Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 65 of 145
Found at i:21590623 original size:10 final size:10
Alignment explanation
Indices: 21590608--21590654 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
21590598 AAGAAATATT
21590608 TTAAAAAATC
1 TTAAAAAATC
21590618 TTAAAAAAT-
1 TTAAAAAATC
21590627 TTAAAAAATC
1 TTAAAAAATC
* *
21590637 ATAAATAAATA
1 TTAAA-AAATC
21590648 TTAAAAA
1 TTAAAAA
21590655 TTATGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.28
10 15 0.47
11 8 0.25
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAATC
Found at i:21590633 original size:20 final size:20
Alignment explanation
Indices: 21590607--21590654 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
21590597 CAAGAAATAT
*
21590607 TTTAAAAAATCTTAAA-AAA
1 TTTAAAAAATCATAAATAAA
21590626 TTTAAAAAATCATAAATAAA
1 TTTAAAAAATCATAAATAAA
21590646 TATTAAAAA
1 T-TTAAAAA
21590655 TTATGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.58
20 4 0.15
21 7 0.27
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTTAAAAAATCATAAATAAA
Found at i:21590652 original size:11 final size:10
Alignment explanation
Indices: 21590608--21590665 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
21590598 AAGAAATATT
*
21590608 TTAAAAAATC
1 TTAAAAAATA
21590618 TTAAAAAAT-
1 TTAAAAAATA
21590627 TTAAAAAATCA
1 TTAAAAAAT-A
21590638 -TAAATAAATA
1 TTAAA-AAATA
*
21590648 TTAAAAATTA
1 TTAAAAAATA
*
21590658 TGAAAAAA
1 TTAAAAAA
21590666 ACTCTTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 9 0.22
10 24 0.59
11 8 0.20
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:21591729 original size:22 final size:21
Alignment explanation
Indices: 21591683--21591739 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
21591673 GGGTGAGAAG
21591683 TAAAAG-TTT-AGGGGGAAAA
1 TAAAAGTTTTGAGGGGGAAAA
*
21591702 TAAAAAGTTTTGAGGGAGTAAAA
1 T-AAAAGTTTTGAGGG-GGAAAA
21591725 TAAAAGTTTTGAGGG
1 TAAAAGTTTTGAGGG
21591740 TTTTGGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 3 0.09
22 18 0.55
23 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (21 bp):
TAAAAGTTTTGAGGGGGAAAA
Found at i:21596701 original size:16 final size:15
Alignment explanation
Indices: 21596665--21596703 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21596655 TAAAGAGAGC
*
21596665 TAATGTTCATGTATG
1 TAATGTGCATGTATG
21596680 TAAATGTGCATGTATGG
1 T-AATGTGCATGTAT-G
21596697 TAATGTG
1 TAATGTG
21596704 ATAAGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (15 bp):
TAATGTGCATGTATG
Found at i:21603837 original size:22 final size:22
Alignment explanation
Indices: 21603811--21603855 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21603801 AACAAATAAC
21603811 TTAGGTATATGCTCATAACCAA
1 TTAGGTATATGCTCATAACCAA
21603833 TTAGGTATATGCTCATAACCAA
1 TTAGGTATATGCTCATAACCAA
21603855 T
1 T
21603856 CACTTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (22 bp):
TTAGGTATATGCTCATAACCAA
Found at i:21607888 original size:20 final size:20
Alignment explanation
Indices: 21607863--21607900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21607853 CCTATGATTG
*
21607863 ATTAAATCACTAATTATCTA
1 ATTAAATAACTAATTATCTA
*
21607883 ATTAAATAATTAATTATC
1 ATTAAATAACTAATTATC
21607901 CTAAATTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAATAACTAATTATCTA
Found at i:21608275 original size:21 final size:21
Alignment explanation
Indices: 21608241--21608281 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21608231 AATGCTAATT
*
21608241 AATAAAGTTAATGAAAATATA
1 AATAAAGCTAATGAAAATATA
* *
21608262 AATAAAGCTCATGAACATAT
1 AATAAAGCTAATGAAAATAT
21608282 TGAATTGCGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (21 bp):
AATAAAGCTAATGAAAATATA
Found at i:21609464 original size:17 final size:16
Alignment explanation
Indices: 21609430--21609468 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
21609420 AACATCAATT
*
21609430 AATCTAATTAACCTAAA
1 AATC-AATTAAACTAAA
21609447 AATCAATTAAACTAAA
1 AATCAATTAAACTAAA
21609463 AATCAA
1 AATCAA
21609469 CCAATTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCAATTAAACTAAA
Found at i:21619191 original size:22 final size:22
Alignment explanation
Indices: 21619166--21619379 Score: 275
Period size: 22 Copynumber: 9.7 Consensus size: 22
21619156 AGCAATTATC
**
21619166 CAACATTCAGACAGCATTTAAT
1 CAACATTTGGACAGCATTTAAT
* * *
21619188 CAACAATTGGATAGCATTAAAT
1 CAACATTTGGACAGCATTTAAT
*
21619210 CAACATTTGGACAACATTTAAT
1 CAACATTTGGACAGCATTTAAT
* *
21619232 CAACAATTGGACAGCATTCAAT
1 CAACATTTGGACAGCATTTAAT
*
21619254 CAATATTTGGACAGCATTTAAT
1 CAACATTTGGACAGCATTTAAT
* * *
21619276 CAACATCTGGACAACATTAAAT
1 CAACATTTGGACAGCATTTAAT
21619298 CAACATTTGGACAGCATTTAAT
1 CAACATTTGGACAGCATTTAAT
* * *
21619320 CAACAATTGGACATCATTCAAT
1 CAACATTTGGACAGCATTTAAT
*
21619342 CAATATTTGGACAGCATTTAAT
1 CAACATTTGGACAGCATTTAAT
*
21619364 CAACAATTGGACAGCA
1 CAACATTTGGACAGCA
21619380 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 31, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 161 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (22 bp):
CAACATTTGGACAGCATTTAAT
Found at i:21619214 original size:44 final size:44
Alignment explanation
Indices: 21619166--21619379 Score: 322
Period size: 44 Copynumber: 4.9 Consensus size: 44
21619156 AGCAATTATC
** *
21619166 CAACATTCAGACAGCATTTAATCAACAATTGGATAGCATTAAAT
1 CAACATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAAT
* *
21619210 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTCAAT
1 CAACATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAAT
* *
21619254 CAATATTTGGACAGCATTTAATCAAC-ATCTGGACAACATTAAAT
1 CAACATTTGGACAGCATTTAATCAACAAT-TGGACAGCATTAAAT
* *
21619298 CAACATTTGGACAGCATTTAATCAACAATTGGACATCATTCAAT
1 CAACATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAAT
*
21619342 CAATATTTGGACAGCATTTAATCAACAATTGGACAGCA
1 CAACATTTGGACAGCATTTAATCAACAATTGGACAGCA
21619380 NNNNNNNNNN
Statistics
Matches: 154, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 150 0.97
45 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (44 bp):
CAACATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAAT
Found at i:21619280 original size:88 final size:88
Alignment explanation
Indices: 21619175--21619379 Score: 358
Period size: 88 Copynumber: 2.3 Consensus size: 88
21619165 CCAACATTCA
*
21619175 GACAGCATTTAATCAACAATTGGATAGCATTAAATCAACATTTGGACAACATTTAATCAACAATT
1 GACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATTTGGACAACATTTAATCAACAATT
21619240 GGACAGCATTCAATCAATATTTG
66 GGACAGCATTCAATCAATATTTG
* *
21619263 GACAGCATTTAATCAAC-ATCTGGACAACATTAAATCAACATTTGGACAGCATTTAATCAACAAT
1 GACAGCATTTAATCAACAAT-TGGACAGCATTAAATCAACATTTGGACAACATTTAATCAACAAT
*
21619327 TGGACATCATTCAATCAATATTTG
65 TGGACAGCATTCAATCAATATTTG
21619351 GACAGCATTTAATCAACAATTGGACAGCA
1 GACAGCATTTAATCAACAATTGGACAGCA
21619380 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
87 2 0.02
88 106 0.96
89 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (88 bp):
GACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATTTGGACAACATTTAATCAACAATT
GGACAGCATTCAATCAATATTTG
Found at i:21620341 original size:43 final size:42
Alignment explanation
Indices: 21620275--21620433 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 42
21620265 AGCTCGTACA
* * * *
21620275 ATGCCAACGTCCCAAAC-GTGGTCTTTCATGTAATCAAACAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAA-AACG
* * *
21620318 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAAAACG
* * * * *
21620360 ATGCCAATGTCCTAGACATGGTCTTACACGTAAATCTCAAATCA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGT-AATC-AAAAACG
* *
21620404 AGGCCAACGTCCCAGAC-GTGGTCTTACACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG
21620434 ACATCACATT
Statistics
Matches: 93, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 31 0.33
43 34 0.37
44 28 0.30
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAAAACG
Found at i:21622844 original size:19 final size:18
Alignment explanation
Indices: 21622817--21622855 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
21622807 AATCATGTAC
21622817 AAAAGATGAAAAACATAAA
1 AAAAGATGAAAAACA-AAA
*
21622836 AAAATATGAAAAACAAAA
1 AAAAGATGAAAAACAAAA
21622854 AA
1 AA
21622856 GAAAGTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAGATGAAAAACAAAA
Found at i:21623256 original size:15 final size:15
Alignment explanation
Indices: 21623236--21623265 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21623226 ATTTAAGATC
21623236 CTTTAATAGAAATTG
1 CTTTAATAGAAATTG
21623251 CTTTAATAGAAATTG
1 CTTTAATAGAAATTG
21623266 TGAATAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
CTTTAATAGAAATTG
Found at i:21624323 original size:80 final size:80
Alignment explanation
Indices: 21624188--21624352 Score: 244
Period size: 80 Copynumber: 2.1 Consensus size: 80
21624178 TAGAAGTGCG
* * *
21624188 TGCAAGTAAAATGCTTGGCTCCTTATAAAATAGAGTAATGATACTTTTAACCCTCTGATAATTAA
1 TGCAATTAAAATGCTTGGCCCCTTATAAAATAGAGTAATGATACTTTTAACCCTCTAATAATTAA
21624253 TAATTTAATTTAATT
66 TAATTTAATTTAATT
* *
21624268 TGCAATTAAAAGTGCTT-GCCCCTTATAAAATAGAGTAATGGTACTTTTAATCCTCTAATAATTA
1 TGCAATTAAAA-TGCTTGGCCCCTTATAAAATAGAGTAATGATACTTTTAACCCTCTAATAATTA
* *
21624332 ATAATTTGATTTTATT
65 ATAATTTAATTTAATT
21624348 T-CAAT
1 TGCAAT
21624353 CTAACTCTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
79 4 0.05
80 68 0.88
81 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (80 bp):
TGCAATTAAAATGCTTGGCCCCTTATAAAATAGAGTAATGATACTTTTAACCCTCTAATAATTAA
TAATTTAATTTAATT
Found at i:21626386 original size:13 final size:12
Alignment explanation
Indices: 21626364--21626393 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
21626354 AAATCAATTT
21626364 TAAATTTTTATA
1 TAAATTTTTATA
21626376 TAAATTTTT-TA
1 TAAATTTTTATA
21626387 TAAATTT
1 TAAATTT
21626394 ATTACATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTTATA
Found at i:21626539 original size:44 final size:45
Alignment explanation
Indices: 21626490--21626579 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
21626480 ATTTAATCAG
*
21626490 GGAAATAGGTCA-TTTTTAGGAGAGAGAAACAAAAAGCACGTCCA
1 GGAAATAGATCATTTTTTAGGAGAGAGAAACAAAAAGCACGTCCA
21626534 GGAAATAGATCATTTTTTAGGAGAGAGAAACAAAAAGCACGTCCA
1 GGAAATAGATCATTTTTTAGGAGAGAGAAACAAAAAGCACGTCCA
21626579 G
1 G
21626580 CTTTTTGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 11 0.25
45 33 0.75
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (45 bp):
GGAAATAGATCATTTTTTAGGAGAGAGAAACAAAAAGCACGTCCA
Found at i:21630863 original size:25 final size:25
Alignment explanation
Indices: 21630829--21630882 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
21630819 TATGACCTCC
21630829 TCGAAATTATCCTTCAACTAGCTCA
1 TCGAAATTATCCTTCAACTAGCTCA
*
21630854 TCGAAATTATCCTTCAACTAGTTCA
1 TCGAAATTATCCTTCAACTAGCTCA
21630879 TCGA
1 TCGA
21630883 TATCCGACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (25 bp):
TCGAAATTATCCTTCAACTAGCTCA
Found at i:21631504 original size:19 final size:19
Alignment explanation
Indices: 21631482--21631527 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21631472 GTTGAGAGGC
* *
21631482 TTGAGAGGGTTTGAGAAAG
1 TTGAGAGAGTTTAAGAAAG
*
21631501 TTGAGAGAGTTTAAGAGAG
1 TTGAGAGAGTTTAAGAAAG
*
21631520 CTGAGAGA
1 TTGAGAGA
21631528 ATGATGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (19 bp):
TTGAGAGAGTTTAAGAAAG
Found at i:21631526 original size:9 final size:9
Alignment explanation
Indices: 21631465--21631527 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
21631455 ACAATCAAAA
21631465 TGAGAGAGT
1 TGAGAGAGT
21631474 TGAGAG-GCT
1 TGAGAGAG-T
*
21631483 TGAGAGGGTT
1 TGAGAGAG-T
*
21631493 TGAGAAAGT
1 TGAGAGAGT
21631502 TGAGAGAGTT
1 TGAGAGAG-T
* *
21631512 TAAGAGAGC
1 TGAGAGAGT
21631521 TGAGAGA
1 TGAGAGA
21631528 ATGATGTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 1 0.02
9 27 0.61
10 16 0.36
ACGTcount: A:0.33, C:0.03, G:0.41, T:0.22
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:21631837 original size:28 final size:29
Alignment explanation
Indices: 21631781--21631839 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
21631771 ACCTATTTCT
* * *
21631781 CTAATTAATTTTAAAATCGGCCTAAAGGC
1 CTAATTAATTTAAAAAACAGCCTAAAGGC
*
21631810 CTAATTAA-TTAAAAAACAGCCTATAGGC
1 CTAATTAATTTAAAAAACAGCCTAAAGGC
21631838 CT
1 CT
21631840 TATTTTGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (29 bp):
CTAATTAATTTAAAAAACAGCCTAAAGGC
Found at i:21632234 original size:22 final size:22
Alignment explanation
Indices: 21632207--21632259 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
21632197 TTCAGTGCCA
21632207 GTTTTTAAAATTAGGGTTCTTT-
1 GTTTTTAAAATTAGGGTT-TTTG
**
21632229 GTTTTTAAGGTTAGGGTTTTTG
1 GTTTTTAAAATTAGGGTTTTTG
*
21632251 GTATTTAAA
1 GTTTTTAAA
21632260 GTATGGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.53
Consensus pattern (22 bp):
GTTTTTAAAATTAGGGTTTTTG
Found at i:21634136 original size:56 final size:56
Alignment explanation
Indices: 21634046--21634153 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 56
21634036 ATCATCAGAG
*
21634046 GATGGGTTGGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTTAGAT
1 GATGGGTTGGAGTTTGCAAAACTACTACACAGAAGGTCAGGCCACGCGAGTTAGAT
*
21634102 GATGGGTTGGAGTTTGCAAAACTACTACATAGAAGGTCAGGCCACGCGAGTT
1 GATGGGTTGGAGTTTGCAAAACTACTACACAGAAGGTCAGGCCACGCGAGTT
21634154 CTTCGTTGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (56 bp):
GATGGGTTGGAGTTTGCAAAACTACTACACAGAAGGTCAGGCCACGCGAGTTAGAT
Found at i:21636640 original size:21 final size:25
Alignment explanation
Indices: 21636616--21636670 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 25
21636606 AAAATATATA
21636616 TAAAATAATACAT-TAT-G-AAA-T
1 TAAAATAATACATATATGGAAAACT
21636637 T-AAATAATA-ATATATGGAAAACT
1 TAAAATAATACATATATGGAAAACT
21636660 TAAAATAATAC
1 TAAAATAATAC
21636671 TACATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 11 0.39
21 2 0.07
22 3 0.11
23 2 0.07
24 8 0.29
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (25 bp):
TAAAATAATACATATATGGAAAACT
Found at i:21641606 original size:109 final size:109
Alignment explanation
Indices: 21641493--21641707 Score: 421
Period size: 109 Copynumber: 2.0 Consensus size: 109
21641483 TTTTTGGCAT
21641493 TCTTTTATAACTTTTTGAAACTTTATGTAATTTTGTATATGTTTTGAGTTTTCTAGACTTTTTAT
1 TCTTTTATAACTTTTTGAAACTTTATGTAATTTTGTATATGTTTTGAGTTTTCTAGACTTTTTAT
*
21641558 CTTTTAAAATTTTAAATAAAAATAAAATAAATTTTATTTTAGGC
66 CTTTTAAAATTTTAAAAAAAAATAAAATAAATTTTATTTTAGGC
21641602 TCTTTTATAACTTTTTGAAACTTTATGTAATTTTGTATATGTTTTGAGTTTTCTAGACTTTTTAT
1 TCTTTTATAACTTTTTGAAACTTTATGTAATTTTGTATATGTTTTGAGTTTTCTAGACTTTTTAT
21641667 CTTTTAAAATTTTAAAAAAAAATAAAATAAATTTTATTTTA
66 CTTTTAAAATTTTAAAAAAAAATAAAATAAATTTTATTTTA
21641708 AATATTAATA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (109 bp):
TCTTTTATAACTTTTTGAAACTTTATGTAATTTTGTATATGTTTTGAGTTTTCTAGACTTTTTAT
CTTTTAAAATTTTAAAAAAAAATAAAATAAATTTTATTTTAGGC
Found at i:21642561 original size:14 final size:15
Alignment explanation
Indices: 21642537--21642587 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
21642527 TTATCTCGAA
21642537 TTATATTTTAATTAT
1 TTATATTTTAATTAT
*
21642552 TTAT-TTTTAA-AAT
1 TTATATTTTAATTAT
*
21642565 ATTATATTTTAGTTAT
1 -TTATATTTTAATTAT
21642581 TTATATT
1 TTATATT
21642588 ATTATCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 16 0.53
16 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:21642600 original size:20 final size:20
Alignment explanation
Indices: 21642563--21642600 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21642553 TATTTTTAAA
*
21642563 ATATTATATTTTAGTTATTT
1 ATATTATATCTTAGTTATTT
21642583 ATATTATTATCTTA-TTAT
1 ATATTA-TATCTTAGTTAT
21642601 AAAATGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
ATATTATATCTTAGTTATTT
Found at i:21642737 original size:18 final size:16
Alignment explanation
Indices: 21642705--21642748 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
21642695 ATAAGATGAT
21642705 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
21642721 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
21642735 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
21642749 ACCCTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:21642829 original size:15 final size:15
Alignment explanation
Indices: 21642787--21642834 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
21642777 ATGTCCTCTG
*
21642787 TTTTTTAGTTTTCTT
1 TTTTTTAGTATTCTT
* * *
21642802 TTTTGT-CTCTTCTT
1 TTTTTTAGTATTCTT
21642816 TTTTTTAGTATTCTT
1 TTTTTTAGTATTCTT
21642831 TTTT
1 TTTT
21642835 ATTTGACTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (15 bp):
TTTTTTAGTATTCTT
Found at i:21643033 original size:14 final size:14
Alignment explanation
Indices: 21643001--21643033 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
21642991 TTTTCTTCGC
21643001 AAAAAAGAAACCCT
1 AAAAAAGAAACCCT
*
21643015 TAAAAAG-AACCCT
1 AAAAAAGAAACCCT
21643028 AAAAAA
1 AAAAAA
21643034 TCTAATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (14 bp):
AAAAAAGAAACCCT
Found at i:21644742 original size:43 final size:43
Alignment explanation
Indices: 21644695--21644942 Score: 200
Period size: 43 Copynumber: 5.8 Consensus size: 43
21644685 TTTTACGGCG
* *
21644695 TTTAGTGGTGCTTTTAT-ATAAAACGCCGCTAAAGAACATGACC
1 TTTAGCGGCGCTTTTATCA-AAAACGCCGCTAAAGAACATGACC
* *
21644738 TTTAGTGGCGC-TTTACCCACAAAA-GCCGCTAAA-AAGCATGACC
1 TTTAGCGGCGCTTTTA-TCA-AAAACGCCGCTAAAGAA-CATGACC
* * * *
21644781 TTTAGCAGCGCTATTATCACAAATGCCGCTAAAGAACATGACC
1 TTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGAACATGACC
** * * *
21644824 TTTAGCGATGCTTTTATCACAGACGCTGCTAAAGAACATGACC
1 TTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGAACATGACC
* * * * * *
21644867 TTTACCGGCGCTTTTATCACAAATGTCGCTATAGAGA-ATGACT
1 TTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGA-ACATGACC
** * * *
21644910 TTTAGCGGCTTTTTTTTCACAAACGCCACTAAA
1 TTTAGCGGCGCTTTTATCAAAAACGCCGCTAAA
21644943 AATACTATTC
Statistics
Matches: 166, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
42 9 0.05
43 146 0.88
44 11 0.07
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGAACATGACC
Found at i:21644942 original size:86 final size:85
Alignment explanation
Indices: 21644719--21644944 Score: 235
Period size: 86 Copynumber: 2.6 Consensus size: 85
21644709 TATATAAAAC
* * * *
21644719 GCCGCTAAAGAACATGACCTTTAGTG-GCGCTTTACCCACAAAAGCCGCTAAAAAGCATGACCTT
1 GCCGCTAAAGAACATGACCTTTAGCGAGC-TTTTA-TCACAAACGCCGCTAAAAAGCATGACCTT
*
21644783 TAGCAGCGCTATTATCACAAAT
64 TACCAGCGCTATTATCACAAAT
* *
21644805 GCCGCTAAAGAACATGACCTTTAGCGATGCTTTTATCACAGACGCTGCTAAAGAA-CATGACCTT
1 GCCGCTAAAGAACATGACCTTTAGCGA-GCTTTTATCACAAACGCCGCTAAA-AAGCATGACCTT
* *
21644869 TACCGGCGCTTTTATCACAAAT
64 TACCAGCGCTATTATCACAAAT
* * * * *
21644891 GTCGCTATAGAGA-ATGACTTTTAGCG-GCTTTTTTTTCACAAACGCCACTAAAAA
1 GCCGCTAAAGA-ACATGACCTTTAGCGAGC--TTTTATCACAAACGCCGCTAAAAA
21644945 TACTATTCTT
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
84 2 0.02
85 2 0.02
86 105 0.89
87 7 0.06
88 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (85 bp):
GCCGCTAAAGAACATGACCTTTAGCGAGCTTTTATCACAAACGCCGCTAAAAAGCATGACCTTTA
CCAGCGCTATTATCACAAAT
Found at i:21647754 original size:13 final size:13
Alignment explanation
Indices: 21647736--21647764 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21647726 ATGTAATTAT
21647736 TATTATTTATATA
1 TATTATTTATATA
21647749 TATTATTTATATA
1 TATTATTTATATA
21647762 TAT
1 TAT
21647765 GTGTATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTTATATA
Found at i:21654652 original size:3 final size:3
Alignment explanation
Indices: 21654644--21655464 Score: 1642
Period size: 3 Copynumber: 273.7 Consensus size: 3
21654634 TAAGTCGCAA
21654644 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654692 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654740 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654788 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654836 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654884 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654932 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21654980 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655028 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655076 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655124 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655172 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655220 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655268 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655316 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655364 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655412 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21655460 AAG AA
1 AAG AA
21655465 CATATGTGAA
Statistics
Matches: 818, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 818 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21656677 original size:50 final size:50
Alignment explanation
Indices: 21656609--21656726 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 50
21656599 AAGACATTAG
* * * *
21656609 TCTTATCGCCTTGACGTTGTAATGGAAAAGATTGAAGCCACAACAGCGAA
1 TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACAGCGAA
* ** * * *
21656659 TCTTATTTCCCTGGCGTTGTAACGGAGTAGATTGAAGCCACGACGGTGAA
1 TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACAGCGAA
*
21656709 TCTTATCTCCTTGGCGTT
1 TCTTATCTCCCTGGCGTT
21656727 AAGGCCTGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (50 bp):
TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACAGCGAA
Found at i:21656857 original size:50 final size:50
Alignment explanation
Indices: 21656796--21657079 Score: 166
Period size: 50 Copynumber: 5.7 Consensus size: 50
21656786 TTGGCATTAC
*
21656796 AGTGGAGCAGATTGAAG-TAGCAACGACGAATCTTACTCCCCTGGCGATGT
1 AGTGGAACAGATTGAAGCTA-CAACGACGAATCTTACTCCCCTGGCGATGT
* ** ** **
21656846 AGTGGAACAGATTGAAGCTACGACGGTGAATCTTGTTTCCCC-AAC-AT-T
1 AGTGGAACAGATTGAAGCTACAACGACGAATCTT-ACTCCCCTGGCGATGT
* ** * * ** * *
21656894 ACAATTAAAAAGATTGAGGCCGCAACGACGAATCTTACTTCCCTGGCGTTGT
1 --AGTGGAACAGATTGAAGCTACAACGACGAATCTTACTCCCCTGGCGATGT
* * * ** * *
21656946 AGTGGAATAGATTGAAGCTACGACGGCGAATCTTGTTTCCCC-AGC-ATTGC
1 AGTGGAACAGATTGAAGCTACAACGACGAATCTT-ACTCCCCTGGCGA-TGT
* ** * ** * *
21656996 AATTAAAAAGATTGAAGCCGCAACGTCGAATCTTACTCCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCTACAACGACGAATCTTACTCCCCTGGCGATGT
* *
21657046 AGTGGAACAAATTGAAGCTACGACGACGAATCTT
1 AGTGGAACAGATTGAAGCTACAACGACGAATCTT
21657080 GTTTCCCCAA
Statistics
Matches: 162, Mismatches: 61, Indels: 22
0.66 0.25 0.09
Matches are distributed among these distances:
48 1 0.01
49 11 0.07
50 137 0.85
51 12 0.07
52 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCTACAACGACGAATCTTACTCCCCTGGCGATGT
Found at i:21656919 original size:100 final size:100
Alignment explanation
Indices: 21656804--21657312 Score: 730
Period size: 100 Copynumber: 5.1 Consensus size: 100
21656794 ACAGTGGAGC
** * *
21656804 AGATTGAAGTAGCAACGACGAATCTTACTCCCCTGGCGATGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
21656869 CGGTGAATCTTGTTTCCCCAACATTACAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * *
21656904 AGATTGAGGCCGCAACGACGAATCTTACTTCCCTGGCGTTGTAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
21656969 CGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * *
21657004 AGATTGAAGCCGCAACGTCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAAATTGAAGCTACGA
1 AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
21657069 CGACGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* ** * * * *
21657104 AGATTGAAGCCGCAATGGTGAATCTTACTTCCTTGGTGGTATAGTGGAACAAATTGAAGCTACGA
1 AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
21657169 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * * * *
21657204 AGATTGAAGCCACAATGTCGAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGATGCTACGA
1 AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
21657269 CGGCGAATCTTGTTTCCCCGACATTCCAGTTAAAC
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
21657304 AGATTGAAG
1 AGATTGAAG
21657313 ATGGCGGATC
Statistics
Matches: 375, Mismatches: 34, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 375 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:21657110 original size:50 final size:50
Alignment explanation
Indices: 21656854--21657113 Score: 191
Period size: 50 Copynumber: 5.2 Consensus size: 50
21656844 GTAGTGGAAC
** * *
21656854 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCAACATTACAATTAAAA
1 AGATTGAAGCTACGACGACGAATCTTGTTTCCCCAGCATTGCAATTAAAA
* ** * ** ** * * * ** *
21656904 AGATTGAGGCCGCAACGACGAATCTTACTTCCCTGGCGTTGTAGTGGAAT
1 AGATTGAAGCTACGACGACGAATCTTGTTTCCCCAGCATTGCAATTAAAA
*
21656954 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
1 AGATTGAAGCTACGACGACGAATCTTGTTTCCCCAGCATTGCAATTAAAA
** * * ** * ** * * * *
21657004 AGATTGAAGCCGCAACGTCGAATCTT-ACTCCCCTGGCGGTGTAGTGGAACA
1 AGATTGAAGCTACGACGACGAATCTTGTTTCCCC-AGCATTGCAAT-TAAAA
*
21657055 A-ATTGAAGCTACGACGACGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGACGAATCTTGTTTCCCCAGCATTGCAATTAAAA
21657104 AGATTGAAGC
1 AGATTGAAGC
21657114 CGCAATGGTG
Statistics
Matches: 146, Mismatches: 60, Indels: 8
0.68 0.28 0.04
Matches are distributed among these distances:
49 9 0.06
50 128 0.88
51 9 0.06
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACGACGACGAATCTTGTTTCCCCAGCATTGCAATTAAAA
Found at i:21657127 original size:50 final size:50
Alignment explanation
Indices: 21656854--21657229 Score: 186
Period size: 50 Copynumber: 7.5 Consensus size: 50
21656844 GTAGTGGAAC
** * * * *
21656854 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCAACATTACAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
* * ** ** * * * ** *
21656904 AGATTGAGGCCGCAACGACGAATCTTACTTCCCTGGCGTTGTAGTGGAAT
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
** *
21656954 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
* ** * ** * * * *
21657004 AGATTGAAGCCGCAACGTCGAATCTT-ACTCCCCTGGCGGTGTAGTGGAACA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCC-AGCATTGCAAT-TAAAA
** * * *
21657055 A-ATTGAAGCTACGACGACGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
* * ** ** * * * * *
21657104 AGATTGAAGCCGCAATGGTGAATCTTACTT-CCTTG-GTGGTATAGTGGAACA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCA-A-T-TAAAA
** * *
21657155 A-ATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
* * *
21657204 AGATTGAAGCCACAATGTCGAATCTT
1 AGATTGAAGCCGCAACGGCGAATCTT
21657230 ACTTCCTTGG
Statistics
Matches: 221, Mismatches: 95, Indels: 20
0.66 0.28 0.06
Matches are distributed among these distances:
48 3 0.01
49 16 0.07
50 183 0.83
51 16 0.07
52 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCGCAACGGCGAATCTTGTTTCCCCAGCATTGCAATTAAAA
Found at i:21657276 original size:50 final size:50
Alignment explanation
Indices: 21657123--21657279 Score: 129
Period size: 50 Copynumber: 3.1 Consensus size: 50
21657113 CCGCAATGGT
*
21657123 GAATCTTACTTCCTTGGTGGTATAGTGGAACAAATTGAAGCTACGACGGC
1 GAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGAAGCTACGACGGC
** **** * * ** * * * * *
21657173 GAATCTTGTTTCCCCAACATTGCA-A-TTAAAAAGATTGAAGCCACAATGTC
1 GAATCTTACTT--CCTTGGTGGTATAGTGGAACAGATTGAAGCTACGACGGC
*
21657223 GAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGATGCTACGACGGC
1 GAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGAAGCTACGACGGC
21657273 GAATCTT
1 GAATCTT
21657280 GTTTCCCCGA
Statistics
Matches: 71, Mismatches: 32, Indels: 8
0.64 0.29 0.07
Matches are distributed among these distances:
48 5 0.07
49 1 0.01
50 59 0.83
51 1 0.01
52 5 0.07
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (50 bp):
GAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGAAGCTACGACGGC
Found at i:21659332 original size:10 final size:10
Alignment explanation
Indices: 21659307--21659338 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
21659297 ATTTTAACAC
21659307 ATATTT-TAT
1 ATATTTATAT
21659316 A-ATTTATAT
1 ATATTTATAT
21659325 ATATTTATAT
1 ATATTTATAT
21659335 ATAT
1 ATAT
21659339 ATTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.19
9 5 0.24
10 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATAT
Found at i:21661005 original size:9 final size:9
Alignment explanation
Indices: 21660991--21661217 Score: 373
Period size: 9 Copynumber: 25.2 Consensus size: 9
21660981 TATGTATTAC
21660991 GTAAGTTAT
1 GTAAGTTAT
21661000 GTAAGTTAT
1 GTAAGTTAT
*
21661009 GTGAGTTAT
1 GTAAGTTAT
21661018 GTAAGTTAT
1 GTAAGTTAT
21661027 GTAAGTTAT
1 GTAAGTTAT
*
21661036 GTGAGTTAT
1 GTAAGTTAT
21661045 GTAAGTTAT
1 GTAAGTTAT
21661054 GTAAGTTAT
1 GTAAGTTAT
*
21661063 GTGAGTTAT
1 GTAAGTTAT
21661072 GTAAGTTAT
1 GTAAGTTAT
21661081 GTAAGTTAT
1 GTAAGTTAT
*
21661090 GTGAGTTAT
1 GTAAGTTAT
21661099 GTAAGTTAT
1 GTAAGTTAT
21661108 GTAAGTTAT
1 GTAAGTTAT
*
21661117 GTGAGTTAT
1 GTAAGTTAT
21661126 GTAAGTTAT
1 GTAAGTTAT
21661135 GTAAGTTAT
1 GTAAGTTAT
*
21661144 GTGAGTTAT
1 GTAAGTTAT
21661153 GTAAGTTAT
1 GTAAGTTAT
21661162 GTAAGTTAT
1 GTAAGTTAT
*
21661171 GTGAGTTAT
1 GTAAGTTAT
21661180 GTAAGTTAT
1 GTAAGTTAT
21661189 GTAAGTTAT
1 GTAAGTTAT
*
21661198 GTGAGTTAT
1 GTAAGTTAT
*
21661207 GTGAGTTAT
1 GTAAGTTAT
21661216 GT
1 GT
21661218 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 203 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:21661023 original size:27 final size:27
Alignment explanation
Indices: 21660991--21661217 Score: 445
Period size: 27 Copynumber: 8.4 Consensus size: 27
21660981 TATGTATTAC
21660991 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661018 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661045 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661072 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661099 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661126 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661153 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
21661180 GTAAGTTATGTAAGTTATGTGAGTTAT
1 GTAAGTTATGTAAGTTATGTGAGTTAT
*
21661207 GTGAGTTATGT
1 GTAAGTTATGT
21661218 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 199 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (27 bp):
GTAAGTTATGTAAGTTATGTGAGTTAT
Found at i:21661384 original size:43 final size:43
Alignment explanation
Indices: 21661323--21661404 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
21661313 NNNNNNNNNN
* *
21661323 ACAAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTC
1 ACAAACGCCGCTATAGCTCAAGACATTTAGCGACGCTTTTTTC
21661366 ACAAACGCCGCTATAGCTCAAGACATTTAGCGACGCTTT
1 ACAAACGCCGCTATAGCTCAAGACATTTAGCGACGCTTT
21661405 GATTACAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
ACAAACGCCGCTATAGCTCAAGACATTTAGCGACGCTTTTTTC
Found at i:21664137 original size:30 final size:30
Alignment explanation
Indices: 21664103--21664166 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
21664093 TATATGGAAA
* *
21664103 TAAACCCTAAACCCTAAAA-CTCTAAAATTC
1 TAAACCCTAAACACTAAAACCT-TAAAACTC
* *
21664133 TAAACCTTAAATACTAAAACCTTAAAACTC
1 TAAACCCTAAACACTAAAACCTTAAAACTC
21664163 TAAA
1 TAAA
21664167 TTCTAAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (30 bp):
TAAACCCTAAACACTAAAACCTTAAAACTC
Found at i:21664149 original size:14 final size:15
Alignment explanation
Indices: 21664116--21664158 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21664106 ACCCTAAACC
* *
21664116 CTAAAACTCTAAAATT
1 CTAAAAC-CTTAAATA
21664132 CT-AAACCTTAAATA
1 CTAAAACCTTAAATA
21664146 CTAAAACCTTAAA
1 CTAAAACCTTAAA
21664159 ACTCTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 14 0.58
16 2 0.08
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
CTAAAACCTTAAATA
Found at i:21664183 original size:38 final size:38
Alignment explanation
Indices: 21664111--21664183 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
21664101 AATAAACCCT
**
21664111 AAACCCTAAAACTCTAAAATTCTAAACCTTAAATACTA
1 AAACCCTAAAACTCTAAAATTCTAAACCCAAAATACTA
*
21664149 AAACCTTAAAACTCT-AAATTCTAAAACCCAAAATA
1 AAACCCTAAAACTCTAAAATTCT-AAACCCAAAATA
21664184 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 7 0.23
38 24 0.77
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (38 bp):
AAACCCTAAAACTCTAAAATTCTAAACCCAAAATACTA
Found at i:21664559 original size:40 final size:39
Alignment explanation
Indices: 21664460--21664576 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 39
21664450 CAACTTTTTT
* *
21664460 GCAGCGTTTTGTGAAAAGCGCCGCTAATGCTGATCTATA
1 GCAGCGTTTTGCGAAAAGCACCGCTAATGCTGATCTATA
* *
21664499 GCAGCATTTTTC-AAATAGCACCGCTAATGCTCGATCTATTA
1 GCAGCGTTTTGCGAAA-AGCACCGCTAATGCT-GATCTA-TA
* *
21664540 -CGGGGTTTTGCGAAAAGCACCGCTAATGCTTGATCTA
1 GCAGCGTTTTGCGAAAAGCACCGCTAATGC-TGATCTA
21664577 CTGCGACATT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
38 3 0.05
39 23 0.35
40 33 0.51
41 6 0.09
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (39 bp):
GCAGCGTTTTGCGAAAAGCACCGCTAATGCTGATCTATA
Found at i:21664693 original size:40 final size:40
Alignment explanation
Indices: 21664649--21664798 Score: 201
Period size: 40 Copynumber: 3.8 Consensus size: 40
21664639 CAACTTTATT
*
21664649 GCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* *
21664689 GCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCAATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* * * * * * *
21664729 GCAGCGTTTTTTAAAAAGCGTCGCTAATGCTTGACCTTTT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
*
21664769 GCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGC
21664799 CACTAAAGCT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:21664904 original size:187 final size:188
Alignment explanation
Indices: 21664441--21664984 Score: 565
Period size: 190 Copynumber: 2.9 Consensus size: 188
21664431 ACAAACGACG
* *
21664441 TCGTTTT-CTCAACTTTTTTGCAGCGTTTTGT-GAAAAGCGCCGCTAATGCT-GATCTATAGCAG
1 TCGTTTTGCTCAACTTTTATGCAGCGTTTT-TCGAAAAGCGCCGCTAATGCTCGATCTATAGCGG
* * * * * * **
21664503 CATTTTTCAAATAGCACCGCTAATGCTCGATCTATTA-CGGGGTTTTGCGAAAAGCACCGCTAAT
65 CATTTTTCAAAAAGCGCCGCTAATGCTCAATCTA-TAGC-GCGTTTTTCAAAAAGCGTCGCTAAT
* * * *
21664567 GCTTGATCTACTGCGACATTTGTTAAAAAGCGCCGCT-A---ACTAAAGCTCAACAACAAAGGAC
128 GCTTGATCTATTGCGGCGTTTTTTAAAAAGCGCCGCTAATGCACTAAAGCTCAACAAC--A--AC
* * *
21664628 GTCGTTTTGCTCAAC-TTTATTGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
1 -TCGTTTTGCTCAACTTTTA-TGCAGCGTTTTTCGAAAAGCGCCGCTAATGCTCGATCTATAGCG
* * *
21664692 GCGTTTTTCAAAAAGCGCTGCTAATGCTCAATCTATAGCAGCGTTTTTTAAAAAGCGTCGCTAAT
64 GCATTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGC-GCGTTTTTCAAAAAGCGTCGCTAAT
* *
21664757 GCTTGACCTTTTGCGGCGTTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAAC-A-
128 GCTTGATCTATTGCGGCGTTTTTTAAAAAGCGCCGCTAATG-CACTAAAGCTCAACAACAAC
* * **
21664817 T-GTTTTGCTCAACTTTTATGCTGTGTTTTTCGAAAAGCGCCGCTAATGCTCGATCTATAATGGC
1 TCGTTTTGCTCAACTTTTATGCAGCGTTTTTCGAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* ** * **
21664881 ATTTTTCTAGGAGCGCCGCTAATGCTTAATCTAT-GCGACACTTTTCAAAAAGCGTCGCTAATGC
66 ATTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGCG-CGTTTTTCAAAAAGCGTCGCTAATGC
* * * *
21664945 TCGATCTATAGCTGCGTTTTTCAAAAAGCGCCGCTAATGC
130 TTGATCTATTGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
21664985 TTGAGCTTTT
Statistics
Matches: 300, Mismatches: 44, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
185 2 0.01
186 58 0.19
187 80 0.27
188 15 0.05
189 36 0.12
190 92 0.31
191 1 0.00
195 16 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (188 bp):
TCGTTTTGCTCAACTTTTATGCAGCGTTTTTCGAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
ATTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGCGCGTTTTTCAAAAAGCGTCGCTAATGCT
TGATCTATTGCGGCGTTTTTTAAAAAGCGCCGCTAATGCACTAAAGCTCAACAACAAC
Found at i:21665002 original size:40 final size:40
Alignment explanation
Indices: 21664841--21665005 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 40
21664831 TTTATGCTGT
* **
21664841 GTTTTTCGAAAAGCGCCGCTAATGCTCGATCTATAATGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * ** ** *
21664881 ATTTTTCTAGGAGCGCCGCTAATGCTTAATCTAT-GCGAC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
** * *
21664920 ACTTTTCAAAAAGCGTCGCTAATGCTCGATCTATAGCTGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * * *
21664960 GTTTTTCAAAAAGCGCCGCTAATGCTTGAGCTTTTGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
21665000 GTTTTT
1 GTTTTT
21665006 GTCATAAACG
Statistics
Matches: 98, Mismatches: 26, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
39 29 0.30
40 69 0.70
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
Found at i:21667957 original size:75 final size:75
Alignment explanation
Indices: 21667870--21668019 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
21667860 TATTGAGTAA
21667870 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
1 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
21667935 ATATTTAATT
66 ATATTTAATT
21667945 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
1 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
21668010 ATATTTAATT
66 ATATTTAATT
21668020 CCATTTTTAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (75 bp):
GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
ATATTTAATT
Found at i:21668353 original size:16 final size:16
Alignment explanation
Indices: 21668334--21668364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21668324 ATAACAAAAT
21668334 GTTGTTATAGAGAGTG
1 GTTGTTATAGAGAGTG
*
21668350 GTTGTTATAGGGAGT
1 GTTGTTATAGAGAGT
21668365 CTTGACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (16 bp):
GTTGTTATAGAGAGTG
Found at i:21669279 original size:27 final size:27
Alignment explanation
Indices: 21669168--21669284 Score: 135
Period size: 28 Copynumber: 4.2 Consensus size: 27
21669158 CGACAGTGTG
*
21669168 TCCCTTATTTTTCAAATTTTATAATTT
1 TCCCCTATTTTTCAAATTTTATAATTT
*
21669195 TGCCCCTATTTTTCAAATTTTATAGTTT
1 T-CCCCTATTTTTCAAATTTTATAATTT
* * * * *
21669223 ACCTCTATTTTTTAGATTTTATATTTTT
1 TCCCCTATTTTTCAAATTTTATA-ATTT
*
21669251 TCCCCTATTTTTCAGATTTTATAATTT
1 TCCCCTATTTTTCAAATTTTATAATTT
21669278 TCTCCCT
1 TC-CCCT
21669285 TGCTTCACAA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 25 0.33
28 51 0.67
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.57
Consensus pattern (27 bp):
TCCCCTATTTTTCAAATTTTATAATTT
Found at i:21670030 original size:78 final size:78
Alignment explanation
Indices: 21669901--21670056 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
21669891 ACAACAAGTG
* *
21669901 GTAGTAACTGCACATATGCAGTTCAATCATGAACCAAGTGGCAATTTGTTTAATATGCAAATATG
1 GTAGTAACTGCAAATATGCAGTTCAATCATGAACCAAGTGGCAATTTGTTTAATATGAAAATATG
*
21669966 TTGTGCACTCACA
66 TTGTGCACCCACA
** * * *
21669979 GTAGTAACTGCAAATATGTGGTTCGATCATGAATCAAGTGGCAATTTGTTTAATTTGAAAATATG
1 GTAGTAACTGCAAATATGCAGTTCAATCATGAACCAAGTGGCAATTTGTTTAATATGAAAATATG
21670044 TTGTGCACCCACA
66 TTGTGCACCCACA
21670057 ACAAGTGGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (78 bp):
GTAGTAACTGCAAATATGCAGTTCAATCATGAACCAAGTGGCAATTTGTTTAATATGAAAATATG
TTGTGCACCCACA
Found at i:21672412 original size:154 final size:154
Alignment explanation
Indices: 21672120--21672581 Score: 854
Period size: 154 Copynumber: 3.0 Consensus size: 154
21672110 AGAGATTCTG
* *
21672120 GTTT-TACTGACCCAAATTCTCATCCTATAAAACAAACTACAAAGGGTAGACCGCAACAAGAGGT
1 GTTTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
21672184 TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
66 TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
21672249 AGTGTTGGAAGAAATTGAGTGCTT
131 AGTGTTGGAAGAAATTGAGTGCTT
*
21672273 GTTTCTATTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
1 GTTTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
21672338 TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
66 TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
21672403 AGTGTTGGAAGAAATTGAGTGCTT
131 AGTGTTGGAAGAAATTGAGTGCTT
21672427 GTTTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
1 GTTTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
* * * *
21672492 TGTTGTAACTAATTCAAGGGGTTAGACTTCTAGTTATGTGTATTGAGAAAAATACCACATAGGTA
66 TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
21672557 AGTGTTGGAAGAAATTGAGTGCTT
131 AGTGTTGGAAGAAATTGAGTGCTT
21672581 G
1 G
21672582 CTTAAAGTGT
Statistics
Matches: 300, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
153 4 0.01
154 296 0.99
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (154 bp):
GTTTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAACAAGAGGT
TGTTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAGGTA
AGTGTTGGAAGAAATTGAGTGCTT
Found at i:21673543 original size:18 final size:19
Alignment explanation
Indices: 21673508--21673543 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21673498 CCTCTCTTCT
*
21673508 CTTTATTTTTTTCTTTTCC
1 CTTTATTTTTTTCGTTTCC
21673527 CTTTATTTTTTT-GTTTC
1 CTTTATTTTTTTCGTTTC
21673544 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (19 bp):
CTTTATTTTTTTCGTTTCC
Found at i:21677259 original size:13 final size:13
Alignment explanation
Indices: 21677241--21677293 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
21677231 CTTAAACCAA
21677241 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
21677254 ACTTTTCTACAA-C
1 ACTTTTC-AAAAGC
* *
21677267 ACTTTTTAAAATC
1 ACTTTTCAAAAGC
*
21677280 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
21677293 A
1 A
21677294 TTGCTTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:21679258 original size:7 final size:7
Alignment explanation
Indices: 21679246--21679285 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
21679236 AAGTCTGGAG
21679246 TAAAAAT
1 TAAAAAT
21679253 TAAAAAT
1 TAAAAAT
21679260 TAAAAAT
1 TAAAAAT
21679267 TAAAAAT
1 TAAAAAT
21679274 TAAAAAT
1 TAAAAAT
21679281 TAAAA
1 TAAAA
21679286 TAGTCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:21683018 original size:23 final size:23
Alignment explanation
Indices: 21682992--21683064 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
21682982 TAATTAGGGC
21682992 TCGCATACATAAAATGTAAGGCT
1 TCGCATACATAAAATGTAAGGCT
* * * *
21683015 TCGCATGCA-AAATAGGTAGGGGT
1 TCGCATACATAAA-ATGTAAGGCT
*
21683038 TCGCATACATAAATTAGTAAGGCT
1 TCGCATACATAAAAT-GTAAGGCT
21683062 TCG
1 TCG
21683065 TATAAAGGGC
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 3 0.08
23 23 0.61
24 12 0.32
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (23 bp):
TCGCATACATAAAATGTAAGGCT
Found at i:21685063 original size:39 final size:39
Alignment explanation
Indices: 21685009--21685098 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
21684999 CATGGCACAA
** *
21685009 AAGTGCGATCAGGGGTACTGAAGTACAACAAGGACATGT
1 AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
* * *
21685048 AAGTGCGATCAGGGGTACCAAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
*
21685087 AAGTGTGATCAG
1 AAGTGCGATCAG
21685099 AGGTGTAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
Found at i:21687631 original size:27 final size:27
Alignment explanation
Indices: 21687601--21687656 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
21687591 ACTGACGAAC
* *
21687601 ACCAACTCGCTAGTCTTGTTGGCGTAT
1 ACCAACTCGCTAGACTTGCTGGCGTAT
* * *
21687628 ACCATCTCGTTAGACTTGCTGGTGTAT
1 ACCAACTCGCTAGACTTGCTGGCGTAT
21687655 AC
1 AC
21687657 TAGCTCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
ACCAACTCGCTAGACTTGCTGGCGTAT
Found at i:21695893 original size:17 final size:16
Alignment explanation
Indices: 21695840--21695896 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
21695830 AGTAAATGCG
* *
21695840 ATTTAAAAAATTTTAAA
1 ATTTTAAAAATTTT-TA
*
21695857 AATTTAAAAATTTTTA
1 ATTTTAAAAATTTTTA
*
21695873 ATTTTATAAATTTTCTA
1 ATTTTAAAAATTTT-TA
21695890 ATTTTAA
1 ATTTTAA
21695897 TCATTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAAAAATTTTTA
Found at i:21695902 original size:9 final size:9
Alignment explanation
Indices: 21695848--21695912 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
21695838 CGATTTAAAA
21695848 AATTTTAA-
1 AATTTTAAT
* *
21695856 AAATTTAAA
1 AATTTTAAT
21695865 AATTTT--T
1 AATTTTAAT
21695872 AATTTT-AT
1 AATTTTAAT
*
21695880 AAATTTT-CT
1 -AATTTTAAT
21695889 AATTTTAAT
1 AATTTTAAT
*
21695898 CATTTTAAT
1 AATTTTAAT
21695907 AATTTT
1 AATTTT
21695913 TTGTATTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
7 6 0.13
8 14 0.30
9 26 0.57
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
AATTTTAAT
Found at i:21696390 original size:130 final size:130
Alignment explanation
Indices: 21696152--21696480 Score: 491
Period size: 130 Copynumber: 2.5 Consensus size: 130
21696142 ATTAAATGCT
* *
21696152 TGAAGGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTACTTGATTTAAAGTGATTGATTG
1 TGAATGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTG
* * * **
21696217 AATCTATATTTTCACAACTAAATTTGATGACATTAAAATATAATATTAAAATAACATATCATTTA
66 AGTCTATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTA
*
21696282 TGAATGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATGGTATTTGATTTAAAGTGATTGATTG
1 TGAATGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTG
*
21696347 AGTCTATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATCTCATTTA
66 AGTCTATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTA
* * ** * *
21696412 T-ACATGTAGTTGTTTGTCGATGTATTAGATTAGGTTGA-CCAACTTTAATTTAAAATGATTGAT
1 TGA-ATGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTA-TTTGATTTAAAGTGATTGAT
21696475 TGAGTC
64 TGAGTC
21696481 CAGGCTTCTA
Statistics
Matches: 181, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
129 2 0.01
130 179 0.99
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (130 bp):
TGAATGTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTG
AGTCTATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTA
Found at i:21699650 original size:50 final size:52
Alignment explanation
Indices: 21699511--21699665 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
21699501 GAACAAATGA
*
21699511 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCAAGACTTAATTTAAT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
* *
21699563 GATGTAGACTTAAACTAACATGGGAGTTACATAATGCATGTCATT-ATTT-AT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGAC-TTAATTTAAT
* * * * * *
21699614 GATGCATACTT-AACTAGCATGGAAGTTACATAATGCATAACTTTATTAAAT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
21699665 G
1 G
21699666 CAGAACACAC
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.02
50 29 0.32
51 14 0.16
52 43 0.48
53 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (52 bp):
GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
Found at i:21699746 original size:20 final size:19
Alignment explanation
Indices: 21699705--21699746 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
21699695 AAAAATATGC
*
21699705 AAACTTATTAATTCAAATA
1 AAACTTATTAATTCAAAAA
21699724 AAACTATATTGAATT-AAAAA
1 AAACT-TATT-AATTCAAAAA
21699744 AAA
1 AAA
21699747 AGTCCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (19 bp):
AAACTTATTAATTCAAAAA
Found at i:21699747 original size:21 final size:19
Alignment explanation
Indices: 21699705--21699747 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
21699695 AAAAATATGC
* *
21699705 AAACTTATTAATTCAAATA
1 AAACTTATTAATTAAAAAA
21699724 AAACTATATTGAATTAAAAAA
1 AAACT-TATT-AATTAAAAAA
21699745 AAA
1 AAA
21699748 GTCCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
AAACTTATTAATTAAAAAA
Found at i:21700032 original size:57 final size:58
Alignment explanation
Indices: 21699892--21700047 Score: 163
Period size: 57 Copynumber: 2.7 Consensus size: 58
21699882 TTGTTTCATG
* * * * *
21699892 TATTTATTTATTATTCTTTTACCTTTTAAATATTTAAATTCGATATTATTTATATTTGTT
1 TATTTATTTATTATTCTTTT--TTTTTAAATACTTAAATTCAATATTATTTATATTTCTC
* * ** * *
21699952 TATCTATTTATTCTT-TTACTTTTTAAATACTTAAATTTAATATTATTTGT-TTTCTC
1 TATTTATTTATTATTCTTTTTTTTTAAATACTTAAATTCAATATTATTTATATTTCTC
21700008 TATTTATTTATTATTCTTTTTTTTTTGAAATACTTAAATT
1 TATTTATTTATTATTC-TTTTTTTTT-AAATACTTAAATT
21700048 GGATACTACT
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
56 17 0.22
57 26 0.33
58 7 0.09
59 15 0.19
60 13 0.17
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (58 bp):
TATTTATTTATTATTCTTTTTTTTTAAATACTTAAATTCAATATTATTTATATTTCTC
Found at i:21701337 original size:6 final size:6
Alignment explanation
Indices: 21701326--21701350 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21701316 AAAGGAGAAT
21701326 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
21701351 TGGTTCACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:21701775 original size:7 final size:7
Alignment explanation
Indices: 21701763--21701792 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
21701753 TGTTAAGCTT
21701763 AATGGAG
1 AATGGAG
21701770 AATGGAG
1 AATGGAG
21701777 AATGGAG
1 AATGGAG
21701784 AATGGAG
1 AATGGAG
21701791 AA
1 AA
21701793 AGATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.40, T:0.13
Consensus pattern (7 bp):
AATGGAG
Found at i:21718593 original size:34 final size:35
Alignment explanation
Indices: 21718528--21718595 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
21718518 TACGAAACAT
*
21718528 AAGGATACTAATCTTCATAAAATAAACATTAAATA
1 AAGGATACTAATATTCATAAAATAAACATTAAATA
* *
21718563 AAGGATACTAATATT-ATAAAATACAGATTAAAT
1 AAGGATACTAATATTCATAAAATAAACATTAAAT
21718596 TAGGGATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.29
Consensus pattern (35 bp):
AAGGATACTAATATTCATAAAATAAACATTAAATA
Found at i:21719037 original size:43 final size:43
Alignment explanation
Indices: 21718989--21719216 Score: 262
Period size: 43 Copynumber: 5.3 Consensus size: 43
21718979 TTTTAGAAAT
* *
21718989 AAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTATCCCAC
1 AAACGCCGCTAAAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* *
21719032 AAACGCCGCTATAGATCATGATTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGATCATGACTTTTAGCGGCGCTTTTCCCAC
*
21719075 AAACGCCGCTATAAG-TCATGACTTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTA-AAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * ***
21719118 TAACGCCGCTATAGATCATCACTTTTAGCGACGCTTTTTTGTAC
1 AAACGCCGCTAAAGATCATGACTTTTAGCGGCGC-TTTTCCCAC
* * * * * *
21719162 AAACGCCGTTATAGAACA-GACCTTTAGCGGGGCTTTTCACAC
1 AAACGCCGCTAAAGATCATGACTTTTAGCGGCGCTTTTCCCAC
21719204 AAACGCCGCTAAA
1 AAACGCCGCTAAA
21719217 AACATATCTT
Statistics
Matches: 155, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
42 19 0.12
43 113 0.73
44 23 0.15
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:21719554 original size:43 final size:42
Alignment explanation
Indices: 21719482--21719572 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 42
21719472 ACATATGTAA
* ** *
21719482 TGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCT
1 TGTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
* * *
21719524 TGGTAATAAAAGATATAATACATTGACTTAATGAAGGAAATCT
1 T-GTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
21719567 TGTAAT
1 TGTAAT
21719573 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 6 0.15
43 35 0.85
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (42 bp):
TGTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
Found at i:21720047 original size:41 final size:41
Alignment explanation
Indices: 21719983--21720074 Score: 134
Period size: 41 Copynumber: 2.2 Consensus size: 41
21719973 AATACTCATT
* *
21719983 GCATTAGCGGCGCTTTTCTAAAAACGCTGCTAAAACCC-CGA
1 GCATTAGCGGCGCTTTTCTAAAAACACCGCTAAAACCCAC-A
21720024 GCATTAGCGGCGCTTTATC-AAAAACACCGCTAAAACCCACA
1 GCATTAGCGGCGCTTT-TCTAAAAACACCGCTAAAACCCACA
21720065 GCATTAGCGG
1 GCATTAGCGG
21720075 TGCTACTCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 44 0.94
42 3 0.06
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTCTAAAAACACCGCTAAAACCCACA
Found at i:21720087 original size:41 final size:40
Alignment explanation
Indices: 21719983--21720103 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 40
21719973 AATACTCATT
* * *
21719983 GCATTAGCGGCGCTTTTCTAAAAACGCTGCTAAAACCCCGA
1 GCATTAGCGGCGC-TATCCAAAAACGCCGCTAAAACCCCGA
*
21720024 GCATTAGCGGCGCTTTAT-CAAAAACACCGCTAAAACCCAC-A
1 GCATTAGCGGCGC--TATCCAAAAACGCCGCTAAAACCC-CGA
* * *
21720065 GCATTAGCGGTGCTACTCCAAAAACGCCACTAAAGCCCC
1 GCATTAGCGGCGCTA-TCCAAAAACGCCGCTAAAACCCC
21720104 CGATAGGTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 60 0.88
42 4 0.06
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.18
Consensus pattern (40 bp):
GCATTAGCGGCGCTATCCAAAAACGCCGCTAAAACCCCGA
Found at i:21742906 original size:68 final size:67
Alignment explanation
Indices: 21742807--21742942 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 67
21742797 AATTCAGGAT
* ** *
21742807 TACCAAAGTACAAACAGGGCACGTATATGCATTC-AGGGATACTTAAGTACAAATAGGGGCATGT
1 TACCAAAGTACAAACAGAGCACGTATATGCATTCAAGGG-TACCAAAGTACAAATAGGGGCACGT
21742871 ATG
65 ATG
* * * *
21742874 TACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATTAGGGGCACGT
1 TACCAAAGTACAAAC-AGAGCACGTATATGCATTCAAGGGTACCAAAGTACAAATAGGGGCACGT
21742939 ATG
65 ATG
21742942 T
1 T
21742943 GCATTCAGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
67 13 0.22
68 42 0.71
69 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (67 bp):
TACCAAAGTACAAACAGAGCACGTATATGCATTCAAGGGTACCAAAGTACAAATAGGGGCACGTA
TG
Found at i:21742937 original size:40 final size:40
Alignment explanation
Indices: 21742873--21743189 Score: 338
Period size: 40 Copynumber: 7.9 Consensus size: 40
21742863 GGGCATGTAT
* *
21742873 GTACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* *
21742913 GTACCAAAGTACAATTAGGGGCACGTATGTGCATTC-AGAG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAG-G
** * * *
21742953 GTATGGAAGTATAAACAGGGGCATGTATGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* *
21742993 GTACCGAAGTACAATCAGGAGCACGTGTGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * *
21743033 GTACTGAAGTACAATCAGAGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * *
21743073 GTATCGAAGTACAATCAGAGGG-ACGCATGTGCATTCAGGG
1 GTACCGAAGTACAATCAG-GGGCACGTATGTGCATTCAAGG
* * *
21743113 GTACCGAAGTACAAACAAGGGG-ACATATGTGCATT-TAGG
1 GTACCGAAGTACAATC-AGGGGCACGTATGTGCATTCAAGG
* * * *
21743152 TGTATCGAAGTACAAAT-ATGGGAATGTATGTGCATTCA
1 -GTACCGAAGTAC-AATCAGGGGCACGTATGTGCATTCA
21743190 TTCAATAATT
Statistics
Matches: 230, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
39 8 0.03
40 214 0.93
41 8 0.03
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (40 bp):
GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
Found at i:21743103 original size:120 final size:120
Alignment explanation
Indices: 21742873--21743147 Score: 381
Period size: 120 Copynumber: 2.3 Consensus size: 120
21742863 GGGCATGTAT
* *
21742873 GTACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATTAGGGGCACG
1 GTACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACG
* * * *
21742938 TATGTGCATTCAGAGGTATGGAAGTATAAACAGGGGCATGTATGTGCATTCAAGG
66 TATGTGCATTCAGAGGTATCGAAGTACAAACAGGGGCACGCATGTGCATTCAAGG
* * **
21742993 GTACCGAAGTACAATCAGGAGCACGTGTGTGCATTCAAGGGTACTGAAGTACAATCAGAGGCACG
1 GTACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACG
* * *
21743058 TATGTGCATTCAGGGGTATCGAAGTACAATCAGAGGG-ACGCATGTGCATTCAGGG
66 TATGTGCATTCAGAGGTATCGAAGTACAAACAG-GGGCACGCATGTGCATTCAAGG
* * * *
21743113 GTACCGAAGTACAAACAAGGGGACATATGTGCATT
1 GTACCGAAGTACAATCAAGAGCACGTATGTGCATT
21743148 TAGGTGTATC
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
120 132 0.98
121 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (120 bp):
GTACCGAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACG
TATGTGCATTCAGAGGTATCGAAGTACAAACAGGGGCACGCATGTGCATTCAAGG
Found at i:21751513 original size:21 final size:21
Alignment explanation
Indices: 21751435--21751514 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
21751425 AGCTCTCATA
* *
21751435 AGCTTCAG-TTAACTCATATG
1 AGCTTCAGTTTAACTCTTTTG
* * *
21751455 AGTTTCAGTTTAACCCTATTG
1 AGCTTCAGTTTAACTCTTTTG
* * * *
21751476 GGTTTCCGTTTAGCTCTTTTG
1 AGCTTCAGTTTAACTCTTTTG
21751497 AGCTTCAGTTTAACTCTT
1 AGCTTCAGTTTAACTCTT
21751515 ATAGGTTTCC
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 7 0.16
21 38 0.84
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (21 bp):
AGCTTCAGTTTAACTCTTTTG
Found at i:21751522 original size:42 final size:42
Alignment explanation
Indices: 21751453--21751535 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
21751443 TTAACTCATA
* * *
21751453 TGAGTTTCAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTT
1 TGAGCTTCAGTTTAACCCTATTAGGTTTCCGTTCAGCTCTTT
*
21751495 TGAGCTTCAGTTTAACTCT-TATAGGTTTCCGTTCAGCTCTT
1 TGAGCTTCAGTTTAACCCTAT-TAGGTTTCCGTTCAGCTCTT
21751536 ACGAGTCTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
TGAGCTTCAGTTTAACCCTATTAGGTTTCCGTTCAGCTCTTT
Found at i:21754893 original size:192 final size:192
Alignment explanation
Indices: 21754566--21755145 Score: 1110
Period size: 192 Copynumber: 3.0 Consensus size: 192
21754556 TGTTTTACTA
*
21754566 AAAACCTTATTTAATAAATATACAACTATTTTAAATGCATGCATCCACAATGATATAGGTAATAA
1 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAATAA
21754631 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
66 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
21754696 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
131 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
21754758 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAATAA
1 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAATAA
21754823 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
66 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
21754888 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
131 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
21754950 AAAACCTTATTTAATAAATATATACAACTA--TTAAGTGCATGCATCCACAATGATATAGGTAAT
1 AAAACCTTATTTAAT-AA-ATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAAT
*
21755013 AAGGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTATGCCTTTCTACAATATC
64 AAGGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATC
21755078 ATTTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
129 ATTTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
21755142 AAAA
1 AAAA
21755146 TGGACCTGGA
Statistics
Matches: 384, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
192 371 0.97
193 2 0.01
194 11 0.03
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (192 bp):
AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAATAA
GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
Found at i:21759729 original size:195 final size:194
Alignment explanation
Indices: 21759220--21759797 Score: 912
Period size: 190 Copynumber: 3.0 Consensus size: 194
21759210 TAAAGGTGAA
* * *
21759220 AAAAAATGCCACTATAAATAGAATTTCTTATAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAGAAGTGCAA
*
21759285 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATGTTCATGGAGAAAATGCAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
*
21759350 CAATTAAGGAAAGAAATGTATAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATA-T
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATATT
21759413 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAG---CAACATAGTACCAGAAGTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAGAAGTGCAA
* * * *
21759475 CTGATCTTGACAACATTAATCAAAGCTAGCTGTTGAATAAGGATATATTCATAGAGAAAATGCAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
* * *
21759540 TAGTTAAGGAAAGAAATATAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATATTT
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATA-TT
* * *
21759605 AAAAAATGCCACTATAAACAAAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAAAACTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAGAAGTGCAA
* * *
21759670 TTGATCCTGACAACATTAATCAAAGCTAACAGTTGAATGAGGATATATCCATGGAGAAAATGCAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
* * * * *
21759735 CAATTAAGTAAAGAAATGTAAAAGTATAAGAAATCAACATCATTCGACTAACTAATAAAATAT
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATAT
21759798 ACCAAGAAGC
Statistics
Matches: 350, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
190 139 0.40
192 40 0.11
193 38 0.11
194 1 0.00
195 132 0.38
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (194 bp):
AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAGAAGTGCAA
CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATATT
Found at i:21771020 original size:26 final size:22
Alignment explanation
Indices: 21770943--21771022 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 22
21770933 AATTCAATAT
21770943 CGAGCTGAAGAACAGTAAGCTC-TA
1 CGAGCTG-A-AAC-GTAAGCTCATA
21770967 TCGAGCTGAAACGTAAGCTCATA
1 -CGAGCTGAAACGTAAGCTCATA
*
21770990 AGAGCTGATATATCGATAAGCTCATA
1 CGAGCTGA-A-A-CG-TAAGCTCATA
21771016 CGAGCTG
1 CGAGCTG
21771023 TGGTGAGTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
22 15 0.31
23 6 0.12
24 2 0.04
25 9 0.19
26 16 0.33
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (22 bp):
CGAGCTGAAACGTAAGCTCATA
Found at i:21771230 original size:14 final size:14
Alignment explanation
Indices: 21771211--21771239 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21771201 TTCATTTCAT
21771211 ACAATTGCAATTAA
1 ACAATTGCAATTAA
21771225 ACAATTGCAATTAA
1 ACAATTGCAATTAA
21771239 A
1 A
21771240 TGAAAGTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
ACAATTGCAATTAA
Found at i:21776186 original size:17 final size:19
Alignment explanation
Indices: 21776158--21776192 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21776148 TTTCTTTTCT
21776158 CTTTACCAAGCTC-TTCAG
1 CTTTACCAAGCTCATTCAG
21776176 CTTTA-CAAGCTCATTCA
1 CTTTACCAAGCTCATTCA
21776193 ACCAGGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (19 bp):
CTTTACCAAGCTCATTCAG
Found at i:21778692 original size:468 final size:468
Alignment explanation
Indices: 21777816--21778752 Score: 1874
Period size: 468 Copynumber: 2.0 Consensus size: 468
21777806 ACTTCTATGA
21777816 GTTCAAACGTACCAAGAAATCGACTGGATAGTGTGATGTTTATCTCCGACATCGTCCGAATCGAG
1 GTTCAAACGTACCAAGAAATCGACTGGATAGTGTGATGTTTATCTCCGACATCGTCCGAATCGAG
21777881 CTAGCTAACGAACCTCTATAAAACACGAAGAAATAAACTGAGTAAGCATTAAAGCTTAGTAAGTT
66 CTAGCTAACGAACCTCTATAAAACACGAAGAAATAAACTGAGTAAGCATTAAAGCTTAGTAAGTT
21777946 GATATGTAAATAATAAGCAATCTTTAACATGCTTTTACCAATCCTCACAACATGTTCTCAAGATA
131 GATATGTAAATAATAAGCAATCTTTAACATGCTTTTACCAATCCTCACAACATGTTCTCAAGATA
21778011 ATACAATCAAAATTGCAAATAGTTACACTATTTACTCATGTTCACATCAAGTTGTGTACTCGAGT
196 ATACAATCAAAATTGCAAATAGTTACACTATTTACTCATGTTCACATCAAGTTGTGTACTCGAGT
21778076 CATAGTCACTAAACTATTTATATCTTGCGCTACGGAACTTCAAATTCCGTTTAACTTTCCCGAAA
261 CATAGTCACTAAACTATTTATATCTTGCGCTACGGAACTTCAAATTCCGTTTAACTTTCCCGAAA
21778141 CTAGATTCAAAGATCTTGTTACCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACAGTT
326 CTAGATTCAAAGATCTTGTTACCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACAGTT
21778206 AATTCTTCAAAGTCGTCCCTGTTATGTTGTCTGACAGTTCCGACCCTTTTTCTCTAAAAATTAAT
391 AATTCTTCAAAGTCGTCCCTGTTATGTTGTCTGACAGTTCCGACCCTTTTTCTCTAAAAATTAAT
21778271 TATCTCTTAGTAC
456 TATCTCTTAGTAC
21778284 GTTCAAACGTACCAAGAAATCGACTGGATAGTGTGATGTTTATCTCCGACATCGTCCGAATCGAG
1 GTTCAAACGTACCAAGAAATCGACTGGATAGTGTGATGTTTATCTCCGACATCGTCCGAATCGAG
21778349 CTAGCTAACGAACCTCTATAAAACACGAAGAAATAAACTGAGTAAGCATTAAAGCTTAGTAAGTT
66 CTAGCTAACGAACCTCTATAAAACACGAAGAAATAAACTGAGTAAGCATTAAAGCTTAGTAAGTT
21778414 GATATGTAAATAATAAGCAATCTTTAACATGCTTTTACCAATCCTCACAACATGTTCTCAAGATA
131 GATATGTAAATAATAAGCAATCTTTAACATGCTTTTACCAATCCTCACAACATGTTCTCAAGATA
21778479 ATACAATCAAAATTGCAAATAGTTACACTATTTACTCATGTTCACATCAAGTTGTGTACTCGAGT
196 ATACAATCAAAATTGCAAATAGTTACACTATTTACTCATGTTCACATCAAGTTGTGTACTCGAGT
21778544 CATAGTCACTAAACTATTTATATCTTGCGCTACGGAACTTCAAATTCCGTTTAACTTTCCCGAAA
261 CATAGTCACTAAACTATTTATATCTTGCGCTACGGAACTTCAAATTCCGTTTAACTTTCCCGAAA
21778609 CTAGATTCAAAGATCTTGTTACCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACAGTT
326 CTAGATTCAAAGATCTTGTTACCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACAGTT
21778674 AATTCTTCAAAGTCGTCCCTGTTATGTTGTCTGACAGTTCCGACCCTTTTTCTCTAAAAATTAAT
391 AATTCTTCAAAGTCGTCCCTGTTATGTTGTCTGACAGTTCCGACCCTTTTTCTCTAAAAATTAAT
21778739 TATCTCTTAGTAC
456 TATCTCTTAGTAC
21778752 G
1 G
21778753 GGATTCAGAT
Statistics
Matches: 469, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
468 469 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (468 bp):
GTTCAAACGTACCAAGAAATCGACTGGATAGTGTGATGTTTATCTCCGACATCGTCCGAATCGAG
CTAGCTAACGAACCTCTATAAAACACGAAGAAATAAACTGAGTAAGCATTAAAGCTTAGTAAGTT
GATATGTAAATAATAAGCAATCTTTAACATGCTTTTACCAATCCTCACAACATGTTCTCAAGATA
ATACAATCAAAATTGCAAATAGTTACACTATTTACTCATGTTCACATCAAGTTGTGTACTCGAGT
CATAGTCACTAAACTATTTATATCTTGCGCTACGGAACTTCAAATTCCGTTTAACTTTCCCGAAA
CTAGATTCAAAGATCTTGTTACCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACAGTT
AATTCTTCAAAGTCGTCCCTGTTATGTTGTCTGACAGTTCCGACCCTTTTTCTCTAAAAATTAAT
TATCTCTTAGTAC
Found at i:21779377 original size:26 final size:24
Alignment explanation
Indices: 21779347--21779405 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 24
21779337 CAATGATCGT
21779347 TAAGCTCAT-TCCGAGCTGAAGAACGG
1 TAAGCTCATAT-CGAGCT-AA-AACGG
*
21779373 TAAGCTC-TATCGAGCTAAATCGG
1 TAAGCTCATATCGAGCTAAAACGG
21779396 TAAGCTCATA
1 TAAGCTCATA
21779406 AGAGCTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 11 0.37
24 4 0.13
25 7 0.23
26 8 0.27
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
TAAGCTCATATCGAGCTAAAACGG
Found at i:21779410 original size:23 final size:26
Alignment explanation
Indices: 21779342--21779438 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 26
21779332 TCGAGCAATG
* * *
21779342 ATCGTTAAGCTCATTCCGAGCTGA-AG
1 ATCGGTAAGCTCA-TACGAGCTGATAT
*
21779368 AACGGTAAGCTC-TATCGAGCT-A-A-
1 ATCGGTAAGCTCATA-CGAGCTGATAT
*
21779391 ATCGGTAAGCTCATAAGAGCTGATAT
1 ATCGGTAAGCTCATACGAGCTGATAT
*
21779417 ATCGGTAAGCCCATACGAGCTG
1 ATCGGTAAGCTCATACGAGCTG
21779439 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.27
24 6 0.10
25 7 0.12
26 30 0.51
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (26 bp):
ATCGGTAAGCTCATACGAGCTGATAT
Found at i:21783150 original size:15 final size:16
Alignment explanation
Indices: 21783120--21783151 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21783110 TAAGTGTGTT
21783120 AATGTAATATTCTTTA
1 AATGTAATATTCTTTA
21783136 AATGTAATATT-TTTA
1 AATGTAATATTCTTTA
21783151 A
1 A
21783152 TAAATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
AATGTAATATTCTTTA
Found at i:21783302 original size:22 final size:24
Alignment explanation
Indices: 21783271--21783325 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
21783261 TGAACTATTT
*
21783271 TTTATGTTTTT-CATAAGTT-AAA
1 TTTATATTTTTACATAAGTTAAAA
* *
21783293 TTTATATTTTTACATTATTTAAAA
1 TTTATATTTTTACATAAGTTAAAA
21783317 TTTA-ATTTT
1 TTTATATTTT
21783326 GTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTATATTTTTACATAAGTTAAAA
Found at i:21783675 original size:31 final size:31
Alignment explanation
Indices: 21783637--21783715 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
21783627 ACTACAAAAA
*
21783637 TAGTCACTTTTGTTTG-CTTCAAATTACATTT
1 TAGTCACTTATGTTTGAC-TCAAATTACATTT
**
21783668 TAGTCACTTATGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGACTCAAATTACATTT
*
21783699 TAGTCACTTATATTTGA
1 TAGTCACTTATGTTTGA
21783716 AATGTTACGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (31 bp):
TAGTCACTTATGTTTGACTCAAATTACATTT
Found at i:21784983 original size:2 final size:2
Alignment explanation
Indices: 21784976--21785001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21784966 GGGATCATGA
21784976 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
21785002 GTTACCGGTG
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:21788298 original size:37 final size:35
Alignment explanation
Indices: 21788243--21788352 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 35
21788233 TACTAGATAG
*
21788243 TTTAATATTATTTTAATAGTTTAATATTAAATTTAA
1 TTTAATATTATCTTAATAGTTTAATATT-AATTTAA
*
21788279 TTTAATACTTATCTTAATAGTATT-TTATTAATTTAA
1 TTTAATA-TTATCTTAATAGT-TTAATATTAATTTAA
*
21788315 TATTAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAA
1 T-TT-AA-T-ATTATCTTAATAGTTTAATATTAATTTAA
21788352 T
1 T
21788353 GTTTATCTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
36 15 0.24
37 29 0.46
38 6 0.10
39 12 0.19
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (35 bp):
TTTAATATTATCTTAATAGTTTAATATTAATTTAA
Found at i:21790007 original size:113 final size:113
Alignment explanation
Indices: 21789890--21790244 Score: 710
Period size: 113 Copynumber: 3.1 Consensus size: 113
21789880 ACTTCTAGTT
21789890 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
1 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
21789955 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
66 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
21790003 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
1 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
21790068 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
66 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
21790116 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
1 AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
21790181 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
66 GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
21790229 AAGCGCCGCAAGATAT
1 AAGCGCCGCAAGATAT
21790245 ATTAACCGAA
Statistics
Matches: 242, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 242 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (113 bp):
AAGCGCCGCAAGATATGCACACCAAAACGCAGAGCTTGGTATTGAGGTATATTAGATGTAGTGGT
GCTTTCTGGAAACGCCGCAAAGGTATACTATTAGCGGCGCTTTCTTAG
Found at i:21792597 original size:42 final size:42
Alignment explanation
Indices: 21792538--21792635 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
21792528 NNNNNNNNNN
21792538 AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TA
1 AGCGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTTCGTA
*
21792580 AGCGCCGCTAAAGAACATGATCTTTAGGGGCTTTTTTTCTGTA
1 AGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTTC-GTA
*
21792623 AGCGCCGCAAAAG
1 AGCGCCGCTAAAG
21792636 TTTGCGACGT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 8 0.15
42 30 0.58
43 14 0.27
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (42 bp):
AGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTTCGTA
Found at i:21794154 original size:20 final size:21
Alignment explanation
Indices: 21794129--21794181 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
21794119 GATAACATTT
*
21794129 TATTTTGAATTTTTTG-TTTA
1 TATTTTGAATTTTTAGTTTTA
*
21794149 TATTTT-TATTTTTAGTTTTA
1 TATTTTGAATTTTTAGTTTTA
*
21794169 TTTTTTGAATTTT
1 TATTTTGAATTTT
21794182 AAAGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.74
Consensus pattern (21 bp):
TATTTTGAATTTTTAGTTTTA
Found at i:21794161 original size:19 final size:18
Alignment explanation
Indices: 21794126--21794173 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
21794116 TTAGATAACA
* *
21794126 TTTTATTTTGAATTTTTTG
1 TTTTATTTT-TATTTTTAG
21794145 TTTATATTTTTATTTTTAG
1 TTT-TATTTTTATTTTTAG
21794164 TTTTATTTTT
1 TTTTATTTTT
21794174 TGAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 13 0.50
20 6 0.23
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTATTTTTAG
Found at i:21795445 original size:36 final size:36
Alignment explanation
Indices: 21795376--21795461 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
21795366 CTACCTTCAT
** *
21795376 CCGATTTGCTTCCTTGTTTCTTTGCTTTTCTTTTCTG
1 CCGATTTGC-TCCCAGTTTATTTGCTTTTCTTTTCTG
*
21795413 CCGATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTG
1 CCGATTTGCTCCCAGTTTATTTGCTTTTCTTTTCTG
21795449 CCGATTTGCTCCC
1 CCGATTTGCTCCC
21795462 CCCCGTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 36 0.80
37 9 0.20
ACGTcount: A:0.06, C:0.28, G:0.13, T:0.53
Consensus pattern (36 bp):
CCGATTTGCTCCCAGTTTATTTGCTTTTCTTTTCTG
Found at i:21799548 original size:18 final size:17
Alignment explanation
Indices: 21799520--21799554 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21799510 NNNNNNNAGA
*
21799520 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21799537 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21799555 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21799745 original size:39 final size:40
Alignment explanation
Indices: 21799702--21799806 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
21799692 TTCCATTATG
21799702 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
21799741 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
21799786 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
21799807 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:21799800 original size:45 final size:44
Alignment explanation
Indices: 21799700--21799809 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
21799690 TTTTCCATTA
21799700 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
21799739 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
21799784 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
21799810 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:21799809 original size:16 final size:16
Alignment explanation
Indices: 21799788--21799857 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
21799778 TTGATTTGCT
*
21799788 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
21799804 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
21799820 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
21799836 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
21799852 AATACA
1 ATTACA
21799858 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:21802159 original size:17 final size:18
Alignment explanation
Indices: 21802137--21802219 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 18
21802127 TTATTTTGGA
* *
21802137 ATTTTTGTTTATATTT-T
1 ATTTTTATTTTTATTTAT
*
21802154 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATTTAT
***
21802172 ATTTTTTATTTTTAAAGAT
1 A-TTTTTATTTTTATTTAT
*
21802191 -TTTTTATTTTT-TTCAT
1 ATTTTTATTTTTATTTAT
21802207 ATTTTTATTTTTA
1 ATTTTTATTTTTA
21802220 AACAAATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.04
17 36 0.68
18 2 0.04
19 13 0.25
ACGTcount: A:0.20, C:0.01, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTATTTTTATTTAT
Found at i:21802159 original size:18 final size:17
Alignment explanation
Indices: 21802138--21802178 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
21802128 TATTTTGGAA
21802138 TTTTTGTTTATATTTTAT
1 TTTTTGTTTAT-TTTTAT
*
21802156 TTTTATTTTTATTTTTAT
1 TTTT-TGTTTATTTTTAT
21802174 TTTTT
1 TTTTT
21802179 ATTTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTGTTTATTTTTAT
Found at i:21802171 original size:13 final size:13
Alignment explanation
Indices: 21802144--21802185 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
21802134 GGAATTTTTG
*
21802144 TTTATATTTTATT
1 TTTATTTTTTATT
21802157 TTTA-TTTTTATT
1 TTTATTTTTTATT
21802169 TTTATTTTTTATT
1 TTTATTTTTTATT
21802182 TTTA
1 TTTA
21802186 AAGATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:21802177 original size:19 final size:19
Alignment explanation
Indices: 21802144--21802185 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
21802134 GGAATTTTTG
21802144 TTTATATTTTATTTTTATT
1 TTTATATTTTATTTTTATT
21802163 TTTAT-TTTTATTTTTTATT
1 TTTATATTTTA-TTTTTATT
21802182 TTTA
1 TTTA
21802186 AAGATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATATTTTATTTTTATT
Found at i:21802201 original size:6 final size:6
Alignment explanation
Indices: 21802144--21802185 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
21802134 GGAATTTTTG
21802144 TTTATAT TTTATT TTTATT TTTATT TTTATTT TTTATT TTTA
1 TTTAT-T TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTA
21802186 AAGATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 23 0.68
7 11 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:21802234 original size:24 final size:22
Alignment explanation
Indices: 21802205--21802266 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
21802195 TATTTTTTTC
*
21802205 ATATTTTTATTTTTAAACAAATT
1 ATATTTTTATTTTTAAA-AAAAT
21802228 ATAATTTTTATTTTTAAAAAAAT
1 AT-ATTTTTATTTTTAAAAAAAT
*
21802251 ATTTTTTTAATTTTTA
1 ATATTTTT-ATTTTTA
21802267 TGTTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 5 0.14
23 15 0.43
24 15 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATTTTTAAAAAAAT
Found at i:21802236 original size:34 final size:32
Alignment explanation
Indices: 21802167--21802242 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 32
21802157 TTTATTTTTA
* ** * *
21802167 TTTTTATTTTTTATTTTTAAAGATTTTTTATT
1 TTTTTATTTTTTATTTTTAAACAAATTATAAT
21802199 TTTTTCATATTTTTATTTTTAAACAAATTATAA-
1 TTTTT-AT-TTTTTATTTTTAAACAAATTATAAT
21802232 TTTTTATTTTT
1 TTTTTATTTTT
21802243 AAAAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
31 4 0.11
32 7 0.19
33 7 0.19
34 19 0.51
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (32 bp):
TTTTTATTTTTTATTTTTAAACAAATTATAAT
Found at i:21802258 original size:23 final size:24
Alignment explanation
Indices: 21802207--21802266 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
21802197 TTTTTTTCAT
*
21802207 ATTTTTATTTTTAAACAAATTATA
1 ATTTTTATTTTTAAACAAAATATA
21802231 ATTTTTATTTTTAAA-AAAATAT-
1 ATTTTTATTTTTAAACAAAATATA
*
21802253 TTTTTTAATTTTTA
1 ATTTTT-ATTTTTA
21802267 TGTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 5 0.15
23 13 0.39
24 15 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTATTTTTAAACAAAATATA
Found at i:21811016 original size:18 final size:18
Alignment explanation
Indices: 21810965--21811030 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
21810955 TTAGAATTTT
*
21810965 TTTTGAAATTTTTAT-AA
1 TTTTGAAATATTTATAAA
* * *
21810982 -TTTAAAAAATATATAAA
1 TTTTGAAATATTTATAAA
21810999 TTTTGAAATATTTATAAA
1 TTTTGAAATATTTATAAA
*
21811017 TATTTTAAAT-TTTA
1 T-TTTGAAATATTTA
21811031 AAAAGTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
16 10 0.26
17 2 0.05
18 19 0.50
19 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTTGAAATATTTATAAA
Found at i:21811070 original size:21 final size:20
Alignment explanation
Indices: 21810998--21811061 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
21810988 AAATATATAA
* *
21810998 ATTTTGAAATATTTATAAA-T
1 ATTTT-AAATTTTTAAAAAGT
21811018 ATTTTAAA-TTTTAAAAAGT
1 ATTTTAAATTTTTAAAAAGT
*
21811037 ATTTTAAATTTTTAAAAATT
1 ATTTTAAATTTTTAAAAAGT
21811057 ATTTT
1 ATTTT
21811062 GTAATTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 7 0.18
19 12 0.31
20 20 0.51
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTAAATTTTTAAAAAGT
Found at i:21814142 original size:26 final size:27
Alignment explanation
Indices: 21814090--21814148 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
21814080 ATTGAGAATG
** *
21814090 AAAAAAAGAAAGTAAAATGTTATTAAA
1 AAAAAAAGAAAGTAAAATGAAAGTAAA
*
21814117 AAAAAAAGAAAG-AAAGTGAAAGTAAA
1 AAAAAAAGAAAGTAAAATGAAAGTAAA
21814143 AAAAAA
1 AAAAAA
21814149 GTAATTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (27 bp):
AAAAAAAGAAAGTAAAATGAAAGTAAA
Found at i:21817483 original size:30 final size:28
Alignment explanation
Indices: 21817449--21817505 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
21817439 CGTTATTTCA
* *
21817449 GCCTAGTCTCGTAAATTTTTTAAAAAAATG
1 GCCTAATCTCGT-AA-TTTTAAAAAAAATG
*
21817479 GCCTAATCTGGTAATTTTAAAAAAAAT
1 GCCTAATCTCGTAATTTTAAAAAAAAT
21817506 CAGTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.50
29 2 0.08
30 10 0.42
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (28 bp):
GCCTAATCTCGTAATTTTAAAAAAAATG
Found at i:21817515 original size:18 final size:18
Alignment explanation
Indices: 21817492--21817527 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21817482 TAATCTGGTA
21817492 ATTTTAAAAAAAATCAGT
1 ATTTTAAAAAAAATCAGT
* *
21817510 ATTTTAAAGAAATTCAGT
1 ATTTTAAAAAAAATCAGT
21817528 CCATCTGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (18 bp):
ATTTTAAAAAAAATCAGT
Found at i:21822473 original size:116 final size:116
Alignment explanation
Indices: 21822268--21822518 Score: 412
Period size: 116 Copynumber: 2.2 Consensus size: 116
21822258 AACCTAAACA
*
21822268 CCTCAAGCCCTAAGGCTCCTCGTCGTGTATTCTTGAAAACCAATACTTCATATTTAAAGGGAGTT
1 CCTCAAGCCCCAAGGCTCCTCGTCGTGTATTCTTGAAAACCAATACTTCATATTTAAAGGGAGTT
*
21822333 CAATTAGTTAACGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
66 CAAGTAGTTAACGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
* * * * *
21822384 CCTCAAGCCCCAAGGCTCCTTGTCGTGTATTCTTGAAAGCTAGTACTTCATATTTAAGGGGAGTT
1 CCTCAAGCCCCAAGGCTCCTCGTCGTGTATTCTTGAAAACCAATACTTCATATTTAAAGGGAGTT
* *
21822449 CAAGTAGTTAAGGAAAACTGTAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
66 CAAGTAGTTAACGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
21822500 CCTCAAGCCCTCAAGGCTC
1 CCTCAAGCCC-CAAGGCTC
21822519 TTCATCAACA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
116 117 0.94
117 8 0.06
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (116 bp):
CCTCAAGCCCCAAGGCTCCTCGTCGTGTATTCTTGAAAACCAATACTTCATATTTAAAGGGAGTT
CAAGTAGTTAACGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
Found at i:21822883 original size:36 final size:36
Alignment explanation
Indices: 21822842--21822913 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
21822832 CGAAAGTAAT
* *
21822842 CAAATTTATTGAAAGGCTAATATGCCATCTATCAAG
1 CAAATTGATTGAAAGACTAATATGCCATCTATCAAG
*
21822878 CAAATTGATTGAAAGACTAATATGCCGTCTATCAAG
1 CAAATTGATTGAAAGACTAATATGCCATCTATCAAG
21822914 TCTAGAGGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (36 bp):
CAAATTGATTGAAAGACTAATATGCCATCTATCAAG
Found at i:21827391 original size:17 final size:17
Alignment explanation
Indices: 21827371--21827408 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21827361 AAAAGAGTCT
21827371 GCCAAGCCCTAGAGTTC
1 GCCAAGCCCTAGAGTTC
* *
21827388 GCC-AGCCTTAGAGTTT
1 GCCAAGCCCTAGAGTTC
21827404 GCCAA
1 GCCAA
21827409 ATGGTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (17 bp):
GCCAAGCCCTAGAGTTC
Done.