Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 21
Found at i:1376887 original size:75 final size:74
Alignment explanation
Indices: 1376754--1376939 Score: 173
Period size: 75 Copynumber: 2.5 Consensus size: 74
1376744 CCAAGAAATA
** * * * *
1376754 GGGTATCGATACCATGGTAAGG-GTATCGATACCA-GTAAAAATATCGAATCTAAATTGGGTATC
1 GGGTATCGATACCATAATAGGGAGTATCGATACCAGGT---TATATAGAAGCTAAATTGGGTATC
1376817 GATAC-CTAGAAG
63 GATACACTA-AAG
* * *
1376829 GGGTATCGGTACCATATCATAGGG-GTATCGATACCAGGTTATATAGAAGCTAATTTGGGTATTG
1 GGGTATCGATACCATA--ATAGGGAGTATCGATACCAGGTTATATAGAAGCTAAATTGGGTATCG
* *
1376893 ATACATTAAGG
64 ATACACTAAAG
*
1376904 GGGTATCGATACCCTAATAGGGTAGTATCGATACCA
1 GGGTATCGATACCATAATAGGG-AGTATCGATACCA
1376940 TAGAAGGGGT
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
73 6 0.07
75 66 0.72
76 2 0.02
77 16 0.17
78 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (74 bp):
GGGTATCGATACCATAATAGGGAGTATCGATACCAGGTTATATAGAAGCTAAATTGGGTATCGAT
ACACTAAAG
Found at i:1376953 original size:20 final size:20
Alignment explanation
Indices: 1376903--1376955 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1376893 ATACATTAAG
*
1376903 GGGGTATCGATACCCTAATA
1 GGGGTATCGATACCATAATA
1376923 GGGTAGTATCGATACCATAGA-A
1 GGG--GTATCGATACCATA-ATA
1376945 GGGGTATCGAT
1 GGGGTATCGAT
1376956 TCTGAAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 11 0.38
22 17 0.59
23 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCATAATA
Found at i:1377368 original size:57 final size:57
Alignment explanation
Indices: 1377298--1377668 Score: 548
Period size: 57 Copynumber: 6.5 Consensus size: 57
1377288 GTGAAAACTA
* *
1377298 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACTCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
* *
1377355 TAAGAAATAATACTAAGT-TATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
*
1377411 TAAGAACTCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
* * ** *
1377468 TAAGAAATCATACCAAGTGTATGAATTTCAGATTGGGTGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
* * * * * *
1377525 TAAAAAAATCATACTAAGTGTATGAATTTCAGATAGGGTGA-TTCGCATGTTAAAATAT
1 T-AAGAAATCATACTAAGTGTATGAATTTCAGATAGGG-CATTTCGTACGCTAAAATGT
* *
1377583 TAAGAAATCATACTAAGTGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1377640 TAAGAAATCATACTAAGTGTATGAATTTC
1 TAAGAAATCATACTAAGTGTATGAATTTC
1377669 GGTATTGGAC
Statistics
Matches: 279, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
56 52 0.19
57 181 0.65
58 46 0.16
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
Found at i:1377579 original size:115 final size:114
Alignment explanation
Indices: 1377298--1377668 Score: 550
Period size: 115 Copynumber: 3.3 Consensus size: 114
1377288 GTGAAAACTA
*
1377298 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACT-CTAAAATGTTAAGAAA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTA-TGCTAAAATGTTAAGAAA
*
1377362 TAATACTAAGT-TATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
65 TCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1377411 TAAGAACTCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGTTAAGAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTATGCTAAAATGTTAAGAAAT
* * * *
1377476 CATACCAAGTGTATGAATTTCAGATTGGGTGTTTTGTACGCTAAAATGT
66 CATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * *
1377525 TAAAAAAATCATACTAAGTGTATGAATTTCAGATAGGGTGA-TTCGCATGTTAAAATATTAAGAA
1 T-AAGAAATCATACTAAGTGTATGAATTTCAGATAGGG-CATTTCGTATGCTAAAATGTTAAGAA
* * *
1377589 ATCATACTAAGTGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
64 ATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1377640 TAAGAAATCATACTAAGTGTATGAATTTC
1 TAAGAAATCATACTAAGTGTATGAATTTC
1377669 GGTATTGGAC
Statistics
Matches: 231, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
113 69 0.30
114 63 0.27
115 98 0.42
116 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (114 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTATGCTAAAATGTTAAGAAAT
CATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1377620 original size:172 final size:170
Alignment explanation
Indices: 1377298--1377668 Score: 580
Period size: 172 Copynumber: 2.2 Consensus size: 170
1377288 GTGAAAACTA
* *
1377298 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACTCTAAAATGTTAAGAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACGCTAAAATGTTAAAAAAT
* * * *
1377363 AATACTAAGTTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAACTCATACTAAG
66 AATACTAAGTTATGAATTTCAGATAGGGCGATTCGCACGCTAAAATATTAAGAAATCATACTAAG
* *
1377428 TGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
131 TGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
* * **
1377468 TAAGAAATCATACCAAGTGTATGAATTTCAGATTGGGTGTTTTGTACGCTAAAATGTTAAAAAAA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACGCTAAAATGTT-AAAAAA
* * * *
1377533 TCATACTAAGTGTATGAATTTCAGATAGGGTGATTCGCATGTTAAAATATTAAGAAATCATACTA
65 TAATACTAAGT-TATGAATTTCAGATAGGGCGATTCGCACGCTAAAATATTAAGAAATCATACTA
1377598 AGTGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
129 AGTGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
1377640 TAAGAAATCATACTAAGTGTATGAATTTC
1 TAAGAAATCATACTAAGTGTATGAATTTC
1377669 GGTATTGGAC
Statistics
Matches: 182, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
170 53 0.29
171 15 0.08
172 114 0.63
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (170 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTTGTACGCTAAAATGTTAAAAAAT
AATACTAAGTTATGAATTTCAGATAGGGCGATTCGCACGCTAAAATATTAAGAAATCATACTAAG
TGTATGAATTTCAAATAGGGCATTTCGTACACTAAAATGT
Found at i:1378161 original size:81 final size:81
Alignment explanation
Indices: 1378023--1378173 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 81
1378013 GGCTTAGTTG
* * * **
1378023 TGCAATTGACAGAAAAGTGTCAATTACGCCAATTAGATAAATGGTTAAGTATCGTTGAGTAAAAG
1 TGCAATTGACAGAAAAGTATCAATTACACCAATTAGATAAAGGGTTAAACATCGTTGAGTAAAAG
1378088 AATAATGGTCTTTCTA
66 AATAATGGTCTTTCTA
* * * * * *
1378104 TGCAATTGGCAGAAATGTATCAATTATACCAGTTAGATAAAGGGTTAAACATTGTTGAGTAGAAG
1 TGCAATTGACAGAAAAGTATCAATTACACCAATTAGATAAAGGGTTAAACATCGTTGAGTAAAAG
1378169 AATAA
66 AATAA
1378174 AGGAATTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 59 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (81 bp):
TGCAATTGACAGAAAAGTATCAATTACACCAATTAGATAAAGGGTTAAACATCGTTGAGTAAAAG
AATAATGGTCTTTCTA
Found at i:1380185 original size:15 final size:15
Alignment explanation
Indices: 1380157--1380201 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1380147 GGGATAATTA
*
1380157 AAATCATATGTATATC
1 AAAT-ATATATATATC
*
1380173 AAATATATATATATT
1 AAATATATATATATC
*
1380188 AAATATAGATATAT
1 AAATATATATATAT
1380202 TTTAGTAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (15 bp):
AAATATATATATATC
Found at i:1380993 original size:24 final size:24
Alignment explanation
Indices: 1380966--1381011 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1380956 ATTGTCCATT
1380966 CCCATAATAATACTTGACTATGTG
1 CCCATAATAATACTTGACTATGTG
1380990 CCCATAATAATACTTGACTATG
1 CCCATAATAATACTTGACTATG
1381012 GATCTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (24 bp):
CCCATAATAATACTTGACTATGTG
Found at i:1388461 original size:2 final size:2
Alignment explanation
Indices: 1388454--1388478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1388444 TGTCAAAAAG
1388454 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1388479 AGCTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1390710 original size:20 final size:20
Alignment explanation
Indices: 1390660--1390715 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
1390650 TACATTAAGG
*
1390660 GGGGTATCGATACCCTAATA
1 GGGGTATCGATACCATAATA
1390680 GGGTAGTATCGATACCATAGA-A
1 GGG--GTATCGATACCATA-ATA
1390702 GGGGTATCGATACC
1 GGGGTATCGATACC
1390716 GAAGGACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 14 0.44
22 17 0.53
23 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (20 bp):
GGGGTATCGATACCATAATA
Found at i:1391121 original size:57 final size:57
Alignment explanation
Indices: 1391056--1391547 Score: 743
Period size: 57 Copynumber: 8.6 Consensus size: 57
1391046 GTGCAAAATA
* *
1391056 TAAGAAATCATACTAAGTGTATGAATTTCAGTTAGGGCGTTTCGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1391113 TAATAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGAACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1391170 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGCACGCTAAAATTT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
1391227 TAAGAAATCATACTAAGTGTGTGAATTTCAGATAGGGTGTTTCGTACGGTAGAA-GT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1391283 TAAGAAATCATACTAAGTGTATGAATTTTAGATCGGGCGTTTCGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * * *
1391340 TAAGAAATCATATTAAGTGTACGAAATTCAGATATGGTGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1391397 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGACGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
1391454 TAAGAAATCATACTAAGTGTATGAAATTCAGATAGGGCATTTTGTACGATAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1391511 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGG
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGG
1391548 TTAAGTACCG
Statistics
Matches: 388, Mismatches: 46, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 0.12
57 340 0.88
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1391451 original size:227 final size:228
Alignment explanation
Indices: 1391056--1391547 Score: 772
Period size: 227 Copynumber: 2.2 Consensus size: 228
1391046 GTGCAAAATA
* *
1391056 TAAGAAATCATACTAAGTGTATGAATTTCAGTTAGGGCGTTTCGTACACTAAAATGTTAATAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACACTAAAATGTTAAGAAAT
* *
1391121 CATACTAAGTGTATGAATTTCAGATAGGGCATTTCGAACGCTAAAATGTTAAGAAATCATACTAA
66 CATACTAAGTGTACGAAATTCAGATAGGGCATTTCGAACGCTAAAATGTTAAGAAATCATACTAA
* ** *
1391186 GTGTATGAATTTCAGATAGGGCGTTTCGCACGCTAAAATTTTAAGAAATCATACTAAGTGTGTGA
131 GTGTATGAATTTCAGATAGGACGTTTCGCACGCTAAAATGATAAGAAATCATACTAAGTGTATGA
* ** * *
1391251 ATTTCAGATAGGGTGTTTCGTACGGTAGAA-GT
196 AATTCAGATAGGGCATTTCGTACGATAAAATGT
* *
1391283 TAAGAAATCATACTAAGTGTATGAATTTTAGATCGGGCGTTTCGTACACTAAAATGTTAAGAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACACTAAAATGTTAAGAAAT
* * **
1391348 CATATTAAGTGTACGAAATTCAGATATGGTGTTTC-ATACGCTAAAATGTTAAGAAATCATACTA
66 CATACTAAGTGTACGAAATTCAGATAGGGCATTTCGA-ACGCTAAAATGTTAAGAAATCATACTA
*
1391412 AGTGTATGAATTTCAGATAGGACGTTTCGTACGCTAAAATGATAAGAAATCATACTAAGTGTATG
130 AGTGTATGAATTTCAGATAGGACGTTTCGCACGCTAAAATGATAAGAAATCATACTAAGTGTATG
*
1391477 AAATTCAGATAGGGCATTTTGTACGATAAAATGT
195 AAATTCAGATAGGGCATTTCGTACGATAAAATGT
1391511 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGG
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGG
1391548 TTAAGTACCG
Statistics
Matches: 240, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
226 1 0.00
227 202 0.84
228 37 0.15
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (228 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACACTAAAATGTTAAGAAAT
CATACTAAGTGTACGAAATTCAGATAGGGCATTTCGAACGCTAAAATGTTAAGAAATCATACTAA
GTGTATGAATTTCAGATAGGACGTTTCGCACGCTAAAATGATAAGAAATCATACTAAGTGTATGA
AATTCAGATAGGGCATTTCGTACGATAAAATGT
Found at i:1394825 original size:20 final size:23
Alignment explanation
Indices: 1394777--1394831 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
1394767 GAACCTACAA
*
1394777 AAATAAAATAAGATATGTAAGTCG
1 AAATAAAA-AATATATGTAAGTCG
1394801 AAATAAAAAATATAT-TAA-T-G
1 AAATAAAAAATATATGTAAGTCG
*
1394821 AAATAATAAAT
1 AAATAAAAAAT
1394832 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
22 3 0.10
23 6 0.21
24 8 0.28
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (23 bp):
AAATAAAAAATATATGTAAGTCG
Found at i:1396535 original size:47 final size:47
Alignment explanation
Indices: 1396429--1396560 Score: 162
Period size: 47 Copynumber: 2.8 Consensus size: 47
1396419 GGTCTTAGAA
* * * * *
1396429 ATTTACTCCACTCCTACAAAACAAAGG-ATGTT-GAGGCTTGGTCATG
1 ATTTTCTCTACTCCTCCAAAACAAAGGAATGTTAGA-GCTCGCTCATG
1396475 ATTTTCTCTACTCCTCCAAAACAAAGGAATGTTAGAGCTCGCTCAT-
1 ATTTTCTCTACTCCTCCAAAACAAAGGAATGTTAGAGCTCGCTCATG
* *
1396521 AGTTTTTTCTACTCCTCCATAACAAAGGAATGTTAGAGCT
1 A-TTTTCTCTACTCCTCCAAAACAAAGGAATGTTAGAGCT
1396561 AGTTCGGTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 25 0.33
47 49 0.64
48 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (47 bp):
ATTTTCTCTACTCCTCCAAAACAAAGGAATGTTAGAGCTCGCTCATG
Found at i:1396591 original size:8 final size:8
Alignment explanation
Indices: 1396578--1396602 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1396568 TTATAGAAAT
1396578 TTGCTCCA
1 TTGCTCCA
1396586 TTGCTCCA
1 TTGCTCCA
1396594 TTGCTCCA
1 TTGCTCCA
1396602 T
1 T
1396603 AAGATAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.36, G:0.12, T:0.40
Consensus pattern (8 bp):
TTGCTCCA
Found at i:1396759 original size:46 final size:46
Alignment explanation
Indices: 1396702--1396810 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 46
1396692 ACTCCATAAT
* ** *
1396702 AACATAGGATGTTGGTGCTTGCTCATGATTTGCTCTACTCCTCCAA
1 AACAAAGGATGTTGGTGCTCACTCATAATTTGCTCTACTCCTCCAA
*** * *
1396748 AACAAAGGATGTTACAGCTCACTCATAATTTGCTCTACTCGTCCAT
1 AACAAAGGATGTTGGTGCTCACTCATAATTTGCTCTACTCCTCCAA
* *
1396794 AATAAATGAATGTTGGT
1 AACAAA-GGATGTTGGT
1396811 TACACCCATT
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
46 42 0.88
47 6 0.12
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (46 bp):
AACAAAGGATGTTGGTGCTCACTCATAATTTGCTCTACTCCTCCAA
Found at i:1402215 original size:11 final size:10
Alignment explanation
Indices: 1402169--1402219 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
1402159 GATGTAGGTG
1402169 TTTTTCTTTC
1 TTTTTCTTTC
*
1402179 TCTTTGCTTTC
1 T-TTTTCTTTC
*
1402190 TTTTTCATTTG
1 TTTTTC-TTTC
1402201 TTTTTCTTT-
1 TTTTTCTTTC
1402210 TCTTTTCTTT
1 T-TTTTCTTT
1402220 TCCTTTGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 1 0.03
10 16 0.46
11 18 0.51
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:1404923 original size:20 final size:22
Alignment explanation
Indices: 1404891--1404930 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1404881 AATGGATATT
1404891 TAATTTGAATTAATT-AAAAAA
1 TAATTTGAATTAATTCAAAAAA
1404912 TAATTT-AATTAATTCAAAA
1 TAATTTGAATTAATTCAAAA
1404931 TAACTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (22 bp):
TAATTTGAATTAATTCAAAAAA
Found at i:1409155 original size:18 final size:18
Alignment explanation
Indices: 1409128--1409175 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1409118 AATGCAATTA
1409128 GTATCGATACTATTGTGG
1 GTATCGATACTATTGTGG
*
1409146 GTATCAATACTATTGTGG
1 GTATCGATACTATTGTGG
1409164 GTATCGATACTA
1 GTATCGATACTA
1409176 AGCAGAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (18 bp):
GTATCGATACTATTGTGG
Found at i:1409210 original size:22 final size:21
Alignment explanation
Indices: 1409164--1409223 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
1409154 ACTATTGTGG
*
1409164 GTATCGATACTA-AGCAGAAA
1 GTATCGATACTATAGTAGAAA
*
1409184 GTATCGATACTATAGTATAGAA
1 GTATCGATACTATAGTAGA-AA
*
1409206 GTATCGATACCATAGTAG
1 GTATCGATACTATAGTAG
1409224 GGTAGCGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.35
21 4 0.12
22 18 0.53
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (21 bp):
GTATCGATACTATAGTAGAAA
Found at i:1414219 original size:5 final size:5
Alignment explanation
Indices: 1414209--1414244 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
1414199 TTTTTATTGC
1414209 TTTAA TTTAA TTTAA TTT-A TTT-A TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1414245 TTCTATACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTTAA
Found at i:1414227 original size:23 final size:23
Alignment explanation
Indices: 1414201--1414244 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1414191 TTTTCTTGTT
*
1414201 TTTATTGCTTTAATTTAATTTAA
1 TTTATTGATTTAATTTAATTTAA
*
1414224 TTTATTTATTTAATTTAATTT
1 TTTATTGATTTAATTTAATTT
1414245 TTCTATACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATTGATTTAATTTAATTTAA
Found at i:1414234 original size:13 final size:14
Alignment explanation
Indices: 1414209--1414244 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1414199 TTTTTATTGC
1414209 TTTAATTTAATTTAA
1 TTTAATTT-ATTTAA
1414224 TTT-ATTTATTTAA
1 TTTAATTTATTTAA
1414237 TTTAATTT
1 TTTAATTT
1414245 TTCTATACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 8 0.40
15 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTATTTAA
Found at i:1415660 original size:32 final size:33
Alignment explanation
Indices: 1415624--1415693 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
1415614 ACCTTACAAC
*
1415624 TCCCTA-CTTTTTAC-GGGCTAAACTAGAACCTT
1 TCCCTAGC-TTTTACAGGGATAAACTAGAACCTT
*
1415656 TCCCTAGCTTTTACAGGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACA-GGGATAAACTAGAACCTT
1415690 TCCC
1 TCCC
1415694 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTACAGGGATAAACTAGAACCTT
Found at i:1416067 original size:20 final size:19
Alignment explanation
Indices: 1416042--1416106 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
1416032 CCGTTAGACA
1416042 GGGGGAATCGGTACACCCTG
1 GGGGGAATCGGTAC-CCCTG
* *
1416062 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATC-GGTACCCCTG
1416082 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCC-TG
1416102 GGGGG
1 GGGGG
1416107 GGGAATCTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.15
20 30 0.77
21 3 0.08
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (19 bp):
GGGGGAATCGGTACCCCTG
Found at i:1417895 original size:19 final size:20
Alignment explanation
Indices: 1417852--1417899 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1417842 TCTAAATCCT
*
1417852 TTTTCAAAATTTCATTTTCG
1 TTTTCAAAATCTCATTTTCG
* *
1417872 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTCG
1417891 TTTTCAAAA
1 TTTTCAAAA
1417900 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTCG
Found at i:1418803 original size:32 final size:33
Alignment explanation
Indices: 1418759--1418828 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
1418749 ACCTTACAAC
* *
1418759 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
* *
1418791 TCCCTAGCTTTTACACGGGATAAGCTATAACCTT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACCTT
1418825 TCCC
1 TCCC
1418829 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:1419204 original size:20 final size:20
Alignment explanation
Indices: 1419179--1419239 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
1419169 CGTTACACAT
*
1419179 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
1419199 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
1419219 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
1419239 G
1 G
1419240 ACAATCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.13, C:0.30, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:1427324 original size:20 final size:21
Alignment explanation
Indices: 1427287--1427327 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1427277 GATTCTTGGG
**
1427287 TTAGAGTGTTATTTGAAGATT
1 TTAGAGTGTTATAGGAAGATT
1427308 TTAGA-TGTTATAGGAAGATT
1 TTAGAGTGTTATAGGAAGATT
1427328 AGTCAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (21 bp):
TTAGAGTGTTATAGGAAGATT
Found at i:1434436 original size:19 final size:21
Alignment explanation
Indices: 1434393--1434436 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1434383 GGAATTTCGG
*
1434393 TACCATAGTATAGAAGTATCGA
1 TACCATAGTATAG-AGTAGCGA
1434415 TACCATAGTA-AG-GTAGCGA
1 TACCATAGTATAGAGTAGCGA
1434434 TAC
1 TAC
1434437 TATTATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (21 bp):
TACCATAGTATAGAGTAGCGA
Found at i:1445025 original size:25 final size:25
Alignment explanation
Indices: 1444983--1445073 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
1444973 CGAACCACCT
*
1444983 TAGCTCGCTAGCTCCTCTCGGATACC
1 TAGCTCGCCA-CTCCTCTCGGATACC
* *
1445009 TAGCTCGTCACTCCTCTCGAATACC
1 TAGCTCGCCACTCCTCTCGGATACC
*
1445034 TAGCTCGCCACTCCTCTCGGAAACC
1 TAGCTCGCCACTCCTCTCGGATACC
1445059 TAGCTCGCCACTCCT
1 TAGCTCGCCACTCCT
1445074 TGGAGCTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 51 0.86
26 8 0.14
ACGTcount: A:0.18, C:0.42, G:0.15, T:0.25
Consensus pattern (25 bp):
TAGCTCGCCACTCCTCTCGGATACC
Found at i:1447394 original size:25 final size:27
Alignment explanation
Indices: 1447365--1447417 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1447355 TATTTTTAAG
*
1447365 TAAAA-TTCTTAAAAA-ATTTAAAAAT
1 TAAAATTTCTTAAAAATATATAAAAAT
*
1447390 TAAAATTTTTTAAAAATATATAAAAAT
1 TAAAATTTCTTAAAAATATATAAAAAT
1447417 T
1 T
1447418 CATTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 9 0.38
27 10 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAAATTTCTTAAAAATATATAAAAAT
Found at i:1449469 original size:20 final size:21
Alignment explanation
Indices: 1449444--1449495 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1449434 TTTTCCCAAT
*
1449444 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1449464 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1449485 TCGCAATGCGA
1 TCGCAATGCGA
1449496 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1450135 original size:19 final size:19
Alignment explanation
Indices: 1450111--1450155 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1450101 GCAACGAGAG
*
1450111 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
1450130 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
1450149 AATCGCA
1 AATCGCA
1450156 TTGCGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1450173 original size:19 final size:19
Alignment explanation
Indices: 1450151--1450296 Score: 100
Period size: 19 Copynumber: 8.1 Consensus size: 19
1450141 GAAACCAAAA
*
1450151 TCGCATTGCGATTATCATT
1 TCGCGTTGCGATTATCATT
*
1450170 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTATCATT
1450189 TCGCGTTGCGA-T-TC---
1 TCGCGTTGCGATTATCATT
* *
1450203 TCTCGTCGCGA-TAGTCATT
1 TCGCGTTGCGATTA-TCATT
1450222 TCGCGTTGCGA-T-TC---
1 TCGCGTTGCGATTATCATT
*
1450236 TCTCGTTGCGA-TAGTCATT
1 TCGCGTTGCGATTA-TCATT
*
1450255 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTATCATT
* *
1450275 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTATCATT
1450295 TC
1 TC
1450297 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 11, Indels: 26
0.74 0.08 0.19
Matches are distributed among these distances:
14 21 0.20
16 4 0.04
17 4 0.04
18 1 0.01
19 41 0.40
20 30 0.29
21 2 0.02
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTATCATT
Found at i:1450221 original size:33 final size:33
Alignment explanation
Indices: 1450184--1450271 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
1450174 GTTGCGATTT
1450184 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1450217 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1450250 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1450272 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1452454 original size:21 final size:21
Alignment explanation
Indices: 1452430--1452496 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1452420 TCATTCCTCG
1452430 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1452451 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1452472 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1452493 AGAG
1 AGAG
1452497 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1452454 original size:42 final size:42
Alignment explanation
Indices: 1452378--1452496 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1452368 GACTCGCCTG
* * * * * * *
1452378 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1452420 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1452462 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1452497 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1453865 original size:14 final size:14
Alignment explanation
Indices: 1453846--1453881 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1453836 ATTGTTTAAT
1453846 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1453860 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1453874 TGATTTGT
1 TGATTTGT
1453882 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1454025 original size:14 final size:14
Alignment explanation
Indices: 1454006--1454062 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1453996 GCGAAATGAA
1454006 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1454020 AATCGCAACGCAAAATGAA
1 AATCGCAACG----A-GAG
1454039 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1454053 AATCGTAACG
1 AATCGCAACG
1454063 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 21 0.60
15 1 0.03
18 1 0.03
19 12 0.34
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1454036 original size:33 final size:33
Alignment explanation
Indices: 1453988--1454077 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
1453978 AAAAAGTACT
*
1453988 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
1454021 ATCGCAACGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
1454054 ATCGTAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1454078 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1454047 original size:19 final size:18
Alignment explanation
Indices: 1453988--1454048 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
1453978 AAAAAGTACT
*
1453988 ATCGCAATGCGAAATGAAA
1 ATCGCAACGC-AAATGAAA
*
1454007 ATCGCAACG---A-GAGA
1 ATCGCAACGCAAATGAAA
1454021 ATCGCAACGCAAAATGAAA
1 ATCGCAACGC-AAATGAAA
1454040 ATCGCAACG
1 ATCGCAACG
1454049 AGAGAATCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 12 0.35
15 1 0.03
18 1 0.03
19 20 0.59
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (18 bp):
ATCGCAACGCAAATGAAA
Found at i:1454095 original size:19 final size:19
Alignment explanation
Indices: 1454073--1454203 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1454063 CGAAATTAAA
*
1454073 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1454092 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1454108 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1454125 TTCGCATTGTGA-----AA
1 TTCGCATTGCGATTTTCAT
*
1454139 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1454158 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1454174 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1454191 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1454204 AGTAATTTCT
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 23 0.27
16 13 0.15
17 13 0.15
19 35 0.42
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1454119 original size:33 final size:32
Alignment explanation
Indices: 1454077--1454203 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1454067 ATTAAATTCG
1454077 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
1454110 CGTTGCGATTTTCATTTCGCATTGTGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1454143 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1454176 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1454204 AGTAATTTCT
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1454146 original size:66 final size:66
Alignment explanation
Indices: 1454070--1454199 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
1454060 ACGCGAAATT
1454070 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1454135 G
66 G
*
1454136 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
1454200 CGATAGTAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:1456506 original size:12 final size:12
Alignment explanation
Indices: 1456489--1456513 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1456479 TCTTCGGGGA
1456489 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1456501 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1456513 C
1 C
1456514 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1456715 original size:24 final size:24
Alignment explanation
Indices: 1456688--1456741 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1456678 TTGAAACATC
*
1456688 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1456712 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1456736 ATCAAA
1 ATCAAA
1456742 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1457513 original size:20 final size:20
Alignment explanation
Indices: 1457488--1457535 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1457478 TGTATTATCT
1457488 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
1457508 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
1457528 CGTTGCGA
1 CGTTGCGA
1457536 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1457598 original size:41 final size:41
Alignment explanation
Indices: 1457504--1457598 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1457494 GAAAGTCAGA
* * * * *
1457504 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTATAAT
1457545 ATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTATCAAT
1 ATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTAT-AAT
1457587 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1457599 TTACTTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTATAAT
Found at i:1457688 original size:21 final size:21
Alignment explanation
Indices: 1457648--1457688 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1457638 ACTGTAGACC
* *
1457648 ATCGCAACGCGATATCCAACT
1 ATCGCAACGCGAAATACAACT
1457669 ATCGCAACGCGAAATACAAC
1 ATCGCAACGCGAAATACAAC
1457689 GCGAATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.15, T:0.15
Consensus pattern (21 bp):
ATCGCAACGCGAAATACAACT
Found at i:1461105 original size:17 final size:18
Alignment explanation
Indices: 1461069--1461109 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1461059 ATATTATGTA
*
1461069 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1461087 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1461104 TTTACT
1 TTTACT
1461110 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1463467 original size:35 final size:33
Alignment explanation
Indices: 1463427--1463511 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1463417 GTATTTCAGT
1463427 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
1463462 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1463497 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1463512 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1466842 original size:12 final size:12
Alignment explanation
Indices: 1466818--1466850 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1466808 AATAAGTATA
1466818 ATAA-AAAAATT
1 ATAACAAAAATT
*
1466829 ATAACAAAATTT
1 ATAACAAAAATT
1466841 ATAACAAAAA
1 ATAACAAAAA
1466851 ATCACACGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACAAAAATT
Found at i:1468336 original size:21 final size:21
Alignment explanation
Indices: 1468310--1468365 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1468300 GGGAGCGTCA
1468310 GTGCATCGATGCATACCCATG
1 GTGCATCGATGCATACCCATG
*
1468331 GTGCATCGGTGCATACCCATG
1 GTGCATCGATGCATACCCATG
*
1468352 GTGCATCGCTGCAT
1 GTGCATCGATGCAT
1468366 CAGTGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATACCCATG
Found at i:1468562 original size:65 final size:64
Alignment explanation
Indices: 1468427--1468582 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
1468417 CTAAGAGTGT
* * * *
1468427 ATCGATGCATCAAGTGCATTCGATGATTTAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTGGTAC
* * * *
1468491 ATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATGT
1 ATCGATGCATCAAATGCATTCGATGTTTT-A-AAATAGCCACAGTGCATCGATGCATGGCT-GGT
1468554 AC
63 AC
* *
1468556 ATCGATGCATGAAATGCATTCAATGTT
1 ATCGATGCATCAAATGCATTCGATGTT
1468583 CAATTTAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.35
65 48 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (64 bp):
ATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTGGTAC
Found at i:1468624 original size:65 final size:63
Alignment explanation
Indices: 1468467--1468632 Score: 176
Period size: 65 Copynumber: 2.6 Consensus size: 63
1468457 AAATAGCCAG
* *
1468467 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAAT-CTC
* * * **
1468532 AGTGCATCGGTGCATGGTAT-GTACATCGATGCATGAAATGCATTCAATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCAATGTTTC-ATAAAATCTC
*
1468594 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
1468633 CACTGAAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.25
65 56 0.67
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAATGTTTCATAAAATCTC
Found at i:1477037 original size:8 final size:8
Alignment explanation
Indices: 1477026--1477052 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1477016 CATACCCATG
1477026 GTGCATCA
1 GTGCATCA
1477034 GTGCATCA
1 GTGCATCA
1477042 GTGCATCA
1 GTGCATCA
1477050 GTG
1 GTG
1477053 TAAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (8 bp):
GTGCATCA
Found at i:1477630 original size:42 final size:42
Alignment explanation
Indices: 1477570--1477669 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
1477560 CACATAGTAG
*
1477570 CCCTAGAACCCTCTCAATCGACCTCTAAATGAAAAAAACCAGT
1 CCCTA-AACCCTCTCAATCAACCTCTAAATGAAAAAAACCAGT
***
1477613 CCCTAAACCCTCTCAATCAACCTCTAAATGGCCAAAACCAGT
1 CCCTAAACCCTCTCAATCAACCTCTAAATGAAAAAAACCAGT
1477655 CCCTAAA-CCTCTCAA
1 CCCTAAACCCTCTCAA
1477670 AGCCAAACCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 8 0.15
42 40 0.75
43 5 0.09
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (42 bp):
CCCTAAACCCTCTCAATCAACCTCTAAATGAAAAAAACCAGT
Found at i:1478787 original size:17 final size:17
Alignment explanation
Indices: 1478746--1478788 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1478736 CAAAAATGTA
*
1478746 ATAATAATATTAATCAT
1 ATAATAATAATAATCAT
*
1478763 ATACTAATAATAAT-AT
1 ATAATAATAATAATCAT
1478779 ATAATTAATA
1 ATAA-TAATA
1478789 TTATAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAATAATAATCAT
Found at i:1479171 original size:135 final size:135
Alignment explanation
Indices: 1478936--1479266 Score: 461
Period size: 135 Copynumber: 2.5 Consensus size: 135
1478926 AACAAGTTAC
* *
1478936 TCTCATTATGAACTTCTTCTCTCT--TATGGACGAGTTCTTCTCATTATGAACTCTTCACTAAAA
1 TCTCATTATGAACTTCTTCTCTCTCGT-TGGATGAGTTCTTCTCATTATGAACTCTTCACTGAAA
* * * * *
1478999 ATGTTGATCCCTCAAGCGAGTCATCACTGATTTGAAATGTCGTGAATCGAGTGATGGGTCGAACA
65 ATGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACA
1479064 AGCTCT
130 AGCTCT
*
1479070 TCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTTATTATGAACTCTTCACTGAAAA
1 TCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGAAAA
* * * *
1479135 TGTTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGTCGTGAATCAAGTGATAGGTTAAACAA
66 TGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACAA
*
1479200 GTTCT
131 GCTCT
* * * *
1479205 TCTCATTATAAACTTCTTCTCCCTCTGTCGGAT-AGGTTCTTCTCATTATGAACTCTCCACTG
1 TCTCATTATGAACTTCTTCTCTCTC-GTTGGATGA-GTTCTTCTCATTATGAACTCTTCACTG
1479267 GAAACACTGA
Statistics
Matches: 175, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
134 24 0.14
135 119 0.68
136 32 0.18
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (135 bp):
TCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGAAAA
TGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACAA
GCTCT
Found at i:1480319 original size:15 final size:15
Alignment explanation
Indices: 1480293--1480340 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
1480283 TTCAAACATC
*
1480293 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
1480309 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
1480326 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
1480341 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:1482141 original size:21 final size:22
Alignment explanation
Indices: 1482115--1482195 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
1482105 CTGAACCCCA
*
1482115 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* *
1482136 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-TCAT
* *
1482159 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
*
1482180 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
1482196 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:1482189 original size:20 final size:21
Alignment explanation
Indices: 1482116--1482197 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
1482106 TGAACCCCAG
* *
1482116 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
1482136 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TCAAT
*
1482160 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
1482180 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1482198 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.33
21 13 0.25
22 6 0.12
23 13 0.25
24 2 0.04
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Found at i:1486343 original size:153 final size:152
Alignment explanation
Indices: 1486142--1486444 Score: 572
Period size: 153 Copynumber: 2.0 Consensus size: 152
1486132 AGTTGTTTAA
*
1486142 TTTGAAAATTTCTTTTTCAAAGTTTCAGATTTTATTTTGAAAGCTCTAACTCCTTTTTCAACATT
1 TTTGAAAATTTCTTTTTCAAAGTTTCAGATTTTATTTTGAAAGCTCTAACTCCTTTCTCAACATT
1486207 TCATTTTGATTTTCCAAGTCTGTTATAGCTTTCAAAAAAAGATCATTTTTAGCAA-AAATTTAGA
66 TCATTTTGATTTTCCAAGTCTGTTATAGCTTTCAAAAAAAGATCATTTTTAGCAATAAATTTAGA
1486271 AATTAATTTATTGTATTTGGGT
131 AATTAATTTATTGTATTTGGGT
1486293 TTTGAAAATTTCTTTTTCAAAGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTTTCTCAACA
1 TTTGAAAATTTCTTTTTCAAAG-TTTCAGATTTTA-TTTTGAAAGCTCTAACTCCTTTCTCAACA
1486358 TTTCATTTTGATTTTCCAAGTCTGTTATAGCTTTCAAAAAAAGATCATTTTTAGCAATAAATTTA
64 TTTCATTTTGATTTTCCAAGTCTGTTATAGCTTTCAAAAAAAGATCATTTTTAGCAATAAATTTA
1486423 GAAATTAATTTATTGTATTTGG
129 GAAATTAATTTATTGTATTTGG
1486445 AGTTCATGGT
Statistics
Matches: 148, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
151 22 0.15
152 12 0.08
153 85 0.57
154 29 0.20
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (152 bp):
TTTGAAAATTTCTTTTTCAAAGTTTCAGATTTTATTTTGAAAGCTCTAACTCCTTTCTCAACATT
TCATTTTGATTTTCCAAGTCTGTTATAGCTTTCAAAAAAAGATCATTTTTAGCAATAAATTTAGA
AATTAATTTATTGTATTTGGGT
Found at i:1491575 original size:28 final size:26
Alignment explanation
Indices: 1491525--1491577 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
1491515 ATGTAAACGC
*
1491525 AAAAATGAAAATGTAAATACAAATGT
1 AAAAATGAAAATGCAAATACAAATGT
*
1491551 AAAAATGCAAAGATGCAAATGCAAATG
1 AAAAATG-AAA-ATGCAAATACAAATG
1491578 CAAATGTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 3 0.13
28 13 0.57
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAAATGAAAATGCAAATACAAATGT
Found at i:1493932 original size:78 final size:80
Alignment explanation
Indices: 1493821--1493975 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 80
1493811 CACATGTACT
1493821 AATGAAAATAATCCAAAAATGAAATTAGAACTAAAGTGCAACAAATC-AAAACTTGAAGGCTAAA
1 AATGAAAATAATCCAAAAATGAAATTAGAACTAAAGTGCAACAAATCAAAAACTTGAAGGCTAAA
1493885 TCAC-ATTAAACTAA
66 TCACAATTAAACTAA
1493899 AATGAAAATAATCC-AAAATGAAATTTAGAACTAAAGTGCAACAAATCAAAAACTTGAAGGCTAA
1 AATGAAAATAATCCAAAAATGAAA-TTAGAACTAAAGTGCAACAAATCAAAAACTTGAAGGCTAA
1493963 ATCACAATTAAAC
65 ATCACAATTAAAC
1493976 CAAATTAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
77 9 0.12
78 37 0.50
79 21 0.28
80 7 0.09
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (80 bp):
AATGAAAATAATCCAAAAATGAAATTAGAACTAAAGTGCAACAAATCAAAAACTTGAAGGCTAAA
TCACAATTAAACTAA
Found at i:1504915 original size:24 final size:24
Alignment explanation
Indices: 1504887--1504932 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1504877 ATATTTAATT
*
1504887 TTATTCTTTTTTAATTAATTTCAC
1 TTATTCATTTTTAATTAATTTCAC
*
1504911 TTATTCATTTTTATTTAATTTC
1 TTATTCATTTTTAATTAATTTC
1504933 GTTTGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTCATTTTTAATTAATTTCAC
Found at i:1512406 original size:13 final size:13
Alignment explanation
Indices: 1512388--1512416 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1512378 AATATCATTA
1512388 TAAATACCCGAAC
1 TAAATACCCGAAC
1512401 TAAATACCCGAAC
1 TAAATACCCGAAC
1512414 TAA
1 TAA
1512417 GATTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (13 bp):
TAAATACCCGAAC
Found at i:1521386 original size:30 final size:30
Alignment explanation
Indices: 1521352--1521441 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
1521342 GCTTTAGCTA
* *
1521352 TTTAAGTTTATGTTTTTGCCATTTTAGTCC
1 TTTAAGTTTATGTTTTTGCTATTTTGGTCC
* * * *
1521382 TTTAA-ATTACTATTTATACTATTTTGGTCC
1 TTTAAGTTTA-TGTTTTTGCTATTTTGGTCC
*
1521412 TTTGAGTTTATGTTTTTGCTATTTTGGTCC
1 TTTAAGTTTATGTTTTTGCTATTTTGGTCC
1521442 CTTATAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 3 0.06
30 41 0.87
31 3 0.06
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (30 bp):
TTTAAGTTTATGTTTTTGCTATTTTGGTCC
Found at i:1521558 original size:22 final size:21
Alignment explanation
Indices: 1521533--1521573 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1521523 TATGTACATG
*
1521533 TTGTAAATGTTGTTATTTTATA
1 TTGTAAATATT-TTATTTTATA
1521555 TTGTAAATATTTTATTTTA
1 TTGTAAATATTTTATTTTA
1521574 CATCATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TTGTAAATATTTTATTTTATA
Found at i:1525361 original size:15 final size:14
Alignment explanation
Indices: 1525335--1525427 Score: 91
Period size: 15 Copynumber: 6.5 Consensus size: 14
1525325 AAAGAGAAAA
1525335 AGAAAAAAACAAAG
1 AGAAAAAAACAAAG
1525349 AGAAAAGAAACAAAG
1 AGAAAA-AAACAAAG
* * *
1525364 -CAAAAAACCAATG
1 AGAAAAAAACAAAG
1525377 AGAAAAGAAACAAAG
1 AGAAAA-AAACAAAG
*
1525392 AGAAAAAAGCAAAG
1 AGAAAAAAACAAAG
*
1525406 CATGAAATAAACAAAG
1 -A-GAAAAAAACAAAG
1525422 A-AAAAA
1 AGAAAAA
1525428 CGAAAAGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
13 10 0.16
14 21 0.33
15 22 0.34
16 11 0.17
ACGTcount: A:0.72, C:0.10, G:0.15, T:0.03
Consensus pattern (14 bp):
AGAAAAAAACAAAG
Found at i:1525423 original size:28 final size:27
Alignment explanation
Indices: 1525325--1525427 Score: 111
Period size: 28 Copynumber: 3.7 Consensus size: 27
1525315 AAATCACAAC
1525325 AAAGAGAA-AAAGAAAAAAACAAAGAGA
1 AAAGA-AACAAAGAAAAAAACAAAGAGA
* *
1525352 AAAGAAACAAAGCAAAAAACCAATGAGA
1 AAAGAAACAAAG-AAAAAAACAAAGAGA
1525380 AAAGAAACAAAGAGAAAAAAGCAAAGCATG-
1 AAAGAAACAAAGA-AAAAAA-CAAAG-A-GA
*
1525410 AAATAAACAAAGAAAAAA
1 AAAGAAACAAAGAAAAAA
1525428 CGAAAAGAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.03
27 10 0.15
28 30 0.46
29 9 0.14
30 13 0.20
31 1 0.02
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.03
Consensus pattern (27 bp):
AAAGAAACAAAGAAAAAAACAAAGAGA
Found at i:1525424 original size:43 final size:40
Alignment explanation
Indices: 1525333--1525427 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 40
1525323 ACAAAGAGAA
*
1525333 AAAGAAAAAAACAAAGAGAAAAGAAACAAAGCAAAAAACC
1 AAAGAAAAAAACAAAGAGAAAAGAAACAAAGCAAAAAAAC
*
1525373 AATGAGAAAAGAAACAAAGAGAAAA-AAGCAAAGCATGAAATAAAC
1 AA--AGAAAA-AAACAAAGAGAAAAGAAACAAAGCA--AAA-AAAC
1525418 AAAGAAAAAA
1 AAAGAAAAAA
1525428 CGAAAAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
40 2 0.04
42 17 0.36
43 20 0.43
44 3 0.06
45 5 0.11
ACGTcount: A:0.73, C:0.09, G:0.15, T:0.03
Consensus pattern (40 bp):
AAAGAAAAAAACAAAGAGAAAAGAAACAAAGCAAAAAAAC
Found at i:1525446 original size:30 final size:30
Alignment explanation
Indices: 1525384--1525446 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1525374 ATGAGAAAAG
* * *
1525384 AAACAAAGAGAAAAAAGCAAAGCATGAAAT
1 AAACAAAGAGAAAAAAGAAAAGAAAGAAAT
*
1525414 AAACAAAGA-AAAAACGAAAAGAAAGAAGAT
1 AAACAAAGAGAAAAAAGAAAAGAAAGAA-AT
1525444 AAA
1 AAA
1525447 AAGCACACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (30 bp):
AAACAAAGAGAAAAAAGAAAAGAAAGAAAT
Found at i:1526496 original size:32 final size:32
Alignment explanation
Indices: 1526455--1526524 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1526445 TGAAGCAAGA
** * *
1526455 AACATCGAATATTGGGGCATCTTTGGAGATTC
1 AACATCGAATATTGGAACATATTTGGAGAGTC
*
1526487 AACATCGAATATTGGAACATATTTGGGGAGTC
1 AACATCGAATATTGGAACATATTTGGAGAGTC
1526519 AACATC
1 AACATC
1526525 CTGAAACGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (32 bp):
AACATCGAATATTGGAACATATTTGGAGAGTC
Found at i:1526709 original size:37 final size:38
Alignment explanation
Indices: 1526668--1526752 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 38
1526658 TTTGAGTTTG
* * *
1526668 TTTCCTTTGAAACA-AAATTTTTTCTCATTTGAGACAT
1 TTTCCTTTGAAAAATAAATTTTGTCTCACTTGAGACAT
* *
1526705 TTTCC-TTCAAAAATAAATTTTGTCTCGCTTGAGACAT
1 TTTCCTTTGAAAAATAAATTTTGTCTCACTTGAGACAT
1526742 TTTCCCTTTGA
1 TTT-CCTTTGA
1526753 GATACAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 6 0.15
37 28 0.72
38 2 0.05
39 3 0.08
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (38 bp):
TTTCCTTTGAAAAATAAATTTTGTCTCACTTGAGACAT
Found at i:1527157 original size:32 final size:33
Alignment explanation
Indices: 1527116--1527180 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1527106 TCTTTTGAAG
1527116 AAAAATCTTTGAGT-CGTTTCTTTTGAAACAAA
1 AAAAATCTTTGAGTACGTTTCTTTTGAAACAAA
*
1527148 AAAAATCTTTGAGTATGTTTCTTTTGAAACAAA
1 AAAAATCTTTGAGTACGTTTCTTTTGAAACAAA
1527181 GTTTTGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (33 bp):
AAAAATCTTTGAGTACGTTTCTTTTGAAACAAA
Found at i:1527197 original size:98 final size:92
Alignment explanation
Indices: 1527068--1527243 Score: 244
Period size: 98 Copynumber: 1.8 Consensus size: 92
1527058 TAACAATCTT
1527068 TTTCTCTTAAAACAAATTTTGTCTCTATTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCGT
1 TTTCTCTTAAAACAAATTTTGTCTCTATTGAGACAGTTT-TTTTG-AGAAAAATC--TGAGTCGT
1527133 TTCTTTTGAAACAAAAAAAATCTTTGAGTATG
62 TTCTTTTGAAA-AAAAAAAATCTTTGAGTATG
* * * * * *
1527165 TTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTTTTTGTGAAAAATCTGAGTCTTTTC
1 TTTCTCTTAAAACAAA-TTTTGTCTCTATTGAGACAGTTTTTTTGAGAAAAATCTGAGTCGTTTC
1527230 TTTTGAAAAAAAAA
65 TTTTGAAAAAAAAA
1527244 TTGAGTCTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
93 6 0.08
94 18 0.25
96 8 0.11
97 19 0.26
98 21 0.29
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (92 bp):
TTTCTCTTAAAACAAATTTTGTCTCTATTGAGACAGTTTTTTTGAGAAAAATCTGAGTCGTTTCT
TTTGAAAAAAAAAAATCTTTGAGTATG
Found at i:1527242 original size:27 final size:26
Alignment explanation
Indices: 1527212--1527263 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1527202 TTTTTTTGTG
1527212 AAAAATCTGAGTCTTTTCTTTTGAAAA
1 AAAAAT-TGAGTCTTTTCTTTTGAAAA
1527239 AAAAATTGAGTCTTTTCTTTTGAAA
1 AAAAATTGAGTCTTTTCTTTTGAAA
1527264 CACCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (26 bp):
AAAAATTGAGTCTTTTCTTTTGAAAA
Found at i:1527770 original size:134 final size:130
Alignment explanation
Indices: 1527395--1527775 Score: 394
Period size: 130 Copynumber: 2.9 Consensus size: 130
1527385 TGAAACCATT
* * *
1527395 ATCCCTAAATATGGTCTA-TCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
1 ATCCCTAAAGATGG-CTAGACATCCTCATCACGTAGGAA-AGTGTCATCCCCCGACCAGACCTCC
** * * * * *
1527459 TCATCTTGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCATAACGTAGGAACCGTGTTA
64 TCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCCTCTTCATCACGTAAGAACCGAGTTA
1527524 TC
129 TC
* * * *
1527526 ATCCCTAAAGATGGCTTGTCATCCTCATCACGTAGGAAAATGTCATCTCCCGACCAGACCTCCTC
1 ATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAAAGTGTCATCCCCCGACCAGACCTCCTC
* *
1527591 ATCACGTAGGAGTCGTGTCACCCCTAGATAACCA-TCCAT-TCTCATCGCGTAAGAACCGAGTTA
66 ATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCC-TCT-TCATCACGTAAGAACCGAGTTA
1527654 TC
129 TC
* * * ** * *
1527656 ACCCTTCCTAAAGATGGCTAGA-ACTCTTCATCATGTATGGGCAGTGTCATCCCCCGACTAGATC
1 A---TCCCTAAAGATGGCTAGACA-TCCTCATCACGTA-GGAAAGTGTCATCCCCCGACCAGACC
* ** *
1527720 TCCTCATCACGTAGGAG-CTATGTCACCCTTAGACGACCAGACCTCTTCATCACGTA
61 TCCTCATCACGTAGGAGTC-GTGTCACCCTTAGATAACCAGTCCTCTTCATCACGTA
1527776 TGAGCAGTGT
Statistics
Matches: 208, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
129 2 0.01
130 79 0.38
131 33 0.16
132 1 0.00
133 27 0.13
134 63 0.30
135 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (130 bp):
ATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAAAGTGTCATCCCCCGACCAGACCTCCTC
ATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCCTCTTCATCACGTAAGAACCGAGTTATC
Found at i:1529646 original size:30 final size:30
Alignment explanation
Indices: 1529453--1529705 Score: 142
Period size: 30 Copynumber: 8.5 Consensus size: 30
1529443 TTTATAACTT
* * * *
1529453 CTATTTTAGCCCTTTATGTTTCTGTATTTG
1 CTATTTTAGTCCTTTAAGTTTATGTTTTTG
* *
1529483 -TATTTTGGTCCTTAAAGTTCTAT-TTTTTG
1 CTATTTTAGTCCTTTAAGTT-TATGTTTTTG
* * * * * *
1529512 CAATCTTAGTCCTCTAGGTTTCTGTTTTTA
1 CTATTTTAGTCCTTTAAGTTTATGTTTTTG
* * *
1529542 TTGTTTTAGTCC-TTAAGTTTATGTTTTTA
1 CTATTTTAGTCCTTTAAGTTTATGTTTTTG
* **
1529571 CTATTTATA-CCCTTTAAGTTTCA--AATTTG
1 CTATTT-TAGTCCTTTAAGTTT-ATGTTTTTG
* * *
1529600 GTGTTTTAGAT-ATTTAAGTTTATGTTTTTG
1 CTATTTTAG-TCCTTTAAGTTTATGTTTTTG
* * ** * * *
1529630 CCATTTTAGTCCTTTAAATTCCTATTTGTA
1 CTATTTTAGTCCTTTAAGTTTATGTTTTTG
* *
1529660 CTATTTTGGTCCTTTGAGTTTATGTTTTTG
1 CTATTTTAGTCCTTTAAGTTTATGTTTTTG
*
1529690 CTATTTTGGTCCTTTA
1 CTATTTTAGTCCTTTA
1529706 TAATTTCAAA
Statistics
Matches: 159, Mismatches: 53, Indels: 22
0.68 0.23 0.09
Matches are distributed among these distances:
28 3 0.02
29 59 0.37
30 96 0.60
31 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAGTTTATGTTTTTG
Found at i:1531545 original size:24 final size:22
Alignment explanation
Indices: 1531491--1531545 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1531481 TTACTTCAAT
* *
1531491 TTTTATATTTATTTTATGTTAC
1 TTTTATATTAATTTTATGTTAA
*
1531513 TTTTTTATTAATATTTATGTTAA
1 TTTTATATTAAT-TTTATGTTAA
1531536 TTTATATATT
1 TTT-TATATT
1531546 TAAAGATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 10 0.37
23 12 0.44
24 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTATATTAATTTTATGTTAA
Found at i:1531727 original size:22 final size:20
Alignment explanation
Indices: 1531702--1531759 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
1531692 TATTTTTATT
1531702 TTTTATATTTTTTATTAA-TTAA
1 TTTTA-ATTTTTTA--AATTTAA
1531724 TTTTAATTATTTTAAATTTAA
1 TTTTAATT-TTTTAAATTTAA
*
1531745 TTTTAAATTTTTAAA
1 TTTTAATTTTTTAAA
1531760 ATAAAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 9 0.27
21 14 0.42
22 10 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATTTTTTAAATTTAA
Found at i:1537267 original size:357 final size:357
Alignment explanation
Indices: 1536608--1537320 Score: 1273
Period size: 357 Copynumber: 2.0 Consensus size: 357
1536598 TGGAGCATAT
* *
1536608 TCAGACTTTTAATCTTGCTCACTCAAACCAGATGAGGATTGATGATGAGATAAGGATTCATGCTG
1 TCAGACTTTTAATCTTGCTCACTCAAACCAGAGGAGGATTGATGATGAGAGAAGGATTCATGCTG
*
1536673 AACTTGTTGATTTGGAAATTGTAGAATCTGGTTTTTATAAACAACATGCTAAGGTGCACTAGCTT
66 AACTTGTTGATTTGGAAATTGCAGAATCTGGTTTTTATAAACAACATGCTAAGGTGCACTAGCTT
* *
1536738 AGAGAGGGTGACTAGAACACCAAGTTCTTCTACCAGAGGATACAAGCTAATAAAAAGAAGAATGC
131 AGAGAGGGTGACTAGAACACCAAGTTCTTCTACCAGAGGATACAAGCTAATAAAAAAAAGAATAC
1536803 TATAAGAGTTATAAGAGATGAGGATGGACAAATCCATGAATCGTTTGAAGGAATATCAGCTGAAC
196 TATAAGAGTTATAAGAGATGAGGATGGACAAATCCATGAATCGTTTGAAGGAATATCAGCTGAAC
* *
1536868 TAGTGGGATTTTTTACTAGTCTCATTGGTTCCCCTTATCCTCTAGTCAAAGGCTGCTCTATTGAA
261 TAGTGGGATTTTTTACTAGTCTCATTGGTTCCCCTGATCCTCTAGTCAAAGGCTGCTCTATTAAA
1536933 AATTTGAAGGACTTGCTAAGTTACTCCATTCA
326 AATTTGAAGGACTTGCTAAGTTACTCCATTCA
*
1536965 TCAGACTTTTAATCTTGCTCACTCAAACCAGAGGAGGATTGATGATGAGAGAATGATTCATGCTG
1 TCAGACTTTTAATCTTGCTCACTCAAACCAGAGGAGGATTGATGATGAGAGAAGGATTCATGCTG
* * *
1537030 AACTTGTTGATTTGGAAATTGCAGAATCTTGTTTTTATAAGCAGCATGCTAAGGTGCACTAGCTT
66 AACTTGTTGATTTGGAAATTGCAGAATCTGGTTTTTATAAACAACATGCTAAGGTGCACTAGCTT
1537095 AGAGAGGGTGACTAGAACACCAAGTTCTTCTACCAGAGGATACAAGCTAATAAAAAAAAGAATAC
131 AGAGAGGGTGACTAGAACACCAAGTTCTTCTACCAGAGGATACAAGCTAATAAAAAAAAGAATAC
* * ** *
1537160 TATAAGGGTTATAAGAGATGAGGATGGGCTGATCCATGAATCTTTTGAAGGAATATCAGCTGAAC
196 TATAAGAGTTATAAGAGATGAGGATGGACAAATCCATGAATCGTTTGAAGGAATATCAGCTGAAC
*
1537225 TAGTGGGATTTTTTACTAGTCTCATTGGTTCCCCTGATCCTCTAGTCAAAGGTTGCTCTATTAAA
261 TAGTGGGATTTTTTACTAGTCTCATTGGTTCCCCTGATCCTCTAGTCAAAGGCTGCTCTATTAAA
1537290 AATTTGAAGGACTTGCTAAGTTACTCCATTC
326 AATTTGAAGGACTTGCTAAGTTACTCCATTC
1537321 CTGAAGGTGT
Statistics
Matches: 339, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
357 339 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (357 bp):
TCAGACTTTTAATCTTGCTCACTCAAACCAGAGGAGGATTGATGATGAGAGAAGGATTCATGCTG
AACTTGTTGATTTGGAAATTGCAGAATCTGGTTTTTATAAACAACATGCTAAGGTGCACTAGCTT
AGAGAGGGTGACTAGAACACCAAGTTCTTCTACCAGAGGATACAAGCTAATAAAAAAAAGAATAC
TATAAGAGTTATAAGAGATGAGGATGGACAAATCCATGAATCGTTTGAAGGAATATCAGCTGAAC
TAGTGGGATTTTTTACTAGTCTCATTGGTTCCCCTGATCCTCTAGTCAAAGGCTGCTCTATTAAA
AATTTGAAGGACTTGCTAAGTTACTCCATTCA
Found at i:1539287 original size:12 final size:13
Alignment explanation
Indices: 1539265--1539294 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1539255 TCCAAAGTAA
1539265 TTCTCTCATCTTC
1 TTCTCTCATCTTC
1539278 TTCT-TCATCTTC
1 TTCTCTCATCTTC
1539290 TTCTC
1 TTCTC
1539295 CCAAACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTCTCATCTTC
Found at i:1540286 original size:21 final size:21
Alignment explanation
Indices: 1540260--1540300 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1540250 GCCGAGGGTT
*
1540260 TCATAGGTCCTCCGGGACAAC
1 TCATAGGTCCTCCGGAACAAC
*
1540281 TCATAGGTCCTTCGGAACAA
1 TCATAGGTCCTCCGGAACAA
1540301 ATTTCATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (21 bp):
TCATAGGTCCTCCGGAACAAC
Found at i:1540780 original size:25 final size:25
Alignment explanation
Indices: 1540744--1540792 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1540734 TAACATTTTG
*
1540744 GGTACTGCAGCAGGTTACTGTTCAC
1 GGTACTGCAGCAAGTTACTGTTCAC
* *
1540769 GGTACTGTAGCAAGTTATTGTTCA
1 GGTACTGCAGCAAGTTACTGTTCA
1540793 TTACTGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (25 bp):
GGTACTGCAGCAAGTTACTGTTCAC
Found at i:1542708 original size:20 final size:21
Alignment explanation
Indices: 1542660--1542719 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
1542650 AACTCAGTTT
*
1542660 TCAA-ATTCGCAACGCGAATA
1 TCAAGATTCGCAACGCGATTA
* *
1542680 TCCAGATTCGCAACGCGATTG
1 TCAAGATTCGCAACGCGATTA
1542701 T-AAGATTCGCAACGCGATT
1 TCAAGATTCGCAACGCGATT
1542720 TTGAAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGATTCGCAACGCGATTA
Found at i:1543243 original size:19 final size:19
Alignment explanation
Indices: 1543205--1543307 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 19
1543195 GATTTTTAAA
*
1543205 ATCGCAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGGACT
1543226 ATCGCAACGAATTTGGACT
1 ATCGCAACGAATTTGGACT
* * **
1543245 AACG-TA--AATTTGGAAA
1 ATCGCAACGAATTTGGACT
* **
1543261 ATCGTAACGAATTTGGAAA
1 ATCGCAACGAATTTGGACT
*
1543280 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGACT
1543301 ATCGCAA
1 ATCGCAA
1543308 AATCGCGTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
16 11 0.17
17 1 0.02
18 1 0.02
19 29 0.44
21 24 0.36
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (19 bp):
ATCGCAACGAATTTGGACT
Found at i:1543258 original size:35 final size:35
Alignment explanation
Indices: 1543210--1543277 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1543200 TTAAAATCGC
* **
1543210 AACGTGAACTTGGACTATCGCAACGAATTTGGACT
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
* *
1543245 AACGTAAATTTGGAAAATCGTAACGAATTTGGA
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGA
1543278 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (35 bp):
AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
Found at i:1545351 original size:18 final size:19
Alignment explanation
Indices: 1545316--1545352 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1545306 CACGGAATGT
1545316 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1545336 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1545353 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1552226 original size:24 final size:24
Alignment explanation
Indices: 1552120--1552228 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
1552110 GAATGTTTTA
** * *
1552120 TCTGATTTCCAATTTGAATTATGT
1 TCTGATTTCTGATCTGAATTTTGT
*
1552144 TCTGATTTCTTATCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTTTGT
* *
1552168 TCTGATTTCTTATCTGGATTTTGT
1 TCTGATTTCTGATCTGAATTTTGT
* *
1552192 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTTTGT
* *
1552216 TTTGTTTTCTGAT
1 TCTGATTTCTGAT
1552229 ATATCCGTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.55
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTTTGT
Found at i:1556801 original size:24 final size:25
Alignment explanation
Indices: 1556773--1556881 Score: 120
Period size: 24 Copynumber: 4.6 Consensus size: 25
1556763 GAATGTTTTA
*
1556773 TCTGATTTTC-GATTTGAATTCTGT
1 TCTGATTTTCTGATCTGAATTCTGT
* *
1556797 TCTGA-TTTATGATCTGAATTATGT
1 TCTGATTTTCTGATCTGAATTCTGT
*
1556821 TCTGA-TTTCTGATCTGGATTCTGT
1 TCTGATTTTCTGATCTGAATTCTGT
* *
1556845 TATGA-TATCTGATCTGAATTCTGT
1 TCTGATTTTCTGATCTGAATTCTGT
*
1556869 TTTG-TTTTCTGAT
1 TCTGATTTTCTGAT
1556882 ATATCCTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
23 3 0.04
24 69 0.96
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.52
Consensus pattern (25 bp):
TCTGATTTTCTGATCTGAATTCTGT
Found at i:1556825 original size:48 final size:49
Alignment explanation
Indices: 1556773--1556881 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
1556763 GAATGTTTTA
* * *
1556773 TCTGATTTTC-GATTTGAATTCTGTTCTGATTTATGATCTGAATTATGT
1 TCTGATTTTCTGATCTGAATTCTGTTATGATATATGATCTGAATTATGT
* * *
1556821 TCTGA-TTTCTGATCTGGATTCTGTTATGATATCTGATCTGAATTCTGT
1 TCTGATTTTCTGATCTGAATTCTGTTATGATATATGATCTGAATTATGT
*
1556869 TTTG-TTTTCTGAT
1 TCTGATTTTCTGAT
1556882 ATATCCTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 4 0.08
48 48 0.92
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.52
Consensus pattern (49 bp):
TCTGATTTTCTGATCTGAATTCTGTTATGATATATGATCTGAATTATGT
Found at i:1559459 original size:16 final size:16
Alignment explanation
Indices: 1559438--1559495 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
1559428 TAATAAATAA
1559438 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1559454 ACGAACAAAAACGAAC
1 ACGAACATAAACGAAC
*
1559470 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1559486 TCGAACATAA
1 ACGAACATAA
1559496 GCGTTGGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1560442 original size:24 final size:24
Alignment explanation
Indices: 1560406--1560474 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1560396 GATTGAATTA
** * *
1560406 AACATAAATGAATGAATATAAATG
1 AACATAACCGAATGAACATAAACG
1560430 AACATAACCGAATGAACATAAACG
1 AACATAACCGAATGAACATAAACG
*
1560454 AACATAACCGAACGAACATAA
1 AACATAACCGAATGAACATAA
1560475 CCAAACGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (24 bp):
AACATAACCGAATGAACATAAACG
Found at i:1560443 original size:14 final size:14
Alignment explanation
Indices: 1560429--1560481 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
1560419 GAATATAAAT
*
1560429 GAACATAACCGAAT
1 GAACATAACCGAAC
1560443 GAACAT-A---AAC
1 GAACATAACCGAAC
1560453 GAACATAACCGAAC
1 GAACATAACCGAAC
*
1560467 GAACATAACCAAAC
1 GAACATAACCGAAC
1560481 G
1 G
1560482 TTCACGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.09
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:1562926 original size:23 final size:22
Alignment explanation
Indices: 1562879--1562926 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1562869 CTCTAAATTC
* *
1562879 TTTTTTCTTTTTTACTTTGTGT
1 TTTTTTCTTCTTTACTTTGTCT
1562901 TTTTCTTCTTCTTTA-TTTCGTCT
1 TTTT-TTCTTCTTTACTTT-GTCT
1562924 TTT
1 TTT
1562927 ATTTTTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTTCTTCTTTACTTTGTCT
Found at i:1566350 original size:15 final size:15
Alignment explanation
Indices: 1566330--1566362 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1566320 ATATACATAC
1566330 ATATATATATTCTTT
1 ATATATATATTCTTT
1566345 ATATATATATTCTTT
1 ATATATATATTCTTT
1566360 ATA
1 ATA
1566363 AATAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATATATTCTTT
Found at i:1569771 original size:29 final size:29
Alignment explanation
Indices: 1569739--1569821 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
1569729 ACACCCATTT
* * *
1569739 CGAATTAATTACTAGCATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1569768 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1569797 CGAATTATTTACCAGAATAGCACCA
1 CGAATTATTTACCAGAATAGCACCA
1569822 GTCAACGGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1569850 original size:17 final size:17
Alignment explanation
Indices: 1569828--1569870 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1569818 ACCAGTCAAC
*
1569828 GGTCAACGATCTGGTCG
1 GGTCAACGATCGGGTCG
*
1569845 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GATCGGGTCG
1569863 GGTCAACG
1 GGTCAACG
1569871 GGTTGGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:1569863 original size:18 final size:18
Alignment explanation
Indices: 1569840--1569879 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1569830 TCAACGATCT
1569840 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
*
1569858 GGTCGGGTCAACGGGTTG
1 GGTCGGGTCAACGGGTCG
1569876 GGTC
1 GGTC
1569880 AAAAAGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:1577181 original size:29 final size:29
Alignment explanation
Indices: 1577149--1577230 Score: 139
Period size: 28 Copynumber: 2.9 Consensus size: 29
1577139 CACCCATTTC
*
1577149 GAATTAATTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
1577178 GAATTATTTACCAGAATAGCACC-AAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
1577206 AAATTATTTACCAGAATAGCACCAA
1 GAATTATTTACCAGAATAGCACCAA
1577231 TTAACGGTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 27 0.54
29 23 0.46
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACT
Found at i:1579215 original size:72 final size:72
Alignment explanation
Indices: 1579131--1579273 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
1579121 ATTCATACTT
1579131 TTAATTATATTTAATACTAATTGTATTAAAAAATTGCAGACATTTTATTCTAGTATACATGCCAA
1 TTAATTATATTTAATACTAATTGTATTAAAAAATTGCAGACATTTTATTCTAGTATACATGCCAA
*
1579196 TTAGAAG
66 CTAGAAG
* * *
1579203 TTAATTATATTTAATACTAATTGTTTTAAGAAATTGCAGACATTTTATTCTCGTATACATGCCAA
1 TTAATTATATTTAATACTAATTGTATTAAAAAATTGCAGACATTTTATTCTAGTATACATGCCAA
1579268 CTAGAA
66 CTAGAA
1579274 CTAGAACACA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (72 bp):
TTAATTATATTTAATACTAATTGTATTAAAAAATTGCAGACATTTTATTCTAGTATACATGCCAA
CTAGAAG
Found at i:1581069 original size:22 final size:22
Alignment explanation
Indices: 1581044--1581097 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1581034 AATCTCTACT
* *
1581044 ATCAAAGCCCTAACTTAATTTA
1 ATCAAAACACTAACTTAATTTA
*
1581066 ATCAAAACACTAACTTAATTTC
1 ATCAAAACACTAACTTAATTTA
*
1581088 ATTAAAACAC
1 ATCAAAACAC
1581098 ATCTTTCCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (22 bp):
ATCAAAACACTAACTTAATTTA
Found at i:1581726 original size:43 final size:42
Alignment explanation
Indices: 1581679--1581965 Score: 313
Period size: 42 Copynumber: 6.8 Consensus size: 42
1581669 ATAGGTCAAG
* *
1581679 ATCTATAGCGACGTTTTTGAAACAAACGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AT
* * * *
1581722 ATCTATAGCGGCGTTTTTGGAACAAACGCTGCAAAAAGTTGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGC-AAAAGGTCAT
* *
1581765 ATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
* * * * * * *
1581807 ATCTATAGCGACGTTTCTGGAACAAACGCTGTAAAAAGTTGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCG-CAAAAGGTCAT
* *
1581850 ATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
* * * *
1581892 ATCTAAAGTGGCGTTTTTGGAAGAAACGTCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
** ** *
1581934 ATCTATAGCAACGTTTTTTAAACAAACACCGC
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGC
1581966 TAATTACCTT
Statistics
Matches: 197, Mismatches: 45, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
42 99 0.50
43 92 0.47
44 6 0.03
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
Found at i:1581847 original size:85 final size:85
Alignment explanation
Indices: 1581677--1581960 Score: 392
Period size: 85 Copynumber: 3.3 Consensus size: 85
1581667 CCATAGGTCA
* *
1581677 AGATCTATAGCGACGTTTTTGAAACAAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGG
1 AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTC-ATATCTATAGCGGCGTTTTTGG
1581742 AACAAACGCTGCAAAAAGTTG
65 AACAAACGCTGCAAAAAGTTG
* *
1581763 AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCATATCTATAGCGACGTTTCTGGA
1 AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCATATCTATAGCGGCGTTTTTGGA
*
1581828 ACAAACGCTGTAAAAAGTTG
66 ACAAACGCTGCAAAAAGTTG
* * * *
1581848 AGATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCATATCTAAAGTGGCGTTTTTGGA
1 AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCATATCTATAGCGGCGTTTTTGGA
* * *
1581913 AGAAACG-TCGC-AAAAGGTC
66 ACAAACGCT-GCAAAAAGTTG
* ** *
1581932 ATATCTATAGCAACGTTTTTTAAACAAAC
1 AGATCTATAGCGGCGTTTTTGAAACAAAC
1581961 ACCGCTAATT
Statistics
Matches: 176, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
84 30 0.17
85 106 0.60
86 40 0.23
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (85 bp):
AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCATATCTATAGCGGCGTTTTTGGA
ACAAACGCTGCAAAAAGTTG
Found at i:1586998 original size:79 final size:81
Alignment explanation
Indices: 1586787--1587000 Score: 240
Period size: 79 Copynumber: 2.7 Consensus size: 81
1586777 ATGGCATTTT
* * * * *
1586787 TATAAAAAGGCCGCTAAAGTACAAATCTGTTGTGGCGTTTG-TCAAAAAACGCCACAATAGATGG
1 TATAAAAACGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTTAAAAAACGCCACAATA-ATGG
1586851 ACCTATTACGACGTATA
65 ACCTATTACGACGTATA
* * * *
1586868 TATAAAAACGCCGCTAAAGTACTACTCTTTTGTGGCATTT-TTTGAAAAAACGCTAC-AT-ATGT
1 TATAAAAACGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTT-AAAAAACGCCACAATAATGG
* *
1586930 ACCTATTGC-AGCGTTTA
65 ACCTATTACGA-CGTATA
* * *
1586947 TATAAAAACGTCGCTAAAGTACTACTCTATTGTGGTGTTTGTTTAAGAAACGCC
1 TATAAAAACGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTTAAAAAACGCC
1587001 GCTAAAGTAT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.53
80 3 0.03
81 38 0.34
82 11 0.10
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (81 bp):
TATAAAAACGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTTAAAAAACGCCACAATAATGGA
CCTATTACGACGTATA
Found at i:1602347 original size:21 final size:21
Alignment explanation
Indices: 1602321--1602360 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1602311 CCCCCTTTGA
*
1602321 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1602342 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1602361 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1606113 original size:24 final size:24
Alignment explanation
Indices: 1606086--1606144 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1606076 CTGGCCAAGG
* * **
1606086 AGTACCGATACTACTTTGTAGTGT
1 AGTATCGATACTACTATGTAAAGT
*
1606110 AGTATCGATATTACTATGTAAAGT
1 AGTATCGATACTACTATGTAAAGT
1606134 AGTATCGATAC
1 AGTATCGATAC
1606145 CGATCGTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (24 bp):
AGTATCGATACTACTATGTAAAGT
Found at i:1606233 original size:21 final size:21
Alignment explanation
Indices: 1606208--1606303 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
1606198 AAAAGGGGTA
*
1606208 GTATCGGTACCATTGATCATG
1 GTATCGATACCATTGATCATG
* *
1606229 GTATCGATACTACT-ATC---
1 GTATCGATACCATTGATCATG
* *
1606246 -TATCGGTACCATTGACCATG
1 GTATCGATACCATTGATCATG
* *
1606266 GTATCGATACTACTATGTATAATG
1 GTATCGATACCA-T-TG-ATCATG
1606290 GTATCGATA-CATTG
1 GTATCGATACCATTG
1606304 TAGGGTATCG
Statistics
Matches: 55, Mismatches: 12, Indels: 16
0.66 0.14 0.19
Matches are distributed among these distances:
16 10 0.18
17 2 0.04
20 3 0.05
21 22 0.40
22 2 0.04
23 3 0.05
24 13 0.24
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
GTATCGATACCATTGATCATG
Found at i:1606259 original size:37 final size:37
Alignment explanation
Indices: 1606209--1606281 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
1606199 AAAGGGGTAG
*
1606209 TATCGGTACCATTGATCATGGTATCGATACTACTATC
1 TATCGGTACCATTGACCATGGTATCGATACTACTATC
1606246 TATCGGTACCATTGACCATGGTATCGATACTACTAT
1 TATCGGTACCATTGACCATGGTATCGATACTACTAT
1606282 GTATAATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (37 bp):
TATCGGTACCATTGACCATGGTATCGATACTACTATC
Found at i:1606552 original size:18 final size:18
Alignment explanation
Indices: 1606529--1606564 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1606519 ATTCAAATAA
1606529 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
1606547 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
1606565 CTTAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:1609132 original size:5 final size:5
Alignment explanation
Indices: 1609122--1609192 Score: 80
Period size: 5 Copynumber: 14.8 Consensus size: 5
1609112 ATAACTAAAC
*
1609122 ATAAT ATAAT ATAAT ATAAT A-AAT ATAAA ATAAT A-AAT AATAAT ATAA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
1609170 ATAAT AT-AT A-ATAT ATAAT ATAA
1 ATAAT ATAAT ATA-AT ATAAT ATAA
1609193 ACTATATAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
4 14 0.25
5 39 0.68
6 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:1609155 original size:29 final size:29
Alignment explanation
Indices: 1609117--1609192 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
1609107 AATGAATAAC
1609117 TAAACATAATATAATATAATAT-AATAAATA
1 TAAA-ATAATATAATATAATATAAAT-AATA
1609147 TAAAATAATA-AATAATAATATAAATAATA
1 TAAAATAATATAAT-ATAATATAAATAATA
*
1609176 TATAAT-ATATAATATAA
1 TAAAATAATATAATATAA
1609193 ACTATATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 10 0.24
29 25 0.60
30 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAATAATATAATATAATATAAATAATA
Found at i:1609159 original size:7 final size:7
Alignment explanation
Indices: 1609122--1609189 Score: 63
Period size: 7 Copynumber: 9.9 Consensus size: 7
1609112 ATAACTAAAC
1609122 ATAATATA
1 ATAATA-A
1609130 AT-ATAA
1 ATAATAA
1609136 TATAATAA
1 -ATAATAA
1609144 AT-ATAAA
1 ATAAT-AA
1609151 ATAATAA
1 ATAATAA
1609158 ATAAT-A
1 ATAATAA
1609164 AT-ATAA
1 ATAATAA
*
1609170 ATAATAT
1 ATAATAA
*
1609177 ATAATAT
1 ATAATAA
1609184 ATAATA
1 ATAATA
1609190 TAAACTATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
5 2 0.04
6 9 0.17
7 34 0.64
8 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
ATAATAA
Found at i:1609190 original size:7 final size:7
Alignment explanation
Indices: 1609130--1609213 Score: 72
Period size: 7 Copynumber: 12.6 Consensus size: 7
1609120 ACATAATATA
1609130 ATATAAT
1 ATATAAT
1609137 ATAATAA-
1 AT-ATAAT
1609144 ATATAA-
1 ATATAAT
1609150 A-ATAAT
1 ATATAAT
*
1609156 AAATAAT
1 ATATAAT
1609163 A-AT-AT
1 ATATAAT
*
1609168 AAATAAT
1 ATATAAT
1609175 ATATAAT
1 ATATAAT
1609182 ATATAAT
1 ATATAAT
1609189 ATA-AACT
1 ATATAA-T
*
1609196 ATATAAC
1 ATATAAT
*
1609203 ATATATT
1 ATATAAT
1609210 ATAT
1 ATAT
1609214 TTTCAAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
5 7 0.11
6 12 0.18
7 41 0.62
8 6 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (7 bp):
ATATAAT
Found at i:1609233 original size:20 final size:21
Alignment explanation
Indices: 1609204--1609243 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1609194 CTATATAACA
*
1609204 TATATTATA-TTTTCAAAAAT
1 TATATAATAGTTTTCAAAAAT
1609224 TATATAATATGTTTTCAAAA
1 TATATAATA-GTTTTCAAAA
1609244 TATGTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
TATATAATAGTTTTCAAAAAT
Found at i:1609247 original size:13 final size:13
Alignment explanation
Indices: 1609229--1609256 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1609219 AAAATTATAT
1609229 AATATGTTTTCAA
1 AATATGTTTTCAA
1609242 AATATGTTTTCAA
1 AATATGTTTTCAA
1609255 AA
1 AA
1609257 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
AATATGTTTTCAA
Found at i:1609287 original size:16 final size:16
Alignment explanation
Indices: 1609266--1609300 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1609256 ACTATATTAT
1609266 ATACGTTTTCAAAATC
1 ATACGTTTTCAAAATC
*
1609282 ATACGTTTTCAAAGTC
1 ATACGTTTTCAAAATC
1609298 ATA
1 ATA
1609301 TATTATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (16 bp):
ATACGTTTTCAAAATC
Done.