Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007847.1 Hibiscus syriacus cultivar Beakdansim tig00110204_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: 1444154
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1039500 original size:17 final size:18
Alignment explanation
Indices: 1039478--1039511 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1039468 TTGAAAGGTC
*
1039478 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
1039495 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
1039512 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:1046870 original size:20 final size:20
Alignment explanation
Indices: 1046847--1046888 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1046837 AATGCGTTTA
1046847 AATTTTAAATAAATTTTAAT
1 AATTTTAAATAAATTTTAAT
** *
1046867 AATTTTATTTAAATTTTTAT
1 AATTTTAAATAAATTTTAAT
1046887 AA
1 AA
1046889 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTAAATAAATTTTAAT
Found at i:1048114 original size:41 final size:41
Alignment explanation
Indices: 1048055--1048147 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
1048045 GGACACTATG
*
1048055 TAATACTAGTATCCTTATTGCAGCCCATAGGATTAGGACAT
1 TAATACTAGCATCCTTATTGCAGCCCATAGGATTAGGACAT
* *
1048096 TAATTCTAGCATCGTTATTGCAGCCCATAGGATTAGGACAT
1 TAATACTAGCATCCTTATTGCAGCCCATAGGATTAGGACAT
1048137 TAATACTAGCA
1 TAATACTAGCA
1048148 CACGGTGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (41 bp):
TAATACTAGCATCCTTATTGCAGCCCATAGGATTAGGACAT
Found at i:1054333 original size:14 final size:14
Alignment explanation
Indices: 1054310--1054346 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1054300 ATTTTGGTCA
1054310 TTTAAGTTTAATTAT
1 TTTAA-TTTAATTAT
1054325 TTTAATTTAATTAT
1 TTTAATTTAATTAT
*
1054339 TTAAATTT
1 TTTAATTT
1054347 CAAATTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAATTTAATTAT
Found at i:1054750 original size:26 final size:27
Alignment explanation
Indices: 1054717--1054768 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1054707 TGGTATAGAT
1054717 ATATATGGGTTAA-ATTTTAC-TATATA
1 ATATATGGGTTAATA-TTTACTTATATA
1054743 ATATATGGGTTAATATTTACTTATAT
1 ATATATGGGTTAATATTTACTTATAT
1054769 TGTGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (27 bp):
ATATATGGGTTAATATTTACTTATATA
Found at i:1058901 original size:21 final size:21
Alignment explanation
Indices: 1058875--1058919 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1058865 TTAGAAATAT
* * *
1058875 TAAAAACATTGATGTTTTAGA
1 TAAAAACAATAATGTTTTAAA
*
1058896 TAAAAATAATAATGTTTTAAA
1 TAAAAACAATAATGTTTTAAA
1058917 TAA
1 TAA
1058920 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
TAAAAACAATAATGTTTTAAA
Found at i:1060010 original size:14 final size:15
Alignment explanation
Indices: 1059989--1060027 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1059979 AAATTTTGTT
*
1059989 TTTAAAAATATTATA
1 TTTAAAAATATAATA
*
1060004 TTTAAAAATATAATT
1 TTTAAAAATATAATA
1060019 TTTAAAAAT
1 TTTAAAAAT
1060028 TCACTACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAAATATAATA
Found at i:1060067 original size:6 final size:6
Alignment explanation
Indices: 1060062--1060142 Score: 144
Period size: 6 Copynumber: 13.5 Consensus size: 6
1060052 TCCCCTCTCT
* *
1060062 CCCTCT CCCTCT CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA
1060110 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCC
1060143 ACACAAATAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.14, C:0.68, G:0.00, T:0.19
Consensus pattern (6 bp):
CCCTCA
Found at i:1061992 original size:17 final size:18
Alignment explanation
Indices: 1061955--1061994 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1061945 TAATAGTGAG
1061955 TTATTATAAAATATATCT
1 TTATTATAAAATATATCT
* *
1061973 TTATTAT-AATTATATTT
1 TTATTATAAAATATATCT
1061990 TTATT
1 TTATT
1061995 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAAAATATATCT
Found at i:1062251 original size:519 final size:518
Alignment explanation
Indices: 1061180--1062724 Score: 2633
Period size: 519 Copynumber: 3.0 Consensus size: 518
1061170 AAAAATTGTG
* *
1061180 ATTTATAGCTTTTTCATATTCAACTTTGCATTTAGAAACACATTTAAATTTTTATCTTTACTAAT
1 ATTTCTAGCTTTTTCATATTCAACTTTGCATTTAGAAGCACATTTAAATTTTTATCTTTACTAAT
*
1061245 ACATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTAAAATTCATTTTTCTTTATTAATTATGT
66 ACATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTGAAATTCATTTTTCTTTATTAATTATGT
*
1061310 ATTTACATTTTATTTAAAAAAATATAACACTAACATCCTTAAAAAATAATTTATTGTTTAGTAAT
131 ATTTACATTTTATTT-AAAAAATATAATACTAACATCCTTAAAAAATAATTTATTGTTTAGTAAT
1061375 TTATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTT
195 TTATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTT
*
1061440 ATTATAAAATATATCTTTATTATAATTATA----TA--TATATTTTAATATTTTTAATATAGTTT
260 ATTATAAAATATATCTTTATTATAATTATATTTTTATTTTTATTTTAATATTTTTAATATAGTTT
1061499 AAATTGATATATTTCATATATATATATATATAATACTAATTTTTTTTAATTTATTTATAATATAT
325 AAATTG--ATA--T-ATATATATATATATATAATACTAA-TTTTTTTAATTTATTTATAATATAT
*
1061564 ATTTTTA-TTTTTTCTATTTTTTAATGGTTAAAATGATAAATATATCATTTAAATTATATTATTT
384 ATTTTTATTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATTATATTATTT
* * *
1061628 AAAATTTTAAATGAATGATTGTGATTAAATCAGAATAATACAAATAGTGTTTTAAAATTCAAATG
449 TAAATTTTAAATGAATGATTGTGATTAAATCAGAATAATAAAAATATTGTTTTAAAATTCAAATG
1061693 TTAAA
514 TTAAA
*
1061698 ATTTCTAGCTTTTTCATATTCAACTTTTCATTTAGAAGCACATTTAAATTTTTATCTTTACTAAT
1 ATTTCTAGCTTTTTCATATTCAACTTTGCATTTAGAAGCACATTTAAATTTTTATCTTTACTAAT
* *
1061763 CCATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTGAAATTCATTTTCCTTTATTAATTATGT
66 ACATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTGAAATTCATTTTTCTTTATTAATTATGT
*
1061828 ATTTACATTTTATTTAAAAAATATAATACTAACATCCTTAAAAAATAATTTATTATTTAGTAATT
131 ATTTACATTTTATTTAAAAAATATAATACTAACATCCTTAAAAAATAATTTATTGTTTAGTAATT
1061893 TATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTTA
196 TATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTTA
1061958 TTATAAAATATATCTTTATTATAATTATATTTTTATTTTTATTTTTAATATTTTTAATATAGTTT
261 TTATAAAATATATCTTTATTATAATTATATTTTTATTTTTA-TTTTAATATTTTTAATATAGTTT
*
1062023 AAATTGATATATATATATATATATATAATACTAATTTTTTTAATTTATTTATAATATATATTTAT
325 AAATTGATATATATATATATATATATAATACTAATTTTTTTAATTTATTTATAATATATATTTTT
1062088 ATTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATT-TCATTATTTTAAAT
390 ATTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATTAT-ATTATTTTAAAT
*
1062152 TTTAAATGAATGATTGTGATTAAATCTGAATAATAAAAATATTGTTTTAAAATTCAAATGTTAAA
454 TTTAAATGAATGATTGTGATTAAATCAGAATAATAAAAATATTGTTTTAAAATTCAAATGTTAAA
* *
1062217 ATTTCTAGCTTTTTCATATTCAACGTTGCATTTAGAAGCATATTTAAATTTTTATCTTTACTAAT
1 ATTTCTAGCTTTTTCATATTCAACTTTGCATTTAGAAGCACATTTAAATTTTTATCTTTACTAAT
* *
1062282 GCATGAACTTCACTCATTTGCCTTGAAAAATAAATTTGAAATTCATTTTTCTTTATTAATTATGT
66 ACATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTGAAATTCATTTTTCTTTATTAATTATGT
1062347 ATTTACATTTTATTTAAAAAATATAATACTAACATCCTTAAAAAATAATTTATTGTTTAGTAATT
131 ATTTACATTTTATTTAAAAAATATAATACTAACATCCTTAAAAAATAATTTATTGTTTAGTAATT
*
1062412 TATTTTAATTACTTAAAACTAAATAAAGTTTATTAATTATAGATTAAAATATTAATAGTGAGTTA
196 TATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTTA
* * *
1062477 TTATAAAATATATCTTTATTATAATTATATTTTTATTTTTA--TT-ATA-GTTTAA-ATTG-ATA
261 TTATAAAATATATCTTTATTATAATTATATTTTTATTTTTATTTTAATATTTTTAATATAGTTTA
* * * *
1062536 TATT--T-CACATATATATATATGTAATACT-A-TTTTTTAATTTATTTATAATATATATTTTTA
326 AATTGATATATATATATATATATATAATACTAATTTTTTTAATTTATTTATAATATATATTTTTA
1062596 TTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATTATATTATTTTAAATTT
391 TTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATTATATTATTTTAAATTT
1062661 TAAATGAATGATTGTGATTAAATCAGAATAATAAAAATATTGTTTTAAAATTCAAATGTTAAA
456 TAAATGAATGATTGTGATTAAATCAGAATAATAAAAATATTGTTTTAAAATTCAAATGTTAAA
1062724 A
1 A
1062725 AGTATAGATA
Statistics
Matches: 985, Mismatches: 32, Indels: 31
0.94 0.03 0.03
Matches are distributed among these distances:
507 156 0.16
508 2 0.00
509 20 0.02
510 1 0.00
512 5 0.01
513 3 0.00
514 5 0.01
515 3 0.00
516 2 0.00
517 142 0.14
518 171 0.17
519 437 0.44
520 1 0.00
521 2 0.00
522 3 0.00
523 3 0.00
524 29 0.03
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (518 bp):
ATTTCTAGCTTTTTCATATTCAACTTTGCATTTAGAAGCACATTTAAATTTTTATCTTTACTAAT
ACATGAACTTCACTCATTTGCCTTGAAAAAGAAATTTGAAATTCATTTTTCTTTATTAATTATGT
ATTTACATTTTATTTAAAAAATATAATACTAACATCCTTAAAAAATAATTTATTGTTTAGTAATT
TATTTTAATTACTTAAAACTAAATAAAGTTTATTATTTATAGATTAAAATATTAATAGTGAGTTA
TTATAAAATATATCTTTATTATAATTATATTTTTATTTTTATTTTAATATTTTTAATATAGTTTA
AATTGATATATATATATATATATATAATACTAATTTTTTTAATTTATTTATAATATATATTTTTA
TTTTTTTCTATTTTTGAATGGTTAAAATGATAAATATATCATTTAAATTATATTATTTTAAATTT
TAAATGAATGATTGTGATTAAATCAGAATAATAAAAATATTGTTTTAAAATTCAAATGTTAAA
Found at i:1062511 original size:17 final size:18
Alignment explanation
Indices: 1062474--1062513 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1062464 TAATAGTGAG
1062474 TTATTATAAAATATATCT
1 TTATTATAAAATATATCT
* *
1062492 TTATTAT-AATTATATTT
1 TTATTATAAAATATATCT
1062509 TTATT
1 TTATT
1062514 TTTATTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAAAATATATCT
Found at i:1065785 original size:168 final size:169
Alignment explanation
Indices: 1065507--1065843 Score: 610
Period size: 168 Copynumber: 2.0 Consensus size: 169
1065497 AAACAAATCA
1065507 AATCCAATCAACTAATGACACCTCTATTTTAAGTATATGAAAGAACATTTATATTTAATACCTAT
1 AATCCAATCAACTAATGACACCTCTATTTTAAGTATATGAAAGAACATTTATATTTAATACCTAT
1065572 ATATGTGGTCACTTGTTTTCATGGAATGCATGTCCATTTTAAAA-TT-GT-TCTA-TTTATTTAA
66 ATATGTGGTCACTTGTTTTCATGGAATGCATGTCCATTTTAAAATTTCGTGTCTATTTTATTTAA
*
1065633 AAATTTATATTATATATATAATATATATATATATGATTGAAG
131 AAATAT-TA-TATATATAT-ATATATATATATATGATTGAAG
1065675 AATCCAATCAACTAATGACACCTCTATTTTAAGTATATGAAAGAACATTTATATTTAATACCTAT
1 AATCCAATCAACTAATGACACCTCTATTTTAAGTATATGAAAGAACATTTATATTTAATACCTAT
1065740 ATATGTGGTCACTTGTTTTCATGGAATGCATGTCCATTTTAAAATTTCGTGTCTATTTTATTTAA
66 ATATGTGGTCACTTGTTTTCATGGAATGCATGTCCATTTTAAAATTTCGTGTCTATTTTATTTAA
1065805 AAATATTATATATATATATATATATATATATGATTGAAG
131 AAATATTATATATATATATATATATATATATGATTGAAG
1065844 TTAATATTTT
Statistics
Matches: 164, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
168 109 0.66
169 24 0.15
170 11 0.07
171 6 0.04
172 14 0.09
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (169 bp):
AATCCAATCAACTAATGACACCTCTATTTTAAGTATATGAAAGAACATTTATATTTAATACCTAT
ATATGTGGTCACTTGTTTTCATGGAATGCATGTCCATTTTAAAATTTCGTGTCTATTTTATTTAA
AAATATTATATATATATATATATATATATATGATTGAAG
Found at i:1065818 original size:2 final size:2
Alignment explanation
Indices: 1065807--1065835 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1065797 TTATTTAAAA
1065807 AT AT -T 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
1065836 GATTGAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1075033 original size:18 final size:20
Alignment explanation
Indices: 1075000--1075039 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1074990 AACATTAAAG
*
1075000 ATGAACAAAGAAAATGCTAA
1 ATGAACAAAGAAAATGCAAA
1075020 ATGAA-AAA-AAAATGCAAA
1 ATGAACAAAGAAAATGCAAA
1075038 AT
1 AT
1075040 AATGAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.15
Consensus pattern (20 bp):
ATGAACAAAGAAAATGCAAA
Found at i:1076652 original size:16 final size:16
Alignment explanation
Indices: 1076633--1076663 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1076623 GTTATGACCC
*
1076633 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
1076649 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
1076664 ATAGAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:1080398 original size:16 final size:16
Alignment explanation
Indices: 1080377--1080407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1080367 GTTATGACCC
*
1080377 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
1080393 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
1080408 ATAGAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:1085177 original size:41 final size:41
Alignment explanation
Indices: 1085115--1085194 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
1085105 AAAAATGAAA
1085115 GGTAAGTCAAACATGAAAATGCAGTAGCAAAGTAAAGACAG
1 GGTAAGTCAAACATGAAAATGCAGTAGCAAAGTAAAGACAG
*
1085156 GGTAGGTCAAACATGAAAATGCAGTAGCAAAGTAAAGAC
1 GGTAAGTCAAACATGAAAATGCAGTAGCAAAGTAAAGAC
1085195 GAACATTGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (41 bp):
GGTAAGTCAAACATGAAAATGCAGTAGCAAAGTAAAGACAG
Found at i:1088015 original size:14 final size:15
Alignment explanation
Indices: 1087998--1088036 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1087988 GGTAATGATA
1087998 TTGAAGGAATG-AAT
1 TTGAAGGAATGTAAT
* *
1088012 TTGAAAGAATGTCAT
1 TTGAAGGAATGTAAT
1088027 TTGAAGGAAT
1 TTGAAGGAAT
1088037 TTGACATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.31
Consensus pattern (15 bp):
TTGAAGGAATGTAAT
Found at i:1103074 original size:23 final size:23
Alignment explanation
Indices: 1103047--1103093 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1103037 GTCACCACAG
*
1103047 CTCGTATAATTGCACCGAAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
*
1103070 CTCGTAGAATTGCACCGTAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
1103093 C
1 C
1103094 ATATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (23 bp):
CTCGTAGAATTGCACCGAAGTGC
Found at i:1103312 original size:150 final size:149
Alignment explanation
Indices: 1103072--1103376 Score: 538
Period size: 150 Copynumber: 2.0 Consensus size: 149
1103062 CGAAGTGCCT
* *
1103072 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTATAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* * *
1103137 CATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAATAT
66 CATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGTTCCAAAGAATAT
*
1103202 ATATATATCCCGAAGGACCG
130 ACATATATCCCGAAGGACCG
1103222 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1103287 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAATATA
*
1103352 CATATGTCCCGAAGGACCG
131 CATATATCCCGAAGGACCG
1103371 CGTAGA
1 CGTAGA
1103377 CCCTCTACCC
Statistics
Matches: 148, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 97 0.66
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAATATA
CATATATCCCGAAGGACCG
Found at i:1104464 original size:19 final size:20
Alignment explanation
Indices: 1104418--1104454 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1104408 CCACGTTTGG
*
1104418 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
1104438 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
1104455 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:1110014 original size:23 final size:23
Alignment explanation
Indices: 1109988--1110032 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1109978 CACCACAGCT
*
1109988 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1110011 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1110033 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1110205 original size:150 final size:149
Alignment explanation
Indices: 1110000--1110315 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
1109990 TATAATTGCA
*
1110000 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* * *
1110064 TTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACATATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACATATGT
* *
1110129 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
*
1110150 CTGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1110215 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACATATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACATATGTTC
*
1110280 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1110299 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1110316 CCCTCTACCC
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 51 0.33
150 105 0.67
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACATATGTTC
CAAAGAATATACATATATC
Found at i:1111377 original size:8 final size:8
Alignment explanation
Indices: 1111354--1111416 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
1111344 TCCACGTTTG
1111354 GAGAAGGAA
1 GAGAA-GAA
1111363 GAGAAGAA
1 GAGAAGAA
*
1111371 GATAAGAA
1 GAGAAGAA
1111379 -AGAAGGAA
1 GAGAA-GAA
1111387 GAGAAGAA
1 GAGAAGAA
*
1111395 GATAAGAA
1 GAGAAGAA
*
1111403 -AGAAGGA
1 GAGAAGAA
1111410 -AGAAGAA
1 GAGAAGAA
1111417 ATGAGAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 14 0.30
8 23 0.50
9 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (8 bp):
GAGAAGAA
Found at i:1111387 original size:24 final size:24
Alignment explanation
Indices: 1111355--1111412 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
1111345 CCACGTTTGG
1111355 AGAAGGAAGAGAAGAAGATAAGAA
1 AGAAGGAAGAGAAGAAGATAAGAA
1111379 AGAAGGAAGAGAAGAAGATAAGAA
1 AGAAGGAAGAGAAGAAGATAAGAA
1111403 AGAAGGAAGA
1 AGAAGGAAGA
1111413 AGAAATGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (24 bp):
AGAAGGAAGAGAAGAAGATAAGAA
Found at i:1112593 original size:19 final size:19
Alignment explanation
Indices: 1112564--1112613 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1112554 AAGATAATCA
1112564 AAAGA-TAAAGAAGTTATG
1 AAAGATTAAAGAAGTTATG
1112582 AAAGATTAAAGAAGTTATG
1 AAAGATTAAAGAAGTTATG
1112601 AAAGATTAAAGAA
1 AAAGATTAAAGAA
1112614 AATGAGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (19 bp):
AAAGATTAAAGAAGTTATG
Found at i:1113788 original size:31 final size:31
Alignment explanation
Indices: 1113750--1113843 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
1113740 AGGGTCGAGG
1113750 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1113781 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1113812 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1113843 G
1 G
1113844 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1116220 original size:39 final size:38
Alignment explanation
Indices: 1116142--1116222 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
1116132 ATTGAACGTG
* * *
1116142 ATATATTTTTATATAAATTATGTTGAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTGAAATAAAATATTA
**
1116180 ATATATTTTTTAAATAAATTTATGTT-AAATTTAATATTA
1 ATATA-TTTTTAAATAAA-TTATGTTGAAATAAAATATTA
1116219 ATAT
1 ATAT
1116223 TAATTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 5 0.14
39 24 0.67
40 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTGAAATAAAATATTA
Found at i:1116305 original size:15 final size:15
Alignment explanation
Indices: 1116285--1116357 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
1116275 ATCGATGAAA
1116285 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
1116300 TTTTATTTAAAT-A-
1 TTTTATATAAATAAT
* **
1116313 TATTA-A-CGATGAAT
1 TTTTATATAAAT-AAT
1116327 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
1116342 TTTTATTTAAATAAT
1 TTTTATATAAATAAT
1116357 T
1 T
1116358 AGAATTTCAC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 2 0.05
13 5 0.11
14 5 0.11
15 30 0.68
16 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTTATATAAATAAT
Found at i:1116313 original size:42 final size:42
Alignment explanation
Indices: 1116267--1116358 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
1116257 ATAATAAAAT
*
1116267 AATATATTATCGATGAAATTTTATATAAATAATTTTTATTTA
1 AATATATTAACGATGAAATTTTATATAAATAATTTTTATTTA
*
1116309 AATATATTAACGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTAACGATGAAATTTTATATAAATAATTTTTATTTA
1116351 AATA-ATTA
1 AATATATTA
1116359 GAATTTCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (42 bp):
AATATATTAACGATGAAATTTTATATAAATAATTTTTATTTA
Found at i:1132452 original size:29 final size:29
Alignment explanation
Indices: 1132419--1132474 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1132409 CTATAGTTAT
1132419 AGAATCATTTTGTAAATTTTAATAATTGA
1 AGAATCATTTTGTAAATTTTAATAATTGA
* *
1132448 AGAATTATTTTGTAATTTTTAATAATT
1 AGAATCATTTTGTAAATTTTAATAATT
1132475 ATATAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (29 bp):
AGAATCATTTTGTAAATTTTAATAATTGA
Found at i:1132482 original size:29 final size:29
Alignment explanation
Indices: 1132415--1132482 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
1132405 CGTTCTATAG
*
1132415 TTATAGAATCATTTTGTAAATTTTAATAA
1 TTATAGAATTATTTTGTAAATTTTAATAA
*
1132444 TTGA-AGAATTATTTTGTAATTTTTAATAA
1 TT-ATAGAATTATTTTGTAAATTTTAATAA
*
1132473 TTATATAATT
1 TTATAGAATT
1132483 CAATAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 32 0.94
30 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (29 bp):
TTATAGAATTATTTTGTAAATTTTAATAA
Found at i:1133127 original size:22 final size:22
Alignment explanation
Indices: 1133102--1133163 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1133092 CAAACGACCG
*
1133102 AAAAACATGTCA-AAAGGCAAAA
1 AAAAATATGTCATAAAGG-AAAA
* *
1133124 AAAAATGTGTCATAAATGAAAA
1 AAAAATATGTCATAAAGGAAAA
1133146 AGAAAATATGTCATAAAG
1 A-AAAATATGTCATAAAG
1133164 ACATAAGACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.18
Consensus pattern (22 bp):
AAAAATATGTCATAAAGGAAAA
Found at i:1133171 original size:23 final size:23
Alignment explanation
Indices: 1133103--1133171 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1133093 AAACGACCGA
* * *
1133103 AAAACATGTCA-AAAGGCAAAAA
1 AAAATATGTCATAAAGACAAAAG
*
1133125 AAAATGTGTCATAAATGA-AAAAG
1 AAAATATGTCATAAA-GACAAAAG
*
1133148 AAAATATGTCATAAAGACATAAG
1 AAAATATGTCATAAAGACAAAAG
1133171 A
1 A
1133172 CAAACATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 11 0.29
23 26 0.68
24 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.17
Consensus pattern (23 bp):
AAAATATGTCATAAAGACAAAAG
Found at i:1133594 original size:20 final size:21
Alignment explanation
Indices: 1133534--1133615 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
1133524 GACTATCGTA
* *
1133534 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTACCTAATTCGCG
* *
1133555 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACCTAATTCGCG
*
1133576 TTGCGATTTACGT-ATTCGCG
1 TTGCGATTTACCTAATTCGCG
* *
1133596 TTGCGATTTTCATAATTCGC
1 TTGCGATTTACCTAATTCGC
1133616 AATGCGAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.33
21 35 0.67
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (21 bp):
TTGCGATTTACCTAATTCGCG
Found at i:1133637 original size:20 final size:20
Alignment explanation
Indices: 1133612--1133705 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
1133602 TTTTCATAAT
1133612 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1133632 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1133652 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1133673 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1133693 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1133706 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1133643 original size:41 final size:40
Alignment explanation
Indices: 1133612--1133705 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
1133602 TTTTCATAAT
*
1133612 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
* * *
1133652 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
1133693 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1133706 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
Found at i:1134313 original size:33 final size:33
Alignment explanation
Indices: 1134252--1134344 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
1134242 CGAGAATGAA
**
1134252 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
1134286 AATCGCAACGCGAAATGAAAATTGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* **
1134319 AATTGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
1134345 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 40 0.78
34 11 0.22
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:1134391 original size:33 final size:33
Alignment explanation
Indices: 1134345--1134466 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
1134335 CAAAATCGCA
1134345 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1134378 TTGTGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
1134411 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
1134451 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1134467 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
33 43 0.58
34 8 0.11
39 1 0.01
40 22 0.30
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1134443 original size:20 final size:21
Alignment explanation
Indices: 1134403--1134466 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
1134393 CACGTTGCGA
* **
1134403 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
1134424 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
1134443 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
1134464 TTC
1 TTC
1134467 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:1136289 original size:94 final size:93
Alignment explanation
Indices: 1136102--1136477 Score: 582
Period size: 94 Copynumber: 4.1 Consensus size: 93
1136092 TAGATTGCTT
* *
1136102 AGTAAATTTATTCGGTTGCTGTCAA-TACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTA-TGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
*
1136162 TATTTGTCTTTTATTTTGTCTTTTGGTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
1136192 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1136257 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
1136286 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1136351 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * * *
1136380 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1136445 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1136473 AGTAA
1 AGTAA
1136478 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 10, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
90 32 0.12
91 2 0.01
92 3 0.01
93 27 0.10
94 206 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1136595 original size:20 final size:20
Alignment explanation
Indices: 1136570--1136612 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1136560 TTTTGGTTGA
1136570 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1136590 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1136610 AAT
1 AAT
1136613 CGCAACGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1136731 original size:19 final size:19
Alignment explanation
Indices: 1136651--1136734 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
1136641 GAAACTATAA
* *
1136651 TCGCGTTGTGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCGTT
**
1136671 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCGTT
1136690 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCGTT
*
1136704 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCGTT
1136723 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1136735 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 2 0.04
19 28 0.53
20 10 0.19
ACGTcount: A:0.07, C:0.19, G:0.26, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCGTT
Found at i:1138654 original size:14 final size:14
Alignment explanation
Indices: 1138635--1138666 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1138625 ATTGTTTAAT
1138635 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1138649 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1138663 TGAT
1 TGAT
1138667 ATGTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1138884 original size:19 final size:19
Alignment explanation
Indices: 1138862--1139012 Score: 107
Period size: 19 Copynumber: 8.7 Consensus size: 19
1138852 CGAAACTAAA
1138862 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1138881 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1138897 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1138914 TTTGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1138930 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1138947 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1138963 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
1138980 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
1138999 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
1139013 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 18 0.18
16 19 0.19
17 19 0.19
19 36 0.35
20 10 0.10
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1138910 original size:33 final size:33
Alignment explanation
Indices: 1138868--1138992 Score: 223
Period size: 33 Copynumber: 3.8 Consensus size: 33
1138858 TAAATTCGCA
* *
1138868 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1138901 TTGCGATTTTCATTTTGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1138934 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1138967 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1138993 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1138937 original size:14 final size:14
Alignment explanation
Indices: 1138920--1138974 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1138910 TCATTTTGCA
1138920 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1138934 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1138951 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1138967 TTGCGATT
1 TTGCGATT
1138975 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1139011 original size:20 final size:20
Alignment explanation
Indices: 1138965--1139058 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1138955 GCGATTCTCT
**
1138965 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1138984 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
1139004 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
1139023 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
1139045 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1139059 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1141487 original size:24 final size:24
Alignment explanation
Indices: 1141460--1141513 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
1141450 CTGAAAAATC
1141460 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAATCCAG-GTATTGACCAAG
*
1141484 ATCAAAGTCCAGGTATTGACCAAG
1 ATCAAAATCCAGGTATTGACCAAG
1141508 ATCAAA
1 ATCAAA
1141514 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAGGTATTGACCAAG
Found at i:1142432 original size:21 final size:21
Alignment explanation
Indices: 1142388--1142525 Score: 174
Period size: 21 Copynumber: 6.7 Consensus size: 21
1142378 GCGATTTACT
* *
1142388 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
1142408 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTAGGA
1142429 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
1142450 AAATCGCAATGTG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
1142470 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
1142491 AAATCGCAATACGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
1142512 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1142526 TAGTCAGAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 27 0.26
21 71 0.70
22 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:1142439 original size:41 final size:42
Alignment explanation
Indices: 1142388--1142525 Score: 174
Period size: 41 Copynumber: 3.3 Consensus size: 42
1142378 GCGATTTACT
* *
1142388 AAATCGCAATGCG-ATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGAAAATCGCAA-TGCGAATTAGGA
* * *
1142429 AAATCGCAATGCGAATTAGGAAAATCGCAATGTG-ATTACGT
1 AAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGA
* * *
1142470 AAATCGCAATGCGAATTAGGAAAATCGCAATACGAATTTGGG
1 AAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGA
1142512 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1142526 TAGTCAGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 50 0.60
42 32 0.38
43 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (42 bp):
AAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGA
Found at i:1142538 original size:62 final size:62
Alignment explanation
Indices: 1142388--1142526 Score: 226
Period size: 62 Copynumber: 2.2 Consensus size: 62
1142378 GCGATTTACT
*
1142388 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGAAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGAAAATCGCAATACGAATTAGGA
* * *
1142450 AAATCGCAATGTGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATTTGGG
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATTAGGA
1142512 AAATCGCAATGCGAT
1 AAATCGCAATGCGAT
1142527 AGTCAGAATC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 69 0.97
63 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (62 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATTAGGA
Found at i:1142554 original size:62 final size:61
Alignment explanation
Indices: 1142388--1142547 Score: 207
Period size: 62 Copynumber: 2.6 Consensus size: 61
1142378 GCGATTTACT
* *
1142388 AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCG-CGTGCGAATTAGGAAAATCGCAATACGAATTAGGA
* * * *
1142450 AAATCGCAATGTGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATTTGGG
1 AAATCGCAATGCGATTACGTAAATCGC-GTGCGAATTAGGAAAATCGCAATACGAATTAGGA
1142512 AAATCGCAATGCGA-TA-GTCAGAATCGCGTTGCGAAT
1 AAATCGCAATGCGATTACGT-A-AATCGCG-TGCGAAT
1142548 CTGGAAACTG
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 81 0.94
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (61 bp):
AAATCGCAATGCGATTACGTAAATCGCGTGCGAATTAGGAAAATCGCAATACGAATTAGGA
Found at i:1143553 original size:21 final size:20
Alignment explanation
Indices: 1143467--1143556 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
1143457 TCAAAATGGA
*
1143467 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
1143487 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1143509 GTGCATGGATGCACTGCAGAG
1 GTGCATGGATGCACTGCAG-G
*
1143530 GTGCATGGATGCACTACCAGG
1 GTGCATGGATGCACT-GCAGG
1143551 GTGCAT
1 GTGCAT
1143557 ATATGCACTT
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.07
20 13 0.21
21 23 0.38
22 17 0.28
23 4 0.07
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1143554 original size:42 final size:41
Alignment explanation
Indices: 1143467--1143565 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
1143457 TCAAAATGGA
* *
1143467 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAAGGTGCATCGATGCACTAG-CCAG
*
1143509 GTGCATGGATGCACTGCAGAGGTGCATGGATGCACTA-CCAGG
1 GTGCATGGATGCACTGCA-AGGTGCATCGATGCACTAGCCA-G
**
1143551 GTGCATATATGCACT
1 GTGCATGGATGCACT
1143566 TTGACACCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.04
42 32 0.64
43 16 0.32
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAAGGTGCATCGATGCACTAGCCAG
Found at i:1143811 original size:21 final size:21
Alignment explanation
Indices: 1143787--1143826 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1143777 ATGTTTAATG
1143787 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
* *
1143808 AAAATGTTATCAATTGTTA
1 AAAAAGATATCAATTGTTA
1143827 CCAATTGTTT
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:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:1145522 original size:22 final size:22
Alignment explanation
Indices: 1145475--1145522 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1145465 ACAGAATGTC
*
1145475 AAGG-GGGAACTGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* * *
1145496 CAGGAGGGAACCGATTCCCCTA
1 AAGGAGGGAACCGATACCCCCA
1145518 AAGGA
1 AAGGA
1145523 AAATGTGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.33, C:0.27, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1146467 original size:31 final size:31
Alignment explanation
Indices: 1146423--1146500 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1146413 GGTCGAGGGT
1146423 TTTACCT-TGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
*
1146453 TTTACCTATGTTCTTCGGGACATATTGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* *
1146484 ATTACCTAGGTTCTTCG
1 TTTACCTATGTTCTTCG
1146501 AAATCTATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 7 0.16
31 37 0.84
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTG
Found at i:1146514 original size:31 final size:31
Alignment explanation
Indices: 1146431--1146514 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
1146421 GTTTTACCTT
** * *
1146431 GTTCTTCGGGACATATGGACTGTTTACCTAT
1 GTTCTTCGAAACATATGGACTGATTACCTAG
** *
1146462 GTTCTTCGGGACATATTGACTGATTACCTAG
1 GTTCTTCGAAACATATGGACTGATTACCTAG
1146493 GTTCTTCGAAATC-TATGGACTG
1 GTTCTTCGAAA-CATATGGACTG
1146515 GTCTTTCGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 45 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTCTTCGAAACATATGGACTGATTACCTAG
Found at i:1146962 original size:59 final size:61
Alignment explanation
Indices: 1146895--1147014 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 61
1146885 ATATGTACTG
1146895 TATATAGAGTGTAG-TGGCATGTAGTCTAAAGATATAAATTGTATGAA-CTGATATATTTT
1 TATATAGAGTGTAGTTGGCATGTAGTCTAAAGATATAAATTGTATGAACCTGATATATTTT
1146954 TATATAGAGTGTAGTTGGCATGTAGTCTAAAGATATAAATTGTATGAACCTGATATATTTT
1 TATATAGAGTGTAGTTGGCATGTAGTCTAAAGATATAAATTGTATGAACCTGATATATTTT
1147015 GTAAACGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 14 0.24
60 33 0.56
61 12 0.20
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (61 bp):
TATATAGAGTGTAGTTGGCATGTAGTCTAAAGATATAAATTGTATGAACCTGATATATTTT
Found at i:1154498 original size:17 final size:16
Alignment explanation
Indices: 1154476--1154511 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
1154466 AATTTGGCAA
1154476 AAAATAAACTTAAAATG
1 AAAATAAACTTAAAA-G
1154493 AAAATAAACTTAAAAG
1 AAAATAAACTTAAAAG
1154509 AAA
1 AAA
1154512 CATACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAATAAACTTAAAAG
Found at i:1161327 original size:16 final size:17
Alignment explanation
Indices: 1161303--1161336 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1161293 ATACGTTTTT
1161303 AAATAATAAAT-AAATA
1 AAATAATAAATCAAATA
*
1161319 AAATTATAAATCAAATA
1 AAATAATAAATCAAATA
1161336 A
1 A
1161337 TGTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATAAATCAAATA
Found at i:1173942 original size:228 final size:229
Alignment explanation
Indices: 1173545--1174003 Score: 911
Period size: 228 Copynumber: 2.0 Consensus size: 229
1173535 TTATTTACAA
1173545 ATATCGAGACCAGATCTTAAAGATATAACAACCTTTTCTCGATATATTTAAATAAACGAACATTT
1 ATATCGAGACCAGATCTTAAAGATATAACAACCTTTTCTCGATATATTTAAATAAACGAACATTT
1173610 CTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAAATTTTTTTTGGTTTCACTTTCGGGATA
66 CTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAAATTTTTTTTGGTTTCACTTTCGGGATA
1173675 CACTTTTAATTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGACTGCCCACTTAAAATAA-
131 CACTTTTAATTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGACTGCCCACTTAAAATAAT
1173739 TTTAAATTAAAAGGATATTACCCTTAATCCAATT
196 TTTAAATTAAAAGGATATTACCCTTAATCCAATT
1173773 ATATCGAGACCAGATCTTAAAGATATAACAACCTTTTCTCGATATATTTAAATAAACGAACATTT
1 ATATCGAGACCAGATCTTAAAGATATAACAACCTTTTCTCGATATATTTAAATAAACGAACATTT
1173838 CTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAAATTTTTTTTGGTTTCACTTTCGGGATA
66 CTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAAATTTTTTTTGGTTTCACTTTCGGGATA
1173903 CACTTTTAATTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGACTGCCCACTTAAAATAAT
131 CACTTTTAATTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGACTGCCCACTTAAAATAAT
1173968 TTTAAATTAAAAGGATATTACCCTTAATCCAATT
196 TTTAAATTAAAAGGATATTACCCTTAATCCAATT
1174002 AT
1 AT
1174004 GTAATATGTC
Statistics
Matches: 230, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 194 0.84
229 36 0.16
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (229 bp):
ATATCGAGACCAGATCTTAAAGATATAACAACCTTTTCTCGATATATTTAAATAAACGAACATTT
CTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAAATTTTTTTTGGTTTCACTTTCGGGATA
CACTTTTAATTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGACTGCCCACTTAAAATAAT
TTTAAATTAAAAGGATATTACCCTTAATCCAATT
Found at i:1175856 original size:53 final size:53
Alignment explanation
Indices: 1175797--1175993 Score: 326
Period size: 53 Copynumber: 3.7 Consensus size: 53
1175787 GTGGGTTCGT
* *
1175797 TCCCTCTTGCTTCAAGGAATAGAACTC-AAAATATCTTCTTCCTACGGGTTCAC
1 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACA-ATCTTCTTCCTACGGGTTCAC
1175850 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGT-CTACGGGTTCAC
1 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCT-TCCTACGGGTTCAC
*
1175903 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTACGGGTTCGC
1 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTACGGGTTCAC
*
1175956 TCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTC
1 TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTC
1175994 CGGTGTGATT
Statistics
Matches: 137, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
52 1 0.01
53 132 0.96
54 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (53 bp):
TCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTACGGGTTCAC
Found at i:1176654 original size:41 final size:41
Alignment explanation
Indices: 1176597--1176703 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1176587 CCCGAAGGTT
** * *
1176597 TTACAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCAAGCTCGAAAGAC
* * *
1176638 TTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCAAGCTCGAAAGAC
*
1176680 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
1176704 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 21 0.39
42 33 0.61
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCAAGCTCGAAAGAC
Found at i:1176866 original size:41 final size:41
Alignment explanation
Indices: 1176811--1176917 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
1176801 CCCGAAGGTT
* ** * *
1176811 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCAAGCTCGAAAGAC
* * *
1176852 TTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCAAGCTCGAAAGAC
*
1176894 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
1176918 AAATTGTGAA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCAAGCTCGAAAGAC
Found at i:1177078 original size:41 final size:41
Alignment explanation
Indices: 1177023--1177129 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1177013 CCCGAAGGTT
* * * *
1177023 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
1177064 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
1177106 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
1177130 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:1177120 original size:212 final size:214
Alignment explanation
Indices: 1176432--1177246 Score: 1427
Period size: 214 Copynumber: 3.8 Consensus size: 214
1176422 CTTATGAATA
* *
1176432 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * * *
1176497 AAATTTTAAAAATCGCATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAACATCGTTTTTTCATT
66 AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATC-ATTTTTCATT
* * * *
1176562 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTATCATCTT
130 TTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTT
1176627 GCTCTAAAGGCTTACAGATG
195 GCTCTAAAGGCTTACAGATG
1176647 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1176712 AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTCATTT
66 AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTCATTT
1176777 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTG
131 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTG
1176842 CTCTAAAGGCTTACAGATG
196 CTCTAAAGGCTTACAGATG
1176861 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1176926 AAATTTTGAAAATCACATTCTTTGTTTTC-AAAATTTCATCTTCTC-AAACATCATTTTTCATTT
66 AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTCATTT
1176989 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTG
131 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTG
1177054 CTCTAAAGGCTTACAGATG
196 CTCTAAAGGCTTACAGATG
* *
1177073 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * * * * *
1177138 AAATTTTGACAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTATTT
66 AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTCATTT
* *
1177203 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
131 TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGG
1177247 TTTGCTTCAC
Statistics
Matches: 578, Mismatches: 20, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
212 191 0.33
213 30 0.05
214 243 0.42
215 114 0.20
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (214 bp):
ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAACATCATTTTTCATTT
TCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTG
CTCTAAAGGCTTACAGATG
Found at i:1177228 original size:426 final size:429
Alignment explanation
Indices: 1176432--1177246 Score: 1438
Period size: 426 Copynumber: 1.9 Consensus size: 429
1176422 CTTATGAATA
* *
1176432 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* *
1176497 AAATTTTAAAAATCGCATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAACATCGTTTTTTCATT
66 AAATTTTAAAAATCACATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAACATCGATTTTTCATT
1176562 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTATCATCTT
1176627 GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCC
196 GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCC
* *
1176692 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCT
261 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
*
1176757 CAAAACATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGC
326 CAAAACATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGC
1176822 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATG
391 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATG
1176861 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
1176926 AAATTTTGAAAATCACATTCTTTGTTTTCAAAA-TTTCATCTTCTC-AAACATC-ATTTTTCATT
66 AAATTTTAAAAATCACATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAACATCGATTTTTCATT
* * * *
1176988 TTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTATCATCTT
* *
1177053 GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
196 GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCC
* *
1177118 CGAAGGACTTATAAATTGTGAAATTTTGACAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCT
261 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
* * *
1177183 TAAAACATCATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
326 CAAAACATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGG
1177247 TTTGCTTCAC
Statistics
Matches: 367, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
426 254 0.69
427 7 0.02
428 12 0.03
429 94 0.26
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (429 bp):
ACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTAAAAATCACATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAACATCGATTTTTCATT
TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTATCATCTT
GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGGCC
CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
CAAAACATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGC
CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATG
Found at i:1193180 original size:3 final size:3
Alignment explanation
Indices: 1193166--1193196 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1193156 AATTTTTAGC
*
1193166 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1193197 ACTTATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1195132 original size:19 final size:20
Alignment explanation
Indices: 1195108--1195149 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1195098 TACTTCAACA
1195108 AAAATTATT-AAAAGT-AAAT
1 AAAATTATTCAAAA-TAAAAT
1195127 AAAATTATTCAAAATAAAAT
1 AAAATTATTCAAAATAAAAT
1195147 AAA
1 AAA
1195150 CCACTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATTATTCAAAATAAAAT
Found at i:1195500 original size:16 final size:16
Alignment explanation
Indices: 1195457--1195500 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1195447 TATAATATTG
* *
1195457 GAACTCGAAAATGCTC
1 GAACTCAAAAAAGCTC
1195473 GAACTCAAAAAAGCTC
1 GAACTCAAAAAAGCTC
1195489 GAACTCAAAAAA
1 GAACTCAAAAAA
1195501 TTTCAAGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (16 bp):
GAACTCAAAAAAGCTC
Found at i:1195524 original size:11 final size:11
Alignment explanation
Indices: 1195508--1195545 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1195498 AAATTTCAAG
1195508 AGCTCGATTGA
1 AGCTCGATTGA
1195519 AGCTCGATTTTG-
1 AGCTCGA--TTGA
1195531 AGCTCGATTGA
1 AGCTCGATTGA
1195542 AGCT
1 AGCT
1195546 TGAACTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
12 7 0.29
13 3 0.12
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:1195609 original size:14 final size:14
Alignment explanation
Indices: 1195590--1195667 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
1195580 TTATATTACA
1195590 TTTAAAAATATATT
1 TTTAAAAATATATT
1195604 TTTAAAAATTTATAATT
1 TTTAAAAA--TAT-ATT
* * * *
1195621 ATCAATAATGTATT
1 TTTAAAAATATATT
1195635 TTT---AATATATT
1 TTTAAAAATATATT
* *
1195646 TTTAATAATATAAT
1 TTTAAAAATATATT
1195660 TTTAAAAA
1 TTTAAAAA
1195668 AATCTAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
11 10 0.20
14 26 0.53
15 2 0.04
16 3 0.06
17 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:1197327 original size:2 final size:2
Alignment explanation
Indices: 1197320--1197357 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1197310 AAACCCGGTA
1197320 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
1197358 TAACAACGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1197890 original size:13 final size:13
Alignment explanation
Indices: 1197872--1197897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1197862 GATCGACAAA
1197872 AATATTTAAATAT
1 AATATTTAAATAT
1197885 AATATTTAAATAT
1 AATATTTAAATAT
1197898 TATTTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:1199401 original size:81 final size:81
Alignment explanation
Indices: 1199265--1199414 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
1199255 GAGCCATGAT
*
1199265 TTAATTTAAGGTTAAAAAATAGTAGTTTTAAAGTGTAATCGAAAATGTGATAAAAAAATATAATA
1 TTAATTTAAGGTTAAAAAATAATAGTTTTAAAGTGTAATCGAAAATGTGAT-AAAAAATATAATA
1199330 TTTTATTGTTGTGCTAC
65 TTTTATTGTTGTGCTAC
* * *
1199347 TTAATTTAAGGTT-AAAAATAAT-GATTTT-AGGATGTAATTGAAAATGTGATAAAAATTATAAT
1 TTAATTTAAGGTTAAAAAATAATAG-TTTTAAAG-TGTAATCGAAAATGTGATAAAAAATATAAT
1199409 ATTTTA
64 ATTTTA
1199415 AGTTGAACAC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 20 0.32
81 29 0.47
82 13 0.21
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (81 bp):
TTAATTTAAGGTTAAAAAATAATAGTTTTAAAGTGTAATCGAAAATGTGATAAAAAATATAATAT
TTTATTGTTGTGCTAC
Found at i:1204994 original size:20 final size:20
Alignment explanation
Indices: 1204969--1205022 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1204959 GACCAACAAA
1204969 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
1204989 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
1205009 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
1205023 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:1205101 original size:20 final size:20
Alignment explanation
Indices: 1205046--1205102 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1205036 TGCGATTTTA
* * *
1205046 CAAATTCATAACCCGATAGT
1 CAAATTCGTAACGCGAAAGT
* *
1205066 CAAATTCGCAATGCGAAAGT
1 CAAATTCGTAACGCGAAAGT
1205086 CAAATTCGTAACGCGAA
1 CAAATTCGTAACGCGAA
1205103 TTTAATTTCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTCGTAACGCGAAAGT
Found at i:1208689 original size:20 final size:20
Alignment explanation
Indices: 1208664--1208705 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1208654 CGCGAAATAA
*
1208664 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
1208684 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
1208704 GC
1 GC
1208706 AACGCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:1208742 original size:20 final size:20
Alignment explanation
Indices: 1208714--1208755 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1208704 GCAACGCTTA
*
1208714 TTTCGCGTTGCGAATTTACC
1 TTTCACGTTGCGAATTTACC
1208734 TTTCACGTTGCGAATTTACC
1 TTTCACGTTGCGAATTTACC
1208754 TT
1 TT
1208756 CAACAGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTCACGTTGCGAATTTACC
Found at i:1209273 original size:18 final size:18
Alignment explanation
Indices: 1209252--1209288 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1209242 GTAATTGGAG
1209252 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1209270 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1209288 T
1 T
1209289 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1209295 original size:24 final size:24
Alignment explanation
Indices: 1209244--1209296 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1209234 TTTCATATGT
* * *
1209244 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1209268 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1209292 AATTT
1 AATTT
1209297 CGACTTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1209606 original size:35 final size:35
Alignment explanation
Indices: 1209531--1209606 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1209521 AATAATAACA
* * *
1209531 AAAATAATAAGTCCGAAATGCTTCTGAGTACCACC
1 AAAATCATAAGTCCAAAATGCTTCCGAGTACCACC
* *
1209566 CAAATCATAAGTCCAAAATGCTTCCGA-TACTCATC
1 AAAATCATAAGTCCAAAATGCTTCCGAGTAC-CACC
1209601 AAAATC
1 AAAATC
1209607 CAAATATGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (35 bp):
AAAATCATAAGTCCAAAATGCTTCCGAGTACCACC
Found at i:1209636 original size:34 final size:36
Alignment explanation
Indices: 1209598--1209679 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 36
1209588 TCCGATACTC
1209598 ATCAAAATCC-AA-ATATGGTGCCAAGCAAAAGAAA
1 ATCAAAATCCAAATATATGGTGCCAAGCAAAAGAAA
*
1209632 ATCAAAATCCAAATCTTATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAA---TATATGGTGCCAAGCAAAAGAAA
1209671 ATCAAAATC
1 ATCAAAATC
1209680 TACAACTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 10 0.24
35 2 0.05
39 30 0.71
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (36 bp):
ATCAAAATCCAAATATATGGTGCCAAGCAAAAGAAA
Found at i:1210162 original size:61 final size:62
Alignment explanation
Indices: 1210032--1210171 Score: 176
Period size: 61 Copynumber: 2.2 Consensus size: 62
1210022 TTTTAGAAAC
*
1210032 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACAAATCAAATTA
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAATAAATCTTATTTACAAATCAAATTA
* * ** *
1210097 AACAAATCAACTTTTACAAATCAATT-AATCAAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAAATT-A
1210158 AACAAATCAACTTT
1 AACAAATCAACTTT
1210172 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 4 0.06
61 38 0.56
65 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (62 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:1210226 original size:16 final size:16
Alignment explanation
Indices: 1210207--1210240 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1210197 AAAAGAAACC
*
1210207 ACAATCATACGAGAGG
1 ACAAGCATACGAGAGG
1210223 ACAAGCATACGAGAGG
1 ACAAGCATACGAGAGG
1210239 AC
1 AC
1210241 CACAATCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (16 bp):
ACAAGCATACGAGAGG
Found at i:1211588 original size:32 final size:34
Alignment explanation
Indices: 1211547--1211616 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1211537 ACCTTACAAC
*
1211547 TCCCTAGCTTTT-C-CAGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
* *
1211579 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
1211613 TCCC
1 TCCC
1211617 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
Found at i:1211926 original size:21 final size:21
Alignment explanation
Indices: 1211900--1211942 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1211890 CCCAGAATTG
*
1211900 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1211921 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1211942 A
1 A
1211943 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1212074 original size:22 final size:22
Alignment explanation
Indices: 1212049--1212091 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1212039 ATATGTTCCC
* *
1212049 GGGGTATCTGTACCCCCTGGGG
1 GGGGAATCTATACCCCCTGGGG
1212071 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
1212092 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
GGGGAATCTATACCCCCTGGGG
Found at i:1212213 original size:29 final size:31
Alignment explanation
Indices: 1212181--1212240 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1212171 AAACTTTGAA
1212181 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1212210 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1212241 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:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1213522 original size:19 final size:19
Alignment explanation
Indices: 1213479--1213526 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1213469 TCTAAATCCT
*
1213479 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
1213498 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
1213518 TTTTCAAAA
1 TTTTCAAAA
1213527 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:1214453 original size:34 final size:32
Alignment explanation
Indices: 1214385--1214454 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1214375 ACCTTACAAC
*
1214385 TCCCTAGCTTTTCCAGGCTAAACTAGAACATT
1 TCCCTAGCTTTTCCAGGATAAACTAGAACATT
* * *
1214417 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTT-C-CAGGATAAACTAGAACATT
1214451 TCCC
1 TCCC
1214455 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 12 0.38
33 1 0.03
34 19 0.59
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (32 bp):
TCCCTAGCTTTTCCAGGATAAACTAGAACATT
Found at i:1214694 original size:20 final size:22
Alignment explanation
Indices: 1214669--1214708 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1214659 AGTCGTATAT
1214669 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1214689 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1214709 TATACTAAAA
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:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1214762 original size:21 final size:21
Alignment explanation
Indices: 1214736--1214778 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214726 CCCAGAACAG
*
1214736 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1214757 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1214778 A
1 A
1214779 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1214841 original size:21 final size:21
Alignment explanation
Indices: 1214816--1214857 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214806 GTTGAACAGG
1214816 GGGGGAATCGGTACCCCCTGA
1 GGGGGAATCGGTACCCCCTGA
1214837 GGGGGAATCGGTACCCCCTGA
1 GGGGGAATCGGTACCCCCTGA
1214858 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.38, T:0.14
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGA
Found at i:1214932 original size:21 final size:21
Alignment explanation
Indices: 1214908--1214949 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214898 ATATGTTCCC
* *
1214908 GGGGTATCTGTACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
1214929 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
1214950 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGAATCTATACCCCCTGGG
Found at i:1215071 original size:29 final size:31
Alignment explanation
Indices: 1215039--1215098 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1215029 AAACTTTGAA
1215039 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1215068 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1215099 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:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1216364 original size:19 final size:19
Alignment explanation
Indices: 1216321--1216368 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1216311 TCTAAATCAT
*
1216321 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
1216340 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
1216360 TTTTCAAAA
1 TTTTCAAAA
1216369 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:1217269 original size:32 final size:34
Alignment explanation
Indices: 1217228--1217297 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1217218 ACCTTACAAC
*
1217228 TCCCTAGCTTTT-C-CAGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
* *
1217260 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
1217294 TCCC
1 TCCC
1217298 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACAGGATAAACTAGAACCTT
Found at i:1217603 original size:21 final size:21
Alignment explanation
Indices: 1217579--1217621 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1217569 CCCAGAATAG
*
1217579 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1217600 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1217621 A
1 A
1217622 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1217774 original size:21 final size:21
Alignment explanation
Indices: 1217750--1217791 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1217740 ATATGTTCCC
* *
1217750 GGGGTATCTGTACCCCTTGGG
1 GGGGAATCTATACCCCTTGGG
1217771 GGGGAATCTATACCCCTTGGG
1 GGGGAATCTATACCCCTTGGG
1217792 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.36, T:0.26
Consensus pattern (21 bp):
GGGGAATCTATACCCCTTGGG
Found at i:1217913 original size:29 final size:31
Alignment explanation
Indices: 1217881--1217940 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1217871 AAACTTTGAA
1217881 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1217910 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1217941 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:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1218507 original size:12 final size:12
Alignment explanation
Indices: 1218490--1218515 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1218480 ACTTGTATAC
1218490 GCCGGTGATTAA
1 GCCGGTGATTAA
1218502 GCCGGTGATTAA
1 GCCGGTGATTAA
1218514 GC
1 GC
1218516 AAAACTCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (12 bp):
GCCGGTGATTAA
Found at i:1219669 original size:21 final size:21
Alignment explanation
Indices: 1219645--1219763 Score: 57
Period size: 21 Copynumber: 5.8 Consensus size: 21
1219635 CATTTGACTT
1219645 TCGCGTTGCGAATTTGTAAAA
1 TCGCGTTGCGAATTTGTAAAA
*** *
1219666 TCGCAACGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGTAAAA
** ** * *
1219687 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGTAAAA
* *
1219707 TCGCGTTGCGAAATTGGAAAA
1 TCGCGTTGCGAATTTGTAAAA
* * *
1219728 T-GGGTTGCGAA-AT-TAGAAT
1 TCGCGTTGCGAATTTGTA-AAA
*
1219747 TCGCGTCGCGAATTTGT
1 TCGCGTTGCGAATTTGT
1219764 TGGTCATTTT
Statistics
Matches: 70, Mismatches: 23, Indels: 9
0.69 0.23 0.09
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 31 0.44
21 33 0.47
22 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGTAAAA
Found at i:1224349 original size:17 final size:18
Alignment explanation
Indices: 1224306--1224346 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1224296 AAATTATATT
1224306 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1224323 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1224341 ATTAAA
1 AGTAAA
1224347 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1224402 original size:10 final size:10
Alignment explanation
Indices: 1224387--1224417 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1224377 CCTTAAACGA
1224387 GAGAGAATTT
1 GAGAGAATTT
1224397 GAGAGAATTT
1 GAGAGAATTT
*
1224407 AAGAGAATTT
1 GAGAGAATTT
1224417 G
1 G
1224418 GTGTGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1225044 original size:11 final size:12
Alignment explanation
Indices: 1225004--1225047 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1224994 TATTTAAACG
*
1225004 GGTATTGGGCCA
1 GGTATTGGGTCA
*
1225016 GGTATTGGGTCG
1 GGTATTGGGTCA
1225028 GGTATTGGGTC-
1 GGTATTGGGTCA
1225039 GGTATTGGG
1 GGTATTGGG
1225048 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:1225046 original size:23 final size:24
Alignment explanation
Indices: 1225002--1225047 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1224992 ATTATTTAAA
1225002 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
1225026 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
1225048 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:1225072 original size:2 final size:2
Alignment explanation
Indices: 1225065--1225160 Score: 78
Period size: 2 Copynumber: 51.0 Consensus size: 2
1225055 TCGGGCCGGG
* * *
1225065 TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1225105 TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
1225143 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1225161 ATTATTTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
1 6 0.08
2 69 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1226742 original size:2 final size:2
Alignment explanation
Indices: 1226731--1226784 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
1226721 TAAATATCCT
*
1226731 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1226772 TA TG TA TA TA TA T
1 TA TA TA TA TA TA T
1226785 CGAGTTAGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1228023 original size:24 final size:24
Alignment explanation
Indices: 1227996--1228041 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1227986 GAACGTGGAT
1227996 TTTTTTTAAAAAAATTAATTTTAA
1 TTTTTTTAAAAAAATTAATTTTAA
* * *
1228020 TTTTTTTATAAAAGTTATTTTT
1 TTTTTTTAAAAAAATTAATTTT
1228042 TTATTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTTTTAAAAAAATTAATTTTAA
Found at i:1228625 original size:2 final size:2
Alignment explanation
Indices: 1228618--1228678 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1228608 ATTAAGGTGT
1228618 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
1228660 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1228679 TATTAGTAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1230788 original size:18 final size:18
Alignment explanation
Indices: 1230765--1230801 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1230755 GTCCGATTCT
1230765 TTTGACCGGTCGAACCAG
1 TTTGACCGGTCGAACCAG
*
1230783 TTTGACCGGTTGAACCAG
1 TTTGACCGGTCGAACCAG
1230801 T
1 T
1230802 GAACCGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (18 bp):
TTTGACCGGTCGAACCAG
Found at i:1234118 original size:23 final size:24
Alignment explanation
Indices: 1234079--1234131 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
1234069 AAAAACCTAG
* *
1234079 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
1234103 ACCGGTTTTTAT-CCGGAAAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
1234126 ACCGGT
1 ACCGGT
1234132 CTGGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGAAAAAAA
Found at i:1236431 original size:21 final size:21
Alignment explanation
Indices: 1236407--1236448 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1236397 AGTTTATTTT
1236407 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1236428 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1236449 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1236496 original size:33 final size:33
Alignment explanation
Indices: 1236443--1236541 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1236433 TTTGTTTCAA
1236443 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1236475 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1236508 TTATCAAACTTGGAAGTATTTAAGTATTTTAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1236541 T
1 T
1236542 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1237269 original size:21 final size:21
Alignment explanation
Indices: 1237240--1237293 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1237230 TCGTTGAATA
1237240 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
*
1237261 GGGGAAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
1237282 GGGGGAATCGGT
1 GGGGGAATCGGT
1237294 TCCCTCCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAT
Found at i:1237395 original size:22 final size:21
Alignment explanation
Indices: 1237335--1237389 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1237325 AAATCATTCA
1237335 GGGGGGAATCGGTACCTCCTT
1 GGGGGGAATCGGTACCTCCTT
1237356 GGGGGGAATCGGTACCTCCTT
1 GGGGGGAATCGGTACCTCCTT
1237377 GGGGGGAATCGGT
1 GGGGGGAATCGGT
1237390 TCCCTCTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGGTACCTCCTT
Found at i:1237742 original size:16 final size:15
Alignment explanation
Indices: 1237690--1237746 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1237680 TTTAATAATA
*
1237690 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
1237705 TTATAACCGGATTTTT
1 TTAAAACC-GATTTTT
**
1237721 AGAAAAACCGATTTTT
1 -TTAAAACCGATTTTT
1237737 TTAAAACCGA
1 TTAAAACCGA
1237747 AACCGATTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 14 0.42
16 14 0.42
17 5 0.15
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Done.