Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2321123 original size:20 final size:20
Alignment explanation
Indices: 2321098--2321136 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2321088 TCAGCGGCTC
2321098 GGCTCGGCTCGGTCCAGACT
1 GGCTCGGCTCGGTCCAGACT
2321118 GGCTCGGCTCGGTCCAGAC
1 GGCTCGGCTCGGTCCAGAC
2321137 CGGTTCAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.36, G:0.36, T:0.18
Consensus pattern (20 bp):
GGCTCGGCTCGGTCCAGACT
Found at i:2323365 original size:12 final size:12
Alignment explanation
Indices: 2323348--2323390 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2323338 CGGAGATATG
2323348 AGAAATCAGAGC
1 AGAAATCAGAGC
*
2323360 AGAAATTAGAGC
1 AGAAATCAGAGC
* *
2323372 AG-AACCAGAAC
1 AGAAATCAGAGC
2323383 AGAAATCA
1 AGAAATCA
2323391 AAGAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.53, C:0.16, G:0.21, T:0.09
Consensus pattern (12 bp):
AGAAATCAGAGC
Found at i:2326052 original size:45 final size:45
Alignment explanation
Indices: 2325997--2326167 Score: 245
Period size: 45 Copynumber: 3.8 Consensus size: 45
2325987 ACTCTAACAT
* * *
2325997 TTTTCTGTTGAAAATGCACCCATACGCATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGTATAC
* * * *
2326042 TTTTATGTTGATAATGTACCCATATACATCTCAACCATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGTATAC
2326087 TTTTCTGTTGATAATGTACCCATATGCATTT-AACCTATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATGCATTTCAA-CTATAGTATAC
* *
2326132 TTTTCTATTGATAATGTACCCATATTCATTTCAACT
1 TTTTCTGTTGATAATGTACCCATATGCATTTCAACT
2326168 CTGGCATCCT
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 2 0.02
45 107 0.96
46 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGTATAC
Found at i:2326191 original size:90 final size:90
Alignment explanation
Indices: 2326009--2326206 Score: 240
Period size: 90 Copynumber: 2.2 Consensus size: 90
2325999 TTCTGTTGAA
* *
2326009 AATGCACCCATACGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCATATACATCTC
1 AATGCACCCATATGCATTTCAACTATAGTATACTTTTATATTGATAATGTACCCATATACATCTC
* * ***
2326074 AACCATAGTATACTTTTCTGTTGAT
66 AACCATAGCATACCTTTCTGACAAT
* * * *
2326099 AATGTACCCATATGCATTT-AACCTATAGTATACTTTTCTATTGATAATGTACCCATATTCATTT
1 AATGCACCCATATGCATTTCAA-CTATAGTATACTTTTATATTGATAATGTACCCATATACATCT
*
2326163 CAACTC-TGGCAT-CCTTTCATGACAAT
65 CAAC-CATAGCATACCTTTC-TGACAAT
2326189 AATGCACCCATATGCATT
1 AATGCACCCATATGCATT
2326207 ATTTTGTTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
89 7 0.08
90 84 0.91
91 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (90 bp):
AATGCACCCATATGCATTTCAACTATAGTATACTTTTATATTGATAATGTACCCATATACATCTC
AACCATAGCATACCTTTCTGACAAT
Found at i:2326272 original size:79 final size:79
Alignment explanation
Indices: 2326141--2326376 Score: 339
Period size: 81 Copynumber: 3.0 Consensus size: 79
2326131 CTTTTCTATT
* * * ** * *
2326141 GATAATGTACCCATATTCATTTCAACTCTGGCATCCTTTCATGACAATAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
2326206 TATT-TTGTTATGCC
66 TATTCTT-TTATGCC
* *
2326220 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACACCCATGTGT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATG--CACCCATATGC
2326285 ATTATTCTTTTATGCC
64 ATTATTCTTTTATGCC
* *
2326301 AATAATGTACCCATATACATATAAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
2326366 TATTCTTTTAT
66 TATTCTTTTAT
2326377 TCATTAATTT
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 67 0.48
81 72 0.51
82 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (79 bp):
GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
TATTCTTTTATGCC
Found at i:2331332 original size:16 final size:16
Alignment explanation
Indices: 2331311--2331345 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2331301 ATAAATTATA
* *
2331311 AATTTATAATTAATTT
1 AATTTACAAGTAATTT
2331327 AATTTACAAGTAATTT
1 AATTTACAAGTAATTT
2331343 AAT
1 AAT
2331346 AAAGATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
AATTTACAAGTAATTT
Found at i:2332601 original size:3 final size:3
Alignment explanation
Indices: 2332595--2332698 Score: 115
Period size: 3 Copynumber: 34.0 Consensus size: 3
2332585 TAATATTATT
2332595 TAA TAA TAA TAA TAAA TAA TAA TATA TAA TAA T-A TAA TATA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA
* * *
2332642 TAT TAG T-A TAA TATA TAA TTA TATA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
2332687 TAA TAA TAA TAA
1 TAA TAA TAA TAA
2332699 GACCGGACGA
Statistics
Matches: 88, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
2 5 0.06
3 68 0.77
4 15 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2332612 original size:10 final size:10
Alignment explanation
Indices: 2332595--2332695 Score: 89
Period size: 10 Copynumber: 9.6 Consensus size: 10
2332585 TAATATTATT
2332595 TAAT-AATAA
1 TAATAAATAA
2332604 TAATAAATAA
1 TAATAAATAA
*
2332614 TAATATATAA
1 TAATAAATAA
2332624 TAATATAATATA
1 TAATA-AATA-A
2332636 TAATAATATTAGTA
1 TAATAA-A-TA--A
*
2332650 TAATATATAA
1 TAATAAATAA
* *
2332660 TTATATATAA
1 TAATAAATAA
2332670 TAAT-AATAA
1 TAATAAATAA
2332679 TAATAATATAA
1 TAATAA-ATAA
2332690 TAATAA
1 TAATAA
2332696 TAAGACCGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
9 12 0.15
10 33 0.42
11 14 0.18
12 9 0.12
13 3 0.04
14 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (10 bp):
TAATAAATAA
Found at i:2332623 original size:23 final size:23
Alignment explanation
Indices: 2332597--2332698 Score: 120
Period size: 23 Copynumber: 4.4 Consensus size: 23
2332587 ATATTATTTA
2332597 ATAATAATAATAAATAATAATAT
1 ATAATAATAATAAATAATAATAT
*
2332620 ATAATAATATAATATATAATAATAT
1 ATAAT-A-ATAATAAATAATAATAT
* * *
2332645 -TAGT-ATAATATATAATTATAT
1 ATAATAATAATAAATAATAATAT
2332666 ATAATAATAAT-AATAATAATAT
1 ATAATAATAATAAATAATAATAT
2332688 AATAATAATAA
1 -ATAATAATAA
2332699 GACCGGACGA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
21 16 0.24
22 12 0.18
23 20 0.29
24 4 0.06
25 16 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAATAATAATAAATAATAATAT
Found at i:2341300 original size:20 final size:21
Alignment explanation
Indices: 2341275--2341314 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2341265 TTTCTAGCTG
2341275 TTTCTAGCCG-TTGGGGATGA
1 TTTCTAGCCGATTGGGGATGA
2341295 TTTCTAGCCGATTGGGGATG
1 TTTCTAGCCGATTGGGGATG
2341315 TTTTATCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (21 bp):
TTTCTAGCCGATTGGGGATGA
Found at i:2344877 original size:20 final size:21
Alignment explanation
Indices: 2344840--2344880 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2344830 TAGTCATTGG
2344840 GCCTAATGGAATCAATACTAA
1 GCCTAATGGAATCAATACTAA
* *
2344861 GCCT-ATGGTATCGATACTAA
1 GCCTAATGGAATCAATACTAA
2344881 TATGTAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (21 bp):
GCCTAATGGAATCAATACTAA
Found at i:2361648 original size:21 final size:20
Alignment explanation
Indices: 2361568--2361649 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
2361558 CGCAAATCAG
2361568 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
2361589 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
**
2361609 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
2361630 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
2361650 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 26 0.55
22 5 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:2361664 original size:20 final size:21
Alignment explanation
Indices: 2361639--2361690 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2361629 TTTTCCCAAT
*
2361639 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2361659 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2361680 TCGCAATGCGA
1 TCGCAATGCGA
2361691 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2361669 original size:41 final size:41
Alignment explanation
Indices: 2361624--2361855 Score: 132
Period size: 41 Copynumber: 5.7 Consensus size: 41
2361614 AATTTCGCGT
*
2361624 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
2361665 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
2361706 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * *
2361747 TGCGATTTTCATAATTCGCAATGTGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
2361788 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
2361829 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
2361856 CTTACTATCG
Statistics
Matches: 144, Mismatches: 40, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.01
40 25 0.17
41 115 0.80
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:2361734 original size:21 final size:21
Alignment explanation
Indices: 2361700--2361766 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2361690 ATACTGACTA
* * *
2361700 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
2361721 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
2361741 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
2361762 TCGCA
1 TCGCA
2361767 ATGTGAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:2361787 original size:20 final size:20
Alignment explanation
Indices: 2361762--2361873 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2361752 TTTTCATAAT
*
2361762 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2361782 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2361802 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2361823 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2361843 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2361863 TCGCAATGCGA
1 TCGCAATGCGA
2361874 TTTACATAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2362140 original size:27 final size:27
Alignment explanation
Indices: 2362083--2362135 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2362073 CATCGCTGGC
* *
2362083 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
2362110 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
2362136 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:2362446 original size:19 final size:19
Alignment explanation
Indices: 2362422--2362466 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2362412 GCAACGAGAG
**
2362422 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
2362441 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2362460 AATCGCA
1 AATCGCA
2362467 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:2362484 original size:19 final size:18
Alignment explanation
Indices: 2362462--2362654 Score: 76
Period size: 19 Copynumber: 11.1 Consensus size: 18
2362452 GAAACCAAAA
2362462 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
2362481 TCGCATTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
2362497 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
* *
2362514 TTGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
2362530 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
* *
2362547 TCGCGTTTCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
* **
2362563 TCG-TTGAGATAGTCATT
1 TCGCTTGCGATTTTCATT
*
2362580 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
**
2362596 TCG-TTGCGATAGTCATT
1 TCGCTTGCGATTTTCATT
*
2362613 TCCGCGTTGCGATTCTCATT
1 T-CGC-TTGCGATTTTCATT
*
2362633 ATCTCGTTGCGATTTTCATT
1 -TCGC-TTGCGATTTTCATT
2362653 TC
1 TC
2362655 AACCAAAAGA
Statistics
Matches: 131, Mismatches: 21, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
14 22 0.17
16 25 0.19
17 24 0.18
18 2 0.02
19 29 0.22
20 28 0.21
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:2362505 original size:14 final size:14
Alignment explanation
Indices: 2362486--2362605 Score: 60
Period size: 14 Copynumber: 7.5 Consensus size: 14
2362476 TCATTTCGCA
2362486 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2362500 TTGCGATTTTCATTTTGCG
1 TTGCGA--TTC--TCT-CG
2362519 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2362533 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
*
2362552 TTTCGATTCTCTCG
1 TTGCGATTCTCTCG
* *
2362566 TTGAGATAGTCATTTCGCG
1 TTGCGAT--TC---TCTCG
2362585 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
2362599 TTGCGAT
1 TTGCGAT
2362606 AGTCATTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 34 0.42
15 2 0.02
16 8 0.10
17 8 0.10
18 2 0.02
19 27 0.33
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2362509 original size:33 final size:33
Alignment explanation
Indices: 2362467--2362629 Score: 245
Period size: 33 Copynumber: 4.9 Consensus size: 33
2362457 CAAAATCGCA
*
2362467 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2362500 TTGCGATTTTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2362533 TTGCGATTTTCATTTCGCGTTTCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
2362566 TTGAGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
2362599 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
2362630 ATTATCTCGT
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 105 0.88
34 15 0.12
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2362631 original size:20 final size:20
Alignment explanation
Indices: 2362597--2362654 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2362587 GCGATTCTCT
**
2362597 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
2362617 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
2362637 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
2362655 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:2364846 original size:21 final size:20
Alignment explanation
Indices: 2364787--2364847 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
2364777 CTCGACAGTC
2364787 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
2364807 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
2364828 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
2364848 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:2366161 original size:14 final size:14
Alignment explanation
Indices: 2366142--2366177 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2366132 ATTGTTTAAT
2366142 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2366156 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2366170 TGATTTGT
1 TGATTTGT
2366178 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2366308 original size:19 final size:19
Alignment explanation
Indices: 2366284--2366401 Score: 107
Period size: 19 Copynumber: 6.7 Consensus size: 19
2366274 AAAAAGTACT
*
2366284 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2366303 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
2366317 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2366336 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
2366350 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
2366369 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
2366388 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2366402 CTAAATTCGC
Statistics
Matches: 85, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 53 0.62
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2366329 original size:33 final size:33
Alignment explanation
Indices: 2366284--2366401 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
2366274 AAAAAGTACT
* * *
2366284 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2366317 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2366350 ATCGCAACGCGAAACT-AAAATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAA--CG--AC-AAA
2366388 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2366402 CTAAATTCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
33 54 0.71
34 1 0.01
35 2 0.03
37 2 0.03
38 17 0.22
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2366418 original size:19 final size:19
Alignment explanation
Indices: 2366316--2366411 Score: 132
Period size: 19 Copynumber: 5.3 Consensus size: 19
2366306 GCAACGAGAG
2366316 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
2366335 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
2366349 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
2366368 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
2366387 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
2366406 ATTCGC
1 AATCGC
2366412 GTTGCGATTT
Statistics
Matches: 70, Mismatches: 1, Indels: 12
0.84 0.01 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 53 0.76
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:2366429 original size:19 final size:19
Alignment explanation
Indices: 2366407--2366524 Score: 58
Period size: 19 Copynumber: 6.7 Consensus size: 19
2366397 CGAAACTAAA
2366407 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
2366426 TTCGCATTGC-A----AAA
1 TTCGCGTTGCGATTTTCAT
* *
2366440 TTCACGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2366459 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2366474 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2366492 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2366511 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2366525 AGACATTAAG
Statistics
Matches: 69, Mismatches: 19, Indels: 21
0.63 0.17 0.19
Matches are distributed among these distances:
14 17 0.25
15 1 0.01
16 3 0.04
17 3 0.04
18 1 0.01
19 34 0.49
20 10 0.14
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2366502 original size:33 final size:32
Alignment explanation
Indices: 2366411--2366504 Score: 134
Period size: 33 Copynumber: 2.9 Consensus size: 32
2366401 ACTAAATTCG
* *
2366411 CGTTGCGATTTTCATTTCGCATTGCAAAATTCA
1 CGTTGCGATTTTCATTTCGCATTGC-GATTTCA
* *
2366444 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-TCA
2366477 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2366505 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTCA
Found at i:2368725 original size:12 final size:12
Alignment explanation
Indices: 2368708--2368742 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2368698 ATTCGGGGAC
2368708 TTTTCTTCTTCT
1 TTTTCTTCTTCT
2368720 TTTTCTTCTTCT
1 TTTTCTTCTTCT
2368732 TTTTCTTCTTC
1 TTTTCTTCTTC
2368743 AGGATTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:2368973 original size:24 final size:24
Alignment explanation
Indices: 2368927--2368973 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2368917 CAAAATCTGA
* *
2368927 GTATTGACCAATATTAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
2368951 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
2368974 AATACTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:2369778 original size:20 final size:20
Alignment explanation
Indices: 2369731--2369780 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2369721 GATATAATAC
2369731 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
2369751 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
2369771 AAAATCGCAA
1 AAAATCGCAA
2369781 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:2371583 original size:41 final size:42
Alignment explanation
Indices: 2371538--2371629 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
2371528 CCTCTTCAAC
* *
2371538 GATGACAGTGGCCTCTTAAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTCTTGAGG
* * *
2371579 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTCTTGAGG
* *
2371621 AATGGCAGG
1 GATGACAGG
2371630 TGAGTCGAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 19 0.45
42 23 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTCTTGAGG
Found at i:2371991 original size:20 final size:20
Alignment explanation
Indices: 2371966--2372004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2371956 GAAGAATAGT
2371966 TTACTTTCGAAACACGAAAC
1 TTACTTTCGAAACACGAAAC
* *
2371986 TTACTTTCGCAACGCGAAA
1 TTACTTTCGAAACACGAAA
2372005 ATGACTATCG
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:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGAAACACGAAAC
Found at i:2372015 original size:20 final size:20
Alignment explanation
Indices: 2371992--2372078 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
2371982 AAACTTACTT
2371992 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
2372012 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
2372032 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
2372052 TCGCAATGC-AAAATGAAAA
1 TCGCAACGCGAAAATGACTA
2372071 TCGCAACG
1 TCGCAACG
2372079 ACAAAATTGC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 13 0.22
20 46 0.78
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2372167 original size:20 final size:19
Alignment explanation
Indices: 2372133--2372187 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2372123 TTGCGATTTT
*
2372133 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2372152 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2372172 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2372188 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2372751 original size:18 final size:18
Alignment explanation
Indices: 2372728--2372775 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2372718 CGGTTCGATC
2372728 AGGTGATGGCTCTGGGTA
1 AGGTGATGGCTCTGGGTA
* *
2372746 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTA
2372764 AGGTGATGGCTC
1 AGGTGATGGCTC
2372776 CCAAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTA
Found at i:2374143 original size:20 final size:20
Alignment explanation
Indices: 2374095--2374153 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2374085 AATAGTTTCT
* *
2374095 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2374115 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2374135 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2374154 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2374656 original size:20 final size:20
Alignment explanation
Indices: 2374631--2374697 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2374621 GTATTATCTC
*
2374631 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
2374651 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
2374671 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
2374691 GTTGCGA
1 GTTGCGA
2374698 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:2374724 original size:41 final size:41
Alignment explanation
Indices: 2374605--2374742 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
2374595 CGCTTTGAAA
* * *
2374605 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
2374646 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
2374686 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
2374727 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
2374743 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2374758 original size:41 final size:41
Alignment explanation
Indices: 2374672--2374760 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
2374662 AAGTATCGAG
* * * ** * *
2374672 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGAACCGCGTTGCGATTTTCAAATATCGCA
2374713 TTGCGATAGTCAGAACCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGAACCGCGTTGCGATTTT-CAAATATCGCA
2374754 TTGCGAT
1 TTGCGAT
2374761 TTACTTATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGAACCGCGTTGCGATTTTCAAATATCGCA
Found at i:2374759 original size:21 final size:20
Alignment explanation
Indices: 2374733--2374779 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2374723 CAGAACCGCG
*
2374733 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
2374754 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
2374774 TTGCGA
1 TTGCGA
2374780 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:2374821 original size:21 final size:22
Alignment explanation
Indices: 2374769--2374821 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2374759 ATTTACTTAT
2374769 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2374790 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2374811 TCGCATTGCGA
1 TCGCATTGCGA
2374822 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2376215 original size:21 final size:23
Alignment explanation
Indices: 2376189--2376236 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
2376179 ACTGGTATAG
*
2376189 TTTACCTTT-TATTTT-AAATAA
1 TTTACCTTTAAATTTTCAAATAA
*
2376210 TTTACCTTTAAATTTTCAACTAA
1 TTTACCTTTAAATTTTCAAATAA
2376233 TTTA
1 TTTA
2376237 TAATTATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTACCTTTAAATTTTCAAATAA
Found at i:2380568 original size:20 final size:20
Alignment explanation
Indices: 2380540--2380583 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2380530 TTTTGTAGAA
* *
2380540 AAATTATCCCCAACGGGTCC
1 AAATCATCCCCAACAGGTCC
2380560 AAATCATCCCCAACAGGTCC
1 AAATCATCCCCAACAGGTCC
2380580 AAAT
1 AAAT
2380584 AACCACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.18
Consensus pattern (20 bp):
AAATCATCCCCAACAGGTCC
Found at i:2386461 original size:2 final size:2
Alignment explanation
Indices: 2386454--2386481 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2386444 ATTTGTGATC
2386454 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
2386482 TATGTATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2387817 original size:13 final size:13
Alignment explanation
Indices: 2387801--2387842 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2387791 TAAATATATA
2387801 TTTTTTATATTTC
1 TTTTTTATATTTC
*
2387814 TTTTTTGACT-TTTA
1 TTTTTT-A-TATTTC
2387828 TTTTTTATATTTC
1 TTTTTTATATTTC
2387841 TT
1 TT
2387843 AAAGTCGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTATATTTC
Found at i:2390626 original size:2 final size:2
Alignment explanation
Indices: 2390611--2390662 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
2390601 TGATACTTTT
*
2390611 TA TA TA GA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2390654 TA TA TA TA T
1 TA TA TA TA T
2390663 TTCATCTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2390948 original size:17 final size:18
Alignment explanation
Indices: 2390926--2390961 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2390916 AAATAACTAT
2390926 ATATTTTT-AATTATAAA
1 ATATTTTTAAATTATAAA
2390943 ATATTTTTAAATTATAAA
1 ATATTTTTAAATTATAAA
2390961 A
1 A
2390962 AAATTTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTTTAAATTATAAA
Found at i:2394221 original size:45 final size:45
Alignment explanation
Indices: 2394157--2394293 Score: 238
Period size: 45 Copynumber: 3.0 Consensus size: 45
2394147 AGAGCCCATT
* *
2394157 TTACATCCGCCACTCAGATTTTGCATATTGATGATATGTTATAGA
1 TTACATCCGCCATTGAGATTTTGCATATTGATGATATGTTATAGA
*
2394202 TTACATCCGCCATTGAGATTTTGCATATTGATAATATGTTATAGA
1 TTACATCCGCCATTGAGATTTTGCATATTGATGATATGTTATAGA
*
2394247 TTTCATCCGCCATTGAGATTTTGCATATTGATGATATGTTATAGA
1 TTACATCCGCCATTGAGATTTTGCATATTGATGATATGTTATAGA
2394292 TT
1 TT
2394294 TTATCATTTG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (45 bp):
TTACATCCGCCATTGAGATTTTGCATATTGATGATATGTTATAGA
Found at i:2394954 original size:21 final size:21
Alignment explanation
Indices: 2394929--2394968 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2394919 TTTTAAATAG
2394929 AAAATATATAG-AATGTTTTTA
1 AAAATATATAGTAAT-TTTTTA
2394950 AAAATATATAGTAATTTTT
1 AAAATATATAGTAATTTTT
2394969 GTTGGAAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
AAAATATATAGTAATTTTTTA
Found at i:2395070 original size:8 final size:8
Alignment explanation
Indices: 2395056--2395098 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
2395046 GACGTTACCC
2395056 CAATATTA
1 CAATATTA
*
2395064 TAATATTA
1 CAATATTA
*
2395072 CAATACTA
1 CAATATTA
2395080 CAATATTA
1 CAATATTA
*
2395088 CAATACTA
1 CAATATTA
2395096 CAA
1 CAA
2395099 CACTAGCTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (8 bp):
CAATATTA
Found at i:2395083 original size:24 final size:24
Alignment explanation
Indices: 2395056--2395103 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2395046 GACGTTACCC
* * *
2395056 CAATATTATAATATTACAATACTA
1 CAATATTACAATACTACAACACTA
2395080 CAATATTACAATACTACAACACTA
1 CAATATTACAATACTACAACACTA
2395104 GCTGTGGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (24 bp):
CAATATTACAATACTACAACACTA
Found at i:2395084 original size:16 final size:16
Alignment explanation
Indices: 2395065--2395098 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2395055 CCAATATTAT
2395065 AATATTACAATACTAC
1 AATATTACAATACTAC
2395081 AATATTACAATACTAC
1 AATATTACAATACTAC
2395097 AA
1 AA
2395099 CACTAGCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATTACAATACTAC
Found at i:2395103 original size:8 final size:8
Alignment explanation
Indices: 2395065--2395103 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2395055 CCAATATTAT
*
2395065 AATATTAC
1 AATACTAC
2395073 AATACTAC
1 AATACTAC
*
2395081 AATATTAC
1 AATACTAC
2395089 AATACTAC
1 AATACTAC
*
2395097 AACACTA
1 AATACTA
2395104 GCTGTGGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (8 bp):
AATACTAC
Found at i:2398580 original size:19 final size:19
Alignment explanation
Indices: 2398552--2398591 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2398542 AACTTCTCTC
2398552 TGCCGCCATTCTTCTTTCT
1 TGCCGCCATTCTTCTTTCT
*
2398571 TGCCGTCATTCTTCTTTCT
1 TGCCGCCATTCTTCTTTCT
2398590 TG
1 TG
2398592 TCGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.33, G:0.12, T:0.50
Consensus pattern (19 bp):
TGCCGCCATTCTTCTTTCT
Found at i:2400312 original size:14 final size:15
Alignment explanation
Indices: 2400287--2400327 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
2400277 ATTCATAAGC
2400287 AAAATAAATTATTAT
1 AAAATAAATTATTAT
2400302 AAAAT-AATTATTAT
1 AAAATAAATTATTAT
* *
2400316 AGAGTAAATTAT
1 AAAATAAATTAT
2400328 AAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (15 bp):
AAAATAAATTATTAT
Found at i:2400349 original size:26 final size:26
Alignment explanation
Indices: 2400297--2400349 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2400287 AAAATAAATT
* *
2400297 ATTATAAAATAATTATTATAGAGTAA
1 ATTATAAAATAATTATTAAAGAATAA
* * *
2400323 ATTATAAAATTATTTTTAAATAATAA
1 ATTATAAAATAATTATTAAAGAATAA
2400349 A
1 A
2400350 AAGTAATTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTATAAAATAATTATTAAAGAATAA
Found at i:2401721 original size:2 final size:2
Alignment explanation
Indices: 2401714--2401751 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2401704 GATTCTTCTC
2401714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2401752 TGCATATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2402095 original size:106 final size:106
Alignment explanation
Indices: 2401910--2402116 Score: 389
Period size: 106 Copynumber: 2.0 Consensus size: 106
2401900 TAAGGAATCC
2401910 AAAATGTATATAAGAGGAATATAATAACTTTGCTTGAGTAGAGAAAATAAAGAAAATATGACAAT
1 AAAATGTATATAAGAGGAATATAATAACTTTGCTTGAGTAGAGAAAATAAAGAAAATATGACAAT
2401975 TGCAGTACTGAATCTTCATTGTATACGTTTAGAGATACTTT
66 TGCAGTACTGAATCTTCATTGTATACGTTTAGAGATACTTT
2402016 AAAATGTATATAAGAGGAATATAATAACTGTT-CTTGAGTAGAGAAAATAAAGAAAATATGACAA
1 AAAATGTATATAAGAGGAATATAATAACT-TTGCTTGAGTAGAGAAAATAAAGAAAATATGACAA
*
2402080 TTGTAGTACTGAATCTTCATTGTATACGTTTAGAGAT
65 TTGCAGTACTGAATCTTCATTGTATACGTTTAGAGAT
2402117 GAAAGTAAGA
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
106 97 0.98
107 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (106 bp):
AAAATGTATATAAGAGGAATATAATAACTTTGCTTGAGTAGAGAAAATAAAGAAAATATGACAAT
TGCAGTACTGAATCTTCATTGTATACGTTTAGAGATACTTT
Found at i:2403728 original size:14 final size:14
Alignment explanation
Indices: 2403709--2403750 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2403699 CGAGTCTGGA
2403709 GAACATAAACGAAC
1 GAACATAAACGAAC
*
2403723 GAACATAAACAAAC
1 GAACATAAACGAAC
* *
2403737 GAGCATAAATGAAC
1 GAACATAAACGAAC
2403751 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.10
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:2404938 original size:93 final size:94
Alignment explanation
Indices: 2404774--2404964 Score: 366
Period size: 93 Copynumber: 2.0 Consensus size: 94
2404764 GTACACCAAG
*
2404774 ATCTGAGAAAAAGTTTTCTACCGGTGAACAATTTGTGAGCAAATTAGAGAGCTTTATAATAGTTA
1 ATCTGAGAAAAAGTTTTCTACCGGTGAACAATTTGTGAGCAAATTAGAGAGCTTTATAATAATTA
2404839 AAGCATGCACCTAGGAATTGGAATTCTAC
66 AAGCATGCACCTAGGAATTGGAATTCTAC
2404868 ATCT-AGAAAAAGTTTTCTACCGGTGAACAATTTGTGAGCAAATTAGAGAGCTTTATAATAATTA
1 ATCTGAGAAAAAGTTTTCTACCGGTGAACAATTTGTGAGCAAATTAGAGAGCTTTATAATAATTA
2404932 AAGCATGCACCTAGGAATTGGAATTCTAC
66 AAGCATGCACCTAGGAATTGGAATTCTAC
2404961 ATCT
1 ATCT
2404965 CGATCATTCT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 92 0.96
94 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (94 bp):
ATCTGAGAAAAAGTTTTCTACCGGTGAACAATTTGTGAGCAAATTAGAGAGCTTTATAATAATTA
AAGCATGCACCTAGGAATTGGAATTCTAC
Found at i:2406047 original size:12 final size:12
Alignment explanation
Indices: 2406032--2406073 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2406022 CGATTTTTTT
2406032 ACCGGATTAAAA
1 ACCGGATTAAAA
*
2406044 ACCGGTTTGAAAA
1 ACCGGATT-AAAA
*
2406057 ACCGGATAAAAA
1 ACCGGATTAAAA
2406069 ACCGG
1 ACCGG
2406074 TTTTTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (12 bp):
ACCGGATTAAAA
Found at i:2413726 original size:19 final size:19
Alignment explanation
Indices: 2413699--2413743 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2413689 AGTGTAGACT
2413699 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
*
2413718 ATTGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
2413737 ATCGCAA
1 ATCGCAA
2413744 TGACAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:2413784 original size:20 final size:20
Alignment explanation
Indices: 2413759--2413856 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
2413749 ACTGTAGACT
2413759 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
2413779 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
** * **
2413800 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
2413821 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
2413841 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
2413857 CAACGCGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 30 0.45
21 36 0.55
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:2413805 original size:21 final size:21
Alignment explanation
Indices: 2413779--2413832 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2413769 GAAATGAAAA
2413779 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
2413800 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
2413821 ATCGCAACGCGA
1 ATCGCAACGCGA
2413833 AATGGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:2414929 original size:37 final size:38
Alignment explanation
Indices: 2414826--2414987 Score: 150
Period size: 37 Copynumber: 4.3 Consensus size: 38
2414816 GTGGTATTCT
* * *
2414826 AATCGAATATAAATTTGT-AATAATATATTCATATTTT
1 AATCAAATATAAATTTATAAATAATATATTCATATTTC
** * * **
2414863 AATTGAACATAAATTCATAAATAATATATTTGTATTT-
1 AATCAAATATAAATTTATAAATAATATATTCATATTTC
* *
2414900 AGTCAAATATATATTTATAAATAATATATTCATATTTC
1 AATCAAATATAAATTTATAAATAATATATTCATATTTC
* * * *
2414938 AATTAAATATAAATTTAT-AATAACATGTTCATATTTT
1 AATCAAATATAAATTTATAAATAATATATTCATATTTC
**
2414975 AATTGAATATAAA
1 AATCAAATATAAA
2414988 AACTTAAATA
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
37 71 0.70
38 31 0.30
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (38 bp):
AATCAAATATAAATTTATAAATAATATATTCATATTTC
Found at i:2414984 original size:75 final size:75
Alignment explanation
Indices: 2414820--2414987 Score: 187
Period size: 75 Copynumber: 2.3 Consensus size: 75
2414810 TACAATGTGG
* * * *
2414820 TATTCTAATCGAATATAAATTTGTAATAATATATTCATATTTTAATTGAACATAAATTCATAAAT
1 TATTTTAATCGAATATAAATTTATAATAATATATTCATATTTCAATTAAACATAAATTCATAAAT
* **
2414885 AATATATTTG
66 AACATATTCA
* * * * *
2414895 TA-TTTAGTCAAATATATATTTATAAATAATATATTCATATTTCAATTAAATATAAATTTAT-AA
1 TATTTTAATCGAATATAAATTTAT-AATAATATATTCATATTTCAATTAAACATAAATTCATAAA
*
2414958 TAACATGTTCA
65 TAACATATTCA
*
2414969 TATTTTAATTGAATATAAA
1 TATTTTAATCGAATATAAA
2414988 AACTTAAATA
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
74 27 0.36
75 47 0.64
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (75 bp):
TATTTTAATCGAATATAAATTTATAATAATATATTCATATTTCAATTAAACATAAATTCATAAAT
AACATATTCA
Found at i:2425097 original size:29 final size:29
Alignment explanation
Indices: 2425056--2425112 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2425046 AATATTTAAT
*
2425056 TTAATATATTATTGTTTTAAA-AATTAAAA
1 TTAATATATTATT-TATTAAATAATTAAAA
2425085 TTAAT-TATATATTTATTAAATAATTAAA
1 TTAATATAT-TATTTATTAAATAATTAAA
2425113 TTTCTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAATATATTATTTATTAAATAATTAAAA
Found at i:2425113 original size:28 final size:29
Alignment explanation
Indices: 2425046--2425114 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
2425036 TTAAGTAATT
* * *
2425046 AATATTTAATTTAATATATTATTGTTTTA
1 AATAATTAAATTAATATATTATTGTATTA
2425075 AA-AATTAAAATTAAT-TATATATT-TATTA
1 AATAATT-AAATTAATATAT-TATTGTATTA
2425103 AATAATTAAATT
1 AATAATTAAATT
2425115 TCTAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
AATAATTAAATTAATATATTATTGTATTA
Found at i:2425189 original size:4 final size:4
Alignment explanation
Indices: 2425180--2425206 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2425170 AGGGTTTGTT
2425180 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2425207 TTAGAGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2429638 original size:14 final size:14
Alignment explanation
Indices: 2429619--2429645 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2429609 TCTCTGTCGT
2429619 TTGCATTCTTTCCG
1 TTGCATTCTTTCCG
2429633 TTGCATTCTTTCC
1 TTGCATTCTTTCC
2429646 TCCAACAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (14 bp):
TTGCATTCTTTCCG
Found at i:2431486 original size:42 final size:42
Alignment explanation
Indices: 2431375--2431471 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
2431365 TTGCAGGGAC
*
2431375 ACCTCATTCAGCAGGAGAATCTAGAACAGCATAACAAAGTAA
1 ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
* * *
2431417 ACCTCATTCATCAGGAGAATCTAGAACTGCATAACAAATTTA
1 ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
*
2431459 ACCTCATGCAGCA
1 ACCTCATTCAGCA
2431472 AGAAAATACT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (42 bp):
ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
Found at i:2437672 original size:39 final size:39
Alignment explanation
Indices: 2437627--2437703 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
2437617 AAGTTTTAGT
*
2437627 TTATATTTTATTTTAATATCTCGTTGTTAAAAATTTAAG
1 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAAG
2437666 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAA
1 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAA
2437704 CAAAACTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (39 bp):
TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAAG
Found at i:2437780 original size:49 final size:50
Alignment explanation
Indices: 2437725--2437828 Score: 158
Period size: 49 Copynumber: 2.1 Consensus size: 50
2437715 CACGTTATAT
2437725 TTTTTCA-TGTGTAATTACATCATTTATCCCTTAAT-TATTCTCACTCCTA
1 TTTTTCATTG-GTAATTACATCATTTATCCCTTAATATATTCTCACTCCTA
* *
2437774 TTTTTCATTGGTAATTACATCATTTATCCCTTAATCATCTTCTCACTCTTA
1 TTTTTCATTGGTAATTACATCATTTATCCCTTAAT-ATATTCTCACTCCTA
2437825 TTTT
1 TTTT
2437829 GGTCATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
49 32 0.64
50 2 0.04
51 16 0.32
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.51
Consensus pattern (50 bp):
TTTTTCATTGGTAATTACATCATTTATCCCTTAATATATTCTCACTCCTA
Found at i:2441902 original size:20 final size:20
Alignment explanation
Indices: 2441852--2441904 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2441842 AGTTGTTTCT
*
2441852 AGCCATTGGGAATGTTTTGG
1 AGCCATTGGGGATGTTTTGG
2441872 AGCCATTGGGGATGTTTTGG
1 AGCCATTGGGGATGTTTTGG
*
2441892 AGTCATTGGGGAT
1 AGCCATTGGGGAT
2441905 TTATTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.09, G:0.38, T:0.34
Consensus pattern (20 bp):
AGCCATTGGGGATGTTTTGG
Found at i:2442017 original size:21 final size:21
Alignment explanation
Indices: 2441991--2442046 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2441981 GGGCTTGATA
2441991 GTATCGATACTACTATTCACG
1 GTATCGATACTACTATTCACG
* * *
2442012 GTATCGATACTAGTGTTCATG
1 GTATCGATACTACTATTCACG
2442033 GTATCGATACTACT
1 GTATCGATACTACT
2442047 GTAGCAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
GTATCGATACTACTATTCACG
Found at i:2442121 original size:21 final size:21
Alignment explanation
Indices: 2442095--2442145 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2442085 TTAGTATCGG
*
2442095 TACTGTTCATGGTATCGATAC
1 TACTGTTCATGGTATCAATAC
2442116 TACTGTTCATGGTATCAATAC
1 TACTGTTCATGGTATCAATAC
*
2442137 TATTGTTCA
1 TACTGTTCA
2442146 CAAATTATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (21 bp):
TACTGTTCATGGTATCAATAC
Found at i:2442174 original size:20 final size:20
Alignment explanation
Indices: 2442151--2442226 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
2442141 GTTCACAAAT
2442151 TATCGGTACTATTCATACAA
1 TATCGGTACTATTCATACAA
* *
2442171 TATCGATAATATTCATACAA
1 TATCGGTACTATTCATACAA
* *
2442191 TATCAGTACTATTCATATAA
1 TATCGGTACTATTCATACAA
*
2442211 T-GCGGTACTATTCATA
1 TATCGGTACTATTCATA
2442227 AAAAATTTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 13 0.27
20 35 0.73
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
TATCGGTACTATTCATACAA
Found at i:2444656 original size:22 final size:20
Alignment explanation
Indices: 2444611--2444681 Score: 92
Period size: 22 Copynumber: 3.5 Consensus size: 20
2444601 AAGCAAAAAT
*
2444611 GGTATCGATACCATAAT-A-
1 GGTATCGATACCATAGTAAG
2444629 GGTATCGATACCATAGTAAG
1 GGTATCGATACCATAGTAAG
*
2444649 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
2444671 GGTATCGATAC
1 GGTATCGATAC
2444682 TTAGGAGCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 16 0.34
19 1 0.02
20 11 0.23
22 19 0.40
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:2445095 original size:54 final size:54
Alignment explanation
Indices: 2445023--2445154 Score: 185
Period size: 54 Copynumber: 2.4 Consensus size: 54
2445013 TGCAAAAAGT
* * *
2445023 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGCATTTTGTGTGCAAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGC-AAAC
* * *
2445078 -AATAAATTCATATTAAGTGTATGAATTTCCGTATGGGAACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGCAAAC
*
2445131 TAAGAAATCCATACTAAGTGTATG
1 TAAGAAATTCATACTAAGTGTATG
2445155 TGTTGAGTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 4 0.06
54 63 0.94
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (54 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGCAAAC
Found at i:2450433 original size:42 final size:42
Alignment explanation
Indices: 2450370--2450488 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
2450360 TTCCCCGAAA
* **
2450370 TCCCGTGTTTGTTTCATGTAATTCGTTTTCTGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
2450412 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
*
2450454 TCCCGTGTTTGTTTCACGTAATTCATTTTCCAGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAA
2450489 TATAATTCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
Found at i:2450690 original size:21 final size:23
Alignment explanation
Indices: 2450647--2450697 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
2450637 CATTTTCATC
2450647 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
2450671 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
2450692 ATAATA
1 AAAATA
2450698 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:2450708 original size:53 final size:51
Alignment explanation
Indices: 2450649--2450765 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
2450639 TTTTCATCAA
* **
2450649 AATATTAT-TTATTAA-AATATTTAAAATATATTTATTAATATTTATAATAATAT
1 AATATTATATTATTAATAATATATAAAATA-ATCAATT-ATA-TTATAATAA-AT
* *
2450702 AATATTATATTTTTAATATTATATAAAATAATCAATTATATTATAATAAAT
1 AATATTATATTATTAATAATATATAAAATAATCAATTATATTATAATAAAT
**
2450753 AATAAGATATTAT
1 AATATTATATTAT
2450766 ATTTTTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
51 12 0.22
52 9 0.17
53 11 0.20
54 11 0.20
55 11 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
AATATTATATTATTAATAATATATAAAATAATCAATTATATTATAATAAAT
Found at i:2450711 original size:22 final size:23
Alignment explanation
Indices: 2450664--2450724 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
2450654 TATTTATTAA
* *
2450664 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
2450685 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
2450708 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
2450725 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:2450742 original size:22 final size:21
Alignment explanation
Indices: 2450717--2450767 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
2450707 TATATTTTTA
*
2450717 ATATTATATA-AAATAATCAATT
1 ATATTATATATAAATAAT-AA-G
2450739 ATATTATA-ATAAATAATAAG
1 ATATTATATATAAATAATAAG
2450759 ATATTATAT
1 ATATTATAT
2450768 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 15 0.58
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATTATATATAAATAATAAG
Found at i:2450749 original size:61 final size:60
Alignment explanation
Indices: 2450673--2450834 Score: 148
Period size: 56 Copynumber: 2.8 Consensus size: 60
2450663 AAATATTTAA
2450673 AATATATT-TATTA-ATATTTATAATAATATAATATTATATTTTTAATATTATATAA-A-AT
1 AATA-ATTATATTATATATTTATAATAATATAATATTATATTTTTAATATTA-ATAATATAT
*
2450731 AATCAATTATATTATA-A--TA-AATAATA-AGATATTATATTTTT-ATTTTAATAATATAT
1 AAT-AATTATATTATATATTTATAATAATATA-ATATTATATTTTTAATATTAATAATATAT
* * *
2450787 AATAATT-TTTTATATATTTAATAATGAATAATATTATTATATATTTAA
1 AATAATTATATTATATATTT-ATAAT-AAT-ATAATATTATATTTTTAA
2450835 ATAATATTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 26
0.74 0.03 0.23
Matches are distributed among these distances:
54 10 0.12
55 12 0.14
56 25 0.29
57 3 0.04
58 7 0.08
59 10 0.12
60 4 0.05
61 12 0.14
62 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (60 bp):
AATAATTATATTATATATTTATAATAATATAATATTATATTTTTAATATTAATAATATAT
Found at i:2450829 original size:29 final size:28
Alignment explanation
Indices: 2450771--2450841 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
2450761 ATTATATTTT
*
2450771 TATTTTAATAATATATAATAATTTTTTA
1 TATTTTAATAATATATAATAATTTTATA
2450799 TATATTTAATAATGA-ATAAT-ATTATTATA
1 TAT-TTTAATAAT-ATATAATAATT-TTATA
*
2450828 TATTTAAATAATAT
1 TATTTTAATAATAT
2450842 TTTAGTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.38
29 21 0.57
30 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TATTTTAATAATATATAATAATTTTATA
Found at i:2451204 original size:20 final size:21
Alignment explanation
Indices: 2451166--2451217 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
2451156 TTTCCAGATG
2451166 TTTTCCAGAAATGTGTAATTCA
1 TTTTCCAGAAA-GTGTAATTCA
2451188 TTTTCCAGAAA-TGTAATTCA
1 TTTTCCAGAAAGTGTAATTCA
2451208 TTTTCCAGAA
1 TTTTCCAGAA
2451218 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.63
22 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTTCCAGAAAGTGTAATTCA
Found at i:2451225 original size:20 final size:20
Alignment explanation
Indices: 2451182--2451226 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2451172 AGAAATGTGT
**
2451182 AATTCATTTTCCAGAAATGT
1 AATTCATTTTCCAGAAATCA
*
2451202 AATTCATTTTCCAGAATTCA
1 AATTCATTTTCCAGAAATCA
2451222 AATTC
1 AATTC
2451227 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (20 bp):
AATTCATTTTCCAGAAATCA
Found at i:2451257 original size:15 final size:15
Alignment explanation
Indices: 2451200--2451251 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
2451190 TTCCAGAAAT
**
2451200 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2451215 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
2451229 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2451244 GTAATTCA
1 GTAATTCA
2451252 TTTTCCGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2459680 original size:15 final size:15
Alignment explanation
Indices: 2459639--2459673 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2459629 ATCAAAGGAA
*
2459639 GAAACGAAAAATGAG
1 GAAACAAAAAATGAG
2459654 GAAACAAAAAATGAG
1 GAAACAAAAAATGAG
2459669 GAAAC
1 GAAAC
2459674 TCAAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAACAAAAAATGAG
Found at i:2465292 original size:68 final size:68
Alignment explanation
Indices: 2465094--2465280 Score: 311
Period size: 68 Copynumber: 2.8 Consensus size: 68
2465084 TATTAATGGT
* *
2465094 CTAACTGTGTATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
2465159 GGC
66 GGC
* *
2465162 CTAACTGTGCATTTGACATAAAGGTGTCAATCATGCTAGTAAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
2465227 GGC
66 GGC
***
2465230 CTAACTGTGCATTTGACAGAATTTTGTCAATCATGCTAGTTAGATGAAAGG
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAAGG
2465281 TTAAATACCT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 110 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:2465362 original size:81 final size:81
Alignment explanation
Indices: 2465254--2465464 Score: 323
Period size: 81 Copynumber: 2.6 Consensus size: 81
2465244 GACAGAATTT
* *
2465254 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTAAGTAAAAGATTAATGGCCTAGTTTT
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
*
2465319 GCACTTGACAGAAAGG
66 GCACTTGACAAAAAGG
* * * *
2465335 TGTCACTCATGCCAGTTAGATAAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGTCTAGTTGT
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
*
2465400 GCATTTGACAAAAAGG
66 GCACTTGACAAAAAGG
* **
2465416 TGTCAATCATGTTAGTTAGATGAAAGGTTAAATGTCTTTGAGTAAAAGA
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
2465465 CTAGATGTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 116 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
GCACTTGACAAAAAGG
Found at i:2465653 original size:46 final size:46
Alignment explanation
Indices: 2465478--2465669 Score: 257
Period size: 45 Copynumber: 4.2 Consensus size: 46
2465468 GATGTATAAC
*
2465478 AATGTATAATAT-TGTATAAAAGGCATGAAAGGATGTCATAAATGA
1 AATGTATAATATGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
2465523 AATATATAAT-TGTGTATAAAAGGAATGAAAGGATGCCATAAATGA
1 AATGTATAATATGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
2465568 AATGTATAATA-GTGTATAAAAGGCATGAAAGGTTGCCATAAATGA
1 AATGTATAATATGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * * *
2465613 AATGTATAATAGTGTGTA-AAAAGGCATTAACGGTTACCATAAATGAA
1 AATGTATAATA-TGTGTATAAAAGGCATGAAAGGATGCCATAAATG-A
*
2465660 AATGCATAAT
1 AATGTATAAT
2465670 GGTGCATTAT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.01
45 92 0.70
46 24 0.18
47 15 0.11
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (46 bp):
AATGTATAATATGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:2466292 original size:2 final size:2
Alignment explanation
Indices: 2466287--2466329 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2466277 AATAAAAAAT
*
2466287 TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2466328 TA
1 TA
2466330 ATAAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2469402 original size:32 final size:32
Alignment explanation
Indices: 2469361--2469425 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2469351 TTCATGCATG
*
2469361 CAGTGTTTGAGGGAGATTGTCGATCAGTGATT
1 CAGTGTTTGAGGGAGATTGTCGATCAGTAATT
2469393 CAGTGTTTGAGGGAGATTGTCGATCAGTAATT
1 CAGTGTTTGAGGGAGATTGTCGATCAGTAATT
2469425 C
1 C
2469426 TTAAAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34
Consensus pattern (32 bp):
CAGTGTTTGAGGGAGATTGTCGATCAGTAATT
Found at i:2470275 original size:24 final size:25
Alignment explanation
Indices: 2470238--2470297 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
2470228 AACTTTTCAC
2470238 TTATAATATAAATACTTAA-A-ATATT
1 TTAT-ATATAAATA-TTAATACATATT
2470263 TTATATATAAATATTAATATCATATT
1 TTATATATAAATATTAATA-CATATT
2470289 TTA-ATATAA
1 TTATATATAA
2470298 TTTTAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 10 0.31
25 10 0.31
26 8 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATATATAAATATTAATACATATT
Found at i:2470294 original size:13 final size:12
Alignment explanation
Indices: 2470258--2470304 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2470248 AATACTTAAA
2470258 ATATTTTATATAT
1 ATATTTTA-ATAT
* *
2470271 AAATATTAATAT
1 ATATTTTAATAT
2470283 CATATTTTAATAT
1 -ATATTTTAATAT
2470296 A-ATTTTAAT
1 ATATTTTAAT
2470305 GAATATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 8 0.28
12 5 0.17
13 16 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTTAATAT
Found at i:2470330 original size:42 final size:44
Alignment explanation
Indices: 2470264--2470346 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 44
2470254 TAAAATATTT
2470264 TATATATAAATATTAATATCATATTTTAAT-ATAATTTTAATGAA
1 TATATATAAATATTAATATCATA-TTTAATAATAATTTTAATGAA
* * *
2470308 TATAT-TAATTATTAA-ATTATATTTATTAATAATTTTAAT
1 TATATATAAATATTAATATCATATTTAATAATAATTTTAAT
2470347 ATTATAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 5 0.14
42 16 0.46
43 9 0.26
44 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (44 bp):
TATATATAAATATTAATATCATATTTAATAATAATTTTAATGAA
Found at i:2470356 original size:8 final size:8
Alignment explanation
Indices: 2470331--2470416 Score: 54
Period size: 8 Copynumber: 10.9 Consensus size: 8
2470321 AAATTATATT
2470331 TATTAATAA
1 TATT-ATAA
2470340 T-TT-TAA
1 TATTATAA
2470346 TATTATAA
1 TATTATAA
*
2470354 TATTATAT
1 TATTATAA
*
2470362 TTTTA-AA
1 TATTATAA
*
2470369 TGTTATAA
1 TATTATAA
* *
2470377 TAATATATT
1 TATTATA-A
*
2470386 TAATTATAT
1 T-ATTATAA
*
2470395 TATTATAG
1 TATTATAA
2470403 TA-TATAA
1 TATTATAA
2470410 TATTATA
1 TATTATA
2470417 TTTTATATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
6 4 0.07
7 13 0.21
8 35 0.57
9 4 0.07
10 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (8 bp):
TATTATAA
Found at i:2470357 original size:23 final size:22
Alignment explanation
Indices: 2470313--2470416 Score: 65
Period size: 23 Copynumber: 4.7 Consensus size: 22
2470303 ATGAATATAT
*
2470313 TAATTATTAA-ATTATATTTATTAA
1 TAATT-TTAATATTATA-ATATT-A
2470337 TAATTTTAATATTATAATATTA
1 TAATTTTAATATTATAATATTA
* * *
2470359 TATTTTTAAATGTTATAATAATA
1 TAATTTT-AATATTATAATATTA
*
2470382 T-A-TTT-A-ATTATATTATTA
1 TAATTTTAATATTATAATATTA
* *
2470400 TAGTATATAATATTATA
1 TAAT-TTTAATATTATA
2470417 TTTTATATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
18 10 0.16
19 1 0.02
21 5 0.08
22 8 0.13
23 28 0.44
24 11 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TAATTTTAATATTATAATATTA
Found at i:2470395 original size:33 final size:33
Alignment explanation
Indices: 2470355--2470419 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2470345 ATATTATAAT
*
2470355 ATTATATTTTTAAATGT-TATAATAATATATTTA
1 ATTATATTATTAAA-GTATATAATAATATATTTA
* *
2470388 ATTATATTATTATAGTATATAATATTATATTT
1 ATTATATTATTAAAGTATATAATAATATATTT
2470420 TATATTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
ATTATATTATTAAAGTATATAATAATATATTTA
Found at i:2470574 original size:14 final size:15
Alignment explanation
Indices: 2470555--2470596 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2470545 TTATTTTTAA
2470555 TATTATTATAAT-AG
1 TATTATTATAATAAG
*
2470569 TATTATTTTAATAAG
1 TATTATTATAATAAG
*
2470584 TAATTAATATAAT
1 T-ATTATTATAAT
2470597 TAATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 3 0.13
16 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
TATTATTATAATAAG
Found at i:2470623 original size:42 final size:42
Alignment explanation
Indices: 2470571--2470658 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
2470561 TATAATAGTA
** * *
2470571 TTATTTTAATAAGTAATTAATATAATTAATAATATATTATTC
1 TTATTTTAATAAACAATGAATAAAATTAATAATATATTATTC
* * *
2470613 TTATTTTAATAAACAATGAATAAAATTTATAATATTTTATTT
1 TTATTTTAATAAACAATGAATAAAATTAATAATATATTATTC
2470655 TTAT
1 TTAT
2470659 AAAATAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (42 bp):
TTATTTTAATAAACAATGAATAAAATTAATAATATATTATTC
Found at i:2470730 original size:14 final size:15
Alignment explanation
Indices: 2470674--2470731 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 15
2470664 AAAATAATCT
*
2470674 TAATATTTAAAAACAA
1 TAATATTTAAATA-AA
2470690 TAAT-TTT-AAT-AA
1 TAATATTTAAATAAA
*
2470702 TAATATTGAAATAAA
1 TAATATTTAAATAAA
2470717 TAAT-TTTAAATAAA
1 TAATATTTAAATAAA
2470731 T
1 T
2470732 TATTATAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 6 0.17
13 2 0.06
14 15 0.42
15 9 0.25
16 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TAATATTTAAATAAA
Found at i:2471899 original size:29 final size:29
Alignment explanation
Indices: 2471857--2471927 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
2471847 CATTTTTCAT
*
2471857 ATCTTATATTCCTTCAACCAAACACTGTA
1 ATCTTACATTCCTTCAACCAAACACTGTA
2471886 ATCTTACATTCCTTCAACCAAACACTGTA
1 ATCTTACATTCCTTCAACCAAACACTGTA
2471915 ATCTTACATTCCT
1 ATCTTACATTCCT
2471928 GCCAAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (29 bp):
ATCTTACATTCCTTCAACCAAACACTGTA
Found at i:2476921 original size:13 final size:13
Alignment explanation
Indices: 2476903--2476936 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2476893 TGCATCATAA
2476903 ATTTATGACACGC
1 ATTTATGACACGC
*
2476916 ATTTATGACACGT
1 ATTTATGACACGC
2476929 ATTTATGA
1 ATTTATGA
2476937 TGCTCATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:2477108 original size:2 final size:2
Alignment explanation
Indices: 2477101--2477141 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2477091 TGTCGTAAAT
2477101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2477142 TGTAGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2482285 original size:16 final size:15
Alignment explanation
Indices: 2482259--2482288 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2482249 TGTTTTGGAC
2482259 AAAAGGAAAAAGGGA
1 AAAAGGAAAAAGGGA
2482274 AAAAGAGAAAAAGGG
1 AAAAG-GAAAAAGGG
2482289 GAAGCATGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAAGGAAAAAGGGA
Found at i:2483961 original size:23 final size:24
Alignment explanation
Indices: 2483925--2483970 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
2483915 TACTTTATTA
2483925 TTTTTAATATAAATATATATATAC
1 TTTTTAATATAAATATATATATAC
*
2483949 TTTTTAATA-AAATTTATATATA
1 TTTTTAATATAAATATATATATA
2483971 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTAATATAAATATATATATAC
Found at i:2483966 original size:25 final size:25
Alignment explanation
Indices: 2483925--2483989 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
2483915 TACTTTATTA
*
2483925 TTTTTAATATAAA--TATATATATAC
1 TTTTTAATA-AAATTTATATATAAAC
*
2483949 TTTTTAATAAAATTTATATATAAAT
1 TTTTTAATAAAATTTATATATAAAC
*
2483974 TTTTTTATAAAATTTA
1 TTTTTAATAAAATTTA
2483990 AAAGATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.08
24 9 0.25
25 24 0.67
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTAATAAAATTTATATATAAAC
Found at i:2483976 original size:23 final size:24
Alignment explanation
Indices: 2483926--2483976 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2483916 ACTTTATTAT
**
2483926 TTTTAATATAAATATATATATACT
1 TTTTAATATAAATATATATATAAA
*
2483950 TTTTAATA-AAATTTATATATAAA
1 TTTTAATATAAATATATATATAAA
2483973 TTTT
1 TTTT
2483977 TTTATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAATATAAATATATATATAAA
Found at i:2483997 original size:26 final size:25
Alignment explanation
Indices: 2483949--2484000 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2483939 ATATATATAC
* *
2483949 TTTTTAATAAAATTTATATATAAAT
1 TTTTTAATAAAATTTAAAGATAAAT
*
2483974 TTTTTTATAAAATTTAAAAGATAAAT
1 TTTTTAATAAAATTT-AAAGATAAAT
2484000 T
1 T
2484001 AGTAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTTTAATAAAATTTAAAGATAAAT
Found at i:2507523 original size:21 final size:21
Alignment explanation
Indices: 2507484--2507523 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2507474 TACTATATAT
* *
2507484 TTAATTTAAGTATTTATCTTC
1 TTAAATTAAGTATTAATCTTC
*
2507505 TTAAATTAAGTGTTAATCT
1 TTAAATTAAGTATTAATCT
2507524 CATCCTTCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
TTAAATTAAGTATTAATCTTC
Found at i:2509923 original size:23 final size:23
Alignment explanation
Indices: 2509888--2509954 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
2509878 GCCTCACTAT
*
2509888 TCGAGTTTGAGCTCGATTCAAGC
1 TCGACTTTGAGCTCGATTCAAGC
* *
2509911 TTGACTTTGAGCTCAATTCAAGC
1 TCGACTTTGAGCTCGATTCAAGC
* *
2509934 TCGACTTTAAACTCGATTCAA
1 TCGACTTTGAGCTCGATTCAA
2509955 TCTCAAAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (23 bp):
TCGACTTTGAGCTCGATTCAAGC
Found at i:2511496 original size:7 final size:7
Alignment explanation
Indices: 2511484--2511580 Score: 72
Period size: 7 Copynumber: 13.9 Consensus size: 7
2511474 AATCAAATTA
2511484 AGGGTTT
1 AGGGTTT
2511491 AGGGTTT
1 AGGGTTT
**
2511498 AAAGTTT
1 AGGGTTT
*
2511505 AGGATTT
1 AGGGTTT
2511512 AGGGTTT
1 AGGGTTT
*
2511519 AAGGTTT
1 AGGGTTT
* *
2511526 ATGGCTT
1 AGGGTTT
* *
2511533 AAGGCTT
1 AGGGTTT
2511540 -GAGGTTT
1 AG-GGTTT
*
2511547 AGAGTTT
1 AGGGTTT
2511554 -GTGGTTT
1 AG-GGTTT
2511561 AGGGTTT
1 AGGGTTT
2511568 AGGGTTT
1 AGGGTTT
*
2511575 AAGGTT
1 AGGGTT
2511581 CATTGCAAAG
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
6 1 0.01
7 68 0.96
8 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.35, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:2511580 original size:21 final size:21
Alignment explanation
Indices: 2511485--2511580 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
2511475 ATCAAATTAA
*
2511485 GGGTTTAGGGTTTAAAGTTTA
1 GGGTTTAGGGTTTAAGGTTTA
*
2511506 GGATTTAGGGTTTAAGGTTTA
1 GGGTTTAGGGTTTAAGGTTTA
* * * * *
2511527 TGGCTTAAGGCTTGAGGTTTA
1 GGGTTTAGGGTTTAAGGTTTA
* *
2511548 GAGTTT-GTGGTTTAGGGTTTA
1 GGGTTTAG-GGTTTAAGGTTTA
*
2511569 GGGTTTAAGGTT
1 GGGTTTAGGGTT
2511581 CATTGCAAAG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (21 bp):
GGGTTTAGGGTTTAAGGTTTA
Found at i:2512999 original size:16 final size:16
Alignment explanation
Indices: 2512978--2513030 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
2512968 CGCGTATCCG
2512978 TAAATCGCAACGATAA
1 TAAATCGCAACGATAA
*
2512994 TAAATCGCAACGAGAA
1 TAAATCGCAACGATAA
2513010 TCTGTAAATCGCAACGATAA
1 ----TAAATCGCAACGATAA
2513030 T
1 T
2513031 CCGTAAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 16 0.52
20 15 0.48
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (16 bp):
TAAATCGCAACGATAA
Found at i:2513017 original size:76 final size:77
Alignment explanation
Indices: 2512937--2513104 Score: 225
Period size: 76 Copynumber: 2.2 Consensus size: 77
2512927 AAGCGTATCC
* * *
2512937 GTAAATCGCAATGCG-T-ATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA-TAAAT
1 GTAAATCGCAA--CGATAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAACTAAAT
2512999 CGCAACGAGAATCT
64 CGCAACGAGAATCT
*
2513013 GTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
1 GTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAA--C-TAAA
2513078 TCGCAACGAGAATCT
63 TCGCAACGAGAATCT
*
2513093 GTAAATCACAAC
1 GTAAATCGCAAC
2513105 ACTGAAATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
74 2 0.02
75 1 0.01
76 48 0.59
80 30 0.37
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (77 bp):
GTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAACTAAATCG
CAACGAGAATCT
Done.