Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold179
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: 2991183
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 65816 characters in sequence are not A, C, G, or T
File 18 of 18
Found at i:2799544 original size:13 final size:13
Alignment explanation
Indices: 2799526--2799550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2799516 ACAATACTTA
2799526 TGTATCGATACAT
1 TGTATCGATACAT
2799539 TGTATCGATACA
1 TGTATCGATACA
2799551 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2799548 original size:32 final size:32
Alignment explanation
Indices: 2799507--2799569 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2799497 TAGCTAATTA
*
2799507 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2799539 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2799570 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2799652 original size:21 final size:21
Alignment explanation
Indices: 2799626--2799682 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2799616 ACATTTGGGG
2799626 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2799647 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2799668 ATGTATCGATACATT
1 ATGTATCGATACATT
2799683 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2799693 original size:1 final size:1
Alignment explanation
Indices: 2799687--2799731 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
2799677 TACATTTAAA
**
2799687 TTTTTTTTTTTTTTTTTTTTTCATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2799732 CAAACACTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.02, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:2799714 original size:21 final size:21
Alignment explanation
Indices: 2799689--2799728 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2799679 CATTTAAATT
2799689 TTTTTTTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTTTTTTCA
2799710 TTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTT
2799729 TTTCAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.95
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTTTTCA
Found at i:2799715 original size:22 final size:22
Alignment explanation
Indices: 2799688--2799729 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2799678 ACATTTAAAT
2799688 TTTTTTTTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTTTTTTTCA
2799710 TTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
2799730 TTCAAACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.02, C:0.02, G:0.00, T:0.95
Consensus pattern (22 bp):
TTTTTTTTTTTTTTTTTTTTCA
Found at i:2799716 original size:23 final size:23
Alignment explanation
Indices: 2799686--2799730 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2799676 ATACATTTAA
2799686 ATTTTTTTTTTTTTTTTTTTTTC
1 ATTTTTTTTTTTTTTTTTTTTTC
2799709 ATTTTTTTTTTTTTTTTTTTTT
1 ATTTTTTTTTTTTTTTTTTTTT
2799731 TCAAACACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.93
Consensus pattern (23 bp):
ATTTTTTTTTTTTTTTTTTTTTC
Found at i:2799719 original size:24 final size:24
Alignment explanation
Indices: 2799687--2799733 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2799677 TACATTTAAA
2799687 TTTTTTTTTTTTTTTTTTTTTCAT
1 TTTTTTTTTTTTTTTTTTTTTCAT
2799711 TTTTTTTTTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTTTTTTTTCA
2799734 AACACTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.04, G:0.00, T:0.91
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTTTCAT
Found at i:2800413 original size:55 final size:55
Alignment explanation
Indices: 2800327--2801169 Score: 1316
Period size: 55 Copynumber: 15.3 Consensus size: 55
2800317 ATAAATTGTA
* * * * * *
2800327 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2800382 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2800437 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2800492 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2800547 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2800602 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2800657 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2800712 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2800767 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2800822 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2800877 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2800932 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2800987 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2801042 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2801097 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2801152 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
2801170 AAAAAGCGGA
Statistics
Matches: 743, Mismatches: 24, Indels: 42
0.92 0.03 0.05
Matches are distributed among these distances:
53 4 0.01
54 22 0.03
55 693 0.93
56 20 0.03
57 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2802155 original size:1 final size:1
Alignment explanation
Indices: 2802151--2802208 Score: 80
Period size: 1 Copynumber: 58.0 Consensus size: 1
2802141 CTTTTCTCTC
* * * *
2802151 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2802209 GAAGAGAAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (1 bp):
T
Found at i:2814790 original size:105 final size:104
Alignment explanation
Indices: 2814662--2815006 Score: 272
Period size: 105 Copynumber: 3.3 Consensus size: 104
2814652 CCGATGAAAT
* * *
2814662 AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
*
2814727 TATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAA
66 TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * * * * *
2814766 AACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGA
1 AA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
* * * * * ** *
2814830 GTATCCCCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-T
65 GTAT-CCC-C-G-ATTAAAGGAGAAATTGGTGT-T--CTGAAAATAA
* *
2814873 AACGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTT
1 AACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGAGTT
* ** * *
2814938 GGAGTATCCCCGATTATA-GA-AAATTAATGTTTTGAAAGTAA
62 GGAGTATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * *
2814979 AATCGGAGTTGGAATATCCTCGATTGTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG
2815007 GAGAATTGAG
Statistics
Matches: 180, Mismatches: 43, Indels: 33
0.70 0.17 0.13
Matches are distributed among these distances:
104 27 0.15
105 43 0.24
106 30 0.17
107 33 0.18
108 16 0.09
109 1 0.01
110 4 0.02
111 26 0.14
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (104 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
Found at i:2814827 original size:51 final size:51
Alignment explanation
Indices: 2814667--2814837 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2814657 GAAATAACGA
* * *
2814667 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2814719 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2814772 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2814823 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2814838 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2814883 original size:27 final size:28
Alignment explanation
Indices: 2814820--2814895 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2814810 AAAATAAAGT
*
2814820 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2814848 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2814875 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2814896 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2817384 original size:13 final size:13
Alignment explanation
Indices: 2817366--2817391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2817356 ACAAAGATCC
2817366 ATGTATCGATACA
1 ATGTATCGATACA
2817379 ATGTATCGATACA
1 ATGTATCGATACA
2817392 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2817387 original size:33 final size:33
Alignment explanation
Indices: 2817345--2817411 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2817335 AAAATTTCCA
***
2817345 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2817378 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2817411 A
1 A
2817412 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2817455 original size:19 final size:18
Alignment explanation
Indices: 2817431--2817498 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2817421 CAGTAGCTAA
2817431 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2817450 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2817465 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2817482 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2817499 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2817471 original size:13 final size:13
Alignment explanation
Indices: 2817453--2817477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2817443 ACAATACTTA
2817453 TGTATCGATACAT
1 TGTATCGATACAT
2817466 TGTATCGATACA
1 TGTATCGATACA
2817478 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2817475 original size:32 final size:32
Alignment explanation
Indices: 2817434--2817496 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2817424 TAGCTAATTA
*
2817434 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2817466 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2817497 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2817578 original size:21 final size:21
Alignment explanation
Indices: 2817554--2817610 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2817544 CATTTGTAGG
2817554 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2817575 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2817596 ATGTATCGATACATT
1 ATGTATCGATACATT
2817611 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2817621 original size:1 final size:1
Alignment explanation
Indices: 2817615--2817667 Score: 79
Period size: 1 Copynumber: 53.0 Consensus size: 1
2817605 TACATTTAAA
***
2817615 TTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2817668 CAAACACTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:2817655 original size:26 final size:26
Alignment explanation
Indices: 2817619--2817670 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2817609 TTTAAATTTT
2817619 TTTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTTCAA
2817645 TTTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTTCAA
2817671 ACACTTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (26 bp):
TTTTTTTTTTTTTTTTTTTTTTTCAA
Found at i:2818392 original size:20 final size:20
Alignment explanation
Indices: 2818367--2818421 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
2818357 TTTTACCCAG
2818367 ATGTATCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
2818387 ATGTATCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
2818407 ATGTATCGATACATT
1 ATGTATCGATACATT
2818422 CAAGCATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCA
Found at i:2821108 original size:80 final size:79
Alignment explanation
Indices: 2820772--2821130 Score: 367
Period size: 79 Copynumber: 4.6 Consensus size: 79
2820762 TCATTCATGT
* * * * * *
2820772 TTTTATTTCTAAAATACCGA-TTTTCTACCATCGGGTATACTCCAACCC-GTTATTTTTGAGAGG
1 TTTTATTTCTAAAACATCGATTTTTC-ACAATCGGGGATACTCCAACCCTATTATTTTTGAAAGG
* **
2820835 ATAATCCAACCTTGG
65 ATACTCCAACCCCGG
* * * **
2820850 TTTTACTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCATTATTTTTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTTGAAAGGA
**
2820915 TACTTTAA-CCC--
66 TACTCCAACCCCGG
* * * *
2820926 ---TAGTTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCGACCCTATTATTTTCG-AGGG
1 TTTTA-TTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTTGAAAGG
*
2820987 AATACTCCAACACCGG
65 -ATACTCCAACCCCGG
* * * * *
2821003 CTTCATTTCTAAAACATTGATTTTTCATAATCGGGGATGCTCCAACCCTATTATTTTTGAAAAGG
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTTG-AAAGG
**
2821068 ATACTCCAACCCCAA
65 ATACTCCAACCCCGG
2821083 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
2821131 CGTTATTTCC
Statistics
Matches: 230, Mismatches: 39, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
73 5 0.02
74 55 0.24
75 2 0.01
78 37 0.16
79 72 0.31
80 56 0.24
81 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTTGAAAGGA
TACTCCAACCCCGG
Found at i:2828986 original size:13 final size:13
Alignment explanation
Indices: 2828968--2828997 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2828958 ACAATTCTTC
*
2828968 ATGTATCGATACA
1 ATGTATCAATACA
2828981 ATGTATCAATACA
1 ATGTATCAATACA
2828994 ATGT
1 ATGT
2828998 TCCCTGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:2829087 original size:19 final size:19
Alignment explanation
Indices: 2829042--2829097 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
2829032 CTGCCAGTTT
2829042 CATGTATCGATACAATCGAG
1 CATGTATCGATACAAT-GAG
*
2829062 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
2829081 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2829098 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:2831511 original size:21 final size:21
Alignment explanation
Indices: 2831470--2831513 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2831460 GATGTGAAAA
* *
2831470 TGAAGAATTTTAAAAAGGATT
1 TGAAGAAATTGAAAAAGGATT
2831491 TGAAGAAATTGAAGAAA-GATT
1 TGAAGAAATTGAA-AAAGGATT
2831512 TG
1 TG
2831514 TTAAGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (21 bp):
TGAAGAAATTGAAAAAGGATT
Found at i:2837724 original size:20 final size:20
Alignment explanation
Indices: 2837699--2837751 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2837689 GTTGGGCATA
*
2837699 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-CC
2837719 ATGTATCGATACAATGTCCC
1 ATGTATCGATACAATGTCCC
2837739 ATGTATCGATACA
1 ATGTATCGATACA
2837752 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:2837806 original size:20 final size:19
Alignment explanation
Indices: 2837780--2837833 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
2837770 CTACCAGTTT
2837780 CATGTATCGATGCAATTGAG
1 CATGTATCGATGCAA-TGAG
* **
2837800 TATGTATCGATATAATGAG
1 CATGTATCGATGCAATGAG
2837819 CATGTATCGATGCAA
1 CATGTATCGATGCAA
2837834 AGTATAATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (19 bp):
CATGTATCGATGCAATGAG
Found at i:2848165 original size:61 final size:61
Alignment explanation
Indices: 2848070--2848505 Score: 448
Period size: 61 Copynumber: 7.0 Consensus size: 61
2848060 AAATTTTTGT
* *
2848070 CCTTTTAGTCTTCAAAGAGCAGGACG-TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
2848131 CCTTTTGGTCTTCAAAGAGTAGGATGCTTTTTCCTTTTAAAGCCTATACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
2848192 CCTTTCAGTCCTTAAAGAGCATGACGCCTTTTCCTTTTAAATCCCACACAAGTTGGTGGTA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
2848253 CCTTTCAGTCCTCAAAAAATAGGAC-ATCTTTTCCTTTTAAAGCCCATACAATTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
2848314 CCTTTCAGTCCTCAAAGAGTAGGATGC-TTTTCCTTCTTAGAGCCCACATAAGTTGGTAGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTTTCCTT-TTAAAGCCCACACAAGTTGGTGGCA
** * * *
2848375 CCTTTTAGTCCTCAAAGAACAGGACACTTCCTTT-CTTTTAAAGCCCGCACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTT--TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
2848437 CCTTCTAGTCCTCAAAGAGTAGGACGCCTCTCTCTTTTTCCATTTTAAAGCCCACACAAGTTGGT
1 CCTTTTAGTCCTCAAAGAGTAGGACG-------CTTTTTCC-TTTTAAAGCCCACACAAGTTGGT
2848502 GGCA
58 GGCA
2848506 TCTATCTACT
Statistics
Matches: 306, Mismatches: 53, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
60 8 0.03
61 216 0.71
62 44 0.14
63 3 0.01
64 3 0.01
67 3 0.01
68 1 0.00
69 28 0.09
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (61 bp):
CCTTTTAGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2849021 original size:20 final size:20
Alignment explanation
Indices: 2848996--2849043 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2848986 TTTGCATCAC
*
2848996 TACATTCTTTATTGTATCGA
1 TACATTCTTCATTGTATCGA
2849016 TACATTCTTCATTGTATCGA
1 TACATTCTTCATTGTATCGA
2849036 TACATTCT
1 TACATTCT
2849044 GGGTTTCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (20 bp):
TACATTCTTCATTGTATCGA
Found at i:2851667 original size:157 final size:157
Alignment explanation
Indices: 2851410--2851700 Score: 354
Period size: 157 Copynumber: 1.9 Consensus size: 157
2851400 TCATTCATGT
* * * * *
2851410 TTTTATTTCTAAAATACCGATTTTTCACTATCGGGGATACTCCAATCACGTTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACCGATTTTTCACTATCGGGGATACTCCAACCACGTTATTTTCGAAGGAA
* * * *
2851475 TACTCAAATTCCGATTTTATTTTTAAAACACCAATTTTTTATAATCG-GAGATACTCCAACCCCA
66 TACTCAAATCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGAG-GATACTCCAACCCCA
*
2851539 TTTTTTAGAGGGGATACTTTAACCCAGA
130 ATTTTTAGAGGGGATACTTTAACCCAGA
** * * *
2851567 TTTTATTTCCAAAACATTGATTTTTCA-TAATCGGGGATACTCCAGCCCCGTTATTTTTGAAGGA
1 TTTTATTTCCAAAACACCGATTTTTCACT-ATCGGGGATACTCCAACCACGTTATTTTCGAAGGA
* * * * *
2851631 ATACTCCAA-CCCTGGTTTTATTTCTAAAAGATCAATTTTTCACAATCGAGGATATTCCAACCCC
65 ATACTCAAATCCC-GATTTTATTTCTAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCC
2851695 AATTTT
129 AATTTT
2851701 ATTTTCAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
156 3 0.03
157 107 0.96
158 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (157 bp):
TTTTATTTCCAAAACACCGATTTTTCACTATCGGGGATACTCCAACCACGTTATTTTCGAAGGAA
TACTCAAATCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCAA
TTTTTAGAGGGGATACTTTAACCCAGA
Found at i:2851669 original size:79 final size:78
Alignment explanation
Indices: 2851410--2851694 Score: 277
Period size: 79 Copynumber: 3.6 Consensus size: 78
2851400 TCATTCATGT
* * * * *
2851410 TTTTATTTCTAAAATACCGATTTTTCACT-ATCGGGGATACTCCAATCACGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACACCAATTTTTCA-TAATCGGGGATACTCCAACCCCGTTATTTTAGAGGGG
*
2851474 ATACTCAAATTCCGA
65 ATACTCAAA-CCCGA
* * * *
2851489 TTTTATTTTTAAAACACCAATTTTTTATAATCGGAGATACTCCAACCCCATT-TTTTAGAGGGGA
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTAGAGGGGA
**
2851553 TACTTTAACCCAGA
66 TACTCAAACCC-GA
* *** * * * *
2851567 TTTTATTTCCAAAACATTGATTTTTCATAATCGGGGATACTCCAGCCCCGTTATTTTTGAAGGAA
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTAGAGGGGA
* *
2851632 TACTCCAACCCTGG
66 TACTCAAACCC-GA
* * * * *
2851646 TTTTATTTCTAAAAGATCAATTTTTCACAATCGAGGATATTCCAACCCC
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCC
2851695 AATTTTATTT
Statistics
Matches: 167, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
77 2 0.01
78 63 0.38
79 102 0.61
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (78 bp):
TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTAGAGGGGA
TACTCAAACCCGA
Found at i:2851701 original size:51 final size:51
Alignment explanation
Indices: 2851631--2851744 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
2851621 TTTTGAAGGA
*** *
2851631 ATACTCCAACCCTGGTTTTA-TTTCTAAAAGATCAATTTTTCACAATCGAGG
1 ATACTCCAACCCCAATTTTATTTTC-AAAACATCAATTTTTCACAATCGAGG
* * * * *
2851682 ATATTCCAACCCCAATTTTATTTTCAAAACATCGATTTTTCACCATTGGGG
1 ATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCACAATCGAGG
2851733 ATACTCCAACCC
1 ATACTCCAACCC
2851745 TGTTATTTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 48 0.92
52 4 0.08
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
ATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCACAATCGAGG
Found at i:2851798 original size:130 final size:131
Alignment explanation
Indices: 2851561--2851802 Score: 301
Period size: 130 Copynumber: 1.9 Consensus size: 131
2851551 GATACTTTAA
* * * *
2851561 CCCAGATTTTATTTCCAAAACATTGATTTTTCATAATCGGGGATACTCCAGCCCCGTTATTTTTG
1 CCCAGATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCG
* ** * *
2851626 AAGGAATACTCCAACCCTGGTTTTATTTCTAAAAGATCAATTTTTCACAATCGAGGATATTCCAA
66 AAGGAACACTCCAACCCTCATTTTATTTCCAAAAGATAAATTTTTCACAATCGAGGATATTCCAA
2851691 C
131 C
* * * *
2851692 CCCA-ATTTTATTTTCAAAACATCGATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTTCG
1 CCCAGATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCG
* * *
2851756 AGGGGACACTCCAACCC-CATTTT-TTCTCCAAAATATTAAATTTTTCA
66 AAGGAACACTCCAACCCTCATTTTATT-TCCAAAAGA-TAAATTTTTCA
2851803 TCGGGGAATG
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 2 0.02
129 11 0.12
130 76 0.82
131 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (131 bp):
CCCAGATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCG
AAGGAACACTCCAACCCTCATTTTATTTCCAAAAGATAAATTTTTCACAATCGAGGATATTCCAA
C
Found at i:2860711 original size:19 final size:20
Alignment explanation
Indices: 2860684--2860737 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
2860674 ACATTATGCT
* *
2860684 TTGTTTCGATACATGTTC-A
1 TTGTATCGATACATGCTCAA
* *
2860703 TTGTATCGATTCATACTCAA
1 TTGTATCGATACATGCTCAA
2860723 TTGTATCGATACATG
1 TTGTATCGATACATG
2860738 AAACTAGTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:2870356 original size:51 final size:50
Alignment explanation
Indices: 2870275--2870404 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 50
2870265 CAGTATCCCC
2870275 TCAAAAAT--AACGGGGTTGGAGTATCCCCGATGGTGAAAAATCTG-TGTT
1 TCAAAAATAAAACGGGGTTGGAGTATCCCCGATGGTGAAAAATC-GATGTT
* * *
2870323 TCAGAAATAAAATCGGGGTTGGAGTATCTCCGATGGTGGAAAATCGATGTT
1 TCAAAAATAAAA-CGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTT
* *
2870374 TTAAAAATAAAACTGGGGTTCGAGTATCCCC
1 TCAAAAATAAAAC-GGGGTTGGAGTATCCCC
2870405 TGACAAATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
48 7 0.10
50 4 0.06
51 59 0.84
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (50 bp):
TCAAAAATAAAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTT
Found at i:2870439 original size:79 final size:78
Alignment explanation
Indices: 2870339--2870622 Score: 320
Period size: 79 Copynumber: 3.6 Consensus size: 78
2870329 ATAAAATCGG
* * *
2870339 GGTTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTAAAAATAAAA-CTGGGGTTCGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAAAAATAAAATC-GGGGTTGGAGTATCC
2870403 CCTGACAAATAACGA
65 CCTGA-AAATAACGA
* ** * ** *
2870418 GGTTGAAGTATCCCTAATGGTGAAAAATTGATGTTTTGGAAATAAAATCAGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAAAAATAAAATCGGGGTTGGAGTATCCC
2870483 CTTGAAAATAACGA
66 C-TGAAAATAACGA
* * * * *
2870497 GGCTGGAGTATCCCCGATGGTGGAAAATTG-GGATTTTGAAAATAAAATCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCGATG-TTTTAAAAATAAAATCGGGGTTGGAGTATCC
* *
2870561 TCTTGAAAATAACGG
65 -CCTGAAAATAACGA
* * * *
2870576 GGTTGGAGTATCCCCGATTGTGAAAAATCTATATTTTAGAAATAAAA
1 GGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAAAAATAAAA
2870623 CATCAATGAA
Statistics
Matches: 171, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
79 165 0.96
80 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAAAAATAAAATCGGGGTTGGAGTATCCC
CTGAAAATAACGA
Found at i:2870444 original size:130 final size:129
Alignment explanation
Indices: 2870212--2870480 Score: 389
Period size: 130 Copynumber: 2.1 Consensus size: 129
2870202 TCCCTCAAAA
** *
2870212 TTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTGGAAATAAATCGGGGTTGCAGTATCCCCTC
1 TTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACGGGGTTGCAGTATCCCCTC
* * * *
2870277 AAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCTG-TGTTTCAGAAATAAAATCGGGG
66 AAAAATAACGAGGTTGAAGTATCCCCAATGGTGAAAAAT-TGATGTTTCAGAAATAAAATCAGGG
2870341 TTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACTGGGGTT-CGAGTATCCCC
1 TTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTAAAAATAAAAC-GGGGTTGC-AGTATCCCC
* * * **
2870405 TGACAAATAACGAGGTTGAAGTATCCCTAATGGTGAAAAATTGATGTTTTGGAAATAAAATCAGG
64 TCAAAAATAACGAGGTTGAAGTATCCCCAATGGTGAAAAATTGATGTTTCAGAAATAAAATCAGG
2870470 G
129 G
2870471 TTGGAGTATC
1 TTGGAGTATC
2870481 CCCTTGAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
129 46 0.37
130 79 0.63
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (129 bp):
TTGGAGTATCTCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACGGGGTTGCAGTATCCCCTC
AAAAATAACGAGGTTGAAGTATCCCCAATGGTGAAAAATTGATGTTTCAGAAATAAAATCAGGG
Found at i:2875924 original size:21 final size:20
Alignment explanation
Indices: 2875877--2875930 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2875867 CATTTTAGGC
2875877 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
2875897 ATGTATCGATATATTGC-CTT
1 ATGTATCGATACATT-CACTT
2875917 ATTGTATCGATACA
1 A-TGTATCGATACA
2875931 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:2875987 original size:17 final size:17
Alignment explanation
Indices: 2875965--2875997 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2875955 ACCATTAGGA
2875965 CCTTGTATCGATACATT
1 CCTTGTATCGATACATT
2875982 CCTTGTATCGATACAT
1 CCTTGTATCGATACAT
2875998 GTGGGCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (17 bp):
CCTTGTATCGATACATT
Found at i:2876972 original size:6 final size:7
Alignment explanation
Indices: 2876955--2876981 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2876945 TTCATTCGAT
2876955 TTTTTTC
1 TTTTTTC
2876962 TTTTTTC
1 TTTTTTC
2876969 TTTTTTC
1 TTTTTTC
2876976 TTTTTT
1 TTTTTT
2876982 TATGCATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:2889104 original size:159 final size:157
Alignment explanation
Indices: 2888565--2889170 Score: 622
Period size: 159 Copynumber: 3.8 Consensus size: 157
2888555 TATTTTATTT
*
2888565 TTTTA-TT-TTTTTG-AAAATATCATTTCATACCTTAATGGAAACCTGAAAAGATACAAAAATTT
1 TTTTATTTATTTTTGAAAAATATCATTTCATACCTTAATGGAAACCTGAAAAGATACGAAAA---
* * * *
2888627 TTTTTTTGAAATCTTTTATACCCTTACGGA-CCCTCATAGGAGTATAAAATATTAAAAAGATTAA
63 -GTTTTTGAAATCTTTTATACCCTTACGGATACC-CATAGGAATATAAAAGATTAAAAAGATTAA
* * *** * * * *
2888691 TGTTTCTTTCGGTTGTATA-AGTATTACTTTTA
126 TATTTATTTTAATTAT-TAGAGTGTTAATTTAA
* ** * * * *
2888723 TTTTATTTATTCATTTTCAAGAAATGCCTTTTTCATACCTTAAT-GAGACCCGAAAAGATATGAA
1 TTTTATTTA-T--TTTTGAA-AAATATC-ATTTCATACCTTAATGGAAACCTGAAAAGATACGAA
* * *
2888787 AAGTTTTT-AAGATCCTTTATACTCC-TACAGACACCCATAGGAATATAAAAGATTAAAAACG-T
61 AAGTTTTTGAA-ATCTTTTATAC-CCTTACGGATACCCATAGGAATATAAAAGATTAAAAA-GAT
* *
2888849 TAATATTTATTTTAATTATGAGAGTGTTAATTCAA
123 TAATATTTATTTTAATTATTAGAGTGTTAATTTAA
* * * *
2888884 TTTTATTTATTTTTGAAAAATATCATTTCGTACTTTAATAG-AAGCTCGAAAAGATACGAAAAGT
1 TTTTATTTATTTTTGAAAAATATCATTTCATACCTTAATGGAAACCT-GAAAAGATACGAAAAGT
* *
2888948 TTTTGAAATCTTTTATACCCTTACGGATACCCATAAGAATATAAAAGATTAAAAATGAATAATAT
65 TTTTGAAATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAGATTAAAAA-GATTAATAT
*
2889013 TTATTTTAATAATTAGAGTGTTAATTTAA
129 TTATTTTAATTATTAGAGTGTTAATTTAA
* *
2889042 TTTTTATTTATTTTTGAAAAATATCATTTCATACCTTAATGGAAACCTAAAAAGATATGAAAAG-
1 -TTTTATTTATTTTTGAAAAATATCATTTCATACCTTAATGGAAACCTGAAAAGATACGAAAAGT
* * * *
2889106 TTTTCAGAATCTTTTATACCCTTACGAATACCCATAGGAATATAAAAGATCAAAAAAATTAATAT
65 TTTTGA-AATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAGATTAAAAAGATTAATAT
2889171 GAAAATATCT
Statistics
Matches: 371, Mismatches: 56, Indels: 42
0.79 0.12 0.09
Matches are distributed among these distances:
156 16 0.04
157 68 0.18
158 57 0.15
159 100 0.27
160 8 0.02
161 75 0.20
162 5 0.01
163 4 0.01
164 1 0.00
165 23 0.06
166 14 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (157 bp):
TTTTATTTATTTTTGAAAAATATCATTTCATACCTTAATGGAAACCTGAAAAGATACGAAAAGTT
TTTGAAATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAGATTAAAAAGATTAATATTT
ATTTTAATTATTAGAGTGTTAATTTAA
Found at i:2889262 original size:28 final size:29
Alignment explanation
Indices: 2889226--2889284 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
2889216 CTTTTGCCTT
* * *
2889226 ATTTGCAATTTAGTCT-TAAATTTTCAAA
1 ATTTACAATTTAGCCTCTAAATATTCAAA
*
2889254 ATTTACAATTTCGCCTCTAAATATTCAAA
1 ATTTACAATTTAGCCTCTAAATATTCAAA
2889283 AT
1 AT
2889285 ATCACTCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTTACAATTTAGCCTCTAAATATTCAAA
Found at i:2890173 original size:14 final size:14
Alignment explanation
Indices: 2890146--2890206 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
2890136 GTAGTTTATT
* *
2890146 TTTTTTTCGATTTTG
1 TTTTTTTC-TTTTTA
2890161 TTTTTTTCTTTTTA
1 TTTTTTTCTTTTTA
* *
2890175 TTCTTTTCTTTGCTA
1 TTTTTTTCTTT-TTA
* *
2890190 TTTCTTTCTTCTTA
1 TTTTTTTCTTTTTA
2890204 TTT
1 TTT
2890207 GCTATTGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 19 0.51
15 18 0.49
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTTTTTCTTTTTA
Found at i:2890297 original size:26 final size:27
Alignment explanation
Indices: 2890243--2890302 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
2890233 CTCCTTTTAA
2890243 TGCAGCTGTTTCGATGACTTTCTTCAT
1 TGCAGCTGTTTCGATGACTTTCTTCAT
*
2890270 TGCAGCTGTTTC-ATTTA-TTTCTTCAT
1 TGCAGCTGTTTCGA-TGACTTTCTTCAT
2890296 TGCAGCT
1 TGCAGCT
2890303 ATCAGTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (27 bp):
TGCAGCTGTTTCGATGACTTTCTTCAT
Found at i:2890745 original size:14 final size:14
Alignment explanation
Indices: 2890726--2890774 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2890716 TTTTTAATTA
2890726 ATTAATATTTTATT
1 ATTAATATTTTATT
2890740 ATTAATATTTT-TT
1 ATTAATATTTTATT
* *
2890753 ATTTATTTATTTATT
1 ATTAATAT-TTTATT
*
2890768 TTTAATA
1 ATTAATA
2890775 AACCAATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 8 0.29
14 14 0.50
15 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAATATTTTATT
Found at i:2890751 original size:15 final size:17
Alignment explanation
Indices: 2890716--2890751 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
2890706 CCTTTCTCTT
2890716 TTTTTAATTAATTAATA
1 TTTTTAATTAATTAATA
2890733 -TTTT-ATT-ATTAATA
1 TTTTTAATTAATTAATA
2890747 TTTTT
1 TTTTT
2890752 TATTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.39
15 7 0.39
16 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATTAATTAATA
Found at i:2890752 original size:16 final size:17
Alignment explanation
Indices: 2890715--2890755 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2890705 CCCTTTCTCT
2890715 TTTTTTAATTAATTAATA
1 TTTTTT-ATTAATTAATA
2890733 --TTTTATT-ATTAATA
1 TTTTTTATTAATTAATA
2890747 TTTTTTATT
1 TTTTTTATT
2890756 TATTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.33
15 3 0.14
16 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTATTAATTAATA
Found at i:2893335 original size:51 final size:51
Alignment explanation
Indices: 2893259--2893362 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
2893249 AGCATGCAAA
*
2893259 AATGATAGTATTGTGATGACATAGAAGTGGTGATAGAATGTTAAAAACGAC
1 AATGATAGTATTGTGATGACATAGAAGTGGTGATAGAATGATAAAAACGAC
*
2893310 AATGATAGTATTGTGATGACATAGAAGTGGTGATAGAATGATAAAAATGAC
1 AATGATAGTATTGTGATGACATAGAAGTGGTGATAGAATGATAAAAACGAC
2893361 AA
1 AA
2893363 ACAACATACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (51 bp):
AATGATAGTATTGTGATGACATAGAAGTGGTGATAGAATGATAAAAACGAC
Found at i:2894462 original size:52 final size:52
Alignment explanation
Indices: 2894379--2894496 Score: 184
Period size: 52 Copynumber: 2.3 Consensus size: 52
2894369 TTGAAGAATG
* * *
2894379 TATCGATAGA-TTGGATAAAAAGCCCAAAATGTATCGATACAAAGCAAATTA
1 TATCGATACATTTGGATAAAAAACCCAAAATGTATCGATACAAACCAAATTA
* *
2894430 TATCGATACATTTGGATAAAAAACCCAGAATGTATCGATACAAACCAAATTG
1 TATCGATACATTTGGATAAAAAACCCAAAATGTATCGATACAAACCAAATTA
2894482 TATCGATACATTTGG
1 TATCGATACATTTGG
2894497 GAATGCATCG
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
51 9 0.15
52 52 0.85
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (52 bp):
TATCGATACATTTGGATAAAAAACCCAAAATGTATCGATACAAACCAAATTA
Found at i:2895937 original size:36 final size:36
Alignment explanation
Indices: 2895890--2895989 Score: 200
Period size: 36 Copynumber: 2.8 Consensus size: 36
2895880 ATAATGTATG
2895890 GATACATTGATTTGAAATTATAGCCATTACAATATC
1 GATACATTGATTTGAAATTATAGCCATTACAATATC
2895926 GATACATTGATTTGAAATTATAGCCATTACAATATC
1 GATACATTGATTTGAAATTATAGCCATTACAATATC
2895962 GATACATTGATTTGAAATTATAGCCATT
1 GATACATTGATTTGAAATTATAGCCATT
2895990 TATAGCTGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (36 bp):
GATACATTGATTTGAAATTATAGCCATTACAATATC
Found at i:2896034 original size:20 final size:21
Alignment explanation
Indices: 2896009--2896060 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
2895999 TACAAGCAAC
*
2896009 GTATCGATACAATT-CATCAT
1 GTATCGATACAATTGCACCAT
*
2896029 GTATCGATAC-ATTGTACCAT
1 GTATCGATACAATTGCACCAT
2896049 GTATCGATACAA
1 GTATCGATACAA
2896061 ACAGTGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (21 bp):
GTATCGATACAATTGCACCAT
Found at i:2896114 original size:20 final size:20
Alignment explanation
Indices: 2896089--2896143 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2896079 CTACCAATTT
**
2896089 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
2896109 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
2896128 CATCTATCGATACAAT
1 CATGTATCGATACAAT
2896144 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2897180 original size:53 final size:53
Alignment explanation
Indices: 2897100--2897235 Score: 227
Period size: 53 Copynumber: 2.6 Consensus size: 53
2897090 AGATTGCATA
*
2897100 GTATCGATAAACACAATATGTATCGATACAAGACATTAGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACATTAGCAGTAGCCAAATTT
* * *
2897153 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACATTAGCAGTAGCCAAATTT
*
2897206 GTATCGATACACACAATATGTATTGATACA
1 GTATCGATACACACAATATGTATCGATACA
2897236 TTAGCAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 78 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACATTAGCAGTAGCCAAATTT
Found at i:2897323 original size:9 final size:10
Alignment explanation
Indices: 2897259--2897327 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 10
2897249 AATCTCATTT
2897259 TCACTGTTCA
1 TCACTGTTCA
2897269 TCACTGTTCA
1 TCACTGTTCA
* *
2897279 TGTA-TCGATACA
1 T-CACT-G-TTCA
2897291 TCACT-TTCA
1 TCACTGTTCA
2897300 TCACT-TTCA
1 TCACTGTTCA
2897309 TCACTGTTCA
1 TCACTGTTCA
2897319 T-ACTGTTCA
1 TCACTGTTCA
2897328 CGTATCACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 25 0.50
10 17 0.34
11 3 0.06
12 5 0.10
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.41
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2897393 original size:47 final size:46
Alignment explanation
Indices: 2897308--2897398 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
2897298 CATCACTTTC
* * *
2897308 ATCACTGTTCATACTGTTCACGTATCACTATCCATGTATCGATAAAA
1 ATCACTGTACATACTATTCACGTATCAC-ATACATGTATCGATAAAA
*
2897355 ATCACTGTACATCACTATTCATGTATCA-ATACATTGTATCGATA
1 ATCACTGTACAT-ACTATTCACGTATCACATACA-TGTATCGATA
2897399 CAGTGTATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 4 0.11
47 21 0.55
48 13 0.34
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (46 bp):
ATCACTGTACATACTATTCACGTATCACATACATGTATCGATAAAA
Found at i:2897394 original size:13 final size:13
Alignment explanation
Indices: 2897376--2897414 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2897366 TCACTATTCA
*
2897376 TGTATCAATACAT
1 TGTATCGATACAT
*
2897389 TGTATCGATACAG
1 TGTATCGATACAT
2897402 TGTATCGATACAT
1 TGTATCGATACAT
2897415 CATAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2902926 original size:13 final size:13
Alignment explanation
Indices: 2902908--2902940 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2902898 ACAATTCATC
2902908 ATGTATCGATACA
1 ATGTATCGATACA
2902921 ATGTATCGATACA
1 ATGTATCGATACA
*
2902934 TTGTATC
1 ATGTATC
2902941 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2902926 original size:33 final size:33
Alignment explanation
Indices: 2902886--2902954 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2902876 CCGTTACAAG
*
2902886 CAATGTATTGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCATCATGTATCGATA
*
2902919 CAATGTATCGATACATTGTATCATGTATCGATA
1 CAATGTATCGATACATTGCATCATGTATCGATA
2902952 CAA
1 CAA
2902955 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATTGCATCATGTATCGATA
Found at i:2904246 original size:51 final size:49
Alignment explanation
Indices: 2904182--2904314 Score: 176
Period size: 51 Copynumber: 2.7 Consensus size: 49
2904172 TTTTACTGTT
** *
2904182 TGTATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTACTTAGA
1 TGTATCGATACATTATTCATTGTATCAATACATTCT-GAATTTTAC-CAGA
* *
2904233 TGTATCGATACATTCTTCATTGTATCGATACATTCTGAATTTTACCAGA
1 TGTATCGATACATTATTCATTGTATCAATACATTCTGAATTTTACCAGA
* * *
2904282 TGCATCGATACTTTATTCAATGTATCAATACAT
1 TGTATCGATACATTATTCATTGTATCAATACAT
2904315 GTAGGCAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 31 0.43
50 7 0.10
51 34 0.47
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (49 bp):
TGTATCGATACATTATTCATTGTATCAATACATTCTGAATTTTACCAGA
Found at i:2909671 original size:14 final size:14
Alignment explanation
Indices: 2909652--2909680 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2909642 ATAAAGAAAA
2909652 ATGAAGAATGAATC
1 ATGAAGAATGAATC
2909666 ATGAAGAATGAATC
1 ATGAAGAATGAATC
2909680 A
1 A
2909681 AATCATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
ATGAAGAATGAATC
Found at i:2910340 original size:85 final size:85
Alignment explanation
Indices: 2910251--2910478 Score: 246
Period size: 84 Copynumber: 2.7 Consensus size: 85
2910241 GAAGATACCA
*
2910251 TTACCCCTATGGTGACCTGTCAG-TTCAATTTTCGGTCAACCTTCATCTCTTTGTTTACCTGTTG
1 TTACCCCTATGGTGACCTGTCAGCTT-AATTTTCGGTCAACCTTCATCTCTTTGTTTACCTGTCG
* *
2910315 ACTTAGTCCTCGGTAAACCCC
65 ACTCAGTCCCCGGTAAACCCC
* * * * * *
2910336 TTACCCCTATAGTGACCTGTCAGCTTAGTCTTT-AGTCATCCTTTATC-CTTTGTTTACTTGTCG
1 TTACCCCTATGGTGACCTGTCAGCTTAAT-TTTCGGTCAACCTTCATCTCTTTGTTTACCTGTCG
*
2910399 GCTCAGTCCCCGGTAAACCCC
65 ACTCAGTCCCCGGTAAACCCC
* * * * * * * * *
2910420 TTACCCTTTTGGTGACTTGTCAGCTTAATCTCCGATCAATCTCCATCTCATTGTTTACC
1 TTACCCCTATGGTGACCTGTCAGCTTAATTTTCGGTCAACCTTCATCTCTTTGTTTACC
2910479 CATTGGCCCA
Statistics
Matches: 114, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
83 1 0.01
84 64 0.56
85 44 0.39
86 5 0.04
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (85 bp):
TTACCCCTATGGTGACCTGTCAGCTTAATTTTCGGTCAACCTTCATCTCTTTGTTTACCTGTCGA
CTCAGTCCCCGGTAAACCCC
Found at i:2912329 original size:16 final size:16
Alignment explanation
Indices: 2912304--2912334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2912294 TGGAAAATGG
2912304 AAAAAGAAAAAATAAT
1 AAAAAGAAAAAATAAT
*
2912320 AAAAATAAAAAATAA
1 AAAAAGAAAAAATAA
2912335 AGGGGCCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAGAAAAAATAAT
Found at i:2912462 original size:21 final size:21
Alignment explanation
Indices: 2912436--2912475 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2912426 TAAAGGAACT
*
2912436 AAAAAAAAGAGAGAAAAAAAG
1 AAAAAAAAGAAAGAAAAAAAG
2912457 AAAAAAAAGAAAGAAAAAA
1 AAAAAAAAGAAAGAAAAAA
2912476 TAACTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAGAAAAAAAG
Found at i:2912469 original size:13 final size:12
Alignment explanation
Indices: 2912436--2912475 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2912426 TAAAGGAACT
*
2912436 AAAAAAAAGAGA
1 AAAAAAAAGAAA
*
2912448 GAAAAAAAGAAA
1 AAAAAAAAGAAA
2912460 AAAAAGAAAGAAA
1 AAAAA-AAAGAAA
2912473 AAA
1 AAA
2912476 TAACTAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:2913891 original size:3 final size:3
Alignment explanation
Indices: 2913883--2913929 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2913873 CTATCCTAAA
2913883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2913930 AGATTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2916208 original size:13 final size:13
Alignment explanation
Indices: 2916190--2916229 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
2916180 ACAATTGTCC
2916190 ATGTATCGATACA
1 ATGTATCGATACA
2916203 ATGTATCGATACA
1 ATGTATCGATACA
2916216 ATGTATCGATACA
1 ATGTATCGATACA
2916229 A
1 A
2916230 AGCATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2918748 original size:13 final size:13
Alignment explanation
Indices: 2918727--2918768 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
2918717 AAATAGTATC
2918727 CAATGTATCGATA
1 CAATGTATCGATA
*
2918740 CAGTGTATCGATA
1 CAATGTATCGATA
2918753 CAATGTATCGATA
1 CAATGTATCGATA
2918766 CAA
1 CAA
2918769 GGAATATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2924946 original size:20 final size:21
Alignment explanation
Indices: 2924919--2924974 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
2924909 CCATTACAAG
2924919 CTATGTATCGATACAATTCAT-
1 CTATGTATCGATACAATT-ATA
*
2924940 C-ATGTATCGATAC-ATTGTA
1 CTATGTATCGATACAATTATA
2924959 CTATGTATCGATACAA
1 CTATGTATCGATACAA
2924975 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 24 0.77
21 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (21 bp):
CTATGTATCGATACAATTATA
Found at i:2925055 original size:19 final size:19
Alignment explanation
Indices: 2925003--2925057 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2924993 CTGCCAATCT
**
2925003 CATGTATCGATACAATTGT
1 CATGTATCGATACAATTAA
* *
2925022 CTATATATTGATACAATTAA
1 C-ATGTATCGATACAATTAA
2925042 CATGTATCGATACAAT
1 CATGTATCGATACAAT
2925058 GTATCGATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
CATGTATCGATACAATTAA
Found at i:2925061 original size:13 final size:13
Alignment explanation
Indices: 2925043--2925069 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2925033 TACAATTAAC
2925043 ATGTATCGATACA
1 ATGTATCGATACA
2925056 ATGTATCGATACA
1 ATGTATCGATACA
2925069 A
1 A
2925070 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2925582 original size:39 final size:39
Alignment explanation
Indices: 2925534--2925629 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
2925524 TTAATTATAC
* * *
2925534 TTTTCAAATTTCAATAAATAATCTATACATT-ACTAATAT
1 TTTTTAAATTTCAATAAAGAATCCATACATTAAC-AATAT
*
2925573 TTTTTAAATTTCAATAAAGAATCCATGCATTAACAATAT
1 TTTTTAAATTTCAATAAAGAATCCATACATTAACAATAT
* *
2925612 CTTTTAAATTTTAATAAA
1 TTTTTAAATTTCAATAAA
2925630 CTTTAAATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 48 0.96
40 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (39 bp):
TTTTTAAATTTCAATAAAGAATCCATACATTAACAATAT
Found at i:2926271 original size:2 final size:2
Alignment explanation
Indices: 2926264--2926316 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2926254 TGCATTCCCT
2926264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2926306 TA TA TA TA TA T
1 TA TA TA TA TA T
2926317 CGAATTTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2926393 original size:15 final size:16
Alignment explanation
Indices: 2926344--2926400 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
2926334 ATATAAAATT
*
2926344 AATTAATTTTATATATT
1 AATTAATTTT-TATATA
*
2926361 TATATAATTTTTATAT-
1 AAT-TAATTTTTATATA
2926377 AATTAATATTTTA-ATA
1 AATTAAT-TTTTATATA
2926393 AATTAATT
1 AATTAATT
2926401 ATTAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 7 0.20
16 14 0.40
17 7 0.20
18 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTAATTTTTATATA
Found at i:2926396 original size:16 final size:17
Alignment explanation
Indices: 2926349--2926399 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
2926339 AAATTAATTA
*
2926349 ATTTT-ATATATTTATAT
1 ATTTTAATATAATTA-AT
*
2926366 AATTTTTATATAATTAAT
1 -ATTTTAATATAATTAAT
2926384 ATTTTAATA-AATTAAT
1 ATTTTAATATAATTAAT
2926400 TATTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.23
17 8 0.27
18 7 0.23
19 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAATATAATTAAT
Found at i:2926403 original size:17 final size:17
Alignment explanation
Indices: 2926335--2926403 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 17
2926325 TTTAAATTAA
*
2926335 TATAAAATTAATTAATTT
1 TATATAATTAATT-ATTT
* *
2926353 TATATATTTATATAATTTT
1 TATATAATTA-ATTA-TTT
2926372 TATATAATTAA-TATTT
1 TATATAATTAATTATTT
2926388 TA-ATAAATTAATTATT
1 TATAT-AATTAATTATT
2926404 AAATTTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
17 5 0.12
18 10 0.24
19 14 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATAATTAATTATTT
Found at i:2926587 original size:24 final size:24
Alignment explanation
Indices: 2926544--2926589 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2926534 TTAAATTTTT
* **
2926544 TAATTTATTTAAATTTAATATATA
1 TAATTTATGTAAATAAAATATATA
2926568 TAATTTATGTAAATAAAATATA
1 TAATTTATGTAAATAAAATATA
2926590 AAATATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TAATTTATGTAAATAAAATATATA
Found at i:2926605 original size:13 final size:13
Alignment explanation
Indices: 2926578--2926613 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2926568 TAATTTATGT
2926578 AAATAAAAT-ATA
1 AAATAAAATAATA
*
2926590 AAATATAATAATA
1 AAATAAAATAATA
2926603 AAATAAAATAA
1 AAATAAAATAA
2926614 ATATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:2927500 original size:17 final size:17
Alignment explanation
Indices: 2927461--2927501 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2927451 TTAAAAATTA
2927461 AATTTAAAAAATAATGT
1 AATTTAAAAAATAATGT
* *
2927478 AGATTTTAAAAATATTGT
1 A-ATTTAAAAAATAATGT
2927496 AATTTA
1 AATTTA
2927502 TGTAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
AATTTAAAAAATAATGT
Found at i:2931293 original size:23 final size:23
Alignment explanation
Indices: 2931265--2931308 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2931255 GTTATGCATA
*
2931265 TTTATAAATTTTAAATTTATATT
1 TTTATAAATTTTAAATATATATT
**
2931288 TTTATACTTTTTAAATATATA
1 TTTATAAATTTTAAATATATA
2931309 ATTATATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATAAATTTTAAATATATATT
Found at i:2937140 original size:21 final size:21
Alignment explanation
Indices: 2937098--2937157 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2937088 GAATTAGAGG
2937098 AGAAAATGAATGAGTTAGAAA
1 AGAAAATGAATGAGTTAGAAA
2937119 AGAAAA-GAAATGAGTT-GCAAA
1 AGAAAATG-AATGAGTTAG-AAA
2937140 ATGAAAATG-ATGAGTTAG
1 A-GAAAATGAATGAGTTAG
2937158 CTAATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.06
21 25 0.74
22 6 0.18
23 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.20
Consensus pattern (21 bp):
AGAAAATGAATGAGTTAGAAA
Found at i:2938655 original size:13 final size:13
Alignment explanation
Indices: 2938637--2938662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2938627 ACAATCAAAT
2938637 TTATATCGATATA
1 TTATATCGATATA
2938650 TTATATCGATATA
1 TTATATCGATATA
2938663 ATTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTATATCGATATA
Found at i:2939986 original size:10 final size:10
Alignment explanation
Indices: 2939967--2939997 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2939957 ATCTCATTTT
2939967 TCACTGTTCA
1 TCACTGTTCA
*
2939977 TCACTATTCA
1 TCACTGTTCA
2939987 TCACTGTTCA
1 TCACTGTTCA
2939997 T
1 T
2939998 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2940016 original size:22 final size:22
Alignment explanation
Indices: 2939985--2940061 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
2939975 CATCACTATT
2939985 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
* * * *
2940007 CATCATTGTTCA--TAACTATT
1 CATCACTGTTCATGTATCGATA
*
2940027 CATTACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2940049 CATCACTGTTCAT
1 CATCACTGTTCAT
2940062 CACTGTACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 15 0.35
22 28 0.65
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2940035 original size:42 final size:42
Alignment explanation
Indices: 2939967--2940061 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
2939957 ATCTCATTTT
*
2939967 TCACTGTTCATCACTATTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
* *
2940009 TCATTGTTCATAACTATTCATTACTGTTCATGTATCGATACA
1 TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
2940051 TCACTGTTCAT
1 TCACTGTTCAT
2940062 CACTGTACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (42 bp):
TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
Found at i:2940146 original size:22 final size:22
Alignment explanation
Indices: 2940118--2940160 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2940108 ATTCATCACA
2940118 GTATCGATACATCACTGTTCAT
1 GTATCGATACATCACTGTTCAT
2940140 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
2940161 CACTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:2941772 original size:21 final size:21
Alignment explanation
Indices: 2941746--2941787 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2941736 AATCAAACGT
* *
2941746 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
2941767 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
2941788 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:2942333 original size:84 final size:84
Alignment explanation
Indices: 2942173--2942333 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 84
2942163 ACTCAAAGAA
* * * *
2942173 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
2942238 TATGAAAGAGTTTCAAAAT
66 TAAGAAAGAGTTTCAAAAT
* * *
2942257 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
2942320 AA-AAGAAATGAGTT
64 AATAAGAAA-GAGTT
2942334 GCAAGTGGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 56 0.85
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTTCAAAAT
Found at i:2944591 original size:99 final size:99
Alignment explanation
Indices: 2944420--2944615 Score: 367
Period size: 99 Copynumber: 2.0 Consensus size: 99
2944410 TGGTATAAAT
2944420 TTGGTTTTATCAACTTAGCTTATGAACCAAAAAAGGGGAGAGATTATTGTTAATTGGTTTAAGGG
1 TTGGTTTTATCAACTTAGCTTATGAACCAAAAAAGGGGAGAGATTATTGTTAATTGGTTTAAGGG
2944485 TGAGAACGTATTAAGAGGGAGAGTTTGCATAAGC
66 TGAGAACGTATTAAGAGGGAGAGTTTGCATAAGC
*
2944519 TTGGTTTTATCAACTTAGCTTATGAACC-AAAAAGGGGAAGAGATTATTGTTTATTGGTTTAAGG
1 TTGGTTTTATCAACTTAGCTTATGAACCAAAAAAGGGG-AGAGATTATTGTTAATTGGTTTAAGG
2944583 GTGAGAACGTATTAAGAGGGAGAGTTTGCATAA
65 GTGAGAACGTATTAAGAGGGAGAGTTTGCATAA
2944616 AATTCGTATT
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
98 9 0.09
99 86 0.91
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (99 bp):
TTGGTTTTATCAACTTAGCTTATGAACCAAAAAAGGGGAGAGATTATTGTTAATTGGTTTAAGGG
TGAGAACGTATTAAGAGGGAGAGTTTGCATAAGC
Found at i:2945354 original size:21 final size:21
Alignment explanation
Indices: 2945330--2945373 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2945320 TTTTTCTAAG
*
2945330 TAAAAATACGTGTT-GTATCAA
1 TAAAAATAC-TATTGGTATCAA
*
2945351 TAAATATACTATTGGTATCAA
1 TAAAAATACTATTGGTATCAA
2945372 TA
1 TA
2945374 CACAAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
TAAAAATACTATTGGTATCAA
Found at i:2945528 original size:10 final size:10
Alignment explanation
Indices: 2945509--2945581 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
2945499 ATCTCATTTT
2945509 TCACTGTTCA
1 TCACTGTTCA
*
2945519 TCACTATTCA
1 TCACTGTTCA
2945529 TCACTGTTCA
1 TCACTGTTCA
* *
2945539 TGTA-TCGATACA
1 T-CACT-G-TTCA
*
2945551 TCATTGTTCA
1 TCACTGTTCA
* *
2945561 TAACTATTCA
1 TCACTGTTCA
2945571 TCACTGTTCA
1 TCACTGTTCA
2945581 T
1 T
2945582 GTATCGATAC
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 39 0.81
11 4 0.08
12 5 0.10
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2945558 original size:22 final size:22
Alignment explanation
Indices: 2945527--2945602 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
2945517 CATCACTATT
2945527 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
* * * *
2945549 CATCATTGTTCA--TAACTATT
1 CATCACTGTTCATGTATCGATA
2945569 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2945591 CATCACTGTTCA
1 CATCACTGTTCA
2945603 CACTATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.36
22 28 0.64
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2945572 original size:42 final size:42
Alignment explanation
Indices: 2945509--2945602 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
2945499 ATCTCATTTT
*
2945509 TCACTGTTCATCACTATTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
*
2945551 TCATTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
2945593 TCACTGTTCA
1 TCACTGTTCA
2945603 CACTATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (42 bp):
TCACTGTTCATAACTATTCATCACTGTTCATGTATCGATACA
Found at i:2946106 original size:34 final size:35
Alignment explanation
Indices: 2946043--2946109 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2946033 CTAAGTGATT
2946043 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2946079 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2946110 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2948165 original size:20 final size:20
Alignment explanation
Indices: 2948140--2948333 Score: 176
Period size: 20 Copynumber: 9.6 Consensus size: 20
2948130 GTTGGGCTCA
2948140 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACC
2948160 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACC
2948180 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACC
* * * *
2948200 ATGTATTGATATAATTCATC
1 ATGTATCGATACATTTCACC
* **
2948220 ATGTATCGATATATTTCAAG
1 ATGTATCGATACATTTCACC
* ** *
2948240 GTGTATCGATACCA--AGAAC
1 ATGTATCGATA-CATTTCACC
2948259 ATGTATCGATATAACATTTCACC
1 ATGTATCG--AT-ACATTTCACC
* * *
2948282 ATGTATAGATACAATTCATC
1 ATGTATCGATACATTTCACC
* **
2948302 ATGTATCGATATATTTCAAG
1 ATGTATCGATACATTTCACC
*
2948322 GTGTATCGATAC
1 ATGTATCGATAC
2948334 CAAGAACATG
Statistics
Matches: 141, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
19 9 0.06
20 115 0.82
21 7 0.05
22 1 0.01
23 9 0.06
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTCACC
Found at i:2948187 original size:40 final size:40
Alignment explanation
Indices: 2948140--2948333 Score: 203
Period size: 40 Copynumber: 4.8 Consensus size: 40
2948130 GTTGGGCTCA
* *
2948140 ATGTATCGATACATTTCACCATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACCATGTATCGATACAATTCATC
* *
2948180 ATGTATCGATACATTTCACCATGTATTGATATAATTCATC
1 ATGTATCGATACATTTCACCATGTATCGATACAATTCATC
* *** * *
2948220 ATGTATCGATATATTTCAAGGTGTATCGATACCAA--GAAC
1 ATGTATCGATACATTTCACCATGTATCGATA-CAATTCATC
*
2948259 ATGTATCGATATAACATTTCACCATGTATAGATACAATTCATC
1 ATGTATCG--AT-ACATTTCACCATGTATCGATACAATTCATC
* ***
2948302 ATGTATCGATATATTTCAAGGTGTATCGATAC
1 ATGTATCGATACATTTCACCATGTATCGATAC
2948334 CAAGAACATG
Statistics
Matches: 124, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 10 0.08
40 79 0.64
41 9 0.07
42 16 0.13
43 10 0.08
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (40 bp):
ATGTATCGATACATTTCACCATGTATCGATACAATTCATC
Found at i:2948270 original size:39 final size:39
Alignment explanation
Indices: 2948219--2948353 Score: 164
Period size: 39 Copynumber: 3.4 Consensus size: 39
2948209 TATAATTCAT
2948219 CATGTATCGATATATTTCAAGGTGTATCGATACCAAGAA
1 CATGTATCGATATATTTCAAGGTGTATCGATACCAAGAA
*** * * *
2948258 CATGTATCGATATAACATTTCACCATGTATAGATA-CAATTCAT
1 CATGTATCGATAT---ATTTCAAGGTGTATCGATACCAA--GAA
2948301 CATGTATCGATATATTTCAAGGTGTATCGATACCAAGAA
1 CATGTATCGATATATTTCAAGGTGTATCGATACCAAGAA
2948340 CATGTATCGATATA
1 CATGTATCGATATA
2948354 ATGTATCAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
39 28 0.36
40 15 0.19
41 6 0.08
42 15 0.19
43 14 0.18
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (39 bp):
CATGTATCGATATATTTCAAGGTGTATCGATACCAAGAA
Found at i:2948305 original size:82 final size:82
Alignment explanation
Indices: 2948179--2948354 Score: 313
Period size: 82 Copynumber: 2.2 Consensus size: 82
2948169 TACATTTCAC
* *
2948179 CATGTATCG--AT-ACATTTCACCATGTATTGATATAATTCATCATGTATCGATATATTTCAAGG
1 CATGTATCGATATAACATTTCACCATGTATAGATACAATTCATCATGTATCGATATATTTCAAGG
2948241 TGTATCGATACCAAGAA
66 TGTATCGATACCAAGAA
2948258 CATGTATCGATATAACATTTCACCATGTATAGATACAATTCATCATGTATCGATATATTTCAAGG
1 CATGTATCGATATAACATTTCACCATGTATAGATACAATTCATCATGTATCGATATATTTCAAGG
2948323 TGTATCGATACCAAGAA
66 TGTATCGATACCAAGAA
2948340 CATGTATCGATATAA
1 CATGTATCGATATAA
2948355 TGTATCAATA
Statistics
Matches: 92, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
79 9 0.10
81 2 0.02
82 81 0.88
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (82 bp):
CATGTATCGATATAACATTTCACCATGTATAGATACAATTCATCATGTATCGATATATTTCAAGG
TGTATCGATACCAAGAA
Found at i:2952923 original size:13 final size:13
Alignment explanation
Indices: 2952905--2952930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2952895 CATACCCAGA
2952905 TGTATCGATACAT
1 TGTATCGATACAT
2952918 TGTATCGATACAT
1 TGTATCGATACAT
2952931 GTTCATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2952960 original size:20 final size:19
Alignment explanation
Indices: 2952914--2952970 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2952904 ATGTATCGAT
*
2952914 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2952933 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2952952 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2952971 AGATTGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2953057 original size:33 final size:33
Alignment explanation
Indices: 2953002--2953067 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2952992 CCACTGTTTT
* *
2953002 TATCGATACATGGTACAATGTATCAATATATTG
1 TATCGATACATGATACAATGTATCAATACATTG
* *
2953035 TATCGATACATGATGA-ATTGTATCGATACATTG
1 TATCGATACATGAT-ACAATGTATCAATACATTG
2953068 CTTGTAACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TATCGATACATGATACAATGTATCAATACATTG
Found at i:2959259 original size:20 final size:20
Alignment explanation
Indices: 2959234--2959299 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2959224 TATCGATACA
2959234 TTGTATCGATACAATATTCC
1 TTGTATCGATACAATATTCC
2959254 TTGTATCGATAC---A----
1 TTGTATCGATACAATATTCC
*
2959267 TTATATCGATACAATATTCC
1 TTGTATCGATACAATATTCC
2959287 TTGTATCGATACA
1 TTGTATCGATACA
2959300 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.30
16 1 0.03
17 1 0.03
20 24 0.65
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACAATATTCC
Found at i:2959261 original size:33 final size:33
Alignment explanation
Indices: 2959223--2959312 Score: 171
Period size: 33 Copynumber: 2.7 Consensus size: 33
2959213 TAGATGTATC
2959223 GTATCGATACATTGTATCGATACAATATTCCTT
1 GTATCGATACATTGTATCGATACAATATTCCTT
*
2959256 GTATCGATACATTATATCGATACAATATTCCTT
1 GTATCGATACATTGTATCGATACAATATTCCTT
2959289 GTATCGATACATTGTATCGATACA
1 GTATCGATACATTGTATCGATACA
2959313 TAGGGTACTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (33 bp):
GTATCGATACATTGTATCGATACAATATTCCTT
Found at i:2959305 original size:13 final size:13
Alignment explanation
Indices: 2959287--2959313 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2959277 ACAATATTCC
2959287 TTGTATCGATACA
1 TTGTATCGATACA
2959300 TTGTATCGATACA
1 TTGTATCGATACA
2959313 T
1 T
2959314 AGGGTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2961236 original size:21 final size:21
Alignment explanation
Indices: 2961196--2961273 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
2961186 TAGATTTGAC
*
2961196 TAAGGGGGAGAAATGCTTTAAT
1 TAAGGGGGAGAAAT-TTTTAAT
*
2961218 TAAGGGGGAGAAATTTTTAAA
1 TAAGGGGGAGAAATTTTTAAT
* * *
2961239 TAAAGAGAAGAAATTCTTTAAT
1 TAAGGGGGAGAAATT-TTTAAT
*
2961261 TAAGGGAGAGAAA
1 TAAGGGGGAGAAA
2961274 AACGAAAACT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 17 0.38
22 28 0.62
ACGTcount: A:0.45, C:0.03, G:0.27, T:0.26
Consensus pattern (21 bp):
TAAGGGGGAGAAATTTTTAAT
Found at i:2961825 original size:13 final size:13
Alignment explanation
Indices: 2961807--2961833 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2961797 GTATTGTGCT
2961807 TTGTATCGATACA
1 TTGTATCGATACA
2961820 TTGTATCGATACA
1 TTGTATCGATACA
2961833 T
1 T
2961834 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2961842 original size:19 final size:19
Alignment explanation
Indices: 2961817--2961873 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2961807 TTGTATCGAT
*
2961817 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2961836 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
2961855 ACAATTATATCGATACATG
1 AC-ATTGTATCGATACATG
2961874 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2961948 original size:20 final size:20
Alignment explanation
Indices: 2961905--2961955 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2961895 CCACTGTTTG
*
2961905 TATCGATACATGATACAATG
1 TATCGATACATGATACAATA
*
2961925 TATCGATACATGATGA-ATTA
1 TATCGATACATGAT-ACAATA
2961945 TATCGATACAT
1 TATCGATACAT
2961956 TGCTTGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACATGATACAATA
Found at i:2974490 original size:11 final size:11
Alignment explanation
Indices: 2974474--2974503 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2974464 CTTTCGTACA
2974474 AAAAAAAAAAC
1 AAAAAAAAAAC
2974485 AAAAAAAAAAC
1 AAAAAAAAAAC
2974496 AAAAAAAA
1 AAAAAAAA
2974504 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:2975529 original size:26 final size:26
Alignment explanation
Indices: 2975482--2975538 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
2975472 TAGACTTTGT
* * **
2975482 ATCATGCAACCATGATAGCATTCCAC
1 ATCATGCAACCATAATACCATTAAAC
**
2975508 ATCATGCATTCATAATACCATTAAAC
1 ATCATGCAACCATAATACCATTAAAC
2975534 ATCAT
1 ATCAT
2975539 TATTTTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (26 bp):
ATCATGCAACCATAATACCATTAAAC
Found at i:2975761 original size:28 final size:28
Alignment explanation
Indices: 2975729--2976043 Score: 298
Period size: 28 Copynumber: 11.2 Consensus size: 28
2975719 TCATCTCTTG
*
2975729 AAAGCCCACAAGTCATTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
2975757 AAAGCCCACAAGTCAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * * *
2975785 AATGCCTACAAGTCAATGGCATTCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * **
2975813 AAAGTCCACAAGTCGGTGGCATATTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
2975841 AAAGCCCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
2975869 AAAGTCCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
2975897 TAAGCCTACAAGTCGGTGGCA-CCTTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTT-C
* * *
2975925 AAAGCCCATAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCATCCTTTC
* * * *
2975953 TAAGCCCACAAGTCGGTGGCACCCTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
2975981 AAAGCCCACAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCATCCTTTC
* *
2976009 TAAGCCCACAAGTCAGTGGCA-CTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTT-C
2976037 AAAGCCC
1 AAAGCCC
2976044 GCAACCTTTT
Statistics
Matches: 233, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
27 13 0.06
28 211 0.91
29 9 0.04
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:2975806 original size:56 final size:55
Alignment explanation
Indices: 2975730--2976162 Score: 327
Period size: 56 Copynumber: 7.9 Consensus size: 55
2975720 CATCTCTTGA
* *
2975730 AAGCCCACAAGTCATTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTC
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * * *
2975785 AATGCCTACAAGTCAATGGCATTCTTTCAAAGTCCACAAGTCGGTGGCATATTTTC
1 AA-GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * *
2975841 AAAGCCCATAGGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCACCCTTTTT
1 -AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTC
* * * * *
2975898 AAGCCTACAAGTCGGTGGCA-CCTTTCCAAAGCCCATAAG-CAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACAAGTC-AGTGGCA-TCTTTTC
* * * * *
2975954 AAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAG-CAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC-AGTGGCA-TCTTTTC
* * *
2976010 AAGCCCACAAGTCAGTGGCA-CTTTTCCAAAGCCCGCAA--C-----C-T-TTTTT
1 AAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * ** * * *
2976056 AAGCCCATAGGTCGGTGGCACCCTTTTTAAGCCCATAAG-CAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC-AGTGGCA-TCTTTTC
* * *
2976112 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAGGTCAGTGGCATCT
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCT
2976163 CTTTTCAAAG
Statistics
Matches: 311, Mismatches: 48, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
46 30 0.10
47 5 0.02
49 1 0.00
53 1 0.00
55 14 0.05
56 249 0.80
57 11 0.04
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (55 bp):
AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:2975880 original size:84 final size:82
Alignment explanation
Indices: 2975729--2976189 Score: 263
Period size: 84 Copynumber: 5.6 Consensus size: 82
2975719 TCATCTCTTG
** * * *
2975729 AAAGCCCACAAGTCATTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT-CTCTTCAATGCCTA
1 AAAG-CCACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCATCCT-TTCAAAGCC-A
**
2975793 CAAGTCAATGGCATTCTTTC
63 CAAGTCAATGGCACCCTTTC
* *
2975813 AAAGTCCACAAGTCGGTGGCATATTTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGTCCAC
1 AAAG-CCACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAG-CCAC
* *
2975878 AAGTCAGTGGCACCCTTTT
64 AAGTCAATGGCACCCTTTC
* * * * **
2975897 TAAGCCTACAAGTCGGTGGCACCTTTCCAAAGCCCATAAG-CAAGTGGCACCCTTTTTAAGCCCA
1 AAAGCC-ACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTC-AGTGGCATCCTTTCAAAG-CCA
** *
2975961 CAAGTCGGTGGCACCCTTCC
63 CAAGTCAATGGCACCCTTTC
* * * * *
2975981 AAAGCCCACAAG-CAAGTGGCACCCTTTT-TAAGCCCACAAGTCAGTGGCA-CTTTTCCAAAGCC
1 AAAG-CCACAAGTC-GGTGGCA-TCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTT-CAAAGCC
* *
2976043 -C--G-C-A----ACCTTTTT
62 ACAAGTCAATGGCACCCTTTC
* * * * **
2976055 TAAGCC-CATAGGTCGGTGGCACCCTTTT-TAAGCCCATAAG-CAAGTGGCACCCTTTTTAAGCC
1 AAAGCCACA-A-GTCGGTGGCA-TCTTTTCAAAGCCCATAAGTC-AGTGGCATCCTTTCAAAG-C
* *
2976117 CACAAGTCAGTGGCACCCTTCC
61 CACAAGTCAATGGCACCCTTTC
* * *
2976139 AAAGCCCACAGGTCAGTGGCATCTCTTTTCAAAGTCCACATAAGTCGGTGG
1 AAAG-CCACAAGTCGGTGGCA--TCTTTTCAAAG-CC-CATAAGTCAGTGG
2976190 TAACTTTTTT
Statistics
Matches: 294, Mismatches: 52, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
72 2 0.01
73 4 0.01
74 43 0.15
75 7 0.02
76 1 0.00
78 1 0.00
79 2 0.01
80 1 0.00
82 1 0.00
83 10 0.03
84 184 0.63
85 20 0.07
86 5 0.02
87 2 0.01
88 10 0.03
89 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (82 bp):
AAAGCCACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCACAA
GTCAATGGCACCCTTTC
Found at i:2976111 original size:29 final size:28
Alignment explanation
Indices: 2976051--2976159 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 28
2976041 CCCGCAACCT
* *
2976051 TTTTTAAGCCCATAGGTCGGTGGCACCC
1 TTTTTAAGCCCATAAGTCAGTGGCACCC
2976079 TTTTTAAGCCCATAAG-CAAGTGGCACCC
1 TTTTTAAGCCCATAAGTC-AGTGGCACCC
*
2976107 TTTTTAAGCCCACAAGTCAGTGGCACCC
1 TTTTTAAGCCCATAAGTCAGTGGCACCC
*** * *
2976135 TTCCAAAGCCCACAGGTCAGTGGCA
1 TTTTTAAGCCCATAAGTCAGTGGCA
2976160 TCTCTTTTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
27 1 0.01
28 70 0.97
29 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (28 bp):
TTTTTAAGCCCATAAGTCAGTGGCACCC
Found at i:2976125 original size:102 final size:102
Alignment explanation
Indices: 2975949--2976145 Score: 322
Period size: 102 Copynumber: 1.9 Consensus size: 102
2975939 AGTGGCACCC
2975949 TTTTTAAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTTAAGC
1 TTTTTAAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTTAAGC
**
2976014 CCACAAGTCAGTGGCACTTTTCCAAAGCCCGCAACCT
66 CCACAAGTCAGTGGCACCCTTCCAAAGCCCGCAACCT
* * *** *
2976051 TTTTTAAGCCCATAGGTCGGTGGCACCCTTTTTAAGCCCATAAGCAAGTGGCACCCTTTTTAAGC
1 TTTTTAAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTTAAGC
2976116 CCACAAGTCAGTGGCACCCTTCCAAAGCCC
66 CCACAAGTCAGTGGCACCCTTCCAAAGCCC
2976146 ACAGGTCAGT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 87 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (102 bp):
TTTTTAAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTTAAGC
CCACAAGTCAGTGGCACCCTTCCAAAGCCCGCAACCT
Found at i:2980472 original size:13 final size:13
Alignment explanation
Indices: 2980454--2980478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2980444 CATAAAGTAT
2980454 TGTATCGATACAA
1 TGTATCGATACAA
2980467 TGTATCGATACA
1 TGTATCGATACA
2980479 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2980490 original size:33 final size:33
Alignment explanation
Indices: 2980434--2980500 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2980424 TTCAACGATT
*
2980434 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATAGATACAA
*** *
2980467 TGTATCGATACATATTTTTTTGTATAGATACAA
1 TGTATCGATACATAAAGTATTGTATAGATACAA
2980500 T
1 T
2980501 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATAGATACAA
Found at i:2980559 original size:13 final size:13
Alignment explanation
Indices: 2980541--2980565 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2980531 ATCACTTAAA
2980541 TGTATCGATACAT
1 TGTATCGATACAT
2980554 TGTATCGATACA
1 TGTATCGATACA
2980566 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2984787 original size:10 final size:10
Alignment explanation
Indices: 2984772--2984798 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2984762 TGCTAACTAA
2984772 GTTTTTGTTT
1 GTTTTTGTTT
2984782 GTTTTTGTTT
1 GTTTTTGTTT
2984792 GTTTTTG
1 GTTTTTG
2984799 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.