Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008140.1 Hibiscus syriacus cultivar Beakdansim tig00110698_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 511555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:203593 original size:26 final size:27
Alignment explanation
Indices: 203536--203596 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
203526 ATATAATGTA
*
203536 GTCATTTTACACTTCAAAGGTATTTTG
1 GTCATTTTACACTTCAAAGGCATTTTG
* * *
203563 CTCATTTTACACTT-TAGGGCATTTTG
1 GTCATTTTACACTTCAAAGGCATTTTG
203589 GTCATTTT
1 GTCATTTT
203597 TACCTCATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (27 bp):
GTCATTTTACACTTCAAAGGCATTTTG
Found at i:217951 original size:57 final size:57
Alignment explanation
Indices: 217854--217994 Score: 205
Period size: 57 Copynumber: 2.5 Consensus size: 57
217844 TGTTAAAAGG
* *
217854 TTGAACAAGTTCTTCTTATTATGAACTCTCTGTTCGTCCATCAATG-TCATTCTGAGA
1 TTGAACAAGTTCTTCTCATTATGAACTCTATGTTCGTCCATCAA-GCTCATTCTGAGA
* * *
217911 TTGAACAAGTTATTCTCATTATGAACTCTATGTTAC-TCCATGAAGCTTATTCTGAGA
1 TTGAACAAGTTCTTCTCATTATGAACTCTATGTT-CGTCCATCAAGCTCATTCTGAGA
217968 TTGAACAAGTTCTTCTCATTATGAACT
1 TTGAACAAGTTCTTCTCATTATGAACT
217995 TCATCTACCT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.01
57 74 0.97
58 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (57 bp):
TTGAACAAGTTCTTCTCATTATGAACTCTATGTTCGTCCATCAAGCTCATTCTGAGA
Found at i:223668 original size:10 final size:10
Alignment explanation
Indices: 223641--223697 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 10
223631 AAAAATGGAA
223641 AATAACAAAAT
1 AATAA-AAAAT
*
223652 ACGTAAAAAAT
1 A-ATAAAAAAT
223663 AATAAAAAAT
1 AATAAAAAAT
223673 AAT-AAAAAT
1 AATAAAAAAT
*
223682 AA-ACAAAAT
1 AATAAAAAAT
223691 GAATAAA
1 -AATAAA
223698 TGTTAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.34
10 13 0.34
11 9 0.24
12 3 0.08
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:223679 original size:19 final size:19
Alignment explanation
Indices: 223657--223697 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
223647 AAAATACGTA
223657 AAAAATAATAAAAAAT-AAT
1 AAAAATAA-AAAAAATGAAT
*
223676 AAAAATAAACAAAATGAAT
1 AAAAATAAAAAAAATGAAT
223695 AAA
1 AAA
223698 TGTTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAAAATGAAT
Found at i:223970 original size:39 final size:37
Alignment explanation
Indices: 223927--224011 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
223917 GTAAAAATAT
223927 AATATATATAAATAA-ATACAAAAAATAGAATATTAAGAA
1 AATATATATAAA-AACAT--AAAAAATAGAATATTAAGAA
* *
223966 AATATATATAAAAACATATAAAATATAATATTAAGAA
1 AATATATATAAAAACATAAAAAATAGAATATTAAGAA
224003 AA-ATATATA
1 AATATATATA
224012 CATAGTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 7 0.16
37 20 0.47
38 2 0.05
39 14 0.33
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (37 bp):
AATATATATAAAAACATAAAAAATAGAATATTAAGAA
Found at i:224086 original size:25 final size:25
Alignment explanation
Indices: 224041--224088 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
224031 TTAATACATC
* *
224041 TATATATATATATAATGATATAAGA
1 TATATATATATAAAATAATATAAGA
224066 TATATATA-ATAAAAATAATATAA
1 TATATATATAT-AAAATAATATAA
224089 TATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATATATATAAAATAATATAAGA
Found at i:234727 original size:21 final size:20
Alignment explanation
Indices: 234698--234747 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
234688 CGTAAGAGAT
* *
234698 TATCAATACCATAGATAGTAG
1 TATCGATACCAT-GATAGGAG
* *
234719 TATCGATACCATGGTAGGGG
1 TATCGATACCATGATAGGAG
234739 TATCGATAC
1 TATCGATAC
234748 TAATGAGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (20 bp):
TATCGATACCATGATAGGAG
Found at i:235142 original size:57 final size:57
Alignment explanation
Indices: 235070--235534 Score: 681
Period size: 57 Copynumber: 8.3 Consensus size: 57
235060 GACCGAATGT
* * * * *
235070 CACTTTGTGTACAAAAAGTTGAGAAAATCATACTAAGTGTATGAATTTCCGTATGGA
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
235127 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * *
235184 CACTTTGTGTGCAAAAATCTAAGAAATTCATACTTAGTGTATGAATTTCTGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * * *
235241 CACTATGTGTGC--AAA-CTAAGAAATTCATACTAATTGTGTGAATTTTCGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
235295 CACATTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* *
235352 CACTTTGTGTGCAAAAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * * *
235409 TACTATGTGTGC--AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* *
235463 CACTTTGTGTACAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGG
1 CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
235520 CACTATGTGTGCAAA
1 CACTTTGTGTGCAAA
235535 GAAGTTCATA
Statistics
Matches: 369, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
54 89 0.24
55 6 0.02
56 6 0.02
57 268 0.73
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (57 bp):
CACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
Found at i:235311 original size:111 final size:112
Alignment explanation
Indices: 235074--235534 Score: 641
Period size: 111 Copynumber: 4.1 Consensus size: 112
235064 GAATGTCACT
* * * *
235074 TTGTGTACAAAAAGT-TGAGAAAATCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTG
1 TTGTGTGCAAAAA-TCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTG
235138 CAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCAC
65 C-AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCAC
* * *
235187 TTTGTGTGCAAAAATCTAAGAAATTCATACTTAGTGTATGAATTTCTGTATGGGCACTATGTGTG
1 -TTGTGTGCAAAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTG
* *
235252 C-AAA-CTAAGAAATTCATACTAATTGTGTGAATTT-TCGTATGGGCAC
65 CAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATGGGCAC
*
235298 ATTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTG
1 -TTGTGTGCAAAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTG
* *
235363 CAAAAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGTAC
65 C-AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCAC
* * *
235412 TATGTGTGC--AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTA
1 T-TGTGTGCAAAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTG
235474 CAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATGGGCAC
65 C-AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATGGGCAC
235523 TATGTGTGCAAA
1 T-TGTGTGCAAA
235535 GAAGTTCATA
Statistics
Matches: 315, Mismatches: 22, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
110 2 0.01
111 200 0.63
112 6 0.02
113 6 0.02
114 100 0.32
115 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (112 bp):
TTGTGTGCAAAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCAC
Found at i:235376 original size:168 final size:168
Alignment explanation
Indices: 235091--235534 Score: 771
Period size: 168 Copynumber: 2.6 Consensus size: 168
235081 CAAAAAGTTG
* * * *
235091 AGAAAATCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTGCAAAAAGCTAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTGCAAAAAGCTAAGAAATTC
* * *
235156 ATACTAAGTGTATGAATTTCTGTATGGGCACTTTGTGTGCAAAAATCTAAGAAATTCATACTTAG
66 ATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTCATACTAAG
235221 TGTATGAATTTCTGTATGGGCACTATGTGTGCAAACTA
131 TGTATGAATTTCTGTATGGGCACTATGTGTGCAAACTA
* *
235259 AGAAATTCATACTAATTGTGTGAATTTTCGTATGGGCACATTGTGTGCAAAAAGCTAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTGCAAAAAGCTAAGAAATTC
235324 ATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTCATACTAAG
66 ATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTCATACTAAG
*
235389 TGTATGAATTTCTGTATGGGTACTATGTGTGCAAACTA
131 TGTATGAATTTCTGTATGGGCACTATGTGTGCAAACTA
*
235427 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTACAAAAAGCTAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTGCAAAAAGCTAAGAAATTC
* *
235492 ATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGCAAA
66 ATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAA
235535 GAAGTTCATA
Statistics
Matches: 261, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
168 261 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (168 bp):
AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTGCAAAAAGCTAAGAAATTC
ATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTCATACTAAG
TGTATGAATTTCTGTATGGGCACTATGTGTGCAAACTA
Found at i:235637 original size:104 final size:105
Alignment explanation
Indices: 235091--235598 Score: 393
Period size: 111 Copynumber: 4.6 Consensus size: 105
235081 CAAAAAGTTG
* * * * *
235091 AGAAAATCATACTAAGTGTATGAATTTCCGTAT-GGACACTTTGTGTGCAAAAAGCTAAGAAATT
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGA-AATTTGTGT--AAAAAACTAAGAAATT
** *
235155 CATACTAAGTGTATGAA-TTTCTGTATGGGCACTTTGTGTGCAAAAATCTA
63 CATACTAAGTGTATGAATTTTC-GTATGGGCACTAGGTATGC----A---A
* * * * * **
235205 AGAAATTCATACTTAGTGTATGAA-TTTCTGTATGGGCACTATGTGT-GCAAACTAAGAAATTCA
1 AGAAATTCATACTAAGTGTGTGAATTTTC-GTATGGGAAATTTGTGTAAAAAACTAAGAAATTCA
* * * * *
235268 TACTAATTGTGTGAATTTTCGTATGGGCACATTGTGTGCAAAAAGCTA
65 TACTAAGTGTATGAATTTTCGTATGGGCAC-TAG-GT-----ATGCAA
* * * *
235316 AGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAAATTTGTGT--AAAAAACTAAGAAATTC
* * *
235381 ATACTAAGTGTATGAA-TTTCTGTATGGGTACTATGTGTGCAAACTA
64 ATACTAAGTGTATGAATTTTC-GTATGGGCACTAGGTATGC--A--A
* *
235427 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTTTGTGTACAAAAAGCTAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAAATTTGTGTA-AAAAA-CTAAGAAATTC
* *
235492 ATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGCAA
64 ATACTAAGTGTATGAATTTTCGTATGGGCACTAGGTATGCAA
* *
235534 AGAAGTTCATACTAAGTG-GTGAATTTTCGTATGGGAAATATATGTGT-AAACA-TAAGAAATTC
1 AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAAAT-T-TGTGTAAAAAACTAAGAAATTC
235596 ATA
64 ATA
235599 ACAAGTAGGT
Statistics
Matches: 336, Mismatches: 34, Indels: 58
0.79 0.08 0.14
Matches are distributed among these distances:
104 13 0.04
106 23 0.07
107 21 0.06
108 5 0.01
109 2 0.01
110 5 0.01
111 167 0.50
112 15 0.04
113 10 0.03
114 71 0.21
115 2 0.01
118 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (105 bp):
AGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAAATTTGTGTAAAAAACTAAGAAATTCAT
ACTAAGTGTATGAATTTTCGTATGGGCACTAGGTATGCAA
Found at i:241655 original size:60 final size:60
Alignment explanation
Indices: 241515--241995 Score: 677
Period size: 60 Copynumber: 8.1 Consensus size: 60
241505 TAAGCACCAT
* * *
241515 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAAATACACTGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCC-AAAATGCACCGTTAGGCATTTAAC
* * *
241576 TTTTCATCTAACTTGCATTAGGGGTACCTTTCTGCCAAAACGCACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * *
241636 TTTTCATCTAAATTGCATTAGTGGCACCTTTCTGCCAAAATACACCGTTATGCA-TTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
**
241695 --TTCATCTAACTTGCATTAGTGGCACCTTTCTTACAAAATGCACCGTT-GGTCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGG-CATTTAAC
*
241753 TTTTCATCTAAC-TGCATTAGTGGCACCTTTTCTGTCAAAATGCACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACC-TTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * * * *
241813 TTTTAATCTTACTTGCATTAGTGGCACCTTTCAGCCAAAATACACCGTTAAGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * *
241873 TTTTCATCTAACTTGCATTAGTGGCACCTTTTTGCCAAAATGCACCATTAGGAATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * * *
241933 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTTCAAAAATGCACC-TTAGTCATTTAAA
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
241992 TTTT
1 TTTT
241996 ATTTTAGAGC
Statistics
Matches: 374, Mismatches: 39, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.00
57 45 0.12
58 5 0.01
59 34 0.09
60 239 0.64
61 50 0.13
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGGCATTTAAC
Found at i:245776 original size:153 final size:153
Alignment explanation
Indices: 245498--245803 Score: 612
Period size: 153 Copynumber: 2.0 Consensus size: 153
245488 TCACAATCAT
245498 TGTCGATATCACCTTGAACAATGATTTTGCTTTCTCTCAAAAACTATAATTTCCATATCCTCTGT
1 TGTCGATATCACCTTGAACAATGATTTTGCTTTCTCTCAAAAACTATAATTTCCATATCCTCTGT
245563 ATCTTTATGAAATAATCATTTCTGGAGACAAACAACATATACCCAATATGATCTTAACTCATCAA
66 ATCTTTATGAAATAATCATTTCTGGAGACAAACAACATATACCCAATATGATCTTAACTCATCAA
245628 TTGATAATTCCATCAGATTCACC
131 TTGATAATTCCATCAGATTCACC
245651 TGTCGATATCACCTTGAACAATGATTTTGCTTTCTCTCAAAAACTATAATTTCCATATCCTCTGT
1 TGTCGATATCACCTTGAACAATGATTTTGCTTTCTCTCAAAAACTATAATTTCCATATCCTCTGT
245716 ATCTTTATGAAATAATCATTTCTGGAGACAAACAACATATACCCAATATGATCTTAACTCATCAA
66 ATCTTTATGAAATAATCATTTCTGGAGACAAACAACATATACCCAATATGATCTTAACTCATCAA
245781 TTGATAATTCCATCAGATTCACC
131 TTGATAATTCCATCAGATTCACC
245804 GGGAACATAG
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.35
Consensus pattern (153 bp):
TGTCGATATCACCTTGAACAATGATTTTGCTTTCTCTCAAAAACTATAATTTCCATATCCTCTGT
ATCTTTATGAAATAATCATTTCTGGAGACAAACAACATATACCCAATATGATCTTAACTCATCAA
TTGATAATTCCATCAGATTCACC
Found at i:245845 original size:48 final size:48
Alignment explanation
Indices: 245774--245869 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
245764 TGATCTTAAC
245774 TCATCAATTGATAATTCCATCAGATTCACCGGGAACATAGTCCCTGAA
1 TCATCAATTGATAATTCCATCAGATTCACCGGGAACATAGTCCCTGAA
245822 TCATCAATTGATAATTCCATCAGATTCACCGGGAACATAGTCCCTGAA
1 TCATCAATTGATAATTCCATCAGATTCACCGGGAACATAGTCCCTGAA
245870 ATATTTATCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (48 bp):
TCATCAATTGATAATTCCATCAGATTCACCGGGAACATAGTCCCTGAA
Found at i:248022 original size:238 final size:229
Alignment explanation
Indices: 247640--248071 Score: 611
Period size: 238 Copynumber: 1.8 Consensus size: 229
247630 TTTATTTTGG
* * *
247640 TCGGGTTGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTTGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAA
* * * *
247705 AATATCCAACCTGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTATAATAATACCC
66 AATATCCAACCTCAAAAAATATATAATTTTACCTTATAAATTTAGGAATAATTACAATAATACCC
* *
247770 CTCTATATATATA-TTTTTT-CAATTAAGTCATTGTTTTTATTGAATATAAATAAATTTTTTTAT
131 CTATATATATATATTTTTTTCCAATTAAGTC--TGTTTTTATTGAATAAAAAT-AATTTTTTTAT
247833 TTCAGGTGGGGTCGGGTCGGATTTCTAATTCATATCT
193 TTCAGGTGGGGTCGGGTCGGATTTCTAATTCATATCT
*
247870 TCGGGTCGGGTCAG-TTTTTTAAGTGTGATATTCGGGTCGGGTCTAGTTCGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAA
*
247934 AATACCTGACCCGATCCGACC-CAAAAAATATATAATTTTACCTTATAAATTTATGAATAATTAC
66 AATA--T---CC-A----ACCTCAAAAAATATATAATTTTACCTTATAAATTTAGGAATAATTAC
247998 AATAATACCCCTATATATATATATTTTTTTTCCAATTAAGTCTGTTTTTATTGAATAAAAATAAT
121 AATAATACCCCTATATATATATA-TTTTTTTCCAATTAAGTCTGTTTTTATTGAATAAAAATAAT
248063 TTTTTTATT
185 TTTTTTATT
248072 ATTTCGGGTC
Statistics
Matches: 178, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
229 52 0.29
230 12 0.07
231 1 0.01
234 2 0.01
235 1 0.01
238 72 0.40
239 22 0.12
240 6 0.03
241 10 0.06
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (229 bp):
TCGGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAA
AATATCCAACCTCAAAAAATATATAATTTTACCTTATAAATTTAGGAATAATTACAATAATACCC
CTATATATATATATTTTTTTCCAATTAAGTCTGTTTTTATTGAATAAAAATAATTTTTTTATTTC
AGGTGGGGTCGGGTCGGATTTCTAATTCATATCT
Found at i:249045 original size:60 final size:60
Alignment explanation
Indices: 248912--249336 Score: 566
Period size: 60 Copynumber: 7.1 Consensus size: 60
248902 TATGCACCAT
* * * *
248912 TTTTCATCTAACTTGCATTAGTGGA-ACTTTTCTACCAAAAATGCACCATTAGGCATTTAGC
1 TTTTCATCTAACTTGCATTAGT-GACACATTTCTGCC-AAAATGCACCGTTAGGCATTTAAC
* * *
248973 TTTTCATATAACTTGCATTAGTGACACATTTCTGCCAAACTGCACTGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * *
249033 TTTTCATCTAACTTGCATTA-TAGACACATTTTTGCCAATATGCACCGTTGGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGT-GACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * *
249093 TTTTCATCTAACTTGCATTAGTGGCACATTTTTGCCAAAATGCACCGTTAGACATTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * * *
249153 TTTTCATCTAACTTTCATTAGTGCCACTTTTCTGCCAAAATTCACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * * *
249213 TTTTCATCTAACTTGCATTAGTGGCACCTTTATGCCAAAATGCACCGTTAGGCTTTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
* * * * * *
249273 GTTTCATCTAACTTGCATTAGTGGCACATTTATGGCAAAATGCACCATTAGGCATTAAAC
1 TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
249333 TTTT
1 TTTT
249337 ATTTTAGAGC
Statistics
Matches: 325, Mismatches: 36, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
59 1 0.00
60 293 0.90
61 31 0.10
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTTAGGCATTTAAC
Found at i:251062 original size:30 final size:28
Alignment explanation
Indices: 250990--251066 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
250980 GATTCTCAAG
* *
250990 TAGTATGTTTTAAATATATTATTATTTAT
1 TAGT-TGTTTTAAATATATTAGTATATAT
**
251019 TAGTTGAAATTAAATATATTAGTAGTATAT
1 TAGTTG-TTTTAAATATATTAGTA-TATAT
251049 TATGTTGTTTTAAATATA
1 TA-GTTGTTTTAAATATA
251067 GTTGTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.05
29 18 0.46
30 15 0.38
31 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (28 bp):
TAGTTGTTTTAAATATATTAGTATATAT
Found at i:273241 original size:31 final size:31
Alignment explanation
Indices: 273203--273279 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
273193 ACATTCACTC
273203 GCGTTATTGGTTGCCGTGACAAAATATGCAT
1 GCGTTATTGGTTGCCGTGACAAAATATGCAT
273234 GCGTTATTGGTTGCCGTGACAAAATATGCAT
1 GCGTTATTGGTTGCCGTGACAAAATATGCAT
273265 GCGTTATTGGTTGCC
1 GCGTTATTGGTTGCC
273280 TTAACTTCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (31 bp):
GCGTTATTGGTTGCCGTGACAAAATATGCAT
Found at i:277753 original size:23 final size:23
Alignment explanation
Indices: 277698--277758 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
277688 CAGCTCGTAT
* *
277698 AAATGCACTGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
277721 AATTGTACCGTAGTGCCGCATAG
1 AAATGCACCGAAGTGCCACATAG
277744 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
277759 ATATATAAGG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:282755 original size:14 final size:16
Alignment explanation
Indices: 282718--282769 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
282708 TGCAATCACC
*
282718 CATATCACACATATAT
1 CATATCATACATATAT
*
282734 CATGTCATACA-AT-T
1 CATATCATACATATAT
282748 CATATCATACATCATAT
1 CATATCATACAT-ATAT
282765 ACATA
1 -CATA
282770 ATTACTACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.38
15 2 0.07
16 11 0.38
17 1 0.03
18 4 0.14
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (16 bp):
CATATCATACATATAT
Found at i:287210 original size:23 final size:23
Alignment explanation
Indices: 287176--287241 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
287166 CACCACAACT
*
287176 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
287199 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
287222 CGTAGAAATGTACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
287242 TTATATAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:291935 original size:46 final size:46
Alignment explanation
Indices: 291868--291960 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
291858 AGTGTTTCAT
291868 TAAATTCTTGTATTAAGAATGATTTCTAATTGTATTCGAATGAACA
1 TAAATTCTTGTATTAAGAATGATTTCTAATTGTATTCGAATGAACA
291914 TAAATTCTTGTATTAAGAATGATTTCTAATTGTATTCGAATGAACA
1 TAAATTCTTGTATTAAGAATGATTTCTAATTGTATTCGAATGAACA
291960 T
1 T
291961 TTTGTTGGGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (46 bp):
TAAATTCTTGTATTAAGAATGATTTCTAATTGTATTCGAATGAACA
Found at i:291944 original size:25 final size:25
Alignment explanation
Indices: 291870--291944 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
291860 TGTTTCATTA
291870 AATTCTTGTATTAAGAATGATTTCT
1 AATTCTTGTATTAAGAATGATTTCT
* *
291895 AA---TTGTATT-CGAATGA--ACAT
1 AATTCTTGTATTAAGAATGATTTC-T
291915 AAATTCTTGTATTAAGAATGATTTCT
1 -AATTCTTGTATTAAGAATGATTTCT
291941 AATT
1 AATT
291945 GTATTCGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 8 0.21
22 7 0.18
24 7 0.18
25 12 0.32
26 1 0.03
27 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
AATTCTTGTATTAAGAATGATTTCT
Found at i:291956 original size:21 final size:22
Alignment explanation
Indices: 291875--291949 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
291865 CATTAAATTC
291875 TTGTATTAAGAATGATTTCTAA
1 TTGTATTAAGAATGATTTCTAA
* *
291897 TTGTATT-CGAATGA--ACATAAA
1 TTGTATTAAGAATGATTTC-T-AA
291918 TTCTTGTATTAAGAATGATTTCTAA
1 ---TTGTATTAAGAATGATTTCTAA
291943 TTGTATT
1 TTGTATT
291950 CGAATGAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 8 0.20
22 14 0.34
24 7 0.17
25 8 0.20
26 1 0.02
27 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (22 bp):
TTGTATTAAGAATGATTTCTAA
Found at i:301015 original size:81 final size:81
Alignment explanation
Indices: 300728--301303 Score: 846
Period size: 81 Copynumber: 7.3 Consensus size: 81
300718 TGCCAAAAAA
*
300728 CACAGTTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC---ATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
300790 ACATTTCTGTCAAATG
66 ACATTTCTGTCAAATG
*
300806 CACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC---ATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
* *
300868 ACATTTCTTTAAAATG
66 ACATTTCTGTCAAATG
300884 --CAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
300947 ACATTTATGTCAAATG
66 ACATTTCTGTCAAATG
* * *
300963 CACAGCTAGGCAATTAATCTTTTACTCAAATGTATTTAACCTTTCATTTAACT-GCATGATCGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
301027 ACATATT-TGTTAAATG
66 ACAT-TTCTGTCAAATG
*
301043 CACAGCTAGGCAA-TAATCATGTTTACTCAAAGGTATTTAACATTTCATCTAACT-GCATGATTG
1 CACAGCTAGGCAATTAATC-T-TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTG
301106 ACACATTT-T-T-AAATG
64 ACACATTTCTGTCAAATG
* *
301121 CACAACTAGGCAATTAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
301186 ACCTTTCTGTCAAATG
66 ACATTTCTGTCAAATG
* * *
301202 CACAGCTAGACAATTAATCTTTTACTCAAAGATATTTAACC-TTCATCTAACTAGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
301266 ACCTTTCTGTCAAATG
66 ACATTTCTGTCAAATG
301282 --CAGCTAGGCAATTAATCTTTTA
1 CACAGCTAGGCAATTAATCTTTTA
301304 TTTTAAAACA
Statistics
Matches: 461, Mismatches: 24, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
76 53 0.11
77 31 0.07
78 129 0.28
79 31 0.07
80 78 0.17
81 139 0.30
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (81 bp):
CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
ACATTTCTGTCAAATG
Found at i:301166 original size:239 final size:236
Alignment explanation
Indices: 300728--301303 Score: 843
Period size: 239 Copynumber: 2.4 Consensus size: 236
300718 TGCCAAAAAA
* *
300728 CACAGTTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCAT--TGACA
1 CACAGCTAGGCAATTAATCTTTTACTCAAA-GTATTTAACCTTTCATCTAACTAGCATGATGACA
* *
300791 CATTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTA
65 CATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTA
* *
300856 ACTGGCATTGACACATTTCTTTAAAATGCAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAA
130 ACTGGCATTGACACATTTCTTTAAAATGCAACTAGGCAATTAATCTTTTACTCAAAGATATTTAA
300921 CCTTTCATCTAACTGGCATGATTGACACATTTATGTCAAATG
195 CCTTTCATCTAACTGGCATGATTGACACATTTATGTCAAATG
*
300963 CACAGCTAGGCAATTAATCTTTTACTCAAATGTATTTAACCTTTCATTTAACT-GCATGATCGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAA-GTATTTAACCTTTCATCTAACTAGCATGAT-GAC
*
301027 ACATATT-TGTTAAATGCACAGCTAGGCAA-TAATCATGTTTACTCAAAGGTATTTAACATTTCA
64 ACAT-TTCTGTCAAATGCACAGCTAGGCAATTAATC-T-TTTACTCAAAGGTATTTAACATTTCA
301090 TCTAACT-GCATGATTGACACA-TT-TTT-AAATGCACAACTAGGCAATTAATCTTTTACTCAAA
126 TCTAACTGGC---ATTGACACATTTCTTTAAAATG--CAACTAGGCAATTAATCTTTTACTCAAA
* *
301151 GATATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATG
186 GATATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTCAAATG
*
301202 CACAGCTAGACAATTAATCTTTTACTCAAAGATATTTAACC-TTCATCTAACTAGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAG-TATTTAACCTTTCATCTAACTAGCATGA-TGAC
*
301266 ACCTTTCTGTCAAATG--CAGCTAGGCAATTAATCTTTTA
64 ACATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTA
301304 TTTTAAAACA
Statistics
Matches: 311, Mismatches: 14, Indels: 31
0.87 0.04 0.09
Matches are distributed among these distances:
234 4 0.01
235 50 0.16
236 10 0.03
237 47 0.15
238 55 0.18
239 135 0.43
240 10 0.03
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (236 bp):
CACAGCTAGGCAATTAATCTTTTACTCAAAGTATTTAACCTTTCATCTAACTAGCATGATGACAC
ATTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
CTGGCATTGACACATTTCTTTAAAATGCAACTAGGCAATTAATCTTTTACTCAAAGATATTTAAC
CTTTCATCTAACTGGCATGATTGACACATTTATGTCAAATG
Found at i:304196 original size:46 final size:46
Alignment explanation
Indices: 304113--304200 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
304103 ACCGTTATGT
* ** * *
304113 ATTTTCATTTGTGGCATCATTTCATTTCAATTTTGCACTGTTATAC
1 ATTTTCATTTATGGCATCATTTCATGACAAGTATGCACTGTTATAC
*
304159 ATTTTCATTTATGGCATCCTTTCATGACAAGTATGCACTGTT
1 ATTTTCATTTATGGCATCATTTCATGACAAGTATGCACTGTT
304201 CCTCATCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCATTTCATGACAAGTATGCACTGTTATAC
Found at i:304387 original size:81 final size:81
Alignment explanation
Indices: 304297--304637 Score: 520
Period size: 81 Copynumber: 4.2 Consensus size: 81
304287 AAAACACAGT
*
304297 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCCATGATTGACACATTT
1 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTT
**
304362 CTATCAAATAAACAAC
66 CTATCAAATGCACAAC
* *
304378 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATGATTGACACCTTT
1 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTT
*
304443 CTGTCAAATGCACAAC
66 CTATCAAATGCACAAC
*
304459 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATATTT
1 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTT
**
304524 CTATCAAATGCACAGT
66 CTATCAAATGCACAAC
* ** * *
304540 TAGGCAATTAATCTTTTACTCAAAGGTATTTATCCTTTCATCTAGTTGGCATAATTAACACATTT
1 TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTT
* * *
304605 CTGTAAAATGCACATC
66 CTATCAAATGCACAAC
*
304621 TAGACAATTAATCTTTT
1 TAGGCAATTAATCTTTT
304638 TTTTAAATAG
Statistics
Matches: 237, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 237 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (81 bp):
TAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTT
CTATCAAATGCACAAC
Found at i:305223 original size:94 final size:94
Alignment explanation
Indices: 305047--305223 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 94
305037 ATGGTATCGA
* * * * *
305047 TACTTCTATATTGTGGTACCGATACTCCTTTTCAGTATCGATATCATTTCTACATTCTGGATCCA
1 TACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCAACATTCTGGATCCA
*
305112 TGGTATCAATATTTTTCTCCTAGTACCGG
66 TGGTATCAATATATTTCTCCTAGTACCGG
* *
305141 TACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGGTACCATTTCAACATTTTGGAATCC
1 TACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCAACATTCTGG-ATCC
305206 ATGGTA-CAGATA-ATTTCT
65 ATGGTATCA-ATATATTTCT
305224 TTTTTGGTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 60 0.82
95 13 0.18
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (94 bp):
TACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCAACATTCTGGATCCA
TGGTATCAATATATTTCTCCTAGTACCGG
Found at i:312785 original size:55 final size:55
Alignment explanation
Indices: 312719--313097 Score: 618
Period size: 55 Copynumber: 6.9 Consensus size: 55
312709 CAAATGGCAA
*
312719 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGACAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACAC
* *
312774 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACAC
*
312829 TTTGTGTGCAAAACTATGAAATTCATAATAAGTTTATGAATTTCTGTATAGG-CAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT-GGACAC
* * *
312884 TTTGTGTACAAAACTAAGAAATTCATAATAAGATTATGAATTTCTGTATGGGCAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACAC
* *
312939 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACAC
*
312994 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATTAATTTCCT-TATGGACAC
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT-CTGTATGGACAC
* *
313049 TTTGTATGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
313098 TGGTAGTGGG
Statistics
Matches: 302, Mismatches: 18, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
54 3 0.01
55 296 0.98
56 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (55 bp):
TTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACAC
Found at i:313114 original size:55 final size:55
Alignment explanation
Indices: 312713--313169 Score: 609
Period size: 55 Copynumber: 8.3 Consensus size: 55
312703 GATTACCAAA
* **
312713 TGGCAATTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTTGTA-
1 TGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
312767 TGGACACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGG-CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
312823 GGGCACTTTGTGTGCAAAACTATGAAATTCATAATAAGTTTATGAATTTCTGTAT
1 TGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * *
312878 AGGCACTTTGTGTACAAAACTAAGAAATTCATAATAAGATTATGAATTTCTGTAT
1 TGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
*
312933 GGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTA-
1 TGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* *
312987 TGGTCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATTAATTTCCTTA-
1 TGG-CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
*
313042 TGGACACTTTGTATGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGG-CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * ** * * * * * *
313098 TGGTAGTGGGTGTGC-AACCCACGCAAATT-ATAATAAGATTGTGAATTACCGTAT
1 TGGCACTTTGTGTGCAAAACTAAG-AAATTCATAATAAGTTTATGAATTTCCGTAT
**
313152 TGGCACTACGTGTGCAAA
1 TGGCACTTTGTGTGCAAA
313170 CTATATAGTT
Statistics
Matches: 361, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
54 43 0.12
55 313 0.87
56 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (55 bp):
TGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
Found at i:314901 original size:106 final size:104
Alignment explanation
Indices: 314685--314906 Score: 239
Period size: 105 Copynumber: 2.1 Consensus size: 104
314675 GTTCTACTTG
* * * * * * *
314685 GTCTATGTAATTACATGAAAAGGTAAAATAAGCTATGTGACATTTACTTATGTGATATATGAAGA
1 GTCTATGTGATTACATGAAAAGATAAAATAAGCTATGTGACATTAACTTAAGCGATATATAAACA
* * *
314750 TGTGATATATACTATGTGACCATGATATATGTCTTATGT
66 TGTGATATATACTATGTGACAAGGATATATGTCTTATAT
* * * * **
314789 GATCTATGTGATTACATGAGAATATGATATAAGCTATGTGTTATTAACTTAAGCGATTATATAAA
1 G-TCTATGTGATTACATGAAAAGATAAAATAAGCTATGTGACATTAACTTAAGCGA-TATATAAA
* *
314854 CATGTGATATA-AGCTATGTGATAAGGATCTATGTGCTTATAT
64 CATGTGATATATA-CTATGTGACAAGGATATATGT-CTTATAT
314896 GTCTATGTGAT
1 GTCTATGTGAT
314907 ATTGAACTAC
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
104 1 0.01
105 44 0.46
106 44 0.46
107 7 0.07
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (104 bp):
GTCTATGTGATTACATGAAAAGATAAAATAAGCTATGTGACATTAACTTAAGCGATATATAAACA
TGTGATATATACTATGTGACAAGGATATATGTCTTATAT
Found at i:314925 original size:31 final size:31
Alignment explanation
Indices: 314867--314926 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
314857 GTGATATAAG
* * *
314867 CTATGTGATAAGGATCTATGTGCTTATATGT
1 CTATGTGATAAGGAACTACGTGATTATATGT
**
314898 CTATGTGATATTGAACTACGTGATTATAT
1 CTATGTGATAAGGAACTACGTGATTATAT
314927 AAATATGTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (31 bp):
CTATGTGATAAGGAACTACGTGATTATATGT
Found at i:315096 original size:23 final size:23
Alignment explanation
Indices: 315064--315147 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
315054 GAGTCGAAGG
*
315064 TTCTATGTGGTCCTTCAGGATAA
1 TTCTACGTGGTCCTTCAGGATAA
** *
315087 TTCTACGTGGTCCTTTGGGATAT
1 TTCTACGTGGTCCTTCAGGATAA
*** *
315110 TTCTACACAGTCCTTCATGATAA
1 TTCTACGTGGTCCTTCAGGATAA
* *
315133 TACTATGTGGTCCTT
1 TTCTACGTGGTCCTT
315148 TGAGACATTT
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCAGGATAA
Found at i:315123 original size:46 final size:46
Alignment explanation
Indices: 315073--315160 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
315063 GTTCTATGTG
* * *
315073 GTCCTTCAGGATAATTCTACGTGGTCCTTTGGGATATTTCTACACA
1 GTCCTTCAGGATAATACTACGTGGTCCTTTGAGACATTTCTACACA
* *
315119 GTCCTTCATGATAATACTATGTGGTCCTTTGAGACATTTCTA
1 GTCCTTCAGGATAATACTACGTGGTCCTTTGAGACATTTCTA
315161 TGTGGCACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (46 bp):
GTCCTTCAGGATAATACTACGTGGTCCTTTGAGACATTTCTACACA
Found at i:315325 original size:6 final size:6
Alignment explanation
Indices: 315314--315370 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
315304 AATGAACAGA
* * * * *
315314 GATAAT GATAAT GATAGT GATAAT GATAAG GATATT GATGAT GATGAT
1 GATAAT GATAAT GATAAT GATAAT GATAAT GATAAT GATAAT GATAAT
*
315362 GATGAT GAT
1 GATAAT GAT
315371 GATATATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.33
Consensus pattern (6 bp):
GATAAT
Found at i:315357 original size:3 final size:3
Alignment explanation
Indices: 315349--315373 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
315339 ATAAGGATAT
315349 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
315374 ATATGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:316864 original size:33 final size:33
Alignment explanation
Indices: 316826--316890 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
316816 GTTCAGCACC
316826 ATCAAAGAGAGGCAGAGA-TCATGGTTTTCAACA
1 ATCAAAGAGAGGCAGAGATTC-TGGTTTTCAACA
316859 ATCAAAGAGAGGCAGAGATTCTGGTTTTCAAC
1 ATCAAAGAGAGGCAGAGATTCTGGTTTTCAAC
316891 CTGAGACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (33 bp):
ATCAAAGAGAGGCAGAGATTCTGGTTTTCAACA
Found at i:318190 original size:54 final size:54
Alignment explanation
Indices: 318123--318570 Score: 646
Period size: 54 Copynumber: 8.3 Consensus size: 54
318113 ATTCCATAGT
* * * * **
318123 TTGCACCCGTAGTGCCAATACAGATATTCATAAACTCATTATGAATTTCTTAAT
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
* * *
318177 TTGCACATATAGTGTCAATACGGAAATTCAGAAACTCATTATGAATGTT-TTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAAT-TTCTTAGG
* ** *
318231 TTGCACATATAGTGCCAATACATAAATTCATAAACTCGTTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
318285 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
* * *
318339 TTGCACACATAGTGTCAATACTGAAATTCATAAACTCATTATGAATTTCATAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
* *
318393 TTACACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
* * *
318447 TTGCACACATAGTGCCAATATGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
* * *
318501 TTGCACACATAGTGCCAATATGAAAATTCATAAACTCATTATGAATTTATTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
**
318555 TTGCACGTATAGTGCC
1 TTGCACACATAGTGCC
318571 CATTCGGTAA
Statistics
Matches: 359, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 2 0.01
54 355 0.99
55 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGG
Found at i:327309 original size:23 final size:22
Alignment explanation
Indices: 327275--327335 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
327265 GAGTCGAGGG
*
327275 TTCTACACGGTCCTTCAGAACAA
1 TTCTACGCGGTCCTTCAGAAC-A
* * *
327298 TTCTACGTGGTCCTTCGGGACA
1 TTCTACGCGGTCCTTCAGAACA
327320 TTCTACGCGGTCCTTC
1 TTCTACGCGGTCCTTC
327336 GGACAATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (22 bp):
TTCTACGCGGTCCTTCAGAACA
Found at i:327325 original size:22 final size:23
Alignment explanation
Indices: 327275--327342 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
327265 GAGTCGAGGG
* *
327275 TTCTACACGGTCCTTCAGAACAA
1 TTCTACGCGGTCCTTCGGAACAA
* *
327298 TTCTACGTGGTCCTTCGGGAC-A
1 TTCTACGCGGTCCTTCGGAACAA
327320 TTCTACGCGGTCCTTCGG-ACAA
1 TTCTACGCGGTCCTTCGGAACAA
327342 T
1 T
327343 ACAATATGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.05
22 20 0.51
23 17 0.44
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGAACAA
Found at i:330221 original size:15 final size:16
Alignment explanation
Indices: 330180--330223 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
330170 TTACCCGACT
330180 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
* *
330196 TGTTATGAACCTG-CA
1 TGTTTTCAACCTGACA
*
330211 TGTTTTTAACCTG
1 TGTTTTCAACCTG
330224 GCCTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:330810 original size:11 final size:11
Alignment explanation
Indices: 330786--330818 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
330776 ATGATAATTA
330786 AATAACATTT-
1 AATAACATTTG
*
330796 AATAAAATTTG
1 AATAACATTTG
330807 AATAACATTTG
1 AATAACATTTG
330818 A
1 A
330819 GTCAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (11 bp):
AATAACATTTG
Found at i:333868 original size:3 final size:3
Alignment explanation
Indices: 333855--333930 Score: 100
Period size: 3 Copynumber: 25.0 Consensus size: 3
333845 TTACCCATTT
* * *
333855 TTA TT- TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
333902 TATA TATA TTA TTA TTA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA TTA TTA TTA
333931 AAAAAAATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.88
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:335328 original size:17 final size:18
Alignment explanation
Indices: 335286--335330 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
335276 TTTTTATTAT
* *
335286 TATTATATAGTCATATAA
1 TATTATATAATAATATAA
335304 TATATATATAATAATATAA
1 TAT-TATATAATAATATAA
335323 T-TTATATA
1 TATTATATA
335331 TTTTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 14 0.58
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTATATAATAATATAA
Found at i:348012 original size:93 final size:93
Alignment explanation
Indices: 347892--348089 Score: 344
Period size: 93 Copynumber: 2.1 Consensus size: 93
347882 AACAAGTGCC
*
347892 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTT-GATATGAACCCT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGGA-ATGAACCCC
* *
347956 GAAAACCAATCATTGGATTTGAAAGATGA
65 AAAAACCAATCATTAGATTTGAAAGATGA
*
347985 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGGAATGAACCCCA
348050 AAAACCAATCATTAGATTTGAAAGATGA
66 AAAACCAATCATTAGATTTGAAAGATGA
348078 ATGTGCTCATAG
1 ATGTGCTCATAG
348090 TAGAAATAAG
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 98 0.98
94 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGGAATGAACCCCA
AAAACCAATCATTAGATTTGAAAGATGA
Found at i:349162 original size:114 final size:114
Alignment explanation
Indices: 348876--349499 Score: 1148
Period size: 114 Copynumber: 5.5 Consensus size: 114
348866 TAGCAAAGAT
* *
348876 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
*
348941 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
348989 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCACCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
349054 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
349103 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
349168 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
349217 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
349282 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
349331 TCAAATCCATCATTTAATGGATCA-CTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
349394 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
349443 TTAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAAC
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAAC
349500 ATTGTTCAAC
Statistics
Matches: 498, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
112 100 0.20
113 145 0.29
114 253 0.51
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:349530 original size:74 final size:73
Alignment explanation
Indices: 349402--349540 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 73
349392 TGAAGAAGGA
* **
349402 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATCA
349467 GCTTTTCC
66 GCTTTTCC
* * *
349475 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AGAAGAAA-TTCATAATGAGAAGAA-ATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGAT
349539 CA
64 CA
349541 ACATTACCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 3 0.05
73 20 0.34
74 35 0.60
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (73 bp):
AGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATCA
GCTTTTCC
Found at i:349530 original size:186 final size:186
Alignment explanation
Indices: 349290--349685 Score: 537
Period size: 186 Copynumber: 2.1 Consensus size: 186
349280 TGAAGAAGGA
* *
349290 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGAT
1 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
* * *
349353 C-ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
65 CAACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA-AAGAAATTCATAA
* * *
349417 TGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAGCTTTTCC
129 TGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
* ** *
349475 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
**** *
349540 AACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAAAGAAGTTCATAATG
66 AACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAAAGAAATTCATAATG
* * * *
349605 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGGATTAACATTGCC
131 AGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
** *
349661 AGGTAGAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAAC
349686 TCGTCATCTG
Statistics
Matches: 184, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
184 3 0.02
185 20 0.11
186 119 0.65
187 42 0.23
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (186 bp):
AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
AACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
Found at i:349559 original size:74 final size:74
Alignment explanation
Indices: 349402--349573 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 74
349392 TGAAGAAGGA
* **
349402 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGAT
1 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGAT
* * *
349465 CAGCTTTTCC
65 CAACATTACC
* * *
349475 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATC
349540 AACATTACC
66 AACATTACC
**** *
349549 AGTTCGAGTTCATAATAAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAAC
349574 TCATCTGAAG
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 3 0.04
73 20 0.24
74 60 0.72
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (74 bp):
AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATC
AACATTACC
Found at i:349636 original size:112 final size:108
Alignment explanation
Indices: 349475--349847 Score: 413
Period size: 112 Copynumber: 3.4 Consensus size: 108
349465 CAGCTTTTCC
* * * * *
349475 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTTAAATTCATCATT-GATGGATC
* * *
349540 AACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGA
64 AACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
349585 AGGAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGGA
1 A-G--AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGA
* * *
349650 TTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
62 TCAACATTACCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * * *
349700 AGAAGAAATTCATACTGAGAAGAATTTGTTCAACCTTTTGCTAAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCA
* * * * * *
349765 GCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
65 ACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* ** *
349809 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACATTTT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
349848 ACATAATTTT
Statistics
Matches: 223, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
109 44 0.20
110 2 0.01
111 1 0.00
112 139 0.62
113 23 0.10
114 2 0.01
115 12 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (108 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCAA
CATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:349737 original size:298 final size:301
Alignment explanation
Indices: 349176--349797 Score: 884
Period size: 298 Copynumber: 2.1 Consensus size: 301
349166 TGAAGAAGGA
* *
349176 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGAT
1 AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
* * * *
349239 CAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
66 CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* * *
349304 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATCACTTTTCCAGAGAAA
131 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATAACATTGCCAGAGAAA
349369 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
196 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* *
349434 ACCTTTTGCTTAAATCCATCATTTGATGGATCAGCTTTTCC
261 ACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
* ** *
349475 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
**** *
349539 CAACATTACCAG-TTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA-AAGAAGTTCATA
66 CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* * * * *
349602 ATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGGATTAACATTGCCAG-GTA
131 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGA-TAACATTGCCAGAG-A
* * ** *
349666 GAGTTCATAATGAGAAGAACTCGTCAT-CTGAA-GAAGAAGAAATTCATACTGAGAAGAATTTGT
194 AAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
349729 TCAACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
258 TCAACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
349773 A-AAGAAAGTTCATAATGAGAAGAAC
1 AGAAGAAAGTTCATAATGAGAAGAAC
349798 TCATCTGAAG
Statistics
Matches: 287, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
297 2 0.01
298 152 0.53
299 90 0.31
300 43 0.15
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (301 bp):
AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATAACATTGCCAGAGAAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
Found at i:350088 original size:3 final size:3
Alignment explanation
Indices: 350075--350124 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
350065 TTACCCATTT
* * *
350075 TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA -TA ATA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
350119 TTA TTA
1 TTA TTA
350125 AAAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:350103 original size:18 final size:18
Alignment explanation
Indices: 350076--350124 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
350066 TACCCATTTT
350076 TATT-TTATTATTATA-A
1 TATTATTATTATTATATA
*
350092 TAATTATTATTATAATATA
1 T-ATTATTATTATTATATA
350111 TATTATTATTATTA
1 TATTATTATTATTA
350125 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 22 0.79
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTATTATTATATA
Found at i:350114 original size:12 final size:15
Alignment explanation
Indices: 350080--350119 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
350070 CATTTTTATT
350080 TTATTATTATAATAA
1 TTATTATTATAATAA
350095 TTATTATTATAAT-A
1 TTATTATTATAATAA
350109 TATATTATTAT
1 T-TATTATTAT
350120 TATTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATAATAA
Found at i:352515 original size:6 final size:6
Alignment explanation
Indices: 352478--352556 Score: 66
Period size: 6 Copynumber: 14.3 Consensus size: 6
352468 AGTATTTATA
* *
352478 ATTAAT ATTAAA ATAAAT A-T-AT ATT-AT AATTAAT ATTAAT ATT-A-
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT -ATTAAT ATTAAT ATTAAT
*
352522 ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
352557 AGTTTATAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.12
5 14 0.24
6 36 0.61
7 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:352523 original size:16 final size:16
Alignment explanation
Indices: 352476--352585 Score: 88
Period size: 16 Copynumber: 7.0 Consensus size: 16
352466 AAAGTATTTA
*
352476 TAATTAATATTAA-AA
1 TAATTAATATTAATAT
* *
352491 TAAAT-ATA-TATTA-
1 TAATTAATATTAATAT
352504 TAATTAATATTAATAT
1 TAATTAATATTAATAT
352520 TAATTAATATTAATAT
1 TAATTAATATTAATAT
352536 TAACTT-ATATTAATA-
1 TAA-TTAATATTAATAT
* * *
352551 TAATATAGTTTATAATTT
1 TAAT-TAATAT-TAATAT
352569 GTAATTAATATTAATAT
1 -TAATTAATATTAATAT
352586 AAAATATAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
13 6 0.08
14 8 0.11
15 12 0.16
16 30 0.40
17 11 0.15
18 4 0.05
19 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTAATATTAATAT
Found at i:352609 original size:31 final size:30
Alignment explanation
Indices: 352571--352755 Score: 135
Period size: 31 Copynumber: 5.8 Consensus size: 30
352561 TATAATTTGT
352571 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAAATATAGT-TATAA
*
352602 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAAATATA-GTTATAA
* * *
352632 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTT-ATAA
*
352668 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAAATATAG-TTATAA
*
352697 ACTATATACTATATTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATATTAATATAAAATATAGTTATA-A
*
352732 TAATTAACATTAATATAAAATATA
1 -AATTAATATTAATATAAAATATA
352756 TAGTACATTA
Statistics
Matches: 127, Mismatches: 9, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
29 10 0.08
30 8 0.06
31 49 0.39
32 5 0.04
33 6 0.05
34 17 0.13
35 20 0.16
36 12 0.09
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATAGTTATAA
Found at i:352623 original size:24 final size:25
Alignment explanation
Indices: 352578--352624 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
352568 TGTAATTAAT
**
352578 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
352603 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
352625 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:352651 original size:14 final size:14
Alignment explanation
Indices: 352634--352695 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
352624 ATGTTATAAA
352634 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
352648 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
352662 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
352677 TAATATAGTATAGT
1 TTATATAGTATAGT
352691 TTATA
1 TTATA
352696 AACTATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:352685 original size:43 final size:40
Alignment explanation
Indices: 352636--352726 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
352626 GTTATAAATT
*
352636 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
352679 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
352719 ATTATAGT
1 A-TATAGT
352727 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 11 0.24
43 24 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:352689 original size:29 final size:29
Alignment explanation
Indices: 352656--352748 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
352646 GTTTATAAAC
352656 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
352685 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
352721 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
352749 AAATATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:352690 original size:131 final size:133
Alignment explanation
Indices: 352529--352791 Score: 315
Period size: 131 Copynumber: 2.0 Consensus size: 133
352519 TTAATTAATA
** * *
352529 TTAATATTAACTTATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATAT
1 TTAATATTAACTTATATTAATATAATATAGTTTATAAACTATATACT-ATATTAATATAAAATAT
* * * * *
352593 AGTCTATA-A-AATTAATATTAATATAAACTATAT-GT-TATAAATTATATAGTATAGTTTATAA
65 AGT-TA-AGATAATTAACATTAATATAAAATATATAGTACATAAA-TATAAACTATAGTTTATAA
352654 ACTATAG
127 ACTATAG
* *
352661 TTAATA-TAA-TTAATATTAATATAGTATAGTTTATAAACTATATACTATATTAATATAAATTAT
1 TTAATATTAACTT-ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATAT
* *
352724 AGTTAAGATAATTAACATTAATATAAAATATATAGTACATTAATATAAACTATAGTTTATAAATT
65 AGTTAAGATAATTAACATTAATATAAAATATATAGTACATAAATATAAACTATAGTTTATAAACT
352789 ATA
130 ATA
352792 TACTATAGGT
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
129 1 0.01
130 5 0.04
131 70 0.62
132 32 0.29
133 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (133 bp):
TTAATATTAACTTATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATATA
GTTAAGATAATTAACATTAATATAAAATATATAGTACATAAATATAAACTATAGTTTATAAACTA
TAG
Found at i:352796 original size:21 final size:21
Alignment explanation
Indices: 352767--352819 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
352757 AGTACATTAA
* *
352767 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
352788 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
352809 TATAAACTATA
1 TATAAACTATA
352820 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:352911 original size:57 final size:55
Alignment explanation
Indices: 352850--352984 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 55
352840 TTGTTTATAA
* *
352850 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATAC-TATAAATAG-TT-TATACATACATAT
* * * *
352907 ACTATATGTTATATATATAGTTTATATATACTATACATAGTTTATACATACATGT
1 ACTATAAGTTACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
352962 ACTATAAGTTACATATATA-TTTA
1 ACTATAAGTTACATATATAGTTTA
352985 CATTTATATA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
54 4 0.06
55 28 0.40
56 2 0.03
57 34 0.49
58 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
Found at i:352932 original size:20 final size:20
Alignment explanation
Indices: 352866--352957 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 20
352856 GGTTACATAT
*
352866 ATAGTTTATATA-ACATATAA
1 ATAGTTTATATATAC-TATAC
352886 ATAGATTGTATATATACATATAC
1 ATAG-TT-TATATATAC-TATAC
* *
352909 -TA---TATGT-TA-TATAT
1 ATAGTTTATATATACTATAC
352923 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTATAC
*
352943 ATAGTTTATACATAC
1 ATAGTTTATATATAC
352958 ATGTACTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
14 4 0.07
15 2 0.04
16 2 0.04
17 4 0.07
18 4 0.07
19 2 0.04
20 22 0.39
21 2 0.04
22 8 0.14
23 7 0.12
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:352997 original size:55 final size:57
Alignment explanation
Indices: 352850--352997 Score: 153
Period size: 55 Copynumber: 2.6 Consensus size: 57
352840 TTGTTTATAA
* * * * *
352850 ACTATAGGTTACATATATAGTTT-ATATAACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTAAT-TTATATATACATAGATTGTATACATACATAT
* * * *
352907 ACTATATGTTATATATATAGTTT-ATATATACTATACATAG-TT-TATACATACATGT
1 ACTATAAGTTACATATATAGTTTAATTTATA-TATACATAGATTGTATACATACATAT
352962 ACTATAAGTTACATATATA-TTTACATTTATATATAC
1 ACTATAAGTTACATATATAGTTTA-ATTTATATATAC
352998 TACTATAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
54 3 0.04
55 33 0.43
56 10 0.13
57 31 0.40
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (57 bp):
ACTATAAGTTACATATATAGTTTAATTTATATATACATAGATTGTATACATACATAT
Found at i:353050 original size:7 final size:7
Alignment explanation
Indices: 353038--353172 Score: 60
Period size: 7 Copynumber: 19.6 Consensus size: 7
353028 TATGCATAGT
353038 GTTTAGG
1 GTTTAGG
353045 GTTTA-G
1 GTTTAGG
*
353051 GTTTATG
1 GTTTAGG
353058 GTTTAGG
1 GTTTAGG
*
353065 GTATAGG
1 GTTTAGG
* *
353072 TTTTATG
1 GTTTAGG
*
353079 ATTTAGG
1 GTTTAGG
*
353086 GTTTAGA
1 GTTTAGG
* *
353093 ATTTATG
1 GTTTAGG
* *
353100 ATTTAAG
1 GTTTAGG
*
353107 ATTTAGG
1 GTTTAGG
*
353114 GTTTATG
1 GTTTAGG
* **
353121 ATTTATA
1 GTTTAGG
*
353128 ATTTA-G
1 GTTTAGG
*
353134 GTTTA-T
1 GTTTAGG
** *
353140 GCATAGT
1 GTTTAGG
353147 GTTTAGG
1 GTTTAGG
353154 GTTTAGG
1 GTTTAGG
353161 GTTTTAGG
1 G-TTTAGG
353169 GTTT
1 GTTT
353173 CTATAAACTA
Statistics
Matches: 99, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
6 13 0.13
7 79 0.80
8 7 0.07
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:353085 original size:14 final size:14
Alignment explanation
Indices: 353039--353125 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
353029 ATGCATAGTG
*
353039 TTTAGGGTTTA-GG
1 TTTAGGGTTTATGA
* * *
353052 TTTATGGTTTAGGG
1 TTTAGGGTTTATGA
* *
353066 TATAGGTTTTATGA
1 TTTAGGGTTTATGA
353080 TTTAGGGTTTA-GAA
1 TTTAGGGTTTATG-A
* * *
353094 TTTATGATTTAAGA
1 TTTAGGGTTTATGA
353108 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
353122 TTTA
1 TTTA
353126 TAATTTAGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
13 11 0.19
14 46 0.79
15 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:353097 original size:21 final size:21
Alignment explanation
Indices: 353039--353172 Score: 105
Period size: 21 Copynumber: 6.5 Consensus size: 21
353029 ATGCATAGTG
*
353039 TTTAGGGTTTA-GGTTTATGG
1 TTTAGGGTTTAGGGTTTATGA
* *
353059 TTTAGGGTATAGGTTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
**
353080 TTTAGGGTTTAGAATTTATGA
1 TTTAGGGTTTAGGGTTTATGA
* *
353101 TTTAAGATTTAGGGTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
***
353122 TTTATAATTTA-GGTTTATGCA
1 TTTAGGGTTTAGGGTTTATG-A
* * *
353143 --TAGTGTTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGTTTA-TGA
353163 TTTAGGGTTT
1 TTTAGGGTTT
353173 CTATAAACTA
Statistics
Matches: 90, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
19 6 0.07
20 24 0.27
21 53 0.59
22 7 0.08
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATGA
Found at i:353124 original size:28 final size:28
Alignment explanation
Indices: 353073--353132 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
353063 GGGTATAGGT
* *
353073 TTTATGATTTAGGGTTTAGAATTTATGA
1 TTTAAGATTTAGGGTTTAGAATTTATAA
353101 TTTAAGATTTAGGGTTTATG-ATTTATAA
1 TTTAAGATTTAGGGTTTA-GAATTTATAA
353129 TTTA
1 TTTA
353133 GGTTTATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (28 bp):
TTTAAGATTTAGGGTTTAGAATTTATAA
Found at i:353291 original size:20 final size:18
Alignment explanation
Indices: 353248--353302 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 18
353238 TAATTTACTT
*
353248 TATATGGTTTATATATA-
1 TATATAGTTTATATATAC
353265 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
353283 TATACATAGTTTATACATAC
1 TAT--ATAGTTTATATATAC
353303 ATGTACTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 16 0.48
18 3 0.09
20 14 0.42
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:353542 original size:2 final size:2
Alignment explanation
Indices: 353528--353763 Score: 66
Period size: 2 Copynumber: 118.5 Consensus size: 2
353518 ATTTATAAAC
* * * *
353528 TA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
353569 TA TA TA TA TA AA T- TA TA GTT TA TA AA CTA TA TA CTT TT TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA
* * * ** *
353611 GTT TA TA CA TA TA TA GTT TA TA TA CC TA GTT TA TA TA TA TA GT-
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * *
353654 TCA TA TA AA CA TA -A TA TA TA TA TA TA TA TC T- TA TA -A TA -A
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
353693 T- TA TA TA GTT TA TA -A TA TA AA TA TA GTT TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* *
353735 T- TT TA TA TA TA AA CT- TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T
353764 TTTTTCAATT
Statistics
Matches: 169, Mismatches: 40, Indels: 50
0.65 0.15 0.19
Matches are distributed among these distances:
1 13 0.08
2 145 0.86
3 11 0.07
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:353553 original size:68 final size:71
Alignment explanation
Indices: 353468--353651 Score: 229
Period size: 68 Copynumber: 2.6 Consensus size: 71
353458 TATAGATTAC
* *
353468 TTATATTAG-TTATACATACATATATATATACTTTAT-TA-ATATAAATTATAATTTATAAACTA
1 TTATA-TAGTTTATACATATATATATATATACTATATATATATATAAATTATAATTTATAAACTA
353530 TATA-TT
65 TATACTT
* *
353536 TTATATAGTTTATACATATATA-ATTTATA-TATATATATATATAAATTATAGTTTATAAACTAT
1 TTATATAGTTTATACATATATATATATATACTATATATATATATAAATTATAATTTATAAACTAT
353599 ATACTT
66 ATACTT
* *
353605 TT-TATAGTTTATACATATATAGTTTATATACCTAGTTTATATATATA
1 TTATATAGTTTATACATATATA-TATATATA-CTA-TATATATATATA
353652 GTTCATATAA
Statistics
Matches: 100, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
66 4 0.04
67 11 0.11
68 63 0.63
69 4 0.04
70 5 0.05
72 2 0.02
73 11 0.11
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (71 bp):
TTATATAGTTTATACATATATATATATATACTATATATATATATAAATTATAATTTATAAACTAT
ATACTT
Found at i:353555 original size:15 final size:15
Alignment explanation
Indices: 353537--353732 Score: 89
Period size: 15 Copynumber: 13.4 Consensus size: 15
353527 CTATATATTT
*
353537 TATATAGTTTATACA
1 TATATAGTTTATAAA
* *
353552 TATATAATTTATATA
1 TATATAGTTTATAAA
*
353567 TATATA-TATATAAA
1 TATATAGTTTATAAA
353581 T-TATAGTTTATAAA
1 TATATAGTTTATAAA
*
353595 CTATATA-CTT-T---
1 -TATATAGTTTATAAA
*
353606 T-TATAGTTTATACA
1 TATATAGTTTATAAA
353620 TATATAGTTTAT--A
1 TATATAGTTTATAAA
**
353633 TACCTAGTTTAT--A
1 TATATAGTTTATAAA
353646 TATATAGTTCATATAAA
1 TATATAGTT--TATAAA
* * *
353663 CATA-A-TATATATA
1 TATATAGTTTATAAA
353676 TATATA-TCTTATAATAA
1 TATATAGT-TTAT-A-AA
353693 TTATATAGTTTATAATA
1 -TATATAGTTTATAA-A
*
353710 TAAATATAGTTTATATA
1 T--ATATAGTTTATAAA
353727 TATATA
1 TATATA
353733 TATTTTATAT
Statistics
Matches: 141, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
9 4 0.03
10 3 0.02
11 1 0.01
13 31 0.22
14 18 0.13
15 44 0.31
16 8 0.06
17 9 0.06
18 22 0.16
19 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (15 bp):
TATATAGTTTATAAA
Found at i:353585 original size:28 final size:27
Alignment explanation
Indices: 353553--353735 Score: 107
Period size: 28 Copynumber: 6.9 Consensus size: 27
353543 GTTTATACAT
*
353553 ATATAATTTATATATATATATATATAA
1 ATATAGTTTATATATATATATATATAA
*
353580 ATTATAGTTTATA-A-ACTATATACT-T-T
1 A-TATAGTTTATATATA-TATATA-TATAA
* * * *
353606 TTATAGTTTATACATATATAGTTTATAT
1 ATATAGTTTATATATATATA-TATATAA
**
353634 ACCTAGTTTATATATATAGT-TCATATAA
1 ATATAGTTTATATATATA-TAT-ATATAA
* * * *
353662 ACATAATATATATATATATATCT-TATA
1 ATATAGTTTATATATATATATATATA-A
*
353689 ATA-A--TTATATAGTTTATA-ATATAA
1 ATATAGTTTATATA-TATATATATATAA
353713 ATATAGTTTATATATATATATAT
1 ATATAGTTTATATATATATATAT
353736 TTTATATATA
Statistics
Matches: 119, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
24 11 0.09
25 19 0.16
26 15 0.13
27 27 0.23
28 46 0.39
29 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATAGTTTATATATATATATATATAA
Found at i:353661 original size:68 final size:68
Alignment explanation
Indices: 353468--353743 Score: 222
Period size: 68 Copynumber: 4.1 Consensus size: 68
353458 TATAGATTAC
* * * *
353468 TTATATTAG-TTATACATACAT-ATATATATAC-TTTATTAATATAAATTATAATTTATAAACTA
1 TTATA-TAGTTTATACATATATAATTTATATACATATA-T-ATATAAATTATAGTTTATAAACTA
353530 TATATT
63 TATATT
*
353536 TTATATAGTTTATACATATATAATTTATATATATATATATATAAATTATAGTTTATAAACTATAT
1 TTATATAGTTTATACATATATAATTTATATACATATATATATAAATTATAGTTTATAAACTATAT
353601 ACTT
66 A-TT
* * *
353605 TT-TATAGTTTATACATATATAGTTTATATACCTAGT-T-TATATA-TATAGTTCATATAAAC-A
1 TTATATAGTTTATACATATATAATTTATATACATA-TATATATAAATTATAGTT--TATAAACTA
353665 TA-A-T
63 TATATT
* * * * *
353669 ATATATA-TATATATCTTATAATAA-TTATATA-GTTTATAATATAAA-TATAGTTTATATATA-
1 TTATATAGTTTATA-CATAT-ATAATTTATATACATATAT-ATATAAATTATAGTTTATA-A-AC
353729 TATATATT
61 TATATATT
353737 TTATATA
1 TTATATA
353744 TAAACTTATA
Statistics
Matches: 173, Mismatches: 17, Indels: 36
0.77 0.08 0.16
Matches are distributed among these distances:
63 1 0.01
64 13 0.08
65 16 0.09
66 27 0.16
67 12 0.07
68 87 0.50
69 14 0.08
70 3 0.02
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (68 bp):
TTATATAGTTTATACATATATAATTTATATACATATATATATAAATTATAGTTTATAAACTATAT
ATT
Found at i:353741 original size:15 final size:15
Alignment explanation
Indices: 353537--353766 Score: 69
Period size: 15 Copynumber: 14.7 Consensus size: 15
353527 CTATATATTT
* *
353537 TATATAGTTTATACA
1 TATATATTTTATATA
*
353552 TATATAATTTATATA
1 TATATATTTTATATA
* *
353567 TATATA-TATATAAA
1 TATATATTTTATATA
* *
353581 T-TATAGTTTATAAA
1 TATATATTTTATATA
353595 CTATATACTTTT-TATA
1 -TATATA-TTTTATATA
* * * *
353611 GTTTATACATATATAGTT
1 -TATATA-TTTTATA-TA
*
353629 TATATACCTAGTT-TATA
1 TATATA--T-TTTATATA
* *
353646 TATATAGTTCATATA
1 TATATATTTTATATA
* * * *
353661 AACATAATATATATA
1 TATATATTTTATATA
*
353676 TATATATCTTATAATAA
1 TATATATTTTAT-AT-A
353693 TTATATAGTTTATAATATA
1 -TATATA-TTT-T-ATATA
*
353712 AATATAGTTTATATATA
1 TATATA-TTT-TATATA
353729 TATATATTTTATATA
1 TATATATTTTATATA
*
353744 TA-A-A-CTTATATA
1 TATATATTTTATATA
353756 TATTATATTTT
1 TA-TATATTTT
353767 TTCAATTTTT
Statistics
Matches: 161, Mismatches: 35, Indels: 37
0.69 0.15 0.16
Matches are distributed among these distances:
12 9 0.06
13 5 0.03
14 17 0.11
15 50 0.31
16 22 0.14
17 28 0.17
18 21 0.13
19 4 0.02
20 3 0.02
21 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATTTTATATA
Found at i:353754 original size:19 final size:17
Alignment explanation
Indices: 353668--353747 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
353658 ATAAACATAA
*
353668 TATATATATATATA-TCT
1 TATATATAAATATAGT-T
353685 TATA-ATAATTATATAGTT
1 TATATATAA--ATATAGTT
353703 TATAATATAAATATAGTT
1 TAT-ATATAAATATAGTT
* *
353721 TATATATATATATATTT
1 TATATATAAATATAGTT
353738 TATATATAAA
1 TATATATAAA
353748 CTTATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.06
17 25 0.46
18 20 0.37
19 2 0.04
20 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATATAAATATAGTT
Found at i:357143 original size:23 final size:22
Alignment explanation
Indices: 357117--357166 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
357107 AAACGTGTCA
*
357117 AAAGCAAGAGGAAAATACGTTAT
1 AAAGCAA-AGGAAAACACGTTAT
* *
357140 AAAGGTAAAGGAAAACATGTTAT
1 AAA-GCAAAGGAAAACACGTTAT
357163 AAAG
1 AAAG
357167 GAATAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 19 0.83
24 3 0.13
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (22 bp):
AAAGCAAAGGAAAACACGTTAT
Found at i:366200 original size:6 final size:6
Alignment explanation
Indices: 366189--366339 Score: 154
Period size: 6 Copynumber: 25.7 Consensus size: 6
366179 AAAATAACTT
* * *
366189 CTTCTC CTTCTC CTTCT- CTTCTT TTTCCTT CTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTT-CTC CTTCTC CTTCTC CTTCTC
* * *
366237 CTTCTC CTTCTGC TTCTTCTT CTTCTC ATTCTC CTTGTC CTTCTC CTTCTC
1 CTTCTC CTTCT-C --CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
366288 CTTCTC CTTCTC CTTCT- C--CTC CTTCTC CTTCTC CTT-T- -TTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
*
366330 CTTCTT CTTC
1 CTTCTC CTTC
366340 CTATTCTTCT
Statistics
Matches: 124, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
3 4 0.03
4 2 0.02
5 7 0.06
6 100 0.81
7 6 0.05
9 5 0.04
ACGTcount: A:0.01, C:0.44, G:0.01, T:0.54
Consensus pattern (6 bp):
CTTCTC
Found at i:366253 original size:33 final size:32
Alignment explanation
Indices: 366186--366354 Score: 172
Period size: 30 Copynumber: 5.4 Consensus size: 32
366176 AAAAAAATAA
**
366186 CTTCTTCTCCTTCTCCTTCT-CTTCTTTTTC-
1 CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTCT
366216 CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTCT
1 CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTCT
* * *
366248 GCTTCTTCTTCTTCTCATTCTCCTTGTCCTTCT
1 -CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTCT
*
366281 C--CTTCTCCTTCTCCTTCTCCTTCTCCTCCTT
1 CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTC-T
* *
366312 CTCCTTCTCCTT-T--TTCTCCTTCTTCTTCCT
1 CTTCTTCTCCTTCTCCTTCTCCTTCTCCTT-CT
* *
366342 ATTCTTCTTCTTC
1 CTTCTTCTCCTTC
366355 ATCATCTTCT
Statistics
Matches: 117, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
30 66 0.56
31 11 0.09
32 2 0.02
33 38 0.32
ACGTcount: A:0.01, C:0.43, G:0.01, T:0.55
Consensus pattern (32 bp):
CTTCTTCTCCTTCTCCTTCTCCTTCTCCTTCT
Found at i:366348 original size:15 final size:15
Alignment explanation
Indices: 366330--366398 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
366320 CCTTTTTCTC
*
366330 CTTCTTCTTCCT-ATT
1 CTTCTTCTTCATCA-T
366345 CTTCTTCTTCATCAT
1 CTTCTTCTTCATCAT
*
366360 CTTCTTCTTTC-TCCT
1 CTTCTTC-TTCATCAT
* * *
366375 CTTCCTCCTCTTC-T
1 CTTCTTCTTCATCAT
366389 CTTCTTCTTC
1 CTTCTTCTTC
366399 TTCTTCTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
14 11 0.24
15 30 0.67
16 4 0.09
ACGTcount: A:0.04, C:0.39, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTCTTCTTCATCAT
Found at i:366352 original size:6 final size:6
Alignment explanation
Indices: 366186--366407 Score: 137
Period size: 6 Copynumber: 37.2 Consensus size: 6
366176 AAAAAAATAA
* * * * *
366186 CTTCTT CTCCTT CTCCTT C-TCTT CTTTTT CCTTCTT CTCCTT CTCCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT -CTTCTT CTTCTT CTTCTT
* * * * * * *
366234 CTCCTT CTCCTT CTGCTT CTTCTT CTTC-T CATTCTC CTTGTC CTTCTC
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT C-TTCTT CTTCTT CTTCTT
* * * * * * * * *
366282 CTTCTC CTTCTC CTTCTC CTTCTC CTCCTT CTCCTT CTCCTT TTTCTC
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * *
366330 CTTCTT CTTCCT ATTCTT CTTCTT CATCAT CTTCTT CTT-TCT CCTCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCT-T CTTCTT
* *
366378 CCTCCT CTTC-T CTTCTT CTTCTT CTTCTT C
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT C
366408 AAAACAAAAC
Statistics
Matches: 181, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
5 12 0.07
6 162 0.90
7 7 0.04
ACGTcount: A:0.02, C:0.42, G:0.01, T:0.55
Consensus pattern (6 bp):
CTTCTT
Found at i:367649 original size:3 final size:3
Alignment explanation
Indices: 367641--367665 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
367631 GTTGGTATTT
367641 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
367666 CATCTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:368319 original size:31 final size:31
Alignment explanation
Indices: 368264--368326 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
368254 TTAACGGTGG
** *
368264 GGGACTTAAACCGAATGGACCGATAACTTTA
1 GGGACTTAAACCGAACAGACCGATAACGTTA
*
368295 GGGACTTAAACCGAACAGATCGATAACGTTA
1 GGGACTTAAACCGAACAGACCGATAACGTTA
368326 G
1 G
368327 AAACCATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (31 bp):
GGGACTTAAACCGAACAGACCGATAACGTTA
Found at i:371006 original size:23 final size:23
Alignment explanation
Indices: 370972--371023 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
370962 TTGTATAATG
*
370972 TTAAACAAACATGTTAGTGAACA
1 TTAAACAAACATGTTAGCGAACA
* * *
370995 TTAAACATACATGTTCGCGAACG
1 TTAAACAAACATGTTAGCGAACA
371018 TTAAAC
1 TTAAAC
371024 GAACCAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (23 bp):
TTAAACAAACATGTTAGCGAACA
Found at i:374381 original size:2 final size:2
Alignment explanation
Indices: 374374--374403 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
374364 GTAACTAGAT
374374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
374404 ATCATGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:375283 original size:60 final size:60
Alignment explanation
Indices: 375213--375384 Score: 195
Period size: 60 Copynumber: 2.9 Consensus size: 60
375203 TCTGGTGACT
* * * *
375213 ATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAACCTATACTC-TATAGTCATG-GGATC
1 ATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAATA-TCACATAGTCA-GAGGATC
* * *
375273 ATTTTATAACTTTTAATAGTCGATGGACTCAACAAAAGAATATCACATAGTCAGAGGATC
1 ATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAATATCACATAGTCAGAGGATC
** * * * *
375333 ATTTTATAACTTTTAATAGTTGAGAAACTCAATAAGATAATATCATATAGTC
1 ATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAATATCACATAGTC
375385 GGGAACCACT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 3 0.03
60 92 0.97
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAATATCACATAGTCAGAGGATC
Found at i:381215 original size:22 final size:22
Alignment explanation
Indices: 381172--381215 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
381162 AACCAGATTA
381172 CCCAGAGGGTACAGATACCCCC
1 CCCAGAGGGTACAGATACCCCC
* *
381194 CCCATGAGGTTACCGATACCCC
1 CCCA-GAGGGTACAGATACCCC
381216 TGTGTAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.41, G:0.20, T:0.14
Consensus pattern (22 bp):
CCCAGAGGGTACAGATACCCCC
Found at i:383228 original size:21 final size:21
Alignment explanation
Indices: 383202--383241 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
383192 AAGACTTTAT
383202 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
383223 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
383242 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:385151 original size:18 final size:18
Alignment explanation
Indices: 385128--385162 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
385118 CCATTGAAGA
385128 AAGGGAAGTCTCTTACCC
1 AAGGGAAGTCTCTTACCC
385146 AAGGGAAGTCTCTTACC
1 AAGGGAAGTCTCTTACC
385163 AAAGAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGGGAAGTCTCTTACCC
Found at i:385805 original size:82 final size:82
Alignment explanation
Indices: 385668--385835 Score: 309
Period size: 82 Copynumber: 2.0 Consensus size: 82
385658 AACAACCTCC
* *
385668 TGGTTTTGAAGATTCAAAATTTCCAGATCATGTTTTCAAATTGACAAAAGTACTTTATGGTTTAA
1 TGGTTTTGAAGATTCAAAATTTCCAGATCATGTTTTCAAATTAACAAAAGCACTTTATGGTTTAA
385733 AACAAGCTCCTAGAGCT
66 AACAAGCTCCTAGAGCT
*
385750 TGGTTTTGAAGATTCAAAATTTCCAGATCATGTTTTTAAATTAACAAAAGCACTTTATGGTTTAA
1 TGGTTTTGAAGATTCAAAATTTCCAGATCATGTTTTCAAATTAACAAAAGCACTTTATGGTTTAA
385815 AACAAGCTCCTAGAGCT
66 AACAAGCTCCTAGAGCT
385832 TGGT
1 TGGT
385836 ATGAAAGACT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (82 bp):
TGGTTTTGAAGATTCAAAATTTCCAGATCATGTTTTCAAATTAACAAAAGCACTTTATGGTTTAA
AACAAGCTCCTAGAGCT
Found at i:387181 original size:23 final size:22
Alignment explanation
Indices: 387150--387210 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
387140 TCTGACGATA
* *
387150 GGTATCGATACCCCCTTTGCATG
1 GGTACCGATACCCCC-TTGAATG
387173 GGTACCGATACCCTCCTTGAATG
1 GGTACCGATACCC-CCTTGAATG
387196 GGTACCGATACCCCC
1 GGTACCGATACCCCC
387211 ACATGAGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.20, C:0.34, G:0.21, T:0.25
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:387223 original size:22 final size:23
Alignment explanation
Indices: 387150--387230 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
387140 TCTGACGATA
* ** *
387150 GGTATCGATACCCCCTTTGCATG
1 GGTACCGATACCCCCCATGAATG
* *
387173 GGTACCGATACCCTCCTTGAATG
1 GGTACCGATACCCCCCATGAATG
387196 GGTACCGATACCCCCACATG-A-G
1 GGTACCGATACCCCC-CATGAATG
*
387218 GGTACCTATACCC
1 GGTACCGATACCC
387231 TACACGAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 13 0.26
23 34 0.68
24 3 0.06
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.23
Consensus pattern (23 bp):
GGTACCGATACCCCCCATGAATG
Found at i:398878 original size:43 final size:43
Alignment explanation
Indices: 398772--398925 Score: 148
Period size: 43 Copynumber: 3.6 Consensus size: 43
398762 AGACATATAA
*
398772 CGGCGTTTGTCTTTACAAACGCCGCTATTAACTGTGTATTTAG
1 CGGCATTTGTCTTTACAAACGCCGCTATTAACTGTGTATTTAG
* *** * *
398815 CGGCATTTTTAAATACAAACGCTGTTAATT-ACTGTGTATTTAG
1 CGGCATTTGTCTTTACAAACGCCGCT-ATTAACTGTGTATTTAG
* * * * *
398858 GGGCGTTTGTCTTTATAAACGCCGCTATTGACTATGTATTTAG
1 CGGCATTTGTCTTTACAAACGCCGCTATTAACTGTGTATTTAG
* ** *
398901 TGGCATTTGTAATTAAAAACGCCGC
1 CGGCATTTGTCTTTACAAACGCCGC
398926 AAATAAGCCA
Statistics
Matches: 87, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
42 3 0.03
43 81 0.93
44 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (43 bp):
CGGCATTTGTCTTTACAAACGCCGCTATTAACTGTGTATTTAG
Found at i:408663 original size:23 final size:23
Alignment explanation
Indices: 408633--408708 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
408623 GAGTAGAGGG
*
408633 ATCTATGTGGTCCTTCGGGACAA
1 ATCTATGTGGTTCTTCGGGACAA
* *
408656 ATCTATGTGGTTCTTTGGGATAA
1 ATCTATGTGGTTCTTCGGGACAA
*
408679 ATCTATATGGTTCTTCGGGACAA
1 ATCTATGTGGTTCTTCGGGACAA
408702 ATTCTAT
1 A-TCTAT
408709 ATGACACTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 41 0.89
24 5 0.11
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (23 bp):
ATCTATGTGGTTCTTCGGGACAA
Found at i:413181 original size:34 final size:34
Alignment explanation
Indices: 413129--413272 Score: 108
Period size: 34 Copynumber: 3.9 Consensus size: 34
413119 CCTTAGCTGA
*
413129 AATGTATATGGGTACATTATCGGCATAAAAGAAT
1 AATGCATATGGGTACATTATCGGCATAAAAGAAT
* * *
413163 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCTTAGCT
1 AATGCATATGGGTACATTATCGGCAT-AAA--A-G----A-AT
* *
413206 GAAATGTATATGGGAACATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTACATTATCGGCATAAAAGAAT
* * *
413242 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTACATTATCGGCATAAAAG
413273 GATGCATTAG
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
34 49 0.58
35 3 0.04
36 1 0.01
37 2 0.02
38 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
44 3 0.04
45 22 0.26
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTACATTATCGGCATAAAAGAAT
Found at i:413226 original size:79 final size:79
Alignment explanation
Indices: 413095--413540 Score: 662
Period size: 79 Copynumber: 5.7 Consensus size: 79
413085 GGCACTGTGT
* * *
413095 GTGCATTATTGGCACGAAATGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
413160 AATAATGCATATGG
66 AATAATGCATATGG
*
413174 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGAACATTATCGGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
413239 AATAATGCATATGG
66 AATAATGCATATGG
* ** * *
413253 GTGCATTATTGGCATGAAAGGATG-CATTAGCTTAAATGTATATGAATACATTATTGTCATAAAA
1 GTGCATTATTGGCATGAAAGGATGTC-TTAGCTGAAATGTATATGGGTACATTATCGGCATAAAA
* *
413317 AAATAATTCATATGG
65 GAATAATGCATATGG
** * * * *
413332 GTGCATTATTGGCACAAAAGGATGCCTTAGCTGAAATTTATATGGGTACATTATCGGTATAAAAT
1 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
413397 AATAATGCATATGG
66 AATAATGCATATGG
*
413411 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATTGGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
413476 AATAATGCATATGG
66 AATAATGCATATGG
** * * *
413490 GTGCATTATTATCATGAAAGGATGTC-AAGTTGAAATGTATATGGGTGCATT
1 GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATT
413541 TTCAATATAA
Statistics
Matches: 330, Mismatches: 35, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
78 23 0.07
79 306 0.93
80 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (79 bp):
GTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACATTATCGGCATAAAAG
AATAATGCATATGG
Found at i:417912 original size:34 final size:34
Alignment explanation
Indices: 417856--418072 Score: 119
Period size: 34 Copynumber: 5.7 Consensus size: 34
417846 AGAAATGTAT
* **
417856 TATGGGTACATTATCGAAATAAAAGAATAATGCA
1 TATGGGTACATTATTGGCATAAAAGAATAATGCA
* *
417890 TATGGGTACATTATTTGCATAAAATGATACCTTAGCTGAAACGTA
1 TATGGGTACATTATTGGCATAAAA-GA-A---TA-ATG---C--A
* *
417935 TATGGGTACATTATCGGTATAAAAGAATAATGCA
1 TATGGGTACATTATTGGCATAAAAGAATAATGCA
* * *
417969 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTA
1 TATGGGTACATTATTGGCAT-AAA--A-G----A-AT--AATGCA
*
418014 TATGGGTACATTATCGGCATAAAAGAATAATGCA
1 TATGGGTACATTATTGGCATAAAAGAATAATGCA
* *
418048 TATGGGTGCATTATTGGCATGAAAG
1 TATGGGTACATTATTGGCATAAAAG
418073 GATGCCTTAG
Statistics
Matches: 140, Mismatches: 21, Indels: 44
0.68 0.10 0.21
Matches are distributed among these distances:
34 65 0.46
35 5 0.04
36 3 0.02
37 2 0.01
38 1 0.01
39 4 0.03
40 4 0.03
41 1 0.01
42 2 0.01
43 3 0.02
44 5 0.04
45 45 0.32
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (34 bp):
TATGGGTACATTATTGGCATAAAAGAATAATGCA
Found at i:417957 original size:45 final size:44
Alignment explanation
Indices: 417889--418118 Score: 140
Period size: 45 Copynumber: 5.6 Consensus size: 44
417879 AGAATAATGC
**
417889 ATATGGGTACATTATTTGCATAAAATGATACCTTAGCTGAAACGT
1 ATATGGGTACATTATCGGCATAAAA-GATACCTTAGCTGAAACGT
* *
417934 ATATGGGTACATTATCGGTATAAAAGA-A---TA-ATG---C--
1 ATATGGGTACATTATCGGCATAAAAGATACCTTAGCTGAAACGT
* * * * *
417968 ATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGT
1 ATATGGGTACATTATCGGCAT-AAAAGATACCTTAGCTGAAACGT
*
418013 ATATGGGTACATTATCGGCATAAAAGA-A---TA-ATG---C--
1 ATATGGGTACATTATCGGCATAAAAGATACCTTAGCTGAAACGT
* * * * *
418047 ATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGT
1 ATATGGGTACATTATCGGCAT-AAAAGATACCTTAGCTGAAACGT
* *
418092 ATATGGGTATATTATCAGCATAAAAGA
1 ATATGGGTACATTATCGGCATAAAAGA
418119 ATAATGCATA
Statistics
Matches: 135, Mismatches: 28, Indels: 45
0.65 0.13 0.22
Matches are distributed among these distances:
34 37 0.27
35 10 0.07
36 1 0.01
39 8 0.06
40 8 0.06
43 1 0.01
44 12 0.09
45 58 0.43
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (44 bp):
ATATGGGTACATTATCGGCATAAAAGATACCTTAGCTGAAACGT
Found at i:417973 original size:79 final size:79
Alignment explanation
Indices: 417731--418199 Score: 668
Period size: 79 Copynumber: 5.9 Consensus size: 79
417721 GTATGGGCAC
* * **
417731 TATGTGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGTATATATGTACATTATCGGCAT
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
417796 AAAAGAATAATGCA
66 AAAAGAATAATGCA
* **
417810 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCAGAAATGTATTATGGGTACATTATCGAAA
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTA-TATGGGTACATTATCGGCA
417875 TAAAAGAATAATGCA
65 TAAAAGAATAATGCA
* * * * * * *
417890 TATGGGTACATTATTTGCATAAAATGATACCTTAGCTGAAACGTATATGGGTACATTATCGGTAT
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
417955 AAAAGAATAATGCA
66 AAAAGAATAATGCA
417969 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
418034 AAAAGAATAATGCA
66 AAAAGAATAATGCA
* *
418048 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTATATTATCAGCAT
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
418113 AAAAGAATAATGCA
66 AAAAGAATAATGCA
*** * * ** * * * * **
418127 TACATGTGCATTATTAGCAAGAAAGGATGCCAAAGTTGAAATGCATATGGGTTCATTTTCAACAT
1 TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
418192 AAAAGAAT
66 AAAAGAAT
418200 GCTATAATTA
Statistics
Matches: 351, Mismatches: 38, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
79 283 0.81
80 68 0.19
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (79 bp):
TATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACATTATCGGCAT
AAAAGAATAATGCA
Found at i:420246 original size:3 final size:3
Alignment explanation
Indices: 420234--420264 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
420224 ATTTGGTTTA
420234 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
420265 CCCCACCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:421539 original size:23 final size:24
Alignment explanation
Indices: 421509--421561 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
421499 TAGAGGGATA
*
421509 TATGTGGTCCTTCGGGATAAA-TC
1 TATGTGGTCCTTCGGGACAAATTC
*
421532 TATGTGGTCTTTCGGGACAAATTC
1 TATGTGGTCCTTCGGGACAAATTC
421556 TATGTG
1 TATGTG
421562 TCACTTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (24 bp):
TATGTGGTCCTTCGGGACAAATTC
Found at i:423988 original size:14 final size:14
Alignment explanation
Indices: 423969--423999 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
423959 AATTTTATTA
*
423969 AAAAAGCTAATCCT
1 AAAAAGATAATCCT
423983 AAAAAGATAATCCT
1 AAAAAGATAATCCT
423997 AAA
1 AAA
424000 CTTAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAAGATAATCCT
Found at i:425854 original size:14 final size:12
Alignment explanation
Indices: 425815--425931 Score: 70
Period size: 10 Copynumber: 9.8 Consensus size: 12
425805 CATATAAATG
425815 ACGAACAAACGTAA
1 ACGAAC-AAC-TAA
425829 ACGAA-AAC-AA
1 ACGAACAACTAA
425839 ACGAACGAACGTAA
1 ACGAAC-AAC-TAA
425853 ACGAAC-AC-AA
1 ACGAACAACTAA
425863 ACGAACGAACATAA
1 ACGAAC-AAC-TAA
* *
425877 ATGAACATAATAA
1 ACGAACA-ACTAA
*
425890 ATGAAC-A-TAA
1 ACGAACAACTAA
*
425900 ACGAACACAATAA
1 ACGAACA-ACTAA
425913 ACGAAC-A-TAA
1 ACGAACAACTAA
425923 ACGAACAAC
1 ACGAACAAC
425932 ACAAACACAA
Statistics
Matches: 86, Mismatches: 3, Indels: 30
0.72 0.03 0.25
Matches are distributed among these distances:
10 32 0.37
11 3 0.03
12 11 0.13
13 19 0.22
14 21 0.24
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.09
Consensus pattern (12 bp):
ACGAACAACTAA
Found at i:425882 original size:24 final size:25
Alignment explanation
Indices: 425815--425929 Score: 125
Period size: 24 Copynumber: 4.8 Consensus size: 25
425805 CATATAAATG
* * *
425815 ACGAACAAACGTAAACGAAAACAA-
1 ACGAACGAACATAAACGAACACAAT
*
425839 ACGAACGAACGTAAACGAACACAA-
1 ACGAACGAACATAAACGAACACAAT
* *
425863 ACGAACGAACATAAATGAACATAAT
1 ACGAACGAACATAAACGAACACAAT
*
425888 A--AATGAACATAAACGAACACAAT
1 ACGAACGAACATAAACGAACACAAT
425911 A--AACGAACATAAACGAACA
1 ACGAACGAACATAAACGAACA
425930 ACACAAACAC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
23 37 0.46
24 43 0.53
25 1 0.01
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (25 bp):
ACGAACGAACATAAACGAACACAAT
Found at i:425891 original size:13 final size:13
Alignment explanation
Indices: 425873--425899 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
425863 ACGAACGAAC
425873 ATAAATGAACATA
1 ATAAATGAACATA
425886 ATAAATGAACATA
1 ATAAATGAACATA
425899 A
1 A
425900 ACGAACACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAATGAACATA
Found at i:425899 original size:23 final size:23
Alignment explanation
Indices: 425842--425929 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
425832 AAAACAAACG
*
425842 AACGAACGTAAACGAACACAA-A
1 AACGAACATAAACGAACACAATA
* *
425864 CGAACGAACATAAATGAACATAATA
1 --AACGAACATAAACGAACACAATA
*
425889 AATGAACATAAACGAACACAATA
1 AACGAACATAAACGAACACAATA
425912 AACGAACATAAACGAACA
1 AACGAACATAAACGAACA
425930 ACACAAACAC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 37 0.66
24 18 0.32
25 1 0.02
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.10
Consensus pattern (23 bp):
AACGAACATAAACGAACACAATA
Found at i:425937 original size:23 final size:22
Alignment explanation
Indices: 425834--425937 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 22
425824 CGTAAACGAA
* *
425834 AACAAACGAACGAACGTAAACG
1 AACAAACAAACGAACATAAACG
* *
425856 AACACAAACGAACGAACATAAATG
1 -A-ACAAACAAACGAACATAAACG
* *
425880 AACATAATAAATGAACATAAACG
1 AACA-AACAAACGAACATAAACG
*
425903 AACACAATAAACGAACATAAACG
1 AACA-AACAAACGAACATAAACG
425926 AACAACACAAAC
1 AACAA-ACAAAC
425938 ACAAAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.06
23 46 0.67
24 19 0.28
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.09
Consensus pattern (22 bp):
AACAAACAAACGAACATAAACG
Found at i:426209 original size:10 final size:10
Alignment explanation
Indices: 426194--426241 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
426184 CCCTCTGTTC
426194 GAACATAAAT
1 GAACATAAAT
426204 GAACATAAAT
1 GAACATAAAT
426214 GAACGAACATAAAT
1 ----GAACATAAAT
426228 GAACATAAAT
1 GAACATAAAT
426238 GAAC
1 GAAC
426242 GAACATAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 24 0.71
14 10 0.29
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:426222 original size:24 final size:24
Alignment explanation
Indices: 426193--426268 Score: 125
Period size: 24 Copynumber: 3.1 Consensus size: 24
426183 GCCCTCTGTT
426193 CGAACATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
426217 CGAACATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
*
426241 CGAACATAAAGGAACATATAATCGAA
1 CGAACATAAATGAACATA-AAT-GAA
426267 CG
1 CG
426269 TTCACGAACG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 41 0.84
25 3 0.06
26 5 0.10
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.16
Consensus pattern (24 bp):
CGAACATAAATGAACATAAATGAA
Found at i:426223 original size:14 final size:14
Alignment explanation
Indices: 426204--426255 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
426194 GAACATAAAT
426204 GAACATAAATGAAC
1 GAACATAAATGAAC
426218 GAACATAAAT----
1 GAACATAAATGAAC
426228 GAACATAAATGAAC
1 GAACATAAATGAAC
*
426242 GAACATAAAGGAAC
1 GAACATAAATGAAC
426256 ATATAATCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 10 0.30
14 23 0.70
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.13
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:429434 original size:36 final size:36
Alignment explanation
Indices: 429387--429469 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
429377 ACCGAATTAA
* * *
429387 ACGGAGACGGGGAAAAATCGTTTATGCTAAACGGGG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGAG
*
429423 ACGGGGACGGGGAAAAACCGTTTATGTTAAACGGAG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGAG
429459 ACGGGGACGGG
1 ACGGGGACGGG
429470 ACGGGTTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.31, C:0.14, G:0.40, T:0.14
Consensus pattern (36 bp):
ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGAG
Found at i:429595 original size:41 final size:41
Alignment explanation
Indices: 429538--429615 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
429528 ATAATTATTT
429538 TATATATATATATAATATTAATAAATTTAATTTAAATTAAA
1 TATATATATATATAATATTAATAAATTTAATTTAAATTAAA
* *
429579 TATATATATATATAATATTTATATATTTAATTTAAAT
1 TATATATATATATAATATTAATAAATTTAATTTAAAT
429616 ATATATACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (41 bp):
TATATATATATATAATATTAATAAATTTAATTTAAATTAAA
Found at i:429601 original size:15 final size:15
Alignment explanation
Indices: 429542--429622 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
429532 TTATTTTATA
429542 TATATATATAATATT
1 TATATATATAATATT
* * *
429557 AATAAAT-TTA-ATT
1 TATATATATAATATT
* *
429570 TAAAT-TA-AATATA
1 TATATATATAATATT
429583 TATATATATAATATT
1 TATATATATAATATT
*
429598 TATATATTTAAT-TT
1 TATATATATAATATT
*
429612 AAATATATATA
1 -TATATATATA
429623 CCCGGCCCGA
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
12 2 0.04
13 11 0.23
14 6 0.12
15 29 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATAATATT
Found at i:429764 original size:25 final size:25
Alignment explanation
Indices: 429730--429778 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
429720 ATCCCCGTGA
* *
429730 TTTTTTAAACGGGGACGGGTACGGG
1 TTTTTTAAACGGAGACGGGGACGGG
429755 TTTTTTAAACGGAGACGGGGACGG
1 TTTTTTAAACGGAGACGGGGACGG
429779 AGGATCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.39, T:0.27
Consensus pattern (25 bp):
TTTTTTAAACGGAGACGGGGACGGG
Found at i:434200 original size:19 final size:19
Alignment explanation
Indices: 434178--434216 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
434168 GTTTACCAGC
* *
434178 AATTGTAAAGTTTTTATTT
1 AATTATAAACTTTTTATTT
*
434197 AATTATGAACTTTTTATTT
1 AATTATAAACTTTTTATTT
434216 A
1 A
434217 TTTTGTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (19 bp):
AATTATAAACTTTTTATTT
Found at i:437243 original size:298 final size:302
Alignment explanation
Indices: 436704--437303 Score: 1172
Period size: 298 Copynumber: 2.0 Consensus size: 302
436694 AGAATGTTTC
436704 AATTATCATCTTGGATAACTGCTAATAGTAAAACTTGCTTGTATTTTCCATACAAGAATGTCTCA
1 AATTATCATCTTGGATAACTGCTAATAGTAAAACTTGCTTGTATTTTCCATACAAGAATGTCTCA
436769 TCAATTTGGACCACGAGCTTGATGTATTTCACAACATTAATGCACTGTGAGTAAGTCAAAAAAAT
66 TCAATTTGGACCACGAGCTTGATGTATTTCACAACATTAATGCACTGTGAGTAAGTCAAAAAAAT
436834 GGATAGAATTGGTATCGATCGTGAAGCACTCGATCATTACGGTATGCATGGAAAGTTTCGAAGTC
131 GGATAGAATTGGTATCGATCGTGAAGCACTCGATCATTACGGTATGCATGGAAAGTTTCGAAGTC
436899 AACAATTTTCCCATGGTTCAATATGCGTATTACCTTAAACCAACTTGGTAGTTCGTTATAAGATG
196 AACAATTTTCCCATGGTTCAATATGCGTATTACCTTAAACCAACTTGGTAGTTCGTTATAAGATG
436964 CAACCCATTCATCGTGAAGTTTTTTAATGGCATT-TACTTTG
261 CAACCCATTCATCGTGAAGTTTTTTAATGGCATTATACTTTG
437005 AATTATCATCTTGGATAACTGCTAATAGTAAAACTTGCTTGTA-TTTCCATACAAGAATGTCTCA
1 AATTATCATCTTGGATAACTGCTAATAGTAAAACTTGCTTGTATTTTCCATACAAGAATGTCTCA
437069 TCAATTTGGACCACGAGCTTGATGTATTTCAC-A-ATTAATGCACTGTGAGTAAGTCAAAAAAAT
66 TCAATTTGGACCACGAGCTTGATGTATTTCACAACATTAATGCACTGTGAGTAAGTCAAAAAAAT
437132 GGATAGAATTGGTATCGATCGTGAAGCACTCGATCATTACGGTATGCATGGAAAGTTTCGAAGTC
131 GGATAGAATTGGTATCGATCGTGAAGCACTCGATCATTACGGTATGCATGGAAAGTTTCGAAGTC
437197 AACAATTTTCCCATGGTTCAATATGCGTATTACCTTAAACCAACTTGGTAGTTCGTTATAAGATG
196 AACAATTTTCCCATGGTTCAATATGCGTATTACCTTAAACCAACTTGGTAGTTCGTTATAAGATG
437262 CAACCCATTCATCGTGAAGTTTTTTAATGGCATTATACTTTG
261 CAACCCATTCATCGTGAAGTTTTTTAATGGCATTATACTTTG
437304 CCTTCCATGC
Statistics
Matches: 298, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
298 194 0.65
299 8 0.03
300 53 0.18
301 43 0.14
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (302 bp):
AATTATCATCTTGGATAACTGCTAATAGTAAAACTTGCTTGTATTTTCCATACAAGAATGTCTCA
TCAATTTGGACCACGAGCTTGATGTATTTCACAACATTAATGCACTGTGAGTAAGTCAAAAAAAT
GGATAGAATTGGTATCGATCGTGAAGCACTCGATCATTACGGTATGCATGGAAAGTTTCGAAGTC
AACAATTTTCCCATGGTTCAATATGCGTATTACCTTAAACCAACTTGGTAGTTCGTTATAAGATG
CAACCCATTCATCGTGAAGTTTTTTAATGGCATTATACTTTG
Found at i:440156 original size:60 final size:59
Alignment explanation
Indices: 440016--440185 Score: 150
Period size: 60 Copynumber: 2.8 Consensus size: 59
440006 ATCCTTATTT
*
440016 TAAATTGGTCCCTAAACTTTTAA-ATATTCTAATTACATCCCTAAACTATAACTATCATTC
1 TAAATTGGTCCCTAAACTTTTAACAT-TTC-AATTACATCCCCAAACTATAACTATCATTC
* * * * * *
440076 TAAATTAGTCCTTAATCTTTTCAACATTTCAATTCCATCCCCAAACTCTGATCT-TCGA-TC
1 TAAATTGGTCCCTAAACTTTT-AACATTTCAATTACATCCCCAAACTAT-AACTATC-ATTC
* * * *
440136 TAAATTGGTCCCCAAACTTTTTAAACATTCCAATTTCAT-CCCAAATTATA
1 TAAATTGGTCCCTAAAC-TTTT-AACATTTCAATTACATCCCCAAACTATA
440186 TGTGTATACT
Statistics
Matches: 89, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
59 1 0.01
60 59 0.66
61 27 0.30
62 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
TAAATTGGTCCCTAAACTTTTAACATTTCAATTACATCCCCAAACTATAACTATCATTC
Done.