATTCCCTTG
Found at i:56877 original size:29 final size:29
Alignment explanation
Indices: 56844--56918 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
56834 TTTTGAGACA
56844 GTTTCCCTTGAAACAAAATCTTTGAATCT
1 GTTTCCCTTGAAACAAAATCTTTGAATCT
*
56873 GTTTCTCTTGAAACAAAATCTTTGAATCT
1 GTTTCCCTTGAAACAAAATCTTTGAATCT
56902 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
56919 TTTTGTCTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (29 bp):
GTTTCCCTTGAAACAAAATCTTTGAATCT
Found at i:57017 original size:65 final size:65
Alignment explanation
Indices: 56874--57019 Score: 220
Period size: 65 Copynumber: 2.2 Consensus size: 65
56864 TTTGAATCTG
* * * * *
56874 TTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTGAAACAAAATCTTAGAATCCGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
* *
56939 TTTCCCCTGAAACAAAATCTTAGAATCCGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAAATCTTAGAATCCGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
*
57004 TTTCTCTTAAAACAAA
1 TTTCTCTTGAAACAAA
57020 GTTTTGTCTC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (65 bp):
TTTCTCTTGAAACAAAATCTTAGAATCCGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
Found at i:57133 original size:66 final size:67
Alignment explanation
Indices: 57039--57316 Score: 352
Period size: 66 Copynumber: 4.2 Consensus size: 67
57029 CTCTTAAAAT
* **
57039 AGTTTCTCTTGAAACA-AAATCTTTGA-ATCTGTTTCCCTTTAAACAAATTTCGTCTCCCTTGAG
1 AGTTTCTCTTGAAACACAAATCTTTGAGATCTGTTTCCCTTGAAACAAATTTTATCTCCCTTGAG
57102 AC
66 AC
* * *
57104 AATTTCTCTTGAAACACCAATCTTTGA-ATCAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAG
1 AGTTTCTCTTGAAACACAAATCTTTGAGATCTGTTTCCCTTGAAACAAATTTTATCTCCCTTGAG
57168 AC
66 AC
** *
57170 AGTTTCTCTTGAAACACAAATCTTTGAGATC-GTTTCCCTTGAAATGAATTTTATCTCTCTTGAG
1 AGTTTCTCTTGAAACACAAATCTTTGAGATCTGTTTCCCTTGAAACAAATTTTATCTCCCTTGAG
57234 AC
66 AC
* * * ** * *
57236 AGTTTCCCTTGAAACACCAACCTTTGAGAT-TGTTTCCCTT-AGAACATGTTTTGTCTCTCTTGA
1 AGTTTCTCTTGAAACACAAATCTTTGAGATCTGTTTCCCTTGA-AACAAATTTTATCTCCCTTGA
57299 GAC
65 GAC
*
57302 GGTTTCTCTTGAAAC
1 AGTTTCTCTTGAAAC
57317 CATCATACCC
Statistics
Matches: 188, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
65 16 0.09
66 169 0.90
67 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (67 bp):
AGTTTCTCTTGAAACACAAATCTTTGAGATCTGTTTCCCTTGAAACAAATTTTATCTCCCTTGAG
AC
Found at i:57205 original size:30 final size:31
Alignment explanation
Indices: 57097--57213 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 31
57087 TTCGTCTCCC
* * *
57097 TTGAGA-CAATTTCTCTTGAAACACCAATCT
1 TTGAGATCAGTTTCCCTTGAAACACAAATCT
57127 TTGA-ATCAGTTTCCCTTGAAACA-AATTTTATCT
1 TTGAGATCAGTTTCCCTTGAAACACAA----ATCT
*
57160 CCCTTGAGA-CAGTTTCTCTTGAAACACAAATCT
1 ---TTGAGATCAGTTTCCCTTGAAACACAAATCT
57193 TTGAGATC-GTTTCCCTTGAAA
1 TTGAGATCAGTTTCCCTTGAAA
57214 TGAATTTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
29 2 0.03
30 37 0.52
31 1 0.01
33 8 0.11
36 20 0.28
37 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (31 bp):
TTGAGATCAGTTTCCCTTGAAACACAAATCT
Found at i:57241 original size:36 final size:35
Alignment explanation
Indices: 57133--57249 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 35
57123 ATCTTTGAAT
*
57133 CAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGA
1 CAGTTTCCCTTGAAA-AAATTTTATCTCTCTTGAGA
*
57169 CAGTTTCTCTTGAAACACAA----A--TCT-TTGAGA
1 CAGTTTCCCTTGAAA-A-AATTTTATCTCTCTTGAGA
*
57199 TC-GTTTCCCTTGAAATGAATTTTATCTCTCTTGAGA
1 -CAGTTTCCCTTGAAA-AAATTTTATCTCTCTTGAGA
57235 CAGTTTCCCTTGAAA
1 CAGTTTCCCTTGAAA
57250 CACCAACCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
29 2 0.03
30 18 0.27
31 3 0.05
33 2 0.03
35 4 0.06
36 35 0.53
37 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (35 bp):
CAGTTTCCCTTGAAAAAATTTTATCTCTCTTGAGA
Found at i:58010 original size:19 final size:20
Alignment explanation
Indices: 57978--58018 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
57968 AATGATTTTC
*
57978 AAAGAAAAATGAGAGAGAGA
1 AAAGAAAAATGAGAGAAAGA
57998 AAAGAAAAA-GAGAGAAAGA
1 AAAGAAAAATGAGAGAAAGA
58017 AA
1 AA
58019 GAGTGAACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
AAAGAAAAATGAGAGAAAGA
Found at i:60879 original size:30 final size:30
Alignment explanation
Indices: 60843--60900 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
60833 ATATTTTTCT
60843 TATTAACATTCAGAAACTCATAAACACACA
1 TATTAACATTCAGAAACTCATAAACACACA
60873 TATTAACATTCAGAAACTCATAAACACA
1 TATTAACATTCAGAAACTCATAAACACA
60901 TATAGATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.22, G:0.03, T:0.24
Consensus pattern (30 bp):
TATTAACATTCAGAAACTCATAAACACACA
Found at i:62453 original size:2 final size:2
Alignment explanation
Indices: 62446--62472 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62436 AAAAAGTTAA
62446 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
62473 AACAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65460 original size:21 final size:21
Alignment explanation
Indices: 65428--65484 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
65418 ATGTGAAGCG
*
65428 AGAACGAGAAGAGAGAGAAGA
1 AGAAGGAGAAGAGAGAGAAGA
* **
65449 AG-AGGAAGAAGAAAGAGGGGA
1 AGAAGG-AGAAGAGAGAGAAGA
65470 AGAAGGAGAAGAGAG
1 AGAAGGAGAAGAGAG
65485 GGCGCGGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.83
22 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.44, T:0.00
Consensus pattern (21 bp):
AGAAGGAGAAGAGAGAGAAGA
Found at i:65918 original size:31 final size:31
Alignment explanation
Indices: 65883--65944 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
65873 AAGTTTAATT
65883 TTAACATCAAATTCAAATAGATTAAAAGTTC
1 TTAACATCAAATTCAAATAGATTAAAAGTTC
*
65914 TTAACATCAAATTCCAATAGATTAAAAGTTC
1 TTAACATCAAATTCAAATAGATTAAAAGTTC
65945 GATCCACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (31 bp):
TTAACATCAAATTCAAATAGATTAAAAGTTC
Found at i:68282 original size:45 final size:45
Alignment explanation
Indices: 68184--68440 Score: 290
Period size: 45 Copynumber: 5.8 Consensus size: 45
68174 TGACGTCGGA
* * * * *
68184 GCCTACTTTACCAACACCAGCATCTTTAG-TTTGTTTGAAGCATC
1 GCCTGCTTTATCAGCACCAACATCTTTAGTTTTATTTGAAGCATC
* * *
68228 GCCTGCTTCATCAGCACCAACATCTTTAGTTTTATTCGAAGCACC
1 GCCTGCTTTATCAGCACCAACATCTTTAGTTTTATTTGAAGCATC
* *
68273 GCCTGCTTCATCAGCACCAACATC-TTATTTTTATTTGAAGCATC
1 GCCTGCTTTATCAGCACCAACATCTTTAGTTTTATTTGAAGCATC
* *
68317 GTCTGCTTTATCAGCATCAACATCTTTAGTTTT-TTT-ATCAGCATC
1 GCCTGCTTTATCAGCACCAACATCTTTAGTTTTATTTGA--AGCATC
* *
68362 GCCTGCTTTATCAGCATCAACATCTTTAGTGTTT-TTTGAAGTATC
1 GCCTGCTTTATCAGCACCAACATCTTTAGT-TTTATTTGAAGCATC
* * * *
68407 GCCTACTTTATCGGCATCAACATCTTTATTTTTA
1 GCCTGCTTTATCAGCACCAACATCTTTAGTTTTA
68441 CTTGGATCTT
Statistics
Matches: 186, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.01
44 68 0.37
45 110 0.59
46 6 0.03
47 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (45 bp):
GCCTGCTTTATCAGCACCAACATCTTTAGTTTTATTTGAAGCATC
Found at i:68315 original size:89 final size:90
Alignment explanation
Indices: 68198--68440 Score: 303
Period size: 89 Copynumber: 2.7 Consensus size: 90
68188 ACTTTACCAA
* * * *
68198 CACCAGCATCTTTAGT-TTGTTTGAAGCATCGCCTGCTTCATCAGCACCAACATCTTTAGTTTTA
1 CACCAACATCTTTAGTGTTTTTTGAAGCATCGCCTGCTTTATCAGCATCAACATCTTTAGTTTTA
*
68262 TTCGAAGCACCGCCTGCTTCATCAG
66 TTAGAAGCACCGCCTGCTTCATCAG
* *
68287 CACCAACATC-TTA-TTTTTATTTGAAGCATCGTCTGCTTTATCAGCATCAACATCTTTAGTTTT
1 CACCAACATCTTTAGTGTTT-TTTGAAGCATCGCCTGCTTTATCAGCATCAACATCTTTAGTTTT
* ** * *
68350 TTTATCAGCATCGCCTGCTTTATCAG
65 ATTAGAAGCACCGCCTGCTTCATCAG
* * * * *
68376 CATCAACATCTTTAGTGTTTTTTGAAGTATCGCCTACTTTATCGGCATCAACATCTTTATTTTTA
1 CACCAACATCTTTAGTGTTTTTTGAAGCATCGCCTGCTTTATCAGCATCAACATCTTTAGTTTTA
68441 CTTGGATCTT
Statistics
Matches: 131, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
87 1 0.01
88 5 0.04
89 79 0.60
90 42 0.32
91 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (90 bp):
CACCAACATCTTTAGTGTTTTTTGAAGCATCGCCTGCTTTATCAGCATCAACATCTTTAGTTTTA
TTAGAAGCACCGCCTGCTTCATCAG
Found at i:69367 original size:24 final size:25
Alignment explanation
Indices: 69334--69382 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
69324 CGTTCGTTAA
*
69334 AATGATAAACGAACACAAATGAACG
1 AATGATAAACGAACACAAACGAACG
*
69359 AATG-TAAACGAATACAAACGAACG
1 AATGATAAACGAACACAAACGAACG
69383 TACACAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.12
Consensus pattern (25 bp):
AATGATAAACGAACACAAACGAACG
Found at i:69869 original size:128 final size:128
Alignment explanation
Indices: 69651--69916 Score: 381
Period size: 128 Copynumber: 2.1 Consensus size: 128
69641 CGTAAATAAG
* * *
69651 CATAAATAAATGAGTTATCGAAAGTTCACAAACATAAACAAAAGAACGAGCCTTTTGTTCGTGTT
1 CATAAACAAAAGAGTTACCGAAAGTTCACAAACATAAACAAAAGAACGAGCCTTTTGTTCGTGTT
* * *
69716 CTTTCATTTAATTAAACGAACATAAAATC-TGATTCATGTTCGTTCGTTTAATAAATAAACAAA
66 CGTTCATTTAATTAAACGAACATAAAATCTTG-TTCATATTCATTCGTTTAATAAATAAACAAA
* * * * * *
69779 CATAAACAAAAGAGTTACCGAATGTTCACAAACGTATACGAACGAACGAGCCTTTTGTTTGTGTT
1 CATAAACAAAAGAGTTACCGAAAGTTCACAAACATAAACAAAAGAACGAGCCTTTTGTTCGTGTT
* * *
69844 CGTTCATTTAATTAAACGAATATAAAATCTTGTTCATATTTATTCGTTTAATAAATAAACATA
66 CGTTCATTTAATTAAACGAACATAAAATCTTGTTCATATTCATTCGTTTAATAAATAAACAAA
69907 CATAAACAAA
1 CATAAACAAA
69917 CTTTCCGTCA
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
128 120 0.98
129 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (128 bp):
CATAAACAAAAGAGTTACCGAAAGTTCACAAACATAAACAAAAGAACGAGCCTTTTGTTCGTGTT
CGTTCATTTAATTAAACGAACATAAAATCTTGTTCATATTCATTCGTTTAATAAATAAACAAA
Found at i:77711 original size:14 final size:14
Alignment explanation
Indices: 77692--77724 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
77682 GAATTGGAAT
77692 TTAAATTAGTTGAA
1 TTAAATTAGTTGAA
77706 TTAAATTAGTTGAA
1 TTAAATTAGTTGAA
77720 TTAAA
1 TTAAA
77725 CATGGACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (14 bp):
TTAAATTAGTTGAA
Found at i:79452 original size:41 final size:41
Alignment explanation
Indices: 79414--79834 Score: 172
Period size: 41 Copynumber: 10.2 Consensus size: 41
79404 TGCATGTTAT
* * * *
79414 CATGATCGAATCAAATTGAATGGTCAACTATTATATGTTGC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * * ** * * * * *
79455 CTTGATTGTATTGAATCGAACGGTAAATTATTGCATGCTAC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * * * *
79496 CATGATCAAATCAAATTGAATGATGAACTATTATATGATGC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * ** * * *
79537 CTTGATTGAATTGAATCGAATGGTGAATTATTGCATGCTAC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* **
79578 CATGATCGAATCAAATTGAACGATGAAGGTGAATTATTGTATGCTAC
1 CATGATCGAATCAAATTG-A--AT---GGTGAACTATTACATGCTAC
* * * * * *
79625 CATGATTGAATCAAATTGAATGATGAAATATTATATGATGC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * * ** * * * *
79666 CTTAATTGAATTGAATCGAATGGTTAATTATTGTA-AT-CTAG
1 CATGATCGAATCAAATTGAATGGTGAACTA-T-TACATGCTAC
* * * * * ** *
79707 CATGATCAAATCAAGTTGAACGATGAACTAATGTATGCTGC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * * *
79748 CATGAT----T-GAATTGAATGGTGAATTATTGCATGTTAC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
* * * *
79784 CATGATCGAATCAAGTTGAATGATGAACTATTGCATACTAC
1 CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
*
79825 CAAGATCGAA
1 CATGATCGAA
79835 CTCAGTTGAA
Statistics
Matches: 270, Mismatches: 95, Indels: 30
0.68 0.24 0.08
Matches are distributed among these distances:
36 26 0.10
37 1 0.00
39 1 0.00
40 3 0.01
41 192 0.71
42 4 0.01
43 2 0.01
44 4 0.01
46 1 0.00
47 36 0.13
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (41 bp):
CATGATCGAATCAAATTGAATGGTGAACTATTACATGCTAC
Found at i:79525 original size:82 final size:82
Alignment explanation
Indices: 79400--79604 Score: 320
Period size: 82 Copynumber: 2.5 Consensus size: 82
79390 GATAAATTGG
* * * * * *
79400 TTATTGCATGTTATCATGATCGAATCAAATTGAATGGTCAACTATTATATGTTGCCTTGATTGTA
1 TTATTGCATGCTACCATGATCGAATCAAATTGAATGATGAACTATTATATGATGCCTTGATTGAA
79465 TTGAATCGAACGGTAAA
66 TTGAATCGAACGGTAAA
*
79482 TTATTGCATGCTACCATGATCAAATCAAATTGAATGATGAACTATTATATGATGCCTTGATTGAA
1 TTATTGCATGCTACCATGATCGAATCAAATTGAATGATGAACTATTATATGATGCCTTGATTGAA
* *
79547 TTGAATCGAATGGTGAA
66 TTGAATCGAACGGTAAA
*
79564 TTATTGCATGCTACCATGATCGAATCAAATTGAACGATGAA
1 TTATTGCATGCTACCATGATCGAATCAAATTGAATGATGAA
79605 GGTGAATTAT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 112 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (82 bp):
TTATTGCATGCTACCATGATCGAATCAAATTGAATGATGAACTATTATATGATGCCTTGATTGAA
TTGAATCGAACGGTAAA
Found at i:79611 original size:47 final size:47
Alignment explanation
Indices: 79558--79651 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
79548 TGAATCGAAT
79558 GGTGAATTATTGCATGCTACCATGATCGAATCAAATTGAACGATGAA
1 GGTGAATTATTGCATGCTACCATGATCGAATCAAATTGAACGATGAA
* * *
79605 GGTGAATTATTGTATGCTACCATGATTGAATCAAATTGAATGATGAA
1 GGTGAATTATTGCATGCTACCATGATCGAATCAAATTGAACGATGAA
79652 ATATTATATG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (47 bp):
GGTGAATTATTGCATGCTACCATGATCGAATCAAATTGAACGATGAA
Found at i:79627 original size:129 final size:129
Alignment explanation
Indices: 79480--79733 Score: 402
Period size: 129 Copynumber: 2.0 Consensus size: 129
79470 TCGAACGGTA
* *
79480 AATTATTGCATGCTACCATGATCAAATCAAATTGAATGATGAACTATTATATGATGCCTTGATTG
1 AATTATTGCATGCTACCATGATCAAATCAAATTGAATGATGAAATATTATATGATGCCTTAATTG
* *
79545 AATTGAATCGAATGGTGAATTATTG-CATGCTACCATGATCGAATCAAATTGAACGATGAAGGTG
66 AATTGAATCGAATGGTGAATTATTGTAAT-CTACCATGATCAAATCAAATTGAACGATGAAGGTG
* **
79609 AATTATTGTATGCTACCATGATTGAATCAAATTGAATGATGAAATATTATATGATGCCTTAATTG
1 AATTATTGCATGCTACCATGATCAAATCAAATTGAATGATGAAATATTATATGATGCCTTAATTG
* * *
79674 AATTGAATCGAATGGTTAATTATTGTAATCTAGCATGATCAAATCAAGTTGAACGATGAA
66 AATTGAATCGAATGGTGAATTATTGTAATCTACCATGATCAAATCAAATTGAACGATGAA
79734 CTAATGTATG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
129 112 0.98
130 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (129 bp):
AATTATTGCATGCTACCATGATCAAATCAAATTGAATGATGAAATATTATATGATGCCTTAATTG
AATTGAATCGAATGGTGAATTATTGTAATCTACCATGATCAAATCAAATTGAACGATGAAGGTG
Found at i:79711 original size:82 final size:82
Alignment explanation
Indices: 79609--79810 Score: 200
Period size: 77 Copynumber: 2.5 Consensus size: 82
79599 GATGAAGGTG
** * * *
79609 AATTATTGTATGCTACCATGATTGAATCAAATTGAATGATGAAATATTATATGATGCCTTAATTG
1 AATTATTGTATGCTACCATGATCAAATCAAATTGAACGATGAAATAATATATGATGCCATAATTG
79674 AATTGAATCGAATGGTT
66 AATTGAATCGAATGGTT
* * * * *
79691 AATTATTGTAAT-CTAGCATGATCAAATCAAGTTGAACGATGAACTAATGTATGCTGCC---A-T
1 AATTATTGT-ATGCTACCATGATCAAATCAAATTGAACGATGAAATAATATATGATGCCATAATT
* *
79751 G-ATTGAATTGAATGGTG
65 GAATTGAATCGAATGGTT
* * * * *
79768 AATTATTGCATGTTACCATGATCGAATCAAGTTGAATGATGAA
1 AATTATTGTATGCTACCATGATCAAATCAAATTGAACGATGAA
79811 CTATTGCATA
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
76 2 0.02
77 49 0.48
78 2 0.02
79 1 0.01
82 46 0.45
83 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (82 bp):
AATTATTGTATGCTACCATGATCAAATCAAATTGAACGATGAAATAATATATGATGCCATAATTG
AATTGAATCGAATGGTT
Found at i:79842 original size:41 final size:41
Alignment explanation
Indices: 79758--79845 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
79748 CATGATTGAA
* * ** *
79758 TTGAATGGTGAATTATTGCATGTTACCATGATCGAATCAAG
1 TTGAATGATGAACTATTGCATACTACCAAGATCGAATCAAG
79799 TTGAATGATGAACTATTGCATACTACCAAGATCGAACTC-AG
1 TTGAATGATGAACTATTGCATACTACCAAGATCGAA-TCAAG
79840 TTGAAT
1 TTGAAT
79846 TGAAATCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (41 bp):
TTGAATGATGAACTATTGCATACTACCAAGATCGAATCAAG
Found at i:94304 original size:22 final size:22
Alignment explanation
Indices: 94279--94332 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 22
94269 AAGGTATCAG
94279 TACCATAGTATAGAAATATCGA
1 TACCATAGTATAGAAATATCGA
* *
94301 TACCATAGAGTATAGAAGTATTGA
1 TACCAT--AGTATAGAAATATCGA
94325 TACCATAG
1 TACCATAG
94333 AGGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
24 20 0.71
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (22 bp):
TACCATAGTATAGAAATATCGA
Found at i:94312 original size:24 final size:24
Alignment explanation
Indices: 94285--94334 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
94275 TCAGTACCAT
94285 AGTATAGAAATATCGATACCATAG
1 AGTATAGAAATATCGATACCATAG
* *
94309 AGTATAGAAGTATTGATACCATAG
1 AGTATAGAAATATCGATACCATAG
94333 AG
1 AG
94335 GTATCGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (24 bp):
AGTATAGAAATATCGATACCATAG
Found at i:103723 original size:24 final size:24
Alignment explanation
Indices: 103694--103777 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
103684 AGAAATTCAT
103694 AATGAGTTTATAGAGATTAGAGAA
1 AATGAGTTTATAGAGATTAGAGAA
* * *
103718 AATGAGTTTTTGAAGGATATGTTG-GAA
1 AATGAGTTTAT--A-GAGAT-TAGAGAA
* * *
103745 TATGAGTTAATGGAGATTAGAGAA
1 AATGAGTTTATAGAGATTAGAGAA
103769 AATGAGTTT
1 AATGAGTTT
103778 TTGAATGATA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
23 2 0.05
24 24 0.55
26 1 0.02
27 15 0.34
28 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (24 bp):
AATGAGTTTATAGAGATTAGAGAA
Found at i:103761 original size:51 final size:51
Alignment explanation
Indices: 103695--103803 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 51
103685 GAAATTCATA
*
103695 ATGAGTTTATAGAGATTAGAGAAAATGAGTTTTTGAAGGATATGTTGGAAT
1 ATGAGTTAATAGAGATTAGAGAAAATGAGTTTTTGAAGGATATGTTGGAAT
* * *
103746 ATGAGTTAATGGAGATTAGAGAAAATGAGTTTTTGAATGATATGTTGTAAT
1 ATGAGTTAATAGAGATTAGAGAAAATGAGTTTTTGAAGGATATGTTGGAAT
103797 ATGAGTT
1 ATGAGTT
103804 TTTACTGATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (51 bp):
ATGAGTTAATAGAGATTAGAGAAAATGAGTTTTTGAAGGATATGTTGGAAT
Found at i:103800 original size:27 final size:26
Alignment explanation
Indices: 103719--103814 Score: 74
Period size: 27 Copynumber: 3.7 Consensus size: 26
103709 ATTAGAGAAA
*
103719 ATGAGTTTTTGAAGGATATGTTGGAAT
1 ATGAGTTTTTGAATGATATGTT-GAAT
** * * *
103746 ATGAGTTAATGGA-GAT-TAG-AGAAA
1 ATGAGTTTTTGAATGATAT-GTTGAAT
103770 ATGAGTTTTTGAATGATATGTTGTAAT
1 ATGAGTTTTTGAATGATATGTTG-AAT
*
103797 ATGAGTTTTT-ACTGATAT
1 ATGAGTTTTTGAATGATAT
103815 TTATTAGTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
24 13 0.25
25 5 0.09
26 13 0.25
27 22 0.42
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (26 bp):
ATGAGTTTTTGAATGATATGTTGAAT
Found at i:104558 original size:56 final size:56
Alignment explanation
Indices: 104477--105373 Score: 1164
Period size: 56 Copynumber: 16.1 Consensus size: 56
104467 ATTACCGAAT
*
104477 GGCACTATATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACT-T-TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* ** **
104535 AGCACTTTGTGAACAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTTGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * *
104591 GGCACTATGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGAATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * *
104647 GGAACTTTGTGTG-TAAAACTAAGAAATTCATAATGAATTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * **
104702 TGCACTTTGTGTGCAAACACTAAGAAATTCATAATG-GATTTAAGAATTTCTATATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAG-TTTATGAATTTCCGTATG
* ** * *
104758 GGCACTTTGTGTTCAAAAGGTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
104814 GGCACTTTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
*
104869 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATTAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
104925 GACACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * *
104981 GGTATTTTGTGAGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
105036 GGCACTTTGTGTGCAAAAGCTAAGAAAATCATAATGAGTTTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
*
105092 GGCAC-TTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * **
105147 GTCACTTTGTGTGCAAAAGCTAACAAATTCATAATGAGTTTATAAATTTTTGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
105203 GGTAC-TTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * * *
105258 GTCACTTTCTGTGC-AAAACTAAGAAATTCATAAT-AATTTCTTGAATTTCCTTATA
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTT-ATGAATTTCCGTATG
* * * ** * *
105313 TGCACTTTGTGTGC-AAAACTAAGAAAATCATAATAAGTTTACAAATTTCCATATT
1 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
105368 GGCACT
1 GGCACT
105374 ACGTGTATAA
Statistics
Matches: 734, Mismatches: 96, Indels: 21
0.86 0.11 0.02
Matches are distributed among these distances:
54 4 0.01
55 323 0.44
56 400 0.54
57 2 0.00
58 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (56 bp):
GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
Found at i:104716 original size:111 final size:110
Alignment explanation
Indices: 104475--105353 Score: 1182
Period size: 111 Copynumber: 7.9 Consensus size: 110
104465 TGATTACCGA
* *
104475 ATGGCACTATATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCAC
1 ATGGCACT-T-TGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCAC
** *
104540 TTTGTGAACAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTTGT
64 TTTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGT
* * * *
104588 ATGGGCACTATGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGAATGGGAACT
1 AT-GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACT
* *
104653 TTGTGTGTAAAACTAAGAAATTCATAATGAATTTATGAATTTTCGT
65 TTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGT
* *
104699 ATGTGCACTTTGTGTGCAAACA-CTAAGAAATTCATAATG-GATTTAAGAATTTCTATATGGGCA
1 ATG-GCACTTTGTGTGCAAA-AGCTAAGAAATTCATAATGAG-TTTATGAATTTCTGTATGGGCA
* * * *
104762 CTTTGTGTTCAAAAGGTAAGAAATTCATAATAAGTTTATGAATTTCCGT
63 CTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGT
*
104811 ATAGGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACT
1 AT-GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACT
* *
104875 TTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATTAATTTCCGT
65 TTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGT
* * * *
104922 ATGGACACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTATT
1 ATGG-CACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACT
*
104987 TTGTGAGCAAAACTAAGAAATTCATAATGAGTTTATGAA-TTTCTGT
65 TTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GT
*
105033 ATGGGCACTTTGTGTGCAAAAGCTAAGAAAATCATAATGAGTTTATGAATTTCTGTATGGGCAC-
1 AT-GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACT
*
105097 TTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGT
65 TTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGT
* * * *
105144 ATGGTCACTTTGTGTGCAAAAGCTAACAAATTCATAATGAGTTTATAAATTTTTGTATGGGTAC-
1 ATGG-CACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACT
105208 TTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTTCGT
65 TTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGT
* * * **
105255 ATGGTCACTTTCTGTGCAAAA-CTAAGAAATTCATAAT-AATTTCTTGAATTTCCT-TATATGCA
1 ATGG-CACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTT-ATGAATTT-CTGTATGGGCA
* *
105317 CTTTGTGTGCAAAACTAAGAAAATCATAATAAGTTTA
63 CTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTA
105354 CAAATTTCCA
Statistics
Matches: 688, Mismatches: 60, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
109 4 0.01
110 68 0.10
111 446 0.65
112 161 0.23
113 3 0.00
114 6 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (110 bp):
ATGGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
TGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGT
Found at i:104784 original size:167 final size:166
Alignment explanation
Indices: 104477--105353 Score: 1237
Period size: 167 Copynumber: 5.2 Consensus size: 166
104467 ATTACCGAAT
* *
104477 GGCACTATATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCACTT
1 GGCACT-T-TGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
** * *
104542 TGTGAACAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTATGTGTGCAA
63 TGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAA
* *
104607 AAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGAATG
127 AAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
104647 GGAACTTTGTGTGTAAAACTAAGAAATTCATAATGAATTTATGAATTTTCGTATGTGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
* * *
104712 GTGCAAACACTAAGAAATTCATAATG-GATTTAAGAATTTCTATATGGGCACTTTGTGTTCAAAA
66 GTGCAAA-ACTAAGAAATTCATAATGAG-TTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAA
* *
104776 GGTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
129 GCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
104814 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
* * *
104879 GTGCAAAAACTAAGAAATTCATAATGAGTTTATTAATTTCCGTATGGACACTTTGTGTGCAAAAG
66 GTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAAG
104944 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
130 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
104981 GGTATTTTGTGAGCAAAACTAAGAAATTCATAATGAGTTTATGAA-TTTCTGTATGGGCACTTTG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATGGGCACTTTG
*
105045 TGTGCAAAAGCTAAGAAAATCATAATGAGTTTATGAATTTCTGTATGGGCAC-TTGTGTGCAAAA
65 TGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAA
*
105109 GCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
129 GCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * *
105147 GTCACTTTGTGTGCAAAAGCTAACAAATTCATAATGAGTTTATAAATTTTTGTATGGGTAC-TTG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTG
* *
105211 TGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTT-TCGTATGGTCACTTTCTGTGCAAA
65 TGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCT-GTATGGGCACTTTGTGTGCAAA
* * *
105275 A-CTAAGAAATTCATAATAA-TTTCTTGAATTTCCTTATA
128 AGCTAAGAAATTCATAATAAGTTT-ATGAATTTCCGTATG
* * *
105313 TGCACTTTGTGTGCAAAACTAAGAAAATCATAATAAGTTTA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTA
105354 CAAATTTCCA
Statistics
Matches: 638, Mismatches: 58, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
165 24 0.04
166 170 0.27
167 421 0.66
168 17 0.03
169 1 0.00
170 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (166 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAAGC
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:105587 original size:82 final size:81
Alignment explanation
Indices: 105457--105765 Score: 413
Period size: 82 Copynumber: 3.8 Consensus size: 81
105447 CTATTCTAAA
* * * *
105457 ATAAAAGACTAATGTCCAACTGTTCATTTGACAGAAAGGTGCCAATAATGTAAGTTATAAGAAAG
1 ATAAAAGACTAATGTCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGAAGAAAG
*
105522 GTTAAATGCCTTTAGG
66 GTTAAATGCATTTAGG
* * * *
105538 ATAAAAGACTAATGTATAACTGTGCAATTTGGTAGAAAAGTGCCAATAATGTAAGTTAGAAGGAA
1 ATAAAAGACTAATGTCTAACTGTGC-ATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGAAGAAA
105603 GGTTAAATGCATTTAGG
65 GGTTAAATGCATTTAGG
* * *
105620 ATAAAAGACTAATGTCTAACTGTGCATTTGGCATAAAGGTGCCAATAATGCAAGTTAGAAGAAAA
1 ATAAAAGACTAATGTCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGAAGAAAG
*
105685 GTTAAATGCATTTATG
66 GTTAAATGCATTTAGG
* * * ** *
105701 ATAAAAGACTAATGCCTAA-TGGTGCAATTTGGTAGAAAGGTGCCACTAATACAAGTTAGATGAA
1 ATAAAAGACTAATGTCTAACT-GTGC-ATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGAAGAA
105765 A
64 A
105766 AACATTGCAT
Statistics
Matches: 202, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 1 0.00
81 93 0.46
82 108 0.53
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (81 bp):
ATAAAAGACTAATGTCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGAAGAAAG
GTTAAATGCATTTAGG
Found at i:105728 original size:163 final size:163
Alignment explanation
Indices: 105457--105760 Score: 457
Period size: 163 Copynumber: 1.9 Consensus size: 163
105447 CTATTCTAAA
* * * *
105457 ATAAAAGACTAATGTCCAACTGTTCATTTGACAGAAAGGTGCCAATAATGTAAGTTATAAGAAAG
1 ATAAAAGACTAATGTCCAACTGTGCATTTGACAGAAAGGTGCCAATAATGCAAGTTAGAAGAAAA
* *
105522 GTTAAATGCCTTTAGGATAAAAGACTAATGTATAACTGTGCAATTTGGTAGAAAAGTGCCAATAA
66 GTTAAATGCATTTAGGATAAAAGACTAATGCATAACTGTGCAATTTGGTAGAAAAGTGCCAATAA
**
105587 TGTAAGTTAGAAGGAAGGTTAAATGCATTTAGG
131 TACAAGTTAGAAGGAAGGTTAAATGCATTTAGG
* * *
105620 ATAAAAGACTAATGTCTAACTGTGCATTTGGCATAAAGGTGCCAATAATGCAAGTTAGAAGAAAA
1 ATAAAAGACTAATGTCCAACTGTGCATTTGACAGAAAGGTGCCAATAATGCAAGTTAGAAGAAAA
* * * *
105685 GTTAAATGCATTTATGATAAAAGACTAATGCCTAA-TGGTGCAATTTGGTAGAAAGGTGCCACTA
66 GTTAAATGCATTTAGGATAAAAGACTAATGCATAACT-GTGCAATTTGGTAGAAAAGTGCCAATA
105749 ATACAAGTTAGA
130 ATACAAGTTAGA
105761 TGAAAAACAT
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
162 1 0.01
163 124 0.99
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (163 bp):
ATAAAAGACTAATGTCCAACTGTGCATTTGACAGAAAGGTGCCAATAATGCAAGTTAGAAGAAAA
GTTAAATGCATTTAGGATAAAAGACTAATGCATAACTGTGCAATTTGGTAGAAAAGTGCCAATAA
TACAAGTTAGAAGGAAGGTTAAATGCATTTAGG
Found at i:105818 original size:46 final size:46
Alignment explanation
Indices: 105766--105858 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
105756 TTAGATGAAA
* * *
105766 AACATTGCATAATTGGCATGAAAGGATATCATAAATGAAAATTTAT
1 AACATTGCATAATTGGCATGAAAGGATACCACAAATGAAAATATAT
* *
105812 AACATTGCATAATTGGCATGAAATGATGCCACAAATGAAAATATAT
1 AACATTGCATAATTGGCATGAAAGGATACCACAAATGAAAATATAT
105858 A
1 A
105859 GTGGTATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (46 bp):
AACATTGCATAATTGGCATGAAAGGATACCACAAATGAAAATATAT
Found at i:112646 original size:21 final size:21
Alignment explanation
Indices: 112616--112663 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
112606 TCAGCGTTTT
* * **
112616 AATATTGATACTGGGATGGAC
1 AATATCGATACTAGGATAAAC
112637 AATATCGATACTAGGATAAAC
1 AATATCGATACTAGGATAAAC
112658 AATATC
1 AATATC
112664 AATATTGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
AATATCGATACTAGGATAAAC
Found at i:116228 original size:11 final size:13
Alignment explanation
Indices: 116204--116235 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
116194 GACTTTTGGA
116204 TTAAATTACA-TT
1 TTAAATTACATTT
116216 TTAAATT-CATTT
1 TTAAATTACATTT
116228 TTAAATTA
1 TTAAATTA
116236 GAATAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATTACATTT
Found at i:135345 original size:26 final size:26
Alignment explanation
Indices: 135309--135361 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
135299 TGTTTGAATG
135309 TTTCAGAACACCTTGAAAAGTTAATT
1 TTTCAGAACACCTTGAAAAGTTAATT
135335 TTTCAGAACACCTTGAAAAGTTAATT
1 TTTCAGAACACCTTGAAAAGTTAATT
135361 T
1 T
135362 GGAGGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (26 bp):
TTTCAGAACACCTTGAAAAGTTAATT
Found at i:153427 original size:20 final size:20
Alignment explanation
Indices: 153386--153441 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
153376 GAAAAGGAGA
* * *
153386 TAGTATCGATACTGGCACAT
1 TAGTATCAATACTGACAAAT
153406 TAGTATCAATACTGACAAAT
1 TAGTATCAATACTGACAAAT
* *
153426 TAATATCAATATTGAC
1 TAGTATCAATACTGAC
153442 TTAGGAGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (20 bp):
TAGTATCAATACTGACAAAT
Found at i:153576 original size:18 final size:19
Alignment explanation
Indices: 153531--153576 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
153521 CCCCTACGGG
*
153531 GAGTATCGATACTCAGCCCTT
1 GAGTATCGATACT-A-CCCAT
153552 G-GTATCGATACT-CCCAT
1 GAGTATCGATACTACCCAT
153569 GAGTATCG
1 GAGTATCG
153577 GTACCAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
20 11 0.48
21 1 0.04
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (19 bp):
GAGTATCGATACTACCCAT
Found at i:161023 original size:14 final size:14
Alignment explanation
Indices: 160992--161124 Score: 85
Period size: 14 Copynumber: 9.6 Consensus size: 14
160982 CTCTAGACTC
*
160992 TAAACACTAAA-CT
1 TAAACCCTAAACCT
* *
161005 ATAAACCCTAAGCCC
1 -TAAACCCTAAACCT
* * *
161020 TAAA-CTTTAACCC
1 TAAACCCTAAACCT
*
161033 TAAGCCC-AAAGCCT
1 TAAACCCTAAA-CCT
161047 TAAACCCTAAACCT
1 TAAACCCTAAACCT
161061 TAAACCCTAAACCT
1 TAAACCCTAAACCT
* *
161075 TAAACCATAATCCT
1 TAAACCCTAAACCT
* * * *
161089 TGATCCTTAAACCC
1 TAAACCCTAAACCT
* *
161103 TAAA-TCTAAATCT
1 TAAACCCTAAACCT
161116 TAAACCCTA
1 TAAACCCTA
161125 CACTTAAAGT
Statistics
Matches: 89, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
13 20 0.22
14 65 0.73
15 4 0.04
ACGTcount: A:0.41, C:0.32, G:0.03, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:161057 original size:7 final size:7
Alignment explanation
Indices: 160976--161080 Score: 70
Period size: 7 Copynumber: 15.1 Consensus size: 7
160966 TGTTGAAATA
160976 CCTAAAC
1 CCTAAAC
* *
160983 TCTAGAC
1 CCTAAAC
*
160990 TCTAAAC
1 CCTAAAC
*
160997 ACTAAAC
1 CCTAAAC
**
161004 TATAAAC
1 CCTAAAC
*
161011 CCTAAGC
1 CCTAAAC
161018 CCTAAA-
1 CCTAAAC
* *
161024 CTTTAAC
1 CCTAAAC
*
161031 CCTAAGC
1 CCTAAAC
161038 CC-AAAGC
1 CCTAAA-C
*
161045 CTTAAAC
1 CCTAAAC
161052 CCTAAAC
1 CCTAAAC
*
161059 CTTAAAC
1 CCTAAAC
161066 CCTAAAC
1 CCTAAAC
*
161073 CTTAAAC
1 CCTAAAC
161080 C
1 C
161081 ATAATCCTTG
Statistics
Matches: 74, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
6 6 0.08
7 65 0.88
8 3 0.04
ACGTcount: A:0.41, C:0.34, G:0.04, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:161071 original size:21 final size:21
Alignment explanation
Indices: 161048--161124 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
161038 CCAAAGCCTT
* *
161048 AAACCCTAAACCTTAAACCCT
1 AAACCTTAAACCCTAAACCCT
* * *
161069 AAACCTTAAACCATAATCCTT
1 AAACCTTAAACCCTAAACCCT
* * *
161090 GATCCTTAAACCCTAAA-TCT
1 AAACCTTAAACCCTAAACCCT
*
161110 AAATCTTAAACCCTA
1 AAACCTTAAACCCTA
161125 CACTTAAAGT
Statistics
Matches: 43, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 13 0.30
21 30 0.70
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (21 bp):
AAACCTTAAACCCTAAACCCT
Found at i:162188 original size:21 final size:21
Alignment explanation
Indices: 162164--162204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
162154 CAAATTACTA
*
162164 ACTAAATAATAAACCCTAAAT
1 ACTAAACAATAAACCCTAAAT
**
162185 ACTAAACCTTAAACCCTAAA
1 ACTAAACAATAAACCCTAAA
162205 CCTAACTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (21 bp):
ACTAAACAATAAACCCTAAAT
Found at i:162803 original size:14 final size:14
Alignment explanation
Indices: 162784--162814 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
162774 ACAACTTGAA
162784 CCGGTTTGACCGAC
1 CCGGTTTGACCGAC
162798 CCGGTTTGACCGAC
1 CCGGTTTGACCGAC
162812 CCG
1 CCG
162815 ACCCGGTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.39, G:0.29, T:0.19
Consensus pattern (14 bp):
CCGGTTTGACCGAC
Found at i:163039 original size:15 final size:16
Alignment explanation
Indices: 163019--163049 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
163009 TAACTTTGAC
163019 CAAAAAGTCA-ATTTT
1 CAAAAAGTCATATTTT
163034 CAAAAAGTCATATTTT
1 CAAAAAGTCATATTTT
163050 ATGTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
CAAAAAGTCATATTTT
Found at i:163525 original size:24 final size:24
Alignment explanation
Indices: 163504--163561 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
163494 GATTGTTTTC
163504 TCTGATTTGAAATATAATGTTTGA
1 TCTGATTTGAAATATAATGTTTGA
163528 TCTGATTTGAAATATAATGTTTGA
1 TCTGATTTGAAATATAATGTTTGA
163552 TCTGATTTGA
1 TCTGATTTGA
163562 CTACTGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTGAAATATAATGTTTGA
Found at i:170879 original size:29 final size:29
Alignment explanation
Indices: 170837--170892 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
170827 CTCCCGTTAT
*
170837 CTCCTCCTCCTCCTTCTCTTCTCCTTCAG
1 CTCCTCCTCCTCCTTCTCCTCTCCTTCAG
*
170866 CTCCTCCTCCTCCTTCTCCTCTTCTTC
1 CTCCTCCTCCTCCTTCTCCTCTCCTTC
170893 TTCTACTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.02, C:0.54, G:0.02, T:0.43
Consensus pattern (29 bp):
CTCCTCCTCCTCCTTCTCCTCTCCTTCAG
Found at i:175395 original size:15 final size:15
Alignment explanation
Indices: 175375--175404 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
175365 AAATTAATGT
175375 TTAATTATAAAATAA
1 TTAATTATAAAATAA
*
175390 TTAATTATAAGATAA
1 TTAATTATAAAATAA
175405 ATAGATTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TTAATTATAAAATAA
Found at i:177721 original size:42 final size:43
Alignment explanation
Indices: 177603--178002 Score: 393
Period size: 42 Copynumber: 9.4 Consensus size: 43
177593 TGTGAAATAA
** **
177603 AAACGCCGCAAAAAATCAAGATCTATAGCGGTATTTTTAT-ATAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTT-TGATAC
* * *
177647 AAACCCCACAAAAGGTTGAGATCTATAGCGGCGTTTTTTGA-AC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTTGATAC
* * *
177690 AAACACCGCAAAAGGTCAGATCTATAGCGGCG-ATTTTGTATAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTG-ATAC
* *
177733 AAACGCCGCAAAAGGTCAGATCTGTAGCAGCGTTTTTTGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
* *
177775 AAACGCCGCAAAAGGTCATATCTATAGCGGCG-GTTTTGTATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTG-ATAC
* * * *
177818 AAACACCGCAAAAGATCAGATCTGTAGCGCCGTTTTTTGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
* * * * * *
177860 AAACGCCACAAAAAGTCATATTTGTAGCGGCATTTTTTGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
* * * * *
177902 AAACGCCACAAAAAGTCATATCTATAGCGGCG-GTTTTAATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
* * * *
177944 AAACGCTGCAAAAGGTCAGATCTATAGTGGCATTTTTTTATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
*
177987 AAACGCTGCAAAAGGT
1 AAACGCCGCAAAAGGT
178003 TATATTTGTA
Statistics
Matches: 298, Mismatches: 48, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
41 15 0.05
42 141 0.47
43 101 0.34
44 40 0.13
45 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
Found at i:177784 original size:85 final size:84
Alignment explanation
Indices: 177603--178033 Score: 427
Period size: 85 Copynumber: 5.1 Consensus size: 84
177593 TGTGAAATAA
** * * * * *
177603 AAACGCCGCAAAAAATCAAGATCTATAGCGGTATTTTTATATACAAACCCCACAAAAGGTTGAGA
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCA-TTTTGTATACAAACGCCGCAAAAGG-TCAGA
* *
177668 TCTATAGCGGCGTTTTTTGAAC
63 TCTGTAGCAGCGTTTTTTGAAC
* *
177690 AAACACCGCAAAAGGTCAGATCTATAGCGGCGATTTTGTATATAAACGCCGCAAAAGGTCAGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC-ATTTTGTATACAAACGCCGCAAAAGGTCAGATC
177755 TGTAGCAGCGTTTTTTGAAC
65 TGTAGCAGCGTTTTTTGAAC
* * * *
177775 AAACGCCGCAAAAGGTCATATCTATAGCGGCGGTTTTGTATACAAACACCGCAAAAGATCAGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC-ATTTTGTATACAAACGCCGCAAAAGGTCAGATC
177840 TGTAGC-GCCGTTTTTTGAAC
65 TGTAGCAG-CGTTTTTTGAAC
* * * * * * * * *
177860 AAACGCCACAAAAAGTCATATTTGTAGCGGCATTTTTTGA-ACAAACGCCACAAAAAGTCATATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTGT-ATACAAACGCCGCAAAAGGTCAGATC
* * * *
177924 TATAGCGGCG-GTTTTAATAC
65 TGTAGCAGCGTTTTTTGA-AC
* * * * * * *
177944 AAACGCTGCAAAAGGTCAGATCTATAGTGGCATTTTTTTATACAAACGCTGCAAAAGGTTATATT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCA-TTTTGTATACAAACGCCGCAAAAGGTCAGATC
* *
178009 TGTAGTAGCGTTTTTGGAAC
65 TGTAGCAGCGTTTTTTGAAC
178029 AAACG
1 AAACG
178034 TCGCTAATTA
Statistics
Matches: 287, Mismatches: 49, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
83 5 0.02
84 60 0.21
85 169 0.59
86 38 0.13
87 15 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTGTATACAAACGCCGCAAAAGGTCAGATCT
GTAGCAGCGTTTTTTGAAC
Found at i:177914 original size:127 final size:127
Alignment explanation
Indices: 177645--178033 Score: 469
Period size: 127 Copynumber: 3.1 Consensus size: 127
177635 ATTTTTATAT
* * * *
177645 ACAAACCCCACAAAAGGTTGAGATCTATAGCGGCGTTTTTTGA-ACAAACACCGCAAAAGGTCAG
1 ACAAACGCCACAAAAGG-TCATATCTATAGCGGCGGTTTTT-ATACAAACACCGCAAAAGGTCAG
* * * * *
177709 ATCTATAGCGGCG-ATTTTGTATATAAACGCCGCAAAAGGTCAGATCTGTAGCAGCGTTTTTTGA
64 ATCTATAGCGGCGTTTTTTG-ATACAAACGCCGCAAAAGGTCATATTTGTAGCAGCATTTTTTGA
* *
177773 ACAAACGCCGCAAAAGGTCATATCTATAGCGGCGGTTTTGTATACAAACACCGCAAAAGATCAGA
1 ACAAACGCCACAAAAGGTCATATCTATAGCGGCGGTTTT-TATACAAACACCGCAAAAGGTCAGA
* * * * *
177838 TCTGTAGCGCCGTTTTTTGA-ACAAACGCCACAAAAAGTCATATTTGTAGCGGCATTTTTTGA
65 TCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCATATTTGTAGCAGCATTTTTTGA
* * * *
177900 ACAAACGCCACAAAAAGTCATATCTATAGCGGCGGTTTTAATACAAACGCTGCAAAAGGTCAGAT
1 ACAAACGCCACAAAAGGTCATATCTATAGCGGCGGTTTTTATACAAACACCGCAAAAGGTCAGAT
* * * * * * * *
177965 CTATAGTGGCATTTTTTTATACAAACGCTGCAAAAGGTTATATTTGTAGTAGCGTTTTTGGA
66 CTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCATATTTGTAGCAGCATTTTTTGA
178027 ACAAACG
1 ACAAACG
178034 TCGCTAATTA
Statistics
Matches: 222, Mismatches: 35, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
126 36 0.16
127 133 0.60
128 48 0.22
129 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (127 bp):
ACAAACGCCACAAAAGGTCATATCTATAGCGGCGGTTTTTATACAAACACCGCAAAAGGTCAGAT
CTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCATATTTGTAGCAGCATTTTTTGA
Found at i:181597 original size:41 final size:41
Alignment explanation
Indices: 181522--181879 Score: 468
Period size: 41 Copynumber: 8.8 Consensus size: 41
181512 ACGGCATTTT
*
181522 TAGCGGCGTTTGTA-AAAAATGCCACTAAAG-ACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
** * * *
181561 TAATGGCATTTTTATAAAAACGCCACTAATGTACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
* *
181602 TAGCGGCGTTTGTACAAAAATGCCACTAAAGTACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*** *
181643 TAGCATTGTTTGTTTAAAAACGCCACTAAAGTACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*** * * * *
181684 TAGCATTGTTTGTTTAAAAACGCCACTAAAGTACCAGTTTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
* *
181725 TAGCGGTGTTTGTATAAAAACGCCACTAAAGTACGAGTATA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
* *
181766 TAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
* *
181807 TAGTGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTATA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*
181848 TAGCGGCGTTTGTATAAAAACGCCGCTAAAGT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGT
181880 TACCATTTTG
Statistics
Matches: 279, Mismatches: 38, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 10 0.04
40 14 0.05
41 255 0.91
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
Found at i:188705 original size:21 final size:21
Alignment explanation
Indices: 188681--188726 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
188671 ATTTATTATA
*
188681 ATGGATTTAAAGTTGGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
*
188702 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
188723 ATGG
1 ATGG
188727 CTGTCATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:189747 original size:15 final size:15
Alignment explanation
Indices: 189727--189758 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
189717 AATTAATGTT
189727 TAATTATAAAATAAA
1 TAATTATAAAATAAA
*
189742 TAATTATAAGATAAA
1 TAATTATAAAATAAA
189757 TA
1 TA
189759 GATTTCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TAATTATAAAATAAA
Found at i:194402 original size:28 final size:28
Alignment explanation
Indices: 194370--194435 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
194360 GCGGCAAGAT
* * *
194370 CGACCATATATTATTCATGCGGTATAA-C
1 CGACCATATATAAATCAGGCGGTA-AAGC
*
194398 TGACCATATATAAATCAGGCGGTAAAGC
1 CGACCATATATAAATCAGGCGGTAAAGC
194426 CGACCATATA
1 CGACCATATA
194436 ATAGAACTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (28 bp):
CGACCATATATAAATCAGGCGGTAAAGC
Found at i:194514 original size:15 final size:15
Alignment explanation
Indices: 194491--194524 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
194481 TTAACCGGGA
*
194491 AACTTAAGAGAAGAG
1 AACTCAAGAGAAGAG
194506 AACTCAAGAGAAGAG
1 AACTCAAGAGAAGAG
194521 AACT
1 AACT
194525 TTTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (15 bp):
AACTCAAGAGAAGAG
Found at i:199599 original size:25 final size:27
Alignment explanation
Indices: 199558--199608 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
199548 AAATAAATTA
* *
199558 AAATTTCAAAGTATTATGAAATTATTC
1 AAATTTCAAAGTATTATAAAAATATTC
199585 AAATTT-AAA-TATTATAAAAATATT
1 AAATTTCAAAGTATTATAAAAATATT
199609 AAAGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATTTCAAAGTATTATAAAAATATTC
Found at i:199605 original size:17 final size:16
Alignment explanation
Indices: 199585--199629 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
199575 GAAATTATTC
199585 AAATTTAAATATTATAA
1 AAATTTAAATATTA-AA
199602 AAATATTAAAGTATTAAA
1 AAAT-TTAAA-TATTAAA
*
199620 ATATTTAAAT
1 AAATTTAAAT
199630 TCAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 9 0.36
18 10 0.40
19 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTTAAATATTAAA
Found at i:202087 original size:2 final size:2
Alignment explanation
Indices: 202080--202124 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
202070 ATACATAACG
202080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202122 AT A
1 AT A
202125 CACATACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:203314 original size:2 final size:2
Alignment explanation
Indices: 203307--203356 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
203297 ATGGTAAATT
203307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
203349 TA TA TA TA
1 TA TA TA TA
203357 CACATACATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:206260 original size:2 final size:2
Alignment explanation
Indices: 206253--206280 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
206243 TTTTTAGTAT
206253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
206281 GTAATTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209575 original size:4 final size:4
Alignment explanation
Indices: 209546--209591 Score: 58
Period size: 4 Copynumber: 11.0 Consensus size: 4
209536 AACAAAAAAT
209546 ATAA TATAA TATAA TATAA A-AA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA -ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
209592 TATGAACAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.08
4 23 0.57
5 14 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:210458 original size:20 final size:21
Alignment explanation
Indices: 210405--210450 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
210395 ACTTTCATGT
* *
210405 AGTTTCGAAACTAT-CTTAAG
1 AGTTTCAAAACTTTCCTTAAG
210425 AGTTTCAAAACTTTCCTTAA-
1 AGTTTCAAAACTTTCCTTAAG
210445 AGTTTC
1 AGTTTC
210451 TATACTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (21 bp):
AGTTTCAAAACTTTCCTTAAG
Found at i:218793 original size:51 final size:51
Alignment explanation
Indices: 218682--218786 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
218672 TCTTGATAAA
218682 ATTTATGATGCATGTGCTAAGGGCAAACACAAAAGATCTTATTTTAAACCT
1 ATTTATGATGCATGTGCTAAGGGCAAACACAAAAGATCTTATTTTAAACCT
218733 ATTTATGATGCATGTGCTAAGGGCAAACACAAAAGATCTTATTTTAAACCT
1 ATTTATGATGCATGTGCTAAGGGCAAACACAAAAGATCTTATTTTAAACCT
218784 ATT
1 ATT
218787 AGTGATGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (51 bp):
ATTTATGATGCATGTGCTAAGGGCAAACACAAAAGATCTTATTTTAAACCT
Found at i:233378 original size:21 final size:21
Alignment explanation
Indices: 233336--233379 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
233326 TTGGGATCAG
*
233336 TTTAGTGTATATGATAATAAT
1 TTTAGTGTATATGATAAAAAT
*
233357 TTTA-TGTATATGCTTAAAAAT
1 TTTAGTGTATATG-ATAAAAAT
233378 TT
1 TT
233380 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTAGTGTATATGATAAAAAT
Found at i:233608 original size:15 final size:15
Alignment explanation
Indices: 233590--233618 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
233580 TTAATTTCAA
233590 AATTTTATAAAATAC
1 AATTTTATAAAATAC
233605 AATTTTATAAAATA
1 AATTTTATAAAATA
233619 ACTTAAAAAT
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:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Done.