Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1853766 original size:23 final size:23
Alignment explanation
Indices: 1853737--1853781 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1853727 AGTGTTATAT
1853737 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
1853760 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
1853782 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:1853787 original size:23 final size:23
Alignment explanation
Indices: 1853738--1853806 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1853728 GTGTTATATT
* * **
1853738 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
1853761 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
1853784 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
1853807 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:1853844 original size:19 final size:19
Alignment explanation
Indices: 1853776--1853856 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
1853766 TTAAATATAT
1853776 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
1853795 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
1853814 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
1853834 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
1853852 -TATTA
1 TTATTA
1853857 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:1853949 original size:23 final size:20
Alignment explanation
Indices: 1853919--1853983 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 20
1853909 TATTAAAATA
*
1853919 AAAATATATTTTCTTATATTATT
1 AAAATATATTTT-AT-TATT-TT
*
1853942 AAAATATAATTTATTATTTT
1 AAAATATATTTTATTATTTT
*
1853962 -AAATATATTTTAAATATTTT
1 AAAATATATTTT-ATTATTTT
1853982 AA
1 AA
1853984 TAATTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 10 0.28
20 9 0.25
21 5 0.14
22 1 0.03
23 11 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAATATATTTTATTATTTT
Found at i:1853963 original size:20 final size:21
Alignment explanation
Indices: 1853934--1853991 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 21
1853924 ATATTTTCTT
1853934 ATATTATTAAAATATAATTT-A
1 ATATT-TTAAAATATAATTTAA
* *
1853955 TTATTTT-AAATATATTTTAA
1 ATATTTTAAAATATAATTTAA
1853975 ATATTTTAATAAT-TAAT
1 ATATTTTAA-AATATAAT
1853992 ATTTTGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.33
20 9 0.30
21 8 0.27
22 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTTAAAATATAATTTAA
Found at i:1854036 original size:24 final size:25
Alignment explanation
Indices: 1853989--1854037 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1853979 TTTAATAATT
*
1853989 AATATTTTGATTAAAATGATATTAA
1 AATATTTTGATTAAAATGAAATTAA
* *
1854014 AATATTTT-ATTAATATTAAATTAA
1 AATATTTTGATTAAAATGAAATTAA
1854038 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAATGAAATTAA
Found at i:1854254 original size:42 final size:43
Alignment explanation
Indices: 1854194--1854288 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
1854184 TCCTCCAACC
* * *
1854194 AAACACTGGAAAACA-TTTTCCGGAAAATGAATTACGTGAAAA
1 AAACACGGGAAAACATTTTTCCGAAAAACGAATTACGTGAAAA
* *
1854236 AAACACGGGAAAATATTTTTCCGAAAAACGAATTACGTGAAAT
1 AAACACGGGAAAACATTTTTCCGAAAAACGAATTACGTGAAAA
1854279 AAACACGGGA
1 AAACACGGGA
1854289 TTTCCGATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 13 0.28
43 34 0.72
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACACGGGAAAACATTTTTCCGAAAAACGAATTACGTGAAAA
Found at i:1857085 original size:6 final size:6
Alignment explanation
Indices: 1857051--1857082 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1857041 CTCGTCTCGA
*
1857051 GTCGTG GTCGTG GTCGTG GTCGTG GTAGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1857083 AGTACGTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.12, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:1857232 original size:21 final size:21
Alignment explanation
Indices: 1857208--1857254 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1857198 AAATCACAAC
*
1857208 GCGAACTTCGACTGTCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1857229 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
1857250 GCGAA
1 GCGAA
1857255 TATGTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:1865955 original size:26 final size:26
Alignment explanation
Indices: 1865919--1865971 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1865909 ACTATCTACG
1865919 TCATATTGTTTAATATAAAACAGAAA
1 TCATATTGTTTAATATAAAACAGAAA
1865945 TCATATTGTTTAATATAAAACAGAAA
1 TCATATTGTTTAATATAAAACAGAAA
1865971 T
1 T
1865972 AAGTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
TCATATTGTTTAATATAAAACAGAAA
Found at i:1868415 original size:19 final size:19
Alignment explanation
Indices: 1868391--1868451 Score: 122
Period size: 19 Copynumber: 3.2 Consensus size: 19
1868381 ATGGTGGGAT
1868391 TTCTTTACAAGCCCATGTC
1 TTCTTTACAAGCCCATGTC
1868410 TTCTTTACAAGCCCATGTC
1 TTCTTTACAAGCCCATGTC
1868429 TTCTTTACAAGCCCATGTC
1 TTCTTTACAAGCCCATGTC
1868448 TTCT
1 TTCT
1868452 CACTTTCCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (19 bp):
TTCTTTACAAGCCCATGTC
Found at i:1873680 original size:2 final size:2
Alignment explanation
Indices: 1873673--1873708 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1873663 ACATGATTGG
*
1873673 AT AT AT AT AC 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
1873709 GAGGCTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1882221 original size:27 final size:27
Alignment explanation
Indices: 1882191--1882243 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1882181 TTCTAACTCA
1882191 GAAGTTTCAACAATTTCAAGAGAGTTT
1 GAAGTTTCAACAATTTCAAGAGAGTTT
1882218 GAAGTTTCAACAATTTCAAGAGAGTT
1 GAAGTTTCAACAATTTCAAGAGAGTT
1882244 GTAATCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (27 bp):
GAAGTTTCAACAATTTCAAGAGAGTTT
Found at i:1883022 original size:23 final size:24
Alignment explanation
Indices: 1882991--1883037 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1882981 ATTATTTTTA
1882991 ATATATATACTTTTTAATAAAATGT
1 ATATATA-ACTTTTTAATAAAATGT
* *
1883016 ATATATAATTTTTTTATAAAAT
1 ATATATAACTTTTTAATAAAAT
1883038 TTAAAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATATAACTTTTTAATAAAATGT
Found at i:1890782 original size:16 final size:17
Alignment explanation
Indices: 1890756--1890787 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1890746 GCATCATACA
1890756 TATGAAACCTATTAGAT
1 TATGAAACCTATTAGAT
1890773 TATG-AACCTATTAGA
1 TATGAAACCTATTAGA
1890788 GTTTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (17 bp):
TATGAAACCTATTAGAT
Found at i:1903557 original size:60 final size:60
Alignment explanation
Indices: 1903411--1903557 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
1903401 TACATAATGA
** *
1903411 ATAGTCGGATGATCATTTTGTAACTTTTAACAGTAGAGGGACTCAACAAAACAACTCCCT
1 ATAGTCGGGGGATCATTTTGTAACTTTTAACAGTAGAAGGACTCAACAAAACAACTCCCT
* * * * *
1903471 ATAGTCGGGGGACCATTTTATAACTTTTAATAGTGGAAGGACTCAACAAAATAGTA-T-CCT
1 ATAGTCGGGGGATCATTTTGTAACTTTTAACAGTAGAAGGACTCAACAAAACA--ACTCCCT
*
1903531 ATAGTCGGGGGATTATTTGTGT-ACTTT
1 ATAGTCGGGGGATCATTT-TGTAACTTT
1903558 ACCCTTAATT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
60 69 0.95
61 3 0.04
62 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (60 bp):
ATAGTCGGGGGATCATTTTGTAACTTTTAACAGTAGAAGGACTCAACAAAACAACTCCCT
Found at i:1910556 original size:60 final size:60
Alignment explanation
Indices: 1910428--1910569 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 60
1910418 GTTCAAATAA
* * **
1910428 TTTAGGGACCAATTTAGAATGAAGATCATAGTTTAGGGATGAAAGTGAAATGCTCAAAAG
1 TTTAAGGACCAATTTAGAATGAAGATCATAGTTTAAGGATGAAAGTGAAACACTCAAAAG
* * * * * * *
1910488 TTTGAGGACTAATTTAGAATGATAG-TCATTGTTTAAGGATGAAATTGAAACATTTAAATG
1 TTTAAGGACCAATTTAGAATGA-AGATCATAGTTTAAGGATGAAAGTGAAACACTCAAAAG
*
1910548 TTTAAGGACCAATTTAAAATGA
1 TTTAAGGACCAATTTAGAATGA
1910570 GGGTCATGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 65 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTAAGGACCAATTTAGAATGAAGATCATAGTTTAAGGATGAAAGTGAAACACTCAAAAG
Found at i:1921459 original size:6 final size:6
Alignment explanation
Indices: 1921448--1921478 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1921438 GACACGTATT
*
1921448 ACCACG ACCACG ACCACG ACCAAG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
1921479 GATGAGACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.39, C:0.45, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1922264 original size:30 final size:30
Alignment explanation
Indices: 1922228--1922288 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1922218 TGGAATAAAT
*
1922228 CGCAACGC-AATCTTTGACTATCGCAACGAA
1 CGCAACGCGAA-CTTCGACTATCGCAACGAA
1922258 CGCAACGCGAACTTCGACTATCGCAACGAA
1 CGCAACGCGAACTTCGACTATCGCAACGAA
1922288 C
1 C
1922289 TTGAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (30 bp):
CGCAACGCGAACTTCGACTATCGCAACGAA
Found at i:1922284 original size:21 final size:21
Alignment explanation
Indices: 1922258--1922582 Score: 296
Period size: 21 Copynumber: 15.5 Consensus size: 21
1922248 TCGCAACGAA
*
1922258 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTGGACTAT
* *
1922279 CGCAA--CGAACTTGAAATAAAT
1 CGCAACGCGAACTTGGACT--AT
*
1922300 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTGGACTAT
*
1922321 AGCAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTGGACTAT
*
1922342 CGCAACGCGAACTTGGAATAAAT
1 CGCAACGCGAACTTGGACT--AT
*
1922365 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTGGACTAT
*
1922386 CGCAA--CGAACTTGGAATAAAT
1 CGCAACGCGAACTTGGACT--AT
*
1922407 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTGGACTAT
*
1922428 CGCAA--CGAACTTGGAATAAAT
1 CGCAACGCGAACTTGGACT--AT
*
1922449 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTGGACTAT
* *
1922470 CGCAA--CGAATTTGGAATAAAT
1 CGCAACGCGAACTTGGACT--AT
1922491 CGCAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTGGACTAT
* *
1922512 CGCAA--CGAATTTGGAATAAAT
1 CGCAACGCGAACTTGGACT--AT
1922533 CGCAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTGGACTAT
* **
1922554 CGCAA--CGAATTTGGAAAAT
1 CGCAACGCGAACTTGGACTAT
1922573 CGCAACGCGA
1 CGCAACGCGA
1922583 TAGTCGAAGT
Statistics
Matches: 248, Mismatches: 32, Indels: 48
0.76 0.10 0.15
Matches are distributed among these distances:
19 64 0.26
21 116 0.47
23 68 0.27
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
CGCAACGCGAACTTGGACTAT
Found at i:1922395 original size:42 final size:42
Alignment explanation
Indices: 1922322--1922582 Score: 436
Period size: 42 Copynumber: 6.2 Consensus size: 42
1922312 TTCGACTATA
*
1922322 GCAACGCGAACTTGGACTATCGCAACGCGAACTTGGAATAAATC
1 GCAACGCGAACTTCGACTATCGCAA--CGAACTTGGAATAAATC
1922366 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
1 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
1922408 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
1 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
*
1922450 GCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATC
1 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
* *
1922492 GCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATC
1 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
* *
1922534 GCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AAATC
1 GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
1922574 GCAACGCGA
1 GCAACGCGA
1922583 TAGTCGAAGT
Statistics
Matches: 214, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
40 14 0.07
41 1 0.00
42 175 0.82
44 24 0.11
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (42 bp):
GCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATC
Found at i:1924740 original size:2 final size:2
Alignment explanation
Indices: 1924733--1924758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1924723 AAGTGCAATG
1924733 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
1924759 GACAGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1926708 original size:2 final size:2
Alignment explanation
Indices: 1926703--1926728 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1926693 TTACAACATA
1926703 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
1926729 TTGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1930758 original size:60 final size:60
Alignment explanation
Indices: 1930685--1930805 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
1930675 ATATTAATTG
1930685 AATGTTTCAACTTATTCATGACCTAAAACATCAACATATCAATCTGAGTTGAATTTCAAA
1 AATGTTTCAACTTATTCATGACCTAAAACATCAACATATCAATCTGAGTTGAATTTCAAA
1930745 AATGTTTCAACTTATTCATGACCTAAAACATCAACATATCAATCTGAGTTGAATTTCAAA
1 AATGTTTCAACTTATTCATGACCTAAAACATCAACATATCAATCTGAGTTGAATTTCAAA
1930805 A
1 A
1930806 TTAATGCTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (60 bp):
AATGTTTCAACTTATTCATGACCTAAAACATCAACATATCAATCTGAGTTGAATTTCAAA
Found at i:1940408 original size:58 final size:58
Alignment explanation
Indices: 1940338--1940449 Score: 183
Period size: 58 Copynumber: 1.9 Consensus size: 58
1940328 TTAAGCTACT
*
1940338 TGATGATTAATTATGTTAAAATAATTTTTC-ATAT-TTAAACTTTCTAAAGTTACACAAG
1 TGATGATTAATTATGTTAAAATAA-TTTTCGAT-TGTTAAACTTTCTAAAATTACACAAG
1940396 TGATGATTAATTATGTTAAAATAATTTTCGATTGTTAAACTTTCTAAAATTACA
1 TGATGATTAATTATGTTAAAATAATTTTCGATTGTTAAACTTTCTAAAATTACA
1940450 AAATATATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
57 6 0.12
58 45 0.88
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (58 bp):
TGATGATTAATTATGTTAAAATAATTTTCGATTGTTAAACTTTCTAAAATTACACAAG
Found at i:1941185 original size:2 final size:2
Alignment explanation
Indices: 1941180--1941209 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1941170 AAAAAATCAA
1941180 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
1941210 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1942273 original size:23 final size:23
Alignment explanation
Indices: 1942246--1942337 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
1942236 CACCACAGCT
* *
1942246 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1942269 CGTATAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1942292 CGTAGAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1942315 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1942338 TATAAGGTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1947740 original size:32 final size:29
Alignment explanation
Indices: 1947704--1947766 Score: 72
Period size: 32 Copynumber: 2.1 Consensus size: 29
1947694 ATGTATGCTA
* *
1947704 AATTTTAGATAGATTATAAATATGTAATTATT
1 AATTTTAGATAAAAT-TAAATATG-AATT-TT
*
1947736 AATTTTATATAAAATTAAATATGAATTTT
1 AATTTTAGATAAAATTAAATATGAATTTT
1947765 AA
1 AA
1947767 CTTAATGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 4 0.14
31 8 0.29
32 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
AATTTTAGATAAAATTAAATATGAATTTT
Found at i:1949064 original size:29 final size:29
Alignment explanation
Indices: 1948974--1949064 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
1948964 CTATAATCCT
*
1948974 CATTTTAAATTAGTCCTTAAATTTTTGAA
1 CATTTTAAATTAGTCCTTAAACTTTTGAA
* * * * * *
1949003 TATTTCAATTTTA-T-CTATGAAC-TATGACT
1 CATTTTAA-ATTAGTCCT-TAAACTTTTGA-A
1949032 CATTTTAAATTAGTCCTTAAACTTTTGAA
1 CATTTTAAATTAGTCCTTAAACTTTTGAA
1949061 CATT
1 CATT
1949065 CTAATTTCAT
Statistics
Matches: 43, Mismatches: 13, Indels: 12
0.63 0.19 0.18
Matches are distributed among these distances:
28 9 0.21
29 25 0.58
30 9 0.21
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (29 bp):
CATTTTAAATTAGTCCTTAAACTTTTGAA
Found at i:1952898 original size:25 final size:24
Alignment explanation
Indices: 1952874--1952919 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1952864 ATTCAATGAA
*
1952874 AATATTTAAAAT-TAAATAATTTG
1 AATATTAAAAATATAAATAATTTG
1952897 AATATTAAAAATAATAAATAATT
1 AATATTAAAAAT-ATAAATAATT
1952920 ATACTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATTAAAAATATAAATAATTTG
Found at i:1957892 original size:30 final size:31
Alignment explanation
Indices: 1957831--1957899 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1957821 TTACTGCATC
*
1957831 GACACTTAAAAATGTAATGAAAAAAATGTTA
1 GACACTTAAAAATGTAAAGAAAAAAATGTTA
*
1957862 GACACTTAAAAGTGTAACAG-AAAAAA-GTTA
1 GACACTTAAAAATGTAA-AGAAAAAAATGTTA
1957892 GACACTTA
1 GACACTTA
1957900 TTTTTAACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 12 0.34
31 22 0.63
32 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (31 bp):
GACACTTAAAAATGTAAAGAAAAAAATGTTA
Found at i:1959659 original size:17 final size:17
Alignment explanation
Indices: 1959637--1959671 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1959627 ATATTTTTTT
1959637 ATTTAATATAAAAAATA
1 ATTTAATATAAAAAATA
*
1959654 ATTTAATATATAAAATA
1 ATTTAATATAAAAAATA
1959671 A
1 A
1959672 AAACAGACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAATATAAAAAATA
Found at i:1960874 original size:285 final size:284
Alignment explanation
Indices: 1960338--1960905 Score: 1019
Period size: 285 Copynumber: 2.0 Consensus size: 284
1960328 GAAAGTAAAT
* *
1960338 TGAGTAAAATAGAAGAAAGGTAAAGTTCAATTAGGAATGATGTAGTTTACCCTTCATTGATTTTA
1 TGAGTAAAATAGAAGAAAGATAAAGTTCAATTAGGAATGATGTAATTTACCCTTCATTGATTTTA
*
1960403 CTTTATAAAATTGAGAAAGGGATTAGACTAAAAAAATAACAAACAGTGATTTAAAATATAAGCTT
66 CTTTATAAAATTGAGAAAGGGATTAGACTAAAAAAATAACAAAAAGTGATTTAAAATATAAGCTT
*
1960468 ATAGTGAGCAAACCGTTTCTCATTTTCTCTCAAAAGATTTTCCTAAGCTGTTGTCATCAGCCAAA
131 ATAGTGAGCAAACCGTTTCTCATTTTCTCTCAAAAGATTTTCCGAAGCTGTTGTCATCAGCCAAA
* *
1960533 CAGAACCCAATCTGACTCATCCTTTCACTCTCTCAGCTCTTCCTTCGGAGTTGGTAAGTCTCGCT
196 AAGAACCCAATCTGACTCATCCTTTCACTCTCTCAGCTCTTCCTTCGGACTTGGTAAGTCTCGCT
*
1960598 CCTCGGTGATTCCATTCTCCAAAG
261 CCTCAGTGATTCCATTCTCCAAAG
* *
1960622 TGAGTAGAATAGGAGAAAAGATAAAGTTCAATTAGGAATGATGTAATTTACCCTTCATTGATTTT
1 TGAGTAAAATAGAAG-AAAGATAAAGTTCAATTAGGAATGATGTAATTTACCCTTCATTGATTTT
*
1960687 ACTTTATAAAATTGAGAAAGGGATTAGACTAAAAAAATAACAAAAAGTGATTTAGAATATAAGCT
65 ACTTTATAAAATTGAGAAAGGGATTAGACTAAAAAAATAACAAAAAGTGATTTAAAATATAAGCT
* *
1960752 TTTAGTGAGCAAACCGTTTCTCATTTTCTCTCAACAGATTTTCCGAAGCTGTTGTCATCAGCCAA
130 TATAGTGAGCAAACCGTTTCTCATTTTCTCTCAAAAGATTTTCCGAAGCTGTTGTCATCAGCCAA
1960817 AAAGAACCCAATCTGACTCATCCTTTCACTCTCTCAGCTCTTCCTTCGGACTTGGTAAGTCTCGC
195 AAAGAACCCAATCTGACTCATCCTTTCACTCTCTCAGCTCTTCCTTCGGACTTGGTAAGTCTCGC
1960882 TCCTCAGTGATTCCATTCTCCAAA
260 TCCTCAGTGATTCCATTCTCCAAA
1960906 TATACTTCCG
Statistics
Matches: 271, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
284 13 0.05
285 258 0.95
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (284 bp):
TGAGTAAAATAGAAGAAAGATAAAGTTCAATTAGGAATGATGTAATTTACCCTTCATTGATTTTA
CTTTATAAAATTGAGAAAGGGATTAGACTAAAAAAATAACAAAAAGTGATTTAAAATATAAGCTT
ATAGTGAGCAAACCGTTTCTCATTTTCTCTCAAAAGATTTTCCGAAGCTGTTGTCATCAGCCAAA
AAGAACCCAATCTGACTCATCCTTTCACTCTCTCAGCTCTTCCTTCGGACTTGGTAAGTCTCGCT
CCTCAGTGATTCCATTCTCCAAAG
Found at i:1973563 original size:30 final size:28
Alignment explanation
Indices: 1973514--1973605 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 28
1973504 ACAATTTTTT
*
1973514 ATCAATAAATTTTTAAATGTTATAAAATA
1 ATCATTAAA-TTTTAAATGTTATAAAATA
* *
1973543 ATCATTAAATGTTCTAAATGTTCACAAAATG
1 ATCATTAAAT-TT-TAAATGTT-ATAAAATA
* * *
1973574 ATCGTTAAACATTTAAACGATTATAAAATA
1 ATCATTAAA-TTTTAAATG-TTATAAAATA
1973604 AT
1 AT
1973606 TTATGTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 21 0.42
31 18 0.36
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (28 bp):
ATCATTAAATTTTAAATGTTATAAAATA
Found at i:1973582 original size:31 final size:29
Alignment explanation
Indices: 1973514--1973582 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
1973504 ACAATTTTTT
* * *
1973514 ATCAATAAATTTTTAAATGTTATAAAATA
1 ATCATTAAATTTCTAAATGTTACAAAATA
*
1973543 ATCATTAAATGTTCTAAATGTTCACAAAATG
1 ATCATTAAAT-TTCTAAATGTT-ACAAAATA
*
1973574 ATCGTTAAA
1 ATCATTAAA
1973583 CATTTAAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 9 0.27
30 10 0.30
31 14 0.42
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (29 bp):
ATCATTAAATTTCTAAATGTTACAAAATA
Found at i:1981016 original size:16 final size:17
Alignment explanation
Indices: 1980986--1981017 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1980976 ATTCACATGA
1980986 CAAAATTTCACTATTCG
1 CAAAATTTCACTATTCG
1981003 CAAAATTT-ACTATTC
1 CAAAATTTCACTATTC
1981018 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (17 bp):
CAAAATTTCACTATTCG
Found at i:1982135 original size:16 final size:17
Alignment explanation
Indices: 1982107--1982141 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1982097 CGTATCGCCG
1982107 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
1982124 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
1982140 AC
1 AC
1982142 GTAAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:1989681 original size:2 final size:2
Alignment explanation
Indices: 1989674--1989719 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
1989664 TAACATTGTT
1989674 TA TA TA TA TA -A TA TA TA TA TA TA T- TA TA TA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1989712 TA TA TA TA
1 TA TA TA TA
1989720 ACGCCAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1989689 original size:7 final size:7
Alignment explanation
Indices: 1989677--1989720 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1989667 CATTGTTTAT
1989677 ATATATA
1 ATATATA
1989684 ATATATA
1 ATATATA
*
1989691 TATATATT
1 -ATATATA
*
1989699 ATATATT
1 ATATATA
*
1989706 ATATATT
1 ATATATA
1989713 ATATATA
1 ATATATA
1989720 A
1 A
1989721 CGCCAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
ATATATA
Found at i:1989689 original size:9 final size:9
Alignment explanation
Indices: 1989675--1989719 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1989665 AACATTGTTT
1989675 ATATATATA
1 ATATATATA
1989684 ATATATATA
1 ATATATATA
1989693 TATATTATATA
1 -ATA-TATATA
* *
1989704 TTATATATT
1 ATATATATA
1989713 ATATATA
1 ATATATA
1989720 ACGCCAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 20 0.65
10 5 0.16
11 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATATATA
Found at i:1990629 original size:19 final size:20
Alignment explanation
Indices: 1990605--1990653 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1990595 AAAGAATAGT
1990605 TAAATAACTTTAAAAAT-AA
1 TAAATAACTTTAAAAATAAA
***
1990624 TAAATAAAAATAAAAATAAA
1 TAAATAACTTTAAAAATAAA
*
1990644 TATATAACTT
1 TAAATAACTT
1990654 CAATTTATAT
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATAACTTTAAAAATAAA
Found at i:1993971 original size:37 final size:40
Alignment explanation
Indices: 1993907--1993981 Score: 104
Period size: 38 Copynumber: 1.9 Consensus size: 40
1993897 TCAATATTTC
1993907 TTTTTCTTTGTTGATTTTGTGTTTCC-TTTGTT-TTGAAA
1 TTTTTCTTTGTTGATTTTGTGTTTCCTTTTGTTGTTGAAA
*
1993945 TTTTTCTTTTTTG-TTATT-TGTTTCCTTTTGTTGTTGA
1 TTTTTCTTTGTTGATT-TTGTGTTTCCTTTTGTTGTTGA
1993982 TGTTGTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 9 0.27
38 20 0.61
39 4 0.12
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (40 bp):
TTTTTCTTTGTTGATTTTGTGTTTCCTTTTGTTGTTGAAA
Found at i:1996043 original size:16 final size:16
Alignment explanation
Indices: 1996022--1996054 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1996012 TAATAAATAG
1996022 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1996038 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1996054 A
1 A
1996055 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1996150 original size:14 final size:15
Alignment explanation
Indices: 1996124--1996182 Score: 93
Period size: 14 Copynumber: 3.9 Consensus size: 15
1996114 TAATAAATAA
1996124 ACGAACATAAACGAC
1 ACGAACATAAACGAC
1996139 ACGAACAT-AACGAC
1 ACGAACATAAACGAC
*
1996153 ACGAACATAAATGAAC
1 ACGAACATAAACG-AC
1996169 ACGAACATAAACGA
1 ACGAACATAAACGA
1996183 ACATAAACGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
14 14 0.35
15 12 0.30
16 14 0.35
ACGTcount: A:0.54, C:0.24, G:0.14, T:0.08
Consensus pattern (15 bp):
ACGAACATAAACGAC
Found at i:1996172 original size:16 final size:16
Alignment explanation
Indices: 1996124--1996185 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
1996114 TAATAAATAA
1996124 ACGAACATAAACG-AC
1 ACGAACATAAACGAAC
1996139 ACGAACAT-AACG-AC
1 ACGAACATAAACGAAC
*
1996153 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1996169 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1996185 A
1 A
1996186 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
14 14 0.33
15 11 0.26
16 18 0.42
ACGTcount: A:0.55, C:0.24, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1996955 original size:14 final size:14
Alignment explanation
Indices: 1996938--1996993 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1996928 AATGAACATA
*
1996938 AACGAACATAATCG
1 AACGAACATAACCG
1996952 AACGAACAT-A---
1 AACGAACATAACCG
1996962 AACGAACATAACCG
1 AACGAACATAACCG
1996976 AACGAACATAACCG
1 AACGAACATAACCG
1996990 AACG
1 AACG
1996994 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1996958 original size:24 final size:24
Alignment explanation
Indices: 1996918--1996992 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
1996908 GATTGGGTTA
*
1996918 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1996942 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
1996966 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1996990 AAC
1 AAC
1996993 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1996992 original size:10 final size:10
Alignment explanation
Indices: 1996931--1996978 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1996921 ATAAATGAAT
1996931 GAACATAAAC
1 GAACATAAAC
1996941 GAACATAATCGAAC
1 GAACAT-A---AAC
1996955 GAACATAAAC
1 GAACATAAAC
*
1996965 GAACATAACC
1 GAACATAAAC
1996975 GAAC
1 GAAC
1996979 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:2006063 original size:34 final size:33
Alignment explanation
Indices: 2006039--2006118 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 33
2006029 CGATCTACTA
2006039 AGGAGAAAACAATGATAATTCTCTCTTGATAAAT
1 AGGAGAAAACAATGATAATTCTCTC-TGATAAAT
2006073 AGGAGAAAACAATGATAATTCTCTCTTGATAAAT
1 AGGAGAAAACAATGATAATTCTCTC-TGATAAAT
2006107 AGGAGAAAACAA
1 AGGAGAAAACAA
2006119 CTCTCAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (33 bp):
AGGAGAAAACAATGATAATTCTCTCTGATAAAT
Found at i:2011715 original size:13 final size:14
Alignment explanation
Indices: 2011697--2011725 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2011687 AGCAAGCAAT
2011697 AATATATG-GAGAA
1 AATATATGTGAGAA
2011710 AATATATGTGAGAA
1 AATATATGTGAGAA
2011724 AA
1 AA
2011726 CACAGACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (14 bp):
AATATATGTGAGAA
Found at i:2020423 original size:18 final size:18
Alignment explanation
Indices: 2020402--2020437 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2020392 ATATAATATG
*
2020402 TATTTAAATTCAAAATTC
1 TATTTAAACTCAAAATTC
2020420 TATTTAAACTCAAAATTC
1 TATTTAAACTCAAAATTC
2020438 AAAAGAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTTAAACTCAAAATTC
Found at i:2028466 original size:2 final size:2
Alignment explanation
Indices: 2028453--2028504 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2028443 GTAAGCACAG
*
2028453 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2028495 GA GA GA GA GA
1 GA GA GA GA GA
2028505 ATGGTGGGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2032660 original size:25 final size:25
Alignment explanation
Indices: 2032630--2032680 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2032620 TCTTGAGCAG
*
2032630 TAAAATCCTTTCTTAATATTTTCCA
1 TAAAATCCTTTCCTAATATTTTCCA
2032655 TAAAATCCTTTCCTAATATTTTCCA
1 TAAAATCCTTTCCTAATATTTTCCA
2032680 T
1 T
2032681 CTATGCCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAATCCTTTCCTAATATTTTCCA
Found at i:2044897 original size:2 final size:2
Alignment explanation
Indices: 2044890--2044917 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2044880 CATTAGTTGG
2044890 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2044918 ATGCTGTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2057293 original size:179 final size:180
Alignment explanation
Indices: 2056979--2057337 Score: 704
Period size: 178 Copynumber: 2.0 Consensus size: 180
2056969 CCTCTGCCCT
2056979 CCGCCGTGAACCCATAGTTGGGAGCACAGAAATTGTGGCGGTGACAATGATCGATGGTCCCAGGT
1 CCGCCGTGAACCCATAGTTGGGAGCACAGAAATTGTGGCGGTGACAATGATCGATGGTCCCAGGT
2057044 ATGCACCATCGCAGGTCATCCACGCACCTAAGCTCGAAGCACGCACCGTAGATCTGCCCACGCTA
66 ATGCACCATCGCAGGTCATCCACGCACCTAAGCTCGAAGCACGCACCGTAGATCTGCCCACGCTA
2057109 AAAAAAAGCCTCGCTTAAAACCACC-TCATAATCCCGTAGCCAGCTTTGA
131 AAAAAAAGCCTCGCTTAAAACCACCGTCATAATCCCGTAGCCAGCTTTGA
2057158 CCGCCGTGAACCCATAGTTGGGAGCACAGAAATTGTGGCGGTGACAATGATCGA-GGTCCCAGGT
1 CCGCCGTGAACCCATAGTTGGGAGCACAGAAATTGTGGCGGTGACAATGATCGATGGTCCCAGGT
2057222 ATGCACCATCGCAGGTCATCCACGCACCTAAGCTCGAAGCACGCACCGTAGATCTGCCCACGCTA
66 ATGCACCATCGCAGGTCATCCACGCACCTAAGCTCGAAGCACGCACCGTAGATCTGCCCACGCTA
2057287 AAAAAAAGCCTCGCTTAAAACCACCGTCATAATCCCGTAGCCAGCTTTGA
131 AAAAAAAGCCTCGCTTAAAACCACCGTCATAATCCCGTAGCCAGCTTTGA
2057337 C
1 C
2057338 GAGGTCCCCA
Statistics
Matches: 179, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
178 100 0.56
179 79 0.44
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (180 bp):
CCGCCGTGAACCCATAGTTGGGAGCACAGAAATTGTGGCGGTGACAATGATCGATGGTCCCAGGT
ATGCACCATCGCAGGTCATCCACGCACCTAAGCTCGAAGCACGCACCGTAGATCTGCCCACGCTA
AAAAAAAGCCTCGCTTAAAACCACCGTCATAATCCCGTAGCCAGCTTTGA
Found at i:2058776 original size:21 final size:22
Alignment explanation
Indices: 2058736--2058776 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2058726 GCTTGAATAT
*
2058736 ATCTCTGTTTAGCTTGTTTCTG
1 ATCTCTGTTCAGCTTGTTTCTG
*
2058758 ATCTTTGTTCAGC-TGTTTC
1 ATCTCTGTTCAGCTTGTTTC
2058777 CAGAAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.54
Consensus pattern (22 bp):
ATCTCTGTTCAGCTTGTTTCTG
Found at i:2088342 original size:31 final size:31
Alignment explanation
Indices: 2088211--2088344 Score: 80
Period size: 31 Copynumber: 4.4 Consensus size: 31
2088201 ATAATGAGTG
* * * *
2088211 TAAAATTTTGATAAATTTAATTATTATTTTA
1 TAAAAATTTAATAAATTTAATAATTATTATA
* * *
2088242 TAACAA-TTAACTCTAATTTAATGA-TATT-T-
1 TAAAAATTTAA-T-AAATTTAATAATTATTATA
* * * *
2088271 TAATAGTTTTATAAAATTTAATGATTATTATA
1 TAAAAATTTAAT-AAATTTAATAATTATTATA
* *
2088303 TAATAATTTAATAAATTTAATAATTATT-TT
1 TAAAAATTTAATAAATTTAATAATTATTATA
2088333 TAAAAAATTTAA
1 T-AAAAATTTAA
2088345 AACGATTTCT
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
29 15 0.19
30 13 0.16
31 34 0.42
32 19 0.23
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
TAAAAATTTAATAAATTTAATAATTATTATA
Found at i:2099168 original size:23 final size:22
Alignment explanation
Indices: 2099119--2099194 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
2099109 AATATTGTAT
* * **
2099119 TTTAAGTAAATTATATTTATATT
1 TTTAA-TAATTTATAATTATACG
2099142 TTTAACTAATTTATAATTATACG
1 TTTAA-TAATTTATAATTATACG
*
2099165 TTTAATACTTTATAATT-TAACG
1 TTTAATAATTTATAATTAT-ACG
*
2099187 TTTGATAA
1 TTTAATAA
2099195 ATTAATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.02
22 20 0.45
23 23 0.52
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAATAATTTATAATTATACG
Found at i:2099179 original size:22 final size:23
Alignment explanation
Indices: 2099142--2099189 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2099132 TATTTATATT
2099142 TTTAACTAATTTATAA-TTATACG
1 TTTAACTAATTTATAATTTA-ACG
*
2099165 TTTAA-TACTTTATAATTTAACG
1 TTTAACTAATTTATAATTTAACG
2099187 TTT
1 TTT
2099190 GATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACG
Found at i:2105046 original size:22 final size:22
Alignment explanation
Indices: 2105021--2105063 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2105011 TCCTTGTCCA
*
2105021 TTTTAAGGCAACT-TTTGTTTCC
1 TTTTAA-GCAAATGTTTGTTTCC
*
2105043 TTTTGAGCAAATGTTTGTTTC
1 TTTTAAGCAAATGTTTGTTTC
2105064 GCTACTACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (22 bp):
TTTTAAGCAAATGTTTGTTTCC
Found at i:2107605 original size:19 final size:17
Alignment explanation
Indices: 2107573--2107608 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2107563 TAAAGAATTT
2107573 ATTATTATTTTAATTCA
1 ATTATTATTTTAATTCA
2107590 ATTATTGATATTTAATTCA
1 ATTATT-AT-TTTAATTCA
2107609 TTAGTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTATTATTTTAATTCA
Found at i:2108276 original size:38 final size:40
Alignment explanation
Indices: 2108178--2108286 Score: 98
Period size: 38 Copynumber: 2.8 Consensus size: 40
2108168 TTTTTGGTTA
* * *
2108178 AACCTAAAATGTTACGAAAAGTGTAACATTTCCGGTTGTC
1 AACCGAAAATGTTAAGAAAAATGTAACATTTCCGGTTGTC
* * *
2108218 TACGGAAAATGTTAACAAAAATGTAACATTATCC-G-T-TC
1 AACCGAAAATGTTAAGAAAAATGTAACATT-TCCGGTTGTC
* * * *
2108256 AACCGCAAATGTTAGGAAAAATATAATATTT
1 AACCGAAAATGTTAAGAAAAATGTAACATTT
2108287 TAGGTTGTGT
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
37 1 0.02
38 25 0.45
39 1 0.02
40 25 0.45
41 3 0.05
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (40 bp):
AACCGAAAATGTTAAGAAAAATGTAACATTTCCGGTTGTC
Found at i:2111200 original size:18 final size:19
Alignment explanation
Indices: 2111174--2111213 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2111164 ATTTATATAT
*
2111174 TTTTTAAATTAT-TTTAAA
1 TTTTAAAATTATATTTAAA
*
2111192 TTTTAAAATTATATTTTAA
1 TTTTAAAATTATATTTAAA
2111211 TTT
1 TTT
2111214 GATATTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATTATATTTAAA
Found at i:2111201 original size:35 final size:34
Alignment explanation
Indices: 2111140--2111205 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
2111130 ATTATTTTTA
* * *
2111140 TTTTAATTTATTTAAGTATTTGAAATTTATATATT
1 TTTTAAATTATTTAAATATTT-AAAATTATATATT
2111175 TTTTAAATTATTTTAAAT-TTTAAAATTATAT
1 TTTTAAATTA-TTTAAATATTTAAAATTATAT
2111206 TTTAATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 9 0.33
35 12 0.44
36 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (34 bp):
TTTTAAATTATTTAAATATTTAAAATTATATATT
Found at i:2111566 original size:24 final size:24
Alignment explanation
Indices: 2111510--2111560 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2111500 GTTGGAAAAC
* * *
2111510 ATTCTCAATCCCCGGTAATCCTTT
1 ATTCTCAACCCCCGATAATCATTT
2111534 ATTCTCAACCCCCGATAATCATTT
1 ATTCTCAACCCCCGATAATCATTT
2111558 ATT
1 ATT
2111561 ACCAACAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTCTCAACCCCCGATAATCATTT
Found at i:2111931 original size:37 final size:37
Alignment explanation
Indices: 2111854--2111931 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
2111844 TTATTTTTTT
** * *
2111854 AATTTTGTAAAGAAATTATATAAATTTTTTAAATTTA
1 AATTTTGTAAAGAAATTATATAAATTAGTTAAAGTAA
* *
2111891 AATTTTTTAAA-AAATATATATAAATTAGTTATAGTAA
1 AATTTTGTAAAGAAAT-TATATAAATTAGTTAAAGTAA
2111928 AATT
1 AATT
2111932 ATAATAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (37 bp):
AATTTTGTAAAGAAATTATATAAATTAGTTAAAGTAA
Found at i:2120804 original size:30 final size:29
Alignment explanation
Indices: 2120768--2120830 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2120758 CCCGAAAAAT
* *
2120768 CACCGGTAATAGGTATATTTACTGATCTAA
1 CACCGGTAAGA-GTATATTTACCGATCTAA
* * *
2120798 CACCGGTCAGATTATATTTCCCGATCTAA
1 CACCGGTAAGAGTATATTTACCGATCTAA
2120827 CACC
1 CACC
2120831 CTTAGCAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (29 bp):
CACCGGTAAGAGTATATTTACCGATCTAA
Found at i:2121010 original size:41 final size:41
Alignment explanation
Indices: 2120960--2121042 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
2120950 ACCCCTGATC
* *
2120960 CGCGTTATATGCCACGTAGGGGTATAGCGCGGATCAAGGGG
1 CGCGCTATATGCCACGTAGGGATATAGCGCGGATCAAGGGG
2121001 CGCGCTATATGCCACGTAGGGATATAGCGCGGATCAAGGGG
1 CGCGCTATATGCCACGTAGGGATATAGCGCGGATCAAGGGG
2121042 C
1 C
2121043 ATACTATACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.37, T:0.18
Consensus pattern (41 bp):
CGCGCTATATGCCACGTAGGGATATAGCGCGGATCAAGGGG
Found at i:2125941 original size:56 final size:56
Alignment explanation
Indices: 2125853--2126004 Score: 193
Period size: 55 Copynumber: 2.7 Consensus size: 56
2125843 GGGCATGGGA
* *
2125853 ATGTGTGAGCTCTCTGAATATATACTTACATATATAGTATATCAAAGCTCGAGTTC-
1 ATGTGTGAGCTCTCTGAATATATACTTACATATA-AATATATCAAAGCTAGAGTTCG
* * * *
2125909 ATGTGTGAACTCTTTGAATATATACTTGCATATAAATATATCAAAGTTAGAGTTCG
1 ATGTGTGAGCTCTCTGAATATATACTTACATATAAATATATCAAAGCTAGAGTTCG
*
2125965 A-GTGTGAGCTCTCT-AATTATATACTTACAGATAAAATATA
1 ATGTGTGAGCTCTCTGAA-TATATACTTACATAT-AAATATA
2126005 GGTGCACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
54 2 0.02
55 42 0.51
56 39 0.47
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (56 bp):
ATGTGTGAGCTCTCTGAATATATACTTACATATAAATATATCAAAGCTAGAGTTCG
Found at i:2129527 original size:50 final size:50
Alignment explanation
Indices: 2129473--2129570 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
2129463 AGACACCCAG
* * *
2129473 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAACACGGAGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* *
2129523 GTATATCACGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA
1 GTATAACACGGAGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA
2129571 ACATATAGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (50 bp):
GTATAACACGGAGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:2133841 original size:2 final size:2
Alignment explanation
Indices: 2133834--2133858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2133824 GCTGATAGAA
2133834 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
2133859 GTATTTGCTG
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:2139906 original size:21 final size:22
Alignment explanation
Indices: 2139852--2139909 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
2139842 GCAATACAAT
*
2139852 TTGGAATAAATAGCAACGCGAAC
1 TTGGAATAAATCGCAAC-CGAAC
* *
2139875 TTCGACT--ATCGCAA-CGAAC
1 TTGGAATAAATCGCAACCGAAC
2139894 TTGGAATAAATCGCAA
1 TTGGAATAAATCGCAA
2139910 TGCGATAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 10 0.36
21 13 0.46
23 5 0.18
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (22 bp):
TTGGAATAAATCGCAACCGAAC
Found at i:2145779 original size:15 final size:15
Alignment explanation
Indices: 2145756--2145809 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2145746 GTCTACAGAC
2145756 ATAATTGTTAATTAT
1 ATAATTGTTAATTAT
* *
2145771 ATAACTGTTTATTACTTT
1 ATAATTGTTAATTA---T
*
2145789 TTAATTGTTAATTAT
1 ATAATTGTTAATTAT
2145804 ATAATT
1 ATAATT
2145810 TTGGATTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (15 bp):
ATAATTGTTAATTAT
Found at i:2151599 original size:25 final size:24
Alignment explanation
Indices: 2151562--2151608 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
2151552 CCAAATACCT
*
2151562 ATTAATTAGATTTTTTTATTTAACA
1 ATTAATTAGATTTATTT-TTTAACA
2151587 ATTAA-TAGAATTTATTTTTTAA
1 ATTAATTAG-ATTTATTTTTTAA
2151609 ATAATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTAATTAGATTTATTTTTTAACA
Found at i:2153869 original size:21 final size:20
Alignment explanation
Indices: 2153783--2153940 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
2153773 AAATGACCAA
**
2153783 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2153802 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2153822 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2153842 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2153863 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2153884 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
2153904 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
2153926 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2153941 ACACATAAAT
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2153931 original size:20 final size:20
Alignment explanation
Indices: 2153843--2153959 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
2153833 ATCAGTTTCC
* *
2153843 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
2153863 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
2153883 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
2153904 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
2153926 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
2153945 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
2153960 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:2153969 original size:20 final size:20
Alignment explanation
Indices: 2153927--2154117 Score: 226
Period size: 20 Copynumber: 9.6 Consensus size: 20
2153917 GCGAATATTA
* *
2153927 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2153947 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2153967 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2153987 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2154007 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2154027 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2154047 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2154067 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2154087 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
2154107 AAATCGCAACG
1 AAATCGCAACG
2154118 AGAATATGTA
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 145 0.98
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2154128 original size:20 final size:20
Alignment explanation
Indices: 2153907--2154136 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
2153897 CGATTTTCCA
**
2153907 AAATCGCAACGCGAAT-ATT
1 AAATCGCAACGCGAATCCGT
*
2153926 AAAATCGCAACGCGAA-CACAT
1 -AAATCGCAACGCGAATC-CGT
*
2153947 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2153967 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
2153987 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
2154007 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2154027 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
2154047 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2154067 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2154087 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* **
2154107 AAATCGCAACGAGAATATGT
1 AAATCGCAACGCGAATCCGT
*
2154127 AAATCACAAC
1 AAATCGCAAC
2154137 ACTGAAATTT
Statistics
Matches: 182, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
20 180 0.99
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2154860 original size:24 final size:22
Alignment explanation
Indices: 2154818--2154862 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
2154808 AAATTTGGTC
2154818 TTGGTCAATCCGGACTTTGATA
1 TTGGTCAATCCGGACTTTGATA
*
2154840 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAAT-C-CGGACTTTGAT
2154863 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
TTGGTCAATCCGGACTTTGATA
Found at i:2155972 original size:14 final size:14
Alignment explanation
Indices: 2155953--2156009 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2155943 GCGAAATGAA
*
2155953 AATCGCAACGACAG
1 AATCGCAACGAAAG
2155967 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2155984 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2156000 AATCGCAACG
1 AATCGCAACG
2156010 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2155980 original size:33 final size:33
Alignment explanation
Indices: 2155934--2156026 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2155924 GCGAAACCAA
*
2155934 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2155967 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2156000 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2156027 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2155991 original size:19 final size:19
Alignment explanation
Indices: 2155899--2156031 Score: 124
Period size: 19 Copynumber: 7.5 Consensus size: 19
2155889 GTTTACTTTT
* *
2155899 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TGAAAATC
**
2155919 GCAACGCGAAACCAAAATC
1 GCAACGCGAAATGAAAATC
2155938 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
2155957 GCAA--CGACA-G--AATC
1 GCAACGCGAAATGAAAATC
*
2155971 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
2155990 GCAA--CGAAA-G--AATC
1 GCAACGCGAAATGAAAATC
2156004 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
2156023 GCAATGCGA
1 GCAACGCGA
2156032 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 47 0.49
20 10 0.11
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:2156049 original size:19 final size:19
Alignment explanation
Indices: 2156027--2156155 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2156017 AAAATCGCAA
2156027 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2156046 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2156060 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2156079 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2156093 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2156112 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2156131 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2156151 TGCGA
1 TGCGA
2156156 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2156069 original size:33 final size:33
Alignment explanation
Indices: 2156027--2156118 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2156017 AAAATCGCAA
2156027 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2156060 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2156093 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2156119 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2156542 original size:184 final size:184
Alignment explanation
Indices: 2156202--2156573 Score: 687
Period size: 184 Copynumber: 2.0 Consensus size: 184
2156192 ATGGATTGCA
2156202 TTAC-TTCAACCAAAGACAAAACAAAGACAAATACTATTCACAGTGTTAAAGAATACACAGTTTA
1 TTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTCACAGTGTTAAAGAATACACAGTTTA
2156266 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
2156331 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
*
2156385 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
2156450 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAAC-AAGACAAATACT
64 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
2156513 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
129 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
2156569 TTACT
1 TTACT
2156574 AAGCAATCTA
Statistics
Matches: 184, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
183 4 0.02
184 79 0.43
185 35 0.19
186 66 0.36
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
TTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2156569 original size:91 final size:93
Alignment explanation
Indices: 2156202--2156573 Score: 691
Period size: 93 Copynumber: 4.1 Consensus size: 93
2156192 ATGGATTGCA
2156202 TTAC-TTCAACC-AAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2156264 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2156292 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2156357 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
2156385 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2156450 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2156478 TTACTTTCAACC-AAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2156541 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2156569 TTACT
1 TTACT
2156574 AAGCAATCTA
Statistics
Matches: 276, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
90 4 0.01
91 79 0.29
92 35 0.13
93 158 0.57
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2158289 original size:14 final size:14
Alignment explanation
Indices: 2158270--2158359 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
2158260 TTGAAATGAA
2158270 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2158284 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
2158303 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2158317 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2158336 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2158350 AATCACAACG
1 AATCGCAACG
2158360 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2158301 original size:33 final size:33
Alignment explanation
Indices: 2158262--2158376 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2158252 TCTTTTGGTT
2158262 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2158295 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2158328 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2158361 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2158377 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2158308 original size:19 final size:19
Alignment explanation
Indices: 2158284--2158381 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2158274 GCAACGAGAG
*
2158284 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
2158303 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2158317 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2158336 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
2158350 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2158369 AATCGCAATGCGA
1 AATCGCAACGCGA
2158382 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2158412 original size:14 final size:14
Alignment explanation
Indices: 2158393--2158449 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2158383 TTTGGTTTCG
2158393 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2158407 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2158426 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2158440 CGTTGCGATT
1 CGTTGCGATT
2158450 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2158425 original size:33 final size:33
Alignment explanation
Indices: 2158377--2158457 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2158367 AAAATCGCAA
**
2158377 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2158410 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2158443 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2158458 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2158460 original size:21 final size:21
Alignment explanation
Indices: 2158434--2158509 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2158424 CGCGTTGCGA
2158434 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2158455 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2158475 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2158496 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2158510 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2158490 original size:41 final size:41
Alignment explanation
Indices: 2158433--2158510 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2158423 TCGCGTTGCG
*
2158433 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
2158474 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2158511 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2158630 original size:33 final size:33
Alignment explanation
Indices: 2158588--2158658 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2158578 AATACTAACT
*
2158588 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2158621 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2158654 TGAAA
1 TGAAA
2158659 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2158890 original size:22 final size:22
Alignment explanation
Indices: 2158838--2158892 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2158828 ATGGTTGTGA
**
2158838 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2158860 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2158882 GGATTTCTTCG
1 GGATTTCTTCG
2158893 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2159064 original size:20 final size:20
Alignment explanation
Indices: 2159039--2159232 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
2159029 CTTTAAATAT
2159039 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2159059 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2159081 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2159100 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
** **
2159120 CGTATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2159140 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2159160 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2159180 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2159200 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2159220 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2159233 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2159226 original size:60 final size:60
Alignment explanation
Indices: 2159039--2159232 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
2159029 CTTTAAATAT
**
2159039 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* ** *** *
2159100 CGCGTTGCGATATACGGATACGTATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2159160 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2159220 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2159233 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2159249 original size:21 final size:21
Alignment explanation
Indices: 2159219--2159301 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2159209 ATTTTCATAT
*
2159219 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2159240 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2159261 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2159282 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2159302 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2159292 original size:42 final size:43
Alignment explanation
Indices: 2159199--2159297 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2159189 ATTTATGTGT
* *
2159199 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2159240 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2159282 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2159298 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2159545 original size:28 final size:28
Alignment explanation
Indices: 2159497--2159580 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
2159487 GTATTTGTTT
*
2159497 ACATTATGTTGTCGA-CTTAGTGCTTGAA
1 ACATTATGTCGTCGAGC-TAGTGCTTGAA
* **
2159525 ACATTATGTCGTTGAGCTAGT-AATGAA
1 ACATTATGTCGTCGAGCTAGTGCTTGAA
* * * *
2159552 ATATTATATCGTCAAGCCAGTGCTTGAA
1 ACATTATGTCGTCGAGCTAGTGCTTGAA
2159580 A
1 A
2159581 GCAACAACAA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
27 20 0.47
28 22 0.51
29 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (28 bp):
ACATTATGTCGTCGAGCTAGTGCTTGAA
Found at i:2163071 original size:29 final size:31
Alignment explanation
Indices: 2163002--2163071 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 31
2162992 ATTTAAAAAT
2163002 CATAATATAATTCAAATTATTAAAAGAATTATA
1 CATAATAT--TTCAAATTATTAAAAGAATTATA
*
2163035 -A-AATTATTTCAGATT-TTAAAAGAA-TATA
1 CATAA-TATTTCAAATTATTAAAAGAATTATA
2163063 CATAATATT
1 CATAATATT
2163072 ATATACAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
28 4 0.12
29 14 0.42
30 9 0.27
31 2 0.06
32 4 0.12
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
CATAATATTTCAAATTATTAAAAGAATTATA
Found at i:2181198 original size:41 final size:41
Alignment explanation
Indices: 2181152--2181232 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
2181142 TAAATTATTA
*
2181152 AAATTATCTTTTTATTTTTTCTTCAAAATATATTCTCATTG
1 AAATTATCTTTCTATTTTTTCTTCAAAATATATTCTCATTG
*
2181193 AAATTATCTTTCTATTTTTTCTTTAAAATATATTCTCATT
1 AAATTATCTTTCTATTTTTTCTTCAAAATATATTCTCATT
2181233 TTCTACTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.12, G:0.01, T:0.57
Consensus pattern (41 bp):
AAATTATCTTTCTATTTTTTCTTCAAAATATATTCTCATTG
Found at i:2182237 original size:24 final size:25
Alignment explanation
Indices: 2182201--2182248 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2182191 ATAATACAAA
2182201 AAATAGATGTTAACT-GTTTTTAAT
1 AAATAGATGTTAACTGGTTTTTAAT
*
2182225 AAATAGTAT-TTAAGTGGTTTTTAA
1 AAATAG-ATGTTAACTGGTTTTTAA
2182249 ATTTTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.46
Consensus pattern (25 bp):
AAATAGATGTTAACTGGTTTTTAAT
Found at i:2182372 original size:21 final size:20
Alignment explanation
Indices: 2182348--2182389 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2182338 TAATATTATA
2182348 TATTAGGGTAAACTATATGTT
1 TATTA-GGTAAACTATATGTT
**
2182369 TATTATTTAAACTATATGTT
1 TATTAGGTAAACTATATGTT
2182389 T
1 T
2182390 GGTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (20 bp):
TATTAGGTAAACTATATGTT
Found at i:2182395 original size:20 final size:20
Alignment explanation
Indices: 2182356--2182396 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2182346 TATATTAGGG
*
2182356 TAAACTATATGTTTATTATT
1 TAAACTATATGTTTAGTATT
*
2182376 TAAACTATATGTTTGGTATT
1 TAAACTATATGTTTAGTATT
2182396 T
1 T
2182397 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
TAAACTATATGTTTAGTATT
Found at i:2183543 original size:20 final size:20
Alignment explanation
Indices: 2183518--2183570 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2183508 TTTTCTCATG
2183518 ATTATTAAAATTATAAAATA
1 ATTATTAAAATTATAAAATA
* *
2183538 ATTATTAAATTTATTAAATTA
1 ATTATTAAAATTA-TAAAATA
2183559 A-TA-TAAAATTAT
1 ATTATTAAAATTAT
2183571 TATTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 7 0.24
20 14 0.48
21 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATTAAAATTATAAAATA
Found at i:2183567 original size:31 final size:31
Alignment explanation
Indices: 2183529--2183613 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
2183519 TTATTAAAAT
2183529 TATAAAATAATTATTAAATTTATTAAATTAA
1 TATAAAATAATTATTAAATTTATTAAATTAA
* * *
2183560 TATAAAATTATTATTAAAGTTT-TTATATTAT
1 TATAAAATAATTATTAAA-TTTATTAAATTAA
* * *
2183591 TATAAAATAGTCATTAAAATTAT
1 TATAAAATAATTATTAAATTTAT
2183614 CAAAATTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 40 0.89
32 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
TATAAAATAATTATTAAATTTATTAAATTAA
Found at i:2183705 original size:21 final size:22
Alignment explanation
Indices: 2183668--2183711 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2183658 TTTTATAATA
2183668 ATTTTAATAAATGTAATA-TTT
1 ATTTTAATAAATGTAATAGTTT
*
2183689 ATTTT-ATAAATTTTAATAGTTT
1 ATTTTAATAAA-TGTAATAGTTT
2183711 A
1 A
2183712 AATTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAATAAATGTAATAGTTT
Found at i:2188123 original size:12 final size:12
Alignment explanation
Indices: 2188088--2188133 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2188078 TGAAAATATT
*
2188088 AATATTTTTTAA
1 AATATTATTTAA
* **
2188100 CATATTCGTTAA
1 AATATTATTTAA
2188112 AATATTATTTAA
1 AATATTATTTAA
2188124 AATATTATTT
1 AATATTATTT
2188134 TTATTAGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (12 bp):
AATATTATTTAA
Found at i:2188239 original size:22 final size:24
Alignment explanation
Indices: 2188172--2188239 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 24
2188162 ATTTCGATAG
*
2188172 AAAAAATAACATTTTATGTAGCAC
1 AAAAAATAACATTTTAAGTAGCAC
* * **
2188196 ATAATATTAACATTTTCGGTAG-A-
1 A-AAAAATAACATTTTAAGTAGCAC
2188219 AAAAAATAACATTTTAAGTAG
1 AAAAAATAACATTTTAAGTAG
2188240 TATTTTATCG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 16 0.46
23 1 0.03
24 2 0.06
25 16 0.46
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (24 bp):
AAAAAATAACATTTTAAGTAGCAC
Found at i:2188282 original size:80 final size:82
Alignment explanation
Indices: 2188179--2188342 Score: 217
Period size: 80 Copynumber: 2.0 Consensus size: 82
2188169 TAGAAAAAAT
* * * *
2188179 AACATTTTATGTAGCACATAATATTAACATTTTCGGTAGAAAAAAA-TAACATTTTAAG-TAGTA
1 AACATTTTAGGTAACACATAATATTAACATTTCCGGTAGAAAAAAAGTAACATTTTAAGATAATA
*
2188242 TTTTATCGAAAATATTA
66 TTTTACCGAAAATATTA
* * *
2188259 AACATTTTAGGTAACA-ATCAATATTAACATTTCCGGTAGAAAAAAAGTGATATTTTAGGATAAT
1 AACATTTTAGGTAACACAT-AATATTAACATTTCCGGTAGAAAAAAAGTAACATTTTAAGATAAT
*
2188323 GTTTTACCGAAAATATTA
65 ATTTTACCGAAAATATTA
2188341 AA
1 AA
2188343 AAAATTAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
79 2 0.03
80 40 0.56
81 9 0.12
82 21 0.29
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (82 bp):
AACATTTTAGGTAACACATAATATTAACATTTCCGGTAGAAAAAAAGTAACATTTTAAGATAATA
TTTTACCGAAAATATTA
Found at i:2190540 original size:16 final size:17
Alignment explanation
Indices: 2190507--2190540 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2190497 CAATTCATAT
*
2190507 TTTTTTCTAACATACAA
1 TTTTTTATAACATACAA
2190524 TTTTTTATAACAT-CAA
1 TTTTTTATAACATACAA
2190540 T
1 T
2190541 ATTATATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTTATAACATACAA
Found at i:2200295 original size:29 final size:28
Alignment explanation
Indices: 2200261--2200356 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 28
2200251 AGTGAAGGAT
*
2200261 ATAGTTTGGGGATGAAATTGAAATATTTA
1 ATAGTTTGAGGATGAAATT-AAATATTTA
* *
2200290 ATAGTTTGAGGACT-AAATTAGAATGATAATC
1 ATAGTTTGAGGA-TGAAATTA-AAT-AT-TTA
2200321 ATAGTTT-ATGGATGAAATTAAAATATTTA
1 ATAGTTTGA-GGATGAAATT-AAATATTTA
*
2200350 AAAGTTT
1 ATAGTTT
2200357 AGAGACCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
28 1 0.02
29 26 0.48
30 7 0.13
31 19 0.35
32 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (28 bp):
ATAGTTTGAGGATGAAATTAAATATTTA
Found at i:2200296 original size:60 final size:59
Alignment explanation
Indices: 2200200--2200369 Score: 184
Period size: 60 Copynumber: 2.8 Consensus size: 59
2200190 GGTACATGTG
* * * *
2200200 TATAGTTTGGGG-TGAAATTGGAATGTTCAAAAAGTTTGAGGACCAATTTAGAGTGA-AGGA
1 TATAGTTTGGGGATGAAATTGAAATATT-TAAAAGTTTGAGGACCAATTTAGAATGATA--A
* * *
2200260 TATAGTTTGGGGATGAAATTGAAATATTTAATAGTTTGAGGACTAAATTAGAATGATAA
1 TATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTGAGGACCAATTTAGAATGATAA
** *
2200319 TCATAGTTTATGGATGAAATTAAAATATTTAAAAGTTT-AGAGACCAATTTA
1 T-ATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTGAG-GACCAATTTA
2200370 AAAGGAAGGT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.04
60 75 0.81
61 14 0.15
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (59 bp):
TATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTGAGGACCAATTTAGAATGATAA
Found at i:2200915 original size:15 final size:15
Alignment explanation
Indices: 2200895--2201039 Score: 157
Period size: 15 Copynumber: 9.3 Consensus size: 15
2200885 AATCAATCCA
*
2200895 TATTTTATAATAATT
1 TATTTTAAAATAATT
2200910 TATTTTAAAATAATT
1 TATTTTAAAATAATT
2200925 TATTTTAAAATAATT
1 TATTTTAAAATAATT
*
2200940 TATTATAAAATAATT
1 TATTTTAAAATAATT
* *
2200955 TATTATAAAATAAAT
1 TATTTTAAAATAATT
*
2200970 TATTTTAAAATAAAT
1 TATTTTAAAATAATT
*
2200985 TATTATAAAATATGGATTGATT
1 TATT-TTAAA-AT--A---ATT
2201007 TATTTTAAAATAATT
1 TATTTTAAAATAATT
*
2201022 TATTTT-AAATGATT
1 TATTTTAAAATAATT
2201036 TATT
1 TATT
2201040 AGTATAGATT
Statistics
Matches: 115, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
14 11 0.10
15 84 0.73
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TATTTTAAAATAATT
Found at i:2200953 original size:45 final size:45
Alignment explanation
Indices: 2200903--2201065 Score: 175
Period size: 45 Copynumber: 3.4 Consensus size: 45
2200893 CATATTTTAT
2200903 AATAATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAA
1 AATAATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAA
* * *
2200948 AATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAA
1 AATAATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAT-AA
*
2200994 ATATGGATTGATTTATTTTAAAATAATTTATTTT-AAATGATTTATTAGTATA
1 A-AT--A---ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTA-TA-A
* *
2201046 GATTTATTTATTTTAAAATA
1 -AATAATTTATTTTAAAATA
2201066 TGGATTGATT
Statistics
Matches: 99, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
45 40 0.40
46 3 0.03
47 17 0.17
49 1 0.01
51 12 0.12
52 25 0.25
53 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.50
Consensus pattern (45 bp):
AATAATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAA
Found at i:2201059 original size:32 final size:31
Alignment explanation
Indices: 2201019--2201313 Score: 152
Period size: 32 Copynumber: 9.4 Consensus size: 31
2201009 TTTTAAAATA
* *
2201019 ATTTATTTTAAATGATTTATTAGTATAGATTT
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
2201051 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
2201073 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
*
2201105 ATTTATTTTAAATAATTTATTTGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
** *
2201137 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTA-TGATTG
* * * * *
2201166 ATTGTAGTTGTATAGATTGATTTATTTA-AATAATTT
1 ATT-TA-TT-T-TA-AATAATTTA-TTAGTATGATTG
* * * * * *
2201202 ATTAGTATGGATTGATTTATTT-TAAAATATGGATTG
1 ATT--TAT--TTTAAATAATTTAT-TAGTAT-GATTG
2201238 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
*
2201270 ATTTATTTTAAATAATTTATTTGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
2201302 ATTTATTTTAAA
1 ATTTATTTTAAA
2201314 ATATGGATTG
Statistics
Matches: 207, Mismatches: 25, Indels: 62
0.70 0.09 0.21
Matches are distributed among these distances:
22 13 0.06
23 2 0.01
24 2 0.01
26 3 0.01
27 2 0.01
28 3 0.01
29 3 0.01
30 7 0.03
31 9 0.04
32 120 0.58
33 4 0.02
34 8 0.04
35 15 0.07
36 12 0.06
37 4 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:2201082 original size:54 final size:54
Alignment explanation
Indices: 2201019--2201464 Score: 451
Period size: 54 Copynumber: 8.1 Consensus size: 54
2201009 TTTTAAAATA
* * *
2201019 ATTTATTTTAAATGATTTATTAGTATAGATTTATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2201073 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *** *
2201123 ATTTGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
2201185 ATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2201238 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *** *
2201288 ATTTGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
2201350 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2201404 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2201458 ATTTATT
1 ATTTATT
2201465 ATTGTAGTTG
Statistics
Matches: 320, Mismatches: 47, Indels: 50
0.77 0.11 0.12
Matches are distributed among these distances:
50 34 0.11
52 4 0.01
53 23 0.07
54 173 0.54
55 6 0.02
56 7 0.02
57 18 0.06
58 14 0.04
59 6 0.02
60 2 0.01
61 9 0.03
62 24 0.08
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2201093 original size:165 final size:162
Alignment explanation
Indices: 2201019--2201447 Score: 743
Period size: 165 Copynumber: 2.6 Consensus size: 162
2201009 TTTTAAAATA
* *
2201019 ATTTATTTTAAATGATTTATTAGTATAGATTTATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2201084 ATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAA
65 ATAATTTATTA-TATGGATTGATTTATTTTAAATAATTTA-TTGTATGAATTGATTTATTTTAAA
2201149 ATATGGATTGATTTATTATTGTAGTTGTATAGATTG
128 ATA-GGATTGATTTATTATTGTAGTTGTATAGATTG
2201185 ATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2201249 ATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAA
65 ATAATTTATTA-TATGGATTGATTTATTTTAAATAATTTA-TTGTATGAATTGATTTATTTTAAA
2201314 ATATGGATTGATTTATTATTGTAGTTGTATAGATTG
128 ATA-GGATTGATTTATTATTGTAGTTGTATAGATTG
2201350 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2201415 ATAATTTATTAGTATGGATTGATTTATTTTAAA
65 ATAATTTATTA-TATGGATTGATTTATTTTAAA
2201448 ATATGGATTG
Statistics
Matches: 258, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
165 163 0.63
166 95 0.37
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (162 bp):
ATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
TAATTTATTATATGGATTGATTTATTTTAAATAATTTATTGTATGAATTGATTTATTTTAAAATA
GGATTGATTTATTATTGTAGTTGTATAGATTG
Found at i:2201232 original size:22 final size:22
Alignment explanation
Indices: 2201207--2201249 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2201197 AATTTATTAG
2201207 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2201229 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2201250 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Done.