Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 29
Found at i:983373 original size:18 final size:17
Alignment explanation
Indices: 983349--983395 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
983339 GGTAGTTGAC
983349 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* *
983366 TCATTTAAACTGGTTCAT
1 T-AATTAAACTAGTTCAT
983384 TAATTAAACTAG
1 TAATTAAACTAG
983396 CTCTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:985066 original size:15 final size:16
Alignment explanation
Indices: 985046--985076 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
985036 GGAGTGTTTG
985046 GTGAGGTT-TTTTTTT
1 GTGAGGTTATTTTTTT
985061 GTGAGGTTATTTTTTT
1 GTGAGGTTATTTTTTT
985077 TACTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.65
Consensus pattern (16 bp):
GTGAGGTTATTTTTTT
Found at i:986762 original size:18 final size:17
Alignment explanation
Indices: 986738--986784 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
986728 GGTAGTTGAC
986738 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* *
986755 TCATTTAAACTGGTTCAT
1 T-AATTAAACTAGTTCAT
986773 TAATTAAACTAG
1 TAATTAAACTAG
986785 CTCTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:990135 original size:18 final size:17
Alignment explanation
Indices: 990111--990157 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
990101 GGTAGTTGAC
990111 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* *
990128 TCATTTAAACTGGTTCAT
1 T-AATTAAACTAGTTCAT
990146 TAATTAAACTAG
1 TAATTAAACTAG
990158 CTCTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:991920 original size:49 final size:49
Alignment explanation
Indices: 991848--991958 Score: 204
Period size: 49 Copynumber: 2.3 Consensus size: 49
991838 AGCATGATAC
*
991848 TTCATTTAAGTATGAGTTCATCAAAGCATGTAGGTTTTTATGAAGCTAT
1 TTCATTTAAGTATGAGTTCATCAAAGCATGTAGGTTTTTAAGAAGCTAT
991897 TTCATTTAAGTATGAGTTCATCAAAGCATGTAGGTTTTTAAGAAGCTAT
1 TTCATTTAAGTATGAGTTCATCAAAGCATGTAGGTTTTTAAGAAGCTAT
*
991946 TTCATTTATGTAT
1 TTCATTTAAGTAT
991959 CCTCTTTCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (49 bp):
TTCATTTAAGTATGAGTTCATCAAAGCATGTAGGTTTTTAAGAAGCTAT
Found at i:992011 original size:18 final size:17
Alignment explanation
Indices: 991987--992033 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
991977 GGTAGTTGAC
991987 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* *
992004 TCATTTAAACTGGTTCAT
1 T-AATTAAACTAGTTCAT
992022 TAATTAAACTAG
1 TAATTAAACTAG
992034 CTCTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:996505 original size:16 final size:16
Alignment explanation
Indices: 996484--996516 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
996474 TTTTAAGGAC
996484 GTTCGTCCATCTTTGT
1 GTTCGTCCATCTTTGT
996500 GTTCGTCCATCTTTGT
1 GTTCGTCCATCTTTGT
996516 G
1 G
996517 AGTAGATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.21, T:0.48
Consensus pattern (16 bp):
GTTCGTCCATCTTTGT
Found at i:997475 original size:75 final size:74
Alignment explanation
Indices: 997313--997513 Score: 180
Period size: 75 Copynumber: 2.7 Consensus size: 74
997303 ATAAATATAT
* * * * *
997313 ATAAA-AAATCATAA-AT-AAA-ATCAAATATCAAGACTCAACCCACAATATTAAGTTTCGAACA
1 ATAAACAAATCATAATATAAAATATCAAATTTCAAGACTCAAACCACAATATTAACTCTAGAACA
*
997374 GTAAAATCC
66 ATAAAATCC
* *
997383 ATAAACAAA-CTACAATATGAAAATATCAAATTTCAAGATTCAAACCACAATATTAACTCTAGAA
1 ATAAACAAATC-ATAATAT-AAAATATCAAATTTCAAGACTCAAACCACAATATTAACTCTAGAA
* **
997447 TAATAAAATTT
64 CAATAAAATCC
* * * * *
997458 ATAATCAAATCATAATATTAAAGTGTCAAATCTT-AATACTCAAACCATAATATTAA
1 ATAAACAAATCATAATA-TAAAATATCAAAT-TTCAAGACTCAAACCACAATATTAA
997514 GTATAGAAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
70 6 0.06
71 6 0.06
72 2 0.02
74 3 0.03
75 83 0.80
76 4 0.04
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.27
Consensus pattern (74 bp):
ATAAACAAATCATAATATAAAATATCAAATTTCAAGACTCAAACCACAATATTAACTCTAGAACA
ATAAAATCC
Found at i:998519 original size:21 final size:21
Alignment explanation
Indices: 998489--998547 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
998479 TTCAATAAAT
*
998489 ATGATCCAAAGCTGCCGCTTC
1 ATGATACAAAGCTGCCGCTTC
998510 ATGATACAAAGCTGCCGCTTC
1 ATGATACAAAGCTGCCGCTTC
998531 ATGATACAAAGCTGCCG
1 ATGATACAAAGCTGCCG
998548 TTTTAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
ATGATACAAAGCTGCCGCTTC
Found at i:998711 original size:2 final size:2
Alignment explanation
Indices: 998704--998736 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
998694 TATCTTTGTT
998704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
998737 TCTAGTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1009747 original size:17 final size:17
Alignment explanation
Indices: 1009727--1009773 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1009717 GATTTTTGGT
1009727 TATCAGATATTTACAAA
1 TATCAGATATTTACAAA
*
1009744 TATCAGATGA-TTACAAT
1 TATCAGAT-ATTTACAAA
*
1009761 TATCAAATATTTA
1 TATCAGATATTTA
1009774 TAGATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (17 bp):
TATCAGATATTTACAAA
Found at i:1010709 original size:2 final size:2
Alignment explanation
Indices: 1010702--1010756 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1010692 TTAGACAGTA
1010702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1010744 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1010757 CTTATGATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1023341 original size:15 final size:16
Alignment explanation
Indices: 1023321--1023353 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1023311 TCGATTTAAG
*
1023321 TATTG-ATTTTATTTT
1 TATTGAATTTTATATT
1023336 TATTGAATTTTATATT
1 TATTGAATTTTATATT
1023352 TA
1 TA
1023354 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TATTGAATTTTATATT
Found at i:1024427 original size:17 final size:17
Alignment explanation
Indices: 1024376--1024482 Score: 67
Period size: 17 Copynumber: 6.2 Consensus size: 17
1024366 GATGAATTCT
* *
1024376 AAATATTTACAGTTTTC
1 AAATATTTACAGATATC
* * *
1024393 AGAAGATTTTCAGTTATC
1 A-AATATTTACAGATATC
1024411 AAATATTTACAGATATC
1 AAATATTTACAGATATC
1024428 AAATGA-TTACA-ATTATC
1 AAAT-ATTTACAGA-TATC
* *
1024445 AGATATTTATAGATAT-
1 AAATATTTACAGATATC
* *
1024461 AAGATGTTTTACAGTTATC
1 AA-AT-ATTTACAGATATC
1024480 AAA
1 AAA
1024483 AAAAGATTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
16 3 0.04
17 39 0.56
18 26 0.37
19 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (17 bp):
AAATATTTACAGATATC
Found at i:1026866 original size:23 final size:23
Alignment explanation
Indices: 1026789--1026866 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
1026779 ACAATAAACA
* * *
1026789 AACGCTAAACCAACATATTTGTG
1 AACGCTAAACAAACATGTTTATG
* * **
1026812 AGCACTAAACAAACATGTTTACA
1 AACGCTAAACAAACATGTTTATG
* * *
1026835 AATGTTAAACAAACATGTTCATG
1 AACGCTAAACAAACATGTTTATG
1026858 AACGCTAAA
1 AACGCTAAA
1026867 TGAATTAACA
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (23 bp):
AACGCTAAACAAACATGTTTATG
Found at i:1040152 original size:131 final size:130
Alignment explanation
Indices: 1039919--1040262 Score: 317
Period size: 129 Copynumber: 2.6 Consensus size: 130
1039909 ACTCCACCAT
* * *
1039919 TCTTTAAGGAAAATTAGATCTAAAAACTTAGATTCACTTCACTACATTTTAGGGAAGATTAAATC
1 TCTTTAGGGAAGATCAGATCTAAAAACTTAGATTCACTTCACTACATTTTAGGGAAGATTAAATC
* * * *
1039984 GAGGTAGATTTTGTCCACTGCTCCACTGGGAAAATCAAATGTTGGAAGAAGGGATCATATCCACT
66 CAGGTAGATTTTGCCCACTGATCCACTGGGAAAATCAAAT-TT-GAACAAGGGATCATATCCACT
1040049 AC
129 AC
*
1040051 TCTTTAGGGAATG-TCAGATCTAAAAACTT-GATTCACTTCACTACTTTTCTA-GGAAGATTAAA
1 TCTTTAGGGAA-GATCAGATCTAAAAACTTAGATTCACTTCACTACATTT-TAGGGAAGATTAAA
* * ** * * ** * *
1040113 TCCATGTAGA-TTTGCCCTAGTGAT-CTTTGGGAATGATCAAATTTGAACATGGGATTTTCTCCG
64 TCCAGGTAGATTTTGCCC-ACTGATCCACTGGGAA-AATCAAATTTGAACAAGGGATCATATCCA
1040176 CTAC
127 CTAC
* * ** * * *
1040180 TCTTTAGGGAAGATCAGATCTGAAGACTTTCATT-ACTGCACT-CTTTTTCAGGGAAGATTGAAT
1 TCTTTAGGGAAGATCAGATCTAAAAACTTAGATTCACTTCACTACATTTT-AGGGAAGATTAAAT
* *
1040243 CAAGGTACA-TTTGCTCCACT
65 CCAGGTAGATTTTGC-CCACT
1040263 TCTTCTTAGG
Statistics
Matches: 176, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
127 1 0.01
128 7 0.04
129 73 0.41
130 20 0.11
131 48 0.27
132 27 0.15
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (130 bp):
TCTTTAGGGAAGATCAGATCTAAAAACTTAGATTCACTTCACTACATTTTAGGGAAGATTAAATC
CAGGTAGATTTTGCCCACTGATCCACTGGGAAAATCAAATTTGAACAAGGGATCATATCCACTAC
Found at i:1041207 original size:17 final size:17
Alignment explanation
Indices: 1041155--1041209 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1041145 ATTCATACAT
*
1041155 CTAGTTCATTGAATAAAG
1 CTAGTTCATT-AATAAAA
* *
1041173 TTAGTTCATTAATTAAA
1 CTAGTTCATTAATAAAA
*
1041190 CTAGTTCATTCATAAAA
1 CTAGTTCATTAATAAAA
1041207 CTA
1 CTA
1041210 ATTCCAACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (17 bp):
CTAGTTCATTAATAAAA
Found at i:1043057 original size:45 final size:47
Alignment explanation
Indices: 1042977--1043067 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 47
1042967 GATAATTACA
* **
1042977 ATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAA-GAAAT
1 ATATATATATAGTAATAATAGAAATATAAGTAAAATA-TAAATGAAAT
1043024 ATATATATATA-TAATAATA-AAATAT-AGTAAAAATATAAATGAAA
1 ATATATATATAGTAATAATAGAAATATAAGT-AAAATATAAATGAAA
1043068 ATAATTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
44 7 0.18
45 14 0.36
46 7 0.18
47 11 0.28
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (47 bp):
ATATATATATAGTAATAATAGAAATATAAGTAAAATATAAATGAAAT
Found at i:1043117 original size:18 final size:17
Alignment explanation
Indices: 1043096--1043138 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1043086 ATATATACAT
1043096 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1043114 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1043131 ATAA-AATA
1 ATAATAATA
1043139 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1043146 original size:60 final size:59
Alignment explanation
Indices: 1043022--1043146 Score: 128
Period size: 62 Copynumber: 2.1 Consensus size: 59
1043012 TATTAAAGAA
* * * * *
1043022 ATATATATATATATAATAATAAAATATAGTAAAAATATAAATGAAAATAATTTAATATATAT
1 ATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAATATACAT
*
1043084 ATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATATCCAT
1 ATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAATATACAT
1043144 ATA
1 ATA
1043147 ATAAATAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
60 10 0.19
62 21 0.39
63 9 0.17
64 4 0.07
65 10 0.19
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (59 bp):
ATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAATATACAT
Found at i:1044478 original size:105 final size:105
Alignment explanation
Indices: 1044291--1044740 Score: 696
Period size: 105 Copynumber: 4.3 Consensus size: 105
1044281 GCATTGTTCA
* * ** *
1044291 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1044351 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1044391 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1044456 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1044496 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-ACGATTGGGAAGTTGTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-GATTGGGAAGTTGTTGTTGACAA
1044560 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1044601 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1044666 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1044706 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1044741 CGCGGATGGC
Statistics
Matches: 324, Mismatches: 16, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
100 37 0.11
101 1 0.00
102 1 0.00
104 6 0.02
105 253 0.78
106 4 0.01
108 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1045477 original size:67 final size:68
Alignment explanation
Indices: 1045313--1045480 Score: 205
Period size: 68 Copynumber: 2.5 Consensus size: 68
1045303 GATAGAATTC
* * * *
1045313 GTTTCAAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAA
1 GTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACGGTCTCAAGGGAAACAA
1045377 AATTAT
63 AATTAT
** * * *
1045383 GTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAAT
1 GTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAAT
1045448 T-T
66 TAT
*
1045450 GTTTTAGGGGAAATAAATTCAAAGATTTTGT
1 GTTTTAAGGGAAATAAATTCAAAGATTTTGT
1045481 TTCAAGGGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
67 29 0.34
68 32 0.38
69 3 0.04
70 19 0.22
71 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (68 bp):
GTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAAT
TAT
Found at i:1045562 original size:37 final size:37
Alignment explanation
Indices: 1045510--1045735 Score: 199
Period size: 37 Copynumber: 6.4 Consensus size: 37
1045500 AAGATATATG
* *
1045510 TTGTTTCATGAGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
1045547 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1045583 TTGTTTCAA-AGAAAACATAT-TC-------A-AATATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
1045612 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1045648 TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1045685 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1045721 TTATTTCAAGGGAAA
1 TTGTTTCAAGAGAAA
1045736 TGTTTTCAAT
Statistics
Matches: 154, Mismatches: 21, Indels: 29
0.75 0.10 0.14
Matches are distributed among these distances:
28 4 0.03
29 17 0.11
30 1 0.01
35 2 0.01
36 64 0.42
37 66 0.43
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (37 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1045640 original size:102 final size:102
Alignment explanation
Indices: 1045505--1045693 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
1045495 TCTCAAAGAT
*
1045505 ATATGTTGTTTCATGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCA
1 ATATGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCA
* *
1045570 AGGGAGACGAAA-TTTGTTTCAAAGAAAACATATTCAA
65 AGAGAGACAAAATTTTGTTTCAAAGAAAACATATTCAA
* * * * *
1045607 ATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAA
1 ATATGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAA
1045672 GAGAGACAAAATTTTGTTTCAA
66 GAGAGACAAAATTTTGTTTCAA
1045694 GGGAAACTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 28 0.36
102 50 0.64
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (102 bp):
ATATGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAA
GAGAGACAAAATTTTGTTTCAAAGAAAACATATTCAA
Found at i:1045663 original size:36 final size:36
Alignment explanation
Indices: 1045615--1045735 Score: 197
Period size: 36 Copynumber: 3.3 Consensus size: 36
1045605 AAATATTTTG
1045615 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* *
1045651 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTA
* *
1045688 TTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
1045724 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1045736 TGTTTTCAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 46 0.59
37 32 0.41
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:1045715 original size:138 final size:139
Alignment explanation
Indices: 1045413--1045783 Score: 450
Period size: 138 Copynumber: 2.7 Consensus size: 139
1045403 GAAGATTTTG
* * * * * *
1045413 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
* * * *
1045478 TGTTTCAAGGGAAA-TGATCTC-A-A-AGA-TATATGTTGTTTCATGAGAAACTGTCTCAAGAGA
66 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATGTTATTTCAAGAGAAACTGTCTCAAGAGA
1045538 GACAAAACTT
130 GACAAAACTT
* * * * * *
1045548 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
1045613 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-TTATTTCAAGAGAAACTGTCTCAAGAGAG
66 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATGTTATTTCAAGAGAAACTGTCTCAAGAGAG
*
1045677 ACAAAATTT
131 ACAAAACTT
* * * * * * *
1045686 TGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
*
1045750 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
66 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1045784 TCTTGTTTTA
Statistics
Matches: 199, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
135 71 0.36
136 3 0.02
137 7 0.04
138 115 0.58
139 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (139 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATGTTATTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAACTT
Found at i:1046726 original size:22 final size:22
Alignment explanation
Indices: 1046701--1046744 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1046691 ATTTTTGTTC
1046701 ATTTGATGCT-AAATGGTTTGAT
1 ATTTGATGCTCAAA-GGTTTGAT
1046723 ATTTGATGCTCAAAGGTTTGAT
1 ATTTGATGCTCAAAGGTTTGAT
1046745 GGGGTAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGTTTGAT
Found at i:1047358 original size:12 final size:11
Alignment explanation
Indices: 1047342--1047400 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
1047332 TTTTTGTCCC
1047342 TTTTTCTTTTT
1 TTTTTCTTTTT
1047353 TCTTTT-TGTTCTT
1 T-TTTTCT-TT-TT
1047366 TTTTTGCTTTTT
1 TTTTT-CTTTTT
1047378 TTTTTGCTTTTT
1 TTTTT-CTTTTT
*
1047390 CTTTTCTTTTT
1 TTTTTCTTTTT
1047401 GCCCTTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
11 8 0.19
12 28 0.67
13 5 0.12
14 1 0.02
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1047358 original size:23 final size:22
Alignment explanation
Indices: 1047332--1047409 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
1047322 TTGCATGTGT
1047332 TTTTTGTCCCTTTTTCTTTTTTC
1 TTTTTGT-CCTTTTTCTTTTTTC
*
1047355 TTTTTGTTCTTTTT-TTGCTTTT-
1 TTTTTGTCCTTTTTCTT--TTTTC
*
1047377 TTTTT-TGCTTTTTC--TTTTC
1 TTTTTGTCCTTTTTCTTTTTTC
*
1047396 TTTTTGCCCTTTTT
1 TTTTTGTCCTTTTT
1047410 ATTCTGATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.09
19 5 0.11
20 6 0.13
21 9 0.20
22 11 0.24
23 11 0.24
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTGTCCTTTTTCTTTTTTC
Found at i:1047364 original size:9 final size:8
Alignment explanation
Indices: 1047342--1047394 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
1047332 TTTTTGTCCC
1047342 TTTTTC-T
1 TTTTTCTT
1047349 TTTTTCTT
1 TTTTTCTT
1047357 TTTGTTCTT
1 TTT-TTCTT
1047366 TTTTTGCTT
1 TTTTT-CTT
*
1047375 TTTTTTTT
1 TTTTTCTT
1047383 GCTTTTTCTT
1 --TTTTTCTT
1047393 TT
1 TT
1047395 CTTTTTGCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.15
8 10 0.26
9 16 0.41
10 7 0.18
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1047388 original size:30 final size:31
Alignment explanation
Indices: 1047341--1047402 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
1047331 TTTTTTGTCC
* *
1047341 CTTTTTCTTTTTTCTTTTTGTTCTT-TTTTTG
1 CTTTTTCTTTTTGCTTTTTCTT-TTCTTTTTG
1047372 CTTTTT-TTTTTGCTTTTTCTTTTCTTTTTG
1 CTTTTTCTTTTTGCTTTTTCTTTTCTTTTTG
1047402 C
1 C
1047403 CCTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 20 0.71
31 6 0.21
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (31 bp):
CTTTTTCTTTTTGCTTTTTCTTTTCTTTTTG
Found at i:1047399 original size:18 final size:19
Alignment explanation
Indices: 1047366--1047402 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1047356 TTTTGTTCTT
*
1047366 TTTTTGCTTTTTTTTTTGC
1 TTTTTGCTTTTCTTTTTGC
1047385 TTTTT-CTTTTCTTTTTGC
1 TTTTTGCTTTTCTTTTTGC
1047403 CCTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTTGCTTTTCTTTTTGC
Found at i:1047414 original size:23 final size:22
Alignment explanation
Indices: 1047332--1047414 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 22
1047322 TTGCATGTGT
1047332 TTTTTGTCCCTTTTTCTT-TTTTC
1 TTTTTG-CCCTTTTT-TTCTTTTC
** *
1047355 TTTTTGTTCTTTTTTTGCTTTTT
1 TTTTTGCCCTTTTTTT-CTTTTC
1047378 TTTTTG--C--TTTTTCTTTTC
1 TTTTTGCCCTTTTTTTCTTTTC
1047396 TTTTTGCCCTTTTTATTCT
1 TTTTTGCCCTTTTT-TTCT
1047415 GATTAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
18 11 0.22
19 5 0.10
20 1 0.02
21 3 0.06
22 9 0.18
23 20 0.41
ACGTcount: A:0.01, C:0.17, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTTTGCCCTTTTTTTCTTTTC
Found at i:1048605 original size:15 final size:15
Alignment explanation
Indices: 1048585--1048615 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1048575 ATTGTAGATG
1048585 AAAATGCAAAAATGC
1 AAAATGCAAAAATGC
*
1048600 AAAATGCAAGAATGC
1 AAAATGCAAAAATGC
1048615 A
1 A
1048616 TGAAATGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAATGCAAAAATGC
Found at i:1051752 original size:18 final size:17
Alignment explanation
Indices: 1051729--1051771 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1051719 ATATATACAT
1051729 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1051747 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1051764 ATAA-AATA
1 ATAATAATA
1051772 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1058349 original size:23 final size:23
Alignment explanation
Indices: 1058323--1058367 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1058313 GTAATAAGTT
1058323 TCTTTTAATAAAACAAATAAATC
1 TCTTTTAATAAAACAAATAAATC
*
1058346 TCTTTTAATAAAAGAAATAAAT
1 TCTTTTAATAAAACAAATAAAT
1058368 ATCCTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TCTTTTAATAAAACAAATAAATC
Found at i:1058375 original size:23 final size:23
Alignment explanation
Indices: 1058326--1058375 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1058316 ATAAGTTTCT
* *
1058326 TTTAATAAAACAAATAAATCTCT
1 TTTAATAAAACAAATAAATATCC
*
1058349 TTTAATAAAAGAAATAAATATCC
1 TTTAATAAAACAAATAAATATCC
1058372 TTTA
1 TTTA
1058376 TTTTTATCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (23 bp):
TTTAATAAAACAAATAAATATCC
Found at i:1062870 original size:12 final size:12
Alignment explanation
Indices: 1062853--1062877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1062843 TCTGAAAAGA
1062853 AAGAAAAATAAT
1 AAGAAAAATAAT
1062865 AAGAAAAATAAT
1 AAGAAAAATAAT
1062877 A
1 A
1062878 CTAATAATTA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAGAAAAATAAT
Found at i:1063914 original size:27 final size:26
Alignment explanation
Indices: 1063884--1063943 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
1063874 TTTTAATTCC
* *
1063884 AATAAAAGAGCTATTAAATTTATTTT
1 AATAAAAGAGCTAATAAATCTATTTT
* *
1063910 AAATAAAAGAGGTAATAAATCTCTTTT
1 -AATAAAAGAGCTAATAAATCTATTTT
1063937 AATAAAA
1 AATAAAA
1063944 TAAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (26 bp):
AATAAAAGAGCTAATAAATCTATTTT
Found at i:1067311 original size:12 final size:12
Alignment explanation
Indices: 1067294--1067320 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1067284 GAAAAATACA
1067294 AAAAAGAAGTGC
1 AAAAAGAAGTGC
1067306 AAAAAGAAGTGC
1 AAAAAGAAGTGC
1067318 AAA
1 AAA
1067321 GTCAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (12 bp):
AAAAAGAAGTGC
Found at i:1067373 original size:28 final size:27
Alignment explanation
Indices: 1067342--1067397 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1067332 AGAAAAAATC
* *
1067342 AGAAAAAGAAGCACTCCAAAAGAAAGAA
1 AGAAAAACAAGCACTCAAAAAG-AAGAA
* *
1067370 AGAAAATCCAGCACTCAAAAAGAAGAA
1 AGAAAAACAAGCACTCAAAAAGAAGAA
1067397 A
1 A
1067398 AGCAAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.62, C:0.16, G:0.16, T:0.05
Consensus pattern (27 bp):
AGAAAAACAAGCACTCAAAAAGAAGAA
Found at i:1071639 original size:28 final size:28
Alignment explanation
Indices: 1071608--1071668 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1071598 AGAAAAAATC
* *
1071608 AGAAAAAGAAGCACTCCAAAAGAA-AGAA
1 AGAAAAACAAGCACTCAAAAAGAAGA-AA
* *
1071636 AGAAAATCCAGCACTCAAAAAGAAGAAA
1 AGAAAAACAAGCACTCAAAAAGAAGAAA
1071664 AGAAA
1 AGAAA
1071669 GAAAGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.64, C:0.15, G:0.16, T:0.05
Consensus pattern (28 bp):
AGAAAAACAAGCACTCAAAAAGAAGAAA
Found at i:1080598 original size:21 final size:21
Alignment explanation
Indices: 1080519--1080604 Score: 79
Period size: 20 Copynumber: 4.2 Consensus size: 21
1080509 TTCGGAATCG
*
1080519 ATACCA-AATGCTTGGTATCG
1 ATACCAGAATGCTTGGTATCC
* *
1080539 ATACTAG-ATGCTTGGTATCA
1 ATACCAGAATGCTTGGTATCC
***
1080559 ATACCAGATAAAATT-GTATCC
1 ATACCAGA-ATGCTTGGTATCC
*
1080580 ATACCAGAAGGCTTGGTATCC
1 ATACCAGAATGCTTGGTATCC
1080601 ATAC
1 ATAC
1080605 TGAATGAACT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
20 26 0.50
21 23 0.44
22 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (21 bp):
ATACCAGAATGCTTGGTATCC
Found at i:1083850 original size:190 final size:191
Alignment explanation
Indices: 1083471--1083855 Score: 682
Period size: 190 Copynumber: 2.0 Consensus size: 191
1083461 CACAATCTAA
* *
1083471 ATAAGCATCATTACCAAAAATATACAAATTCAAATCAAATGTTAGAATCTTACTAACATAGGCAT
1 ATAAGAATCATTACCAAAAATATACAAATTCAAACCAAATGTTAGAATCTTACTAACATAGGCAT
*
1083536 ACTTTGGAAAATAAATTTCTAACAATTTTTCCGATGCTTATTCGATATAATTTCCATGTCAAAAC
66 ACTTTGGAAAATAAATTCCTAACAATTTTTCCGATGCTTATTCGATATAATTTCCATGTCAAAAC
*
1083601 ATAAATGTTGACCTTAATACTTTCAATTGACCATTCAAATTCCTTTTTATCCCAACTTCAT
131 ATAAATGTTGACCTTAATACTTCCAATTGACCATTCAAATTCCTTTTTATCCCAACTTCAT
*
1083662 ATAAGAATCATTACCAAACATATACAAATTCAAACCAAATGTTAGAATCTTACTAACATAGGCAT
1 ATAAGAATCATTACCAAAAATATACAAATTCAAACCAAATGTTAGAATCTTACTAACATAGGCAT
1083727 ACTTTGGAAAATAAATTCCTAACAA-TTTTCCGATGCTTATTCGATATAATTTCCATGTCAAAAC
66 ACTTTGGAAAATAAATTCCTAACAATTTTTCCGATGCTTATTCGATATAATTTCCATGTCAAAAC
* * * *
1083791 ATAAATGTTGACCTTAATACTTCCAATTTACCATTCTAGTTCTTTTTTATCCCAACTTCAT
131 ATAAATGTTGACCTTAATACTTCCAATTGACCATTCAAATTCCTTTTTATCCCAACTTCAT
1083852 ATAA
1 ATAA
1083856 CATTTTCACT
Statistics
Matches: 185, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
190 99 0.54
191 86 0.46
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.35
Consensus pattern (191 bp):
ATAAGAATCATTACCAAAAATATACAAATTCAAACCAAATGTTAGAATCTTACTAACATAGGCAT
ACTTTGGAAAATAAATTCCTAACAATTTTTCCGATGCTTATTCGATATAATTTCCATGTCAAAAC
ATAAATGTTGACCTTAATACTTCCAATTGACCATTCAAATTCCTTTTTATCCCAACTTCAT
Found at i:1092444 original size:24 final size:23
Alignment explanation
Indices: 1092401--1092446 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1092391 TTTAAAGAAA
1092401 TTTTAAGATTATTTTCGATTCAT
1 TTTTAAGATTATTTTCGATTCAT
*
1092424 TTTTCAAGTTTATATTT-GATTCA
1 TTTT-AAGATTAT-TTTCGATTCA
1092447 ATCATTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTTAAGATTATTTTCGATTCAT
Found at i:1102796 original size:44 final size:44
Alignment explanation
Indices: 1102733--1102884 Score: 216
Period size: 44 Copynumber: 3.5 Consensus size: 44
1102723 AGGTTTGATA
* * *
1102733 CCATCACATAAGGAGTTGGATCAGCATTACCACTTCCCTCAATT
1 CCATCACATAAGGAGTTGGATCAACATTACCACTTCACTTAATT
*
1102777 CCATCACATAAGGAGTTGGATCAACATTACCACTTCACTTGATT
1 CCATCACATAAGGAGTTGGATCAACATTACCACTTCACTTAATT
* * *
1102821 CCATTACATAAGGAGTTGGATCAACATCACCA-TCTCACTTATTT
1 CCATCACATAAGGAGTTGGATCAACATTACCACT-TCACTTAATT
*
1102865 CCATCACATAATGAGTTGGA
1 CCATCACATAAGGAGTTGGA
1102885 GAAGTATCTA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.01
44 96 0.99
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (44 bp):
CCATCACATAAGGAGTTGGATCAACATTACCACTTCACTTAATT
Found at i:1108536 original size:3 final size:3
Alignment explanation
Indices: 1108522--1108560 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1108512 CATCTATTTG
*
1108522 CAT CAT -AT CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1108561 TAATTCACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:1110767 original size:22 final size:21
Alignment explanation
Indices: 1110734--1110778 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1110724 AAAATATACA
* *
1110734 ATATATATAGTTTTTGAAGAT
1 ATATATATAGTTTTCGAAAAT
1110755 ATATAGTATAGTTTTCGAAAAT
1 ATATA-TATAGTTTTCGAAAAT
1110777 AT
1 AT
1110779 TTTTTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (21 bp):
ATATATATAGTTTTCGAAAAT
Found at i:1110856 original size:38 final size:37
Alignment explanation
Indices: 1110784--1111022 Score: 247
Period size: 37 Copynumber: 6.4 Consensus size: 37
1110774 AATATTTTTT
* * *
1110784 AAACATATAATATATAGTTTTTAAAAA-TGGTTTTGA
1 AAACATATAATATATAGGTTTTAAAAACAGTTTTTGA
1110820 AAACATATAATATATAGGTTTTAAAAGACAGTTTTTGA
1 AAACATATAATATATAGGTTTTAAAA-ACAGTTTTTGA
* * * * *
1110858 AAATATTTAATATATA-GTTTTTAAAACGGTTTTTTTA
1 AAACATATAATATATAGGTTTTAAAAACAG-TTTTTGA
*
1110895 AAACATATAATATATAGTTTTTAAAAGACAGTTTTTGA
1 AAACATATAATATATAGGTTTTAAAA-ACAGTTTTTGA
* *
1110933 AAACGTATAA-ATATAGTTTTTAAAAATCAGTTTTTGA
1 AAACATATAATATATAGGTTTTAAAAA-CAGTTTTTGA
** *
1110970 AAATGTAT-ATAATATA-GTTTTGAAAACA-TATTTTGA
1 AAACATATAAT-ATATAGGTTTTAAAAACAGT-TTTTGA
1111006 AAACATATATATATATA
1 AAACATATA-ATATATA
1111023 TATATATATA
Statistics
Matches: 172, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
35 1 0.01
36 44 0.26
37 74 0.43
38 50 0.29
39 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (37 bp):
AAACATATAATATATAGGTTTTAAAAACAGTTTTTGA
Found at i:1110918 original size:75 final size:73
Alignment explanation
Indices: 1110784--1111022 Score: 272
Period size: 75 Copynumber: 3.2 Consensus size: 73
1110774 AATATTTTTT
*
1110784 AAACATATAATATATAGTTTTTAAAAATGGTTTTGAAAACATATAATATATAGGTTTTAAAAGAC
1 AAACATATAATATATAGTTTTT-AAAACGGTTTTGAAAACATATAATATATAGGTTTTAAAAGAC
1110849 AGTTTTTGA
65 AGTTTTTGA
* * * *
1110858 AAATATTTAATATATAGTTTTTAAAACGGTTTTTTTAAAACATATAATATATAGTTTTTAAAAGA
1 AAACATATAATATATAGTTTTTAAAACGG--TTTTGAAAACATATAATATATAGGTTTTAAAAGA
1110923 CAGTTTTTGA
64 CAGTTTTTGA
* * ** *
1110933 AAACGTATAA-ATATAGTTTTTAAAAATCAGTTTTTGAAAATGTAT-ATAATATA-GTTTTGAAA
1 AAACATATAATATATAGTTTTT-AAAA-C-GGTTTTGAAAACATATAAT-ATATAGGTTTTAAAA
1110995 -ACA-TATTTTGA
62 GACAGT-TTTTGA
1111006 AAACATATATATATATA
1 AAACATATA-ATATATA
1111023 TATATATATA
Statistics
Matches: 141, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
72 1 0.01
73 23 0.16
74 41 0.29
75 74 0.52
76 1 0.01
77 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (73 bp):
AAACATATAATATATAGTTTTTAAAACGGTTTTGAAAACATATAATATATAGGTTTTAAAAGACA
GTTTTTGA
Found at i:1111005 original size:13 final size:13
Alignment explanation
Indices: 1110987--1111013 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1110977 TATAATATAG
1110987 TTTTGAAAACATA
1 TTTTGAAAACATA
1111000 TTTTGAAAACATA
1 TTTTGAAAACATA
1111013 T
1 T
1111014 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:1111017 original size:2 final size:2
Alignment explanation
Indices: 1111010--1111062 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1111000 TTTTGAAAAC
1111010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1111052 AT AT AT AT AT A
1 AT AT AT AT AT A
1111063 GTTTTGAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1111098 original size:38 final size:38
Alignment explanation
Indices: 1110788--1111100 Score: 217
Period size: 38 Copynumber: 8.3 Consensus size: 38
1110778 TTTTTTAAAC
* *
1110788 ATATAATATATAGTTTTTAAAAA-TGGTTTTGAAAAC--
1 ATATAATATATAG-TTTTAAAAACAGTTTTTGAAAACAT
1110824 ATATAATATATAGGTTTTAAAAGACAGTTTTTG-AAA-AT
1 ATATAATATATA-GTTTTAAAA-ACAGTTTTTGAAAACAT
* * * *
1110862 ATTTAATATATAGTTTTTAAAACGGTTTTTTTAAAAC--
1 ATATAATATATAGTTTTAAAAACAG-TTTTTGAAAACAT
1110899 ATATAATATATAGTTTTTAAAAGACAGTTTTTGAAAAC--
1 ATATAATATATAG-TTTTAAAA-ACAGTTTTTGAAAACAT
* **
1110937 GTATAA-ATATAGTTTTTAAAAATCAGTTTTTGAAAATGT
1 ATATAATATATAG-TTTTAAAAA-CAGTTTTTGAAAACAT
*
1110976 ATAT-A-ATATAGTTTTGAAAACA-TATTTTGAAAACAT
1 ATATAATATATAGTTTTAAAAACAGT-TTTTGAAAACAT
* * * * * * * *
1111012 ATATATATATATA-TATATATATATA-TATAT-ATATATAT
1 ATATA-ATATATAGT-TTTAAAAACAGTTTTTGA-AAACAT
* *
1111050 ATATATATATATAGTTTTGAAAACGGTTTTTGAAAACAT
1 ATATA-ATATATAGTTTTAAAAACAGTTTTTGAAAACAT
1111089 ATATAATATATA
1 ATATAATATATA
1111101 TAATTTTTAA
Statistics
Matches: 220, Mismatches: 35, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
35 1 0.00
36 40 0.18
37 67 0.30
38 81 0.37
39 30 0.14
40 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (38 bp):
ATATAATATATAGTTTTAAAAACAGTTTTTGAAAACAT
Found at i:1111122 original size:22 final size:22
Alignment explanation
Indices: 1111096--1111145 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1111086 CATATATAAT
1111096 ATATATAATTTTTAAAAACATA
1 ATATATAATTTTTAAAAACATA
* * * *
1111118 TTATATAGTTTTTGAAAATATA
1 ATATATAATTTTTAAAAACATA
1111140 ATATAT
1 ATATAT
1111146 GTTATGTAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATATAATTTTTAAAAACATA
Found at i:1111139 original size:77 final size:77
Alignment explanation
Indices: 1110975--1111124 Score: 191
Period size: 77 Copynumber: 2.0 Consensus size: 77
1110965 TTTGAAAATG
* * *
1110975 TATAT-AATATAGTTTTGAAAACATATTTTGAAAACATATATATATATATATATATATATATATA
1 TATATAAATATAGTTTTGAAAACATATTTTGAAAACATATATATATATATATATATATAAAAACA
1111039 TATATATATATA
66 TATATATATATA
* * * *
1111051 TATATATATATAGTTTTGAAAACGGT-TTTTGAAAACATATATA-ATATATATAATTTTTAAAAA
1 TATATAAATATAGTTTTGAAAAC-ATATTTTGAAAACATATATATATATATAT-ATATATAAAAA
1111114 CATAT-TATATA
64 CATATATATATA
1111125 GTTTTTGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
76 19 0.30
77 44 0.69
78 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (77 bp):
TATATAAATATAGTTTTGAAAACATATTTTGAAAACATATATATATATATATATATATAAAAACA
TATATATATATA
Found at i:1111150 original size:29 final size:26
Alignment explanation
Indices: 1111118--1111171 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
1111108 TAAAAACATA
1111118 TTATATAGTTTTTGAAAATATAATATATG
1 TTATATAGTTTTT--AAATA-AATATATG
*
1111147 TTATGTAGTTTTTAAATAAATATAT
1 TTATATAGTTTTTAAATAAATATAT
1111172 AGTACGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
29 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (26 bp):
TTATATAGTTTTTAAATAAATATATG
Found at i:1118948 original size:19 final size:19
Alignment explanation
Indices: 1118914--1118954 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1118904 TTCTTTTTGA
1118914 TTTATTCCTTTCTTTT-AT
1 TTTATTCCTTTCTTTTAAT
1118932 TTTATTTCCTTAT-TTTTAAT
1 TTTA-TTCCTT-TCTTTTAAT
1118952 TTT
1 TTT
1118955 CTCTCTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTCCTTTCTTTTAAT
Found at i:1127464 original size:24 final size:24
Alignment explanation
Indices: 1127437--1127486 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1127427 TCAAGGAGAC
* *
1127437 TCATTTGCTGTAAAAGCACAAGCT
1 TCATCTGCTGCAAAAGCACAAGCT
*
1127461 TCATCTGTTGCAAAAGCACAAGCT
1 TCATCTGCTGCAAAAGCACAAGCT
1127485 TC
1 TC
1127487 TGTAACTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (24 bp):
TCATCTGCTGCAAAAGCACAAGCT
Found at i:1134880 original size:20 final size:22
Alignment explanation
Indices: 1134855--1134895 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1134845 TGAGTCATAT
1134855 AATTTAT-CTTTAATT-TTTAA
1 AATTTATACTTTAATTATTTAA
*
1134875 AATTTATATTTTAATTATTTA
1 AATTTATACTTTAATTATTTA
1134896 TAAACAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTTATACTTTAATTATTTAA
Found at i:1138000 original size:99 final size:98
Alignment explanation
Indices: 1137740--1138018 Score: 328
Period size: 99 Copynumber: 2.8 Consensus size: 98
1137730 AAGAGAAGCT
* ** * *
1137740 ATCTCAGGTGAGAAAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGCATTTCAAAGGAAAA
1 ATCTCAAGTGAGATCAA-TTTTGTTTCAAGTGAAACAATTTCAAAATTTGC--TTCAAGGGAAAA
* *
1137805 CTATCTTAAGAGAGACGAATTTTTTTTAGGAAAAAA
63 CTGTCTCAAGAGAGACGAATTTTTTTTAGGAAAAAA
* * * *
1137841 ATCTCAAGTGAGATCAAATTTGTTTCAAGTGAAACAATTTCAAAATTTTTGTTTCGAGGGAAAAT
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAA--TTTGCTTCAAGGGAAAAC
* * *
1137906 TGTCTCAAGCGAGATGAA-TTTTTTTAGGAAAACA
64 TGTCTCAAGAGAGACGAATTTTTTTTAGGAAAAAA
* *
1137940 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTCGAAATTTAGGCTTCAAGGG-AAAC
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTT--GCTTCAAGGGAAAAC
*
1138004 TGTCTCAAGTGAGAC
64 TGTCTCAAGAGAGAC
1138019 AAAACTTTGT
Statistics
Matches: 152, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
97 3 0.02
98 16 0.11
99 65 0.43
100 50 0.33
101 14 0.09
102 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (98 bp):
ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGCTTCAAGGGAAAACTG
TCTCAAGAGAGACGAATTTTTTTTAGGAAAAAA
Found at i:1138030 original size:66 final size:65
Alignment explanation
Indices: 1137941--1138246 Score: 305
Period size: 66 Copynumber: 4.6 Consensus size: 65
1137931 AGGAAAACAA
* * * * * *
1137941 TCTCAAGTGAGATC-AATTTTGTTTCAAGTGAAACAA-CTTCGAAA-TTTAGGCTTCAAGGGAAA
1 TCTCAAGCGAGA-CAAAATTTGTTTCAAGAGAAACAATC-TC-AAAGTTTATGTTTCAAGAGAAA
1138003 CTG
63 CTG
* * **
1138006 TCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAATGTTTATGTTTCAAGAGAAGT
1 TCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAA-GTTTATGTTTCAAGAGAAAC
1138071 TG
64 TG
* * * * *
1138073 TCTCAAGCGAGA-TAAATTTTTTATCAAGAGAAACAATCTCAAAGGTTTCTGTTTCTAGAAAAAC
1 TCTCAAGCGAGACAAAATTTGTT-TCAAGAGAAACAATCTCAAA-GTTTATGTTTCAAGAGAAAC
1138137 TG
64 TG
* * * * *
1138139 TCTCAAGAGATACCAAATTTGTTTCAAGAGAAACAATTTGAAACGTTTATGTTTCAAGAGAAACT
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAA-GTTTATGTTTCAAGAGAAACT
*
1138204 A
65 G
* *
1138205 TCTCAAGCGAGACAGAATTTGTTTCAAGAGAAACTATCTCAA
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA
1138247 GCAAGACAAA
Statistics
Matches: 198, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
64 1 0.01
65 22 0.11
66 139 0.70
67 36 0.18
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (65 bp):
TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
Found at i:1138106 original size:132 final size:130
Alignment explanation
Indices: 1137935--1138246 Score: 340
Period size: 132 Copynumber: 2.4 Consensus size: 130
1137925 TTTTTTAGGA
* * * *
1137935 AAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAA-CTTCGAAA-TTTAGGCTTCAAG
1 AAACTATCTCAAGCGAGATAAATTTT-TTTCAAGAGAAACAATC-TC-AAAGTTTAGGCTTCAAG
** * * *
1137998 GGAAACTGTCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAATGTTTATGTTTCA
63 AAAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAACGTTTATGTTTCA
1138063 AGAG
127 AGAG
** * ** * *
1138067 AAGTTGTCTCAAGCGAGATAAATTTTTTATCAAGAGAAACAATCTCAAAGGTTTCTGTTTCTAGA
1 AAACTATCTCAAGCGAGATAAATTTTTT-TCAAGAGAAACAATCTCAAA-GTTTAGGCTTCAAGA
* * * *
1138132 AAAACTGTCTCAAGAGATACCAAATTTGTTTCAAGAGAAACAATTTGAAACGTTTATGTTTCAAG
64 AAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAACGTTTATGTTTCAAG
1138197 AG
129 AG
* * *
1138199 AAACTATCTCAAGCGAGACAGAATTTGTTTCAAGAGAAACTATCTCAA
1 AAACTATCTCAAGCGAGATA-AATTTTTTTCAAGAGAAACAATCTCAA
1138247 GCAAGACAAA
Statistics
Matches: 149, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
131 5 0.03
132 107 0.72
133 37 0.25
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (130 bp):
AAACTATCTCAAGCGAGATAAATTTTTTTCAAGAGAAACAATCTCAAAGTTTAGGCTTCAAGAAA
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAACGTTTATGTTTCAAGAG
Found at i:1138235 original size:36 final size:36
Alignment explanation
Indices: 1138188--1138292 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
1138178 GAAACGTTTA
1138188 TGTTTCAAGAGAAACTATCTCAAGCGAGACAGAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAGAATT
* *
1138224 TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAGAATT
*
1138260 TGTTTCAAGAGAAACTATCTCAAGGGAGACAGA
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
1138293 CAATCTGCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAGAATT
Found at i:1143328 original size:64 final size:64
Alignment explanation
Indices: 1143173--1143328 Score: 181
Period size: 64 Copynumber: 2.4 Consensus size: 64
1143163 TACACTAGGG
* ** * *
1143173 GTGCATCGGTACACTAATTACATTCCATGTTTCAAAAGAGCCTGGAGTACATCGATGCATGGTTT
1 GTGCATCGGTACACTAA-TGCATTTGATGTTTCAAAAGACCCTGGAGTACATCGATGCATGGTCT
* ** *
1143238 GTGCATCGGTACACAAAATGTTTTTGATGTTTCAATAA-ACCCT-GAGTGCATCGATGCATGGTC
1 GTGCATCGGTACAC-TAATGCATTTGATGTTTCAA-AAGACCCTGGAGTACATCGATGCATGGTC
1143301 T
64 T
1143302 GTGCATCGGTACACTTAATGCATTTGA
1 GTGCATCGGTACAC-TAATGCATTTGA
1143329 AATAGGGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 42 0.55
65 30 0.39
66 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCGGTACACTAATGCATTTGATGTTTCAAAAGACCCTGGAGTACATCGATGCATGGTCT
Found at i:1145468 original size:12 final size:13
Alignment explanation
Indices: 1145447--1145488 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
1145437 CCTAATGGAC
1145447 AATGTTTGAAAAT
1 AATGTTTGAAAAT
*
1145460 AAT-TTTGAAAAC
1 AATGTTTGAAAAT
1145472 AATGTTTGAAAACT
1 AATGTTTGAAAA-T
1145486 AAT
1 AAT
1145489 ATGTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 11 0.44
14 3 0.12
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (13 bp):
AATGTTTGAAAAT
Found at i:1145481 original size:13 final size:13
Alignment explanation
Indices: 1145445--1145484 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1145435 ATCCTAATGG
1145445 ACAATGTTTGAAA
1 ACAATGTTTGAAA
*
1145458 ATAAT-TTTGAAA
1 ACAATGTTTGAAA
1145470 ACAATGTTTGAAA
1 ACAATGTTTGAAA
1145483 AC
1 AC
1145485 TAATATGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (13 bp):
ACAATGTTTGAAA
Found at i:1147060 original size:23 final size:22
Alignment explanation
Indices: 1147034--1147101 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
1147024 AGTGCATTGA
1147034 TGCACATTCAAGGAATGCATCGG
1 TGCACATTCAAGG-ATGCATCGG
* * *
1147057 TGCATC-TTC-ACGATGTATCGA
1 TGCA-CATTCAAGGATGCATCGG
1147078 TGCACATTCAAGGGATGCATCGG
1 TGCACATTCAA-GGATGCATCGG
1147101 T
1 T
1147102 ACACTCTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
20 1 0.03
21 14 0.40
22 3 0.09
23 16 0.46
24 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCACATTCAAGGATGCATCGG
Found at i:1147087 original size:21 final size:22
Alignment explanation
Indices: 1147026--1147087 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
1147016 CACAACAAAG
* *
1147026 TGCATTGATGCACATTCAAGGAA
1 TGCATCGATGCACATTC-ACGAA
*
1147049 TGCATCGGTGCATC-TTCACG-A
1 TGCATCGATGCA-CATTCACGAA
*
1147070 TGTATCGATGCACATTCA
1 TGCATCGATGCACATTCA
1147088 AGGGATGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 2 0.06
23 13 0.41
24 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCACATTCACGAA
Found at i:1154087 original size:16 final size:17
Alignment explanation
Indices: 1154066--1154102 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1154056 AAGGCCTTTT
1154066 AAAACAATTTTAAGA-A
1 AAAACAATTTTAAGATA
*
1154082 AAAACATTTTTAAGATA
1 AAAACAATTTTAAGATA
1154099 AAAA
1 AAAA
1154103 TTGGTCTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAACAATTTTAAGATA
Found at i:1160670 original size:13 final size:13
Alignment explanation
Indices: 1160652--1160683 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1160642 CACAATACGC
*
1160652 GTCATAAATGCGT
1 GTCATAAATGCGA
1160665 GTCATAAATGCGA
1 GTCATAAATGCGA
1160678 GTCATA
1 GTCATA
1160684 GATTTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (13 bp):
GTCATAAATGCGA
Found at i:1162025 original size:21 final size:21
Alignment explanation
Indices: 1161999--1162055 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1161989 TCCAACAAAA
1161999 ATTCAGGTCGATTTCGATTCG
1 ATTCAGGTCGATTTCGATTCG
1162020 ATTCAGGTCGATTTCGATTCG
1 ATTCAGGTCGATTTCGATTCG
1162041 ATTCAGGTC-ATTTCG
1 ATTCAGGTCGATTTCG
1162056 GGTTTCAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (21 bp):
ATTCAGGTCGATTTCGATTCG
Found at i:1164137 original size:20 final size:20
Alignment explanation
Indices: 1164112--1164150 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1164102 ATCAACAAAA
1164112 AGCAAAGTGGAGGGGACAAC
1 AGCAAAGTGGAGGGGACAAC
1164132 AGCAAAGTGGAGGGGACAA
1 AGCAAAGTGGAGGGGACAA
1164151 AATATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.41, T:0.05
Consensus pattern (20 bp):
AGCAAAGTGGAGGGGACAAC
Found at i:1165205 original size:2 final size:2
Alignment explanation
Indices: 1165198--1165259 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1165188 TGTTGCCTAA
1165198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1165240 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1165260 CTGAAATGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1168583 original size:22 final size:23
Alignment explanation
Indices: 1168539--1168584 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1168529 GCACTCCCAT
*
1168539 TTTTGCATTTTTGCATATGCATA
1 TTTTGCATTTTTGCATATACATA
1168562 TTTT-CATTTTTGCAT-TAACATA
1 TTTTGCATTTTTGCATAT-ACATA
1168584 T
1 T
1168585 ACACATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 16 0.76
23 4 0.19
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (23 bp):
TTTTGCATTTTTGCATATACATA
Found at i:1169778 original size:41 final size:42
Alignment explanation
Indices: 1169722--1169812 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 42
1169712 GAAAGAAGAG
* *
1169722 AAAATATAGCAAAAAAG-GGAAAAA-GATAGAAAAGAAATAAAT
1 AAAAAATAGCAAAAAAGAGGAAAAAGGA-A-AAAAGAAAAAAAT
1169764 AAAAAATAG-AAAAAAGAGGAAAAAGGAAAAAAGAAAAAAAT
1 AAAAAATAGCAAAAAAGAGGAAAAAGGAAAAAAGAAAAAAAT
*
1169805 AAAGAATA
1 AAAAAATA
1169813 AAGAAGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
41 26 0.59
42 16 0.36
43 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (42 bp):
AAAAAATAGCAAAAAAGAGGAAAAAGGAAAAAAGAAAAAAAT
Found at i:1170994 original size:32 final size:32
Alignment explanation
Indices: 1170936--1171022 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
1170926 TTAATTAAAT
*
1170936 TAAAATAAAGAAAAAACAAATTAAATAG-AAG
1 TAAAATAAAGAAAAAACAAATAAAATAGTAAG
* *
1170967 ATAAGATAAAGAAAGAAA-AGATAAAATAGTAAG
1 -TAAAATAAAGAAA-AAACAAATAAAATAGTAAG
* *
1171000 TAAAATAAATAAATAAATAAATA
1 TAAAATAAAGAAA-AAACAAATA
1171023 TTAAAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 35 0.78
33 10 0.22
ACGTcount: A:0.70, C:0.01, G:0.10, T:0.18
Consensus pattern (32 bp):
TAAAATAAAGAAAAAACAAATAAAATAGTAAG
Found at i:1171009 original size:4 final size:4
Alignment explanation
Indices: 1171002--1171192 Score: 60
Period size: 4 Copynumber: 47.5 Consensus size: 4
1170992 ATAGTAAGTA
* * *
1171002 AAAT AAAT AAAT AAAT AAAT ATTAA- AAAT -ATT AAA- AAAT AAAG AATAA
1 AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AA-AT
*
1171050 AAAT AAA- AAAT ATATAT GAAT AAAAT AAAT AAAT AAA- ATAAT AAA-
1 AAAT AAAT AAAT A-A-AT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT
* * * * * * *
1171095 AAA- AAGT AAAA ATAAT ATAT ATAT ATAT ATAAT TAAT AAA- AACAT AAAA
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT AA-AT AAAT
* * * * * *
1171144 AAAT -AGT AAAT ATAT ATAT AAAT TAAT AAA- ACAT ATAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
1171191 AA
1 AA
1171193 CATATATATA
Statistics
Matches: 140, Mismatches: 27, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
3 22 0.16
4 94 0.67
5 20 0.14
6 4 0.03
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:1171061 original size:13 final size:13
Alignment explanation
Indices: 1171006--1171109 Score: 59
Period size: 13 Copynumber: 7.5 Consensus size: 13
1170996 TAAGTAAAAT
1171006 AAATAAATAAATAA
1 AAATAAA-AAATAA
*
1171020 ATATTAAAAATATTAAA
1 A-AATAAAAA-A-T-AA
*
1171037 AAATAAAGAATAA
1 AAATAAAAAATAA
*
1171050 AAATAAAAAATAT
1 AAATAAAAAATAA
*
1171063 ATATGAATAAAATAA
1 AAAT-AA-AAAATAA
*
1171078 ATAA-ATAAAATAA
1 A-AATAAAAAATAA
*
1171091 TAAA-AAAAAGTAA
1 -AAATAAAAAATAA
1171104 AAATAA
1 AAATAA
1171110 TATATATATA
Statistics
Matches: 70, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
12 3 0.04
13 34 0.49
14 8 0.11
15 14 0.20
16 8 0.11
17 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:1171097 original size:23 final size:21
Alignment explanation
Indices: 1171006--1171097 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 21
1170996 TAAGTAAAAT
*
1171006 AAATAAATAAATAAATATTAAA
1 AAATAAA-AAATAAATAATAAA
*
1171028 AATATTAAAAAATAAAGAAT-AA
1 AA-A-TAAAAAATAAATAATAAA
*
1171050 AAATAAAAAATATAT-ATGAATA
1 AAATAAAAAATAAATAAT-AA-A
1171072 AAATAAATAAATAAAATAATAAA
1 AAATAAA-AAAT-AAATAATAAA
1171095 AAA
1 AAA
1171098 AAGTAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
19 2 0.04
20 10 0.18
21 2 0.04
22 14 0.25
23 18 0.32
24 9 0.16
25 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATAAAAAATAAATAATAAA
Found at i:1171199 original size:20 final size:21
Alignment explanation
Indices: 1171138--1171204 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 21
1171128 TAATAAAAAC
1171138 ATAAAAAAATAGTAAATATATAT
1 ATAAAAAAATA--AAATATATAT
** *
1171161 ATAAATTAATAAAACATATA-
1 ATAAAAAAATAAAATATATAT
*
1171181 ATAAAAAAATAACATATATAT
1 ATAAAAAAATAAAATATATAT
1171202 ATA
1 ATA
1171205 TATATATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 16 0.44
21 11 0.31
23 9 0.25
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (21 bp):
ATAAAAAAATAAAATATATAT
Found at i:1172745 original size:106 final size:106
Alignment explanation
Indices: 1172614--1173147 Score: 783
Period size: 106 Copynumber: 5.0 Consensus size: 106
1172604 TGTATTGTTC
* *
1172614 CGAGTCCAATAT-CTTCCGCCGTGAAGTTGAAATTGGCT-TTAGAACTGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTT-CGCTGTGAAGTTGAAATTGGCTCTGA-AACTGGGAAATTGTTTGTTGA
1172677 CAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCTT
64 CAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCTT
1172720 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* * *
1172785 ACCAGCCGTCCCTTCGTCGTGAAGTTGACATTGCGGATTGTATTG-TT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGA-A---C---TTGTGTTGCTT
* *
1172832 CCGAGTCCAATAT-CTTCCGCCGTGAAGTTGAAATTGGCT-TTAGAACTGGGAAATTGTTTGTTG
1 -CGAGTCCAATATCCTT-CGCTGTGAAGTTGAAATTGGCTCTGA-AACTGGGAAATTGTTTGTTG
1172895 ACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCTT
63 ACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCTT
*
1172939 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
1173004 ACCAGCCATCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CTT
* * *
1173046 -GCGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
1173110 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1173148 TCTTGAATGA
Statistics
Matches: 391, Mismatches: 21, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
106 276 0.71
107 16 0.04
109 1 0.00
110 1 0.00
112 8 0.02
113 89 0.23
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCTT
Found at i:1172888 original size:219 final size:219
Alignment explanation
Indices: 1172574--1173147 Score: 934
Period size: 219 Copynumber: 2.7 Consensus size: 219
1172564 TGTGCACGAT
*
1172574 TCCCTTCGTCGTGAAGTTGACATCGCGGATTGTATTGTTCCGAGTCCAATATCTTCCGCCGTGAA
1 TCCCTTCGTCGTGAAGTTGACATTGCGGATTGTATTGTTCCGAGTCCAATATCTTCCGCCGTGAA
1172639 GTTGAAATTGGCTTTAGAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGT
66 GTTGAAATTGGCTTTAGAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGT
*
1172704 TGAACTTGTGTTGCTTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
131 TGAACTTGTGTTGCTTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGG
*
1172769 AAATTGTTTGTTGACAACCAGCCG
196 AAATTGTTTGTTGACAACCAGCCA
1172793 TCCCTTCGTCGTGAAGTTGACATTGCGGATTGTATTGTTCCGAGTCCAATATCTTCCGCCGTGAA
1 TCCCTTCGTCGTGAAGTTGACATTGCGGATTGTATTGTTCCGAGTCCAATATCTTCCGCCGTGAA
1172858 GTTGAAATTGGCTTTAGAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGT
66 GTTGAAATTGGCTTTAGAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGT
1172923 TGAACTTGTGTTGCTTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGG
131 TGAACTTGTGTTGCTTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGG
1172988 AAATTGTTTGTTGACAACCAGCCA
196 AAATTGTTTGTTGACAACCAGCCA
* * * * *
1173012 TCCCTTCATTGTGAAGTTGA-ACTTG-TG-TTGTCTTG---C--GTCCAATATCCTT-CGCTGTG
1 TCCCTTCGTCGTGAAGTTGACA-TTGCGGATTGTATTGTTCCGAGTCCAATAT-CTTCCGCCGTG
* * * * *
1173068 AAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGA
64 AAGTTGAAATTGGCTTTAG-AACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGA
1173132 AGTTGAACTTGTGTTG
128 AGTTGAACTTGTGTTG
1173148 TCTTGAATGA
Statistics
Matches: 339, Mismatches: 13, Indels: 13
0.93 0.04 0.04
Matches are distributed among these distances:
211 1 0.00
212 88 0.26
213 3 0.01
214 1 0.00
217 7 0.02
218 2 0.01
219 237 0.70
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (219 bp):
TCCCTTCGTCGTGAAGTTGACATTGCGGATTGTATTGTTCCGAGTCCAATATCTTCCGCCGTGAA
GTTGAAATTGGCTTTAGAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGT
TGAACTTGTGTTGCTTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGG
AAATTGTTTGTTGACAACCAGCCA
Found at i:1175637 original size:14 final size:14
Alignment explanation
Indices: 1175620--1175657 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1175610 TGATTTTTAT
*
1175620 TTCTTTTTTTTTCG
1 TTCTTTTTTTTTCC
*
1175634 TTCTTGTTTTTTCC
1 TTCTTTTTTTTTCC
1175648 TT-TTTTTTTT
1 TTCTTTTTTTT
1175658 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (14 bp):
TTCTTTTTTTTTCC
Found at i:1175656 original size:11 final size:10
Alignment explanation
Indices: 1175613--1175674 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 10
1175603 TTCCTTTTGA
*
1175613 TTTTTATTTC
1 TTTTTTTTTC
1175623 TTTTTTTTTC
1 TTTTTTTTTC
1175633 GTTCTTGTTTTTTCC
1 --T-TT-TTTTTT-C
1175648 TTTTTTTTTTC
1 -TTTTTTTTTC
1175659 TTTTCTTTTTC
1 TTTT-TTTTTC
1175670 TTTTT
1 TTTTT
1175675 GCCCTTTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
10 14 0.31
11 11 0.24
12 7 0.16
13 4 0.09
14 8 0.18
15 1 0.02
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1175659 original size:22 final size:23
Alignment explanation
Indices: 1175619--1175674 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
1175609 TTGATTTTTA
*
1175619 TTTCTTTTTTTTTCGTTCTTGTT-T
1 TTTCCTTTTTTTTC-TTCTT-TTCT
1175643 TTTCCTTTTTTTT-TTCTTTTCT
1 TTTCCTTTTTTTTCTTCTTTTCT
*
1175665 TTTTCTTTTT
1 TTTCCTTTTT
1175675 GCCCTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 15 0.52
24 12 0.41
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTCCTTTTTTTTCTTCTTTTCT
Found at i:1180177 original size:14 final size:15
Alignment explanation
Indices: 1180158--1180189 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1180148 GGTAAGAAAT
1180158 AAAT-AAATAAAGAA
1 AAATAAAATAAAGAA
1180172 AAATAAAATAAAGAA
1 AAATAAAATAAAGAA
1180187 AAA
1 AAA
1180190 ACAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAATAAAATAAAGAA
Found at i:1180195 original size:15 final size:14
Alignment explanation
Indices: 1180151--1180195 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
1180141 ATAAAAAGGT
1180151 AAGAAATAAATAAATA
1 AAGAAA-AAA-AAATA
1180167 AAGAAAAATAAAATA
1 AAGAAAAA-AAAATA
1180182 AAGAAAAAACAAAT
1 AAGAAAAAA-AAAT
1180196 TAAATAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (14 bp):
AAGAAAAAAAAATA
Found at i:1180233 original size:32 final size:33
Alignment explanation
Indices: 1180174--1180247 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
1180164 ATAAAGAAAA
*
1180174 ATAAAATAAAGAAAAAACAAATTAAATAG-AAG
1 ATAAAATAAAGAAAAAACAAATAAAATAGTAAG
* *
1180206 ATAAGATAAAGAAAGAAA-AGATAAAATAGTAAG
1 ATAAAATAAAGAAA-AAACAAATAAAATAGTAAG
1180239 -TAAAATAAA
1 ATAAAATAAA
1180248 TAAATACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 30 0.83
33 6 0.17
ACGTcount: A:0.70, C:0.01, G:0.12, T:0.16
Consensus pattern (33 bp):
ATAAAATAAAGAAAAAACAAATAAAATAGTAAG
Found at i:1180351 original size:42 final size:42
Alignment explanation
Indices: 1180304--1180429 Score: 154
Period size: 42 Copynumber: 3.0 Consensus size: 42
1180294 GAATAAAACA
*
1180304 AATAAATAAAATAATAAAAAAAGTAAAAATATATATATATAT
1 AATAAATAAAATAATAAAAAAAGTAAATATATATATATATAT
*
1180346 AATAAATAAAA-ACATAAAAAATAGTAAATATATATATAAAT-T
1 AATAAATAAAATA-ATAAAAAA-AGTAAATATATATATATATAT
*
1180388 AATAAA-ACATATAAT-AAAAAA-TAACATATATATATATATAT
1 AATAAATA-AAATAATAAAAAAAGTAA-ATATATATATATATAT
1180429 A
1 A
1180430 TATTTAATCT
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
39 3 0.04
40 14 0.19
41 9 0.12
42 30 0.41
43 18 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (42 bp):
AATAAATAAAATAATAAAAAAAGTAAATATATATATATATAT
Found at i:1180410 original size:35 final size:36
Alignment explanation
Indices: 1180327--1180421 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 36
1180317 ATAAAAAAAG
1180327 TAAAAATATATATATATATAATAAATAAAAACATAAA
1 TAAAAA-ATATATATATATAATAAATAAAAACATAAA
* *
1180364 AAATAGTAAATATATATATA-AATTAAT-AAAACATATAA
1 TAA-A--AAATATATATATATAATAAATAAAAACATA-AA
*
1180402 TAAAAAATAACATATATATA
1 TAAAAAAT-ATATATATATA
1180422 TATATATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
35 4 0.08
36 8 0.17
37 12 0.25
38 11 0.23
39 11 0.23
40 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (36 bp):
TAAAAAATATATATATATAATAAATAAAAACATAAA
Found at i:1180477 original size:23 final size:22
Alignment explanation
Indices: 1180447--1180497 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1180437 TCTAAAAAAT
1180447 AAAAATATATACT-AAA-GTAAA
1 AAAAATATATA-TAAAATGTAAA
*
1180468 AAATATATATATAAAATGTAAA
1 AAAAATATATATAAAATGTAAA
1180490 AAAAATAT
1 AAAAATAT
1180498 TGCATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATATATATAAAATGTAAA
Found at i:1182550 original size:42 final size:42
Alignment explanation
Indices: 1182498--1182579 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1182488 CCAAAATTTA
*
1182498 TAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCAAGATGCT
* ** * *
1182540 TAAATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCAAGATG
1182580 ATAAGTCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (42 bp):
TAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCAAGATGCT
Found at i:1182941 original size:233 final size:234
Alignment explanation
Indices: 1182353--1183325 Score: 1477
Period size: 234 Copynumber: 4.2 Consensus size: 234
1182343 ATTTATAAAC
* * * * *
1182353 CATTTGGGCCATCCATAAGACCTTTGGGCAGGATG-TTTTCACATGTCTATCAAAATATGAGAAA
1 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
* * * * * * *
1182417 GGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAAAAAGGTTTCTTACTTAGTAAA
66 GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
* **
1182482 ATATTTCCAAAATTTATAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
131 CTATTTCCAAAATTTATAAATCCTTCGGGCCATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
1182547 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
196 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
* *
1182586 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATTTTTTTTAAATGTCTATTAAAATATGAGAAA
1 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
* *
1182651 GATTTCACATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
66 GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
* *
1182716 CTATTTCCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
131 CTATTTCCAAAATTTATAAATCCTTCGGGCCATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
1182781 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA-AAGT
196 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
* * *
1182819 CTTTCAGGCCATCCATAAGTCCTCCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
1 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
1182884 GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
66 GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
* * * *
1182949 CTATTTCCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTGT-CGAGCATGATTCTTAAATC
131 CTATTTCCAAAATTTATAAATCCTTCGGGCCATCAGTAAGTCT-TCCGAGCATGATGCTTAAATT
* * *
1183013 CTTCGGATCATTTGTAAGTCTTTCGAGCAAGATGACAAGT
195 CTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
* *
1183053 CATTCGGGCCATCCATAAGTCCTTTGGGCAGGATGATTTTCAAATGTCTATTAAAATATGAGAAA
1 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
* *
1183118 TGTTTCTCATTTAAATCTGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
66 GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
* * * *
1183183 CTATTTCCAAAATTTATAAATCCTTCGGGTCGTCAGTAAGTCTTTCGAGCATGATGCATAAA-TC
131 CTATTTCCAAAATTTATAAATCCTTCGGGCCATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
* *
1183247 ATTCGGGTAATCTGTAAGCCTTTCGAGCAAGATGATAAGT
196 -TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
* * * * * *
1183287 CCTTTGGGCTATCCATAAGTCCTTCAGGTAGGATATTTT
1 CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTT
1183326 CGCATGATTT
Statistics
Matches: 676, Mismatches: 59, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
233 253 0.37
234 423 0.63
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (234 bp):
CATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAA
GGTTTCTCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
CTATTTCCAAAATTTATAAATCCTTCGGGCCATCAGTAAGTCTTCCGAGCATGATGCTTAAATTC
TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
Found at i:1183245 original size:42 final size:41
Alignment explanation
Indices: 1183198--1183290 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
1183188 TCCAAAATTT
** * *
1183198 ATAAATCCTTCGGGTCGTCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGTAATCAGTAAGCCTTTCGAGCAAGATG
* *
1183239 CATAAATCATTCGGGTAATCTGTAAGCCTTTCGAGCAAGATG
1 -ATAAATCCTTCGGGTAATCAGTAAGCCTTTCGAGCAAGATG
*
1183281 ATAAGTCCTT
1 ATAAATCCTT
1183291 TGGGCTATCC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 8 0.19
42 35 0.81
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGTAATCAGTAAGCCTTTCGAGCAAGATG
Found at i:1183272 original size:467 final size:467
Alignment explanation
Indices: 1182359--1183309 Score: 1480
Period size: 467 Copynumber: 2.0 Consensus size: 467
1182349 AAACCATTTG
* ** *
1182359 GGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAATATGAGAAAGGTTTCT
1 GGCCATCCATAAGTCCTCCGGGCAGGATGTTTTCAAATGTCTATCAAAATATGAGAAAGGTTTCT
* * *
1182424 CATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAAAAAGGTTTCTTACTTAGTAAAATATTTC
66 CATTCAAATATGAAAATTGAAATTGTTGAAAAGTAAAAAAGGTTTCTTACCTAGTAAAATATTTC
* *
1182489 CAAAATTTATAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCATGATGCTTAAATTCTTCGGGT
131 CAAAATTTATAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGAT
*
1182554 CATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAGGA
196 CATCTGTAAGTCTTTCGAGCAAGATGACAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAGGA
** *
1182619 TTTTTTTTAAATGTCTATTAAAATATGAGAAAGATTTCACATTTAAATATGAGATTTGAAATTGT
261 TGATTTTCAAATGTCTATTAAAATATGAGAAAGATTTCACATTTAAATATGAGATTTGAAATTGT
* *
1182684 TGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGGGCCAT
326 TGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAATCCTTCGGGCCAT
* * *
1182749 CAGTAAGTCTTCCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
391 CAGTAAGTCTTCCGAGCATGATGCATAAATTCTTCGGGTAATCTGTAAGCCTTTCGAGCAAGATG
1182814 A-AAGT-CTTTCA
456 ATAAGTCCTTT-A
*
1182825 GGCCATCCATAAGTCCTCCGGGCAGGATGTTTTTCAAATGTCTATTAAAATATGAGAAAGGTTTC
1 GGCCATCCATAAGTCCTCCGGGCAGGATG-TTTTCAAATGTCTATCAAAATATGAGAAAGGTTTC
* * * * *
1182890 TCATTTAAATATGAGATTTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTT
65 TCATTCAAATATGAAAATTGAAATTGTTGAAAAGTAAAAAAGGTTTCTTACCTAGTAAAATATTT
* * ** *
1182955 CCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTGT-CGAGCATGATTCTTAAATCCTTCGG
130 CCAAAATTTATAAATCCTTCGGGAAATCAGTAAGTCT-TCCGAGCATGATGCTTAAATCCTTCGG
* *
1183019 ATCATTTGTAAGTCTTTCGAGCAAGATGACAAGTCATTCGGGCCATCCATAAGTCCTTTGGGCAG
194 ATCATCTGTAAGTCTTTCGAGCAAGATGACAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAG
* *
1183084 GATGATTTTCAAATGTCTATTAAAATATGAGAAATG-TTTCTCATTTAAATCTGAGATTTGAAAT
259 GATGATTTTCAAATGTCTATTAAAATATGAGAAA-GATTTCACATTTAAATATGAGATTTGAAAT
*
1183148 TGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAATCCTTCGGGT
323 TGTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAATCCTTCGGGC
* *
1183213 CGTCAGTAAGTCTTTCGAGCATGATGCATAAA-TCATTCGGGTAATCTGTAAGCCTTTCGAGCAA
388 CATCAGTAAGTCTTCCGAGCATGATGCATAAATTC-TTCGGGTAATCTGTAAGCCTTTCGAGCAA
*
1183277 GATGATAAGTCCTTTG
452 GATGATAAGTCCTTTA
*
1183293 GGCTATCCATAAGTCCT
1 GGCCATCCATAAGTCCT
1183310 TCAGGTAGGA
Statistics
Matches: 441, Mismatches: 38, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
466 28 0.06
467 387 0.88
468 22 0.05
469 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (467 bp):
GGCCATCCATAAGTCCTCCGGGCAGGATGTTTTCAAATGTCTATCAAAATATGAGAAAGGTTTCT
CATTCAAATATGAAAATTGAAATTGTTGAAAAGTAAAAAAGGTTTCTTACCTAGTAAAATATTTC
CAAAATTTATAAATCCTTCGGGAAATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGAT
CATCTGTAAGTCTTTCGAGCAAGATGACAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAGGA
TGATTTTCAAATGTCTATTAAAATATGAGAAAGATTTCACATTTAAATATGAGATTTGAAATTGT
TGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAATCCTTCGGGCCAT
CAGTAAGTCTTCCGAGCATGATGCATAAATTCTTCGGGTAATCTGTAAGCCTTTCGAGCAAGATG
ATAAGTCCTTTA
Found at i:1183714 original size:48 final size:48
Alignment explanation
Indices: 1183587--1183720 Score: 205
Period size: 48 Copynumber: 2.8 Consensus size: 48
1183577 TTTAATTTGC
* * * *
1183587 AGATCTGATATTCCATTCAGAGTAAACAGAACATGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAACGGAACAAGTCTCTCTTCTCCA
*
1183635 AGATTTAATATTCCCTTCAGAGTAAACGGAACAAGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAACGGAACAAGTCTCTCTTCTCCA
**
1183683 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAACGGAACAAGTCT
1183721 GCTTCGATTC
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAACGGAACAAGTCTCTCTTCTCCA
Found at i:1183834 original size:48 final size:48
Alignment explanation
Indices: 1183748--1183882 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 48
1183738 CAACTCCCAC
* * * * *
1183748 AGATCTGATACTCCCTTCAGAGTAAGCGGAATAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCGTCTCAA
*
1183796 AGATTTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCGTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCGTCTCAA
*
1183844 AGATTTGATATTCCCTTCAGAAGTAAGTGGAACATGTCT
1 AGATTTGATATTCCCTTCAG-AGTAAGCGGAACATGTCT
1183883 GCCCCGACTG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
48 62 0.79
49 16 0.21
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCGTCTCAA
Found at i:1183836 original size:161 final size:162
Alignment explanation
Indices: 1183586--1183973 Score: 494
Period size: 161 Copynumber: 2.4 Consensus size: 162
1183576 GTTTAATTTG
* * * * *
1183586 CAGATCTGATATTCCATTCAGAGTAAACAGAACATGTCTCTCTTCTCCAAGATTTAATATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCT
* * *
1183651 TCAGAGTAAACGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAG-AGTAAGTGGAAC
66 TCAGAGTAAACGAAACAAGTCTCTCGTCTCAAAGATTTGATATTCCCTTCAGAAGTAAGTGGAAC
** *
1183715 AAGTCTGCTTCGATTCAATGGATCAACTCC-C
131 AAGTCTGCCCCGACTCAATGGATCAACTCCAC
* * * *
1183746 ACAGATCTGATACTCCCTTCAGAGTAAGCGGAATAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 -CAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
1183811 TTCAGAGTAAGCGAAACATGTCTCTCGTCTCAAAGATTTGATATTCCCTTCAGAAGTAAGTGGAA
65 TTCAGAGTAAACGAAACAAGTCTCTCGTCTCAAAGATTTGATATTCCCTTCAGAAGTAAGTGGAA
* * * *
1183876 CATGTCTGCCCCGACTGAGTGGATCAAGTCCAC
130 CAAGTCTGCCCCGACTCAATGGATCAACTCCAC
* * * * * *
1183909 CAAATCTGATTTTACCTTCA-ACATAAGCGGAACAAGTCTCTCTTTTCCAAGGTTTGATATTCCC
1 CAGATCTGATATTCCCTTCAGA-GTAAGCGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCC
1183973 T
65 T
1183974 GAGTGACAGT
Statistics
Matches: 194, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
161 105 0.54
162 88 0.45
163 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (162 bp):
CAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCT
TCAGAGTAAACGAAACAAGTCTCTCGTCTCAAAGATTTGATATTCCCTTCAGAAGTAAGTGGAAC
AAGTCTGCCCCGACTCAATGGATCAACTCCAC
Found at i:1184338 original size:3 final size:3
Alignment explanation
Indices: 1184332--1184384 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1184322 TCGTCCTAAA
1184332 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1184380 TAT TA
1 TAT TA
1184385 ATATAACTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1185880 original size:2 final size:2
Alignment explanation
Indices: 1185873--1185915 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1185863 CTAAATAATT
1185873 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1185915 T
1 T
1185916 TCTAAAATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1188152 original size:20 final size:20
Alignment explanation
Indices: 1188127--1188198 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
1188117 TTGCAACCTT
*
1188127 GATGCATTGATGCATAGCAG
1 GATGCATCGATGCATAGCAG
1188147 GATGCATCGATGCATAGCAAG
1 GATGCATCGATGCATAGC-AG
* *
1188168 GATGCATCGATGCATAACAA
1 GATGCATCGATGCATAGCAG
1188188 GATGCATCGAT
1 GATGCATCGAT
1188199 ACACTAATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 29 0.60
21 19 0.40
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.22
Consensus pattern (20 bp):
GATGCATCGATGCATAGCAG
Found at i:1188294 original size:21 final size:21
Alignment explanation
Indices: 1188268--1188317 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1188258 AGTGCAGATA
1188268 CATGGATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGGATG
* *
1188289 CATGGATGCACTGTAGGGGTG
1 CATGGATGCACTGCAGGGATG
1188310 CATGGATG
1 CATGGATG
1188318 AACTTTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGATG
Found at i:1188448 original size:30 final size:30
Alignment explanation
Indices: 1188401--1188460 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1188391 AAACTTTGAA
1188401 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
*
1188430 TAAATTTAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
1188461 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:1191499 original size:20 final size:22
Alignment explanation
Indices: 1191474--1191513 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1191464 TGTTGTATAT
1191474 AGTCG-TTGGGGATG-TTTTGG
1 AGTCGTTTGGGGATGATTTTGG
1191494 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
1191514 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:1191647 original size:21 final size:21
Alignment explanation
Indices: 1191604--1191674 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 21
1191594 TGCAGCCTTA
* *
1191604 ATGCATGGATGCGTAGC-AGG
1 ATGCATCGATGCATAGCAAGG
1191624 ATGCATCGATGCATAGCAAGG
1 ATGCATCGATGCATAGCAAGG
*
1191645 ATGCATCGATGCATAACAA-G
1 ATGCATCGATGCATAGCAAGG
1191665 ATGCATCGAT
1 ATGCATCGAT
1191675 ACACTAATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 26 0.55
21 21 0.45
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.21
Consensus pattern (21 bp):
ATGCATCGATGCATAGCAAGG
Found at i:1191723 original size:12 final size:12
Alignment explanation
Indices: 1191700--1191744 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1191690 GATGTTTGGA
1191700 TGCATGGATGCAT
1 TGCAT-GATGCAT
1191713 TGCATGATGCA-
1 TGCATGATGCAT
1191724 TG---GATGCAT
1 TGCATGATGCAT
1191733 TGCATGATGCAT
1 TGCATGATGCAT
1191745 CGATGCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
8 6 0.21
9 2 0.07
11 2 0.07
12 13 0.46
13 5 0.18
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (12 bp):
TGCATGATGCAT
Found at i:1191723 original size:20 final size:20
Alignment explanation
Indices: 1191697--1191815 Score: 123
Period size: 20 Copynumber: 5.8 Consensus size: 20
1191687 TTCGATGTTT
1191697 GGATGCATGGATGCATTGCA
1 GGATGCATGGATGCATTGCA
*
1191717 TGATGCATGGATGCATTGCA
1 GGATGCATGGATGCATTGCA
* *
1191737 TGATGCATCGATGCATTAGTGCA
1 GGATGCATGGATGCA-T--TGCA
*
1191760 -GATGCATGGATGCACTGCA
1 GGATGCATGGATGCATTGCA
* *
1191779 GGGATGCATAGATGCACTGCA
1 -GGATGCATGGATGCATTGCA
*
1191800 GGGGTGCATGGATGCA
1 -GGATGCATGGATGCA
1191816 CTTTGACACC
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.05
20 33 0.38
21 33 0.38
22 13 0.15
23 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (20 bp):
GGATGCATGGATGCATTGCA
Found at i:1191749 original size:28 final size:28
Alignment explanation
Indices: 1191696--1191752 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1191686 ATTCGATGTT
*
1191696 TGGATGCATGGATGCATTGCATGATGCA
1 TGGATGCATGCATGCATTGCATGATGCA
1191724 TGGATGCATTGCATG-A-TGCATCGATGCA
1 TGGATGCA-TGCATGCATTGCAT-GATGCA
1191752 T
1 T
1191753 TAGTGCAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
28 16 0.62
29 5 0.19
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGGATGCATGCATGCATTGCATGATGCA
Found at i:1191793 original size:8 final size:7
Alignment explanation
Indices: 1191698--1191773 Score: 63
Period size: 8 Copynumber: 10.9 Consensus size: 7
1191688 TCGATGTTTG
1191698 GATGCAT
1 GATGCAT
1191705 GGATGCAT
1 -GATGCAT
1191713 --TGCAT
1 GATGCAT
1191718 GATGCAT
1 GATGCAT
1191725 GGATGCAT
1 -GATGCAT
1191733 --TGCAT
1 GATGCAT
1191738 GATGCAT
1 GATGCAT
1191745 CGATGCAT
1 -GATGCAT
*
1191753 TAGTGCA-
1 GA-TGCAT
1191760 GATGCAT
1 GATGCAT
1191767 GGATGCA
1 -GATGCA
1191774 CTGCAGGGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
5 10 0.18
6 4 0.07
7 12 0.21
8 31 0.54
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (7 bp):
GATGCAT
Found at i:1191918 original size:29 final size:29
Alignment explanation
Indices: 1191897--1191954 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1191887 AAACTTTGAA
1191897 TAAATTCAATT-AAGCCCAAAAACATTTTG
1 TAAATTCAATTCAAGCCCAAAAACA-TTTG
*
1191926 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGCCCAAAAA-CATTT
1191955 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (29 bp):
TAAATTCAATTCAAGCCCAAAAACATTTG
Found at i:1191948 original size:30 final size:30
Alignment explanation
Indices: 1191897--1191956 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1191887 AAACTTTGAA
1191897 TAAATTCAATTAAGCCCAAAAA-CATTTTG
1 TAAATTCAATTAAGCCCAAAAACCATTTTG
*
1191926 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGCCCAAAAACCATTTTG
1191957 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAATTCAATTAAGCCCAAAAACCATTTTG
Found at i:1195182 original size:20 final size:20
Alignment explanation
Indices: 1195157--1195231 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1195147 TTGCAGCCTT
*
1195157 GATGCATGGATGCATAGCAG
1 GATGCATCGATGCATAGCAG
*
1195177 GATGCATGGATGCATAGCAAG
1 GATGCATCGATGCATAGC-AG
* *
1195198 GATGCATCGATGCATAACAA
1 GATGCATCGATGCATAGCAG
1195218 GATGCATCGATGCA
1 GATGCATCGATGCA
1195232 CTAATTGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 33 0.65
21 18 0.35
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (20 bp):
GATGCATCGATGCATAGCAG
Found at i:1195320 original size:21 final size:21
Alignment explanation
Indices: 1195251--1195351 Score: 100
Period size: 21 Copynumber: 4.8 Consensus size: 21
1195241 TTCGATGTTT
*
1195251 GGATGCATGGATGCATTGCA-
1 GGATGCATGGATGCACTGCAG
* * *
1195271 TGATGCATCGATGCA-T-TAG
1 GGATGCATGGATGCACTGCAG
1195290 TGCAGATGCATGGATGCACTGCAG
1 -G--GATGCATGGATGCACTGCAG
1195314 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCACTGCAG
* *
1195335 GGGTGCATGGATACACT
1 GGATGCATGGATGCACT
1195352 TTGACACCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 13 0.19
21 35 0.52
22 13 0.19
23 2 0.03
24 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
GGATGCATGGATGCACTGCAG
Found at i:1195453 original size:29 final size:29
Alignment explanation
Indices: 1195432--1195489 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1195422 AAACTTTGAA
1195432 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTAAAGTCCAAAAACA-TTTG
1195461 TAAATTCAATTAAAGTCCAAAAACCATTT
1 TAAATTCAATTAAAGTCCAAAAA-CATTT
1195490 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTAAAGTCCAAAAACATTTG
Found at i:1195479 original size:30 final size:30
Alignment explanation
Indices: 1195432--1195491 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1195422 AAACTTTGAA
1195432 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1195461 TAAATTCAATTAAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1195492 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1195592 original size:24 final size:26
Alignment explanation
Indices: 1195551--1195598 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1195541 TTAATTTTAA
1195551 ATTATAAACAACATAATTATTTATAT
1 ATTATAAACAACATAATTATTTATAT
*
1195577 ATTATAAA-AATA-AATTATTTAT
1 ATTATAAACAACATAATTATTTAT
1195599 TGATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTATAAACAACATAATTATTTATAT
Found at i:1196894 original size:16 final size:16
Alignment explanation
Indices: 1196872--1196931 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
1196862 GTTTTCAGTA
*
1196872 CGGGTTGATTTCGATT
1 CGGGTTGATTTCAATT
*
1196888 CGTGTTGATTTCAATT
1 CGGGTTGATTTCAATT
*
1196904 CGGGTTGATTTCAGTT
1 CGGGTTGATTTCAATT
*
1196920 CGGGTTGCTTTC
1 CGGGTTGATTTC
1196932 GGTTAGGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (16 bp):
CGGGTTGATTTCAATT
Found at i:1196940 original size:16 final size:16
Alignment explanation
Indices: 1196891--1196951 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
1196881 TTCGATTCGT
* * *
1196891 GTTGATTTCAATTCGG
1 GTTGCTTTCAGTTAGG
* *
1196907 GTTGATTTCAGTTCGG
1 GTTGCTTTCAGTTAGG
*
1196923 GTTGCTTTCGGTTAGG
1 GTTGCTTTCAGTTAGG
*
1196939 GTTACTTTCAGTT
1 GTTGCTTTCAGTT
1196952 CAACTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.13, C:0.13, G:0.28, T:0.46
Consensus pattern (16 bp):
GTTGCTTTCAGTTAGG
Found at i:1196941 original size:32 final size:32
Alignment explanation
Indices: 1196873--1196952 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
1196863 TTTTCAGTAC
* *
1196873 GGGTTGATTTC-GATTCGTGTTGATTTCAATTC
1 GGGTTGATTTCAG-TTCGGGTTGATTTCAATTA
* **
1196905 GGGTTGATTTCAGTTCGGGTTGCTTTCGGTTA
1 GGGTTGATTTCAGTTCGGGTTGATTTCAATTA
1196937 GGGTT-ACTTTCAGTTC
1 GGGTTGA-TTTCAGTTC
1196953 AACTAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 1 0.02
32 39 0.95
33 1 0.02
ACGTcount: A:0.12, C:0.14, G:0.29, T:0.45
Consensus pattern (32 bp):
GGGTTGATTTCAGTTCGGGTTGATTTCAATTA
Found at i:1197702 original size:31 final size:30
Alignment explanation
Indices: 1197652--1197718 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1197642 TCTTAATATT
* *
1197652 AAAA-ATATATTCTATTCTTATC-TTAACTAA
1 AAAATATATATTCTAGTCTTAACTTTAA--AA
*
1197682 AAAATATATATTTTAGTCTTAACTTTAAAA
1 AAAATATATATTCTAGTCTTAACTTTAAAA
1197712 AAAATAT
1 AAAATAT
1197719 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 13 0.41
31 15 0.47
32 4 0.12
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAATATATATTCTAGTCTTAACTTTAAAA
Done.