Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008727.1 Hibiscus syriacus cultivar Beakdansim tig00111794_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: 1388410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:991071 original size:15 final size:15
Alignment explanation
Indices: 991053--991094 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
991043 TCAGTGTTGC
991053 TGTTATTGGAGTCGT
1 TGTTATTGGAGTCGT
**
991068 TGTTAAAGGAGTCGT
1 TGTTATTGGAGTCGT
991083 TGTTATTGGAGT
1 TGTTATTGGAGT
991095 ATCGGAGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.43
Consensus pattern (15 bp):
TGTTATTGGAGTCGT
Found at i:994727 original size:54 final size:54
Alignment explanation
Indices: 994693--995061 Score: 576
Period size: 54 Copynumber: 6.8 Consensus size: 54
994683 CCATAGGGTC
* * * *
994693 ATTCATAAATATATTATGAATTCCGTGGATTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* *
994747 ATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * *
994801 ATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTTCTGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* *
994855 ATTCATCAATATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * *
994909 ATTCATCAACATATGATGAATTCCGTTAATTGCACACTTAGTGCCAAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * *
994963 ATTTATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCAAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
*
995017 ATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCC
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
995062 TATTTGTTAA
Statistics
Matches: 287, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 287 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
Found at i:1000047 original size:2 final size:2
Alignment explanation
Indices: 1000042--1000263 Score: 183
Period size: 2 Copynumber: 111.0 Consensus size: 2
1000032 AAAATTAATA
* * *
1000042 AT AT AT AT AT AT AT AT AT -T AT AT GT ACT AT AT AT -T TT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * * *
1000083 AT ACT AT ACG AT AT AT A- AT AT AT AT GT -T TT CAA AA AT AT ACC
1 AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T
* *
1000125 AT AT A- AT AC AT AT AT TT AT AGT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1000167 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
* *
1000209 AT AT AT AT AT AT AT AT -T A- AA AT A- AT AC AT AT ACT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT
1000250 ACT AT AT AT A- AT AT
1 A-T AT AT AT AT AT AT
1000264 CTACACTACT
Statistics
Matches: 184, Mismatches: 19, Indels: 34
0.78 0.08 0.14
Matches are distributed among these distances:
1 9 0.05
2 160 0.87
3 15 0.08
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1002722 original size:21 final size:21
Alignment explanation
Indices: 1002710--1002807 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
1002700 AAGGGTTAAG
1002710 TCCTTTTGATGAAAGGACTTA
1 TCCTTTTGATGAAAGGACTTA
1002731 TCCTTTTGATGAAAGGACTTA
1 TCCTTTTGATGAAAGGACTTA
*
1002752 TCCTTTTGATGAAAGTACTTA
1 TCCTTTTGATGAAAGGACTTA
*
1002773 TCCTTTTGATGAAAGGGCTTAA
1 TCCTTTTGATGAAAGGACTT-A
*
1002795 T-CTTTTCATGAAA
1 TCCTTTTGATGAAA
1002808 AGATTTAATC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 70 0.97
22 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (21 bp):
TCCTTTTGATGAAAGGACTTA
Found at i:1002925 original size:35 final size:35
Alignment explanation
Indices: 1002877--1002948 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1002867 TAAATTAAAA
1002877 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
* *
1002912 AATAAGTCTATTCACCAAGTGACTTGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
1002947 AA
1 AA
1002949 ATAGCATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (35 bp):
AATAAGTCCATTCACCAAGTGACATGACTTATTAT
Found at i:1005489 original size:15 final size:16
Alignment explanation
Indices: 1005459--1005491 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1005449 CAAAACTCCA
1005459 ACAATCTTCTTTTATC
1 ACAATCTTCTTTTATC
1005475 ACAATCTTC-TTTATC
1 ACAATCTTCTTTTATC
1005490 AC
1 AC
1005492 TTTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (16 bp):
ACAATCTTCTTTTATC
Found at i:1006971 original size:2 final size:2
Alignment explanation
Indices: 1006964--1006990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1006954 CTAAGGTGAA
1006964 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1006991 ATTCAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1009344 original size:13 final size:13
Alignment explanation
Indices: 1009321--1009365 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
1009311 GAGACGACAA
1009321 AAATC-AATTTCT
1 AAATCAAATTTCT
1009333 AAATCAAATTTCT
1 AAATCAAATTTCT
1009346 AAATCAAATTTCT
1 AAATCAAATTTCT
1009359 AAATCAA
1 AAATCAA
1009366 TCCCTGGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 5 0.16
13 27 0.84
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATCAAATTTCT
Found at i:1012028 original size:83 final size:83
Alignment explanation
Indices: 1011889--1012052 Score: 274
Period size: 83 Copynumber: 2.0 Consensus size: 83
1011879 ACACCGATGG
*
1011889 TTAAATCATGAACCGGTTGGAATCTTTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCAAG
1 TTAAATCATGAACCGGTTGGAATCTCTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCAAG
1011954 CCTGTAAAAAAAACCCTA
66 CCTGTAAAAAAAACCCTA
* ** *
1011972 TTAAATCATGAACCGGTTGGAATCTCTTGTCGGTAAACTGCAAGATTAAACATGATTTTCCCACG
1 TTAAATCATGAACCGGTTGGAATCTCTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCAAG
*
1012037 CTTGTAAAAAAAACCC
66 CCTGTAAAAAAAACCC
1012053 CAATTAAAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (83 bp):
TTAAATCATGAACCGGTTGGAATCTCTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCAAG
CCTGTAAAAAAAACCCTA
Found at i:1012938 original size:74 final size:74
Alignment explanation
Indices: 1012811--1012954 Score: 195
Period size: 74 Copynumber: 1.9 Consensus size: 74
1012801 TTGGCACGTA
* *
1012811 TCCACCCTGAAATTTGAATTTCCTTCGATCAATTACTTATTTTATTGATGGTG-CT-CACTCTGA
1 TCCAACCTGAAATTTGAATTTCCTTCGATCAATTACTTATTTTATTGACGGTGCCTAC-CT-TGA
1012874 AATTTTACATG
64 AATTTTACATG
** *
1012885 TCCAACCTGAAATTTGAATTTTGTTCGATTAATTACTTATTTTA-TGAACGGTGCCTACCTTGAA
1 TCCAACCTGAAATTTGAATTTCCTTCGATCAATTACTTATTTTATTG-ACGGTGCCTACCTTGAA
1012949 ATTTTA
65 ATTTTA
1012955 TTTGTACTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 2 0.03
74 55 0.89
75 4 0.06
76 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (74 bp):
TCCAACCTGAAATTTGAATTTCCTTCGATCAATTACTTATTTTATTGACGGTGCCTACCTTGAAA
TTTTACATG
Found at i:1013267 original size:11 final size:11
Alignment explanation
Indices: 1013251--1013283 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1013241 AAACAAAAGA
1013251 TGCATCAGAGG
1 TGCATCAGAGG
1013262 TGCATCAGAGG
1 TGCATCAGAGG
1013273 TGCATCAGAGG
1 TGCATCAGAGG
1013284 ATTCAATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (11 bp):
TGCATCAGAGG
Found at i:1014645 original size:26 final size:26
Alignment explanation
Indices: 1014616--1014668 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1014606 AACTTTAGTT
* *
1014616 GAATAGTTTGATTGTTTTGTAATTCA
1 GAATAGTTTGATTATATTGTAATTCA
1014642 GAATAGTTTGATTATATTGTAATTCA
1 GAATAGTTTGATTATATTGTAATTCA
1014668 G
1 G
1014669 TCTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (26 bp):
GAATAGTTTGATTATATTGTAATTCA
Found at i:1027524 original size:156 final size:152
Alignment explanation
Indices: 1027323--1027734 Score: 494
Period size: 156 Copynumber: 2.7 Consensus size: 152
1027313 AAAAAGTAAA
* * * *
1027323 AATTGAAGTTACGTAGGTATTATATTGTGGTATATAAGCATGTGGTTCAAATTTGGTAAAAACTG
1 AATTGAAGTTACATATGTATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTGGTAAAAACTG
1027388 ACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTAAGAGACTAAATTGAAA
66 ACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTAAGAGACTAAATTG---
*
1027453 ATTAAAAAATTATTAT-CAAAAAGAGG
128 A--AAAAAATTATTATAAAAAAAGAGG
*
1027479 AATTGAAGTTACATATGCATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTGGTAAAAAC-G
1 AATTGAAGTTACATATGTATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTGGTAAAAACTG
* * *
1027543 AACATAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATGAAAAATTAAGGGACTAAATTGAA
66 -ACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTAAGAGACTAAATTGAA
* *
1027608 ACAAATTGTTATAAAAAAAGAGG
130 AAAAATTATTATAAAAAAAGAGG
* * * *
1027631 AATTGAGAG-TACATATGTATTCTA-TGATGGCT-TATGAGCATATTGTTAAAATTTGTTAAAAA
1 AATTGA-AGTTACATATGTATTCTATTG-TGG-TATATGAGCATGTGGTTCAAATTTGGT-AAAA
* * * * *
1027693 AATGGACTTAAAATGAAGAAGGAATTGAATG-AATAATGAAAT
62 ACT-GACTTAAAATAAAGGATGAATTGAA-GAAATAAGGAAAT
1027735 CAGAGACTAA
Statistics
Matches: 225, Mismatches: 22, Indels: 20
0.84 0.08 0.07
Matches are distributed among these distances:
151 13 0.06
152 53 0.24
153 9 0.04
154 30 0.13
155 3 0.01
156 117 0.52
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (152 bp):
AATTGAAGTTACATATGTATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTGGTAAAAACTG
ACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTAAGAGACTAAATTGAAA
AAAATTATTATAAAAAAAGAGG
Found at i:1030466 original size:55 final size:55
Alignment explanation
Indices: 1030382--1030858 Score: 636
Period size: 55 Copynumber: 8.5 Consensus size: 55
1030372 AATATGTTGC
* * *
1030382 AATTTCCGAATTGGCACTATGTGTGCAACCTCACGAAATTAATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1030437 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* *
1030492 AATTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCAAAATTAGTTTATG
1 -A----AT---TTT-CGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
*
1030556 AA-TTTCTGTATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTC-GTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* *
1030611 AATTTAT-GTATTGGCATTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATG
1 AATTT-TCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * *
1030666 AATTTCCATATTGACACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * *
1030721 AATTTTCGTATTGTCACTATGTGTGCAACTTCACGAAATTCATAATAAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * * *
1030776 AATTTCCGTATTGGTACTATGTGTGCAACCCCA-TATAATTCATAATGAGTTTGTG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGA-AATTCATAATGAGTTTATG
**
1030831 AATTACCGTATTGGCACTATGTGTGCAA
1 AATTTTCGTATTGGCACTATGTGTGCAA
1030859 AACCATGGAA
Statistics
Matches: 379, Mismatches: 29, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
54 2 0.01
55 319 0.84
56 3 0.01
57 1 0.00
59 1 0.00
60 2 0.01
63 4 0.01
64 47 0.12
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (55 bp):
AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
Found at i:1036375 original size:20 final size:20
Alignment explanation
Indices: 1036350--1036399 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1036340 ATTTAAAGAA
*
1036350 GTATCGATACCGAG-GTGTAG
1 GTATCGATACCAAGAG-GTAG
1036370 GTATCGATACCAAGAGGTAG
1 GTATCGATACCAAGAGGTAG
1036390 GTATCGATAC
1 GTATCGATAC
1036400 TATAATCAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAAGAGGTAG
Found at i:1036871 original size:55 final size:55
Alignment explanation
Indices: 1036811--1037380 Score: 793
Period size: 55 Copynumber: 10.4 Consensus size: 55
1036801 GTAATTTCCA
*
1036811 TATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
1036866 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTAC-G
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTT-CTG
** * ***
1036921 TATTGATACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAAGAATTGAAG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* * *
1036976 TATTGGAACTAAGTGTGTAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* *
1037031 TATTGGCACTATATGTGTAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* *
1037086 TATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCGG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* * * *
1037141 TATTGGCACTATGTATACAACCTCACGAAATTTATAATGAGTTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* * * * *
1037196 TATTGGCATTATGTGTGAAACCTCATGAAACTCATAATGAGTTTATGAATTT-TCA
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCT-G
*
1037251 TATTGGCACTATGTGTGCAACCTCGCGAAATTCATAATGAGTTTATGAATTTCTG
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* * * * * * * **
1037306 TATTGGCACTCTGTGTGTAACCCCATGTAATTCATAATGAGTTTGTGAATTACCA
1 TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
* *
1037361 TATCGACACTATGTGTGCAA
1 TATTGGCACTATGTGTGCAA
1037381 AACCATGGAA
Statistics
Matches: 456, Mismatches: 55, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
55 454 1.00
56 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (55 bp):
TATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTG
Found at i:1039289 original size:20 final size:20
Alignment explanation
Indices: 1039264--1039308 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1039254 AAATGGTTCG
1039264 ATTTC-ACACTCTTAACATCA
1 ATTTCAACACTCTT-ACATCA
*
1039284 ATTTCAACACTCTTACATTA
1 ATTTCAACACTCTTACATCA
1039304 ATTTC
1 ATTTC
1039309 CAGCATAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTCAACACTCTTACATCA
Found at i:1043925 original size:42 final size:42
Alignment explanation
Indices: 1043875--1043971 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
1043865 ATAATATGAG
* *
1043875 AATGTTATATGAGATATATGAGAAACGGTATATGAAAGTGAT
1 AATGTTATATGAGATATATAAGAAAAGGTATATGAAAGTGAT
*
1043917 AATGTTATATGAGATATATAAGAAAAGGTATGTGAAAGTGAT
1 AATGTTATATGAGATATATAAGAAAAGGTATATGAAAGTGAT
*
1043959 AATGTGATATGAG
1 AATGTTATATGAG
1043972 TCTCTATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.43, C:0.01, G:0.25, T:0.31
Consensus pattern (42 bp):
AATGTTATATGAGATATATAAGAAAAGGTATATGAAAGTGAT
Found at i:1048134 original size:21 final size:21
Alignment explanation
Indices: 1048083--1048134 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1048073 CAAAATGGCC
*
1048083 CAATTTC-ATACTCTTAACAT
1 CAATTTCAACACTCTTAACAT
1048103 CAATTTCAACACTC-TAACAT
1 CAATTTCAACACTCTTAACAT
*
1048123 TAATTTCTAACA
1 CAATTTC-AACA
1048135 TAGTACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (21 bp):
CAATTTCAACACTCTTAACAT
Found at i:1053938 original size:24 final size:24
Alignment explanation
Indices: 1053906--1053951 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1053896 AGAGAAACAA
*
1053906 AGAAAAGAAAAAATAATAAAAATG
1 AGAAAAGAAAAAATAAAAAAAATG
* *
1053930 AGAATAGAAGAAATAAAAAAAA
1 AGAAAAGAAAAAATAAAAAAAA
1053952 GAAAAAATAT
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:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (24 bp):
AGAAAAGAAAAAATAAAAAAAATG
Found at i:1053966 original size:3 final size:3
Alignment explanation
Indices: 1053960--1053984 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1053950 AAGAAAAAAT
1053960 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1053985 AGAAGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1054490 original size:5 final size:5
Alignment explanation
Indices: 1054480--1054504 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1054470 ATACTTATCC
1054480 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
1054505 CTTTCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1055451 original size:44 final size:44
Alignment explanation
Indices: 1055391--1055503 Score: 190
Period size: 44 Copynumber: 2.6 Consensus size: 44
1055381 AATCAACGTG
*
1055391 TCCAGATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
1 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
*
1055435 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATGTCATTTT
1 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
* *
1055479 TTCATATTTGATCTTCCTTAAAGAG
1 TCCATATTTGATCTTCCTTGAAGAG
1055504 AAATAGAGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (44 bp):
TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
Found at i:1055633 original size:130 final size:131
Alignment explanation
Indices: 1055475--1055766 Score: 318
Period size: 130 Copynumber: 2.2 Consensus size: 131
1055465 AATCATGTCA
* * *
1055475 TTTTTTCATATTTGATCTTCCTTAAAGAGAAATAGAGCAAATCTACCT-CAATTCAATCTTCCCT
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGC-ATTCAATCTTCCCT
** * ** * *
1055539 AAAGAGTAGTAAAGTGAATCAACGTTTCCAAATATGATCTACCCTGAAGAGCAGTGAAGCAGAT-
65 AAAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATC
1055603 CC
130 CC
* * * * * * *
1055605 TTTTTCCATATTTGATCTTCCCTGAAGAGCAGTGGAGCAAATCTACTTGCATTTAATCTTCCTTG
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGCATTCAATCTTCCCTA
* * * * * * *
1055670 AAGAACAATAAAGTGAATCAAAATTTCTAGATTTGATTTTCCTTGAAGAACAGTGGAGCAAATCC
66 AAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATCC
1055735 C
131 C
***
1055736 TTTTAGTATATTTGATCTTCCCTGAAGAGAA
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAA
1055767 GTGAAACAAA
Statistics
Matches: 132, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
130 102 0.77
131 30 0.23
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (131 bp):
TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGCATTCAATCTTCCCTA
AAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATCC
C
Found at i:1059464 original size:27 final size:27
Alignment explanation
Indices: 1059434--1059495 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1059424 TAAAACATTA
1059434 AAAATAATATATACAATTTATAAAAGT
1 AAAATAATATATACAATTTATAAAAGT
*
1059461 AAAATAATATATATAATTTATAAAAGT
1 AAAATAATATATACAATTTATAAAAGT
1059488 AAAATAAT
1 AAAATAAT
1059496 TATTTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAATAATATATACAATTTATAAAAGT
Found at i:1059485 original size:21 final size:20
Alignment explanation
Indices: 1059460--1059511 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1059450 TTTATAAAAG
1059460 TAAAATAATATATATAATTTA
1 TAAAATAATATA-ATAATTTA
* *
1059481 TAAAAGTAAAATAATTATTTA
1 TAAAA-TAATATAATAATTTA
*
1059502 TTAAA-AATAT
1 TAAAATAATAT
1059512 CAGAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
21 16 0.62
22 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATAATATAATAATTTA
Found at i:1060300 original size:33 final size:33
Alignment explanation
Indices: 1060257--1060343 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
1060247 GTTAGAGGCC
*
1060257 GGCCACCACCAGCCACCGTTCTACGACGGTGAT
1 GGCCATCACCAGCCACCGTTCTACGACGGTGAT
*
1060290 GGCCATCACCAGCCACCGTTCTACGGCGGTGAT
1 GGCCATCACCAGCCACCGTTCTACGACGGTGAT
1060323 GGCCATCACCAGCCACCGTTC
1 GGCCATCACCAGCCACCGTTC
1060344 GATCTAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (33 bp):
GGCCATCACCAGCCACCGTTCTACGACGGTGAT
Found at i:1060995 original size:3 final size:3
Alignment explanation
Indices: 1060983--1061041 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
1060973 GTGTCATTAT
*
1060983 TAA TAA -AA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA T-A TGA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1061027 TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1061042 AAATTTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1061581 original size:74 final size:73
Alignment explanation
Indices: 1061200--1061795 Score: 942
Period size: 73 Copynumber: 8.1 Consensus size: 73
1061190 ATGTCTTATG
*
1061200 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTTGAAAACATCGTGCACTGT
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC--TTTTTGAAAACATCATGCACTGT
* *
1061265 AGGCCTTACG
64 AGGTCTTACA
* *
1061275 GATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCGAGGGCTTTTTGAAAACATCATGCACT-TAG
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1061339 GTCTTACA
66 GTCTTACA
* *
1061347 GATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCGTGCACTGTAG
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1061412 GTCTTACA
66 GTCTTACA
* * *
1061420 GATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCAAAAGCTTTTTGAAAACATCATGCACTGTAG
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1061485 GTCTTACA
66 GTCTTACA
*
1061493 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCTCGAAGGCGTTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTA
1061558 GGTCTTACA
65 GGTCTTACA
*
1061567 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGATGGCTTTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTA
1061632 GGTCTTACA
65 GGTCTTACA
* *
1061641 GATAACCCCGAGGCTTTAAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCAC
1 GATGACCCTGAGGCTTT---AAA-ATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCAC
1061706 TGTAGGTCTTACA
61 TGTAGGTCTTACA
* * * *
1061719 GATGACCATGAGGCTCTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAATGTAG
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1061784 GTCTTACA
66 GTCTTACA
1061792 GATG
1 GATG
1061796 TGGGAAATAA
Statistics
Matches: 485, Mismatches: 30, Indels: 14
0.92 0.06 0.03
Matches are distributed among these distances:
72 66 0.14
73 171 0.35
74 139 0.29
75 40 0.08
77 3 0.01
78 66 0.14
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (73 bp):
GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
GTCTTACA
Found at i:1061592 original size:147 final size:147
Alignment explanation
Indices: 1061200--1061795 Score: 953
Period size: 147 Copynumber: 4.0 Consensus size: 147
1061190 ATGTCTTATG
*
1061200 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTTGAAAACATCGTGCACTGT
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTTGAAAACATCATGCACTGT
* * * *
1061265 AGGCCTTACGGATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCGAGGGCTTTTTGAAAACATCA
65 AGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCA
1061330 TGCACT-TAGGTCTTACA
130 TGCACTGTAGGTCTTACA
* *
1061347 GATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCGTGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
* * *
1061411 GGTCTTACAGATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCAAAAGCTTTTTGAAAACATCAT
66 GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
1061476 GCACTGTAGGTCTTACA
131 GCACTGTAGGTCTTACA
* *
1061493 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCTCGAAGGCGTTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
*
1061558 GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGATGGCTTTTTTGAAAACATCA
66 GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCA
1061623 TGCACTGTAGGTCTTACA
130 TGCACTGTAGGTCTTACA
* *
1061641 GATAACCCCGAGGCTTTAAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCAC
1 GATGACCCTGAGGCTTT---AAA-ATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCAC
* * *
1061706 TGTAGGTCTTACAGATGACCATGAGGCTCTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
62 TGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
*
1061771 TCATGCAATGTAGGTCTTACA
127 TCATGCACTGTAGGTCTTACA
1061792 GATG
1 GATG
1061796 TGGGAAATAA
Statistics
Matches: 419, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
145 89 0.21
146 49 0.12
147 107 0.26
148 48 0.11
151 38 0.09
152 88 0.21
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (147 bp):
GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
GCACTGTAGGTCTTACA
Found at i:1062484 original size:22 final size:22
Alignment explanation
Indices: 1062459--1062511 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1062449 TAAGGTTTTT
*
1062459 ATCTTTGAAAAGAAAATCTATC
1 ATCTTTGAAAAGAAAATATATC
** *
1062481 ATCTTTGAGGAGAGAATATATC
1 ATCTTTGAAAAGAAAATATATC
1062503 ATCTTTGAA
1 ATCTTTGAA
1062512 GAGTGTAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAAAATATATC
Found at i:1062968 original size:54 final size:54
Alignment explanation
Indices: 1062881--1063015 Score: 153
Period size: 54 Copynumber: 2.5 Consensus size: 54
1062871 TAATTGGTTC
* * ** *
1062881 GTAAAACATTTGACAAAACATTCATCATCTCATGTGGTTTATGCTCAGATACTA
1 GTAAAACATTTGACAAAACATTCATCCTCTCATGCGACTTATGCACAGATACTA
* * * * ** *
1062935 GTAAAACATTTGACAACACGTTCATCCTTTCATGCGACTTCTGCACAGATGTTT
1 GTAAAACATTTGACAAAACATTCATCCTCTCATGCGACTTATGCACAGATACTA
*
1062989 GTAAAACATTTGACAATACATTCATCC
1 GTAAAACATTTGACAAAACATTCATCC
1063016 AGTTGTGGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (54 bp):
GTAAAACATTTGACAAAACATTCATCCTCTCATGCGACTTATGCACAGATACTA
Found at i:1066068 original size:8 final size:8
Alignment explanation
Indices: 1066030--1066075 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
1066020 ATTGGTTCAA
*
1066030 TTTTTTCC
1 TTTTTTCT
*
1066038 TTTTTCCTT
1 TTTTTTC-T
1066047 TTTTTTCT
1 TTTTTTCT
1066055 TTTTTTCT
1 TTTTTTCT
1066063 TTTTTT-T
1 TTTTTTCT
1066070 TTTTTT
1 TTTTTT
1066076 TTAAGTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.21
8 21 0.62
9 6 0.18
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1066077 original size:17 final size:17
Alignment explanation
Indices: 1066030--1066076 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1066020 ATTGGTTCAA
* *
1066030 TTTTTTCCTTTTTCCTT
1 TTTTTTCTTTTTTTCTT
1066047 TTTTTTCTTTTTTTCTT
1 TTTTTTCTTTTTTTCTT
1066064 TTTTTT-TTTTTTT
1 TTTTTTCTTTTTTT
1066077 TAAGTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTCTTTTTTTCTT
Found at i:1071782 original size:29 final size:29
Alignment explanation
Indices: 1071749--1071812 Score: 114
Period size: 27 Copynumber: 2.3 Consensus size: 29
1071739 TAAAACATTA
1071749 AAAATAATATATATATAATTTATAAAAGT
1 AAAATAATATATATATAATTTATAAAAGT
1071778 AAAAT-A-ATATATATAATTTATAAAAGT
1 AAAATAATATATATATAATTTATAAAAGT
1071805 AAAATAAT
1 AAAATAAT
1071813 TATTTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 26 0.79
28 2 0.06
29 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATAATATATATATAATTTATAAAAGT
Found at i:1073317 original size:3 final size:3
Alignment explanation
Indices: 1073305--1073367 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
1073295 GTGTAATTAT
* * *
1073305 TAA TAA -AA TAA TAA TAC T-A TTA TAA TAA TAA TAA TAA TAA T-A TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1073350 TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1073368 AAAAAGGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 5 0.10
3 46 0.90
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1073337 original size:23 final size:23
Alignment explanation
Indices: 1073300--1073367 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1073290 GCTTGGTGTA
*
1073300 ATTATTAATAA-AATAATAATACT
1 ATTA-TAATAATAATAATAATAAT
1073323 ATTATAATAATAATAATAATAAT
1 ATTATAATAATAATAATAATAAT
* *
1073346 ATGATATTAATAATAATAATAA
1 ATTATAATAATAATAATAATAA
1073368 AAAAAGGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.15
23 35 0.85
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (23 bp):
ATTATAATAATAATAATAATAAT
Found at i:1073364 original size:20 final size:20
Alignment explanation
Indices: 1073307--1073366 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1073297 GTAATTATTA
* *
1073307 ATAA-AATAATAATACTATT
1 ATAATAATAATAATAATAAT
1073326 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
* *
1073346 ATGATATTAATAATAATAAT
1 ATAATAATAATAATAATAAT
1073366 A
1 A
1073367 AAAAAAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:1076363 original size:74 final size:75
Alignment explanation
Indices: 1076241--1076385 Score: 220
Period size: 74 Copynumber: 1.9 Consensus size: 75
1076231 ATAATCATTT
* * * * *
1076241 AGGATTATTAAAAATATATACCCACCATGACCAAAACTATATTACTTATCAATATACCATATTCT
1 AGGATAATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTAT
1076306 GGACTCTCAC
66 GGACTCTCAC
* *
1076316 AGGATAATTAAAAAAATATA-CCACCATGACTAAAACTATGTAACTTATCAATATACCAAATTAT
1 AGGATAATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTAT
1076380 GGACTC
66 GGACTC
1076386 ACATCTAGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 45 0.71
75 18 0.29
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (75 bp):
AGGATAATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTAT
GGACTCTCAC
Found at i:1078621 original size:8 final size:9
Alignment explanation
Indices: 1078606--1078633 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1078596 ATTATAACTC
1078606 AATAAAAAT
1 AATAAAAAT
1078615 AATAAAAAT
1 AATAAAAAT
1078624 AATAAAAAT
1 AATAAAAAT
1078633 A
1 A
1078634 GGAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1081463 original size:24 final size:24
Alignment explanation
Indices: 1081434--1081483 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1081424 TGGTGGTTGA
*
1081434 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1081458 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1081482 TT
1 TT
1081484 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1081989 original size:17 final size:16
Alignment explanation
Indices: 1081958--1081991 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1081948 CACGTGAGGA
1081958 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1081974 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1081991 T
1 T
1081992 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1088375 original size:19 final size:21
Alignment explanation
Indices: 1088338--1088380 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1088328 TAACTTTTTC
1088338 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1088358 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1088378 TTT
1 TTT
1088381 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1088386 original size:19 final size:20
Alignment explanation
Indices: 1088337--1088386 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1088327 TTAACTTTTT
*
1088337 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1088357 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1088376 CTTTTACCTTT
1 CTTTTACCTTT
1088387 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1091672 original size:24 final size:24
Alignment explanation
Indices: 1091643--1091692 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1091633 TGGTGGTTGA
*
1091643 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1091667 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1091691 TT
1 TT
1091693 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1092198 original size:17 final size:16
Alignment explanation
Indices: 1092167--1092200 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1092157 CACGTGAGGA
1092167 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1092183 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1092200 T
1 T
1092201 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1093141 original size:21 final size:21
Alignment explanation
Indices: 1093117--1093189 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1093107 TATGCCACCA
1093117 CCACAGGGTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
* * *
1093138 CCACAGGGGTACATACCCAGC
1 CCACAGGGTTACATTCCTAGC
* *
1093159 CCGCAAGGTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
1093180 CC-CTAGGGTT
1 CCAC-AGGGTT
1093190 TTATGACACC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (21 bp):
CCACAGGGTTACATTCCTAGC
Found at i:1093637 original size:19 final size:19
Alignment explanation
Indices: 1093593--1093637 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1093583 GTTGTATTTC
*
1093593 AATTTTAATGTAATTTTGT
1 AATTTTTATGTAATTTTGT
1093612 AATTTTTATGTAATTTTGT
1 AATTTTTATGTAATTTTGT
1093631 AATTTTT
1 AATTTTT
1093638 TTAAATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
AATTTTTATGTAATTTTGT
Found at i:1093717 original size:27 final size:29
Alignment explanation
Indices: 1093687--1093748 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1093677 ATTCAACTTG
*
1093687 AAATGTTTAA-ATTATG-T-AATGTTTTTT
1 AAATGTTTAATATT-TGTTGAATGTTTTTA
1093714 AAATGTTTAATATTTGTTGAATGTTTTTA
1 AAATGTTTAATATTTGTTGAATGTTTTTA
1093743 AAATGT
1 AAATGT
1093749 AAATTCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 12 0.39
28 4 0.13
29 15 0.48
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (29 bp):
AAATGTTTAATATTTGTTGAATGTTTTTA
Found at i:1097758 original size:26 final size:28
Alignment explanation
Indices: 1097721--1097784 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
1097711 TATGTATTTG
1097721 TTTCTA-ATATTT-CAATGTAAT-TGCAT
1 TTTCTACATATTTCCAATGT-ATGTGCAT
*
1097747 TTTCTACA-ATTTCCCAATGTATGTGTAT
1 TTTCTACATATTT-CCAATGTATGTGCAT
1097775 TTTCTACATA
1 TTTCTACATA
1097785 AATTTCCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 18 0.56
29 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTCTACATATTTCCAATGTATGTGCAT
Found at i:1097877 original size:25 final size:24
Alignment explanation
Indices: 1097849--1097965 Score: 76
Period size: 25 Copynumber: 4.6 Consensus size: 24
1097839 CTTACCCTAA
1097849 ACCACTTTAACCTATACAACCCTT
1 ACCACTTTAACCTATACAACCCTT
* * *
1097873 GACCACTCTCACCTTAAATA-AACCCTAA
1 -ACCACTTTAACC-T--ATACAACCCT-T
* * *
1097901 ACCACTTTAACCTACAAAATCCTT
1 ACCACTTTAACCTATACAACCCTT
*
1097925 CACCACTTTTACCT-TAACGAACCCTAT
1 -ACCACTTTAACCTAT-AC-AACCCT-T
1097952 ACCACTTTAACCTA
1 ACCACTTTAACCTA
1097966 AAATCACTCC
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
24 2 0.03
25 28 0.41
26 19 0.28
27 17 0.25
28 3 0.04
ACGTcount: A:0.35, C:0.36, G:0.02, T:0.27
Consensus pattern (24 bp):
ACCACTTTAACCTATACAACCCTT
Found at i:1097930 original size:52 final size:51
Alignment explanation
Indices: 1097842--1097965 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 51
1097832 ATTGAACCTT
* * * *
1097842 ACCCTAAACCACTTTAACCTATACAACCCTTGACCACTCTCACCTTAAATAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTT-AACAA
* * * *
1097894 ACCCTAAACCACTTTAACCTACAAAATCCTTCACCACTTTTACCTTAACGA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
*
1097945 ACCCTATACCACTTTAACCTA
1 ACCCTAAACCACTTTAACCTA
1097966 AAATCACTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 23 0.37
52 40 0.63
ACGTcount: A:0.35, C:0.36, G:0.02, T:0.27
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
Found at i:1099100 original size:39 final size:39
Alignment explanation
Indices: 1099042--1099123 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
1099032 GGTGGTCTAA
*
1099042 TTCATATTTTAATACCATATTGTTAAATGGAAATCGTGC
1 TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
**
1099081 TTCATATTTTAATGGCATATTGTTAAATGAAAATCGTGC
1 TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
1099120 TTCA
1 TTCA
1099124 GTGGAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
Found at i:1099491 original size:16 final size:13
Alignment explanation
Indices: 1099456--1099487 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1099446 ATATTCGAAA
1099456 TTACAATAATAGT
1 TTACAATAATAGT
1099469 TTACAATAATAGT
1 TTACAATAATAGT
1099482 TTACAA
1 TTACAA
1099488 CAATCATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (13 bp):
TTACAATAATAGT
Found at i:1099847 original size:23 final size:23
Alignment explanation
Indices: 1099821--1099894 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
1099811 GAGTCGTCAA
* **
1099821 ATAAATGTGCCACAAGAGTAGAG
1 ATAAATGTGCCACAAAAACAGAG
*
1099844 ATAAATGTGTCACAAAAACAGAG
1 ATAAATGTGCCACAAAAACAGAG
* * * *
1099867 ATAAACGTGCAACATAATCAGAG
1 ATAAATGTGCCACAAAAACAGAG
1099890 ATAAA
1 ATAAA
1099895 CATATAACAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.18
Consensus pattern (23 bp):
ATAAATGTGCCACAAAAACAGAG
Found at i:1099946 original size:11 final size:12
Alignment explanation
Indices: 1099924--1099952 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1099914 TATTTTTAAT
1099924 AAAAAATAAAAG
1 AAAAAATAAAAG
1099936 AAAAAAT-AAAG
1 AAAAAATAAAAG
1099947 AAAAAA
1 AAAAAA
1099953 GAGAATTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAATAAAAG
Found at i:1104609 original size:32 final size:31
Alignment explanation
Indices: 1104572--1104631 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
1104562 TCACTATTAT
*
1104572 TATTTATAATTGTGATAATAACAATTTTTTTC
1 TATTTATAATTGTGACAATAAC-ATTTTTTTC
*
1104604 TATTTATAATTGTGACAGTAACATTTTT
1 TATTTATAATTGTGACAATAACATTTTT
1104632 CACTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (31 bp):
TATTTATAATTGTGACAATAACATTTTTTTC
Found at i:1105546 original size:11 final size:11
Alignment explanation
Indices: 1105530--1105559 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1105520 AAGATATATT
1105530 AAAATAAAATA
1 AAAATAAAATA
*
1105541 AAAATAATATA
1 AAAATAAAATA
1105552 AAAATAAA
1 AAAATAAA
1105560 TATTAATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1105550 original size:22 final size:22
Alignment explanation
Indices: 1105525--1105582 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1105515 TTGAAAAGAT
1105525 ATATTAAAATAAAATAAAAATA
1 ATATTAAAATAAAATAAAAATA
* **
1105547 ATATAAAAAT-AAATATTAATA
1 ATATTAAAATAAAATAAAAATA
*
1105568 GTATTAAATATAAAA
1 ATATTAAA-ATAAAA
1105583 GGGAGATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.52
22 11 0.38
23 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
ATATTAAAATAAAATAAAAATA
Found at i:1105649 original size:22 final size:23
Alignment explanation
Indices: 1105608--1105660 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1105598 AAGTTGTGGT
*
1105608 TAAAATAAAAAATAAGAATTAAA
1 TAAAACAAAAAATAAGAATTAAA
*
1105631 TAAAACAAAAAA-AATAATTAAA
1 TAAAACAAAAAATAAGAATTAAA
1105653 T-AAACAAA
1 TAAAACAAA
1105661 TTAAGAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.25
22 10 0.36
23 11 0.39
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (23 bp):
TAAAACAAAAAATAAGAATTAAA
Found at i:1106327 original size:62 final size:67
Alignment explanation
Indices: 1106255--1106431 Score: 206
Period size: 76 Copynumber: 2.6 Consensus size: 67
1106245 AAATCTTAAT
*
1106255 TAAAA-CTATTTAAACTAAAATACTAAA-A-AAAATATAAT-AT-T-CTAAATCCTAATTAAAAT
1 TAAAACCTATTTAAACTAAAATACTAAAGATAAAATATAATAATATCCTAAAACCTAATTAAAAT
1106314 AC
66 AC
*
1106316 TAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAAAATAATATCCTAAAACTTA
1 TAAAACCTATTTAAACTAAAATAC-----TAAAGATAAAATAT---AATAATATCCTAAAACCTA
1106381 ATTAAAATAC
58 ATTAAAATAC
1106391 TAAAAACCTATTTAAACTAAAATAC-AAAGATAAAATATAAT
1 T-AAAACCTATTTAAACTAAAATACTAAAGATAAAATATAAT
1106432 GTTTAAAATA
Statistics
Matches: 99, Mismatches: 2, Indels: 24
0.79 0.02 0.19
Matches are distributed among these distances:
61 5 0.05
62 18 0.18
67 7 0.07
68 1 0.01
69 7 0.07
70 13 0.13
72 3 0.03
73 2 0.02
74 1 0.01
75 19 0.19
76 23 0.23
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (67 bp):
TAAAACCTATTTAAACTAAAATACTAAAGATAAAATATAATAATATCCTAAAACCTAATTAAAAT
AC
Found at i:1106383 original size:75 final size:76
Alignment explanation
Indices: 1106283--1106451 Score: 243
Period size: 76 Copynumber: 2.2 Consensus size: 76
1106273 AATACTAAAA
* *
1106283 AAAATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATA
1 AAAA-ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATA
1106347 AAGATAAAAT-AT
65 AA-ATAAAATGAT
*
1106359 AAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAA
1 AAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAA
* *
1106424 AATATAATGTT
66 AATAAAATGAT
* *
1106435 TAAAATATTATCCTAAA
1 AAAAATAATATCCTAAA
1106452 TTTGAGTTTA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
75 32 0.38
76 52 0.62
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
AAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAA
AATAAAATGAT
Found at i:1113463 original size:23 final size:23
Alignment explanation
Indices: 1113431--1113480 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1113421 AAGTTGTGGT
* *
1113431 TAAAATAAAAAATAAGAATTAAA
1 TAAAAGAAAAAAAAAGAATTAAA
*
1113454 TAAAAGAAAAAAAAATAATTAAA
1 TAAAAGAAAAAAAAAGAATTAAA
1113477 TAAA
1 TAAA
1113481 CAAATTAAAG
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:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAGAAAAAAAAAGAATTAAA
Found at i:1114161 original size:19 final size:19
Alignment explanation
Indices: 1114106--1114167 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1114096 CAATTTAAAC
**
1114106 TAAAATACTAAAAAATAAT
1 TAAAATACTAAAACCTAAT
* * *
1114125 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1114145 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1114164 TAAA
1 TAAA
1114168 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1114212 original size:75 final size:76
Alignment explanation
Indices: 1114125--1114289 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1114115 AAAAAATAAT
* *
1114125 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATACTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1114189 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
1114200 ATAATATCCTAAAAATTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATACTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
1114265 TAATGTTTAAA
66 AAATGATAAAA
*
1114276 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1114290 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 31 0.39
76 48 0.61
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATACTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:1119689 original size:23 final size:23
Alignment explanation
Indices: 1119655--1119715 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1119645 CTCATATAAA
*
1119655 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
1119678 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
1119701 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1119716 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:1121418 original size:21 final size:21
Alignment explanation
Indices: 1121394--1121437 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1121384 TTTTTGTTCG
*
1121394 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTATCGATTCCC
* *
1121415 CTTGAATGGGTATTGATTCCC
1 CTTGAAGGGGTATCGATTCCC
1121436 CT
1 CT
1121438 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTGAAGGGGTATCGATTCCC
Found at i:1122340 original size:104 final size:105
Alignment explanation
Indices: 1122149--1122368 Score: 334
Period size: 104 Copynumber: 2.1 Consensus size: 105
1122139 TAGTGAAGAC
* * *
1122149 TTTATTAATAATAGTGTCGAACATTTGGTCACTAAAAAAATACTTAGTGTGATAACATTGGTGAT
1 TTTATTGAT-ATAGTATCGAACAGTTGGTCACTAAAAAAATACTTAGTGTGATAACATTGGTGAT
* *
1122214 CACAAAATATATTTTTAGTGTCAAACAAATTTATCATAATT
65 CACAAAATATATTTTTAGTGTCAAACAAATTCATCACAATT
* * * *
1122255 TTTATTGATATAGTATCGAACAGTTGGTCACT-AAATATTACTTAGTGTGATAATATTGGTGGTC
1 TTTATTGATATAGTATCGAACAGTTGGTCACTAAAAAAATACTTAGTGTGATAACATTGGTGATC
1122319 ACAAAATATATTTTTAGTGTCAAACAAATTCATCACAATT
66 ACAAAATATATTTTTAGTGTCAAACAAATTCATCACAATT
*
1122359 TATATTGATA
1 TTTATTGATA
1122369 ATTGTATCAA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
104 75 0.72
105 21 0.20
106 8 0.08
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (105 bp):
TTTATTGATATAGTATCGAACAGTTGGTCACTAAAAAAATACTTAGTGTGATAACATTGGTGATC
ACAAAATATATTTTTAGTGTCAAACAAATTCATCACAATT
Found at i:1124666 original size:14 final size:14
Alignment explanation
Indices: 1124649--1124681 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1124639 TTTATGAATT
1124649 TAATTTCTCTATAA
1 TAATTTCTCTATAA
*
1124663 TAATTTCTCTGTAA
1 TAATTTCTCTATAA
1124677 TAATT
1 TAATT
1124682 CAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (14 bp):
TAATTTCTCTATAA
Found at i:1125368 original size:3 final size:3
Alignment explanation
Indices: 1125360--1125389 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1125350 AGGTGGCAAT
1125360 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1125390 CGAGGGGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:1127777 original size:32 final size:32
Alignment explanation
Indices: 1127741--1127804 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1127731 CATCTACAGA
*
1127741 ACATTGTATGACA-TAAAAAATCAAGTAGGAAT
1 ACATTATATGA-AGTAAAAAATCAAGTAGGAAT
* *
1127773 ACATTATATGAAGTCAAAAATGAAGTAGGAAT
1 ACATTATATGAAGTAAAAAATCAAGTAGGAAT
1127805 GCTGAGTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (32 bp):
ACATTATATGAAGTAAAAAATCAAGTAGGAAT
Found at i:1130880 original size:31 final size:31
Alignment explanation
Indices: 1130845--1130908 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1130835 TTACATTGGA
1130845 GACCATATTGCAAAC-AGACTAAATGTTGGGG
1 GACCATATTGCAAACGA-ACTAAATGTTGGGG
*
1130876 GACCATATTGTAAACGAACTAAATGTTGGGG
1 GACCATATTGCAAACGAACTAAATGTTGGGG
1130907 GA
1 GA
1130909 ATGTATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (31 bp):
GACCATATTGCAAACGAACTAAATGTTGGGG
Found at i:1131094 original size:45 final size:45
Alignment explanation
Indices: 1131014--1131099 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1131004 TGATAGTTTA
* * **
1131014 ATTCAAATATTATTTATTTTATATTTTATTTTAT-AATATATCAT
1 ATTCAAATATTATTAATCTTATATTTTATGATATAAATATATCAT
*
1131058 ATTCAAGTATTAATTAATCTTATATTTTATGATATAAATATA
1 ATTCAAATATT-ATTAATCTTATATTTTATGATATAAATATA
1131100 ATTAGAGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 10 0.29
45 19 0.54
46 6 0.17
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (45 bp):
ATTCAAATATTATTAATCTTATATTTTATGATATAAATATATCAT
Found at i:1131425 original size:56 final size:56
Alignment explanation
Indices: 1131311--1131425 Score: 167
Period size: 56 Copynumber: 2.1 Consensus size: 56
1131301 CTCAAGAAGG
* * ** **
1131311 TGTCAGTTAAAGCTGTCAAATCAGGTAATCGGTCAGGTTTCAGTCGGATTTTGACA
1 TGTCAGTTAAAGCTGTAAAATCAGGTAATCAGTCAGAATTCAGTCGGATCCTGACA
*
1131367 TGTCAGTTAAAGCTGTAAAATCAGGTAATCAGTCAGAATTCAGTCGGATCCTGGCA
1 TGTCAGTTAAAGCTGTAAAATCAGGTAATCAGTCAGAATTCAGTCGGATCCTGACA
1131423 TGT
1 TGT
1131426 TAGGTAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (56 bp):
TGTCAGTTAAAGCTGTAAAATCAGGTAATCAGTCAGAATTCAGTCGGATCCTGACA
Found at i:1132027 original size:31 final size:30
Alignment explanation
Indices: 1131989--1132068 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
1131979 CTTTTAAAAC
* *
1131989 TTGCAATATAATCTCCCAACATTTAGTATGT
1 TTGCAATATGATC-CCCAACATTTAGTATAT
* * *
1132020 TTGCAATATGGTACCCTAACATTTAGTCTAT
1 TTGCAATATGAT-CCCCAACATTTAGTATAT
1132051 TTGCAATATGATCCCCAA
1 TTGCAATATGATCCCCAA
1132069 AGTAACTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.12
31 35 0.85
32 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (30 bp):
TTGCAATATGATCCCCAACATTTAGTATAT
Found at i:1132256 original size:43 final size:43
Alignment explanation
Indices: 1132195--1132286 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
1132185 TACTTTACCC
*
1132195 TTAAAACTAATGTAACAATCCACAAATTCACCAAACCAACAAA
1 TTAAAACTAATGTAACAATCCACAAATACACCAAACCAACAAA
* * * *
1132238 TTAAAACTAGA-GTAACAATCCGCAAATACATCAAACTAACATA
1 TTAAAACTA-ATGTAACAATCCACAAATACACCAAACCAACAAA
1132281 TTAAAA
1 TTAAAA
1132287 GTATTCTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.22, G:0.04, T:0.21
Consensus pattern (43 bp):
TTAAAACTAATGTAACAATCCACAAATACACCAAACCAACAAA
Found at i:1134829 original size:34 final size:34
Alignment explanation
Indices: 1134780--1134859 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 34
1134770 TTAATAATAT
**
1134780 TTTATTATTTATTAAAAAATTGATAGATTAGTTAA
1 TTTATTATTT-TTAAAAAATAAATAGATTAGTTAA
*
1134815 TTTATCATTTTTAAAAAATAAATAGATTAGTTAA
1 TTTATTATTTTTAAAAAATAAATAGATTAGTTAA
1134849 TTTATTATTTT
1 TTTATTATTTT
1134860 ATTAATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 32 0.78
35 9 0.22
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (34 bp):
TTTATTATTTTTAAAAAATAAATAGATTAGTTAA
Found at i:1138594 original size:58 final size:58
Alignment explanation
Indices: 1138475--1138597 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 58
1138465 AAACATATGA
* * * * *
1138475 ATAATTAGACGATCATTTTCTAACTTTAATAGTTGGGGAGTTAACAAAACAATATTAT
1 ATAATTGGACGATCATTTTCTAACTTTAATAGTAGGAGACTTAACAAAACAATATCAT
* * *
1138533 ATAATTGGA-GATCATTTTGTAACTTATAATAGTCAGGAGACTTAACAATACAAT-TCCT
1 ATAATTGGACGATCATTTTCTAACTT-TAATAGT-AGGAGACTTAACAAAACAATATCAT
1138591 ATAATTG
1 ATAATTG
1138598 AGGGGTCATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 15 0.27
58 24 0.44
59 16 0.29
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (58 bp):
ATAATTGGACGATCATTTTCTAACTTTAATAGTAGGAGACTTAACAAAACAATATCAT
Found at i:1139184 original size:20 final size:20
Alignment explanation
Indices: 1139154--1139309 Score: 118
Period size: 20 Copynumber: 7.7 Consensus size: 20
1139144 GTTTCCAGAT
*
1139154 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
1139174 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
* *
1139194 TTCGCGATGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
1139217 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
1139237 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
1139257 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
*
1139277 TCGCAATGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
1139297 TCGCAATGCGATT
1 TCGCAATGCGATT
1139310 TTCAAAGCAC
Statistics
Matches: 103, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 3 0.03
20 76 0.74
21 10 0.10
22 10 0.10
23 3 0.03
24 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:1139524 original size:22 final size:22
Alignment explanation
Indices: 1139484--1139525 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1139474 GGCGACATCT
*
1139484 GTCCCCACCTCCAATGAAATCA
1 GTCCCCACCTCCAACGAAATCA
* *
1139506 GTCCCCATCTCCGACGAAAT
1 GTCCCCACCTCCAACGAAAT
1139526 TCGTCTATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.40, G:0.12, T:0.19
Consensus pattern (22 bp):
GTCCCCACCTCCAACGAAATCA
Found at i:1140016 original size:20 final size:20
Alignment explanation
Indices: 1139912--1140018 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
1139902 AGAATCGCAA
*
1139912 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1139931 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
* ** **
1139950 GGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1139970 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1139990 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1140010 TGCGATTTT
1 TGCGATTTT
1140019 AAGTTTCAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 25 0.33
20 51 0.67
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1141682 original size:18 final size:18
Alignment explanation
Indices: 1141659--1141708 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1141649 TTTACTCGTA
1141659 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1141677 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1141695 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1141709 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1141968 original size:18 final size:19
Alignment explanation
Indices: 1141926--1141972 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1141916 GCGATTCTCT
1141926 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
1141946 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
1141964 TGTTGCGAT
1 CGTTGCGAT
1141973 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:1143412 original size:14 final size:14
Alignment explanation
Indices: 1143393--1143419 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1143383 TCTCGTGGCA
1143393 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1143407 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
1143420 TTTCTTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1144522 original size:20 final size:20
Alignment explanation
Indices: 1144494--1144559 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1144484 AAATTCAGTG
* *
1144494 TTGCAACAGTCAGAATCGCG
1 TTGCGACAGTCAGAATCGCA
1144514 TTGCGACAGTCAGAATCGCA
1 TTGCGACAGTCAGAATCGCA
* *
1144534 TTGCGATAGTCATAATCGCA
1 TTGCGACAGTCAGAATCGCA
1144554 TTGCGA
1 TTGCGA
1144560 TTTACATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (20 bp):
TTGCGACAGTCAGAATCGCA
Found at i:1144560 original size:20 final size:20
Alignment explanation
Indices: 1144501--1144604 Score: 104
Period size: 20 Copynumber: 5.2 Consensus size: 20
1144491 GTGTTGCAAC
* * *
1144501 AGTCAGAATCGCGTTGCGAC
1 AGTCATAATCGCATTGCGAT
*
1144521 AGTCAGAATCGCATTGCGAT
1 AGTCATAATCGCATTGCGAT
1144541 AGTCATAATCGCATTGCGAT
1 AGTCATAATCGCATTGCGAT
* *
1144561 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
* *
1144581 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
1144601 AGTC
1 AGTC
1144605 GGAAAATCGC
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 74 0.97
21 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTCATAATCGCATTGCGAT
Found at i:1144620 original size:22 final size:22
Alignment explanation
Indices: 1144589--1144647 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
1144579 ATTTACATAT
*
1144589 TCGCATTGCGATAGTCGGAAAA
1 TCGCAATGCGATAGTCGGAAAA
* *
1144611 TCGCAATGCGA-ATTTGGAAAA
1 TCGCAATGCGATAGTCGGAAAA
1144632 TCGCAATGCGATAGTC
1 TCGCAATGCGATAGTC
1144648 AGAATCGCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (22 bp):
TCGCAATGCGATAGTCGGAAAA
Found at i:1144655 original size:20 final size:20
Alignment explanation
Indices: 1144501--1144655 Score: 100
Period size: 20 Copynumber: 7.6 Consensus size: 20
1144491 GTGTTGCAAC
* *
1144501 AGTCAGAATCGCGTTGCGAC
1 AGTCAGAATCGCATTGCGAT
1144521 AGTCAGAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
*
1144541 AGTCATAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
* * *
1144561 -TTACATATTCGCATTGCGAT
1 AGT-CAGAATCGCATTGCGAT
* * *
1144581 -TTACATATTCGCATTGCGAT
1 AGT-CAGAATCGCATTGCGAT
* *
1144601 AGTCGGAAAATCGCAATGCGA-
1 AGTC--AGAATCGCATTGCGAT
* * * *
1144622 ATTTGGAAAATCGCAATGCGAT
1 A-GT-CAGAATCGCATTGCGAT
1144644 AGTCAGAATCGC
1 AGTCAGAATCGC
1144656 GTTGTGAATC
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.01
20 81 0.71
21 18 0.16
22 14 0.12
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (20 bp):
AGTCAGAATCGCATTGCGAT
Found at i:1147039 original size:15 final size:15
Alignment explanation
Indices: 1147012--1147054 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1147002 ATGGCTACTT
1147012 AGAGAAGATGAAG-GA
1 AGAGAA-ATGAAGAGA
1147027 AGAAGAAATGAAGAGA
1 AG-AGAAATGAAGAGA
1147043 AGAGAAAT-AAGA
1 AGAGAAATGAAGA
1147055 TGAGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (15 bp):
AGAGAAATGAAGAGA
Found at i:1150930 original size:31 final size:31
Alignment explanation
Indices: 1150863--1150922 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1150853 CAATTTAAGG
*
1150863 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1150894 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1150923 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1151014 original size:19 final size:19
Alignment explanation
Indices: 1150987--1151053 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
1150977 AATGTTTTTA
*
1150987 TGAATAGTAATTCACTATT
1 TGAACAGTAATTCACTATT
1151006 TGAACAGTAAATT-ACTATT
1 TGAACAGT-AATTCACTATT
* *
1151025 TGAACAGTAAATCACTGTT
1 TGAACAGTAATTCACTATT
1151044 TGAACAGTAA
1 TGAACAGTAA
1151054 CCCGAGGCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 3 0.07
19 36 0.84
20 4 0.09
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (19 bp):
TGAACAGTAATTCACTATT
Found at i:1151184 original size:21 final size:21
Alignment explanation
Indices: 1151160--1151199 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1151150 TTTGAATATT
*
1151160 TGAAGGGGTATTGATTCCCTA
1 TGAAGGGGTATCGATTCCCTA
1151181 TGAAGGGGTATCGATTCCC
1 TGAAGGGGTATCGATTCCC
1151200 CCCATTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TGAAGGGGTATCGATTCCCTA
Found at i:1151261 original size:21 final size:21
Alignment explanation
Indices: 1151228--1151267 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1151218 TTTTTGCTGA
*
1151228 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1151250 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1151268 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1155994 original size:37 final size:36
Alignment explanation
Indices: 1155887--1156341 Score: 511
Period size: 37 Copynumber: 12.0 Consensus size: 36
1155877 AATTTTTAAA
*
1155887 AAAATATATATAATATATAGTTTTTAAAACACTTTG
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
*
1155923 AATATATATATATATATATATATAGTTTTTAAAACGTTTTTG
1 -A-A-A-ATATATATA-ATATATAGTTTTTAAAAC-ATTTTG
* *
1155965 AAAATATATATAATATATAGTTTTCAAAACATTTTA
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
* *
1156001 AAATATATATATAATATATATTTTTTAAAACATTTTAA
1 AAA-ATATATATAATATATAGTTTTTAAAACATTTT-G
1156039 AAATATATATATAATATATAGTTTTTAAAACATTTTG
1 AAA-ATATATATAATATATAGTTTTTAAAACATTTTG
*
1156076 AAAA-ATTATATACTATATAGTTTTTTAAAACATTTTG
1 AAAATA-TATATAATATATAG-TTTTTAAAACATTTTG
*
1156113 AAAATAAATACATAATATATAGTTTTTAAAACATTTTG
1 AAAAT--ATATATAATATATAGTTTTTAAAACATTTTG
*
1156151 AAAATTTATATAATATATAGTTTTTAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
*
1156187 -AAATATATATAATATATAGTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
*
1156222 AATATATATATATATATATATATATATATAGTTTTGAAAACATTTTG
1 -------A-A-A-ATATATATA-ATATATAGTTTTTAAAACATTTTG
*
1156269 AAAAGTATATATAATATATAGTTTTTAAAATCGGTTTTG
1 AAAA-TATATATAATATATAGTTTTTAAAA-C-ATTTTG
* * *
1156308 AAAA-ACATATAATATATAATTTTTAAAATATTTT
1 AAAATATATATAATATATAGTTTTTAAAACATTTT
1156342 TTTGTTTTTG
Statistics
Matches: 369, Mismatches: 22, Indels: 56
0.83 0.05 0.13
Matches are distributed among these distances:
35 38 0.10
36 50 0.14
37 110 0.30
38 77 0.21
39 24 0.07
40 12 0.03
41 19 0.05
42 4 0.01
44 1 0.00
45 1 0.00
46 9 0.02
47 24 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTTAAAACATTTTG
Found at i:1156057 original size:75 final size:75
Alignment explanation
Indices: 1155845--1156341 Score: 530
Period size: 75 Copynumber: 6.5 Consensus size: 75
1155835 GAGTTTTTTT
* *
1155845 ATATATAATATTATCATATAGTTTTTTAAATAAATTTTTAAAAAAATATATATAATATATAGTTT
1 ATATAT-ATATAAT-ATATA-TTTTTTAAA-ACA-TTTT-AAAAAATATATATAATATATAGTTT
*
1155910 TTAAAACACTTTGAATA
60 TTAAAACATTTTGAA-A
* * ** *
1155927 TATATATATATATATATATAGTTTTTAAAACGTTTTTGAAAATATATATAATATATAGTTTTCAA
1 -ATATATATATA-ATATATATTTTTTAAAACATTTTAAAAAATATATATAATATATAGTTTTTAA
1155992 AACATTTT-AAA
64 AACATTTTGAAA
1156003 ATATATATATAATATATATTTTTTAAAACATTTTAAAAATATATATATAATATATAGTTTTTAAA
1 ATATATATATAATATATATTTTTTAAAACATTTTAAAAA-ATATATATAATATATAGTTTTTAAA
1156068 ACATTTTGAAA
65 ACATTTTGAAA
* *
1156079 A-AT-TATATACTATATAGTTTTTTAAAACATTTTGAAAATAA-ATACATAATATATAGTTTTTA
1 ATATATATATAATATATA-TTTTTTAAAACATTTT-AAAA-AATATATATAATATATAGTTTTTA
1156141 AAACATTTTGAAA
63 AAACATTTTGAAA
* * *
1156154 AT-T-TATATAATATATAGTTTTTAAAACATTTT--GAAATATATATAATATATAGTTTTGAAAA
1 ATATATATATAATATATATTTTTTAAAACATTTTAAAAAATATATATAATATATAGTTTTTAAAA
1156215 CATTTTGAATATA
66 CATTTTG-A-A-A
* *
1156228 TATATATATATATATATATATATAGTTTTGAAAACATTTTGAAAAGTATATATAATATATAGTTT
1 -ATATATATATA-ATATATAT-T--TTTT-AAAACATTTTAAAAAATATATATAATATATAGTTT
*
1156293 TTAAAATCGGTTTTG-AA
60 TTAAAA-C-ATTTTGAAA
* * *
1156310 A-A-ACATATAATATATAATTTTTAAAATATTTT
1 ATATATATATAATATATATTTTTTAAAACATTTT
1156342 TTTGTTTTTG
Statistics
Matches: 363, Mismatches: 28, Indels: 55
0.81 0.06 0.12
Matches are distributed among these distances:
70 2 0.01
71 30 0.08
72 1 0.00
73 1 0.00
74 61 0.17
75 113 0.31
76 11 0.03
77 10 0.03
78 47 0.13
79 11 0.03
80 2 0.01
81 13 0.04
82 20 0.06
83 9 0.02
84 26 0.07
85 1 0.00
86 5 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (75 bp):
ATATATATATAATATATATTTTTTAAAACATTTTAAAAAATATATATAATATATAGTTTTTAAAA
CATTTTGAAA
Found at i:1156230 original size:2 final size:2
Alignment explanation
Indices: 1156223--1156251 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1156213 AACATTTTGA
1156223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1156252 GTTTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1156255 original size:47 final size:46
Alignment explanation
Indices: 1156188--1156288 Score: 168
Period size: 47 Copynumber: 2.2 Consensus size: 46
1156178 AACATTTTGA
*
1156188 AATATATATAATATATAGTTTTGAAAACATTTTGAATA-TATATAT
1 AATATATATAATATATAGTTTTGAAAACATTTTGAAAAGTATATAT
1156233 ATATATATATATATATATAGTTTTGAAAACATTTTGAAAAGTATATAT
1 A-ATATATATA-ATATATAGTTTTGAAAACATTTTGAAAAGTATATAT
1156281 AATATATA
1 AATATATA
1156289 GTTTTTAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
45 1 0.02
46 9 0.17
47 34 0.65
48 8 0.15
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (46 bp):
AATATATATAATATATAGTTTTGAAAACATTTTGAAAAGTATATAT
Found at i:1156323 original size:82 final size:81
Alignment explanation
Indices: 1156157--1156327 Score: 233
Period size: 82 Copynumber: 2.1 Consensus size: 81
1156147 TTTGAAAATT
*
1156157 TATATAATATATAGTTTTTAAAACATTTTGAAATATATATAATATATAGTTTTGAAAACATTTTG
1 TATATAATATATAGTTTTGAAAACATTTTGAAATATATATAATATATAGTTTTGAAAACATTTTG
*
1156222 AATATATATATATATA
66 AATATATACATATATA
* *
1156238 TATATATATATATAGTTTTGAAAACATTTTGAAAAGTATATATAATATATAGTTTTTAAAATCGG
1 TATATA-ATATATAGTTTTGAAAACATTTTG-AAA-TATATATAATATATAGTTTTGAAAA-C-A
1156303 TTTTGAA-A-A-ACATATA-A
61 TTTTGAATATATACATATATA
1156320 TATATAAT
1 TATATAAT
1156328 TTTTAAAATA
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
81 8 0.10
82 30 0.37
83 9 0.11
84 25 0.31
85 2 0.02
86 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (81 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAATATATATAATATATAGTTTTGAAAACATTTTG
AATATATACATATATA
Found at i:1156474 original size:28 final size:26
Alignment explanation
Indices: 1156411--1156474 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
1156401 TTTGGAAATG
*
1156411 TAATATTATATATATTATTTTATTTTT
1 TAATATT-TTTATATTATTTTATTTTT
*
1156438 TATTATTTTTATATTATATCTTATTTATT
1 TAATATTTTTATATTAT-T-TTATTT-TT
1156467 TAAT-TTTT
1 TAATATTTT
1156475 CTTTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.29
27 7 0.23
28 10 0.32
29 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
TAATATTTTTATATTATTTTATTTTT
Found at i:1157720 original size:9 final size:8
Alignment explanation
Indices: 1157708--1157831 Score: 52
Period size: 9 Copynumber: 14.1 Consensus size: 8
1157698 AAATTTAACC
*
1157708 TTTTTAAT
1 TTTTTTAT
1157716 TTTTTTAT
1 TTTTTTAT
*
1157724 TTTTTTCGT
1 TTTTTT-AT
*
1157733 TTATTTA-
1 TTTTTTAT
*
1157740 TTTATTAT
1 TTTTTTAT
*
1157748 TTATTTAT
1 TTTTTTAT
*
1157756 TTATTTTCCT
1 TT-TTTT-AT
*
1157766 TTTTACTCAAT
1 TTTT--T-TAT
1157777 TTTATTTAT
1 TTT-TTTAT
1157786 CTTTATTTAT
1 -TTT-TTTAT
*
1157796 TTATTTAT
1 TTTTTTAT
*
1157804 CTATTTTAT
1 -TTTTTTAT
1157813 TTTATTTAT
1 TTT-TTTAT
1157822 TTTTATTAT
1 TTTT-TTAT
1157831 T
1 T
1157832 ATATTAATAT
Statistics
Matches: 87, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
7 5 0.06
8 29 0.33
9 34 0.39
10 13 0.15
11 5 0.06
12 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1157741 original size:4 final size:4
Alignment explanation
Indices: 1157732--1157823 Score: 64
Period size: 4 Copynumber: 21.8 Consensus size: 4
1157722 ATTTTTTTCG
**
1157732 TTTA TTTA TTTA -TTA TTTA TTTA TTTA TTT- TCCTT- TTTA CTCAA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T--TTA TTTA -TTTA -TTTA
*
1157781 TTTA TCTTTA TTTA TTTA TTTA TCTA TTTTA TTTTA TTTA TTT
1 TTTA --TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTT
1157824 TTATTATTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
3 6 0.08
4 48 0.66
5 15 0.21
6 4 0.05
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1157800 original size:18 final size:17
Alignment explanation
Indices: 1157716--1157849 Score: 82
Period size: 18 Copynumber: 7.5 Consensus size: 17
1157706 CCTTTTTAAT
1157716 TTTTTTATTT-TTT-TC
1 TTTTTTATTTATTTATC
1157731 GTTTATTTATTTA-TTAT-
1 -TTT-TTTATTTATTTATC
*
1157748 TTATTTATTTATTT-TCC
1 TTTTTTATTTATTTAT-C
1157765 TTTTTACTCAATTTTATTTATC
1 TTTTT--T--A-TTTATTTATC
1157787 TTTATTTATTTATTTATC
1 TTT-TTTATTTATTTATC
*
1157805 TATTTTATTTTATTTAT-
1 TTTTTTA-TTTATTTATC
* *
1157822 TTTTATTATTATATTAATA
1 TTTT-TTATT-TATTTATC
1157841 TTTTTTATT
1 TTTTTTATT
1157850 ATCTTTCCAT
Statistics
Matches: 96, Mismatches: 5, Indels: 32
0.72 0.04 0.24
Matches are distributed among these distances:
15 9 0.09
16 7 0.07
17 22 0.23
18 36 0.38
19 6 0.06
21 2 0.02
22 11 0.11
23 3 0.03
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (17 bp):
TTTTTTATTTATTTATC
Found at i:1157821 original size:40 final size:40
Alignment explanation
Indices: 1157732--1157836 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 40
1157722 ATTTTTTTCG
1157732 TTTATTTATTTATTATTTATTTATTTATTTTCCTTTTTAC
1 TTTATTTATTTATTATTTATTTATTTATTTTCCTTTTTAC
** * *
1157772 TCAATTTTATTTA-TCTTTATTTATTTATTTAT-CTATTTTAT
1 TTTA-TTTATTTATTATTTATTTATTTATTT-TCCT-TTTTAC
1157813 TTTATTTATTT-TTA-TTATTATATT
1 TTTATTTATTTATTATTTATT-TATT
1157837 AATATTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
39 5 0.09
40 32 0.60
41 16 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (40 bp):
TTTATTTATTTATTATTTATTTATTTATTTTCCTTTTTAC
Found at i:1157833 original size:21 final size:21
Alignment explanation
Indices: 1157791--1157851 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1157781 TTTATCTTTA
1157791 TTTATTTATTTATCTATT-TTAT
1 TTTATTTATTT-T-TATTATTAT
1157813 TTTATTTATTTTTATTATTAT
1 TTTATTTATTTTTATTATTAT
* *
1157834 ATTA-ATATTTTTTATTAT
1 TTTATTTA-TTTTTATTAT
1157852 CTTTCCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 6 0.17
21 18 0.51
22 11 0.31
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTATTTTTATTATTAT
Found at i:1157847 original size:36 final size:36
Alignment explanation
Indices: 1157775--1157849 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
1157765 TTTTTACTCA
* *
1157775 ATTTTATTTATCTTTATTTATTTATTTATCTATTTT
1 ATTTTATTTATCTTTATTTATTTATTAATATATTTT
* *
1157811 ATTTTATTTATTTTTA-TTATTATATTAATATTTTTT
1 ATTTTATTTATCTTTATTTATT-TATTAATATATTTT
1157847 ATT
1 ATT
1157850 ATCTTTCCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (36 bp):
ATTTTATTTATCTTTATTTATTTATTAATATATTTT
Found at i:1158985 original size:26 final size:26
Alignment explanation
Indices: 1158950--1158999 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1158940 ATTTCACTTT
*
1158950 TTTTAATTTAATTATTAATTTATTTG
1 TTTTAATTTAAATATTAATTTATTTG
* *
1158976 TTTTATTTTAAATATTATTTTATT
1 TTTTAATTTAAATATTAATTTATT
1159000 CTAAAAGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTAATTTAAATATTAATTTATTTG
Found at i:1163098 original size:17 final size:17
Alignment explanation
Indices: 1163066--1163195 Score: 93
Period size: 17 Copynumber: 7.5 Consensus size: 17
1163056 ATGTTTACAA
1163066 TTATCAAATGATTTTCAG
1 TTATCAAAT-ATTTTCAG
*
1163084 TTATCAAATATTTTCAC
1 TTATCAAATATTTTCAG
* * *
1163101 ATATCATATGATTTTAAG
1 TTATCAAAT-ATTTTCAG
* *
1163119 TTATCATATATTTACAG
1 TTATCAAATATTTTCAG
* *
1163136 ATATCAAATGA-TTACAG
1 TTATCAAAT-ATTTTCAG
* *
1163153 TTATCAGATATTTACA-
1 TTATCAAATATTTTCAG
* *
1163169 TATATCAGATGTTTTACAG
1 T-TATCAAATATTTT-CAG
1163188 TTATCAAA
1 TTATCAAA
1163196 CACAGATTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.02
17 56 0.62
18 32 0.35
19 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (17 bp):
TTATCAAATATTTTCAG
Found at i:1163106 original size:35 final size:35
Alignment explanation
Indices: 1163054--1163195 Score: 155
Period size: 35 Copynumber: 4.1 Consensus size: 35
1163044 GATGAATTCT
*
1163054 AAATGTTTACA-ATTATCAAATGATTTTCAGTTATC
1 AAATATTTACACA-TATCAAATGATTTTCAGTTATC
* * *
1163089 AAATATTTTCACATATCATATGATTTTAAGTTATC
1 AAATATTTACACATATCAAATGATTTTCAGTTATC
* * *
1163124 ATATATTTACAGATATCAAATGA-TTACAGTTATC
1 AAATATTTACACATATCAAATGATTTTCAGTTATC
* * *
1163158 AGATATTTACATATATCAGATG-TTTTACAGTTATC
1 AAATATTTACACATATCAAATGATTTT-CAGTTATC
1163193 AAA
1 AAA
1163196 CACAGATTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
34 30 0.34
35 58 0.65
36 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (35 bp):
AAATATTTACACATATCAAATGATTTTCAGTTATC
Found at i:1163164 original size:69 final size:70
Alignment explanation
Indices: 1163059--1163193 Score: 186
Period size: 69 Copynumber: 1.9 Consensus size: 70
1163049 ATTCTAAATG
* * *
1163059 TTTACAATTATCAAATGATTTTCAGTTATCAAATATTTTCACATATCATATGATTTTA-AGTTAT
1 TTTACAATTATCAAATGATTTACAGTTATCAAATATTTACACATATCAGATG-TTTTACAGTTAT
1163123 CATATA
65 CATATA
* *
1163129 TTTACAGA-TATCAAATGA-TTACAGTTATCAGATATTTACATATATCAGATGTTTTACAGTTAT
1 TTTACA-ATTATCAAATGATTTACAGTTATCAAATATTTACACATATCAGATGTTTTACAGTTAT
1163192 CA
65 CA
1163194 AACACAGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
68 5 0.09
69 36 0.62
70 16 0.28
71 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (70 bp):
TTTACAATTATCAAATGATTTACAGTTATCAAATATTTACACATATCAGATGTTTTACAGTTATC
ATATA
Found at i:1169947 original size:35 final size:35
Alignment explanation
Indices: 1169903--1169992 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
1169893 TACATTTATT
* * *
1169903 AGATAATTTTCAGTTATCATATATTTACGGATATC
1 AGATGATTTTCAGTTATCATATATTTACAGATATA
* * *
1169938 ATATGATTTTTAGTTATCAAATATTTACAGATATA
1 AGATGATTTTCAGTTATCATATATTTACAGATATA
*
1169973 AGATGA-TTACAGTTATCATA
1 AGATGATTTTCAGTTATCATA
1169993 CGTGCATCTA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 11 0.24
35 34 0.76
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (35 bp):
AGATGATTTTCAGTTATCATATATTTACAGATATA
Found at i:1171005 original size:37 final size:37
Alignment explanation
Indices: 1170948--1171052 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1170938 CCTTTTCGTC
*
1170948 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1170985 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * *
1171022 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1171053 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1171498 original size:23 final size:23
Alignment explanation
Indices: 1171470--1171516 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1171460 TATATGTATA
1171470 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
1171493 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
1171516 T
1 T
1171517 TTCTTTACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:1171774 original size:24 final size:22
Alignment explanation
Indices: 1171744--1171799 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1171734 CTATTTAATA
1171744 TTTTATTATATTATACATACATT
1 TTTTATTAT-TTATACATACATT
* *
1171767 TTTATATT-TTTATATATATATT
1 TTT-TATTATTTATACATACATT
1171789 TTTTATTATTT
1 TTTTATTATTT
1171800 TATTTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTATACATACATT
Found at i:1171779 original size:22 final size:21
Alignment explanation
Indices: 1171744--1171822 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 21
1171734 CTATTTAATA
1171744 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
1171767 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
**
1171789 TTTTATTATTTTATTTATACTATT
1 TTTTA-T-TTTTATACATAC-ATT
1171813 TATTTATTTT
1 T-TTTATTTT
1171823 CATTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 17 0.36
24 9 0.19
25 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:1171795 original size:21 final size:21
Alignment explanation
Indices: 1171765--1171834 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
1171755 TATACATACA
1171765 TTTTTATATTTTTATATATATAT
1 TTTTTATA-TTTTAT-TATATAT
1171788 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTTA-TTATA-TAT
*
1171812 TTATTTAT-TTTCATTATAT-T
1 TT-TTTATATTTTATTATATAT
1171832 TTT
1 TTT
1171835 AGTTTCTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 1 0.02
22 5 0.12
23 19 0.45
24 9 0.21
25 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTATTATATAT
Found at i:1171830 original size:45 final size:44
Alignment explanation
Indices: 1171744--1171834 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
1171734 CTATTTAATA
*
1171744 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-TT
* **
1171789 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATTT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTT
1171833 TT
1 TT
1171835 AGTTTCTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 22 0.55
46 12 0.30
47 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (44 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATTT
Found at i:1171831 original size:28 final size:27
Alignment explanation
Indices: 1171775--1171832 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1171765 TTTTTATATT
* *
1171775 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
1171802 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
1171830 TTT
1 TTT
1171833 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:1171943 original size:15 final size:15
Alignment explanation
Indices: 1171925--1171954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1171915 ATCTTCATTT
1171925 ATTTTATTTTATTCA
1 ATTTTATTTTATTCA
*
1171940 ATTTTATTTTTTTCA
1 ATTTTATTTTATTCA
1171955 TCAATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTATTCA
Found at i:1176936 original size:22 final size:22
Alignment explanation
Indices: 1176908--1176961 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
1176898 CTACCCCATC
1176908 AAACCTTTGAGCATCAAATGCT
1 AAACCTTTGAGCATCAAATGCT
1176930 AAACCTTTGAGCATCAAATGCT
1 AAACCTTTGAGCATCAAATGCT
1176952 AAACCTTTGA
1 AAACCTTTGA
1176962 CCAAACACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (22 bp):
AAACCTTTGAGCATCAAATGCT
Found at i:1178051 original size:106 final size:106
Alignment explanation
Indices: 1177923--1179197 Score: 1967
Period size: 106 Copynumber: 12.0 Consensus size: 106
1177913 ATATCGTGCC
* * * *
1177923 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1177988 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1178029 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCTCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1178094 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1178135 ACTCCAGACAACGCAAGTTCAACTTCACGACGAACGAACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1178200 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1178241 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCGC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1178306 AATTTCAAACCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1178347 ACTCCAGACAACGCAAGTTTAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1178412 AATTTCAGAACCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1178453 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1178518 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1178559 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1178624 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1178665 ACTCTATACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1178730 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1178771 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1178836 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1178877 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1178942 AATTTCATAGCCAATTTCAACTTCACAGCAAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1178983 ACTCGAGACAACGCAAGTTCAACGTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1179048 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1179089 AATCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * * * * *
1179153 CGATTCCAGAGCCAATTTTAACTTCACGACGGAGCATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1179195 ACT
1 ACT
1179198 TGGAACAATG
Statistics
Matches: 1076, Mismatches: 92, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 2 0.00
106 1074 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Done.