Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1514301 original size:131 final size:130
Alignment explanation
Indices: 1514164--1514498 Score: 453
Period size: 131 Copynumber: 2.6 Consensus size: 130
1514154 AACAATTTCC
*
1514164 AATTGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCAATCGAAATGAAGAG
1 AATTGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAG
* *
1514229 ATATCACTATTTCATCTGAAAAATCAATATTGATTCGAGAGAAA-ATGGTAATATCCAATTATAT
66 ATATCACTATTTCATCTGAAAAATCAATATTGATTCGAGAGAAACA--CTAATATACAATTATAT
1514293 CA
129 CA
* * *
1514295 AATTGAGATTAAATGACCTCTCATGCCTTAAAACAGTCATTTATTACTCCAATCGAAATGAAGAT
1 AATTGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAG
* * * * * *
1514360 ATATCACTATTTCGTCTTAAAAATCAATATTTATTCGAGAGAAACACTAATATATAATTATTTCC
66 ATATCACTATTTCATCTGAAAAATCAATATTGATTCGAGAGAAACACTAATATACAATTATATCA
* * * * * *
1514425 AATGGAGAATAAATTACCTCTAATGCCATAAAGCAGTCATTTATTA---CAACCGAAATGAAAAG
1 AATTGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAG
*
1514487 ATATTACTATTT
66 ATATCACTATTT
1514499 TCAACAATAA
Statistics
Matches: 181, Mismatches: 22, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
127 24 0.13
130 54 0.30
131 102 0.56
132 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (130 bp):
AATTGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAG
ATATCACTATTTCATCTGAAAAATCAATATTGATTCGAGAGAAACACTAATATACAATTATATCA
Found at i:1514972 original size:24 final size:23
Alignment explanation
Indices: 1514934--1514978 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1514924 AATTAATGAC
* *
1514934 TAAAATGAAATAACATGCAAAAAT
1 TAAAATAAAACAACATG-AAAAAT
1514958 TAAAATAAAACAACATGAAAA
1 TAAAATAAAACAACATGAAAA
1514979 TAGGACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAAATAAAACAACATGAAAAAT
Found at i:1515515 original size:109 final size:108
Alignment explanation
Indices: 1515277--1515507 Score: 286
Period size: 109 Copynumber: 2.1 Consensus size: 108
1515267 TATGACCAAA
* * * *
1515277 ATGTAAAAACACGCTAAACATATAGGGACTAAGAAGTAAATAACCTTAAAAATATATAACATGCA
1 ATGTAAAAACACGCTAAAC-TATAGGGACTAAGAAGAAAATAACCCTAAAAATATATAAAATACA
* * * *
1515342 TAAAAATGGGTAAATTGTAGAATCGGTCCCTACAGGTGACTACT
65 TAAAAATGGGTAAATAGAAGAATCGATCCCTACAGATGACTACT
* * * *
1515386 ATGAAAAAACACGGCCAAACTATGGGGACTAA-ATAGAAAATAACCCTAAAATTATA-AAGAATA
1 ATGTAAAAACAC-GCTAAACTATAGGGACTAAGA-AGAAAATAACCCTAAAAATATATAA-AATA
*
1515449 CATAAAAATGGGTAAATAGAAGAATTGATCCCTACAGATGACTACT
63 CATAAAAATGGGTAAATAGAAGAATCGATCCCTACAGATGACTACT
*
1515495 TTGTAAAAACACG
1 ATGTAAAAACACG
1515508 TTTAAACTGG
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
108 4 0.04
109 94 0.90
110 6 0.06
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (108 bp):
ATGTAAAAACACGCTAAACTATAGGGACTAAGAAGAAAATAACCCTAAAAATATATAAAATACAT
AAAAATGGGTAAATAGAAGAATCGATCCCTACAGATGACTACT
Found at i:1516519 original size:3 final size:3
Alignment explanation
Indices: 1516502--1516546 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1516492 AAAATTTAAA
* *
1516502 AAT AAT AAC ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1516547 GGGATGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1518352 original size:21 final size:19
Alignment explanation
Indices: 1518318--1518363 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1518308 TTATGGGTAC
*
1518318 CGATACTGACCTTTTAGTAT
1 CGATACTAACC-TTTAGTAT
*
1518338 CGATACTAAACCTTTGGTAT
1 CGATACT-AACCTTTAGTAT
1518358 CGATAC
1 CGATAC
1518364 CCCTTGACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (19 bp):
CGATACTAACCTTTAGTAT
Found at i:1518877 original size:15 final size:15
Alignment explanation
Indices: 1518857--1518887 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1518847 AGCTGCATAT
1518857 GGTATAGTTAGGTTA
1 GGTATAGTTAGGTTA
1518872 GGTATAGTTAGGTTA
1 GGTATAGTTAGGTTA
1518887 G
1 G
1518888 AAGTGAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (15 bp):
GGTATAGTTAGGTTA
Found at i:1520789 original size:20 final size:20
Alignment explanation
Indices: 1520764--1520810 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1520754 ATTAGGCTTT
1520764 GTTTGAGCCTTGTGTGGTTA
1 GTTTGAGCCTTGTGTGGTTA
**
1520784 GTTTGAGTTTTGTGTGGTTA
1 GTTTGAGCCTTGTGTGGTTA
1520804 GTTTGAG
1 GTTTGAG
1520811 TTGGCCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.04, G:0.36, T:0.49
Consensus pattern (20 bp):
GTTTGAGCCTTGTGTGGTTA
Found at i:1520811 original size:20 final size:20
Alignment explanation
Indices: 1520773--1520812 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1520763 TGTTTGAGCC
1520773 TTGTGTGGTTAGTTTGAGTT
1 TTGTGTGGTTAGTTTGAGTT
1520793 TTGTGTGGTTAGTTTGAGTT
1 TTGTGTGGTTAGTTTGAGTT
1520813 GGCCCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.35, T:0.55
Consensus pattern (20 bp):
TTGTGTGGTTAGTTTGAGTT
Found at i:1521183 original size:4 final size:4
Alignment explanation
Indices: 1521174--1521198 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1521164 TCATTAGATT
1521174 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
1521199 GTATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:1521398 original size:14 final size:13
Alignment explanation
Indices: 1521381--1521432 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1521371 CCTCAAATTA
1521381 TAAACCTTAAACTC
1 TAAACCTTAAA-TC
* *
1521395 TAAACTTTATATC
1 TAAACCTTAAATC
1521408 TTAAACCTTAAATCC
1 -TAAACCTTAAAT-C
*
1521423 TAAACTTTAA
1 TAAACCTTAA
1521433 CCCTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 28 0.90
15 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAACCTTAAATC
Found at i:1521771 original size:30 final size:31
Alignment explanation
Indices: 1521700--1521776 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1521690 TAAAAAAAAC
*
1521700 TTAATTTTTGGTCACTTATGTTATCAATTTA
1 TTAAATTTTGGTCACTTATGTTATCAATTTA
** *
1521731 TTAAATTTTGGTCACTTATGTTATTGA-TTG
1 TTAAATTTTGGTCACTTATGTTATCAATTTA
*
1521761 TTATATTTTGGTCACT
1 TTAAATTTTGGTCACT
1521777 GAATCATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (31 bp):
TTAAATTTTGGTCACTTATGTTATCAATTTA
Found at i:1522176 original size:8 final size:8
Alignment explanation
Indices: 1522163--1522188 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1522153 ATATTCCTTT
1522163 AAAAATTA
1 AAAAATTA
1522171 AAAAATTA
1 AAAAATTA
1522179 AAAAATTA
1 AAAAATTA
1522187 AA
1 AA
1522189 TCTATATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATTA
Found at i:1528760 original size:12 final size:12
Alignment explanation
Indices: 1528743--1528779 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1528733 TCGATTAAAG
1528743 CTCAAACTCGAA
1 CTCAAACTCGAA
1528755 CTCAAACTCGAA
1 CTCAAACTCGAA
*
1528767 CTCAAACTTGAA
1 CTCAAACTCGAA
1528779 C
1 C
1528780 ATTAAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.32, G:0.08, T:0.19
Consensus pattern (12 bp):
CTCAAACTCGAA
Found at i:1530341 original size:118 final size:118
Alignment explanation
Indices: 1530138--1530494 Score: 610
Period size: 118 Copynumber: 3.0 Consensus size: 118
1530128 GCTACTACGT
*
1530138 CATAAACTAATTAAACTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATGGCAT
1 CATAAACTAATTAAAGTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATGGCAT
*
1530203 AAAAAAACAAGATCCTAAAAAATAGAATATTATAAGTACCAAAACAGTGCATG
66 AAAAAAACAAGATCCTAAAAAACAGAATATTATAAGTACCAAAACAGTGCATG
*
1530256 CATAAACTAATTAAAGTTTGCTATAATCATAAAGATCTATTAAATAATATGTATACATATGGCAT
1 CATAAACTAATTAAAGTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATGGCAT
* *
1530321 AAAAAAACAAGATCCTAAAAAACAGAATACTATAAGTACCAAAACAGTGCACG
66 AAAAAAACAAGATCCTAAAAAACAGAATATTATAAGTACCAAAACAGTGCATG
* *
1530374 CATAAATTAATTAAAGTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATTGCAT
1 CATAAACTAATTAAAGTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATGGCAT
* *
1530439 -AAAAAACAAGATCCT-AAAGACAGAATATTATAAGTACCAAAACATTGCATG
66 AAAAAAACAAGATCCTAAAAAACAGAATATTATAAGTACCAAAACAGTGCATG
*
1530490 AATAA
1 CATAA
1530495 TTTTAAAATA
Statistics
Matches: 226, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
116 36 0.16
117 15 0.07
118 175 0.77
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (118 bp):
CATAAACTAATTAAAGTTTGCTATAATAATAAAGATCTATTAAATAATATGTATACATATGGCAT
AAAAAAACAAGATCCTAAAAAACAGAATATTATAAGTACCAAAACAGTGCATG
Found at i:1531015 original size:2 final size:2
Alignment explanation
Indices: 1531004--1531044 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1530994 TTTAACCGAA
1531004 AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1531045 CTTTCAACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1532836 original size:20 final size:20
Alignment explanation
Indices: 1532807--1532844 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1532797 TTTCAAAGTG
1532807 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1532827 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1532845 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1532913 original size:45 final size:46
Alignment explanation
Indices: 1532864--1532950 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 46
1532854 AAACATCGAA
* *
1532864 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1532909 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
1532951 AAGACCATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1532942 original size:20 final size:20
Alignment explanation
Indices: 1532917--1532970 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1532907 AGTGCATTTG
1532917 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
1532937 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
1532957 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1532971 TCAGGCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:1538784 original size:24 final size:23
Alignment explanation
Indices: 1538757--1538837 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
1538747 ACACTTAACA
1538757 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CCTTTGAAT
* *
1538781 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATGCATCCT-TTGAAT
* *
1538803 -TGCACCGATGCAT-GTCTTGAAT
1 GTGCATCGATGCATCCT-TTGAAT
1538825 GTGCATCGATGCA
1 GTGCATCGATGCA
1538838 CGGGGTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
23 14 0.30
24 16 0.35
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTTGAAT
Found at i:1547467 original size:3 final size:3
Alignment explanation
Indices: 1547459--1547558 Score: 175
Period size: 3 Copynumber: 33.7 Consensus size: 3
1547449 TTAATATATT
*
1547459 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1547507 TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1547554 TAA TA
1 TAA TA
1547559 TGGATAAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 90 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1548015 original size:113 final size:113
Alignment explanation
Indices: 1547875--1548626 Score: 1234
Period size: 113 Copynumber: 6.6 Consensus size: 113
1547865 ATAATTATGC
* * * *
1547875 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
1547940 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
* *
1547988 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1548053 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1548101 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
1548166 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1548214 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1548279 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1548327 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * ***
1548392 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAAAC
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
*
1548440 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * **
1548505 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTAAGCA
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGAT-GAATTCAGGT
1548554 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1548619 TATGAACT
66 TATGAACT
1548627 CGAACTGGAA
Statistics
Matches: 599, Mismatches: 39, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
113 522 0.87
114 77 0.13
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
Found at i:1549575 original size:84 final size:84
Alignment explanation
Indices: 1549242--1549587 Score: 541
Period size: 84 Copynumber: 4.1 Consensus size: 84
1549232 GTAATTTTTA
* * *
1549242 CCAAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
***
1549307 AATTCAATGATTGGTTTTA
66 AATTCAATGATTGGTTCCG
* * * *
1549326 CCAAACCAAATCAGATAATTCAAAGAACACTTCCAGAATATGCTATTGAGCACATTCATCTTCTA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1549391 AATTCAATGATTGGTTCCG
66 AATTCAATGATTGGTTCCG
* *
1549410 TCCAACT-AGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCT
1 -CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCT
1549474 AAATTCAATGATTGGTTCCG
65 AAATTCAATGATTGGTTCCG
*
1549494 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCATATTCATCTTCTA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
*
1549559 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCCG
*
1549578 CTAAATCAGA
1 CCAAATCAGA
1549588 ACACTTATTT
Statistics
Matches: 241, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
83 5 0.02
84 232 0.96
85 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (84 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
AATTCAATGATTGGTTCCG
Found at i:1550717 original size:17 final size:17
Alignment explanation
Indices: 1550695--1550759 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
1550685 TCCCTTTCTT
*
1550695 TTTCTTCTTCTTTTTTC
1 TTTCTTTTTCTTTTTTC
1550712 TTTCTTTTTTCTTTTTTC
1 TTTC-TTTTTCTTTTTTC
*
1550730 TATT-TTTTTCTATTTTC
1 T-TTCTTTTTCTTTTTTC
1550747 TTTCTTTTCTCTT
1 TTTCTTTT-TCTT
1550760 AAGCATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 2 0.05
17 21 0.51
18 16 0.39
19 2 0.05
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTTC
Found at i:1550749 original size:24 final size:24
Alignment explanation
Indices: 1550688--1550752 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
1550678 TTGACCCTCC
*
1550688 CTTTCTTTTTC-TTCTTCTTTTTT
1 CTTTCTTTTTCTTTCTTCTATTTT
*
1550711 CTTTCTTTTTTCTTTTTTCTATTTT
1 CTTTC-TTTTTCTTTCTTCTATTTT
1550736 -TTTCTATTTTCTTTCTT
1 CTTTCT-TTTTCTTTCTT
1550753 TTCTCTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.56
25 10 0.28
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (24 bp):
CTTTCTTTTTCTTTCTTCTATTTT
Found at i:1557968 original size:14 final size:15
Alignment explanation
Indices: 1557949--1557980 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1557939 ATTTTTTTTA
1557949 AATTTTAA-TTAATG
1 AATTTTAACTTAATG
1557963 AATTTTAACTTAATG
1 AATTTTAACTTAATG
1557978 AAT
1 AAT
1557981 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTTAACTTAATG
Found at i:1561348 original size:29 final size:28
Alignment explanation
Indices: 1561288--1561350 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1561278 CTTCGACAGA
1561288 AAAAT-AAATAATAACATAAAATACTTG
1 AAAATAAAATAATAACATAAAATACTTG
* *
1561315 CAAATAAAATAA-AACATATAAATATTATG
1 AAAATAAAATAATAACATA-AAATACT-TG
1561344 AAAATAA
1 AAAATAA
1561351 TAAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 10 0.33
28 12 0.40
29 8 0.27
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAATAAAATAATAACATAAAATACTTG
Found at i:1561352 original size:27 final size:27
Alignment explanation
Indices: 1561288--1561364 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 27
1561278 CTTCGACAGA
1561288 AAAATAAATAATAACATA-AAATACTTGC
1 AAAAT-AATAA-AACATATAAATACTTGC
* *
1561316 AAATAAAATAAAACATATAAATATTATG-
1 AAA-ATAATAAAACATATAAATACT-TGC
*
1561344 AAAATAATAAATATATATAAA
1 AAAATAATAAA-ACATATAAA
1561365 AATTTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 13 0.32
28 25 0.61
29 3 0.07
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAATAATAAAACATATAAATACTTGC
Found at i:1561353 original size:18 final size:19
Alignment explanation
Indices: 1561323--1561367 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1561313 TGCAAATAAA
1561323 ATAAAACAT-ATAAATAT-T
1 ATAAAA-ATAATAAATATAT
*
1561341 ATGAAAATAATAAATATAT
1 ATAAAAATAATAAATATAT
1561360 ATAAAAAT
1 ATAAAAAT
1561368 TTTAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATAATAAATATAT
Found at i:1563526 original size:3 final size:3
Alignment explanation
Indices: 1563518--1563621 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
1563508 TTAATATATT
*
1563518 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1563566 AAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1563614 TAA TAA TA
1 TAA TAA TA
1563622 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1564361 original size:16 final size:16
Alignment explanation
Indices: 1564340--1564373 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1564330 TTAAATGATG
1564340 TGTCATTATTGTATGA
1 TGTCATTATTGTATGA
1564356 TGTCATTATTGTATGA
1 TGTCATTATTGTATGA
1564372 TG
1 TG
1564374 ACATATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.50
Consensus pattern (16 bp):
TGTCATTATTGTATGA
Found at i:1564729 original size:21 final size:21
Alignment explanation
Indices: 1564696--1564741 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 21
1564686 GTTGTTATAT
*
1564696 TCAAGACAAAAAGAAAAGAAA
1 TCAAAACAAAAAGAAAAGAAA
1564717 TCAAAACAGAAAGAGAAGAAGAAA
1 TCAAAACA-AAA-AGAA-AAGAAA
1564741 T
1 T
1564742 ATGATGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 4 0.19
24 7 0.33
ACGTcount: A:0.67, C:0.09, G:0.17, T:0.07
Consensus pattern (21 bp):
TCAAAACAAAAAGAAAAGAAA
Found at i:1565252 original size:5 final size:5
Alignment explanation
Indices: 1565233--1565311 Score: 74
Period size: 5 Copynumber: 15.4 Consensus size: 5
1565223 TGCCCCGTTC
*
1565233 TTTTA -TTTA -TTTA TTTTA TTTTTA TTTTTA TTTT- CTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
*
1565282 TCTTTA TGTTA TTTTA TTATTA TTATTA TT
1 T-TTTA TTTTA TTTTA TT-TTA TT-TTA TT
1565312 GCTGGCCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
4 11 0.17
5 27 0.42
6 27 0.42
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1565261 original size:25 final size:25
Alignment explanation
Indices: 1565233--1565311 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 25
1565223 TGCCCCGTTC
1565233 TTTTATTTATTTATTTTATTTTTAT
1 TTTTATTTATTTATTTTATTTTTAT
*
1565258 TTTTATTTTCTTTATTTTA-TTTTAT
1 TTTTA-TTTATTTATTTTATTTTTAT
* *
1565283 CTTTATGTTATTTTATTATTATTATTAT
1 TTTTAT-TTA-TTTATT-TTATTTTTAT
1565311 T
1 T
1565312 GCTGGCCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.02
25 17 0.39
26 18 0.41
27 3 0.07
28 5 0.11
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTATTTATTTATTTTATTTTTAT
Found at i:1565264 original size:21 final size:20
Alignment explanation
Indices: 1565238--1565305 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
1565228 CGTTCTTTTA
1565238 TTTATTTATTTTATTTTTATT
1 TTTATTTATTTTA-TTTTATT
1565259 TTTATTT-TCTTTATTTTATT
1 TTTATTTAT-TTTATTTTATT
* *
1565279 TTATCTTTATGTTATTTTATT
1 TT-TATTTATTTTATTTTATT
*
1565300 ATTATT
1 TTTATT
1565306 ATTATTGCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 13 0.32
21 26 0.65
22 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTATTTATTTTATTTTATT
Found at i:1574749 original size:25 final size:26
Alignment explanation
Indices: 1574710--1574759 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1574700 AATCTCGAAT
1574710 ATTTAATTTAATTT-AAATAAATAAAG
1 ATTTAATTTAATTTAAAAT-AATAAAG
1574736 ATTTAA-TTAATTTAAAATAATAAA
1 ATTTAATTTAATTTAAAATAATAAA
1574760 ATCCCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTTAATTTAATTTAAAATAATAAAG
Found at i:1582392 original size:44 final size:44
Alignment explanation
Indices: 1582319--1582421 Score: 163
Period size: 44 Copynumber: 2.3 Consensus size: 44
1582309 TTTATGTGCA
* *
1582319 ATGCATCGATACACTATGATAGTGTACCGATGCA-TCCCTTGAAT
1 ATGCATCGATACACTATGAAAGTGCACCGATGCAGT-CCTTGAAT
1582363 ATGCATCGATACACTATGAAAGTGCACCGATGCAGTCCTTGAAT
1 ATGCATCGATACACTATGAAAGTGCACCGATGCAGTCCTTGAAT
*
1582407 GTGCATCGATACACT
1 ATGCATCGATACACT
1582422 CTGCAGTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 54 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCATCGATACACTATGAAAGTGCACCGATGCAGTCCTTGAAT
Found at i:1582933 original size:13 final size:14
Alignment explanation
Indices: 1582903--1582937 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1582893 TCCATATTGA
1582903 TTTTCAAACATAGT
1 TTTTCAAACATAGT
1582917 TTTTCAAACATAG-
1 TTTTCAAACATAGT
1582930 TTTTCAAA
1 TTTTCAAA
1582938 ATTGCCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTTCAAACATAGT
Found at i:1584428 original size:2 final size:2
Alignment explanation
Indices: 1584421--1584447 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1584411 CTTGAATGCT
1584421 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 T
1584448 TTGATTTGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1584741 original size:36 final size:36
Alignment explanation
Indices: 1584701--1584772 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1584691 AAAGGGAGAG
1584701 AATAAAGTAAGGGGGAGTAATTTCAAAAATTGATGA
1 AATAAAGTAAGGGGGAGTAATTTCAAAAATTGATGA
1584737 AATAAAGTAAGGGGGAGTAATTTCAAAAATTGATGA
1 AATAAAGTAAGGGGGAGTAATTTCAAAAATTGATGA
1584773 TTTCAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (36 bp):
AATAAAGTAAGGGGGAGTAATTTCAAAAATTGATGA
Found at i:1587043 original size:119 final size:119
Alignment explanation
Indices: 1586832--1587056 Score: 315
Period size: 119 Copynumber: 1.9 Consensus size: 119
1586822 ATCTACCCTG
** * * * * * *
1586832 AAGAGCAACGGAGTAGATCCCTTTTTCAGATTTGATCTTCCTTGAGAAGCAGTTGAAGAAATCTG
1 AAGAGCAACAAAGCAGATCCCTTTTACAGATTTGATCTTCCCTGAGAAGCAGTGGAACAAATATG
1586897 GCTAGATTCAATCTTCCCTGAAGAGCAGTAAAATGAATCAATGTTTTAGATCTA
66 GCTAGATTCAATCTTCCCTGAAGAGCAGTAAAATGAATCAATGTTTTAGATCTA
* * *
1586951 AAGAGCAACAAAGCAGATTCCTTTTACATATTTGATCTTCCCTGAGGAGCAGTGGAACAAATATG
1 AAGAGCAACAAAGCAGATCCCTTTTACAGATTTGATCTTCCCTGAGAAGCAGTGGAACAAATATG
* * * *
1587016 GCTCGATTCAATTTTCCCTGAAGAGCAGTGAAGTGAATCAA
66 GCTAGATTCAATCTTCCCTGAAGAGCAGTAAAATGAATCAA
1587057 CATTTCCAGA
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
119 91 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (119 bp):
AAGAGCAACAAAGCAGATCCCTTTTACAGATTTGATCTTCCCTGAGAAGCAGTGGAACAAATATG
GCTAGATTCAATCTTCCCTGAAGAGCAGTAAAATGAATCAATGTTTTAGATCTA
Found at i:1588784 original size:2 final size:2
Alignment explanation
Indices: 1588777--1588830 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1588767 ATAACATGTT
1588777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1588818 TA TA TA CA TA TA T
1 TA TA TA TA TA TA T
1588831 TTACATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1588835 original size:10 final size:10
Alignment explanation
Indices: 1588777--1588841 Score: 69
Period size: 10 Copynumber: 6.6 Consensus size: 10
1588767 ATAACATGTT
*
1588777 TATATATATA
1 TATATATACA
*
1588787 TATATATATA
1 TATATATACA
*
1588797 TATATATATA
1 TATATATACA
*
1588807 TATATAT-TA
1 TATATATACA
1588816 TATATATACA
1 TATATATACA
*
1588826 TATATTTACA
1 TATATATACA
*
1588836 TTTATA
1 TATATA
1588842 CTAAAATACA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
9 9 0.18
10 41 0.82
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATATACA
Found at i:1590682 original size:23 final size:23
Alignment explanation
Indices: 1590655--1590744 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 23
1590645 GAAGTGCCAT
*
1590655 ATAGATTTTTCCCGAAGGACCAC
1 ATAGATTTGTCCCGAAGGACCAC
*
1590678 GTAGAATTTGTCCCGAA-GACCAC
1 ATAG-ATTTGTCCCGAAGGACCAC
* *
1590701 ATAGAATTGTCTCGAAGGACCAC
1 ATAGATTTGTCCCGAAGGACCAC
*
1590724 ATAGATTTGTCCCGAATGACC
1 ATAGATTTGTCCCGAAGGACC
1590745 GCGTATAACC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
22 10 0.18
23 36 0.63
24 11 0.19
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
ATAGATTTGTCCCGAAGGACCAC
Found at i:1596909 original size:3 final size:3
Alignment explanation
Indices: 1596903--1596935 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1596893 ATAATACCGG
1596903 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1596936 CAGAAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1604570 original size:23 final size:22
Alignment explanation
Indices: 1604522--1604570 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1604512 TTTGTAAATT
* * *
1604522 TTTAAATTTATTTATCCTTTTT
1 TTTAAATTTATTTATCATATTA
1604544 TTTAAATTTTATTTATCATATTA
1 TTTAAA-TTTATTTATCATATTA
1604567 TTTA
1 TTTA
1604571 GATGGAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAAATTTATTTATCATATTA
Found at i:1605149 original size:12 final size:12
Alignment explanation
Indices: 1605132--1605156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1605122 GTAATTCCCA
1605132 AAAATTTTGACT
1 AAAATTTTGACT
1605144 AAAATTTTGACT
1 AAAATTTTGACT
1605156 A
1 A
1605157 CTAATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTTTGACT
Found at i:1606461 original size:20 final size:20
Alignment explanation
Indices: 1606417--1606455 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1606407 TACTTTTTTG
1606417 GAATTTAATGTTAGAATGTT
1 GAATTTAATGTTAGAATGTT
* *
1606437 GAATTTGATGTTATAATGT
1 GAATTTAATGTTAGAATGT
1606456 GAAATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
GAATTTAATGTTAGAATGTT
Found at i:1607414 original size:81 final size:81
Alignment explanation
Indices: 1607327--1607485 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 81
1607317 TTTAGAGTCA
* * *
1607327 TTTTTTATAAATGCTGCTATAACTCATTCTTAGTGGTGTTTTTGAGACAAACGCCGTTAAAGACT
1 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGTTTTTGAGACAAACGCCGCTAAAGACT
1607392 AATGCGTTAGTGGTGT
66 AATGCGTTAGTGGTGT
* *
1607408 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGTTTTTTAGACTAACGCCGCTAAAGACT
1 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGTTTTTGAGACAAACGCCGCTAAAGACT
* *
1607473 CATGTGTTAGTGG
66 AATGCGTTAGTGG
1607486 CATTTTTCTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (81 bp):
TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGTTTTTGAGACAAACGCCGCTAAAGACT
AATGCGTTAGTGGTGT
Found at i:1607450 original size:39 final size:39
Alignment explanation
Indices: 1607327--1607451 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 39
1607317 TTTAGAGTCA
* *
1607327 TTTTTTATAAATGCTGCTATAACTCATTCTTAGTGGTGT
1 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGT
** * * * * *
1607366 TTTTGAGACAAACGCCGTTAAAGACTAATGCGTTAGTGGTGT
1 TTTT-TTATAAACGCCGCTATA-ACTCATTC-TTAGTGGTGT
1607408 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGT
1 TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGT
1607447 TTTTT
1 TTTTT
1607452 AGACTAACGC
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
39 19 0.28
40 16 0.24
41 18 0.27
42 14 0.21
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (39 bp):
TTTTTTATAAACGCCGCTATAACTCATTCTTAGTGGTGT
Found at i:1607492 original size:42 final size:41
Alignment explanation
Indices: 1607348--1607485 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
1607338 TGCTGCTATA
* * *
1607348 ACTCATTCTTAGTGGTGTTTTTGAGACAAACGCCGTTAAAG
1 ACTCATTCTTAGTGGTGTTTTTTAGACTAACGCCGCTAAAG
* * * *
1607389 ACTAATGCGTTAGTGGTGTTTTTT-TA-TAAACGCCGCTATA-
1 ACTCATTC-TTAGTGGTGTTTTTTAGACT-AACGCCGCTAAAG
1607429 ACTCATTCTTAGTGGTGTTTTTTAGACTAACGCCGCTAAAG
1 ACTCATTCTTAGTGGTGTTTTTTAGACTAACGCCGCTAAAG
*
1607470 ACTCATGTGTTAGTGG
1 ACTCAT-TCTTAGTGG
1607486 CATTTTTCTA
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
39 15 0.19
40 18 0.23
41 24 0.30
42 22 0.28
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (41 bp):
ACTCATTCTTAGTGGTGTTTTTTAGACTAACGCCGCTAAAG
Found at i:1609369 original size:43 final size:44
Alignment explanation
Indices: 1609318--1609434 Score: 164
Period size: 44 Copynumber: 2.7 Consensus size: 44
1609308 AAAAAGGGCG
1609318 CTATAGAACCTGACCTGTTGCAGCGTTTGTA-TAAAAAACGTCA
1 CTATAGAACCTGACCTGTTGCAGCGTTTGTATTAAAAAACGTCA
* * * *
1609361 TTATAGAACATGACCTGTTGCAACGTTTGTATTAAAAAACGTCG
1 CTATAGAACCTGACCTGTTGCAGCGTTTGTATTAAAAAACGTCA
* **
1609405 CTATAGAACCTAACCTGTTGTGGCGTTTGT
1 CTATAGAACCTGACCTGTTGCAGCGTTTGT
1609435 GAAAGTAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 28 0.44
44 35 0.56
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (44 bp):
CTATAGAACCTGACCTGTTGCAGCGTTTGTATTAAAAAACGTCA
Found at i:1609434 original size:44 final size:43
Alignment explanation
Indices: 1609298--1609424 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 43
1609288 ACTAGTTGTG
* *
1609298 ACGTTTGTAT-AAAAAGGGCGCTATAGAACCTGACCTGTTGCA
1 ACGTTTGTATAAAAAACGTCGCTATAGAACCTGACCTGTTGCA
* ** *
1609340 GCGTTTGTATAAAAAACGTCATTATAGAACATGACCTGTTGCA
1 ACGTTTGTATAAAAAACGTCGCTATAGAACCTGACCTGTTGCA
*
1609383 ACGTTTGTATTAAAAAACGTCGCTATAGAACCTAACCTGTTG
1 ACGTTTGTA-TAAAAAACGTCGCTATAGAACCTGACCTGTTG
1609425 TGGCGTTTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 9 0.12
43 35 0.49
44 28 0.39
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (43 bp):
ACGTTTGTATAAAAAACGTCGCTATAGAACCTGACCTGTTGCA
Found at i:1610138 original size:28 final size:29
Alignment explanation
Indices: 1610076--1610144 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
1610066 TGGTGCAAGT
* *
1610076 TATAAGAGGCACTTTCGAGTGCATATTCC
1 TATATGAGGCACTTTCGAGTGCATATTCA
*
1610105 TA-ATGAGGCACTTTCGAGTGCA-ATTGA
1 TATATGAGGCACTTTCGAGTGCATATTCA
1610132 TATATGATGGCAC
1 TATATGA-GGCAC
1610145 ATGGAGTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.14
28 23 0.66
29 7 0.20
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (29 bp):
TATATGAGGCACTTTCGAGTGCATATTCA
Found at i:1610665 original size:172 final size:172
Alignment explanation
Indices: 1610379--1610723 Score: 681
Period size: 172 Copynumber: 2.0 Consensus size: 172
1610369 ATTGATTTGA
1610379 CACTATATGCCTTATGCATATATGTGAAAGGATGGTTTTATAAGTTACTATTACCGTATAAGGAA
1 CACTATATGCCTTATGCATATATGTGAAAGGATGGTTTTATAAGTTACTATTACCGTATAAGGAA
1610444 AAAGGTTTGAAGTATCAATTTTATATATTTTTATATGACAGTGGTAGCACTTTAGTTATGTATAA
66 AAAGGTTTGAAGTATCAATTTTATATATTTTTATATGACAGTGGTAGCACTTTAGTTATGTATAA
1610509 TCTTTTCATAGTTTAAAATATCTTACCTTAGTTTATATGGCC
131 TCTTTTCATAGTTTAAAATATCTTACCTTAGTTTATATGGCC
1610551 CACTATATGCCTTATGCATATATGTGAAAGGATGGTTTTATAAGTTACTATTACCGTATAAGGAA
1 CACTATATGCCTTATGCATATATGTGAAAGGATGGTTTTATAAGTTACTATTACCGTATAAGGAA
*
1610616 AAAGGTTTGAATTATCAATTTTATATATTTTTATATGACAGTGGTAGCACTTTAGTTATGTATAA
66 AAAGGTTTGAAGTATCAATTTTATATATTTTTATATGACAGTGGTAGCACTTTAGTTATGTATAA
1610681 TCTTTTCATAGTTTAAAATATCTTACCTTAGTTTATATGGCC
131 TCTTTTCATAGTTTAAAATATCTTACCTTAGTTTATATGGCC
1610723 C
1 C
1610724 CCTAGTGAAA
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (172 bp):
CACTATATGCCTTATGCATATATGTGAAAGGATGGTTTTATAAGTTACTATTACCGTATAAGGAA
AAAGGTTTGAAGTATCAATTTTATATATTTTTATATGACAGTGGTAGCACTTTAGTTATGTATAA
TCTTTTCATAGTTTAAAATATCTTACCTTAGTTTATATGGCC
Found at i:1611169 original size:16 final size:17
Alignment explanation
Indices: 1611148--1611180 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1611138 AATTTTTGAT
1611148 TTTTAGTAATT-AAATA
1 TTTTAGTAATTGAAATA
*
1611164 TTTTAGTGATTGAAATA
1 TTTTAGTAATTGAAATA
1611181 AATTTGACGA
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:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTTAGTAATTGAAATA
Found at i:1614743 original size:21 final size:22
Alignment explanation
Indices: 1614719--1614774 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1614709 TTCTTTTGAC
1614719 GGATCGATCATTTTCTCC-AAG
1 GGATCGATCATTTTCTCCTAAG
* * *
1614740 GGATCAATC-CTTTCTCCTGAG
1 GGATCGATCATTTTCTCCTAAG
1614761 GGATCGATCATTTT
1 GGATCGATCATTTT
1614775 GAAAAGCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (22 bp):
GGATCGATCATTTTCTCCTAAG
Found at i:1623230 original size:26 final size:26
Alignment explanation
Indices: 1623201--1623254 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1623191 ATCAAAAGAG
*
1623201 TTGGTTCAAAGGCTTATTAGCTAGTA
1 TTGGTTCAAAAGCTTATTAGCTAGTA
1623227 TTGGTTCAAAAGCTTATTAGCTAGTA
1 TTGGTTCAAAAGCTTATTAGCTAGTA
1623253 TT
1 TT
1623255 ACCCCGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (26 bp):
TTGGTTCAAAAGCTTATTAGCTAGTA
Found at i:1624891 original size:20 final size:20
Alignment explanation
Indices: 1624847--1624885 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1624837 CACTATGCTG
1624847 GAATTTAATGTTAGAATGTT
1 GAATTTAATGTTAGAATGTT
1624867 GAATTTAATGTTAGAATGT
1 GAATTTAATGTTAGAATGT
1624886 GAAATTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (20 bp):
GAATTTAATGTTAGAATGTT
Found at i:1637543 original size:16 final size:16
Alignment explanation
Indices: 1637530--1637563 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1637520 GAATTTTTTT
1637530 AAAAAAATATTTTTAA
1 AAAAAAATATTTTTAA
1637546 AAAAAAATATTTTTAA
1 AAAAAAATATTTTTAA
1637562 AA
1 AA
1637564 TTATTTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAAATATTTTTAA
Found at i:1637544 original size:14 final size:14
Alignment explanation
Indices: 1637525--1637563 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
1637515 GTGACGAATT
1637525 TTTTTAAAAAAATA
1 TTTTTAAAAAAATA
1637539 TTTTTAAAAAAAAATA
1 TTTTT--AAAAAAATA
1637555 TTTTTAAAA
1 TTTTTAAAA
1637564 TTATTTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
16 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTTAAAAAAATA
Found at i:1638685 original size:14 final size:14
Alignment explanation
Indices: 1638666--1638698 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1638656 CTTAAAATCC
*
1638666 TAAATTTTAAAATT
1 TAAATTCTAAAATT
1638680 TAAATTCTAAAATT
1 TAAATTCTAAAATT
1638694 TAAAT
1 TAAAT
1638699 AATAAATTAT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTCTAAAATT
Found at i:1646681 original size:47 final size:47
Alignment explanation
Indices: 1646612--1646705 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1646602 ATCAGAGAGT
1646612 GGCAGTTAGGGAAGAATTGTTGAAGCGAGGAGTGATAGGGATTGATG
1 GGCAGTTAGGGAAGAATTGTTGAAGCGAGGAGTGATAGGGATTGATG
1646659 GGCAGTTAGGGAAGAATTGTTGAAGCGAGGAGTGATAGGGATTGATG
1 GGCAGTTAGGGAAGAATTGTTGAAGCGAGGAGTGATAGGGATTGATG
1646706 ACTCTTTGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.04, G:0.43, T:0.23
Consensus pattern (47 bp):
GGCAGTTAGGGAAGAATTGTTGAAGCGAGGAGTGATAGGGATTGATG
Found at i:1646702 original size:25 final size:25
Alignment explanation
Indices: 1646627--1646702 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
1646617 TTAGGGAAGA
1646627 ATTGTTGAAGCGAGGAGTGATAGGG
1 ATTGTTGAAGCGAGGAGTGATAGGG
* * * * *
1646652 ATTGATG-GGC-AGTTAGGGA-A-GA
1 ATTGTTGAAGCGAG-GAGTGATAGGG
1646674 ATTGTTGAAGCGAGGAGTGATAGGG
1 ATTGTTGAAGCGAGGAGTGATAGGG
1646699 ATTG
1 ATTG
1646703 ATGACTCTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 7 0.19
23 9 0.25
24 9 0.25
25 11 0.31
ACGTcount: A:0.29, C:0.04, G:0.42, T:0.25
Consensus pattern (25 bp):
ATTGTTGAAGCGAGGAGTGATAGGG
Found at i:1656360 original size:31 final size:30
Alignment explanation
Indices: 1656320--1656384 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
1656310 TGTAAACTTC
*
1656320 AAGATTAATCACTTCCATTTTTATTTAATT
1 AAGATTAATCACTTCCATCTTTATTTAATT
* *
1656350 AAGATTTAATCACTTTCATCTTTATTTAGTT
1 AAGA-TTAATCACTTCCATCTTTATTTAATT
1656381 AAGA
1 AAGA
1656385 CATGGTCACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (30 bp):
AAGATTAATCACTTCCATCTTTATTTAATT
Found at i:1658600 original size:17 final size:17
Alignment explanation
Indices: 1658578--1658611 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1658568 AAATCATCTT
1658578 CGATTCTCATTTTGTAA
1 CGATTCTCATTTTGTAA
*
1658595 CGATTCTTATTTTGTAA
1 CGATTCTCATTTTGTAA
1658612 ACTGGGGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (17 bp):
CGATTCTCATTTTGTAA
Found at i:1658727 original size:13 final size:13
Alignment explanation
Indices: 1658709--1658733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1658699 AGCAAAGGTT
1658709 CTTTACATTTTAG
1 CTTTACATTTTAG
1658722 CTTTACATTTTA
1 CTTTACATTTTA
1658734 TTATTATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
CTTTACATTTTAG
Found at i:1659786 original size:2 final size:2
Alignment explanation
Indices: 1659735--1659768 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1659725 AAATCCTACT
1659735 TA TA -A 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 T
1659769 TTACTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1659928 original size:2 final size:2
Alignment explanation
Indices: 1659921--1659960 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1659911 TAAAAACCTA
1659921 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
1659961 GTATGTATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1663720 original size:10 final size:10
Alignment explanation
Indices: 1663705--1663780 Score: 70
Period size: 10 Copynumber: 7.5 Consensus size: 10
1663695 CATTAATCAT
1663705 AAAAAAGAAG
1 AAAAAAGAAG
1663715 AAAAAA-AAG
1 AAAAAAGAAG
1663724 AGAAAAAG-AG
1 A-AAAAAGAAG
1663734 AAAAAA-AAG
1 AAAAAAGAAG
1663743 AAAAAAAGAA-
1 -AAAAAAGAAG
1663753 AAGAAAAGAAAAG
1 AA-AAAAG--AAG
*
1663766 AAAAAAGATG
1 AAAAAAGAAG
1663776 AAAAA
1 AAAAA
1663781 TAAAATAAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
9 13 0.23
10 32 0.57
11 2 0.04
12 7 0.12
13 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:1663724 original size:9 final size:9
Alignment explanation
Indices: 1663705--1663769 Score: 78
Period size: 10 Copynumber: 6.9 Consensus size: 9
1663695 CATTAATCAT
1663705 AAAAAAGAAG
1 AAAAAA-AAG
1663715 AAAAAAAAG
1 AAAAAAAAG
*
1663724 AGAAAAAGAG
1 A-AAAAAAAG
1663734 AAAAAAAAG
1 AAAAAAAAG
1663743 -AAAAAAAG
1 AAAAAAAAG
1663751 AAAAGAAAAG
1 AAAA-AAAAG
1663761 AAAAGAAAA
1 AAAA-AAAA
1663770 AAGATGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
8 8 0.16
9 14 0.28
10 28 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1663735 original size:19 final size:18
Alignment explanation
Indices: 1663705--1663764 Score: 86
Period size: 18 Copynumber: 3.2 Consensus size: 18
1663695 CATTAATCAT
1663705 AAAAAAGAAGAAAAAAAAG
1 AAAAAAG-AGAAAAAAAAG
1663724 AGAAAAAGAGAAAAAAAAG
1 A-AAAAAGAGAAAAAAAAG
1663743 AAAAAA-AGAAAAGAAAAG
1 AAAAAAGAGAAAA-AAAAG
1663761 AAAA
1 AAAA
1663765 GAAAAAAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.15
18 14 0.36
19 13 0.33
20 6 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:1663737 original size:17 final size:17
Alignment explanation
Indices: 1663712--1663780 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
1663702 CATAAAAAAG
*
1663712 AAGAAAAAAAAGAGAAA
1 AAGAGAAAAAAGAGAAA
*
1663729 AAGAGAAAAAAAAGAAA
1 AAGAGAAAAAAGAGAAA
*
1663746 AA-A-AGAAAAGA-AAA
1 AAGAGAAAAAAGAGAAA
*
1663760 GAAAAGAAAAAAGATGAAA
1 -AAGAGAAAAAAGA-GAAA
1663779 AA
1 AA
1663781 TAAAATAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.07
15 8 0.19
16 2 0.05
17 24 0.57
18 2 0.05
19 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (17 bp):
AAGAGAAAAAAGAGAAA
Found at i:1666113 original size:54 final size:54
Alignment explanation
Indices: 1666031--1666186 Score: 231
Period size: 54 Copynumber: 2.9 Consensus size: 54
1666021 GAGAATTAAA
*
1666031 GCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGG
1 GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGG
* * * * **
1666085 GCAGAAACCACAGGAAAGGATGATTGTGTTGTCAAATGTTTTATGAACATCTTT
1 GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGG
* *
1666139 GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATATTTCACGAAC
1 GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1666187 CAGAGATTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (54 bp):
GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGG
Found at i:1666576 original size:20 final size:20
Alignment explanation
Indices: 1666551--1666616 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
1666541 ACATCTACAT
*
1666551 TCTTCAAAGATGATAGATTC
1 TCTTCAAAGATGATAAATTC
1666571 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAA-T-TC
*
1666593 TCTTCAAAGATGATATATTC
1 TCTTCAAAGATGATAAATTC
1666613 TCTT
1 TCTT
1666617 TTTAAAGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.52
21 2 0.05
22 18 0.43
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
TCTTCAAAGATGATAAATTC
Found at i:1666597 original size:22 final size:22
Alignment explanation
Indices: 1666551--1666627 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
1666541 ACATCTACAT
*
1666551 TCTTCAAAGATGATAGA-T-TC
1 TCTTCAAAGATGATAAATTCTC
1666571 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
1666593 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAAATTCTC
* *
1666615 TTTTTAAAGATGA
1 TCTTCAAAGATGA
1666628 AAGCTCTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.31
21 1 0.02
22 34 0.67
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:1667437 original size:73 final size:73
Alignment explanation
Indices: 1667315--1667575 Score: 441
Period size: 73 Copynumber: 3.6 Consensus size: 73
1667305 TGATGTTTTC
*
1667315 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAATTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
1667380 TTCACTTG
66 TTCACTTG
* *
1667388 AAATATCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTTTCTTGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
1667453 TTCACTTG
66 TTCACTTG
* * * * *
1667461 AAATAGCAATTTATCTAACTTGAGATTGTTTTTCTTAAAACAAACTATTTTTCGCTGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
1667526 TTCACTTG
66 TTCACTTG
*
1667534 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
1667576 TTTGAATGAG
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 177 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
TTCACTTG
Found at i:1667637 original size:39 final size:39
Alignment explanation
Indices: 1667583--1667837 Score: 348
Period size: 39 Copynumber: 6.5 Consensus size: 39
1667573 ACATTTGAAT
* **
1667583 GAGTTCATATTCTGAAGAACTCGGCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
*
1667622 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * *
1667661 GAGTTCATAGTATGAATAACTCATCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * *
1667700 GAGTTCATAGTCTGAAGAACTCATATGAAGAGCAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * * *
1667739 GAGTTTATAATATGAAGAACTCGTCTGAAGAGGAAGAAA
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
1667778 AAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAA
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
1667817 AAGTTCATAGTCTGAAGAACT
1 GAGTTCATAATCTGAAGAACT
1667838 TATTCAACCT
Statistics
Matches: 194, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 194 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (39 bp):
GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
Found at i:1667799 original size:117 final size:117
Alignment explanation
Indices: 1667583--1667837 Score: 384
Period size: 117 Copynumber: 2.2 Consensus size: 117
1667573 ACATTTGAAT
* * * * *
1667583 GAGTTCATATTCTGAAGAACTCGGCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCT
1 GAGTTCATAGTCTGAAGAACTCAGATGAAGAGCAAGAAGGAGTTCATAATATGAAGAACTCGTCT
** * * *
1667648 GAAGAGGAAGAAGGAGTTCATAGTATGAATAACTCATCTGAAGAGGAAGAAG
66 GAAGAGGAAGAAAAAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAA
* *
1667700 GAGTTCATAGTCTGAAGAACTCATATGAAGAGCAAGAAGGAGTTTATAATATGAAGAACTCGTCT
1 GAGTTCATAGTCTGAAGAACTCAGATGAAGAGCAAGAAGGAGTTCATAATATGAAGAACTCGTCT
*
1667765 GAAGAGGAAGAAAAAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAA
66 GAAGAGGAAGAAAAAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAA
*
1667817 AAGTTCATAGTCTGAAGAACT
1 GAGTTCATAGTCTGAAGAACT
1667838 TATTCAACCT
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 124 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (117 bp):
GAGTTCATAGTCTGAAGAACTCAGATGAAGAGCAAGAAGGAGTTCATAATATGAAGAACTCGTCT
GAAGAGGAAGAAAAAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAA
Found at i:1668049 original size:120 final size:120
Alignment explanation
Indices: 1667779--1668202 Score: 557
Period size: 120 Copynumber: 3.5 Consensus size: 120
1667769 AGGAAGAAAA
* * *
1667779 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAA-AAAGTTCATAGTCTGAAGAACTTATTC
1 AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAA-TTCATAATCTGAAGAACTT-GTC
* * * * *
1667843 AACCTTTTGCTTGACTTTATCGCAGAAGGAGATAGAGCAACA-AAATATTTCCAGAAAGG
64 AACC-TTAGCTCGA-TTCATCGCAGAAGGAGATAGATCAACATAAACATTTCCAG-AAGG
* *
1667902 AGTTCATAATCTGAAGAACTCATCTAAAAAGGAAGAAGAAATTCATAATATGAAGAACTTGT-AA
1 AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTGTCAA
* * * *
1667966 CCTTAGCTCGATTCATCGTAGAAGGAGATAGATCAACATCAACATTTCTATACAGG
66 CCTTAGCTCGATTCATCGCAGAAGGAGATAGATCAACATAAACATTTCCAGA-AGG
*
1668022 AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTGTTCA
1 AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTG-TCA
*
1668087 ACCTTAGCTCGATTCATCGCAGAAGGAGATAGATCAACATTAACATTTCCAGAAGG
65 ACCTTAGCTCGATTCATCGCAGAAGGAGATAGATCAACATAAACATTTCCAGAAGG
* ** * * * *
1668143 AGTTCGTAATGAGAAGAACTCATTTGAAGAGAAAGAAGAAGTTCATAATCTGAAGAACTT
1 AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTT
1668203 ATTCAACATT
Statistics
Matches: 269, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
119 25 0.09
120 76 0.28
121 62 0.23
122 51 0.19
123 52 0.19
124 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (120 bp):
AGTTCATAATCTGAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTGTCAA
CCTTAGCTCGATTCATCGCAGAAGGAGATAGATCAACATAAACATTTCCAGAAGG
Found at i:1669735 original size:2 final size:2
Alignment explanation
Indices: 1669682--1669718 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1669672 AAATTCTACT
1669682 TA TA -A 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
1669719 CACTTAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1673801 original size:46 final size:44
Alignment explanation
Indices: 1673730--1673845 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 44
1673720 CTCTTACTAT
* *
1673730 TTATCCCATAAGCTCGTAAGATTATTTTACCAA-ACTACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TACTTGCCA
* *
1673774 TTTAAATTCCATAAGC-CGTAAGCTTATTTTATCAATATACTTGTCA
1 -TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1673820 TTATT-CATAAGCTCGTAAGCTTATTT
1 TTATTCCATAAGCTCGTAAGCTTATTT
1673846 GCATACTTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
42 7 0.11
43 16 0.25
45 4 0.06
46 25 0.40
47 11 0.17
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:1674386 original size:67 final size:67
Alignment explanation
Indices: 1674276--1674416 Score: 257
Period size: 67 Copynumber: 2.1 Consensus size: 67
1674266 CATGTCAATT
1674276 TATAAAAATGACATAATAAAATGCTGTTATAAACGAGGTCGACTTATCGCAAGGCTTCCCGATGA
1 TATAAAAATGACATAATAAAATGCTGTTATAAACGAGGTCGACTTATCGCAAGGCTTCCCGATGA
1674341 TG
66 TG
*
1674343 TAATAAAAATGACATAAT-AAATGCTGTTATAAACGAGGTCGACTTATCGCAAGTCTTCCCGATG
1 T-ATAAAAATGACATAATAAAATGCTGTTATAAACGAGGTCGACTTATCGCAAGGCTTCCCGATG
1674407 ATG
65 ATG
1674410 TATAAAA
1 TATAAAA
1674417 TCCATATATA
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
66 6 0.08
67 50 0.69
68 16 0.22
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (67 bp):
TATAAAAATGACATAATAAAATGCTGTTATAAACGAGGTCGACTTATCGCAAGGCTTCCCGATGA
TG
Found at i:1675697 original size:49 final size:49
Alignment explanation
Indices: 1675640--1675736 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
1675630 TCTTCTTAAT
1675640 TACCATAAAACCATGACAACTCATCCTTATCATATTTCAAAGTCAAAGC
1 TACCATAAAACCATGACAACTCATCCTTATCATATTTCAAAGTCAAAGC
*
1675689 TACCATAAAACCATGACAATTCATCCTTATCATATTTCAAAGTCAAAG
1 TACCATAAAACCATGACAACTCATCCTTATCATATTTCAAAGTCAAAG
1675737 ATGAATTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (49 bp):
TACCATAAAACCATGACAACTCATCCTTATCATATTTCAAAGTCAAAGC
Found at i:1676276 original size:84 final size:84
Alignment explanation
Indices: 1676135--1676303 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
1676125 ACAGGCTACA
1676135 TGTCACATAAGAATCCTTATAACAGCTATATTGATGAGTACTCACAGGTTGTTTTCTTGTAGATT
1 TGTCACATAAGAATCCTTATAACAGCTATATTGATGAGTACTCACAGGTTGTTTTCTTGTAGATT
1676200 GCAGCTTTATCTGTGGCAT
66 GCAGCTTTATCTGTGGCAT
1676219 TGTCACATAAGAATCCTTATAACAGCTATATTGATGAGTACTCACAGGTTGTTTTCTTGTAGATT
1 TGTCACATAAGAATCCTTATAACAGCTATATTGATGAGTACTCACAGGTTGTTTTCTTGTAGATT
1676284 GCAGCTTTATCTGTGGCAT
66 GCAGCTTTATCTGTGGCAT
1676303 T
1 T
1676304 ATTCAGAGCT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (84 bp):
TGTCACATAAGAATCCTTATAACAGCTATATTGATGAGTACTCACAGGTTGTTTTCTTGTAGATT
GCAGCTTTATCTGTGGCAT
Found at i:1676801 original size:27 final size:27
Alignment explanation
Indices: 1676771--1676826 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1676761 GTTGATGAAT
1676771 TGACTGATGGAAAATCAATCTGTAATG
1 TGACTGATGGAAAATCAATCTGTAATG
1676798 TGACTGATGGAAAATCAATCTGTAATG
1 TGACTGATGGAAAATCAATCTGTAATG
1676825 TG
1 TG
1676827 CAGTCGGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (27 bp):
TGACTGATGGAAAATCAATCTGTAATG
Found at i:1683515 original size:30 final size:30
Alignment explanation
Indices: 1683479--1683539 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1683469 ACACATACAG
1683479 TGGCAATATGATGAAGACATTCAGCCCTTT
1 TGGCAATATGATGAAGACATTCAGCCCTTT
1683509 TGGCAATATGATGAAGACATTCAGCCCTTT
1 TGGCAATATGATGAAGACATTCAGCCCTTT
1683539 T
1 T
1683540 TCTTCACACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (30 bp):
TGGCAATATGATGAAGACATTCAGCCCTTT
Found at i:1691653 original size:3 final size:3
Alignment explanation
Indices: 1691645--1691688 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1691635 AACAAAAAAC
* *
1691645 AAT AAT AAT AAT AAT AATT TAT AAT ACT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
1691689 GATTAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1692154 original size:133 final size:133
Alignment explanation
Indices: 1691891--1692246 Score: 464
Period size: 133 Copynumber: 2.7 Consensus size: 133
1691881 GTTCTGGTCG
* * * *
1691891 TCTAAGGGTGACATGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACGACTCATACGT
1 TCTAGGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGT
*
1691956 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACACTGG
66 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACACTGG
1692021 TTA
131 TTA
* * * * *
1692024 TCTAGGGGTGACACGGCTCCTACGCGATGAGGAGATCTAGTCGGGGGATGACACGGCTCATACAT
1 TCTAGGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGT
* * * * * *
1692089 GATGAAGTGTTTTGGTCATCTTTTGGAA-GGTGATAACTCGGTTCTTATGCGATGAGGACGGCTG
66 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGAC-ACTG
1692153 GTTA
130 GTTA
* * * * * *
1692157 TCTAGGGGTGACATGGCTCCTACATGATGAAGAGGTCTGGTCAAGGGATGACACGGTTCCTACGT
1 TCTAGGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGT
* *
1692222 GATGAAGAAG-GCTGGCCATCTTTAG
66 GATGAAG-AGTTCTGGTCATCTTTAG
1692247 TGATTATGGT
Statistics
Matches: 189, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
132 28 0.15
133 160 0.85
134 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (133 bp):
TCTAGGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGT
GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACACTGG
TTA
Found at i:1692324 original size:28 final size:28
Alignment explanation
Indices: 1692271--1692334 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
1692261 AGGGAAACCG
* *
1692271 ACTCAAAGATTTGTTTTAAAAGAAACAT
1 ACTCAAAGATTTGTTTGAAAAGAAACAA
1692299 ACTCAAAGATTTGTTTGAAGAA-AAACAA
1 ACTCAAAGATTTGTTTGAA-AAGAAACAA
1692327 ACTCAAAG
1 ACTCAAAG
1692335 GTGATGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (28 bp):
ACTCAAAGATTTGTTTGAAAAGAAACAA
Found at i:1692518 original size:32 final size:34
Alignment explanation
Indices: 1692471--1692541 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 34
1692461 CAAAGATCGG
* *
1692471 TGTTTCGAGATAAACAAACTAAAAG-TTGTT-TT
1 TGTTTCAAGAAAAACAAACTAAAAGATTGTTGTT
* * *
1692503 TGTTTCAAGAAAAACATACTCAAAGATTTTTGTT
1 TGTTTCAAGAAAAACAAACTAAAAGATTGTTGTT
1692537 TGTTT
1 TGTTT
1692542 TGTTTCAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 21 0.66
33 4 0.12
34 7 0.22
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (34 bp):
TGTTTCAAGAAAAACAAACTAAAAGATTGTTGTT
Found at i:1692666 original size:65 final size:65
Alignment explanation
Indices: 1692572--1692693 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
1692562 CAAAGATGGT
* *
1692572 AAATTTTCTTTCCAAGAAATATACTCAAAGATTTTTCTT-AAAAGAAACTGTCTCAAAATAGACA
1 AAATTTTATTTCCAAGAAATAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAATAGACA
*
1692636 AAATTTTATTTCCAAAGAAATAAATTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAA
1 AAATTTTATTTCC-AAGAAATAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAA
1692694 GGGATAAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
64 12 0.23
65 24 0.45
66 17 0.32
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (65 bp):
AAATTTTATTTCCAAGAAATAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAATAGACA
Found at i:1692849 original size:31 final size:31
Alignment explanation
Indices: 1692776--1692841 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
1692766 TCAAAATTCG
* *
1692776 TTTCAAGAGAAA-TAACTCAAAGATGGTTTTA
1 TTTCAGGAGAAACAAACTCAAAGAT-GTTTTA
1692807 TTTCAGGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAGGAGAAACAAACTCAAAGATGTTT-TA
1692838 TTTC
1 TTTC
1692842 TTGAGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.10
31 17 0.55
32 11 0.35
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (31 bp):
TTTCAGGAGAAACAAACTCAAAGATGTTTTA
Found at i:1693073 original size:59 final size:62
Alignment explanation
Indices: 1692994--1693118 Score: 141
Period size: 63 Copynumber: 2.0 Consensus size: 62
1692984 TAAAATTTGG
* * *
1692994 TTTCAAAAGAAAAATACTC-AA-AGAT-GAGTTTTGTT-TCAAGGGAAACATACTCAAAGATT
1 TTTCAAAAGAAAAATACTCAAACAGATAAAATTTTGTTATCAA-AGAAACATACTCAAAGATT
** * *
1693053 TTTCAAAAGAAACTTTCTCAAACGAGATAAAATTTTGTTATCAAAGACACATACTCAAAGATT
1 TTTCAAAAGAAAAATACTCAAAC-AGATAAAATTTTGTTATCAAAGAAACATACTCAAAGATT
1693116 TTT
1 TTT
1693119 TCATTTTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 16 0.30
60 2 0.04
62 4 0.07
63 28 0.52
64 4 0.07
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (62 bp):
TTTCAAAAGAAAAATACTCAAACAGATAAAATTTTGTTATCAAAGAAACATACTCAAAGATT
Found at i:1693266 original size:36 final size:35
Alignment explanation
Indices: 1693219--1693292 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
1693209 ATAATTTGGA
*
1693219 AAATTGTCTCAAGTAAGACAACA-TTTGTTTTTAGAG
1 AAATTGTCTCAAGCAAGACAA-AGTTTGTTTTT-GAG
*
1693255 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAG
1 AAATTGTCTCAAGCAAGACAAAGTTTGTTTTTGAG
1693290 AAA
1 AAA
1693293 ACGATCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 7 0.20
36 28 0.80
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (35 bp):
AAATTGTCTCAAGCAAGACAAAGTTTGTTTTTGAG
Found at i:1693301 original size:36 final size:36
Alignment explanation
Indices: 1693224--1693317 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
1693214 TTGGAAAATT
* **
1693224 GTCTCAAGTAAGACAACATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAACATTTGTTTTTAGAGAAAAC
*
1693260 GTCTCAAGCGAGACAA-AGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAACA-TTTGTTTTTAGAGAAAAC
1693295 GATCTCAAGTGAGATCAAC-TTTG
1 G-TCTCAAGTGAGA-CAACATTTG
1693318 CTTAATGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
35 8 0.16
36 38 0.78
37 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (36 bp):
GTCTCAAGTGAGACAACATTTGTTTTTAGAGAAAAC
Found at i:1693502 original size:107 final size:104
Alignment explanation
Indices: 1693259--1693503 Score: 275
Period size: 107 Copynumber: 2.3 Consensus size: 104
1693249 TTAGAGAAAT
* ** *
1693259 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAG-AA-AACGATCTCAAGTGAGATCAACTTTGCTTA
1 TGTCTCAAGCGAGACGAAGTTTGTTTAAGAGAAATAACAATCTCAAGTGAGATCAACTTTGCTTA
*
1693322 ATGTGAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
66 ATGTGAACAAATTCAAAATTTGTATTATCAAAGGAAAAA
* * * * *
1693361 TGTCTCAAACGAGACGAAATTTGTTTTGAA-AGAAATAACAATCTCAAGTGAGATTAATTTTTGT
1 TGTCTCAAGCGAGACGAAGTTTG-TTT-AAGAGAAATAACAATCTCAAGTGAGATCAA-CTTTGC
* *
1693425 TTCAA-GTGAATTAAATTCGAAATTTGTA-TATCAAAGGGAAAAA
63 TT-AATGTGAA-CAAATTCAAAATTTGTATTATCAAA-GGAAAAA
*
1693468 TGTCTCAAGCAAGACGAAGTTTGTTTCAAGAGAAAT
1 TGTCTCAAGCGAGACGAAGTTTGTTT-AAGAGAAAT
1693504 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
102 20 0.17
103 5 0.04
104 2 0.02
105 19 0.16
106 22 0.19
107 50 0.42
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (104 bp):
TGTCTCAAGCGAGACGAAGTTTGTTTAAGAGAAATAACAATCTCAAGTGAGATCAACTTTGCTTA
ATGTGAACAAATTCAAAATTTGTATTATCAAAGGAAAAA
Found at i:1693644 original size:48 final size:48
Alignment explanation
Indices: 1693514--1693645 Score: 110
Period size: 48 Copynumber: 2.7 Consensus size: 48
1693504 TTTCTTAAAT
* *
1693514 GAGACAAAATTTGTTTTAAAATTCTCAAAATTTATGGGAAATGTCTCAAGT
1 GAGACAAAATTTGTTTTAAAATTCTCAAAATTTA---GAAATGTATCAAGC
* * * * *
1693565 GAGA-AAGAATTT-TGTTTCAAGTAC-AACAAATTTA-AATTTGTATCAAGC
1 GAGACAA-AATTTGT-TTTAAAATTCTCA-AAATTTAGAA-ATGTATCAAGC
1693613 GAGACAAAATTTGTTTTAAAATTCTCAAAATTT
1 GAGACAAAATTTGTTTTAAAATTCTCAAAATTT
1693646 GTGGAAAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
47 2 0.03
48 30 0.48
49 4 0.06
50 4 0.06
51 23 0.37
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (48 bp):
GAGACAAAATTTGTTTTAAAATTCTCAAAATTTAGAAATGTATCAAGC
Found at i:1694663 original size:11 final size:11
Alignment explanation
Indices: 1694649--1694693 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
1694639 CATATTTTTG
1694649 TTCTTTGCTTT
1 TTCTTTGCTTT
*
1694660 TTCTTTGTTTT
1 TTCTTTGCTTT
*
1694671 TTCTTTTC-TT
1 TTCTTTGCTTT
*
1694681 TTCTTTTCTTT
1 TTCTTTGCTTT
1694692 TT
1 TT
1694694 TTTCCTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (11 bp):
TTCTTTGCTTT
Found at i:1694677 original size:5 final size:5
Alignment explanation
Indices: 1694658--1694707 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
1694648 GTTCTTTGCT
* * *
1694658 TTTTC TTTGTT TTTTC TTTTC TTTTC TTTTC TTTT- TTTTC CTTTG TTTTC
1 TTTTC TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1694708 CTTTGCTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
6 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1694681 original size:22 final size:22
Alignment explanation
Indices: 1694644--1694686 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1694634 TTTGTCATAT
1694644 TTTTGTTCTTTGCTTTTTCTTTG
1 TTTTGTTCTTTGC-TTTTCTTTG
*
1694667 TTTT-TTCTTTTCTTTTCTTT
1 TTTTGTTCTTTGCTTTTCTTT
1694687 TCTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTGTTCTTTGCTTTTCTTTG
Found at i:1694692 original size:22 final size:22
Alignment explanation
Indices: 1694644--1694694 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1694634 TTTGTCATAT
*
1694644 TTTTGTTCTTTGCTTTTTCTTTG
1 TTTT-TTCTTTGCTTTTTCTTTC
*
1694667 TTTTTTCTTTTC-TTTTCTTTTC
1 TTTTTTCTTTGCTTTTTC-TTTC
1694689 TTTTTT
1 TTTTTT
1694695 TTCCTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 4 0.16
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (22 bp):
TTTTTTCTTTGCTTTTTCTTTC
Found at i:1695182 original size:26 final size:24
Alignment explanation
Indices: 1695150--1695200 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
1695140 GAAGATCACT
*
1695150 TCGAGATGCCCCCACATTGTTTCTTC
1 TCGAGATG-CCCCACATT-TTTATTC
1695176 TCGAGATGCCCCACATTTTTATTC
1 TCGAGATGCCCCACATTTTTATTC
1695200 T
1 T
1695201 GGTAGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 9 0.38
26 8 0.33
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (24 bp):
TCGAGATGCCCCACATTTTTATTC
Found at i:1698654 original size:8 final size:8
Alignment explanation
Indices: 1698641--1698677 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1698631 GTTTAACATT
*
1698641 TAAAAACA
1 TAAAAAAA
1698649 TAAAAAAA
1 TAAAAAAA
1698657 T--AAAAA
1 TAAAAAAA
1698663 TAAAAAAA
1 TAAAAAAA
1698671 TAAAAAA
1 TAAAAAA
1698678 TATGTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1698667 original size:14 final size:14
Alignment explanation
Indices: 1698643--1698676 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1698633 TTAACATTTA
1698643 AAAACATAAAAAAAT
1 AAAA-ATAAAAAAAT
1698658 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
1698672 AAAAA
1 AAAAA
1698677 ATATGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:1700652 original size:15 final size:15
Alignment explanation
Indices: 1700632--1700663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1700622 CTGTAAAACA
1700632 AAAAAAAAAAATAAT
1 AAAAAAAAAAATAAT
*
1700647 AAAAAAAATAATAAT
1 AAAAAAAAAAATAAT
1700662 AA
1 AA
1700664 TAATAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAAAAAATAAT
Found at i:1700654 original size:18 final size:18
Alignment explanation
Indices: 1700631--1700666 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1700621 CCTGTAAAAC
1700631 AAAAAAAAAAAATAATAA
1 AAAAAAAAAAAATAATAA
* *
1700649 AAAAAATAATAATAATAA
1 AAAAAAAAAAAATAATAA
1700667 TAGATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAAAAAAAATAATAA
Found at i:1700668 original size:12 final size:12
Alignment explanation
Indices: 1700635--1700660 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1700625 TAAAACAAAA
1700635 AAAAAAAATAAT
1 AAAAAAAATAAT
1700647 AAAAAAAATAAT
1 AAAAAAAATAAT
1700659 AA
1 AA
1700661 TAATAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAATAAT
Found at i:1710340 original size:21 final size:21
Alignment explanation
Indices: 1710299--1710340 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1710289 ACAATTCCTA
* *
1710299 GATTTAAGTTATCTAAGATAG
1 GATTTAAGTGATCTAAAATAG
1710320 GATTTAAGTGATC-ACAAATAG
1 GATTTAAGTGATCTA-AAATAG
1710341 CACGAGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
GATTTAAGTGATCTAAAATAG
Found at i:1712077 original size:25 final size:24
Alignment explanation
Indices: 1712025--1712082 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1712015 TGTGTAGCAG
1712025 AGCTGGCAGTGGTCCCCTCTGGGA
1 AGCTGGCAGTGGTCCCCTCTGGGA
* *
1712049 AGCTGGTC-GTGGTCCCTTCCTGGGC
1 AGCTGG-CAGTGGTCCCCT-CTGGGA
*
1712074 AGCTTGCAG
1 AGCTGGCAG
1712083 CTAGGCGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.10, C:0.29, G:0.36, T:0.24
Consensus pattern (24 bp):
AGCTGGCAGTGGTCCCCTCTGGGA
Found at i:1712386 original size:20 final size:20
Alignment explanation
Indices: 1712357--1712395 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1712347 TTTCCACCAC
*
1712357 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1712377 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
1712396 TATTAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1724304 original size:3 final size:3
Alignment explanation
Indices: 1724298--1724396 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
1724288 TTTTTATCCA
* *
1724298 TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAC TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1724344 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1724392 TAT TA
1 TAT TA
1724397 AATATATTAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 4 0.05
3 82 0.95
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1725955 original size:42 final size:40
Alignment explanation
Indices: 1725887--1725964 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
1725877 ATATTTTTAA
1725887 ATAAATAAATATTTTTATATATAATTTTGAAATAATAGGATT
1 ATAAATAAATATTTTTATATATAATTTT--AATAATAGGATT
*
1725929 ATAAATTAAATATATTTT-TTTA-AATTTTAATAATAG
1 ATAAA-TAAATAT-TTTTATATATAATTTTAATAATAG
1725965 AGACAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 8 0.24
42 11 0.33
43 10 0.30
44 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (40 bp):
ATAAATAAATATTTTTATATATAATTTTAATAATAGGATT
Found at i:1727904 original size:15 final size:14
Alignment explanation
Indices: 1727879--1727920 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1727869 TTTTCATGCA
1727879 TACAT-TTGCATTT
1 TACATCTTGCATTT
1727892 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
1727907 TTCATTTTGCATTT
1 TACATCTTGCATTT
1727921 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:1731249 original size:8 final size:8
Alignment explanation
Indices: 1731233--1731275 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
1731223 TCCAGCAAAG
*
1731233 AAAGGAAA
1 AAAGAAAA
1731241 AAAG-AAA
1 AAAGAAAA
*
1731248 AAAGAGGAA
1 AAAGA-AAA
1731257 AAAGAAAA
1 AAAGAAAA
1731265 AAAGAAAA
1 AAAGAAAA
1731273 AAA
1 AAA
1731276 TTAAATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.23
8 17 0.55
9 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1731257 original size:17 final size:16
Alignment explanation
Indices: 1731233--1731274 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1731223 TCCAGCAAAG
1731233 AAAGGAAAAAAGAAAA
1 AAAGGAAAAAAGAAAA
1731249 AAGAGG-AAAAAGAAAA
1 AA-AGGAAAAAAGAAAA
1731265 AAA-GAAAAAA
1 AAAGGAAAAAA
1731275 ATTAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 6 0.25
16 14 0.58
17 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAGGAAAAAAGAAAA
Found at i:1733906 original size:113 final size:113
Alignment explanation
Indices: 1733612--1733925 Score: 477
Period size: 113 Copynumber: 2.8 Consensus size: 113
1733602 TAATGAGGCT
1733612 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACTCCAAAATCA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACTCCAAAATCA
* * * *
1733677 ATCATTGAATTTGGAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCT
66 ATCATTGAA-TTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
1733726 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACTCCAAAATCA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACTCCAAAATCA
*
1733791 ATCATTGGATTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
66 ATCATTGAATTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
* * * * * * * *
1733839 CAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTCGGTAGGAA-TCCCATAACC
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACT-CCAAAATC
1733903 AATCATTGAAATTGAAAGATGAA
65 AATCATTG-AATTGAAAGATGAA
1733926 CTGCATGATC
Statistics
Matches: 184, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
112 1 0.01
113 97 0.53
114 86 0.47
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (113 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTAATCTGATTTGGTATGAACTCCAAAATCA
ATCATTGAATTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
Found at i:1736109 original size:40 final size:40
Alignment explanation
Indices: 1736054--1736133 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1736044 TGAGCAGAGT
1736054 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
* *
1736094 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1736134 TAAGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
Found at i:1736547 original size:22 final size:22
Alignment explanation
Indices: 1736518--1736572 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1736508 ATCTACACTC
*
1736518 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
1736540 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
1736562 TTCAAAGATGA
1 TTCAAAGATGA
1736573 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:1737332 original size:113 final size:114
Alignment explanation
Indices: 1736973--1738301 Score: 1693
Period size: 113 Copynumber: 11.7 Consensus size: 114
1736963 CAAAGATATA
* ***
1736973 AATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAG-
**
1737038 AAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* *
1737087 AATTCATCATTCGATGATTCAGTATTTCCAGTAAAAGTTCATAATGAGAAGAACTCATCTGAAG-
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1737151 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* ***
1737199 AATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
1737264 AAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* * *
1737312 AATTCATCATTCGATGATTCAGTATTTCCAGTAAAAATTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1737377 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* ***
1737425 AATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
** *
1737490 AAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* * *
1737538 AATTCATCATTCGATGATTCAGTATTTCCAGTAAAAGTTCATAATGAGAAGAACTCATCTAAAGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1737603 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
*
1737651 AATTCATCATTCGATGATTCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAA--C-TCATCTGA
1737716 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-C-TG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-CGCTTG
* * * * *
1737767 AATCCATCATTTGATGGA-TCAGCTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCATCTG
1 AATTCATCATTCGAT-GATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAA--C-TCATCTG
1737831 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-C-TG
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-CGCTTG
* * *
1737883 AATTCATCAAATT-GATGGATT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 AATTCATC--ATTCGAT-GATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGA
1737946 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-C-TG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-CGCTTG
* * * *
1737997 AAGTCATCAAATT-GATGGA-TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGA
1 AATTCATC--ATTCGAT-GATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGA
* **
1738060 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTC-TG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* * *
1738111 AATTCATCAAATT-GATGGATT-ATCTTTTCCA--GAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC--ATTCGAT-GATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAA--C-TCATC
*
1738172 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTT-GCTTG
60 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
* * ** *
1738226 AATTCATCATTTGATGGA-TCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATCATTCGAT-GATTCAGCATTTCCAG-TGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
1738290 GAAAG-AGAAGAA
64 GAAGGAAGAAGAA
1738302 TTTATTCAAT
Statistics
Matches: 1103, Mismatches: 85, Indels: 55
0.89 0.07 0.04
Matches are distributed among these distances:
112 126 0.11
113 392 0.36
114 289 0.26
115 65 0.06
116 168 0.15
117 59 0.05
118 4 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (114 bp):
AATTCATCATTCGATGATTCAGCATTTCCAGTGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTG
Found at i:1738447 original size:3 final size:3
Alignment explanation
Indices: 1738441--1738526 Score: 138
Period size: 3 Copynumber: 28.7 Consensus size: 3
1738431 TTTTTATCCA
1738441 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1738488 TATT TAT TAT TAT TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1738527 AATATATTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 72 0.94
4 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Done.