Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002875.1 Hibiscus syriacus cultivar Beakdansim tig00005929_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: 1473696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:987691 original size:17 final size:16
Alignment explanation
Indices: 987631--987698 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 16
987621 TTTATGAATT
987631 CAAATGTTAAATTTTAA
1 CAAAT-TTAAATTTTAA
987648 CAAATTTAAATAATTTATGAA
1 CAAATTT--A-AATTT-T-AA
987669 TTCAAATGTTAAATTTTAA
1 --CAAAT-TTAAATTTTAA
987688 CAAATTTAAAT
1 CAAATTTAAAT
987699 ATAAAAGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
16 8 0.19
17 10 0.23
18 1 0.02
19 7 0.16
20 2 0.05
21 7 0.16
22 1 0.02
23 5 0.12
24 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (16 bp):
CAAATTTAAATTTTAA
Found at i:1003753 original size:2 final size:2
Alignment explanation
Indices: 1003746--1003773 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1003736 CAACTCAGTT
1003746 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
1003774 ACATAGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1010088 original size:60 final size:60
Alignment explanation
Indices: 1009982--1010094 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1009972 GTCAGATAAT
* * * *
1009982 CATTTTGTAACTTTTAATAGAGGAGTGACTTAACAAAGCAACACTCTGTAGTCGAATGAC
1 CATTTTATAACTTTTAATAGAGAAGTGACTTAACAAAACAACACTCTATAGTCGAATGAC
* * * *
1010042 CATTTTATAACTTTTAATAGTCGAAG-GAGTTAATAAAACAATACTCTATAGTC
1 CATTTTATAACTTTTAATAG-AGAAGTGACTTAACAAAACAACACTCTATAGTC
1010095 AGGGGACCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 41 0.93
61 3 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGAGAAGTGACTTAACAAAACAACACTCTATAGTCGAATGAC
Found at i:1023179 original size:53 final size:53
Alignment explanation
Indices: 1023116--1023223 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 53
1023106 TATTCTCGTA
* *
1023116 CGCTGTTGGTAGATGCAATGCTTATTAG-TACTTAATATTAGCTTACAATTAAC
1 CGCTGTTGGTAGATACAATGCTTATTAGAT-CTTAACATTAGCTTACAATTAAC
* *
1023169 CGCTGTTGGTAGGTACAATGTTTATTAGATCTTAACATTAGCTTACAATTAAC
1 CGCTGTTGGTAGATACAATGCTTATTAGATCTTAACATTAGCTTACAATTAAC
1023222 CG
1 CG
1023224 AACAGTTATG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 49 0.98
54 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (53 bp):
CGCTGTTGGTAGATACAATGCTTATTAGATCTTAACATTAGCTTACAATTAAC
Found at i:1027083 original size:29 final size:29
Alignment explanation
Indices: 1027027--1027083 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1027017 AAAATTTAAC
*
1027027 TTTTGAAAAATTAATAAAAGACACTTTTT
1 TTTTGAAAAATTAATAAAAGAAACTTTTT
*
1027056 TTTTGAAAAGTTAATAAAAGAAA-TTTTT
1 TTTTGAAAAATTAATAAAAGAAACTTTTT
1027084 AATGGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTGAAAAATTAATAAAAGAAACTTTTT
Found at i:1036379 original size:30 final size:30
Alignment explanation
Indices: 1036337--1036425 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
1036327 TAAACCACTT
* * *
1036337 AAATAAATTTAATATTTTATTTTTAATTAA
1 AAATGAATTTAATATTTTATTTTAAATAAA
* * * *
1036367 ACAT-TATATTAATGTTATATTTTAAATAAA
1 AAATGAAT-TTAATATTTTATTTTAAATAAA
1036397 AAATGAATTTAATATTTTA-TTTAAATAAA
1 AAATGAATTTAATATTTTATTTTAAATAAA
1036426 TACCGTATAG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (30 bp):
AAATGAATTTAATATTTTATTTTAAATAAA
Found at i:1039660 original size:13 final size:13
Alignment explanation
Indices: 1039642--1039667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1039632 ATACGGAATC
1039642 TTCCTAAAATTCG
1 TTCCTAAAATTCG
1039655 TTCCTAAAATTCG
1 TTCCTAAAATTCG
1039668 GAATCTTCCT
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
TTCCTAAAATTCG
Found at i:1043258 original size:15 final size:15
Alignment explanation
Indices: 1043240--1043269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1043230 AAAACCATGT
1043240 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
*
1043255 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
1043270 GAAATAAATA
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:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1043426 original size:28 final size:28
Alignment explanation
Indices: 1043358--1043428 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1043348 ATAGTAAGTA
*
1043358 AAATAAATTAAAAAATAAAGAAAAAGAAG
1 AAATAAA-TAAAAAATAAAGAAAAAGAAC
* *
1043387 AAA-AAGAAAAAAAATATAGAAATAA-AAC
1 AAATAA-ATAAAAAATAAAGAAA-AAGAAC
1043415 AAATAAATAAAAAA
1 AAATAAATAAAAAA
1043429 AGTAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.79, C:0.01, G:0.07, T:0.13
Consensus pattern (28 bp):
AAATAAATAAAAAATAAAGAAAAAGAAC
Found at i:1043451 original size:30 final size:29
Alignment explanation
Indices: 1043417--1043479 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
1043407 AATAAAACAA
* * *
1043417 ATAAATAAAAAAAGTAAAAATAATATATAT
1 ATAAATAAAAAAA-TAAAAAAAGTAAATAT
1043447 ATAAAATAAAAAAATAAAAAAAGTAAATAT
1 ATA-AATAAAAAAATAAAAAAAGTAAATAT
1043477 ATA
1 ATA
1043480 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (29 bp):
ATAAATAAAAAAATAAAAAAAGTAAATAT
Found at i:1043451 original size:39 final size:39
Alignment explanation
Indices: 1043378--1043489 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 39
1043368 AAAAATAAAG
* * * *
1043378 AAAAAGAAGAAAAAG-AAAAAAAATATAGAAATAAAACAA
1 AAAAATAA-AAAAAGTAAAAATAATATATATATAAAACAA
* *
1043417 ATAAATAAAAAAAGTAAAAATAATATATATATAAAATAA
1 AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
*
1043456 AAAAATAAAAAAAGTAAATATATATATATATATA
1 AAAAATAAAAAAAGTAAAAATA-ATATATATATA
1043490 TATATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 6 0.10
39 46 0.73
40 11 0.17
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (39 bp):
AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
Found at i:1043478 original size:2 final size:2
Alignment explanation
Indices: 1043473--1043499 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1043463 AAAAAAGTAA
1043473 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
1043500 AATTAATAAA
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:1043565 original size:26 final size:25
Alignment explanation
Indices: 1043536--1043593 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
1043526 ATATATTTAT
1043536 ATATATAATCTAAAATAAAAATA-AAA
1 ATATATAA-CTAAAATAAAAA-AGAAA
*
1043562 ATATAT-ACTAAAGTAAAAAAGAAA
1 ATATATAACTAAAATAAAAAAGAAA
1043586 ATATATAA
1 ATATATAA
1043594 AATGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 20 0.69
25 2 0.07
26 6 0.21
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (25 bp):
ATATATAACTAAAATAAAAAAGAAA
Found at i:1043591 original size:24 final size:23
Alignment explanation
Indices: 1043536--1043606 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
1043526 ATATATTTAT
*
1043536 ATATATAATCTAAAATAAAAATAAAA
1 ATATAT-A-CTAAAGTAAAAA-AAAA
1043562 ATATATACTAAAGTAAAAAAGAAA
1 ATATATACTAAAGTAAAAAA-AAA
1043586 ATATATA--AAATGTAAAAAAAA
1 ATATATACTAAA-GTAAAAAAAA
1043607 TATTACATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 5 0.12
23 9 0.21
24 21 0.50
25 1 0.02
26 6 0.14
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (23 bp):
ATATATACTAAAGTAAAAAAAAA
Found at i:1043989 original size:34 final size:34
Alignment explanation
Indices: 1043946--1044014 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1043936 GAATCCTAGC
1043946 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
1043980 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1044014 A
1 A
1044015 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:1044779 original size:98 final size:98
Alignment explanation
Indices: 1044610--1044868 Score: 277
Period size: 98 Copynumber: 2.6 Consensus size: 98
1044600 TGGAACCGGA
* * * *
1044610 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
* * * *
1044675 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 ATATCCTCCGCTGTGAAGTTAAAATTGGCTCCG
** * * * *
1044708 AAATTATTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTTTTGGGTCCA
1 AAATTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
1044773 ATATCCTCCGCTGTGAAGTTAAAATTGGC-CCTG
66 ATATCCTCCGCTGTGAAGTTAAAATTGGCTCC-G
* * * *
1044806 AAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAA-T----TA-T-TTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTC
1044869 ATAGGTAGCA
Statistics
Matches: 131, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
97 2 0.02
98 84 0.64
99 1 0.01
103 1 0.01
104 1 0.01
105 42 0.32
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (98 bp):
AAATTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
ATATCCTCCGCTGTGAAGTTAAAATTGGCTCCG
Found at i:1045707 original size:31 final size:31
Alignment explanation
Indices: 1045672--1045800 Score: 75
Period size: 31 Copynumber: 3.9 Consensus size: 31
1045662 AGGAAATAAA
1045672 CTCAAAG-ATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAACT-T
** * *
1045703 CTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACAAT
1 CTCAA---AG--AATTTTGTGTTTCAAGAGAAAC-TT
*
1045739 CTCAAAG-GTTTTGTGTTTCAAGAGAAACATT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAAC-TT
* **
1045770 TTCAAAGGTTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAA-G-AATTTTGTGTTTCAAGAGAAAC
1045801 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
30 2 0.03
31 26 0.34
32 1 0.01
33 2 0.03
34 22 0.29
36 20 0.26
37 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (31 bp):
CTCAAAGAATTTTGTGTTTCAAGAGAAACTT
Found at i:1045759 original size:67 final size:67
Alignment explanation
Indices: 1045574--1045766 Score: 233
Period size: 67 Copynumber: 2.8 Consensus size: 67
1045564 GTCTTAAAAA
** * * * * *
1045574 AGACAAAATTCATTTCAATGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAAGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
1045639 AGGG
64 AGGG
* * * * *
1045643 AGACAAAATTTTGTTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
1 AGACAAAA-TTTGTTTCAAAGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAA
1045708 GGG
65 GGG
* *
1045711 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAAGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
1045767 ATTTTCAAAG
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 43 0.41
68 31 0.29
69 11 0.10
70 21 0.20
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAAGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:1045827 original size:36 final size:34
Alignment explanation
Indices: 1045721--1045836 Score: 166
Period size: 34 Copynumber: 3.4 Consensus size: 34
1045711 AGACAAAATT
* *
1045721 TGTTTCAAGGGAAACAATCTCAAAGG---TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
*
1045752 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
1045786 TGTTTCAAGAGAAACAATTTCAAAGGTTTGTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TT-TTTTTG
1045822 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1045837 TGTATCAAGG
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.30
34 30 0.39
35 2 0.03
36 21 0.28
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
Found at i:1046641 original size:21 final size:21
Alignment explanation
Indices: 1046597--1046641 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1046587 TGATTCTGGG
* * *
1046597 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1046618 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1046639 CAA
1 CAA
1046642 ACGAACATAG
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:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1047406 original size:31 final size:31
Alignment explanation
Indices: 1047368--1047433 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1047358 TCGAGGGTTT
**
1047368 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
1047399 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
1047430 TACC
1 TACC
1047434 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:1047576 original size:29 final size:30
Alignment explanation
Indices: 1047421--1047580 Score: 232
Period size: 30 Copynumber: 5.3 Consensus size: 30
1047411 AAGGAACATA
1047421 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
1047452 TGGACAGTTTACCGAGGATCTTTAAGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1047483 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1047513 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
1047543 TGGATAGTTATCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1047572 TGGATAGTT
1 TGGACAGTT
1047581 CCTTCAGGAC
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 22 0.18
30 63 0.52
31 37 0.30
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1050842 original size:21 final size:21
Alignment explanation
Indices: 1050798--1050842 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1050788 TGATTCTGGG
* * *
1050798 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1050819 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1050840 CAA
1 CAA
1050843 ACGAACATAG
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:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1051697 original size:30 final size:30
Alignment explanation
Indices: 1051622--1051776 Score: 240
Period size: 30 Copynumber: 5.1 Consensus size: 30
1051612 AAGGAACATA
1051622 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
1051653 TGGACAGTTTACCGAGGATCTTTAAGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1051684 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1051714 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1051744 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1051773 TGGA
1 TGGA
1051777 TAGGTCCTTC
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
29 17 0.14
30 64 0.54
31 37 0.31
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1052550 original size:36 final size:36
Alignment explanation
Indices: 1052450--1052795 Score: 140
Period size: 36 Copynumber: 10.1 Consensus size: 36
1052440 GGGGTGTTAC
* *
1052450 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAG
1 AGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAG
* * *
1052487 AAAAACATGTCTTAAGATAGACAAAATTTGTTTCAAG
1 AGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAG
*
1052524 AGAAACTGTCTCAAGAGAGACGAAATTTGTTT-AATG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-G
* *
1052560 TA-AAACATAT-TC-A-A-AG----ATTTTGTTTCAAG
1 -AGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAG
* * * *
1052589 GGAAACTGTTTTC-A-A-AG-----TTTATGTTTCAAT
1 AGAAACTG-TCTCAAGAGAGACAAAATT-TGTTTCAAG
*
1052619 AAAAACTGTCTCAA-AGGAGACAAAATTTGTTTCAAG
1 AGAAACTGTCTCAAGA-GAGACAAAATTTGTTTCAAG
* * **
1052655 GGAAACTATCTCAAGAGAGACAAAATTCATTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
* * * *
1052691 GGAAA-TGTTTTC-A-A-TG-----TTTATGTTTCAAG
1 AGAAACTG-TCTCAAGAGAGACAAAATT-TGTTTCAAG
* *
1052720 AGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAG
* * *
1052757 GGAAACTATCTCAAGAGAGAC--AATTTATTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
*
1052791 GGAAA
1 AGAAA
1052796 TGCTTTCAAT
Statistics
Matches: 239, Mismatches: 40, Indels: 63
0.70 0.12 0.18
Matches are distributed among these distances:
28 3 0.01
29 34 0.14
30 27 0.11
32 3 0.01
33 3 0.01
34 17 0.07
35 7 0.03
36 75 0.31
37 52 0.22
38 18 0.08
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (36 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
Found at i:1052625 original size:30 final size:30
Alignment explanation
Indices: 1052569--1052627 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1052559 GTAAAACATA
**
1052569 TTCAAAGATTTTGTTTCAAGGGAAACTGTT
1 TTCAAAGATTTTGTTTCAAGAAAAACTGTT
*
1052599 TTCAAAG-TTTATGTTTCAATAAAAACTGT
1 TTCAAAGATTT-TGTTTCAAGAAAAACTGT
1052628 CTCAAAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (30 bp):
TTCAAAGATTTTGTTTCAAGAAAAACTGTT
Found at i:1052773 original size:102 final size:102
Alignment explanation
Indices: 1052582--1052884 Score: 450
Period size: 102 Copynumber: 3.0 Consensus size: 102
1052572 AAAGATTTTG
* * * *
1052582 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAAAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1052646 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1052684 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
1052749 GTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * *
1052784 TTTCAAGGGAAATGCTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
1052849 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1052885 CTTGTTTTAA
Statistics
Matches: 183, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
100 62 0.34
101 47 0.26
102 71 0.39
104 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1052793 original size:34 final size:36
Alignment explanation
Indices: 1052713--1052795 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
1052703 AATGTTTATG
* * * * *
1052713 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTTTA
1052750 TTTCAAGGGAAACTATCTCAAGAGAGAC-AA-TTTA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAATTTTA
1052784 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1052796 TGCTTTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 15 0.37
35 2 0.05
37 24 0.59
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAATTTTA
Found at i:1054381 original size:183 final size:183
Alignment explanation
Indices: 1054073--1054426 Score: 654
Period size: 183 Copynumber: 1.9 Consensus size: 183
1054063 ATCAGGTTTA
1054073 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
1054138 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
1054203 TTCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
1054256 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
1054321 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1054386 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1054427 CGGATTTAAT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1057293 original size:53 final size:53
Alignment explanation
Indices: 1057226--1057331 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1057216 AACACCTTTT
1057226 CAGGGATCAGTAACCTCTTGTTATGATGCAAAATGCTCTAAAACAAACACAAA
1 CAGGGATCAGTAACCTCTTGTTATGATGCAAAATGCTCTAAAACAAACACAAA
1057279 CAGGGATCAGTAACCTCTTGTTATGATGCAAAATGCTCTAAAACAAACACAAA
1 CAGGGATCAGTAACCTCTTGTTATGATGCAAAATGCTCTAAAACAAACACAAA
1057332 GGCAAAAAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (53 bp):
CAGGGATCAGTAACCTCTTGTTATGATGCAAAATGCTCTAAAACAAACACAAA
Found at i:1058257 original size:15 final size:15
Alignment explanation
Indices: 1058239--1058268 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1058229 AAAACCATGT
1058239 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1058254 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1058269 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1058275 original size:15 final size:15
Alignment explanation
Indices: 1058242--1058276 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1058232 ACCATGTTAG
* *
1058242 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1058257 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1058272 ATAAA
1 ATAAA
1058277 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1058393 original size:21 final size:20
Alignment explanation
Indices: 1058367--1058422 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1058357 AAATAAATAT
*
1058367 AAAAAATAAAGAAAAAGAAGA
1 AAAAAATAAAGAAAAA-AACA
*
1058388 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAA-AAAACA
*
1058409 AATAAATAAA-AAAA
1 AAAAAATAAAGAAAA
1058423 GTAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 3 0.10
21 24 0.80
22 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (20 bp):
AAAAAATAAAGAAAAAAACA
Found at i:1058403 original size:38 final size:39
Alignment explanation
Indices: 1058361--1058436 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
1058351 TAAGTAAAAT
1058361 AAATATAAA-AAATAAAGAAAAAGAAG-AAAAA-AATATAG
1 AAATA-AAACAAATAAAGAAAAA-AAGTAAAAATAATATAG
*
1058399 AAATAAAACAAATAAATAAAAAAAGTAAAAATAATATA
1 AAATAAAACAAATAAAGAAAAAAAGTAAAAATAATATA
1058437 TATATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 6 0.18
38 22 0.65
39 6 0.18
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (39 bp):
AAATAAAACAAATAAAGAAAAAAAGTAAAAATAATATAG
Found at i:1058427 original size:13 final size:12
Alignment explanation
Indices: 1058356--1058467 Score: 59
Period size: 13 Copynumber: 9.1 Consensus size: 12
1058346 AATAGTAAGT
1058356 AAAATAAATATAA
1 AAAATAAATA-AA
*
1058369 AAAATAAAGAAA
1 AAAATAAATAAA
*
1058381 AAGAAGAAA-AAA
1 AA-AATAAATAAA
* *
1058393 ATATAGAAATAAA
1 A-AAATAAATAAA
1058406 ACAAATAAATAAA
1 A-AAATAAATAAA
*
1058419 AAAAGTAAA-AAT
1 AAAA-TAAATAAA
* * *
1058431 AATATATATATA
1 AAAATAAATAAA
* *
1058443 TATATATAATAAA
1 AAAATA-AATAAA
1058456 AAAATAAA-AAA
1 AAAATAAATAAA
1058467 A
1 A
1058468 GTAAATATAT
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
11 7 0.09
12 29 0.38
13 41 0.53
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:1058550 original size:26 final size:25
Alignment explanation
Indices: 1058521--1058578 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
1058511 ATATATTTAT
1058521 ATATATAATCTAAAATAAAAATA-AAA
1 ATATATAA-CTAAAATAAAAA-AGAAA
*
1058547 ATATAT-ACTAAAGTAAAAAAGAAA
1 ATATATAACTAAAATAAAAAAGAAA
*
1058571 ATACATAA
1 ATATATAA
1058579 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 1 0.04
24 19 0.68
25 2 0.07
26 6 0.21
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.24
Consensus pattern (25 bp):
ATATATAACTAAAATAAAAAAGAAA
Found at i:1058598 original size:23 final size:22
Alignment explanation
Indices: 1058543--1058604 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1058533 AAATAAAAAT
1058543 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
1058564 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
1058587 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
1058605 AAAAATAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:1058962 original size:34 final size:34
Alignment explanation
Indices: 1058919--1058987 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
1058909 GAATCCTAGC
1058919 AAAATTCTA-TCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATTC-TATCTTTAGGAGTTTGAATCCT
*
1058953 AAAATTCTATTCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATTCTATCTTTAGGAGTTTGAATCCT
1058987 A
1 A
1058988 GTGGGACGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 31 0.94
35 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (34 bp):
AAAATTCTATTCTATCTTTAGGAGTTTGAATCCT
Found at i:1062772 original size:11 final size:11
Alignment explanation
Indices: 1062756--1062814 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
1062746 ATAATCGATG
1062756 ATTAAAATATA
1 ATTAAAATATA
*
1062767 ATTAAAATGTA
1 ATTAAAATATA
* *
1062778 ATATTAGATATA
1 AT-TAAAATATA
1062790 GATTAAAATATA
1 -ATTAAAATATA
* *
1062802 AATAAAATGTA
1 ATTAAAATATA
1062813 AT
1 AT
1062815 ATTAGATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 22 0.59
12 13 0.35
13 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (11 bp):
ATTAAAATATA
Found at i:1062794 original size:35 final size:35
Alignment explanation
Indices: 1062755--1062825 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1062745 AATAATCGAT
*
1062755 GATTAAAATATAATTAAAATGTAATATTAGATATA
1 GATTAAAATATAAATAAAATGTAATATTAGATATA
1062790 GATTAAAATATAAATAAAATGTAATATTAGATATA
1 GATTAAAATATAAATAAAATGTAATATTAGATATA
1062825 G
1 G
1062826 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (35 bp):
GATTAAAATATAAATAAAATGTAATATTAGATATA
Found at i:1067555 original size:26 final size:27
Alignment explanation
Indices: 1067501--1067571 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
1067491 ATATGATTAA
* *
1067501 AATAATAATAATAATTACTAATTTAAAT
1 AATAACAATAA-AATTACTAATGTAAAT
1067529 ATATAACAATAAAATTAC-AATGT-AAT
1 A-ATAACAATAAAATTACTAATGTAAAT
*
1067555 AAAAACAAATAAAATTA
1 AATAAC-AATAAAATTA
1067572 AAATTATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.11
26 14 0.37
27 4 0.11
28 7 0.18
29 9 0.24
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (27 bp):
AATAACAATAAAATTACTAATGTAAAT
Found at i:1068782 original size:3 final size:3
Alignment explanation
Indices: 1068767--1068837 Score: 81
Period size: 3 Copynumber: 23.3 Consensus size: 3
1068757 ATATTTAATT
*
1068767 TAA TAA TAT TAA TAA T-A TATA TATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA
** *
1068813 TAA TAA TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1068838 TTAAATAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.03
3 49 0.84
4 7 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1078977 original size:16 final size:16
Alignment explanation
Indices: 1078956--1078986 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1078946 TAAATTAAAC
*
1078956 TCTATATTTTTTCGTA
1 TCTATATTTGTTCGTA
1078972 TCTATATTTGTTCGT
1 TCTATATTTGTTCGT
1078987 TTACTGATAC
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:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (16 bp):
TCTATATTTGTTCGTA
Found at i:1083252 original size:29 final size:29
Alignment explanation
Indices: 1083219--1083274 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1083209 ATAATTAGGA
* *
1083219 GATCATTTTGTAACTTTTAATAGTTAAAT
1 GATCATTTTATAACTTTTAATAATTAAAT
1083248 GATCATTTTATAACTTTTAATAATTAA
1 GATCATTTTATAACTTTTAATAATTAA
1083275 GGACTCAAAA
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:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (29 bp):
GATCATTTTATAACTTTTAATAATTAAAT
Found at i:1087676 original size:2 final size:2
Alignment explanation
Indices: 1087664--1087700 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1087654 AATAATTCAT
1087664 TA TA T- 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
1087701 AATAAAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1096134 original size:21 final size:21
Alignment explanation
Indices: 1096108--1096152 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1096098 ACTGAGGGTC
1096108 AGCTTGTTGTAAATTAGGATA
1 AGCTTGTTGTAAATTAGGATA
1096129 AGCTTGTTGTAAATTAGGATA
1 AGCTTGTTGTAAATTAGGATA
1096150 AGC
1 AGC
1096153 AGTATCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (21 bp):
AGCTTGTTGTAAATTAGGATA
Found at i:1097786 original size:45 final size:45
Alignment explanation
Indices: 1097729--1097820 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
1097719 AGAGGATTTA
1097729 AAGAAATATTTCCATCACTAGCAGGGATGCTAAGAGGAACTGAAG
1 AAGAAATATTTCCATCACTAGCAGGGATGCTAAGAGGAACTGAAG
* *
1097774 AAGAAATGTTTCCATCACTAGCAGGGATGCTAGGAGGAACTGAAG
1 AAGAAATATTTCCATCACTAGCAGGGATGCTAAGAGGAACTGAAG
1097819 AA
1 AA
1097821 TCACCCTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (45 bp):
AAGAAATATTTCCATCACTAGCAGGGATGCTAAGAGGAACTGAAG
Found at i:1104870 original size:42 final size:42
Alignment explanation
Indices: 1104823--1104907 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1104813 CATCTGTTTG
1104823 GAATTTGATCGATAGACTTGTTACTACAATTGGAATTGCCGA
1 GAATTTGATCGATAGACTTGTTACTACAATTGGAATTGCCGA
1104865 GAATTTGATCGATAGACTTGTTACTACAATTGGAATTGCCGA
1 GAATTTGATCGATAGACTTGTTACTACAATTGGAATTGCCGA
1104907 G
1 G
1104908 GCATGTGGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (42 bp):
GAATTTGATCGATAGACTTGTTACTACAATTGGAATTGCCGA
Found at i:1113111 original size:35 final size:35
Alignment explanation
Indices: 1113064--1113177 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 35
1113054 AAAACAGTCA
* *
1113064 TCAATTTCATTCTAAACCCCAAATTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
1113099 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* *
1113134 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
1113169 TCAATTTAA
1 TCAATTTAA
1113178 GGTTTAGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1113217 original size:35 final size:35
Alignment explanation
Indices: 1113171--1113245 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1113161 AAAATACTTC
* * *
1113171 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
*
1113206 AATTTAGGGTTTAAAATGAAATTGAATTACTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
1113241 AATTT
1 AATTT
1113246 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
Found at i:1113249 original size:24 final size:24
Alignment explanation
Indices: 1113222--1113293 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
1113212 GGGTTTAAAA
1113222 TGAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
*
1113246 TGAACA-TGAATTTACTATTTAGAA---
1 TGAA-ATTGAA-TTAC--TTTGGAATTT
*
1113270 TAAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
1113294 GGGGTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
21 6 0.16
23 5 0.14
24 15 0.41
25 5 0.14
27 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (24 bp):
TGAAATTGAATTACTTTGGAATTT
Found at i:1114251 original size:174 final size:178
Alignment explanation
Indices: 1113950--1114301 Score: 660
Period size: 174 Copynumber: 2.0 Consensus size: 178
1113940 AACTAAATGT
1113950 ATTTAAGGGTCGACTACAATATTAATTACTTATGTTTATGTTATGTTCGTTTTTCCTTACTTATT
1 ATTTAAGGGTCGACTACAATATTAATTACTTATGTTTATGTTATGTTCGTTTTTCCTTACTTATT
1114015 TCAAAAAACATAACATGTGGTCATTTTTATTTTTAGTTAATCGAAGCATGATCACTTTCATTTTT
66 TCAAAAAACATAACATGTGGTCATTTTTATTTTTAGTTAATCGAAGCATGATCACTTTCATTTTT
1114080 ATTTAATTAATATGTGGTCACCACATGTTAGCTGTCGTTAACAGTTAA
131 ATTTAATTAATATGTGGTCACCACATGTTAGCTGTCGTTAACAGTTAA
1114128 ATTTAAGGGGTCGACTAC-A-A-T-ATTACTTATGTTTATGTTATGTTCG-TTTTCCTTACTTAT
1 ATTTAA-GGGTCGACTACAATATTAATTACTTATGTTTATGTTATGTTCGTTTTTCCTTACTTAT
1114188 TTCAAAAAACATAACATGTGGTCATTTTTATTTTTAGTTAATCGAAGCATGATCACTTTCATTTT
65 TTCAAAAAACATAACATGTGGTCATTTTTATTTTTAGTTAATCGAAGCATGATCACTTTCATTTT
1114253 TATTTAATTAATATGTGGTCACCACATGTTAGCTGTCGTTAACAGTTAA
130 TATTTAATTAATATGTGGTCACCACATGTTAGCTGTCGTTAACAGTTAA
1114302 CATATTAGGT
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
174 128 0.74
175 25 0.14
176 1 0.01
177 1 0.01
178 7 0.04
179 11 0.06
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (178 bp):
ATTTAAGGGTCGACTACAATATTAATTACTTATGTTTATGTTATGTTCGTTTTTCCTTACTTATT
TCAAAAAACATAACATGTGGTCATTTTTATTTTTAGTTAATCGAAGCATGATCACTTTCATTTTT
ATTTAATTAATATGTGGTCACCACATGTTAGCTGTCGTTAACAGTTAA
Found at i:1114802 original size:8 final size:8
Alignment explanation
Indices: 1114789--1114839 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
1114779 TTATAATAAT
1114789 TATTATTA
1 TATTATTA
1114797 TATTATTA
1 TATTATTA
1114805 TATTATAATA
1 TATTAT--TA
1114815 TATTATTAA
1 TATTATT-A
*
1114824 TAATATTAA
1 TATTATT-A
1114833 TATTATT
1 TATTATT
1114840 TATGTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
8 15 0.39
9 15 0.39
10 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTATTA
Found at i:1114810 original size:28 final size:27
Alignment explanation
Indices: 1114770--1114838 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
1114760 CCGGATTATA
*
1114770 AATATTATGTTATAATA-ATTATTATTAT
1 AATATTATATTATAATATATTATTA--AT
*
1114798 ATTATTATATTATAATATATTATTAAT
1 AATATTATATTATAATATATTATTAAT
1114825 AATATTAATATTAT
1 AATATT-ATATTAT
1114839 TTATGTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 7 0.19
28 22 0.61
29 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATATTATATTATAATATATTATTAAT
Found at i:1114828 original size:14 final size:14
Alignment explanation
Indices: 1114764--1114829 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
1114754 TTTTGTCCGG
* *
1114764 ATTATAAATATTAT
1 ATTATTAATAATAT
*
1114778 GTTA-TAATAAT-T
1 ATTATTAATAATAT
1114790 ATTATT-AT-AT-T
1 ATTATTAATAATAT
*
1114801 ATTATATTATAATAT
1 ATTAT-TAATAATAT
1114816 ATTATTAATAATAT
1 ATTATTAATAATAT
1114830 TAATATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
11 8 0.19
12 7 0.17
13 8 0.19
14 13 0.31
15 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
ATTATTAATAATAT
Found at i:1114837 original size:33 final size:27
Alignment explanation
Indices: 1114764--1114842 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 27
1114754 TTTTGTCCGG
1114764 ATTATAAATATTATGTTATAATAATTATT
1 ATTAT-AATATTAT-TTATAATAATTATT
*
1114793 ATTATATTATTATATTATAATATATTATT
1 ATTATAATATTAT-TTATAATA-ATTATT
1114822 AATAATATTAATATTATTTAT
1 -AT--TA-TAATATTATTTAT
1114843 GTTTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 15 0.36
29 11 0.26
30 2 0.05
32 6 0.14
33 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTATAATATTATTTATAATAATTATT
Found at i:1117682 original size:3 final size:3
Alignment explanation
Indices: 1117674--1117705 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1117664 CTTATGAACT
1117674 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1117706 TTAACAGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1123700 original size:60 final size:61
Alignment explanation
Indices: 1123623--1123741 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 61
1123613 AGTTGAGTGA
* *
1123623 TCATTTTATAATGTTTAATAGTCGAAGGACTCAACAAAGCAACACTCTATAGTT-GGAGGG
1 TCATTTTATAATGTTTAACAGTAGAAGGACTCAACAAAGCAACACTCTATAGTTAGGAGGG
* * * * * * *
1123683 TCATTTTGTAACT-TTTAACATTATAAGGACTTAATAAATCAATACTCTATAGTTAGGAG
1 TCATTTTATAA-TGTTTAACAGTAGAAGGACTCAACAAAGCAACACTCTATAGTTAGGAG
1123742 ACCATTTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (61 bp):
TCATTTTATAATGTTTAACAGTAGAAGGACTCAACAAAGCAACACTCTATAGTTAGGAGGG
Found at i:1123748 original size:60 final size:59
Alignment explanation
Indices: 1123647--1123760 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 59
1123637 TTAATAGTCG
**
1123647 AAGGACTCAACAAAGCAACACTCTATAGTTGGAGGGTCATTT-TGTAACTTTTAACATTAT
1 AAGGACTCAACAAAGCAACACTCTATAGTTGGAGGACCATTTGTGT-A-TTTTAACATTAT
* * * *
1123707 AAGGACTTAATAAATCAATACTCTATAGTTAGGA-GACCATTTGTGTATTTTAAC
1 AAGGACTCAACAAAGCAACACTCTATAGTT-GGAGGACCATTTGTGTATTTTAAC
1123761 CAAAATATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
59 7 0.15
60 33 0.72
61 6 0.13
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (59 bp):
AAGGACTCAACAAAGCAACACTCTATAGTTGGAGGACCATTTGTGTATTTTAACATTAT
Found at i:1124241 original size:33 final size:33
Alignment explanation
Indices: 1124199--1124274 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
1124189 AACACGCTAG
*
1124199 GCATCCGAGGTCATCCGAGCGAGCTATGCGAGA
1 GCATCCGAGGCCATCCGAGCGAGCTATGCGAGA
* *
1124232 GCATCCGAGGCCATCTGAGCGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGAGCGAGCTATGCGAGA
1124265 GCATCCGAGG
1 GCATCCGAGG
1124275 GCAAGAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGAGCGAGCTATGCGAGA
Found at i:1124275 original size:10 final size:10
Alignment explanation
Indices: 1124198--1124277 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
1124188 CAACACGCTA
1124198 GGCATCCGAG
1 GGCATCCGAG
*
1124208 GTCATCCGAG
1 GGCATCCGAG
*
1124218 CGAGCTATGCGAG
1 -G-GC-ATCCGAG
*
1124231 AGCATCCGAG
1 GGCATCCGAG
* *
1124241 GCCATCTGAG
1 GGCATCCGAG
*
1124251 CGAGCTATGCGAG
1 -G-GC-ATCCGAG
1124264 GGCATCCGAG
1 GGCATCCGAG
1124274 GGCA
1 GGCA
1124278 AGAGGAATTA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
10 32 0.62
11 6 0.12
12 3 0.06
13 11 0.21
ACGTcount: A:0.23, C:0.28, G:0.36, T:0.14
Consensus pattern (10 bp):
GGCATCCGAG
Found at i:1124345 original size:29 final size:29
Alignment explanation
Indices: 1124303--1124378 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
1124293 GGAGCAGGAG
* *
1124303 GGAGTGCACGGCGACCTACAAGGTCACCC
1 GGAGTGCATGGCGACCTACAAAGTCACCC
* *
1124332 GGAGTGCATGGCGACCTTCAAAGTCGCCC
1 GGAGTGCATGGCGACCTACAAAGTCACCC
*
1124361 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCGACCTA
1124379 TGCTTGGGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.13
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAAGTCACCC
Found at i:1124653 original size:2 final size:2
Alignment explanation
Indices: 1124648--1124674 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1124638 TTTGTCATCC
1124648 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
1124675 AGAAAGGTTT
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:1135564 original size:2 final size:2
Alignment explanation
Indices: 1135557--1135603 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1135547 TTGAAATAAG
1135557 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
1135599 TA TA T
1 TA TA T
1135604 CATGTATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1136030 original size:32 final size:31
Alignment explanation
Indices: 1135959--1136064 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 31
1135949 GACCTAATCG
* * * * *
1135959 AAACCAACCGATCCGATATTGACCCGATTCG
1 AAACCAACTGATTCGATATTAACCCGACTCA
*
1135990 AAACCAACTGATTCGATATTAACCTGACTCA
1 AAACCAACTGATTCGATATTAACCCGACTCA
* * * * *
1136021 AACACCAACTGATTCAATTTTGACCCAACCCAA
1 AA-ACCAACTGATTCGATATTAACCCGACTC-A
1136054 AAACCAACTGA
1 AAACCAACTGA
1136065 CCCGATTTGA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 27 0.44
32 31 0.51
33 3 0.05
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (31 bp):
AAACCAACTGATTCGATATTAACCCGACTCA
Found at i:1136322 original size:2 final size:2
Alignment explanation
Indices: 1136315--1136342 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1136305 AAATAAGAAT
1136315 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
1136343 AAGATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1138545 original size:8 final size:8
Alignment explanation
Indices: 1138534--1138675 Score: 221
Period size: 8 Copynumber: 17.8 Consensus size: 8
1138524 ACGTACGTAC
1138534 ACGTATGT
1 ACGTATGT
1138542 ACGTATGT
1 ACGTATGT
1138550 ACGTATGT
1 ACGTATGT
1138558 ACGTATGT
1 ACGTATGT
1138566 ACGTATGT
1 ACGTATGT
*
1138574 ATGTATGT
1 ACGTATGT
*
1138582 ACGCATGT
1 ACGTATGT
*
1138590 ACGTATAT
1 ACGTATGT
1138598 ACGTATGT
1 ACGTATGT
1138606 ACGTATGT
1 ACGTATGT
1138614 ACGTATGT
1 ACGTATGT
1138622 ACGTATGT
1 ACGTATGT
1138630 ACGTATGT
1 ACGTATGT
*
1138638 ACGTACGT
1 ACGTATGT
*
1138646 ATGTATGT
1 ACGTATGT
*
1138654 ATGTATGT
1 ACGTATGT
1138662 ACGTATGT
1 ACGTATGT
*
1138670 ATGTAT
1 ACGTAT
1138676 TTCAAGATTT
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 123 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (8 bp):
ACGTATGT
Found at i:1140813 original size:14 final size:14
Alignment explanation
Indices: 1140791--1140824 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1140781 CCTCAAAGAA
*
1140791 TTACAATAATTCTT
1 TTACCATAATTCTT
1140805 TTACCATAATTCTT
1 TTACCATAATTCTT
1140819 TTACCA
1 TTACCA
1140825 CCGATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (14 bp):
TTACCATAATTCTT
Found at i:1142216 original size:33 final size:33
Alignment explanation
Indices: 1142174--1142244 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1142164 AATACTAACT
1142174 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1142207 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1142240 TGAAA
1 TGAAA
1142245 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1142649 original size:20 final size:20
Alignment explanation
Indices: 1142624--1142795 Score: 240
Period size: 20 Copynumber: 8.6 Consensus size: 20
1142614 CTTTAAAAAT
1142624 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1142644 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
1142665 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1142684 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1142704 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1142724 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1142744 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1142764 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1142784 CGCGTTGCGATT
1 CGCGTTGCGATT
1142796 CTTGAAAATC
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 130 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1144393 original size:2 final size:2
Alignment explanation
Indices: 1144386--1144434 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1144376 TTAAACCAAA
1144386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1144426 AT AA AT AT A
1 AT AT AT AT A
1144435 ATAATGAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1144624 original size:15 final size:15
Alignment explanation
Indices: 1144604--1144633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1144594 ATAATTATTA
1144604 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
1144619 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
1144634 TAAGAGCTCC
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:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:1145822 original size:3 final size:3
Alignment explanation
Indices: 1145792--1145856 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
1145782 TCTGGGCTTG
* * *
1145792 TAA TAA TTA TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1145836 TAA TAA TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1145857 ATTTAAGTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:1152481 original size:16 final size:17
Alignment explanation
Indices: 1152450--1152482 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1152440 TATGGAATCC
*
1152450 AGATATTAATAATAAAA
1 AGATATTAAAAATAAAA
1152467 AGATA-TAAAAATAAAA
1 AGATATTAAAAATAAAA
1152483 TAATCATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AGATATTAAAAATAAAA
Found at i:1152707 original size:96 final size:96
Alignment explanation
Indices: 1152543--1152732 Score: 380
Period size: 96 Copynumber: 2.0 Consensus size: 96
1152533 AGTATCATAA
1152543 ACGGAAGCAATGGACTTGGGCACATACGATAGCAATGGACTCCGTTACATACGAAGTTTCTTTAT
1 ACGGAAGCAATGGACTTGGGCACATACGATAGCAATGGACTCCGTTACATACGAAGTTTCTTTAT
1152608 ATGAGTATTATATTGAAGGAATATTCTTTAT
66 ATGAGTATTATATTGAAGGAATATTCTTTAT
1152639 ACGGAAGCAATGGACTTGGGCACATACGATAGCAATGGACTCCGTTACATACGAAGTTTCTTTAT
1 ACGGAAGCAATGGACTTGGGCACATACGATAGCAATGGACTCCGTTACATACGAAGTTTCTTTAT
1152704 ATGAGTATTATATTGAAGGAATATTCTTT
66 ATGAGTATTATATTGAAGGAATATTCTTT
1152733 TTGGCATATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (96 bp):
ACGGAAGCAATGGACTTGGGCACATACGATAGCAATGGACTCCGTTACATACGAAGTTTCTTTAT
ATGAGTATTATATTGAAGGAATATTCTTTAT
Found at i:1157407 original size:25 final size:25
Alignment explanation
Indices: 1157343--1157413 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
1157333 ATGGATATCG
*
1157343 ATCTTTCAAAATATA-AATATATATTTT
1 ATCTTT-AAAATTTATAA-ATA-ATTTT
1157370 ATCTTTAAAATTTTATAAATAATTTT
1 ATCTTTAAAA-TTTATAAATAATTTT
*
1157396 -TCTTTAATATTTATAAAT
1 ATCTTTAAAATTTATAAAT
1157414 TCGTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.22
25 8 0.20
26 9 0.22
27 12 0.30
28 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
ATCTTTAAAATTTATAAATAATTTT
Found at i:1157413 original size:24 final size:26
Alignment explanation
Indices: 1157365--1157413 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
1157355 ATAAATATAT
1157365 ATTTTATCTTTAAAATTTTATAAATA
1 ATTTTATCTTTAAAATTTTATAAATA
*
1157391 ATTTT-TCTTTAATA-TTTATAAAT
1 ATTTTATCTTTAAAATTTTATAAAT
1157414 TCGTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTATCTTTAAAATTTTATAAATA
Found at i:1157623 original size:13 final size:13
Alignment explanation
Indices: 1157605--1157631 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1157595 AGTATTTGTT
1157605 AGTGTAGTAGAGA
1 AGTGTAGTAGAGA
1157618 AGTGTAGTAGAGA
1 AGTGTAGTAGAGA
1157631 A
1 A
1157632 TTTTAGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (13 bp):
AGTGTAGTAGAGA
Found at i:1158227 original size:6 final size:6
Alignment explanation
Indices: 1158216--1158247 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1158206 CCGTCTCGTC
1158216 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1158248 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:1158361 original size:34 final size:34
Alignment explanation
Indices: 1158323--1158418 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 34
1158313 CTTTTTTTTT
*
1158323 CAACGAATTTAGAAAATCGCACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCACTGTAGACTATCG
1158357 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAAT-----CG-C-ACTGTAGACTATCG
1158398 CAACGAATTTGGAAAATCGCA
1 CAACGAATTTGGAAAATCGCA
1158419 ACGACAACTG
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
34 17 0.31
35 1 0.02
36 2 0.04
39 2 0.04
40 1 0.02
41 31 0.57
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (34 bp):
CAACGAATTTGGAAAATCGCACTGTAGACTATCG
Found at i:1158377 original size:19 final size:19
Alignment explanation
Indices: 1158353--1158422 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
1158343 ACTGTAGACT
1158353 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
1158372 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG--AA-TTTGGAAA
1158394 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1158413 ATCGCAACGA
1 ATCGCAACGA
1158423 CAACTGCAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 23 0.57
20 2 0.05
21 2 0.05
22 13 0.32
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1158400 original size:22 final size:20
Alignment explanation
Indices: 1158343--1158443 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 20
1158333 AGAAAATCGC
1158343 ACTGTAGACTATCGCAACGA
1 ACTGTAGACTATCGCAACGA
* * **
1158363 A-TTTGGAAAATCGCAACGACA
1 ACTGTAGACTATCGCAACG--A
1158384 ACTGTAGACTATCGCAACGA
1 ACTGTAGACTATCGCAACGA
* * **
1158404 A-TTTGGAAAATCGCAACGACA
1 ACTGTAGACTATCGCAACG--A
*
1158425 ACTGCAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
1158444 CGAAATGGAA
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
19 26 0.45
20 3 0.05
21 4 0.07
22 25 0.43
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTGTAGACTATCGCAACGA
Found at i:1158400 original size:41 final size:41
Alignment explanation
Indices: 1158343--1158463 Score: 199
Period size: 41 Copynumber: 2.9 Consensus size: 41
1158333 AGAAAATCGC
1158343 ACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACA
1 ACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACA
1158384 ACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACA
1 ACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACA
* *
1158425 ACTGCAGACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACG
1158464 CGATTTTCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
41 57 0.75
42 15 0.20
43 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACA
Found at i:1158460 original size:20 final size:20
Alignment explanation
Indices: 1158435--1158589 Score: 148
Period size: 20 Copynumber: 7.6 Consensus size: 20
1158425 ACTGCAGACT
1158435 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1158455 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1158476 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
1158496 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1158517 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1158537 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1158558 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1158578 AACGCAACGCGA
1 ATCGCAACGCGA
1158590 TTTTCAACTA
Statistics
Matches: 103, Mismatches: 29, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
20 57 0.55
21 46 0.45
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1158477 original size:41 final size:41
Alignment explanation
Indices: 1158432--1158614 Score: 339
Period size: 41 Copynumber: 4.5 Consensus size: 41
1158422 ACAACTGCAG
1158432 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1158473 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1158514 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1158555 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1158596 ACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATG
1158615 CAACGTGAAT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1158481 original size:21 final size:21
Alignment explanation
Indices: 1158432--1158611 Score: 143
Period size: 20 Copynumber: 8.8 Consensus size: 21
1158422 ACAACTGCAG
* **
1158432 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
1158453 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1158473 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
1158494 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1158514 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
1158535 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1158555 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* * *
1158576 A-AAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
*
1158596 ACTATCGCAATGCGAA
1 ACTATCGCAACGCGAA
1158612 ATGCAACGTG
Statistics
Matches: 117, Mismatches: 38, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
20 60 0.51
21 57 0.49
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:1158518 original size:82 final size:82
Alignment explanation
Indices: 1158391--1158614 Score: 346
Period size: 82 Copynumber: 2.7 Consensus size: 82
1158381 ACAACTGTAG
* * *
1158391 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-AACTGCAGACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGAATTTCA-ACTATCGCAACGCGAAATGGA
1158453 AAATCGCAACGCGATTTTCA
63 AAATCGCAACGCGATTTTCA
1158473 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
1158538 TCGCAACGCGATTTTCA
66 TCGCAACGCGATTTTCA
* * *
1158555 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATG
1158615 CAACGTGAAT
Statistics
Matches: 133, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
82 109 0.82
83 20 0.15
84 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
TCGCAACGCGATTTTCA
Found at i:1158518 original size:123 final size:122
Alignment explanation
Indices: 1158350--1158614 Score: 344
Period size: 123 Copynumber: 2.1 Consensus size: 122
1158340 CGCACTGTAG
* *
1158350 ACTATCGCAA-CGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ACTATCGCAAGCGAA-ATGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAA-ATGGAAA
*
1158413 ATCGCAACGAC-AACTGCAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
64 ATCGCAACG-CGAACTGCA-ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
*
1158473 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAAATGGA
1 ACTATCGCAA-GCGAAATGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAAC-CGAAATGGA
** *
1158535 AAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
62 AAATCGCAACGCGAACTGCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
1158596 ACTATCGCAATGCGAAATG
1 ACTATCGCAA-GCGAAATG
1158615 CAACGTGAAT
Statistics
Matches: 127, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
123 82 0.65
124 37 0.29
125 8 0.06
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (122 bp):
ACTATCGCAAGCGAAATGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAAATGGAAAAT
CGCAACGCGAACTGCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
Found at i:1159193 original size:20 final size:20
Alignment explanation
Indices: 1159177--1159227 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1159167 CACGGAATGT
1159177 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
* *
1159197 AATATTACCAGTGTGAATAA
1 AAGATTACCAGTGGGAATAA
1159217 AAGATTACCAG
1 AAGATTACCAG
1159228 ATAATAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.24
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:1159458 original size:37 final size:37
Alignment explanation
Indices: 1159385--1159459 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1159375 GTAGTAAAAT
* * *
1159385 ATTTATATATTTTATTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTAGTTTAAAAATTCAAAATCATAAA
1159422 ATTTATATAATTTT-GTTTACAAAATTCAAAAT-ATAAA
1 ATTTATAT-ATTTTAGTTTA-AAAATTCAAAATCATAAA
1159459 A
1 A
1159460 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTAGTTTAAAAATTCAAAATCATAAA
Found at i:1160319 original size:21 final size:21
Alignment explanation
Indices: 1160275--1160319 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1160265 GTTTTGATAA
*
1160275 AAAAATGAAAGTTTAAGTACT
1 AAAAATGAAAGTTTAAATACT
* * *
1160296 AAAACTGATAGTTTAAATATT
1 AAAAATGAAAGTTTAAATACT
1160317 AAA
1 AAA
1160320 CGTATAATTT
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:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (21 bp):
AAAAATGAAAGTTTAAATACT
Found at i:1161628 original size:21 final size:21
Alignment explanation
Indices: 1161602--1161800 Score: 234
Period size: 21 Copynumber: 9.6 Consensus size: 21
1161592 GTTCCCAGAT
1161602 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1161623 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1161644 TCACAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1161665 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1161686 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1161707 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1161727 TCGCAATGCG-ATTGTCGACTA
1 TCGCAATGCGAACT-TCGACTA
*
1161748 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1161768 TCGCAATGCG-ATTGTCGACTA
1 TCGCAATGCGAACT-TCGACTA
1161789 TCGCAATGCGAA
1 TCGCAATGCGAA
1161801 TATGTAAATC
Statistics
Matches: 157, Mismatches: 10, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.01
20 31 0.20
21 122 0.78
22 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1161652 original size:42 final size:41
Alignment explanation
Indices: 1161602--1161819 Score: 268
Period size: 41 Copynumber: 5.3 Consensus size: 41
1161592 GTTCCCAGAT
*
1161602 TCGCAATGCGAACTTCGACTATCGCAATGCGAACT-TCG-ACTA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAA-TAT-GTA-AA
* *
1161644 TCACAATGCGAACTTCGACTATCGCAATGCGAACT-TCG-ACTA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAA-TAT-GTA-AA
*
1161686 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
*
1161727 TCGCAATGCG-ATTGTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACT-TCGACTATCGCAATGCGAATATGTAAA
*
1161768 TCGCAATGCG-ATTGTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACT-TCGACTATCGCAATGCGAATATGTAAA
1161809 TCGCAATGCGA
1 TCGCAATGCGA
1161820 TAGTCGAAGT
Statistics
Matches: 166, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
40 2 0.01
41 90 0.54
42 74 0.45
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (41 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
Found at i:1161731 original size:20 final size:20
Alignment explanation
Indices: 1161706--1161819 Score: 128
Period size: 20 Copynumber: 5.6 Consensus size: 20
1161696 AACTTGGACT
1161706 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1161726 ATCGCAATGCG-AT-TGTCGACT
1 ATCGCAATGCGAATATGT--A-A
1161747 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1161767 ATCGCAATGCG-AT-TGTCGACT
1 ATCGCAATGCGAATATGT--A-A
1161788 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1161808 ATCGCAATGCGA
1 ATCGCAATGCGA
1161820 TAGTCGAAGT
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.08
19 4 0.05
20 36 0.45
21 24 0.30
22 4 0.05
23 6 0.08
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1161854 original size:21 final size:21
Alignment explanation
Indices: 1161809--1161862 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1161799 AATATGTAAA
* *
1161809 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAACT
*
1161830 TCGCGTTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAACT
1161850 ATCGCATTGCGAT
1 -TCGCATTGCGAT
1161863 TTACATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAACT
Found at i:1161876 original size:20 final size:20
Alignment explanation
Indices: 1161851--1161891 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1161841 TAGTCGACTA
1161851 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1161871 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1161891 T
1 T
1161892 TTGGACTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1162015 original size:21 final size:21
Alignment explanation
Indices: 1161892--1162015 Score: 153
Period size: 21 Copynumber: 5.9 Consensus size: 21
1161882 TTTACATATT
*
1161892 TTGGACTATCGCAAT--GAAT
1 TTGGACTATCGCAATGCGAAC
* *
1161911 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
1161934 TTTGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
1161955 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
1161976 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
1161997 TTGGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
1162016 TTTACATATT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.07
21 76 0.84
23 8 0.09
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:1162066 original size:29 final size:29
Alignment explanation
Indices: 1162024--1162079 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1162014 GATTTACATA
1162024 TTCGCATTGCGATAGTCAAAGTTCGCAAG
1 TTCGCATTGCGATAGTCAAAGTTCGCAAG
*
1162053 TTCGCATTGCGATAGTCGAAGTTCGCA
1 TTCGCATTGCGATAGTCAAAGTTCGCA
1162080 TTGCGATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (29 bp):
TTCGCATTGCGATAGTCAAAGTTCGCAAG
Found at i:1162076 original size:21 final size:21
Alignment explanation
Indices: 1162050--1162147 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
1162040 CAAAGTTCGC
1162050 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
1162071 AAGTTCGCATTGCGATAGTTG
1 AAGTTCGCATTGCGATAGTCG
* *
1162092 -ACTATCGCATTGCGAT-TTAC-
1 AAGT-TCGCATTGCGATAGT-CG
1162112 ATA-TTCGCATTGCGATAGTCG
1 A-AGTTCGCATTGCGATAGTCG
*
1162133 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
1162148 ATCTGGAAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
20 17 0.27
21 46 0.72
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:1171520 original size:26 final size:26
Alignment explanation
Indices: 1171481--1171545 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1171471 ACCCGAACCG
*
1171481 AACCGAATCAAAAAATGAAGCC-TTTA
1 AACCGAACCAAAAAATGAA-CCGTTTA
* *
1171507 AACCGAACCGAAAACTGAACCGTTTA
1 AACCGAACCAAAAAATGAACCGTTTA
*
1171533 AAGCCAAACCAAA
1 AA-CCGAACCAAA
1171546 CCGAACCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.06
26 22 0.69
27 8 0.25
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14
Consensus pattern (26 bp):
AACCGAACCAAAAAATGAACCGTTTA
Found at i:1177292 original size:12 final size:12
Alignment explanation
Indices: 1177275--1177330 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
1177265 AGAGGGGCTC
1177275 ATTTTTAAAAAT
1 ATTTTTAAAAAT
*
1177287 ATTTTTAAGTTTAAT
1 ATTTTTAA---AAAT
* *
1177302 AATTTAAAAAAT
1 ATTTTTAAAAAT
1177314 A-TTTTAAAAAT
1 ATTTTTAAAAAT
1177325 ATTTTT
1 ATTTTT
1177331 TTATTTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 10 0.29
12 16 0.46
15 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATTTTTAAAAAT
Found at i:1182183 original size:22 final size:22
Alignment explanation
Indices: 1182141--1182185 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1182131 GTAATTAATA
* *
1182141 TATTTAATTATGAGTTTATTTT
1 TATTTAATTATGAGGTGATTTT
1182163 TATTTAATTA-GTAGGTGATTTT
1 TATTTAATTATG-AGGTGATTTT
1182185 T
1 T
1182186 TGTGTGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
TATTTAATTATGAGGTGATTTT
Found at i:1182827 original size:2 final size:2
Alignment explanation
Indices: 1182820--1182860 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1182810 GTTTTCATTT
1182820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1182861 CCACATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1183299 original size:2 final size:2
Alignment explanation
Indices: 1183292--1183345 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1183282 AAAGTCTTTT
1183292 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
1183334 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1183346 AAAGGATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1195958 original size:2 final size:2
Alignment explanation
Indices: 1195951--1196019 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1195941 ATACAGAATC
1195951 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
1195993 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
1196020 GGGCCGGCCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1198942 original size:21 final size:20
Alignment explanation
Indices: 1198915--1198984 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
1198905 ATTTGACGAT
1198915 AAATTTTATTTATTTACTTTA
1 AAATTTTATTTATTTA-TTTA
* * *
1198936 AATTTTTAATTATTT-TTGA
1 AAATTTTATTTATTTATTTA
*
1198955 AAAATTTATTTATTTATTTA
1 AAATTTTATTTATTTATTTA
1198975 ATAATTTTAT
1 A-AATTTTAT
1198985 ACAATTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.38
20 4 0.10
21 20 0.51
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
AAATTTTATTTATTTATTTA
Found at i:1211497 original size:39 final size:39
Alignment explanation
Indices: 1211424--1211498 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1211414 TCCTATACCA
* *
1211424 TATCGAAAATCACATGTGCATCACTTCTCCGGAGTCTGG
1 TATCGAAAATCACATGTGCACCACTTCTACGGAGTCTGG
* *
1211463 TATCGAAAATCACCA-GTGCACCGCTTCTATGGAGTC
1 TATCGAAAATCA-CATGTGCACCACTTCTACGGAGTC
1211499 CAGACTCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 29 0.94
40 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
TATCGAAAATCACATGTGCACCACTTCTACGGAGTCTGG
Found at i:1214482 original size:129 final size:129
Alignment explanation
Indices: 1214252--1214510 Score: 518
Period size: 129 Copynumber: 2.0 Consensus size: 129
1214242 TGTTCAATGA
1214252 TTAAACATTTAAGTATACTCGATCATTTATCTTTCTATATAATACATAGATAACGACATTAGTCA
1 TTAAACATTTAAGTATACTCGATCATTTATCTTTCTATATAATACATAGATAACGACATTAGTCA
1214317 ACATTAATTTATTCAAGATGTTGGTGGAGGATGGACTGACTTGGATCAAATTTGATGAGTATCT
66 ACATTAATTTATTCAAGATGTTGGTGGAGGATGGACTGACTTGGATCAAATTTGATGAGTATCT
1214381 TTAAACATTTAAGTATACTCGATCATTTATCTTTCTATATAATACATAGATAACGACATTAGTCA
1 TTAAACATTTAAGTATACTCGATCATTTATCTTTCTATATAATACATAGATAACGACATTAGTCA
1214446 ACATTAATTTATTCAAGATGTTGGTGGAGGATGGACTGACTTGGATCAAATTTGATGAGTATCT
66 ACATTAATTTATTCAAGATGTTGGTGGAGGATGGACTGACTTGGATCAAATTTGATGAGTATCT
1214510 T
1 T
1214511 ATCAAAAGAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (129 bp):
TTAAACATTTAAGTATACTCGATCATTTATCTTTCTATATAATACATAGATAACGACATTAGTCA
ACATTAATTTATTCAAGATGTTGGTGGAGGATGGACTGACTTGGATCAAATTTGATGAGTATCT
Found at i:1215729 original size:67 final size:68
Alignment explanation
Indices: 1215633--1215767 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 68
1215623 GTTTCTAAAT
*
1215633 TCGCAATGCGATTCTTCAAATTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAA
1 TCGCAACGCGATTCTTCAAATTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAA
1215698 CTC
66 CTC
*
1215701 TCGCAACGCGATTC-TCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAA
1 TCGCAACGCGATTCTTCAAATTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAA
1215765 CTC
66 CTC
1215768 AGTTTTCAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 52 0.80
68 13 0.20
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (68 bp):
TCGCAACGCGATTCTTCAAATTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAA
CTC
Found at i:1220079 original size:95 final size:95
Alignment explanation
Indices: 1219916--1220106 Score: 325
Period size: 95 Copynumber: 2.0 Consensus size: 95
1219906 TGACTCTGTT
1219916 CATCAGTAGAAGCTGCCACTGCTGCTGTCTCAACAATTGATTACCAGAAAGTAATACATTGTTTC
1 CATCAGTAGAAGCTGCCACTGCTGCTGTCTCAACAATTGATTACCAGAAAGTAATACATTGTTTC
*
1219981 TTTTTCGGATTCCCTTCATTA-TCCAGTGCA
66 -TTTTCGGATTCCCTTCATTACACCAGTGCA
1220011 CATCAGTAGAAGCTGCCA-TGCTGCTGTCTCAACAATTGTATTACCCA-AAAGTAATACATTGTT
1 CATCAGTAGAAGCTGCCACTGCTGCTGTCTCAACAATTG-ATTA-CCAGAAAGTAATACATTGTT
1220074 TCTTTTCGGATTCCCTTCATTACACCAGTGCA
64 TCTTTTCGGATTCCCTTCATTACACCAGTGCA
1220106 C
1 C
1220107 CAGAGATAAT
Statistics
Matches: 92, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
94 40 0.43
95 49 0.53
96 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (95 bp):
CATCAGTAGAAGCTGCCACTGCTGCTGTCTCAACAATTGATTACCAGAAAGTAATACATTGTTTC
TTTTCGGATTCCCTTCATTACACCAGTGCA
Found at i:1228785 original size:17 final size:18
Alignment explanation
Indices: 1228762--1228866 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 18
1228752 TCGGGCCGGG
1228762 TATATATATTTAAATTAAA
1 TATATATA-TTAAATTAAA
*
1228781 TATATATATTAATTTAAA
1 TATATATATTAAATTAAA
* *
1228799 TTAAATATATAAATATTATATA
1 -TATATATATTAA-ATTA-A-A
*
1228821 TATATATATTAATTTAAA
1 TATATATATTAAATTAAA
* * *
1228839 TTAAATTTATTAATATTATA
1 -TATATATATTAA-ATTAAA
1228859 TATATATA
1 TATATATA
1228867 ATAATTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
18 10 0.15
19 35 0.52
20 10 0.15
21 11 0.16
22 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATATATTAAATTAAA
Found at i:1228795 original size:23 final size:22
Alignment explanation
Indices: 1228762--1228844 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 22
1228752 TCGGGCCGGG
1228762 TATATA-TATTTAAATTAAATA
1 TATATATTATTTAAATTAAATA
1228783 TATATATTAATTTAAATTAAATA
1 TATATATT-ATTTAAATTAAATA
* *
1228806 TATA-AATA-TT--A-TATATA
1 TATATATTATTTAAATTAAATA
1228823 TATATATTAATTTAAATTAAAT
1 TATATATT-ATTTAAATTAAAT
1228845 TTATTAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
17 9 0.18
18 3 0.06
19 1 0.02
20 4 0.08
21 7 0.14
22 4 0.08
23 22 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATATTATTTAAATTAAATA
Found at i:1228821 original size:15 final size:15
Alignment explanation
Indices: 1228798--1228874 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
1228788 ATTAATTTAA
*
1228798 ATTAAATATATAAAT
1 ATTATATATATAAAT
*
1228813 ATTATATATATATAT
1 ATTATATATATAAAT
1228828 ATTA-AT-T-T-AA-
1 ATTATATATATAAAT
* * *
1228838 ATTAAATTTATTAAT
1 ATTATATATATAAAT
1228853 ATTATATATATATAAT
1 ATTATATATATA-AAT
1228869 AATTAT
1 -ATTAT
1228875 TTTTAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 2 0.04
13 2 0.04
14 4 0.08
15 26 0.53
16 3 0.06
17 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATATATAAAT
Found at i:1228822 original size:38 final size:38
Alignment explanation
Indices: 1228775--1228872 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 38
1228765 ATATATTTAA
*
1228775 ATTAAATATATATATTAATTTAAATTAAATATATAAAT
1 ATTATATATATATATTAATTTAAATTAAATATATAAAT
* *
1228813 ATTATATATATATATATTAATTTAAATTAAATTTATTAAT
1 A-T-TATATATATATATTAATTTAAATTAAATATATAAAT
*
1228853 ATTATATATATATAATAATT
1 ATTATATATATATATTAATT
1228873 ATTTTTAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
38 18 0.33
39 2 0.04
40 34 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
ATTATATATATATATTAATTTAAATTAAATATATAAAT
Found at i:1228824 original size:40 final size:40
Alignment explanation
Indices: 1228780--1228866 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
1228770 TTTAAATTAA
1228780 ATATATATATTAATTTAAATTAAATATATAAATATTATAT
1 ATATATATATTAATTTAAATTAAATATATAAATATTATAT
* *
1228820 ATATATATATTAATTTAAATTAAATTTATTAATATTATAT
1 ATATATATATTAATTTAAATTAAATATATAAATATTATAT
1228860 ATATATA
1 ATATATA
1228867 ATAATTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
ATATATATATTAATTTAAATTAAATATATAAATATTATAT
Found at i:1229673 original size:30 final size:31
Alignment explanation
Indices: 1229615--1229673 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
1229605 ATGGTTGTTT
1229615 TATTTGTTTTTCAATTTGATGATATAAGTGAA
1 TATTTGTTTTTCAATTTGA-GATATAAGTGAA
* * *
1229647 TATTTTTTTTTTAATTTGA-ATTTAAGT
1 TATTTGTTTTTCAATTTGAGATATAAGT
1229674 AATTATATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.29
32 17 0.71
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (31 bp):
TATTTGTTTTTCAATTTGAGATATAAGTGAA
Found at i:1229692 original size:2 final size:2
Alignment explanation
Indices: 1229685--1229709 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1229675 ATTATATTGT
1229685 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1229710 TAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1230805 original size:156 final size:156
Alignment explanation
Indices: 1230521--1230831 Score: 622
Period size: 156 Copynumber: 2.0 Consensus size: 156
1230511 GTTGAAATTA
1230521 GGGTTTCAAGCGTTAAGACATTAGAATTTTGGGATCCCTTGCAATCGGGGCTGTAATAGTCGAGT
1 GGGTTTCAAGCGTTAAGACATTAGAATTTTGGGATCCCTTGCAATCGGGGCTGTAATAGTCGAGT
1230586 AGGCTTATTCAGTAGGTTATTGCTGAGTTACTCATTGGCTTAAGAGATATCCAATATGTTAATGA
66 AGGCTTATTCAGTAGGTTATTGCTGAGTTACTCATTGGCTTAAGAGATATCCAATATGTTAATGA
1230651 CAGCCCTTTACATCTGACCTTTTTTG
131 CAGCCCTTTACATCTGACCTTTTTTG
1230677 GGGTTTCAAGCGTTAAGACATTAGAATTTTGGGATCCCTTGCAATCGGGGCTGTAATAGTCGAGT
1 GGGTTTCAAGCGTTAAGACATTAGAATTTTGGGATCCCTTGCAATCGGGGCTGTAATAGTCGAGT
1230742 AGGCTTATTCAGTAGGTTATTGCTGAGTTACTCATTGGCTTAAGAGATATCCAATATGTTAATGA
66 AGGCTTATTCAGTAGGTTATTGCTGAGTTACTCATTGGCTTAAGAGATATCCAATATGTTAATGA
1230807 CAGCCCTTTACATCTGACCTTTTTT
131 CAGCCCTTTACATCTGACCTTTTTT
1230832 TGTCTTTTAT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (156 bp):
GGGTTTCAAGCGTTAAGACATTAGAATTTTGGGATCCCTTGCAATCGGGGCTGTAATAGTCGAGT
AGGCTTATTCAGTAGGTTATTGCTGAGTTACTCATTGGCTTAAGAGATATCCAATATGTTAATGA
CAGCCCTTTACATCTGACCTTTTTTG
Found at i:1232180 original size:69 final size:70
Alignment explanation
Indices: 1232087--1232227 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 70
1232077 TTCTGACTAT
* * *
1232087 ATCCTTCAAGGAACGTGTCGCTCAGTTCTTATTGTT-ATTATCCGCAACCTTTCATTAGTATGTA
1 ATCCTGCAAGGAACGTGCCACTCAGTTCTTATTGTTAATTATCCGCAACCTTTCATTAGTATGTA
*
1232151 TCAGC
66 GCAGC
* * ** *
1232156 ATCCTGCAAGGAATGTGCCACTCAGTTCTTATTGTTAATTATCTGTGACCTTTCATTAGTTTGTA
1 ATCCTGCAAGGAACGTGCCACTCAGTTCTTATTGTTAATTATCCGCAACCTTTCATTAGTATGTA
1232221 GCAGC
66 GCAGC
1232226 AT
1 AT
1232228 TACAAAGCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
69 32 0.52
70 30 0.48
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (70 bp):
ATCCTGCAAGGAACGTGCCACTCAGTTCTTATTGTTAATTATCCGCAACCTTTCATTAGTATGTA
GCAGC
Found at i:1232398 original size:41 final size:41
Alignment explanation
Indices: 1232353--1232434 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1232343 GATAAGCGAC
1232353 AGTGGGGTTCACATCATAATGAGAACAGGTTGATTATTGGT
1 AGTGGGGTTCACATCATAATGAGAACAGGTTGATTATTGGT
1232394 AGTGGGGTTCACATCATAATGAGAACAGGTTGATTATTGGT
1 AGTGGGGTTCACATCATAATGAGAACAGGTTGATTATTGGT
1232435 GATGAAGCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (41 bp):
AGTGGGGTTCACATCATAATGAGAACAGGTTGATTATTGGT
Done.