Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 6 of 210
Found at i:1592196 original size:23 final size:23
Alignment explanation
Indices: 1592169--1592289 Score: 81
Period size: 23 Copynumber: 5.3 Consensus size: 23
1592159 AAATTAAATT
1592169 TGTTTAAGTGCTGCAAATTGAAG
1 TGTTTAAGTGCTGCAAATTGAAG
* *
1592192 TGTTTAAGTGCTACAAAGTG-AG
1 TGTTTAAGTGCTGCAAATTGAAG
* * *
1592214 ATGTTTTA-TCGCTG-TAATTGATG
1 -TGTTTAAGT-GCTGCAAATTGAAG
* * * **
1592237 TGTATAAATGTTGTTAATTGATA-
1 TGTTTAAGTGCTGCAAATTGA-AG
1592260 TG-TTAAGGTGCTGCAAATTGAAG
1 TGTTTAA-GTGCTGCAAATTGAAG
1592283 TGTTTAA
1 TGTTTAA
1592290 ATTTAACTTG
Statistics
Matches: 73, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
22 19 0.26
23 50 0.68
24 4 0.05
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.40
Consensus pattern (23 bp):
TGTTTAAGTGCTGCAAATTGAAG
Found at i:1592960 original size:43 final size:43
Alignment explanation
Indices: 1592905--1593154 Score: 383
Period size: 43 Copynumber: 5.8 Consensus size: 43
1592895 TTTTCGTGAC
* *
1592905 CTTTAGTGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
* * *
1592948 CTTTAGCGGCGTTTGTGGTAAAAGCACCACTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
* * *
1592991 CTTTAGCGGCGTTTGTGGGAAAAGTGTCACTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
* *
1593034 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCCTGGC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
* *
1593077 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCCTGGC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
*
1593120 CTTTAGCGGCGTTTGTGGGAAAAGCGCCTCTAAAG
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1593155 TTAGCGACGC
Statistics
Matches: 191, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 191 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
Found at i:1593782 original size:19 final size:19
Alignment explanation
Indices: 1593760--1593798 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1593750 AAATAATAAC
1593760 ATAAAACTTATATCTTTAG
1 ATAAAACTTATATCTTTAG
1593779 ATAAAACTTATATCTTTAG
1 ATAAAACTTATATCTTTAG
1593798 A
1 A
1593799 AAAGCTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
ATAAAACTTATATCTTTAG
Found at i:1594634 original size:19 final size:19
Alignment explanation
Indices: 1594592--1594632 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1594582 ATTTTTCATT
1594592 AAAATCATAAAAAATTAAG
1 AAAATCATAAAAAATTAAG
*
1594611 AAAATCATTAAAAATT-AG
1 AAAATCATAAAAAATTAAG
1594629 AAAA
1 AAAA
1594633 ATGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAATCATAAAAAATTAAG
Found at i:1594778 original size:28 final size:27
Alignment explanation
Indices: 1594736--1594799 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
1594726 ACTATAATAT
*
1594736 ATTAAG-AAAAATT-AAATTTTGTAAAA
1 ATTAAGAAAAAATTAAAATATTG-AAAA
1594762 ATTAAGAAAAATATTAAAATATTGAAAA
1 ATTAAGAAAAA-ATTAAAATATTGAAAA
*
1594790 ATTAATAAAA
1 ATTAAGAAAA
1594800 TTTAGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.18
27 4 0.12
28 16 0.48
29 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
ATTAAGAAAAAATTAAAATATTGAAAA
Found at i:1594788 original size:18 final size:17
Alignment explanation
Indices: 1594767--1594817 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
1594757 TAAAAATTAA
1594767 GAAAAATATTAAAATATT
1 GAAAAATATTAAAAT-TT
*
1594785 GAAAAATTAATAAAATTT
1 GAAAAA-TATTAAAATTT
1594803 -AGAAAATATTTAAAA
1 GA-AAAATA-TTAAAA
1594818 AATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
18 17 0.61
19 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
GAAAAATATTAAAATTT
Found at i:1594827 original size:37 final size:35
Alignment explanation
Indices: 1594758--1594835 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 35
1594748 TAAATTTTGT
*
1594758 AAAAATTAAGAAAAATATTAAAATATTGAAAAATTA
1 AAAAATTAAGAAAAATATTAAAAAATTGAAAAA-TA
*
1594794 ATAAAATTTAG-AAAATATTTAAAAAATAT-AAAAATA
1 A-AAAATTAAGAAAAATA-TTAAAAAAT-TGAAAAATA
1594830 AAAAAT
1 AAAAAT
1594836 ACATGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 5 0.14
36 10 0.27
37 21 0.57
38 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (35 bp):
AAAAATTAAGAAAAATATTAAAAAATTGAAAAATA
Found at i:1596879 original size:4 final size:4
Alignment explanation
Indices: 1596870--1596903 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
1596860 AGATTATCTG
1596870 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT
1596904 TATGCATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CTAA
Found at i:1609294 original size:17 final size:17
Alignment explanation
Indices: 1609274--1609306 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1609264 ATAGCATTCA
1609274 ATTTTAATCTTTTTTAT
1 ATTTTAATCTTTTTTAT
*
1609291 ATTTTAATTTTTTTTA
1 ATTTTAATCTTTTTTA
1609307 AAATTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTAATCTTTTTTAT
Found at i:1610159 original size:69 final size:69
Alignment explanation
Indices: 1610077--1610217 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
1610067 AATAAAAGAG
1610077 TAATTGACTAAATGTGTAAAGATTTAGGGCTAAATTTGTTATTATACCTTATATATAAACACAAA
1 TAATTGACTAAATGTGTAAAGATTTAGGGCTAAATTTGTTATTATACCTTATATATAAACACAAA
1610142 ATTT
66 ATTT
1610146 TAATTGACTAAATGTGTAAAGATTTAGGGCTAAATTTGTTATTATACCTTATATATAAACACAAA
1 TAATTGACTAAATGTGTAAAGATTTAGGGCTAAATTTGTTATTATACCTTATATATAAACACAAA
1610211 ATTT
66 ATTT
1610215 TAA
1 TAA
1610218 CAATGGGTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (69 bp):
TAATTGACTAAATGTGTAAAGATTTAGGGCTAAATTTGTTATTATACCTTATATATAAACACAAA
ATTT
Found at i:1612053 original size:22 final size:21
Alignment explanation
Indices: 1611999--1612053 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1611989 AAATAATTAT
*
1611999 AAAAATAAT-AAATTTTAATA
1 AAAAATTATAAAATTTTAATA
* *
1612019 AAAATTTA-AAAATTTTTATA
1 AAAAATTATAAAATTTTAATA
1612039 GAAAAATTATAAAAT
1 -AAAAATTATAAAAT
1612054 ACTTCTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 16 0.57
21 7 0.25
22 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTATAAAATTTTAATA
Found at i:1612170 original size:27 final size:27
Alignment explanation
Indices: 1612103--1612180 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
1612093 ATTTATATTT
*
1612103 CTTTATATTTTGTATAATTTTTTACGA
1 CTTTATATTTTTTATAATTTTTTACGA
**
1612130 CTTTATAAAATTTTAT-ATTTTTTACGA
1 CTTTAT-ATTTTTTATAATTTTTTACGA
* *
1612157 TTTTTATATTTTTTTCTAATTTTT
1 -CTTTATA-TTTTTTATAATTTTT
1612181 AATATTTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
27 18 0.45
28 16 0.40
29 6 0.15
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (27 bp):
CTTTATATTTTTTATAATTTTTTACGA
Found at i:1612474 original size:92 final size:92
Alignment explanation
Indices: 1612265--1612498 Score: 237
Period size: 92 Copynumber: 2.5 Consensus size: 92
1612255 AATTTTTAAT
* * *
1612265 AAAAGCA-ATGGCTTAATTGTTTTTTCTGAAAAAGTTTGAAGGTCTTTTGGATGCATTTTGAAAG
1 AAAAGCAGA-GGCTTAATTGCTTTTTCAGAAAAAGTTTGAAGGCCTTTTGGATGCATTTTGAAAG
* *
1612329 TTCAAGTACCGAATTGAGTGCAAAAAAA
65 TTCAAGTACCCAAATGAGTGCAAAAAAA
** * * *
1612357 AGTA--AG-GGATTAATTGCTTTTTTTTTAGAAAAGGTTT-AAGGGCCTTTCT-GATGCATTTTG
1 AAAAGCAGAGGCTTAATTGC---TTTTTCAGAAAAAGTTTGAA-GGCCTTT-TGGATGCATTTTG
1612417 AAAGTTCAAGTACCCAAATGAGTGCAAAAAAAA
61 AAAGTTCAAGTACCCAAATGAGTGC-AAAAAAA
** * *
1612450 AAAAGCAGAGGCTTAATTGCTTTTTTTGAAAAAGTTTGACGGCTTTTTG
1 AAAAGCAGAGGCTTAATTGCTTTTTCAGAAAAAGTTTGAAGGCCTTTTG
1612499 CACCCTTAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
89 9 0.08
90 1 0.01
91 2 0.02
92 57 0.50
93 31 0.27
94 1 0.01
95 2 0.02
96 10 0.09
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (92 bp):
AAAAGCAGAGGCTTAATTGCTTTTTCAGAAAAAGTTTGAAGGCCTTTTGGATGCATTTTGAAAGT
TCAAGTACCCAAATGAGTGCAAAAAAA
Found at i:1613412 original size:44 final size:44
Alignment explanation
Indices: 1613364--1613518 Score: 147
Period size: 44 Copynumber: 3.5 Consensus size: 44
1613354 GGTTTGCAGA
* * *
1613364 AAAATTCGCCACTGGGCTGTGGATACATAGCAAAATTCGCAGAT
1 AAAATTCGCCACTAGGCTATGGATACATAGCAAAATTCGCAAAT
* * *
1613408 AAAA-TCAACCGA-T-GAACTATGAATACATAG-AAAATTCGCAAAT
1 AAAATTC-GCC-ACTAG-GCTATGGATACATAGCAAAATTCGCAAAT
* * * *
1613451 AAAATTTGCCACTAGGCTATGGGTACACAACAAAATTCGCAAAT
1 AAAATTCGCCACTAGGCTATGGATACATAGCAAAATTCGCAAAT
* *
1613495 AAAATTTGCCACTAGGCTGTGGAT
1 AAAATTCGCCACTAGGCTATGGAT
1613519 GCACTACATA
Statistics
Matches: 90, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
42 1 0.01
43 32 0.36
44 56 0.62
45 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (44 bp):
AAAATTCGCCACTAGGCTATGGATACATAGCAAAATTCGCAAAT
Found at i:1613561 original size:43 final size:43
Alignment explanation
Indices: 1613457--1613583 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
1613447 AAATAAAATT
* * * * ** **
1613457 TGCCACTAGGCTATGGGTACACAACAAAATTCGCAAATAAAATT
1 TGCCACTAGGCTCTGGATGCACAACATAATT-GCAGGTAAAAGC
* *
1613501 TGCCACTAGGCTGTGGATGCACTACATAATTGCAGGTAAAAGC
1 TGCCACTAGGCTCTGGATGCACAACATAATTGCAGGTAAAAGC
* * *
1613544 TGCCACTAGGTTCTGGATGCACAACATACTTGCAGTTAAA
1 TGCCACTAGGCTCTGGATGCACAACATAATTGCAGGTAAA
1613584 GGAAAAATAC
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 43 0.62
44 26 0.38
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (43 bp):
TGCCACTAGGCTCTGGATGCACAACATAATTGCAGGTAAAAGC
Found at i:1613775 original size:38 final size:38
Alignment explanation
Indices: 1613733--1613813 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
1613723 CATGTACAAT
* ** *
1613733 ATGTACTCAATTCATCACTAATGGTAAATATGTTTAAC
1 ATGTACGCAATTCATCACTAAAAGTAAACATGTTTAAC
* *
1613771 ATGTACGCAATTCATCATTAAAAGTAAACATGTTTAAT
1 ATGTACGCAATTCATCACTAAAAGTAAACATGTTTAAC
1613809 ATGTA
1 ATGTA
1613814 TTCATGTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (38 bp):
ATGTACGCAATTCATCACTAAAAGTAAACATGTTTAAC
Found at i:1615437 original size:14 final size:14
Alignment explanation
Indices: 1615410--1615459 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1615400 TTTCTCTAAC
1615410 TTAATTTAACTTTAA
1 TTAA-TTAACTTTAA
*
1615425 TTAATTAATTTTAA
1 TTAATTAACTTTAA
* *
1615439 TTAATTTACTTAAA
1 TTAATTAACTTTAA
*
1615453 ATAATTA
1 TTAATTA
1615460 GTTTTTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATTAACTTTAA
Found at i:1615467 original size:29 final size:29
Alignment explanation
Indices: 1615410--1615464 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1615400 TTTCTCTAAC
* *
1615410 TTAATTTAACTTTAATTAATTAATTTTAA
1 TTAATTTAACTTAAAATAATTAATTTTAA
*
1615439 TTAATTT-ACTTAAAATAATTAGTTTT
1 TTAATTTAACTTAAAATAATTAATTTT
1615465 TAAATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (29 bp):
TTAATTTAACTTAAAATAATTAATTTTAA
Found at i:1616231 original size:14 final size:15
Alignment explanation
Indices: 1616212--1616245 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1616202 ACTTTCACAT
1616212 TTAAAATATAA-AAA
1 TTAAAATATAATAAA
1616226 TTAAAATATAATAAA
1 TTAAAATATAATAAA
1616241 -TAAAA
1 TTAAAA
1616246 AACTCACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAAATATAATAAA
Found at i:1625464 original size:40 final size:40
Alignment explanation
Indices: 1625381--1625487 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
1625371 AGCGGCACTT
* * * *
1625381 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAGAGTGAGCA
1 TTAGCGGCGTTT-AAGCAAAAACGCCGCTAAAGAGCGAACA
* *
1625422 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGCGAACA
1 TTAGCGGCGTTTAAGCAAAAACGCCGCTAAAGAGCGAACA
*
1625462 TTAGCAGCGTTTATA--AAAAACGCCGC
1 TTAGCGGCGTTTA-AGCAAAAACGCCGC
1625488 AAATAATACA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
39 10 0.18
40 34 0.60
41 13 0.23
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.19
Consensus pattern (40 bp):
TTAGCGGCGTTTAAGCAAAAACGCCGCTAAAGAGCGAACA
Found at i:1625837 original size:113 final size:112
Alignment explanation
Indices: 1625439--1626098 Score: 1115
Period size: 113 Copynumber: 5.8 Consensus size: 112
1625429 CGTTTAAGGA
1625439 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
*
1625504 CGGTGCCGTTTTGTGGCCTTTAGG-GGGGAATTAGTGGCGTTTTTTGT
66 CGGTGACGTTTTGTGGCCTTT-GGAGGGGAATTAGTGGCGTTTTTTGT
*
1625551 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGG
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
*
1625616 CGGTGCCGTTTTGTGGCCTTTGGGAGGGGGGAATTAGTGGCGTTTTTTGT
66 CGGTGACGTTTTGTGGCCTTT-GGA--GGGGAATTAGTGGCGTTTTTTGT
*
1625666 AAAGCGCAGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
*
1625731 CGGTGATGTTTTGTGGCCTTTGGAGGGAGAATTAGTGGCGTTTTTTGT
66 CGGTGACGTTTTGTGGCCTTTGGAGGG-GAATTAGTGGCGTTTTTTGT
*
1625779 AAAGCGCCGCTAAAGAGCGGACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
*
1625844 CGGTGATGTTTTGTGGCCTTTGGAGGGAGAATTAGTGGCGTTTTTTGT
66 CGGTGACGTTTTGTGGCCTTTGGAGGG-GAATTAGTGGCGTTTTTTGT
1625892 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAAACGCCGCAAATAATACACCCAG
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTAT-AAAAAACGCCGCAAATAATACACCCAG
* *** *
1625957 ACGGTGATGTTTTGTGGCCTTTGGAGGGGAATTAGTGGCGTTTAAGGA
65 ACGGTGACGTTTTGTGGCCTTTGGAGGGGAATTAGTGGCGTTTTTTGT
*
1626005 AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
* *
1626070 CGGTGCCGTTTTGTGGCCTTTGGGGGGGA
66 CGGTGACGTTTTGTGGCCTTTGGAGGGGA
1626099 NNNNNNNNNN
Statistics
Matches: 526, Mismatches: 17, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
112 144 0.27
113 219 0.42
114 58 0.11
115 105 0.20
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (112 bp):
AAAGCGCCGCTAAAGAGCGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
CGGTGACGTTTTGTGGCCTTTGGAGGGGAATTAGTGGCGTTTTTTGT
Found at i:1626846 original size:60 final size:60
Alignment explanation
Indices: 1626781--1626910 Score: 235
Period size: 60 Copynumber: 2.2 Consensus size: 60
1626771 AGGGGTTAGT
*
1626781 GTTGGGGTTAGCACTTAGGGGTTATTAGGAGTTAATTAAGGATTTAGGGTTTAGTTAGGG
1 GTTGGGGTTAGCACTTAGGGGTTATTAGGAGTTAATTAAGGATTTAGGGTTTAGCTAGGG
*
1626841 GTTGGGGTTAGCACTTAGGGTTTATTAGGAGTTAATTAAGGATTTAGGGTTTAGCTAGGG
1 GTTGGGGTTAGCACTTAGGGGTTATTAGGAGTTAATTAAGGATTTAGGGTTTAGCTAGGG
1626901 GTT-GGGTTAG
1 GTTGGGGTTAG
1626911 GGAACGTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 7 0.10
60 61 0.90
ACGTcount: A:0.22, C:0.04, G:0.37, T:0.37
Consensus pattern (60 bp):
GTTGGGGTTAGCACTTAGGGGTTATTAGGAGTTAATTAAGGATTTAGGGTTTAGCTAGGG
Found at i:1627671 original size:84 final size:84
Alignment explanation
Indices: 1627572--1627851 Score: 506
Period size: 84 Copynumber: 3.3 Consensus size: 84
1627562 TAAACTTTTG
1627572 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
1 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
1627637 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
1627656 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
1 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
1627721 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
* *
1627740 GTGGCTTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
1627805 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
* **
1627824 GTGGCGTTTGTACCAAAAACGCCACAAA
1 GTGGCGTTTTTA-GGAAAACGCCACAAA
1627852 ACGGTGTTAA
Statistics
Matches: 189, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 176 0.93
85 13 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (84 bp):
GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACTGTGTCGTTTCTG
TTCACAGCTGTAATATTTA
Found at i:1630066 original size:34 final size:34
Alignment explanation
Indices: 1630027--1630140 Score: 228
Period size: 34 Copynumber: 3.4 Consensus size: 34
1630017 AAGGTGAACG
1630027 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1630061 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1630095 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1 AATTATCGATTTTCAAGGATCTTGTCAATTAATA
1630129 AATTATCGATTT
1 AATTATCGATTT
1630141 ATTACTAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (34 bp):
AATTATCGATTTTCAAGGATCTTGTCAATTAATA
Found at i:1630945 original size:31 final size:31
Alignment explanation
Indices: 1630907--1630971 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1630897 ACCCCTAGAC
** *
1630907 CCCAAGCCGGTGTATCTGTTGAATGGGATAT
1 CCCAAGCCGGTGTATCCCTGGAATGGGATAT
1630938 CCCAAGCCGGTGTATCCCTGGAATGGGATAT
1 CCCAAGCCGGTGTATCCCTGGAATGGGATAT
1630969 CCC
1 CCC
1630972 TATCTGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (31 bp):
CCCAAGCCGGTGTATCCCTGGAATGGGATAT
Found at i:1631055 original size:20 final size:21
Alignment explanation
Indices: 1631013--1631068 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
1631003 CAGACACATT
*
1631013 AAAAAT-CTGAACCGGCCACC
1 AAAAATACTGAACCGGACACC
* *
1631033 AAAACTGCTGAACCGGACA-C
1 AAAAATACTGAACCGGACACC
1631053 AAAAATACTGAACCGG
1 AAAAATACTGAACCGG
1631069 TATAGGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.43, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
AAAAATACTGAACCGGACACC
Found at i:1636886 original size:78 final size:78
Alignment explanation
Indices: 1636757--1636907 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
1636747 GTACACAAAG
* * *
1636757 TCCATGGTGATCGCTATCAACATGATCACCAACTCTCCTAGCTGATGAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
1636822 TTAATGGTCGAAC
66 TTAATGGTCGAAC
* * *
1636835 TCCATGGTGATCATTATCAACATGATCACCGACTCTCCCAGCTGGTAAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
1636900 TTAATGGT
66 TTAATGGT
1636908 AGAATATGAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (78 bp):
TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
TTAATGGTCGAAC
Found at i:1638956 original size:16 final size:16
Alignment explanation
Indices: 1638937--1638969 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1638927 AAACATTACC
1638937 AATT-TAAATATTATTT
1 AATTGTAAATATT-TTT
1638953 AATTGTAAATATTTTT
1 AATTGTAAATATTTTT
1638969 A
1 A
1638970 CTTATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTGTAAATATTTTT
Found at i:1644285 original size:19 final size:19
Alignment explanation
Indices: 1644251--1644301 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1644241 TAATTTTATA
*
1644251 ATTTATTAGATTTTTATAAT
1 ATTTATAAG-TTTTTATAAT
1644271 ATTTATAAGTTTTTATAAT
1 ATTTATAAGTTTTTATAAT
* *
1644290 TTTTTTAAGTTT
1 ATTTATAAGTTT
1644302 ATATCATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (19 bp):
ATTTATAAGTTTTTATAAT
Found at i:1644294 original size:10 final size:9
Alignment explanation
Indices: 1644244--1644293 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
1644234 GGTTTGTTAA
1644244 TTTTATAAT
1 TTTTATAAT
*
1644253 TTATTA-GAT
1 TT-TTATAAT
1644262 TTTTATAAT
1 TTTTATAAT
*
1644271 ATTTATAAGT
1 TTTTATAA-T
1644281 TTTTATAAT
1 TTTTATAAT
1644290 TTTT
1 TTTT
1644294 TTAAGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.09
9 20 0.59
10 11 0.32
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1644757 original size:27 final size:27
Alignment explanation
Indices: 1644719--1644774 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1644709 TTTAATAGAT
1644719 AATTTTAATTGTATTAAAAAATTTTAA
1 AATTTTAATTGTATTAAAAAATTTTAA
* *
1644746 AATTTTAATTGTATTAATAATTTTTAA
1 AATTTTAATTGTATTAAAAAATTTTAA
1644773 AA
1 AA
1644775 ATTACATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
AATTTTAATTGTATTAAAAAATTTTAA
Found at i:1651980 original size:342 final size:343
Alignment explanation
Indices: 1651340--1652028 Score: 1364
Period size: 342 Copynumber: 2.0 Consensus size: 343
1651330 TATTTATGTA
1651340 TTAT-ATATTTTTAATTTTTTAAATTAGGGTCAATTTTGAGACAATCAAGATCAATTTTTTTTTA
1 TTATAATATTTTTAATTTTTTAAATTAGGGTCAATTTTGAGACAATCAAGATCAATTTTTTTTTA
1651404 AAACCATAATTAAATTGATACAATATATAAGTTTTAAGGATTAAAATAATTAGTATATTAAAATT
66 AAACCATAATTAAATTGATACAATATATAAGTTTTAAGGATTAAAATAATTAGTATATTAAAATT
1651469 TGAACTGACACCTTGTCTTTCTATGGTAAAGTTAAAGTAAGTTAATAGAATTGGAACAAAAAAGA
131 TGAACTGACACCTTGTCTTTCTATGGTAAAGTTAAAGTAAGTTAATAGAATTGGAACAAAAAAGA
1651534 TAAATGTGATTAGTTGAATGAACATTTTGTTATTTTCTATAGTTAGTGAAAAAATTTAAACATAA
196 TAAATGTGATTAGTTGAATGAACATTTTGTTATTTTCTATAGTTAGTGAAAAAATTTAAACATAA
1651599 TTGGTTGATATGTAGGGTCCATTTGTTTGACTGAAAATGGTTTTCGAAAAATGACTTATTTTTCT
261 TTGGTTGATATGTAGGGTCCATTTGTTTGACTGAAAATGGTTTTCGAAAAATGACTTATTTTTCT
1651664 GGAAAAGTTAATATTTTT
326 GGAAAAGTTAATATTTTT
1651682 TTATAATATTTTTAA-TTTTTAAATTAGGGTCAATTTTGAGACAATCAAGATCAATTTTTTTTTA
1 TTATAATATTTTTAATTTTTTAAATTAGGGTCAATTTTGAGACAATCAAGATCAATTTTTTTTTA
1651746 AAACCATAATTAAATTGATACAATATATAAGTTTTAAGGATTAAAATAATTAGTATATTAAAATT
66 AAACCATAATTAAATTGATACAATATATAAGTTTTAAGGATTAAAATAATTAGTATATTAAAATT
1651811 TGAACTGACACCTTGTCTTTCTATGGTAAAGTTAAAGTAAGTTAATAGAATTGGAACAAAAAAGA
131 TGAACTGACACCTTGTCTTTCTATGGTAAAGTTAAAGTAAGTTAATAGAATTGGAACAAAAAAGA
1651876 TAAATGTGATTAGTTGAATGAACATTTTGTTATTTTCTATAGTTAGTGAAAAAATTTAAACATAA
196 TAAATGTGATTAGTTGAATGAACATTTTGTTATTTTCTATAGTTAGTGAAAAAATTTAAACATAA
1651941 TTGGTTGATATGTAGGGTCCATTTGTTTGACTGAAAATGGTTTTCGAAAAATGACTTATTTTTCT
261 TTGGTTGATATGTAGGGTCCATTTGTTTGACTGAAAATGGTTTTCGAAAAATGACTTATTTTTCT
1652006 GGAAAAGTTAATATTTTT
326 GGAAAAGTTAATATTTTT
1652024 TTATA
1 TTATA
1652029 TTTGAATGAA
Statistics
Matches: 346, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
342 336 0.97
343 10 0.03
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (343 bp):
TTATAATATTTTTAATTTTTTAAATTAGGGTCAATTTTGAGACAATCAAGATCAATTTTTTTTTA
AAACCATAATTAAATTGATACAATATATAAGTTTTAAGGATTAAAATAATTAGTATATTAAAATT
TGAACTGACACCTTGTCTTTCTATGGTAAAGTTAAAGTAAGTTAATAGAATTGGAACAAAAAAGA
TAAATGTGATTAGTTGAATGAACATTTTGTTATTTTCTATAGTTAGTGAAAAAATTTAAACATAA
TTGGTTGATATGTAGGGTCCATTTGTTTGACTGAAAATGGTTTTCGAAAAATGACTTATTTTTCT
GGAAAAGTTAATATTTTT
Found at i:1652530 original size:16 final size:16
Alignment explanation
Indices: 1652481--1652533 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1652471 TTGGTTCGCT
*
1652481 GTAATGGAATAGAAGT
1 GTAATGGAATAGAAGC
*
1652497 GTAATGGAATAGATGC
1 GTAATGGAATAGAAGC
*
1652513 GTAATGGAATAGAGGC
1 GTAATGGAATAGAAGC
1652529 GTAAT
1 GTAAT
1652534 AGGTAAATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAAGC
Found at i:1652568 original size:46 final size:44
Alignment explanation
Indices: 1652515--1652603 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
1652505 ATAGATGCGT
*
1652515 AATGGAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAAT-GGT-AATCTTGTGTTTGGTTGAATGG
* *
1652561 AATGGAATAGAGGCGTAGTGGTATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGGCGTAATGGTAATCTTGTGTTTGGTTGAATG
1652604 TAATAGAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 19 0.47
45 3 0.08
46 18 0.45
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATGGTAATCTTGTGTTTGGTTGAATGG
Found at i:1652843 original size:24 final size:24
Alignment explanation
Indices: 1652811--1652860 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1652801 GATAAAGTAT
1652811 TTATCACCTCAAATGTGATTTGGG
1 TTATCACCTCAAATGTGATTTGGG
*
1652835 TTATCACCTCAAATGTGATTTTGG
1 TTATCACCTCAAATGTGATTTGGG
1652859 TT
1 TT
1652861 CAAATTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (24 bp):
TTATCACCTCAAATGTGATTTGGG
Found at i:1655133 original size:23 final size:23
Alignment explanation
Indices: 1655101--1655144 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1655091 ACTACCATTT
1655101 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
1655124 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
1655145 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:1655137 original size:13 final size:11
Alignment explanation
Indices: 1655105--1655147 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1655095 CCATTTTCTA
*
1655105 AATAAAATAAT
1 AATAAAATATT
1655116 AAT-AAATATCT
1 AATAAAATAT-T
1655127 AAGTAAAATATT
1 AA-TAAAATATT
1655139 AATAAAATA
1 AATAAAATA
1655148 ATTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:1660143 original size:38 final size:38
Alignment explanation
Indices: 1660092--1660165 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
1660082 TGCTTTCCAG
1660092 TATCACAGACCAAGAATGACATGTTAAGAATACAAGAC
1 TATCACAGACCAAGAATGACATGTTAAGAATACAAGAC
1660130 TATCACAGACCAAGAATGACATGTTAAGAATACAAG
1 TATCACAGACCAAGAATGACATGTTAAGAATACAAG
1660166 GTAATCTCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (38 bp):
TATCACAGACCAAGAATGACATGTTAAGAATACAAGAC
Found at i:1664100 original size:20 final size:19
Alignment explanation
Indices: 1664057--1664130 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 19
1664047 TATTTTAAGT
* *
1664057 AATT-TTTTCATGTTTTTA
1 AATTATTTTAATGTTTTAA
*
1664075 ACTTATCTTTAATGTTTTAA
1 AATTAT-TTTAATGTTTTAA
* *
1664095 AATTA-TTTAATTTTTTAG
1 AATTATTTTAATGTTTTAA
*
1664113 AA-TATTTTCATGTTTTAA
1 AATTATTTTAATGTTTTAA
1664131 GAATCACTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 2 0.05
18 26 0.59
19 1 0.02
20 15 0.34
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTATTTTAATGTTTTAA
Found at i:1664683 original size:21 final size:21
Alignment explanation
Indices: 1664658--1664708 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1664648 TACATCTATA
1664658 TATGTATCGATACATTGTATT
1 TATGTATCGATACATTGTATT
1664679 TATGTATCGATACATTGTATT
1 TATGTATCGATACATTGTATT
1664700 TATGTATCG
1 TATGTATCG
1664709 GTACTTGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (21 bp):
TATGTATCGATACATTGTATT
Found at i:1668371 original size:215 final size:217
Alignment explanation
Indices: 1667987--1668419 Score: 852
Period size: 215 Copynumber: 2.0 Consensus size: 217
1667977 ATTTGTATTT
1667987 ATTTATTTATAATATAATATTTATATTTGATTATTTTATATCTAAAAAATAATGTTCATTTATTA
1 ATTTATTTATAATATAATATTTATATTTGATTATTTTATATCTAAAAAATAATGTTCATTTATTA
1668052 TTTATTTGCTTATTATTCATGACTATTGTTCGTGAACATGTCTAATTATATGTTAATGAACATCT
66 TTTATTTGCTTATTATTCATGACTATTGTTCGTGAACATGTCTAATTATATGTTAATGAACATCT
1668117 ATGTACGTTTAAGTTAAACAATTACACAAACATATTCGTGAATATTAAATAAACAAATATGAACA
131 ATGTACGTTTAAGTTAAACAATTACACAAACATATTCGTGAATATTAAATAAACAAATATGAACA
1668182 CACATATTTTAAATAAATAAAC
196 CACATATTTTAAATAAATAAAC
1668204 ATTTATTTAT-A-ATAATATTTATATTTGATTATTTTATATCTAAAAAATAATGTTCATTTATTA
1 ATTTATTTATAATATAATATTTATATTTGATTATTTTATATCTAAAAAATAATGTTCATTTATTA
1668267 TTTATTTGCTTATTATTCATGACTATTGTTCGTGAACATGTCTAATTATATGTTAATGAACATCT
66 TTTATTTGCTTATTATTCATGACTATTGTTCGTGAACATGTCTAATTATATGTTAATGAACATCT
1668332 ATGTACGTTTAAGTTAAACAATTACACAAACATATTCGTGAATATTAAATAAACAAATATGAACA
131 ATGTACGTTTAAGTTAAACAATTACACAAACATATTCGTGAATATTAAATAAACAAATATGAACA
1668397 CACATATTTTAAATAAATAAAC
196 CACATATTTTAAATAAATAAAC
1668419 A
1 A
1668420 CGAATAAAAA
Statistics
Matches: 216, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
215 205 0.95
216 1 0.00
217 10 0.05
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (217 bp):
ATTTATTTATAATATAATATTTATATTTGATTATTTTATATCTAAAAAATAATGTTCATTTATTA
TTTATTTGCTTATTATTCATGACTATTGTTCGTGAACATGTCTAATTATATGTTAATGAACATCT
ATGTACGTTTAAGTTAAACAATTACACAAACATATTCGTGAATATTAAATAAACAAATATGAACA
CACATATTTTAAATAAATAAAC
Found at i:1670717 original size:3 final size:3
Alignment explanation
Indices: 1670711--1670746 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1670701 CACCACCACC
*
1670711 AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1670747 CATAGCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1671033 original size:6 final size:6
Alignment explanation
Indices: 1671010--1671042 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1671000 GCCTTGGTTC
*
1671010 TTCTTC TTCTTT TTCTTT TTCTTT TT-TTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
1671043 GTGGGGGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:1691181 original size:12 final size:12
Alignment explanation
Indices: 1691164--1691188 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1691154 CTTGAAATGC
1691164 CTTCTCTTCACT
1 CTTCTCTTCACT
1691176 CTTCTCTTCACT
1 CTTCTCTTCACT
1691188 C
1 C
1691189 CTTTCTGCTG
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:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:1700463 original size:15 final size:16
Alignment explanation
Indices: 1700443--1700477 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1700433 CTTTTTTTTC
*
1700443 TGTTTTCTT-AGAATT
1 TGTTTTCTTCAGAAGT
1700458 TGTTTTCTTCAGAAGT
1 TGTTTTCTTCAGAAGT
1700474 TGTT
1 TGTT
1700478 AAAGAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (16 bp):
TGTTTTCTTCAGAAGT
Found at i:1704585 original size:18 final size:19
Alignment explanation
Indices: 1704558--1704593 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1704548 TATATTTTTA
*
1704558 TTTTTTATCAAA-ATATAC
1 TTTTTAATCAAATATATAC
1704576 TTTTTAATCAAATATATA
1 TTTTTAATCAAATATATA
1704594 TTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAATCAAATATATAC
Found at i:1712246 original size:48 final size:46
Alignment explanation
Indices: 1712176--1712268 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 46
1712166 TCCTTTTAAA
* * *
1712176 TCTCTGAAAGGCATTAAAACACAATACT-TAAGAAAACCAAATGAAAT
1 TCTCTGAAAAGCAGTAAAACACAATACTCCAA-AAAACCAAA-GAAAT
1712223 TCTCTGAAAAAGCAGTAAAACACAATACTCCAAAAAACCAAAGAAA
1 TCTCTG-AAAAGCAGTAAAACACAATACTCCAAAAAACCAAAGAAA
1712269 ACACCAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 10 0.24
48 29 0.71
49 2 0.05
ACGTcount: A:0.54, C:0.19, G:0.10, T:0.17
Consensus pattern (46 bp):
TCTCTGAAAAGCAGTAAAACACAATACTCCAAAAAACCAAAGAAAT
Found at i:1714327 original size:20 final size:20
Alignment explanation
Indices: 1714294--1714334 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1714284 AAGCAAAGAA
* *
1714294 ATGAGAAAGGAGAAATTTTT
1 ATGAGAAAGCAGAAATGTTT
*
1714314 ATGAGAAATCAGAAATGTTT
1 ATGAGAAAGCAGAAATGTTT
1714334 A
1 A
1714335 AGCTCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.29
Consensus pattern (20 bp):
ATGAGAAAGCAGAAATGTTT
Found at i:1722715 original size:16 final size:16
Alignment explanation
Indices: 1722694--1722725 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1722684 TCCTTTTGCC
1722694 GTCTCTCTCTGTCTCT
1 GTCTCTCTCTGTCTCT
*
1722710 GTCTCTGTCTGTCTCT
1 GTCTCTCTCTGTCTCT
1722726 TTTTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (16 bp):
GTCTCTCTCTGTCTCT
Found at i:1722742 original size:2 final size:2
Alignment explanation
Indices: 1722737--1722761 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1722727 TTTTTTTTCT
1722737 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1722762 AAAAGTCGAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1728232 original size:3 final size:3
Alignment explanation
Indices: 1728171--1728220 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1728161 TTGCATTCCT
* *
1728171 TTA TTA TTA TTA TTG TTG 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
1728219 TT
1 TT
1728221 TTGTCATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1734430 original size:12 final size:11
Alignment explanation
Indices: 1734405--1734439 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
1734395 AAGCAAATAC
1734405 AGAAA-AAAAA
1 AGAAAGAAAAA
1734415 AGAAAGAAAGAA
1 AGAAAGAAA-AA
1734427 AGAAAGAAAAA
1 AGAAAGAAAAA
1734438 AG
1 AG
1734440 CTTGGGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 7 0.30
12 11 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:1735292 original size:30 final size:31
Alignment explanation
Indices: 1735233--1735292 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1735223 GCCCAATGTC
1735233 TTAAATAAAAATTTACGAATAGTTTAGTGAT
1 TTAAATAAAAATTTACGAATAGTTTAGTGAT
*
1735264 TTAAATGAAAATTT-CGAATA-TTTCAGTGA
1 TTAAATAAAAATTTACGAATAGTTT-AGTGA
1735293 CTATTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (31 bp):
TTAAATAAAAATTTACGAATAGTTTAGTGAT
Found at i:1740018 original size:31 final size:29
Alignment explanation
Indices: 1739947--1740003 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1739937 GAATTTGACC
1739947 AAATTAAAATTTCATGTATAAAATTATACA
1 AAATTAAAA-TTCATGTATAAAATTATACA
*
1739977 AAATTAAAATTCATGTATATAATTATA
1 AAATTAAAATTCATGTATAAAATTATA
1740004 TATTAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATTAAAATTCATGTATAAAATTATACA
Found at i:1756030 original size:87 final size:88
Alignment explanation
Indices: 1755914--1756088 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 88
1755904 AATAAAATTC
1755914 ACTATGTCGAATTCGAATGATTACAAAAGAAGTTTCGACTACATCTATTTATAGGTTGAAAAAAC
1 ACTATGTCGAATTCGAATGATTACAAAAGAAGTTTCGACTACATCTATTTATAGGTTGAAAAAAC
1755979 CTAACTCTAATCAAAGTCACATA
66 CTAACTCTAATCAAAGTCACATA
1756002 ACTATGTCG-ATTCGAATGATTACAAAAGAAGTTTCGACTACATCTATTTATAGGTTGAAAAAAC
1 ACTATGTCGAATTCGAATGATTACAAAAGAAGTTTCGACTACATCTATTTATAGGTTGAAAAAAC
1756066 CTAACTCTAATCAAAGTCACATA
66 CTAACTCTAATCAAAGTCACATA
1756089 TATTATGCTA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 78 0.90
88 9 0.10
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (88 bp):
ACTATGTCGAATTCGAATGATTACAAAAGAAGTTTCGACTACATCTATTTATAGGTTGAAAAAAC
CTAACTCTAATCAAAGTCACATA
Found at i:1756113 original size:24 final size:24
Alignment explanation
Indices: 1756086--1756135 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1756076 TCAAAGTCAC
* *
1756086 ATATATTATGCTAATAAATGCTAA
1 ATATATTATACTAATAAATACTAA
*
1756110 ATATATTATACTCATAAATACTAA
1 ATATATTATACTAATAAATACTAA
1756134 AT
1 AT
1756136 CTTTTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATTATACTAATAAATACTAA
Found at i:1758682 original size:46 final size:46
Alignment explanation
Indices: 1758610--1758748 Score: 260
Period size: 46 Copynumber: 3.0 Consensus size: 46
1758600 ACATTGCTAT
* *
1758610 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCGC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1758656 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1758702 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1758748 A
1 A
1758749 TTTTTCCATG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:1763655 original size:255 final size:255
Alignment explanation
Indices: 1763204--1763715 Score: 1008
Period size: 255 Copynumber: 2.0 Consensus size: 255
1763194 ACTTAAAAAA
1763204 AAAAAGCTTCAAGAAATGGCGGATTTCTGGAAAGCTTAAAGAAAGCTTAAGAAACAGTGGTTTTC
1 AAAAAGCTTCAAGAAATGGCGGATTTCTGGAAAGCTTAAAGAAAGCTTAAGAAACAGTGGTTTTC
1763269 TCATTTCTGGAAAGCTTCAAGAAACGGTGGTTTTCTGGAAAAATGAACAGTAATTCTGGCCTACT
66 TCATTTCTGGAAAGCTTCAAGAAACGGTGGTTTTCTGGAAAAATGAACAGTAATTCTGGCCTACT
1763334 CATCCAGATATGATGAACGGTGGTTAATATAATTTTATTAGAAATTATTTAATTTAATTTAAAAT
131 CATCCAGATATGATGAACGGTGGTTAATATAATTTTATTAGAAATTATTTAATTTAATTTAAAAT
1763399 ATATTTTATATAAATACTTTTATTATATATTAATAATATAAATAA-AATATTCTTTATTTT
196 ATATTTTATATAAATACTTTTATTATATATTAATAATATAAATAACAA-ATTCTTTATTTT
1763459 AAAAAGCTTCAAGAAATGGCGGATTTCTGGAAAGCTTAAAGAAAGCTTAAGAAACAGTGGTTTTC
1 AAAAAGCTTCAAGAAATGGCGGATTTCTGGAAAGCTTAAAGAAAGCTTAAGAAACAGTGGTTTTC
1763524 TCATTTCTGGAAAGCTTCAAGAAACGGTGGTTTTCTGGAAAAATGAACAGTAATTCTGGCCTACT
66 TCATTTCTGGAAAGCTTCAAGAAACGGTGGTTTTCTGGAAAAATGAACAGTAATTCTGGCCTACT
1763589 CATCCAGATATGATGAACGGTGGTTAATATAATTTTATTAGAAATTATTTAATTTAATTTAAAAT
131 CATCCAGATATGATGAACGGTGGTTAATATAATTTTATTAGAAATTATTTAATTTAATTTAAAAT
1763654 ATATTTTATATAAATACTTTTATTATATATTAATAATATAAATAACAAATTCTTTATTTT
196 ATATTTTATATAAATACTTTTATTATATATTAATAATATAAATAACAAATTCTTTATTTT
1763714 AA
1 AA
1763716 GGGTAAAGTT
Statistics
Matches: 256, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
255 254 0.99
256 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (255 bp):
AAAAAGCTTCAAGAAATGGCGGATTTCTGGAAAGCTTAAAGAAAGCTTAAGAAACAGTGGTTTTC
TCATTTCTGGAAAGCTTCAAGAAACGGTGGTTTTCTGGAAAAATGAACAGTAATTCTGGCCTACT
CATCCAGATATGATGAACGGTGGTTAATATAATTTTATTAGAAATTATTTAATTTAATTTAAAAT
ATATTTTATATAAATACTTTTATTATATATTAATAATATAAATAACAAATTCTTTATTTT
Found at i:1763966 original size:16 final size:16
Alignment explanation
Indices: 1763945--1763975 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1763935 TTATTGATTA
1763945 CAGCTCTATTCCATTT
1 CAGCTCTATTCCATTT
1763961 CAGCTCTATTCCATT
1 CAGCTCTATTCCATT
1763976 ACATTGAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.06, T:0.42
Consensus pattern (16 bp):
CAGCTCTATTCCATTT
Found at i:1780599 original size:33 final size:33
Alignment explanation
Indices: 1780557--1780624 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1780547 GAGTCAATCC
1780557 ATATTAGCTTCTTCAAGCTTTTTCATATATTTT
1 ATATTAGCTTCTTCAAGCTTTTTCATATATTTT
1780590 ATATTAGCTTCTTCAAGCTTTTTCATATATTTT
1 ATATTAGCTTCTTCAAGCTTTTTCATATATTTT
1780623 AT
1 AT
1780625 TTTAAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54
Consensus pattern (33 bp):
ATATTAGCTTCTTCAAGCTTTTTCATATATTTT
Found at i:1795612 original size:12 final size:12
Alignment explanation
Indices: 1795595--1795628 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1795585 CTCTCTTTCT
1795595 CCTCTTCCTCCC
1 CCTCTTCCTCCC
* *
1795607 CCTCTTCATCCT
1 CCTCTTCCTCCC
1795619 CCTCTTCCTC
1 CCTCTTCCTC
1795629 ATCATCTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (12 bp):
CCTCTTCCTCCC
Found at i:1795636 original size:24 final size:24
Alignment explanation
Indices: 1795593--1795640 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1795583 CTCTCTCTTT
* *
1795593 CTCCTCTTCCTCCCCCTCTTCATC
1 CTCCTCTTCCTCACCATCTTCATC
*
1795617 CTCCTCTTCCTCATCATCTTCATC
1 CTCCTCTTCCTCACCATCTTCATC
1795641 TTCGTCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.52, G:0.00, T:0.40
Consensus pattern (24 bp):
CTCCTCTTCCTCACCATCTTCATC
Found at i:1798541 original size:17 final size:18
Alignment explanation
Indices: 1798515--1798549 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1798505 TACAGGAAGA
1798515 AAGAAGATGAT-GAGAAT
1 AAGAAGATGATCGAGAAT
*
1798532 AAGAATATGATCGAGAAT
1 AAGAAGATGATCGAGAAT
1798550 CCTTTGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (18 bp):
AAGAAGATGATCGAGAAT
Found at i:1807654 original size:1 final size:1
Alignment explanation
Indices: 1807648--1807681 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
1807638 TAGCAGAGAG
**
1807648 AAAAAAAAACCAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1807682 CATTACCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1813450 original size:82 final size:82
Alignment explanation
Indices: 1813313--1813481 Score: 302
Period size: 82 Copynumber: 2.1 Consensus size: 82
1813303 AAGTTACTCA
* *
1813313 AAAGAAGTTGGAATTTGGCAATCCTAAGATACATTATCAAGTTGGGGCAAATGAAACTTCAGCAT
1 AAAGAAGTTGGAATTTGACAATCCTAAGATACATTATCAAATTGGGGCAAATGAAACTTCAGCAT
1813378 CCGATCACACCTTAAAT
66 CCGATCACACCTTAAAT
* *
1813395 AAAGAAGTTGGAATTTGACAATCTTAAGATATATTATCAAATTGGGGCAAATGAAACTTCAGCAT
1 AAAGAAGTTGGAATTTGACAATCCTAAGATACATTATCAAATTGGGGCAAATGAAACTTCAGCAT
1813460 CCGATCACACCTTAAAT
66 CCGATCACACCTTAAAT
1813477 AAAGA
1 AAAGA
1813482 CATCTCACAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (82 bp):
AAAGAAGTTGGAATTTGACAATCCTAAGATACATTATCAAATTGGGGCAAATGAAACTTCAGCAT
CCGATCACACCTTAAAT
Found at i:1816302 original size:13 final size:13
Alignment explanation
Indices: 1816268--1816294 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1816258 ATATAAAAAA
1816268 TATATAATTACAT
1 TATATAATTACAT
1816281 TATATAATTACAT
1 TATATAATTACAT
1816294 T
1 T
1816295 TATTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATAATTACAT
Found at i:1824165 original size:20 final size:19
Alignment explanation
Indices: 1824114--1824166 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1824104 TTTCAACAAA
*
1824114 AAAATTTAAAATAATTTTT
1 AAAATTTAAAATAATTTTC
**
1824133 AGAAATTCGAAATAATTTTC
1 A-AAATTTAAAATAATTTTC
1824153 AAAATTTTAAAATA
1 AAAA-TTTAAAATA
1824167 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTTAAAATAATTTTC
Found at i:1824238 original size:20 final size:18
Alignment explanation
Indices: 1824215--1824259 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1824205 ATATATATTT
1824215 AAAAAACTTAAAAATTCTAA
1 AAAAAACTTAAAAA-T-TAA
* *
1824235 AAAATATTTAAAAATTAA
1 AAAAAACTTAAAAATTAA
1824253 AAAAAAC
1 AAAAAAC
1824260 CAAAATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 12 0.57
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAACTTAAAAATTAA
Found at i:1824377 original size:176 final size:177
Alignment explanation
Indices: 1824164--1824516 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 177
1824154 AAATTTTAAA
1824164 ATATTTATAAAAAATCTAAAATTTCATATTTTTTAAACATTATATATATTTAAAAAACTTAAAAA
1 ATATTTATAAAAAATCTAAAATTTCATATTTTTTAAACATTATATATATTTAAAAAACTTAAAAA
1824229 TTCTAAAAAATATTTAAAAATTAAAAAAAACCAAAATAATAAATTTAAGGACATAAACAAGTAAA
66 TTCTAAAAAATATTTAAAAATTAAAAAAAACCAAAATAATAAATTTAAGGACATAAACAAGTAAA
1824294 TTACAATTTCAAGTTTATCATACTAAAAAGTATCTCTAACATAGATT
131 TTACAATTTCAAGTTTATCATACTAAAAAGTATCTCTAACATAGATT
1824341 ATATTTAT-AAAAATCTAAAATTTCATATTTTTTAAACATTATATATATTTAAAAAACTTAAAAA
1 ATATTTATAAAAAATCTAAAATTTCATATTTTTTAAACATTATATATATTTAAAAAACTTAAAAA
1824405 TTCTAAAAAATATTTAAAAATTAAAAAAAACCAAAATAATAAATTTAAGGACATAAACAAGTAAA
66 TTCTAAAAAATATTTAAAAATTAAAAAAAACCAAAATAATAAATTTAAGGACATAAACAAGTAAA
1824470 TTACAATTTCAAGTTTATCATACTAAAAAGTATCTCTAACATAGATT
131 TTACAATTTCAAGTTTATCATACTAAAAAGTATCTCTAACATAGATT
1824517 TAGTTTTATT
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 168 0.95
177 8 0.05
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (177 bp):
ATATTTATAAAAAATCTAAAATTTCATATTTTTTAAACATTATATATATTTAAAAAACTTAAAAA
TTCTAAAAAATATTTAAAAATTAAAAAAAACCAAAATAATAAATTTAAGGACATAAACAAGTAAA
TTACAATTTCAAGTTTATCATACTAAAAAGTATCTCTAACATAGATT
Found at i:1824414 original size:20 final size:18
Alignment explanation
Indices: 1824391--1824435 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1824381 ATATATATTT
1824391 AAAAAACTTAAAAATTCTAA
1 AAAAAACTTAAAAA-T-TAA
* *
1824411 AAAATATTTAAAAATTAA
1 AAAAAACTTAAAAATTAA
1824429 AAAAAAC
1 AAAAAAC
1824436 CAAAATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 12 0.57
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAACTTAAAAATTAA
Found at i:1825815 original size:12 final size:12
Alignment explanation
Indices: 1825798--1825822 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1825788 TGTGGTACCT
1825798 CTTCAATATCTA
1 CTTCAATATCTA
1825810 CTTCAATATCTA
1 CTTCAATATCTA
1825822 C
1 C
1825823 AACAAACAGG
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CTTCAATATCTA
Found at i:1837199 original size:27 final size:27
Alignment explanation
Indices: 1837141--1837235 Score: 156
Period size: 27 Copynumber: 3.5 Consensus size: 27
1837131 AAAAATAAAA
1837141 ATTTACCAAAATATTATAAC-TTTTTT
1 ATTTACCAAAATATTATAACTTTTTTT
1837167 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATATTATAACTTTTTTT
*
1837194 ATTTACCAAAATATTATAAATTTTTTTT
1 ATTTACCAAAATATTAT-AACTTTTTTT
*
1837222 ATTTACTAAAATAT
1 ATTTACCAAAATAT
1837236 ACCCAAAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.31
27 23 0.35
28 22 0.34
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTACCAAAATATTATAACTTTTTTT
Found at i:1837325 original size:27 final size:27
Alignment explanation
Indices: 1837295--1837346 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1837285 AGCCAATCAC
*
1837295 ATTGGCGGCACCAAAAGTGCCAAAGAG
1 ATTGGCAGCACCAAAAGTGCCAAAGAG
**
1837322 ATTGGCAGCACCAATGGTGCCAAAG
1 ATTGGCAGCACCAAAAGTGCCAAAG
1837347 GACTAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.29, T:0.13
Consensus pattern (27 bp):
ATTGGCAGCACCAAAAGTGCCAAAGAG
Found at i:1837925 original size:19 final size:19
Alignment explanation
Indices: 1837901--1837949 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1837891 TCTAATTAAG
*
1837901 TAATAACTCTATTTTAATT
1 TAATAACTCTATTCTAATT
* *
1837920 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTCTAATT
1837938 TAATAACTCTAT
1 TAATAACTCTAT
1837950 AAATGTAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAACTCTATTCTAATT
Found at i:1838601 original size:45 final size:45
Alignment explanation
Indices: 1838545--1838632 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
1838535 AGCAGTAACA
*
1838545 GTAACAGTATTCAACACACAAAGTG-CTGAATCTATAACAGTAATG
1 GTAACAGTATTCAACACACAAAGTGTC-GAATCGATAACAGTAATG
* * *
1838590 GTAACAGTATTCGACACATAAAGTGTCGAATCGGTAACAGTAA
1 GTAACAGTATTCAACACACAAAGTGTCGAATCGATAACAGTAA
1838633 CAGTAGTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (45 bp):
GTAACAGTATTCAACACACAAAGTGTCGAATCGATAACAGTAATG
Found at i:1838881 original size:40 final size:41
Alignment explanation
Indices: 1838837--1838924 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
1838827 AATTCATTAC
* * *
1838837 TTCAGTAATTTCACAGTTCAATGCAATACAC-ATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAAACAATA
* * * *
1838877 TTCAGTACCTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAAACAATA
1838918 TTCAGTA
1 TTCAGTA
1838925 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 25 0.62
41 15 0.38
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.31
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATGCAATACACAAAAACAATA
Found at i:1844967 original size:44 final size:44
Alignment explanation
Indices: 1844897--1844991 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
1844887 TGAATTTGTC
* * * **
1844897 TTAGATTTTATAATTATTTAAGTTTATTTTTGTCTAA-TTAATAT
1 TTAGATATTATAATTATTAAACTTTATTTTTAAC-AATTTAATAT
*
1844941 TTAGATATTGTAATTATTAAACTTTATTTTTAACAATTTAATAT
1 TTAGATATTATAATTATTAAACTTTATTTTTAACAATTTAATAT
1844985 TTAGATA
1 TTAGATA
1844992 CTACTTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (44 bp):
TTAGATATTATAATTATTAAACTTTATTTTTAACAATTTAATAT
Found at i:1846721 original size:9 final size:9
Alignment explanation
Indices: 1846704--1846740 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1846694 TGAGTTTTCG
1846704 AATTCGAAT
1 AATTCGAAT
*
1846713 AACTCGAAT
1 AATTCGAAT
1846722 AATTCGAAT
1 AATTCGAAT
1846731 AATTCGAAT
1 AATTCGAAT
1846740 A
1 A
1846741 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1847961 original size:6 final size:6
Alignment explanation
Indices: 1847950--1847974 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1847940 GGCGGTACCG
1847950 TGAAGC TGAAGC TGAAGC TGAAGC T
1 TGAAGC TGAAGC TGAAGC TGAAGC T
1847975 CAAACTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (6 bp):
TGAAGC
Found at i:1854121 original size:97 final size:100
Alignment explanation
Indices: 1853989--1854322 Score: 271
Period size: 97 Copynumber: 3.4 Consensus size: 100
1853979 GTATGAAGAC
*
1853989 CAAC-TTGTTTGTTGATATTTGA-AGTTGT-AGAGTTTGATCCTTGGCTATTAGAACTATGACTC
1 CAACTTTGTTT-TTGATATTTGAGAGTTGTGAGGGTTTGATCCTTGGCTATTAGAACTATGACTC
*
1854051 AAACACTCTACTAGCAAAGT-ACATGATTGTTGGCT
65 AAGCACTCTACTAGCAAAGTAACATGATTGTTGGCT
* * * * * *
1854086 CAACTTTG-TTTTGATATTTGAGA-TTGTGAGGGTTTGGTCCTTGGCCATCAGAGCTATGAGTTA
1 CAACTTTGTTTTTGATATTTGAGAGTTGTGAGGGTTTGATCCTTGGCTATTAGAACTATGACTCA
* * * * * ***
1854149 AGCAATCTACCAACAGA-TGACATGACCATTGGCT
66 AGCACTCTACTAGCAAAGTAACATGATTGTTGGCT
** * * * * * * *
1854183 TGACTTGGTTTTTGATATTTGAGATTTTTG-GGTTTTGATGCTTGGCTGTTA-AACTATGATTCA
1 CAACTTTGTTTTTGATATTTGAGAGTTGTGAGGGTTTGATCCTTGGCTATTAGAACTATGACTCA
* * *
1854246 AGCTCTCTACT-G-ACAGATAACATGATTGTTAGCT
66 AGCACTCTACTAGCAAAG-TAACATGATTGTTGGCT
* * *
1854280 CAA-TTTGTTTTTATATATTTGAG-GTTGTGTGGATTTGATCCTT
1 CAACTTTGTTTTT-GATATTTGAGAGTTGTGAGGGTTTGATCCTT
1854323 ATCCATTAGA
Statistics
Matches: 181, Mismatches: 46, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
95 2 0.01
96 28 0.15
97 114 0.63
98 33 0.18
99 4 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (100 bp):
CAACTTTGTTTTTGATATTTGAGAGTTGTGAGGGTTTGATCCTTGGCTATTAGAACTATGACTCA
AGCACTCTACTAGCAAAGTAACATGATTGTTGGCT
Found at i:1859940 original size:2 final size:2
Alignment explanation
Indices: 1859927--1859963 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1859917 TTATGCTAAT
*
1859927 AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1859964 AAAGGATCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1867079 original size:20 final size:21
Alignment explanation
Indices: 1867042--1867080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1867032 CAACATTTAA
* *
1867042 AATTTTAAAATTATAAAATAC
1 AATTTAAAAAATATAAAATAC
1867063 AATTTAAAAAATA-AAAAT
1 AATTTAAAAAATATAAAAT
1867081 TATTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAAAAATATAAAATAC
Found at i:1896934 original size:2 final size:2
Alignment explanation
Indices: 1896927--1896954 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1896917 AATCAACTTG
1896927 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
1896955 GTGTGTGTGT
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:1913885 original size:22 final size:21
Alignment explanation
Indices: 1913860--1913901 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1913850 TTAGACATGC
* *
1913860 ATTTTTAAATGAAAAGTAGAAA
1 ATTTTAAAAT-AAAAATAGAAA
1913882 ATTTTAAAATAAAAATAGAA
1 ATTTTAAAATAAAAATAGAA
1913902 GGACGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
ATTTTAAAATAAAAATAGAAA
Found at i:1914163 original size:3 final size:3
Alignment explanation
Indices: 1914155--1914186 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1914145 TCTGTGTTTC
1914155 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1914187 AACTAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1914443 original size:6 final size:6
Alignment explanation
Indices: 1914429--1914459 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1914419 GAAAGATGAC
*
1914429 GGTGGT GGTGAT GGTGAT GGTGAT GGTGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT G
1914460 ATCATGGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.55, T:0.32
Consensus pattern (6 bp):
GGTGAT
Found at i:1914466 original size:18 final size:18
Alignment explanation
Indices: 1914429--1914468 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1914419 GAAAGATGAC
* * *
1914429 GGTGGTGGTGATGGTGAT
1 GGTGATGGTGATGATCAT
1914447 GGTGATGGTGATGATCAT
1 GGTGATGGTGATGATCAT
1914465 GGTG
1 GGTG
1914469 GTGATCAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.50, T:0.33
Consensus pattern (18 bp):
GGTGATGGTGATGATCAT
Found at i:1921754 original size:11 final size:11
Alignment explanation
Indices: 1921738--1921778 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1921728 ATTTTCGACT
1921738 ATTATAAAAAA
1 ATTATAAAAAA
1921749 ATTATAAAAAA
1 ATTATAAAAAA
**
1921760 ATT-TAATTAA
1 ATTATAAAAAA
1921770 ATTATAAAA
1 ATTATAAAA
1921779 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATTATAAAAAA
Found at i:1921782 original size:13 final size:13
Alignment explanation
Indices: 1921738--1921796 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 13
1921728 ATTTTCGACT
1921738 ATTATAAAA--AA
1 ATTATAAAATTAA
1921749 ATTATAAAA--AA
1 ATTATAAAATTAA
1921760 ATT-T--AATTAA
1 ATTATAAAATTAA
1921770 ATTATAAAATTAA
1 ATTATAAAATTAA
*
1921783 A-TAAAAAATTAA
1 ATTATAAAATTAA
1921795 AT
1 AT
1921797 AATATTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.05
10 6 0.15
11 15 0.37
12 11 0.27
13 7 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTATAAAATTAA
Found at i:1921788 original size:29 final size:29
Alignment explanation
Indices: 1921746--1921807 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1921736 CTATTATAAA
* *
1921746 AAAATTATAAAAAAATTTAATTAA-ATTAT
1 AAAATTATAAAAAAAATTAAATAATATT-T
1921775 AAAATTA-AATAAAAAATTAAATAATATTT
1 AAAATTATAA-AAAAAATTAAATAATATTT
1921804 AAAA
1 AAAA
1921808 AATGGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.83
30 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATTATAAAAAAAATTAAATAATATTT
Found at i:1921792 original size:12 final size:12
Alignment explanation
Indices: 1921764--1921798 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1921754 AAAAAAATTT
*
1921764 AATTAAATTATAA
1 AATTAAA-TAAAA
1921777 AATTAAATAAAA
1 AATTAAATAAAA
1921789 AATTAAATAA
1 AATTAAATAA
1921799 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:1931641 original size:21 final size:21
Alignment explanation
Indices: 1931608--1931654 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1931598 ATCCTTAACC
*
1931608 CTAAATCTCAAA-CTCTGAACA
1 CTAAATCTCAAACCTC-AAACA
1931629 CTAAATC-CTAAACCTCAAACA
1 CTAAATCTC-AAACCTCAAACA
1931650 CTAAA
1 CTAAA
1931655 CATCGAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (21 bp):
CTAAATCTCAAACCTCAAACA
Found at i:1939129 original size:12 final size:12
Alignment explanation
Indices: 1939112--1939137 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1939102 AACACTACTC
1939112 TAATTTTTTATT
1 TAATTTTTTATT
1939124 TAATTTTTTATT
1 TAATTTTTTATT
1939136 TA
1 TA
1939138 GGATATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TAATTTTTTATT
Found at i:1940701 original size:26 final size:28
Alignment explanation
Indices: 1940672--1940732 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
1940662 AAAACTAACC
1940672 AAAATATTAT-AA-TTTTTTTATTTACT
1 AAAATATTATAAATTTTTTTTATTTACT
1940698 AAAATATTATAAATTTTTTTTATTTACT
1 AAAATATTATAAATTTTTTTTATTTACT
1940726 AAAATAT
1 AAAATAT
1940733 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 10 0.30
27 2 0.06
28 21 0.64
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
AAAATATTATAAATTTTTTTTATTTACT
Found at i:1941193 original size:18 final size:18
Alignment explanation
Indices: 1941172--1941209 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1941162 AGTAATAACT
*
1941172 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
1941190 CTATTCTCATTTAATAAA
1 CTATTCTAATTTAATAAA
1941208 CT
1 CT
1941210 CTAATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:1941564 original size:26 final size:28
Alignment explanation
Indices: 1941535--1941598 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1941525 TATTTTTGGT
1941535 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1941561 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1941589 ATATTTTGGT
1 ATATTTTGGT
1941599 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:1943926 original size:10 final size:10
Alignment explanation
Indices: 1943911--1943935 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1943901 ATATTAATTG
1943911 TAAAAAAATA
1 TAAAAAAATA
1943921 TAAAAAAATA
1 TAAAAAAATA
1943931 TAAAA
1 TAAAA
1943936 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:1944576 original size:22 final size:22
Alignment explanation
Indices: 1944546--1944589 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1944536 CAAATGTGTT
*
1944546 AAAATTATTAATTTAAAA-AATA
1 AAAAATATT-ATTTAAAATAATA
*
1944568 AAAAATATTTTTTAAAATAATA
1 AAAAATATTATTTAAAATAATA
1944590 CAAATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATTATTTAAAATAATA
Found at i:1945465 original size:394 final size:394
Alignment explanation
Indices: 1944737--1945524 Score: 1567
Period size: 394 Copynumber: 2.0 Consensus size: 394
1944727 ATAGTAAATT
1944737 ATATTTTTATATTCTTACTAAAATATGATAATAATTGATTTGAACATTATTTATATATTTGTTAC
1 ATATTTTTATATTCTTACTAAAATATGATAATAATTGATTTGAACATTATTTATATATTTGTTAC
1944802 TTGATAATACCATGTCTAAAATGGATATTTTATAAAATAACTTTTTGACAGCAATGCTAAACATT
66 TTGATAATACCATGTCTAAAATGGATATTTTATAAAATAACTTTTTGACAGCAATGCTAAACATT
1944867 CAAATCTTAAACCAAACATTTTAAAAGTAATTCTCAAAAGTACTTTTCCACATAGCTTTTTGAAA
131 CAAATCTTAAACCAAACATTTTAAAAGTAATTCTCAAAAGTACTTTTCCACATAGCTTTTTGAAA
1944932 GCATTGCTAAACTAACCCTAAAATAAATAAGGGAAGTTAGAAATTTTGTTTAGGGGTTCAATATA
196 GCATTGCTAAACTAACCCTAAAATAAATAAGGGAAGTTAGAAATTTTGTTTAGGGGTTCAATATA
1944997 ATTATAAAATTTGGAGTTAAAGTTAAATATTTTGTATTATATTTTTTAAAAAGGTTAAATTATAA
261 ATTATAAAATTTGGAGTTAAAGTTAAATATTTTGTATTATATTTTTTAAAAAGGTTAAATTATAA
1945062 TTTTTAATTTTAGAAGAGGTTAAAAAATAATTTGTGTATTTAACAAGGTGTCAAGGCCATGCCGT
326 TTTTTAATTTTAGAAGAGGTTAAAAAATAATTTGTGTATTTAACAAGGTGTCAAGGCCATGCCGT
1945127 TTGG
391 TTGG
*
1945131 ATATTTTTATTTTCTTACTAAAATATGATAATAATTGATTTGAACATTATTTATATATTTGTTAC
1 ATATTTTTATATTCTTACTAAAATATGATAATAATTGATTTGAACATTATTTATATATTTGTTAC
1945196 TTGATAATACCATGTCTAAAATGGATATTTTATAAAATAACTTTTTGACAGCAATGCTAAACATT
66 TTGATAATACCATGTCTAAAATGGATATTTTATAAAATAACTTTTTGACAGCAATGCTAAACATT
1945261 CAAATCTTAAACCAAACATTTTAAAAGTAATTCTCAAAAGTACTTTTCCACATAGCTTTTTGAAA
131 CAAATCTTAAACCAAACATTTTAAAAGTAATTCTCAAAAGTACTTTTCCACATAGCTTTTTGAAA
1945326 GCATTGCTAAACTAACCCTAAAATAAATAAGGGAAGTTAGAAATTTTGTTTAGGGGTTCAATATA
196 GCATTGCTAAACTAACCCTAAAATAAATAAGGGAAGTTAGAAATTTTGTTTAGGGGTTCAATATA
1945391 ATTATAAAATTTGGAGTTAAAGTTAAATATTTTGTATTATATTTTTTAAAAAGGTTAAATTATAA
261 ATTATAAAATTTGGAGTTAAAGTTAAATATTTTGTATTATATTTTTTAAAAAGGTTAAATTATAA
1945456 TTTTTAATTTTAGAAGAGGTTAAAAAATAATTTGTGTATTTAACAAGGTGTCAAGGCCATGCCGT
326 TTTTTAATTTTAGAAGAGGTTAAAAAATAATTTGTGTATTTAACAAGGTGTCAAGGCCATGCCGT
1945521 TTGG
391 TTGG
1945525 TTACGCCACT
Statistics
Matches: 393, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
394 393 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (394 bp):
ATATTTTTATATTCTTACTAAAATATGATAATAATTGATTTGAACATTATTTATATATTTGTTAC
TTGATAATACCATGTCTAAAATGGATATTTTATAAAATAACTTTTTGACAGCAATGCTAAACATT
CAAATCTTAAACCAAACATTTTAAAAGTAATTCTCAAAAGTACTTTTCCACATAGCTTTTTGAAA
GCATTGCTAAACTAACCCTAAAATAAATAAGGGAAGTTAGAAATTTTGTTTAGGGGTTCAATATA
ATTATAAAATTTGGAGTTAAAGTTAAATATTTTGTATTATATTTTTTAAAAAGGTTAAATTATAA
TTTTTAATTTTAGAAGAGGTTAAAAAATAATTTGTGTATTTAACAAGGTGTCAAGGCCATGCCGT
TTGG
Found at i:1946379 original size:61 final size:61
Alignment explanation
Indices: 1946314--1946436 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
1946304 TATTAATTTT
1946314 GCGACATACAATGTTTGATTATTTTATATTCTTTGTCAATTCAACAAACCTAATGGACAGA
1 GCGACATACAATGTTTGATTATTTTATATTCTTTGTCAATTCAACAAACCTAATGGACAGA
1946375 GCGACATACAATGTTTGATTATTTTATATTCTTTGTCAATTCAACAAACCTAATGGACAGA
1 GCGACATACAATGTTTGATTATTTTATATTCTTTGTCAATTCAACAAACCTAATGGACAGA
1946436 G
1 G
1946437 GCAAATTTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (61 bp):
GCGACATACAATGTTTGATTATTTTATATTCTTTGTCAATTCAACAAACCTAATGGACAGA
Found at i:1963971 original size:17 final size:17
Alignment explanation
Indices: 1963949--1964010 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1963939 CATCAATGGC
*
1963949 TACAATTAAAAGTTGTA
1 TACAATTAGAAGTTGTA
**
1963966 TACAATTAGATCTCT-TA
1 TACAATTAGAAGT-TGTA
*
1963983 CACAATTAGAAGTTGTA
1 TACAATTAGAAGTTGTA
1964000 TACAATTAGAA
1 TACAATTAGAA
1964011 CTCTAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 1 0.03
17 34 0.94
18 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (17 bp):
TACAATTAGAAGTTGTA
Found at i:1963996 original size:34 final size:34
Alignment explanation
Indices: 1963950--1964014 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1963940 ATCAATGGCT
*
1963950 ACAATTAAAAGTTGTATACAATTAGATCTCTTAC
1 ACAATTAAAAGTTGTATACAATTAGAACTCTTAC
*
1963984 ACAATTAGAAGTTGTATACAATTAGAACTCT
1 ACAATTAAAAGTTGTATACAATTAGAACTCT
1964015 AAGATTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (34 bp):
ACAATTAAAAGTTGTATACAATTAGAACTCTTAC
Found at i:1969090 original size:17 final size:18
Alignment explanation
Indices: 1969064--1969117 Score: 85
Period size: 17 Copynumber: 3.1 Consensus size: 18
1969054 CAATTAAAAG
*
1969064 CTGTATACAATTAGAACT
1 CTGTACACAATTAGAACT
1969082 CT-TACACAATTAGAACT
1 CTGTACACAATTAGAACT
1969099 -TGTACACAATTAGAACT
1 CTGTACACAATTAGAACT
1969116 CT
1 CT
1969118 AAGATTACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.88
18 3 0.09
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (18 bp):
CTGTACACAATTAGAACT
Found at i:1971183 original size:57 final size:56
Alignment explanation
Indices: 1971073--1971240 Score: 171
Period size: 57 Copynumber: 3.0 Consensus size: 56
1971063 GATATAATAC
** * *
1971073 CTTAAGCCGAGGGGACTGACGAACAACTGGTGATAAAAGATCTGGTTTTGCTACTTT
1 CTTAAGCCGAGGGGACCAACGAACAACTGGTGATAAAAGATCTGATTTGGCTAC-TT
* * * **
1971130 CTTAAGCCGGGGGGACCAATGAACAACTGGTGATAAGATTTCTGATTTGGCTACTT
1 CTTAAGCCGAGGGGACCAACGAACAACTGGTGATAAAAGATCTGATTTGGCTACTT
* * * * *
1971186 CTTTAAGCCGAGTGGACCGACG-AC--CTGGTGATAGAATATCTGATTTGACTACTT
1 C-TTAAGCCGAGGGGACCAACGAACAACTGGTGATAAAAGATCTGATTTGGCTACTT
1971240 C
1 C
1971241 CTTGGGATTT
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
54 27 0.29
56 5 0.05
57 61 0.66
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (56 bp):
CTTAAGCCGAGGGGACCAACGAACAACTGGTGATAAAAGATCTGATTTGGCTACTT
Found at i:1998476 original size:104 final size:105
Alignment explanation
Indices: 1998343--1998562 Score: 415
Period size: 104 Copynumber: 2.1 Consensus size: 105
1998333 AGCTAATGTT
*
1998343 CTAAAATTTTTCATCCCTAGTTTTTTTAGGTATAAAAAAGCAGTGACGGTTTTTTCTTAATTTCA
1 CTAAAATTTTACATCCCTAGTTTTTTTAGGTATAAAAAAGCAGTGACGGTTTTTTCTTAATTTCA
*
1998408 TCCTTAAAACTTAAATTTTATTATGGTATCATATCATTAC
66 TCCTTAAAACTTAAATTTTATTATGGTAACATATCATTAC
1998448 CTAAAATTTTACA-CCCTAGTTTTTTTAGGTATAAAAAAGCAGTGACGGTTTTTTCTTAATTTCA
1 CTAAAATTTTACATCCCTAGTTTTTTTAGGTATAAAAAAGCAGTGACGGTTTTTTCTTAATTTCA
1998512 TCCTTAAAACTTAAATTTTATTATGGTAACATATCATTAC
66 TCCTTAAAACTTAAATTTTATTATGGTAACATATCATTAC
1998552 CTAAAATTTTA
1 CTAAAATTTTA
1998563 AAAAAATTTA
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 101 0.89
105 12 0.11
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (105 bp):
CTAAAATTTTACATCCCTAGTTTTTTTAGGTATAAAAAAGCAGTGACGGTTTTTTCTTAATTTCA
TCCTTAAAACTTAAATTTTATTATGGTAACATATCATTAC
Found at i:1998605 original size:11 final size:11
Alignment explanation
Indices: 1998565--1998605 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1998555 AAATTTTAAA
1998565 AAAATTTATAT
1 AAAATTTATAT
1998576 AAAATTTA-A-
1 AAAATTTATAT
1998585 AATAATTTTATAT
1 AA-AA-TTTATAT
1998598 AAAATTTA
1 AAAATTTA
1998606 GAAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 2 0.08
10 3 0.12
11 16 0.62
12 3 0.12
13 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATTTATAT
Found at i:1998612 original size:21 final size:21
Alignment explanation
Indices: 1998553--1998612 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
1998543 TATCATTACC
*
1998553 TAAAATTTTAAAAAAATTTATA
1 TAAAA-TTTAAAAAATTTTATA
1998575 TAAAATTTAAAATAATTTTATA
1 TAAAATTTAAAA-AATTTTATA
*
1998597 TAAAATTTAGAAAATT
1 TAAAATTTAAAAAATT
1998613 AAAACAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAATTTAAAAAATTTTATA
Found at i:2004132 original size:22 final size:21
Alignment explanation
Indices: 2004090--2004132 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2004080 AAATTCATGA
**
2004090 TTTTAATAATTATAATTTTTT
1 TTTTAATAATTATAAAATTTT
*
2004111 TTTTAATTAATTTTAAAATTTT
1 TTTTAA-TAATTATAAAATTTT
2004133 AAACTATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAATAATTATAAAATTTT
Found at i:2004153 original size:134 final size:135
Alignment explanation
Indices: 2003962--2004237 Score: 529
Period size: 134 Copynumber: 2.1 Consensus size: 135
2003952 CTCGAAGTCG
2003962 AATTATAATTTTTATTTTAAATTAATTTTAAAATTTTAAACTATTGTAATTACATTTTAAATTAT
1 AATTATAATTTTTATTTTAAATTAATTTTAAAATTTTAAACTATTGTAATTACATTTTAAATTAT
2004027 AAATGGCATATCGATAAGTTCTTTTTGTTACTAATATTATTAATATAATGATTAAATTCATGATT
66 AAATGGCATATCGATAAGTTCTTTTTGTTACTAATATTATTAATATAATGATTAAATTCATGATT
2004092 TTAAT
131 TTAAT
*
2004097 AATTATAATTTTT-TTTTTAATTAATTTTAAAATTTTAAACTATTGTAATTACATTTTAAATTAT
1 AATTATAATTTTTATTTTAAATTAATTTTAAAATTTTAAACTATTGTAATTACATTTTAAATTAT
2004161 AAATGGCATATCGATAAGTTCTTTTTGTTACTAATATTATTAATATAATGATTAAATTCATGATT
66 AAATGGCATATCGATAAGTTCTTTTTGTTACTAATATTATTAATATAATGATTAAATTCATGATT
2004226 TTAAT
131 TTAAT
2004231 AA-TATAA
1 AATTATAA
2004238 GTAATTATTT
Statistics
Matches: 140, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
133 5 0.04
134 122 0.87
135 13 0.09
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (135 bp):
AATTATAATTTTTATTTTAAATTAATTTTAAAATTTTAAACTATTGTAATTACATTTTAAATTAT
AAATGGCATATCGATAAGTTCTTTTTGTTACTAATATTATTAATATAATGATTAAATTCATGATT
TTAAT
Found at i:2010586 original size:21 final size:21
Alignment explanation
Indices: 2010562--2010601 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2010552 GCCATAGTCT
2010562 AAGAAA-AATAGATTAGTTTAA
1 AAGAAAGAATAGA-TAGTTTAA
*
2010583 AAGAAAGCATAGATAGTTT
1 AAGAAAGAATAGATAGTTT
2010602 CTTCAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (21 bp):
AAGAAAGAATAGATAGTTTAA
Found at i:2022839 original size:43 final size:43
Alignment explanation
Indices: 2022791--2022877 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
2022781 CCCAAAATGT
**
2022791 TAGAATTTTAATTTAGTCATTTTGATAACCATAATGATATAAG
1 TAGAATTACAATTTAGTCATTTTGATAACCATAATGATATAAG
2022834 TAGAATTACAATTTAGTCATTTTGATAACCATAATGATATAAG
1 TAGAATTACAATTTAGTCATTTTGATAACCATAATGATATAAG
2022877 T
1 T
2022878 CAATACAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.40
Consensus pattern (43 bp):
TAGAATTACAATTTAGTCATTTTGATAACCATAATGATATAAG
Found at i:2025142 original size:11 final size:12
Alignment explanation
Indices: 2025125--2025157 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2025115 AAGGCCTATT
2025125 GGAAAAAAAAAA
1 GGAAAAAAAAAA
*
2025137 AGAAAAAAAAAA
1 GGAAAAAAAAAA
2025149 GGAAAAAAA
1 GGAAAAAAA
2025158 CAATTCAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
GGAAAAAAAAAA
Found at i:2027033 original size:12 final size:12
Alignment explanation
Indices: 2027010--2027046 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2027000 AGAAACATAA
*
2027010 ATAAACCAAAAC
1 ATAAATCAAAAC
*
2027022 ATGAATCAAAAC
1 ATAAATCAAAAC
2027034 ATAAATCAAAAC
1 ATAAATCAAAAC
2027046 A
1 A
2027047 AAACATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.65, C:0.19, G:0.03, T:0.14
Consensus pattern (12 bp):
ATAAATCAAAAC
Found at i:2027402 original size:58 final size:58
Alignment explanation
Indices: 2027248--2027404 Score: 147
Period size: 59 Copynumber: 2.7 Consensus size: 58
2027238 TTTTTGGGGT
* * * *
2027248 CTGAATTTGGCAACTATCCC-CACTTGAGGCCTAAACTTTTTTTTGGTCCAAGTTAGGCC
1 CTGAACTTGGCAATTTTCCCACA-TTGAGGCCTAAACTTTTTTTT-GTCCAAATTAGGCC
* * * * * *
2027307 CTGAACTTGGTAATTTTCCCACATTGGGGCTTGAACTTTTTTTT-TCTAAATTAGTCC
1 CTGAACTTGGCAATTTTCCCACATTGAGGCCTAAACTTTTTTTTGTCCAAATTAGGCC
* ** *
2027364 TTGAACTTGGCAATTGTTCCCATGTTGAGGTCTAAACTTTT
1 CTGAACTTGGCAATT-TTCCCACATTGAGGCCTAAACTTTT
2027405 GGAGTTTTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
57 23 0.29
58 19 0.24
59 34 0.44
60 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (58 bp):
CTGAACTTGGCAATTTTCCCACATTGAGGCCTAAACTTTTTTTTGTCCAAATTAGGCC
Found at i:2031034 original size:17 final size:16
Alignment explanation
Indices: 2031010--2031041 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2031000 GTGAAAATTT
2031010 ATTTATTTACAAAACC
1 ATTTATTTACAAAACC
2031026 ATTTCATTTACAAAAC
1 ATTT-ATTTACAAAAC
2031042 TATAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTATTTACAAAACC
Found at i:2032288 original size:16 final size:18
Alignment explanation
Indices: 2032245--2032290 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
2032235 ACCACCGTTT
2032245 GCCGCCTGCTCTGCCACC
1 GCCGCCTGCTCTGCCACC
** *
2032263 GCCGATTGCT-TG-CTCC
1 GCCGCCTGCTCTGCCACC
2032279 GCCGCCTGCTCT
1 GCCGCCTGCTCT
2032291 TGCCTGGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (18 bp):
GCCGCCTGCTCTGCCACC
Found at i:2043446 original size:41 final size:37
Alignment explanation
Indices: 2043401--2043481 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
2043391 TTAAAAATAC
*
2043401 ATTATAATAAAAAACACTATCATAAATATAACAAATGTTTT
1 ATTAT-AT-AAAAACACTA--ATAAATATAACAAATATTTT
* * *
2043442 ATTATATTAAAATACTAATAAATATAATAAATATTTT
1 ATTATATAAAAACACTAATAAATATAACAAATATTTT
2043479 ATT
1 ATT
2043482 GTATTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 21 0.58
39 8 0.22
40 2 0.06
41 5 0.14
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (37 bp):
ATTATATAAAAACACTAATAAATATAACAAATATTTT
Found at i:2058494 original size:18 final size:18
Alignment explanation
Indices: 2058471--2058517 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
2058461 GGATATGTTC
2058471 TTTCTTTTTGATCCCCCT
1 TTTCTTTTTGATCCCCCT
* * *
2058489 TTTCTTTTTCTATCTCCTT
1 TTTCTTTTT-GATCCCCCT
2058508 TTTCTTTTTG
1 TTTCTTTTTG
2058518 GGTTGTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTCTTTTTGATCCCCCT
Found at i:2062711 original size:4 final size:4
Alignment explanation
Indices: 2062702--2062738 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2062692 ACAAACATCG
2062702 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2062739 TCCCTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2064842 original size:20 final size:20
Alignment explanation
Indices: 2064817--2064855 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2064807 TTAACAAAAA
2064817 AAAAAGCAATATTTATAGAG
1 AAAAAGCAATATTTATAGAG
**
2064837 AAAAAGGTATATTTATAGA
1 AAAAAGCAATATTTATAGA
2064856 AGATTTGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAAAGCAATATTTATAGAG
Done.