Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 118 of 187
Found at i:34963624 original size:224 final size:224
Alignment explanation
Indices: 34963234--34963681 Score: 878
Period size: 224 Copynumber: 2.0 Consensus size: 224
34963224 AACCCAAATC
34963234 GCATCCTTCTTACTTGCGGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGGTCCCATTT
1 GCATCCTTCTTACTTGCGGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGGTCCCATTT
34963299 CCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTT
66 CCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTT
*
34963364 GACATATTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAATCGA
131 GACATATTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCGA
*
34963429 CGTTTCAAGTCGTTGTACATTTTCGTGCT
196 CGTTTCAAGTCATTGTACATTTTCGTGCT
34963458 GCATCCTTCTTACTTGCGGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGGTCCCATTT
1 GCATCCTTCTTACTTGCGGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGGTCCCATTT
34963523 CCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTT
66 CCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTT
34963588 GACATATTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCGA
131 GACATATTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCGA
34963653 CGTTTCAAGTCATTGTACATTTTCGTGCT
196 CGTTTCAAGTCATTGTACATTTTCGTGCT
34963682 CCCCGGGTGG
Statistics
Matches: 222, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
224 222 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (224 bp):
GCATCCTTCTTACTTGCGGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGGTCCCATTT
CCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTT
GACATATTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCGA
CGTTTCAAGTCATTGTACATTTTCGTGCT
Found at i:34968614 original size:27 final size:27
Alignment explanation
Indices: 34968584--34968761 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34968574 ATATTGAGTC
* * * *
34968584 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
34968611 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34968638 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
34968666 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
34968693 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
34968720 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34968747 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34968762 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:34968723 original size:82 final size:81
Alignment explanation
Indices: 34968605--34968760 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34968595 TGCTATATAA
* *
34968605 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34968670 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
34968687 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34968751 CACTTAGTGC
65 CACTTAGTGC
34968761 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:34970346 original size:128 final size:128
Alignment explanation
Indices: 34970214--34970468 Score: 415
Period size: 128 Copynumber: 2.0 Consensus size: 128
34970204 GATGAGACCA
* *
34970214 TTTTTTTTT-CATCACCCTTCCTTTTCATTGTTTAATTACCATGCTCT-TTATTTTATTTTTCTT
1 TTTTTTTTTCCATCACCCTTCC-TTTCATTATTTAATTACCATGCT-TATTATTTTATTTTCCTT
* * *
34970277 AGCATACATCACTAGCATAACATGTTGGTGACATGTTTCCACCCATAGCATGCCCGGCCACTACT
64 ACCATACATCACTAACACAACATGTTGGTGACATGTTTCCACCCATAGCATGCCCGGCCACTACT
*
34970342 TTTTTTTTTCCATCACCCTTCCTTTCATTATTTAATTATCATGCTTATTATTTTATTTTCCTTAC
1 TTTTTTTTTCCATCACCCTTCCTTTCATTATTTAATTACCATGCTTATTATTTTATTTTCCTTAC
*
34970407 CATACATCACTAACACAACATGTTGGTGACATGTTTCCACCCATAGCATGGCCGGCCACTAC
66 CATACATCACTAACACAACATGTTGGTGACATGTTTCCACCCATAGCATGCCCGGCCACTAC
34970469 ATATTAGGGA
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
127 1 0.01
128 105 0.89
129 12 0.10
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.42
Consensus pattern (128 bp):
TTTTTTTTTCCATCACCCTTCCTTTCATTATTTAATTACCATGCTTATTATTTTATTTTCCTTAC
CATACATCACTAACACAACATGTTGGTGACATGTTTCCACCCATAGCATGCCCGGCCACTACT
Found at i:34975828 original size:40 final size:40
Alignment explanation
Indices: 34975784--34976011 Score: 393
Period size: 40 Copynumber: 5.7 Consensus size: 40
34975774 GCAAACACAT
* * *
34975784 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* *
34975824 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* *
34975864 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
34975904 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
34975944 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
34975984 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCATAGCCCGGATATAT
34976012 TCCAATGCTC
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
Found at i:34978862 original size:53 final size:52
Alignment explanation
Indices: 34978793--34978974 Score: 181
Period size: 54 Copynumber: 3.4 Consensus size: 52
34978783 TGTGATTCAT
* * * * **
34978793 GGTAAAATAACCGAAATGCCCTCGATAGGTAAAATGATAAAAATACCCCTGAG
1 GGTAAAATGACTGAAATACCCTC-AAAGGTAAAATGACCAAAATACCCCTGAG
*
34978846 GGTAAAATGACTGAAATACCCTCAAACGGTAAAATGACCAAAATA-CCTTCGAAG
1 GGTAAAATGACTGAAATACCCTCAAA-GGTAAAATGACCAAAATACCCCT-G-AG
* *
34978900 GGTAAAATGA-TCAAAATACCCTCAAAAGGTAAAATGACCGAAATACCCCCAT-AG
1 GGTAAAATGACT-GAAATACCCTC-AAAGGTAAAATGACCAAAATA-CCCC-TGAG
*
34978954 GGTAAAATGACTGATATACCC
1 GGTAAAATGACTGAAATACCC
34978975 CTAGGAATTG
Statistics
Matches: 108, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
52 5 0.05
53 38 0.35
54 58 0.54
55 4 0.04
56 2 0.02
57 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (52 bp):
GGTAAAATGACTGAAATACCCTCAAAGGTAAAATGACCAAAATACCCCTGAG
Found at i:34978957 original size:27 final size:27
Alignment explanation
Indices: 34978793--34978975 Score: 131
Period size: 27 Copynumber: 6.8 Consensus size: 27
34978783 TGTGATTCAT
* * *
34978793 GGTAAAATAACCGAAATGCCCTCGATA-
1 GGTAAAATGACCGAAATACCC-CCATAG
***
34978820 GGTAAAATGATAAAAATA-CCCC-TGAG
1 GGTAAAATGACCGAAATACCCCCAT-AG
* * * *
34978846 GGTAAAATGACTGAAATACCCTCAAAC
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
34978873 GGTAAAATGACCAAAATACCTTCGA-AG
1 GGTAAAATGACCGAAATACC-CCCATAG
* * * * *
34978900 GGTAAAATGATCAAAATACCCTCAAAA
1 GGTAAAATGACCGAAATACCCCCATAG
34978927 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
34978954 GGTAAAATGACTGATATACCCC
1 GGTAAAATGACCGAAATACCCC
34978976 TAGGAATTGA
Statistics
Matches: 120, Mismatches: 30, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
24 1 0.01
25 2 0.02
26 18 0.15
27 98 0.82
28 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:34978973 original size:81 final size:80
Alignment explanation
Indices: 34978793--34978964 Score: 211
Period size: 80 Copynumber: 2.1 Consensus size: 80
34978783 TGTGATTCAT
* * * * ** *
34978793 GGTAAAATAACCGAAATGCCCTCGATA-GGTAAAATGATAAAAATACCCCTGAGGGTAAAATGAC
1 GGTAAAATGACCAAAATACCTTCGA-AGGGTAAAATGATAAAAATACCCCAAAAGGTAAAATGAC
* *
34978857 TGAAATACCCTCAAAC
65 CGAAATACCCCCAAAC
*
34978873 GGTAAAATGACCAAAATACCTTCGAAGGGTAAAATGATCAAAATACCCTCAAAAGGTAAAATGAC
1 GGTAAAATGACCAAAATACCTTCGAAGGGTAAAATGATAAAAATACCC-CAAAAGGTAAAATGAC
* *
34978938 CGAAATACCCCCATAG
65 CGAAATACCCCCAAAC
34978954 GGTAAAATGAC
1 GGTAAAATGAC
34978965 TGATATACCC
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.01
80 41 0.53
81 36 0.46
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (80 bp):
GGTAAAATGACCAAAATACCTTCGAAGGGTAAAATGATAAAAATACCCCAAAAGGTAAAATGACC
GAAATACCCCCAAAC
Found at i:34979208 original size:26 final size:26
Alignment explanation
Indices: 34979144--34979215 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
34979134 ACAAAGAGTG
* *
34979144 TTACTGGCAGCTCTGCTGCGTTACTA
1 TTACTGGCAGCTTTGCTGCGTCACTA
*
34979170 TTACTGGCAGCTTTGCTGTGTCACTA
1 TTACTGGCAGCTTTGCTGCGTCACTA
* *
34979196 TTATTGGCAGCTTTACTGCG
1 TTACTGGCAGCTTTGCTGCG
34979216 ATATTGGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTCACTA
Found at i:34979363 original size:28 final size:28
Alignment explanation
Indices: 34979321--34979410 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 28
34979311 ACGACATTGT
*
34979321 ACTGATTACTATATTGGGCTAAGGACCAC
1 ACTG-TTACTGTATTGGGCTAAGGACCAC
34979350 ACTGTTACTGTATTGGGCTAA-GACCCACAC
1 ACTGTTACTGTATTGGGCTAAGGA--C-CAC
* * *
34979380 ACTATTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGACCAC
34979408 ACT
1 ACT
34979411 ACACTGATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
27 2 0.04
28 22 0.42
29 6 0.11
30 22 0.42
31 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGACCAC
Found at i:34979388 original size:30 final size:30
Alignment explanation
Indices: 34979325--34979409 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
34979315 CATTGTACTG
*
34979325 ATTACTATATTGGGCTAAGGA--C-CACACT
1 ATTACTGTATTGGGCTAA-GACCCACACACT
*
34979353 GTTACTGTATTGGGCTAAGACCCACACACT
1 ATTACTGTATTGGGCTAAGACCCACACACT
* *
34979383 ATTACTGTAATGGGCTAAGGCCCACAC
1 ATTACTGTATTGGGCTAAGACCCACAC
34979410 TACACTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.04
28 16 0.33
29 1 0.02
30 30 0.61
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (30 bp):
ATTACTGTATTGGGCTAAGACCCACACACT
Found at i:34979657 original size:26 final size:26
Alignment explanation
Indices: 34979615--34979681 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
34979605 TCTGCTTTTA
*
34979615 TTGTATTTT-TAACAATAAGTTGGGTT
1 TTGT-TTTTGTAATAATAAGTTGGGTT
34979641 TTGTTTTTGTAATAATAAGTTGGGTT
1 TTGTTTTTGTAATAATAAGTTGGGTT
34979667 TTGTTTTTGTAATAA
1 TTGTTTTTGTAATAA
34979682 GGCCTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 4 0.10
26 35 0.90
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.54
Consensus pattern (26 bp):
TTGTTTTTGTAATAATAAGTTGGGTT
Found at i:34982650 original size:50 final size:50
Alignment explanation
Indices: 34982462--34982708 Score: 185
Period size: 50 Copynumber: 4.8 Consensus size: 50
34982452 GATAATAACA
* ** * * *
34982462 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
34982511 TGCCAATGTCATATCCCAGATATGGCCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
34982561 TGCCCATGCCATGTCTCAAACATGGTCTTA-AGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* * * *
34982611 TGCCAACGCCATGTCCCAGACATGGTCTTATATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* * *
34982667 AGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34982709 TTACCCAAAT
Statistics
Matches: 156, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 72 0.46
51 1 0.01
53 5 0.03
56 39 0.25
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34984758 original size:22 final size:22
Alignment explanation
Indices: 34984733--34984775 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34984723 GCAATTATCC
34984733 AACATTCAGACAACATTTAATT
1 AACATTCAGACAACATTTAATT
** *
34984755 AACATTTGGATAACATTTAAT
1 AACATTCAGACAACATTTAAT
34984776 CAAAAATTGG
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:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (22 bp):
AACATTCAGACAACATTTAATT
Found at i:34984785 original size:22 final size:22
Alignment explanation
Indices: 34984741--34985124 Score: 406
Period size: 22 Copynumber: 17.7 Consensus size: 22
34984731 CCAACATTCA
* *
34984741 GACAACATTTAATTAACATTTG
1 GACAACATTTAATCAACAATTG
* *
34984763 GATAACATTTAATCAAAAATTG
1 GACAACATTTAATCAACAATTG
* * * *
34984785 GACAGCAATCAATCAA-AATTTT
1 GACAACATTTAATCAACAA-TTG
* *
34984807 GA-AAGAATTTAATCAAGAATTG
1 GACAA-CATTTAATCAACAATTG
* *
34984829 GACAACATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
*
34984851 GACAACATTTAATCAACAATTA
1 GACAACATTTAATCAACAATTG
* * * *
34984873 GACAACAGTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
*
34984895 GACAACATTTAATCAATAATTG
1 GACAACATTTAATCAACAATTG
* *
34984917 GACAACATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
34984939 G-----ATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* *
34984956 GACAACATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
34984978 GACAACATTT-ATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * * *
34984999 GGCAACATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
34985021 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* *
34985043 GACAACATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
*
34985065 AACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
34985087 GACAACATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
34985109 GACAACATTTAATCAA
1 GACAACATTTAATCAA
34985125 AAAAATTTAA
Statistics
Matches: 296, Mismatches: 56, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
17 15 0.05
21 21 0.07
22 256 0.86
23 4 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (22 bp):
GACAACATTTAATCAACAATTG
Found at i:34984832 original size:44 final size:44
Alignment explanation
Indices: 34984741--34985124 Score: 512
Period size: 44 Copynumber: 8.9 Consensus size: 44
34984731 CCAACATTCA
* * * *
34984741 GACAACATTTAATTAACATTTGGATAACATTTAATCAAAAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * * * * * *
34984785 GACAGCAATCAATCAAAATTTTGA-AAGAATTTAATCAAGAATTG
1 GACAACATTAAATCAACATTTGGACAA-CATTTAATCAACAATTG
*
34984829 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTA
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * * *
34984873 GACAACAGTCAATCAATATTTGGACAACATTTAATCAATAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
34984917 GACAACATTAAATCAACATTTGG-----ATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
34984956 GACAACATTAAATCAACATTTGGACAACATTT-ATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * *
34984999 GGCAACATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
*
34985043 GACAACATTAAATCAACATTTGAACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* *
34985087 GACAACATTCAATCAATATTTGGACAACATTTAATCAA
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAA
34985125 AAAAATTTAA
Statistics
Matches: 297, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.13
43 42 0.14
44 215 0.72
45 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
Found at i:34984867 original size:11 final size:11
Alignment explanation
Indices: 34984831--34985124 Score: 82
Period size: 11 Copynumber: 27.3 Consensus size: 11
34984821 AAGAATTGGA
*
34984831 CAACATTAAAT
1 CAACATTTAAT
*
34984842 CAACATTTGGA-
1 CAACATTT-AAT
34984853 CAACATTTAAT
1 CAACATTTAAT
*
34984864 CAACAATTAGA-
1 CAACATTTA-AT
* *
34984875 CAACAGTCAAT
1 CAACATTTAAT
* *
34984886 CAATATTTGGA-
1 CAACATTT-AAT
34984897 CAACATTTAAT
1 CAACATTTAAT
* **
34984908 CAATAATTGGA-
1 CAA-CATTTAAT
*
34984919 CAACATTAAAT
1 CAACATTTAAT
34984930 CAACA-TT--T
1 CAACATTTAAT
**
34984938 --GGATTTAAT
1 CAACATTTAAT
**
34984947 CAACAATTGGA-
1 CAAC-ATTTAAT
*
34984958 CAACATTAAAT
1 CAACATTTAAT
*
34984969 CAACATTTGGA-
1 CAACATTT-AAT
34984980 CAACATTT-AT
1 CAACATTTAAT
* ***
34984990 CAACAATTGGG
1 CAACATTTAAT
*
34985001 CAACATTCAAT
1 CAACATTTAAT
* *
34985012 CAATATTTGGA-
1 CAACATTT-AAT
34985023 CAACATTTAAT
1 CAACATTTAAT
**
34985034 CAACAATTGGA-
1 CAAC-ATTTAAT
*
34985045 CAACATTAAAT
1 CAACATTTAAT
34985056 CAACATTTGAA-
1 CAACATTT-AAT
34985067 CAACATTTAAT
1 CAACATTTAAT
**
34985078 CAACAATTGGA-
1 CAAC-ATTTAAT
*
34985089 CAACATTCAAT
1 CAACATTTAAT
* *
34985100 CAATATTTGGA-
1 CAACATTT-AAT
34985111 CAACATTTAAT
1 CAACATTTAAT
34985122 CAA
1 CAA
34985125 AAAAATTTAA
Statistics
Matches: 199, Mismatches: 56, Indels: 56
0.64 0.18 0.18
Matches are distributed among these distances:
6 1 0.01
7 2 0.01
8 1 0.01
9 2 0.01
10 31 0.16
11 138 0.69
12 24 0.12
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (11 bp):
CAACATTTAAT
Found at i:34985028 original size:170 final size:171
Alignment explanation
Indices: 34984769--34985110 Score: 490
Period size: 170 Copynumber: 2.0 Consensus size: 171
34984759 TTTGGATAAC
* * * *
34984769 ATTTAATCAAAAATTGGACAGCAATCAATCAAAATTTTGAAAGAATTTAATCAAGAATTGGACAA
1 ATTTAATCAAAAATTGGACAACAATAAATCAAAATTTGGAAAGAATTTAATCAACAATTGGACAA
* * *
34984834 CATTAAATCAACATTTGGACAACATTTAATCAACAATTAGACAACAGTCAATCAATATTTGGACA
66 CATTAAATCAACATTTGGACAACATTTAATCAACAATTAGACAACAGTAAATCAACATTTGAACA
*
34984899 ACATTTAATCAATAATTGGACAACATTAAATCAACATTTGG
131 ACATTTAATCAACAATTGGACAACATTAAATCAACATTTGG
* * * * *
34984940 ATTTAATCAACAATTGGACAACATTAAATCAACATTTGGACAA-CATTT-ATCAACAATTGGGCA
1 ATTTAATCAAAAATTGGACAACAATAAATCAAAATTTGGA-AAGAATTTAATCAACAATTGGACA
* * * *
34985003 ACATTCAATCAATATTTGGACAACATTTAATCAACAATTGGACAACATTAAATCAACATTTGAAC
65 ACATTAAATCAACATTTGGACAACATTTAATCAACAATTAGACAACAGTAAATCAACATTTGAAC
* *
34985068 AACATTTAATCAACAATTGGACAACATTCAATCAATATTTGG
130 AACATTTAATCAACAATTGGACAACATTAAATCAACATTTGG
34985110 A
1 A
34985111 CAACATTTAA
Statistics
Matches: 151, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
170 111 0.74
171 38 0.25
172 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (171 bp):
ATTTAATCAAAAATTGGACAACAATAAATCAAAATTTGGAAAGAATTTAATCAACAATTGGACAA
CATTAAATCAACATTTGGACAACATTTAATCAACAATTAGACAACAGTAAATCAACATTTGAACA
ACATTTAATCAACAATTGGACAACATTAAATCAACATTTGG
Found at i:34986011 original size:42 final size:42
Alignment explanation
Indices: 34985915--34986063 Score: 181
Period size: 43 Copynumber: 3.5 Consensus size: 42
34985905 GCCAACATCC
* * * * * *
34985915 CAGACGTGGTCTTTCATGTAATCAAAAAACGATGCCAATGTCT
1 CAGACATGGTCTTACACGTAATC-ATATACGACGCCAATGTCT
* *
34985958 CAGACAAGGTCTTACACGTAATCATATACGACGCCAATGTCC
1 CAGACATGGTCTTACACGTAATCATATACGACGCCAATGTCT
* * *
34986000 CAAACATGGTCTTACATGTAAATCATATACGACGCCAATATCT
1 CAGACATGGTCTTACACGT-AATCATATACGACGCCAATGTCT
34986043 CAGACATGGTCTTACACGTAA
1 CAGACATGGTCTTACACGTAA
34986064 ATCTCAAATC
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 33 0.37
43 57 0.63
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
CAGACATGGTCTTACACGTAATCATATACGACGCCAATGTCT
Found at i:34986064 original size:43 final size:43
Alignment explanation
Indices: 34985943--34986066 Score: 187
Period size: 43 Copynumber: 2.9 Consensus size: 43
34985933 TAATCAAAAA
* *
34985943 ACGATGCCAATGTCTCAGACAAGGTCTTACACGT-AATCATAT
1 ACGACGCCAATGTCTCAGACATGGTCTTACACGTAAATCATAT
* * *
34985985 ACGACGCCAATGTCCCAAACATGGTCTTACATGTAAATCATAT
1 ACGACGCCAATGTCTCAGACATGGTCTTACACGTAAATCATAT
*
34986028 ACGACGCCAATATCTCAGACATGGTCTTACACGTAAATC
1 ACGACGCCAATGTCTCAGACATGGTCTTACACGTAAATC
34986067 TCAAATCGGG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 29 0.40
43 43 0.60
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
ACGACGCCAATGTCTCAGACATGGTCTTACACGTAAATCATAT
Found at i:34988073 original size:42 final size:43
Alignment explanation
Indices: 34987990--34988075 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
34987980 TGTTATCCTA
* * *
34987990 GAAAAAATAATTTAAAAGGAGAAGAAGATAATCTTGGGTTGTT
1 GAAAAAATAATTTAAAAGAAGAAGAAGATAAACTTGCGTTGTT
* *
34988033 GAAAAAATAATTTAAAA-AAGGAGAAGCTAAACTTGCGTTGTT
1 GAAAAAATAATTTAAAAGAAGAAGAAGATAAACTTGCGTTGTT
34988075 G
1 G
34988076 GATTTACCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (43 bp):
GAAAAAATAATTTAAAAGAAGAAGAAGATAAACTTGCGTTGTT
Found at i:34989281 original size:15 final size:15
Alignment explanation
Indices: 34989257--34989288 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34989247 CTTAATTTCA
*
34989257 TTAGTTTAATTTAAC
1 TTAGTCTAATTTAAC
34989272 TTAGTCTAATTTAAC
1 TTAGTCTAATTTAAC
34989287 TT
1 TT
34989289 CTACAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAGTCTAATTTAAC
Found at i:34990996 original size:29 final size:30
Alignment explanation
Indices: 34990943--34991012 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
34990933 ATAGCCGAAG
* * *
34990943 CCATCCTTTTTCATAGTTAGATGGTTGTCA
1 CCATCCCTTTTAATAGTTAGATGGTCGTCA
*
34990973 CCATCCCTTTTAATTGTT-GATGGTCGTCA
1 CCATCCCTTTTAATAGTTAGATGGTCGTCA
*
34991002 CCATCTCTTTT
1 CCATCCCTTTT
34991013 CATAATCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.44
Consensus pattern (30 bp):
CCATCCCTTTTAATAGTTAGATGGTCGTCA
Found at i:34999900 original size:30 final size:29
Alignment explanation
Indices: 34999866--35000088 Score: 147
Period size: 29 Copynumber: 7.6 Consensus size: 29
34999856 TAACCAAAGT
34999866 TATCCCTTTTCATAGTTTGATAGTCGAAGC
1 TATCCCTTTTCATA-TTTGATAGTCGAAGC
* * *
34999896 TATCCCTTTTAATAATTTGATGGTCGTTA-C
1 TATCCCTTTTCAT-ATTTGATAGTCG-AAGC
* * * *
34999926 CAT-CCTTTTCCATTGTTTGA-AGGCCGTCA-C
1 TATCCCTTTT-CA-TATTTGATA-GTCG-AAGC
* *
34999956 CATCCCTTTTCATAGTTTGATGGTC-ATTA-C
1 TATCCCTTTTCATA-TTTGATAGTCGA--AGC
* * * * *
34999986 CATCCCTTTTCATAATCGATAGCCAAAGC
1 TATCCCTTTTCATATTTGATAGTCGAAGC
35000015 TATCCCTTTTCATATTTGATAG-CTGAAGC
1 TATCCCTTTTCATATTTGATAGTC-GAAGC
35000044 TATCCCTTTTCATATTTGATAG-CTGAAGC
1 TATCCCTTTTCATATTTGATAGTC-GAAGC
*
35000073 TATCCTTTTTCATATT
1 TATCCCTTTTCATATT
35000089 CAATAACCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.01
29 81 0.51
30 66 0.42
31 9 0.06
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (29 bp):
TATCCCTTTTCATATTTGATAGTCGAAGC
Found at i:34999944 original size:60 final size:60
Alignment explanation
Indices: 34999867--35000086 Score: 186
Period size: 60 Copynumber: 3.7 Consensus size: 60
34999857 AACCAAAGTT
* * * *
34999867 ATCCCTTTTCATAGTTTGATAGTCGAAGCTATCCCTTTTAATAATTTGATGGTCGTTACC
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATTACC
* * *
34999927 AT-CCTTTTCCATTGTTTGA-AGGCCGTCA-CCATCCCTTTTCATAGTTTGATGGTCATTACC
1 ATCCCTTTT-CATTGTTTGATA-GCCG-AAGCTATCCCTTTTCATAATTTGATGGTCATTACC
** * * * * *
34999987 ATCCCTTTTCA-TAATCGATAGCCAAAGCTATCCCTTTTCAT-ATTTGATAG-C-TGAAGCT
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCAT-TA-CC
* * *
35000045 ATCCCTTTTCA-TATTTGATAGCTGAAGCTATCCTTTTTCATA
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATA
35000087 TTCAATAACC
Statistics
Matches: 129, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 45 0.35
59 27 0.21
60 47 0.36
61 7 0.05
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (60 bp):
ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATTACC
Found at i:35000035 original size:29 final size:29
Alignment explanation
Indices: 34999987--35000110 Score: 158
Period size: 29 Copynumber: 4.3 Consensus size: 29
34999977 GGTCATTACC
*
34999987 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* **
35000016 ATCCCTTTTCATATTTGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* **
35000045 ATCCCTTTTCATATTTGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* * *
35000074 ATCCTTTTTCATATTCAATAACCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
35000103 ATCCCTTT
1 ATCCCTTT
35000111 GCATTCATCG
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCAAAGCT
Found at i:35003152 original size:16 final size:17
Alignment explanation
Indices: 35003120--35003152 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35003110 TTTAGATCAA
*
35003120 GAAAATTGAAGAAAATG
1 GAAAATTGAACAAAATG
35003137 GAAAATT-AACAAAATG
1 GAAAATTGAACAAAATG
35003153 CCCCTGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAATTGAACAAAATG
Found at i:35003363 original size:29 final size:29
Alignment explanation
Indices: 35003329--35003573 Score: 262
Period size: 29 Copynumber: 8.4 Consensus size: 29
35003319 AGCTATCGAT
*
35003329 TATGAAAAGGGATGGTGACGACCATCAAG
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * * * * * *
35003358 TTTGAAAAGGTATAGCT-TCGGCTATCAAA
1 TATGAAAAGGGAT-GGTGACGACCATCAAC
* * * * *
35003387 TATGAAAAGGGATAGCT-TCGACTATCGAT
1 TATGAAAAGGGAT-GGTGACGACCATCAAC
*
35003416 TATGAAAATGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
35003445 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
35003474 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * * *
35003503 TATGAAAAGGGATAGCT-TCGACTATCGAC
1 TATGAAAAGGGAT-GGTGACGACCATCAAC
* *
35003532 TATGAAAAGGGATGGTGACAACCATCGAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
35003561 TATGAAAAGGGAT
1 TATGAAAAGGGAT
35003574 AGCTTCGACT
Statistics
Matches: 185, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
28 4 0.02
29 177 0.96
30 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:35003472 original size:87 final size:87
Alignment explanation
Indices: 35003301--35003597 Score: 341
Period size: 87 Copynumber: 3.4 Consensus size: 87
35003291 CCCTCAGATA
* * *
35003301 ATGAAAAGGGATAGCTTC-AGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAGTTTGAAA
1 ATGAAAAGGGATAGCTTCGA-CTATCGACTATGAAAAGGGATGGTGACGACCATCAACTATGAAA
* * * * * *
35003365 AGGTATAGCT-TCGGCTATCAAAT
65 AGGGAT-GGTGACGACCATCAACT
* *
35003388 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAATGGATGGTGACGACCATCAACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCAACTATGAAAA
35003453 GGGATGGTGACGACCATCAACT
66 GGGATGGTGACGACCATCAACT
* * * * * * * *
35003475 ATGAAAAGGGAT-GGTGACGACCATCAACTATGAAAAGGGATAGCT-TCGACTATCGACTATGAA
1 ATGAAAAGGGATAGCT-TCGACTATCGACTATGAAAAGGGAT-GGTGACGACCATCAACTATGAA
* *
35003538 AAGGGATGGTGACAACCATCGACT
64 AAGGGATGGTGACGACCATCAACT
35003562 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
35003598 AAGATGGTTT
Statistics
Matches: 180, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
86 4 0.02
87 171 0.95
88 5 0.03
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCAACTATGAAAA
GGGATGGTGACGACCATCAACT
Found at i:35003605 original size:58 final size:58
Alignment explanation
Indices: 35003381--35003597 Score: 337
Period size: 58 Copynumber: 3.7 Consensus size: 58
35003371 AGCTTCGGCT
* * *
35003381 ATCAAATATGAAAAGGGATAGCTTCGACTATCGATTATGAAAATGGATGGTGACGACC
1 ATCAACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACC
* * * *
35003439 ATCAACTATGAAAAGGGAT-GGTGACGACCATCAACTATGAAAAGGGATGGTGACGACC
1 ATCAACTATGAAAAGGGATAGCT-TCGACTATCGACTATGAAAAGGGATGGTGACGACC
*
35003497 ATCAACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACAACC
1 ATCAACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACC
*
35003555 ATCGACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
1 ATCAACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
35003598 AAGATGGTTT
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
57 2 0.01
58 140 0.97
59 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (58 bp):
ATCAACTATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACC
Found at i:35003612 original size:29 final size:29
Alignment explanation
Indices: 35003301--35003612 Score: 230
Period size: 29 Copynumber: 10.8 Consensus size: 29
35003291 CCCTCAGATA
* * *
35003301 ATGAAAAGGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATGGTTTCGA-CTATCGACT
** * * *
35003330 ATGAAAAGGGATGGTGACGACCATCAAGT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* * * * * * *
35003359 TTGAAAAGGTATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* * *
35003388 ATGAAAAGGGATAGCTTCGACTATCGATT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* ** * *
35003417 ATGAAAATGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** * *
35003446 ATGAAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** * *
35003475 ATGAAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* *
35003504 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** * *
35003533 ATGAAAAGGGATGGTGACAACCATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* *
35003562 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** *
35003591 ATGAAAAAAGATGGTTTTGACT
1 ATGAAAAGGGATGGTTTCGACT
35003613 TTCAATTAAA
Statistics
Matches: 229, Mismatches: 53, Indels: 2
0.81 0.19 0.01
Matches are distributed among these distances:
29 228 1.00
30 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCGACTATCGACT
Found at i:35007767 original size:25 final size:24
Alignment explanation
Indices: 35007710--35007844 Score: 108
Period size: 25 Copynumber: 5.5 Consensus size: 24
35007700 CCACAACTCA
* * *
35007710 TGTGAGCATACCAATTTACAGGTCA
1 TGTGAGCATACCGA-TTACAGCTCG
**
35007735 TGAAAGCATACCGATCTACAGCTCG
1 TGTGAGCATACCGAT-TACAGCTCG
*** * *
35007760 TGTGAGCATAAATATTATAGGTCG
1 TGTGAGCATACCGATTACAGCTCG
*
35007784 TGAGAGCATACCGATCTACAGCTCG
1 TGTGAGCATACCGAT-TACAGCTCG
*
35007809 AGTGAGCATACCGATTCACAGCTCG
1 TGTGAGCATACCGATT-ACAGCTCG
* *
35007834 TATAAGCATAC
1 TGTGAGCATAC
35007845 ATGTACAAGA
Statistics
Matches: 84, Mismatches: 23, Indels: 6
0.74 0.20 0.05
Matches are distributed among these distances:
24 20 0.24
25 64 0.76
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (24 bp):
TGTGAGCATACCGATTACAGCTCG
Found at i:35007792 original size:49 final size:49
Alignment explanation
Indices: 35007710--35007819 Score: 159
Period size: 49 Copynumber: 2.2 Consensus size: 49
35007700 CCACAACTCA
35007710 TGTGAGCATACCAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
1 TGTGAGCATA-CAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
* * *
35007760 TGTGAGCATA-AATATTATAGGTCGTGAGAGCATACCGATCTACAGCTCG
1 TGTGAGCATACAAT-TTACAGGTCATGAAAGCATACCGATCTACAGCTCG
*
35007809 AGTGAGCATAC
1 TGTGAGCATAC
35007820 CGATTCACAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 3 0.06
49 41 0.76
50 10 0.19
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (49 bp):
TGTGAGCATACAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
Found at i:35008634 original size:14 final size:14
Alignment explanation
Indices: 35008615--35008643 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35008605 TTTGTAAGAT
35008615 TATGGTTTCATGAA
1 TATGGTTTCATGAA
35008629 TATGGTTTCATGAA
1 TATGGTTTCATGAA
35008643 T
1 T
35008644 CTTACGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TATGGTTTCATGAA
Found at i:35017988 original size:25 final size:25
Alignment explanation
Indices: 35017954--35018048 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
35017944 GCAGACACAC
* *
35017954 TACAGCTCGT-ATGAGCTTACCTATT
1 TACAGCTCGTGA-GAGCATACCGATT
35017979 TACAGCTCGTGAGAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCGATT
* ** *
35018004 TGCAGCTCAAGAAAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCGATT
* * *
35018029 CACAGCTTGTGTGAGCATAC
1 TACAGCTCGTGAGAGCATAC
35018049 ATGTACTAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
TACAGCTCGTGAGAGCATACCGATT
Found at i:35024444 original size:67 final size:67
Alignment explanation
Indices: 35024335--35024468 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
35024325 AAAACTTATC
35024335 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
35024400 TT
66 TT
* * *
35024402 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAATGAATTATATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
35024467 TT
66 TT
35024469 TAGTGAGATA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (67 bp):
GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
TT
Found at i:35036093 original size:14 final size:14
Alignment explanation
Indices: 35036074--35036101 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35036064 CCAATTTATT
35036074 AATGAATTATTAAA
1 AATGAATTATTAAA
35036088 AATGAATTATTAAA
1 AATGAATTATTAAA
35036102 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:35041912 original size:27 final size:27
Alignment explanation
Indices: 35041882--35042059 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
35041872 ATATTGAGCC
* *
35041882 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
35041909 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
35041936 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
35041964 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
35041991 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
35042018 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
35042045 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35042060 GTACAATTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.02
27 101 0.80
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:35042021 original size:82 final size:81
Alignment explanation
Indices: 35041903--35042058 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
35041893 TGCTATATAA
* * *
35041903 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCA-AACTCGC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACAAAGT-AGAA-TCGC
35041967 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
35041985 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACAAAGTAGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACAAAGTAGAATCGCA
35042049 CACTTAGTGC
65 CACTTAGTGC
35042059 TGTACAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACAAAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:35050099 original size:27 final size:27
Alignment explanation
Indices: 35050069--35050245 Score: 144
Period size: 27 Copynumber: 6.5 Consensus size: 27
35050059 ATATTGAGCC
* * *
35050069 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCCACATAATCAACT
* * *
35050096 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACATAATCAACT
* *
35050123 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACATAAT-CAACT
* ** *
35050151 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAATCAACT
* **
35050178 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CATAATCAACT
* *
35050205 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCCACATAA-TCA-ACT
35050232 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35050246 TGTACAATTT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.02
27 95 0.78
28 24 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAATCAACT
Found at i:35060229 original size:14 final size:15
Alignment explanation
Indices: 35060199--35060232 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35060189 CTGTTTAGGG
*
35060199 TTTCATTTCTATCCA
1 TTTCATTGCTATCCA
35060214 TTTCATTGCT-TCCA
1 TTTCATTGCTATCCA
35060228 TTTCA
1 TTTCA
35060233 CTTTTCTTCA
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:35061966 original size:17 final size:17
Alignment explanation
Indices: 35061946--35062038 Score: 83
Period size: 17 Copynumber: 5.9 Consensus size: 17
35061936 TTATTTTCTA
35061946 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
35061963 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
35061977 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
35061993 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
35062009 TATCAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
35062024 TATAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
35062039 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 11 0.19
16 14 0.24
17 22 0.37
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:35061974 original size:30 final size:30
Alignment explanation
Indices: 35061939--35062056 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
35061929 TATTGTTTTA
*
35061939 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* *
35061969 TTTTCTAAATAATTTTTCTAAATTTATTAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* * *
35061999 TATT-AAAATTTATCAG-TAT-TAAATTTATAAG
1 TTTTCTAAA--TA--AGTTTTCTAAATTTATAAG
* *
35062030 TTTTCTAAAAAAGTGTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
35062057 TATTAATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
28 2 0.03
29 4 0.06
30 40 0.59
31 16 0.24
32 5 0.07
33 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:35061989 original size:13 final size:13
Alignment explanation
Indices: 35061939--35061991 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
35061929 TATTGTTTTA
*
35061939 TTTTCTATATAAG
1 TTTTCTAAATAAG
35061952 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
35061969 TTTTCTAAATAAT
1 TTTTCTAAATAAG
35061982 TTTTCTAAAT
1 TTTTCTAAAT
35061992 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:35062022 original size:15 final size:15
Alignment explanation
Indices: 35061987--35062026 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
35061977 ATAATTTTTC
*
35061987 TAAATTTATTAGTAT
1 TAAATTTATCAGTAT
35062002 TAAAATTTATCAGTAT
1 T-AAATTTATCAGTAT
35062018 TAAATTTAT
1 TAAATTTAT
35062027 AAGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (15 bp):
TAAATTTATCAGTAT
Found at i:35062029 original size:61 final size:61
Alignment explanation
Indices: 35061957--35062104 Score: 215
Period size: 61 Copynumber: 2.4 Consensus size: 61
35061947 ATAAGTTTTC
* * *
35061957 TAAATTTATAAGTTTTCTAAATAATTTTTCTAAATTTATTAGTATTAAAATTTATCAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
35062018 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAAATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
35062079 CAATTTTATAATTTTTCTAAATAATT
1 TAAATTTATAAGTTTTCTAAATAATT
35062105 ATATATTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:35062299 original size:21 final size:21
Alignment explanation
Indices: 35062273--35062349 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
35062263 TAACATAATA
* *
35062273 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
35062294 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
** *
35062315 CATAACTTA-ATACACCACTTA
1 CATAACTTACATA-ATAACTTC
*
35062336 AATAACTTACATAA
1 CATAACTTACATAA
35062350 CTTACATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 37 0.79
22 7 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:35062349 original size:9 final size:9
Alignment explanation
Indices: 35062331--35062799 Score: 167
Period size: 9 Copynumber: 54.3 Consensus size: 9
35062321 TTAATACACC
*
35062331 ACTTAAATA
1 ACTTACATA
35062340 ACTTACATA
1 ACTTACATA
35062349 ACTTACATA
1 ACTTACATA
*
35062358 GCTTACATA
1 ACTTACATA
*
35062367 AC-T-CATT
1 ACTTACATA
35062374 ACTTACATA
1 ACTTACATA
*
35062383 ACATACATA
1 ACTTACATA
**
35062392 AAATAC--A
1 ACTTACATA
35062399 ACTTACATA
1 ACTTACATA
*
35062408 TCTTACATA
1 ACTTACATA
35062417 A--TACATA
1 ACTTACATA
*
35062424 ACTTACAGA
1 ACTTACATA
* *
35062433 AATTAAATA
1 ACTTACATA
* *
35062442 ACCTGCATA
1 ACTTACATA
*
35062451 A--AACATA
1 ACTTACATA
* *
35062458 GCCTACATA
1 ACTTACATA
*
35062467 ACTTATATA
1 ACTTACATA
* *
35062476 GCTTTCATA
1 ACTTACATA
**
35062485 AAGTAC--A
1 ACTTACATA
35062492 ACTTACATA
1 ACTTACATA
**
35062501 TTTTACATAAA
1 ACTTACAT--A
35062512 ACTTACATA
1 ACTTACATA
35062521 A--TACATA
1 ACTTACATA
*
35062528 ACTTAC-TT
1 ACTTACATA
35062536 ACATAATACA-A
1 AC-T--TACATA
*
35062547 CACTTACACA
1 -ACTTACATA
*
35062557 ACTTAAATA
1 ACTTACATA
*
35062566 ACTTGCATA
1 ACTTACATA
35062575 A--TACATA
1 ACTTACATA
35062582 GAC-TACATA
1 -ACTTACATA
*
35062591 ACTTA-ATTTG
1 ACTTACA--TA
*
35062601 CCTTACATA
1 ACTTACATA
35062610 A--TACA-A
1 ACTTACATA
*
35062616 CACTTACACA
1 -ACTTACATA
*
35062626 ACTTAAATA
1 ACTTACATA
*
35062635 ACTTGCATA
1 ACTTACATA
35062644 A--TACATA
1 ACTTACATA
* *
35062651 GCCTACATA
1 ACTTACATA
*
35062660 ACTTA-ATTTG
1 ACTTACA--TA
*
35062670 CCTTACATA
1 ACTTACATA
**
35062679 A--TACAGC
1 ACTTACATA
35062686 ACTTACATA
1 ACTTACATA
35062695 ACTTACATA
1 ACTTACATA
**
35062704 GGTTACATA
1 ACTTACATA
35062713 A--TACATA
1 ACTTACATA
*
35062720 ACTTAAATA
1 ACTTACATA
*
35062729 ACTTATATA
1 ACTTACATA
35062738 A--TACATA
1 ACTTACATA
35062745 ACTTACATA
1 ACTTACATA
* *
35062754 ATTTACTTA
1 ACTTACATA
35062763 A--TACATA
1 ACTTACATA
* *
35062770 A-ATATATA
1 ACTTACATA
* *
35062778 TCATATCATA
1 ACTTA-CATA
35062788 ACTTACATA
1 ACTTACATA
35062797 ACT
1 ACT
35062800 CATTTAATTT
Statistics
Matches: 336, Mismatches: 80, Indels: 88
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.00
7 72 0.21
8 15 0.04
9 215 0.64
10 18 0.05
11 13 0.04
12 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:35062380 original size:16 final size:17
Alignment explanation
Indices: 35062340--35062753 Score: 77
Period size: 16 Copynumber: 24.1 Consensus size: 17
35062330 CACTTAAATA
35062340 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
35062357 AGCTTACATAAC-T-CATT
1 A-CTTACATAACTTACA-T
*
35062374 ACTTACATAACATACAT
1 ACTTACATAACTTACAT
**
35062391 AAAATAC--AACTTACAT
1 -ACTTACATAACTTACAT
35062407 ATCTTACATAA--TACAT
1 A-CTTACATAACTTACAT
* * *
35062423 AACTTACAGAAATTAAAT
1 -ACTTACATAACTTACAT
* * *
35062441 AACCTGCATAA--AACAT
1 -ACTTACATAACTTACAT
* *
35062457 AGCCTACATAACTTATAT
1 A-CTTACATAACTTACAT
* **
35062475 AGCTTTCATAAAGTACA-
1 A-CTTACATAACTTACAT
**
35062492 ACTTACATATTTTACAT
1 ACTTACATAACTTACAT
* *
35062509 AAAACTTACATAATACATAACTT
1 ---ACTTACAT-A-AC-TTACAT
*
35062532 ACTTACATAA--TACAAC
1 ACTTACATAACTTAC-AT
* *
35062548 ACTTACACAACTTAAAT
1 ACTTACATAACTTACAT
*
35062565 AACTTGCATAA--TACAT
1 -ACTTACATAACTTACAT
35062581 AGAC-TACATAACTTA-ATTT
1 --ACTTACATAACTTACA--T
* *
35062600 GCCTTACATAA--TACAAC
1 -ACTTACATAACTTAC-AT
* *
35062617 ACTTACACAACTTAAAT
1 ACTTACATAACTTACAT
*
35062634 AACTTGCATAA--TACAT
1 -ACTTACATAACTTACAT
*
35062650 AGCCTACATAACTTA-ATTT
1 A-CTTACATAACTTACA--T
* *
35062669 GCCTTACATAA--TACAGC
1 -ACTTACATAACTTACA-T
35062686 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
*
35062703 AGGTTACATAA--TACAT
1 A-CTTACATAACTTACAT
* *
35062719 AACTTAAATAACTTATAT
1 -ACTTACATAACTTACAT
*
35062737 A-ATACATAACTTACAT
1 ACTTACATAACTTACAT
35062753 A
1 A
35062754 ATTTACTTAA
Statistics
Matches: 285, Mismatches: 63, Indels: 99
0.64 0.14 0.22
Matches are distributed among these distances:
15 5 0.02
16 130 0.46
17 21 0.07
18 89 0.31
19 19 0.07
20 16 0.06
21 1 0.00
23 4 0.01
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (17 bp):
ACTTACATAACTTACAT
Found at i:35062426 original size:25 final size:25
Alignment explanation
Indices: 35062343--35062770 Score: 114
Period size: 25 Copynumber: 17.3 Consensus size: 25
35062333 TTAAATAACT
*
35062343 TACATAACTTACATAGCTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
35062368 CT-CATTACTTACATAACATACATAA
1 -TACATAACTTACATAACTTACATAA
* * * *
35062393 AATACAACTTACATATCTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
35062418 TACATAACTTACAGAAATTAAATAA
1 TACATAACTTACATAACTTACATAA
* * * *
35062443 CCTGCATAA--AACATAGCCTACATAA
1 --TACATAACTTACATAACTTACATAA
* * * ** *
35062468 CTTATATAGCTTTCATAAAGTACA-ACT
1 --TACATAACTTACATAACTTACATA-A
**
35062495 TACATATTTTACATAAAACTTACATAA
1 TACATAACTTACAT--AACTTACATAA
35062522 TACATAAC-T---T-ACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
35062542 TACA-ACACTTACACAACTTAAATAA
1 TACATA-ACTTACATAACTTACATAA
*
35062567 CTTGCATAA--TACATAGAC-TACATAA
1 --TACATAACTTACATA-ACTTACATAA
**
35062592 CTTA-ATTTGCCTTACATAA--TACA-ACA
1 --TACA--TAACTTACATAACTTACATA-A
* * *
35062618 CTTACACAACTTAAATAACTTGCATAA
1 --TACATAACTTACATAACTTACATAA
* *
35062645 TACATAGCCTACATAACTTA-AT--
1 TACATAACTTACATAACTTACATAA
** * *
35062667 T---TGCCTTACATAA--TACAGCACT
1 TACATAACTTACATAACTTACA-TA-A
**
35062689 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
35062714 TACATAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
35062739 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
35062764 TACATAA
1 TACATAA
35062771 ATATATATCA
Statistics
Matches: 287, Mismatches: 77, Indels: 77
0.65 0.17 0.17
Matches are distributed among these distances:
17 2 0.01
18 1 0.00
19 10 0.03
20 16 0.06
21 1 0.00
22 2 0.01
23 1 0.00
24 3 0.01
25 186 0.65
26 16 0.06
27 40 0.14
28 9 0.03
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:35062614 original size:69 final size:69
Alignment explanation
Indices: 35062533--35062733 Score: 314
Period size: 69 Copynumber: 2.9 Consensus size: 69
35062523 ACATAACTTA
35062533 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
35062598 TTGC
66 TTGC
*
35062602 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATAACTTAAT
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
35062667 TTGC
66 TTGC
* * * ** * *
35062671 CTTACATAATACAGCACTTACATAACTTACATAGGTTACATAATACATA-ACTTAAATAACTTA
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGAC-TACATAACTTA
35062734 TATAATACAT
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
68 1 0.01
69 121 0.99
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (69 bp):
CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
TTGC
Found at i:35062724 original size:34 final size:34
Alignment explanation
Indices: 35062533--35062733 Score: 173
Period size: 34 Copynumber: 5.9 Consensus size: 34
35062523 ACATAACTTA
* *
35062533 CTTACATAATACA-ACACTTACACAACTTAAATAA
1 CTTACATAATACATACACTTACATAACTT-AATAG
* * *
35062567 CTTGCATAATACATAGAC-TACATAACTTAATTTG
1 CTTACATAATACATACACTTACATAACTTAA-TAG
* *
35062601 CCTTACATAATACA-ACACTTACACAACTTAAATAA
1 -CTTACATAATACATACACTTACATAACTT-AATAG
* *
35062636 CTTGCATAATACATAGC-C-TACATAACTTAATTTG
1 CTTACATAATACATA-CACTTACATAACTTAA-TAG
*
35062670 CCTTACATAATACA-GCACTTACATAACTTACATAG
1 -CTTACATAATACATACACTTACATAACTTA-ATAG
* *
35062705 GTTACATAATACATA-ACTTAAATAACTTA
1 CTTACATAATACATACACTTACATAACTTA
35062734 TATAATACAT
Statistics
Matches: 134, Mismatches: 20, Indels: 26
0.74 0.11 0.14
Matches are distributed among these distances:
33 5 0.04
34 73 0.54
35 52 0.39
36 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (34 bp):
CTTACATAATACATACACTTACATAACTTAATAG
Found at i:35065570 original size:142 final size:142
Alignment explanation
Indices: 35065314--35065593 Score: 533
Period size: 142 Copynumber: 2.0 Consensus size: 142
35065304 TGTGAACATT
35065314 TTTTTAACATAGTGAGTACAAACAAATATTGAGATCTCGTTCGCGCTCCCGAAGAACACAACATC
1 TTTTTAACATAGTGAGTACAAACAAATATTGAGATCTCGTTCGCGCTCCCGAAGAACACAACATC
*
35065379 GAGATATCAATAAGTTGTTCATAGAATCTTTTCATGAATGGTTAAGCCAAACGGTATGCAATTGG
66 GAGATATCAATAAGTTGTTCACAGAATCTTTTCATGAATGGTTAAGCCAAACGGTATGCAATTGG
*
35065444 ATCTTTCATCAA
131 AGCTTTCATCAA
35065456 TTTTTAACATAGTGAGTACAAACAAATATTGAGATCTCGTTCGCGCTCCCGAAGAACACAACATC
1 TTTTTAACATAGTGAGTACAAACAAATATTGAGATCTCGTTCGCGCTCCCGAAGAACACAACATC
*
35065521 GAGATATCAATAAGTTGTTCACAGAATCTTTTCATGAATGGTTAAGCCAAACGGTATGTAATTGG
66 GAGATATCAATAAGTTGTTCACAGAATCTTTTCATGAATGGTTAAGCCAAACGGTATGCAATTGG
35065586 AGCTTTCA
131 AGCTTTCA
35065594 CCGACAAATA
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (142 bp):
TTTTTAACATAGTGAGTACAAACAAATATTGAGATCTCGTTCGCGCTCCCGAAGAACACAACATC
GAGATATCAATAAGTTGTTCACAGAATCTTTTCATGAATGGTTAAGCCAAACGGTATGCAATTGG
AGCTTTCATCAA
Found at i:35067161 original size:98 final size:98
Alignment explanation
Indices: 35066987--35067186 Score: 373
Period size: 98 Copynumber: 2.0 Consensus size: 98
35066977 ATTTACTTTC
35066987 TTAACTTGTGTTTTTTGTAGGCGAGATTTGCTCTAGAGGACTCCGATACTTATGTAAAGAAGGCA
1 TTAACTTGTGTTTTTTGTAGGCGAGATTTGCTCTAGAGGACTCCGATACTTATGTAAAGAAGGCA
35067052 TTGGGAAAAAGATGGAGAGACCATAAGAGCACT
66 TTGGGAAAAAGATGGAGAGACCATAAGAGCACT
* * *
35067085 TTAAGTTGTGTTTTTTGTAGGCGAGATTTGCTCTAGAGGTCTCCGATGCTTATGTAAAGAAGGCA
1 TTAACTTGTGTTTTTTGTAGGCGAGATTTGCTCTAGAGGACTCCGATACTTATGTAAAGAAGGCA
35067150 TTGGGAAAAAGATGGAGAGACCATAAGAGCACT
66 TTGGGAAAAAGATGGAGAGACCATAAGAGCACT
35067183 TTAA
1 TTAA
35067187 AGAAAGACTA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (98 bp):
TTAACTTGTGTTTTTTGTAGGCGAGATTTGCTCTAGAGGACTCCGATACTTATGTAAAGAAGGCA
TTGGGAAAAAGATGGAGAGACCATAAGAGCACT
Found at i:35067594 original size:76 final size:76
Alignment explanation
Indices: 35067468--35067614 Score: 294
Period size: 76 Copynumber: 1.9 Consensus size: 76
35067458 AGGTATTTTG
35067468 AATTTTTTAATACTGGCAGATATTTATTACTTTCTATCAAATAATATTTTTACTATTGTATTGTA
1 AATTTTTTAATACTGGCAGATATTTATTACTTTCTATCAAATAATATTTTTACTATTGTATTGTA
35067533 GGAACTATCTC
66 GGAACTATCTC
35067544 AATTTTTTAATACTGGCAGATATTTATTACTTTCTATCAAATAATATTTTTACTATTGTATTGTA
1 AATTTTTTAATACTGGCAGATATTTATTACTTTCTATCAAATAATATTTTTACTATTGTATTGTA
35067609 GGAACT
66 GGAACT
35067615 GTCGTCCGGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (76 bp):
AATTTTTTAATACTGGCAGATATTTATTACTTTCTATCAAATAATATTTTTACTATTGTATTGTA
GGAACTATCTC
Found at i:35068249 original size:66 final size:65
Alignment explanation
Indices: 35068142--35068311 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 65
35068132 GAACAAATTA
* * * *
35068142 CACAACTTAAAACGGAGGCAGCATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
*
35068206 T
65 G
*
35068207 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
35068272 G
65 G
* * * *
35068273 CGCAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
35068312 CTGCAGTGAG
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 35 0.38
66 54 0.58
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:35068317 original size:21 final size:21
Alignment explanation
Indices: 35068282--35068326 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35068272 GCGCAGCTTA
*
35068282 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
* * *
35068303 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
35068324 AAG
1 AAG
35068327 TATTAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.44, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:35068608 original size:86 final size:86
Alignment explanation
Indices: 35068458--35068637 Score: 208
Period size: 86 Copynumber: 2.1 Consensus size: 86
35068448 TTTTCAAAAA
*
35068458 CGCCACTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
1 CGCCGCTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
*
35068523 TAGCAGCGTTTGT-TTGGAAAG
66 TAGCAGCGTTTGTGGT-GAAAG
* * * * *
35068544 CGCCGCTAAAGGTCATTGTC-TTTAGTGGCGTTTTTCAG-ATAAGCGTTGCTAAA-AGTCATG-G
1 CGCCGCTAAAGGTCATGGTCATTT-GCGGCGTTTGT-AGAAAAAGCGTCGCTAAAGA-TCA-GAG
*
35068605 TCTTTAGCGGCGTTTGTGGTGAAAG
62 TCTTTAGCAGCGTTTGTGGTGAAAG
35068630 CGCCGCTA
1 CGCCGCTA
35068638 CAGTTAGCGA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
85 4 0.05
86 73 0.90
87 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (86 bp):
CGCCGCTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
TAGCAGCGTTTGTGGTGAAAG
Found at i:35068631 original size:43 final size:42
Alignment explanation
Indices: 35068463--35068637 Score: 142
Period size: 43 Copynumber: 4.1 Consensus size: 42
35068453 AAAAACGCCA
* *
35068463 CTAAAGGTCATGGTCATTT-GCGGCGTTTGTAGAAAAAGCGTCG
1 CTAAAAGTCATGGTC-TTTAGCGGCGTTTGT-GAGAAAGCGTCG
* *
35068506 CT-AAAGATCA-GAGTCTTTAGCAGCGTTTGTTTG-GAAAGCGCCG
1 CTAAAAG-TCATG-GTCTTTAGCGGCGTTTG--TGAGAAAGCGTCG
* * * * * *
35068549 CTAAAGGTCATTGTCTTTAGTGGCGTTTTTCAGATAAGCGTTG
1 CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGA-AAGCGTCG
* *
35068592 CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGTGAAAGCGCCG
1 CTAAAAGTCATGGTCTTTAGCGGCGTTTGT-GAGAAAGCGTCG
35068635 CTA
1 CTA
35068638 CAGTTAGCGA
Statistics
Matches: 102, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 9 0.09
43 85 0.83
44 6 0.06
45 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (42 bp):
CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAGCGTCG
Found at i:35073458 original size:16 final size:16
Alignment explanation
Indices: 35073433--35073469 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
35073423 TAGTAATAAA
35073433 TACATAGATAAAATGT
1 TACATAGATAAAATGT
*
35073449 TACATGGATAAAATGT
1 TACATAGATAAAATGT
35073465 TACAT
1 TACAT
35073470 TTCATAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (16 bp):
TACATAGATAAAATGT
Found at i:35076487 original size:40 final size:39
Alignment explanation
Indices: 35076456--35076665 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
35076446 GGACTAAGAT
* *
35076456 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
35076496 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
35076536 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
35076576 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
35076616 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
35076655 CCGAAGGCATT
1 CCGAAGGCATT
35076666 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:35076619 original size:120 final size:120
Alignment explanation
Indices: 35076403--35076665 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
35076393 TTGAATGCTG
* *
35076403 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
35076467 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
35076523 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
35076586 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
35076642 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
35076666 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:35076685 original size:79 final size:80
Alignment explanation
Indices: 35076404--35076700 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
35076394 TGAATGCTGT
* ** * * * **
35076404 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
35076467 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
35076484 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
35076548 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
35076564 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
35076628 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
35076643 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
35076701 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:35079535 original size:205 final size:205
Alignment explanation
Indices: 35079168--35079583 Score: 706
Period size: 205 Copynumber: 2.0 Consensus size: 205
35079158 TGAACGTCGA
*
35079168 GACAGGACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
1 GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
* * *
35079233 CTGTTACAAGTGCGGATCAGTTGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGGACAGAATG
66 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
* *
35079298 CAAATCAGAGTGGGAGACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
131 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
35079363 GCTAGTGGTG
196 GCTAGTGGTG
* * *
35079373 GACAGAACGGAATGTCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTTCCTGACCGCTC
1 GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
**
35079438 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTTTGAACAGAATG
66 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
*
35079503 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATATGGGCAAT
131 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
*
35079568 GCTGGTGGTG
196 GCTAGTGGTG
*
35079578 GTCAGA
1 GACAGA
35079584 GAGGATCTAG
Statistics
Matches: 197, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
205 197 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (205 bp):
GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
GCTAGTGGTG
Found at i:35084695 original size:80 final size:79
Alignment explanation
Indices: 35084611--35084782 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
35084601 GGACTAAGAT
*
35084611 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35084675 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * ** * * * *
35084691 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35084756 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35084770 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35084783 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35084762 original size:39 final size:39
Alignment explanation
Indices: 35084558--35084780 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
35084548 TTGAATGCTG
* * * * *
35084558 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
35084598 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
35084637 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
35084678 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
35084718 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
35084757 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35084781 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 102 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:35084800 original size:79 final size:80
Alignment explanation
Indices: 35084638--35084815 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
35084628 AGATACAAAT
* * * *
35084638 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
35084703 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * *
35084718 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35084782 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
35084797 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35084816 TACGTGATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.17
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:35093995 original size:21 final size:19
Alignment explanation
Indices: 35093966--35094022 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 19
35093956 AAAAAAATTG
35093966 AAATATTGAAAAAGAATAAAGA
1 AAAT-TTGAAAAA-AA-AAAGA
35093988 AAATTTGAAGTAAAAAAAAGA
1 AAATTTGAA--AAAAAAAAGA
*
35094009 AGGATTTGAAAAAA
1 A-AATTTGAAAAAA
35094023 TTTGAGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.13
21 11 0.35
22 13 0.42
23 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATTTGAAAAAAAAAAGA
Found at i:35096178 original size:16 final size:18
Alignment explanation
Indices: 35096140--35096181 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
35096130 GTTTACAAAT
*
35096140 AAGAAAGAAAATGAGAGTA
1 AAGAAAAAAAATGAGAG-A
35096159 AAGAAAAAAAAT-AGAG-
1 AAGAAAAAAAATGAGAGA
35096175 AAGAAAA
1 AAGAAAA
35096182 GTGAAAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
18 4 0.18
19 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (18 bp):
AAGAAAAAAAATGAGAGA
Found at i:35096321 original size:17 final size:17
Alignment explanation
Indices: 35096299--35096334 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35096289 ATTGGAAGAA
35096299 AAAATATTGAGTTGATT
1 AAAATATTGAGTTGATT
35096316 AAAATATTGAGTTGATT
1 AAAATATTGAGTTGATT
35096333 AA
1 AA
35096335 TGAGAGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (17 bp):
AAAATATTGAGTTGATT
Found at i:35100891 original size:151 final size:151
Alignment explanation
Indices: 35100607--35100900 Score: 453
Period size: 151 Copynumber: 1.9 Consensus size: 151
35100597 TTCACGAGTT
* * *
35100607 TGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
1 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
* *
35100672 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCTGATTACACATTAAT
66 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
*
35100737 CACAGTTTCACATCACGGGCC
131 CACAATTTCACATCACGGGCC
* *
35100758 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATCT
1 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
* * * * * * *
35100823 GTAACATATGCCGGTATACCCAGCCACTGGTAGAACTTATGACTAGCGCCCGAATCCACTTTATT
66 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
35100888 CACAATTTCACAT
131 CACAATTTCACAT
35100901 AGATCTCTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 128 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (151 bp):
TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
CACAATTTCACATCACGGGCC
Found at i:35105876 original size:5 final size:5
Alignment explanation
Indices: 35105866--35105894 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35105856 CACATGCTCT
35105866 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
35105895 TCACAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:35124955 original size:22 final size:22
Alignment explanation
Indices: 35124912--35124955 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35124902 GAAAATGATC
**
35124912 AAAATTAATCAAAATTTGACAT
1 AAAATTAATCAAAATTAAACAT
*
35124934 AAAATTAATTAAAATTAAACAT
1 AAAATTAATCAAAATTAAACAT
35124956 GTTCATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTAATCAAAATTAAACAT
Found at i:35128510 original size:30 final size:31
Alignment explanation
Indices: 35128452--35128511 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
35128442 GCCTTTTGAA
* *
35128452 AATATTTACAAAAAAATGACATCTAATTTTT
1 AATATTTACAAAAAAATGACACCAAATTTTT
35128483 AATATTTACAAAAAGAAT-A-ACCAAATTTT
1 AATATTTACAAAAA-AATGACACCAAATTTT
35128512 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 15 0.58
32 3 0.12
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (31 bp):
AATATTTACAAAAAAATGACACCAAATTTTT
Found at i:35136269 original size:22 final size:22
Alignment explanation
Indices: 35136226--35136269 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35136216 AAAAATAATC
**
35136226 AAAACTAATCAAAATTTGACAT
1 AAAACTAATCAAAATTCAACAT
* *
35136248 AAAATTAATTAAAATTCAACAT
1 AAAACTAATCAAAATTCAACAT
35136270 GTTCATAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAACTAATCAAAATTCAACAT
Found at i:35142109 original size:19 final size:19
Alignment explanation
Indices: 35142085--35142121 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35142075 TGGAAATGTC
* *
35142085 ATTTCCATTTTCATTTTTT
1 ATTTCCAATTCCATTTTTT
35142104 ATTTCCAATTCCATTTTT
1 ATTTCCAATTCCATTTTT
35142122 GGAAATATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTCCAATTCCATTTTTT
Found at i:35142644 original size:66 final size:66
Alignment explanation
Indices: 35142538--35142669 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
35142528 CTTATTACAT
*
35142538 TAATGTCGCTACATGAGTTAATCCCAGATTGCATTCAGAATTGTT-GCCGCACTTGACAGCTGTC
1 TAATGTCGCTACATGAGTTAATCCCAGATTACATTCAGAATT-TTCGCCGCACTTGACAGCTGTC
35142602 TG
65 TG
* * * ** *
35142604 TAATGTTGCTGCATGAGTTAATTCCAGATTAC-TTCCAGAATTTTCGTTGCACTTGATAGCTGTC
1 TAATGTCGCTACATGAGTTAATCCCAGATTACATT-CAGAATTTTCGCCGCACTTGACAGCTGTC
35142668 TG
65 TG
35142670 GATAAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.07
66 53 0.93
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (66 bp):
TAATGTCGCTACATGAGTTAATCCCAGATTACATTCAGAATTTTCGCCGCACTTGACAGCTGTCT
G
Found at i:35151633 original size:41 final size:37
Alignment explanation
Indices: 35151538--35151634 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 37
35151528 TACAATCACT
* *
35151538 TTAATATTAAATTAATATAATATTTATCTTGATAAATA
1 TTAA-ATTAAATTAATATAATATTTATCTAGATAAACA
* *
35151576 TTATAATCAAAATAATATAATATTTATCTAAAAGATAAACA
1 TTA-AATTAAATTAATATAATATTTATCT---AGATAAACA
35151617 TTAAATTAAATTTAATAT
1 TTAAATTAAA-TTAATAT
35151635 TAAACCATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
38 25 0.52
39 1 0.02
40 6 0.12
41 16 0.33
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (37 bp):
TTAAATTAAATTAATATAATATTTATCTAGATAAACA
Found at i:35153518 original size:27 final size:27
Alignment explanation
Indices: 35153450--35153519 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
35153440 CACACGTGAA
* *
35153450 CACCAACTCGCCGAGCCTACTGGAGAT
1 CACCAACTCGCCAAGCCTACTGGAGAC
**
35153477 CACCAACTCATCAAGCCTACT-GACGAC
1 CACCAACTCGCCAAGCCTACTGGA-GAC
*
35153504 CACCAACTTGCCAAGC
1 CACCAACTCGCCAAGC
35153520 GCCAAACTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.30, C:0.40, G:0.16, T:0.14
Consensus pattern (27 bp):
CACCAACTCGCCAAGCCTACTGGAGAC
Found at i:35154144 original size:12 final size:12
Alignment explanation
Indices: 35154116--35154148 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35154106 CTTCGTTATT
35154116 TTTATG-TTTTC
1 TTTATGTTTTTC
35154127 -TTATGTTTTTC
1 TTTATGTTTTTC
35154138 TTTATGTTTTT
1 TTTATGTTTTT
35154149 ATTTGCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 5 0.25
12 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTATGTTTTTC
Found at i:35161033 original size:16 final size:16
Alignment explanation
Indices: 35161012--35161043 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35161002 GTTTCGTTGC
*
35161012 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
35161028 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
35161044 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:35161476 original size:101 final size:101
Alignment explanation
Indices: 35161264--35161487 Score: 231
Period size: 101 Copynumber: 2.2 Consensus size: 101
35161254 AATGATACCG
* * *
35161264 GTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTAACCGATACACGTAATATC
1 GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACCATCACTAACCGATACACGTAATAGC
* *
35161329 CTGTACATAATACTACACACGTGATCGAAGCTATCT
66 CTGCACATAATACTACACACGTGATCCAAGCTATCT
* * * * * * *
35161365 GGTACGCATAGTAGCCTGCACATAGTACTACAAATGCGACCTATCA-T-TCTGGTACACGTAGTA
1 -GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACC-ATCACTAACCGATACACGTAATA
* * *
35161428 GCCTGCACATAGTACTACACACGTGA-CCATTGCTTTTACT
64 GCCTGCACATAATACTACACACGTGATCCA-AGC-TAT-CT
*
35161468 -TTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
35161488 CAGACCATGC
Statistics
Matches: 99, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
100 2 0.02
101 53 0.54
102 38 0.38
103 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACCATCACTAACCGATACACGTAATAGC
CTGCACATAATACTACACACGTGATCCAAGCTATCT
Found at i:35164872 original size:30 final size:30
Alignment explanation
Indices: 35164838--35164934 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35164828 TAAACTAAAA
*
35164838 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
35164868 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35164898 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35164927 ATGAGCTA
1 -TGAGCTA
35164935 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:35169429 original size:20 final size:20
Alignment explanation
Indices: 35169382--35169429 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
35169372 AGTAAGCTCG
35169382 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
35169402 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
35169422 GTTGAGCT
1 GTTGAGCT
35169430 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:35170637 original size:28 final size:27
Alignment explanation
Indices: 35170596--35170664 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
35170586 GTTTTCACAA
*
35170596 ATTTAAAATTTAATCGATTTATTTTTT
1 ATTTAAAATTTAATCCATTTATTTTTT
* *
35170623 ATTTAAATATTTAATCCTTTTATTTTTAA
1 ATTTAAA-ATTTAATCCATTTATTTTT-T
*
35170652 ATTTTAAATTTAA
1 ATTTAAAATTTAA
35170665 ATTTAATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 7 0.19
28 23 0.64
29 6 0.17
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTAAAATTTAATCCATTTATTTTTT
Found at i:35180785 original size:31 final size:30
Alignment explanation
Indices: 35180747--35180811 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
35180737 AATACAAAGA
* *
35180747 ATTCTTTCATTACTCAATACATTTTCATTC
1 ATTCTTTCAATACTCAATACAGTTTCATTC
* *
35180777 TATTCTTTCAATACTTAGTACAGTTTCATTC
1 -ATTCTTTCAATACTCAATACAGTTTCATTC
35180808 ATTC
1 ATTC
35180812 AATACACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTCTTTCAATACTCAATACAGTTTCATTC
Found at i:35181245 original size:7 final size:7
Alignment explanation
Indices: 35181233--35181266 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
35181223 TGAACAAAAG
35181233 AATTTTA
1 AATTTTA
35181240 AATTTTA
1 AATTTTA
35181247 AATTTTA
1 AATTTTA
35181254 AATTATT-
1 AATT-TTA
35181261 AATTTT
1 AATTTT
35181267 TTTCAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 2 0.08
7 22 0.85
8 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:35183752 original size:16 final size:16
Alignment explanation
Indices: 35183725--35183795 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
35183715 GTTTGGTTCA
35183725 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
35183741 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
35183757 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
35183773 TTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
35183789 CTGTAAT
1 CTGTAAT
35183796 CAGTAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:35184111 original size:22 final size:24
Alignment explanation
Indices: 35184072--35184125 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
35184062 TAAATATTAT
* *
35184072 TTATTT-ATTTTATCAATACAT-A
1 TTATTTAATTTAATCAATAAATAA
35184094 TTATTTAATTTAAT-AATAAATAA
1 TTATTTAATTTAATCAATAAATAA
*
35184117 TAATTTAAT
1 TTATTTAAT
35184126 CATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTATTTAATTTAATCAATAAATAA
Found at i:35186938 original size:13 final size:13
Alignment explanation
Indices: 35186917--35186946 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35186907 ATCAAAAGGC
35186917 CTCTATATTTTCT
1 CTCTATATTTTCT
*
35186930 CTCTCTATTTTCT
1 CTCTATATTTTCT
35186943 CTCT
1 CTCT
35186947 TTTTTGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (13 bp):
CTCTATATTTTCT
Found at i:35189199 original size:17 final size:18
Alignment explanation
Indices: 35189177--35189210 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35189167 AAAACTAAAA
*
35189177 TTAAAAGTAA-AAGAAAG
1 TTAAAAGAAATAAGAAAG
35189194 TTAAAAGAAATAAGAAA
1 TTAAAAGAAATAAGAAA
35189211 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (18 bp):
TTAAAAGAAATAAGAAAG
Found at i:35191247 original size:18 final size:17
Alignment explanation
Indices: 35191214--35191252 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35191204 TTTTATAAAT
35191214 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
35191232 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
35191249 TGTG
1 TGTG
35191253 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:35191497 original size:23 final size:23
Alignment explanation
Indices: 35191470--35191522 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
35191460 AGTGTTATTG
35191470 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35191493 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35191516 ATCAGTG
1 ATCAGTG
35191523 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35191695 original size:38 final size:37
Alignment explanation
Indices: 35191652--35191723 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
35191642 ATGTGTGGAA
*
35191652 TTGAATTGAATATTGACTTGAAA-ATGAAAAAGTGAGTT
1 TTGAATTGAATAGTGA-TT-AAATATGAAAAAGTGAGTT
*
35191690 TTGAATTGAATAGTGATTAAATGTGAAAAAGTGA
1 TTGAATTGAATAGTGATTAAATATGAAAAAGTGA
35191724 AATTATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.10
37 13 0.42
38 15 0.48
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAATATGAAAAAGTGAGTT
Found at i:35200566 original size:30 final size:30
Alignment explanation
Indices: 35200509--35200567 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35200499 TGCCTTTGAA
* *
35200509 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAGCAAATTTTT
35200539 AATATTTACAAAAAGAG-CAAGCAAATTTT
1 AATATTTACAAAAAGAGAC-AGCAAATTTT
35200568 GAAAATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAGCAAATTTTT
Found at i:35201433 original size:14 final size:13
Alignment explanation
Indices: 35201416--35201446 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
35201406 CGAGTATGCC
35201416 TTTGATCTCTTTA
1 TTTGATCTCTTTA
35201429 GTTTGATCTCTTTA
1 -TTTGATCTCTTTA
35201443 TTTG
1 TTTG
35201447 CCAGTTCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (13 bp):
TTTGATCTCTTTA
Found at i:35211059 original size:43 final size:43
Alignment explanation
Indices: 35210975--35211073 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
35210965 CCTGTTCTTT
* ** * *
35210975 CGATGATGCACTATGCGTGCCAGTATATTTTGATGGGTTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
* *
35211018 CGATGATGCACTACGTGTGCCAGTATATTTCCTTCGATTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
**
35211061 TAATGATGCACTA
1 CGATGATGCACTA
35211074 TAGTGCTAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (43 bp):
CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
Found at i:35219103 original size:339 final size:339
Alignment explanation
Indices: 35218483--35219503 Score: 1943
Period size: 339 Copynumber: 3.0 Consensus size: 339
35218473 GGAAATAAAA
35218483 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAGAAGA
1 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAGAAGA
35218548 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
66 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
35218613 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
131 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
*
35218678 GAAATTAGGTTATTTATGAGGGTTGAATTGCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
196 GAAATTAGGTTATTTATGAGGGTTGAATTTCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
*
35218743 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAATTGTTTTAGCTTGAAAGTTA
261 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTTTAGCTTGAAAGTTA
35218808 AGGTTAATATGGCT
326 AGGTTAATATGGCT
*
35218822 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAAAAGA
1 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAGAAGA
35218887 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
66 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
35218952 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
131 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
*
35219017 GAAATTAGGTTATTTATGAGGATTGAATTTCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
196 GAAATTAGGTTATTTATGAGGGTTGAATTTCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
*
35219082 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTCTAGCTTGAAAGTTA
261 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTTTAGCTTGAAAGTTA
35219147 AGGTTAATATGGCT
326 AGGTTAATATGGCT
*
35219161 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGTCGAAACTAGAAGA
1 TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAGAAGA
35219226 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
66 AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
***
35219291 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAAAGCTACTTGAATCTTGGATT
131 TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
*
35219356 GAAATTAGGTTATTTATGAGGGTTGAATTTCGGCCTAGGAGCTTAAAATTTTTAGTAGAAGTTTT
196 GAAATTAGGTTATTTATGAGGGTTGAATTTCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
35219421 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTTTAGCTTGAAAGTTA
261 GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTTTAGCTTGAAAGTTA
*
35219486 AGGTTAATATGGTT
326 AGGTTAATATGGCT
35219500 TATG
1 TATG
35219504 GGATTGCCGA
Statistics
Matches: 668, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
339 668 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (339 bp):
TATGAGAAGTGGGAGGAGAAACCAAAGTGTTTCATCTTTACTTCTCCATTGCCGAAACTAGAAGA
AAGAAAGAAGAAAAACTCTTGTTGAATTTCGGCTAAGGTGTTTTGATACAAAAAGGTATGTTTTA
TGCCACTCTTGAAAATGTATGCATAATTTGGAGGATTGGTTTAAATTTTACTTGAATCTTGGATT
GAAATTAGGTTATTTATGAGGGTTGAATTTCGGCCTAGGAACTTAAAATTTTTAGTAGAAGTTTT
GATGACATTAGATGGATAGTTAGGTTGGATGTGTTAAATTGTTAAGTGTTTTAGCTTGAAAGTTA
AGGTTAATATGGCT
Found at i:35221205 original size:40 final size:40
Alignment explanation
Indices: 35221150--35221656 Score: 1005
Period size: 40 Copynumber: 12.7 Consensus size: 40
35221140 AGCATTGGAT
35221150 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221190 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221230 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221270 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221310 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221350 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221390 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221430 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221470 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221510 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221550 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35221590 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
35221630 TATGTCCGGGCTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
35221657 ATGTGTTTGC
Statistics
Matches: 466, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 466 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:35229501 original size:39 final size:39
Alignment explanation
Indices: 35229337--35229519 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
35229327 TTGAATGCTG
* * * * * * *
35229337 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
35229377 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
35229417 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
35229457 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
35229496 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
35229520 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:35229539 original size:79 final size:80
Alignment explanation
Indices: 35229373--35229554 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
35229363 GCTAAGTGAA
* * * *
35229373 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
35229437 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
35229453 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
35229517 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
35229532 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
35229555 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:35242315 original size:36 final size:36
Alignment explanation
Indices: 35242268--35242337 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
35242258 AACATTCATT
*
35242268 TATTAAAACATACTTATGAAATAAATGATTAAAACA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAACA
35242304 TATTAAAACATACTTATGAAAGAAATGATTAAAA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAA
35242338 TATACTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (36 bp):
TATTAAAACATACTTATGAAAGAAATGATTAAAACA
Found at i:35242353 original size:24 final size:26
Alignment explanation
Indices: 35242305--35242353 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
35242295 ATTAAAACAT
*
35242305 ATTAAAACATACTTATGAAAGAAATG
1 ATTAAAACATACTTATGAAAAAAATG
*
35242331 ATTAAAATATAC-T-TGAAAAAAAT
1 ATTAAAACATACTTATGAAAAAAAT
35242354 TTAAAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 1 0.05
26 11 0.52
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (26 bp):
ATTAAAACATACTTATGAAAAAAATG
Found at i:35247175 original size:6 final size:7
Alignment explanation
Indices: 35247148--35247174 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
35247138 TATAATTATA
35247148 ATTTTTT
1 ATTTTTT
35247155 ATTTTTT
1 ATTTTTT
35247162 ATTTTTT
1 ATTTTTT
35247169 ATTTTT
1 ATTTTT
35247175 AGACATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:35248878 original size:29 final size:28
Alignment explanation
Indices: 35248816--35248878 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
35248806 TTAAATTTAG
* *
35248816 AGTTATTTTTTAATTTTATATATAATTT
1 AGTTATTTTTTAATTTTACATATAAATT
* * *
35248844 ATTTATTTTATTATTTTTACATGTAAATT
1 AGTTATTTT-TTAATTTTACATATAAATT
35248873 AGTTAT
1 AGTTAT
35248879 CAAATCCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
AGTTATTTTTTAATTTTACATATAAATT
Found at i:35256050 original size:25 final size:25
Alignment explanation
Indices: 35256016--35256073 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
35256006 AAATTATTAT
35256016 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
35256041 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
35256066 TTAGTTTT
1 TTAGTTTT
35256074 TTACCTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.59
Consensus pattern (25 bp):
TTAGTTTTCATATTTGATTTCGCTC
Found at i:35260012 original size:47 final size:47
Alignment explanation
Indices: 35259943--35260037 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
35259933 TGTGTGATTG
*
35259943 TTTTATGCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
35259990 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
35260037 T
1 T
35260038 ATGACGCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (47 bp):
TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
Found at i:35260047 original size:47 final size:47
Alignment explanation
Indices: 35259949--35260047 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
35259939 ATTGTTTTAT
* * * *
35259949 GCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATTTTAT
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
35259996 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
35260043 GCTTT
1 GCTTT
35260048 ACTTTTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (47 bp):
GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
Found at i:35260417 original size:23 final size:23
Alignment explanation
Indices: 35260387--35260430 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35260377 GAATGTGGTG
35260387 GTTGTGGATAACTAGGATTGTTA
1 GTTGTGGATAACTAGGATTGTTA
**
35260410 GTTGTGGATATTTAGGATTGT
1 GTTGTGGATAACTAGGATTGT
35260431 ATGTCTGTCG
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:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (23 bp):
GTTGTGGATAACTAGGATTGTTA
Found at i:35264999 original size:27 final size:25
Alignment explanation
Indices: 35264922--35264999 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
35264912 TTTCTCACCC
*
35264922 CAATTTTACCCTAATAAAATTTTGA
1 CAATTTTACCCTGATAAAATTTTGA
* *
35264947 CAATTTTACTCTTGGTAAAATTTTGA
1 CAATTTTAC-CCTGATAAAATTTTGA
*
35264973 CGATTTTAAACCCTGATAAAATTTTGA
1 CAATTTT--ACCCTGATAAAATTTTGA
35265000 GAAAATTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 9 0.20
26 19 0.43
27 14 0.32
28 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (25 bp):
CAATTTTACCCTGATAAAATTTTGA
Found at i:35265275 original size:9 final size:10
Alignment explanation
Indices: 35265248--35265288 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
35265238 CTGAATGTTT
*
35265248 TTCATTTCTC
1 TTCATTTCTA
35265258 TT--TTTCTA
1 TTCATTTCTA
35265266 TTCA-TTCTA
1 TTCATTTCTA
35265275 TTCATTTCTA
1 TTCATTTCTA
35265285 TTCA
1 TTCA
35265289 AACACGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.26
9 9 0.33
10 11 0.41
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (10 bp):
TTCATTTCTA
Found at i:35267652 original size:30 final size:29
Alignment explanation
Indices: 35267456--35267665 Score: 251
Period size: 29 Copynumber: 7.2 Consensus size: 29
35267446 ATATCGACGC
35267456 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * **
35267485 CCATCAAATATGAAAAGGGATGCTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * *
35267514 CCATCAAATAAGAAAAGGGGTAGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
*
35267543 CCATC-AAGTATGAAAAGGGATGGTTTCTA
1 CCATCGAA-TATGAAAAGGGATGGTTTCGA
* **
35267572 CCATCGAATATGAAAAAGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
35267601 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * *
35267630 CCATTGATTAAAGAAAATGGATGGTTTCGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTCGA
35267660 CCATCG
1 CCATCG
35267666 TTTAGCACAC
Statistics
Matches: 152, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 125 0.82
30 25 0.16
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCGA
Found at i:35272508 original size:75 final size:75
Alignment explanation
Indices: 35272376--35272518 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
35272366 GCTTACATAT
* * * * * * *
35272376 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGATTTGATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGGAGATTCGATTAT
35272441 GCAGGTATAC
66 GCAGGTATAC
* * *
35272451 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATATATGTATA-AGGAAGATTCGATTA
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGG-AGATTCGATTA
35272515 TGCA
65 TGCA
35272519 TATATATTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 2 0.04
75 55 0.96
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGGAGATTCGATTAT
GCAGGTATAC
Found at i:35272696 original size:41 final size:41
Alignment explanation
Indices: 35272610--35272703 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
35272600 TCAGATTTAC
* * * * * *
35272610 GTCTAGCAGGTTTGATGCCGGTGAAATATTTAAGACTTTAT
1 GTCTAGCAGGCTTAATGCCAGTGAAAAATTTAAGACTATAA
*
35272651 GTCTAGCAGGCTTAATGCCAGTGAAACAATTT-GGACTATAA
1 GTCTAGCAGGCTTAATGCCAGTGAAA-AATTTAAGACTATAA
*
35272692 GTCTAACAGGCT
1 GTCTAGCAGGCT
35272704 AAAAGCCGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCAGTGAAAAATTTAAGACTATAA
Found at i:35272908 original size:69 final size:67
Alignment explanation
Indices: 35272828--35273043 Score: 233
Period size: 63 Copynumber: 3.2 Consensus size: 67
35272818 TTGAAGAATA
* * * *
35272828 TGTATACACATTCGGTGATAATACTTGTTAGGCATATTTATATATGTATTTAGCTATTCATGTTT
1 TGTATATACATTCGGTGATAATATTTGTTA-GCATATTTATATA-GCATTCAGCTATTCATGTTT
35272893 AAAG
64 AAAG
* * *
35272897 TGTATATACATTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGCTATTCATGTTTAA
1 TGTATATACATTCGGTGATAATATTTGTTAGCATATTTATATAGCATTCAGCTATTCATGTTTAA
35272958 AG
66 AG
* * *
35272960 TGTGTATACATTCGATGATAATATTTGTTAAGCATATATGTATATACACATTCAGCTATTCATGT
1 TGTATATACATTCGGTGATAATATTTGTT-AGCATAT-T-TATATA-GCATTCAGCTATTCATG-
*
35273025 TTTAAAT
61 TTTAAAG
*
35273032 TGTATATGCATT
1 TGTATATACATT
35273044 TGACTATATG
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
63 48 0.39
64 1 0.01
65 7 0.06
67 3 0.02
69 31 0.25
70 1 0.01
71 15 0.12
72 16 0.13
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (67 bp):
TGTATATACATTCGGTGATAATATTTGTTAGCATATTTATATAGCATTCAGCTATTCATGTTTAA
AG
Found at i:35272933 original size:32 final size:32
Alignment explanation
Indices: 35272894--35272991 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
35272884 TTCATGTTTA
35272894 AAGTGTATATACATTCGGTGATAATATTTGTT
1 AAGTGTATATACATTCGGTGATAATATTTGTT
* *
35272926 ATGTGTATA-AGCATTCGGCT-AT--TCATGTT-TA
1 AAGTGTATATA-CATTCGG-TGATAAT-AT-TTGTT
* *
35272957 AAGTGTGTATACATTCGATGATAATATTTGTT
1 AAGTGTATATACATTCGGTGATAATATTTGTT
35272989 AAG
1 AAG
35272992 CATATATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
30 2 0.04
31 21 0.41
32 26 0.51
33 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (32 bp):
AAGTGTATATACATTCGGTGATAATATTTGTT
Found at i:35275379 original size:39 final size:38
Alignment explanation
Indices: 35275325--35275435 Score: 132
Period size: 39 Copynumber: 2.9 Consensus size: 38
35275315 AGTTTGAGTC
35275325 TTTAATTATGTCATAATTTGAACATCATTAATATGAGAT
1 TTTAATTATGTCATAATTTGAACATCATTAATA-GAGAT
* * * * *
35275364 TTTAATTATGTCATAATCTGAACAACATTAGTAGGGGT
1 TTTAATTATGTCATAATTTGAACATCATTAATAGAGAT
* * *
35275402 TTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TTTAATTATGTCATAATTT-GAACATCATTAATA
35275436 CATGTTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 20 0.33
39 40 0.67
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTGAACATCATTAATAGAGAT
Found at i:35288770 original size:11 final size:12
Alignment explanation
Indices: 35288754--35288787 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
35288744 AAATTTTTGA
35288754 ACGAAATTTT-C
1 ACGAAATTTTCC
35288765 ACGAAATATTTCC
1 ACGAAAT-TTTCC
35288778 ACGAAATTTT
1 ACGAAATTTT
35288788 AGGCCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 6 0.29
13 8 0.38
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (12 bp):
ACGAAATTTTCC
Found at i:35288958 original size:39 final size:39
Alignment explanation
Indices: 35288904--35289020 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
35288894 TAATTTAGTT
* *
35288904 TGAATATTCAATTATGTCATAATTTGAACATCATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* *
35288943 TGAATTTTTAATTATGTCATAATCTGAACAACATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* ** * * *
35288982 AG-GGTTTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TGAATTTTTAATTATGTCATAATTT-GAACATCATTAATA
35289021 CATGTTTTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 18 0.28
39 47 0.72
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (39 bp):
TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:35292183 original size:27 final size:27
Alignment explanation
Indices: 35292152--35292329 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35292142 TAAATTGTAC
35292152 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35292179 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35292205 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35292233 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35292261 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35292288 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35292315 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35292330 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Done.