Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 27
Found at i:948225 original size:73 final size:72
Alignment explanation
Indices: 948065--948391 Score: 285
Period size: 73 Copynumber: 4.5 Consensus size: 72
948055 TTTTGACAAA
* * * *
948065 ATATAATATATAATTTTCAAAAAACGATTTTCGAAAATTTATATATTATATAGTTTTTTAAAATA
1 ATATAATATATAGTTTT--AAAAAC-ATTTTTGAAAAATTATATATTATATA-ATTTTTAAAATA
* **
948130 TTTTAAAAAAG
62 TTTGAAAAATT
* *
948141 ATATAATATATAGTTTTGAAAACA-TTTTGAAAACATTTATATATTATATAATTTTTAAAACATT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAA-A-TTATATATTATATAATTTTTAAAATATT
*
948205 TGAAAACTT
64 TGAAAAATT
* * * * * * *
948214 ATATAGTATATAATTTTTAAAACATTTTTGAAAAATTATATAATGTAT-AGTTTAAAAATATTTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATATTATATAATTTTTAAAATA--TT
948278 TGAAAAATT
64 TGAAAAATT
* * *
948287 ATATAATATATAGTTTTAAAAACATTTTTG-AAAACT-TATA-TA-ATAATTTTAAAACATTTTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATATTATATAATTTTTAAA-A--TAT
*
948348 TTG-AAAACT
63 TTGAAAAATT
*
948357 ATAAAATATATAGTTTTAAAAA-ACTTTTT-AAAAAT
1 ATATAATATATAGTTTTAAAAACA-TTTTTGAAAAAT
948392 ATAATGTATA
Statistics
Matches: 211, Mismatches: 29, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
69 3 0.01
70 44 0.21
71 18 0.09
72 24 0.11
73 78 0.37
74 28 0.13
76 16 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (72 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATATTATATAATTTTTAAAATATTTG
AAAAATT
Found at i:948244 original size:37 final size:37
Alignment explanation
Indices: 948065--948443 Score: 265
Period size: 36 Copynumber: 10.4 Consensus size: 37
948055 TTTTGACAAA
* *
948065 ATATAATATATAATTTTCAAAAAACGATTTTCGAAAATTT
1 ATATAATATATAATTTT--AAAAAC-ATTTTTGAAAACTT
* * ** ***
948105 ATATATTATATAGTTTTTTAAA-ATATTTT-AAAAAAG
1 ATATAATATATAATTTTAAAAACAT-TTTTGAAAACTT
* *
948141 ATATAATATATAGTTTTGAAAACA-TTTTGAAAACATTT
1 ATATAATATATAATTTTAAAAACATTTTTGAAAAC--TT
* *
948179 ATATATTATATAATTTTTAAAACA--TTTGAAAACTT
1 ATATAATATATAATTTTAAAAACATTTTTGAAAACTT
* * *
948214 ATATAGTATATAATTTTTAAAACATTTTTGAAAAATT
1 ATATAATATATAATTTTAAAAACATTTTTGAAAACTT
* * * *
948251 ATATAATGTAT-AGTTTAAAAATATTTTTGAAAAATT
1 ATATAATATATAATTTTAAAAACATTTTTGAAAACTT
*
948287 ATATAATATATAGTTTTAAAAACATTTTTGAAAAC-T
1 ATATAATATATAATTTTAAAAACATTTTTGAAAACTT
948323 -TAT-ATA-ATAATTTT-AAAACATTTTTTTGAAAAC-T
1 ATATAATATATAATTTTAAAAACA--TTTTTGAAAACTT
* *
948357 ATAAAATATATAGTTTTAAAAA-ACTTTTT-AAAA---
1 ATATAATATATAATTTTAAAAACA-TTTTTGAAAACTT
* * * *
948390 ATATAATGTATAGTTTAAACAAAATATTTTTGAAATAC--
1 ATATAATATATAATTT-TA-AAAACATTTTTGAAA-ACTT
*
948428 ATATATTATATAATTT
1 ATATAATATATAATTT
948444 ATAATATTTT
Statistics
Matches: 280, Mismatches: 39, Indels: 42
0.78 0.11 0.12
Matches are distributed among these distances:
32 6 0.02
33 21 0.08
34 16 0.06
35 47 0.17
36 74 0.26
37 60 0.21
38 41 0.15
40 15 0.05
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAATATATAATTTTAAAAACATTTTTGAAAACTT
Found at i:948465 original size:14 final size:15
Alignment explanation
Indices: 948448--948481 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
948438 TAATTTATAA
948448 TATTTT-TATTTATT
1 TATTTTCTATTTATT
948462 TATTTTCTATTTATT
1 TATTTTCTATTTATT
*
948477 AATTT
1 TATTT
948482 ATTTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTCTATTTATT
Found at i:956325 original size:18 final size:17
Alignment explanation
Indices: 956311--956359 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
956301 AATAAAAAGG
956311 GCAAAAAGAAAAAAAAA
1 GCAAAAAGAAAAAAAAA
*
956328 GCAAAAAAAAAGCAAAAAA
1 GCAAAAAGAAA--AAAAAA
956347 G-AAAAA-AAAAAAA
1 GCAAAAAGAAAAAAA
956360 GAAAAAGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
17 13 0.45
18 5 0.17
19 7 0.24
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (17 bp):
GCAAAAAGAAAAAAAAA
Found at i:956328 original size:19 final size:19
Alignment explanation
Indices: 956304--956376 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
956294 TAATCAGAAT
956304 AAAAAGGGCAAAAAGAAAA-
1 AAAAAGGGCAAAAA-AAAAG
956323 AAAAA--GCAAAAAAAAAG
1 AAAAAGGGCAAAAAAAAAG
***
956340 CAAAAAAGAAAAAAAAAAAAG
1 --AAAAAGGGCAAAAAAAAAG
956361 AAAAAGGGACAAAAAA
1 AAAAAGGG-CAAAAAA
956377 CACATGCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
16 4 0.09
17 7 0.16
19 16 0.37
20 6 0.14
21 10 0.23
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGGGCAAAAAAAAAG
Found at i:956333 original size:11 final size:10
Alignment explanation
Indices: 956313--956365 Score: 72
Period size: 10 Copynumber: 5.1 Consensus size: 10
956303 TAAAAAGGGC
956313 AAAAAGAAAA
1 AAAAAGAAAA
956323 AAAAAGCAAAA
1 AAAAAG-AAAA
956334 AAAAAGCAAAA
1 AAAAAG-AAAA
956345 AAGAAA-AAAA
1 AA-AAAGAAAA
956355 AAAAAGAAAA
1 AAAAAGAAAA
956365 A
1 A
956366 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.08
10 17 0.43
11 17 0.43
12 3 0.08
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:956337 original size:13 final size:14
Alignment explanation
Indices: 956319--956366 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 14
956309 GGGCAAAAAG
956319 AAAA-AAAAAGC--
1 AAAAGAAAAAGCAA
956330 AAAA-AAAAAGCAA
1 AAAAGAAAAAGCAA
*
956343 AAAAGAAAAA-AAA
1 AAAAGAAAAAGCAA
956356 AAAAGAAAAAG
1 AAAAGAAAAAG
956367 GGACAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.34
13 16 0.50
14 5 0.16
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGCAA
Found at i:956376 original size:30 final size:29
Alignment explanation
Indices: 956304--956376 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
956294 TAATCAGAAT
956304 AAAAAGGGC-AAAAAGAAAAAAAAAGCAAA
1 AAAAAGGGCAAAAAAGAAAAAAAAA-CAAA
*
956333 AAAAA-AGCAAAAAAGAAAAAAAAA-AAA
1 AAAAAGGGCAAAAAAGAAAAAAAAACAAA
956360 GAAAAAGGGACAAAAAA
1 -AAAAAGGG-CAAAAAA
956377 CACATGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.08
28 7 0.18
29 21 0.55
30 7 0.18
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (29 bp):
AAAAAGGGCAAAAAAGAAAAAAAAACAAA
Found at i:956964 original size:21 final size:22
Alignment explanation
Indices: 956927--956969 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
956917 AGCTACCCCA
956927 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
956949 TCAAACCTTT-AGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
956970 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:956975 original size:22 final size:22
Alignment explanation
Indices: 956928--956975 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
956918 GCTACCCCAT
*
956928 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGA
956950 CAAACCTTT-AGCATCAAATGAA
1 CAAACCTTTGAGCATCAAATG-A
956972 CAAA
1 CAAA
956976 AATGCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:958026 original size:36 final size:36
Alignment explanation
Indices: 957910--958041 Score: 160
Period size: 36 Copynumber: 3.7 Consensus size: 36
957900 AACATAAACA
* * *
957910 TTGAAACA-TTTCCCTTGAAATAAATTTCGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
* *
957945 TTGAGATAGTTTCCCTTGGAACTAAGTTTT-GTCTCTC
1 TTGAGACAGTTTCCCTTGAAAC-AA-TTTTCGTCTCTC
* * *
957982 TTAAGACAGTTTCTCTTGAAACAATTTTCGTCTATC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
958018 TTGAGACAGTTTCCCTTGAAACAA
1 TTGAGACAGTTTCCCTTGAAACAA
958042 AACCTTTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
35 10 0.12
36 41 0.51
37 27 0.33
38 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
Found at i:958135 original size:67 final size:68
Alignment explanation
Indices: 958017--958173 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
958007 TTTCGTCTAT
* **
958017 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
958078 CTCC
66 -TCC
* * *
958082 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
958147 TCC
66 TCC
* *
958150 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
958174 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:959242 original size:105 final size:105
Alignment explanation
Indices: 958817--959539 Score: 1149
Period size: 105 Copynumber: 7.0 Consensus size: 105
958807 GCACTCGAGG
* * ** *
958817 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
958882 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
958923 CAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
958987 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
959027 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
959089 ACAAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
959129 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
959194 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * **
959234 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
959299 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
959339 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
959404 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
959444 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
959504 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
959540 TGAACAATGC
Statistics
Matches: 583, Mismatches: 30, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
100 36 0.06
101 1 0.00
102 99 0.17
103 2 0.00
104 86 0.15
105 335 0.57
106 24 0.04
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:960694 original size:12 final size:11
Alignment explanation
Indices: 960677--960715 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
960667 TTATTATGGA
960677 TATTTTATTCAT
1 TATTTTATT-AT
960689 TATTTTATTAT
1 TATTTTATTAT
*
960700 TCATGTTATTAT
1 T-ATTTTATTAT
960712 TATT
1 TATT
960716 ATGTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:960701 original size:15 final size:17
Alignment explanation
Indices: 960677--960717 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
960667 TTATTATGGA
960677 TATT-TTATTCA-TTAT
1 TATTATTATTCAGTTAT
960692 T-TTATTATTCATGTTAT
1 TATTATTATTCA-GTTAT
960709 TATTATTAT
1 TATTATTAT
960718 GTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 8 0.36
17 5 0.23
18 7 0.32
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTATTATTCAGTTAT
Found at i:965222 original size:2 final size:2
Alignment explanation
Indices: 965215--965243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
965205 AACCATAATC
965215 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
965244 GCAAAAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:967933 original size:13 final size:12
Alignment explanation
Indices: 967887--967935 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
967877 TTTTAATATT
*
967887 TATCGGGTCGGG
1 TATCGGGGCGGG
*
967899 TATCGGGTCGGG
1 TATCGGGGCGGG
*
967911 TATTGGGGCGGG
1 TATCGGGGCGGG
967923 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
967936 GATTACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.10, C:0.14, G:0.53, T:0.22
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:968009 original size:36 final size:36
Alignment explanation
Indices: 967957--968037 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
967947 CAGTTCCCGG
*
967957 CCCCATTTAGCATAAACAGTTTTTCCCCGTCCCCAT
1 CCCCGTTTAGCATAAACAGTTTTTCCCCGTCCCCAT
* * *
967993 CCCCGTTTAGCATAAACGGTTTTTCTCCGTCCCCGT
1 CCCCGTTTAGCATAAACAGTTTTTCCCCGTCCCCAT
968029 CCCCGTTTA
1 CCCCGTTTA
968038 TTCGATTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.32
Consensus pattern (36 bp):
CCCCGTTTAGCATAAACAGTTTTTCCCCGTCCCCAT
Found at i:968180 original size:23 final size:23
Alignment explanation
Indices: 968154--968197 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
968144 AAAACATGTC
968154 AAAA-AAAGAAAGAAAACGTGCCA
1 AAAAGAAAG-AAGAAAACGTGCCA
* *
968177 AAAAGACAGATGAAAACGTGC
1 AAAAGAAAGAAGAAAACGTGC
968198 AACACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.07
Consensus pattern (23 bp):
AAAAGAAAGAAGAAAACGTGCCA
Found at i:969708 original size:27 final size:28
Alignment explanation
Indices: 969668--969722 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
969658 AAATTTTAAA
969668 AATTATATTGAAA-TAAAAAACATTCTC
1 AATTATATTGAAATTAAAAAACATTCTC
* *
969695 AATTATAGTT-AAATTACAAAATATTCTC
1 AATTATA-TTGAAATTAAAAAACATTCTC
969723 TATGCTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (28 bp):
AATTATATTGAAATTAAAAAACATTCTC
Found at i:975803 original size:12 final size:12
Alignment explanation
Indices: 975774--975818 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
975764 CTCGAGACTC
975774 GAGCTCGA--TT
1 GAGCTCGATTTT
975784 GAAGCTCGATTTT
1 G-AGCTCGATTTT
975797 GAGCTCGATTTT
1 GAGCTCGATTTT
975809 GAGCTCGATT
1 GAGCTCGATT
975819 CAAGCTCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 7 0.22
12 21 0.66
13 3 0.09
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:975834 original size:17 final size:17
Alignment explanation
Indices: 975812--975850 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
975802 CGATTTTGAG
*
975812 CTCGATTCAAGCTCGAA
1 CTCGATTAAAGCTCGAA
975829 CTCGATTAAAGCTCGAA
1 CTCGATTAAAGCTCGAA
975846 CTCGA
1 CTCGA
975851 ATTTGATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (17 bp):
CTCGATTAAAGCTCGAA
Found at i:975844 original size:11 final size:12
Alignment explanation
Indices: 975775--975827 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
975765 TCGAGACTCG
*
975775 AGCTCGA-TTGA
1 AGCTCGATTTTA
*
975786 AGCTCGATTTTG
1 AGCTCGATTTTA
*
975798 AGCTCGATTTTG
1 AGCTCGATTTTA
*
975810 AGCTCGA-TTCA
1 AGCTCGATTTTA
975821 AGCTCGA
1 AGCTCGA
975828 ACTCGATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (12 bp):
AGCTCGATTTTA
Found at i:976151 original size:22 final size:22
Alignment explanation
Indices: 976121--976179 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
976111 GGCATAACTT
*
976121 AAACCCTAACACATAAACCCTA
1 AAACTCTAACACATAAACCCTA
*
976143 AAACTCTAA-ATCCTAAACCCTA
1 AAACTCTAACA-CATAAACCCTA
* *
976165 AACCT-TATCACATAA
1 AAACTCTAACACATAA
976180 TTAGTTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACTCTAACACATAAACCCTA
Found at i:977333 original size:41 final size:41
Alignment explanation
Indices: 977300--977723 Score: 401
Period size: 41 Copynumber: 10.4 Consensus size: 41
977290 AATACTTGTT
* * * *
977300 CTTTAGTGGCGTTTTTATATAAACACCGCTAAAT-TCTGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * **
977340 CTTTAGTGGCGTTTTTGTATAAACGCCGCTAAATA-ATGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * * **
977380 CTTTAGTGGCGCTTTTGTATAAACGCCGCTAAATA-ATGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * *
977420 CTTTAGTAGCG-TTTTATGCACAAACGCCGCTAAATGA-TCATA
1 CTTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAAT-ACCCGTA
* * **
977462 CTTTAGTGGCGTTTTTGTATAAACGCCGCTAAATA-CTTTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * * ** *
977502 CTTTAGTGGCGTTTTAAGTACAAACGCCGCCAAAGAGTCATA
1 CTTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATACCCGTA
* * * *
977544 CTTTAGTGGTGTTTCTAAACAAACGCCGCTAAATACCCATA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * *
977585 CTTTAGTGGCGTTTTTATACAAACGCCTCCAAAGACCCGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * * **
977626 CTTTCGTGGCGTTTTTATACAAACACCGCCAAAGGCCCGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
* * *
977667 CTTTAATGGCGTTTTTATACAAACGCCGCCAAAGACCCGTA
1 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
977708 CTTTAGTGGCGTTTTT
1 CTTTAGTGGCGTTTTT
977724 TGAATAAACG
Statistics
Matches: 329, Mismatches: 48, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
39 5 0.02
40 103 0.31
41 187 0.57
42 29 0.09
43 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTA
Found at i:979878 original size:23 final size:23
Alignment explanation
Indices: 979851--979894 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
979841 TTTATATATT
979851 TTTTAATAATTATTTATTTAATC
1 TTTTAATAATTATTTATTTAATC
* *
979874 TTTTAATATTTATTTTTTTAA
1 TTTTAATAATTATTTATTTAA
979895 CCTTAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTAATAATTATTTATTTAATC
Found at i:982259 original size:21 final size:20
Alignment explanation
Indices: 982216--982265 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
982206 TAGCGGGTTT
*
982216 AAAATGCCGCTATAGAGCTA
1 AAAAAGCCGCTATAGAGCTA
982236 AAAAAGCCGCTATAGAGCTA
1 AAAAAGCCGCTATAGAGCTA
982256 AAAAACGCCG
1 AAAAA-GCCG
982266 TTAAAAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (20 bp):
AAAAAGCCGCTATAGAGCTA
Found at i:982689 original size:23 final size:24
Alignment explanation
Indices: 982636--982689 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
982626 CAAAAAATTA
*
982636 TGTCTTTGTGGCACATTTTTTATT
1 TGTCTTTGTGGCACATTTTTCATT
* *
982660 TGCCTTTGTGGTACATTTTTCATT
1 TGTCTTTGTGGCACATTTTTCATT
982684 T-TCTTT
1 TGTCTTT
982690 ATCAGTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (24 bp):
TGTCTTTGTGGCACATTTTTCATT
Found at i:983857 original size:21 final size:22
Alignment explanation
Indices: 983831--983872 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
983821 TAGGTATATT
*
983831 ATTTTTTATT-TAAATAATTAA
1 ATTTTTTATTCAAAATAATTAA
*
983852 ATTTTTTGTTCAAAATAATTA
1 ATTTTTTATTCAAAATAATTA
983873 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTTTATTCAAAATAATTAA
Found at i:986116 original size:45 final size:45
Alignment explanation
Indices: 986052--986143 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
986042 TTGTTCCAGA
986052 TTTACTTTGAAAGCTTTTCATAAGATGCAATGTGGTCAATTGAAT
1 TTTACTTTGAAAGCTTTTCATAAGATGCAATGTGGTCAATTGAAT
986097 TTTACTTTGAAAGCTTTTCATAAGATGCAATGTGGTCAATTGAAT
1 TTTACTTTGAAAGCTTTTCATAAGATGCAATGTGGTCAATTGAAT
986142 TT
1 TT
986144 CCGACCTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (45 bp):
TTTACTTTGAAAGCTTTTCATAAGATGCAATGTGGTCAATTGAAT
Found at i:986402 original size:50 final size:50
Alignment explanation
Indices: 986330--986430 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
986320 CATATTATTA
986330 TAGTATGATGCTGCATAAGGGAAGGTCTGTCTTGATTTGCATCTTAGTAT
1 TAGTATGATGCTGCATAAGGGAAGGTCTGTCTTGATTTGCATCTTAGTAT
986380 TAGTATGATGCTGCATAAGGGAAGGTCTGTCTTGATTTGCATCTTAGTAT
1 TAGTATGATGCTGCATAAGGGAAGGTCTGTCTTGATTTGCATCTTAGTAT
986430 T
1 T
986431 TGCCTCAAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.39
Consensus pattern (50 bp):
TAGTATGATGCTGCATAAGGGAAGGTCTGTCTTGATTTGCATCTTAGTAT
Found at i:989697 original size:16 final size:17
Alignment explanation
Indices: 989660--989697 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
989650 GTAGACCAAA
989660 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
989677 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
989693 TTTTT
1 TTTTT
989698 AAAAAGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:992140 original size:32 final size:31
Alignment explanation
Indices: 992094--992155 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
992084 GACAACCACT
*
992094 AAATGAAAAGATTAGCATGTTTATATATAAGA
1 AAATAAAAAGATTAGCATGTTTAT-TATAAGA
992126 AAATAAAAAGATTAGCATGTTTATTATAAG
1 AAATAAAAAGATTAGCATGTTTATTATAAG
992156 CAACCCTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.21
32 23 0.79
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (31 bp):
AAATAAAAAGATTAGCATGTTTATTATAAGA
Found at i:994961 original size:122 final size:123
Alignment explanation
Indices: 994744--994989 Score: 485
Period size: 122 Copynumber: 2.0 Consensus size: 123
994734 AATGTTGGTG
994744 CTTCAGAAGAATTCTTAAAATGAGGCCTGATGTATCACATTTATTTGCTGGCCCTGGTTGCGACC
1 CTTCAGAAGAATTCTTAAAATGAGGCCTGATGTATCACATTTATTTGCTGGCCCTGGTTGCGACC
994809 TTAGCATTAGGAGTATATGGGAGGATTTATGCATACATGGTCTTAA-GTTCCTTGGCA
66 TTAGCATTAGGAGTATATGGGAGGATTTATGCATACATGGTCTTAAGGTTCCTTGGCA
994866 CTTCAGAAGAATTCTTAAAATGAGGCCTGATGTATCACATTTATTTGCTGGCCCTGGTTGCGACC
1 CTTCAGAAGAATTCTTAAAATGAGGCCTGATGTATCACATTTATTTGCTGGCCCTGGTTGCGACC
994931 TTAGCATTAGGAGTATATGGGAGGATTTATGCATACATGGTCTTAAGGTTCCTTGGCA
66 TTAGCATTAGGAGTATATGGGAGGATTTATGCATACATGGTCTTAAGGTTCCTTGGCA
994989 C
1 C
994990 AAGTTGGTCT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 111 0.90
123 12 0.10
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (123 bp):
CTTCAGAAGAATTCTTAAAATGAGGCCTGATGTATCACATTTATTTGCTGGCCCTGGTTGCGACC
TTAGCATTAGGAGTATATGGGAGGATTTATGCATACATGGTCTTAAGGTTCCTTGGCA
Found at i:999965 original size:19 final size:19
Alignment explanation
Indices: 999941--999983 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
999931 AGTTTCAACA
999941 GTGACCGAATAACATTAGG
1 GTGACCGAATAACATTAGG
999960 GTGACCGAATAACATTAGG
1 GTGACCGAATAACATTAGG
999979 GTGAC
1 GTGAC
999984 TGAAAAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (19 bp):
GTGACCGAATAACATTAGG
Found at i:1003426 original size:30 final size:31
Alignment explanation
Indices: 1003383--1003452 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1003373 ACCACCACTC
* *
1003383 ATGTAATTATATTTTCTAAT-GTTTCAATTT
1 ATGTAATTTTATTTTCTAATAGTTTCAATTA
* **
1003413 ATGTTATTTTATTTTCTTTTAGTTTCAATTA
1 ATGTAATTTTATTTTCTAATAGTTTCAATTA
*
1003444 ATGTGATTT
1 ATGTAATTT
1003453 CAACTTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (31 bp):
ATGTAATTTTATTTTCTAATAGTTTCAATTA
Found at i:1003922 original size:13 final size:13
Alignment explanation
Indices: 1003904--1003968 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
1003894 GTCATAAATC
*
1003904 TATGACGCGCATT
1 TATGACACGCATT
1003917 TATGACACGCATT
1 TATGACACGCATT
* *
1003930 TATGACTCACATT
1 TATGACACGCATT
* *
1003943 TATGTCTCGCATT
1 TATGACACGCATT
1003956 TATGACACGCATT
1 TATGACACGCATT
1003969 GAGCGTCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:1004045 original size:85 final size:85
Alignment explanation
Indices: 1003940--1004100 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 85
1003930 TATGACTCAC
* * * * *
1003940 ATTTATGTCTCGCATTTATGACACGCATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATGTATGACACACATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAAACGA
*
1004005 CACGCATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
** * * ** ** *
1004025 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGTTCTTGTCATAAATGAAGACGA
1 ATTTATGACACGCATGTATGACACACATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAAACGA
1004090 CACACATTTGT
66 CACACATTTGT
1004101 ATGAATTACA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACACACATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAAACGA
CACACATTTGTGTGTCATAA
Found at i:1004147 original size:2 final size:2
Alignment explanation
Indices: 1004140--1004185 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1004130 TTTCGTAAAT
*
1004140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1004182 TA TA
1 TA TA
1004186 AGCAATCCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1009978 original size:117 final size:118
Alignment explanation
Indices: 1009772--1010006 Score: 463
Period size: 117 Copynumber: 2.0 Consensus size: 118
1009762 ATTGAGACAA
1009772 ATAATGTGGTTATTTACATAAATTTTTAAAATTTTAAGATAATTGAATATTCATAAAAAAGGGTC
1 ATAATGTGGTTATTTACATAAATTTTTAAAATTTTAAGATAATTGAATATTCATAAAAAAGGGTC
1009837 CCCACGTTAAAGAAGATAAGAGACTTGTACGAAAAAGATTATC-ATTGATATT
66 CCCACGTTAAAGAAGATAAGAGACTTGTACGAAAAAGATTATCAATTGATATT
1009889 ATAATGTGGTTATTTACATAAATTTTTAAAATTTTAAGATAATTGAATATTCATAAAAAAGGGTC
1 ATAATGTGGTTATTTACATAAATTTTTAAAATTTTAAGATAATTGAATATTCATAAAAAAGGGTC
1009954 CCCACGTTAAAGAAGATAAGAGACTTGTACGAAAAAGATTATCAATTGATATT
66 CCCACGTTAAAGAAGATAAGAGACTTGTACGAAAAAGATTATCAATTGATATT
1010007 TCTGCAGGAT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 108 0.92
118 9 0.08
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (118 bp):
ATAATGTGGTTATTTACATAAATTTTTAAAATTTTAAGATAATTGAATATTCATAAAAAAGGGTC
CCCACGTTAAAGAAGATAAGAGACTTGTACGAAAAAGATTATCAATTGATATT
Found at i:1013245 original size:22 final size:22
Alignment explanation
Indices: 1013218--1013265 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1013208 TACCTAAAAT
* * *
1013218 AATAAAAATATTATTTTTATTA
1 AATAAAAATAATAATTTAATTA
1013240 AATAAAAATAATAATTTAATTA
1 AATAAAAATAATAATTTAATTA
1013262 AATA
1 AATA
1013266 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAAATAATAATTTAATTA
Found at i:1017312 original size:13 final size:13
Alignment explanation
Indices: 1017296--1017323 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1017286 AATTAAATTC
1017296 GTTAATGTTCTTA
1 GTTAATGTTCTTA
1017309 GTTAATGTTCTTA
1 GTTAATGTTCTTA
1017322 GT
1 GT
1017324 ATAAAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.54
Consensus pattern (13 bp):
GTTAATGTTCTTA
Found at i:1022878 original size:30 final size:30
Alignment explanation
Indices: 1022842--1022902 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1022832 AACCCTAAAT
1022842 TCAAAAAAAATTACAAAAATTCATATGTTC
1 TCAAAAAAAATTACAAAAATTCATATGTTC
1022872 TCAAAAAAAATTACAAAAATTCATATGTTC
1 TCAAAAAAAATTACAAAAATTCATATGTTC
1022902 T
1 T
1022903 GTCAAAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.31
Consensus pattern (30 bp):
TCAAAAAAAATTACAAAAATTCATATGTTC
Found at i:1029520 original size:2 final size:2
Alignment explanation
Indices: 1029513--1029556 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1029503 GCATACAATA
1029513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1029554 AT A
1 AT A
1029557 ATAGGGTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1029888 original size:27 final size:27
Alignment explanation
Indices: 1029858--1029943 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1029848 GAGCCATACG
1029858 AGTGCGAGCCATGCGAGGTGGCCATGC
1 AGTGCGAGCCATGCGAGGTGGCCATGC
*** * * * *
1029885 AGTG-GAATAGATGCATACG-AGCCATAC
1 AGTGCG-AGCCATGC-GAGGTGGCCATGC
1029912 GAGTGCGAGCCATGCGAGGTGGCCATGC
1 -AGTGCGAGCCATGCGAGGTGGCCATGC
1029940 AGTG
1 AGTG
1029944 GAATAGAGAG
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 17 0.43
29 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.37, T:0.16
Consensus pattern (27 bp):
AGTGCGAGCCATGCGAGGTGGCCATGC
Found at i:1029905 original size:55 final size:54
Alignment explanation
Indices: 1029841--1029950 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 54
1029831 CGAGGTCCCC
1029841 ATGCTACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCTACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1029895 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGC-TACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1029950 A
1 A
1029951 GAGGTCGTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 4 0.07
55 51 0.93
ACGTcount: A:0.27, C:0.22, G:0.35, T:0.16
Consensus pattern (54 bp):
ATGCTACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
Found at i:1029924 original size:137 final size:135
Alignment explanation
Indices: 1029758--1030025 Score: 486
Period size: 137 Copynumber: 2.0 Consensus size: 135
1029748 GGTTCTCCCC
1029758 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1029823 -TCCCCATGCGAGGTCCCCATGC-TACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
66 CT-CCCATGCGA-GT-CCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG-CATGCA
1029886 GTGGAATAG
127 GTGGAATAG
1029895 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1029960 CTCCCATGCGAGTCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCATGCAGTGG
66 CTCCCATGCGAGTCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCATGCAGTGG
1030025 A
131 A
1030026 TGTGGCCATG
Statistics
Matches: 129, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
135 18 0.14
136 36 0.28
137 74 0.57
138 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.34, T:0.18
Consensus pattern (135 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
CTCCCATGCGAGTCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCATGCAGTGG
AATAG
Found at i:1030037 original size:17 final size:16
Alignment explanation
Indices: 1030011--1030042 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1030001 GCCATGCGAG
1030011 GTGGCATGCAGTGGAT
1 GTGGCATGCAGTGGAT
1030027 GTGGCCATGCAGTGGA
1 GTGG-CATGCAGTGGA
1030043 ATAGGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.22
Consensus pattern (16 bp):
GTGGCATGCAGTGGAT
Found at i:1030270 original size:41 final size:41
Alignment explanation
Indices: 1030225--1030312 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
1030215 GTTATGATTG
*
1030225 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAAATATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
1030266 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
1030307 -TAGTTT
1 TTAGTTT
1030313 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
40 5 0.13
41 23 0.59
42 6 0.15
43 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.44
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:1031157 original size:32 final size:32
Alignment explanation
Indices: 1031121--1031184 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1031111 GGAATCTCTG
1031121 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGCTATGATGCAACGCATGCATGCA
1031153 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGCTATGATGCAACGCATGCATGCA
1031185 GCAGGACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (32 bp):
AGCTATGAGCTATGATGCAACGCATGCATGCA
Found at i:1031255 original size:15 final size:15
Alignment explanation
Indices: 1031235--1031402 Score: 112
Period size: 15 Copynumber: 10.6 Consensus size: 15
1031225 ACCATCCTCC
1031235 CATTCCCACCCCATG
1 CATTCCCACCCCATG
*
1031250 CATTCCCACGCCAATG
1 CATTCCCAC-CCCATG
1031266 CACCATCCCCTCCC-CCCCATG
1 ---CAT----TCCCACCCCATG
1031287 CATTCCCA-CCCATG
1 CATTCCCACCCCATG
1031301 CATTCCCACGTCCCATG
1 CATTCCCAC--CCCATG
* *
1031318 CATCCCCTCCCCATG
1 CATTCCCACCCCATG
*
1031333 CATTCCCATCCCATG
1 CATTCCCACCCCATG
*
1031348 -TTGATCCTC-CCCCATG
1 CAT--TCC-CACCCCATG
1031364 CATT-CCACCCCATG
1 CATTCCCACCCCATG
* *
1031378 CATCCCCTCCCCCATG
1 CATTCCC-ACCCCATG
1031394 CATTCCCAC
1 CATTCCCAC
1031403 GTCCCATGTT
Statistics
Matches: 120, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
13 1 0.01
14 30 0.25
15 31 0.26
16 27 0.22
17 15 0.12
18 3 0.03
19 3 0.03
21 5 0.04
22 1 0.01
23 4 0.03
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (15 bp):
CATTCCCACCCCATG
Found at i:1031293 original size:14 final size:14
Alignment explanation
Indices: 1031276--1031400 Score: 99
Period size: 14 Copynumber: 8.3 Consensus size: 14
1031266 CACCATCCCC
1031276 TCCCCCCCATGCAT
1 TCCCCCCCATGCAT
*
1031290 TCCCACCCATGCAT
1 TCCCCCCCATGCAT
1031304 TCCCACGTCCCATGCAT
1 TCCC-C--CCCATGCAT
*
1031321 CCCCTCCCCATGCAT
1 TCCC-CCCCATGCAT
* *
1031336 TCCCATCCCATG-TT
1 TCCC-CCCCATGCAT
1031350 GATCCTCCCCCATGCAT
1 --TCC-CCCCCATGCAT
*
1031367 TCCACCCCATGCAT
1 TCCCCCCCATGCAT
*
1031381 CCCCTCCCCCATGCAT
1 -TCC-CCCCCATGCAT
1031397 TCCC
1 TCCC
1031401 ACGTCCCATG
Statistics
Matches: 88, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
14 29 0.33
15 25 0.28
16 19 0.22
17 15 0.17
ACGTcount: A:0.16, C:0.53, G:0.08, T:0.23
Consensus pattern (14 bp):
TCCCCCCCATGCAT
Found at i:1031339 original size:46 final size:46
Alignment explanation
Indices: 1031235--1031410 Score: 146
Period size: 46 Copynumber: 3.7 Consensus size: 46
1031225 ACCATCCTCC
*
1031235 CATTCCCACCCCATGCATTCCCACGCCAATGCACCATCCCCTCCCCCCCATG
1 CATTCCCACCCCATGCATTCCCACGCCCATG---CATCCCCT---CCCCATG
1031287 CATTCCCA-CCCATGCATTCCCACGTCCCATGCATCCCCTCCCCATG
1 CATTCCCACCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCATG
* * * *
1031333 CATTCCCATCCCATG-TTGATCCTC-C-CCCATGCAT-TCCACCCCATG
1 CATTCCCACCCCATGCAT--TCC-CACGCCCATGCATCCCCTCCCCATG
* *
1031378 CATCCCCTCCCCCATGCATTCCCACGTCCCATG
1 CATTCCC-ACCCCATGCATTCCCACG-CCCATG
1031411 TTGATTGCTG
Statistics
Matches: 106, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
44 1 0.01
45 19 0.18
46 31 0.29
47 13 0.12
48 4 0.04
49 9 0.08
51 16 0.15
52 13 0.12
ACGTcount: A:0.18, C:0.52, G:0.09, T:0.22
Consensus pattern (46 bp):
CATTCCCACCCCATGCATTCCCACGCCCATGCATCCCCTCCCCATG
Found at i:1031347 original size:30 final size:30
Alignment explanation
Indices: 1031281--1031410 Score: 140
Period size: 30 Copynumber: 4.2 Consensus size: 30
1031271 TCCCCTCCCC
* *
1031281 CCCATGCATTCCCACCCATGCATTCCCACGT
1 CCCATGCATCCCCCCCCATGCATTCCCAC-T
1031312 CCCATGCATCCCCTCCCCATGCATTCCCA-T
1 CCCATGCATCCCC-CCCCATGCATTCCCACT
* *
1031342 CCCATGTTGATCCTCCCCCATGCATT-CCAC-
1 CCCATG--CATCCCCCCCCATGCATTCCCACT
1031372 CCCATGCATCCCCTCCCCCATGCATTCCCACGT
1 CCCATGCAT-CCC-CCCCCATGCATTCCCAC-T
1031405 CCCATG
1 CCCATG
1031411 TTGATTGCTG
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
28 2 0.02
29 2 0.02
30 28 0.33
31 27 0.32
32 19 0.23
33 6 0.07
ACGTcount: A:0.17, C:0.51, G:0.09, T:0.23
Consensus pattern (30 bp):
CCCATGCATCCCCCCCCATGCATTCCCACT
Found at i:1031466 original size:17 final size:17
Alignment explanation
Indices: 1031444--1031476 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1031434 ATGCACGTCC
1031444 CCATGTTGATTGCATGT
1 CCATGTTGATTGCATGT
1031461 CCATGTTGATTGCATG
1 CCATGTTGATTGCATG
1031477 GCCCTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (17 bp):
CCATGTTGATTGCATGT
Found at i:1031531 original size:29 final size:29
Alignment explanation
Indices: 1031498--1031586 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
1031488 TAATACACAC
1031498 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1031527 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1031556 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1031585 AG
1 AG
1031587 ACCACTGTAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:1041787 original size:29 final size:29
Alignment explanation
Indices: 1041745--1041804 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1041735 ATATCGATAT
1041745 TGTTCTTACATTATCGATACTGTCGCTAC
1 TGTTCTTACATTATCGATACTGTCGCTAC
1041774 TGTTCTTACATTATCGATACTGTCGCTAC
1 TGTTCTTACATTATCGATACTGTCGCTAC
1041803 TG
1 TG
1041805 GGTGCCTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (29 bp):
TGTTCTTACATTATCGATACTGTCGCTAC
Found at i:1043686 original size:38 final size:39
Alignment explanation
Indices: 1043634--1043718 Score: 163
Period size: 38 Copynumber: 2.2 Consensus size: 39
1043624 TCTTTCCTAC
1043634 TTAAAAAAATTAAATTACATGTCTTGAATTATGGTTTAA
1 TTAAAAAAATTAAATTACATGTCTTGAATTATGGTTTAA
1043673 TTAAAAAAA-TAAATTACATGTCTTGAATTATGGTTTAA
1 TTAAAAAAATTAAATTACATGTCTTGAATTATGGTTTAA
1043711 TTAAAAAA
1 TTAAAAAA
1043719 GTACTAGATG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 37 0.80
39 9 0.20
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (39 bp):
TTAAAAAAATTAAATTACATGTCTTGAATTATGGTTTAA
Found at i:1047606 original size:15 final size:15
Alignment explanation
Indices: 1047586--1047618 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1047576 TGAGACATTA
1047586 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
1047601 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
1047616 CCC
1 CCC
1047619 ACCCAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.70, G:0.18, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1053248 original size:71 final size:72
Alignment explanation
Indices: 1053128--1053262 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 72
1053118 TTAATAAGTT
*
1053128 TCATTCCTAGATCTTACTCTTCAAGCACATTATAGGCATTTGGG-GAAAAATTAATGAGAACTCT
1 TCATTCCTAGATCTTACTCTTCAAGCACATTATAGGCATTTGGGAAAAAAATTAATGAGAACTCT
1053192 ATGATTG
66 ATGATTG
*
1053199 TCATTCCTA-ATTCTTACTCTTCAAGCACATTATAGGCATTTTGGAAAAAAATTAATGAGAACTC
1 TCATTCCTAGA-TCTTACTCTTCAAGCACATTATAGGCATTTGGGAAAAAAATTAATGAGAACTC
1053263 GATAACATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
70 1 0.02
71 41 0.68
72 18 0.30
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (72 bp):
TCATTCCTAGATCTTACTCTTCAAGCACATTATAGGCATTTGGGAAAAAAATTAATGAGAACTCT
ATGATTG
Found at i:1058119 original size:2 final size:2
Alignment explanation
Indices: 1058112--1058169 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1058102 AATAAGAAAC
* * *
1058112 GA GA GA GA GA AA TA GA GA GA GA GA GA GC GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1058154 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1058170 AAATACCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.50, C:0.02, G:0.47, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1074630 original size:2 final size:2
Alignment explanation
Indices: 1074625--1074673 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1074615 CTTTCCTAGC
*
1074625 AT AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1074665 AT AT AT AT A
1 AT AT AT AT A
1074674 AATGATGCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1075527 original size:24 final size:25
Alignment explanation
Indices: 1075476--1075527 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1075466 ATTTGGGTAC
1075476 TTTGCCCAAAGATAAAAAATAAATT
1 TTTGCCCAAAGATAAAAAATAAATT
1075501 TTTGCCCAAAGATAAAAAATAAATT
1 TTTGCCCAAAGATAAAAAATAAATT
1075526 TT
1 TT
1075528 CGAGAAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTGCCCAAAGATAAAAAATAAATT
Found at i:1083382 original size:24 final size:26
Alignment explanation
Indices: 1083339--1083389 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
1083329 AACAAATCAT
1083339 TATTATTTTATATATGTAATATTAATA
1 TATTATTTTATATA-GTAATATTAATA
*
1083366 TATTATTTTA-ATA-TAATTTTAATA
1 TATTATTTTATATAGTAATATTAATA
1083390 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
26 3 0.13
27 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTATTTTATATAGTAATATTAATA
Found at i:1083528 original size:30 final size:31
Alignment explanation
Indices: 1083492--1083550 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1083482 TTACACTTTT
1083492 ATTTTAATAATATATAATAA-ATTATTAATA
1 ATTTTAATAATATATAATAATATTATTAATA
* * *
1083522 ATTTTAATATTATTTAATAATTTTATTAA
1 ATTTTAATAATATATAATAATATTATTAA
1083551 AAAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTAATAATATATAATAATATTATTAATA
Found at i:1087569 original size:17 final size:17
Alignment explanation
Indices: 1087547--1087593 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
1087537 TAATCCCTCC
*
1087547 ACAAGTGCCACCTTAAT
1 ACAAGTGCCACCCTAAT
1087564 ACAAGTGCCACCCTAAT
1 ACAAGTGCCACCCTAAT
*
1087581 ATAAGTGCCACCC
1 ACAAGTGCCACCC
1087594 CTGGGGCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (17 bp):
ACAAGTGCCACCCTAAT
Found at i:1091890 original size:12 final size:12
Alignment explanation
Indices: 1091865--1091981 Score: 76
Period size: 12 Copynumber: 9.8 Consensus size: 12
1091855 ACGGAGATAT
* *
1091865 CAGAAATCAAAA
1 CAGAATTCAGAA
1091877 CAGAATTCAGAA
1 CAGAATTCAGAA
1091889 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * * *
1091901 CATAATCCATAT
1 CAGAATTCAGAA
*
1091913 CAGAAATCAGAA
1 CAGAATTCAGAA
* *
1091925 CAGAATTCATAT
1 CAGAATTCAGAA
* *
1091937 CAGAAATCCGAA
1 CAGAATTCAGAA
**
1091949 CAGAATTCAGGT
1 CAGAATTCAGAA
*
1091961 CA-TATATCAGAA
1 CAGAAT-TCAGAA
1091973 CAGAATTCA
1 CAGAATTCA
1091982 AGTCGAAAAT
Statistics
Matches: 75, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
11 4 0.05
12 66 0.88
13 5 0.07
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1091892 original size:24 final size:24
Alignment explanation
Indices: 1091863--1091981 Score: 130
Period size: 24 Copynumber: 5.0 Consensus size: 24
1091853 AAACGGAGAT
*
1091863 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * * * *
1091887 AACAGATATTAGAACATAATCCAT
1 ATCAGAAATCAGAACAGAATTCAG
*
1091911 ATCAGAAATCAGAACAGAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
*
1091935 ATCAGAAATCCGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1091959 GTCATATATCAGAACAGAATTCA
1 ATCAGAAATCAGAACAGAATTCA
1091982 AGTCGAAAAT
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1091993 original size:24 final size:24
Alignment explanation
Indices: 1091864--1091995 Score: 110
Period size: 24 Copynumber: 5.5 Consensus size: 24
1091854 AACGGAGATA
*
1091864 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * * * *
1091887 AACAGATATTAGAACATAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
1091912 TCAGAAATCAGAACAGAATTCATA-
1 TCAGAAATCAGAACAGAATTCA-AG
* *
1091936 TCAGAAATCCGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* *
1091960 TCATATATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
1091984 TC-GAAAATCAGA
1 TCAG-AAATCAGA
1091996 TAAAATAATT
Statistics
Matches: 85, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
24 84 0.99
26 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:1093157 original size:18 final size:18
Alignment explanation
Indices: 1093136--1093171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1093126 CTTCCATCCG
*
1093136 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1093154 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1093172 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1094498 original size:18 final size:18
Alignment explanation
Indices: 1094477--1094512 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1094467 TCAACGCCGG
1094477 TCAACGGGTCGGGTAAAC
1 TCAACGGGTCGGGTAAAC
1094495 TCAACGGGTCGGGTAAAC
1 TCAACGGGTCGGGTAAAC
1094513 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (18 bp):
TCAACGGGTCGGGTAAAC
Found at i:1094513 original size:13 final size:13
Alignment explanation
Indices: 1094497--1094521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1094487 GGGTAAACTC
1094497 AACGGGTCGGGTA
1 AACGGGTCGGGTA
1094510 AACGGGTCGGGT
1 AACGGGTCGGGT
1094522 CGGGTCGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1096867 original size:7 final size:7
Alignment explanation
Indices: 1096852--1096895 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1096842 AGTTCTTATA
*
1096852 AAAAATT
1 AAAATTT
1096859 AAAATTT
1 AAAATTT
1096866 AAAATTT
1 AAAATTT
1096873 AAAAGTTAT
1 AAAA-TT-T
1096882 AAAA-TT
1 AAAATTT
1096888 AAAATTT
1 AAAATTT
1096895 A
1 A
1096896 TTTATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 5 0.15
7 21 0.64
8 2 0.06
9 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:1096896 original size:15 final size:15
Alignment explanation
Indices: 1096853--1096896 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1096843 GTTCTTATAA
1096853 AAAATTAAAATTTA-
1 AAAATTAAAATTTAT
* *
1096867 AAATTTAAAAGTTAT
1 AAAATTAAAATTTAT
1096882 AAAATTAAAATTTAT
1 AAAATTAAAATTTAT
1096897 TTATAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
AAAATTAAAATTTAT
Found at i:1097154 original size:23 final size:23
Alignment explanation
Indices: 1097102--1097162 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
1097092 TGGGGGGAAA
1097102 TATATTTTTAATTTTTTAGTAATT
1 TATATTTTTAA-TTTTTAGTAATT
1097126 TA-ATTTTTAA-TTTTAGT-ATT
1 TATATTTTTAATTTTTAGTAATT
* *
1097146 TTTATATTTAAGTTTTT
1 TATATTTTTAA-TTTTT
1097163 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 14 0.44
23 12 0.38
24 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TATATTTTTAATTTTTAGTAATT
Found at i:1097184 original size:17 final size:16
Alignment explanation
Indices: 1097102--1097190 Score: 61
Period size: 15 Copynumber: 5.9 Consensus size: 16
1097092 TGGGGGGAAA
1097102 TATATTTTTAAT-TTTT
1 TATA-TTTTAATATTTT
*
1097118 TAGTAATTT-A-ATTTT
1 TA-TATTTTAATATTTT
*
1097133 TA-ATTTTAGTATTTT
1 TATATTTTAATATTTT
1097148 TATA-TTTAAGT-TTTT
1 TATATTTTAA-TATTTT
*
1097163 T-T-TTTAAATATTTT
1 TATATTTTAATATTTT
1097177 TATATTTTAA-ATTT
1 TATATTTTAATATTT
1097191 AAAATATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
13 5 0.09
14 10 0.18
15 28 0.49
16 12 0.21
17 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TATATTTTAATATTTT
Found at i:1098979 original size:28 final size:28
Alignment explanation
Indices: 1098937--1099006 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
1098927 CTTACATGAA
*
1098937 GAAACATTTGTAATGGAAAGGCAGTTCT
1 GAAACATTTGGAATGGAAAGGCAGTTCT
1098965 GAAACATTTGGAATGGAAAGGCAGTTCT
1 GAAACATTTGGAATGGAAAGGCAGTTCT
1098993 GAAACATTT-GAATG
1 GAAACATTTGGAATG
1099007 TGGATATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 5 0.12
28 36 0.88
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (28 bp):
GAAACATTTGGAATGGAAAGGCAGTTCT
Found at i:1100025 original size:13 final size:13
Alignment explanation
Indices: 1100007--1100032 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1099997 GAAGGAAAAA
1100007 AAACGTCTTCATT
1 AAACGTCTTCATT
1100020 AAACGTCTTCATT
1 AAACGTCTTCATT
1100033 GATAAGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
AAACGTCTTCATT
Found at i:1120814 original size:2 final size:2
Alignment explanation
Indices: 1120809--1120841 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1120799 TAACTTTGTC
1120809 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1120842 TCTTTTCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1129191 original size:13 final size:13
Alignment explanation
Indices: 1129173--1129197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1129163 TATTTATTTT
1129173 TTCTTTTTCTTTA
1 TTCTTTTTCTTTA
1129186 TTCTTTTTCTTT
1 TTCTTTTTCTTT
1129198 CGAAAAGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTA
Found at i:1129324 original size:32 final size:35
Alignment explanation
Indices: 1129260--1129324 Score: 100
Period size: 32 Copynumber: 1.9 Consensus size: 35
1129250 TTAAAAAGGT
*
1129260 TTATATTAACTTTGAGATAATATATATTTTTAAGA
1 TTATATTAACTTTGAGATAAAATATATTTTTAAGA
1129295 TTATATTAA-TTTGA-ATAAAAT-TATTTTTAA
1 TTATATTAACTTTGAGATAAAATATATTTTTAA
1129325 AACAATAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 9 0.31
33 6 0.21
34 5 0.17
35 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (35 bp):
TTATATTAACTTTGAGATAAAATATATTTTTAAGA
Found at i:1131350 original size:21 final size:21
Alignment explanation
Indices: 1131310--1131351 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1131300 ATTATTCTAT
**
1131310 TAAAAGAATTGGTATGTTTAG
1 TAAAAGAATTGGTACATTTAG
*
1131331 TAAAAGATTTGGTACATTTAG
1 TAAAAGAATTGGTACATTTAG
1131352 ACACACCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (21 bp):
TAAAAGAATTGGTACATTTAG
Found at i:1139392 original size:32 final size:33
Alignment explanation
Indices: 1139315--1139460 Score: 145
Period size: 32 Copynumber: 4.2 Consensus size: 33
1139305 TGAAAGTATT
*
1139315 AAAATGATTTTC-AAGTTTGGTAACCA-CCTTTGAA
1 AAAATGATTTTCAAAGTTTGGTAA--ATGCTTTG-A
*
1139349 AAAATGGTTTTCAAAGTTTGGTAAATGCTTTG-
1 AAAATGATTTTCAAAGTTTGGTAAATGCTTTGA
1139381 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGATTTTCAAAGTTTGGTAAATG---CTTTGA
* * *
1139417 AAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTGA
1 AAAAT-GATTTTCAAAGTTTGGTAAATG-CT-TTGA
1139453 AAAATGAT
1 AAAATGAT
1139461 AATGGGATAA
Statistics
Matches: 97, Mismatches: 7, Indels: 15
0.82 0.06 0.13
Matches are distributed among these distances:
32 26 0.27
33 1 0.01
34 16 0.16
35 20 0.21
36 14 0.14
37 20 0.21
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (33 bp):
AAAATGATTTTCAAAGTTTGGTAAATGCTTTGA
Found at i:1139433 original size:37 final size:37
Alignment explanation
Indices: 1139342--1139457 Score: 138
Period size: 37 Copynumber: 3.3 Consensus size: 37
1139332 TGGTAACCAC
*
1139342 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATG---
1 CTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
1139376 CTTTG-AAAAT-GATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* *
1139411 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
1139448 -GTTGAAAAAT
1 CTTTGAAAAAT
1139458 GATAATGGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
32 21 0.29
33 4 0.06
34 5 0.07
35 5 0.07
36 14 0.19
37 23 0.32
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (37 bp):
CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1143975 original size:21 final size:21
Alignment explanation
Indices: 1143951--1144016 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1143941 AACTTTGAAA
1143951 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1143972 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1143986 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1144007 AAATGTTTTT
1 AAATGGTTTT
1144017 TTGAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1144042 original size:37 final size:37
Alignment explanation
Indices: 1143944--1144061 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 37
1143934 GGTAACCAAC
*
1143944 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTTT
1143981 TTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
* *
1144016 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
*
1144052 GTTGAAAAAT
1 TTTGAAAAAT
1144062 GATAATGTGA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.39
36 21 0.28
37 24 0.32
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
Found at i:1149847 original size:2 final size:2
Alignment explanation
Indices: 1149840--1149867 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1149830 GTAACAAAGA
1149840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1149868 TATCATCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1152402 original size:42 final size:43
Alignment explanation
Indices: 1152355--1152470 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
1152345 TTGAATTTTT
* *
1152355 GTGTTTGTTTCACGTAATTTGTTTTTTGAAAAAT-ATTTTCTC
1 GTGTTTGTTTCACGTAATTTGTTTTTCGAAAAATGATTTTCCC
*
1152397 GTGTTTGTTTCACGTAATTTGTTTTTCGAAAAATGTTTTTCCC
1 GTGTTTGTTTCACGTAATTTGTTTTTCGAAAAATGATTTTCCC
* *
1152440 GTGTTTGTTTCACGTAATTGGTTTTCCGAAA
1 GTGTTTGTTTCACGTAATTTGTTTTTCGAAA
1152471 TGTAATTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 33 0.49
43 35 0.51
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (43 bp):
GTGTTTGTTTCACGTAATTTGTTTTTCGAAAAATGATTTTCCC
Found at i:1152694 original size:30 final size:29
Alignment explanation
Indices: 1152660--1152726 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
1152650 TTTTTATTTA
*
1152660 TTAATATTGATAATAATATAAT-ATTATATT
1 TTAATATT-AT-ATAAAATAATAATTATATT
1152690 TTAATATTATATAAAATAATCAATTATATT
1 TTAATATTATATAAAATAAT-AATTATATT
*
1152720 ATAATAT
1 TTAATAT
1152727 AAAGATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 9 0.27
29 2 0.06
30 22 0.67
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TTAATATTATATAAAATAATAATTATATT
Found at i:1152760 original size:51 final size:50
Alignment explanation
Indices: 1152663--1152807 Score: 120
Period size: 51 Copynumber: 2.8 Consensus size: 50
1152653 TTATTTATTA
* *
1152663 ATATTGATAATAATATA-ATATTATATTTTAATATTATATAA-A-ATAATCAATT
1 ATATT-ATAAT-ATAAAGATATTATATTTT-ATTTTA-ATAATATATAAT-AATT
1152715 ATATTATAATATAAAGATATTATATTTTATTTTAATAATATATAATAATT
1 ATATTATAATATAAAGATATTATATTTTATTTTAATAATATATAATAATT
* * * *
1152765 -TTTTATATATTATAATGA-ATAATATTATATATTTAAATAATAT
1 ATATTATA-A-TATAAAGATATTATATT-T-TATTTTAATAATAT
1152808 TTTAATAAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
49 10 0.12
50 22 0.28
51 30 0.38
52 18 0.22
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (50 bp):
ATATTATAATATAAAGATATTATATTTTATTTTAATAATATATAATAATT
Found at i:1152774 original size:56 final size:57
Alignment explanation
Indices: 1152644--1152807 Score: 146
Period size: 56 Copynumber: 3.0 Consensus size: 57
1152634 TTTTCATCAA
* * * *
1152644 AATATTTTTTTATTTATTAATATTGATAATAATATAATATTATATTTTAATATTATAT
1 AATAATTTTTTATATATT-ATAATGATAATAATATAATATTATATTTTAATAATATAT
** ** * *
1152702 AA-AATAATCAATTATATTATAAT-ATAA-AGATATTATATTTTATTTTAATAATATAT
1 AATAATTTTTTA-TATATTATAATGATAATA-ATATAATATTATATTTTAATAATATAT
*
1152758 AATAATTTTTTATATATTATAATG--AATAATAT--TA-TATATTTAAATAATAT
1 AATAATTTTTTATATATTATAATGATAATAATATAATATTATATTTTAATAATAT
1152808 TTTAATAAAG
Statistics
Matches: 85, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
52 14 0.16
53 2 0.02
55 7 0.08
56 42 0.49
57 13 0.15
58 7 0.08
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
AATAATTTTTTATATATTATAATGATAATAATATAATATTATATTTTAATAATATAT
Found at i:1152836 original size:23 final size:23
Alignment explanation
Indices: 1152810--1152854 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1152800 AATAATATTT
1152810 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1152833 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1152855 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1153001 original size:24 final size:24
Alignment explanation
Indices: 1152956--1153001 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1152946 ATTATAAAAA
*
1152956 AATATTTAATAAATAAATTATTTT
1 AATATTTAATAAATAAAATATTTT
*
1152980 AATATTTTA-AAATAATAATATT
1 AATATTTAATAAATAA-AATATT
1153002 AAGTTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTAATAAATAAAATATTTT
Found at i:1153186 original size:14 final size:14
Alignment explanation
Indices: 1153152--1153192 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1153142 AAATATAATT
*
1153152 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
1153166 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
*
1153180 CATTTTCCAGAAA
1 CATTTTCCGGAAA
1153193 TGTAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:1153236 original size:15 final size:15
Alignment explanation
Indices: 1153194--1153239 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1153184 TTCCAGAAAT
1153194 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* **
1153209 -AAATTCAAATTCCA
1 GTAATTCATTTTCCA
1153223 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
1153238 GT
1 GT
1153240 TCCAGTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1153244 original size:21 final size:21
Alignment explanation
Indices: 1153209--1153260 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1153199 TCATTTTCCA
* *
1153209 AAATTCAAATTCCAGTAATTC
1 AAATTCCAGTTCCAGTAATTC
**
1153230 ATTTTCCAGTTCCAGTAATTC
1 AAATTCCAGTTCCAGTAATTC
1153251 AAATTCCAGT
1 AAATTCCAGT
1153261 AATTTATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (21 bp):
AAATTCCAGTTCCAGTAATTC
Found at i:1164498 original size:3 final size:3
Alignment explanation
Indices: 1164490--1164514 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1164480 TCAGTTACGA
1164490 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1164515 TTACAACGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1166380 original size:14 final size:13
Alignment explanation
Indices: 1166339--1166389 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
1166329 AAAATAATAG
*
1166339 TTTAAACATTATACT
1 TTTAAA-ATTA-ATT
1166354 TTTAAAA-TAATT
1 TTTAAAATTAATT
1166366 TTTAAATATTAATT
1 TTTAAA-ATTAATT
1166380 TTATAAAATT
1 TT-TAAAATT
1166390 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 11 0.34
15 10 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTAAAATTAATT
Found at i:1166381 original size:25 final size:27
Alignment explanation
Indices: 1166329--1166391 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1166319 AAAAGAATAA
*
1166329 AAAATAATAGTTTAAACATTATACTTTT
1 AAAATAAT-TTTTAAACATTATACTTTT
*
1166357 AAAATAATTTTTAAATATTA-A-TTTT
1 AAAATAATTTTTAAACATTATACTTTT
*
1166382 ATAA-AATTTT
1 AAAATAATTTT
1166392 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 6 0.19
25 7 0.22
26 1 0.03
27 10 0.31
28 8 0.25
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAATTTTTAAACATTATACTTTT
Found at i:1166397 original size:16 final size:17
Alignment explanation
Indices: 1166372--1166411 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1166362 AATTTTTAAA
*
1166372 TATTAATTTTATAAAAT
1 TATTATTTTTATAAAAT
*
1166389 T-TTATTTTTATTAAAT
1 TATTATTTTTATAAAAT
1166405 TATTATT
1 TATTATT
1166412 GAATCGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTTTTATAAAAT
Found at i:1168178 original size:42 final size:43
Alignment explanation
Indices: 1168132--1168219 Score: 142
Period size: 42 Copynumber: 2.0 Consensus size: 43
1168122 CCATGTGCCC
* *
1168132 ATTAAATCTACCTATCTATGCGTCTCT-CTACTCCATGCAACT
1 ATTAAATCTACCTATCTATGCCTCTCTCCTACTCCACGCAACT
1168174 ATTAAATCTACCTATCTATGCCTCTCTCCCTACTCCACGCAACT
1 ATTAAATCTACCTATCTATGCCTCTCT-CCTACTCCACGCAACT
1168218 AT
1 AT
1168220 ATATACATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 26 0.62
44 16 0.38
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (43 bp):
ATTAAATCTACCTATCTATGCCTCTCTCCTACTCCACGCAACT
Found at i:1169686 original size:21 final size:21
Alignment explanation
Indices: 1169662--1169704 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169652 TATTTGAATT
*
1169662 AATTAATATATACCAAACATA
1 AATTAATAAATACCAAACATA
* *
1169683 AATTTATAAATATCAAACATA
1 AATTAATAAATACCAAACATA
1169704 A
1 A
1169705 TATCAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATACCAAACATA
Found at i:1169721 original size:2 final size:2
Alignment explanation
Indices: 1169714--1169745 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1169704 ATATCAAATA
1169714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1169746 TAAATCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1170743 original size:28 final size:26
Alignment explanation
Indices: 1170703--1170756 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
1170693 TATCTTGAGA
1170703 ATATTCTAAAATAAT-ATAAAAATAAT
1 ATATTCTAAAATAATCAT-AAAATAAT
*
1170729 ATATATCTATAAATATTCATAAAATAAT
1 ATAT-TCTA-AAATAATCATAAAATAAT
1170757 CTAGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 4 0.17
28 14 0.58
29 2 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATTCTAAAATAATCATAAAATAAT
Found at i:1176083 original size:128 final size:129
Alignment explanation
Indices: 1175940--1176181 Score: 398
Period size: 128 Copynumber: 1.9 Consensus size: 129
1175930 TAATATTAAA
* *
1175940 TTATATTTAAATAAATTAAATAATTAATTAATTAAACACGTTATG-TATTATTTCTTATGTATGC
1 TTATATTTAAATAAATTAAAGAATTAATTAATTAAACACGTTA-GATACTATTTCTTATGTATGC
* * *
1176004 TACAT-AAAAACGATACTAGTCAAATTAAATTCAGTTGATAAAATAAAATATTTTAATTTTATGT
65 TACATAAAAAACGATACTAGTCAAACTAAACTCAGTCGATAAAATAAAATATTTTAATTTTATGT
* *
1176068 TTATATTTAAATAAATTAAAGAATTAATTAATTAAACATGTTAGATACTATTTCTTATGTATGTT
1 TTATATTTAAATAAATTAAAGAATTAATTAATTAAACACGTTAGATACTATTTCTTATGTATGCT
1176133 ACATAAAAAACGATACTAGTCAAACTAAACTCAGTCGATAAAATAAAAT
66 ACATAAAAAACGATACTAGTCAAACTAAACTCAGTCGATAAAATAAAAT
1176182 GCTTACAAGT
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
127 1 0.01
128 63 0.60
129 41 0.39
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (129 bp):
TTATATTTAAATAAATTAAAGAATTAATTAATTAAACACGTTAGATACTATTTCTTATGTATGCT
ACATAAAAAACGATACTAGTCAAACTAAACTCAGTCGATAAAATAAAATATTTTAATTTTATGT
Found at i:1182776 original size:28 final size:28
Alignment explanation
Indices: 1182745--1182807 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
1182735 TTAATTTTTC
*
1182745 TTTAATATTTATTATTATAGGCTTATTT
1 TTTAATATTTATTATTAGAGGCTTATTT
1182773 TTTAATATTTATTATTAGAGGCTTATTT
1 TTTAATATTTATTATTAGAGGCTTATTT
1182801 TTATAAT
1 TT-TAAT
1182808 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (28 bp):
TTTAATATTTATTATTAGAGGCTTATTT
Found at i:1183184 original size:34 final size:35
Alignment explanation
Indices: 1183119--1183184 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
1183109 AAAATTTATT
* * * * *
1183119 TTTTTTCAACACTTATTTTTTTTGGATAATTAATA
1 TTTTTCCAACACTTATTTATTATGAACAATTAATA
1183154 TTTTTCCAACACTTA-TTATTATGAACAATTA
1 TTTTTCCAACACTTATTTATTATGAACAATTA
1183185 CTTAAATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
34 12 0.46
35 14 0.54
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.52
Consensus pattern (35 bp):
TTTTTCCAACACTTATTTATTATGAACAATTAATA
Found at i:1188664 original size:29 final size:29
Alignment explanation
Indices: 1188624--1188735 Score: 199
Period size: 29 Copynumber: 3.9 Consensus size: 29
1188614 GTGACAGCAT
1188624 AGGTCGCCATGCACGCCCGGCGTCCT-TA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
1188652 TAGGTCGCCATGCACGCCCGGCGTCCTATA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
*
1188682 AGGTCGCCATGCACGCCTGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
1188711 AGGTCGCCATGCACGCCCGGCGTCC
1 AGGTCGCCATGCACGCCCGGCGTCC
1188736 ATCATTCTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 78 0.98
30 2 0.03
ACGTcount: A:0.15, C:0.38, G:0.29, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTATA
Found at i:1189017 original size:13 final size:13
Alignment explanation
Indices: 1188954--1189018 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
1188944 CGGTTCTATC
1188954 GTAGGTCGCCATG
1 GTAGGTCGCCATG
** *
1188967 GCCGG-CGACATG
1 GTAGGTCGCCATG
1188979 GTAGGTCGCCATG
1 GTAGGTCGCCATG
*
1188992 G-A-GTCCCGACATG
1 GTAGGT--CGCCATG
1189005 GTAGGTCGCCATG
1 GTAGGTCGCCATG
1189018 G
1 G
1189019 AGTCCCGGCG
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
11 2 0.05
12 10 0.26
13 24 0.62
14 1 0.03
15 2 0.05
ACGTcount: A:0.17, C:0.26, G:0.38, T:0.18
Consensus pattern (13 bp):
GTAGGTCGCCATG
Found at i:1189040 original size:29 final size:29
Alignment explanation
Indices: 1188954--1189102 Score: 177
Period size: 29 Copynumber: 5.2 Consensus size: 29
1188944 CGGTTCTATC
1188954 GTAGGTCGCCAT-G-G--CCGGCGACATG
1 GTAGGTCGCCATGGAGTCCCGGCGACATG
1188979 GTAGGTCGCCATGGAGT-CC--CGACATG
1 GTAGGTCGCCATGGAGTCCCGGCGACATG
1189005 GTAGGTCGCCATGGAGTCCCGGCGACATG
1 GTAGGTCGCCATGGAGTCCCGGCGACATG
* * *
1189034 GTAGGTCGCGAGTCCGGCGACACCGGCGACATG
1 GTAGGTCGCCA-T--GGAGTC-CCGGCGACATG
*
1189067 GTAGGTCGCCATGGAGTCCCGACGACATG
1 GTAGGTCGCCATGGAGTCCCGGCGACATG
1189096 GTAGGTC
1 GTAGGTC
1189103 TGCATCATCA
Statistics
Matches: 107, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
25 12 0.11
26 25 0.23
27 3 0.03
28 2 0.02
29 34 0.32
30 5 0.05
32 5 0.05
33 21 0.20
ACGTcount: A:0.18, C:0.28, G:0.38, T:0.17
Consensus pattern (29 bp):
GTAGGTCGCCATGGAGTCCCGGCGACATG
Found at i:1190195 original size:23 final size:23
Alignment explanation
Indices: 1190152--1190195 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1190142 TATTGTGTTT
*
1190152 AAAAATATTTAGTGTTGTTTAAA
1 AAAAATATTTAGTGTTATTTAAA
* *
1190175 AAAAATATTTTGTTTTATTTA
1 AAAAATATTTAGTGTTATTTA
1190196 TTGTATGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTATTTAAA
Found at i:1190452 original size:26 final size:25
Alignment explanation
Indices: 1190423--1190482 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
1190413 AAATCATATT
*
1190423 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
1190449 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
1190475 ATTATTAA
1 ATTATTAA
1190483 TATATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 3 0.11
25 1 0.04
26 18 0.64
27 3 0.11
28 3 0.11
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:1190478 original size:21 final size:22
Alignment explanation
Indices: 1190454--1190502 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1190444 AAATCATTAG
*
1190454 ATTAATAATA-ATTATTAAATC-
1 ATTAATAATATATAATT-AATCA
*
1190475 ATTATTAATATATAATTAATCA
1 ATTAATAATATATAATTAATCA
1190497 ATTAAT
1 ATTAAT
1190503 CAAGTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAATATATAATTAATCA
Found at i:1193397 original size:60 final size:60
Alignment explanation
Indices: 1193321--1194230 Score: 1007
Period size: 60 Copynumber: 15.7 Consensus size: 60
1193311 GTATTTATAA
*
1193321 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1193381 GATTTAGTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1193441 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
1193501 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
* *
1193550 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATTATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
1193609 -ATTTAGTAAT-AAT-GAAATTAT--TATTAATT-TTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
*
1193657 GA-TTAGCAATGATTAGTAATAATG-AA--ATTATTAAT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1193712 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1193772 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1193832 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
1193892 GATTTAGTAAT-AAT-GAAATTAT--TATTAATT-TTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
*
1193941 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1194001 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-A--A--T
* *
1194066 AGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATTATTTGATAGTAAT
1 -G--AT--TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1194131 -ATTTAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
1194190 GATTTAGTAATGATTTGATAGTAATG-ATTTATTATAAATAT
1 GATTTAGTAATGATTAG-TAATAATGAAATTATTATTAATAT
1194231 GTCGAATTTG
Statistics
Matches: 728, Mismatches: 60, Indels: 124
0.80 0.07 0.14
Matches are distributed among these distances:
48 20 0.03
49 45 0.06
50 12 0.02
51 13 0.02
52 13 0.02
53 14 0.02
54 5 0.01
55 25 0.03
56 43 0.06
57 17 0.02
58 11 0.02
59 87 0.12
60 354 0.49
61 9 0.01
63 1 0.00
65 2 0.00
66 1 0.00
67 1 0.00
68 2 0.00
69 1 0.00
70 52 0.07
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:1193510 original size:24 final size:24
Alignment explanation
Indices: 1193483--1193563 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1193473 TATTAATTTT
1193483 TAATGATTTAATAGTAATGATTAG
1 TAATGATTTAATAGTAATGATTAG
* ** * * * **
1193507 TAATAATGAAATTATTATTAATTTT
1 TAATGATTTAA-TAGTAATGATTAG
*
1193532 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTAATAGTAATGATTAG
1193556 TAATGATT
1 TAATGATT
1193564 AGTAATAATG
Statistics
Matches: 39, Mismatches: 17, Indels: 2
0.67 0.29 0.03
Matches are distributed among these distances:
24 24 0.62
25 15 0.38
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
TAATGATTTAATAGTAATGATTAG
Found at i:1193556 original size:10 final size:10
Alignment explanation
Indices: 1193543--1193569 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1193533 AATGATTTGA
1193543 TAGTAATGAT
1 TAGTAATGAT
1193553 TAGTAATGAT
1 TAGTAATGAT
1193563 TAGTAAT
1 TAGTAAT
1193570 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1193734 original size:13 final size:13
Alignment explanation
Indices: 1193664--1193737 Score: 53
Period size: 13 Copynumber: 5.4 Consensus size: 13
1193654 AATGATTAGC
1193664 AATGATTAGTAAT
1 AATGATTAGTAAT
*
1193677 AATGAAATTATTAATTTT
1 AATG--ATTAGTAA---T
* *
1193695 AATGATTTGATAGT
1 AATGATTAG-TAAT
1193709 AATGATT--TAAT
1 AATGATTAGTAAT
1193720 AATGATTAGTAAT
1 AATGATTAGTAAT
1193733 AATGA
1 AATGA
1193738 AATTGTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
11 10 0.21
13 13 0.27
14 8 0.17
15 7 0.15
16 3 0.06
17 2 0.04
18 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.42
Consensus pattern (13 bp):
AATGATTAGTAAT
Found at i:1193759 original size:35 final size:35
Alignment explanation
Indices: 1193719--1193881 Score: 132
Period size: 35 Copynumber: 5.2 Consensus size: 35
1193709 AATGATTTAA
1193719 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
* * *
1193754 TAATGATT--TGAT-A-GTAA-TG--ATT--TA-G
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1193779 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
* * *
1193814 TAATGATT--TGAT-A-GTAA-TG--ATT--TA-G
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1193839 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1193874 TAATGATT
1 TAATGATT
1193882 TGATAGTAAT
Statistics
Matches: 96, Mismatches: 12, Indels: 40
0.65 0.08 0.27
Matches are distributed among these distances:
25 16 0.17
26 4 0.04
27 6 0.06
28 8 0.08
29 6 0.06
30 8 0.08
31 6 0.06
32 8 0.08
33 6 0.06
34 4 0.04
35 24 0.25
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTGTTATTAATATT
Found at i:1193944 original size:169 final size:169
Alignment explanation
Indices: 1193321--1194071 Score: 929
Period size: 169 Copynumber: 4.4 Consensus size: 169
1193311 GTATTTATAA
*
1193321 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATT-TTATTAATATTTAATGATTTGATAGT-A--A--T
*
1193386 AGTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
60 -G--AT--TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAA
*
1193451 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAAT
120 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
* * * * * *
1193501 GA-TTAGTAAT-AAT-GAAATTATTATTAA-TTT-TTAATGATTTGAT-AGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAATAATGA--AATTTTATTAAT-ATTTAATGA-T-TTGA-TAGTAAT
* *
1193560 GA-TTAGTAATAATGAAATTATTATTAATTTTTAATTATTTGATAG---T-A---A-T-AT--TT
60 GATTTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATT
1193613 AGTAATAATGAAATTATTATTAA-TTTTAATGATTTGATAGTAAT
125 AGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
1193657 GA-TTAGCAATGATTAGTAATAATGAAA--TTATTAAT-TTTAATGATTTGATAGTAATGATTTA
1 GATTTAGTAATGATTAGTAATAATGAAATTTTATTAATATTTAATGATTTGATAGTAATG-----
*
1193718 ATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAAT
61 ---AT--TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAAT
* *
1193783 GATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
121 GATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1193832 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATT-TTATTAATATTTAATGATTTGATAGTAATGATTT
1193897 AGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAA
65 AGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAA
1193961 TAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
130 TAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
1194001 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATT-TTATTAATATTTAATGATTTGATAGTAATGATTT
1194066 AGTAAT
65 AGTAAT
1194072 GATTAGTAAT
Statistics
Matches: 506, Mismatches: 27, Indels: 87
0.82 0.04 0.14
Matches are distributed among these distances:
152 8 0.02
153 3 0.01
154 6 0.01
155 3 0.01
156 36 0.07
157 27 0.05
158 7 0.01
159 2 0.00
160 2 0.00
161 1 0.00
163 40 0.08
164 1 0.00
165 1 0.00
166 1 0.00
167 1 0.00
168 40 0.08
169 148 0.29
170 26 0.05
171 2 0.00
172 4 0.01
173 1 0.00
174 25 0.05
175 22 0.04
176 31 0.06
177 16 0.03
178 7 0.01
179 22 0.04
180 23 0.05
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (169 bp):
GATTTAGTAATGATTAGTAATAATGAAATTTTATTAATATTTAATGATTTGATAGTAATGATTTA
GTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAAT
AATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
Found at i:1193963 original size:229 final size:235
Alignment explanation
Indices: 1193602--1194230 Score: 855
Period size: 229 Copynumber: 2.6 Consensus size: 235
1193592 AATTATTTGA
* *
1193602 TAGTAAT-ATTTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGA-TTAGC
1 TAGTAATGA-TTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGT
* *
1193664 AATGATTAGTAATAATGAAATTATTAATTTTAATGATTTGATAGTAATGATTTAATAATGATTAG
65 AAT-A--A-TAA-AAT--TATTATTAATTTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
* *
1193729 TAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATA
123 TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATA
1193794 ATGAAATTGTTATTAATATTTAATGATTTGATAGT-A-A-T-G-AT-T
188 ATGAAATTGTTATTAATATTTAATGATTTGATAGTAAGATTAGAATAT
1193836 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
1193901 ATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG
66 ATAATAAAATTATTATTAATTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG
*
1193966 AAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATGAAATT
131 AAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATGAAATT
1194031 GTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
196 GTTATTAATATTTAATGATTTGATAGTAA-GA-TTAG-AAT-AT
*
1194075 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATTATTTGATAGTAATATTTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT-A-A--T-G--A
*
1194140 TGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATT
59 T--TTAGTAATAATAAAATTATTATTAA-TTTTAATGATTTGATAGTAATGATTTAGTAATGATT
* * * *
1194205 TGATAGTAATG-ATTTATTATAAATAT
121 AG-TAATAATGAAATTATTATTAATAT
1194231 GTCGAATTTG
Statistics
Matches: 356, Mismatches: 15, Indels: 33
0.88 0.04 0.08
Matches are distributed among these distances:
229 142 0.40
230 1 0.00
231 3 0.01
232 3 0.01
233 1 0.00
234 33 0.09
235 25 0.07
236 7 0.02
237 2 0.01
239 53 0.15
240 1 0.00
241 1 0.00
243 1 0.00
244 1 0.00
246 2 0.01
248 24 0.07
249 49 0.14
250 7 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (235 bp):
TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATAATAAAATTATTATTAATTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG
AAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATGAAATT
GTTATTAATATTTAATGATTTGATAGTAAGATTAGAATAT
Done.