Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005810.1 Hibiscus syriacus cultivar Beakdansim tig00013620_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: 116035
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:228 original size:11 final size:11
Alignment explanation
Indices: 206--245 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
196 CATATATCAT
206 ATCATA-CACA
1 ATCATATCACA
216 ATCATATCACA
1 ATCATATCACA
227 ATCATAT-AC-
1 ATCATATCACA
236 AT-ATATCACA
1 ATCATATCACA
246 TACATTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.15
9 4 0.15
10 8 0.30
11 11 0.41
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (11 bp):
ATCATATCACA
Found at i:594 original size:23 final size:23
Alignment explanation
Indices: 563--631 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
553 CACCACAGCT
*
563 CGTATAATTGCACCAGAGTGCCA
1 CGTAGAATTGCACCAGAGTGCCA
* *
586 CGTAGAATTGCACTAGAGTGCCG
1 CGTAGAATTGCACCAGAGTGCCA
609 CGTAGAATTGCACC-GTAGTGCCA
1 CGTAGAATTGCACCAG-AGTGCCA
632 TATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCAGAGTGCCA
Found at i:812 original size:101 final size:102
Alignment explanation
Indices: 647--964 Score: 534
Period size: 103 Copynumber: 3.1 Consensus size: 102
637 TAATGTCCAT
* * *
647 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCA-GGATCAAGTATGTGTCTCACCA
*
712 GACTTCACACATGCTCCAAAAGAATACATATATGTCCG
65 GACTTCACACATGTTCCAAAAGAATACATATATGTCCG
*
750 AAGGACCACATATCATTCCTT-ATAATCATTTACATATGCCAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAGGATCAAGTATGTGTCTCACCAG
814 ACTTCACACATGTTCC-AAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAAGAATACATATATGT-CCG
*
851 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCC-AGGATCAAGTATGTGTCTCACCA
916 GACTTCACACATGTTCCAAAA-AATACATATATGTCCG
65 GACTTCACACATGTTCCAAAAGAATACATATATGTCCG
953 AAGGACCACATA
1 AAGGACCACATA
965 GACCTCGACT
Statistics
Matches: 204, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
100 17 0.08
101 62 0.30
102 49 0.24
103 73 0.36
104 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAAGAATACATATATGTCCG
Found at i:2084 original size:21 final size:21
Alignment explanation
Indices: 2059--2104 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2049 TTCAGGTTCG
* * *
2059 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
2080 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
2101 CTTG
1 CTTG
2105 CCCAGAAATC
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:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:4607 original size:16 final size:16
Alignment explanation
Indices: 4588--4640 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4578 CCATAACCCC
4588 TATCACACATATATCA
1 TATCACACATATATCA
* * *
4604 TATCATACACACATCA
1 TATCACACATATATCA
4620 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
4638 TAT
1 TAT
4641 ATCACATACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 21 0.72
17 3 0.10
18 5 0.17
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:4626 original size:12 final size:12
Alignment explanation
Indices: 4588--4634 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4578 CCATAACCCC
4588 TATCACACAT-A
1 TATCACACATCA
*
4599 TAT--CATATCA
1 TATCACACATCA
4609 TA-CACACATCA
1 TATCACACATCA
4620 TATCACACATCA
1 TATCACACATCA
4632 TAT
1 TAT
4635 ACATATATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 11 0.37
12 12 0.40
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.30
Consensus pattern (12 bp):
TATCACACATCA
Found at i:4996 original size:23 final size:23
Alignment explanation
Indices: 4970--5038 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
4960 CACCACAGCT
* *
4970 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
4993 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
5016 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
5039 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 38 0.97
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:5225 original size:103 final size:103
Alignment explanation
Indices: 5054--5374 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
5044 TAATGTCCAT
* * * *
5054 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
5119 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5157 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
5222 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
5260 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAATTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
5325 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5363 AAGGACCACATA
1 AAGGACCACATA
5375 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:9343 original size:45 final size:45
Alignment explanation
Indices: 9294--9387 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
9284 ATAAAGGAAT
*
9294 TTTCTACGTGGTC-CTTAGG-GACATCTTATA-TGGCACTTCGGTGCA
1 TTTCTACGTGG-CACTTAGGTGACAT-TCA-ACTGGCACTTCGGTGCA
*
9339 TTTCTACGTGGCACTTAGGTGCCATTCAACGTGGCACTTCGGTGCA
1 TTTCTACGTGGCACTTAGGTGACATTCAAC-TGGCACTTCGGTGCA
9385 TTT
1 TTT
9388 ATATGAGCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
44 2 0.05
45 19 0.44
46 22 0.51
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (45 bp):
TTTCTACGTGGCACTTAGGTGACATTCAACTGGCACTTCGGTGCA
Found at i:9354 original size:23 final size:23
Alignment explanation
Indices: 9324--9387 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
9314 ACATCTTATA
*
9324 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCAACG
*
9347 TGGCACTTAGGTGCCA-TTCAACG
1 TGGCACTTCGGTG-CATTTCAACG
9370 TGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
9388 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCAACG
Found at i:13880 original size:23 final size:24
Alignment explanation
Indices: 13822--13882 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
13812 ACATCTTATA
13822 TGGCACTTCGGTG-AATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
13845 CGGCAGTTAGGTGCAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
13868 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
13883 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:20398 original size:20 final size:20
Alignment explanation
Indices: 20370--20407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20360 CGTTAGGCCT
* *
20370 TATGGTATTGGTACTACTCA
1 TATGATATTGATACTACTCA
20390 TATGATATTGATACTACT
1 TATGATATTGATACTACT
20408 ATGTAAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
TATGATATTGATACTACTCA
Found at i:20738 original size:3 final size:3
Alignment explanation
Indices: 20730--20784 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
20720 AGTTCAACAT
20730 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20778 ATA ATA A
1 ATA ATA A
20785 AAAACTCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21411 original size:21 final size:21
Alignment explanation
Indices: 21365--21417 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
21355 GATCTGATAT
21365 TATTTTTTAATATTGTAAATCA
1 TATTTTTT-ATATTGTAAATCA
*
21387 -ATTTTTTATATT-TAGAATTA
1 TATTTTTTATATTGTA-AATCA
*
21407 TATTTTATATA
1 TATTTTTTATA
21418 ACTGTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 9 0.33
21 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (21 bp):
TATTTTTTATATTGTAAATCA
Found at i:21574 original size:29 final size:30
Alignment explanation
Indices: 21529--21596 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
21519 ATGGTCACTG
* *
21529 AACATTTCAGAAACTTGCATTTA-GGTCCCCC
1 AACATTT-AGAAACTTGCA-ATACAGTCCCCC
21560 AACATTTA-AAACTTGCAATACAGTCCCCC
1 AACATTTAGAAACTTGCAATACAGTCCCCC
21589 AACATTTA
1 AACATTTA
21597 TTCCGTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 24 0.71
30 1 0.03
31 7 0.21
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (30 bp):
AACATTTAGAAACTTGCAATACAGTCCCCC
Found at i:22287 original size:22 final size:22
Alignment explanation
Indices: 22262--22327 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
22252 GGCGACATCC
22262 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
22284 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* ** *
22306 ATTTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
22328 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:22723 original size:20 final size:20
Alignment explanation
Indices: 22698--22744 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22688 GATTCTTGCA
22698 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
22718 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
22738 TTGCGAT
1 TTGCGAT
22745 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:22750 original size:20 final size:20
Alignment explanation
Indices: 22712--22766 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
22702 GATAGTCAAA
* **
22712 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
22732 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
22752 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
22767 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:22774 original size:20 final size:20
Alignment explanation
Indices: 22731--22774 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
22721 CGATAGTCAT
** *
22731 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
22751 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
22771 TTTC
1 TTTC
22775 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:24655 original size:20 final size:20
Alignment explanation
Indices: 24630--24768 Score: 117
Period size: 20 Copynumber: 7.6 Consensus size: 20
24620 AGAATAGTTT
*
24630 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
24650 ACTATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
24670 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
24686 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
24703 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
24719 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
24737 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
24757 ACTATCGCAATG
1 ACTATCGCAATG
24769 AAAGAATCGC
Statistics
Matches: 99, Mismatches: 6, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
14 14 0.14
16 10 0.10
17 8 0.08
18 4 0.04
19 7 0.07
20 56 0.57
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:24744 original size:53 final size:52
Alignment explanation
Indices: 24686--24804 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 52
24676 GCAACGAGAG
*
24686 AATCGCAATGCGAAATGAAAATCGCAA-CAACAAAATCGCAATGCGAAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAATCAA-AAAATCGCAATGCG-AAATGAA
* ** * *
24739 TATCGCAATGCGAAAATGACTATCGCAATGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AAATGAAAATCGCAATCAAAAAATCGCAATGCGAAATGAA
*
24792 AATCGCATTGCGA
1 AATCGCAATGCGA
24805 TTCTCTCGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.02
53 27 0.48
54 26 0.46
55 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAATCAAAAAATCGCAATGCGAAATGAA
Found at i:24789 original size:21 final size:19
Alignment explanation
Indices: 24686--24804 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
24676 GCAACGAGAG
24686 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
24705 AATCGCAA--C--AA-CAA
1 AATCGCAATGCGAAATGAA
*
24719 AATCGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* *
24739 TATCGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
*
24759 TATCGCAAT--GAAA-G--
1 AATCGCAATGCGAAATGAA
24773 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
24792 AATCGCATTGCGA
1 AATCGCAATGCGA
24805 TTCTCTCGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 18 0.22
15 2 0.02
16 6 0.07
17 5 0.06
18 1 0.01
19 22 0.27
20 29 0.35
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:24818 original size:87 final size:87
Alignment explanation
Indices: 24633--24798 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 87
24623 ATAGTTTACT
* *
24633 ATCGCAATACGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCG
24698 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* * *
24720 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGAAAGAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCG
24785 AAATGAAAATCGCA
66 AAATGAAAATCGCA
24799 TTGCGATTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (87 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:24838 original size:20 final size:20
Alignment explanation
Indices: 24813--24859 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24803 GATTCTCTCG
24813 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
24833 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
24853 TTGCGAT
1 TTGCGAT
24860 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:24872 original size:87 final size:87
Alignment explanation
Indices: 24781--24949 Score: 257
Period size: 87 Copynumber: 1.9 Consensus size: 87
24771 AGAATCGCAA
24781 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
24846 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCGTTGCGATTTTGTTGT
** ** ** ** *
24868 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
24933 TTTCGCGTTGCGATTTT
66 TTTCGCGTTGCGATTTT
24950 AAGTTTCAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (87 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCGTTGCGATTTTGTTGT
Found at i:24890 original size:33 final size:34
Alignment explanation
Indices: 24833--24926 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
24823 CAAATTCGCA
* * *
24833 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
24867 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
24900 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
24927 AGTCATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:24923 original size:20 final size:20
Alignment explanation
Indices: 24898--24946 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
24888 GCGATTCTCT
24898 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
24918 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
24938 CGTTGCGAT
1 CGTTGCGAT
24947 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:24956 original size:20 final size:20
Alignment explanation
Indices: 24898--24956 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
24888 GCGATTCTCT
* *
24898 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
24918 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
24938 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
24957 AGATTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:25527 original size:42 final size:42
Alignment explanation
Indices: 25427--25537 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
25417 CCCGACTCAC
* * * *
25427 CTGTCATCGTTTAAGAGGCCTC-CCCTATCGTTCAACAGGCCC
1 CTGTCATCGTTCAAGAGTCCTCTCCC-ACCGTTCAACAGGCCA
* ** *
25469 CTATCATCCCTCAAGAGTCCTCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAACAGGCCA
*
25511 CTGTCATCGTTGAAGAGGTCC-CTCCCA
1 CTGTCATCGTTCAAGA-GTCCTCTCCCA
25538 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 48 0.87
43 7 0.13
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAACAGGCCA
Found at i:27023 original size:34 final size:34
Alignment explanation
Indices: 26980--27066 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 34
26970 TTGATTTGTT
26980 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
1 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
* *
27014 GATTTTCA-TTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
** *
27047 GATAGTCATTTCCGCATTGC
1 GATTTTCATTTTCGCATTGC
27067 GATAGTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 29 0.62
34 18 0.38
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (34 bp):
GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
Found at i:27068 original size:20 final size:20
Alignment explanation
Indices: 27041--27129 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
27031 GCGATTCTCT
27041 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
27061 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
27081 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
27101 CGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
27121 CGTTGCGAT
1 CGTTGCGAT
27130 TTCCGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:29595 original size:24 final size:24
Alignment explanation
Indices: 29559--29618 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
29549 CTGAAAAATC
*
29559 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
29583 ATCAAAGTTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
29607 ATCAAATTTCGA
1 ATCAAAATTCGA
29619 ATACTGACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:29626 original size:24 final size:24
Alignment explanation
Indices: 29575--29626 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29565 ATCCGAGTAT
* *
29575 TGACCAAGATCAAAGTTCGAGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
29599 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
29623 TGAC
1 TGAC
29627 TAGTACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:30517 original size:21 final size:21
Alignment explanation
Indices: 30491--30604 Score: 228
Period size: 21 Copynumber: 5.4 Consensus size: 21
30481 CGTAATCGTA
30491 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
30512 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
30533 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
30554 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
30575 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
30596 TTGCGATTT
1 TTGCGATTT
30605 ACGTATTCGC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 93 1.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:30641 original size:21 final size:21
Alignment explanation
Indices: 30611--30662 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
30601 ATTTACGTAT
*
30611 TCGCATTGCGAA-TTAGGAAAA
1 TCGCAATGCGAATTTA-GAAAA
30632 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
30653 TCGTAATGCG
1 TCGCAATGCG
30663 GTAGTCAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:35454 original size:20 final size:20
Alignment explanation
Indices: 35429--35500 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
35419 TTTTCCGACT
35429 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
35449 ATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
35469 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATGTAA
35489 ATCGCAATGCGA
1 ATCGCAATGCGA
35501 TTCTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:35512 original size:20 final size:20
Alignment explanation
Indices: 35489--35576 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
35479 GAATATATAA
* *
35489 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
35509 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
35529 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
35549 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
35569 GTCGCAAC
1 ATCGCAAC
35577 ACTGAATTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:35513 original size:40 final size:40
Alignment explanation
Indices: 35367--35515 Score: 140
Period size: 40 Copynumber: 3.6 Consensus size: 40
35357 GTTTCCAGAT
* * * * *
35367 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTTTAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGAATATATAAA
* *
35407 TTCGC-ATAGCGATTTTCCGACTATCGCAATGCGAATATGTAAA
1 -TCGCAAT-GCGA--TTCTGACTATCGCAATGCGAATATATAAA
* * * *
35450 TCGCAATGTGAATATGTA-AATCGCAATGCGAATATATAAA
1 TCGCAATGCGATTCTG-ACTATCGCAATGCGAATATATAAA
35490 TCGCAATGCGATTCTGACTATCGCAA
1 TCGCAATGCGATTCTGACTATCGCAA
35516 CGAGATTCTG
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 43 0.50
41 9 0.10
42 7 0.08
43 26 0.30
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAATGCGAATATATAAA
Found at i:36429 original size:24 final size:24
Alignment explanation
Indices: 36397--36450 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36387 GTATTCGAAA
36397 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
36421 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
36445 TTTGAT
1 TTTGAT
36451 GATTTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:38721 original size:18 final size:18
Alignment explanation
Indices: 38698--38732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38688 AGAAAAAGGC
*
38698 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
38716 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
38733 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:38917 original size:20 final size:20
Alignment explanation
Indices: 38892--39219 Score: 276
Period size: 20 Copynumber: 17.6 Consensus size: 20
38882 TTACACATTC
*
38892 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
38912 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
38931 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
38946 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
38966 ATATGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
38984 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
39000 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
39020 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
39040 ATTTGATTATCGTAACGGGT
1 ATTTGACTATCGCAACGCGA
*
39060 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
39080 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
39094 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
39114 ATTTGACTATCGAAACACGA
1 ATTTGACTATCGCAACGCGA
* *
39134 ATTTGA-TCATCGCAACGGGT
1 ATTTGACT-ATCGCAACGCGA
*
39154 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
39174 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
39188 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
39208 A-TTGACTTTCGC
1 ATTTGACTATCGC
39220 GTTGCGATTT
Statistics
Matches: 247, Mismatches: 35, Indels: 53
0.74 0.10 0.16
Matches are distributed among these distances:
14 39 0.16
15 3 0.01
16 6 0.02
18 6 0.02
19 13 0.05
20 179 0.72
21 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:38974 original size:54 final size:54
Alignment explanation
Indices: 38892--39036 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
38882 TTACACATTC
* **
38892 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
* *
38946 ATTTGACTATCGCAACACGAATATGACTATCGCAACGAAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
39000 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
39037 CGAATTTGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
Found at i:39067 original size:94 final size:93
Alignment explanation
Indices: 38900--39219 Score: 443
Period size: 94 Copynumber: 3.5 Consensus size: 93
38890 TCATTTGAAT
* * *
38900 ATCGCAACGCGAATTTGACTATCGCAACTC-AA---A-AATCGCAACGCGAATTTGACTATCGCA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGCAACGCGAATTTGATTATCGCA
** * * *
38960 ACACGAATATGACTATCGCAACGAAAAA
66 ACGGGTATTTGACTATCGCAACGAGAAA
*
38988 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTGACTATCGCAACGCGAATTTGATTATCGC
39053 AACGGGTATTTGACTATCGCAACGAGAAA
65 AACGGGTATTTGACTATCGCAACGAGAAA
* * *
39082 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGAAACACGAATTTGATCATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTGACTATCGCAACGCGAATTTGATTATCGC
39147 AACGGGTATTTGACTATCGCAACGAGAAA
65 AACGGGTATTTGACTATCGCAACGAGAAA
* * * *
39176 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGC
39220 GTTGCGATTT
Statistics
Matches: 208, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
88 29 0.14
89 2 0.01
93 10 0.05
94 167 0.80
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGCAACGCGAATTTGATTATCGCA
ACGGGTATTTGACTATCGCAACGAGAAA
Found at i:39150 original size:74 final size:74
Alignment explanation
Indices: 38892--39150 Score: 265
Period size: 74 Copynumber: 3.5 Consensus size: 74
38882 TTACACATTC
* * *
38892 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCA-AAAATCGCAACGCGAATTTGACTAT
1 ATTTGACTATCGCAACACGAATTTGACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGACTAT
*
38956 CGCAACACGA
65 CGCAACGCGA
* ** * * * *** **
38966 ATATGACTATCGCAACGAAAAAATCG-C-AACGCGAATTTGACTATCGCAACGCGAATTTGACTA
1 ATTTGACTATCGCAAC-ACGAATTTGACTATCGC-AACGAGAAAATCGCAACGCGAATTTGACTA
39029 TCGCAACGCGA
64 TCGCAACGCGA
* * ** *
39040 ATTTGATTATCGTAACGGGTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
1 ATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
39105 GCAACGCGA
66 GCAACGCGA
*
39114 ATTTGACTATCGAAACACGAATTTGA-TCATCGCAACG
1 ATTTGACTATCGCAACACGAATTTGACT-ATCGCAACG
39151 GGTATTTGAC
Statistics
Matches: 145, Mismatches: 34, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
73 8 0.06
74 129 0.89
75 8 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (74 bp):
ATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
GCAACGCGA
Found at i:39238 original size:20 final size:20
Alignment explanation
Indices: 39209--39266 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
39199 GCAACGCGAA
39209 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
39229 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
39249 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
39267 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:39425 original size:14 final size:14
Alignment explanation
Indices: 39365--39426 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
39355 CACAAATAAG
*
39365 AATTATTTACACATC
1 AATT-TTTACAAATC
**
39380 AATATTAAACAAATC
1 AAT-TTTTACAAATC
* *
39395 AACTTTTACAATTC
1 AATTTTTACAAATC
*
39409 AATTTTTATAAATC
1 AATTTTTACAAATC
39423 AATT
1 AATT
39427 AAACAAGCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 12 0.33
16 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:42517 original size:20 final size:18
Alignment explanation
Indices: 42479--42525 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
42469 GAAACTTAAA
*
42479 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
42497 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
42517 ATCGCAACG
1 ATCGCAACG
42526 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:42811 original size:20 final size:20
Alignment explanation
Indices: 42786--42872 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
42776 TAGTTTACTT
*
42786 TCGCAACGCAAAATGGACTA
1 TCGCAACGCAAAATTGACTA
42806 TCGCAACGCGAAAA-TGACTA
1 TCGCAACGC-AAAATTGACTA
* *
42826 TCGCAACGCGAATTTGACTA
1 TCGCAACGCAAAATTGACTA
* *
42846 TCGCAACGCTAATTTGACTA
1 TCGCAACGCAAAATTGACTA
42866 TCGCAAC
1 TCGCAAC
42873 CAGAGAATCG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.03
20 55 0.90
21 4 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAACGCAAAATTGACTA
Found at i:42941 original size:20 final size:20
Alignment explanation
Indices: 42916--42963 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
42906 GCGATTCTTT
42916 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
42936 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
42956 CGTTGCGA
1 CGTTGCGA
42964 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:43138 original size:18 final size:18
Alignment explanation
Indices: 43111--43160 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
43101 TTTACTAAGC
43111 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
43129 AATTTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
43147 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
43161 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:44946 original size:20 final size:20
Alignment explanation
Indices: 44891--44997 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
44881 TCTGAAACTT
**
44891 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
44911 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
44931 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
44951 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
44970 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
44989 AAAATCGCA
1 AAAATCGCA
44998 TTGTGATTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 24 0.33
20 49 0.67
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:45408 original size:22 final size:22
Alignment explanation
Indices: 45379--45435 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
45369 GATGTAGATA
45379 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* **
45401 GACTGATTTCATCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
45423 GACGGATGTCGCC
1 GACGGATTTCGCC
45436 TTAGAGAATG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:45630 original size:20 final size:20
Alignment explanation
Indices: 45607--45693 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
45597 GAAAATCGTA
*
45607 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGCATCTCG
45627 TTGCGATAGTCAGCATCTCG
1 TTGCGATAGTCAGCATCTCG
*
45647 TTGCGATAGTCAGTATCTCG
1 TTGCGATAGTCAGCATCTCG
* *
45667 TTGCGATAGTCAGAATCACG
1 TTGCGATAGTCAGCATCTCG
45687 TTGCGAT
1 TTGCGAT
45694 TTACATATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGCATCTCG
Found at i:45710 original size:20 final size:20
Alignment explanation
Indices: 45687--45733 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
45677 CAGAATCACG
45687 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
45707 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
45727 TTGCGAT
1 TTGCGAT
45734 AGTCGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:45754 original size:22 final size:22
Alignment explanation
Indices: 45729--45781 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
45719 TATTCGCATT
**
45729 GCGATAGTCGGAAAATCGCAAC
1 GCGATAGTCAAAAAATCGCAAC
* * *
45751 GCGA-ATTTAAAAAATCGCAAT
1 GCGATAGTCAAAAAATCGCAAC
45772 GCGATAGTCA
1 GCGATAGTCA
45782 GAATCGCGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (22 bp):
GCGATAGTCAAAAAATCGCAAC
Found at i:46423 original size:20 final size:20
Alignment explanation
Indices: 46364--46426 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
46354 AAAAAAATAT
46364 ATATTTA-AATTATAA-TTAA
1 ATATTTATAATTA-AATTTAA
46383 ATAATTTCATAA-T--ATTATAA
1 AT-ATTT-ATAATTAAATT-TAA
46403 ATATTTATAATTAAATTTAA
1 ATATTTATAATTAAATTTAA
46423 ATAT
1 ATAT
46427 AAACTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 16 0.44
21 5 0.14
22 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTATAATTAAATTTAA
Found at i:47139 original size:62 final size:62
Alignment explanation
Indices: 47024--47141 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
47014 AAATATAGGG
* * *
47024 TATTGCTTTATTAAGTTCATCGACTATTAAAAGTTACACAATGATCCTTTGACTATAGAGTA
1 TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATCCTCTGACTATAGAGTA
* * * *
47086 TATTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGGTCAC-CTGACTAT
1 TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATC-CTCTGACTAT
47142 TCATTATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 47 0.98
63 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (62 bp):
TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATCCTCTGACTATAGAGTA
Found at i:47421 original size:60 final size:60
Alignment explanation
Indices: 47348--47474 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
47338 ATAGCCAGGT
* * *
47348 GACCATTTTGTAACTTTTAATAATC-AGGGGA-TTCAACAAAACAATACTCTATAGTCGA-AG
1 GACCATTATGTAACCTTTAATAATCGA-GGGACTT-AACAAAACAATACCCTATAGTC-ATAG
* * *
47408 GACCATTATGTAACCTTTAATAATCGATGGACTTAATAAAGCAATACCCTATAGTCATAG
1 GACCATTATGTAACCTTTAATAATCGAGGGACTTAACAAAACAATACCCTATAGTCATAG
47468 GACCATT
1 GACCATT
47475 TGCATTCTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 1 0.02
60 54 0.93
61 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (60 bp):
GACCATTATGTAACCTTTAATAATCGAGGGACTTAACAAAACAATACCCTATAGTCATAG
Found at i:49077 original size:14 final size:15
Alignment explanation
Indices: 49060--49090 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
49050 GTCTCCAATT
49060 TTTTTAAATTT-ATC
1 TTTTTAAATTTCATC
49074 TTTTTAAATTTCATC
1 TTTTTAAATTTCATC
49089 TT
1 TT
49091 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAAATTTCATC
Found at i:49209 original size:29 final size:29
Alignment explanation
Indices: 49167--49249 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
49157 TTTTTTATCA
49167 TGATTTTCTCATATTTTCTCACTAATCCT
1 TGATTTTCTCATATTTTCTCACTAATCCT
49196 TGATTTTCTCATATTTTCTCACTAATCCT
1 TGATTTTCTCATATTTTCTCACTAATCCT
* *
49225 CGATTTTCTC-TCATTTTCTCTCTAA
1 TGATTTTCTCAT-ATTTTCTCACTAA
49250 CTAAATAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (29 bp):
TGATTTTCTCATATTTTCTCACTAATCCT
Found at i:49541 original size:20 final size:19
Alignment explanation
Indices: 49505--49543 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
49495 GTATTTTCGT
* *
49505 AAATAGCATATATAAATAA
1 AAATAGCAAATAGAAATAA
49524 AAATAAGCAAATAGAAATAA
1 AAAT-AGCAAATAGAAATAA
49544 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAGCAAATAGAAATAA
Found at i:51294 original size:2 final size:2
Alignment explanation
Indices: 51287--51311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51277 CGGTAACATA
51287 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 A
51312 CACTTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53430 original size:43 final size:42
Alignment explanation
Indices: 53347--53689 Score: 325
Period size: 43 Copynumber: 8.0 Consensus size: 42
53337 GTTTGAGAAC
* * * *
53347 AAAAAACGCCGCAATAGGTCAATATCTATTA-CGACGTTTTTTG
1 AAAAAACGCCGCAAAAGGTC-AGATCTA-TAGCGGCGTTTTTGG
* *
53390 AAAAAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGG
1 AAAAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGG
* * * * * * *
53433 AATAAACGCCACAAAAAGTTATGATATATAGCGGCGTTTCTAG
1 AAAAAACGCCGCAAAAGGTCA-GATCTATAGCGGCGTTTTTGG
53476 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
1 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
* * * *
53518 ATACAAACGCCGCAAAAGAG-AAGACCTATA-CTGGCGTTTTTAG
1 A-AAAAACGCCGCAAAAG-GTCAGATCTATAGC-GGCGTTTTTGG
* * *
53561 AACAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGG
1 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
* * *
53603 ACACAAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTT-G
1 A-AAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
* * * *
53645 AATACAAACGACACAAAAAGTCAGACCTATAGCGGCGTTTTTGG
1 AA-A-AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
53689 A
1 A
53690 TACAAACACC
Statistics
Matches: 254, Mismatches: 35, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.01
42 60 0.24
43 189 0.74
44 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGG
Found at i:53554 original size:85 final size:84
Alignment explanation
Indices: 53384--53701 Score: 356
Period size: 85 Copynumber: 3.7 Consensus size: 84
53374 ATTACGACGT
* * * * * *
53384 TTTTTGAAAAAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGA-ATAAACGCCACAAA
1 TTTTAGAAAAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
* **
53448 A-AGTTATGATATATAGCGGCG
65 AGAG-TAAGACCTATA-CGGCG
*
53469 TTTCTAGAAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
1 TTT-TAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
53534 AGAG-AAGACCTATACTGGCG
65 AGAGTAAGACCTATAC-GGCG
* * *
53554 TTTTTAGAACAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAA
1 -TTTTAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
*
53619 AG-GTCAGACCTATAACGGCG
65 AGAGTAAGACCTAT-ACGGCG
* * * * *
53639 TTTTTGAATACAAACGACACAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACACCGC
1 TTTTAGAA-A-AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
53702 TAATTACCTT
Statistics
Matches: 203, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
84 9 0.04
85 106 0.52
86 86 0.42
87 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (84 bp):
TTTTAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAA
GAGTAAGACCTATACGGCG
Found at i:53569 original size:128 final size:127
Alignment explanation
Indices: 53347--53696 Score: 359
Period size: 128 Copynumber: 2.7 Consensus size: 127
53337 GTTTGAGAAC
* * * * *
53347 AAAAAACGCCGCAATAGGTCAATATCTATTACGACGTTTTTTGA-AAAAACGCCGCAAAAG-GTC
1 AAAAAACGCCGCAAAAGGTC-AGATCTA-TACGGCGTTTTTGGATACAAACGCCGCAAAAGAGT-
* * * * * * *
53410 GATATCTATAGCGGCATTTTTGGAATAAACGCCACAAAAAGTTATGATATATAGCGGCGTTTCTA
63 AAGACCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCA-GACATATAGCGGCGTTTCTA
53475 G
127 G
53476 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGAG-AA
1 AAAAAACGCCGCAAAAGGTCAGATCTATA-CGGCGTTTTTGGATACAAACGCCGCAAAAGAGTAA
* ** * * * *
53540 GACCTATA-CTGGCGTTTTTAGAACAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGG
65 GACCTATAGC-GGCGTTTTTGGAACAAACGCCACAAAAAGTCAGACATATAGCGGCGTTTCTAG
* * * * * *
53603 ACACAAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAATACAAACGACACAAAA-AGTC
1 A-AAAAACGCCGCAAAAGGTCAGATCTAT-ACGGCGTTTTTGGATACAAACGCCGCAAAAGAGTA
53667 AGACCTATAGCGGCGTTTTTGGATACAAAC
64 AGACCTATAGCGGCGTTTTTGGA-ACAAAC
53697 ACCGCTAATT
Statistics
Matches: 186, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
127 23 0.12
128 120 0.65
129 42 0.23
130 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (127 bp):
AAAAAACGCCGCAAAAGGTCAGATCTATACGGCGTTTTTGGATACAAACGCCGCAAAAGAGTAAG
ACCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCAGACATATAGCGGCGTTTCTAG
Found at i:57246 original size:41 final size:41
Alignment explanation
Indices: 57200--57656 Score: 407
Period size: 41 Copynumber: 11.3 Consensus size: 41
57190 TTGTAAACAC
* * * * *
57200 AAACGCTACTATAGTACAAGTGTATAGCGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
*
57241 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * * *
57282 AAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * * * *
57323 AAATGCCACTAAATTACGAGTCTTTAGCGACATTTGTAAATAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG--AATAA
* * * * *
57366 AAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * * * *
57407 AAATGCCACTAAAGTACGCGTCTTTAGCAGAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* *
57448 AAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * *
57489 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAA-ACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG-AATA-A
* * *
57531 CAAACGCCACTATAGTAC-A-----T----GTGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * *
57563 AAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
* * * *
57604 AAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTG-TTGAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAAT--AA
57646 AAACGCCACTA
1 AAACGCCACTA
57657 TCGATGAACC
Statistics
Matches: 338, Mismatches: 60, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
31 14 0.04
32 3 0.01
33 7 0.02
37 2 0.01
40 1 0.00
41 252 0.75
42 16 0.05
43 43 0.13
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGAATAA
Found at i:57420 original size:125 final size:125
Alignment explanation
Indices: 57236--57620 Score: 359
Period size: 125 Copynumber: 3.2 Consensus size: 125
57226 GCGGCGTTTG
* * * * *
57236 AATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGA
1 AATAAAAACGCCACTAAAGTACAAGTCTATAACGGCGTTTGAATAAAAATGCCAATAAAGTACGA
* * * *
57301 GTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGACATTTGTA
66 GTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACATTTGTA
* * * * *
57361 AATACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTAAAGTACGC
1 AATAAAAACGCCACTAAAGTACAAGTCTATAACGGCGTTTGAATAAAAATGCCAATAAAGTACGA
* * *
57426 GTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGT-
66 GTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACATTTGTA
* * ** * * * * *
57485 -ATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAA-ACACAAACGCCACTATAGTA
1 AATAAAAACGCCACTAAAGTACAAGTCTATAACGGCGTTTG-AATA-A-AAATGCCAATAAAGTA
* * * * *
57548 C-A-----T----GTGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGT-
63 CGAGTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACATTTGTA
57600 -ATAAAAACGCCACTAAAGTAC
1 AATAAAAACGCCACTAAAGTAC
57621 TACTCTTTTG
Statistics
Matches: 221, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
115 63 0.29
119 1 0.00
123 32 0.14
124 3 0.01
125 122 0.55
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (125 bp):
AATAAAAACGCCACTAAAGTACAAGTCTATAACGGCGTTTGAATAAAAATGCCAATAAAGTACGA
GTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACATTTGTA
Found at i:57463 original size:166 final size:165
Alignment explanation
Indices: 57183--57640 Score: 673
Period size: 166 Copynumber: 2.8 Consensus size: 165
57173 TTGTAAACTT
* *
57183 GCGACGTTTGTAAACACAAACGCTACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA-CGGCGTTTGAATAAAAATGCC
* * *
57248 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGC
65 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
57313 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
130 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
* *
57349 GCGACATTTGTAAATACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTAT-ACGGCGTTTGAATAAAAATGCC
* * * *
57414 ACTAAAGTACGCGTCTTTAGCAGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
65 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
*
57479 GTTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
130 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
* *
57515 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-A-TG--T-----GTTTGTATAAAAATGCCA
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATACGGCGTTTGAATAAAAATGCCA
* * * *
57571 CTAAATTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCG
66 CTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCG
57636 TTTGT
131 TTTGT
57641 TGAAAAAACG
Statistics
Matches: 267, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
156 79 0.30
162 1 0.00
164 2 0.01
165 1 0.00
166 183 0.69
167 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (165 bp):
GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATACGGCGTTTGAATAAAAATGCCA
CTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCG
TTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
Found at i:57600 original size:74 final size:72
Alignment explanation
Indices: 57479--57620 Score: 239
Period size: 74 Copynumber: 1.9 Consensus size: 72
57469 CTTTAGCGGC
* *
57479 GTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTAT
1 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAA-A-AAACGCCACTAA
57544 AGTACATGT
64 AGTACATGT
*
57553 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAG
1 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAAAG
57618 TAC
66 TAC
57621 TACTCTTTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 16 0.25
73 1 0.02
74 48 0.74
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (72 bp):
GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAAAG
TACATGT
Found at i:57640 original size:115 final size:114
Alignment explanation
Indices: 57438--57657 Score: 327
Period size: 115 Copynumber: 1.9 Consensus size: 114
57428 CTTTAGCAGA
* * *
57438 GTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAT
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAG
*
57503 TATGAGTCTTTAGCGGCGTTTG-TAAACACAAACGCCACTATAGTACATGT
66 TATGACTCTTTAGCGGCGTTTGTTAAA-A-AAACGCCACTATAGTACATGT
* *
57553 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAG
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAG
* *
57618 TACT-ACTCTTTTGCGGCGTTTGTTGAAAAAACGCCACTAT
66 TA-TGACTCTTTAGCGGCGTTTGTTAAAAAAACGCCACTAT
57658 CGATGAACCT
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
114 12 0.13
115 79 0.83
116 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (114 bp):
GTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAG
TATGACTCTTTAGCGGCGTTTGTTAAAAAAACGCCACTATAGTACATGT
Found at i:60454 original size:21 final size:21
Alignment explanation
Indices: 60428--60467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60418 TCTGCTGAAA
* *
60428 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
60449 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
60468 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:64172 original size:9 final size:9
Alignment explanation
Indices: 64158--64214 Score: 63
Period size: 7 Copynumber: 7.0 Consensus size: 9
64148 CCAAAGATGT
64158 CAACTTTGC
1 CAACTTTGC
64167 CAACTTT--
1 CAACTTTGC
*
64174 CAATTTTGC
1 CAACTTTGC
64183 CAACTTT--
1 CAACTTTGC
64190 CAACTTTGC
1 CAACTTTGC
64199 CAACTTT--
1 CAACTTTGC
64206 CAACTTTGC
1 CAACTTTGC
64215 TAATATTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 20 0.50
9 20 0.50
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.39
Consensus pattern (9 bp):
CAACTTTGC
Found at i:64181 original size:16 final size:16
Alignment explanation
Indices: 64157--64214 Score: 107
Period size: 16 Copynumber: 3.6 Consensus size: 16
64147 ACCAAAGATG
64157 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
64173 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
64189 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
64205 TCAACTTTGC
1 TCAACTTTGC
64215 TAATATTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:67315 original size:22 final size:23
Alignment explanation
Indices: 67251--67315 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
67241 AGTCATATCA
*
67251 ATTCATAATGAATAGTCACATCTT
1 ATTCAT-ATGAATAATCACATCTT
*
67275 TTTCATATGAATCAA-CACATC-T
1 ATTCATATGAAT-AATCACATCTT
67297 ATTCATATGAATAATCACA
1 ATTCATATGAATAATCACA
67316 CCTCTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.06
22 16 0.44
23 12 0.33
24 6 0.17
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.35
Consensus pattern (23 bp):
ATTCATATGAATAATCACATCTT
Found at i:74235 original size:23 final size:24
Alignment explanation
Indices: 74190--74243 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
74180 GATGACATGG
** *
74190 AGATGATGTGGAAGGTGATGTGGC
1 AGATGATGTGGAAGCCGACGTGGC
*
74214 -GATGATGTGGTAGCCGACGTGGC
1 AGATGATGTGGAAGCCGACGTGGC
74237 AGATGAT
1 AGATGAT
74244 CAACAGCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.24, C:0.09, G:0.43, T:0.24
Consensus pattern (24 bp):
AGATGATGTGGAAGCCGACGTGGC
Found at i:74294 original size:23 final size:23
Alignment explanation
Indices: 74242--74294 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
74232 GTGGCAGATG
* *
74242 ATCAACAGCTTCTAGAAGGCCCA
1 ATCAGCAGCTTCTAGAAGACCCA
* *
74265 GTCAGCAGCTTCTAGAAGATCCA
1 ATCAGCAGCTTCTAGAAGACCCA
*
74288 ATTAGCA
1 ATCAGCA
74295 CTGGTTTGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCAGCAGCTTCTAGAAGACCCA
Found at i:78780 original size:14 final size:14
Alignment explanation
Indices: 78754--78786 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
78744 TTTTTATTAA
78754 TTATTAAATATATT
1 TTATTAAATATATT
78768 TTATATAAA-ATATT
1 TTAT-TAAATATATT
78782 TTATT
1 TTATT
78787 CATTTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 13 0.72
15 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTAAATATATT
Found at i:80067 original size:15 final size:15
Alignment explanation
Indices: 80044--80074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
80034 GAAGAGGAGG
*
80044 AGAAGAAGAATAAGA
1 AGAAAAAGAATAAGA
80059 AGAAAAAGAATAAGA
1 AGAAAAAGAATAAGA
80074 A
1 A
80075 TAAGACAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (15 bp):
AGAAAAAGAATAAGA
Found at i:83422 original size:14 final size:15
Alignment explanation
Indices: 83376--83423 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
83366 ACCCGTTTCG
83376 TTTTCTTTTAATTT-
1 TTTTCTTTTAATTTA
*
83390 GTTTCTTTTAATTTA
1 TTTTCTTTTAATTTA
83405 TTTTC-TTTAATTTA
1 TTTTCTTTTAATTTA
83419 TTTTC
1 TTTTC
83424 AATCATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 27 0.87
15 4 0.13
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTAATTTA
Found at i:90905 original size:35 final size:34
Alignment explanation
Indices: 90820--90906 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
90810 AAAATAATTT
* *
90820 TAAATACAACAAACTTACAATAAGTATTAGATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
90854 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
90892 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
90907 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:99139 original size:13 final size:13
Alignment explanation
Indices: 99096--99141 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
99086 TTATGAATAG
99096 AAAATATTAATATT-
1 AAAATA-TAAT-TTA
99110 AAAATATAA-TTA
1 AAAATATAATTTA
*
99122 TAAATATAATTTA
1 AAAATATAATTTA
99135 AAAATAT
1 AAAATAT
99142 TATAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 12 0.43
14 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATATAATTTA
Found at i:99146 original size:22 final size:25
Alignment explanation
Indices: 99097--99151 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 25
99087 TATGAATAGA
99097 AAATATTAATATTAAAATATAATTAT
1 AAATA-TAATATTAAAATATAATTAT
99123 AAATATAAT-TTAAAA-AT-ATTAT
1 AAATATAATATTAAAATATAATTAT
99145 AAATATA
1 AAATATA
99152 TATGATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.41
23 2 0.07
24 6 0.21
25 4 0.14
26 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATATAATATTAAAATATAATTAT
Found at i:99154 original size:13 final size:13
Alignment explanation
Indices: 99105--99159 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 13
99095 GAAAATATTA
99105 ATATTA-AAATAT
1 ATATTATAAATAT
99117 A-ATTATAAATAT
1 ATATTATAAATAT
99129 A-ATT-TAAA-A-
1 ATATTATAAATAT
99138 ATATTATAAATAT
1 ATATTATAAATAT
*
99151 ATATGATAA
1 ATATTATAA
99160 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 1 0.03
10 4 0.11
11 12 0.32
12 12 0.32
13 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTATAAATAT
Found at i:115320 original size:6 final size:6
Alignment explanation
Indices: 115303--115339 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
115293 TCTCGGCTCG
* *
115303 GGTCGT GATCGT GGTCGT GGCCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
115340 ATAATACGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.03, C:0.19, G:0.49, T:0.30
Consensus pattern (6 bp):
GGTCGT
Done.