Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005836.1 Hibiscus syriacus cultivar Beakdansim tig00013680_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: 991970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:798357 original size:19 final size:19
Alignment explanation
Indices: 798335--798427 Score: 106
Period size: 19 Copynumber: 5.1 Consensus size: 19
798325 GAAACCAAAA
*
798335 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
798354 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
798368 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
798387 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
798406 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
798426 TC
1 TC
798428 AACCAAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 28 0.46
20 17 0.28
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:798425 original size:39 final size:33
Alignment explanation
Indices: 798335--798427 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 33
798325 GAAACCAAAA
*
798335 TCGCATTGCGATTTTCATTTCGCGTTGCGATTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
*
798368 TCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGAT--TC
798403 ATTTCCGCGTTGCGATTTTCATTTC
1 ---T-CGCGTTGCGATTTTCATTTC
798428 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
33 29 0.57
35 2 0.04
38 1 0.02
39 19 0.37
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:800266 original size:82 final size:84
Alignment explanation
Indices: 800115--800454 Score: 325
Period size: 94 Copynumber: 3.9 Consensus size: 84
800105 TAGATTGCTT
* * *
800115 AGTAAATTTATTCGGTTGCTGTCAATACTGCTAAAC-A-GT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
800176 A-TTTGTCTTTTGGTTG-A
66 ATTTTGTCTTTTGGTTGAA
* *
800193 AGTAAATTTATTAGGTTGCTGCCAATTCTGCTAAATTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
800258 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 A----------TTTTGTCTTTTGGTTGAA
* * *
800287 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACCGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
800352 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 A----------TTTTGTCTTTTGGTTGAA
* * * * * *
800381 AGTAAATTTGTTTGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
800446 A-TTTGTCTT
66 ATTTTGTCTT
800455 CGTTTTGTCT
Statistics
Matches: 231, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
78 32 0.14
79 1 0.00
80 2 0.01
81 2 0.01
82 20 0.09
83 8 0.03
93 15 0.06
94 151 0.65
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (84 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
ATTTTGTCTTTTGGTTGAA
Found at i:800306 original size:94 final size:93
Alignment explanation
Indices: 800177--800478 Score: 496
Period size: 94 Copynumber: 3.2 Consensus size: 93
800167 GAAGTTAGTA
* * *
800177 TTTGTCTTTTGGTTGAAGTAAATTTATTAGGTTGCTGCCAATTCTGCTAAATTATGTATTCTTTA
1 TTTGTCTTTTGGTTGAAGTAAATTTGTTAGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
800242 ACACTGTGAAGTTAGTATTTGTCTTTGT
66 ACACTGTGAAGTTAGTATTTGTCTTTGT
*
800270 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTG-AAGTAAATTTGTTAGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
*
800335 AACACCGTGAAGTTAGTATTTGTCTTTGT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
* *
800364 TTTGTCTTTTGGTTGAAAGTAAATTTGTTTGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTG-AAGTAAATTTGTTAGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
* * *
800429 AATACTCTGAAGTTAGTATTTGTCTTCGT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
800458 TTTGTCTTTTGGTTGAAGTAA
1 TTTGTCTTTTGGTTGAAGTAA
800479 TGCAATCCAT
Statistics
Matches: 197, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 21 0.11
94 176 0.89
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
TTTGTCTTTTGGTTGAAGTAAATTTGTTAGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
ACACTGTGAAGTTAGTATTTGTCTTTGT
Found at i:800596 original size:20 final size:20
Alignment explanation
Indices: 800571--800632 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
800561 TTTTGGTTGA
800571 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
800591 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
800610 AATAAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
800630 AAT
1 AAT
800633 CGCAATGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.52, C:0.16, G:0.21, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:800619 original size:19 final size:19
Alignment explanation
Indices: 800569--800661 Score: 97
Period size: 19 Copynumber: 5.1 Consensus size: 19
800559 TCTTTTGGTT
*
800569 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
800588 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
800608 GAAATAAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
800625 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
800641 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
800660 GA
1 GA
800662 TTATAGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.46
20 18 0.30
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:800692 original size:20 final size:19
Alignment explanation
Indices: 800667--800759 Score: 96
Period size: 20 Copynumber: 4.8 Consensus size: 19
800657 CGCGATTATA
*
800667 GTTTCGCTTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTT
*
800686 GGTTTCGCGTTGAGATTTTT
1 -GTTTCGCGTTGCGATTTTT
* *
800706 ATTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTT
* * *
800725 ATTCTCTCGTTGCGATTTTC
1 GTT-TCGCGTTGCGATTTTT
*
800745 ATTTCGCGTTGCGAT
1 GTTTCGCGTTGCGAT
800760 AGTCATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 30 0.46
20 35 0.54
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTT
Found at i:800710 original size:19 final size:19
Alignment explanation
Indices: 800668--800783 Score: 115
Period size: 19 Copynumber: 5.9 Consensus size: 19
800658 GCGATTATAG
* **
800668 TTTCGCTTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
* *
800688 TTTCGCGTTGAGATTTTTA
1 TTTCGCGTTGCGATTTTCA
800707 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
800726 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
**
800746 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
800765 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
800784 AAGTTCCAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
19 37 0.46
20 29 0.36
21 14 0.17
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:800711 original size:39 final size:40
Alignment explanation
Indices: 800668--800759 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 40
800658 GCGATTATAG
* ** *
800668 TTTCGCTTTGCGATTTTTGGTT-TCGCGTTGAGATTTTTA
1 TTTCGCGTTGCGATTTTTCATTCTCGCGTTGAGATTTTCA
* *
800707 TTTCGCGTTGCGA-TTTTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTTCATTCTCGCGTTGAGATTTTCA
800746 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
800760 AGTCATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 6 0.13
39 39 0.87
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.50
Consensus pattern (40 bp):
TTTCGCGTTGCGATTTTTCATTCTCGCGTTGAGATTTTCA
Found at i:800766 original size:39 final size:40
Alignment explanation
Indices: 800693--800783 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
800683 TTTGGTTTCG
* * ** *
800693 CGTTGAGATTTTTATTTCGCGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
*
800732 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
800772 CGTTGCGATTTT
1 CGTTGCGATTTT
800784 AAGTTCCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 29 0.64
40 16 0.36
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (40 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
Found at i:802800 original size:19 final size:19
Alignment explanation
Indices: 802786--802862 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
802776 CTATCGTAAT
802786 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
*
802804 -CG--A-GAGAATCGCAAC
1 GCGAAATGAAAATCGCAAC
*
802819 GCGAAATGAAAATCGCAAT
1 GCGAAATGAAAATCGCAAC
802838 GCGAAACT-AAAATCGCAAC
1 GCGAAA-TGAAAATCGCAAC
802857 GCGAAA
1 GCGAAA
802863 CTAAATTCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 32 0.65
20 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:802863 original size:19 final size:19
Alignment explanation
Indices: 802810--802872 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
802800 GCAACGAGAG
802810 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
802829 AATCGCAATGCGAAACTAA
1 AATCGCAACGCGAAACTAA
802848 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
802867 ATTCGC
1 AATCGC
802873 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.98
20 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:802944 original size:33 final size:33
Alignment explanation
Indices: 802907--802979 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
802897 GATTCCCTCG
802907 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
802940 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
802973 TTGCGAT
1 TTGCGAT
802980 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:802944 original size:47 final size:47
Alignment explanation
Indices: 802872--802961 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
802862 ACTAAATTCG
* *
802872 CGTTGCGATTTTCATTTCTCTTTGCGATTCCCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCT
*
802919 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATT
802962 TTCATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.10, C:0.26, G:0.19, T:0.46
Consensus pattern (47 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCT
Found at i:802945 original size:19 final size:19
Alignment explanation
Indices: 802921--802999 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
802911 GATTCTCTCG
802921 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
802940 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
802954 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
802973 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
802993 TTGCGAT
1 TTGCGAT
803000 AGACATTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 7 0.14
19 19 0.39
20 10 0.20
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:802959 original size:14 final size:14
Alignment explanation
Indices: 802888--802961 Score: 76
Period size: 14 Copynumber: 4.9 Consensus size: 14
802878 GATTTTCATT
*
802888 TCTCTTTGCGATTC
1 TCTCGTTGCGATTC
*
802902 CCTCGTTGCGATTC
1 TCTCGTTGCGATTC
802916 TCTCGTTGCGATTTTC
1 TCTCGTTGCGA--TTC
*
802932 ATTTCGCATTGCGATTC
1 -TCTCG--TTGCGATTC
802949 TCTCGTTGCGATT
1 TCTCGTTGCGATT
802962 TTCATTTCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
14 30 0.60
16 7 0.14
17 7 0.14
19 6 0.12
ACGTcount: A:0.09, C:0.27, G:0.19, T:0.45
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:802998 original size:20 final size:19
Alignment explanation
Indices: 802952--803006 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
802942 GCGATTCTCT
**
802952 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
802971 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
802991 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
803007 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:805550 original size:24 final size:24
Alignment explanation
Indices: 805516--805569 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
805506 CTGAAAAATC
805516 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
805540 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
805564 ATCAAA
1 ATCAAA
805570 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:806576 original size:20 final size:20
Alignment explanation
Indices: 806432--806598 Score: 162
Period size: 20 Copynumber: 8.3 Consensus size: 20
806422 AGAATCTCGT
806432 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGT-AATCGCAA
*
806452 TACGA-TTACGTAAATCG-AA
1 TGCGATTTACGT-AATCGCAA
* * *
806471 GTGCGAATTAGGAAAATCGCAA
1 -TGCGATTTACG-TAATCGCAA
*
806493 TGCGA-TTACGTATTCGCAA
1 TGCGATTTACGTAATCGCAA
806512 TGCGATTTACGTAATCGCAA
1 TGCGATTTACGTAATCGCAA
* *
806532 CGCGATTTACGTAATCGCAT
1 TGCGATTTACGTAATCGCAA
806552 TGCGATTTACGTAATCGCAA
1 TGCGATTTACGTAATCGCAA
* ** *
806572 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTTACGTAATCGCAA
806593 TGCGAT
1 TGCGAT
806599 AGTCAAAATC
Statistics
Matches: 124, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.11
20 78 0.63
21 30 0.24
22 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCGATTTACGTAATCGCAA
Found at i:806609 original size:61 final size:59
Alignment explanation
Indices: 806431--806617 Score: 139
Period size: 61 Copynumber: 3.1 Consensus size: 59
806421 CAGAATCTCG
** * *
806431 TTGCGATTACGTAAATCGCAATACGA-TTACGTAAATCG-AAGTGCGAAT-TAGGAAAATCGCA
1 TTGCGATTACGT-AATCGCAACGCGATTTACG-AAATCGCAA-CGCG-ATGTA-CAAAATCGCA
* * * * * **
806492 ATGCGATTACGTATTCGCAATGCGATTTACGTAATCGCAACGCGATTTACGTAATCGCA
1 TTGCGATTACGTAATCGCAACGCGATTTACGAAATCGCAACGCGATGTACAAAATCGCA
** * *
806551 TTGCGATTTACGTAATCGCAACGCGAATTTGGGAAATCGCAATGCGATAGT-CAAAATCGCG
1 TTGCGA-TTACGTAATCGCAACGCG-ATTTACGAAATCGCAACGCGAT-GTACAAAATCGCA
806612 TTGCGA
1 TTGCGA
806618 ATCTGGAAAC
Statistics
Matches: 101, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
59 14 0.14
60 37 0.37
61 49 0.49
62 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (59 bp):
TTGCGATTACGTAATCGCAACGCGATTTACGAAATCGCAACGCGATGTACAAAATCGCA
Found at i:810316 original size:17 final size:16
Alignment explanation
Indices: 810279--810319 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
810269 TAAAAATAAA
810279 AATAA-ATAAATATAT
1 AATAATATAAATATAT
810294 -AT-ATATAAATTATAT
1 AATAATATAAA-TATAT
810309 AATAATATAAA
1 AATAATATAAA
810320 ACTTTAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 7 0.32
15 5 0.23
16 2 0.09
17 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAATATAAATATAT
Found at i:812522 original size:17 final size:18
Alignment explanation
Indices: 812489--812523 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
812479 TATAATTATT
812489 TATTCATATTATCTTTTA
1 TATTCATATTATCTTTTA
*
812507 TATTCA-ATTATGTTTTA
1 TATTCATATTATCTTTTA
812524 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTCATATTATCTTTTA
Found at i:815714 original size:17 final size:18
Alignment explanation
Indices: 815681--815715 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
815671 GAGACAACTA
815681 ATTTTTAATTTTCTTTAT
1 ATTTTTAATTTTCTTTAT
*
815699 ATTTTTAGTTTT-TTTAT
1 ATTTTTAATTTTCTTTAT
815716 TTTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTAATTTTCTTTAT
Found at i:816497 original size:26 final size:27
Alignment explanation
Indices: 816468--816518 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
816458 TATGTTAGGG
*
816468 GATGAACTTATAAAA-TTTGAAGGAGA
1 GATGAACATATAAAACTTTGAAGGAGA
816494 GATGAACATATAAAACTTTGAAGGA
1 GATGAACATATAAAACTTTGAAGGA
816519 ACAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (27 bp):
GATGAACATATAAAACTTTGAAGGAGA
Found at i:816859 original size:19 final size:19
Alignment explanation
Indices: 816832--816883 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
816822 GGATGTTATG
*
816832 GTTAGTATTTTAAAAAGT-T
1 GTTAATATTTTAAAAA-TAT
*
816851 GTTAATATTGT-AAAATAT
1 GTTAATATTTTAAAAATAT
*
816869 GTTGATATTTTAAAA
1 GTTAATATTTTAAAA
816884 GAATACAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 14 0.52
19 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (19 bp):
GTTAATATTTTAAAAATAT
Found at i:817570 original size:20 final size:20
Alignment explanation
Indices: 817542--817579 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
817532 GTGTTTGTGT
817542 TGTTCATTTATGTTCGTTCG
1 TGTTCATTTATGTTCGTTCG
*
817562 TGTTTATTTATGTTCGTT
1 TGTTCATTTATGTTCGTT
817580 TATTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.61
Consensus pattern (20 bp):
TGTTCATTTATGTTCGTTCG
Found at i:819053 original size:21 final size:21
Alignment explanation
Indices: 819029--819068 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
819019 GAAATGATAA
* *
819029 GTCATTTGATCGAAAGGTTAG
1 GTCATTTCATCAAAAGGTTAG
819050 GTCATTTCATCAAAAGGTT
1 GTCATTTCATCAAAAGGTT
819069 TTAACCCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (21 bp):
GTCATTTCATCAAAAGGTTAG
Found at i:827021 original size:18 final size:17
Alignment explanation
Indices: 826998--827043 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
826988 AATGTTTCTG
826998 AGGAATTGGAATCTGTGA
1 AGGAATTGGAATCTGT-A
* *
827016 AGGAATTGAAATCTGTC
1 AGGAATTGGAATCTGTA
827033 AGGAATTGGAA
1 AGGAATTGGAA
827044 ACCAATTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (17 bp):
AGGAATTGGAATCTGTA
Found at i:834107 original size:21 final size:21
Alignment explanation
Indices: 834081--834125 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
834071 GATTTCTGGG
* *
834081 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
834102 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
834123 CAA
1 CAA
834126 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:835141 original size:2 final size:2
Alignment explanation
Indices: 835134--835181 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
835124 GAACATGTGA
835134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
835176 AT AT AT
1 AT AT AT
835182 TTAAGAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:835844 original size:13 final size:13
Alignment explanation
Indices: 835826--835887 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 13
835816 TTATATGGCA
835826 CTACGGTGCAATT
1 CTACGGTGCAATT
835839 CTACGG-GC-A--
1 CTACGGTGCAATT
*
835848 CTTCGGTGCAATT
1 CTACGGTGCAATT
835861 CTACGG-GC-A--
1 CTACGGTGCAATT
*
835870 CTTCGGTGCAATT
1 CTACGGTGCAATT
835883 CTACG
1 CTACG
835888 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
9 10 0.27
10 4 0.11
11 4 0.11
12 4 0.11
13 15 0.41
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:835854 original size:22 final size:22
Alignment explanation
Indices: 835822--835887 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
835812 ATCATTATAT
*
835822 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
835844 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
835866 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
835888 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:839056 original size:21 final size:21
Alignment explanation
Indices: 839030--839074 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
839020 GATTTCTGGG
* *
839030 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
839051 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
839072 CAA
1 CAA
839075 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:840094 original size:2 final size:2
Alignment explanation
Indices: 840087--840150 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
840077 GAACATGTGA
840087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
840129 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
840151 GTTTAAGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:840845 original size:22 final size:22
Alignment explanation
Indices: 840802--840845 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
840792 ATCATTATAT
*
840802 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTATACG
* *
840824 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
840846 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTACGGTGCAATTATACG
Found at i:843615 original size:30 final size:30
Alignment explanation
Indices: 843579--843638 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
843569 CTAAGAATAA
843579 TCCCCCTATCTGAAACAATAGACACAATGT
1 TCCCCCTATCTGAAACAATAGACACAATGT
843609 TCCCCCTATCTGAAACAATAGACACAATGT
1 TCCCCCTATCTGAAACAATAGACACAATGT
843639 CCTTTACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (30 bp):
TCCCCCTATCTGAAACAATAGACACAATGT
Found at i:846620 original size:18 final size:18
Alignment explanation
Indices: 846597--846633 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
846587 TATATGTTCG
846597 TTTATGTTCGTTCATTTA
1 TTTATGTTCGTTCATTTA
846615 TTTATGTTCGTTCATTTA
1 TTTATGTTCGTTCATTTA
846633 T
1 T
846634 GTTCGAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (18 bp):
TTTATGTTCGTTCATTTA
Found at i:846985 original size:16 final size:16
Alignment explanation
Indices: 846964--846994 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
846954 AAAAAAAAAT
846964 TTGTTCGTTTATGTTC
1 TTGTTCGTTTATGTTC
846980 TTGTTCGTTTATGTT
1 TTGTTCGTTTATGTT
846995 GTTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.10, G:0.19, T:0.65
Consensus pattern (16 bp):
TTGTTCGTTTATGTTC
Found at i:848370 original size:38 final size:38
Alignment explanation
Indices: 848273--848362 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
848263 TTGGGCCGGG
* *
848273 TATATATAT-AT-ATTTAAATTAAATATATAAATATTA
1 TATATATATAATAATTTAATTTAAATTTATAAATATTA
* ** *
848309 TATATATTTTTTAATTTAATTTAAATTTATTAATATTA
1 TATATATATAATAATTTAATTTAAATTTATAAATATTA
848347 TATATATATAATAATT
1 TATATATATAATAATT
848363 ATTTTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 8 0.18
37 1 0.02
38 35 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TATATATATAATAATTTAATTTAAATTTATAAATATTA
Found at i:854368 original size:18 final size:18
Alignment explanation
Indices: 854345--854379 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
854335 CTCCCAATAT
854345 TAGTGAGT-TTCTTGTAAG
1 TAGTGAGTGTT-TTGTAAG
854363 TAGTGAGTGTTTTGTAA
1 TAGTGAGTGTTTTGTAA
854380 ATACCTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.46
Consensus pattern (18 bp):
TAGTGAGTGTTTTGTAAG
Found at i:858973 original size:79 final size:79
Alignment explanation
Indices: 858833--859013 Score: 254
Period size: 79 Copynumber: 2.3 Consensus size: 79
858823 TTATAGCATA
* * * * * ** * *
858833 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTTTGGTATCCTTTCATGCCAATAATGCAC
1 CTTTCATGATGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGAAC
858898 CCATATGCATTATT
66 CCATATGCATTATT
* * *
858912 CTTTCATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGAAC
1 CTTTCATGATGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGAAC
858977 CCATATGCATTATT
66 CCATATGCATTATT
858991 CTTTCATGATGATAATGTACCCA
1 CTTTCATGATGATAATGTACCCA
859014 CCTGACTATC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 90 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
CTTTCATGATGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGAAC
CCATATGCATTATT
Found at i:859428 original size:75 final size:76
Alignment explanation
Indices: 859270--859433 Score: 181
Period size: 75 Copynumber: 2.2 Consensus size: 76
859260 ATTACTACCC
* * *
859270 TAGTATCGATACTTCCATACTATGGTACAGATACCCCCCTTCGGGTATCGATACCAAAAATAGGT
1 TAGTATCGATACTACCATACTAGGGTACAGATA-CCCCCTTCGGGTATCGATACCAAAAATAGAT
*
859335 TCGGTGTTGCCA
65 TCGATGTTGCCA
** * *
859347 GGGTATCGATACTACCCTACTAGGGTATC-GATA-CCCCTATC-GGTATCGATACCAAAATTAGA
1 TAGTATCGATACTACCATACTAGGGTA-CAGATACCCCCT-TCGGGTATCGATACCAAAAATAGA
** *
859409 TTCGATGTTTTCT
64 TTCGATGTTGCCA
859422 TAGTATCGATAC
1 TAGTATCGATAC
859434 CTCTTATCAC
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
75 43 0.60
76 2 0.03
77 26 0.36
78 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (76 bp):
TAGTATCGATACTACCATACTAGGGTACAGATACCCCCTTCGGGTATCGATACCAAAAATAGATT
CGATGTTGCCA
Found at i:860522 original size:64 final size:63
Alignment explanation
Indices: 860470--860625 Score: 262
Period size: 64 Copynumber: 2.5 Consensus size: 63
860460 GTGCACTAAG
860470 AGTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AACAAGCCTGAATGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAATGCATCGATGCATGGT
*
860533 ATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 A-GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAATGCATCGATGCATGGT
860597 AGTGCATCGATGCATAAAATGCATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
860626 ATGGTGAGTG
Statistics
Matches: 89, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
63 29 0.33
64 55 0.62
65 3 0.03
66 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAATGCATCGATGCATGGT
Found at i:863192 original size:21 final size:21
Alignment explanation
Indices: 863174--863237 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
863164 TCGGTGCATC
863174 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* *
863195 TTCAAATGGATGCATCGATGCACT
1 TTC--AT-GATGTATCGATGCACA
863219 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
863238 TTATGCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 2 0.06
23 2 0.06
24 17 0.47
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:863230 original size:45 final size:44
Alignment explanation
Indices: 863135--863237 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 44
863125 AAACCCGACG
* * *
863135 GATGCATCGATGCACATTCAAGGCGTGCATCGGTGCATCTTCAT
1 GATGTATCGATGCACATTCAAGGCATGCATCGATGCATCTTCAT
863179 GATGTATCGATGCACATTCAAATGG-ATGCATCGATGCA-CTTTCAT
1 GATGTATCGATGCACATTC-AA-GGCATGCATCGATGCATC-TTCAT
863224 -AGTGTATCGATGCA
1 GA-TGTATCGATGCA
863238 TTATGCACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
44 20 0.38
45 30 0.58
46 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (44 bp):
GATGTATCGATGCACATTCAAGGCATGCATCGATGCATCTTCAT
Found at i:869153 original size:20 final size:20
Alignment explanation
Indices: 869128--869165 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
869118 ATTCGATATG
869128 TGAGTGCATCAATGCATCAA
1 TGAGTGCATCAATGCATCAA
*
869148 TGAGTGCATCGATGCATC
1 TGAGTGCATCAATGCATC
869166 CTTCTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCAATGCATCAA
Found at i:869595 original size:3 final size:3
Alignment explanation
Indices: 869579--869612 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
869569 GCACCCACGT
869579 GAA GAA GGAA -AA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA G
869613 TGTAGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:877474 original size:30 final size:30
Alignment explanation
Indices: 877440--877514 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
877430 CGTATTTTTG
*
877440 AAAAAATGACCGAAAACATTATTA-GATGCT
1 AAAAAATGACCGAAAACATTATCATG-TGCT
* *
877470 -AAAAATGACTGGAAACATTATCATGTGCT
1 AAAAAATGACCGAAAACATTATCATGTGCT
877499 AAAAAATGACCGAAAA
1 AAAAAATGACCGAAAA
877515 TGTTTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (30 bp):
AAAAAATGACCGAAAACATTATCATGTGCT
Found at i:877627 original size:11 final size:11
Alignment explanation
Indices: 877605--877638 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
877595 AATCGATAAC
*
877605 ACCTTATTTTA
1 ACCTTATATTA
*
877616 ATCTTATATTA
1 ACCTTATATTA
877627 ACCTTATATTA
1 ACCTTATATTA
877638 A
1 A
877639 GGTGTCACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (11 bp):
ACCTTATATTA
Found at i:878582 original size:27 final size:27
Alignment explanation
Indices: 878552--878649 Score: 178
Period size: 27 Copynumber: 3.6 Consensus size: 27
878542 AGTTAATTTC
* *
878552 TGTTAACTAACTTGTTTTTTTAACAAT
1 TGTTAAGTAACTTGTTTTTTTAATAAT
878579 TGTTAAGTAACTTGTTTTTTTAATAAT
1 TGTTAAGTAACTTGTTTTTTTAATAAT
878606 TGTTAAGTAACTTGTTTTTTTAATAAT
1 TGTTAAGTAACTTGTTTTTTTAATAAT
878633 TGTTAAGTAACTTGTTT
1 TGTTAAGTAACTTGTTT
878650 ACAACAGACT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (27 bp):
TGTTAAGTAACTTGTTTTTTTAATAAT
Found at i:879028 original size:2 final size:2
Alignment explanation
Indices: 879021--879059 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
879011 TTCTTCCCGC
879021 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
879060 GGGGGGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:889564 original size:60 final size:59
Alignment explanation
Indices: 889488--889600 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
889478 GTCATATGAT
* * *
889488 TATTTTATAACTTTTAATAGTCGAGA-GACTCAACAAAACATCATCCTATAGTTGATGGAC
1 TATTTTATAACATTTAATAGTCGA-ATGACTCAA-AAAACAACACCCTATAGTTGATGGAC
* *
889548 TATTTTATAACATTTAATAGTTGAATGACTCAAAAAATAACACCCTATAGTTG
1 TATTTTATAACATTTAATAGTCGAATGACTCAAAAAACAACACCCTATAGTTG
889601 GGGACCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 18 0.38
60 29 0.62
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (59 bp):
TATTTTATAACATTTAATAGTCGAATGACTCAAAAAACAACACCCTATAGTTGATGGAC
Found at i:890113 original size:7 final size:7
Alignment explanation
Indices: 890101--890126 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
890091 TTAAAGGAGT
890101 GGTTTAG
1 GGTTTAG
890108 GGTTTAG
1 GGTTTAG
890115 GGTTTAG
1 GGTTTAG
890122 GGTTT
1 GGTTT
890127 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:892854 original size:22 final size:24
Alignment explanation
Indices: 892811--892855 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
892801 TTTGTTAACC
892811 AAATATTCTAATATTATTTTAAAAA
1 AAATATTCTAATA-TATTTTAAAAA
892836 AAATA-TCTAATA-ATTTTAAA
1 AAATATTCTAATATATTTTAAA
892856 TCGATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTCTAATATATTTTAAAAA
Found at i:897114 original size:2 final size:2
Alignment explanation
Indices: 897107--897134 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
897097 TTTAATCTTT
897107 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
897135 AAAACTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:898115 original size:26 final size:27
Alignment explanation
Indices: 898060--898137 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
898050 ATTTGATTTT
* *
898060 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATATTTTAATATTA
898085 AATTA-AATATTAATATTTTAATATTA
1 AATTATAATATTAATATTTTAATATTA
*
898111 TATTATAGATATT-A-ATTTTAATATTA
1 AATTATA-ATATTAATATTTTAATATTA
898137 A
1 A
898138 TTTTTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 15 0.33
25 5 0.11
26 18 0.40
27 2 0.04
28 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
AATTATAATATTAATATTTTAATATTA
Found at i:898158 original size:23 final size:24
Alignment explanation
Indices: 898128--898177 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
898118 GATATTAATT
898128 TTAATATTAATTTTTTAA-ATAAA
1 TTAATATTAATTTTTTAATATAAA
*
898151 TTAATATTAATTTTTTAATATATA
1 TTAATATTAATTTTTTAATATAAA
898175 TTA
1 TTA
898178 TAGATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATATTAATTTTTTAATATAAA
Found at i:898189 original size:63 final size:65
Alignment explanation
Indices: 898036--898193 Score: 252
Period size: 64 Copynumber: 2.5 Consensus size: 65
898026 AGAGGTTTTA
* *
898036 TTTAATTTTATATTATTTGAT-TTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATA
1 TTTAATATTATATTA-TAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATA
898100 T
65 T
*
898101 TTTAATATTATATTATAGATA-TTAATTTTAATATTAATTTTTTAAATAAATT-AATATTAATTT
1 TTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATAT
898164 TTTAATA-TATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATATTTAATTTTA
898194 TATCATATAA
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
62 13 0.15
63 26 0.30
64 35 0.40
65 14 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (65 bp):
TTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATAT
Found at i:898222 original size:62 final size:61
Alignment explanation
Indices: 898036--898211 Score: 192
Period size: 64 Copynumber: 2.7 Consensus size: 61
898026 AGAGGTTTTA
* * * *
898036 TTTAATTTTATATTATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATAT
1 TTTAATATTATATTA-TAGATATTAATTTTAATATTAATTATTT-AAT-AATT-AATATTAATAT
* *
898101 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTATTT-AAT-AATTAATATTAATAT
898164 TTTAATA-TATATTATAGATATTTAATTTTATATCATATAAATTATTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA-AT-AT-T-AATTATTTA
898212 TATATTATTA
Statistics
Matches: 101, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
62 13 0.13
63 26 0.26
64 37 0.37
65 16 0.16
66 2 0.02
67 7 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (61 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTATTTAATAATTAATATTAATAT
Found at i:898225 original size:20 final size:19
Alignment explanation
Indices: 898202--898247 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
898192 TATATCATAT
898202 AAATTATTTATATATTATTA
1 AAATTATTTATAT-TTATTA
*
898222 AAA-T-TTTATATTTATTT
1 AAATTATTTATATTTATTA
*
898239 TAATTATTT
1 AAATTATTT
898248 TGATTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.32
18 8 0.36
19 4 0.18
20 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTATTTATATTTATTA
Found at i:898243 original size:17 final size:18
Alignment explanation
Indices: 898187--898237 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
898177 ATAGATATTT
898187 AATTTTATATCA-TA-TAA
1 AATTTTATAT-ATTATTAA
*
898204 ATTATTTATATATTATTAA
1 AAT-TTTATATATTATTAA
898223 AATTTTATAT-TTATT
1 AATTTTATATATTATT
898238 TTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 8 0.28
18 16 0.55
19 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTATATATTATTAA
Found at i:898755 original size:31 final size:31
Alignment explanation
Indices: 898696--898756 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
898686 GTAGTTGTAT
* * **
898696 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATATCAGTATTACAAAACTA
898727 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAGTATTACAAAACT
898757 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAGTATTACAAAACTA
Found at i:899680 original size:2 final size:2
Alignment explanation
Indices: 899673--899701 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
899663 GGCAATACTG
899673 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 T
899702 TATGCATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:902931 original size:2 final size:2
Alignment explanation
Indices: 902924--902962 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
902914 TTCAATTTTG
902924 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 T
902963 TATGAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:905327 original size:22 final size:20
Alignment explanation
Indices: 905278--905327 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
905268 ATATCATACC
*
905278 ATACCATTATATTATGTATAT
1 ATACC-TTATATTATGTATAG
*
905299 ATACCTTATATTATAAGTGTAG
1 ATACCTTATATTAT--GTATAG
905321 ATACCTT
1 ATACCTT
905328 TTTTTGACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 5 0.20
22 11 0.44
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (20 bp):
ATACCTTATATTATGTATAG
Found at i:906291 original size:17 final size:17
Alignment explanation
Indices: 906269--906316 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
906259 CAAGACCAAC
*
906269 CCGAGCCAGACCTAGAA
1 CCGAGCCAGACCCAGAA
*
906286 CCGAGCCAGACCCATAA
1 CCGAGCCAGACCCAGAA
* *
906303 CCGATCCAGGCCCA
1 CCGAGCCAGACCCA
906317 AACAATCCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (17 bp):
CCGAGCCAGACCCAGAA
Found at i:907950 original size:12 final size:13
Alignment explanation
Indices: 907933--907962 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
907923 TATCTTTTAA
907933 TTTTTTTAAATTT
1 TTTTTTTAAATTT
907946 TTTTTTTAAATTT
1 TTTTTTTAAATTT
907959 TTTT
1 TTTT
907963 AAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTAAATTT
Found at i:907957 original size:23 final size:24
Alignment explanation
Indices: 907916--907965 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
907906 CGCAGATCAA
907916 AAATTTTTATCTTTTAATTTTTTT
1 AAATTTTTATCTTTTAATTTTTTT
907940 AAATTTTT-T-TTTTAAATTTTTTT
1 AAATTTTTATCTTTT-AATTTTTTT
907963 AAA
1 AAA
907966 AATATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.16
23 13 0.52
24 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
AAATTTTTATCTTTTAATTTTTTT
Found at i:907975 original size:23 final size:22
Alignment explanation
Indices: 907927--907975 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
907917 AATTTTTATC
** * *
907927 TTTTAATTTTTTTAAATTTTTT
1 TTTTAATTTTTTTAAAAATATA
907949 TTTTAAATTTTTTTAAAAATATA
1 TTTT-AATTTTTTTAAAAATATA
907972 TTTT
1 TTTT
907976 TGGGTATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTAATTTTTTTAAAAATATA
Found at i:908297 original size:145 final size:146
Alignment explanation
Indices: 908116--908435 Score: 423
Period size: 145 Copynumber: 2.2 Consensus size: 146
908106 CGTTTCGATA
** * * *
908116 AGGGACTAAATT-AAAAAATTAAAAA-AGTTATCAAAAAGAGTAATTGAAAGAAAATATTTATTT
1 AGGGACTAAATTGAAAATTTTAAAAATAGTTATCAAAAAGAGGAATTGAAAGAAAATATGTATTC
** * * *
908179 TACGATGGTTTATGAGCTTTTGGTTCAAATTTGGT-AAAAATGGACTTAAAATGAAGGAGGAATT
66 TACGATGACTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAT-GACTTAAAATGAAGGAGGAATT
908243 GAAGGAACAAGGAAATT
130 GAAGGAACAAGGAAATT
* *
908260 AGGGACTAAATTGAAAATTTTAAAAATA-TTATCAAAAAGAGGAATTTAAAGAACATATGTATTC
1 AGGGACTAAATTGAAAATTTTAAAAATAGTTATCAAAAAGAGGAATTGAAAGAAAATATGTATTC
* *
908324 TACGATGACTTAGGAGCATGTGGTTCAGATTTGGTAAAAAATGACTTAAAATGAAGGATGAATTG
66 TACGATGACTTAGGAGCATGTGGTTCAAATTTGGTAAAAAATGACTTAAAATGAAGGAGGAATTG
* *
908389 AAGGAATAAGGGAATT
131 AAGGAACAAGGAAATT
* * *
908405 AGGGACTAAATAGTAAATTTGTCAAAATAGT
1 AGGGACTAAATTGAAAATTT-TAAAAATAGT
908436 CAGCCAAATT
Statistics
Matches: 152, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
144 12 0.08
145 125 0.82
146 14 0.09
147 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (146 bp):
AGGGACTAAATTGAAAATTTTAAAAATAGTTATCAAAAAGAGGAATTGAAAGAAAATATGTATTC
TACGATGACTTAGGAGCATGTGGTTCAAATTTGGTAAAAAATGACTTAAAATGAAGGAGGAATTG
AAGGAACAAGGAAATT
Found at i:909652 original size:22 final size:22
Alignment explanation
Indices: 909627--909674 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
909617 GGTCAACTCG
*
909627 TTGACCGGTCTGACTGTTAACT
1 TTGACCGGTCTGACCGTTAACT
** *
909649 TTGATTGGTCTGACCGTTGACT
1 TTGACCGGTCTGACCGTTAACT
909671 TTGA
1 TTGA
909675 TCGAAAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (22 bp):
TTGACCGGTCTGACCGTTAACT
Found at i:909675 original size:22 final size:22
Alignment explanation
Indices: 909633--909675 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
909623 CTCGTTGACC
*
909633 GGTCTGACTGTTAACTTTGATT
1 GGTCTGACCGTTAACTTTGATT
*
909655 GGTCTGACCGTTGACTTTGAT
1 GGTCTGACCGTTAACTTTGAT
909676 CGAAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (22 bp):
GGTCTGACCGTTAACTTTGATT
Found at i:911330 original size:19 final size:19
Alignment explanation
Indices: 911308--911372 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
911298 CTCTGAACTT
* *
911308 TGATATCTGTTATGATCTC
1 TGATATCTGTTATGATTTA
* *
911327 TGATTTTTGTTATGATTTA
1 TGATATCTGTTATGATTTA
* *
911346 TGATCTCTGTTCTGATTTA
1 TGATATCTGTTATGATTTA
911365 TGATATCT
1 TGATATCT
911373 CTATTTACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (19 bp):
TGATATCTGTTATGATTTA
Found at i:916419 original size:21 final size:21
Alignment explanation
Indices: 916393--916436 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
916383 CTCATTGATA
* *
916393 ACGTACATACGCCTTATAGAG
1 ACGTACACACGCCTTATAAAG
*
916414 ACGTACACACTCCTTATAAAG
1 ACGTACACACGCCTTATAAAG
916435 AC
1 AC
916437 AACTATTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (21 bp):
ACGTACACACGCCTTATAAAG
Found at i:919039 original size:22 final size:22
Alignment explanation
Indices: 919011--919056 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
919001 TGTTAAGGGA
*
919011 TAAATTTATAAAATTTTAGGAG
1 TAAATTTATAAAATTTTAAGAG
919033 TAAATTTATAAAATTTTAAGAG
1 TAAATTTATAAAATTTTAAGAG
919055 TA
1 TA
919057 TTACATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (22 bp):
TAAATTTATAAAATTTTAAGAG
Found at i:925934 original size:2 final size:2
Alignment explanation
Indices: 925927--925951 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
925917 TAGTCCATTC
925927 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
925952 CATTAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:928051 original size:64 final size:64
Alignment explanation
Indices: 927978--928201 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 64
927968 TGTTTGAATG
* * **
927978 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
928041 A
64 A
* * **
928042 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** ** * ** *
928106 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
928170 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
928202 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 126 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:928525 original size:12 final size:12
Alignment explanation
Indices: 928508--928542 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
928498 ATATATGTTC
928508 ATGTGATATGAT
1 ATGTGATATGAT
928520 ATGTGATATGAT
1 ATGTGATATGAT
928532 ATGTGATATGA
1 ATGTGATATGA
928543 GAACATGATA
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:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:928603 original size:29 final size:29
Alignment explanation
Indices: 928561--928631 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
928551 TATGAAGTGG
928561 CATGAGCTACATGATCACAAGAGAAATGA
1 CATGAGCTACATGATCACAAGAGAAATGA
928590 CATGAGCTACATGATCACAAGAGAAATGA
1 CATGAGCTACATGATCACAAGAGAAATGA
928619 CATGAG-TACATGA
1 CATGAGCTACATGA
928632 ACATATGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (29 bp):
CATGAGCTACATGATCACAAGAGAAATGA
Found at i:928734 original size:15 final size:15
Alignment explanation
Indices: 928716--928763 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
928706 GAGGGTATAA
928716 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* *
928731 TAGTCATTCGGGACG
1 TAGTCCTTCGGGATG
928746 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
928761 TAG
1 TAG
928764 GAGTCCTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:934903 original size:64 final size:64
Alignment explanation
Indices: 934826--935043 Score: 208
Period size: 64 Copynumber: 3.4 Consensus size: 64
934816 AATGTGCACT
** ** *
934826 GATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGAAATTCATGCAT
1 GATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCAAATGAAATTCATGCAT
934889 C
64 C
* * **
934890 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCAAATGCAATTGGTGCATC
1 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGAAATTCATGCATC
* ** ** * ** * *
934954 GATGCATAAGGAGTGCATCGATGCATCCCAACAATAATACTACATCGAAT-ACCTTTTATGCACC
1 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGA-AATTCATGCATC
*
935018 GATGCATTAGTAGTGCATCGATGCAT
1 GATGCATAAGTAGTGCATCGATGCAT
935044 ACCTTCATTA
Statistics
Matches: 127, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
64 121 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGAAATTCATGCATC
Found at i:935537 original size:15 final size:15
Alignment explanation
Indices: 935519--935581 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
935509 GAGGGTATAA
935519 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
935534 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
935549 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
935564 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
935579 TAG
1 TAG
935582 GAGTCCTACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:935555 original size:30 final size:30
Alignment explanation
Indices: 935519--935581 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
935509 GAGGGTATAA
935519 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
1 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
935549 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
1 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
935579 TAG
1 TAG
935582 GAGTCCTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (30 bp):
TAGTCCTTCGGGACGTAGTCCTTCGGGATG
Found at i:945942 original size:30 final size:30
Alignment explanation
Indices: 945906--945977 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
945896 TTATTATTGG
945906 CCTTAGTGGCGTTAATTATATAAACGTTGA
1 CCTTAGTGGCGTTAATTATATAAACGTTGA
945936 CCTTAGTGGCGTTAATTATATAAACGTTGA
1 CCTTAGTGGCGTTAATTATATAAACGTTGA
*
945966 TCTTAGTGGCGT
1 CCTTAGTGGCGT
945978 AAGCATAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (30 bp):
CCTTAGTGGCGTTAATTATATAAACGTTGA
Found at i:947166 original size:21 final size:21
Alignment explanation
Indices: 947137--947177 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
947127 TGCACAGAAG
947137 TCGGATTTTAATCGATCCGGA
1 TCGGATTTTAATCGATCCGGA
* *
947158 TCGGTTTTTATTCGATCCGG
1 TCGGATTTTAATCGATCCGG
947178 TTTTTCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (21 bp):
TCGGATTTTAATCGATCCGGA
Found at i:947287 original size:15 final size:15
Alignment explanation
Indices: 947269--947324 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
947259 TAACCGGTTT
947269 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
947284 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
*
947301 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
947316 CGATTTTAA
1 CGGTTTTAA
947325 TATTATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 21 0.58
17 15 0.42
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:947294 original size:17 final size:17
Alignment explanation
Indices: 947272--947322 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
947262 CCGGTTTCGG
947272 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
947289 TTTTAAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
947304 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
947321 TT
1 TT
947323 AATATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:947466 original size:32 final size:32
Alignment explanation
Indices: 947366--947468 Score: 154
Period size: 33 Copynumber: 3.2 Consensus size: 32
947356 ACAAAGTTTA
* *
947366 CGAT-AATTGAAATACTTAAATACTTCTAAGTT
1 CGATAAATTCAAATACTTAAAAACTTC-AAGTT
*
947398 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
947431 CGATAAATTCAAATACTTAAAAACTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCAAGTT
947463 CGATAA
1 CGATAA
947469 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
32 15 0.23
33 49 0.75
34 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (32 bp):
CGATAAATTCAAATACTTAAAAACTTCAAGTT
Found at i:947487 original size:21 final size:21
Alignment explanation
Indices: 947463--947504 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
947453 ACTTCAAGTT
947463 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
947484 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
947505 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:949914 original size:20 final size:20
Alignment explanation
Indices: 949889--949928 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
949879 GTTAAAATAA
* *
949889 CCGGTTTAAAAAAATCCGAT
1 CCGGTTAAAAAAAAACCGAT
949909 CCGGTTAAAAAAAAACCGAT
1 CCGGTTAAAAAAAAACCGAT
949929 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
CCGGTTAAAAAAAAACCGAT
Found at i:950573 original size:13 final size:14
Alignment explanation
Indices: 950550--950595 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
950540 ATCATTGGTA
950550 TTTATTATTATTAT
1 TTTATTATTATTAT
950564 TTTATT-TTATTAT
1 TTTATTATTATTAT
*
950577 ATTATATATT-TT-T
1 TTTAT-TATTATTAT
950590 TTTATT
1 TTTATT
950596 TTTAATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 16 0.57
14 9 0.32
15 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:950581 original size:21 final size:21
Alignment explanation
Indices: 950555--950595 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
950545 TGGTATTTAT
950555 TATTAT-TATTTTATTTTATTA
1 TATTATATATTTT-TTTTATTA
950576 TATTATATATTTTTTTTATT
1 TATTATATATTTTTTTTATT
950596 TTTAATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTATATATTTTTTTTATTA
Found at i:954017 original size:31 final size:32
Alignment explanation
Indices: 953982--954063 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
953972 GTTTCAAAAG
* * *
953982 TTATAAAATTA-CGATTAAA-TTTATCAAATTA
1 TTATAAAATAATC-ATTAAATTTTAGCAAACTA
954013 TTATAAAATAATCATTAAATTTTAGCAAACTA
1 TTATAAAATAATCATTAAATTTTAGCAAACTA
* *
954045 TTATAGAATAGTCATTAAA
1 TTATAAAATAATCATTAAA
954064 GTTATCAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 16 0.36
32 28 0.64
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (32 bp):
TTATAAAATAATCATTAAATTTTAGCAAACTA
Found at i:961935 original size:13 final size:13
Alignment explanation
Indices: 961901--961929 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
961891 CATATGATTA
961901 TATCTATT-ATTT
1 TATCTATTAATTT
961913 TATCTATTAATTT
1 TATCTATTAATTT
961926 TATC
1 TATC
961930 ACTTAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
TATCTATTAATTT
Found at i:962217 original size:21 final size:21
Alignment explanation
Indices: 962188--962229 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
962178 GGAATTATTA
*
962188 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
962209 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
962230 ATTAATTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:962272 original size:11 final size:11
Alignment explanation
Indices: 962258--962287 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
962248 TAAATATCAT
*
962258 AAAATAATTTA
1 AAAAAAATTTA
962269 AAAAAAATTTA
1 AAAAAAATTTA
962280 AAAAAAAT
1 AAAAAAAT
962288 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAAATTTA
Found at i:965720 original size:138 final size:137
Alignment explanation
Indices: 965376--966410 Score: 1527
Period size: 138 Copynumber: 7.5 Consensus size: 137
965366 TTAATACGCA
* ** *
965376 TTCCCGAGGGGCGCCTTTTATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTT
1 TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
* *
965441 ATGTCCCCCGGGGAACTATTTATGTCAGTACC---TATTTCTTAGGGGACTTGGCAAAGTGGTGA
66 ATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGA
*
965503 AAGTGCG
131 AAGCGCG
* *
965510 TTTCCGGGGGACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
1 TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
* * *
965575 ATGTCCCCCGGGAAACTATTCATGTCAGTACCTATTATTTCTGAGTGGATTTGGCAAAGTGGTGA
66 ATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGA
965640 AAGCGCG
131 AAGCGCG
* * * *
965647 TTCCCAGAGGCGCGACTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACT
1 TTCCC-GGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACT
* *
965712 TATGTCCCCAGGGGAACTATTTATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
65 TATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
965777 AAAGCGCG
130 AAAGCGCG
* *
965785 TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTGTCATTGCCCTATTATGTCACTT
1 TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
**
965850 ATGTCCCCCCGGTAAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
66 ATGT-CCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
965915 AAAGCGCG
130 AAAGCGCG
* * * * *
965923 TTCCAGGGGGCACACCTTCCATTATTTTGTCAGAGAATATCTTATCATTGCCTTATTATGTCACT
1 TTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACT
*** * * * * *
965988 TATGTCCTATGGGGAACTATTAATATTAGTACCTATTATTTCTGAGGGGACTTGGTAAAGTGGTA
65 TATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
*
966053 AAAGTGCG
130 AAAGCGCG
* *
966061 TTCCCGGGGGAGCGCCTTCCATTATTTTGTCAGAGAGTATATTATCATTGCCCTATTATGTCACT
1 TTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACT
* * *
966126 TATGTCCCCCGGGGAACTATTTATGTCAGTACCTATTATTTCTGAAGAGACTTGGCAAAGTGGTG
65 TATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
*
966191 AAAGCGTG
130 AAAGCGCG
* * * * **
966199 TTCCCGAGGGCGTGCCTTCCATTATTTTTTCAAAGAATATGTTAAAATTGCCCTATTATGTCACT
1 TTCCCG-GGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACT
* *
966264 CATGTCCCCCGGGGGACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
65 TATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTG
966329 AAAGCGCG
130 AAAGCGCG
* * *
966337 TTCCCGGGGGGCACCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTC
1 TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
966402 ATGTCCCCC
66 ATGTCCCCC
966411 AGAGGCACAG
Statistics
Matches: 803, Mismatches: 91, Indels: 11
0.89 0.10 0.01
Matches are distributed among these distances:
134 89 0.11
137 155 0.19
138 502 0.63
139 57 0.07
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (137 bp):
TTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTT
ATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGA
AAGCGCG
Found at i:966604 original size:23 final size:23
Alignment explanation
Indices: 966556--966605 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
966546 TGAAGTTTAA
* * *
966556 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
966579 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
966602 ATAA
1 ATAA
966606 GTTGGTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:966873 original size:34 final size:34
Alignment explanation
Indices: 966835--966900 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
966825 GAATTTAAAG
966835 TTAAATTTCGAAT-GCTATAATTTGTATTTTAATT
1 TTAAATTTCGAATAG-TATAATTTGTATTTTAATT
*
966869 TTAAATTTTGAATAGTATAATTTGTATTTTAA
1 TTAAATTTCGAATAGTATAATTTGTATTTTAA
966901 AATCATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAGTATAATTTGTATTTTAATT
Found at i:969313 original size:30 final size:30
Alignment explanation
Indices: 969232--969327 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
969222 TAATTAGCAC
*
969232 AAAAAATAATTAATTA-ATAA--ATTTAAAT
1 AAAAAATAA-TATTTATATAATTATTTAAAT
* * * *
969260 AAATAATAAT-TATATAAATATTATTTTAAT
1 AAAAAATAATATTTATATA-ATTATTTAAAT
*
969290 AAAAAATAATATTTATATAATTATATAAAT
1 AAAAAATAATATTTATATAATTATTTAAAT
*
969320 ATAAAATA
1 AAAAAATA
969328 TAACAACTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 9 0.17
30 32 0.62
31 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAAAATAATATTTATATAATTATTTAAAT
Found at i:974773 original size:35 final size:34
Alignment explanation
Indices: 974688--974774 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
974678 ATTTGGTATT
*
974688 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
974722 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
974760 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
974775 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:977099 original size:17 final size:18
Alignment explanation
Indices: 977056--977096 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
977046 GAATTATATT
977056 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
977073 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
977091 ATTAAA
1 AGTAAA
977097 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:987762 original size:23 final size:23
Alignment explanation
Indices: 987735--987789 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
987725 ATATATGATA
*
987735 AATTATATGCTAAAGATTTATGG
1 AATTATATGCTAAAGATCTATGG
987758 AATTATATGCTAAAGATCTATGG
1 AATTATATGCTAAAGATCTATGG
**
987781 GGTTATATG
1 AATTATATG
987790 AAAAGGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
AATTATATGCTAAAGATCTATGG
Found at i:988703 original size:23 final size:23
Alignment explanation
Indices: 988670--988737 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
988660 ATTATTATAT
988670 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
988693 GGCACTCCGGTGCAAGTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
988716 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
988738 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:988789 original size:16 final size:17
Alignment explanation
Indices: 988768--988800 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
988758 TGCACAACCT
988768 CTATAG-ACTCACATAC
1 CTATAGTACTCACATAC
*
988784 CTATAGTTCTCACATAC
1 CTATAGTACTCACATAC
988801 GTCCATGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CTATAGTACTCACATAC
Done.