Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2582966 original size:45 final size:46
Alignment explanation
Indices: 2582892--2582985 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 46
2582882 TTTTCAAAAC
* * *
2582892 TATATATTATATAGTTTTCAAAATGTTTTTGAAAATTATATAATATA
1 TATATATTATATAGTATTCAAAA-GTTTTTAAAAACTATATAATATA
*
2582939 TATATATATATATA-TATTCAAAA-TTTTTAAAAACTATATATTATA
1 TATATAT-TATATAGTATTCAAAAGTTTTTAAAAACTATATAATATA
2582984 TA
1 TA
2582986 AGTTTTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 21 0.50
47 15 0.36
48 6 0.14
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (46 bp):
TATATATTATATAGTATTCAAAAGTTTTTAAAAACTATATAATATA
Found at i:2582977 original size:38 final size:36
Alignment explanation
Indices: 2582937--2583175 Score: 261
Period size: 38 Copynumber: 6.4 Consensus size: 36
2582927 TTATATAATA
*
2582937 TATATATATATATATATATTCAAAAT-TTTTAAAAAC
1 TATATAT-TATATATATTTTCAAAATGTTTTAAAAAC
2582973 TATATATTATATA-AGTTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATA-TTTTCAAAATGTTTTAAAAAC
2583009 TATATATTATATATATTTTCAAAATGTTTTTAAAAAAC
1 TATATATTATATATATTTTCAAAATG-TTTT-AAAAAC
* *
2583047 CATATATTATATA-AGTTTTCAAAATGATTTTCAAAAC
1 TATATATTATATATA-TTTTCAAAATG-TTTTAAAAAC
* * *
2583084 TATATAATATATACATTTTCAAAAATTGTTTTCAAAAC
1 TATATATTATATATATTTTC-AAAA-TGTTTTAAAAAC
* ** *
2583122 TATATATTATATATAAATTTTAAAAATCATTTACAAA-
1 TATATATTATATAT--ATTTTCAAAATGTTTTAAAAAC
2583159 TATATATATATATATAT
1 TATATAT-TATATATAT
2583176 ATATATAAAA
Statistics
Matches: 178, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.01
35 15 0.08
36 43 0.24
37 34 0.19
38 74 0.42
39 6 0.03
40 5 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAAC
Found at i:2583165 original size:2 final size:2
Alignment explanation
Indices: 2583158--2583182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2583148 TCATTTACAA
2583158 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 A
2583183 AAATAAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2583549 original size:19 final size:20
Alignment explanation
Indices: 2583525--2583562 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2583515 ATTAATTTTT
*
2583525 TAAAAT-TAAAAGATTTAAA
1 TAAAATCTAAAAAATTTAAA
2583544 TAAAATCTAAAAAATTTAA
1 TAAAATCTAAAAAATTTAA
2583563 TAATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAAATCTAAAAAATTTAAA
Found at i:2584105 original size:3 final size:3
Alignment explanation
Indices: 2584099--2584124 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2584089 TGGAGGCGGC
2584099 GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GG
2584125 GGAATCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:2590572 original size:42 final size:42
Alignment explanation
Indices: 2590514--2590738 Score: 206
Period size: 42 Copynumber: 5.6 Consensus size: 42
2590504 AGGGTTTAGA
2590514 GTTTAG-GTTTAGAGTTTAGAGTTTATGTGATATGATTTAAG
1 GTTTAGAGTTTAGAGTTTAGAGTTTATGTGATATGATTTAAG
* * *
2590555 GTTTAGGGTTTATAGTTTAGAGTTTATGTAATATGATTTAAG
1 GTTTAGAGTTTAGAGTTTAGAGTTTATGTGATATGATTTAAG
* * * * *
2590597 GTTTAGAGTTTAGTGTTTATAGTTTAAG-G-TTTAGGTATTAAG
1 GTTTAGAGTTTAGAGTTTAGAGTTTATGTGATAT-GAT-TTAAG
* * *
2590639 GTTTAG-GGTTAGAGTTTA-A-TTTA----A-A-GGTTTAAA
1 GTTTAGAGTTTAGAGTTTAGAGTTTATGTGATATGATTTAAG
*
2590672 GTTTAGAATTTAGAGTTTTAGAGTTTATGTGATATGATTTAAG
1 GTTTAGAGTTTAGAG-TTTAGAGTTTATGTGATATGATTTAAG
*
2590715 GTTTATAGTTTATGA-TTTAGAGTT
1 GTTTAGAGTTTA-GAGTTTAGAGTT
2590739 CAGAGTTTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 29
0.75 0.10 0.15
Matches are distributed among these distances:
33 10 0.07
34 9 0.06
35 4 0.03
36 1 0.01
37 4 0.03
39 4 0.03
40 3 0.02
41 19 0.13
42 77 0.52
43 16 0.11
44 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (42 bp):
GTTTAGAGTTTAGAGTTTAGAGTTTATGTGATATGATTTAAG
Found at i:2590683 original size:22 final size:22
Alignment explanation
Indices: 2590656--2590698 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2590646 GTTAGAGTTT
2590656 AATTTAAAGGTTTAAAGTTTAG
1 AATTTAAAGGTTTAAAGTTTAG
* * *
2590678 AATTTAGAGTTTTAGAGTTTA
1 AATTTAAAGGTTTAAAGTTTA
2590699 TGTGATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (22 bp):
AATTTAAAGGTTTAAAGTTTAG
Found at i:2590698 original size:7 final size:7
Alignment explanation
Indices: 2590500--2590755 Score: 96
Period size: 7 Copynumber: 36.7 Consensus size: 7
2590490 ATGTGATAAG
*
2590500 GTTTAGG
1 GTTTAGA
2590507 GTTTAGA
1 GTTTAGA
2590514 GTTTAG-
1 GTTTAGA
2590520 GTTTAGA
1 GTTTAGA
2590527 GTTTAGA
1 GTTTAGA
*
2590534 GTTTA-T
1 GTTTAGA
*
2590540 GTGATATGA
1 GT-TTA-GA
2590549 -TTTA-A
1 GTTTAGA
*
2590554 GGTTTAGG
1 -GTTTAGA
*
2590562 GTTTATA
1 GTTTAGA
2590569 GTTTAGA
1 GTTTAGA
*
2590576 GTTTA-T
1 GTTTAGA
*
2590582 GTAATATGA
1 GT-TTA-GA
2590591 -TTTA-A
1 GTTTAGA
2590596 GGTTTAGA
1 -GTTTAGA
*
2590604 GTTTAGT
1 GTTTAGA
*
2590611 GTTTATA
1 GTTTAGA
2590618 GTTTA-A
1 GTTTAGA
2590624 GGTTTAG-
1 -GTTTAGA
2590631 GTATTA-A
1 GT-TTAGA
2590638 GGTTTAG-
1 -GTTTAGA
*
2590645 GGTTAGA
1 GTTTAGA
2590652 GTTTA-A
1 GTTTAGA
*
2590658 -TTTAAA
1 GTTTAGA
*
2590664 GGTTTAAA
1 -GTTTAGA
2590672 GTTTAGA
1 GTTTAGA
*
2590679 ATTTAGA
1 GTTTAGA
2590686 GTTTTAGA
1 G-TTTAGA
*
2590694 GTTTA-T
1 GTTTAGA
*
2590700 GTGATATGA
1 GT-TTA-GA
2590709 -TTTA-A
1 GTTTAGA
*
2590714 GGTTTATA
1 -GTTTAGA
2590722 GTTTATGA
1 GTTTA-GA
2590730 -TTTAGA
1 GTTTAGA
*
2590736 GTTCAGA
1 GTTTAGA
2590743 GTTTTAGA
1 G-TTTAGA
2590751 GTTTA
1 GTTTA
2590756 TGTGATATGA
Statistics
Matches: 188, Mismatches: 28, Indels: 66
0.67 0.10 0.23
Matches are distributed among these distances:
5 7 0.04
6 24 0.13
7 130 0.69
8 27 0.14
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (7 bp):
GTTTAGA
Found at i:2590725 original size:50 final size:53
Alignment explanation
Indices: 2590657--2590785 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 53
2590647 TTAGAGTTTA
* *
2590657 ATTTAAAGGTTTAAAGTTTAG-A-A-TTTAGAGTTTTAGAGTTTATGTGATATG
1 ATTT-AAGGTTTATAGTTTAGTAGAGTTCAGAGTTTTAGAGTTTATGTGATATG
2590708 ATTTAAGGTTTATAGTTTATGATTTAGAGTTCAGAGTTTTAGAGTTTATGTGATATG
1 ATTTAAGGTTTATAGTTTA-G---TAGAGTTCAGAGTTTTAGAGTTTATGTGATATG
2590765 ATTTAAGGTTTATATGTTTAG
1 ATTTAAGGTTTATA-GTTTAG
2590786 GGTTTATATG
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
50 14 0.21
51 5 0.07
55 1 0.01
56 1 0.01
57 42 0.62
58 5 0.07
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (53 bp):
ATTTAAGGTTTATAGTTTAGTAGAGTTCAGAGTTTTAGAGTTTATGTGATATG
Found at i:2590734 original size:57 final size:58
Alignment explanation
Indices: 2590673--2590784 Score: 199
Period size: 57 Copynumber: 1.9 Consensus size: 58
2590663 AGGTTTAAAG
*
2590673 TTTAGAATTTAGAGTTTTAGAGTTTATGTGATATGATTTAAGGTTTATA-GTTTATGA
1 TTTAGAATTCAGAGTTTTAGAGTTTATGTGATATGATTTAAGGTTTATATGTTTATGA
*
2590730 TTTAGAGTTCAGAGTTTTAGAGTTTATGTGATATGATTTAAGGTTTATATGTTTA
1 TTTAGAATTCAGAGTTTTAGAGTTTATGTGATATGATTTAAGGTTTATATGTTTA
2590785 GGGTTTATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
57 47 0.90
58 5 0.10
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (58 bp):
TTTAGAATTCAGAGTTTTAGAGTTTATGTGATATGATTTAAGGTTTATATGTTTATGA
Found at i:2590789 original size:15 final size:15
Alignment explanation
Indices: 2590760--2590804 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2590750 AGTTTATGTG
*
2590760 ATATGATTTAAGGTTT
1 ATATG-TTTAGGGTTT
2590776 ATATGTTTAGGGTTT
1 ATATGTTTAGGGTTT
*
2590791 ATATGTTAAGGGTT
1 ATATGTTTAGGGTT
2590805 AGGGGTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (15 bp):
ATATGTTTAGGGTTT
Found at i:2592730 original size:11 final size:11
Alignment explanation
Indices: 2592714--2592814 Score: 87
Period size: 11 Copynumber: 8.9 Consensus size: 11
2592704 TAACCCATCC
2592714 TCGAGCTT-AA
1 TCGAGCTTGAA
2592724 GTCGAGCTTGAA
1 -TCGAGCTTGAA
**
2592736 TCGAGCTCACAA
1 TCGAGCT-TGAA
2592748 TCGAGCTTGAA
1 TCGAGCTTGAA
**
2592759 TCGAGCTCACAA
1 TCGAGCT-TGAA
2592771 TCGAGCTTGAA
1 TCGAGCTTGAA
**
2592782 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
2592794 TCGAGCTTCAA
1 TCGAGCTTGAA
*
2592805 TTGAGCTTGA
1 TCGAGCTTGA
2592815 GTCTTGAGCT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
11 43 0.60
12 29 0.40
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2592751 original size:12 final size:12
Alignment explanation
Indices: 2592734--2592800 Score: 75
Period size: 12 Copynumber: 5.8 Consensus size: 12
2592724 GTCGAGCTTG
2592734 AATCGAGCTCAC
1 AATCGAGCTCAC
**
2592746 AATCGAGCT-TG
1 AATCGAGCTCAC
2592757 AATCGAGCTCAC
1 AATCGAGCTCAC
**
2592769 AATCGAGCT-TG
1 AATCGAGCTCAC
*
2592780 AATCGAGCTCAA
1 AATCGAGCTCAC
2592792 AATCGAGCT
1 AATCGAGCT
2592801 TCAATTGAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
11 18 0.40
12 27 0.60
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (12 bp):
AATCGAGCTCAC
Found at i:2592754 original size:23 final size:23
Alignment explanation
Indices: 2592725--2592811 Score: 147
Period size: 23 Copynumber: 3.8 Consensus size: 23
2592715 CGAGCTTAAG
2592725 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
2592748 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
2592771 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
2592794 TCGAGCTTCAATTGAGCT
1 TCGAGCTTGAATCGAGCT
2592812 TGAGTCTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:2592784 original size:34 final size:33
Alignment explanation
Indices: 2592761--2592832 Score: 63
Period size: 34 Copynumber: 2.1 Consensus size: 33
2592751 AGCTTGAATC
*
2592761 GAGCTCACAATCGAGCTTGAATCGAGCTCAAAATC
1 GAGCT-ACAATCGAGCTTGAATCGAGCT-TAAATC
* * * *
2592796 GAGCTTCAATTGAGCTTGAGTCTTGAGCTTCAATC
1 GAGCTACAATCGAGCTTGAATC--GAGCTTAAATC
2592831 GA
1 GA
2592833 TCTCTAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
34 14 0.47
35 11 0.37
36 5 0.17
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (33 bp):
GAGCTACAATCGAGCTTGAATCGAGCTTAAATC
Found at i:2594357 original size:18 final size:17
Alignment explanation
Indices: 2594303--2594351 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2594293 TTGGACCCTT
* *
2594303 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2594321 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2594339 AGTGCATTCGATG
1 AGTGCA-TCGATG
2594352 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2594456 original size:65 final size:65
Alignment explanation
Indices: 2594323--2594482 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
2594313 TGCACTAAGA
* * *
2594323 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
* * * * *
2594387 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATTGGTGCATGGTA-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCAT-G-AC
2594451 T-
64 TG
* *
2594452 GTGCATCGATGCATGAAATACATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
2594483 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.34
65 52 0.63
66 2 0.02
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
Found at i:2594521 original size:65 final size:63
Alignment explanation
Indices: 2594323--2594532 Score: 178
Period size: 65 Copynumber: 3.3 Consensus size: 63
2594313 TGCACTAAGA
* * * * * *
2594323 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGC-CAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATAACATCTC--AGTGCATCGATGCATGATTG
* * * *
2594387 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATTGGTGCATGGTAT
1 GTGCATCGATGCATCAAATACATTCGATG-TTTCATAACAT-CTCAGTGCATCGATGCATGAT-T
2594452 -
63 G
* *
2594452 GTGCATCGATGCATGAAATACATTCGATG-TTCAATTTA-AT-TCATGGTGCATCGATGCATGAA
1 GTGCATCGATGCATCAAATACATTCGATGTTTC-A-TAACATCTCA--GTGCATCGATGCATG-A
2594514 TTG
61 TTG
*
2594517 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2594533 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 45 0.38
65 66 0.55
66 2 0.02
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTCATAACATCTCAGTGCATCGATGCATGATTG
Found at i:2601120 original size:22 final size:21
Alignment explanation
Indices: 2601078--2601117 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2601068 GAGTTTATTT
*
2601078 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2601099 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2601118 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2603179 original size:57 final size:56
Alignment explanation
Indices: 2603061--2603168 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 56
2603051 AGTGCATCGA
* * *
2603061 TGCATCAAGTGCATTAGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACTGG
1 TGCATCAAATGCATTAGATGTTTCAAAACAGCCACAGTGCATCGATGCATGACTGG
* * * *
2603117 TGCATCAAATGCATTAGATGTTTTCATAACATCCTCAGTGCATCGGTGCATG
1 TGCATCAAATGCATTAGATG-TTTCAAAACAGCCACAGTGCATCGATGCATG
2603169 GTATGTGCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 19 0.43
57 25 0.57
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (56 bp):
TGCATCAAATGCATTAGATGTTTCAAAACAGCCACAGTGCATCGATGCATGACTGG
Found at i:2603856 original size:2 final size:2
Alignment explanation
Indices: 2603849--2603885 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2603839 TGACGGTACA
2603849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2603886 ATCATCAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2606286 original size:19 final size:19
Alignment explanation
Indices: 2606262--2606305 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2606252 TTATAGTTAA
*
2606262 AAGATTCGTCTTCTATTAT
1 AAGATTCATCTTCTATTAT
2606281 AAGATTCATCTTCTATTAT
1 AAGATTCATCTTCTATTAT
2606300 AA-ATTC
1 AAGATTC
2606306 TTGATCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (19 bp):
AAGATTCATCTTCTATTAT
Found at i:2608317 original size:27 final size:26
Alignment explanation
Indices: 2608278--2608342 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
2608268 TATTCAATAT
*
2608278 AGAAACAA-AAAAAAGATAA-AAAAGAG
1 AGAAA-AAGAAAAAAGAGAAGAAAA-AG
2608304 AGGAAAAAGAAAAAAGAGAAGAAAAAG
1 A-GAAAAAGAAAAAAGAGAAGAAAAAG
*
2608331 AGAATAAGAAAA
1 AGAAAAAGAAAA
2608343 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 13 0.38
27 17 0.50
28 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (26 bp):
AGAAAAAGAAAAAAGAGAAGAAAAAG
Found at i:2608318 original size:18 final size:18
Alignment explanation
Indices: 2608295--2608331 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2608285 AAAAAAAGAT
*
2608295 AAAAAAGAGAGGAAAAAG
1 AAAAAAGAGAAGAAAAAG
2608313 AAAAAAGAGAAGAAAAAG
1 AAAAAAGAGAAGAAAAAG
2608331 A
1 A
2608332 GAATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAGAAAAAG
Found at i:2608334 original size:20 final size:19
Alignment explanation
Indices: 2608287--2608334 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2608277 TAGAAACAAA
*
2608287 AAAAAGATAAAAAAGAGAG
1 AAAAAGAGAAAAAAGAGAG
*
2608306 GAAAA-AGAAAAAAGAGAAG
1 AAAAAGAGAAAAAAGAG-AG
2608325 AAAAAGAGAA
1 AAAAAGAGAA
2608335 TAAGAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (19 bp):
AAAAAGAGAAAAAAGAGAG
Found at i:2611022 original size:259 final size:260
Alignment explanation
Indices: 2610448--2611141 Score: 1016
Period size: 259 Copynumber: 2.7 Consensus size: 260
2610438 ATGCTTTCAT
*
2610448 ATAATTTGAAAAATGAGAATGCGATTTTCAAAGTTTCTCATTTAG-----T-AGAAAATGAAATT
1 ATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
2610507 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTATCC-AGTAAACTATTTCCAAAATTGGTAA
66 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA-CCTAGTAAACTATTTCCAAAATTGGTAA
* * *
2610571 GTCCTTCAGGTCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCCCTCTGTC
130 GT-CTTCAGGCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCCTTCGGGT-AT-CATCTGTC
* *
2610636 AGTCTTTTGAGCAAGATGACAAGTCCTTCGGACAATCTATAAGACCTTCGTGCAAGATGTTTTCA
192 AGTCTTTTGAGAAAGATGACAAGTCCTTCGGACAATCTATAAGACCTTCGGGCAAGATGTTTTCA
*
2610701 TGTG
257 TATG
*
2610705 ATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGGAAA-
1 ATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAAT-GAAAT
* * *
2610769 ATTTGAAAATTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAA
65 TTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAA
* *
2610834 GTCTTTCAGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGT-T-ATCTGTCAG
130 GTC-TTCAGGCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCCTTCGGGTATCATCTGTCAG
* * * *
2610897 TCTTTTGAGAAAGATGATAAGTCTTTCGGGCCATCTATAAGACCTTCGGGCAAGATGCTTTT-AT
194 TCTTTTGAGAAAGATGACAAGTCCTTCGGACAATCTATAAGACCTTCGGGCAAGATG-TTTTCAT
2610961 ATG
258 ATG
*
2610964 ATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCACATTTAGTATTTTCAGAAAATGAAATT
1 ATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
*
2611029 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACATTA-TAAACTATTTCCAAAATTGGTAA
66 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTAC-CTAGTAAACTATTTCCAAAATTGGTAA
* * * *
2611093 GTACTTCGGGCCATTAATAAGTCTTTAGAGCTTGATGATTAAGTCCTTC
130 GT-CTTCAGGCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCCTTC
2611142 ATGTCATCTG
Statistics
Matches: 396, Mismatches: 28, Indels: 24
0.88 0.06 0.05
Matches are distributed among these distances:
257 43 0.11
258 4 0.01
259 219 0.55
260 7 0.02
261 1 0.00
262 4 0.01
263 114 0.29
264 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (260 bp):
ATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
TCTTCAGGCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCCTTCGGGTATCATCTGTCAGTC
TTTTGAGAAAGATGACAAGTCCTTCGGACAATCTATAAGACCTTCGGGCAAGATGTTTTCATATG
Found at i:2614802 original size:35 final size:35
Alignment explanation
Indices: 2614756--2614840 Score: 161
Period size: 35 Copynumber: 2.4 Consensus size: 35
2614746 TTTTTTAACT
2614756 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
1 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
2614791 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
1 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
*
2614826 TACGAAGCAGACACA
1 TACGAAGCAAACACA
2614841 AGAAAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.53, C:0.21, G:0.15, T:0.11
Consensus pattern (35 bp):
TACGAAGCAAACACATGAGTTACACAAGAAAAACA
Found at i:2614840 original size:24 final size:24
Alignment explanation
Indices: 2614811--2614881 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
2614801 ACACATGAGT
2614811 TACACAAGAAAAACATACGAAGCAG
1 TACACAAGAAAAACATACGAAG-AG
* *
2614836 -ACACAAGAAAAACACAC-ATGAG
1 TACACAAGAAAAACATACGAAGAG
*
2614858 TTACACAAGAAAAACATATGAAGA
1 -TACACAAGAAAAACATACGAAGA
2614882 ACACCCAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 31 0.82
25 3 0.08
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.10
Consensus pattern (24 bp):
TACACAAGAAAAACATACGAAGAG
Found at i:2614851 original size:35 final size:35
Alignment explanation
Indices: 2614756--2614851 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
2614746 TTTTTTAACT
* ***
2614756 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
1 TACGAAGCAAACACAAGAAAAACACAAGAAAAACA
* ***
2614791 TACGAAGCAAACACATGAGTTACACAAGAAAAACA
1 TACGAAGCAAACACAAGAAAAACACAAGAAAAACA
*
2614826 TACGAAGCAGACACAAGAAAAACACA
1 TACGAAGCAAACACAAGAAAAACACA
2614852 CATGAGTTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.55, C:0.21, G:0.15, T:0.09
Consensus pattern (35 bp):
TACGAAGCAAACACAAGAAAAACACAAGAAAAACA
Found at i:2614891 original size:48 final size:48
Alignment explanation
Indices: 2614801--2614892 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
2614791 TACGAAGCAA
* *
2614801 ACACATGAGTTACACAAGAAAAACATACGAAGCAGACACAAGAAAAAC
1 ACACATGAGTTACACAAGAAAAACATACGAAGAACACACAAGAAAAAC
* *
2614849 ACACATGAGTTACACAAGAAAAACATATGAAGAACACCCAAGAA
1 ACACATGAGTTACACAAGAAAAACATACGAAGAACACACAAGAA
2614893 CATTTCAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (48 bp):
ACACATGAGTTACACAAGAAAAACATACGAAGAACACACAAGAAAAAC
Found at i:2615245 original size:33 final size:33
Alignment explanation
Indices: 2615181--2615245 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
2615171 ATATTCTTCT
* * * * *
2615181 TTATTTTTTTACTATTTTTATTGCTTGTTTTTA
1 TTATTTCTTTACTATTATTATTACATATTTTTA
*
2615214 TTATTTCTTTATTATTATTATTACATATTTTT
1 TTATTTCTTTACTATTATTATTACATATTTTT
2615246 TTTTCATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (33 bp):
TTATTTCTTTACTATTATTATTACATATTTTTA
Found at i:2615281 original size:2 final size:2
Alignment explanation
Indices: 2615274--2615343 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
2615264 CTCCTAACAT
2615274 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
2615316 TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2615344 TATCATTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2615552 original size:19 final size:19
Alignment explanation
Indices: 2615528--2615568 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2615518 TCCCTCATTT
*
2615528 TTTATTTTATTTGGTTTTG
1 TTTATTTTATTGGGTTTTG
2615547 TTTATTTTATTGGGTTTTG
1 TTTATTTTATTGGGTTTTG
2615566 TTT
1 TTT
2615569 TGCTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.17, T:0.73
Consensus pattern (19 bp):
TTTATTTTATTGGGTTTTG
Found at i:2615554 original size:24 final size:24
Alignment explanation
Indices: 2615527--2615586 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2615517 TTCCCTCATT
*
2615527 TTTTATTTTATTTGGTTTTGTTTA
1 TTTTATTTTATTTGGTTTTGCTTA
*** *
2615551 TTTTATTGGGTTTTGTTTTGCTTA
1 TTTTATTTTATTTGGTTTTGCTTA
2615575 TTTTA-TTTATTT
1 TTTTATTTTATTT
2615587 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTGGTTTTGCTTA
Found at i:2625933 original size:21 final size:21
Alignment explanation
Indices: 2625907--2625950 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2625897 TTGAAAAAAG
2625907 AAGAGAAAAAG-AAAAGAGAAA
1 AAGAGAAAAAGAAAAAG-GAAA
2625928 AAGAGAAAAAGAAAAAGGAAA
1 AAGAGAAAAAGAAAAAGGAAA
2625949 AA
1 AA
2625951 ATAAGGTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAGAGAAAAAGAAAAAGGAAA
Found at i:2626840 original size:65 final size:64
Alignment explanation
Indices: 2626736--2626914 Score: 222
Period size: 65 Copynumber: 2.8 Consensus size: 64
2626726 GAAGCAACAC
* * * *
2626736 AACTTACAAAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAGTTCAGTGA
1 AACTTAC-TAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
* **
2626801 AACTTACTCAAGATTGGATTTTAACTTCACAATGAAGGATATCCAACTCAAAGCCAATTTGGTGA
1 AACTTACT-AAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
* * *
2626866 AAC--AAT-A-CTTGGATTTTAACTTCACAACGAAGGATATCCAACTTAAAGC
1 AACTTACTAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGC
2626915 TCACCTTCAC
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
60 39 0.38
61 1 0.01
63 2 0.02
65 60 0.59
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (64 bp):
AACTTACTAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
Found at i:2628093 original size:17 final size:17
Alignment explanation
Indices: 2628059--2628110 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2628049 ACCAGACAAA
* *
2628059 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
2628076 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
2628093 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
2628108 TTT
1 TTT
2628111 CTACTGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:2629274 original size:26 final size:27
Alignment explanation
Indices: 2629221--2629284 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
2629211 TATATATATA
* *
2629221 TATTCTTTATTTATTTTTTATGTTTTAT
1 TATT-TTTATTTATTTTTTATCTCTTAT
*
2629249 TATTTTTATTTCTTTTTTA-CTCTTAT
1 TATTTTTATTTATTTTTTATCTCTTAT
*
2629275 TATTATTATT
1 TATTTTTATT
2629285 ACATATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.44
27 14 0.44
28 4 0.12
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (27 bp):
TATTTTTATTTATTTTTTATCTCTTAT
Found at i:2629325 original size:66 final size:66
Alignment explanation
Indices: 2629220--2629400 Score: 242
Period size: 66 Copynumber: 2.7 Consensus size: 66
2629210 ATATATATAT
* *
2629220 ATATTCTTTATTTATTTTTTA-TGTTTTATTATTTTTATTTCTTTT-T-TACTCTTATTATTATT
1 ATATTTTTTATTTA--TTTTACT-TTTT-TTATTTTTATTTATTTTCTATACTCTTATTATTATT
2629282 ATTAC
62 ATTAC
** *
2629287 ATATTTATTTATTTATTTTACTTATTTTTATTTTTATTTATTTTCTATTTTTTTATTATTATTAT
1 ATATTT-TTTATTTATTTTACTT-TTTTTATTTTTATTTATTTTCTATACTCTTATTATTATTAT
2629352 TAC
64 TAC
2629355 ATATTTTTTATTTATTTTACTTTTTTTATTTTTATTTATTTTCTAT
1 ATATTTTTTATTTATTTTACTTTTTTTATTTTTATTTATTTTCTAT
2629401 TTTTTTCATT
Statistics
Matches: 104, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
66 46 0.44
67 26 0.25
68 32 0.31
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.72
Consensus pattern (66 bp):
ATATTTTTTATTTATTTTACTTTTTTTATTTTTATTTATTTTCTATACTCTTATTATTATTATTA
C
Found at i:2629326 original size:10 final size:10
Alignment explanation
Indices: 2629226--2629425 Score: 82
Period size: 9 Copynumber: 19.8 Consensus size: 10
2629216 ATATATATTC
*
2629226 TTTATTTATTT
1 TTTATTT-TTA
2629237 TTTATGTTTTA
1 TTTAT-TTTTA
2629248 -TTATTTTTA
1 TTTATTTTTA
*
2629257 TTTCTTTTTTA
1 TTT-ATTTTTA
*
2629268 CTCTTATTATTA
1 -T-TTATTTTTA
**
2629280 -TTATTACATA
1 TTTATT-TTTA
2629290 TTTATTTATTTA
1 TTTA-TT-TTTA
*
2629302 TTTTACTTATT-
1 -TTTA-TTTTTA
2629313 TTTATTTTTA
1 TTTATTTTTA
2629323 TTTATTTTCTA
1 TTTATTTT-TA
2629334 -TT-TTTTTA
1 TTTATTTTTA
*
2629342 -TTATTATTA
1 TTTATTTTTA
* *
2629351 TTACATATTT-
1 TT-TATTTTTA
*
2629361 TTTATTTAT-
1 TTTATTTTTA
*
2629370 TTTACTTTT-
1 TTTATTTTTA
2629379 TTTATTTTTA
1 TTTATTTTTA
2629389 TTTATTTTCTA
1 TTTATTTT-TA
*
2629400 TTT-TTTTCA
1 TTTATTTTTA
2629409 -TTATTTTTTA
1 TTTA-TTTTTA
2629419 TTT-TTTT
1 TTTATTTT
2629426 CATTATTTGT
Statistics
Matches: 147, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
8 6 0.04
9 47 0.32
10 42 0.29
11 29 0.20
12 15 0.10
13 8 0.05
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:2629351 original size:24 final size:24
Alignment explanation
Indices: 2629311--2629422 Score: 78
Period size: 25 Copynumber: 4.8 Consensus size: 24
2629301 ATTTTACTTA
*
2629311 TTTTTATTTTTATTTATTTTCTATT
1 TTTTTATTATTA-TTATTTTCTATT
*
2629336 TTTTTATTATTATTA-TTAC-A-T
1 TTTTTATTATTATTATTTTCTATT
*
2629357 ATTTT-TTA-T-TTA-TTT-TACTT
1 TTTTTATTATTATTATTTTCTA-TT
*
2629377 TTTTTATTTTTATTTATTTTCTATT
1 TTTTTATTATTA-TTATTTTCTATT
*
2629402 TTTTTCATTATTTTTTATTTT
1 TTTTT-ATTA-TTATTATTTT
2629423 TTTCATTATT
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
18 6 0.09
19 1 0.01
20 8 0.12
21 7 0.10
22 2 0.03
23 3 0.04
24 6 0.09
25 21 0.31
26 12 0.18
27 2 0.03
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTATTATTATTATTTTCTATT
Found at i:2629426 original size:19 final size:19
Alignment explanation
Indices: 2629317--2629433 Score: 100
Period size: 19 Copynumber: 6.1 Consensus size: 19
2629307 CTTATTTTTA
*
2629317 TTTTTATTTATTTTCTATTTT
1 TTTTTATTT-TTTTC-ATTAT
*
2629338 TTTATTATTATTATTACA-TAT
1 TTT-TTATT-TT-TTTCATTAT
*
2629359 TTTTTATTTATTTT-ACT-T
1 TTTTTATTT-TTTTCATTAT
*
2629377 TTTTTATTTTTAT--TTAT
1 TTTTTATTTTTTTCATTAT
*
2629394 TTTCTATTTTTTTCATTAT
1 TTTTTATTTTTTTCATTAT
2629413 TTTTTATTTTTTTCATTAT
1 TTTTTATTTTTTTCATTAT
2629432 TT
1 TT
2629434 GTTTTCCTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.01
17 15 0.19
18 11 0.14
19 28 0.35
20 6 0.08
21 8 0.10
22 7 0.09
23 4 0.05
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTTCATTAT
Found at i:2629431 original size:12 final size:11
Alignment explanation
Indices: 2629295--2629439 Score: 65
Period size: 12 Copynumber: 13.0 Consensus size: 11
2629285 ACATATTTAT
2629295 TTATTTATTTTAC
1 TTATTT-TTTT-C
*
2629308 TTATTTTTATTT
1 TTATTTTT-TTC
2629320 TTATTTATTTTC
1 TTATTT-TTTTC
*
2629332 -TATTTTTTTA
1 TTATTTTTTTC
*
2629342 TTATTATTATTAC
1 TTATT-TT-TTTC
*
2629355 ATATTTTTTAT-
1 TTATTTTTT-TC
*
2629366 TTA--TTTTAC
1 TTATTTTTTTC
*
2629375 TT-TTTTTATTT
1 TTATTTTT-TTC
2629386 TTATTTATTTTC
1 TTATTT-TTTTC
2629398 -TATTTTTTTC
1 TTATTTTTTTC
*
2629408 --ATTATTTT-
1 TTATTTTTTTC
2629416 TTATTTTTTTC
1 TTATTTTTTTC
2629427 ATTATTTGTTTTC
1 -TTATTT-TTTTC
2629440 CTCCTAACAT
Statistics
Matches: 101, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
9 13 0.13
10 19 0.19
11 21 0.21
12 25 0.25
13 23 0.23
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.75
Consensus pattern (11 bp):
TTATTTTTTTC
Found at i:2629432 original size:42 final size:40
Alignment explanation
Indices: 2629230--2629433 Score: 84
Period size: 43 Copynumber: 4.8 Consensus size: 40
2629220 ATATTCTTTA
* * *
2629230 TTTATTTTTTATGTTT-TATTATTTTTATTTCTTTTTTACTCTT
1 TTTATTATTTAT-TTTCTATT-TTTTTA-TTATTTTTTA-TTTT
* * *
2629273 ATTATTA-TTA-TTACATATTTATTTATTTATTTTACTTATTTT
1 TTTATTATTTATTTTC-TATTTTTTTA-TTATTTT--TTATTTT
*
2629315 TATTTTTATTTATTTTCTATTTTTTTATTATTATTATTACATATTT
1 T-TTATTATTTATTTTCTATTTTTTTATTATT-TT-TT--AT-TTT
*
2629361 TTTATTTATTTTACTTTT-T-TTATTTTTATTTATTTTCTATTTT
1 TTTA-TTA-TTTA-TTTTCTATT-TTTTTA-TTATTTTTTATTTT
2629404 TTTCATTA--T-TTTT-TATTTTTTTCATTATTT
1 TTT-ATTATTTATTTTCTATTTTTTT-ATTATTT
2629434 GTTTTCCTCC
Statistics
Matches: 129, Mismatches: 13, Indels: 43
0.70 0.07 0.23
Matches are distributed among these distances:
38 16 0.12
39 3 0.02
40 3 0.02
41 12 0.09
42 10 0.08
43 29 0.22
44 17 0.13
45 7 0.05
46 10 0.08
47 13 0.10
48 9 0.07
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.74
Consensus pattern (40 bp):
TTTATTATTTATTTTCTATTTTTTTATTATTTTTTATTTT
Found at i:2629433 original size:66 final size:67
Alignment explanation
Indices: 2629220--2629413 Score: 272
Period size: 68 Copynumber: 2.9 Consensus size: 67
2629210 ATATATATAT
* * *
2629220 ATATTCTTTATTTATTTT--TTATGTTTTATTATT-TTTA-TTTCTTTTTTACTCTTATTATTAT
1 ATATTTTTTATTTATTTTACTTAT-TTTTATTTTTATTTATTTTCTATTTT--T-TTATTATTAT
2629281 TATTAC
62 TATTAC
2629287 ATATTTATTTATTTATTTTACTTATTTTTATTTTTATTTATTTTCTATTTTTTTATTATTATTAT
1 ATATTT-TTTATTTATTTTACTTATTTTTATTTTTATTTATTTTCTATTTTTTTATTATTATTAT
2629352 TAC
65 TAC
2629355 ATATTTTTTATTTATTTTACTT-TTTTTATTTTTATTTATTTTCTATTTTTTTCATTATT
1 ATATTTTTTATTTATTTTACTTATTTTTATTTTTATTTATTTTCTATTTTTTT-ATTATT
2629414 TTTTATTTTT
Statistics
Matches: 118, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
66 30 0.25
67 27 0.23
68 34 0.29
69 10 0.08
70 8 0.07
71 9 0.08
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.73
Consensus pattern (67 bp):
ATATTTTTTATTTATTTTACTTATTTTTATTTTTATTTATTTTCTATTTTTTTATTATTATTATT
AC
Found at i:2630730 original size:12 final size:12
Alignment explanation
Indices: 2630713--2630750 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2630703 GACACACATT
2630713 AATGAGCTTATA
1 AATGAGCTTATA
2630725 AATGAG-TTGATA
1 AATGAGCTT-ATA
2630737 AATGAGCTTATA
1 AATGAGCTTATA
2630749 AA
1 AA
2630751 GGAGTCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (12 bp):
AATGAGCTTATA
Found at i:2631752 original size:21 final size:21
Alignment explanation
Indices: 2631726--2631766 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2631716 GACTATTGCA
2631726 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
2631747 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
2631767 AATGCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:2631772 original size:21 final size:21
Alignment explanation
Indices: 2631727--2631773 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2631717 ACTATTGCAT
**
2631727 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
2631748 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
2631769 TGCGA
1 TGCGA
2631774 ATACGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:2631788 original size:20 final size:20
Alignment explanation
Indices: 2631763--2631957 Score: 255
Period size: 20 Copynumber: 9.7 Consensus size: 20
2631753 TTTTCCTAAT
2631763 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2631783 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* ** *
2631804 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2631825 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2631845 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2631865 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2631885 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2631905 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2631925 TCGAAATGTGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2631945 TCACAACGCGAAT
1 TCGCAATGCGAAT
2631958 CTGACTATCG
Statistics
Matches: 159, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
20 122 0.77
21 37 0.23
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2631806 original size:21 final size:21
Alignment explanation
Indices: 2631780--2631837 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
2631770 GCGAATACGT
2631780 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
2631801 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
*
2631822 AAATCGCAATGCGAAT
1 AAATCGCAACGCGAAT
2631838 ACGTAAATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:2631971 original size:20 final size:20
Alignment explanation
Indices: 2631948--2631990 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2631938 ATGTAAATCA
*
2631948 CAACGCGAATCTGACTATCG
1 CAACGAGAATCTGACTATCG
*
2631968 CAACGAGATTCTGACTATCG
1 CAACGAGAATCTGACTATCG
2631988 CAA
1 CAA
2631991 TACTGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
CAACGAGAATCTGACTATCG
Found at i:2632027 original size:20 final size:20
Alignment explanation
Indices: 2631997--2632052 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2631987 GCAATACTGA
2631997 ATTTC-AAATTCGCAACTCG
1 ATTTCTAAATTCGCAACTCG
*
2632016 ATTTCTAAATTCGTAACTCG
1 ATTTCTAAATTCGCAACTCG
2632036 ATTTCTAAATTCGCAAC
1 ATTTCTAAATTCGCAAC
2632053 AGGTTTTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (20 bp):
ATTTCTAAATTCGCAACTCG
Found at i:2632875 original size:24 final size:24
Alignment explanation
Indices: 2632848--2632901 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2632838 GTATTCGAAA
2632848 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2632872 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2632896 TTTGAT
1 TTTGAT
2632902 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2635343 original size:20 final size:20
Alignment explanation
Indices: 2635320--2635394 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
2635310 CAATGCGAAT
** *
2635320 ATGACTATCGCAACATGAAA
1 ATGACTATCGCAACGCGGAA
2635340 ATGACTATC-CTAACGCGGAA
1 ATGACTATCGC-AACGCGGAA
*
2635360 TTGACTATCGCAACGCGGAA
1 ATGACTATCGCAACGCGGAA
2635380 ATGACTATCGCAACG
1 ATGACTATCGCAACG
2635395 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATGACTATCGCAACGCGGAA
Found at i:2635416 original size:33 final size:33
Alignment explanation
Indices: 2635377--2635461 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
2635367 TCGCAACGCG
**
2635377 GAAATGACTATCGCAACGAGAGAATCGCAATGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGT
* *
2635410 GAAATGAAAATCGCAACGAGTGAATCGCAATGCA
1 GAAATGAAAATCGCAACGAGAGAATCGCAATG-T
* *
2635444 AAAATGAAAATCGTAACG
1 GAAATGAAAATCGCAACG
2635462 CGAAATTAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 29 0.64
34 16 0.36
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGT
Found at i:2635527 original size:32 final size:32
Alignment explanation
Indices: 2635476--2635568 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
2635466 ATTAGTTTCA
2635476 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATT--CT
2635510 CGTTGCGATTTT-A-TTTCGCATTGCGATTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCT
** *
2635540 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2635569 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
30 12 0.22
31 1 0.02
32 28 0.52
33 1 0.02
34 12 0.22
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCT
Found at i:2637192 original size:42 final size:42
Alignment explanation
Indices: 2637085--2637196 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
2637075 TCTAGAATGT
* * *
2637085 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** * *
2637127 TGGGAGGGGACTCTTGAGGGATGATAGGGGTCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
2637169 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
2637197 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:2637694 original size:20 final size:20
Alignment explanation
Indices: 2637671--2637753 Score: 136
Period size: 20 Copynumber: 4.3 Consensus size: 20
2637661 GAAACTTAAA
2637671 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
2637691 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
2637711 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2637731 ATCGCAATGC---AATGACT
1 ATCGCAACGCGAAAATGACT
2637748 ATCGCA
1 ATCGCA
2637754 CGAATTTGAC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
17 13 0.21
20 49 0.79
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2637840 original size:20 final size:20
Alignment explanation
Indices: 2637815--2637951 Score: 113
Period size: 20 Copynumber: 7.5 Consensus size: 20
2637805 GATTCTTTTG
2637815 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2637835 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
2637855 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
** *
2637869 TTGCGATTTTCA-TTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
2637888 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
2637902 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2637922 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2637942 TTGCGATAGT
1 TTGCGATAGT
2637952 AAACTATTCT
Statistics
Matches: 99, Mismatches: 4, Indels: 28
0.76 0.03 0.21
Matches are distributed among these distances:
14 14 0.14
16 12 0.12
17 6 0.06
18 5 0.05
19 7 0.07
20 55 0.56
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2637915 original size:33 final size:33
Alignment explanation
Indices: 2637835--2637916 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
2637825 CATTTTCGCA
* * *
2637835 TTGCGATAGTCATTTTCGTATTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGTATTGCGATTCTCTCG
**
2637869 TTGCGATTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGTATTGCGATTCTCTCG
2637902 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
2637917 TCGCGTTGCG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 31 0.76
34 10 0.24
ACGTcount: A:0.15, C:0.16, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGTATTGCGATTCTCTCG
Found at i:2637929 original size:87 final size:87
Alignment explanation
Indices: 2637783--2637948 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 87
2637773 AGAATCGCAA
* *
2637783 TGCGATTTTCATTTCGCATTGCGATTCTTTTGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
*
2637848 TTTCGTATTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
* *
2637870 TGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
2637935 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
2637949 AGTAAACTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:2639655 original size:20 final size:20
Alignment explanation
Indices: 2639630--2639667 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2639620 TCTGAAACTT
2639630 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
2639650 AAATCGCAACATGAAAAT
1 AAATCGCAACACGAAAAT
2639668 ACTATCGCAA
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:0.55, C:0.18, G:0.13, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2639738 original size:32 final size:34
Alignment explanation
Indices: 2639671--2639742 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 34
2639661 TGAAAATACT
* * *
2639671 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGACAATCACAACGCAAGA
2639705 ATCGCAACGCGAA-ATGA-AATCACAACG-ACAGA
1 ATCGCAACGCGAATATGACAATCACAACGCA-AGA
2639737 ATCGCA
1 ATCGCA
2639743 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 1 0.03
32 17 0.50
33 3 0.09
34 13 0.38
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGACAATCACAACGCAAGA
Found at i:2640103 original size:21 final size:22
Alignment explanation
Indices: 2640077--2640122 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
2640067 CGCGGAGATA
2640077 GACTGATATCGTC-GAGATGGG
1 GACTGATATCGTCGGAGATGGG
*
2640098 GACTGATTTCGTCGGAGATGGG
1 GACTGATATCGTCGGAGATGGG
2640120 GAC
1 GAC
2640123 GGATGTCGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
GACTGATATCGTCGGAGATGGG
Found at i:2640118 original size:22 final size:22
Alignment explanation
Indices: 2640061--2640122 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 22
2640051 TGACCGTGAA
*
2640061 TGATTTCG-CGGAGAT--AGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2640080 TGATATCGTC-GAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2640101 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2640123 GGATGTCGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 12 0.33
20 1 0.03
21 12 0.33
22 11 0.31
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:2640341 original size:20 final size:20
Alignment explanation
Indices: 2640318--2640451 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
2640308 CGATAGTCAG
**
2640318 ATTCGCATTGCGATTTATAT
1 ATTCGCATTGCGATTTACGT
*
2640338 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2640358 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2640378 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
2640398 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2640419 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2640439 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2640452 ATTAGGAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 84 0.85
21 15 0.15
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2640446 original size:61 final size:60
Alignment explanation
Indices: 2640318--2640465 Score: 188
Period size: 61 Copynumber: 2.5 Consensus size: 60
2640308 CGATAGTCAG
** * * **
2640318 ATTCGCATTGCGATTTATATATTCGTATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
* *
2640378 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACGT
* * *
2640439 ATTCGCATTGCGAATTAGGAAATCGCA
1 ATTCGCATTGCGATTTACGTAATCGCA
2640466 AACGCGAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
60 29 0.38
61 47 0.62
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
Found at i:2640473 original size:21 final size:22
Alignment explanation
Indices: 2640448--2640488 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2640438 TATTCGCATT
2640448 GCGAATTAGG-AAATCGCAAAC
1 GCGAATTAGGAAAATCGCAAAC
*
2640469 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
2640489 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (22 bp):
GCGAATTAGGAAAATCGCAAAC
Found at i:2640493 original size:21 final size:20
Alignment explanation
Indices: 2640441--2640493 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2640431 ATTTACGTAT
*
2640441 TCGCATTGCGAATTAGGAAA
1 TCGCAATGCGAATTAGGAAA
* *
2640461 TCGCAAACGCGAATTTGGAAAA
1 TCGC-AATGCGAATTAGG-AAA
2640483 TCGCAATGCGA
1 TCGCAATGCGA
2640494 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATTAGGAAA
Found at i:2660162 original size:20 final size:20
Alignment explanation
Indices: 2660117--2660172 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
2660107 TGATGAACAT
*
2660117 TATCGATACTAATGTAAGTAG
1 TATCGATACTAATGGAAG-AG
2660138 TATCGATACTAATAGGAAG-G
1 TATCGATACTAAT-GGAAGAG
2660158 TATCGATACT-ATGGA
1 TATCGATACTAATGGA
2660173 TTCCAGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 11 0.33
21 13 0.39
22 4 0.12
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
TATCGATACTAATGGAAGAG
Found at i:2660995 original size:112 final size:112
Alignment explanation
Indices: 2660798--2661000 Score: 334
Period size: 112 Copynumber: 1.8 Consensus size: 112
2660788 TGTGTGACAG
* * ** *
2660798 TATCGATCGATTTTGTTTAATGCACAATGGTGCATTTTTGGCATAAAAGGTGCCACCCATGGTAT
1 TATCGATCGATTTTGCTTAATGCACAACGGTGCATTTTCAGCATAAAAAGTGCCACCCATGGTAT
2660863 TCATAATGAGGTAAATTACCATTTCGACATACTTCATGTATGAAAGT
66 TCATAATGAGGTAAATTACCATTTCGACATACTTCATGTATGAAAGT
* *
2660910 TATCGATTGATTTTGCTTAATGCATAACGGTGCATTTTCAGCATAAAAAGTGCCACCCATGGTAT
1 TATCGATCGATTTTGCTTAATGCACAACGGTGCATTTTCAGCATAAAAAGTGCCACCCATGGTAT
*
2660975 TCATAATGAGGTGAATTACCATTTCG
66 TCATAATGAGGTAAATTACCATTTCG
2661001 GCACTTCGGT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
112 83 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (112 bp):
TATCGATCGATTTTGCTTAATGCACAACGGTGCATTTTCAGCATAAAAAGTGCCACCCATGGTAT
TCATAATGAGGTAAATTACCATTTCGACATACTTCATGTATGAAAGT
Found at i:2664803 original size:5 final size:6
Alignment explanation
Indices: 2664785--2664816 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2664775 TTAGAAATAT
2664785 ATAAAA ATAAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA AT-AAAA ATAAAA ATAAAA ATAAAA A
2664817 GAATTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:2668225 original size:20 final size:20
Alignment explanation
Indices: 2668188--2668226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2668178 AGATTGAGTG
* * *
2668188 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
2668208 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2668227 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:2673032 original size:35 final size:34
Alignment explanation
Indices: 2672979--2673048 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
2672969 AAGAAATAAG
*
2672979 TTTATGGGCCCACTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCACTTTTAATTTAGTATATTAATA
*
2673013 TTTATGGGTCCTACTTTTAATTTAGTATATTAATA
1 TTTATGGG-CCCACTTTTAATTTAGTATATTAATA
2673048 T
1 T
2673049 AGTTTTTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.51
Consensus pattern (34 bp):
TTTATGGGCCCACTTTTAATTTAGTATATTAATA
Found at i:2675056 original size:2 final size:2
Alignment explanation
Indices: 2675051--2675098 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2675041 TGTGTGTGTG
*
2675051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2675093 TA TA TA
1 TA TA TA
2675099 CAGTATGCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2685123 original size:41 final size:41
Alignment explanation
Indices: 2685065--2685143 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
2685055 TGACCCAAGG
* *
2685065 TGATGCTGATCCAACTCCTTATGTGATGGACGAGCGAAATGA
1 TGATGCTAATCCAACTCCTTATATGATGGACGAG-GAAATGA
*
2685107 TGATGCTAAT-CAACTCCTTATATGATGGATGAGGAAA
1 TGATGCTAATCCAACTCCTTATATGATGGACGAGGAAA
2685144 AGTTGGTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 4 0.12
41 21 0.62
42 9 0.26
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (41 bp):
TGATGCTAATCCAACTCCTTATATGATGGACGAGGAAATGA
Found at i:2685336 original size:14 final size:15
Alignment explanation
Indices: 2685307--2685336 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2685297 AATACCTTTT
*
2685307 AAAATAATTTTAAAA
1 AAAAGAATTTTAAAA
2685322 AAAAGAATTTTAAAA
1 AAAAGAATTTTAAAA
2685337 GATAATAATA
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AAAAGAATTTTAAAA
Found at i:2691690 original size:3 final size:3
Alignment explanation
Indices: 2691673--2691719 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
2691663 TTTGGGCCTG
2691673 TAA T-A TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2691718 TA
1 TA
2691720 TGGTGGAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2692159 original size:138 final size:139
Alignment explanation
Indices: 2691954--2692353 Score: 581
Period size: 138 Copynumber: 2.9 Consensus size: 139
2691944 CATGTATTGG
* * * * *
2691954 TGCTG-TTACAACTCCTTATTTGATGGAAACGAGCTAAGGTTGAACAACTTCTTCTCATTATAAA
1 TGCTGATT-CAACTCCATATGTGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAA
** *
2692018 CTTCTTCTCCCTCATCGAACAAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTT
64 CTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTC
2692083 GAGTGAGGTGT
129 GAGTGAGGTGT
* *
2692094 TGTTGATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAAAAAGTTC-TCTCATTATGAACT
1 TGCTGATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
* *
2692158 TCTTCTCCCTCCTC-ATATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCG
66 TCTTCTCCCTCATCGA-ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCG
2692222 AGTGAGGTGT
130 AGTGAGGTGT
* *
2692232 TGCTGATTCAACTCCATATGTGATCAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACT
1 TGCTGATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
* * * * *
2692297 CCTTCTCCCTCATCGGATGAGTTATTCTCATTATGAACTCTCGACTAGAAATGTTGA
66 TCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
2692354 CTAATTATCC
Statistics
Matches: 233, Mismatches: 23, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
137 1 0.00
138 127 0.55
139 85 0.36
140 18 0.08
141 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (139 bp):
TGCTGATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
TCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGA
GTGAGGTGT
Found at i:2692893 original size:98 final size:97
Alignment explanation
Indices: 2692733--2692972 Score: 231
Period size: 98 Copynumber: 2.4 Consensus size: 97
2692723 TAATTTTTTT
**
2692733 TTTTTCAAGGGAAACAATTTCAAAATTTGTTTTCAAGGGAAACTGCTTCAAAAAGACGAAATTGA
1 TTTTTCAAGGGAAACAATTTCAAAATTTGTTTTCAAGGGAAACTGCTTCAAAAAGAAAAAATTGA
2692798 CTTTAAGAGAAACC-ATCTCAAATGAGATAGTAA
66 CTTTAA-A-AAACCAATCTCAAATGAGATAGTAA
* * * *
2692831 TTTTTCGAGTGAAACAATTTCAAAATTTG-TTTCGAA-GGAAATTG-TCTCAAGCAAGAAAAAAT
1 TTTTTCAAGGGAAACAATTTCAAAATTTGTTTTC-AAGGGAAACTGCT-TCAA-AAAGAAAAAAT
* * * *
2692893 TTATTTTAAAAAACCAATCTCAAGTGAGATCA--AT
63 TGACTTTAAAAAACCAATCTCAAATGAGAT-AGTAA
* * *
2692927 TTGCTTTCAAGTGAAACAAATTCCAAATTTTGTGTTTCAAGGGAAA
1 TT--TTTCAAGGGAAAC-AATTTCAAAATTTGT-TTTCAAGGGAAA
2692973 ATTTGTTTCA
Statistics
Matches: 118, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
96 9 0.08
97 29 0.25
98 57 0.48
99 12 0.10
100 2 0.02
101 9 0.08
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (97 bp):
TTTTTCAAGGGAAACAATTTCAAAATTTGTTTTCAAGGGAAACTGCTTCAAAAAGAAAAAATTGA
CTTTAAAAAACCAATCTCAAATGAGATAGTAA
Found at i:2693197 original size:104 final size:101
Alignment explanation
Indices: 2692690--2693237 Score: 496
Period size: 103 Copynumber: 5.4 Consensus size: 101
2692680 ATTTCAAGCA
* * * * *
2692690 AAATTGATTTTAAGAAAAAACCATCTCAAGTG-GTAATTTTTTTTTTTTCAAGGGAAACAATTTC
1 AAATTGATTTTAAG-AAAAACAATCTCAAGTGAG--ATCTATTTTGTTTCAAGTGAAACAATTTC
* * *
2692754 AAAATTTGT-TTTCAAGGGAAACTG-CTTCAA-AAAGACG
63 AAAATTTGTGTTTCAAGGAAAATTGTCTT-AAGCAAGACG
* * * * * * *
2692791 AAATTGACTTTAAGAGAAACCATCTCAAATGAGATAGTA-ATT-TTTCGAGTGAAACAATTTCAA
1 AAATTGATTTTAAGAAAAACAATCTCAAGTGAGAT-CTATTTTGTTTCAAGTGAAACAATTTCAA
* **
2692854 AA-TT-TGTTTCGAAGG-AAATTGTCTCAAGCAAGAAA
65 AATTTGTGTTTC-AAGGAAAATTGTCTTAAGCAAGACG
* * * *
2692889 AAATTTATTTTAA-AAAACCAATCTCAAGTGAGATC-AATTTGCTTTCAAGTGAAACAAATTCCA
1 AAATTGATTTTAAGAAAAACAATCTCAAGTGAGATCTATTTTG-TTTCAAGTGAAAC-AATTTCA
* * *
2692952 AATTTTGTGTTTCAAGGGAAAATTTGT-TTCAAGCAATACT
64 AAATTTGTGTTTCAA-GGAAAA-TTGTCTT-AAGCAAGACG
* * * *
2692992 AAATTTG-GTTT--GAAAAATAATCTCAAGTGAGATCAATTTTGTTTCGAGTGAAACAATTTCAA
1 AAA-TTGATTTTAAGAAAAACAATCTCAAGTGAGATCTATTTTGTTTCAAGTGAAACAATTTCAA
* * * *
2693054 AATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGACG
65 AATTTGTGTTTCAA-GGAAAATTGTCTTAAGCAAGACG
* *
2693092 AAATTGATTTTAAGGAAAAATAATCTCAAGTGAGATCTATTTTGGTTTCAAGTGAATCAATTTCA
1 AAATTGATTTTAA-GAAAAACAATCTCAAGTGAGATCTATTTT-GTTTCAAGTGAAACAATTTCA
* * *
2693157 CAATTTGTGTTTCAAGAGAAAATTGTCTTAAACAATACG
64 AAATTTGTGTTTCAAG-GAAAATTGTCTTAAGCAAGACG
*
2693196 AAATTGATTTTAAGAAAAACAATCTCAAGTGAGATCCATTTT
1 AAATTGATTTTAAGAAAAACAATCTCAAGTGAGATCTATTTT
2693238 TATCTTTGCT
Statistics
Matches: 366, Mismatches: 55, Indels: 50
0.78 0.12 0.11
Matches are distributed among these distances:
95 1 0.00
96 3 0.01
97 30 0.08
98 54 0.15
99 15 0.04
100 35 0.10
101 50 0.14
102 36 0.10
103 78 0.21
104 64 0.17
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (101 bp):
AAATTGATTTTAAGAAAAACAATCTCAAGTGAGATCTATTTTGTTTCAAGTGAAACAATTTCAAA
ATTTGTGTTTCAAGGAAAATTGTCTTAAGCAAGACG
Found at i:2699317 original size:15 final size:15
Alignment explanation
Indices: 2699294--2699341 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
2699284 GTACAGATTA
2699294 AAATAACATAAATTT
1 AAATAACATAAATTT
* *
2699309 AAATGACATAAATGT
1 AAATAACATAAATTT
* *
2699324 AAATAACAAAAAATT
1 AAATAACATAAATTT
2699339 AAA
1 AAA
2699342 GTAATGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (15 bp):
AAATAACATAAATTT
Found at i:2699537 original size:4 final size:4
Alignment explanation
Indices: 2699528--2699558 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2699518 TTTGAACATA
2699528 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2699559 GTAACAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2700372 original size:17 final size:15
Alignment explanation
Indices: 2700334--2700376 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
2700324 GTTTGTTAAA
*
2700334 ACTGAATGGTTTAGC
1 ACTGAATGATTTAGC
2700349 ACTGAATGATTTAGC
1 ACTGAATGATTTAGC
2700364 AGTCTGAATGATT
1 A--CTGAATGATT
2700377 AAGAGGCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
17 10 0.40
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (15 bp):
ACTGAATGATTTAGC
Found at i:2703128 original size:14 final size:14
Alignment explanation
Indices: 2703109--2703139 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2703099 CAGAGTGCAA
2703109 CAATATTGATTCTT
1 CAATATTGATTCTT
2703123 CAATATTGATTCTT
1 CAATATTGATTCTT
2703137 CAA
1 CAA
2703140 CTCTCAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (14 bp):
CAATATTGATTCTT
Found at i:2704835 original size:3 final size:3
Alignment explanation
Indices: 2704823--2704893 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
2704813 TTTTTTACCA
* *
2704823 TAT TATT TAT TAT TA- TATT TAT AAT TAT CAT TAT TA- TAT TAT TAT
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
2704868 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2704894 AATACATTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.85
4 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2706301 original size:13 final size:13
Alignment explanation
Indices: 2706285--2706324 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2706275 AAATATATAA
2706285 TAAATATTTATTT
1 TAAATATTTATTT
*
2706298 TAAATAAATTATTT
1 TAAAT-ATTTATTT
2706312 T-AATATTTATTT
1 TAAATATTTATTT
2706324 T
1 T
2706325 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:2707043 original size:15 final size:13
Alignment explanation
Indices: 2707023--2707060 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
2707013 TATGTTTATT
2707023 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
2707038 TTATTTTATTTCA
1 TTATTTTATTTCA
2707051 TTA-TTTATTT
1 TTATTTTATTT
2707061 TACTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:2714132 original size:10 final size:10
Alignment explanation
Indices: 2714117--2714145 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2714107 CAATCATTCT
2714117 TTACATTTTC
1 TTACATTTTC
2714127 TTACATTTTC
1 TTACATTTTC
2714137 TTACATTTT
1 TTACATTTT
2714146 TACATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (10 bp):
TTACATTTTC
Found at i:2717699 original size:11 final size:11
Alignment explanation
Indices: 2717683--2717758 Score: 84
Period size: 11 Copynumber: 7.0 Consensus size: 11
2717673 AAAAAAAGAG
2717683 AAGAAAGAAAA
1 AAGAAAGAAAA
2717694 AAGAAAGAAAA
1 AAGAAAGAAAA
*
2717705 TA-AAAG-AAA
1 AAGAAAGAAAA
*
2717714 AAGAAAAAAAA
1 AAGAAAGAAAA
*
2717725 AAGAGAGAAAA
1 AAGAAAGAAAA
*
2717736 AGAAAAAGAAAA
1 A-AGAAAGAAAA
*
2717748 AAAAAAGAAAA
1 AAGAAAGAAAA
2717759 GAGGGGGGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
9 4 0.07
10 7 0.13
11 35 0.64
12 9 0.16
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:2717725 original size:31 final size:29
Alignment explanation
Indices: 2717670--2717757 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 29
2717660 ATTATGCTTG
* *
2717670 AAGAAAAAAAG-AGAAGAAAGAAAAAAGA
1 AAGAAAAAAAGAAAAAGAAAAAAAAAAGA
2717698 AAGAAAATAAAAGAAAAAGAAAAAAAAAAG-
1 AAG-AAA-AAAAGAAAAAGAAAAAAAAAAGA
*
2717728 -AGAGAAAAAGAAAAAGAAAAAAAAAAGA
1 AAGAAAAAAAGAAAAAGAAAAAAAAAAGA
2717756 AA
1 AA
2717758 AGAGGGGGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 22 0.42
28 5 0.10
29 6 0.12
30 5 0.10
31 14 0.27
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (29 bp):
AAGAAAAAAAGAAAAAGAAAAAAAAAAGA
Found at i:2717743 original size:16 final size:16
Alignment explanation
Indices: 2717670--2717758 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 16
2717660 ATTATGCTTG
2717670 AAGAAAAA-AAGAGAAGA
1 AAGAAAAAGAA-AGAA-A
2717687 AAGAAAAAAGAAAGAAA
1 AAG-AAAAAGAAAGAAA
2717704 ATA-AAAGAA-AAAGAAA
1 A-AGAAA-AAGAAAGAAA
*
2717720 AA-AAAAAGAGAGAAA
1 AAGAAAAAGAAAGAAA
*
2717735 AAGAAAAAGAAAAAAAA
1 AAGAAAAAG-AAAGAAA
2717752 AAGAAAA
1 AAGAAAA
2717759 GAGGGGGGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.03
15 12 0.19
16 17 0.27
17 19 0.31
18 10 0.16
19 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (16 bp):
AAGAAAAAGAAAGAAA
Found at i:2717759 original size:16 final size:16
Alignment explanation
Indices: 2717673--2717760 Score: 85
Period size: 16 Copynumber: 5.6 Consensus size: 16
2717663 ATGCTTGAAG
*
2717673 AAAAAAAGAGAAGAAA
1 AAAAAAAGAAAAGAAA
*
2717689 GAAAAAAG-AAAG-AA
1 AAAAAAAGAAAAGAAA
*
2717703 AATAAAAGAAAAAGAAA
1 AAAAAAAG-AAAAGAAA
*
2717720 AAAAAAAG-AGAGAAA
1 AAAAAAAGAAAAGAAA
2717735 AAGAAAAAGAAAA-AAA
1 AA-AAAAAGAAAAGAAA
2717751 AAAGAAAAGA
1 AAA-AAAAGA
2717761 GGGGGGATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 8 0.14
15 12 0.20
16 28 0.47
17 11 0.19
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAA
Found at i:2718986 original size:83 final size:83
Alignment explanation
Indices: 2718884--2719296 Score: 718
Period size: 83 Copynumber: 5.0 Consensus size: 83
2718874 ATATCCCAGT
*
2718884 CCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
2718949 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
* * *
2718967 CCAATCATTGAATTTGGAAGCTGAATTTGCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
2719032 TGATCTGATTTGGCAGAA
66 TGATCTGGTTTGGTAAAA
2719050 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
2719115 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
*
2719133 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
2719198 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGTAAAA
*
2719216 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
2719281 TGATCTAGTTTGGTAA
66 TGATCTGGTTTGGTAA
2719297 GAACTACAGA
Statistics
Matches: 309, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 309 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGTAAAA
Found at i:2720188 original size:113 final size:112
Alignment explanation
Indices: 2720001--2721008 Score: 1198
Period size: 113 Copynumber: 8.6 Consensus size: 112
2719991 TGGATTGACA
* * *
2720001 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGGAAGAAGAAATTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
2720066 AGAATTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTACAT-AATTCATCAATTGATGGATCAGCT
* *
2720114 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
2720179 AGAACTTGTTCAACCTTTTACATTAATTCATCATTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTACA-TAATTCATCAATTGATGGATCAGCT
*
2720227 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
2720292 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAACT
66 AGAACTTGTTCAACCTTTTACAT-AATTCATCAATTGATGGATCAGCT
*
2720340 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCACCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
2720405 AGAGCTTGTTTAACCTTTTGC-TCAAATCCATCATTTGATGGATCAGAT
66 AGAACTTGTTCAACCTTTTACAT--AATTCATCAATTGATGGATCAGCT
2720453 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
2720518 AGAACTTGTTTAACCTTTTACATGAATTCATCAATTGATGGATCAGCA
66 AGAACTTGTTCAACCTTTTACAT-AATTCATCAATTGATGGATCAGCT
*
2720566 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
2720630 GGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 AGAACTTGTTCAACCTTTTACATAATTC-AT--C------A-ATTGA-T-GGATCAG-CT
*
2720690 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
2720754 GGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 AGAACTTGTTCAACCTTTTACATAATTC-AT--C------A-ATTGA-T-GGATCAG-CT
*
2720814 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
2720878 GGGACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 AGAACTTGTTCAACCTTTTACATAATTC-AT--C------A-ATTGA-T-GGATCAG-CT
* * * *
2720938 TTTCTAGAGAAAGTTCATAATGAGAAGAATTCATC-GAAAGAATGATGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAAGAAGTTCATAATGAG
2721002 AAGAACT
65 AAGAACT
2721009 CATCAAAAGC
Statistics
Matches: 832, Mismatches: 44, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
111 5 0.01
112 77 0.09
113 425 0.51
114 3 0.00
120 1 0.00
121 4 0.00
122 1 0.00
123 6 0.01
124 257 0.31
125 53 0.06
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (112 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTACATAATTCATCAATTGATGGATCAGCT
Found at i:2720704 original size:124 final size:124
Alignment explanation
Indices: 2720566--2721008 Score: 798
Period size: 124 Copynumber: 3.6 Consensus size: 124
2720556 TGGATCAGCA
2720566 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
2720631 GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
2720690 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
2720755 GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
2720814 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
*
2720879 GGACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
* * * * *
2720938 TTTCTAGAGAAAGTTCATAATGAGAAGAATTCATC-GAAAGAATGATGAAGAAGTTCATAATGAG
1 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAAGAAGTTCATAATAAG
*
2721002 AAGAACT
64 AGGAACT
2721009 CATCAAAAGC
Statistics
Matches: 309, Mismatches: 8, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
124 256 0.83
125 53 0.17
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (124 bp):
TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAG
GAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
Found at i:2721003 original size:40 final size:41
Alignment explanation
Indices: 2720948--2721056 Score: 175
Period size: 42 Copynumber: 2.7 Consensus size: 41
2720938 TTTCTAGAGA
* * *
2720948 AAGTTCATAATGAGAAGAATTCATCGAAA-GAATGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAACGAAGGATGAAG
2720988 AAGTTCATAATGAGAAGAACTCATCAAAAGCGAAGGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAA-CGAAGGATGAAG
2721030 AAGTTCATAATGAGAAGAACTCATCAA
1 AAGTTCATAATGAGAAGAACTCATCAA
2721057 GAGCTTATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 27 0.42
42 37 0.58
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (41 bp):
AAGTTCATAATGAGAAGAACTCATCAAAACGAAGGATGAAG
Found at i:2721316 original size:3 final size:3
Alignment explanation
Indices: 2721303--2721384 Score: 96
Period size: 3 Copynumber: 27.7 Consensus size: 3
2721293 TTTTTACCCA
* * *
2721303 TAT TAT T-T TAT TAT TA- TATT TAT AAT TAT CAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* *
2721347 TAT AAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2721385 AATACATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
2 4 0.06
3 60 0.91
4 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2721846 original size:13 final size:13
Alignment explanation
Indices: 2721830--2721869 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2721820 AAATATATAA
2721830 TAAATATTTATTT
1 TAAATATTTATTT
*
2721843 TAAATAAATTATTT
1 TAAAT-ATTTATTT
2721857 T-AATATTTATTT
1 TAAATATTTATTT
2721869 T
1 T
2721870 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:2722729 original size:13 final size:13
Alignment explanation
Indices: 2722713--2722752 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2722703 AAATATATAA
2722713 TAAATATTTATTT
1 TAAATATTTATTT
*
2722726 TAAATAAATTATTT
1 TAAAT-ATTTATTT
2722740 T-AATATTTATTT
1 TAAATATTTATTT
2722752 T
1 T
2722753 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:2724383 original size:32 final size:32
Alignment explanation
Indices: 2724323--2724383 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
2724313 TCAACCTAAT
* * * *
2724323 TTGATTGAAAGTAAAAATATATATTTTTATTA
1 TTGATTAAAAATAAAAAAATATAGTTTTATTA
*
2724355 TTGATTAAAAATAAAAAAATCTAGTTTTA
1 TTGATTAAAAATAAAAAAATATAGTTTTA
2724384 ATAGATCTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (32 bp):
TTGATTAAAAATAAAAAAATATAGTTTTATTA
Found at i:2725692 original size:230 final size:232
Alignment explanation
Indices: 2725413--2725835 Score: 663
Period size: 231 Copynumber: 1.8 Consensus size: 232
2725403 GGGCGGTGGA
* *
2725413 AAATGTGTGACCATTTTGTTATCTCCAATCAATTTGGGAGTTCGTTAGTAATAG-AATAATACGT
1 AAATGTGTGACAATATTGTTATCTCCAATCAATTTGGGAGTTCGTTAGTAATAGTAATAATACGT
* *
2725477 GGTCCTATATATTATGTGCTTCACGAAGGTTCAGCTACCAATTCTTCTGATGTACCTAATAATGA
66 GGCCCTATATATTATATGCTTCACGAAGGTTCAGCTACCAATTCTTCTGATGTACCTAATAATGA
*
2725542 CTCACTTCATCTGCAAAA-TTTTAGACCTCGATTAATGAAATAATCCTATAT-TTAAAAATAATA
131 CTCACTTCATCTGCAAAATTTTTAGACATCGATTAATGAAATAATCCTAT-TGTTAAAAATAATA
2725605 TTCAATGCTTCACATGCTAGATATATAAAGGTTCAGTG
195 TTCAATGCTTCACATGCTAGATATATAAAGGTTCAGTG
* * *
2725643 AAATGTGTGACAATATTGTTATCTCCAATCGATTTGGGAGTTGGTTAGTAATAGTAATAATATGT
1 AAATGTGTGACAATATTGTTATCTCCAATCAATTTGGGAGTTCGTTAGTAATAGTAATAATACGT
* * * * *
2725708 TGCCCTATTTATTATATGCTTCGCGAGGGTTCAGCTACCAATTCTTCTTATGTACCTAATAATGA
66 GGCCCTATATATTATATGCTTCACGAAGGTTCAGCTACCAATTCTTCTGATGTACCTAATAATGA
* * *
2725773 CTCACTTTATCTGCAAAATTTTTTAGACATCGATTACTGAAATAATTCTATTGTTAAAAATAA
131 CTCACTTCATCTGCAAAA-TTTTTAGACATCGATTAATGAAATAATCCTATTGTTAAAAATAA
2725836 CAATCACTAC
Statistics
Matches: 173, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
230 50 0.29
231 84 0.49
232 1 0.01
233 38 0.22
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (232 bp):
AAATGTGTGACAATATTGTTATCTCCAATCAATTTGGGAGTTCGTTAGTAATAGTAATAATACGT
GGCCCTATATATTATATGCTTCACGAAGGTTCAGCTACCAATTCTTCTGATGTACCTAATAATGA
CTCACTTCATCTGCAAAATTTTTAGACATCGATTAATGAAATAATCCTATTGTTAAAAATAATAT
TCAATGCTTCACATGCTAGATATATAAAGGTTCAGTG
Found at i:2726523 original size:35 final size:35
Alignment explanation
Indices: 2726495--2726602 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 35
2726485 GCATACTCTA
2726495 AATGCGACACATGATACACTGCTATGCATTATCTG
1 AATGCGACACATGATACACTGCTATGCATTATCTG
* * * *
2726530 AATGCGATACATGATACGCTACTGTGCATTATCTG
1 AATGCGACACATGATACACTGCTATGCATTATCTG
* * * *
2726565 AATACGACACATGACACACTG-TGGTGTATTATCTG
1 AATGCGACACATGATACACTGCT-ATGCATTATCTG
2726600 AAT
1 AAT
2726603 CAAACACATG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
34 1 0.02
35 61 0.98
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (35 bp):
AATGCGACACATGATACACTGCTATGCATTATCTG
Found at i:2726610 original size:35 final size:33
Alignment explanation
Indices: 2726557--2726646 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
2726547 GCTACTGTGC
* *
2726557 ATTATCTGAATACGACACATGACACACTGTGGTGT
1 ATTATCTGAATACAACACATGACA-A-TATGGTGT
*
2726592 ATTATCTGAAT-CAAACACATGACAATATTGTGT
1 ATTATCTGAATAC-AACACATGACAATATGGTGT
* * *
2726625 ATTATCTGGATGCGACACATGA
1 ATTATCTGAATACAACACATGA
2726647 TATATTACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
33 24 0.50
34 3 0.06
35 21 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (33 bp):
ATTATCTGAATACAACACATGACAATATGGTGT
Found at i:2726612 original size:70 final size:70
Alignment explanation
Indices: 2726482--2726613 Score: 153
Period size: 70 Copynumber: 1.9 Consensus size: 70
2726472 CTATAATTGT
* * * *
2726482 TGTGCATACTCTAAATGCGACACATGATACACTGCTATGCATTATCTGAATGCGATACATGATAC
1 TGTGCATACTCTAAATACGACACATGACACACTGCTATGCATTATCTGAATGCAACACATGATAC
2726547 GCTAC
66 GCTAC
* * *
2726552 TGTGCATTA-TCTGAATACGACACATGACACACTG-TGGTGTATTATCTGAAT-CAAACACATGA
1 TGTGCA-TACTCTAAATACGACACATGACACACTGCT-ATGCATTATCTGAATGC-AACACATGA
2726614 CAATATTGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
69 2 0.04
70 48 0.92
71 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (70 bp):
TGTGCATACTCTAAATACGACACATGACACACTGCTATGCATTATCTGAATGCAACACATGATAC
GCTAC
Found at i:2726630 original size:33 final size:35
Alignment explanation
Indices: 2726522--2726646 Score: 103
Period size: 35 Copynumber: 3.6 Consensus size: 35
2726512 ACTGCTATGC
* * * * * * *
2726522 ATTATCTGAATGCGATACATGATACGCTACTGTGC
1 ATTATCTGAATACAACACATGACACACTATTGTGT
* * *
2726557 ATTATCTGAATACGACACATGACACACTGTGGTGT
1 ATTATCTGAATACAACACATGACACACTATTGTGT
2726592 ATTATCTGAAT-CAAACACATGACA-A-TATTGTGT
1 ATTATCTGAATAC-AACACATGACACACTATTGTGT
* * *
2726625 ATTATCTGGATGCGACACATGA
1 ATTATCTGAATACAACACATGA
2726647 TATATTACTA
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
33 24 0.32
34 3 0.04
35 48 0.64
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (35 bp):
ATTATCTGAATACAACACATGACACACTATTGTGT
Found at i:2727684 original size:15 final size:15
Alignment explanation
Indices: 2727655--2727722 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
2727645 GGTACTGCAA
* *
2727655 TCACAATATTGGTAC
1 TCACAGTATCGGTAC
*
2727670 TCACAGTATCAGTAC
1 TCACAGTATCGGTAC
2727685 TCACAGTATCGGTAC
1 TCACAGTATCGGTAC
* *
2727700 TCATAGTATTGGTAC
1 TCACAGTATCGGTAC
*
2727715 TCATAGTA
1 TCACAGTA
2727723 CAAATACTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (15 bp):
TCACAGTATCGGTAC
Found at i:2732529 original size:77 final size:79
Alignment explanation
Indices: 2732444--2732590 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 79
2732434 TAATAAAAAA
* *
2732444 TTATTTAATTAATTCAAATTAAATATCTATT-AAAGACTTATAATCTGAATTACAATC-TTTAAT
1 TTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAGAATTACAATCTTTTAAT
2732507 GTTTATTTAAACTC
66 GTTTATTTAAACTC
* ** * * *
2732521 TTATTTAATTATTTTGAATTAAATATCAATTAAAAGAGTTGTAATCAGAATTACATTCTTTTAAT
1 TTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAGAATTACAATCTTTTAAT
2732586 GTTTA
66 GTTTA
2732591 CTTACTATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 27 0.45
78 22 0.37
79 11 0.18
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAGAATTACAATCTTTTAAT
GTTTATTTAAACTC
Found at i:2738661 original size:2 final size:2
Alignment explanation
Indices: 2738649--2738693 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
2738639 AAAAATAAAC
2738649 AT AT CAT 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
2738692 AT
1 AT
2738694 GCAACACTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2746122 original size:29 final size:29
Alignment explanation
Indices: 2746077--2746148 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
2746067 AAGTGCCTTG
2746077 AAAGAAG-AAATGGAGTATCAATATTCAT
1 AAAGAAGAAAATGGAGTATCAATATTCAT
2746105 AAAGAAGAAAATGGAGTATCAATATTCAT
1 AAAGAAGAAAATGGAGTATCAATATTCAT
*
2746134 AAAGAATAAAATGGA
1 AAAGAAGAAAATGGA
2746149 AGAGTGGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (29 bp):
AAAGAAGAAAATGGAGTATCAATATTCAT
Found at i:2749822 original size:18 final size:19
Alignment explanation
Indices: 2749787--2749822 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2749777 TGACCAAACA
*
2749787 AGTTTAGTGCATAAAATTG
1 AGTTTAGTGCACAAAATTG
2749806 AGTTTAGTG-ACAAAATT
1 AGTTTAGTGCACAAAATT
2749823 AATGCAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (19 bp):
AGTTTAGTGCACAAAATTG
Found at i:2750124 original size:20 final size:20
Alignment explanation
Indices: 2750099--2750138 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2750089 TAAAAATACC
2750099 CACAAAAGAAGATCATCATG
1 CACAAAAGAAGATCATCATG
2750119 CACAAAAGAAGATCATCATG
1 CACAAAAGAAGATCATCATG
2750139 ACTGGTTCTG
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:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (20 bp):
CACAAAAGAAGATCATCATG
Found at i:2750990 original size:53 final size:53
Alignment explanation
Indices: 2750928--2751037 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
2750918 CTGAAATCGT
2750928 TATTTCACAACTGCAATACCTGTTATGATCACAATATCACCCACAATTGCTGC
1 TATTTCACAACTGCAATACCTGTTATGATCACAATATCACCCACAATTGCTGC
2750981 TATTTCACAACTGCAATACCTGTTATGATCACAATATCACCCACAATTGCTGC
1 TATTTCACAACTGCAATACCTGTTATGATCACAATATCACCCACAATTGCTGC
2751034 TATT
1 TATT
2751038 GTGAGAAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (53 bp):
TATTTCACAACTGCAATACCTGTTATGATCACAATATCACCCACAATTGCTGC
Found at i:2753235 original size:18 final size:18
Alignment explanation
Indices: 2753203--2753251 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
2753193 TATTATTTTT
*
2753203 TCATGTTTG-GTTGTTGA
1 TCATCTTTGAGTTGTTGA
*
2753220 TCATCTTTGAGTTGTTTA
1 TCATCTTTGAGTTGTTGA
* *
2753238 TCTTCTTTAAGTTG
1 TCATCTTTGAGTTG
2753252 AAACTTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.55
Consensus pattern (18 bp):
TCATCTTTGAGTTGTTGA
Found at i:2753395 original size:105 final size:107
Alignment explanation
Indices: 2753286--2753499 Score: 288
Period size: 105 Copynumber: 2.0 Consensus size: 107
2753276 ATTTTTTAGT
* * * * * *
2753286 TAAAAAAAATTAAAATATTTTTAATTCAATTTATATTTATGATTTTATTTTAATTATTTATGGTT
1 TAAAAAAAATTAAAACATTTTTAATTAAATTTATATTTATAATTTTATTTTAAATATCTATAGTT
**
2753351 AATATGTGGGTTTATGAATTTTCATTTCT-AAAA-AAAAATA
66 AATATGCAGGTTTATGAATTTTCATTTCTAAAAATAAAAATA
* * * *
2753391 TAAAAATATTTTAAACATTTTTAATTAAATTTATATTTATAATTTTATTTTAAATATCTATATTT
1 TAAAAAAAATTAAAACATTTTTAATTAAATTTATATTTATAATTTTATTTTAAATATCTATAGTT
* *
2753456 ATTATGCATGTTTATGAATTTTCATTTCTAAAAATAAAAATA
66 AATATGCAGGTTTATGAATTTTCATTTCTAAAAATAAAAATA
2753498 TA
1 TA
2753500 TACACAAATT
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 80 0.86
106 4 0.04
107 9 0.10
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (107 bp):
TAAAAAAAATTAAAACATTTTTAATTAAATTTATATTTATAATTTTATTTTAAATATCTATAGTT
AATATGCAGGTTTATGAATTTTCATTTCTAAAAATAAAAATA
Found at i:2758442 original size:65 final size:64
Alignment explanation
Indices: 2758373--2758499 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
2758363 CGAATGCATT
* *
2758373 CCATGCATCAATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAA
1 CCATGCATCAATGCAC-CAGAATATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAA
2758437 G
64 G
* **
2758438 CCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCATCAATGCACCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
2758500 CTTGGTACAC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 36 0.64
65 20 0.36
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
CCATGCATCAATGCACCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:2759047 original size:122 final size:122
Alignment explanation
Indices: 2758830--2759076 Score: 494
Period size: 122 Copynumber: 2.0 Consensus size: 122
2758820 TTGCTTTCAA
2758830 GAACACTTTTGTACTCAATTGTATTTATCTTTGAGTGTTCTTTTATTTGTTCTAGAATTGTGCAA
1 GAACACTTTTGTACTCAATTGTATTTATCTTTGAGTGTTCTTTTATTTGTTCTAGAATTGTGCAA
2758895 ACATCTTACCTTGTGAGGTTTTCTTGTAAGTTTGCAAATTTGCAATCTTCTCTTTGG
66 ACATCTTACCTTGTGAGGTTTTCTTGTAAGTTTGCAAATTTGCAATCTTCTCTTTGG
2758952 GAACACTTTTGTACTCAATTGTATTTATCTTTGAGTGTTCTTTTATTTGTTCTAGAATTGTGCAA
1 GAACACTTTTGTACTCAATTGTATTTATCTTTGAGTGTTCTTTTATTTGTTCTAGAATTGTGCAA
2759017 ACATCTTACCTTGTGAGGTTTTCTTGTAAGTTTGCAAATTTGCAATCTTCTCTTTGG
66 ACATCTTACCTTGTGAGGTTTTCTTGTAAGTTTGCAAATTTGCAATCTTCTCTTTGG
2759074 GAA
1 GAA
2759077 AAAGAGTGTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.47
Consensus pattern (122 bp):
GAACACTTTTGTACTCAATTGTATTTATCTTTGAGTGTTCTTTTATTTGTTCTAGAATTGTGCAA
ACATCTTACCTTGTGAGGTTTTCTTGTAAGTTTGCAAATTTGCAATCTTCTCTTTGG
Found at i:2764309 original size:66 final size:66
Alignment explanation
Indices: 2764203--2764362 Score: 223
Period size: 66 Copynumber: 2.4 Consensus size: 66
2764193 TCCCCATGCT
** *
2764203 TGACATGGAGAATAAATACTCATGAAGACATAGGGTATATGAAACC-CAAAAACTACTTGTTAGG
1 TGACATGGAGAATAAATACTCACAAAGACATAGCGTATATG-AACCTCAAAAACTACTTGTTAGG
2764267 TC
65 TC
* * *
2764269 TGACATGGAGAATAAATCCTCACAAAGACATAGCGTATATGAACCTCGAAAGCTACTTGTTAGGT
1 TGACATGGAGAATAAATACTCACAAAGACATAGCGTATATGAACCTCAAAAACTACTTGTTAGGT
*
2764334 T
66 C
* *
2764335 TGACACGGAGAATAAATTCTCACAAAGA
1 TGACATGGAGAATAAATACTCACAAAGA
2764363 TGTCACTTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
65 4 0.05
66 80 0.95
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (66 bp):
TGACATGGAGAATAAATACTCACAAAGACATAGCGTATATGAACCTCAAAAACTACTTGTTAGGT
C
Found at i:2766679 original size:3 final size:3
Alignment explanation
Indices: 2766671--2766779 Score: 138
Period size: 3 Copynumber: 38.0 Consensus size: 3
2766661 TTCGGGCCTG
2766671 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
2766718 T-A TAA TAA TAA TAT TAA TAA TAT TAA TAA -AT TAA TAA -AT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2766763 TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
2766780 AATGGGATAA
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
2 8 0.09
3 83 0.91
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2773277 original size:2 final size:2
Alignment explanation
Indices: 2773270--2773306 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2773260 TAACTTTCAA
2773270 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2773307 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.