Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005274.1 Hibiscus syriacus cultivar Beakdansim tig00011922_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: 315540
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:1661 original size:3 final size:3
Alignment explanation
Indices: 1647--1708 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1637 GTTGTATCTG
* * * *
1647 TAA TAA -AA TAA TAA TAT TAA TAA TAA AAA TAA TAT TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1694 TAA TAA -ATA TAA TAA
1 TAA TAA TA-A TAA TAA
1709 AAAACCAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1679 original size:18 final size:18
Alignment explanation
Indices: 1647--1690 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1637 GTTGTATCTG
*
1647 TAATAA-AATAATAATAT
1 TAATAATAAAAATAATAT
1664 TAATAATAAAAATAATAT
1 TAATAATAAAAATAATAT
1682 TAATAATAA
1 TAATAATAA
1691 TAGTAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAATAAAAATAATAT
Found at i:2301 original size:103 final size:107
Alignment explanation
Indices: 2120--2410 Score: 394
Period size: 113 Copynumber: 2.7 Consensus size: 107
2110 ATAGAGTCAT
* *
2120 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTTA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTA
* *
2185 TTATGAACTTTCTCTGGAAAAGTTGATCCATCCAG-T-A-GC
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGATGATGA
* *
2224 G-AAAA-GTTGAACAGGTTCTTCTCATTATGAACTTCTTTTTCTTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTT
*
2287 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTAATGGATTTGA
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAG--AT-GA--TGA
* * *
2335 GCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTT
2400 ATTATGAACTT
65 ATTATGAACTT
2411 CTTCTTCCTT
Statistics
Matches: 163, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
102 34 0.21
103 57 0.35
104 1 0.01
106 1 0.01
108 1 0.01
111 2 0.01
112 4 0.02
113 62 0.38
114 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (107 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGATGATGA
Found at i:2410 original size:40 final size:40
Alignment explanation
Indices: 2350--2454 Score: 194
Period size: 40 Copynumber: 2.6 Consensus size: 40
2340 AGGTTGAATA
2350 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
2390 AGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
2430 AGTTCTTCTCATTATGAAC-TCTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
2455 GGAAAAGCTG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
39 6 0.10
40 57 0.90
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:2519 original size:152 final size:153
Alignment explanation
Indices: 2242--2566 Score: 546
Period size: 152 Copynumber: 2.1 Consensus size: 153
2232 GAACAGGTTC
* * * *
2242 TTCTCATTATGAACTTCTTTTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAA
* * * *
2307 ATGTTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTC
66 AAGCTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTAAATAAGCTCTTCTCATTATGAACTTC
2372 TTCTTCCTTCTTCAGATGAGTTA
131 TTCTTCCTTCTTCAGATGAGTTA
2395 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAA
*
2459 AAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAATAAGCTCTTCTCATTATGAACTTC
66 AAGCTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTAAATAAGCTCTTCTCATTATGAACTTC
*
2524 TTCTTCCTTCTTCAGATGAGTTC
131 TTCTTCCTTCTTCAGATGAGTTA
2547 TTCTCATTATGAAC-TCTTCT
1 TTCTCATTATGAACTTCTTCT
2567 GGAAAAGCTG
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 6 0.04
152 103 0.64
153 53 0.33
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (153 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAA
AAGCTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTAAATAAGCTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTA
Found at i:2592 original size:112 final size:112
Alignment explanation
Indices: 2395--2820 Score: 773
Period size: 112 Copynumber: 3.8 Consensus size: 112
2385 AGATGAGTTA
2395 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
*
2460 AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAATAAGCTC
66 AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
2507 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
2572 AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
66 AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
* *
2619 TTCTCATTATGAACTTATTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
*
2684 AGATGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
66 AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
2731 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
* * *
2796 TGTTGATCCATTGAA-TGATGGATTT
66 AGCTGATCCA-TCAAGTGATGGATTT
2821 AAATCTTTGC
Statistics
Matches: 304, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
112 301 0.99
113 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAA
AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAGCTC
Found at i:3732 original size:114 final size:114
Alignment explanation
Indices: 3532--3868 Score: 548
Period size: 114 Copynumber: 3.0 Consensus size: 114
3522 AATCATGCAG
* * * * * * ** * *
3532 TTCATCTTTCAATTCTAGTGATTGGTTCTGTGGTTCCTACCGAACCAGATCATATAACTCAAAGA
1 TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
3597 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
3646 TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
*
3711 ACACTTCCAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
3760 TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
* *
3825 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
3869 TAACGTGGCA
Statistics
Matches: 208, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 208 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTTAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4201 original size:16 final size:16
Alignment explanation
Indices: 4180--4224 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
4170 GAATTTTCGA
4180 AAATAAATTGAATCTC
1 AAATAAATTGAATCTC
4196 AAATAAATTGAATCTC
1 AAATAAATTGAATCTC
4212 AAATAAATTGAAT
1 AAATAAATTGAAT
4225 TTAGAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (16 bp):
AAATAAATTGAATCTC
Found at i:4631 original size:22 final size:21
Alignment explanation
Indices: 4574--4615 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4564 TTAATCTTGA
*
4574 CCTTTTTTTTTCTTTTTTTTT
1 CCTTCTTTTTTCTTTTTTTTT
*
4595 CCTTCTTCTTCTCTTTTTTTT
1 CCTTCTT-TTTTCTTTTTTTT
4616 CTTTTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
CCTTCTTTTTTCTTTTTTTTT
Found at i:17586 original size:9 final size:9
Alignment explanation
Indices: 17572--17655 Score: 77
Period size: 9 Copynumber: 9.7 Consensus size: 9
17562 TGTAATAAAA
17572 TAATAATAT
1 TAATAATAT
*
17581 TAATAATAA
1 TAATAATAT
*
17590 AAATAATAT
1 TAATAATAT
*
17599 TAATAATAA
1 TAATAATAT
*
17608 AAATAATAT
1 TAATAATAT
17617 TAATAATA-
1 TAATAATAT
*
17625 -AA-AATAA
1 TAATAATAT
*
17632 TAATAATAG
1 TAATAATAT
17641 TAATAA-AT
1 TAATAATAT
17649 ATAATAA
1 -TAATAA
17656 AAAATAAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
6 4 0.07
7 2 0.03
8 3 0.05
9 52 0.85
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (9 bp):
TAATAATAT
Found at i:17596 original size:18 final size:18
Alignment explanation
Indices: 17564--17649 Score: 129
Period size: 18 Copynumber: 4.8 Consensus size: 18
17554 GTTGTATCTG
*
17564 TAATAA-AATAATAATAT
1 TAATAATAAAAATAATAT
17581 TAATAATAAAAATAATAT
1 TAATAATAAAAATAATAT
17599 TAATAATAAAAATAATAT
1 TAATAATAAAAATAATAT
*
17617 TAATAATAAAAATAATAA
1 TAATAATAAAAATAATAT
*
17635 TAATAGTAATAAATA
1 TAATAATAA-AAATA
17650 TAATAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
17 6 0.09
18 53 0.83
19 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (18 bp):
TAATAATAAAAATAATAT
Found at i:17652 original size:18 final size:18
Alignment explanation
Indices: 17564--17667 Score: 106
Period size: 18 Copynumber: 5.8 Consensus size: 18
17554 GTTGTATCTG
17564 TAATAAAATAATAATATTAA
1 TAAT-AAAT-ATAATATTAA
*
17584 TAATAAAAATAATATTAA
1 TAATAAATATAATATTAA
*
17602 TAATAAAAATAATATTAA
1 TAATAAATATAATATTAA
* *
17620 TAATAAAAATAATAATAA
1 TAATAAATATAATATTAA
*
17638 TAGT-AATA-AATA-TAA
1 TAATAAATATAATATTAA
* *
17653 TAAAAAATAAAATAT
1 TAATAAATATAATAT
17668 ATATAAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
15 5 0.07
16 8 0.11
17 7 0.09
18 48 0.64
19 3 0.04
20 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (18 bp):
TAATAAATATAATATTAA
Found at i:17656 original size:9 final size:9
Alignment explanation
Indices: 17564--17674 Score: 54
Period size: 9 Copynumber: 11.8 Consensus size: 9
17554 GTTGTATCTG
17564 TAATAAA-A
1 TAATAAATA
17572 TAATAATATTAA
1 TAATAA-A-T-A
*
17584 TAATAAAAA
1 TAATAAATA
*
17593 TAAT-ATTAA
1 TAATAAAT-A
*
17602 TAATAAAAA
1 TAATAAATA
17611 TAATATTAATAA
1 TAATA--AAT-A
17623 TAA-AAATAA
1 TAATAAAT-A
17632 TAAT-AATA
1 TAATAAATA
17640 GTAATAAATA
1 -TAATAAATA
17650 TAATAAA-A
1 TAATAAATA
17658 -AATAAAATA
1 TAAT-AAATA
17667 TATATAAA
1 TA-ATAAA
17675 AAAAACTAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 30
0.69 0.05 0.26
Matches are distributed among these distances:
7 3 0.04
8 12 0.15
9 40 0.49
10 9 0.11
11 6 0.07
12 11 0.14
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.32
Consensus pattern (9 bp):
TAATAAATA
Found at i:18130 original size:7 final size:7
Alignment explanation
Indices: 18113--18151 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
18103 CTTGTCTTAT
18113 TTCCATTC
1 TTCC-TTC
18121 TTCCTTC
1 TTCCTTC
18128 TTCCTTC
1 TTCCTTC
18135 TTCCTTC
1 TTCCTTC
18142 TTCCTTC
1 TTCCTTC
18149 TTC
1 TTC
18152 TACCTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCCTTC
Found at i:19936 original size:14 final size:14
Alignment explanation
Indices: 19917--19952 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
19907 CTGTTCAAAC
19917 AATGAACAAACATA
1 AATGAACAAACATA
*
19931 AATGAACGAACATA
1 AATGAACAAACATA
*
19945 AACGAACA
1 AATGAACA
19953 TATAATCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.11
Consensus pattern (14 bp):
AATGAACAAACATA
Found at i:31323 original size:35 final size:35
Alignment explanation
Indices: 31277--31345 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
31267 ACCAGACTGA
31277 TTGATTATTCTTGTAATTGCAGGGTCAAATCAAGC
1 TTGATTATTCTTGTAATTGCAGGGTCAAATCAAGC
*
31312 TTGATTTTTCTTGTAATTGCAGGGTCAAATCAAG
1 TTGATTATTCTTGTAATTGCAGGGTCAAATCAAG
31346 TCACTGACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (35 bp):
TTGATTATTCTTGTAATTGCAGGGTCAAATCAAGC
Found at i:32208 original size:112 final size:112
Alignment explanation
Indices: 32011--32473 Score: 623
Period size: 112 Copynumber: 4.1 Consensus size: 112
32001 TTGTCGGTTT
* * * *
32011 GTGTCGATATTTTATAAAAATATATTGATCCATAACAATATAACAAGT--AAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAAAAAAAATG--AAAA
* *
32074 CCGGTCTATAAATGACAAAACAGATAAAACGCTACCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
32123 GTGTCGATACTTTATAAAAATTTA-TATATCCATAATAATATAACATGTAAAAAAATAAT-AAAA
1 GTGTCGATACTTTATAAAAATGTATTA-ATCCATAACAATATAACAGGTAAAAAAA-AATGAAAA
* *
32186 CCGGACTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** *
32235 GTGTTAATACTTTATAAAAATGTATTAATCTATAACAATATAACAGGTAAAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAAAAAAAATG--AAAA
* *
32300 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** * * *
32349 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAAAAGGT-AAAAAAAATGACAA-C
1 GTGTCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAAAAAAAATGAAAACC
* *
32412 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
32459 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
32474 TATAAGTATC
Statistics
Matches: 316, Mismatches: 27, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
110 63 0.20
111 7 0.02
112 136 0.43
113 12 0.04
114 95 0.30
115 3 0.01
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAAAAAAAATGAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:32790 original size:182 final size:179
Alignment explanation
Indices: 32348--32794 Score: 648
Period size: 180 Copynumber: 2.5 Consensus size: 179
32338 ATATGTTGAT
* * *
32348 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAAAAGGTAAAAAAAATGAC--AA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAA
** * * *
32411 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
65 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
* * * *
32476 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGATAACTCTAATAA
130 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGATAACGCCAATAA
*
32526 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-
32591 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
65 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
*
32656 TAAGTATCGACACTTTTAGAATTTAAAAGAAAATAA-ATTATAGCGCCAATAA
130 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGA-TA-A-CGCCAATAA
* * * *
32708 AGTGTTGATACTTTATAAAAGTGTATCGATCCATAATAATATAACAGATAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-
*
32773 CGATCTCGAAATGACAAAACCG
65 CGGTCTCGAAATGACAAAACCG
32795 ATAGTAAAAA
Statistics
Matches: 242, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
177 9 0.04
178 47 0.19
179 3 0.01
180 95 0.39
181 1 0.00
182 87 0.36
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (179 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
GGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTAT
AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGATAACGCCAATAA
Found at i:33416 original size:23 final size:23
Alignment explanation
Indices: 33370--33417 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
33360 AAATAGGTCA
* * *
33370 ATATAAGTGCTACTTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
33393 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
33416 AT
1 AT
33418 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:33956 original size:38 final size:38
Alignment explanation
Indices: 33905--34048 Score: 288
Period size: 38 Copynumber: 3.8 Consensus size: 38
33895 ATTTAAGCAT
33905 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
1 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
33943 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
1 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
33981 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
1 AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
34019 AACCAAAAGTTATAACCAACCATTTGATTA
1 AACCAAAAGTTATAACCAACCATTTGATTA
34049 TCTTTTGCAT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 106 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (38 bp):
AACCAAAAGTTATAACCAACCATTTGATTAAAACCCTA
Found at i:36817 original size:3 final size:3
Alignment explanation
Indices: 36811--36877 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
36801 TATTTGCTTA
* *
36811 TAT TAT TATT TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
36857 TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
36878 AATAATACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 49 0.89
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:36849 original size:31 final size:31
Alignment explanation
Indices: 36811--36877 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
36801 TATTTGCTTA
* *
36811 TATTATTATTTATTATTAT-TTTTATTTTTAT
1 TATTATTA-TTATTATTATGTTATATTATTAT
36842 TATTATTATTATTATTATGTTATATTATTAT
1 TATTATTATTATTATTATGTTATATTATTAT
36873 TATTA
1 TATTA
36878 AATAATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (31 bp):
TATTATTATTATTATTATGTTATATTATTAT
Found at i:41002 original size:26 final size:27
Alignment explanation
Indices: 40973--41037 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
40963 TACATTTGCA
40973 TTTACATTTTGCATCTT-T-TTTTCATT
1 TTTACATTTTGCAT-TTATATTTTCATT
*
40999 TTTACGTTTAT--ATTTATATTTTCATT
1 TTTACATTT-TGCATTTATATTTTCATT
41025 TTTACA-TTTGCAT
1 TTTACATTTTGCAT
41038 ATTTGCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
24 3 0.09
25 5 0.16
26 23 0.72
27 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (27 bp):
TTTACATTTTGCATTTATATTTTCATT
Found at i:48126 original size:45 final size:48
Alignment explanation
Indices: 48059--48156 Score: 148
Period size: 45 Copynumber: 2.1 Consensus size: 48
48049 TCATTTTCAT
*
48059 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
* *
48106 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCAGTTAGGATTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
48152 TTTTT
1 TTTTT
48157 GTGAATATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 27 0.57
46 11 0.23
47 9 0.19
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
Found at i:54218 original size:8 final size:8
Alignment explanation
Indices: 54205--54232 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
54195 CGATCCTTCC
54205 ATATGTAT
1 ATATGTAT
54213 ATATGTAT
1 ATATGTAT
54221 ATATGTAT
1 ATATGTAT
54229 ATAT
1 ATAT
54233 ATCTTCTCTT
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:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:57746 original size:7 final size:7
Alignment explanation
Indices: 57736--57848 Score: 190
Period size: 7 Copynumber: 15.7 Consensus size: 7
57726 AATAATTAAA
57736 AAAAATG
1 AAAAATG
57743 AAAAATG
1 AAAAATG
57750 AAAAAAATG
1 --AAAAATG
57759 AAAAATG
1 AAAAATG
57766 AAAAATG
1 AAAAATG
57773 AAAAATG
1 AAAAATG
57780 AAAAATG
1 AAAAATG
57787 AAAAATG
1 AAAAATG
57794 AAAAATG
1 AAAAATG
57801 AAAAATG
1 AAAAATG
57808 AAAAATG
1 AAAAATG
57815 AAAAATG
1 AAAAATG
57822 AAAAATG
1 AAAAATG
57829 AAAAATG
1 AAAAATG
*
57836 AAAGAAAG
1 AAA-AATG
57844 AAAAA
1 AAAAA
57849 AAAAGAAATA
Statistics
Matches: 102, Mismatches: 1, Indels: 6
0.94 0.01 0.06
Matches are distributed among these distances:
7 89 0.87
8 6 0.06
9 7 0.07
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:57950 original size:45 final size:45
Alignment explanation
Indices: 57865--57950 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
57855 AATAGAAATA
* * *
57865 AAAGGAGGGTTCAAGATAAAAACCTGAAAAGGGCGTCTTGAAACC
1 AAAGGAGGGTTCAAGATAAAAACCCGAAAAGAGCGACTTGAAACC
* * *
57910 AAAGGA-GGTCTCAAGTTGAAAACCCGCAAAGAGCGACTTGA
1 AAAGGAGGGT-TCAAGATAAAAACCCGAAAAGAGCGACTTGA
57951 GTTGAGTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (45 bp):
AAAGGAGGGTTCAAGATAAAAACCCGAAAAGAGCGACTTGAAACC
Found at i:59422 original size:111 final size:110
Alignment explanation
Indices: 59211--59532 Score: 431
Period size: 111 Copynumber: 2.9 Consensus size: 110
59201 AATACGTTTG
*
59211 ATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCAGACCCATTTTTATGAAGATT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCA-TTTTATGAAGATT
* *
59276 GTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTTT
65 GTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGA-CCGTTTTT
* *
59323 ATGAAGATTGTTCGAGTTCTATACTCTCTG-ATGGAATAGGGAGCGGACCC-GTTTATTGAAGAT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAT-GAATAGGGAGCAGACCCATTTTA-TGAAGAT
* *
59386 T-TTCTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTTTTTT
64 TGTTC-GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCGTTTTT
* * *
59433 ATTGAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGAT
1 A-TGAAGATTGTTCGAGTTC-TATACTCTCTGAATGAATAGGGAGCAGACCCATTTTATGAAGAT
59497 TGTTCGAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
64 TGTTCGAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
59533 AGGCTCGTCA
Statistics
Matches: 187, Mismatches: 13, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
110 20 0.11
111 113 0.60
112 54 0.29
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (110 bp):
ATGAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCATTTTATGAAGATTG
TTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCGTTTTT
Found at i:59552 original size:55 final size:56
Alignment explanation
Indices: 59211--59532 Score: 406
Period size: 56 Copynumber: 5.8 Consensus size: 56
59201 AATACGTTTG
* * * *
59211 ATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCAGACCCATTTTT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
* *
59267 ATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTTT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
* *
59323 ATGAAGATTGTTCGAGTTCTATACTCTCTGATGGAATAGGGAGCGGACCCGTTTAT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
* *
59379 -TGAAGATT-TTCTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CCTTTTTT
1 ATGAAGATTGTTC-GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
* * * * * *
59433 ATTGAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACAC-ATTTT
1 A-TGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
59489 ATGAAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 ATGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
59533 AGGCTCGTCA
Statistics
Matches: 241, Mismatches: 18, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
54 10 0.04
55 80 0.33
56 147 0.61
57 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (56 bp):
ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT
Found at i:64451 original size:13 final size:13
Alignment explanation
Indices: 64433--64457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64423 TCCTTGATTT
64433 ATTATGGTTTTCA
1 ATTATGGTTTTCA
64446 ATTATGGTTTTC
1 ATTATGGTTTTC
64458 TTTAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
ATTATGGTTTTCA
Found at i:69393 original size:24 final size:23
Alignment explanation
Indices: 69366--69417 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
69356 TTTTCGTAAA
*
69366 ATAATTTTAAATCTCTATTTTTTT
1 ATAATTTT-AATCTCTAGTTTTTT
*
69390 ATAA-TTTGATCTCTAGTTTTTT
1 ATAATTTTAATCTCTAGTTTTTT
69412 -TAATTT
1 ATAATTT
69418 ACTGCTCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.12
22 15 0.60
23 3 0.12
24 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.62
Consensus pattern (23 bp):
ATAATTTTAATCTCTAGTTTTTT
Found at i:69415 original size:21 final size:22
Alignment explanation
Indices: 69376--69417 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
69366 ATAATTTTAA
*
69376 ATCTCTATTTTTTTATAATTTG
1 ATCTCTAGTTTTTTATAATTTG
69398 ATCTCTAGTTTTTT-TAATTT
1 ATCTCTAGTTTTTTATAATTT
69418 ACTGCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (22 bp):
ATCTCTAGTTTTTTATAATTTG
Found at i:71873 original size:2 final size:2
Alignment explanation
Indices: 71866--71894 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
71856 GCTTACAAAT
71866 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71895 AAGATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77398 original size:26 final size:26
Alignment explanation
Indices: 77362--77417 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
77352 TTTGCCATAG
77362 TCCTTACTAAAACATTAGAATAATAC
1 TCCTTACTAAAACATTAGAATAATAC
77388 TCCTTACTAAAACATTAGAATAATAC
1 TCCTTACTAAAACATTAGAATAATAC
77414 TCCT
1 TCCT
77418 AGGGAAGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (26 bp):
TCCTTACTAAAACATTAGAATAATAC
Found at i:77975 original size:19 final size:20
Alignment explanation
Indices: 77932--77988 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
77922 AAATGACCAA
*
77932 CAAATTCGTAACGCG-ATCT
1 CAAATTCGCAACGCGAATCT
77951 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATCT
* *
77970 CCAATTTCGCAACGTGAAT
1 -CAAATTCGCAACGCGAAT
77989 ATGTAAATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATCT
Found at i:78020 original size:21 final size:21
Alignment explanation
Indices: 77996--78063 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
77986 AATATGTAAA
* *
77996 TCGCATTACGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
78017 TCGCTTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
78038 TCGCTTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
78059 TCGCA
1 TCGCA
78064 ACGCGATAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:78069 original size:21 final size:21
Alignment explanation
Indices: 77932--78071 Score: 94
Period size: 21 Copynumber: 6.9 Consensus size: 21
77922 AAATGACCAA
* *
77932 CAAATTCGTAACGCGAT-CT-
1 CAAATTCGCAACGCGATATTC
77951 CAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATATTC
* *
77971 CAATTTCGCAACGTGAATATGT-
1 CAAATTCGCAACGCG-ATAT-TC
*** *
77993 -AAA-TCGCATTACGATTTTC
1 CAAATTCGCAACGCGATATTC
***
78012 CAAATTCGCTTTGCGATATTC
1 CAAATTCGCAACGCGATATTC
***
78033 CAAATTCGCTTTGCGATATTC
1 CAAATTCGCAACGCGATATTC
78054 CAAATTCGCAACGCGATA
1 CAAATTCGCAACGCGATA
78072 GTCAAATGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 19 0.20
20 22 0.23
21 52 0.54
22 2 0.02
23 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (21 bp):
CAAATTCGCAACGCGATATTC
Found at i:78070 original size:42 final size:41
Alignment explanation
Indices: 77932--78078 Score: 122
Period size: 42 Copynumber: 3.6 Consensus size: 41
77922 AAATGACCAA
* * **
77932 CAAATTCGTAACGCGAT-CTCAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATATTCAAATTCGCATTGCGATATTC
* * * *
77971 CAATTTCGCAACGTGAATATGT-AAA-TCGCATTACGATTTTC
1 CAAATTCGCAACGCG-ATAT-TCAAATTCGCATTGCGATATTC
*** *
78012 CAAATTCGCTTTGCGATATTCCAAATTCGCTTTGCGATATTC
1 CAAATTCGCAACGCGATATT-CAAATTCGCATTGCGATATTC
*
78054 CAAATTCGCAACGCGATAGTCAAAT
1 CAAATTCGCAACGCGATATTCAAAT
78079 GTTTTTACAC
Statistics
Matches: 81, Mismatches: 20, Indels: 12
0.72 0.18 0.11
Matches are distributed among these distances:
39 13 0.16
40 14 0.17
41 24 0.30
42 30 0.37
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (41 bp):
CAAATTCGCAACGCGATATTCAAATTCGCATTGCGATATTC
Found at i:78239 original size:22 final size:22
Alignment explanation
Indices: 78209--78257 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
78199 CGGCGACATC
*
78209 CGTCCCCA-TCTCTGACGAAATT
1 CGTCTCCATTCTC-GACGAAATT
*
78231 CGTCTCCATTTTCGACGAAATT
1 CGTCTCCATTCTCGACGAAATT
78253 CGTCT
1 CGTCT
78258 ATCTCCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.33
Consensus pattern (22 bp):
CGTCTCCATTCTCGACGAAATT
Found at i:80528 original size:4 final size:4
Alignment explanation
Indices: 80519--80560 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
80509 TTTTTCGGCA
* * *
80519 TTAT TTAT TTAT TTAT TTAT TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
80561 TCAGTGGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:80795 original size:21 final size:21
Alignment explanation
Indices: 80701--80799 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
80691 CCCGATGCAC
*
80701 CTATCATCATTCAAGAGGCGC-
1 CTATCATCGTTCAAGAGGC-CA
* * *
80722 CT-CCTATCGTTCAAGAGTCCC
1 CTATC-ATCGTTCAAGAGGCCA
* *
80743 CTATCATC-ATCGAAGAAGCCA
1 CTATCATCGTTC-AAGAGGCCA
* ** *
80764 ATCCCACCGTTCAAGAGGCCA
1 CTATCATCGTTCAAGAGGCCA
80785 CTATCATCGTTCAAG
1 CTATCATCGTTCAAG
80800 TGGTCCCGCC
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
20 4 0.07
21 48 0.87
22 3 0.05
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.23
Consensus pattern (21 bp):
CTATCATCGTTCAAGAGGCCA
Found at i:82249 original size:14 final size:14
Alignment explanation
Indices: 82230--82269 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
82220 TTTTGATTAA
82230 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
82244 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
82258 TTGATTTGTAAA
1 TTGATTTGTAAA
82270 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:82262 original size:61 final size:66
Alignment explanation
Indices: 82179--82319 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
82169 TTTTACATTG
82179 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
82239 A
66 A
* ** * * *
82240 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
82304 TA
65 TA
82306 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
82320 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.38
62 4 0.06
63 1 0.01
64 6 0.09
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:82453 original size:34 final size:34
Alignment explanation
Indices: 82390--82462 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
82380 AATTCGCAAC
*
82390 GCGAAAGTCAAATTCGCAACGCTTATTTCGCG-TT
1 GCGAAAGTCAAATTCGCAACGCATATTTCG-GTTT
*
82424 GCGATAGTCAAATTCGCAACGCGAT-TTTCGGTTT
1 GCGAAAGTCAAATTCGCAACGC-ATATTTCGGTTT
82458 GCGAA
1 GCGAA
82463 TTTGACATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.03
34 32 0.94
35 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (34 bp):
GCGAAAGTCAAATTCGCAACGCATATTTCGGTTT
Found at i:82509 original size:20 final size:20
Alignment explanation
Indices: 82459--82514 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
82449 TTTCGGTTTG
* *
82459 CGAATTTGACATTCACGTTA
1 CGAATTTGACTTTCGCGTTA
*
82479 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTA
* *
82499 TGAATTTGACTATCGC
1 CGAATTTGACTTTCGC
82515 AACGCTTATT
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:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTA
Found at i:82860 original size:18 final size:18
Alignment explanation
Indices: 82837--82872 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
82827 AAGCCAGATG
82837 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
82855 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
82873 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:84948 original size:3 final size:3
Alignment explanation
Indices: 84940--84976 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
84930 TGGGGACTTT
* *
84940 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTT TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
84977 CCAGGGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:84954 original size:15 final size:15
Alignment explanation
Indices: 84936--84976 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
84926 TCTTTGGGGA
84936 CTTTTTCTTCTTCTT
1 CTTTTTCTTCTTCTT
84951 CTTTTTCTTCTTCTT
1 CTTTTTCTTCTTCTT
84966 CTTTTTCTTCT
1 CTTTTTCTTCT
84977 CCAGGGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTTTCTTCTTCTT
Found at i:86156 original size:21 final size:21
Alignment explanation
Indices: 86132--86219 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
86122 AATTCGCGTT
86132 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
86153 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
86174 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
86195 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
86216 GCGA
1 GCGA
86220 TTTACATATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:88929 original size:18 final size:18
Alignment explanation
Indices: 88906--88940 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
88896 AGAAAAAGGC
*
88906 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
88924 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
88941 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:89252 original size:140 final size:140
Alignment explanation
Indices: 89000--89269 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
88990 AAACGTTGTA
* *
89000 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAATATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
*
89065 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
89130 TATGTGTATT
131 TATGTGTATT
89140 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
*
89205 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCTAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
89270 CGCAATGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:89265 original size:20 final size:20
Alignment explanation
Indices: 89240--89567 Score: 231
Period size: 20 Copynumber: 17.6 Consensus size: 20
89230 TTACACATTC
* *
89240 ATTTGAATATCGCAACGCTA
1 ATTTGACTATCGCAACGCGA
*
89260 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
89280 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
89299 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
89314 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
89334 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
89353 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
89368 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
89388 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
89408 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
89428 A----A--ATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
89442 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
89462 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
89482 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGA
*
89502 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
89522 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
89536 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
89556 A-TTGACTTTCGC
1 ATTTGACTATCGC
89568 GTTGCGATTT
Statistics
Matches: 242, Mismatches: 40, Indels: 53
0.72 0.12 0.16
Matches are distributed among these distances:
14 40 0.17
15 6 0.02
16 2 0.01
18 2 0.01
19 15 0.06
20 176 0.73
21 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:89335 original size:54 final size:54
Alignment explanation
Indices: 89248--89558 Score: 267
Period size: 54 Copynumber: 5.6 Consensus size: 54
89238 TCATTTGAAT
* * *
89248 ATCGCAACGCTAATTTGACTATCGCAATGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* * *
89302 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* * **
89356 ATCGCAACACGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GC-A----AAA
* * *
89416 ATCGCAACGAGAA----A--ATCGCAACGGGAATTTGATTATCGCAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGC-AA----A-A
* * * * *
89470 ATCGCAACGCGAATTTGATTATCGCAATGGGTATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCA-AAA
* * *
89524 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATT
89559 GACTTTCGCG
Statistics
Matches: 208, Mismatches: 31, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
49 1 0.00
53 3 0.01
54 159 0.76
55 3 0.01
56 1 0.00
58 2 0.01
59 1 0.00
60 38 0.18
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
Found at i:89380 original size:74 final size:73
Alignment explanation
Indices: 89302--89496 Score: 259
Period size: 74 Copynumber: 2.6 Consensus size: 73
89292 CAACTCAAAA
*
89302 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACAC
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG-AGAAAATCGCAACAC
89366 GAATTTG-TCT
64 GAATTTGAT-T
* * * **
89376 ATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGGG
1 ATCGCAACGCGAATTTGACTATCGCAACCG-AATTTGACTATCGCAACGAGAAAATCGCAACACG
89441 AATTTGATT
65 AATTTGATT
* *
89450 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAA
89497 TGGGTATTTG
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
73 2 0.02
74 103 0.96
75 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (73 bp):
ATCGCAACGCGAATTTGACTATCGCAACCGAATTTGACTATCGCAACGAGAAAATCGCAACACGA
ATTTGATT
Found at i:89547 original size:94 final size:94
Alignment explanation
Indices: 89356--89567 Score: 318
Period size: 94 Copynumber: 2.3 Consensus size: 94
89346 CAACGCAAAA
* *
89356 ATCGCAACACGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
* * * *
89421 AACGAGAAAATCGCAACGGGAATTTGATT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
* * *
89450 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAATGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
*
89515 AACGAGAAAATCGCAAAGCGTATTAGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
*
89544 ATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGC
89568 GTTGCGATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 9 0.08
94 97 0.92
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
AACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:89773 original size:14 final size:14
Alignment explanation
Indices: 89736--89774 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
89726 TCAATATTAA
*
89736 ATAAATCAACTTTT
1 ATAAATCAATTTTT
*
89750 AGAAATCAATTTTT
1 ATAAATCAATTTTT
89764 ATAAATCAATT
1 ATAAATCAATT
89775 AAACAAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (14 bp):
ATAAATCAATTTTT
Found at i:91810 original size:20 final size:20
Alignment explanation
Indices: 91785--91880 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
91775 TCGCAACACG
*
91785 AATGACTATCGCAACGCAAA
1 AATGACTATCGCAACGCGAA
*
91805 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
91825 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
91845 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
91865 TTTAACTATCGCAACG
1 AATGACTATCGCAACG
91881 AGAGAATCGC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:91948 original size:20 final size:20
Alignment explanation
Indices: 91923--91970 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
91913 GCGATTCTTT
91923 CGTTGCGATAGTCAAATTAG
1 CGTTGCGATAGTCAAATTAG
** *
91943 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTAG
91963 CGTTGCGA
1 CGTTGCGA
91971 AAGTAAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTAG
Found at i:94340 original size:22 final size:22
Alignment explanation
Indices: 94313--94355 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
94303 GAGATAGACG
94313 GATTTCACCGGAGATGAGGACT
1 GATTTCACCGGAGATGAGGACT
** *
94335 GATTTCGTCGGAGATGGGGAC
1 GATTTCACCGGAGATGAGGAC
94356 GGATGTCGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.23
Consensus pattern (22 bp):
GATTTCACCGGAGATGAGGACT
Found at i:94620 original size:71 final size:71
Alignment explanation
Indices: 94503--94656 Score: 272
Period size: 71 Copynumber: 2.2 Consensus size: 71
94493 AAAAAAAATA
* *
94503 CGCGTTGCGATAATAATGGTGCTTTGAAAATCGCATTGCGATAGTCAGCATCGCGTTACGACAGT
1 CGCGTTGCGATAATAATGGCGCTTTGAAAATCGCATTACGATAGTCAGCATCGCGTTACGACAGT
94568 CAGAAT
66 CAGAAT
* *
94574 TGCGTTGCGATAATAATGGCGCTTTGAAAATCGCATTACGATAGTCAGCATCGCGTTGCGACAGT
1 CGCGTTGCGATAATAATGGCGCTTTGAAAATCGCATTACGATAGTCAGCATCGCGTTACGACAGT
94639 CAGAAT
66 CAGAAT
94645 CGCGTTGCGATA
1 CGCGTTGCGATA
94657 GTCAGAATCG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (71 bp):
CGCGTTGCGATAATAATGGCGCTTTGAAAATCGCATTACGATAGTCAGCATCGCGTTACGACAGT
CAGAAT
Found at i:94639 original size:20 final size:20
Alignment explanation
Indices: 94602--94699 Score: 133
Period size: 20 Copynumber: 4.9 Consensus size: 20
94592 GCGCTTTGAA
* *
94602 AATCGCATTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
94622 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
94642 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
94662 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
94682 ATTCGCATTGCGATAGTC
1 AATCGCGTTGCGATAGTC
94700 GGAAAATCGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:97330 original size:24 final size:24
Alignment explanation
Indices: 97303--97374 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 24
97293 TATATATATA
97303 TATTTGTAATTTATAATTTATCCT
1 TATTTGTAATTTATAATTTATCCT
* * *
97327 TA-TT-TCA-TTAT-ATATAT--A
1 TATTTGTAATTTATAATTTATCCT
97345 TATTTGTAATTTATAATTTATCCT
1 TATTTGTAATTTATAATTTATCCT
97369 TATTTG
1 TATTTG
97375 ATGTTGTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 7 0.19
21 8 0.22
22 7 0.19
23 2 0.06
24 8 0.22
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (24 bp):
TATTTGTAATTTATAATTTATCCT
Found at i:97347 original size:42 final size:42
Alignment explanation
Indices: 97293--97373 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
97283 TCATTATATA
97293 TATATATATATATTTGTAATTTATAATTTATCCTTATTTCAT
1 TATATATATATATTTGTAATTTATAATTTATCCTTATTTCAT
97335 TATATATATATATTTGTAATTTATAATTTATCCTTATTT
1 TATATATATATATTTGTAATTTATAATTTATCCTTATTT
97374 GATGTTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (42 bp):
TATATATATATATTTGTAATTTATAATTTATCCTTATTTCAT
Found at i:109702 original size:125 final size:125
Alignment explanation
Indices: 109480--109715 Score: 328
Period size: 125 Copynumber: 1.9 Consensus size: 125
109470 AATACCCACA
* * ** *
109480 TTGGGGCATGACTGAACCCCCATCATTTTGAAATGACAAGATCCAGACGAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATCCAGACCAAGAAGGCATTGAGAA
* * * * *
109545 TAAGCCTTACAATTTGAGGTGTTGGGGTATTTTGAAGACTCGTACCTTTATAAGATAATG
66 TAAGCCTTACAATTTGAGATATTGAGGCATTTTGAAGACCCGTACCTTTATAAGATAATG
* * *
109605 TTGGGGCGCGACTGAACCCACATCATGATGAAATTACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATCCAGACCAAGAAGGCATTGAGAA
* * *
109670 TGAGCCTTATAATTTGAGATATTGAGGCATTTTGAAGGCCCGTACC
66 TAAGCCTTACAATTTGAGATATTGAGGCATTTTGAAGACCCGTACC
109716 AGAACAAAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
125 95 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATCCAGACCAAGAAGGCATTGAGAA
TAAGCCTTACAATTTGAGATATTGAGGCATTTTGAAGACCCGTACCTTTATAAGATAATG
Found at i:110967 original size:36 final size:37
Alignment explanation
Indices: 110927--111161 Score: 191
Period size: 36 Copynumber: 6.5 Consensus size: 37
110917 AAGTCAATCT
110927 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
*
110963 TAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCAT-C
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* * * *
110998 TGAAGCCTTCACCGGAGA-ATAGGGAAGCAATCAAT-C
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* * * *
111034 TGAAGCCATCACCGGAGA-ATAGTGAAGCGAACCATCA
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* * *
111071 TAAGTCTTCACC--AGAGAGTAGTGAAGTAAACCATCT
1 TAAGCCTTCACCGAAGAGA-TAGTGAAGCAAACCATCC
* * * * **
111107 TAAGTCTTCACCAAAAAG-TAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGAAGAGATAGTGAAGCA-AACCATCC
* *
111144 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
111162 TGTTGGAACA
Statistics
Matches: 167, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
34 3 0.02
35 4 0.02
36 137 0.82
37 20 0.12
38 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (37 bp):
TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
Found at i:111116 original size:108 final size:109
Alignment explanation
Indices: 110914--111118 Score: 288
Period size: 108 Copynumber: 1.9 Consensus size: 109
110904 ATGAGATTGG
* * * *
110914 AGCAAGTCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAG
1 AGCAAGTCAATCTGAAGCCATCACCGAAGAGAAGTGAAGCAAACCATCATAAGCCTTCACCAGAG
110979 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGGGA
66 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGGGA
* * *
111023 AGCAA-TCAATCTGAAGCCATCACCGGAGA-ATAGTGAAGCGAACCATCATAAGTCTTCACCAGA
1 AGCAAGTCAATCTGAAGCCATCACCGAAGAGA-AGTGAAGCAAACCATCATAAGCCTTCACCAGA
* * * *
111086 GAGTAGTGAAGTAAACCATCTTAAGTCTTCACC
65 GAATAGTGAAGCAAACCATCTGAAGCCTTCACC
111119 AAAAAGTAGT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 1 0.01
108 78 0.93
109 5 0.06
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (109 bp):
AGCAAGTCAATCTGAAGCCATCACCGAAGAGAAGTGAAGCAAACCATCATAAGCCTTCACCAGAG
AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGGGA
Found at i:111133 original size:72 final size:70
Alignment explanation
Indices: 110927--111118 Score: 231
Period size: 72 Copynumber: 2.7 Consensus size: 70
110917 AAGTCAATCT
* *
110927 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAA
1 TAAGCCTTCACCG-AGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAA
110992 ACCATC
65 ACCATC
* * * * * * *
110998 TGAAGCCTTCACCGGAGAATAGGGAAGCAATCAATCTGAAGCCATCACCGGAGAATAGTGAAGCG
1 T-AAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCA
111063 AACCATC
64 AACCATC
* * *
111070 ATAAGTCTTCACCAGAGAGTAGTGAAGTAAACCATCTTAAGTCTTCACC
1 -TAAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACC
111119 AAAAAGTAGT
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
71 1 0.01
72 96 0.97
73 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (70 bp):
TAAGCCTTCACCGAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAA
CCATC
Found at i:111414 original size:51 final size:51
Alignment explanation
Indices: 111349--111540 Score: 260
Period size: 51 Copynumber: 3.7 Consensus size: 51
111339 AAGATTATTT
*
111349 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGATG-TC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
*
111399 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTC
1 -GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-TGTTC
* * * *
111452 GAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTC
* *
111506 GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAAC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAAC
111541 TCGATTGTTG
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
51 44 0.35
52 40 0.32
53 2 0.02
54 35 0.28
55 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
Found at i:111534 original size:106 final size:103
Alignment explanation
Indices: 111349--111540 Score: 278
Period size: 106 Copynumber: 1.8 Consensus size: 103
111339 AAGATTATTT
* * *
111349 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGATGTCTGAGTTCCATACTCC
1 GAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTTTGAAGATGTCTGAGTTCCATAATCC
*
111414 CTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTC
66 CTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTC
* * *
111452 GAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATAT-TCGAGTTCCATA
1 GAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTTT---GAAGATGTCT-GAGTTCCATA
111516 ATCCCTAGAGAAAGAGGGAACGAAC
62 ATCCCTAGAGAAAGAGGGAACGAAC
111541 TCGATTGTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
103 37 0.47
105 1 0.01
106 40 0.51
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (103 bp):
GAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTTTGAAGATGTCTGAGTTCCATAATCC
CTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTC
Found at i:111700 original size:55 final size:55
Alignment explanation
Indices: 111542--111708 Score: 280
Period size: 55 Copynumber: 3.0 Consensus size: 55
111532 GGAACGAACT
* *
111542 CGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
111597 CGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
111652 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
111707 CG
1 CG
111709 TTTTCAAAAG
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 104 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
Found at i:111720 original size:55 final size:54
Alignment explanation
Indices: 111550--111862 Score: 218
Period size: 55 Copynumber: 5.8 Consensus size: 54
111540 CTCGATTGTT
* * *
111550 GAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT--
1 GAAGATTGTTCGAGTCTCATACTCCCTGAAAGAATAGGGAGCA-ACACG-TT-TTCA
* * *
111605 GAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACACGATTGTT--
1 GAAGATTGTTCGAGTCTCATACTCCCTGAAAGAATAGGGAGCA-ACACG-TT-TTCA
* *
111660 GAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACACGTTTTCA
1 GAAGATTGTTCGAGTCTCATACTCCCTGAAAGAATAGGGAGCA-ACACGTTTTCA
* * * *
111715 AAAGATT-TTCGAGT-TCTATGCTCCCT-AAAGAA-AGTGTGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTCTC-ATACTCCCTGAAAGAATAG-G-GAGC-AACACGTTTTCA
* * * ***
111769 GAAGATT-TTCAAGT-TCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTAGACA
1 GAAGATTGTTCGAGTCTC-ATACTCCCTGAAAG-AATAGGGAGC-AACACGTTTTCA
* * * *
111823 AAAGATTGTACGAGTTTC-TACTCCCTGAAGGAATAGGGAG
1 GAAGATTGTTCGAGTCTCATACTCCCTGAAAGAATAGGGAG
111863 TGAACATGTT
Statistics
Matches: 221, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.01
53 10 0.05
54 92 0.42
55 113 0.51
56 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTCATACTCCCTGAAAGAATAGGGAGCAACACGTTTTCA
Found at i:111828 original size:54 final size:54
Alignment explanation
Indices: 111339--111867 Score: 224
Period size: 54 Copynumber: 9.8 Consensus size: 54
111329 GAAGCAAATG
* * * *
111339 AAGATTATTTGAGTTCCATACTCCCT-AGAGAGAGAGGGAGCGAACCCGTTTG---
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTAGCAA
* * *
111391 AAGA-TGTCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG--A
1 AAGATTTTC-GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTAGCAA
* * * *
111443 AA-ATTGTTCGAGTTCTATACTCCCT-AGAGAAAGAGAGAGCGAACTCGTTTGCAG
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTAGCAA
* * * * * ***
111497 AAGATATTCGAGTTCCATAATCCCT-AGAGAAAGAGGGAACGAACTCGATT-GTTG
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCG-TTAGCAA
* * * * ***
111551 AAGTTTGTTCGAG-TCTTATACTCTCTGAA-AGAATAGGGAGC-AGACACGATT-GTTG
1 AAGATT-TTCGAGTTC-TATACTCCCTGAAGA-AAGAGGGAGCGA-ACCCG-TTAGCAA
* * * * ***
111606 AAGATTATTCGAG-TCTCATACTCTCTGAA-AGAATAGGGAG-TAGACACGATT-GTTG
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGA-AAGAGGGAGCGA-ACCCG-TTAGCAA
* * * * **
111661 AAGATTGTTCGAG-TCTCATACTCTCTGAAGGAATAGGGAGC-ATACACGTTTTCAA
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGA-ACCCGTTAGCAA
* * * * * *
111716 AAGATTTTCGAGTTCTATGCTCCCTAAAGAAAGTGTGAGCGAACCCGTTTGCAG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGCAA
*
111770 AAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TAGACAA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAG-CAA
* * * * *
111824 AAGATTGTACGAGTT-TCTACTCCCTGAAGGAATAGGGAGTGAAC
1 AAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAAC
111868 ATGTTTTCCA
Statistics
Matches: 400, Mismatches: 55, Indels: 42
0.80 0.11 0.08
Matches are distributed among these distances:
50 1 0.00
51 43 0.11
52 46 0.12
53 4 0.01
54 159 0.40
55 146 0.37
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (54 bp):
AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGCAA
Found at i:119426 original size:21 final size:21
Alignment explanation
Indices: 119381--119426 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
119371 TACACTGGTA
* *
119381 AGATTAATTACCATAATAGGT
1 AGATTAATTACCATAATAAGC
* *
119402 AGATTGATTACTATAATAAGC
1 AGATTAATTACCATAATAAGC
119423 AGAT
1 AGAT
119427 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (21 bp):
AGATTAATTACCATAATAAGC
Found at i:119798 original size:18 final size:18
Alignment explanation
Indices: 119775--119814 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
119765 GGAAGGAGGC
*
119775 TTCAATGTATTTACAGTA
1 TTCAATGCATTTACAGTA
119793 TTCAATGCATTTACAGTA
1 TTCAATGCATTTACAGTA
119811 TTCA
1 TTCA
119815 TCCCACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (18 bp):
TTCAATGCATTTACAGTA
Found at i:119934 original size:2 final size:2
Alignment explanation
Indices: 119927--119967 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
119917 TTAGGAATTA
*
119927 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
119968 AGCAAAGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:120330 original size:16 final size:16
Alignment explanation
Indices: 120299--120338 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
120289 TTTACTTCAT
*
120299 AATGATT-AAGTGCTG
1 AATGATTCAAATGCTG
120314 AATGATTCAAATGCTG
1 AATGATTCAAATGCTG
120330 AATGATTCA
1 AATGATTCA
120339 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:129142 original size:7 final size:7
Alignment explanation
Indices: 129130--129159 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
129120 TATTAAATTG
129130 AAATATA
1 AAATATA
129137 AAATATA
1 AAATATA
129144 AAATATA
1 AAATATA
129151 AAATATA
1 AAATATA
129158 AA
1 AA
129160 TTTATATAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:129174 original size:15 final size:18
Alignment explanation
Indices: 129146--129182 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
129136 AAAATATAAA
129146 ATATAAAATATAAATT-T
1 ATATAAAATATAAATTGT
129163 ATAT-AAAT-TAAATTGT
1 ATATAAAATATAAATTGT
129179 ATAT
1 ATAT
129183 TGTAATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 9 0.47
17 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATAAAATATAAATTGT
Found at i:129181 original size:16 final size:17
Alignment explanation
Indices: 129132--129182 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 17
129122 TTAAATTGAA
129132 ATATAAAATATAAA---
1 ATATAAAATATAAATTT
129146 ATATAAAATATAAATTT
1 ATATAAAATATAAATTT
129163 ATAT-AAAT-TAAATTGT
1 ATATAAAATATAAATT-T
129179 ATAT
1 ATAT
129183 TGTAATTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.42
15 6 0.18
16 9 0.27
17 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATAAAATATAAATTT
Found at i:132742 original size:29 final size:29
Alignment explanation
Indices: 132680--132756 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
132670 AGTTAAATTG
* *
132680 ATTTTTTTCAAGTTCAAGGATCAAATTGAT
1 ATTTTTTT-AAGTTTAAGGATCAAATTAAT
*
132710 -TTTTTTTAAGTTTAAGGGTCAAATTAAT
1 ATTTTTTTAAGTTTAAGGATCAAATTAAT
* *
132738 ATTTTTTAAAATTTAAGGA
1 ATTTTTTTAAGTTTAAGGA
132757 CTTATTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 18 0.45
29 22 0.55
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (29 bp):
ATTTTTTTAAGTTTAAGGATCAAATTAAT
Found at i:132745 original size:28 final size:28
Alignment explanation
Indices: 132674--132756 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
132664 TAAATGAGTT
* *
132674 AAATTGATTTTTTTCAAGTTCAAGGATC
1 AAATTGATTTTTTTAAAGTTTAAGGATC
* *
132702 AAATTGATTTTTTTTAAGTTTAAGGGTC
1 AAATTGATTTTTTTAAAGTTTAAGGATC
* *
132730 AAATTAATATTTTTTAAAATTTAAGGA
1 AAATTGAT-TTTTTTAAAGTTTAAGGA
132757 CTTATTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 32 0.68
29 15 0.32
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (28 bp):
AAATTGATTTTTTTAAAGTTTAAGGATC
Found at i:132819 original size:46 final size:45
Alignment explanation
Indices: 132769--132869 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 45
132759 TATTTAATTT
* *
132769 TTAAAAATATATATATAAATTCAAAATAAAAA-AAA-TATTCAAAAAC
1 TTAAAAATATA-ATA-AAACTAAAAATAAAAAGAAATTATTC-AAAAC
* *
132815 TT--AAATATAATAATACTAAAAATAAAAAGTAAATTATTCAAAAG
1 TTAAAAATATAATAAAACTAAAAATAAAAAG-AAATTATTCAAAAC
132859 TTAAAAATATA
1 TTAAAAATATA
132870 CATTATTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
42 13 0.28
43 3 0.07
44 16 0.35
45 5 0.11
46 9 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (45 bp):
TTAAAAATATAATAAAACTAAAAATAAAAAGAAATTATTCAAAAC
Found at i:141290 original size:2 final size:2
Alignment explanation
Indices: 141283--141316 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
141273 AGATAGAAAT
141283 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
141317 GTTGGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:145210 original size:78 final size:78
Alignment explanation
Indices: 145067--145254 Score: 252
Period size: 78 Copynumber: 2.4 Consensus size: 78
145057 CTAATGCCCT
* * *
145067 TCCCCTCATTCCCAGCTAGAAAATTATTTACATTTATCTCATGTGTTGGAGCTTTTGCAAAATTC
1 TCCCCTCATTCCCAGCTGGAAAATTATTTACATTTATCTCATGTGCTGGAGCTTTTACAAAATTC
*
145132 ACACCAGCACTTC
66 ACACCAACACTTC
* * * * **
145145 TCCCCTCATTTCCAGCTGGAATATTATTTACATTTATCTCCTGTGCTGGA-TTGTTTACATTATT
1 TCCCCTCATTCCCAGCTGGAAAATTATTTACATTTATCTCATGTGCTGGAGCT-TTTACAAAATT
145209 CACACCAACACTTC
65 CACACCAACACTTC
* *
145223 TCCCCTCATTCCCAGATGGAACATTATTTACA
1 TCCCCTCATTCCCAGCTGGAAAATTATTTACA
145255 ACATCCTGCT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 95 0.99
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.36
Consensus pattern (78 bp):
TCCCCTCATTCCCAGCTGGAAAATTATTTACATTTATCTCATGTGCTGGAGCTTTTACAAAATTC
ACACCAACACTTC
Found at i:146581 original size:21 final size:20
Alignment explanation
Indices: 146541--146587 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
146531 TAAGTATAAA
146541 TATAATTTAAATGAAATATT
1 TATAATTTAAATGAAATATT
*
146561 TTTAATTTACAAT-ATAATATT
1 TATAATTTA-AATGA-AATATT
146582 TATAAT
1 TATAAT
146588 AGATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATTTAAATGAAATATT
Found at i:147752 original size:2 final size:2
Alignment explanation
Indices: 147745--147774 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
147735 AAAGAATTGA
147745 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
147775 CACATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148152 original size:92 final size:94
Alignment explanation
Indices: 148018--148191 Score: 280
Period size: 93 Copynumber: 1.9 Consensus size: 94
148008 CATAATTTAT
* * * *
148018 TTTATTTTATTCATAATATCAAATTTTAAATTCTAAATATTATTT-AAAAATCTAATATTTCATC
1 TTTATTTTATTCATAATATCAAAATTTAAATTCTAAACATTATTTAAAAAATCTAAAATTTCATA
*
148082 TTTTATAACAACTAATAACTACTTATTAA
66 TCTTATAACAACTAATAACTACTTATTAA
148111 TTTATTTTATTCATAAT-TCAAAATTTAAATTCTAAACATTATTTAAAAAATCTAAAATTTCATA
1 TTTATTTTATTCATAATATCAAAATTTAAATTCTAAACATTATTTAAAAAATCTAAAATTTCATA
*
148175 TCTTATACCAACTAATA
66 TCTTATAACAACTAATA
148192 GGCCAATTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 25 0.34
93 49 0.66
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (94 bp):
TTTATTTTATTCATAATATCAAAATTTAAATTCTAAACATTATTTAAAAAATCTAAAATTTCATA
TCTTATAACAACTAATAACTACTTATTAA
Found at i:153144 original size:21 final size:21
Alignment explanation
Indices: 153083--153137 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
153073 GATTTACATA
* *
153083 TTCGCATTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
153104 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
153125 TTCGCATTGCGAT
1 TTCGCATTGCGAT
153138 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:153690 original size:6 final size:6
Alignment explanation
Indices: 153681--153729 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
153671 CCGTCCCGTC
153681 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
153729 T
1 T
153730 AATGGTAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:153735 original size:6 final size:6
Alignment explanation
Indices: 153726--153756 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
153716 GTCGTGGTCG
153726 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
153757 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:153926 original size:40 final size:42
Alignment explanation
Indices: 153843--153938 Score: 142
Period size: 40 Copynumber: 2.3 Consensus size: 42
153833 CGTTGCGATT
*
153843 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCAAAC
* * *
153885 TTTGACTATCGCAACAAATTTGG-A-AAATCGCAATGCGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCAAAC
153925 TTGGACTATCGCAA
1 TTGGACTATCGCAA
153939 TGCGAATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 27 0.55
41 1 0.02
42 21 0.43
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCAAAC
Found at i:153939 original size:21 final size:20
Alignment explanation
Indices: 153843--153944 Score: 73
Period size: 21 Copynumber: 5.0 Consensus size: 20
153833 CGTTGCGATT
*
153843 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
153862 TTGGAATAAATCGCAACGCAAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
153885 TTTGACTATCGCAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
**
153904 TTGGAAAATCGCAATGCGAAC
1 TTGGACTATCGCAA-GCGAAC
153925 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
153945 TATGTAAATC
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 21 0.33
21 35 0.55
23 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:153957 original size:20 final size:20
Alignment explanation
Indices: 153904--153963 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
153894 CGCAACAAAT
153904 TTGGAAAATCGCAATGCGAAC
1 TTGG-AAATCGCAATGCGAAC
*
153925 TTGGACTATCGCAATGCGAA-
1 TTGGA-AATCGCAATGCGAAC
*
153945 TATGTAAATCGCAATGCGA
1 T-TGGAAATCGCAATGCGA
153964 TAGTCCAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
TTGGAAATCGCAATGCGAAC
Found at i:158134 original size:45 final size:45
Alignment explanation
Indices: 158085--158174 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
158075 CCATCTTTCT
158085 TTAATTTCATTTTAATCTTTATTTAATTTATAAATGTAAGAAAAA
1 TTAATTTCATTTTAATCTTTATTTAATTTATAAATGTAAGAAAAA
158130 TTAATTTCATTTTAATCTTTATTTAATTTATAAATGTAAGAAAAA
1 TTAATTTCATTTTAATCTTTATTTAATTTATAAATGTAAGAAAAA
158175 AACCAGTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (45 bp):
TTAATTTCATTTTAATCTTTATTTAATTTATAAATGTAAGAAAAA
Found at i:166945 original size:46 final size:43
Alignment explanation
Indices: 166849--166949 Score: 121
Period size: 46 Copynumber: 2.3 Consensus size: 43
166839 TAATTTGTAA
* * * *
166849 ATAATATATAATATAAAAATAATATTAATGGTATAAAATTTAT
1 ATAATATAAAATATAAAAATAATATTAATAGTATAAAATATAC
*
166892 ATGAATATAAACATATTATAAATAATATTAATAGTATAAAAATATAC
1 AT-AATATAAA-ATA-TAAAAATAATATTAATAGTAT-AAAATATAC
166939 ATAATATAAAA
1 ATAATATAAAA
166950 AGATAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.04
44 7 0.14
45 4 0.08
46 27 0.55
47 9 0.18
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (43 bp):
ATAATATAAAATATAAAAATAATATTAATAGTATAAAATATAC
Found at i:166946 original size:17 final size:18
Alignment explanation
Indices: 166902--166950 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
166892 ATGAATATAA
*
166902 ACATATTATAAATAATATT
1 ACATAATATAAA-AATATT
*
166921 A-ATAGTATAAAAATA-T
1 ACATAATATAAAAATATT
166937 ACATAATATAAAAA
1 ACATAATATAAAAA
166951 GATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.07
17 15 0.56
18 9 0.33
19 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
ACATAATATAAAAATATT
Found at i:167561 original size:20 final size:20
Alignment explanation
Indices: 167536--167589 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
167526 GACCAACAAA
167536 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
167556 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
167576 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
167590 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:167745 original size:20 final size:20
Alignment explanation
Indices: 167613--167757 Score: 125
Period size: 20 Copynumber: 7.2 Consensus size: 20
167603 TGCGATTTTC
*
167613 CAAATTCGCAATGCGATAGT
1 CAAATTCGCAACGCGATAGT
* * *
167633 TAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
* * *
167653 CAAATTTGCAACACGAATTTGT
1 CAAATTCGCAACGCG-A-TAGT
*
167675 -AAA-TCGCAACACAGA-AGT
1 CAAATTCGCAACGC-GATAGT
* *
167693 CAAATTTGCAACACGATAGT
1 CAAATTCGCAACGCGATAGT
167713 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* * *
167733 GAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACGCGATAGT
167753 CAAAT
1 CAAAT
167758 GTTTTTACGC
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 86 0.86
21 5 0.05
22 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:168234 original size:20 final size:20
Alignment explanation
Indices: 168177--168223 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
168167 CTAAAATCGA
168177 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
*
168197 GTTACGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
168217 GTTGCGA
1 GTTGCGA
168224 ATTTAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGC
Found at i:170207 original size:4 final size:4
Alignment explanation
Indices: 170198--170239 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
170188 TTTTTCGGCA
* * *
170198 TTAT TTAT TTAT TTAT TTAC TTAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
170240 TCAGCGGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:170476 original size:21 final size:21
Alignment explanation
Indices: 170383--170478 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
170373 GATGCACCTA
*
170383 TCATCATTCAAGAGGCGCCTC
1 TCATCATTCAAGAGGCCCCTC
*
170404 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
* *
170425 TCATTA-TCGAAGAAGCCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * * *
170446 CCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
170467 TCATCATTCAAG
1 TCATCATTCAAG
170479 TGGTCCCGCC
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.05
21 51 0.89
22 3 0.05
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:170491 original size:42 final size:42
Alignment explanation
Indices: 170408--170501 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
170398 CGCCTCCTAT
* *
170408 CGTTCAAGAGGCCCCTCTCATTATCGAAGAAGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCAC
* ** *
170450 CGTTCAAGAGGCCCCTGTCATCATTC-AAGTGGTCCCGCCCAC
1 CGTTCAAGAGGCCCCTCTCATCA-TCGAAGAAGCCCCGCCCAC
*
170492 TGTTCAAGAG
1 CGTTCAAGAG
170502 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCAC
Found at i:171765 original size:14 final size:14
Alignment explanation
Indices: 171746--171785 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
171736 TTTTGATTAA
171746 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
171760 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
171774 TTGATTTGTAAA
1 TTGATTTGTAAA
171786 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:171975 original size:20 final size:20
Alignment explanation
Indices: 171952--171990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
171942 GATTTTCGGT
* *
171952 TTGCGAATTTGACTTTCGCG
1 TTGCAAATTTGACTATCGCG
171972 TTGCAAATTTGACTATCGC
1 TTGCAAATTTGACTATCGC
171991 AACGCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCAAATTTGACTATCGCG
Found at i:172280 original size:39 final size:33
Alignment explanation
Indices: 172203--172280 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
172193 CTCAAGTTTT
* *
172203 AGATTTTGATTTCCTTTTGCTTTGCACCATATG
1 AGATTTGGATTTCCTTTTGCTTGGCACCATATG
172236 AGATTTGGATTTCCTTTTGCTTGGCACCATATG
1 AGATTTGGATTTCCTTTTGCTTGGCACCATATG
*
172269 AGCTTTGGATTT
1 AGATTTGGATTT
172281 TAATGAGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (33 bp):
AGATTTGGATTTCCTTTTGCTTGGCACCATATG
Found at i:172315 original size:35 final size:35
Alignment explanation
Indices: 172276--172351 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
172266 ATGAGCTTTG
*
172276 GATTTTAATGAGCA-TCGGAAGCATTTCAGACTTAT
1 GATTTTAATG-GCACTCAGAAGCATTTCAGACTTAT
*** *
172311 GATTTGGGTGGTACTCAGAAGCATTTCAGACTTAT
1 GATTTTAATGGCACTCAGAAGCATTTCAGACTTAT
*
172346 TATTTT
1 GATTTT
172352 TGTTATTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (35 bp):
GATTTTAATGGCACTCAGAAGCATTTCAGACTTAT
Found at i:172618 original size:18 final size:18
Alignment explanation
Indices: 172595--172631 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
172585 CGAAATTTAT
172595 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
172613 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
172631 A
1 A
172632 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:173051 original size:25 final size:25
Alignment explanation
Indices: 173017--173066 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
173007 ATTATTTTTC
*
173017 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
173042 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
173067 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:173266 original size:20 final size:20
Alignment explanation
Indices: 173171--173270 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 20
173161 TTGCGATTTT
*
173171 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTC
* * *
173191 GCATTACGAATTTGTCTTTC
1 GCGTTGCGAATTTGACTTTC
* * * *
173211 CCGTTGCGGATTTAACTATC
1 GCGTTGCGAATTTGACTTTC
**
173231 GC--AACG-A-TT-A-TTTC
1 GCGTTGCGAATTTGACTTTC
173245 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
173265 GCGTTG
1 GCGTTG
173271 ATCGCAACAT
Statistics
Matches: 57, Mismatches: 17, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
14 5 0.09
15 1 0.02
16 4 0.07
17 2 0.04
18 4 0.07
19 1 0.02
20 40 0.70
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:173579 original size:18 final size:18
Alignment explanation
Indices: 173556--173591 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
173546 AAGCCGGTTG
*
173556 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
173574 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
173592 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:177253 original size:17 final size:17
Alignment explanation
Indices: 177233--177289 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
177223 CTTTCATGTC
177233 TTTTTTTTCGAACAGTT
1 TTTTTTTTCGAACAGTT
*
177250 TTTTTTTTCGAACTGCTAT
1 TTTTTTTTCGAACAG-T-T
177269 TTTTTTTTC-AACA-TT
1 TTTTTTTTCGAACAGTT
177284 TTTTTT
1 TTTTTT
177290 GTGATGGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.19
16 1 0.03
17 14 0.39
18 4 0.11
19 10 0.28
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65
Consensus pattern (17 bp):
TTTTTTTTCGAACAGTT
Found at i:182117 original size:13 final size:13
Alignment explanation
Indices: 182099--182142 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
182089 ACTTAGCATA
182099 AAAATAAAACTTG
1 AAAATAAAACTTG
182112 AAAAT-AAA---G
1 AAAATAAAACTTG
182121 AAAAATAAAACTTG
1 -AAAATAAAACTTG
182135 AAAATAAA
1 AAAATAAA
182143 GAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
9 1 0.04
10 5 0.19
11 3 0.12
12 3 0.12
13 13 0.50
14 1 0.04
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (13 bp):
AAAATAAAACTTG
Found at i:182165 original size:27 final size:23
Alignment explanation
Indices: 182098--182153 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
182088 TACTTAGCAT
182098 AAAAATAAAACTTGAAAATAAAG
1 AAAAATAAAACTTGAAAATAAAG
182121 AAAAATAAAACTTGAAAATAAAG
1 AAAAATAAAACTTGAAAATAAAG
182144 AAAAATAAAA
1 AAAAATAAAA
182154 AGAACTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (23 bp):
AAAAATAAAACTTGAAAATAAAG
Found at i:183196 original size:24 final size:24
Alignment explanation
Indices: 183169--183215 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
183159 CAAAATCCGA
*
183169 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGAACAAGATCAAAGTTCGG
*
183193 GTATTGAACAAGATCAAATTTCG
1 GTATTGAACAAGATCAAAGTTCG
183216 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGAACAAGATCAAAGTTCGG
Found at i:184152 original size:20 final size:20
Alignment explanation
Indices: 184116--184306 Score: 153
Period size: 20 Copynumber: 9.6 Consensus size: 20
184106 ACTAAAACCT
*
184116 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
184135 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
184154 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
184174 GTTGCGAATTTG-ACTTCCGC
1 GTTGCGAATTTGAAATT-CGC
*
184194 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
*
184214 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
184235 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
184255 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
184275 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
184295 GTTGCGAATTTG
1 GTTGCGAATTTG
184307 TTGGTCATTT
Statistics
Matches: 137, Mismatches: 23, Indels: 23
0.75 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 36 0.26
20 82 0.60
21 12 0.09
22 5 0.04
23 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:190382 original size:24 final size:24
Alignment explanation
Indices: 190331--190384 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
190321 AATTCTGTTG
* *
190331 TTTTTATTACCTAAAACACTATTA
1 TTTTTTTTACCTAAAACACAATTA
*
190355 TTTTTTTTATCTAAAACATCAATT-
1 TTTTTTTTACCTAAAACA-CAATTA
190379 TTTTTT
1 TTTTTT
190385 AACATTTCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTTTTACCTAAAACACAATTA
Found at i:195106 original size:14 final size:14
Alignment explanation
Indices: 195083--195129 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
195073 CGCTGGGCAT
*
195083 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
195097 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
195111 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
195125 ACGAG
1 CCGAG
195130 CTATGCGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:195150 original size:10 final size:10
Alignment explanation
Indices: 195135--195191 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
195125 ACGAGCTATG
195135 CGAGGGCATC
1 CGAGGGCATC
*
195145 CGAGGGCAAC
1 CGAGGGCATC
*
195155 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
195168 CGAGGGAATC
1 CGAGGGCATC
*
195178 CGAGGGCAAC
1 CGAGGGCATC
195188 CGAG
1 CGAG
195192 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:195163 original size:33 final size:33
Alignment explanation
Indices: 195111--195195 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
195101 GGCCATCCGA
* * * *
195111 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
195144 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
195177 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
195196 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:195232 original size:29 final size:29
Alignment explanation
Indices: 195199--195255 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
195189 GAGCGAGGGT
*
195199 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTACATGGCGACCTACA
195228 AGGTCGCCCGGAGTACATGGCGACCTAC
1 AGGTCGCCCGGAGTACATGGCGACCTAC
195256 GTCGGATGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTACATGGCGACCTACA
Done.