Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold132
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: 2008648
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 78371 characters in sequence are not A, C, G, or T
File 6 of 7
Found at i:1626554 original size:49 final size:49
Alignment explanation
Indices: 1626482--1626579 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
1626472 CGCCTTACAC
* *
1626482 ACATAAAGCTCATTGATGAGACTTTATAGATGTAGTATCAAAATACAGA
1 ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
*
1626531 ACATAAAGCTCACTGATGAGACTTCATATATGTAGTATCAAAATACAGA
1 ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
1626580 TTTAATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (49 bp):
ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
Found at i:1629714 original size:25 final size:25
Alignment explanation
Indices: 1629676--1629728 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1629666 ATTTTTTTTG
*
1629676 AAATTTTATCAGGGGTAAACTCGTC
1 AAATTTTATCAGGGGTAAAATCGTC
*
1629701 AAATTTTA-CTAGGGGTAAAATTGTC
1 AAATTTTATC-AGGGGTAAAATCGTC
1629726 AAA
1 AAA
1629729 CAAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (25 bp):
AAATTTTATCAGGGGTAAAATCGTC
Found at i:1648006 original size:36 final size:36
Alignment explanation
Indices: 1647966--1648038 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1647956 TTAAGTTTGT
1647966 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
1 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
*
1648002 AACTTTTTAACCCTCTACTACTTAGGATTAATTATA
1 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
1648038 A
1 A
1648039 CTCCTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (36 bp):
AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
Found at i:1655683 original size:18 final size:18
Alignment explanation
Indices: 1655660--1655694 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1655650 CAAGAACAGG
1655660 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
1655678 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
1655695 GACACATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:1665783 original size:50 final size:50
Alignment explanation
Indices: 1665708--1665916 Score: 249
Period size: 50 Copynumber: 4.1 Consensus size: 50
1665698 CATGGGATGT
* * * *
1665708 TCTCATCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACC
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
* *
1665758 TCTCATCTCGGTGCCAACGCCATGTCCC-GAACATGGTCTTACATAGAACC
1 TCTCATCTCGGTGCCAACGCCATGTCCCAG-ACATGGTCTTACATGGGACC
*
1665808 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACC
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
* * * *
1665858 TCTCGTAATCTCAATGATGCCAATGCCATGTCCCAGACATGGTCTTACATAGGATC
1 TCTC---ATCTC---GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1665914 TCT
1 TCT
1665917 TTACCCAAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 91 0.66
51 1 0.01
53 5 0.04
56 39 0.28
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (50 bp):
TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
Found at i:1678295 original size:40 final size:39
Alignment explanation
Indices: 1678245--1678510 Score: 273
Period size: 40 Copynumber: 6.7 Consensus size: 39
1678235 TACCGGGTAT
* *
1678245 AAACAAGGGCACGTATGTGCAATCAGGCGTACCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATCAGG-GTACCGAAGTAC
* *
1678285 AAATAGGGGCACGTATGTGCAATCATGGGTACCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
** * * *
1678325 AAACAGGGGCATAAATGTCCAAACAGGGGTACCAAAGTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
* * * *
1678365 AAAAAGGGGTATGAATGTGCAATCAAGGGTACTGAAGTAC
1 AAACAGGGGCACGAATGTGCAATC-AGGGTACCGAAGTAC
* * * *
1678405 AAACAGGGACACGAATGTGCAATTAGGGGTACCAAATTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
*
1678445 AAACAGGGGCAC-ATATGCGCAATCAGTGGTACCGAAGTAC
1 AAACAGGGGCACGA-ATGTGCAATCAG-GGTACCGAAGTAC
* * *
1678485 AAACAAGGGTACGAATGTGTAATCAG
1 AAACAGGGGCACGAATGTGCAATCAG
1678511 ACAATAGTTA
Statistics
Matches: 186, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.02
40 179 0.96
41 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (39 bp):
AAACAGGGGCACGAATGTGCAATCAGGGTACCGAAGTAC
Found at i:1678367 original size:20 final size:20
Alignment explanation
Indices: 1678311--1678453 Score: 81
Period size: 20 Copynumber: 7.2 Consensus size: 20
1678301 GTGCAATCAT
*
1678311 GGGTACCGAAGTACAAACAG
1 GGGTACCAAAGTACAAACAG
* * *
1678331 GGGCA-TAAATGTCCAAACAG
1 GGGTACCAAA-GTACAAACAG
*
1678351 GGGTACCAAAGTACAAAAAG
1 GGGTACCAAAGTACAAACAG
** * * * *
1678371 GGGTATGAATGTGCAATCAA
1 GGGTACCAAAGTACAAACAG
**
1678391 GGGTACTGAAGTACAAACAG
1 GGGTACCAAAGTACAAACAG
** * * * **
1678411 GGACACGAATGTGCAATTAG
1 GGGTACCAAAGTACAAACAG
*
1678431 GGGTACCAAATTACAAACAG
1 GGGTACCAAAGTACAAACAG
1678451 GGG
1 GGG
1678454 CACATATGCG
Statistics
Matches: 83, Mismatches: 38, Indels: 4
0.66 0.30 0.03
Matches are distributed among these distances:
19 2 0.02
20 78 0.94
21 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.15
Consensus pattern (20 bp):
GGGTACCAAAGTACAAACAG
Found at i:1678476 original size:120 final size:121
Alignment explanation
Indices: 1678245--1678509 Score: 331
Period size: 120 Copynumber: 2.2 Consensus size: 121
1678235 TACCGGGTAT
* * * * *
1678245 AAACAAGGGCACGTATGTGCAATC-AGGCGTACCGAAGTACAAATAGGGGCACGTATGTGCAATC
1 AAACAAGGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAATC
* * *
1678309 ATGGGTACCGAAGTACAAACAGGGGCATAAATGTCCAAACAGGGGTACCAAAGTAC
66 AGGGGTACCAAAGTACAAACAGGGGCACAAATGTCCAAACAGGGGTACCAAAGTAC
* *
1678365 AAA-AAGGGGTATGAATGTGCAATCAAGG-GTACTGAAGTACAAACAGGGACACGAATGTGCAAT
1 AAACAA-GGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAAT
* * * * * *
1678428 TAGGGGTACCAAATTACAAACAGGGGCACATATG-CGCAATCAGTGGTACCGAAGTAC
65 CAGGGGTACCAAAGTACAAACAGGGGCACAAATGTC-CAAACAGGGGTACCAAAGTAC
*
1678485 AAACAAGGGTACGAATGTGTAATCA
1 AAACAAGGGTACGAATGTGCAATCA
1678510 GACAATAGTT
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
119 3 0.02
120 115 0.93
121 5 0.04
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (121 bp):
AAACAAGGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAATC
AGGGGTACCAAAGTACAAACAGGGGCACAAATGTCCAAACAGGGGTACCAAAGTAC
Found at i:1694968 original size:34 final size:34
Alignment explanation
Indices: 1694924--1694991 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
1694914 GCACAGTTGA
* *
1694924 ATAGTCTTGGGACTAAGCCCTTTTCAGTATCAGTG
1 ATAGTCTTGGGACTAAGCCCATCTCAGTA-CAGTG
* *
1694959 ATAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ATAGTCTTGGGACTAAGCCCATCTCAGTACAGTG
1694992 TCAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (34 bp):
ATAGTCTTGGGACTAAGCCCATCTCAGTACAGTG
Found at i:1695531 original size:16 final size:16
Alignment explanation
Indices: 1695510--1695545 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1695500 GGCCTTGGCC
1695510 ATGTGATCCATTTTTA
1 ATGTGATCCATTTTTA
1695526 ATGTGATCCATTTTTA
1 ATGTGATCCATTTTTA
1695542 ATGT
1 ATGT
1695546 AACCCATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (16 bp):
ATGTGATCCATTTTTA
Found at i:1695552 original size:16 final size:16
Alignment explanation
Indices: 1695517--1695552 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1695507 GCCATGTGAT
* *
1695517 CCATTTTTAATGTGAT
1 CCATTTTTAATGTAAC
1695533 CCATTTTTAATGTAAC
1 CCATTTTTAATGTAAC
1695549 CCAT
1 CCAT
1695553 GCTAGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (16 bp):
CCATTTTTAATGTAAC
Found at i:1697589 original size:19 final size:19
Alignment explanation
Indices: 1697565--1697602 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1697555 TATGTCGAAA
1697565 TAACAAACTAGTTAACCTT
1 TAACAAACTAGTTAACCTT
1697584 TAACAAACTAGTTAACCTT
1 TAACAAACTAGTTAACCTT
1697603 AATTGCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (19 bp):
TAACAAACTAGTTAACCTT
Found at i:1703492 original size:15 final size:15
Alignment explanation
Indices: 1703472--1703502 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1703462 AAAACTTAAC
1703472 ATGTAGAGCTATCAG
1 ATGTAGAGCTATCAG
1703487 ATGTAGAGCTATCAG
1 ATGTAGAGCTATCAG
1703502 A
1 A
1703503 CTTACTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGTAGAGCTATCAG
Found at i:1704868 original size:18 final size:18
Alignment explanation
Indices: 1704845--1704882 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1704835 ATTGCGACAA
1704845 TTATTTAATTGAAA-TAAT
1 TTATTT-ATTGAAATTAAT
*
1704863 TTATTTATTTAAATTAAT
1 TTATTTATTGAAATTAAT
1704881 TT
1 TT
1704883 TAAGATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATTTATTGAAATTAAT
Found at i:1713715 original size:14 final size:15
Alignment explanation
Indices: 1713687--1713725 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1713677 AGAACAGTTT
1713687 AATAATTTTTAATAA
1 AATAATTTTTAATAA
1713702 AATAATTTTT-ATAA
1 AATAATTTTTAATAA
1713716 AATGAATTTT
1 AAT-AATTTT
1713726 AATTAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATAATTTTTAATAA
Found at i:1714991 original size:20 final size:20
Alignment explanation
Indices: 1714966--1715008 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1714956 TTATGTAAAC
* * *
1714966 AAATGTTTTAATTTTTTTTT
1 AAATGTTCTAATGTGTTTTT
1714986 AAATGTTCTAATGTGTTTTT
1 AAATGTTCTAATGTGTTTTT
1715006 AAA
1 AAA
1715009 ATGTGTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
AAATGTTCTAATGTGTTTTT
Found at i:1715010 original size:21 final size:20
Alignment explanation
Indices: 1714966--1715012 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1714956 TTATGTAAAC
* * *
1714966 AAATGTTTTAATTTTTTTTT
1 AAATGTTCTAATTGTTTTTA
1714986 AAATGTTCTAATGTGTTTTTA
1 AAATGTTCTAAT-TGTTTTTA
1715007 AAATGT
1 AAATGT
1715013 GTTGTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (20 bp):
AAATGTTCTAATTGTTTTTA
Found at i:1715206 original size:29 final size:26
Alignment explanation
Indices: 1715173--1715229 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
1715163 AGAGGTTAAT
1715173 TTATAAATT-TAATGATATTTTAGAATTTC
1 TTATAAATTAT-AT-ATATTTT--AATTTC
1715202 TTATAAATTATATATATTTTAATTTC
1 TTATAAATTATATATATTTTAATTTC
1715228 TT
1 TT
1715230 TATGGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
28 7 0.26
29 11 0.41
30 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATAAATTATATATATTTTAATTTC
Found at i:1715216 original size:26 final size:29
Alignment explanation
Indices: 1715173--1715229 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
1715163 AGAGGTTAAT
1715173 TTATAAATTTAATGATAT-TTTAGAATTTC
1 TTATAAATTTAATGATATATTT-GAATTTC
*
1715202 TTATAAA-TT-AT-ATATATTTTAATTTC
1 TTATAAATTTAATGATATATTTGAATTTC
1715228 TT
1 TT
1715230 TATGGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 5 0.19
28 2 0.08
29 7 0.27
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (29 bp):
TTATAAATTTAATGATATATTTGAATTTC
Found at i:1716358 original size:93 final size:93
Alignment explanation
Indices: 1716176--1716361 Score: 211
Period size: 93 Copynumber: 2.0 Consensus size: 93
1716166 ACGATAAGAG
* * *
1716176 TATTGGTGGATGAACCATCCGTCTATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
1 TATTGGTGGATAAACCATCCATCGATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
* **
1716241 ATCGTGCAGATAAACTGATGACTAAAAT
66 ATCGAGCAGATAAACTGACAACTAAAAT
* *
1716269 TATTGGTGGATAAACCATCCAT-GAGTGCAGATAAAAGTTG-ATTAATATGTTGTGGATGAATCA
1 TATTGGTGGATAAACCATCCATCGA-TGCAGATAAAAGTTGCA--AATATGTTGTGAATGAACCA
*
1716332 CT-AGTCGAGTAGAT-AACT-ACCAACTAAAAT
63 CTGA-TCGAGCAGATAAACTGA-CAACTAAAAT
1716362 AAGTTGTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
92 3 0.04
93 48 0.61
94 28 0.35
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (93 bp):
TATTGGTGGATAAACCATCCATCGATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
ATCGAGCAGATAAACTGACAACTAAAAT
Found at i:1717112 original size:18 final size:19
Alignment explanation
Indices: 1717089--1717130 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1717079 AAACCAAAAG
1717089 TAAATCAA-TTTTACATTC
1 TAAATCAATTTTTACATTC
*
1717107 TAAATCAATTTTTGCATTC
1 TAAATCAATTTTTACATTC
1717126 TAAAT
1 TAAAT
1717131 GTTGGAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (19 bp):
TAAATCAATTTTTACATTC
Found at i:1722058 original size:23 final size:23
Alignment explanation
Indices: 1722015--1722078 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1722005 AACAGAAATA
*
1722015 ATTTTT-TAAAAACTTTGAGATTTT
1 ATTTTTATATAAA-TTT-AGATTTT
1722039 ATTTTTATATAAATTTAGATTTT
1 ATTTTTATATAAATTTAGATTTT
* **
1722062 ATCTTTACGTAAATTTA
1 ATTTTTATATAAATTTA
1722079 AATTAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.60
24 9 0.26
25 5 0.14
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTTTATATAAATTTAGATTTT
Found at i:1723176 original size:23 final size:23
Alignment explanation
Indices: 1723133--1723196 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1723123 AACAGAAATA
*
1723133 ATTTTT-TAAAAACTTTGAGATTTT
1 ATTTTTATATAAA-TTT-AGATTTT
1723157 ATTTTTATATAAATTTAGATTTT
1 ATTTTTATATAAATTTAGATTTT
* **
1723180 ATCTTTACGTAAATTTA
1 ATTTTTATATAAATTTA
1723197 AATTAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.60
24 9 0.26
25 5 0.14
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTTTATATAAATTTAGATTTT
Found at i:1724356 original size:18 final size:18
Alignment explanation
Indices: 1724333--1724368 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1724323 ATGATAAAAA
*
1724333 ATAAAAAATTTAAAATTT
1 ATAAAAAAATTAAAATTT
*
1724351 ATAAAAAAATTATAATTT
1 ATAAAAAAATTAAAATTT
1724369 TTACACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAAAATTAAAATTT
Found at i:1728217 original size:23 final size:24
Alignment explanation
Indices: 1728163--1728219 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1728153 ATAGAAATGT
1728163 ATAAAATAAAATAATAATACCTAA
1 ATAAAATAAAATAATAATACCTAA
* *
1728187 A-AACATAAAATAAT-AT-CTTATA
1 ATAAAATAAAATAATAATACCTA-A
1728209 ATAAAATAAAA
1 ATAAAATAAAA
1728220 GGATCTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.11
22 4 0.14
23 20 0.71
24 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (24 bp):
ATAAAATAAAATAATAATACCTAA
Found at i:1728277 original size:3 final size:3
Alignment explanation
Indices: 1728248--1728311 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
1728238 TAAGAGGAAA
* * * *
1728248 AAT AA- AAT AA- AAT AAA AAG ACT AAT AAT AAT AAT AAT AAT GACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
1728292 AAT AAA AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1728312 ACAAATTAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (3 bp):
AAT
Found at i:1728291 original size:22 final size:21
Alignment explanation
Indices: 1728253--1728305 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
1728243 GGAAAAATAA
1728253 AATAA-AATAAAAAGACTAAT
1 AATAATAATAAAAAGACTAAT
*
1728273 AATAATAATAATAATGACTAAT
1 AATAATAATAA-AAAGACTAAT
*
1728295 AAAAATAATAA
1 AATAATAATAA
1728306 CAATAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 5 0.17
22 19 0.66
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (21 bp):
AATAATAATAAAAAGACTAAT
Found at i:1730931 original size:12 final size:13
Alignment explanation
Indices: 1730914--1730943 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1730904 GGCTCGGAAA
1730914 TGATA-GAAATGT
1 TGATAGGAAATGT
1730926 TGATAGGAAATGT
1 TGATAGGAAATGT
1730939 TGATA
1 TGATA
1730944 ACAGTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (13 bp):
TGATAGGAAATGT
Found at i:1732518 original size:18 final size:18
Alignment explanation
Indices: 1732497--1732532 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1732487 TATGGCATGT
*
1732497 TATAAAAAAATTAAAAAA
1 TATAAAAAAACTAAAAAA
*
1732515 TATAAAAATACTAAAAAA
1 TATAAAAAAACTAAAAAA
1732533 ATGTTTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TATAAAAAAACTAAAAAA
Found at i:1732603 original size:31 final size:32
Alignment explanation
Indices: 1732541--1732603 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1732531 AAATGTTTAG
**
1732541 AATGAACTTGAACAAATGGTTGTCCAGATTCA
1 AATGAACTTGAACAAATCATTGTCCAGATTCA
* *
1732573 AATGAACTTGGAC-AATCATTGTCCATATTCA
1 AATGAACTTGAACAAATCATTGTCCAGATTCA
1732604 TTCTCTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
AATGAACTTGAACAAATCATTGTCCAGATTCA
Found at i:1732662 original size:15 final size:16
Alignment explanation
Indices: 1732625--1732664 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1732615 AAAAATTATA
1732625 ATTTT-TTTTATGAAT
1 ATTTTATTTTATGAAT
1732640 -TTTATATTTTA-GAAT
1 ATTT-TATTTTATGAAT
1732655 ATTTTATTTT
1 ATTTTATTTT
1732665 TTGCCAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
16 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
ATTTTATTTTATGAAT
Found at i:1735080 original size:13 final size:13
Alignment explanation
Indices: 1735030--1735080 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
1735020 TTTAAACAAA
* *
1735030 ACTTTTTAAAATC
1 ACTTTTCAAAAAC
* **
1735043 ACTTTTCTACCAC
1 ACTTTTCAAAAAC
1735056 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
1735069 ACTTTTCAAAAA
1 ACTTTTCAAAAA
1735081 AAATGAAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:1739665 original size:21 final size:22
Alignment explanation
Indices: 1739611--1739667 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1739601 TTAAAAATGT
*
1739611 TTTTTGTATTAATATCTAAATAA
1 TTTTT-TATTAATATCTAAACAA
* *
1739634 TTTTATGTTAA-ATCTAAACAA
1 TTTTTTATTAATATCTAAACAA
1739655 TTTTTTATTAATA
1 TTTTTTATTAATA
1739668 AAAAGCAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 18 0.64
22 6 0.21
23 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTTTATTAATATCTAAACAA
Found at i:1744526 original size:17 final size:17
Alignment explanation
Indices: 1744475--1744529 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
1744465 TATGAAAAAA
1744475 TAAAAAAACTTTAAAATT
1 TAAAAAAA-TTTAAAATT
* * **
1744493 CAAAAATATTT--CTTT
1 TAAAAAAATTTAAAATT
1744508 TAAAAAAATTTAAAATT
1 TAAAAAAATTTAAAATT
1744525 TAAAA
1 TAAAA
1744530 TATAAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
15 11 0.41
17 10 0.37
18 6 0.22
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAAATTTAAAATT
Found at i:1747549 original size:35 final size:34
Alignment explanation
Indices: 1747502--1747584 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
1747492 CATGTACACA
*
1747502 GTTTACACGGTGTCGCACC-AAAGGACTTGTATACC
1 GTTTACATGGTGTCGC-CCGAAA-GACTTGTATACC
*
1747537 GTTTACATGGTGTCGCCCTGAAAGACTTGTATATC
1 GTTTACATGGTGTCGCCC-GAAAGACTTGTATACC
1747572 GTTTACATGGTGT
1 GTTTACATGGTGT
1747585 TACCTCGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 2 0.05
35 39 0.89
36 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (34 bp):
GTTTACATGGTGTCGCCCGAAAGACTTGTATACC
Found at i:1748210 original size:15 final size:15
Alignment explanation
Indices: 1748190--1748221 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1748180 ACGAATATAG
1748190 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
1748205 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
1748220 TA
1 TA
1748222 CTAGTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAAGATTAAGAAGCT
Found at i:1748728 original size:15 final size:15
Alignment explanation
Indices: 1748708--1748739 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1748698 ACGAATATAG
1748708 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
1748723 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
1748738 TA
1 TA
1748740 CTAGTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAAGATTAAGAAGCT
Found at i:1748785 original size:518 final size:518
Alignment explanation
Indices: 1747808--1748844 Score: 2002
Period size: 518 Copynumber: 2.0 Consensus size: 518
1747798 GTCAATACAC
1747808 TACCACATTTACATCTAGAGAACATACTTCCAAACATCTATATATTTATACAACTTTATGCATGC
1 TACCACATTTACATCTAGAGAACATACTTCCAAACATCTATATATTTATACAACTTTATGCATGC
1747873 ATAGCATACTCATTCATCATAATCACACTTAACCATTAAATTTGAACTGAACTCAGAATAGACAT
66 ATAGCATACTCATTCATCATAATCACACTTAACCATTAAATTTGAACTGAACTCAGAATAGACAT
*
1747938 ATGAGCAGAACATTCAAGCAACAAACACCCAAAGTGGAGTATAGGAACTCACGTACTATCCTTTA
131 ATGAGCAGAACATTCAAGCAACAAACACCCAAAGTGGAGTATAGGAACTCACCTACTATCCTTTA
1748003 TCCTCGCCAGGTTAACTCGACTGAATGTCAGAGCCTCCTTCATTGTGGCAACTAAGAATGACAAC
196 TCCTCGCCAGGTTAACTCGACTGAATGTCAGAGCCTCCTTCATTGTGGCAACTAAGAATGACAAC
1748068 CAAATATACCGGTTAAATCGGAGGCATTCAAGGTTTAAATACCAGAATCAAATTTCATGCAAAAA
261 CAAATATACCGGTTAAATCGGAGGCATTCAAGGTTTAAATACCAGAATCAAATTTCATGCAAAAA
1748133 TTTCCAAAGATTTCATAAACCCCTTAACTTCTCTTTTCCTCAACTTCACGAATATAGTAAGATTA
326 TTTCCAAAGATTTCATAAACCCCTTAACTTCTCTTTTCCTCAACTTCACGAATATAGTAAGATTA
1748198 AGAAGCTTAAGATTAAGAAGCTTACTAGTTTACTGTATTCAATACATTCCAGACTTAAACCTTAC
391 AGAAGCTTAAGATTAAGAAGCTTACTAGTTTACTGTATTCAATACATTCCAGACTTAAACCTTAC
1748263 GATCACCATGCCATGCAGGACTTTCCTTAACGTTGTCTTGTTCGGAGCAATCGAAAAAGACGG
456 GATCACCATGCCATGCAGGACTTTCCTTAACGTTGTCTTGTTCGGAGCAATCGAAAAAGACGG
* * *
1748326 TACCACATTTGCATCTAGAGAACATACTTGCAAGCATCTATATATTTATACAACTTTATGCATGC
1 TACCACATTTACATCTAGAGAACATACTTCCAAACATCTATATATTTATACAACTTTATGCATGC
1748391 ATAGCATACTCATTCATCATAATCACACTTAACCATTAAATTTGAACTGAACTCAGAATAGACAT
66 ATAGCATACTCATTCATCATAATCACACTTAACCATTAAATTTGAACTGAACTCAGAATAGACAT
*
1748456 ATGAGCAGAACATTCAAGCAACAAACACCCAAAGTGGAGTATAGGAACTCACCTACTATTCTTTA
131 ATGAGCAGAACATTCAAGCAACAAACACCCAAAGTGGAGTATAGGAACTCACCTACTATCCTTTA
*
1748521 TCCTTGCCAGGTTAACTCGACTGAATGTCAGAGCCTCCTTCATTGTGGCAACTAAGAATGACAAC
196 TCCTCGCCAGGTTAACTCGACTGAATGTCAGAGCCTCCTTCATTGTGGCAACTAAGAATGACAAC
1748586 CAAATATACCGGTTAAATCGGAGGCATTCAAGGTTTAAATACCAGAATCAAATTTCATGCAAAAA
261 CAAATATACCGGTTAAATCGGAGGCATTCAAGGTTTAAATACCAGAATCAAATTTCATGCAAAAA
*
1748651 TTTCCGAAGATTTCATAAACCCCTTAACTTCTCTTTTCCTCAACTTCACGAATATAGTAAGATTA
326 TTTCCAAAGATTTCATAAACCCCTTAACTTCTCTTTTCCTCAACTTCACGAATATAGTAAGATTA
1748716 AGAAGCTTAAGATTAAGAAGCTTACTAGTTTACTGTATTCAATACATTCCAGACTTAAACCTTAC
391 AGAAGCTTAAGATTAAGAAGCTTACTAGTTTACTGTATTCAATACATTCCAGACTTAAACCTTAC
*
1748781 GATCACTATGCCATGCAGGACTTTCCTTAACGTTGTCTTGTTCGGAGCAATCGAAAAAGACGG
456 GATCACCATGCCATGCAGGACTTTCCTTAACGTTGTCTTGTTCGGAGCAATCGAAAAAGACGG
1748844 T
1 T
1748845 GTAGATGAGA
Statistics
Matches: 511, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
518 511 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (518 bp):
TACCACATTTACATCTAGAGAACATACTTCCAAACATCTATATATTTATACAACTTTATGCATGC
ATAGCATACTCATTCATCATAATCACACTTAACCATTAAATTTGAACTGAACTCAGAATAGACAT
ATGAGCAGAACATTCAAGCAACAAACACCCAAAGTGGAGTATAGGAACTCACCTACTATCCTTTA
TCCTCGCCAGGTTAACTCGACTGAATGTCAGAGCCTCCTTCATTGTGGCAACTAAGAATGACAAC
CAAATATACCGGTTAAATCGGAGGCATTCAAGGTTTAAATACCAGAATCAAATTTCATGCAAAAA
TTTCCAAAGATTTCATAAACCCCTTAACTTCTCTTTTCCTCAACTTCACGAATATAGTAAGATTA
AGAAGCTTAAGATTAAGAAGCTTACTAGTTTACTGTATTCAATACATTCCAGACTTAAACCTTAC
GATCACCATGCCATGCAGGACTTTCCTTAACGTTGTCTTGTTCGGAGCAATCGAAAAAGACGG
Found at i:1758613 original size:20 final size:20
Alignment explanation
Indices: 1758580--1758618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1758570 ATTATTTTGG
1758580 AATTTTATACAAAACCATTA
1 AATTTTATACAAAACCATTA
*
1758600 AATTTATATA-AAAATCATT
1 AATTT-TATACAAAACCATT
1758619 GCCATCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTTATACAAAACCATTA
Found at i:1775849 original size:30 final size:30
Alignment explanation
Indices: 1775778--1775849 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1775768 CTAAGGTTAC
* *
1775778 CTCTCAATCTCACCTAGGCTTATAAATTAT
1 CTCTGAATCTCACCTAGGCATATAAATTAT
* * * *
1775808 GTCTTG-GTCTCACCTCGGCATATAGATTAT
1 CTC-TGAATCTCACCTAGGCATATAAATTAT
1775838 CTCTGAATCTCA
1 CTCTGAATCTCA
1775850 TTATTCAGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 2 0.06
30 29 0.91
31 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (30 bp):
CTCTGAATCTCACCTAGGCATATAAATTAT
Found at i:1777436 original size:35 final size:36
Alignment explanation
Indices: 1777396--1777505 Score: 120
Period size: 35 Copynumber: 3.1 Consensus size: 36
1777386 CCCCTCTGTA
* * *
1777396 TGGAAGCGAGCCTTCCGTAAGCCTTCCTTCATGTG-
1 TGGAAGCAAGCCTTCCGTAAGCCTTCCTCCATATGT
* *
1777431 TGGAAGAAAGCC-TCCATAAGCCTCTCC-CCATATGT
1 TGGAAGCAAGCCTTCCGTAAGCCT-TCCTCCATATGT
* *
1777466 TGGAAGCAAGCCTTCCGTAAGCTTTCCTCTATATG-
1 TGGAAGCAAGCCTTCCGTAAGCCTTCCTCCATATGT
1777501 TGGAA
1 TGGAA
1777506 AAAAACACCC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
34 15 0.24
35 32 0.52
36 15 0.24
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (36 bp):
TGGAAGCAAGCCTTCCGTAAGCCTTCCTCCATATGT
Found at i:1777480 original size:70 final size:73
Alignment explanation
Indices: 1777333--1777493 Score: 195
Period size: 70 Copynumber: 2.2 Consensus size: 73
1777323 CAGAGCAAAA
* * * * * * *
1777333 CCTTCCATAACCCTTCCTTATGTGTTGGGAGCAAGACCTGCTATAAGCCACTCCCCCTCTGTATG
1 CCTTCCGTAAGCCTTCCTTATGTGTTGGAAGAAAGACCTGCCATAAGCCACTCCCCATATGTATG
*
1777398 GAAGCGAG
66 GAAGCAAG
*
1777406 CCTTCCGTAAGCCTTCCTTCATGTG-TGGAAGAAAG-CCT-CCATAAGCCTCTCCCCATATGT-T
1 CCTTCCGTAAGCCTTCCTT-ATGTGTTGGAAGAAAGACCTGCCATAAGCCACTCCCCATATGTAT
1777467 GGAAGCAAG
65 GGAAGCAAG
*
1777476 CCTTCCGTAAGCTTTCCT
1 CCTTCCGTAAGCCTTCCT
1777494 CTATATGTGG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 26 0.34
71 18 0.23
72 3 0.04
73 25 0.32
74 5 0.06
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (73 bp):
CCTTCCGTAAGCCTTCCTTATGTGTTGGAAGAAAGACCTGCCATAAGCCACTCCCCATATGTATG
GAAGCAAG
Found at i:1777607 original size:36 final size:36
Alignment explanation
Indices: 1777515--1777607 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
1777505 AAAAAACACC
* *
1777515 CTGTAAGCATTCCCCCATGTACTATGAGCAGGCCTT
1 CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
** * **
1777551 CCATAAGCTTTCCCTTATGTGCTAAGAGCAGGCCTT
1 CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
*
1777587 CTGTAAGCCTTCCCCCATGTG
1 CTGTAAGCATTCCCCCATGTG
1777608 TGTAAGCAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.29
Consensus pattern (36 bp):
CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
Found at i:1777691 original size:107 final size:107
Alignment explanation
Indices: 1777518--1777716 Score: 233
Period size: 107 Copynumber: 1.9 Consensus size: 107
1777508 AAACACCCTG
* * * *
1777518 TAAGCATTCCCCCATGTACTATGAGCAGGCCTTCCATAAGCTTTCCCTTATGTGCTAAGAGCAGG
1 TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCCTTATCTACTAAGAGCAGG
* *
1777583 CCTT-CTGTAAGCCTTCCCCCATGTGTGTAAGCAAGCTCCTCT
66 CCTTAC-ATAAGCATTCCCCCATGTGTGTAAGCAAGCTCCTCT
* * * * * *
1777625 TAAGCCTT-CCCCATGTACTAGGAGTAGACCTTTCGTAAGC-TTCCCTTTTATCTACTAGGAGTA
1 TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCC--TTATCTACTAAGAGCA
*
1777688 GGCCTTACATAAGTATTCCCCCATGTGTG
64 GGCCTTACATAAGCATTCCCCCATGTGTG
1777717 GAAACAGACC
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
105 5 0.07
106 27 0.36
107 43 0.57
108 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.31
Consensus pattern (107 bp):
TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCCTTATCTACTAAGAGCAGG
CCTTACATAAGCATTCCCCCATGTGTGTAAGCAAGCTCCTCT
Found at i:1783304 original size:19 final size:19
Alignment explanation
Indices: 1783280--1783319 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1783270 TGTTTAAGAA
1783280 AACTAGATTTTAACTAAGT
1 AACTAGATTTTAACTAAGT
1783299 AACTAGATTTTAACTAAGT
1 AACTAGATTTTAACTAAGT
1783318 AA
1 AA
1783320 ATTAACTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (19 bp):
AACTAGATTTTAACTAAGT
Found at i:1784797 original size:10 final size:10
Alignment explanation
Indices: 1784770--1784800 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1784760 GCAAATCTAT
*
1784770 TGAAAATATA
1 TGAAAATTTA
1784780 TGAAAATTTA
1 TGAAAATTTA
1784790 TGAAAATTTA
1 TGAAAATTTA
1784800 T
1 T
1784801 TATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (10 bp):
TGAAAATTTA
Found at i:1786435 original size:7 final size:7
Alignment explanation
Indices: 1786423--1786467 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
1786413 GCCATCATCC
1786423 CTCTCAT
1 CTCTCAT
1786430 CTCTCAT
1 CTCTCAT
1786437 CTCTCAT
1 CTCTCAT
1786444 CTCTCAT
1 CTCTCAT
1786451 C-CTC-T
1 CTCTCAT
*
1786456 CTCTCAA
1 CTCTCAT
1786463 CTCTC
1 CTCTC
1786468 TTAGCTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 2 0.06
6 6 0.17
7 27 0.77
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (7 bp):
CTCTCAT
Found at i:1786446 original size:19 final size:19
Alignment explanation
Indices: 1786423--1786467 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1786413 GCCATCATCC
*
1786423 CTCTCATCTCTCATCTCTCAT
1 CTCTCATC-CTC-TCTCTCAA
1786444 CTCTCATCCTCTCTCTCAA
1 CTCTCATCCTCTCTCTCAA
1786463 CTCTC
1 CTCTC
1786468 TTAGCTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCTCATCCTCTCTCTCAA
Found at i:1793318 original size:20 final size:20
Alignment explanation
Indices: 1793293--1793330 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1793283 GTTTTTCTAG
1793293 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
1793313 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
1793331 TAAAGGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:1796929 original size:16 final size:17
Alignment explanation
Indices: 1796908--1796943 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1796898 TCCATCATCC
1796908 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
1796924 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
1796941 CTC
1 CTC
1796944 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:1800655 original size:22 final size:22
Alignment explanation
Indices: 1800619--1800661 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1800609 AACTCATAAC
1800619 ACATTTAGAGAATTTTGTATTT
1 ACATTTAGAGAATTTTGTATTT
* * *
1800641 ACATTTTGAGGATTTTTTATT
1 ACATTTAGAGAATTTTGTATT
1800662 CTCTTCGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (22 bp):
ACATTTAGAGAATTTTGTATTT
Found at i:1803522 original size:107 final size:108
Alignment explanation
Indices: 1803398--1803608 Score: 390
Period size: 107 Copynumber: 2.0 Consensus size: 108
1803388 TGTGTATATT
*
1803398 AAATTTATAATCTTTTTATAATATTAATTTTTGTTTAAAATTTTTAATGAATTTTTTTAAAATAT
1 AAATTTAGAATCTTTTTATAATATTAATTTTTGTTTAAAATTTTTAATGAATTTTTTTAAAATAT
1803463 CATTAAAATTTGACAAAGTAATGTAG-TTAAAATATATTTTAAC
66 CATTAAAATTTGACAAAGTAATGTAGTTTAAAATA-ATTTTAAC
1803506 AAATTTAGAATC-TTTTATAATATTAATTTTTGTTTAAAATTTTTAATGAATTTTTTTAAAATAT
1 AAATTTAGAATCTTTTTATAATATTAATTTTTGTTTAAAATTTTTAATGAATTTTTTTAAAATAT
1803570 CATTAAAATTTGACAAAGTAATGTAGTTTAAAATAATTT
66 CATTAAAATTTGACAAAGTAATGTAGTTTAAAATAATTT
1803609 GTTTAAAATT
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
107 82 0.81
108 19 0.19
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (108 bp):
AAATTTAGAATCTTTTTATAATATTAATTTTTGTTTAAAATTTTTAATGAATTTTTTTAAAATAT
CATTAAAATTTGACAAAGTAATGTAGTTTAAAATAATTTTAAC
Found at i:1812905 original size:85 final size:85
Alignment explanation
Indices: 1812808--1813016 Score: 271
Period size: 88 Copynumber: 2.4 Consensus size: 85
1812798 AAAATATTAC
*
1812808 TGAGATAATAACAAAAATTAAATTTTGTTAAAAAATTACTTTCA-AGAGTACTTTTATTCTATC-
1 TGAGATAATAACAAAAATTAAATTTTG-AAAAAAATTA-TTTCATAGAGTACTTTTATTCTATCA
** *
1812871 AATGGTACGTAAAA-AGAACTTT
64 AAAAGTAAGTAAAAGA-AACTTT
* *
1812893 TGAGATAATAACAAAAATTAAGTTTTGCCAAAAAAAATTATTTCATAGATTACTTTTATTCTATC
1 TGAGATAATAACAAAAATTAAATTTTG---AAAAAAATTATTTCATAGAGTACTTTTATTCTATC
*
1812958 AAAAATTAAGTAAAAGAAACTTT
63 AAAAAGTAAGTAAAAGAAACTTT
*
1812981 TGAGATAATAACAAAAATTAAATTTTGCAAAAAATT
1 TGAGATAATAACAAAAATTAAATTTTGAAAAAAATT
1813017 TTCTTCAAAG
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
85 34 0.31
86 5 0.05
87 27 0.25
88 42 0.39
89 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (85 bp):
TGAGATAATAACAAAAATTAAATTTTGAAAAAAATTATTTCATAGAGTACTTTTATTCTATCAAA
AAGTAAGTAAAAGAAACTTT
Found at i:1812974 original size:87 final size:87
Alignment explanation
Indices: 1812808--1813014 Score: 287
Period size: 87 Copynumber: 2.4 Consensus size: 87
1812798 AAAATATTAC
**
1812808 TGAGATAATAACAAAAATTAAATTTTG-TTAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
1 TGAGATAATAACAAAAATTAAATTTTGCAAAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
** *
1812872 ATGGTACGTAAAAAG-AACTTT
66 AAAGTAAGTAAAAAGAAACTTT
* *
1812893 TGAGATAATAACAAAAATTAAGTTTTGCCAAAAAAAATTA-TTTCATAGATTACTTTTATTCTAT
1 TGAGATAATAACAAAAATTAAATTTTG-CAAAAAAAATTACTTTCA-AGAGTACTTTTATTCTAT
*
1812957 CAAAAATTAAGT-AAAAGAAACTTT
64 C-AAAAGTAAGTAAAAAGAAACTTT
1812981 TGAGATAATAACAAAAATTAAATTTTGCAAAAAA
1 TGAGATAATAACAAAAATTAAATTTTGCAAAAAA
1813015 TTTTCTTCAA
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
85 26 0.24
86 5 0.05
87 39 0.36
88 38 0.35
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (87 bp):
TGAGATAATAACAAAAATTAAATTTTGCAAAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
AAAGTAAGTAAAAAGAAACTTT
Found at i:1822267 original size:18 final size:19
Alignment explanation
Indices: 1822241--1822281 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1822231 CGTTCGTTTC
1822241 CAAAACATTATTCA-TTTA
1 CAAAACATTATTCACTTTA
*
1822259 CAAATCATTATTCACTTTA
1 CAAAACATTATTCACTTTA
1822278 -AAAA
1 CAAAA
1822282 AATTTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAACATTATTCACTTTA
Found at i:1822838 original size:23 final size:24
Alignment explanation
Indices: 1822794--1822838 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1822784 AAAATCCTAC
*
1822794 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
1822818 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
1822839 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:1826259 original size:24 final size:24
Alignment explanation
Indices: 1826214--1826275 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
1826204 ACGAGCTTCC
* *
1826214 CCATTAATGGCTCTTTTAAGCTTT
1 CCATTAATGGCTCATATAAGCTTT
* * *
1826238 CCATTTATGGCTCATATGAGCTTC
1 CCATTAATGGCTCATATAAGCTTT
*
1826262 CCAATAATTGGCTC
1 CCATTAA-TGGCTC
1826276 GCAAGAGCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (24 bp):
CCATTAATGGCTCATATAAGCTTT
Found at i:1826350 original size:25 final size:24
Alignment explanation
Indices: 1826272--1826351 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
1826262 CCAATAATTG
* * *
1826272 GCTCGCAAGAGCTTCACGTTATACA
1 GCTCACAAGAGCTTCCCGAT-TACA
* *
1826297 GCTCACATGAGCTT-CCTATTACA
1 GCTCACAAGAGCTTCCCGATTACA
*
1826320 CGGCTCAGAAGAGCTTCCCGATTACA
1 --GCTCACAAGAGCTTCCCGATTACA
1826346 TGCTCA
1 -GCTCA
1826352 TATGGGTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 4 0.09
24 2 0.05
25 29 0.67
26 8 0.19
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (24 bp):
GCTCACAAGAGCTTCCCGATTACA
Found at i:1831073 original size:18 final size:18
Alignment explanation
Indices: 1831033--1831070 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1831023 GTTAACGAAC
1831033 AAATATATAAATATAAAT
1 AAATATATAAATATAAAT
* *
1831051 AAATATCTATATA-AAAT
1 AAATATATAAATATAAAT
1831068 AAA
1 AAA
1831071 ATAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATAAATATAAAT
Found at i:1831561 original size:20 final size:20
Alignment explanation
Indices: 1831518--1831566 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1831508 ATGAGCAATT
* *
1831518 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATA
**
1831538 AAATCAAATTGATTGGAATA
1 AAATCAAATTGATTAAAATA
*
1831558 AAATAAAAT
1 AAATCAAAT
1831567 CAACATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:1832643 original size:17 final size:17
Alignment explanation
Indices: 1832621--1832655 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1832611 ACATATCCTT
*
1832621 TCAACTTTTATGGCCCA
1 TCAACTTTTATGGACCA
1832638 TCAACTTTTATGGACCA
1 TCAACTTTTATGGACCA
1832655 T
1 T
1832656 ACCCCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (17 bp):
TCAACTTTTATGGACCA
Found at i:1837409 original size:77 final size:80
Alignment explanation
Indices: 1837312--1837490 Score: 204
Period size: 83 Copynumber: 2.2 Consensus size: 80
1837302 CTATTGCACA
* *
1837312 GCAGGATTAAATCCCAAAACAAAATTAT-TTACTTAAATCTT-GTCTGGAAACAAAATC-A-AAA
1 GCAGGAATAAATCCCAAAACAAAATTATCTGA-TTAAATCTTCGTCTGGAAACAAAATCAACAAA
*
1837373 TGAAATATGTTAAACG
65 TAAAATATGTTAAACG
** * * *
1837389 GCAGGAATAAATCCTGAAACAGAATTATCTGATTAAGTCTTCGTTTGGAAACAAAATCAAGATCA
1 GCAGGAATAAATCCCAAAACAAAATTATCTGATTAAATCTTCGTCTGGAAACAAAATC-A-A-CA
* *
1837454 AATAAAATCTGTTAAATG
63 AATAAAATATGTTAAACG
1837472 GCAGGAATAAATCCCAAAA
1 GCAGGAATAAATCCCAAAA
1837491 TAGATTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
77 32 0.39
78 17 0.20
81 1 0.01
83 33 0.40
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (80 bp):
GCAGGAATAAATCCCAAAACAAAATTATCTGATTAAATCTTCGTCTGGAAACAAAATCAACAAAT
AAAATATGTTAAACG
Found at i:1837633 original size:88 final size:84
Alignment explanation
Indices: 1837432--1837722 Score: 300
Period size: 88 Copynumber: 3.4 Consensus size: 84
1837422 TAAGTCTTCG
* * ** * ** *
1837432 TTTGGAAACAAAATCAAGATCAAATAAAATCTGTTAAATGGCAGGAATAAATCCCAAAATAGA--
1 TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGCA-GAATAAATCCCGAAATAGATT
*
1837495 TTATTCAA-TTTAATTCTAA
65 TTATTTAATTTTAATTCTAA
* * *
1837514 TTTGGAAACAAAATTAAAATCGAATAAAATCTATTAAACAGCGAGAATAAATCCCGAAATAAATT
1 TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGC-AGAATAAATCCCGAAATAGATT
**
1837579 TTATTTAATTTTAATTTCTTG
65 TTATTTAATTTTAA-TTCTAA
* * * * *
1837600 TTTGGCAACAAAATAAAAAAATGGAATAAAATCTGTTGAACAGCAAGAATAAATCCTGAAACAGA
1 TTTGGAAACAAAAT--AAAAATGGAATAAAATCTATTAAACAGC-AGAATAAATCCCGAAATAGA
* *
1837665 TTTTATTTAATTTTAATACTCA
63 TTTTATTTAATTTTAATTCTAA
*
1837687 TTTGGAAACAAAATCAAAAATGAAATAAAATCTATT
1 TTTGGAAACAAAAT-AAAAATGGAATAAAATCTATT
1837723 TGAATGGAGG
Statistics
Matches: 175, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
82 53 0.30
83 1 0.01
84 7 0.04
85 5 0.03
86 36 0.21
87 16 0.09
88 57 0.33
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (84 bp):
TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGCAGAATAAATCCCGAAATAGATTT
TATTTAATTTTAATTCTAA
Found at i:1837749 original size:87 final size:85
Alignment explanation
Indices: 1837432--1837765 Score: 288
Period size: 88 Copynumber: 3.9 Consensus size: 85
1837422 TAAGTCTTCG
* * * *
1837432 TTTGGAAACAAAATC-AAGATCAAATAAAATCTGTTAAATGGCAGGAATAAATCCCAAAATAGA-
1 TTTGGAAACAAAATCAAAAATGAAATAAAATCTGTTAAATGG-AAGAATAAATCCCAAAACAGAT
1837495 -TTATTCAA-TTTAATTCTAA
65 TTTATTCAATTTTAATTCTAA
* * * * * *
1837514 TTTGGAAACAAAAT-TAAAATCG-AATAAAATCTATTAAACAGCG-AGAATAAATCCCGAAATAA
1 TTTGGAAACAAAATCAAAAAT-GAAATAAAATCTGTTAAA-TG-GAAGAATAAATCCCAAAACAG
* **
1837576 ATTTTATTTAATTTTAATTTCTTG
63 ATTTTATTCAATTTTAA-TTCTAA
* * * * **
1837600 TTTGGCAACAAAATAAAAAAATGGAATAAAATCTGTTGAACA-GCAAGAATAAATCCTGAAACAG
1 TTTGGAAACAAAAT-CAAAAATGAAATAAAATCTGTT-AA-ATGGAAGAATAAATCCCAAAACAG
* * *
1837664 ATTTTATTTAATTTTAATACTCA
63 ATTTTATTCAATTTTAATTCTAA
* * * *
1837687 TTTGGAAACAAAATCAAAAATGAAATAAAATCTATTTGAATGGAGGGAATAAATCCCAAAACAGG
1 TTTGGAAACAAAATCAAAAATGAAATAAAATCT-GTTAAATGGA-AGAATAAATCCCAAAACAGA
1837752 TTTTATTCAATTTT
64 TTTTATTCAATTTT
1837766 TATTTTTATT
Statistics
Matches: 204, Mismatches: 31, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
82 50 0.25
83 1 0.00
84 8 0.04
85 6 0.03
86 37 0.18
87 48 0.24
88 51 0.25
89 2 0.01
90 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (85 bp):
TTTGGAAACAAAATCAAAAATGAAATAAAATCTGTTAAATGGAAGAATAAATCCCAAAACAGATT
TTATTCAATTTTAATTCTAA
Found at i:1838064 original size:88 final size:89
Alignment explanation
Indices: 1837964--1838150 Score: 252
Period size: 90 Copynumber: 2.1 Consensus size: 89
1837954 TCGTGAAACA
* * * *
1837964 GATTTTATTACTCATTTTGGAACTAAAAT-AAAAAAATGAAATAAAATCTGTTGAACTACAGGAA
1 GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAATGAAATAAAATCTATTGAACGACAGGAA
* *
1838028 TAAATCACGAAATAGATTTTATTT
66 GAAATCACGAAACAGATTTTATTT
* *
1838052 GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAAATGAAATAAAATCTATTGAACGGCGGGA
1 GATTTTAATACTCATTTTGGAAATAAAAT-AAAAAAAATGAAATAAAATCTATTGAACGACAGGA
* *
1838117 AGAAATCCCGAAACGGATTTTATTT
65 AGAAATCACGAAACAGATTTTATTT
1838142 -ACTTTTAAT
1 GA-TTTTAAT
1838151 TTGGAAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 27 0.31
89 1 0.01
90 58 0.67
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (89 bp):
GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAATGAAATAAAATCTATTGAACGACAGGAA
GAAATCACGAAACAGATTTTATTT
Found at i:1839982 original size:2 final size:2
Alignment explanation
Indices: 1839975--1840008 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1839965 GGATTACCTA
1839975 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1840009 TTTGTTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1854873 original size:9 final size:10
Alignment explanation
Indices: 1854830--1854876 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
1854820 ATAAATTATA
1854830 ATTAAAAATC
1 ATTAAAAATC
1854840 ATTAAAAATC
1 ATTAAAAATC
*
1854850 ATT-AAAATT
1 ATTAAAAATC
*
1854859 ATTAAAAATT
1 ATTAAAAATC
1854869 A-TAAAAAT
1 ATTAAAAAT
1854877 ACCAAAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (10 bp):
ATTAAAAATC
Found at i:1854875 original size:19 final size:19
Alignment explanation
Indices: 1854832--1854876 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1854822 AAATTATAAT
1854832 TAAAAATCATTAAAAATCA
1 TAAAAATCATTAAAAATCA
* * *
1854851 TTAAAATTATTAAAAATTA
1 TAAAAATCATTAAAAATCA
1854870 TAAAAAT
1 TAAAAAT
1854877 ACCAAAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATCATTAAAAATCA
Found at i:1855031 original size:148 final size:149
Alignment explanation
Indices: 1854862--1855161 Score: 593
Period size: 148 Copynumber: 2.0 Consensus size: 149
1854852 TAAAATTATT
1854862 AAAAATTATAAAAATACCAAAAAGTATTTTTAAAATTTTAAAAAATAATTAATTGTTTATGTGGA
1 AAAAATTATAAAAATACCAAAAAGTATTTTTAAAATTTTAAAAAATAATTAATTGTTTATGTGGA
1854927 ATACATGTGGATGCAACTTTTCCATTCATTTTGAGATAATTTAACAAACAATGCAAGTTAAAGGG
66 ATACATGTGGATGCAACTTTTCCATTCATTTTGAGATAATTTAACAAACAATGCAAGTTAAAGGG
1854992 CTAAAAAAGAGGAAAAATA
131 CTAAAAAAGAGGAAAAATA
1855011 AAAAATTAT-AAAATACCAAAAAGTATTTTTAAAATTTTAAAAAATAATTAATTGTTTATGTGGA
1 AAAAATTATAAAAATACCAAAAAGTATTTTTAAAATTTTAAAAAATAATTAATTGTTTATGTGGA
1855075 ATACATGTGGATGCAACTTTTCCATTCATTTTGAGATAATTTAACAAACAATGCAAGTTAAAGGG
66 ATACATGTGGATGCAACTTTTCCATTCATTTTGAGATAATTTAACAAACAATGCAAGTTAAAGGG
1855140 CTAAAAAAGAGGAAAAATA
131 CTAAAAAAGAGGAAAAATA
1855159 AAA
1 AAA
1855162 TGGAGGACTA
Statistics
Matches: 151, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 142 0.94
149 9 0.06
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (149 bp):
AAAAATTATAAAAATACCAAAAAGTATTTTTAAAATTTTAAAAAATAATTAATTGTTTATGTGGA
ATACATGTGGATGCAACTTTTCCATTCATTTTGAGATAATTTAACAAACAATGCAAGTTAAAGGG
CTAAAAAAGAGGAAAAATA
Found at i:1869526 original size:15 final size:16
Alignment explanation
Indices: 1869500--1869534 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
1869490 ATTTATAAAT
1869500 TTTAATATTGATAGTA
1 TTTAATATTGATAGTA
1869516 TTTAA-ATTGATAGTA
1 TTTAATATTGATAGTA
1869531 TTTA
1 TTTA
1869535 TAAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAATATTGATAGTA
Found at i:1870428 original size:14 final size:15
Alignment explanation
Indices: 1870398--1870431 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1870388 CTGTTTAGGG
*
1870398 TTTCATTTCTATCCA
1 TTTCATTGCTATCCA
1870413 TTTCATTGCT-TCCA
1 TTTCATTGCTATCCA
1870427 TTTCA
1 TTTCA
1870432 GTTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCATTGCTATCCA
Found at i:1871375 original size:9 final size:9
Alignment explanation
Indices: 1871350--1871408 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
1871340 TAATAACATA
*
1871350 ATAACTAAC
1 ATAACTTAC
1871359 ATAA--TAC
1 ATAACTTAC
*
1871366 ATAACCTAC
1 ATAACTTAC
1871375 ATAACTTAC
1 ATAACTTAC
1871384 ATAACTTAC
1 ATAACTTAC
* *
1871393 ATAAATTAA
1 ATAACTTAC
1871402 ATAACTT
1 ATAACTT
1871409 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
7 6 0.14
9 37 0.86
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1872195 original size:17 final size:17
Alignment explanation
Indices: 1872175--1872267 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 17
1872165 TTATTTTCTA
1872175 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
1872192 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
1872206 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
1872222 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
1872238 TATTAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
*
1872253 TGTAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
1872268 AAAGTGTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 10 0.17
16 15 0.25
17 22 0.37
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:1872203 original size:30 final size:30
Alignment explanation
Indices: 1872168--1872224 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1872158 TATTGTTTTA
*
1872168 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
*
1872198 TTTTCTAAATAATTTTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
1872225 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:1872218 original size:13 final size:13
Alignment explanation
Indices: 1872168--1872220 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
1872158 TATTGTTTTA
*
1872168 TTTTCTATATAAG
1 TTTTCTAAATAAG
1872181 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
1872198 TTTTCTAAATAAT
1 TTTTCTAAATAAG
1872211 TTTTCTAAAT
1 TTTTCTAAAT
1872221 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:1872238 original size:16 final size:16
Alignment explanation
Indices: 1872217--1872250 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1872207 TAATTTTTCT
1872217 AAATTTATTAGTATTA
1 AAATTTATTAGTATTA
1872233 AAATTTATTAGTATTA
1 AAATTTATTAGTATTA
1872249 AA
1 AA
1872251 TTTGTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AAATTTATTAGTATTA
Found at i:1872251 original size:15 final size:15
Alignment explanation
Indices: 1872216--1872253 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
1872206 ATAATTTTTC
1872216 TAAATTTATTAGTAT
1 TAAATTTATTAGTAT
1872231 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
1872247 TAAATTT
1 TAAATTT
1872254 GTAAGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:1872314 original size:15 final size:15
Alignment explanation
Indices: 1872294--1872416 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 15
1872284 TTATTTGCTT
1872294 ACATAATACATAATA
1 ACATAATACATAATA
1872309 ACATAATACATAACTTA
1 ACATAATACATAA--TA
* * *
1872326 TATATAAGCTTGCATAACTT
1 -ACATAA---TACATAA-TA
* *
1872346 ACATAATAACTTCCATA
1 ACATAAT-ACAT-AATA
* *
1872363 ACCT-ATATATAATA
1 ACATAATACATAATA
*
1872377 ACATAAT--A-AATT
1 ACATAATACATAATA
1872389 ACATAATACATAATA
1 ACATAATACATAATA
1872404 ACATAATACATAA
1 ACATAATACATAA
1872417 CTTATATATA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
12 10 0.12
13 1 0.01
14 7 0.09
15 33 0.41
16 3 0.04
17 8 0.10
18 6 0.08
19 5 0.06
20 1 0.01
21 6 0.08
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (15 bp):
ACATAATACATAATA
Found at i:1872343 original size:21 final size:20
Alignment explanation
Indices: 1872317--1872374 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1872307 TAACATAATA
*
1872317 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
*
1872338 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
*
1872359 CATAACCTATATATAA
1 CATAACTTATATATAA
1872375 TAACATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:1872384 original size:8 final size:7
Alignment explanation
Indices: 1872371--1872416 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
1872361 TAACCTATAT
1872371 ATAATAAC
1 ATAAT-AC
1872379 ATAATA-
1 ATAATAC
*
1872385 A-ATTAC
1 ATAATAC
1872391 ATAATAC
1 ATAATAC
1872398 ATAATAAC
1 ATAAT-AC
1872406 ATAATAC
1 ATAATAC
1872413 ATAA
1 ATAA
1872417 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:1872438 original size:21 final size:21
Alignment explanation
Indices: 1872412--1872459 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1872402 TAACATAATA
* *
1872412 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
1872433 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
1872454 CATAAC
1 CATAAC
1872460 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:1872614 original size:35 final size:35
Alignment explanation
Indices: 1872573--1872873 Score: 264
Period size: 34 Copynumber: 8.7 Consensus size: 35
1872563 AAATAACTTG
*
1872573 CATAATACATAGAC-TACATAACTTAATTTTCCTTA
1 CATAATACA-AGACTTACATAACTTAATTTACCTTA
* * * * *
1872608 CATAATACAACACTTACACAACTTAA-ATAACTTG
1 CATAATACAAGACTTACATAACTTAATTTACCTTA
*
1872642 CATAATACATAGAC-TACATAACTTAATTTTCCTTA
1 CATAATACA-AGACTTACATAACTTAATTTACCTTA
* * * *
1872677 CATAATACAACACTTACATAACTTAA-ATAACTTG
1 CATAATACAAGACTTACATAACTTAATTTACCTTA
*
1872711 CATAATACATAGAC-TACATAACTTAATTTTCCTTA
1 CATAATACA-AGACTTACATAACTTAATTTACCTTA
* * * * *
1872746 CATAATACAACACTTACACAACTTAA-ATAACTTG
1 CATAATACAAGACTTACATAACTTAATTTACCTTA
* *
1872780 CATAATACATAG-CCTACATAACTTAATTTGCCTTA
1 CATAATACA-AGACTTACATAACTTAATTTACCTTA
**
1872815 CATAATAC-AGCACTTACATAACTTACA--TAGGTTA
1 CATAATACAAG-ACTTACATAACTTA-ATTTACCTTA
*
1872849 CATAATACACA-ACTTAAATAACTTA
1 CATAATACA-AGACTTACATAACTTA
1872874 TATAATACAT
Statistics
Matches: 212, Mismatches: 40, Indels: 29
0.75 0.14 0.10
Matches are distributed among these distances:
33 2 0.01
34 108 0.51
35 100 0.47
36 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (35 bp):
CATAATACAAGACTTACATAACTTAATTTACCTTA
Found at i:1872700 original size:9 final size:9
Alignment explanation
Indices: 1872688--1872939 Score: 92
Period size: 9 Copynumber: 29.3 Consensus size: 9
1872678 ATAATACAAC
1872688 ACTTACATA
1 ACTTACATA
*
1872697 ACTTAAATA
1 ACTTACATA
*
1872706 ACTTGCATA
1 ACTTACATA
1872715 A--TACATA
1 ACTTACATA
1872722 GAC-TACATA
1 -ACTTACATA
*
1872731 ACTTA-ATTTT
1 ACTTACA--TA
*
1872741 CCTTACATA
1 ACTTACATA
1872750 A--TACA-A
1 ACTTACATA
*
1872756 CACTTACACA
1 -ACTTACATA
*
1872766 ACTTAAATA
1 ACTTACATA
*
1872775 ACTTGCATA
1 ACTTACATA
1872784 A--TACATA
1 ACTTACATA
* *
1872791 GCCTACATA
1 ACTTACATA
*
1872800 ACTTA-ATTTG
1 ACTTACA--TA
*
1872810 CCTTACATA
1 ACTTACATA
**
1872819 A--TACAGC
1 ACTTACATA
1872826 ACTTACATA
1 ACTTACATA
1872835 ACTTACATA
1 ACTTACATA
**
1872844 GGTTACATA
1 ACTTACATA
*
1872853 A--TACACA
1 ACTTACATA
*
1872860 ACTTAAATA
1 ACTTACATA
*
1872869 ACTTATATA
1 ACTTACATA
1872878 A--TACATA
1 ACTTACATA
1872885 ACTTACATA
1 ACTTACATA
* *
1872894 ATTTACTTA
1 ACTTACATA
1872903 A--TACATA
1 ACTTACATA
* *
1872910 A-ATATATA
1 ACTTACATA
* *
1872918 TCATATCATA
1 ACTTA-CATA
1872928 ACTTACATA
1 ACTTACATA
1872937 ACT
1 ACT
1872940 CATTTAATTT
Statistics
Matches: 179, Mismatches: 40, Indels: 48
0.67 0.15 0.18
Matches are distributed among these distances:
6 1 0.01
7 38 0.21
8 10 0.06
9 111 0.62
10 17 0.09
11 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
ACTTACATA
Found at i:1872857 original size:25 final size:25
Alignment explanation
Indices: 1872829--1872910 Score: 101
Period size: 25 Copynumber: 3.3 Consensus size: 25
1872819 ATACAGCACT
**
1872829 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
1872854 TACACAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
1872879 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
1872904 TACATAA
1 TACATAA
1872911 ATATATATCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:1872873 original size:69 final size:69
Alignment explanation
Indices: 1872558--1872857 Score: 519
Period size: 69 Copynumber: 4.3 Consensus size: 69
1872548 NNNNNNNNNN
1872558 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
1 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
1872623 ACAC
66 ACAC
1872627 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
1 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
*
1872692 ACAT
66 ACAC
1872696 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
1 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
1872761 ACAC
66 ACAC
* * *
1872765 AACTTAAATAACTTGCATAATACATAGCCTACATAACTTAATTTGCCTTACATAATACAGCACTT
1 AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
*
1872830 ACAT
66 ACAC
* ** *
1872834 AACTTACATAGGTTACATAATACA
1 AACTTAAATAACTTGCATAATACA
1872858 CAACTTAAAT
Statistics
Matches: 221, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 221 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (69 bp):
AACTTAAATAACTTGCATAATACATAGACTACATAACTTAATTTTCCTTACATAATACAACACTT
ACAC
Found at i:1878378 original size:66 final size:65
Alignment explanation
Indices: 1878272--1878441 Score: 198
Period size: 66 Copynumber: 2.6 Consensus size: 65
1878262 AGCAAATTAC
* * * * * * *
1878272 ACAACTTAAAACGGAGGCAGCATCAAGAGAAGCTGAGGTTCGAA-AAAGATGTGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTC-AACAAAG-TATGAAGAACTCCAA
1878336 CT
64 CT
1878338 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAAC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAC-AAAGTATGAAGAACTCCAAC
1878403 T
65 T
** * * *
1878404 GTAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
1878442 CTGCAGTGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 2 0.02
66 84 0.93
67 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.14
Consensus pattern (65 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAGTATGAAGAACTCCAACT
Found at i:1878438 original size:21 final size:21
Alignment explanation
Indices: 1878412--1878461 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1878402 CTGTAGCTTA
*
1878412 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
* * *
1878433 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
1878454 AAGCAGAG
1 AAGCAGAG
1878462 CAGCGTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:1878869 original size:43 final size:43
Alignment explanation
Indices: 1878795--1878942 Score: 194
Period size: 43 Copynumber: 3.4 Consensus size: 43
1878785 GTGGCGTTTC
* * *
1878795 ATGGTCATTT-GCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATT
1 ATGGTC-TTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTT
* * *
1878838 AGGGTCTTTAGCGGCGTTTGTTTGG-AAAGCGCCGCTAAAGGTC
1 ATGGTCTTTAGCGGCGTTTG-TCGGAAAAGCGCCGCTAAAGGTT
1878881 ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCT
1 ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGT-T
1878925 -TGGTCTTTAGCGGCGTTT
1 ATGGTCTTTAGCGGCGTTT
1878943 ATTTCTAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
42 6 0.06
43 84 0.90
44 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTT
Found at i:1880944 original size:7 final size:7
Alignment explanation
Indices: 1880899--1881032 Score: 164
Period size: 7 Copynumber: 18.9 Consensus size: 7
1880889 ATGCATGATG
1880899 TGATATA
1 TGATATA
1880906 T-AGTATA
1 TGA-TATA
1880913 TGTATATA
1 TG-ATATA
1880921 TGTATATA
1 TG-ATATA
1880929 TGTATATA
1 TG-ATATA
1880937 TGATATA
1 TGATATA
*
1880944 TAATATA
1 TGATATA
*
1880951 TAATATA
1 TGATATA
1880958 TGATATA
1 TGATATA
1880965 TGATATA
1 TGATATA
*
1880972 TAATATA
1 TGATATA
*
1880979 TAATATA
1 TGATATA
1880986 TGATATA
1 TGATATA
1880993 TGATATA
1 TGATATA
*
1881000 TAATATA
1 TGATATA
*
1881007 TAATATA
1 TGATATA
1881014 TGATATA
1 TGATATA
1881021 TGAT-TA
1 TGATATA
1881027 TGATAT
1 TGATAT
1881033 GTATGTTTGT
Statistics
Matches: 117, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
6 7 0.06
7 87 0.74
8 22 0.19
9 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.45
Consensus pattern (7 bp):
TGATATA
Found at i:1880964 original size:28 final size:28
Alignment explanation
Indices: 1880924--1881032 Score: 193
Period size: 28 Copynumber: 3.9 Consensus size: 28
1880914 GTATATATGT
1880924 ATATATGTATATATGATATATAATATATA
1 ATATATG-ATATATGATATATAATATATA
1880953 ATATATGATATATGATATATAATATATA
1 ATATATGATATATGATATATAATATATA
1880981 ATATATGATATATGATATATAATATATA
1 ATATATGATATATGATATATAATATATA
*
1881009 ATATATGATATATGAT-TATGATAT
1 ATATATGATATATGATATATAATAT
1881033 GTATGTTTGT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
27 7 0.09
28 65 0.82
29 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATATATGATATATGATATATAATATATA
Found at i:1881286 original size:5 final size:5
Alignment explanation
Indices: 1881276--1881344 Score: 59
Period size: 5 Copynumber: 13.8 Consensus size: 5
1881266 GGTGGACATT
* * * * *
1881276 ATATG ATATG ATATG TTATG CTATG AT-TCA ATATA ATATG ATATA ATATG
1 ATATG ATATG ATATG ATATG ATATG ATAT-G ATATG ATATG ATATG ATATG
* *
1881326 ATAAG TTATG ATATG ATAT
1 ATATG ATATG ATATG ATAT
1881345 ATTCTGGTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
4 1 0.02
5 49 0.96
6 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:1888169 original size:22 final size:20
Alignment explanation
Indices: 1888144--1888191 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
1888134 ATGCATGACG
1888144 TGATATAT-AGTATATGTATGTA
1 TGATATATGA-TATATG-AT-TA
1888166 TGATATATGATATATGATTA
1 TGATATATGATATATGATTA
1888186 TGATAT
1 TGATAT
1888192 GTATGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 14 0.56
23 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (20 bp):
TGATATATGATATATGATTA
Found at i:1888174 original size:7 final size:7
Alignment explanation
Indices: 1888144--1888191 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
1888134 ATGCATGACG
1888144 TGATATA
1 TGATATA
1888151 T-AGTATA
1 TGA-TATA
*
1888158 TGTATGTA
1 TG-ATATA
1888166 TGATATA
1 TGATATA
1888173 TGATATA
1 TGATATA
1888180 TGAT-TA
1 TGATATA
1888186 TGATAT
1 TGATAT
1888192 GTATGTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 7 0.20
7 22 0.63
8 5 0.14
9 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (7 bp):
TGATATA
Found at i:1888178 original size:20 final size:22
Alignment explanation
Indices: 1888147--1888191 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 22
1888137 CATGACGTGA
*
1888147 TATATAGTATATGT-ATGTATGA
1 TATATAGTATATATGAT-TATGA
1888169 TATAT-G-ATATATGATTATGA
1 TATATAGTATATATGATTATGA
1888189 TAT
1 TAT
1888192 GTATGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 13 0.62
21 3 0.14
22 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (22 bp):
TATATAGTATATATGATTATGA
Found at i:1888187 original size:13 final size:14
Alignment explanation
Indices: 1888144--1888191 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1888134 ATGCATGACG
1888144 TGATATAT-AGTATA
1 TGATATATGA-TATA
*
1888158 TGTATGTATGATATA
1 TG-ATATATGATATA
1888173 TGATATATGAT-TA
1 TGATATATGATATA
1888186 TGATAT
1 TGATAT
1888192 GTATGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 11 0.37
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (14 bp):
TGATATATGATATA
Found at i:1897293 original size:20 final size:20
Alignment explanation
Indices: 1897245--1897293 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1897235 TTATGTCCCG
*
1897245 GATCGCACTTACGTGCCCCT
1 GATCGCACTTACGTACCCCT
*
1897265 G-TTGCACTT-CGGTACCCCT
1 GATCGCACTTAC-GTACCCCT
1897284 GATCGCACTT
1 GATCGCACTT
1897294 TTGTGCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 8 0.33
ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29
Consensus pattern (20 bp):
GATCGCACTTACGTACCCCT
Found at i:1898251 original size:18 final size:18
Alignment explanation
Indices: 1898228--1898263 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1898218 GTCAATAAGT
1898228 TACACGAGCATG-GACACA
1 TACACGAGC-TGAGACACA
1898246 TACACGAGCTGAGACACA
1 TACACGAGCTGAGACACA
1898264 ACCGTGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
TACACGAGCTGAGACACA
Found at i:1907108 original size:25 final size:25
Alignment explanation
Indices: 1907074--1907130 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
1907064 TTCTGTACAT
1907074 ATATGCTTACACGAGCTGTAAATCA
1 ATATGCTTACACGAGCTGTAAATCA
* * * *
1907099 GTATGGTTACATGAGCTGTGAATCA
1 ATATGCTTACACGAGCTGTAAATCA
1907124 ATATGCT
1 ATATGCT
1907131 CACCCAAGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
ATATGCTTACACGAGCTGTAAATCA
Found at i:1911456 original size:20 final size:19
Alignment explanation
Indices: 1911410--1911461 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1911400 AAAAAATCTT
*
1911410 AAAATATTTAACAATTACA
1 AAAATATTTAAAAATTACA
1911429 AAAATATTTAAAAATTACA
1 AAAATATTTAAAAATTACA
1911448 AAAATTATTTAAAA
1 AAAA-TATTTAAAA
1911462 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTTAAAAATTACA
Found at i:1911491 original size:20 final size:19
Alignment explanation
Indices: 1911410--1911491 Score: 83
Period size: 19 Copynumber: 4.2 Consensus size: 19
1911400 AAAAAATCTT
* *
1911410 AAAATATTTAACAATTACA
1 AAAATATTTAAAAAATACA
*
1911429 AAAATATTTAAAAATTACA
1 AAAATATTTAAAAAATACA
* *
1911448 AAAATTATTTAAAATAAAATA
1 AAAA-TATTTAAAA-AATACA
* *
1911469 AAATTATTTAAAAAATAGA
1 AAAATATTTAAAAAATACA
1911488 AAAA
1 AAAA
1911492 AAAATCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 29 0.55
20 18 0.34
21 6 0.11
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAATATTTAAAAAATACA
Found at i:1911518 original size:10 final size:10
Alignment explanation
Indices: 1911505--1911532 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1911495 ATCAAAATAT
1911505 TAAAATTTAC
1 TAAAATTTAC
1911515 TAAAATTTAC
1 TAAAATTTAC
1911525 TAAAATTT
1 TAAAATTT
1911533 TTAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TAAAATTTAC
Found at i:1911539 original size:9 final size:9
Alignment explanation
Indices: 1911504--1911575 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
1911494 AATCAAAATA
1911504 TTAAAATTT
1 TTAAAATTT
*
1911513 ACTAAAATTT
1 -TTAAAATTT
*
1911523 ACTAAAATTT
1 -TTAAAATTT
*
1911533 TTAAAATATA
1 TTAAAAT-TT
*
1911543 TTAAAAATT
1 TTAAAATTT
* *
1911552 TTAATATTC
1 TTAAAATTT
1911561 TTAAAATTT
1 TTAAAATTT
1911570 TATAAA
1 T-TAAA
1911576 TCATATTTGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
9 21 0.42
10 29 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTT
Found at i:1911539 original size:19 final size:19
Alignment explanation
Indices: 1911409--1911555 Score: 59
Period size: 19 Copynumber: 7.6 Consensus size: 19
1911399 AAAAAAATCT
*
1911409 TAAAATATTTAACAAT-TAC
1 TAAAATTTTTAA-AATATAC
* *
1911428 AAAAATATTTAAAA-ATTAC
1 TAAAATTTTTAAAATA-TAC
* * *
1911447 AAAAATTATTTAAAATAAAA
1 TAAAATT-TTTAAAATATAC
* *
1911467 TAAAATTATTTAAAAAATAGA
1 TAAAATT-TTTAAAATATA-C
* *** *
1911488 AAAAAAAATCAAAATAT--
1 TAAAATTTTTAAAATATAC
* *
1911505 TAAAATTTACTAAAATTTAC
1 TAAAATTT-TTAAAATATAC
*
1911525 TAAAATTTTTAAAATATAT
1 TAAAATTTTTAAAATATAC
*
1911544 TAAAAATTTTAA
1 TAAAATTTTTAA
1911556 TATTCTTAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
17 4 0.04
18 8 0.08
19 39 0.41
20 39 0.41
21 6 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (19 bp):
TAAAATTTTTAAAATATAC
Found at i:1911576 original size:9 final size:8
Alignment explanation
Indices: 1911498--1911576 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 8
1911488 AAAAAAAATC
*
1911498 AAAATATT
1 AAAATTTT
1911506 AAAATTTACT
1 AAAATTT--T
1911516 AAAATTTACT
1 AAAATTT--T
1911526 AAAATTTTT
1 AAAA-TTTT
1911535 AAAATATATT
1 AAAAT-T-TT
1911545 AAAAATTTT
1 -AAAATTTT
*
1911554 AATATTCTT
1 AAAATT-TT
1911563 AAAATTTT
1 AAAATTTT
1911571 ATAAAT
1 A-AAAT
1911577 CATATTTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
8 15 0.25
9 19 0.32
10 18 0.30
11 8 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:1918228 original size:31 final size:29
Alignment explanation
Indices: 1918186--1918264 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
1918176 TATTAAATCT
*
1918186 ATACATAAACTTTTATTTAATGTGCAATGTC
1 ATACATGAACTTTTATTT--TGTGCAATGTC
* * * *
1918217 ATACATGAACTTTGATTTTGTTCGATTTC
1 ATACATGAACTTTTATTTTGTGCAATGTC
*
1918246 ATACATGAAATTTTGATTT
1 ATACATGAACTTTT-ATTT
1918265 GATTAAGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.50
30 4 0.10
31 16 0.40
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (29 bp):
ATACATGAACTTTTATTTTGTGCAATGTC
Found at i:1920367 original size:33 final size:31
Alignment explanation
Indices: 1920306--1920372 Score: 73
Period size: 33 Copynumber: 2.1 Consensus size: 31
1920296 ATAAAAGATG
* *
1920306 TATAAAATTTTTAAATATTAAAATAATAAAA
1 TATAAAATTTTTAAAAATTAAAAAAATAAAA
*
1920337 TATAAATATTTTTTAAAAAATT-AAAAAATAATA
1 TATAAA-A-TTTTT-AAAAATTAAAAAAATAAAA
1920370 TAT
1 TAT
1920373 GCAGCCAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.20
32 1 0.03
33 17 0.57
34 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TATAAAATTTTTAAAAATTAAAAAAATAAAA
Found at i:1920968 original size:20 final size:19
Alignment explanation
Indices: 1920925--1920961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1920915 CAAAAAATTG
1920925 TAAAAATTATTTTTAAAAAT
1 TAAAAATTA-TTTTAAAAAT
1920945 TAAAAATTA-TTTAAAAA
1 TAAAAATTATTTTAAAAA
1920962 GTATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAATTATTTTAAAAAT
Found at i:1922719 original size:42 final size:42
Alignment explanation
Indices: 1922612--1922966 Score: 530
Period size: 42 Copynumber: 8.4 Consensus size: 42
1922602 ACGTCGCTAA
* *
1922612 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
1922656 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAATCATGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTT
* * *
1922699 CTATAGTGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
1922741 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * *
1922783 CTTTAGCGACGCTTAGAGACAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
1922825 ATTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
1922867 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAATCATGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTT
* * *
1922910 CTATAGTGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1922952 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
1922967 NNNNNNNNNN
Statistics
Matches: 280, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
42 190 0.68
43 77 0.28
44 13 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:1922772 original size:127 final size:126
Alignment explanation
Indices: 1922612--1922966 Score: 539
Period size: 127 Copynumber: 2.8 Consensus size: 126
1922602 ACGTCGCTAA
*
1922612 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTT--ATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AAAA
* * *
1922677 AAACGCCGCTAAAAATCATGTTCTATAGTGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
63 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
* * *
1922741 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTAGAGACAAA
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
* * *
1922806 CGCCGCTAAAGATCATGTTATTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
* * * *
1922867 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAATCATGTTCTATAGTGGCGCTTAGAAAAAA
1 CTTTAGCGGCGCTTA-TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAA
*
1922932 ACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTTA
65 ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
1922967 NNNNNNNNNN
Statistics
Matches: 206, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
126 75 0.36
127 118 0.57
129 13 0.06
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (126 bp):
CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
Found at i:1922782 original size:84 final size:84
Alignment explanation
Indices: 1922612--1922966 Score: 530
Period size: 85 Copynumber: 4.2 Consensus size: 84
1922602 ACGTCGCTAA
* *
1922612 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AAAA
*
1922677 AAACGCCGCTAAAAATCATGTT
63 AAACGCCGCTAAAGATCATGTT
* * * *
1922699 CTATAGTGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTTATAAAAAAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1922764 CGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGTT
* * * * *
1922783 CTTTAGCGACGCTTAGAGACAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1922848 CGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGTT
* * *
1922867 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAATCATGTTCTATAGTGGCGCTTAGAAAAAA
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAA
*
1922932 ACGCAGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTT
1922952 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
1922967 NNNNNNNNNN
Statistics
Matches: 242, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
84 115 0.48
85 116 0.48
87 11 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (84 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
CGCCGCTAAAGATCATGTT
Found at i:1930773 original size:24 final size:24
Alignment explanation
Indices: 1930738--1930788 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1930728 ATACACTAAC
1930738 ACACACACATATCTGCACATATAG
1 ACACACACATATCTGCACATATAG
*
1930762 ACACACATATATCTGCACATATAG
1 ACACACACATATCTGCACATATAG
1930786 ACA
1 ACA
1930789 ACTAGGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (24 bp):
ACACACACATATCTGCACATATAG
Found at i:1933284 original size:114 final size:114
Alignment explanation
Indices: 1933077--1933292 Score: 256
Period size: 114 Copynumber: 1.9 Consensus size: 114
1933067 ATTAAGTTTC
* * *
1933077 TTGCGGCGTTTTAATCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTCCAAATAAGCGCCA
1 TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
* * ** * *
1933142 CTAATGAATCTATACGTGTAGTCGAAACGATGCGTTTTCCTAAGAAATG
66 CTAAAGAAGCTATACGTCAAGACAAAACGATGCGTTTTCCTAAGAAATG
* **
1933191 TTGCGGCG-CTTAAACATAAGCGCCACTAAAAGCTGATATTCAGCGGCGTTTACGGATAAGCGCC
1 TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATA-TCAGCGGCGTTTACAAATAAGCGCC
* ** *
1933255 AGTAAAGGCGCTATA-GCTCAAGACAAAACGTTGCGTTT
65 ACTAAAGAAGCTATACG-TCAAGACAAAACGATGCGTTT
1933293 CGGCTTCACA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
113 28 0.33
114 56 0.67
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (114 bp):
TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
CTAAAGAAGCTATACGTCAAGACAAAACGATGCGTTTTCCTAAGAAATG
Found at i:1933666 original size:114 final size:114
Alignment explanation
Indices: 1933414--1933741 Score: 548
Period size: 114 Copynumber: 2.9 Consensus size: 114
1933404 TAATAATGTG
* * *
1933414 CTTCAGCGGCGTTTTTATAGAAATGCCACCAATTCTACTATACGTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
*
1933479 TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
66 TGTTTAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
* * *
1933529 CTTCAGCGGCGTTTCTATAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGTTGCGTTT
1 CTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
* *
1933594 TGTTTAACATTTTTTGCAGCGCTTACAAACAAACGCTGCTAATGATACA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
* *
1933643 CTTCAGCGGCGTTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1933708 TGTTTAACATTTTTTGCGGCGCTTACAAACAAAC
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAAC
1933742 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
114 130 0.66
115 68 0.34
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (114 bp):
CTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
Found at i:1936800 original size:39 final size:37
Alignment explanation
Indices: 1936731--1936807 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 37
1936721 TCACATCGAT
*
1936731 AATTACTTAAAATTTTAAAAATATAGAAAATTATTTA
1 AATTACTTAAAATTTTAAAAATATAGAAAATTAATTA
* *
1936768 AATTATTTAAATATTTTGTAAAATATTA-AAAATTAATTA
1 AATTACTTAAA-ATTTT-AAAAATA-TAGAAAATTAATTA
1936807 A
1 A
1936808 TAGTTCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 10 0.29
38 5 0.15
39 17 0.50
40 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
AATTACTTAAAATTTTAAAAATATAGAAAATTAATTA
Found at i:1944463 original size:17 final size:17
Alignment explanation
Indices: 1944441--1944474 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1944431 CATAGTCCTG
1944441 ATTCAGGCAATCTATAT
1 ATTCAGGCAATCTATAT
* *
1944458 ATTCAGGTAGTCTATAT
1 ATTCAGGCAATCTATAT
1944475 TGAGATAGGC
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:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (17 bp):
ATTCAGGCAATCTATAT
Found at i:1945031 original size:113 final size:114
Alignment explanation
Indices: 1944740--1945320 Score: 526
Period size: 114 Copynumber: 5.1 Consensus size: 114
1944730 CCTGAAGAAC
* * *
1944740 TAGTGTCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAT-TGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
*
1944804 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGA-AT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAA-TGTATATTAGATAT
* * * * **
1944853 TCA-TGGCGTTTTTTATAAAAAAACACCGCT-AAAGAATAGT-ATTAGCGGCGTTTAACAAAAAG
1 T-AGTGGCG--TTTT-TAAAAAAACGCCG-TAAAAGAACA-TAATTAGTGGCGTTTATCTGAAAG
* ** * * * *
1944915 CGCCGC-AAATATCTTAAGGAAAACGCACCGTTTTGTCTTAAGGTAGATTA-ATAT
60 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TTAATGTATATTAGATAT
* * *
1944969 TAGTGGCGTTTTTAAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATCTGGAGGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
*
1945034 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACT-T
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAA-TGTATATTAGA-TAT
* * * * * *
1945084 T-GTGGCGTTTTCT-ATAAAACGCCGCAAAAGAATAGT-ATTAGCGGTGTTT-TCGTTAAAGCGC
1 TAGTGGCGTTTT-TAAAAAAACGCCGTAAAAGAACA-TAATTAGTGGCGTTTATC-TGAAAGCGC
* ** * * ** * * *
1945145 CGC-AAATATCTTAATGAAAACACACCGTTTCATCTTGAGGTAGATTAG-TAT
63 CGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TTAATGTATATTAGATAT
* * * ** *
1945196 TAGTGGCATTTTTAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
*
1945261 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGA-AT
66 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTTAATGTATATTAGATAT
1945310 TAGTGGCGTTT
1 TAGTGGCGTTT
1945321 ACGATAAAAC
Statistics
Matches: 368, Mismatches: 72, Indels: 55
0.74 0.15 0.11
Matches are distributed among these distances:
111 1 0.00
112 6 0.02
113 130 0.35
114 133 0.36
115 11 0.03
116 73 0.20
117 14 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAATGTATATTAGATAT
Found at i:1945224 original size:227 final size:226
Alignment explanation
Indices: 1944752--1945338 Score: 847
Period size: 227 Copynumber: 2.6 Consensus size: 226
1944742 GTGTCGTTTC
1944752 TAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCAAAATACCTTAAC
1 TAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCAAAATACCTTAAC
* *
1944817 CAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTCA-TGGCGTTTTTTATAAAAAAACACCG
66 CAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATT-AGTGGCGTTTTCTAT---AAAACGCCG
* *
1944881 CTAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACGCACCGT
127 CAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACACACCGT
** *
1944946 TTTGTCTTAAGGTAGATTAATATTAGTGGCGTTTT
192 TTCATCTTAAGGTAGATTAATATTAGTGGCATTTT
* * *
1944981 TAAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATCTGGAGGCGCCGCAAAATACCTTAA
1 TAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAT-TGTAAGCGCCGCAAAATACCTTAA
* *
1945046 CCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACTTTGTGGCGTTTTCTATAAAACGCCGCAA
65 CCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTATAAAACGCCGCAA
* * ** *
1945111 AAGAATAGTATTAGCGGTGTTT-TCGTTAAAGCGCCGCAAATATCTTAATGAAAACACACCGTTT
130 AAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCGCAAATATCTTAAGGAAAACACACCGTTT
* *
1945175 CATCTTGAGGTAGATTAGTATTAGTGGCATTTT
194 CATCTTAAGGTAGATTAATATTAGTGGCATTTT
* * *
1945208 TAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGCAAAATACCTTAA
1 TAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGCAAAATACCTTAA
** * *
1945273 CCAAAACGCAGCGTTTGGTTTTGA-TGTATATTAGAATTAGTGGCGTTTACGATAAAACGCCGCA
65 CCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCTATAAAACGCCGCA
1945337 AA
129 AA
1945339 TATCTTAAAG
Statistics
Matches: 323, Mismatches: 30, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
226 1 0.00
227 208 0.64
228 4 0.01
229 39 0.12
230 71 0.22
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (226 bp):
TAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCAAAATACCTTAAC
CAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTATAAAACGCCGCAAA
AGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACACACCGTTTCA
TCTTAAGGTAGATTAATATTAGTGGCATTTT
Found at i:1945363 original size:74 final size:75
Alignment explanation
Indices: 1945255--1945394 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 75
1945245 TATTTTTATG
* * * * *
1945255 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGA-ATTAGTGGCGT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1945319 TTACGATAAAA
65 TTACGATAAAA
* *
1945330 CGCCGC-AAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1945394 T
66 T
1945395 TTAAAAAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
73 1 0.02
74 50 0.88
75 6 0.11
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
TACGATAAAA
Found at i:1945387 original size:188 final size:188
Alignment explanation
Indices: 1945137--1945523 Score: 630
Period size: 188 Copynumber: 2.1 Consensus size: 188
1945127 GTGTTTTCGT
* * *
1945137 TAAAGCGCCGCAAATATCTTAATGAAAACACACCGTTTCATCTTGAGGTAGATTAGTATTAGTGG
1 TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
* * ** *
1945202 CATTTTTAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGCAAAATA
66 CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
1945267 CCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTACGA
131 CCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTACGA
* **
1945325 TAAAACGCCGCAAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGG
1 TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
* *
1945390 CGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATG
66 CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
* * *
1945455 CCTTAACCAAAATGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTATGG
131 CCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTACGA
1945513 TAAAACGCCGC
1 TAAAACGCCGC
1945524 TAAAGAATAG
Statistics
Matches: 183, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
188 183 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (188 bp):
TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
CCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTACGA
Found at i:1945404 original size:74 final size:75
Alignment explanation
Indices: 1945255--1945413 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 75
1945245 TATTTTTATG
* * * * *
1945255 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
* *
1945320 TACGATAAAA
66 TACAAAAAAA
* *
1945330 CGCCGC-AAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGA-ATTAGTGGCGT
**
1945393 TTTTAAAAAAA
65 TTACAAAAAAA
*
1945404 CGCCGTAAAA
1 CGCCGCAAAA
1945414 GAACATAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
73 1 0.01
74 60 0.86
75 9 0.13
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
TACAAAAAAA
Done.