Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009269.1 Hibiscus syriacus cultivar Beakdansim tig00112928_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: 362859
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:351 original size:14 final size:15
Alignment explanation
Indices: 322--350 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
312 AGTTTTAAGA
322 GCATTTTATTTTTTT
1 GCATTTTATTTTTTT
337 GCATTTTATTTTTT
1 GCATTTTATTTTTT
351 GTATAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
GCATTTTATTTTTTT
Found at i:10944 original size:35 final size:34
Alignment explanation
Indices: 10859--10945 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
10849 ATTTGATATT
*
10859 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
10893 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
10931 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
10946 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:11563 original size:18 final size:18
Alignment explanation
Indices: 11540--11577 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11530 AGGCGATGGT
11540 GGCATCATATATGGTTGC
1 GGCATCATATATGGTTGC
11558 GGCATCATATATGGTTGC
1 GGCATCATATATGGTTGC
11576 GG
1 GG
11578 TGGCTGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (18 bp):
GGCATCATATATGGTTGC
Found at i:13222 original size:111 final size:113
Alignment explanation
Indices: 13084--13310 Score: 368
Period size: 111 Copynumber: 2.0 Consensus size: 113
13074 ATTACAAAAA
* *
13084 TTAATTATTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAA-T-TTAAAT
1 TTAATTATTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAAT
* *
13147 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
*
13195 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA-TT--ATTA
13260 AATTAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
63 AATTAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
13311 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
111 53 0.50
113 1 0.01
116 52 0.49
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (113 bp):
TTAATTATTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAAT
TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
Found at i:14401 original size:25 final size:26
Alignment explanation
Indices: 14373--14428 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
14363 ATTTTAAACT
*
14373 TTTTAGGGT-TTTTTTT-AAATAATAA
1 TTTTA-GGTATTTTTTTAAAATAAAAA
*
14398 TTTTATGTATTTTTTTAAAATAAAAA
1 TTTTAGGTATTTTTTTAAAATAAAAA
14424 TTTTA
1 TTTTA
14429 AAATTTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 12 0.44
26 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (26 bp):
TTTTAGGTATTTTTTTAAAATAAAAA
Found at i:14434 original size:25 final size:26
Alignment explanation
Indices: 14381--14435 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
14371 CTTTTTAGGG
* * **
14381 TTTTTTTTAAATAATAATTTTATGTA
1 TTTTTTTAAAATAAAAATTTTATAAA
14407 TTTTTTTAAAATAAAAATTTTA-AAA
1 TTTTTTTAAAATAAAAATTTTATAAA
14432 TTTT
1 TTTT
14436 AAGATAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTTTAAAATAAAAATTTTATAAA
Found at i:18672 original size:64 final size:61
Alignment explanation
Indices: 18604--18803 Score: 190
Period size: 64 Copynumber: 3.1 Consensus size: 61
18594 TACACTAAAA
18604 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGG-TG
* * * * *
18668 GTGCATCGATGCATCATTACATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGT-G
* * *
18732 GTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCATGG--
18795 TG
60 TG
18797 GTGCATC
1 GTGCATC
18804 AGTGCATCAC
Statistics
Matches: 112, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
62 1 0.01
63 17 0.15
64 69 0.62
65 24 0.21
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (61 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGTG
Found at i:19183 original size:15 final size:15
Alignment explanation
Indices: 19163--19192 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19153 ACTTTAACAC
19163 TTCTCCCCTTTAAAA
1 TTCTCCCCTTTAAAA
19178 TTCTCCCCTTTAAAA
1 TTCTCCCCTTTAAAA
19193 CATTTTAAAA
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:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCTCCCCTTTAAAA
Found at i:27300 original size:65 final size:65
Alignment explanation
Indices: 27162--27318 Score: 187
Period size: 65 Copynumber: 2.4 Consensus size: 65
27152 ACTAAGAGTG
* * * *
27162 CATCGATGCATAAAATGTATTCGATG-TTTCAAAATAGCTTGAGTGCATTGATGCATGTCTGGTG
1 CATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCTTGAGTGCATCGATGCATGTATGGTA
* * *
27226 CATCAATGCATCAAATGCATTCGGTGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGTAT-
1 CATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCT-TGAGTGCATCGATGCAT-GTATG
27288 GTA
63 GTA
*
27291 CATCGATGCATGAAATGCATTCGATGTT
1 CATCGATGCATAAAATGCATTCGATGTT
27319 CAATTTATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
64 24 0.30
65 49 0.62
66 6 0.08
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
CATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCTTGAGTGCATCGATGCATGTATGGTA
Found at i:33730 original size:2 final size:2
Alignment explanation
Indices: 33723--33747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33713 AAGAAATTTG
33723 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 T
33748 TTTTATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38341 original size:31 final size:31
Alignment explanation
Indices: 38306--38404 Score: 144
Period size: 31 Copynumber: 3.2 Consensus size: 31
38296 TAACAAATCA
*
38306 ATCACTGACGTTATCGATTTGTAACAAAATG
1 ATCACTAACGTTATCGATTTGTAACAAAATG
38337 ATCACTAACGTTATCGATTTGTAACAAAATG
1 ATCACTAACGTTATCGATTTGTAACAAAATG
* * * * *
38368 GTCATTAATGTTATTGATTTGTAACAAAATC
1 ATCACTAACGTTATCGATTTGTAACAAAATG
38399 ATCACT
1 ATCACT
38405 CTACTGTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (31 bp):
ATCACTAACGTTATCGATTTGTAACAAAATG
Found at i:40086 original size:20 final size:22
Alignment explanation
Indices: 40049--40112 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 22
40039 AATTGAAAAT
* *
40049 AGAGTAGAGTATCAATACCTAA
1 AGAGAAGAGTATCGATACCTAA
40071 AGAG-AG-GTATCGATA-CT-A
1 AGAGAAGAGTATCGATACCTAA
* *
40089 AGGGAAGAGTATCGATACCGAA
1 AGAGAAGAGTATCGATACCTAA
40111 AG
1 AG
40113 GCCAGTGTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 17 0.49
21 3 0.09
22 7 0.20
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (22 bp):
AGAGAAGAGTATCGATACCTAA
Found at i:40639 original size:38 final size:38
Alignment explanation
Indices: 40568--40642 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
40558 AGAAGAGAGT
***
40568 GAGTCATAACTTATTTTTAAACTATGTTTTGTATATTC
1 GAGTCATAACTTATTTTTAAACTATGGCCTGTATATTC
40606 GAGTCATAACTTATTTTTAAA-TGATGGCCTGTATATT
1 GAGTCATAACTTATTTTTAAACT-ATGGCCTGTATATT
40643 TTGATTTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (38 bp):
GAGTCATAACTTATTTTTAAACTATGGCCTGTATATTC
Found at i:50471 original size:23 final size:21
Alignment explanation
Indices: 50444--50486 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
50434 ATATAAAAAA
50444 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
50465 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
50486 T
1 T
50487 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:51921 original size:53 final size:52
Alignment explanation
Indices: 51819--51923 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 52
51809 AATAAAGAAA
* * *
51819 AAGTGTTATGAGCAAAGAGCAGCGGATAATCATAAGGTAACATTAGATAGAG
1 AAGTGTTATGAACAAAGAGCAGCGGATAATCATAAGGTAAAACTAGATAGAG
* *
51871 AAGTGTTCTGAACAAAAGAGCAGCAGG-TAATCATGAA-GTAAAACTCGATAGAG
1 AAGTGTTATGAAC-AAAGAGCAGC-GGATAATCAT-AAGGTAAAACTAGATAGAG
51924 CACCTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 11 0.24
53 30 0.67
54 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (52 bp):
AAGTGTTATGAACAAAGAGCAGCGGATAATCATAAGGTAAAACTAGATAGAG
Found at i:57580 original size:3 final size:3
Alignment explanation
Indices: 57572--57616 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
57562 ATGGACTATA
*
57572 AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57617 TAATAATGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:70352 original size:10 final size:10
Alignment explanation
Indices: 70337--70370 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
70327 TTCATTTACC
70337 ATTTATTTTT
1 ATTTATTTTT
70347 ATTTATTTTT
1 ATTTATTTTT
* *
70357 ATCTATTTCT
1 ATTTATTTTT
70367 ATTT
1 ATTT
70371 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:73087 original size:39 final size:39
Alignment explanation
Indices: 73016--73093 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
73006 CCCGGAATAT
* *
73016 TACCCGGGGACGCATCTGCTACTAAAGGGAAAGTAGCAC
1 TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
* * *
73055 TACCCGGGGACTCAT-TCGTTACCAAAGCGAAAGTTGCAC
1 TACCCGGGGACGCATCT-GCTACCAAAGCGAAAGTAGCAC
73094 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (39 bp):
TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
Found at i:80743 original size:105 final size:105
Alignment explanation
Indices: 80561--81639 Score: 1849
Period size: 105 Copynumber: 10.4 Consensus size: 105
80551 AGGTTTTACC
80561 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80626 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
80666 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80731 ACGAAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
80771 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80836 ACGAAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
80876 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80941 ACGAAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
80981 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81046 ACGAAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
81086 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81151 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
81191 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81256 ACGAAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
81296 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG------TT----
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81351 -C-AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
*
81389 CAGAGCCAATTTCAATTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * **
81454 ACGAAGGGATCGCTGGTTGTCAACAAACATTTCTCAGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
* *
81494 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
81559 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
* ** *
81599 CCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 -CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
81640 GGAACAATAC
Statistics
Matches: 935, Mismatches: 26, Indels: 25
0.95 0.03 0.03
Matches are distributed among these distances:
93 87 0.09
94 1 0.00
99 4 0.00
104 1 0.00
105 806 0.86
106 36 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAAATT
Found at i:81418 original size:93 final size:93
Alignment explanation
Indices: 81259--81551 Score: 415
Period size: 93 Copynumber: 3.0 Consensus size: 93
81249 CTTCACGACG
* *
81259 AAGGGACCGCTGGTTGTCACCAAACACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
1 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
81324 GATATTGGACTCCAGACAACGCAAGTTC
66 GATATTGGACTCCAGACAACGCAAGTTC
*
81352 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAATTTCACAACGAAG
1 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
81417 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
66 GATATTGGACTCCAGACAACGCAAG------TT-----C
* **
81456 GAAGGGATCGCTGGTTGTCAACAAACATTTCTCAGTTTCAGAGCCAATTTCAACTTCACAACGAA
1 -AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAA
*
81521 GGATATTGGACTCCAGACAACACAAGTTC
65 GGATATTGGACTCCAGACAACGCAAGTTC
81550 AA
1 AA
81552 CTTCACAACG
Statistics
Matches: 180, Mismatches: 8, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
93 89 0.49
94 1 0.01
99 4 0.02
104 1 0.01
105 85 0.47
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (93 bp):
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
GATATTGGACTCCAGACAACGCAAGTTC
Found at i:83694 original size:12 final size:13
Alignment explanation
Indices: 83677--83707 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
83667 GGGTAACTTA
83677 AATTTTAA-TTTT
1 AATTTTAATTTTT
83689 AATTTTAATTTTT
1 AATTTTAATTTTT
83702 AATTTT
1 AATTTT
83708 CGCAATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTTAATTTTT
Found at i:83701 original size:7 final size:6
Alignment explanation
Indices: 83677--83707 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
83667 GGGTAACTTA
83677 AATTTT AATTTT AATTTT AATTTTT AATTTT
1 AATTTT AATTTT AATTTT AA-TTTT AATTTT
83708 CGCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
AATTTT
Found at i:84584 original size:2 final size:2
Alignment explanation
Indices: 84577--84614 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
84567 AAACTAAAAC
84577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84615 AAAATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87826 original size:28 final size:29
Alignment explanation
Indices: 87794--87855 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
87784 ATTTTGTTAG
*
87794 AATTTTTA-GGAATTT-AGGAGTTTTTTGA
1 AATTTTTATGAAATTTAAGG-GTTTTTTGA
*
87822 AA-TTTTATGAAATTTAAGGGTTTTTTGG
1 AATTTTTATGAAATTTAAGGGTTTTTTGA
87850 AATTTT
1 AATTTT
87856 AATAACTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 5 0.17
28 18 0.62
29 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (29 bp):
AATTTTTATGAAATTTAAGGGTTTTTTGA
Found at i:88589 original size:14 final size:14
Alignment explanation
Indices: 88570--88597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
88560 TCACGACAAA
88570 GTCTTATGCTACAT
1 GTCTTATGCTACAT
88584 GTCTTATGCTACAT
1 GTCTTATGCTACAT
88598 CGGCGGCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
GTCTTATGCTACAT
Found at i:89946 original size:66 final size:66
Alignment explanation
Indices: 89838--90092 Score: 270
Period size: 66 Copynumber: 3.9 Consensus size: 66
89828 TGCAGCAGCA
* * * * *
89838 GCAGCAACAACAACTAGTTCAAGATTCTAGTTATACATTGCAGCAACCCCATTTTGATCATCAGT
1 GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCATCAGT
89903 T
66 T
* * *
89904 GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTTGATCAACGGT
1 GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCATCAGT
89969 T
66 T
* * * *
89970 GCAGCAGCAACAACAACGTGTTCCGGATTGT-GATTATAT-CTTTCAGCAACCCCAATTTGATC-
1 GCAGCAGCAACAACTA---GTTCAGGATTCTAG-TTATATAC-TGCAGCAACCCCAATTTGATCA
90032 TACAGTT
61 T-CAGTT
* * * *
90039 GCAGCAG---CAACTAGTTCCGGATTCTGGTTATATATTGCAGCAACTCCAATTTGA
1 GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGA
90093 ACAACAGCAG
Statistics
Matches: 161, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
63 34 0.21
64 1 0.01
66 78 0.48
68 2 0.01
69 46 0.29
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (66 bp):
GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCATCAGT
T
Found at i:89984 original size:69 final size:67
Alignment explanation
Indices: 89803--90175 Score: 332
Period size: 69 Copynumber: 5.4 Consensus size: 67
89793 TTATATGTCA
*
89803 CAGCAACCCCAATTTGATCAACAGTTGCAGCAGCAGCAGCAACAACAACTAGTTCAAGATTCTAG
1 CAGCAACCCCAATTTGATCAACAGTT------GCAGCAG-AACAACAACTAGTTCAGGATTCT-G
*
89868 TTATACATTG
58 TTATATATTG
* *
89878 CAGCAACCCCATTTTGATCATCAGTTGCAGCAG--CAACAACTAGTTCAGGATTCTAGTTATATA
1 CAGCAACCCCAATTTGATCAACAGTTGCAGCAGAACAACAACTAGTTCAGGATTCT-GTTATATA
*
89941 CTG
65 TTG
* * * *
89944 CAGCAACCTCAATTTGATCAACGGTTGCAGCAGCAACAACAACGT-GTTCCGGATTGTGATTATA
1 CAGCAACCCCAATTTGATCAACAGTTGCAGCAG-AACAACAAC-TAGTTCAGGATTCTG-TTATA
* *
90008 TCTTT
63 TATTG
* *
90013 CAGCAACCCCAATTTGATCTACAGTTGCAGCAG-----CAACTAGTTCCGGATTCTGGTTATATA
1 CAGCAACCCCAATTTGATCAACAGTTGCAGCAGAACAACAACTAGTTCAGGATTCT-GTTATATA
90073 TTG
65 TTG
* * ** * * *
90076 CAGCAACTCCAATTTGAACAACAGCAGCAGCAGAGATAACATCAACAACTTCAGGATTCTGTTTA
1 CAGCAACCCCAATTTGATCAACAGTTGCAGC--AG--AACAACAACTAGTTCAGGATTCTG-TTA
90141 TATATTG
61 TATATTG
90148 TC-GCAACCCCAATTTGATCAACAGTTGC
1 -CAGCAACCCCAATTTGATCAACAGTTGC
90176 GACAACCATC
Statistics
Matches: 248, Mismatches: 32, Indels: 39
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.00
63 49 0.20
64 1 0.00
65 2 0.01
66 59 0.24
68 1 0.00
69 61 0.25
70 1 0.00
71 1 0.00
72 47 0.19
73 1 0.00
75 24 0.10
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (67 bp):
CAGCAACCCCAATTTGATCAACAGTTGCAGCAGAACAACAACTAGTTCAGGATTCTGTTATATAT
TG
Found at i:90089 original size:132 final size:136
Alignment explanation
Indices: 89772--90175 Score: 366
Period size: 135 Copynumber: 3.0 Consensus size: 136
89762 GGTTTCCATT
* ** * **
89772 ACAACTTGTTCAGGAACCTGGTTATATGTCACAGCAACCCCAATTTGATCAACAGTTGCAGCAGC
1 ACAACTAGTTCAGGATTCTGGTTATATATTGCAGCAA-CCCAATTTGATCAACAGTTGCAGCAGC
*
89837 AGCAGCAACAACAACTAGTTCAAGATTCTAGTTATACATTGCAGCAACCCCATTTTGATCATCAG
65 A-CAGCAACAAC-ACTAGTTCAAGATTCTAGTTATACATTGCAGCAACCCCAATTTGATCATCAG
89902 TTGCAGCAG
128 TTGCAGCAG
* * *
89911 CAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTTGATCAACGGTTGCAGCA
1 --ACAACTAGTTCAGGATTCTGGTTATATATTGCAGCAACC-CAATTTGATCAACAGTTGCAGCA
* ** * *
89976 GCA-A-CAACAAC-GT-GTTCCGGATTGT-GATTATATC-TTTCAGCAACCCCAATTTGATC-TA
63 GCACAGCAACAACACTAGTTCAAGATTCTAG-TTATA-CATTGCAGCAACCCCAATTTGATCAT-
90034 CAGTTGCAGCAG
125 CAGTTGCAGCAG
* *
90046 -CAACTAGTTCCGGATTCTGGTTATATATTGCAGCAACTCCAATTTGAACAACA---GCAGCAGC
1 ACAACTAGTTCAGGATTCTGGTTATATATTGCAGCAAC-CCAATTTGATCAACAGTTGCAGCAGC
* * * * * * * *
90107 AGAGATAACATCAACAACTTCAGGATTCT-GTTTATATATTGTC-GCAACCCCAATTTGATCAAC
65 ACAG-CAACAAC-ACTAGTTCAAGATTCTAG-TTATACATTG-CAGCAACCCCAATTTGATCATC
90170 AGTTGC
126 AGTTGC
90176 GACAACCATC
Statistics
Matches: 218, Mismatches: 31, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
129 9 0.04
130 1 0.00
132 51 0.23
133 1 0.00
134 2 0.01
135 87 0.40
136 3 0.01
138 7 0.03
139 1 0.00
140 2 0.01
141 54 0.25
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (136 bp):
ACAACTAGTTCAGGATTCTGGTTATATATTGCAGCAACCCAATTTGATCAACAGTTGCAGCAGCA
CAGCAACAACACTAGTTCAAGATTCTAGTTATACATTGCAGCAACCCCAATTTGATCATCAGTTG
CAGCAG
Found at i:92863 original size:3 final size:3
Alignment explanation
Indices: 92850--92887 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
92840 ACCAATAAAA
92850 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
92888 TTTCTAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:104458 original size:152 final size:150
Alignment explanation
Indices: 104164--104432 Score: 397
Period size: 152 Copynumber: 1.8 Consensus size: 150
104154 ATTATGAAGA
104164 AATATATTAATTTAGATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGAC
1 AATATATTAATTTAGATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGAC
* *
104229 TTCTAGGTGCTTTAAGACAGCTCTTTTCTTAATATTAAAAAATAAATAATATTAAAAAACATCTT
66 TTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATT--AAAATAAATAATATTAAAAAACATCTT
104294 TCTAAAAATAATTAAATAAATT
129 TCTAAAAATAATTAAATAAATT
* **
104316 AATATA-T-ATTTATATATAATTTATAAAATATGATATTTATTTATTTA-AGAATATCAGAAAAG
1 AATATATTAATTTAGATAT-ATTTAT-AAATAAAATATTTATTTATTTAGA-AATATCAGAAAAG
*
104378 GACTTCTAGGTGCTTTAAGACAGCCCATTTCTTGATATT-AAA-AAA-AATATTAAAA
63 GACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATTAAAATAAATAATATTAAAA
104433 TATGATTATT
Statistics
Matches: 108, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
147 10 0.09
148 3 0.03
149 3 0.03
150 9 0.08
151 8 0.07
152 75 0.69
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (150 bp):
AATATATTAATTTAGATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGAC
TTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATTAAAATAAATAATATTAAAAAACATCTTTC
TAAAAATAATTAAATAAATT
Found at i:106190 original size:123 final size:120
Alignment explanation
Indices: 106056--106352 Score: 386
Period size: 123 Copynumber: 2.5 Consensus size: 120
106046 GAACAAATTC
* * *
106056 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTAT
*
106121 CT-CATTCTGTGATAGAA-TCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
66 CTGC-TTCTGTGATAAAATTCAAA-AAAGGTTGAACAAGCTCTTCTCATTATGAA---CT
* * * *
106179 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAATGTTGATGCTAATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTAT
* *** *
106244 TTGCTTCTGTGATAAAATTTTGTAAAAGGTTGAACAAGCTCTTCTCATTGTGAACT
66 CTGCTTCTGTGATAAAA-TTCAAAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
*
106300 TCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTCTGGAAAAGCTGAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGAT
106353 CCATCAAGTG
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
119 14 0.09
120 31 0.20
121 6 0.04
123 71 0.46
124 30 0.19
125 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (120 bp):
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTAT
CTGCTTCTGTGATAAAATTCAAAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
Found at i:106496 original size:112 final size:109
Alignment explanation
Indices: 106267--107157 Score: 875
Period size: 112 Copynumber: 8.0 Consensus size: 109
106257 AAAATTTTGT
** * *
106267 AAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGAT-GAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATAGAGTTCTTCTCATTAT
** * * *
106331 GAACTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
66 GAACTTACCTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
*
106375 AAAAGGTTGAAAAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCATT
* * *
106440 ATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGGATTTGAGC
64 ATGAACT-TACCTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
**
106487 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTC-AGATA-GAGTTCTTCTCAT
* * * *
106552 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGAT-GAATTCAGGC
63 TATGAACTTAC-CTGGAAATGTTAATCCATCAAGTGATGGATTTGA-GC
* *
106600 AAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATA-AGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-T--TCTTCAGATAGAGTTCTTCTCAT
* * *
106664 TATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
63 TATGAACTTAC-CTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
* * *
106712 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATA-AGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATAGAGTTCTTCTCAT
* *** * * * *
106776 TATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGAT-GAATTCAGGG
63 TATGAACTTAC-CTGGAAATGTTAATCCATCAAGTGATGGATTTGA-GC
* *
106824 AAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTCTTCAAAT-GAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-T--TCTTCAGATAGAGTTCTTCTCAT
* * * * * * ** * *
106888 TATGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGC
63 TATGAACT-TACCTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
* * *
106936 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAAT-GAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATAGAGTTCTTCTCAT
* * * * * * *
107000 TATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGC
63 TATGAACT-TACCTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
* *
107048 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATAGAGTTCTTCTCA
* * *
107112 TTATGAACTCGACCTGG-AATGTTGATCCATTGAA-TGATGGATTTGA
62 TTATGAACT-TACCTGGAAATGTTAATCCA-TCAAGTGATGGATTTGA
107158 ACTTTGCTAA
Statistics
Matches: 674, Mismatches: 82, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
108 43 0.06
109 6 0.01
110 1 0.00
111 24 0.04
112 439 0.65
113 135 0.20
114 9 0.01
115 16 0.02
116 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (109 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATAGAGTTCTTCTCATTAT
GAACTTACCTGGAAATGTTAATCCATCAAGTGATGGATTTGAGC
Found at i:106539 original size:24 final size:23
Alignment explanation
Indices: 106504--106548 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
106494 TGAACAAATT
*
106504 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
106528 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
106549 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:107040 original size:336 final size:335
Alignment explanation
Indices: 106267--107130 Score: 1098
Period size: 336 Copynumber: 2.6 Consensus size: 335
106257 AAAATTTTGT
* * *
106267 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTA
* * * * *
106330 TGAACTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAA-AAATTCT
66 TGAACTTATCTGGAAATGATGATCCATCAAGTGATGAATTTGAGCAAAAGGTT-AAACAAGTTCT
* *
106394 TCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
130 TCTCATTATGAACTTCTTCTTCCTCTTCAGAT-A--AGTTCTTCTCATTATGAACTCTACCTGGA
*** * *
106456 AATGTTAATCCATCAAATAATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
192 AAAAATAATCCATCAAATAATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
* * ** * *
106521 CTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTAATCCATCAAG
257 CTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTAATCCACCAAG
*
106586 TGATGAATTCAGGC
322 TGATGAATTCAAGC
* * * *
106600 AAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTTCTTCTTCAAATGAGTTCTTCTCATT
* * * *
106665 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTC
65 ATGAAC-TTATCTGGAAATGATGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAGTTC
*
106730 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAA
129 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC-CTGGAA
* * * * *
106794 AAAATAATTCATCAAGTGATGAATTCAG-GGAAAAGGTTGAACAAATTCTTCTTATTATGAATTT
193 AAAATAATCCATCAAATAATGAATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
* ** * **
106858 CTTCTTCC-TCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGGG
257 CTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTAATCCACCAAG
*
106922 TGATGAATTTAAGC
322 TGATGAATTCAAGC
*
106936 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTTCTTCTTCAAATGAGTTCTTCTCATT
* * * * * *
107001 ATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAGTTC
65 ATGAACT-TATCTGGAAATGATGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAGTTC
* *
107066 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAA
129 TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAA
107131 TGTTGATCCA
Statistics
Matches: 458, Mismatches: 60, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
333 27 0.06
335 1 0.00
336 231 0.50
337 180 0.39
338 2 0.00
339 2 0.00
340 15 0.03
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (335 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTA
TGAACTTATCTGGAAATGATGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAGTTCTT
CTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAAAA
ATAATCCATCAAATAATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC
TTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTAATCCACCAAGTGAT
GAATTCAAGC
Found at i:107140 original size:224 final size:224
Alignment explanation
Indices: 106267--107141 Score: 1147
Period size: 224 Copynumber: 3.9 Consensus size: 224
106257 AAAATTTTGT
* *
106267 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* * * ** *
106329 ATGAACTTT-TCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAAAAATTC
66 ATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTC
*
106393 TTCTCATTATGAATTTCTTC-T--TCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGG
131 TTCTCATTATGAATTTCTTCTTCCTCTTCA-A--ATGAGTTCTTCTCATTATGAACTCTACCTGG
* * *
106455 CAATGTTAATCCATCAAATAATGGATTTGAGC
193 CAATGTTAATCCATCAAGTGATGAATTTGAGC
* * *
106487 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
* * *
106552 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAATT
65 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATT
* * *
106617 CTTCTCATTATGAATTTCTTCTTCCTCTTCAAATAAGTTCTTCTCATTATGAACT-TTCTCTGGA
130 CTTCTCATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTCTAC-CTGGC
*
106681 AATGTTAATCCATCAAGTGATGAATTCGAGC
194 AATGTTAATCCATCAAGTGATGAATTTGAGC
* * *
106712 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* * * *
106777 ATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTC
* * *
106842 TTCTTATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGCAC
131 TTCTCATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTCTACCTGGCAA
* * * ** *
106907 TGCTGATCCACCGGGTGATGAATTTAAGC
196 TGTTAATCCATCAAGTGATGAATTTGAGC
* *
106936 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * * *
107001 ATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAGTTC
66 ATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTC
* * *
107066 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGG-A
131 TTCTCATTATGAATTTCTTCTTCC-TCTTCAAATGAGTTCTTCTCATTATGAACTCTACCTGGCA
*
107130 ATGTTGATCCAT
195 ATGTTAATCCAT
107142 TGAATGATGG
Statistics
Matches: 573, Mismatches: 71, Indels: 18
0.87 0.11 0.03
Matches are distributed among these distances:
220 28 0.05
223 6 0.01
224 339 0.59
225 192 0.34
226 1 0.00
227 1 0.00
228 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (224 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTCTACCTGGCAA
TGTTAATCCATCAAGTGATGAATTTGAGC
Found at i:107582 original size:22 final size:22
Alignment explanation
Indices: 107557--107611 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
107547 GATAAAACTT
* *
107557 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
107579 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
107601 TCATCTTTAAA
1 TCATCTTTAAA
107612 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:110140 original size:83 final size:83
Alignment explanation
Indices: 110001--110476 Score: 740
Period size: 83 Copynumber: 5.7 Consensus size: 83
109991 GTAGTTCCTA
* * * * *
110001 CCAAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
*
110066 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTCTG
*
110084 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
*
110149 ATTCAATGATTGATTCTG
66 ATTCAATGATTGGTTCTG
* *
110167 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTAACAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCA
110231 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * *
110250 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCC
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCA
110314 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * *
110333 CTAAACCAGGTCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTAACAAATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
110398 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
110416 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
110477 TCAGTTAATG
Statistics
Matches: 368, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
82 1 0.00
83 365 0.99
84 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:112620 original size:10 final size:9
Alignment explanation
Indices: 112601--112635 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
112591 TCAATTTTCC
112601 TTTTTCTTT
1 TTTTTCTTT
112610 TTTTTCTTT
1 TTTTTCTTT
112619 TTTTT-TTT
1 TTTTTCTTT
*
112627 TCTTTCTTT
1 TTTTTCTTT
112636 GCTGGATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:112623 original size:13 final size:14
Alignment explanation
Indices: 112602--112635 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
112592 CAATTTTCCT
112602 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
112616 TTTT-TTTTTTTTC
1 TTTTCTTTTTTTTC
112629 -TTTCTTT
1 TTTTCTTT
112636 GCTGGATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 12 0.63
14 4 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:112627 original size:17 final size:17
Alignment explanation
Indices: 112601--112635 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
112591 TCAATTTTCC
*
112601 TTTTTCTTTTTTTTCTT
1 TTTTTCTTTTCTTTCTT
*
112618 TTTTTTTTTTCTTTCTT
1 TTTTTCTTTTCTTTCTT
112635 T
1 T
112636 GCTGGATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTCTTTTCTTTCTT
Found at i:114607 original size:27 final size:27
Alignment explanation
Indices: 114577--114632 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
114567 GTAATTATGT
*
114577 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
114604 AAAAATGCAAATGCAAATTCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
114631 AA
1 AA
114633 TATGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:114705 original size:14 final size:14
Alignment explanation
Indices: 114671--114723 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
114661 TTGTGCAATA
*
114671 CAAATGCAAAAATG
1 CAAATGTAAAAATG
*
114685 CCAAATGTAAATATG
1 -CAAATGTAAAAATG
114700 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
114714 TAAATGTAAA
1 CAAATGTAAA
114724 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:119285 original size:109 final size:109
Alignment explanation
Indices: 119090--119289 Score: 348
Period size: 109 Copynumber: 1.8 Consensus size: 109
119080 TTCAAAATTA
119090 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
1 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
**
119155 CAACACAAAGGATTTTGCGATAGGGAAGACAGGTAGGACTCAAT
66 CAACACAAAGGATTTCACGATAGGGAAGACAGGTAGGACTCAAT
*
119199 TCACCATAAGACTTAGATAGTTAGATTTAGCACAAG-AGCTTTTGCATTAAATAGGAACTAGGAC
1 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCA-CTTTTGCATTAAATAGGAACTAGGAC
*
119263 ACAACACAAAGGGTTTCACGATAGGGA
65 ACAACACAAAGGATTTCACGATAGGGA
119290 CACAACACAA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 85 0.99
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (109 bp):
TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
CAACACAAAGGATTTCACGATAGGGAAGACAGGTAGGACTCAAT
Found at i:124095 original size:60 final size:60
Alignment explanation
Indices: 124020--124153 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
124010 TGTTTAGGGT
* *
124020 AAAG-TACACAAATGGTCCCCTGACTATAGAGTATTATTTTATTAAGTCTCTCAACAATTA
1 AAAGTTACA-AAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTA
* * ** * * * * * *
124080 AAAGTTATAAAATGGTTATTTGGCTATAGAATGTTGTTTTATTGAGTCTCTCGACTATTA
1 AAAGTTACAAAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTA
124140 AAAGTTACAAAATG
1 AAAGTTACAAAATG
124154 ATCTCTCGAC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 57 0.95
61 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTA
Found at i:124500 original size:60 final size:59
Alignment explanation
Indices: 124373--124501 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 59
124363 AGTCTCGTGT
* * * * *
124373 GACCATTTTGTAATTTTTAATAGTCGATGGACTTAATAAAGCAATATTCTATAGTCGAAG
1 GACCATTTTGTAATTTTTAATAATCAAGGGACTTAATAAAGCAATATCCTATAATC-AAG
* * * *
124433 GATCATTTTGTAATTTTTAATAATTAAGGGATTTAATAAAGTAATATCCTATAAT-AAGGG
1 GACCATTTTGTAATTTTTAATAATCAAGGGACTTAATAAAGCAATATCCTATAATCAA--G
124493 GACCATTTT
1 GACCATTTT
124502 TGTACTTTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.04
60 55 0.96
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (59 bp):
GACCATTTTGTAATTTTTAATAATCAAGGGACTTAATAAAGCAATATCCTATAATCAAG
Found at i:130321 original size:16 final size:16
Alignment explanation
Indices: 130300--130332 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
130290 TAATTAAGTT
130300 ATAATAACTCTTATTA
1 ATAATAACTCTTATTA
130316 ATAATAACTCTTATTA
1 ATAATAACTCTTATTA
130332 A
1 A
130333 CTGGACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATAACTCTTATTA
Found at i:136931 original size:2 final size:2
Alignment explanation
Indices: 136890--136915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136880 ATTTGAATGG
136890 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
136916 TAGGGTTTCA
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:142357 original size:13 final size:13
Alignment explanation
Indices: 142339--142363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142329 TATTCGTACA
142339 AAAATAATATTTT
1 AAAATAATATTTT
142352 AAAATAATATTT
1 AAAATAATATTT
142364 AATCAGTCTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:142928 original size:3 final size:3
Alignment explanation
Indices: 142920--142968 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
142910 ACATAAGTTT
142920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
142968 T
1 T
142969 GTTAGCAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:144729 original size:20 final size:20
Alignment explanation
Indices: 144701--144748 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
144691 AAACAGTACT
144701 ATCGCAACGCGAATAGGAAA
1 ATCGCAACGCGAATAGGAAA
* *
144721 ATTGCAACGCGAATAGTAAA
1 ATCGCAACGCGAATAGGAAA
144741 ATCGCAAC
1 ATCGCAAC
144749 ATGATTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAATAGGAAA
Found at i:144729 original size:57 final size:57
Alignment explanation
Indices: 144604--144730 Score: 200
Period size: 57 Copynumber: 2.2 Consensus size: 57
144594 CACAGGTTTC
* *
144604 AAAATCGCAACGTTAATTACCGATATAGGTAAACAATACTATCGCAGCGCGAATAGG
1 AAAATCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCGAATAGG
* * *
144661 AAAATCACAACGCTAATTACCGATTTAGGTAAACAGTACTATCGCAACGCGAATAGG
1 AAAATCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCGAATAGG
*
144718 AAAATTGCAACGC
1 AAAATCGCAACGC
144731 GAATAGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (57 bp):
AAAATCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCGAATAGG
Found at i:145083 original size:20 final size:20
Alignment explanation
Indices: 145060--145113 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
145050 AGTTTGAAAA
* *
145060 TCGCGTTGCGATTTCCTTAT
1 TCGCGTTGTGATTTCCCTAT
*
145080 TCGCGTTGTAATTTCCCTAT
1 TCGCGTTGTGATTTCCCTAT
145100 TCGCGTTGTGATTT
1 TCGCGTTGTGATTT
145114 TGGAACCTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (20 bp):
TCGCGTTGTGATTTCCCTAT
Found at i:147131 original size:111 final size:112
Alignment explanation
Indices: 146795--147256 Score: 737
Period size: 112 Copynumber: 4.1 Consensus size: 112
146785 TTGTCGGTTT
* * ** *
146795 GTGTTGATACTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAAAGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
146860 GGTTTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
146907 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAACAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
146972 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCTGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
147019 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
147083 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** * * *
147130 GTGTTAATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
147195 GGTTTATAAATGACAAAACAGGTGAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
147242 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
147257 TATAAATATC
Statistics
Matches: 325, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
111 104 0.32
112 221 0.68
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:147194 original size:223 final size:224
Alignment explanation
Indices: 146795--147265 Score: 737
Period size: 223 Copynumber: 2.1 Consensus size: 224
146785 TTGTCGGTTT
* *
146795 GTGTTGATACTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAAAGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCAATCCATAACAATATAACAGGTAAAAAAAAGACAAAACC
* * *
146860 GGTTTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATATTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
* *
146925 AATGTATCGATCCATAACAATATAACAGGTAACAAAATGACAAAACCGGTCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAA
*
146990 CAGGTAAAGCGCTACCTGATATATTGAAA
196 CAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
147019 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCAATCCATAACAATATAACAGGTAAAAAAAAGACAAAACC
* *
147083 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTTAATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
* * *
147148 AATGTATCGATCCATAATAATATAACATGTAAAAAAATAACAAAACCGGTTTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAA
* * *
147213 CAGGTGAAGCGCTACCGGATATGTTGATA
196 CAGGTAAAGCGCTACCGGATATATTGAAA
*
147242 GTGTCGATACTTTATTATAAATAT
1 GTGTCGATACTTTA-TAAAAATAT
147266 CAACACTTTT
Statistics
Matches: 223, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
223 173 0.78
224 50 0.22
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATATCAATCCATAACAATATAACAGGTAAAAAAAAGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAA
CAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:147434 original size:182 final size:181
Alignment explanation
Indices: 147127--147581 Score: 626
Period size: 182 Copynumber: 2.5 Consensus size: 181
147117 GGATATATTG
* * * *
147127 AAAGTGTTAATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAAAATAACAAA
1 AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAACAAA
* * * * * *
147192 ACCGGTTTATAAATGACAAAA-CAGGTGAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTA
66 ACCGGTCT-GAAATGACAAAACCA-GTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTA
* *
147256 TTATAAATATCAACACTTTTGGAATTTAAAAGAGAAGAAGTTACAACG-CTAAT
129 TTATAAATATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAACGTC-AAT
* * *
147309 AAAGTGTCAATACTTTATAAAATTGTATCGATCTATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAACAAA
* *
147374 ACCGGTCTCGAAATGACAAAACCAGTAAAGAGTTACCGAATATGTTGAAAGTTTCGATACTTTAT
66 ACCGGTCT-GAAATGACAAAACCAGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
* ** * *
147439 TATAAGTATTGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
130 TATAAATATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAACGTCAAT
* *
147491 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAA
1 AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAACAAA
* *
147556 ATCGGTCTGGAATGACAAAACCAGTA
66 ACCGGTCTGAAATGACAAAACCAGTA
147582 GTAAAAAAGT
Statistics
Matches: 241, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
181 17 0.07
182 221 0.92
183 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (181 bp):
AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAACAAA
ACCGGTCTGAAATGACAAAACCAGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTATT
ATAAATATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAACGTCAAT
Found at i:148044 original size:23 final size:23
Alignment explanation
Indices: 148015--148062 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
148005 AAATATGTTA
*
148015 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTAATACATT
* *
148038 ATATAAGCGCTACCTAATATATT
1 ATATAAGCACTACCTAATACATT
148061 AT
1 AT
148063 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTAATACATT
Found at i:151211 original size:17 final size:18
Alignment explanation
Indices: 151191--151225 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
151181 GAAAAAAAAC
*
151191 CAAAAATA-AGAAATATA
1 CAAAAATAGAAAAATATA
151208 CAAAAATAGAAAAATATA
1 CAAAAATAGAAAAATATA
151226 ACTAAAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
CAAAAATAGAAAAATATA
Found at i:153139 original size:106 final size:106
Alignment explanation
Indices: 152955--153944 Score: 1680
Period size: 106 Copynumber: 9.4 Consensus size: 106
152945 GCATTGTTCC
* * * * * *
152955 GAGTCCAATACCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * *
153020 CCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
153061 GAGTCCAATATCCTTTGCAGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
153126 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
153167 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
153231 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
153272 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
153337 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
153378 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
153442 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
153483 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
153548 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
153589 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
153653 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
153694 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
153759 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTTCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
153800 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
153865 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
153906 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
153945 AAAGGCTGTA
Statistics
Matches: 840, Mismatches: 41, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
105 306 0.36
106 534 0.64
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:153254 original size:211 final size:211
Alignment explanation
Indices: 152955--153944 Score: 1728
Period size: 211 Copynumber: 4.7 Consensus size: 211
152945 GCATTGTTCC
* * * * * *
152955 GAGTCCAATACCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * * * * **
153020 CCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGCAGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * * *
153085 GTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
153150 TGAACTTGCGTTGTCTT
195 TGAACTTGCGTTGTCTG
153167 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
153232 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
153297 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
153362 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
153378 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
153443 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
153508 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
153573 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
153589 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
153654 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
153719 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
153784 AAACTTTCGTTGTCTG
196 GAACTTGCGTTGTCTG
* *
153800 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
*
153865 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
153930 GTTGAAATTGGCTCT
130 GTTGAAATTGACTCT
153945 AAAGGCTGTA
Statistics
Matches: 751, Mismatches: 26, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
211 616 0.82
212 135 0.18
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (211 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTG
Found at i:153547 original size:317 final size:318
Alignment explanation
Indices: 152955--153944 Score: 1698
Period size: 317 Copynumber: 3.1 Consensus size: 318
152945 GCATTGTTCC
* * * * *
152955 GAGTCCAATACCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGAGAAATTGTTTGTTGACAA
* * * * * * **
153020 CCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGCAGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
153085 GTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
153150 TGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
153215 AAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
261 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
153272 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGAGAAATTGTTTGTTGACAA
153337 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
153402 GTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
153466 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
153531 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
261 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
153589 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGAGAAATTGTTTGTTGACAA
153653 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
153718 GTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
153783 TAAACTTTCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* *
153848 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
261 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
153906 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
153945 AAAGGCTGTA
Statistics
Matches: 638, Mismatches: 33, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
316 204 0.32
317 434 0.68
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (318 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:157611 original size:10 final size:11
Alignment explanation
Indices: 157596--157639 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
157586 GATCATAGCA
157596 AATAAT-AAAT
1 AATAATAAAAT
157606 AATAATAAAAT
1 AATAATAAAAT
*
157617 AA-AGTAAAAT
1 AATAATAAAAT
*
157627 AATAATAATAT
1 AATAATAAAAT
157638 AA
1 AA
157640 AAAAGGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 15 0.52
11 14 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:160979 original size:186 final size:184
Alignment explanation
Indices: 160664--161040 Score: 587
Period size: 186 Copynumber: 2.0 Consensus size: 184
160654 ATAAAATTTT
* *
160664 AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAATCCAATTAGTAA
1 AAATATTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAATCCAATTAATAA
* * *
160729 TTTAAGATCCAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAATTTT
66 TCTAAGATCCAATAAATTTTAAAACTAAATAAATATTAATTAATTAAAAAATTTATATAAA-TTT
*
160794 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTATGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTAT-AACTATTTTTATGAATTAAA
* * *
160850 AAATATTAAATATATAATATATAACATATGGGCTCAACTCAAATCATTTAAAA-CCTAATTAATA
1 AAATATTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAATCC-AATTAATA
* *
160914 ATCTAAGGTCCAATAAATTTTAAAACTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATT
65 ATCTAAGATCCAATAAATTTTAAAACTAAATAAATATTAATTAATTAAAAAATTTATAT-AAATT
* *
160978 TTTATTTTATAATTATATATTATTTAAATTAATTATAACTATTTTTTTGAATTATA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAACTATTTTTATGAATTAAA
161034 AAATATT
1 AAATATT
161041 TAATTTTTAT
Statistics
Matches: 176, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
184 25 0.14
185 45 0.26
186 106 0.60
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAATCCAATTAATAA
TCTAAGATCCAATAAATTTTAAAACTAAATAAATATTAATTAATTAAAAAATTTATATAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAACTATTTTTATGAATTAAA
Found at i:162016 original size:30 final size:30
Alignment explanation
Indices: 161980--162038 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
161970 GAAGATCCAG
*
161980 CTGAAAACCGGGAAAACCGGGGTGAACCGA
1 CTGAAAACCGGCAAAACCGGGGTGAACCGA
**
162010 CTGAAAACCGGCAAAACCGGTTTGAACCG
1 CTGAAAACCGGCAAAACCGGGGTGAACCG
162039 CCGGTTCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.10
Consensus pattern (30 bp):
CTGAAAACCGGCAAAACCGGGGTGAACCGA
Found at i:162829 original size:8 final size:8
Alignment explanation
Indices: 162816--162840 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
162806 TGAATCCGGT
162816 TGAACCAG
1 TGAACCAG
162824 TGAACCAG
1 TGAACCAG
162832 TGAACCAG
1 TGAACCAG
162840 T
1 T
162841 ACCTTCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (8 bp):
TGAACCAG
Found at i:166424 original size:29 final size:30
Alignment explanation
Indices: 166359--166428 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
166349 AATGTTTGTA
166359 ACTTTAGGCACCGGGATGAGTCAAAAAAAT
1 ACTTTAGGCACCGGGATGAGTCAAAAAAAT
166389 ACTTTAGGCACCGGGATGAGTC-AAAAAAT
1 ACTTTAGGCACCGGGATGAGTCAAAAAAAT
*
166418 ATTTTAGGCAC
1 ACTTTAGGCAC
166429 ATATTCATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (30 bp):
ACTTTAGGCACCGGGATGAGTCAAAAAAAT
Found at i:174105 original size:38 final size:39
Alignment explanation
Indices: 174063--174150 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 39
174053 GTAAGGTATA
*
174063 ATTATTTTTATAATTTATTTTTTATTC-ATTAACATT-TT
1 ATTATTTTTATAATTAATTTTTTATTCGATT-ACATTATT
* **
174101 ATTA-TTTGAGTAATTAATTTTTTATTCGATTAGTTTATT
1 ATTATTTTTA-TAATTAATTTTTTATTCGATTACATTATT
174140 ATTATTTTTAT
1 ATTATTTTTAT
174151 TTGATTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
37 4 0.10
38 23 0.56
39 10 0.24
40 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (39 bp):
ATTATTTTTATAATTAATTTTTTATTCGATTACATTATT
Found at i:176515 original size:26 final size:26
Alignment explanation
Indices: 176479--176528 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
176469 CAATGACACA
*
176479 TCGATATATCTAATAAAATTGTAATC
1 TCGATAGATCTAATAAAATTGTAATC
176505 TCGATAGATCTAATAAAATTGTAA
1 TCGATAGATCTAATAAAATTGTAA
176529 CCTTTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (26 bp):
TCGATAGATCTAATAAAATTGTAATC
Found at i:179307 original size:16 final size:16
Alignment explanation
Indices: 179286--179317 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
179276 TTTGTTTGAC
179286 GGAAAATAGATTTCGA
1 GGAAAATAGATTTCGA
179302 GGAAAATAGATTTCGA
1 GGAAAATAGATTTCGA
179318 AAAATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
GGAAAATAGATTTCGA
Found at i:179734 original size:16 final size:16
Alignment explanation
Indices: 179697--179749 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
179687 TTAAAACAAG
*
179697 AATAATATATTATTAT
1 AATAATATATTATTAA
*
179713 ATTAAT-TACTTATTAA
1 AATAATATA-TTATTAA
179729 AATAATAATATTATTAA
1 AATAAT-ATATTATTAA
179746 AATA
1 AATA
179750 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.06
16 16 0.52
17 11 0.35
18 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATATATTATTAA
Found at i:179749 original size:14 final size:14
Alignment explanation
Indices: 179723--179781 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
179713 ATTAATTACT
179723 TATTAAAATAATAA
1 TATTAAAATAATAA
*
179737 TATT--ATTAA-AA
1 TATTAAAATAATAA
*
179748 TATTAAAAATAAAAA
1 TATT-AAAATAATAA
*
179763 TATTAAAATAAAAA
1 TATTAAAATAATAA
179777 TATTA
1 TATTA
179782 TATTATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
14 23 0.59
15 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:179753 original size:8 final size:8
Alignment explanation
Indices: 179723--179781 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
179713 ATTAATTACT
179723 TATTAAAA
1 TATTAAAA
* *
179731 TAATAATAT
1 TATTAA-AA
179740 TATTAAAA
1 TATTAAAA
179748 TATTAAAA
1 TATTAAAA
*
179756 -ATAAAAA
1 TATTAAAA
179763 TATTAAAA
1 TATTAAAA
179771 TA--AAAA
1 TATTAAAA
179777 TATTA
1 TATTA
179782 TATTATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 23 0.56
9 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TATTAAAA
Found at i:179764 original size:15 final size:15
Alignment explanation
Indices: 179744--179781 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
179734 TAATATTATT
179744 AAAATATTAAAAATA
1 AAAATATTAAAAATA
179759 AAAATATT-AAAATA
1 AAAATATTAAAAATA
179773 AAAATATTA
1 AAAATATTA
179782 TATTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATTAAAAATA
Found at i:197129 original size:17 final size:16
Alignment explanation
Indices: 197105--197136 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
197095 TTTTAGAAAG
197105 AATAAATTTTTTTATA
1 AATAAATTTTTTTATA
197121 AATATAATTTTTTTAT
1 AATA-AATTTTTTTAT
197137 TATTTTATAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATAAATTTTTTTATA
Found at i:209622 original size:241 final size:240
Alignment explanation
Indices: 209190--209673 Score: 927
Period size: 241 Copynumber: 2.0 Consensus size: 240
209180 TAGTGTTCTG
209190 ATTATAATTGGAACAAATCATCTTCTTCCAAATTGATTCGCTATCATTTGCAAAACTTCCAAAAC
1 ATTATAATTGGAACAAATCATCTTCTTCCAAATTGATTCGCTATCATTTGCAAAACTTCCAAAAC
209255 CATTTCTCTATAAGCCCTATTCATAAAATTAAGATTCAGCACACCCAGACCACTACAACTTCTTG
66 CATTTCTCTATAAGCCCTATTCATAAAATTAAGATTCAGCACACCCAGACCACTACAACTTCTTG
209320 ATTTACACAACTGTTGACCAGTTAACCCAGTGTATTTTCTTAGATTCTGCCCTCCTCCCCACAAA
131 ATTTACACAACTGTTGACCAGTTAACCCAGTGTATTTTCTTAGATTCTGCCCTCCTCCCCACAAA
209385 AAATTGGCCATGATGGATTGCAACTTAGAATTCACTGCTGCTGGA
196 AAATTGGCCATGATGGATTGCAACTTAGAATTCACTGCTGCTGGA
209430 ATTATAATTGGAACAAATCATCTTCTTCC-AATTGATTCGCTATCATTTGCAAAACTTCCAAAAC
1 ATTATAATTGGAACAAATCATCTTCTTCCAAATTGATTCGCTATCATTTGCAAAACTTCCAAAAC
209494 CATTTCTCTAATAAGGCCCTATTCATAAAATTAAGATTCAGCACACCCAGACCACTACAACTTCT
66 CATTTCTCT-ATAA-GCCCTATTCATAAAATTAAGATTCAGCACACCCAGACCACTACAACTTCT
209559 TGATTTACAC-ACTGTTGACCAGTTAACCCAGTGTATTTTCTTAGATTCTGCCCCTCCTCCCCAC
129 TGATTTACACAACTGTTGACCAGTTAACCCAGTGTATTTTCTTAGATTCTG-CCCTCCTCCCCAC
209623 AAAAAATTGGCCATGATGGATTGCAACTTAGAATTCACTGCTGCTGGA
193 AAAAAATTGGCCATGATGGATTGCAACTTAGAATTCACTGCTGCTGGA
209671 ATT
1 ATT
209674 TTAAACATAG
Statistics
Matches: 241, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
239 44 0.18
240 73 0.30
241 124 0.51
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (240 bp):
ATTATAATTGGAACAAATCATCTTCTTCCAAATTGATTCGCTATCATTTGCAAAACTTCCAAAAC
CATTTCTCTATAAGCCCTATTCATAAAATTAAGATTCAGCACACCCAGACCACTACAACTTCTTG
ATTTACACAACTGTTGACCAGTTAACCCAGTGTATTTTCTTAGATTCTGCCCTCCTCCCCACAAA
AAATTGGCCATGATGGATTGCAACTTAGAATTCACTGCTGCTGGA
Found at i:212439 original size:18 final size:17
Alignment explanation
Indices: 212411--212444 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
212401 CAATGAAGAA
212411 GAGGAGAAGATGAAAGT
1 GAGGAGAAGATGAAAGT
212428 GAGGAGGAAGATGAAAG
1 GAGGA-GAAGATGAAAG
212445 CTTAGGTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (17 bp):
GAGGAGAAGATGAAAGT
Found at i:217555 original size:17 final size:17
Alignment explanation
Indices: 217533--217566 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
217523 GCCAGTCTTT
217533 CTAGCCCAGTAAATTTG
1 CTAGCCCAGTAAATTTG
217550 CTAGCCCAGTAAATTTG
1 CTAGCCCAGTAAATTTG
217567 GAACCATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
CTAGCCCAGTAAATTTG
Found at i:220897 original size:75 final size:74
Alignment explanation
Indices: 220805--220955 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 74
220795 AAATTCATAT
220805 ACAACAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTCT
1 ACAACAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTCT
220870 CAAACAAGG
66 CAAACAAGG
220879 ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
1 ACAAC-AAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
220944 TCAAACAAGG
65 TCAAACAAGG
220954 AC
1 AC
220956 CTCTCGGTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 5 0.07
75 71 0.93
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (74 bp):
ACAACAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTCT
CAAACAAGG
Found at i:221406 original size:20 final size:19
Alignment explanation
Indices: 221378--221416 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
221368 AGCCAAACAT
221378 AGAAATTCTCAAACAGTAAA
1 AGAAATTCTCAAACA-TAAA
* *
221398 AGAACTTCTGAAACATAAA
1 AGAAATTCTCAAACATAAA
221417 TGCAGTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (19 bp):
AGAAATTCTCAAACATAAA
Found at i:234135 original size:22 final size:22
Alignment explanation
Indices: 234104--234152 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
234094 TTGAAAATCG
*
234104 CGTTGCGATAGTCTACAGTTGT
1 CGTTGAGATAGTCTACAGTTGT
*
234126 CGTTGAGATAGTTTACAGTTGT
1 CGTTGAGATAGTCTACAGTTGT
234148 CGTTG
1 CGTTG
234153 CGATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (22 bp):
CGTTGAGATAGTCTACAGTTGT
Found at i:234281 original size:15 final size:15
Alignment explanation
Indices: 234261--234291 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
234251 ATTACCATGA
234261 ACACGACCCGACCCG
1 ACACGACCCGACCCG
234276 ACACGACCCGACCCG
1 ACACGACCCGACCCG
234291 A
1 A
234292 GACGGACAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.19, T:0.00
Consensus pattern (15 bp):
ACACGACCCGACCCG
Found at i:234506 original size:42 final size:42
Alignment explanation
Indices: 234429--234530 Score: 170
Period size: 42 Copynumber: 2.5 Consensus size: 42
234419 CCAACTGTAG
* *
234429 ACTATCGTAACGCGAAAT-GGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGGGAAAATCGCAACGCGATTTTCA
*
234470 ACTATCGCAACGCGAAATGGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGGAAAATCGCAACGCGATTTTCA
234512 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
234531 CAACGCTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 17 0.30
42 40 0.70
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
ACTATCGCAACGCGAAATGGGAAAATCGCAACGCGATTTTCA
Found at i:234534 original size:21 final size:21
Alignment explanation
Indices: 234429--234534 Score: 72
Period size: 21 Copynumber: 5.1 Consensus size: 21
234419 CCAACTGTAG
* *
234429 ACTATCGTAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
234450 A-AATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
234470 ACTATCGCAACGCGAAATGGGA
1 ACTATCGCAACGCGAAAT-GCA
* * ** *
234492 A-AATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
234512 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
234533 AC
1 AC
234535 GCTAATTTGC
Statistics
Matches: 58, Mismatches: 24, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
20 15 0.26
21 41 0.71
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:238040 original size:198 final size:201
Alignment explanation
Indices: 237699--238098 Score: 770
Period size: 198 Copynumber: 2.0 Consensus size: 201
237689 TAGCTCTTTC
237699 ATTCGATTCAATAGTTCACCAGCCTAGATTGTCCGAAAAATTAACTTTCGTTTGTGTCCAAATCT
1 ATTCGATTCAATAGTTCACCAGCCTAGATTGTCCGAAAAATTAACTTTCGTTTGTGTCCAAATCT
237764 CCACATTTATTTCTATTTGTCACTTTTTTTTTAATGAAGTTGACCTATATGGTTATCAAAATCTT
66 CCACATTTATTTCTATTTGTCACTTTTTTTTTAATGAAGTTGACCTATATGGTTATCAAAATCTT
237829 TGCAGAATGGGTAGTCAACCTGCTGCCAACAGGTCAACCGGAACCATCAAAATGAAGGGACAGTC
131 TGCAGAATGGGTAGTCAACCTGCTGCCAACAGGTCAACCGGAACCATCAAAATGAAGGGACAGTC
237894 GATTGA
196 GATTGA
237900 ATTCGATTCAATAGTTCACCAGCCTAGATTGTCCG-AAAATT-ACTTTCGTTTGTGTCC-AATCT
1 ATTCGATTCAATAGTTCACCAGCCTAGATTGTCCGAAAAATTAACTTTCGTTTGTGTCCAAATCT
237962 CCACATTTATTTCTATTTGTCACTTTTTTTTTAATGAAGTTGACCTATATGGTTATCAAAATCTT
66 CCACATTTATTTCTATTTGTCACTTTTTTTTTAATGAAGTTGACCTATATGGTTATCAAAATCTT
*
238027 TGCAGAATGGGTAGTCAACCTGCTGCCAACAGGTCAACCGGAACCATCGAAATGAAGGGACAGTC
131 TGCAGAATGGGTAGTCAACCTGCTGCCAACAGGTCAACCGGAACCATCAAAATGAAGGGACAGTC
238092 GATTGA
196 GATTGA
238098 A
1 A
238099 CAGAACAACT
Statistics
Matches: 198, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
198 141 0.71
199 16 0.08
200 6 0.03
201 35 0.18
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (201 bp):
ATTCGATTCAATAGTTCACCAGCCTAGATTGTCCGAAAAATTAACTTTCGTTTGTGTCCAAATCT
CCACATTTATTTCTATTTGTCACTTTTTTTTTAATGAAGTTGACCTATATGGTTATCAAAATCTT
TGCAGAATGGGTAGTCAACCTGCTGCCAACAGGTCAACCGGAACCATCAAAATGAAGGGACAGTC
GATTGA
Found at i:239861 original size:17 final size:17
Alignment explanation
Indices: 239839--239879 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
239829 ATGGTTTTCA
239839 GAACCGGACCGATTAGC
1 GAACCGGACCGATTAGC
*
239856 GAACCGGACCGGTTAGC
1 GAACCGGACCGATTAGC
239873 GAACCGG
1 GAACCGG
239880 TCATGCTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.34, T:0.10
Consensus pattern (17 bp):
GAACCGGACCGATTAGC
Found at i:242443 original size:17 final size:19
Alignment explanation
Indices: 242417--242451 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
242407 AATCCGAATA
242417 AAAAAGAGAAAT-TCAAAT
1 AAAAAGAGAAATATCAAAT
242435 AAAAA-AGAAATATCAAA
1 AAAAAGAGAAATATCAAA
242452 CAAGGAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (19 bp):
AAAAAGAGAAATATCAAAT
Found at i:247406 original size:17 final size:17
Alignment explanation
Indices: 247365--247408 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
247355 TATACTATTG
*
247365 TTAAAAGTAGTATCAGTA
1 TTAAAA-TAGTATCAATA
* *
247383 CTGAAATAGTATCAATA
1 TTAAAATAGTATCAATA
247400 TTAAAATAG
1 TTAAAATAG
247409 CTTACTCGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (17 bp):
TTAAAATAGTATCAATA
Found at i:250127 original size:2 final size:2
Alignment explanation
Indices: 250120--250152 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
250110 GTATTTGACA
250120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250153 ATTTGGGCAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:250790 original size:73 final size:73
Alignment explanation
Indices: 250733--250898 Score: 221
Period size: 73 Copynumber: 2.3 Consensus size: 73
250723 TTTACGAGTT
250733 TTAATT-AAG-GGTTTTGAGTTCGAGTCAGACTTTAAAATTTTTAGGTTTGCAAGTTTTCGAACT
1 TTAATTCAAGAGGTTTTGAGTTCGAGTCAGACTTTAAAATTTTTAGGTTTGCAAGTTTTCGAACT
250796 GAATCAGC
66 GAATCAGC
* * * * * *
250804 TTCATTCTAGAGTTTTTGAGTTCGAGTCGGGCTTTAAAATTTTTAGGTTTGCGAGTTTTCGAACT
1 TTAATTCAAGAGGTTTTGAGTTCGAGTCAGACTTTAAAATTTTTAGGTTTGCAAGTTTTCGAACT
250869 GAATCAAGC
66 GAATC-AGC
* *
250878 TTCATTCTAGA-GTTTTCGAGT
1 TTAATTCAAGAGGTTTT-GAGT
250899 CGATATGAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
71 5 0.06
72 2 0.02
73 59 0.70
74 18 0.21
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (73 bp):
TTAATTCAAGAGGTTTTGAGTTCGAGTCAGACTTTAAAATTTTTAGGTTTGCAAGTTTTCGAACT
GAATCAGC
Found at i:261187 original size:51 final size:51
Alignment explanation
Indices: 261015--261536 Score: 767
Period size: 51 Copynumber: 10.1 Consensus size: 51
261005 TCATAAAATG
* * * ** *
261015 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACT
* * * * ** *
261071 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * *
261126 GGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
261177 AGTCCGCTCCCTATTCCTTCACG-GAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCA-GAGAGTATAGGACTCAATCTTCAACGAACT
261228 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
261279 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
261330 TGTCCGCTCCCTATTCATTAAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
261381 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
261432 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
261483 TGTCCGCTACCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
261534 TGT
1 TGT
261537 TTGCTTCACT
Statistics
Matches: 439, Mismatches: 21, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.00
51 361 0.82
52 2 0.00
55 37 0.08
56 38 0.09
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:262694 original size:27 final size:26
Alignment explanation
Indices: 262664--262783 Score: 92
Period size: 27 Copynumber: 4.6 Consensus size: 26
262654 TTGAACCCTC
262664 CTTTTATTTCTCTTTTTTCATTTTTCT
1 CTTTT-TTTCTCTTTTTTCATTTTTCT
*
262691 CTTTTCCTTC-C-TTTTTCAATTTTTTCT
1 CTTTT-TTTCTCTTTTTTC-A-TTTTTCT
262718 CTTTTTTT-TCTTTTCGTT--TTTTTCAT
1 CTTTTTTTCTCTTTT--TTCATTTTTC-T
*
262744 CATTTTTTCT-TTTTTCTCATTTTT-T
1 CTTTTTTTCTCTTTTT-TCATTTTTCT
*
262769 CTTCTTTTCTCTTTT
1 CTTTTTTTCTCTTTT
262784 ATTTCTTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
24 1 0.01
25 22 0.29
26 21 0.28
27 29 0.39
29 2 0.03
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (26 bp):
CTTTTTTTCTCTTTTTTCATTTTTCT
Found at i:262707 original size:18 final size:16
Alignment explanation
Indices: 262670--262783 Score: 63
Period size: 18 Copynumber: 6.6 Consensus size: 16
262660 CCTCCTTTTA
262670 TTTCTCTTTTTTCATT
1 TTTCTCTTTTTTCATT
*
262686 TTTCTCTTTTCCTTCCTT
1 TTTCTCTTTT--TTCATT
*
262704 TTTCAAT-TTTTTCTCTTT
1 TTTC--TCTTTTT-TCATT
*
262722 TTTTTCTTTTCGTT--TT
1 TTTCTCTTTT--TTCATT
*
262738 TTTCATCATTTTTTCTTT
1 TTTC-TC-TTTTTTCATT
*
262756 TTTCTCATTTTTTCTTCT
1 TTTCTC-TTTTTTCAT-T
262774 TTTCTCTTTT
1 TTTCTCTTTT
262784 ATTTCTTCTT
Statistics
Matches: 81, Mismatches: 4, Indels: 25
0.74 0.04 0.23
Matches are distributed among these distances:
16 18 0.22
17 23 0.28
18 34 0.42
19 5 0.06
20 1 0.01
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTCTCTTTTTTCATT
Found at i:262732 original size:43 final size:43
Alignment explanation
Indices: 262670--262783 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 43
262660 CCTCCTTTTA
* *
262670 TTTCTCTTTTTTCAT-TTTTCTCTTTTCCTTC-CTTTTTCAATTT
1 TTTCTCTTTTTTCTTCTTTTCTCTTTTCCATCACTTTTTC--TTT
* * *
262713 TTTCTCTTTTTT-TTCTTTTCGTTTTTTTCATCATTTTTTCTTT
1 TTTCTCTTTTTTCTTCTTTTC-TCTTTTCCATCACTTTTTCTTT
262756 TTTCTCATTTTTTCTTCTTTTCTCTTTT
1 TTTCTC-TTTTTTCTTCTTTTCTCTTTT
262784 ATTTCTTCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 1 0.02
43 26 0.43
44 19 0.32
45 14 0.23
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (43 bp):
TTTCTCTTTTTTCTTCTTTTCTCTTTTCCATCACTTTTTCTTT
Found at i:262757 original size:20 final size:18
Alignment explanation
Indices: 262728--262790 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
262718 CTTTTTTTTC
262728 TTTTCGTTTTTTTCATCATT
1 TTTTC-TTTTTTTC-TCATT
262748 TTTTC-TTTTTTCTCATT
1 TTTTCTTTTTTTCTCATT
* *
262765 TTTTCTTCTTTTCTCTTT
1 TTTTCTTTTTTTCTCATT
262783 TATTTCTT
1 T-TTTCTT
262791 CTTCAAGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.26
18 18 0.46
19 6 0.15
20 5 0.13
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTTTTCTCATT
Found at i:262777 original size:36 final size:34
Alignment explanation
Indices: 262670--262790 Score: 99
Period size: 36 Copynumber: 3.5 Consensus size: 34
262660 CCTCCTTTTA
* *
262670 TTTCTC-TTTTTTCATTTTTCTC-TTTTCCTTCCT
1 TTTCTCATTTTTTCTTTTTTCTCTTTTTTCTT-CT
*
262703 TTT-TCAATTTTTTCTCTTTTT-T-TTCTTTTCGTTTT
1 TTTCTC-ATTTTTTCT-TTTTTCTCTT-TTTTC-TTCT
262738 TTTCATCATTTTTTCTTTTTTCTCATTTTTTCTTCT
1 TTTC-TCATTTTTTCTTTTTTCTC-TTTTTTCTTCT
*
262774 TTTCTCTTTTATTTCTT
1 TTTCTCATTT-TTTCTT
262791 CTTCAAGCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
32 2 0.03
33 3 0.04
34 9 0.13
35 23 0.32
36 25 0.35
37 7 0.10
38 2 0.03
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.74
Consensus pattern (34 bp):
TTTCTCATTTTTTCTTTTTTCTCTTTTTTCTTCT
Found at i:262788 original size:19 final size:18
Alignment explanation
Indices: 262670--262793 Score: 86
Period size: 17 Copynumber: 7.1 Consensus size: 18
262660 CCTCCTTTTA
*
262670 TTTCTC-TTTTTTCAT-T
1 TTTCTCATTTTTTCTTCT
*
262686 TTTCTC--TTTTCCTTCCT
1 TTTCTCATTTTTTCTT-CT
262703 TTT-TCAATTTTTTC-TCT
1 TTTCTC-ATTTTTTCTTCT
* *
262720 TTT-T-TTTCTTTTCGTTTT
1 TTTCTCATT-TTTTC-TTCT
262738 TTTCATCATTTTTTCTT-T
1 TTTC-TCATTTTTTCTTCT
262756 TTTCTCATTTTTTCTTCT
1 TTTCTCATTTTTTCTTCT
*
262774 TTTCTCTTTTATTTCTTCT
1 TTTCTCATTT-TTTCTTCT
262793 T
1 T
262794 CAAGCAAAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.09
16 13 0.15
17 22 0.25
18 21 0.24
19 16 0.18
20 6 0.07
21 2 0.02
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTCTCATTTTTTCTTCT
Found at i:272490 original size:44 final size:47
Alignment explanation
Indices: 272426--272522 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 47
272416 TGTTATCCAT
*
272426 AAAAAGAAATCCTAACCGCATGATATCTAATTCACATGC-TTATTC-
1 AAAAACAAATCCTAACCGCATGATATCTAATTCACATGCATTATTCG
* *
272471 AAAAACAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAACAAATCCTAACCGCATGATATCTAATTCACATGCA-TTATTCG
272518 AAAAA
1 AAAAA
272523 ACGAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 27 0.59
45 8 0.17
46 6 0.13
47 5 0.11
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (47 bp):
AAAAACAAATCCTAACCGCATGATATCTAATTCACATGCATTATTCG
Found at i:276349 original size:21 final size:21
Alignment explanation
Indices: 276324--276364 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
276314 TTTGAAAAAG
276324 AATTAA-AAGTTTAGATACTAA
1 AATTAATAA-TTTAGATACTAA
276345 AATTAATAATTTAGATACTA
1 AATTAATAATTTAGATACTA
276365 GACAATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (21 bp):
AATTAATAATTTAGATACTAA
Found at i:276833 original size:20 final size:20
Alignment explanation
Indices: 276783--276833 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
276773 AATTAACTAT
*
276783 TTATATTTTATAAATATTTT
1 TTATATTTTATAAATATTTA
* **
276803 TTCTAGATTATAAAT-TTTCA
1 TTATATTTTATAAATATTT-A
276823 TTATATTTTAT
1 TTATATTTTAT
276834 TTTTGTTTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATATTTTATAAATATTTA
Found at i:277611 original size:13 final size:13
Alignment explanation
Indices: 277595--277620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
277585 AACTTTATTA
277595 AAACTATTTAAGT
1 AAACTATTTAAGT
277608 AAACTATTTAAGT
1 AAACTATTTAAGT
277621 TAAGGGTAAA
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AAACTATTTAAGT
Found at i:279491 original size:8 final size:8
Alignment explanation
Indices: 279480--279531 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
279470 CCAAAACACA
279480 CTCCCTCT
1 CTCCCTCT
279488 CTCCCTCT
1 CTCCCTCT
279496 CTCCCTCT
1 CTCCCTCT
*
279504 C-CCTCTCC
1 CTCC-CTCT
279512 CTCTCC-CT
1 CTC-CCTCT
*
279520 CTCCCTGT
1 CTCCCTCT
279528 CTCC
1 CTCC
279532 GATCTCCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 4 0.11
8 30 0.81
9 2 0.05
10 1 0.03
ACGTcount: A:0.00, C:0.63, G:0.02, T:0.35
Consensus pattern (8 bp):
CTCCCTCT
Found at i:279503 original size:6 final size:6
Alignment explanation
Indices: 279494--279525 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
279484 CTCTCTCCCT
279494 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
279526 GTCTCCGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:284778 original size:23 final size:24
Alignment explanation
Indices: 284726--284790 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
284716 AACACACATG
*
284726 AACGAACATAAACAAACAGATGTA
1 AACGAACATAAACAAACAGATATA
284750 AACGAACATAAACAAACAGA-ATA
1 AACGAACATAAACAAACAGATATA
*
284773 AACGAACGTAAACAAACA
1 AACGAACATAAACAAACA
284791 TAAATGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.62, C:0.18, G:0.11, T:0.09
Consensus pattern (24 bp):
AACGAACATAAACAAACAGATATA
Found at i:289679 original size:18 final size:18
Alignment explanation
Indices: 289656--289703 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
289646 ACCCTACTCC
289656 TCGGCGATGAAGGATTCA
1 TCGGCGATGAAGGATTCA
*
289674 TCGGCGATGACGGATTCA
1 TCGGCGATGAAGGATTCA
*
289692 TTGGCGATGAAG
1 TCGGCGATGAAG
289704 CCAGTCCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (18 bp):
TCGGCGATGAAGGATTCA
Found at i:290204 original size:22 final size:22
Alignment explanation
Indices: 290176--290219 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
290166 ATTCAGGTTC
290176 AGGCCGCTTCGATCAACCGATT
1 AGGCCGCTTCGATCAACCGATT
290198 AGGCCGCTTCGATCAACCGATT
1 AGGCCGCTTCGATCAACCGATT
290220 CATCTATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (22 bp):
AGGCCGCTTCGATCAACCGATT
Found at i:290753 original size:15 final size:15
Alignment explanation
Indices: 290730--290768 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
290720 TAACAACATT
*
290730 ATGAATTATTTAAGT
1 ATGAATTATTTAAGC
*
290745 ATTAATTATTTAAGC
1 ATGAATTATTTAAGC
290760 ATGAATTAT
1 ATGAATTAT
290769 ATAAACGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (15 bp):
ATGAATTATTTAAGC
Found at i:291922 original size:79 final size:81
Alignment explanation
Indices: 291824--291983 Score: 306
Period size: 79 Copynumber: 2.0 Consensus size: 81
291814 ACTCTTACTA
291824 TTAGAAAAAGAACAAATCAATCCTTATTAGGGATGGACATGGAACTCG-ATCCGACGGGTTTCGA
1 TTAGAAAAAGAACAAATCAATCCTTATTAGGGATGGACATGGAACTCGAATCCGACGGGTTTCGA
291888 TCCGACCTGATTCGAT
66 TCCGACCTGATTCGAT
291904 TTAG-AAAAGAACAAATCAATCCTTATTAGGGATGGACATGGAACTCGAATCCGACGGGTTTCGA
1 TTAGAAAAAGAACAAATCAATCCTTATTAGGGATGGACATGGAACTCGAATCCGACGGGTTTCGA
291968 TCCGACCTGATTCGAT
66 TCCGACCTGATTCGAT
291984 CAGATATGAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 43 0.54
80 36 0.46
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (81 bp):
TTAGAAAAAGAACAAATCAATCCTTATTAGGGATGGACATGGAACTCGAATCCGACGGGTTTCGA
TCCGACCTGATTCGAT
Found at i:293190 original size:19 final size:19
Alignment explanation
Indices: 293139--293192 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
293129 AAACGAAACC
*
293139 GGTTTTTTCGGTTC-GTTCG
1 GGTTTTTT-TGTTCGGTTCG
**
293158 GG-TTTTTT-AACGGTTCG
1 GGTTTTTTTGTTCGGTTCG
293175 GGTTTTTTTGTTCGGTTC
1 GGTTTTTTTGTTCGGTTC
293193 AGTTCGGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 11 0.41
19 8 0.30
ACGTcount: A:0.04, C:0.13, G:0.30, T:0.54
Consensus pattern (19 bp):
GGTTTTTTTGTTCGGTTCG
Found at i:295794 original size:14 final size:16
Alignment explanation
Indices: 295777--295809 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
295767 CCAATTTTTT
295777 ATTTAAT-AATT-AAA
1 ATTTAATAAATTGAAA
295791 ATTTAATAAATTGAAA
1 ATTTAATAAATTGAAA
295807 ATT
1 ATT
295810 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTAATAAATTGAAA
Found at i:302656 original size:2 final size:2
Alignment explanation
Indices: 302651--302679 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
302641 AAACCCAAAG
302651 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
302680 CCAAATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:312434 original size:18 final size:18
Alignment explanation
Indices: 312413--312448 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
312403 TATTGATTGC
312413 TGGTACAGGTTTGATCAG
1 TGGTACAGGTTTGATCAG
312431 TGGTACAGGTTTGATCAG
1 TGGTACAGGTTTGATCAG
312449 ATGTTCACTG
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:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (18 bp):
TGGTACAGGTTTGATCAG
Found at i:313826 original size:22 final size:22
Alignment explanation
Indices: 313785--313865 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
313775 CTCGTATAAA
313785 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
313808 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
313830 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
313852 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
313866 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:313861 original size:13 final size:13
Alignment explanation
Indices: 313799--313861 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
313789 CCGAAGTGCC
313799 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
313812 CC---GAAGTGC-
1 CCGTAGAATTGCA
313821 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
313834 CC---GAAGTGC-
1 CCGTAGAATTGCA
313843 CCGTAGAATTGCA
1 CCGTAGAATTGCA
313856 CCGTAG
1 CCGTAG
313862 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:315574 original size:21 final size:21
Alignment explanation
Indices: 315550--315594 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
315540 TCTTGTTCGT
* *
315550 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
315571 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
315592 TTG
1 TTG
315595 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:329361 original size:6 final size:6
Alignment explanation
Indices: 329350--329378 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
329340 GAAACTAGCC
329350 GGGGGT GGGGGT GGGGGT GGGGGT GGGGG
1 GGGGGT GGGGGT GGGGGT GGGGGT GGGGG
329379 GGAATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
GGGGGT
Found at i:330889 original size:14 final size:14
Alignment explanation
Indices: 330870--330916 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
330860 TGCCTACTCT
330870 CTCTCTCCCCCTCC
1 CTCTCTCCCCCTCC
*
330884 CTCTCT--CCCTCT
1 CTCTCTCCCCCTCC
*
330896 CTCTCTCCCTCTCC
1 CTCTCTCCCCCTCC
330910 CTCTCTC
1 CTCTCTC
330917 TTATTAGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
14 17 0.61
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (14 bp):
CTCTCTCCCCCTCC
Found at i:330895 original size:6 final size:6
Alignment explanation
Indices: 330866--330914 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
330856 TGTATGCCTA
* * *
330866 CTCTCT CTCTCC CCCTCCC TCTCTCC CTCTCT CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCT-CC -CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
330915 TCTTATTAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 29 0.81
7 4 0.11
8 3 0.08
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCTCC
Found at i:330902 original size:26 final size:26
Alignment explanation
Indices: 330866--330916 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
330856 TGTATGCCTA
330866 CTCTCTCTCTCCCCCTCCCTCTCTCC
1 CTCTCTCTCTCCCCCTCCCTCTCTCC
*
330892 CTCTCTCTCTCCCTCTCCCTCTCTC
1 CTCTCTCTCTCCCCCTCCCTCTCTC
330917 TTATTAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (26 bp):
CTCTCTCTCTCCCCCTCCCTCTCTCC
Found at i:337681 original size:29 final size:28
Alignment explanation
Indices: 337647--337775 Score: 159
Period size: 29 Copynumber: 4.5 Consensus size: 28
337637 ACCGTGTTAC
*
337647 ATTTTGGGAATTAATTTGAAATAGGTGTT
1 ATTTTGGGAATTAATTCGAAA-AGGTGTT
*
337676 ATTTTGGGAATTTAATTCGAAAATGTGTT
1 ATTTTGGGAA-TTAATTCGAAAAGGTGTT
* * *
337705 ATTTTGGGAATTTAATTAGAAAAAGTATT
1 ATTTTGGGAA-TTAATTCGAAAAGGTGTT
*
337734 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAAA-GGTGTT
*
337763 ATTTTGGTAATTA
1 ATTTTGGGAATTA
337776 TTTTAAAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 11 0.12
29 67 0.76
30 10 0.11
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCGAAAAGGTGTT
Found at i:337784 original size:29 final size:29
Alignment explanation
Indices: 337647--337795 Score: 117
Period size: 29 Copynumber: 5.1 Consensus size: 29
337637 ACCGTGTTAC
* * *
337647 ATTTTGGGAATTAATTTGAAATA-GGTGTT
1 ATTTTGGGAATTAA-TTCAAAAAGGGTGCT
* * *
337676 ATTTTGGGAATTTAATTCGAAAA-TGTGTT
1 ATTTTGGGAA-TTAATTCAAAAAGGGTGCT
* **
337705 ATTTTGGGAATTTAATT-AGAAAA-AGTATT
1 ATTTTGGGAA-TTAATTCA-AAAAGGGTGCT
*
337734 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCAAAAAGGGTGCT
* * *
337763 ATTTTGGTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTAATTCAAAAAGGGTGCT
337792 ATTT
1 ATTT
337796 CTGTAAAATG
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
28 10 0.10
29 87 0.86
30 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCAAAAAGGGTGCT
Found at i:337795 original size:58 final size:57
Alignment explanation
Indices: 337647--337795 Score: 158
Period size: 58 Copynumber: 2.6 Consensus size: 57
337637 ACCGTGTTAC
* * * *
337647 ATTTTGGGAATTAATTTGAAATAGGTGTTATTTTGGGAATTTAATTCGAAAATGTGTT
1 ATTTTGGGAATT-ATTTTAAAAAGGTGTTATTTTGGGAATTTAATTCGAAAAGGTGCT
* * *
337705 ATTTTGGGAATT-TAATTAGAAAAAGTATTATTTTGGGAA-TTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAT-TTTA-AAAAGGTGTTATTTTGGGAATTTAATTCGAAAA-GGTGCT
* *
337763 ATTTTGGTAATTATTTTAAAAAGGGTGCTATTT
1 ATTTTGGGAATTATTTTAAAAA-GGTGTTATTT
337796 CTGTAAAATG
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
56 1 0.01
57 18 0.24
58 54 0.73
59 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (57 bp):
ATTTTGGGAATTATTTTAAAAAGGTGTTATTTTGGGAATTTAATTCGAAAAGGTGCT
Done.