Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 24
Found at i:1677777 original size:18 final size:19
Alignment explanation
Indices: 1677742--1677791 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
1677732 TATTTTAATC
*
1677742 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
1677761 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
1677779 TTCTATATATTAA
1 AACTATATATTAA
1677792 ATAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:1679626 original size:18 final size:18
Alignment explanation
Indices: 1679579--1679627 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1679569 TGGACACTTT
* *
1679579 TAATATTTATTATAAAGTT
1 TAAT-TTTATTTTAAAGTA
*
1679598 TATTTTTATTTTAAAGTA
1 TAATTTTATTTTAAAGTA
1679616 TAATTTTATTTT
1 TAATTTTATTTT
1679628 GAAATCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TAATTTTATTTTAAAGTA
Found at i:1686406 original size:174 final size:173
Alignment explanation
Indices: 1686116--1686463 Score: 687
Period size: 174 Copynumber: 2.0 Consensus size: 173
1686106 TTTAAAGACG
1686116 CGCCTCGGGCGAGCCTAGGCGCCAGGCACTGAAGATGGCGCCCGCCCGGGTTGAGACGAGGCGAG
1 CGCCTCGGGCGAGCCTAGGCGCCAGGCACTGAAGATGGCGCCCGCCCGGGTTGAGACGAGGCGAG
1686181 ATACAAGAGGCGCGCGCCTACGGGCTTTAGGCGCCAGGCGCCGGGCGCAGCGCCTTGGAGCTTCT
66 ATACAAGAGGCGCGCGCCTACGGGCTTTAGGCGCCAGGCGCCGGGCGCAGCGCCTTGGAGCTTCT
1686246 GGGGTTAAAAACCCTAACATTCAAAATCTGTCTTTGGTTGAATC
131 GGGGTT-AAAACCCTAACATTCAAAATCTGTCTTTGGTTGAATC
1686290 CGCCTCGGGCGAGCCTAGGCGCCAGGCACTGAAGATGGCGCCCGCCCGGGTTGAGACGAGGCGAG
1 CGCCTCGGGCGAGCCTAGGCGCCAGGCACTGAAGATGGCGCCCGCCCGGGTTGAGACGAGGCGAG
1686355 ATACAAGAGGCGCGCGCCTACGGGCTTTAGGCGCCAGGCGCCGGGCGCAGCGCCTTGGAGCTTCT
66 ATACAAGAGGCGCGCGCCTACGGGCTTTAGGCGCCAGGCGCCGGGCGCAGCGCCTTGGAGCTTCT
1686420 GGGGTTAAAACCCTAACATTCAAAATCTGTCTTTGGTTGAATC
131 GGGGTTAAAACCCTAACATTCAAAATCTGTCTTTGGTTGAATC
1686463 C
1 C
1686464 TTTGGTGGTG
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 38 0.22
174 136 0.78
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (173 bp):
CGCCTCGGGCGAGCCTAGGCGCCAGGCACTGAAGATGGCGCCCGCCCGGGTTGAGACGAGGCGAG
ATACAAGAGGCGCGCGCCTACGGGCTTTAGGCGCCAGGCGCCGGGCGCAGCGCCTTGGAGCTTCT
GGGGTTAAAACCCTAACATTCAAAATCTGTCTTTGGTTGAATC
Found at i:1686531 original size:5 final size:5
Alignment explanation
Indices: 1686521--1686552 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1686511 GACATTTGAT
*
1686521 AAAGG AAAGG AAAGG AAAGG AGAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
1686553 TATAGGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:1687749 original size:27 final size:25
Alignment explanation
Indices: 1687719--1687779 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
1687709 AAACTATCAC
1687719 GATACCACACAAAAGGTGGCTCTGAAT
1 GATACCA-AC-AAAGGTGGCTCTGAAT
* *
1687746 GATA-TAACAGAGGTGGCTCTGAAT
1 GATACCAACAAAGGTGGCTCTGAAT
*
1687770 GATACTAACA
1 GATACCAACA
1687780 GATTAAGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 19 0.61
25 7 0.23
26 1 0.03
27 4 0.13
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (25 bp):
GATACCAACAAAGGTGGCTCTGAAT
Found at i:1687759 original size:24 final size:25
Alignment explanation
Indices: 1687732--1687781 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1687722 ACCACACAAA
1687732 AGGTGGCTCTGAATGATA-TAACAG
1 AGGTGGCTCTGAATGATACTAACAG
1687756 AGGTGGCTCTGAATGATACTAACAG
1 AGGTGGCTCTGAATGATACTAACAG
1687781 A
1 A
1687782 TTAAGTGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (25 bp):
AGGTGGCTCTGAATGATACTAACAG
Found at i:1688576 original size:17 final size:17
Alignment explanation
Indices: 1688554--1688587 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1688544 TTTCGGTTTG
*
1688554 AAAAAACCGATTTTTAA
1 AAAAAAACGATTTTTAA
*
1688571 AAAAAAACGGTTTTTAA
1 AAAAAAACGATTTTTAA
1688588 TCCGGTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAAAAACGATTTTTAA
Found at i:1688639 original size:20 final size:20
Alignment explanation
Indices: 1688614--1688658 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1688604 GTCATCCAAT
1688614 TTTTTAAACCCCATACCAGA
1 TTTTTAAACCCCATACCAGA
*
1688634 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCATACCAGA
1688654 TTTTT
1 TTTTT
1688659 TTCCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCATACCAGA
Found at i:1688798 original size:20 final size:20
Alignment explanation
Indices: 1688758--1688799 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1688748 CGGTTATACT
* *
1688758 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTTAAAAAAACCG
1688778 ATCCGGTTTTAAAAAAACCG
1 ATCCGGTTTTAAAAAAACCG
1688798 AT
1 AT
1688800 TTTTCTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
ATCCGGTTTTAAAAAAACCG
Found at i:1691670 original size:21 final size:20
Alignment explanation
Indices: 1691643--1691740 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
1691633 AATCAGTGTC
1691643 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
1691664 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
1691684 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1691704 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1691725 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1691741 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1691693 original size:41 final size:41
Alignment explanation
Indices: 1691584--1691740 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
1691574 AAATGACCAA
* **
1691584 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
1691623 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
1691664 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
1691705 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
1691741 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:1691750 original size:20 final size:20
Alignment explanation
Indices: 1691727--1691837 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
1691717 GCGAATATGA
1691727 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
1691747 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1691767 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
1691787 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1691807 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
1691827 AAATCGCAACG
1 AAATCGCAACG
1691838 ATAATCCGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 78 0.98
21 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:1691771 original size:40 final size:40
Alignment explanation
Indices: 1691727--1691897 Score: 172
Period size: 40 Copynumber: 4.3 Consensus size: 40
1691717 GCGAATATGA
*
1691727 AAATCGCAACGCG-AACACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGCGTAAC-CGTAAATCGCAA--CGATAATCCGT
* * * *
1691767 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGCGTAACCGTAAATCGCAACG-ATAATCCGT
* *
1691807 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGTAACCGTAAATCGCAACGATAATCCGT
* * *
1691847 TAATCGCAACGAG-AATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGTAA-CCGTAAATCGCAACGATAATCCGT
1691887 AAATCGCAACG
1 AAATCGCAACG
1691898 AGATCTGTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 106 0.95
41 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGCGTAACCGTAAATCGCAACGATAATCCGT
Found at i:1691792 original size:60 final size:57
Alignment explanation
Indices: 1691727--1691915 Score: 191
Period size: 60 Copynumber: 3.2 Consensus size: 57
1691717 GCGAATATGA
*
1691727 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGTAAATCGCAACGTG-ATCCGT
** * *
1691787 AAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGTAAATCGCAACG-TGATCCGT
* * * * *
1691847 TAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGTAAATCGCAACGAGATCTGT
1 AAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGTAAATCGCAACGTGATCCGT
*
1691906 AAATCACAAC
1 AAATCGCAAC
1691916 ACTGAAATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.02
59 14 0.13
60 89 0.83
61 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (57 bp):
AAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGTAAATCGCAACGTGATCCGT
Found at i:1691844 original size:20 final size:20
Alignment explanation
Indices: 1691761--1691898 Score: 156
Period size: 20 Copynumber: 6.9 Consensus size: 20
1691751 CGCAATGCGT
*
1691761 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
1691781 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
1691801 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
1691821 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
* *
1691841 ATCCGTTAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
1691861 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
1691881 ATCCGTAAATCGCAACGA
1 ATCCGTAAATCGCAACGA
1691899 GATCTGTAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 102 0.98
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:1691898 original size:40 final size:40
Alignment explanation
Indices: 1691761--1691915 Score: 197
Period size: 40 Copynumber: 3.9 Consensus size: 40
1691751 CGCAATGCGT
* *
1691761 ATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACGAGTATCCGTAAATCGCAACG-ATA
* * *
1691801 TTCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGTATCCGTAAATCGCAACGATA
* * *
1691841 ATCCGTTAATCGCAACGAGAATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGTATCCGTAAATCGCAACGATA
* *
1691881 ATCCGTAAATCGCAACGAG-ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAACGAGTATCCGTAAATCGCAAC
1691916 ACTGAAATTT
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 16 0.16
40 86 0.84
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
ATCCGTAAATCGCAACGAGTATCCGTAAATCGCAACGATA
Found at i:1692659 original size:18 final size:18
Alignment explanation
Indices: 1692636--1692673 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1692626 CACGGATTTT
1692636 GATGATGTTTCAGAAGAA
1 GATGATGTTTCAGAAGAA
1692654 GATGATGTTTCAGAAGAA
1 GATGATGTTTCAGAAGAA
1692672 GA
1 GA
1692674 AACAGACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.26
Consensus pattern (18 bp):
GATGATGTTTCAGAAGAA
Found at i:1692848 original size:12 final size:12
Alignment explanation
Indices: 1692831--1692855 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1692821 ATATAATCCT
1692831 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1692843 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1692855 G
1 G
1692856 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1694733 original size:19 final size:19
Alignment explanation
Indices: 1694711--1694944 Score: 269
Period size: 19 Copynumber: 13.4 Consensus size: 19
1694701 CGGAAATTAC
*
1694711 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1694730 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1694744 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1694764 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1694778 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1694797 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1694816 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1694830 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1694849 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1694868 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1694887 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1694905 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1694919 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
1694937 AATCGCAA
1 AATCGCAA
1694945 CGAGAGAATC
Statistics
Matches: 188, Mismatches: 6, Indels: 43
0.79 0.03 0.18
Matches are distributed among these distances:
14 40 0.21
15 5 0.03
16 13 0.07
17 4 0.02
18 20 0.11
19 93 0.49
20 13 0.07
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1694826 original size:52 final size:52
Alignment explanation
Indices: 1694739--1694912 Score: 278
Period size: 52 Copynumber: 3.2 Consensus size: 52
1694729 AAATCCCAAC
1694739 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1694792 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1694844 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
1694901 ATG-AAATCGCAA
1 ATGAAAATCGCAA
1694913 CGAAAGAATC
Statistics
Matches: 115, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
52 68 0.59
53 16 0.14
54 2 0.02
56 10 0.09
57 19 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1694881 original size:38 final size:36
Alignment explanation
Indices: 1694711--1694966 Score: 271
Period size: 33 Copynumber: 7.4 Consensus size: 36
1694701 CGGAAATTAC
* *
1694711 AATCGCAACGCGAAATGAAAATCCCAAC---ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAA
*
1694744 AATCGCAATGCGGAAATGAAAATCGCAACG--A-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAAATGAA
1694778 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAA
*
1694816 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAA
1694849 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAA
1694887 AATCGCAATGCGAAATG-AAATCGCAACGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAA
*
1694919 AATCGCAATGCG-AATGAAAATCGCAACG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAA
1694951 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1694967 TATAAACGCA
Statistics
Matches: 201, Mismatches: 6, Indels: 32
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.01
31 4 0.02
32 35 0.17
33 58 0.29
34 31 0.15
35 10 0.05
36 2 0.01
37 11 0.05
38 48 0.24
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (36 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATGAA
Found at i:1695082 original size:19 final size:19
Alignment explanation
Indices: 1694973--1695074 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1694963 AAATTATAAA
1694973 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1694992 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1695012 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1695028 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1695045 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1695064 CGCATTGCGAT
1 CGCATTGCGAT
1695075 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1695200 original size:14 final size:14
Alignment explanation
Indices: 1695181--1695217 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1695171 CATCAATTAC
1695181 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1695195 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1695209 ACAAATCAA
1 ACAAATCAA
1695218 TTAAATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1697206 original size:33 final size:33
Alignment explanation
Indices: 1697155--1697247 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1697145 GCGAAACCAA
*
1697155 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
1697188 AATTGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1697221 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1697248 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1697226 original size:14 final size:14
Alignment explanation
Indices: 1697174--1697230 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1697164 GCGAAATGAA
*
1697174 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
1697188 AATTGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1697205 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1697221 AATCGCAACG
1 AATCGCAACG
1697231 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1697245 original size:19 final size:19
Alignment explanation
Indices: 1697118--1697252 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1697108 TAGTTTACTT
* *
1697118 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1697138 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1697157 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1697176 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
1697190 TTGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1697209 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1697223 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1697242 TCGCAATGCGA
1 TCGCAACGCGA
1697253 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1697270 original size:19 final size:19
Alignment explanation
Indices: 1697248--1697359 Score: 111
Period size: 19 Copynumber: 6.5 Consensus size: 19
1697238 AAAATCGCAA
1697248 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1697267 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1697281 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1697300 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1697314 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1697333 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1697351 TGCGATTTT
1 TGCGATTTT
1697360 AACTTTCGTG
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 18 0.24
19 30 0.40
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1697290 original size:33 final size:33
Alignment explanation
Indices: 1697248--1697339 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1697238 AAAATCGCAA
1697248 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1697281 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1697314 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1697340 TGGTTTCGCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1697372 original size:20 final size:18
Alignment explanation
Indices: 1697278--1697375 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 18
1697268 GCGATCTTGT
*
1697278 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
* *
1697297 CGTTGCGA--TTCTGT--
1 CGTTGCGATTTTATTTCG
1697311 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
**
1697330 CGTTGCGATTTGGTTTCG
1 CGTTGCGATTTTATTTCG
1697348 CGTTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-A-TTTCG
*
1697368 TGTTGCGA
1 CGTTGCGA
1697376 AAGTAAACTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 4 0.06
18 16 0.25
19 19 0.30
20 12 0.19
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:1697539 original size:93 final size:93
Alignment explanation
Indices: 1697423--1697890 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
1697413 ATGGATTGCA
*
1697423 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697487 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1697515 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697580 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
1697608 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAATATTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697672 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1697700 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697765 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1697793 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1697858 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1697886 TTACT
1 TTACT
1697891 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 95 0.26
93 275 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1697740 original size:185 final size:186
Alignment explanation
Indices: 1697423--1697890 Score: 895
Period size: 185 Copynumber: 2.5 Consensus size: 186
1697413 ATGGATTGCA
*
1697423 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697487 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1697552 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
*
1697608 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAATATTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1697672 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1697737 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1697793 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1697858 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1697891 AAGCAATCTA
Statistics
Matches: 277, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
185 187 0.68
186 90 0.32
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1699628 original size:19 final size:20
Alignment explanation
Indices: 1699584--1699645 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1699574 TTTTGGTATA
*
1699584 AATGAAAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
** *
1699604 AATGACTGTCGCAACGCGA-
1 AATGACAATCGCAACGAGAG
1699623 AATGACAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
1699643 AAT
1 AAT
1699646 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAG
Found at i:1699648 original size:14 final size:14
Alignment explanation
Indices: 1699629--1699685 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1699619 GCGAAATGAC
1699629 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1699643 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1699662 AATCGCAATGAGAG
1 AATCGCAACGAGAG
1699676 AATCGCAACG
1 AATCGCAACG
1699686 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1699654 original size:33 final size:33
Alignment explanation
Indices: 1699583--1699702 Score: 150
Period size: 33 Copynumber: 3.5 Consensus size: 33
1699573 CTTTTGGTAT
1699583 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
1699622 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
1699655 AAATGAAAATCGCAATGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1699688 AAACCAAAATCGCAA
1 AAATGAAAATCGCAA
1699703 ATCGCAATGC
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
33 54 0.71
36 1 0.01
38 1 0.01
39 20 0.26
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1699667 original size:19 final size:19
Alignment explanation
Indices: 1699583--1699669 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 19
1699573 CTTTTGGTAT
*
1699583 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
***
1699602 AGAATGACTGTCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
1699622 AAATGACAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
1699639 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
1699655 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
1699670 TGAGAGAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 23 0.43
20 15 0.28
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:1699745 original size:14 final size:14
Alignment explanation
Indices: 1699726--1699782 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1699716 TTTGGTTTCG
1699726 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1699740 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1699759 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1699773 CGTTGCGATT
1 CGTTGCGATT
1699783 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1699764 original size:19 final size:19
Alignment explanation
Indices: 1699740--1699828 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
1699730 GCGATTCTCT
1699740 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1699759 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
1699773 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
1699792 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
1699812 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
1699829 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1699820 original size:39 final size:33
Alignment explanation
Indices: 1699710--1699828 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
1699700 CAAATCGCAA
**
1699710 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1699743 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1699776 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
1699815 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1699829 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1699962 original size:33 final size:33
Alignment explanation
Indices: 1699920--1699990 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1699910 AATACTAACT
1699920 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1699953 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1699986 TGAAA
1 TGAAA
1699991 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1700223 original size:22 final size:22
Alignment explanation
Indices: 1700171--1700225 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1700161 TGGTTGTGAG
**
1700171 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1700193 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1700215 GGATTTCTTCG
1 GGATTTCTTCG
1700226 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1700397 original size:20 final size:20
Alignment explanation
Indices: 1700372--1700565 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
1700362 CTTTAAATAT
1700372 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1700392 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
1700414 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
1700433 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
1700453 CGCATTGTGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1700473 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1700493 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1700513 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1700533 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1700553 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1700566 TGGAAAATCG
Statistics
Matches: 141, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.87
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1700537 original size:60 final size:60
Alignment explanation
Indices: 1700374--1700545 Score: 227
Period size: 60 Copynumber: 2.9 Consensus size: 60
1700364 TTAAATATCG
* ** *
1700374 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* * *** * *
1700435 CGTTGCGATATACGGATACGCATTGTGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
1700495 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
1700546 TCATATTCGC
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 68 0.73
61 25 0.27
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:1700559 original size:60 final size:60
Alignment explanation
Indices: 1700371--1700686 Score: 223
Period size: 60 Copynumber: 5.2 Consensus size: 60
1700361 GCTTTAAATA
* ** * *
1700371 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *** * * *
1700432 ACGCGTTGCGATATACGGATACGCATTGTGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
1700492 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
1700552 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
1700614 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
1700673 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1700687 TGTTGGTCAT
Statistics
Matches: 206, Mismatches: 39, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
59 16 0.08
60 91 0.44
61 77 0.37
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:1700582 original size:21 final size:20
Alignment explanation
Indices: 1700532--1700629 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1700522 ATTTATGTGT
* * * *
1700532 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
1700552 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
1700573 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
1700593 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
1700614 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
1700630 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:1700605 original size:61 final size:60
Alignment explanation
Indices: 1700532--1700688 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
1700522 ATTTATGTGT
*
1700532 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
1700593 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
1700654 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
1700689 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:1700624 original size:41 final size:41
Alignment explanation
Indices: 1700532--1700688 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
1700522 ATTTATGTGT
* * *
1700532 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
1700573 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
1700614 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
1700654 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
1700689 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:1702223 original size:21 final size:21
Alignment explanation
Indices: 1702181--1702233 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1702171 ATTCTGACTA
1702181 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* ** *
1702202 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1702223 TCGCAATGCGA
1 TCGCATTGCGA
1702234 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1702869 original size:14 final size:14
Alignment explanation
Indices: 1702850--1702910 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
1702840 GGAAATGACT
*
1702850 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
1702864 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
1702883 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
1702897 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1702911 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1702887 original size:33 final size:33
Alignment explanation
Indices: 1702829--1702921 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
1702819 CGAGAATGAA
**
1702829 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
1702863 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
1702896 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
1702922 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.80
34 11 0.20
ACGTcount: A:0.43, C:0.25, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:1702939 original size:19 final size:19
Alignment explanation
Indices: 1702917--1703081 Score: 170
Period size: 19 Copynumber: 9.1 Consensus size: 19
1702907 GAAACCAAAA
*
1702917 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1702936 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1702952 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1702969 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1702988 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1703002 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * **
1703021 TCGCATTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1703040 TACGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
1703060 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1703080 TC
1 TC
1703082 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
14 18 0.15
16 8 0.07
17 8 0.07
19 54 0.45
20 31 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1703000 original size:52 final size:52
Alignment explanation
Indices: 1702917--1703081 Score: 222
Period size: 52 Copynumber: 3.0 Consensus size: 52
1702907 GAAACCAAAA
*
1702917 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
1702969 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
* **
1703021 TCGCATTGTGATAGTCATTTACGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCGTTGCGATTTTCATT
1703080 TC
1 TC
1703082 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
52 66 0.66
53 9 0.09
59 25 0.25
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1703059 original size:39 final size:36
Alignment explanation
Indices: 1702917--1703073 Score: 132
Period size: 33 Copynumber: 4.4 Consensus size: 36
1702907 GAAACCAAAA
*
1702917 TCGCATTGCGATTTTCATTTCGCGTTGCGA--TTC-TG
1 TCGCATTGCGA--TTCATTTCGCGTTGCGATTTTCATT
1702952 TCG--TTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGA--TTCATTTCGCGTTGCGATTTTCATT
* *
1702988 TCGCGTTGCGATTC---TCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCATTTCGCGTTGCGATTTTCATT
*
1703021 TCGCATTGTGATAGTCATTTACGCGTTGCGATTTTCATT
1 TCGCATTGCGAT--TCATTT-CGCGTTGCGATTTTCATT
* *
1703060 CTCTCGTTGCGATT
1 -TCGCATTGCGATT
1703074 TTCATTTCAA
Statistics
Matches: 102, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
33 53 0.52
35 8 0.08
36 7 0.07
38 8 0.08
39 17 0.17
40 9 0.09
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (36 bp):
TCGCATTGCGATTCATTTCGCGTTGCGATTTTCATT
Found at i:1704958 original size:94 final size:93
Alignment explanation
Indices: 1704768--1705331 Score: 902
Period size: 94 Copynumber: 6.1 Consensus size: 93
1704758 TAGATTGCTT
* * *
1704768 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1704829 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
1704858 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1704923 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1704952 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1705017 ATTTGTCTTTTGTTTTGTCTTTTGATTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
1705046 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
1705111 ATTTGTCTTTGTTTTATCTTTTGTTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1705140 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1705205 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * * *
1705234 AGTAAATTTGTTCGTTTGCTGTCAATTCTGCTAAATTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1705299 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1705327 AGTAA
1 AGTAA
1705332 TGCAATCCAT
Statistics
Matches: 445, Mismatches: 22, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
90 33 0.07
92 3 0.01
93 46 0.10
94 344 0.77
95 19 0.04
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1705449 original size:20 final size:20
Alignment explanation
Indices: 1705424--1705485 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1705414 TTTTGGTTGA
*
1705424 AATGAAAATCGCAACAAGAG
1 AATGAAAATCGCAACGAGAG
*
1705444 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
1705463 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1705483 AAT
1 AAT
1705486 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.52, C:0.18, G:0.21, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1705470 original size:39 final size:33
Alignment explanation
Indices: 1705422--1705545 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
1705412 TCTTTTGGTT
1705422 GAAATGAAAATCGCAACAAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
*
1705461 GAAACGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1705494 GAAATGAAAATCGCAACGACAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1705527 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
1705546 CGAAACTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
33 45 0.58
34 12 0.15
35 1 0.01
36 1 0.01
37 3 0.04
39 16 0.21
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.08
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1705492 original size:33 final size:33
Alignment explanation
Indices: 1705448--1705545 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 33
1705438 CAAGAGAATG
*
1705448 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* *
1705481 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
1705514 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
1705546 CGAAACTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:1705537 original size:20 final size:20
Alignment explanation
Indices: 1705514--1705551 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1705504 TCGCAACGAC
1705514 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
1705534 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1705552 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:1705579 original size:19 final size:19
Alignment explanation
Indices: 1705557--1705649 Score: 98
Period size: 20 Copynumber: 4.8 Consensus size: 19
1705547 GAAACTATAA
*
1705557 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
1705576 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1705595 CTCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
**
1705615 TCG-GTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1705635 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1705650 AAGTTCCAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
18 10 0.17
19 20 0.33
20 21 0.35
21 9 0.15
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1705632 original size:38 final size:40
Alignment explanation
Indices: 1705560--1705649 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
1705550 ACTATAATCG
* ** *
1705560 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
* *
1705599 CGTTGCGATTTTTATTTCG-GTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
1705638 CGTTGCGATTTT
1 CGTTGCGATTTT
1705650 AAGTTCCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
38 11 0.25
39 33 0.75
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (40 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCTCA
Found at i:1706126 original size:21 final size:22
Alignment explanation
Indices: 1706105--1706168 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
1706095 TTCCTCGAGA
1706105 GTCCCTTCCCACCGTTCAAGAG
1 GTCCCTTCCCACCGTTCAAGAG
* * *
1706127 GTCACTGT--CATCGTTGAAGAG
1 GTCCCT-TCCCACCGTTCAAGAG
*
1706148 GTCCC-TCCCACCATTCAAGAG
1 GTCCCTTCCCACCGTTCAAGAG
1706169 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
21 25 0.78
22 5 0.16
23 1 0.03
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (22 bp):
GTCCCTTCCCACCGTTCAAGAG
Found at i:1707539 original size:14 final size:14
Alignment explanation
Indices: 1707520--1707555 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1707510 ATTGTTTAAT
1707520 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1707534 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1707548 TGATTTGT
1 TGATTTGT
1707556 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1707709 original size:33 final size:33
Alignment explanation
Indices: 1707663--1707740 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
1707653 AAAATGACTA
*
1707663 TCGCAATGCGATTCTCTCGTAGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTAGCGATTTTCATT
* *
1707696 TCGCATTGTGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTAGCGATTTTCATT
1707729 TCGCATTGCGAT
1 TCGCATTGCGAT
1707741 AGTCATTTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTAGCGATTTTCATT
Found at i:1707739 original size:19 final size:19
Alignment explanation
Indices: 1707684--1707760 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
1707674 TTCTCTCGTA
1707684 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
* *
1707703 GTGA--TTC-TCTCG--TT
1 GCGATTTTCATTTCGCATT
1707717 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
** *
1707736 GCGATAGTCATTTCCGCGTT
1 GCGATTTTCATTT-CGCATT
1707756 GCGAT
1 GCGAT
1707761 AGACATTAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
14 5 0.11
16 7 0.16
17 7 0.16
19 16 0.36
20 10 0.22
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATT
Found at i:1707759 original size:20 final size:20
Alignment explanation
Indices: 1707713--1707806 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1707703 GTGATTCTCT
**
1707713 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1707732 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
1707752 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
1707771 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
1707793 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1707807 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1710304 original size:24 final size:24
Alignment explanation
Indices: 1710277--1710330 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1710267 TTGAAAAATC
1710277 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1710301 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1710325 ATCAAA
1 ATCAAA
1710331 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:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1710344 original size:24 final size:24
Alignment explanation
Indices: 1710277--1710344 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1710267 TTGAAAAATC
* * *
1710277 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1710301 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1710325 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1710345 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1711228 original size:21 final size:21
Alignment explanation
Indices: 1711204--1711259 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
1711194 GCGATTACGT
*
1711204 AAATCGCATTGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * * *
1711225 AAATCACAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
1711246 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1711260 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:1712089 original size:35 final size:33
Alignment explanation
Indices: 1712005--1712089 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 33
1711995 AATATATTTT
* *
1712005 TTATTCAAAAAAATACTACTTTATACTCATTGAA
1 TTATT-AAAAAAATACTACTTTATAATCATTCAA
* * *
1712039 TGTGTATACACAAATACTACTTTATAATCACCTTCAA
1 T-TAT-TAAAAAAATACTACTTTATAATCA--TTCAA
1712076 TTATTAAAAAAATA
1 TTATTAAAAAAATA
1712090 TTTTCTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
34 1 0.03
35 30 0.77
36 3 0.08
37 5 0.13
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (33 bp):
TTATTAAAAAAATACTACTTTATAATCATTCAA
Found at i:1715512 original size:4 final size:4
Alignment explanation
Indices: 1715505--1715529 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1715495 CACACTTGCA
1715505 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1715530 ATATCTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1716949 original size:2 final size:2
Alignment explanation
Indices: 1716942--1716977 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1716932 AATAATTTGA
1716942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1716978 ACTTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1717723 original size:2 final size:2
Alignment explanation
Indices: 1717718--1717742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1717708 ATATTTAAAA
1717718 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
1717743 ATTTAAATTT
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:1718822 original size:8 final size:8
Alignment explanation
Indices: 1718806--1718835 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1718796 CTGACCTCCA
*
1718806 TTGTGAAT
1 TTGTAAAT
1718814 TTGTAAAT
1 TTGTAAAT
1718822 TTGTAAAT
1 TTGTAAAT
1718830 TTGTAA
1 TTGTAA
1718836 TTGTTATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (8 bp):
TTGTAAAT
Found at i:1722949 original size:16 final size:16
Alignment explanation
Indices: 1722923--1722957 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1722913 CATTAGGGGA
1722923 GAAAATAAAT-AGTTG
1 GAAAATAAATAAGTTG
1722938 GAAAACTAAATAAGTTG
1 GAAAA-TAAATAAGTTG
1722955 GAA
1 GAA
1722958 TGAATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (16 bp):
GAAAATAAATAAGTTG
Found at i:1723294 original size:21 final size:22
Alignment explanation
Indices: 1723262--1723309 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1723252 TGGTCTGATC
*
1723262 GAAGA-ATCTAAAAAATTTCTA
1 GAAGATATCTAAAAAATCTCTA
*
1723283 GAAGATAT-TAAAAGATCTCTA
1 GAAGATATCTAAAAAATCTCTA
1723304 GAAGAT
1 GAAGAT
1723310 TAATTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
GAAGATATCTAAAAAATCTCTA
Found at i:1727168 original size:2 final size:2
Alignment explanation
Indices: 1727163--1727190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1727153 TAAAAAAATA
1727163 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
1727191 TTCTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1727507 original size:20 final size:20
Alignment explanation
Indices: 1727482--1727522 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1727472 ACTTCTTATC
*
1727482 TATAAGAATATTCTGTTAAT
1 TATAAGAATATTATGTTAAT
1727502 TATAAGAATATTATGTTAAT
1 TATAAGAATATTATGTTAAT
1727522 T
1 T
1727523 TATGTTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
TATAAGAATATTATGTTAAT
Found at i:1739069 original size:15 final size:17
Alignment explanation
Indices: 1739049--1739085 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1739039 TTTTCACCTT
1739049 TCATTA-TTA-CATTTC
1 TCATTATTTATCATTTC
*
1739064 TCATTATTTATTATTTC
1 TCATTATTTATCATTTC
1739081 TCATT
1 TCATT
1739086 TGAGCACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 10 0.53
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (17 bp):
TCATTATTTATCATTTC
Found at i:1740895 original size:19 final size:19
Alignment explanation
Indices: 1740871--1740908 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1740861 AACTTGTCCA
1740871 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
1740890 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
1740909 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:1744105 original size:33 final size:33
Alignment explanation
Indices: 1744068--1744139 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
1744058 CTAGGGACTA
1744068 TTATATTTCTGTTTTCATGCTACCTCAGTAACC
1 TTATATTTCTGTTTTCATGCTACCTCAGTAACC
1744101 TTATATTTCTGTTTTCATGCTACCTCAGTAACC
1 TTATATTTCTGTTTTCATGCTACCTCAGTAACC
1744134 TTATAT
1 TTATAT
1744140 ATACTCACGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (33 bp):
TTATATTTCTGTTTTCATGCTACCTCAGTAACC
Found at i:1747357 original size:18 final size:18
Alignment explanation
Indices: 1747334--1747368 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1747324 CGTAGAAATA
* *
1747334 TCCCGAAGGTCCACTATG
1 TCCCGAAAGACCACTATG
1747352 TCCCGAAAGACCACTAT
1 TCCCGAAAGACCACTAT
1747369 CCATATGTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TCCCGAAAGACCACTATG
Found at i:1748373 original size:20 final size:20
Alignment explanation
Indices: 1748350--1748402 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1748340 CCAATACCTG
*
1748350 GGTATCGATACCCACAAGCA
1 GGTAACGATACCCACAAGCA
*
1748370 GGTAAGGATACCCACAAGCA
1 GGTAACGATACCCACAAGCA
*
1748390 GGGTAACAATACC
1 -GGTAACGATACC
1748403 TGTGAATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (20 bp):
GGTAACGATACCCACAAGCA
Found at i:1758036 original size:197 final size:194
Alignment explanation
Indices: 1757704--1758095 Score: 757
Period size: 197 Copynumber: 2.0 Consensus size: 194
1757694 TTTTAAACAC
1757704 TAAGTGAAGATAGGTTAGTTAAACCTAATCTCCTAAGTGTCCAAAAACGTTCCTTGTCTAAAGGC
1 TAAGTGAAGATAGGTTAGTTAAACCTAATCTCCTAAGTGTCCAAAAACGTTCCTTGTCTAAAGGC
1757769 TTTGTAAAAATATCCGCTAATTGATGCAAAGTATCAACAAATTCTAGAACTACATCTTCCTTAGT
66 TTTGTAAAAATATCCGCTAATTGATGCAAAGTATCAACAAATTCTAGAACTACATCTTCCTTAGT
1757834 GACATGGTCTCTAATGAAGTGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGGATGGGA
131 GACATGGTCTCTAATGAAGTGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGGATGGGA
1757898 TAAGTGAAGATAGGTTAGTTAAACCTAATTCTCCTAAGTGTCCAAAAACGTTCCTTGTCTAAAGG
1 TAAGTGAAGATAGGTTAGTTAAACCTAA-TCTCCTAAGTGTCCAAAAACGTTCCTTGTCTAAAGG
1757963 CTTTGTAAAAAAATATCCGCTAATTGATGCAAAGTATCAACAAATTCTAGAACTACATCTTCCTT
65 CTTTGT--AAAAATATCCGCTAATTGATGCAAAGTATCAACAAATTCTAGAACTACATCTTCCTT
1758028 AGTGACATGGTCTCTAATGAAGTGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGGATGG
128 AGTGACATGGTCTCTAATGAAGTGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGGATGG
1758093 GA
193 GA
1758095 T
1 T
1758096 TTTTAGTGAG
Statistics
Matches: 195, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
194 28 0.14
195 42 0.22
197 125 0.64
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (194 bp):
TAAGTGAAGATAGGTTAGTTAAACCTAATCTCCTAAGTGTCCAAAAACGTTCCTTGTCTAAAGGC
TTTGTAAAAATATCCGCTAATTGATGCAAAGTATCAACAAATTCTAGAACTACATCTTCCTTAGT
GACATGGTCTCTAATGAAGTGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGGATGGGA
Found at i:1763263 original size:18 final size:18
Alignment explanation
Indices: 1763240--1763278 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1763230 TCTCTTCTTG
1763240 AGAAAT-GAAGAAGAAATA
1 AGAAATGGAAGAAG-AATA
1763258 AGAAATGGAAGAAGAATA
1 AGAAATGGAAGAAGAATA
1763276 AGA
1 AGA
1763279 GTATTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (18 bp):
AGAAATGGAAGAAGAATA
Found at i:1765309 original size:2 final size:2
Alignment explanation
Indices: 1765302--1765329 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1765292 AATTATATGG
1765302 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
1765330 CCATTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1769035 original size:2 final size:2
Alignment explanation
Indices: 1769028--1769056 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1769018 CGTTTATCTT
1769028 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
1769057 TCTGTAAGTA
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:1770638 original size:3 final size:3
Alignment explanation
Indices: 1770632--1770667 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1770622 TTGGATTTAC
1770632 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1770668 GATTAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1770872 original size:43 final size:43
Alignment explanation
Indices: 1770824--1770911 Score: 160
Period size: 43 Copynumber: 2.0 Consensus size: 43
1770814 TCTTTTATGC
1770824 TTTGTCTTAGGAAACCAAAGCTTT-CTTTCAACATATCAAATCA
1 TTTGTCTTAGGAAACCAAAGCTTTCCTTT-AACATATCAAATCA
1770867 TTTGTCTTAGGAAACCAAAGCTTTCCTTTAACATATCAAATCA
1 TTTGTCTTAGGAAACCAAAGCTTTCCTTTAACATATCAAATCA
1770910 TT
1 TT
1770912 ATTCATTAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTGTCTTAGGAAACCAAAGCTTTCCTTTAACATATCAAATCA
Found at i:1773534 original size:24 final size:25
Alignment explanation
Indices: 1773482--1773548 Score: 100
Period size: 24 Copynumber: 2.7 Consensus size: 25
1773472 ATGTGAAATT
* *
1773482 TGTCCCAAATGACCTCTGTATACTA
1 TGTCCCAAAGGACCTGTGTATACTA
*
1773507 TGTCCCGAAGGACCTGTGT-TACTA
1 TGTCCCAAAGGACCTGTGTATACTA
1773531 TGTCCCAAAGGACCTGTG
1 TGTCCCAAAGGACCTGTG
1773549 AAACCCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (25 bp):
TGTCCCAAAGGACCTGTGTATACTA
Found at i:1787022 original size:17 final size:16
Alignment explanation
Indices: 1786991--1787024 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1786981 CACGTGATGA
1786991 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1787007 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1787024 T
1 T
1787025 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1797227 original size:16 final size:16
Alignment explanation
Indices: 1797191--1797224 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1797181 CACGTGAGGA
1797191 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1797207 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1797224 T
1 T
1797225 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1800110 original size:23 final size:23
Alignment explanation
Indices: 1800078--1800145 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1800068 CACTTAATTC
*
1800078 CTAATTAATAGTAAATTAAAAGTA
1 CTAA-TAATAGTAAATTAAAAATA
* *
1800102 CTAATAATA-AATAATTAAAAATC
1 CTAATAATAGTA-AATTAAAAATA
*
1800125 CTAAATAATAGTAAACTAAAA
1 CT-AATAATAGTAAATTAAAA
1800146 TTCCATGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 16 0.44
24 18 0.50
25 1 0.03
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.29
Consensus pattern (23 bp):
CTAATAATAGTAAATTAAAAATA
Found at i:1800146 original size:23 final size:23
Alignment explanation
Indices: 1800076--1800146 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
1800066 AACACTTAAT
*
1800076 TCCTAATTAATAGTAAATTAAAA
1 TCCTAAATAATAGTAAATTAAAA
* *
1800099 GTACT-AATAATA-AATAATTAAAAA
1 -TCCTAAATAATAGTA-AATT-AAAA
*
1800123 TCCTAAATAATAGTAAACTAAAA
1 TCCTAAATAATAGTAAATTAAAA
1800146 T
1 T
1800147 TCCATGCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.03
23 18 0.49
24 17 0.46
25 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (23 bp):
TCCTAAATAATAGTAAATTAAAA
Found at i:1823480 original size:21 final size:21
Alignment explanation
Indices: 1823454--1823516 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1823444 CACATTGATC
*
1823454 CAAAGCTTCCAATCAACAGGA
1 CAAAGCTTCCAATCAACAAGA
*
1823475 CAAAGCTTCCAATTAACAAGA
1 CAAAGCTTCCAATCAACAAGA
*
1823496 CAAAGCTTCCCATCAA-AAGA
1 CAAAGCTTCCAATCAACAAGA
1823516 C
1 C
1823517 CAACAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 5 0.13
21 33 0.87
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (21 bp):
CAAAGCTTCCAATCAACAAGA
Found at i:1824068 original size:194 final size:195
Alignment explanation
Indices: 1823842--1824228 Score: 735
Period size: 195 Copynumber: 2.0 Consensus size: 195
1823832 AGAAATAAAT
1823842 TTTCCTTCAACAAAAACTACACCAACATTACAAGAAAT-AATTTCCTTCAACAACAATTGTCTTA
1 TTTCCTTCAACAAAAACTACACCAACATTACAAGAAATAAATTTCCTTCAACAACAATTGTCTTA
1823906 CCATCATTCATCTAAATACCAAATTTCACCATGAAGTACATTATCC-AGAAGTAAAGAATATTAT
66 CCATCATTCATCTAAATACCAAATTTCACCATGAAGTACATTATCCAAGAAGTAAAGAATATTAT
1823970 CTTATAGAATAAAGCAC-TGTCCCTTCTCTTTGTACATTTTACAATTTTCTTCAATTGTTGGTTT
131 C-TATAGAATAAAGCACTTGT-CCTTCTCTTTGTACATTTTACAATTTTCTTCAATTGTTGGTTT
1824034 AA
194 AA
1824036 TTTCCTTCAACAAAAACTACACCAACATTACAAGAAATAAATTTCCTTCAACAACAATTGTCTTA
1 TTTCCTTCAACAAAAACTACACCAACATTACAAGAAATAAATTTCCTTCAACAACAATTGTCTTA
1824101 CCATCATTCATCTAAATACCAAATTTCACCATGAAGTACATTATCCAAGAAGTAAAGAATATTAT
66 CCATCATTCATCTAAATACCAAATTTCACCATGAAGTACATTATCCAAGAAGTAAAGAATATTAT
1824166 CTATAGAATAAAGCACTTGTCCTTCTCTTTGTACATTTTACAATTTTCTTCAATTGTTGGTTT
131 CTATAGAATAAAGCACTTGTCCTTCTCTTTGTACATTTTACAATTTTCTTCAATTGTTGGTTT
1824229 TCAACTTTCA
Statistics
Matches: 190, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
194 38 0.20
195 130 0.68
196 22 0.12
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (195 bp):
TTTCCTTCAACAAAAACTACACCAACATTACAAGAAATAAATTTCCTTCAACAACAATTGTCTTA
CCATCATTCATCTAAATACCAAATTTCACCATGAAGTACATTATCCAAGAAGTAAAGAATATTAT
CTATAGAATAAAGCACTTGTCCTTCTCTTTGTACATTTTACAATTTTCTTCAATTGTTGGTTTAA
Found at i:1836806 original size:23 final size:23
Alignment explanation
Indices: 1836763--1836822 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1836753 TAACAAATAT
1836763 GTGTCACAAAGAC--AGATAAAC
1 GTGTCACAAAGACAAAGATAAAC
*
1836784 GTGTCATAAAGACAAAGATAAAC
1 GTGTCACAAAGACAAAGATAAAC
* *
1836807 ATATCACAAAGACAAA
1 GTGTCACAAAGACAAA
1836823 ATTATTCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.36
23 21 0.64
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (23 bp):
GTGTCACAAAGACAAAGATAAAC
Found at i:1839320 original size:2 final size:2
Alignment explanation
Indices: 1839307--1839367 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
1839297 TAAAAATAAT
* * *
1839307 TA TA TG TA TA TA TA TG TA TA TA TA TG TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1839347 TGC TA TA TA TA TA TA TG TA TA
1 T-A TA TA TA TA TA TA TA TA TA
1839368 ATTAAATATT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
1 2 0.04
2 43 0.93
3 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1839320 original size:10 final size:10
Alignment explanation
Indices: 1839307--1839341 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
1839297 TAAAAATAAT
1839307 TATATGTATA
1 TATATGTATA
1839317 TATATGTATA
1 TATATGTATA
1839327 TATATGTATA
1 TATATGTATA
1839337 TATAT
1 TATAT
1839342 AATAATGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (10 bp):
TATATGTATA
Found at i:1841432 original size:120 final size:123
Alignment explanation
Indices: 1841231--1841572 Score: 451
Period size: 124 Copynumber: 2.8 Consensus size: 123
1841221 TGTGAGCACG
* *
1841231 ATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * * * *
1841296 GATAT-CTTTCGTCGTGAAGTTGAAATCCAA-GT-A-TTGTATATTGCTT-GTGGGCATA
66 GATATCCTTT-GTCGTGAAGTTGAAATCCAATCTAAGATGAATATTG-TTGGTGGACACA
* * * * *
1841351 ATATCCTTCGTAATGAAGTTGAAATCGTGGATGACCCCTTTGTTGTGAAGTTGAGCCTTGAATTA
1 ATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * *
1841416 GATATCCTTTGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGTTGTTGGTGGACACG
66 GATATCCTTTGTCGTGAAGTTGAAATCCAATCT-AAGATGAATATTGTTGGTGGACACA
* * *
1841475 ATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCCTTCATTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
*
1841540 GATATCCTTCGTCGTGAAGTTGAAATCCAATCT
66 GATATCCTTTGTCGTGAAGTTGAAATCCAATCT
1841573 TTGTTTCACC
Statistics
Matches: 191, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
120 82 0.43
121 5 0.03
123 3 0.02
124 101 0.53
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (123 bp):
ATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
GATATCCTTTGTCGTGAAGTTGAAATCCAATCTAAGATGAATATTGTTGGTGGACACA
Found at i:1852686 original size:32 final size:31
Alignment explanation
Indices: 1852650--1852711 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1852640 AAACAAAGTG
* * *
1852650 AATAAAATGATAATATAAATAAAAATAAAAAC
1 AATAAAATAAGAATA-AAACAAAAATAAAAAC
*
1852682 AATAAAATAAGACTAAAACAAAAATAAAAA
1 AATAAAATAAGAATAAAACAAAAATAAAAA
1852712 ACAAAGGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (31 bp):
AATAAAATAAGAATAAAACAAAAATAAAAAC
Found at i:1852986 original size:19 final size:20
Alignment explanation
Indices: 1852964--1853004 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1852954 AATAGTAGAG
1852964 AAATAAAATAA-TAAAAATA
1 AAATAAAATAATTAAAAATA
* *
1852983 AAATATAATAATTACAAATA
1 AAATAAAATAATTAAAAATA
1853003 AA
1 AA
1853005 GGATTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAATAATTAAAAATA
Found at i:1854087 original size:2 final size:2
Alignment explanation
Indices: 1854080--1854130 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
1854070 ATGTAAATAA
1854080 AT AT AT AT AT -T AT A- ACT -T AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1854119 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1854131 ATTTAAGCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1854649 original size:40 final size:39
Alignment explanation
Indices: 1854543--1854654 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 39
1854533 TTAAAGAATT
* *
1854543 AATTTAGAACGTTA-ATGTGAAATAATTTAAGATATTAAG
1 AATTTAGAATGTTATA-GTGAAATAATTTAAGAAATTAAG
* *
1854582 AATTTAGAATGTTATGGTGATAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTATAGTGA-AATAATTTAAGAAATTAAG
** *
1854621 AATTTTTTAATGTTATAGTGAAATAATTTGAGAA
1 AA-TTTAGAATGTTATAGTGAAATAATTTAAGAA
1854655 TTATAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 35 0.57
40 26 0.43
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTATAGTGAAATAATTTAAGAAATTAAG
Found at i:1868798 original size:21 final size:21
Alignment explanation
Indices: 1868756--1868798 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1868746 TTTCTGGGCT
* *
1868756 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1868777 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1868798 A
1 A
1868799 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1877262 original size:29 final size:28
Alignment explanation
Indices: 1877220--1877275 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
1877210 CCCAAGAGTT
1877220 TGGGAGTTCCTAGTGAGAAGGACATATTA
1 TGGGAGTTCCTAGTGAGAA-GACATATTA
1877249 TGGGAGTTCCTAGTGAGAAGACATATT
1 TGGGAGTTCCTAGTGAGAAGACATATT
1877276 GAATTCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (28 bp):
TGGGAGTTCCTAGTGAGAAGACATATTA
Found at i:1882805 original size:10 final size:10
Alignment explanation
Indices: 1882790--1882822 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1882780 TGTTTGGATT
1882790 AAGGGGAAGG
1 AAGGGGAAGG
1882800 AAGGGGAAGG
1 AAGGGGAAGG
1882810 AAGGGG-AGG
1 AAGGGGAAGG
1882819 AAGG
1 AAGG
1882823 AAGGGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (10 bp):
AAGGGGAAGG
Found at i:1893046 original size:57 final size:59
Alignment explanation
Indices: 1892969--1893082 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 59
1892959 TCGAGTGACT
* *
1892969 ATTTTATAACTTTTAATAATTGTAGGATTCAATAAAACAACAC-CT-TAGTCGGAGATC
1 ATTTTATAACATTTAATAATTGTAAGATTCAATAAAACAACACTCTATAGTCGGAGATC
* * ** * *
1893026 ATTTTGTAACATTTATTAATTGTAAGATTTGATAAAATAACACTTTATAGTCGGAGA
1 ATTTTATAACATTTAATAATTGTAAGATTCAATAAAACAACACTCTATAGTCGGAGA
1893083 AAATTTATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
57 36 0.77
58 1 0.02
59 10 0.21
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (59 bp):
ATTTTATAACATTTAATAATTGTAAGATTCAATAAAACAACACTCTATAGTCGGAGATC
Found at i:1893909 original size:3 final size:3
Alignment explanation
Indices: 1893901--1893958 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
1893891 TCATTTAAAT
**
1893901 TTA TTA TTA TTA -TA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1893948 TTA -TA TTA TTA
1 TTA TTA TTA TTA
1893959 AATATTACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1895194 original size:19 final size:19
Alignment explanation
Indices: 1895152--1895195 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1895142 TTTTAATTTC
*
1895152 ATTATTTTTAATTATTGTT
1 ATTATTTTTAATTATTATT
* *
1895171 TTTATTTTTTATTATTATT
1 ATTATTTTTAATTATTATT
1895190 ATTATT
1 ATTATT
1895196 ATGTATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTATTTTTAATTATTATT
Found at i:1895910 original size:17 final size:18
Alignment explanation
Indices: 1895878--1895928 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
1895868 TTTTCTTTCA
*
1895878 AATTTTTATTA-CTTATT
1 AATTTTTATTATTTTATT
1895895 -ATTTTTATTATTTTATT
1 AATTTTTATTATTTTATT
*
1895912 AATATTTATT-TTTTATT
1 AATTTTTATTATTTTATT
1895929 TATTCAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.33
17 12 0.40
18 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTTTATTATTTTATT
Found at i:1897432 original size:14 final size:15
Alignment explanation
Indices: 1897400--1897434 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1897390 TTCATACACA
1897400 TTTGCATTTTTCATC
1 TTTGCATTTTTCATC
*
1897415 TTTGCATTTTTTAT-
1 TTTGCATTTTTCATC
1897429 TTTGCA
1 TTTGCA
1897435 ATTATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (15 bp):
TTTGCATTTTTCATC
Found at i:1898021 original size:16 final size:17
Alignment explanation
Indices: 1897981--1898023 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1897971 GGTTAAAGCT
**
1897981 AAATGAATTTTGTACTG
1 AAATGAATTTTGTACCC
1897998 ATAATGAATTTTG-ACCC
1 A-AATGAATTTTGTACCC
1898015 AAATGAATT
1 AAATGAATT
1898024 AGTTGAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 11 0.48
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (17 bp):
AAATGAATTTTGTACCC
Found at i:1900795 original size:161 final size:164
Alignment explanation
Indices: 1900586--1900911 Score: 606
Period size: 164 Copynumber: 2.0 Consensus size: 164
1900576 CACTCTGGTT
1900586 ATACTGTGATACTGGCTCAAGTCGAGAAACATATTGCTACTTTTTCCATATTGATCA-TTTCTTT
1 ATACTGTGATACT-GCTCAAGTCGAGAAACATATTGCTACTTTTTCCATATTGATCATTTTCTTT
1900650 GTCAGGATT-AATCCATTATGTCCTTCAG-AGATTGTTGAATTTGAATTTGAGGACTTATGGCAC
65 GTCAGGATTAAATCCATTATGTCCTTCAGAAGATTGTTGAATTTGAATTTGAGGACTTATGGCAC
1900713 AGAATAAGACATTGGAACAGAATCTACCCTTATAG
130 AGAATAAGACATTGGAACAGAATCTACCCTTATAG
1900748 ATACTGTGATACT-CTCAAGTCGAGAAACATCATTGCTACTTTTTCCATATTGATCATTTTCTTT
1 ATACTGTGATACTGCTCAAGTCGAGAAACAT-ATTGCTACTTTTTCCATATTGATCATTTTCTTT
1900812 GTCAGGATTAAATCCATTATGTCCTTCAGAAGATTGTTGAATTTGAATTTGAGGACTTATGGCAC
65 GTCAGGATTAAATCCATTATGTCCTTCAGAAGATTGTTGAATTTGAATTTGAGGACTTATGGCAC
1900877 AGAATAAGACATTGGAACAGAATCTACCCTTATAG
130 AGAATAAGACATTGGAACAGAATCTACCCTTATAG
1900912 GCCTTTTATA
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 17 0.11
161 25 0.16
162 29 0.18
163 19 0.12
164 70 0.44
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (164 bp):
ATACTGTGATACTGCTCAAGTCGAGAAACATATTGCTACTTTTTCCATATTGATCATTTTCTTTG
TCAGGATTAAATCCATTATGTCCTTCAGAAGATTGTTGAATTTGAATTTGAGGACTTATGGCACA
GAATAAGACATTGGAACAGAATCTACCCTTATAG
Found at i:1904115 original size:21 final size:22
Alignment explanation
Indices: 1904066--1904116 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1904056 TACACTCTTC
1904066 AAAGATGATAGATTCTCTTTTA
1 AAAGATGATAGATTCTCTTTTA
1904088 AAAGATGATAGATTCTCTTTT-
1 AAAGATGATAGATTCTCTTTTA
*
1904109 CAAGATGA
1 AAAGATGA
1904117 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTA
Found at i:1904911 original size:37 final size:37
Alignment explanation
Indices: 1904820--1905309 Score: 210
Period size: 37 Copynumber: 13.6 Consensus size: 37
1904810 GTTTTCAAAT
** ** *
1904820 AGAAATTTATCTCACTTGAGATTGTTTTTCT-TAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * *
1904856 --AAATTGTTTCTCGCTTGAGAAAGTTTCCCTCGAAAC
1 AGAAATT-TATCTCACTTGAGACAGTTTCCCTCGAAAC
* * ** *
1904892 A-ACAATGTATCTCACTTGAGATTA-TTTTTCTCAAAAC
1 AGA-AATTTATCTCACTTGAGA-CAGTTTCCCTCGAAAC
* * * *
1904929 AGAACTTTGTCTCACTCGAGACAGTTTCACTCGAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * * * *
1904966 AGAACTTTGTCTCTCTCGAGACAGTTTCACATCGAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTC-CCTCGAAAC
** ** *
1905004 A-ACAATTTATCTCACTT--GATTGTTT-TTTCTTAAAC
1 AGA-AATTTATCTCACTTGAGACAGTTTCCCTC-GAAAC
* *
1905039 --AAATTTGTCTCGCTTGAGACAGTTT-CCTCGAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * ** ** *
1905073 AAAAATTTATCTCACTTGACATTGTTT-TTTCTTAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTC-GAAAC
* * *
1905110 --AAATTTGTCTCGCTTGAGACAGTTTCACTCG-AAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* ** ** **
1905144 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * * *
1905181 A-AAATTTTGTCTCGCTTAAGACA-TTTCACTCGAAAC
1 AGAAA-TTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * ** ** *
1905217 AAAAATTTGTCTCACTTGAGATTGTTTTTCT-TAAA-
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
* * * *
1905252 ACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
1 AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
*
1905289 AGAACTTTATCTCACTTGAGA
1 AGAAATTTATCTCACTTGAGA
1905310 TTGTTTTTTC
Statistics
Matches: 336, Mismatches: 94, Indels: 47
0.70 0.20 0.10
Matches are distributed among these distances:
33 12 0.04
34 15 0.04
35 75 0.22
36 89 0.26
37 122 0.36
38 23 0.07
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
AGAAATTTATCTCACTTGAGACAGTTTCCCTCGAAAC
Found at i:1905213 original size:144 final size:143
Alignment explanation
Indices: 1904962--1905348 Score: 558
Period size: 144 Copynumber: 2.7 Consensus size: 143
1904952 GTTTCACTCG
* * *
1904962 AAACAGAACTTTGTCTCTCTCGAGACAGTTTCACATCGAAACA-ACAATTTATCTCACTT--GAT
1 AAACA-AA-TTTGTCTCGCTTGAGACAGTTTCAC-TCGAAACAGA-ACTTTATCTCACTTGAGAT
*
1905024 TGTTTTTTCTTAAAC-AAATTTGTCTCGCTTGAGACAGTTTCCTCGAAACAAAAATTTATCTCAC
62 TGTTTTTTCTTAAACAAAATTTGTCTCGCTTAAGACA-TTTCCTCGAAACAAAAATTTATCTCAC
1905088 TTGACATTGTTTTTTCTT-
126 TTGACATTG-TTTTTCTTA
1905106 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCG-AACAGAACTTTATCTCACTTGAGATTG-T
1 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTT
*
1905169 TTTTCTTAAAACAAAATTTTGTCTCGCTTAAGACATTTCACTCGAAACAAAAATTTGTCTCACTT
66 TTTTCTT-AAACAAAA-TTTGTCTCGCTTAAGACATTTC-CTCGAAACAAAAATTTATCTCACTT
*
1905234 GAGATTGTTTTTCTTA
128 GACATTGTTTTTCTTA
1905250 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTT
1 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTT
*
1905315 TTTTCTTAAACAAGGA-TT-TCTCGCTTAAGACATT
66 TTTTCTTAAACAA-AATTTGTCTCGCTTAAGACATT
1905349 ATTTTGAGTT
Statistics
Matches: 225, Mismatches: 7, Indels: 23
0.88 0.03 0.09
Matches are distributed among these distances:
140 17 0.08
141 12 0.05
142 32 0.14
143 33 0.15
144 89 0.40
145 33 0.15
146 9 0.04
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (143 bp):
AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTT
TTTTCTTAAACAAAATTTGTCTCGCTTAAGACATTTCCTCGAAACAAAAATTTATCTCACTTGAC
ATTGTTTTTCTTA
Found at i:1905346 original size:72 final size:72
Alignment explanation
Indices: 1904962--1905327 Score: 530
Period size: 71 Copynumber: 5.1 Consensus size: 72
1904952 GTTTCACTCG
* * *
1904962 AAACAGAACTTTGTCTCTCTCGAGACAGTTTCACATCGAAACAACAATTTATCTCACTT--GATT
1 AAACA-AA-TTTGTCTCGCTTGAGACAGTTTCAC-TCGAAACAAAAATTTATCTCACTTGAGATT
1905025 GTTTTTTCTT
63 GTTTTTTCTT
*
1905035 AAACAAATTTGTCTCGCTTGAGACAGTTTC-CTCGAAACAAAAATTTATCTCACTTGACATTGTT
1 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTT
1905099 TTTTCTT
66 TTTTCTT
* *
1905106 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCG-AACAGAACTTTATCTCACTTGAGATTG-T
1 AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTT
1905169 TTTTCTT
66 TTTTCTT
* *
1905176 AAAACAAAATTTTGTCTCGCTTAAGACA-TTTCACTCGAAACAAAAATTTGTCTCACTTGAGATT
1 -AAAC-AAA-TTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTTGAGATT
1905240 G-TTTTTCTT
63 GTTTTTTCTT
* *
1905249 AAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGT
1 -AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGT
1905314 TTTTTCTT
65 TTTTTCTT
1905322 AAACAA
1 AAACAA
1905328 GGATTTCTCG
Statistics
Matches: 269, Mismatches: 15, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
69 23 0.09
70 9 0.03
71 109 0.41
72 61 0.23
73 67 0.25
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (72 bp):
AAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTT
TTTTCTT
Found at i:1905692 original size:45 final size:45
Alignment explanation
Indices: 1905558--1905704 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
1905548 CGGAGCTTTT
* *
1905558 TGATGTTTTCAAAGCCTTAGGGTCAT-TGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1905602 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
**
1905648 TGATGTTTTTCAAAACCTTCGGGTC-TCTGTAACCCCTTCAGTGCA
1 TGATG-TTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1905693 TGATGTTTTCAA
1 TGATGTTTTCAA
1905705 CATTTCCATC
Statistics
Matches: 96, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
44 17 0.18
45 37 0.39
46 37 0.39
47 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:1905814 original size:99 final size:101
Alignment explanation
Indices: 1905639--1905840 Score: 358
Period size: 99 Copynumber: 2.0 Consensus size: 101
1905629 CTGTAAGTCC
1905639 TTCAGTGCATGATGTTTTTCAAAACCTTCGGGTCTCTGTAACCCCTTCAGTGCATGATGTTTTCA
1 TTCAGTGCATGATGTTTTTCAAAACCTTCGGGTCTCTGTAACCCCTTCAGTGCATGATGTTTTCA
1905704 ACATTTCCATCCTGCTCAAAAG-AGCCAATGAAAAA
66 ACATTTCCATCCTGCTCAAAAGAAGCCAATGAAAAA
1905739 TTCAGTGCATGATG-TTTTCAAAACCTTC-GGTCATC-GTAACCCCTTCAGTGCATGATGTTTTC
1 TTCAGTGCATGATGTTTTTCAAAACCTTCGGGTC-TCTGTAACCCCTTCAGTGCATGATGTTTTC
1905801 AAACATTTCCATCCTGCTCAAAAGAAGCCAATGAAAAA
65 -AACATTTCCATCCTGCTCAAAAGAAGCCAATGAAAAA
1905839 TT
1 TT
1905841 ATTGTCTTTT
Statistics
Matches: 99, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
98 31 0.31
99 39 0.39
100 29 0.29
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (101 bp):
TTCAGTGCATGATGTTTTTCAAAACCTTCGGGTCTCTGTAACCCCTTCAGTGCATGATGTTTTCA
ACATTTCCATCCTGCTCAAAAGAAGCCAATGAAAAA
Found at i:1905934 original size:3 final size:3
Alignment explanation
Indices: 1905928--1905995 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
1905918 TTATTTAAAT
**
1905928 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1905976 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
1905996 AATATTACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1907226 original size:27 final size:28
Alignment explanation
Indices: 1907184--1907249 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
1907174 ATTACTAGTT
* *
1907184 TTTTTATTTATAGTTTTA-ATTTCATTA
1 TTTTTAATTATTGTTTTATATTTCATTA
*
1907211 TTTTTAATTATTGTTTTATATTTTATTA
1 TTTTTAATTATTGTTTTATATTTCATTA
*
1907239 TTATT-ATTATT
1 TTTTTAATTATT
1907250 ATGTATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTTTAATTATTGTTTTATATTTCATTA
Done.