Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 17 of 27
Found at i:2597545 original size:80 final size:79
Alignment explanation
Indices: 2597461--2597668 Score: 245
Period size: 80 Copynumber: 2.6 Consensus size: 79
2597451 TTCCCTAGCT
2597461 TAATGTCACTGGCCTTGAATCAGCACATTGGCACACCATCAATGTCAAAAGGCACTTGTCGTATA
1 TAATGTCACTGGCCTTGAATCAGCACATTGGCACACCATCAATGTCAAAAGGCACTTGTCGTATA
*
2597526 GTTCTAGTCTAAGCC
66 GTTCTAGTCAAAG-C
* * * * * * *
2597541 TAATGTCACTAGCCTTGAATCAGCACATTGGCACCCCACCTATGCCAAAAGGCACTTGTTGTGTA
1 TAATGTCACTGGCCTTGAATCAGCACATTGGCACACCATCAATGTCAAAAGGCACTTGTCGTATA
2597606 GTTCTAGTCAAAGC
66 GTTCTAGTCAAAGC
* ** * * * ** *
2597620 TCAATATTGCTGGCCTTGAATTAGCATATTAGCATTCCATCACTGTCAA
1 T-AATGTCACTGGCCTTGAATCAGCACATTGGCACACCATCAATGTCAA
2597669 GAATCTTTAA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
79 2 0.02
80 104 0.98
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (79 bp):
TAATGTCACTGGCCTTGAATCAGCACATTGGCACACCATCAATGTCAAAAGGCACTTGTCGTATA
GTTCTAGTCAAAGC
Found at i:2611535 original size:15 final size:14
Alignment explanation
Indices: 2611498--2611536 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2611488 CAAGAATACA
2611498 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
2611512 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
2611528 AAAAAAAAA
1 AAAAAAAAA
2611537 ACCAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:2612306 original size:12 final size:11
Alignment explanation
Indices: 2612284--2612359 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
2612274 AGAGAAAGAA
*
2612284 GAGAGAGGAGG
1 GAGATAGGAGG
2612295 GATGATAGGAGG
1 GA-GATAGGAGG
*
2612307 AGAGACAGGA--
1 -GAGATAGGAGG
*
2612317 GAGATAGTA--
1 GAGATAGGAGG
2612326 GAGATAGGAGG
1 GAGATAGGAGG
2612337 GATGATAGGAGG
1 GA-GATAGGAGG
*
2612349 AGAGACAGGAG
1 -GAGATAGGAG
2612360 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:2612335 original size:42 final size:42
Alignment explanation
Indices: 2612274--2612392 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
2612264 TAGCCCTCAA
* *
2612274 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
2612316 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
2612358 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2612393 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2612376 original size:18 final size:18
Alignment explanation
Indices: 2612349--2612398 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2612339 TGATAGGAGG
*
2612349 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
2612367 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
2612385 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
2612399 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:2629380 original size:42 final size:42
Alignment explanation
Indices: 2629325--2629443 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
2629315 TTCTTCTCTC
* *
2629325 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
2629367 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
2629409 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
2629444 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:2629384 original size:12 final size:11
Alignment explanation
Indices: 2629358--2629433 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
2629348 TCTATTATCT
*
2629358 CTCCTGTCTCTC
1 CTCCTATCTC-C
2629370 CTCCTATCATCC
1 CTCCTATC-TCC
2629382 CTCCTATCT--
1 CTCCTATCTCC
*
2629391 CTACTATCT--
1 CTCCTATCTCC
*
2629400 CTCCTGTCTCTC
1 CTCCTATCTC-C
2629412 CTCCTATCATCC
1 CTCCTATC-TCC
*
2629424 CTCCTCTCTC
1 CTCCTATCTC
2629434 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:2629385 original size:24 final size:24
Alignment explanation
Indices: 2629349--2629434 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2629339 CCTCCTCTCT
* *
2629349 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
2629373 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
2629394 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
2629415 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
2629435 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:2629409 original size:18 final size:18
Alignment explanation
Indices: 2629340--2629410 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
2629330 CCTGTCATCC
* *
2629340 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
2629358 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
2629380 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
2629400 CTCCTGTCTCT
1 CTCCTGTCTCT
2629411 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:2634139 original size:26 final size:26
Alignment explanation
Indices: 2634103--2634160 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2634093 TTTTGATATT
*
2634103 TGATTTGGGATGAAGAACCTAGATTA
1 TGATTCGGGATGAAGAACCTAGATTA
2634129 TGATTCGGGATGAAGAACCTAGATTA
1 TGATTCGGGATGAAGAACCTAGATTA
2634155 TGATTC
1 TGATTC
2634161 TAGGTTCGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (26 bp):
TGATTCGGGATGAAGAACCTAGATTA
Found at i:2634800 original size:34 final size:34
Alignment explanation
Indices: 2634749--2634885 Score: 91
Period size: 35 Copynumber: 3.9 Consensus size: 34
2634739 GACAAGTTTG
*
2634749 GTGCCACTAGA-TAGTGTGGACTT-CAAAGAGGATT
1 GTGCCACT-GACTTGTGTGGACTTGCAAA-AGGATT
* * *
2634783 GTGCCACTGACTTGTGTGAACTTTGGAAAAGGTTT
1 GTGCCACTGACTTGTGTGGAC-TTGCAAAAGGATT
* ** * *
2634818 GTGCCATTGACTTAAGTGGACTTTGGAAAAGGTTT
1 GTGCCACTGACTTGTGTGGAC-TTGCAAAAGGATT
**
2634853 GATTGCCACCAACTTGTGTGGACTTTG-AAAAGG
1 G--TGCCACTGACTTGTGTGGAC-TTGCAAAAGG
2634886 GTTTGGTTGC
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 16 0.19
35 39 0.46
36 9 0.11
37 19 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (34 bp):
GTGCCACTGACTTGTGTGGACTTGCAAAAGGATT
Found at i:2634829 original size:35 final size:35
Alignment explanation
Indices: 2634781--2634890 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
2634771 TCAAAGAGGA
*
2634781 TTGTGCCACTGACTTGTGTGAACTTTGGAAAAGGT
1 TTGTGCCACTGACTTGTGTGGACTTTGGAAAAGGT
* **
2634816 TTGTGCCATTGACTTAAGTGGACTTTGGAAAAGGT
1 TTGTGCCACTGACTTGTGTGGACTTTGGAAAAGGT
**
2634851 TTGATTGCCACCAACTTGTGTGGACTTT-GAAAAGGGT
1 TTG--TGCCACTGACTTGTGTGGACTTTGGAAAA-GGT
2634888 TTG
1 TTG
2634891 GTTGCCATCA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
35 34 0.54
36 5 0.08
37 24 0.38
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.35
Consensus pattern (35 bp):
TTGTGCCACTGACTTGTGTGGACTTTGGAAAAGGT
Found at i:2634874 original size:37 final size:36
Alignment explanation
Indices: 2634792--2634910 Score: 134
Period size: 37 Copynumber: 3.3 Consensus size: 36
2634782 TGTGCCACTG
* **
2634792 ACTTGTGTGAACTTTGGAAAAGGTTTG-TGCCATTG
1 ACTTGTGTGGACTTTGGAAAAGGTTTGTTGCCATCA
** *
2634827 ACTTAAGTGGACTTTGGAAAAGGTTTGATTGCCACCA
1 ACTTGTGTGGACTTTGGAAAAGGTTTG-TTGCCATCA
2634864 ACTTGTGTGGACTTT-GAAAAGGGTTTGGTTGCCATCA
1 ACTTGTGTGGACTTTGGAAAA-GGTTT-GTTGCCATCA
*
2634901 ACTCGTGTGG
1 ACTTGTGTGG
2634911 GCTTAAAAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
35 24 0.34
36 5 0.07
37 40 0.57
38 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (36 bp):
ACTTGTGTGGACTTTGGAAAAGGTTTGTTGCCATCA
Found at i:2634920 original size:36 final size:37
Alignment explanation
Indices: 2634833--2634920 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
2634823 ATTGACTTAA
* *
2634833 GTGGACTTTGGAAAA-GGTTTGATTGCCACCAACTTGT
1 GTGGACTTT-AAAAAGGGTTTGATTGCCACCAACTCGT
* * *
2634870 GTGGACTTTGAAAAGGGTTTGGTTGCCATCAACTCGT
1 GTGGACTTTAAAAAGGGTTTGATTGCCACCAACTCGT
*
2634907 GTGGGC-TTAAAAAG
1 GTGGACTTTAAAAAG
2634921 AGGTCGCCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.31
Consensus pattern (37 bp):
GTGGACTTTAAAAAGGGTTTGATTGCCACCAACTCGT
Found at i:2634944 original size:33 final size:32
Alignment explanation
Indices: 2634894--2635092 Score: 218
Period size: 32 Copynumber: 6.2 Consensus size: 32
2634884 GGGTTTGGTT
* *
2634894 GCCATCAACTCGTGTGGGCTTAAAAAGAGGTC
1 GCCACCAACTCGTGTGGGCTTAAGAAGAGGTC
* *
2634926 GCCACCACACTCGGGTGGGCTTAAGAAGAGGTT
1 GCCACCA-ACTCGTGTGGGCTTAAGAAGAGGTC
* * * * *
2634959 GACACTAACTCATTTTGGCTTAAGAAGAGGTC
1 GCCACCAACTCGTGTGGGCTTAAGAAGAGGTC
* * *
2634991 ACCACCAAACTTGTGTGGGCTTAAGAAGAGGTT
1 GCCACC-AACTCGTGTGGGCTTAAGAAGAGGTC
*
2635024 GCCACTAACTCGTGTGGGCTTAAGAAGAGGTC
1 GCCACCAACTCGTGTGGGCTTAAGAAGAGGTC
* * * * *
2635056 ACCACCAATTCTTGCGGGCTTAAGAAAAGGTC
1 GCCACCAACTCGTGTGGGCTTAAGAAGAGGTC
2635088 GCCAC
1 GCCAC
2635093 TGTAGACACC
Statistics
Matches: 135, Mismatches: 30, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
32 83 0.61
33 52 0.39
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (32 bp):
GCCACCAACTCGTGTGGGCTTAAGAAGAGGTC
Found at i:2634979 original size:65 final size:65
Alignment explanation
Indices: 2634900--2635063 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 65
2634890 GGTTGCCATC
* * * *
2634900 AACTCGTGTGGGCTTAAAAAGAGGTCGCCACCACACTCGGGTGGGCTTAAGAAGAGGTTGACACT
1 AACTCATGTGGGCTTAAGAAGAGGTCACCACCAAACTCGGGTGGGCTTAAGAAGAGGTTGACACT
* * * * *
2634965 AACTCATTTTGGCTTAAGAAGAGGTCACCACCAAACTTGTGTGGGCTTAAGAAGAGGTTGCCACT
1 AACTCATGTGGGCTTAAGAAGAGGTCACCACCAAACTCGGGTGGGCTTAAGAAGAGGTTGACACT
*
2635030 AACTCGTGTGGGCTTAAGAAGAGGTCACCACCAA
1 AACTCATGTGGGCTTAAGAAGAGGTCACCACCAA
2635064 TTCTTGCGGG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 87 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (65 bp):
AACTCATGTGGGCTTAAGAAGAGGTCACCACCAAACTCGGGTGGGCTTAAGAAGAGGTTGACACT
Found at i:2634982 original size:32 final size:32
Alignment explanation
Indices: 2634900--2635054 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 32
2634890 GGTTGCCATC
* * * *
2634900 AACTCGTGTGGGCTTAAAAAGAGGTCGCCACC
1 AACTCGTGTGGGCTTAAGAAGAGGTTGACACT
*
2634932 ACACTCGGGTGGGCTTAAGAAGAGGTTGACACT
1 A-ACTCGTGTGGGCTTAAGAAGAGGTTGACACT
* * * * *
2634965 AACTCATTTTGGCTTAAGAAGAGG-TCACCACCA
1 AACTCGTGTGGGCTTAAGAAGAGGTTGA-CA-CT
* *
2634998 AACTTGTGTGGGCTTAAGAAGAGGTTGCCACT
1 AACTCGTGTGGGCTTAAGAAGAGGTTGACACT
2635030 AACTCGTGTGGGCTTAAGAAGAGGT
1 AACTCGTGTGGGCTTAAGAAGAGGT
2635055 CACCACCAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
31 2 0.02
32 47 0.47
33 50 0.50
34 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (32 bp):
AACTCGTGTGGGCTTAAGAAGAGGTTGACACT
Found at i:2635076 original size:97 final size:98
Alignment explanation
Indices: 2634900--2635092 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 98
2634890 GGTTGCCATC
* *
2634900 AACTCGTGTGGGCTTAAAAAGAGGTCGCCACCACACTCGGGTGGGCTTAAGAAGAGGTTGACACT
1 AACTCGTGTGGGCTTAAAAAGAGGTCGCCACCACACTCGGGTGGGCTTAAGAAGAGGTTCACACC
** *
2634965 AACTCATTTTGGCTTAAGAAGAGGTCACCACCA
66 AACTCATTCGGGCTTAAGAAAAGGTCACCACCA
* * * * *
2634998 AACTTGTGTGGGCTTAAGAAGAGGTTGCCACTA-ACTCGTGTGGGCTTAAGAAGAGG-TCACCAC
1 AACTCGTGTGGGCTTAAAAAGAGGTCGCCACCACACTCGGGTGGGCTTAAGAAGAGGTTCA-CAC
* *
2635061 CAATTC-TTGCGGGCTTAAGAAAAGGTCGCCAC
65 CAACTCATT-CGGGCTTAAGAAAAGGTCACCAC
2635093 TGTAGACACC
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
96 4 0.05
97 48 0.59
98 29 0.36
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (98 bp):
AACTCGTGTGGGCTTAAAAAGAGGTCGCCACCACACTCGGGTGGGCTTAAGAAGAGGTTCACACC
AACTCATTCGGGCTTAAGAAAAGGTCACCACCA
Found at i:2635432 original size:22 final size:23
Alignment explanation
Indices: 2635404--2635453 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2635394 GTTCCCATGA
2635404 CAGCAACCA-TTTCAGCTACTGG
1 CAGCAACCATTTTCAGCTACTGG
**
2635426 CAGCAACCATTTTCAGCTGGTGG
1 CAGCAACCATTTTCAGCTACTGG
2635449 CAGCA
1 CAGCA
2635454 GCTAATCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (23 bp):
CAGCAACCATTTTCAGCTACTGG
Found at i:2637826 original size:202 final size:203
Alignment explanation
Indices: 2637480--2637853 Score: 556
Period size: 202 Copynumber: 1.8 Consensus size: 203
2637470 TTTATTCATG
* *
2637480 GGGATACTCCAACCCTTCTCTTCAAAATTTATCTAGATTTGAACTCCTTCTTTGTCAAAATTATT
1 GGGATACTCCAACCCTGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAAATTATT
* * *
2637545 TGTTATCCATAGGGATACTCCAATCCTGACCTTTCAAGTGGATACTCCAACCACGCTCTTCAAAA
66 TGTTATCCATAGGGATACTCCAATCCCGACCTTTCAAGGGGATACTCCAACCACACTCTTCAAAA
* *
2637610 TTTATCTAGATTTGAA-CTCTTTTGTCAAAATTATTTGTTATCCACGAGGATACTCCAACCCGAC
131 TTTATCAAGATTTGAACCTCTTTTATCAAAATTATTTGTTATCCACGAGGATACTCCAACCCGAC
2637674 CTTTTAAA
196 CTTTTAAA
* *
2637682 GGGATACTCTAA-CCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAAGTTAT
1 GGGATACTCCAACCCT-GCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAAATTAT
* * * * *
2637746 TTGTTATCCATGGGGATACTCCAA-CCACGACTTTTCGAGGGGATACTCTAACCTCACTCTTCAA
65 TTGTTATCCATAGGGATACTCCAATCC-CGACCTTTCAAGGGGATACTCCAACCACACTCTTCAA
*
2637810 AATTTATCAAGATTTGAACTCCTCTTTTATTAAAATTATTTGTT
129 AATTTATCAAGATTTGAA--CCTCTTTTATCAAAATTATTTGTT
2637854 CTCTATAGGG
Statistics
Matches: 152, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
201 5 0.03
202 126 0.83
205 21 0.14
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (203 bp):
GGGATACTCCAACCCTGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAAATTATT
TGTTATCCATAGGGATACTCCAATCCCGACCTTTCAAGGGGATACTCCAACCACACTCTTCAAAA
TTTATCAAGATTTGAACCTCTTTTATCAAAATTATTTGTTATCCACGAGGATACTCCAACCCGAC
CTTTTAAA
Found at i:2637827 original size:103 final size:102
Alignment explanation
Indices: 2637474--2637869 Score: 516
Period size: 103 Copynumber: 3.9 Consensus size: 102
2637464 CAAAATTTTA
* * *
2637474 TTCATGGGGATACTCCAACC-CTTCTCTTCAAAATTTATCTAGATTTGAACTCCTTCTTTGTCAA
1 TTCAAGGGGATACTCCAACCTC-GCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAA
* *
2637538 AATTATTTGTTATCCATAGGGATACTCCAATCCTGACCT
65 AATTATTTGTTATCCATAGGGATACTCCAA-CCCGACTT
* *
2637577 TTCAAGTGGATACTCCAACCACGCTCTTCAAAATTTATCTAGATTTGAACT-CT--TTTGTCAAA
1 TTCAAGGGGATACTCCAACCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAA
*
2637639 ATTATTTGTTATCCA-CGAGGATACTCCAACCCGACCTT
66 ATTATTTGTTATCCATAG-GGATACTCCAACCCGA-CTT
* *
2637677 TT-AAAGGGATACTCTAACCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAA
1 TTCAAGGGGATACTCCAACCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAA
* *
2637741 GTTATTTGTTATCCATGGGGATACTCCAACCACGACTT
66 ATTATTTGTTATCCATAGGGATACTCCAACC-CGACTT
* * * * * * *
2637779 TTCGAGGGGATACTCTAACCTCACTCTTCAAAATTTATCAAGATTTGAACTCCTCTTTTATTAAA
1 TTCAAGGGGATACTCCAACCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAA
* *
2637844 ATTATTTGTTCTCTATAGGGATACTC
66 ATTATTTGTTATCCATAGGGATACTC
2637870 TAAACCCATC
Statistics
Matches: 261, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
99 49 0.19
100 41 0.16
102 43 0.16
103 127 0.49
104 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (102 bp):
TTCAAGGGGATACTCCAACCTCGCTCTTCAAAATTTATCTAGATTTGAACTCCTCCTTTGTCAAA
ATTATTTGTTATCCATAGGGATACTCCAACCCGACTT
Found at i:2656330 original size:77 final size:78
Alignment explanation
Indices: 2656203--2656358 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 78
2656193 AAATGGGAAA
* * * **
2656203 GAAAGTTTTTGGCAAGAAGAAAACTCCATAGATACAGACGACAGAAGTGGAAAAAAAAGATGAAA
1 GAAAGTTTTTGGCAAGAAGAAAACTCCAGAAATACAGACAACAGAAGTGGAAAAAAAAGACAAAA
*
2656268 AT-GAAACAAAGT
66 ATAAAAACAAAGT
* *
2656280 GAAAGTTTTTGGCAAGAAGAAAACTCCAGAAATATAGACAAGAGAAGTGGAAAAAAAAGACAAAA
1 GAAAGTTTTTGGCAAGAAGAAAACTCCAGAAATACAGACAACAGAAGTGGAAAAAAAAGACAAAA
2656345 ATAAAAACAAAGT
66 ATAAAAACAAAGT
2656358 G
1 G
2656359 GCCCTAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
77 60 0.86
78 10 0.14
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (78 bp):
GAAAGTTTTTGGCAAGAAGAAAACTCCAGAAATACAGACAACAGAAGTGGAAAAAAAAGACAAAA
ATAAAAACAAAGT
Found at i:2659017 original size:30 final size:30
Alignment explanation
Indices: 2658919--2659020 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
2658909 CTAGCAAATG
*
2658919 ACCTTGGGCAAAACTAAGAGTAAACAAAC-
1 ACCTTGGGCAAAACCAAGAGTAAACAAACA
* * ** * *
2658948 AGCTTAGGTGAAACCAAGAATCAAACAAATA
1 ACCTTGGGCAAAACCAAGAGT-AAACAAACA
* *
2658979 ATCTTGGGCAAAACCAAGAGTAAACCAACA
1 ACCTTGGGCAAAACCAAGAGTAAACAAACA
2659009 ACCTTGGGCAAA
1 ACCTTGGGCAAA
2659021 GATACGATCA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
29 15 0.27
30 25 0.45
31 16 0.29
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (30 bp):
ACCTTGGGCAAAACCAAGAGTAAACAAACA
Found at i:2663509 original size:28 final size:28
Alignment explanation
Indices: 2663475--2663724 Score: 239
Period size: 28 Copynumber: 9.0 Consensus size: 28
2663465 CACCAGCTAG
*
2663475 TGTGGGCTTT-AAAGAGGTGCCATTGACT
1 TGTGGGCTTTGAAA-AGGTGCCACTGACT
*
2663503 CGTGGGCTTT-AAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAA-GGTGCCACTGACT
2663531 TGTGGGCTTT-AAAAGGGTG-C-C--ACT
1 TGTGGGCTTTGAAAA-GGTGCCACTGACT
* **
2663555 TGTGGGCTTTG-AAAGAATGCCTTTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * *
2663583 TATGGGCTTTGAAAGGGTGCCAGTCACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2663611 TATGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2663639 TGT-GGCTTTGAGAAAAAGTGCCATTGACT
1 TGTGGGCTTT--GAAAAGGTGCCACTGACT
* *
2663668 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
2663696 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2663724 T
1 T
2663725 ATGGAGGGTT
Statistics
Matches: 186, Mismatches: 25, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.01
24 18 0.10
25 1 0.01
26 1 0.01
27 8 0.04
28 130 0.70
29 21 0.11
30 6 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:2663684 original size:85 final size:84
Alignment explanation
Indices: 2663475--2663724 Score: 307
Period size: 85 Copynumber: 3.0 Consensus size: 84
2663465 CACCAGCTAG
* * * * *
2663475 TGTGGGCTTT-AAAGAGGTGCCATTGACTCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
2663539 TT-AAAAGGGTG-C-C-ACT
66 TTGAAAA-GGTGCCACTACT
* * * * * *
2663555 TGTGGGCTTTGAAAGAA-TGCCTTTGACTTATGGGCTTTGAAAGGGTGCCAGTCACTTATGGGCT
1 TGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
2663619 TTGAAAAGGTGCCACTAACT
66 TTGAAAAGGTGCCACT-ACT
2663639 TGT-GGCTTTGAGAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGA-AAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
*
2663703 TTTGAAAAGATGCCACTGACT
65 TTTGAAAAGGTGCCACT-ACT
2663724 T
1 T
2663725 ATGGAGGGTT
Statistics
Matches: 146, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
80 56 0.38
81 10 0.07
82 1 0.01
83 8 0.05
84 10 0.07
85 61 0.42
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (84 bp):
TGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
TTGAAAAGGTGCCACTACT
Found at i:2663717 original size:113 final size:108
Alignment explanation
Indices: 2663505--2663728 Score: 254
Period size: 113 Copynumber: 2.0 Consensus size: 108
2663495 CATTGACTCG
* **
2663505 TGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTTGTGGGCTTTGAAAG
1 TGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTAAAAAAGTGCCACTTGTGGGCTTTGAAAG
** * * * *
2663570 AATGCCTTTGACTTATGGGCTTTGAAAGGGTGCCAGTCACTTA
66 AATGCCACTAACTTATGGGCTTTGAAAAGATGCCACTCACTTA
2663613 TGGGCTTTGAAAA-GGTGCCACTAACTTGT-GGCTTTGAGAAAAAGTGCCATTGACTTGTGGGCT
1 TGGGCTTT-AAAAGGGTGCCACTAACTTGTGGGCTTT-A-AAAAAGTGCC----ACTTGTGGGCT
** * *
2663676 TTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTA
59 TTGAAAGAATGCCACTAACTTATGGGCTTTGAAAAGATGCCACTCACTTA
2663726 TGG
1 TGG
2663729 AGGGTTGGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
107 6 0.06
108 24 0.25
109 12 0.12
113 54 0.56
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (108 bp):
TGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTAAAAAAGTGCCACTTGTGGGCTTTGAAAG
AATGCCACTAACTTATGGGCTTTGAAAAGATGCCACTCACTTA
Found at i:2663812 original size:37 final size:36
Alignment explanation
Indices: 2663733--2664066 Score: 380
Period size: 37 Copynumber: 9.1 Consensus size: 36
2663723 TTATGGAGGG
* *
2663733 TTGGTTGCCACTGACTTGTGTGGACTTTGGAAAGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGAAAAGGT
*
2663769 TTGGTTGCCACCGATTTGTGTGGACTTTGAGAAAGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGA-AAAGGT
*
2663806 TTGGTTGCCACCGACTTCTGTGGACTTTGAAAAAAGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTG--AAAAGGT
* ** * * * *
2663844 TTAGTTGCCATTGACATATGTGGACTTTGAAAAAAGC
1 TTGGTTGCCACCGACTTGTGTGGACTTTG-AAAAGGT
* * **
2663881 TTGATTGCCACTGACTTGTGTGGACTTTGAATGGGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGAA-AAGGT
* **
2663918 TTGGTTGCCACCAACTTGTGTGGACTTTGAATGGGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGAA-AAGGT
**
2663955 TTGGTTGCCACCGACTTGTGTGGACTTTGAATGGGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGAA-AAGGT
*
2663992 TTGGTTGCCACCGACTTATGTGGACTTTGAAAAAGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTG-AAAAGGT
* * *
2664029 TTGGTTGCCACTGACTTGTGTAGACTTTTAAAAGGT
1 TTGGTTGCCACCGACTTGTGTGGACTTTGAAAAGGT
2664065 TT
1 TT
2664067 AGCACAGGTG
Statistics
Matches: 261, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
36 38 0.15
37 190 0.73
38 32 0.12
39 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.35
Consensus pattern (36 bp):
TTGGTTGCCACCGACTTGTGTGGACTTTGAAAAGGT
Found at i:2665263 original size:49 final size:49
Alignment explanation
Indices: 2665191--2665308 Score: 200
Period size: 49 Copynumber: 2.4 Consensus size: 49
2665181 ATTTTTTATA
* * * *
2665191 AGAAAGGTGATACGATTTGGTTCATTTCCAAGAAAATGGTCTGATGACT
1 AGAAAAGTGATGCAATTTGGTTCATTTCCAAGAAAACGGTCTGATGACT
2665240 AGAAAAGTGATGCAATTTGGTTCATTTCCAAGAAAACGGTCTGATGACT
1 AGAAAAGTGATGCAATTTGGTTCATTTCCAAGAAAACGGTCTGATGACT
2665289 AGAAAAGTGATGCAATTTGG
1 AGAAAAGTGATGCAATTTGG
2665309 GCCAATGATG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (49 bp):
AGAAAAGTGATGCAATTTGGTTCATTTCCAAGAAAACGGTCTGATGACT
Found at i:2671778 original size:27 final size:27
Alignment explanation
Indices: 2671758--2671825 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
2671748 GAAAGGCAGG
2671758 GTTGGAGTATCCCCTCGGAAAGAAGGA
1 GTTGGAGTATCCCCTCGGAAAGAAGGA
2671785 GTTGGAGTATCCCCTCGGAAAGAAGGA
1 GTTGGAGTATCCCCTCGGAAAGAAGGA
*
2671812 GTTTGAGTATCCCC
1 GTTGGAGTATCCCC
2671826 ATGAATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (27 bp):
GTTGGAGTATCCCCTCGGAAAGAAGGA
Found at i:2678650 original size:42 final size:42
Alignment explanation
Indices: 2678595--2678755 Score: 268
Period size: 42 Copynumber: 3.8 Consensus size: 42
2678585 TTCTTCTCTC
* * *
2678595 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
2678637 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
2678679 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
* * *
2678721 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
2678756 TTGAGGGCTA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 113 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:2678654 original size:12 final size:11
Alignment explanation
Indices: 2678628--2678745 Score: 72
Period size: 12 Copynumber: 10.9 Consensus size: 11
2678618 TCTATTATCT
*
2678628 CTCCTGTCTCTC
1 CTCCTATCTC-C
2678640 CTCCTATCATCC
1 CTCCTATC-TCC
2678652 CTCCTATCT--
1 CTCCTATCTCC
*
2678661 CTACTATCT--
1 CTCCTATCTCC
*
2678670 CTCCTGTCTCTC
1 CTCCTATCTC-C
2678682 CTCCTATCATCC
1 CTCCTATC-TCC
2678694 CTCCTATCT--
1 CTCCTATCTCC
*
2678703 CTACTATCT--
1 CTCCTATCTCC
*
2678712 CTCCTGTCTCTC
1 CTCCTATCTC-C
2678724 CTCCTATCATCC
1 CTCCTATC-TCC
*
2678736 CTCCTCTCTC
1 CTCCTATCTC
2678746 TTCTTTCTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
9 30 0.34
11 4 0.05
12 47 0.54
13 6 0.07
ACGTcount: A:0.10, C:0.47, G:0.03, T:0.40
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:2678721 original size:9 final size:9
Alignment explanation
Indices: 2678623--2678725 Score: 65
Period size: 9 Copynumber: 12.1 Consensus size: 9
2678613 CTCTCTCTAT
2678623 TATCTCTCC
1 TATCTCTCC
*
2678632 TGTCTCTCC
1 TATCTCTCC
* *
2678641 T-CCTAT-C
1 TATCTCTCC
*
2678648 -ATCCCTCC
1 TATCTCTCC
*
2678656 TATCTCTAC
1 TATCTCTCC
2678665 TATCTCTCC
1 TATCTCTCC
*
2678674 TGTCTCTCC
1 TATCTCTCC
* *
2678683 T-CCTAT-C
1 TATCTCTCC
*
2678690 -ATCCCTCC
1 TATCTCTCC
*
2678698 TATCTCTAC
1 TATCTCTCC
2678707 TATCTCTCC
1 TATCTCTCC
*
2678716 TGTCTCTCC
1 TATCTCTCC
2678725 T
1 T
2678726 CCTATCATCC
Statistics
Matches: 69, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
7 6 0.09
8 8 0.12
9 55 0.80
ACGTcount: A:0.11, C:0.45, G:0.03, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:2681712 original size:44 final size:44
Alignment explanation
Indices: 2681660--2681796 Score: 256
Period size: 44 Copynumber: 3.1 Consensus size: 44
2681650 TTGTTATTTT
2681660 GGTTTAATTAAGAATTGGGCTTGTTAGCATAATAAGTCCATTAG
1 GGTTTAATTAAGAATTGGGCTTGTTAGCATAATAAGTCCATTAG
*
2681704 GGTTTAATTAAGAATTGGGCTTGTTAGCACAATAAGTCCATTAG
1 GGTTTAATTAAGAATTGGGCTTGTTAGCATAATAAGTCCATTAG
*
2681748 GGTTTAATTAAGAATTGGGTTTGTTAGCATAATAAGTCCATTAG
1 GGTTTAATTAAGAATTGGGCTTGTTAGCATAATAAGTCCATTAG
2681792 GGTTT
1 GGTTT
2681797 GTGTTAATGT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (44 bp):
GGTTTAATTAAGAATTGGGCTTGTTAGCATAATAAGTCCATTAG
Found at i:2682364 original size:26 final size:27
Alignment explanation
Indices: 2682335--2682389 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
2682325 AAAGAAGAAG
*
2682335 AAGAAGAAAGAATACAAAACAA-AAAA
1 AAGAAGAAAGAATACAAAAAAATAAAA
2682361 AAGAAGAAAGAATACAAAAAAATAAAA
1 AAGAAGAAAGAATACAAAAAAATAAAA
2682388 AA
1 AA
2682390 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (27 bp):
AAGAAGAAAGAATACAAAAAAATAAAA
Found at i:2682390 original size:9 final size:9
Alignment explanation
Indices: 2682350--2682399 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
2682340 GAAAGAATAC
*
2682350 AAAACAAAA
1 AAAATAAAA
*
2682359 AAAAGAAGAA
1 AAAATAA-AA
*
2682369 AGAATACAAA
1 AAAATA-AAA
2682379 AAAATAAAA
1 AAAATAAAA
2682388 AAAATAAAA
1 AAAATAAAA
2682397 AAA
1 AAA
2682400 CTAGCATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 21 0.60
10 13 0.37
11 1 0.03
ACGTcount: A:0.84, C:0.04, G:0.06, T:0.06
Consensus pattern (9 bp):
AAAATAAAA
Found at i:2684436 original size:16 final size:16
Alignment explanation
Indices: 2684415--2684461 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
2684405 TTGGTGTATC
2684415 TAGTGTTTATCAAACA
1 TAGTGTTTATCAAACA
* *
2684431 TAGTGTTAGAATGAAACA
1 TAGTGTT--TATCAAACA
2684449 TAGTGTTTATCAA
1 TAGTGTTTATCAA
2684462 TTTTGTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (16 bp):
TAGTGTTTATCAAACA
Found at i:2687465 original size:52 final size:52
Alignment explanation
Indices: 2687377--2687505 Score: 152
Period size: 52 Copynumber: 2.5 Consensus size: 52
2687367 GGTTTTAGAG
* * * * * *
2687377 ATGACAAAGGTACCAATGTGCTAATCTAAAGCCAGCGACATTGGTCTTCAAA
1 ATGACAAAGGTGCCAATGTGCTGATCCAAAGCCAGCGACACTGGACTTAAAA
* *
2687429 ATGACAAAGGTGCCAATGTGCTGATCC-AAGATCAGCGATACTGGACTTAAAA
1 ATGACAAAGGTGCCAATGTGCTGATCCAAAG-CCAGCGACACTGGACTTAAAA
* *
2687481 ATGATAAAGGTGCCAATATGCTGAT
1 ATGACAAAGGTGCCAATGTGCTGAT
2687506 TCATGGCCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
51 3 0.05
52 63 0.95
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (52 bp):
ATGACAAAGGTGCCAATGTGCTGATCCAAAGCCAGCGACACTGGACTTAAAA
Found at i:2687530 original size:52 final size:52
Alignment explanation
Indices: 2687414--2687539 Score: 135
Period size: 52 Copynumber: 2.4 Consensus size: 52
2687404 AAAGCCAGCG
* * * * * *
2687414 ACATTGGTCTTCAAAATGACAAAGGTGCCAATGTGCTGATCCAAGATCAGCG
1 ACATTGGTCTTAAAAATGATAAAGGTGCCAATATGCTGATCCAAGACCAACA
* * * * * *
2687466 ATACTGGACTTAAAAATGATAAAGGTGCCAATATGCTGATTCATGGCCAACA
1 ACATTGGTCTTAAAAATGATAAAGGTGCCAATATGCTGATCCAAGACCAACA
*
2687518 ACATTGGTCTTAAAGATGATAA
1 ACATTGGTCTTAAAAATGATAA
2687540 GTGATGACAA
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (52 bp):
ACATTGGTCTTAAAAATGATAAAGGTGCCAATATGCTGATCCAAGACCAACA
Found at i:2691824 original size:42 final size:42
Alignment explanation
Indices: 2691769--2691887 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
2691759 TTCTTCTCTC
* *
2691769 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
2691811 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
2691853 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
2691888 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:2691828 original size:12 final size:11
Alignment explanation
Indices: 2691802--2691877 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
2691792 TCTATTATCT
*
2691802 CTCCTGTCTCTC
1 CTCCTATCTC-C
2691814 CTCCTATCATCC
1 CTCCTATC-TCC
2691826 CTCCTATCT--
1 CTCCTATCTCC
*
2691835 CTACTATCT--
1 CTCCTATCTCC
*
2691844 CTCCTGTCTCTC
1 CTCCTATCTC-C
2691856 CTCCTATCATCC
1 CTCCTATC-TCC
*
2691868 CTCCTCTCTC
1 CTCCTATCTC
2691878 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:2691829 original size:24 final size:24
Alignment explanation
Indices: 2691793--2691878 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2691783 CCTCCTCTCT
* *
2691793 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
2691817 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
2691838 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
2691859 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
2691879 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:2691853 original size:18 final size:18
Alignment explanation
Indices: 2691784--2691854 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
2691774 CCTGTCATCC
* *
2691784 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
2691802 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
2691824 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
2691844 CTCCTGTCTCT
1 CTCCTGTCTCT
2691855 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:2695818 original size:36 final size:36
Alignment explanation
Indices: 2695778--2695849 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2695768 GTTGTCTAGG
2695778 ATGATTTGCTAGTTTAAACAAGCAATGCAACTTGTT
1 ATGATTTGCTAGTTTAAACAAGCAATGCAACTTGTT
*
2695814 ATGATTTGCTAGTTTAAACAAGCAATGCAGCTTGTT
1 ATGATTTGCTAGTTTAAACAAGCAATGCAACTTGTT
2695850 TACCTCTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (36 bp):
ATGATTTGCTAGTTTAAACAAGCAATGCAACTTGTT
Found at i:2697172 original size:81 final size:81
Alignment explanation
Indices: 2697061--2697218 Score: 223
Period size: 81 Copynumber: 2.0 Consensus size: 81
2697051 TTAAGCTTGA
* *
2697061 GAAGAAGATTTAGATAGATGCTGCATACTTAGCGCAAGGTGCCAATGTACTGA-TTCAAGGCCAG
1 GAAGAAGATTTAGACAGATGCTGCATACTTAGCGCAAGGTGCCAATGTACT-ACTTCAAGGCCAA
2697125 CAACATTGGGCTTTAGT
65 CAACATTGGGCTTTAGT
* * *
2697142 GAAGAAGATTT-GACAGATGCCT-CATGACTTAGGGCAAGGTGTCAATGTACTACTTTAAGGCCA
1 GAAGAAGATTTAGACAGATG-CTGCAT-ACTTAGCGCAAGGTGCCAATGTACTACTTCAAGGCCA
2697205 ACAACATTGGGCTT
64 ACAACATTGGGCTT
2697219 AGAATGAAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 11 0.16
81 58 0.84
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (81 bp):
GAAGAAGATTTAGACAGATGCTGCATACTTAGCGCAAGGTGCCAATGTACTACTTCAAGGCCAAC
AACATTGGGCTTTAGT
Found at i:2697291 original size:79 final size:79
Alignment explanation
Indices: 2697208--2697358 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 79
2697198 AAGGCCAACA
* * * *
2697208 ACATTGGGCTTAGAATGAAAGG-TTTGACAAATACCGCCTAACTAGGGCAGAATGCTAATGTGTT
1 ACATTGGGCTTAGAA-GAAAGGTTTTGACAAATACCACATAACTAAGGCAGAATGCTAATGTGCT
2697272 GATTCAAGCTAAGCG
65 GATTCAAGCTAAGCG
* * * * * *
2697287 ACATTGGGCTTAGAAGGAAGGTTTTGATAGATGCCACATGACTAAGGTAGAATGCTAATGTGCTG
1 ACATTGGGCTTAGAAGAAAGGTTTTGACAAATACCACATAACTAAGGCAGAATGCTAATGTGCTG
2697352 ATTCAAG
66 ATTCAAG
2697359 GCTAGTAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
78 5 0.08
79 56 0.92
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (79 bp):
ACATTGGGCTTAGAAGAAAGGTTTTGACAAATACCACATAACTAAGGCAGAATGCTAATGTGCTG
ATTCAAGCTAAGCG
Found at i:2697548 original size:31 final size:31
Alignment explanation
Indices: 2697510--2697890 Score: 285
Period size: 31 Copynumber: 11.9 Consensus size: 31
2697500 TGCAAGCTTA
2697510 GGTGCCACCAACTCGTGTGGACTTT-AACTAT
1 GGTGCCACCAACTCGTGTGGACTTTGAA-TAT
2697541 GGTGCCACCAACTCGTGTGGACTTT-AACTAT
1 GGTGCCACCAACTCGTGTGGACTTTGAA-TAT
* *
2697572 GGTGCCACCAACTCATGTGGACTTTGAA-AA
1 GGTGCCACCAACTCGTGTGGACTTTGAATAT
* * * *
2697602 GGTACCACCAACTTGTGTGGACTTTGACTGGGCT
1 GGTGCCACCAACTCGTGTGGACTTTGAAT---AT
* * * *
2697636 TGTGCCACCGACTTGTGTGGAATTTGGAA-A-
1 GGTGCCACCAACTCGTGTGGACTTT-GAATAT
* * *
2697666 GGATGCCACCAGCTTGTGTGGACTTTGAATAG
1 GG-TGCCACCAACTCGTGTGGACTTTGAATAT
2697698 GGTGCCACCAACTCGTGTGGACTTT-AAT-T
1 GGTGCCACCAACTCGTGTGGACTTTGAATAT
* *
2697727 GGGATGCCACCAACTCATGTGGACTTTGAATGGGTTT
1 -GG-TGCCACCAACTCGTGTGGACTTTGAA----TAT
* * * *
2697764 GGTTGCCATCGACTTGTGTGGACTTTGAAAAAGTTT
1 GG-TGCCACCAACTCGTGTGGACTTTG---AA-TAT
* * *
2697800 GGTTGCCACCGACTTGTGTGGACTTTGAATAG
1 GG-TGCCACCAACTCGTGTGGACTTTGAATAT
*
2697832 GGTGCCACCAACTCGTGTGGACTTT-AACT-G
1 GGTGCCACCAACTCGTGTGGACTTTGAA-TAT
* *
2697862 GGATGCCACCAACTCATATGGACTTTGAA
1 GG-TGCCACCAACTCGTGTGGACTTTGAA
2697891 AAGGTTATGT
Statistics
Matches: 293, Mismatches: 34, Indels: 45
0.79 0.09 0.12
Matches are distributed among these distances:
30 39 0.13
31 162 0.55
32 11 0.04
33 2 0.01
34 21 0.07
35 2 0.01
36 53 0.18
37 1 0.00
39 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (31 bp):
GGTGCCACCAACTCGTGTGGACTTTGAATAT
Found at i:2697784 original size:36 final size:36
Alignment explanation
Indices: 2697744--2697999 Score: 178
Period size: 36 Copynumber: 7.4 Consensus size: 36
2697734 CACCAACTCA
*
2697744 TGTGGACTTTGAATGGGTTTGGTTGCCATCGACTTG
1 TGTGGACTTTGAATGGGTTTGGTTGCCACCGACTTG
***
2697780 TGTGGACTTTGAAAAAGTTTGGTTGCCACCGACTTG
1 TGTGGACTTTGAATGGGTTTGGTTGCCACCGACTTG
* * *
2697816 TGTGGACTTTGAAT-AG---GG-TGCCACCAACTCG
1 TGTGGACTTTGAATGGGTTTGGTTGCCACCGACTTG
* * **
2697847 TGTGGACTTT-AACT--G---GGATGCCACCAACTCA
1 TGTGGACTTTGAA-TGGGTTTGGTTGCCACCGACTTG
* ** *
2697878 TATGGACTTTGAAAAGGTTAT-GTTGCCACCGACTTA
1 TGTGGACTTTGAATGGGTT-TGGTTGCCACCGACTTG
* * **
2697914 TGTGGACTTTGACTAGGGTTTAGTTGCCATTGACTTG
1 TGTGGACTTTGAAT-GGGTTTGGTTGCCACCGACTTG
* *
2697951 TGTGGACTTTGGAA-GGGTTTGGTTGCCACTGACTTC
1 TGTGGACTTT-GAATGGGTTTGGTTGCCACCGACTTG
* *
2697987 TATGCACTTTGAA
1 TGTGGACTTTGAA
2698000 AAAGGTTTGA
Statistics
Matches: 182, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.03
31 43 0.24
32 4 0.02
33 1 0.01
35 5 0.03
36 96 0.53
37 26 0.14
38 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (36 bp):
TGTGGACTTTGAATGGGTTTGGTTGCCACCGACTTG
Found at i:2697828 original size:134 final size:132
Alignment explanation
Indices: 2697543--2697961 Score: 478
Period size: 134 Copynumber: 3.2 Consensus size: 132
2697533 TTAACTATGG
* * * * ** *
2697543 TGCCACCAACTCGTGTGGACTTT-AACTATGGTGCCACCAACTCATGTGGACTTTGAAAAGG-TA
1 TGCCACCGACTTGTGTGGACTTTGAA-TAGGGTGCCACCAACTCGTGTGGACTTT-AATGGGATG
** * * * *
2697606 CCACCAACTTGTGTGGACTTTGACTGGGCTTG-TGCCACCGACTTGTGTGGAATTTG-GAAA---
64 CCACCAACTCATGTGGACTTTGAATGGGTTTGTTGCCACCGACTTGTGTGGACTTTGAAAAAGTT
*
2697666 -GGA
129 TGGT
2697669 TGCCACC-AGCTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTAATTGGGATG
1 TGCCACCGA-CTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTAA-TGGGATG
*
2697733 CCACCAACTCATGTGGACTTTGAATGGGTTTGGTTGCCATCGACTTGTGTGGACTTTGAAAAAGT
64 CCACCAACTCATGTGGACTTTGAATGGGTTT-GTTGCCACCGACTTGTGTGGACTTTGAAAAAGT
2697798 TTGGT
128 TTGGT
2697803 TGCCACCGACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTAACTGGGATGC
1 TGCCACCGACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTAA-TGGGATGC
* ** * * **
2697868 CACCAACTCATATGGACTTTGAAAAGGTTATGTTGCCACCGACTTATGTGGACTTTGACTAGGGT
65 CACCAACTCATGTGGACTTTGAATGGGTT-TGTTGCCACCGACTTGTGTGGACTTTGA-AAAAGT
*
2697933 TTAGT
128 TTGGT
**
2697938 TGCCATTGACTTGTGTGGACTTTG
1 TGCCACCGACTTGTGTGGACTTTG
2697962 GAAGGGTTTG
Statistics
Matches: 253, Mismatches: 26, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
125 3 0.01
126 48 0.19
127 30 0.12
128 1 0.00
129 22 0.09
130 3 0.01
134 115 0.45
135 31 0.12
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (132 bp):
TGCCACCGACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTAATGGGATGCC
ACCAACTCATGTGGACTTTGAATGGGTTTGTTGCCACCGACTTGTGTGGACTTTGAAAAAGTTTG
GT
Found at i:2697918 original size:98 final size:95
Alignment explanation
Indices: 2697511--2697932 Score: 326
Period size: 98 Copynumber: 4.3 Consensus size: 95
2697501 GCAAGCTTAG
* * **
2697511 GTGCCACCAACTCGTGTGGACTTT-AACTATGGTGCCACCAACTCGTGTGGACTTT-AACTATGG
1 GTGCCACCAACTTGTGTGGACTTTGAA-TAGGGTGCCACCAACTCGTGTGGACTTTGAA-TGGGG
2697574 -TGCCACCAACTCATGTGGACTTTGAAAA-G-
64 ATGCCACCAACTCATGTGGACTTTGAAAAGGT
* * * * * * *
2697603 GTACCACCAACTTGTGTGGACTTTGACTGGGCTTGTGCCACCGACTTGTGTGGAATTTGGAA--A
1 GTGCCACCAACTTGTGTGGACTTTGAATAGG---GTGCCACCAACTCGTGTGGACTTT-GAATGG
* ** *
2697666 GGATGCCACCAGCTTGTGTGGACTTTGAATAGG-
62 GGATGCCACCAACTCATGTGGACTTTGAAAAGGT
* * *
2697699 GTGCCACCAACTCGTGTGGACTTT-AATTGGGATGCCACCAACTCATGTGGACTTTGAATGGGTT
1 GTGCCACCAACTTGTGTGGACTTTGAATAGGG-TGCCACCAACTCGTGTGGACTTTGAAT-GG--
* * * ** *
2697763 TGGTTGCCATCGACTTGTGTGGACTTTGAAAAAGTTT
62 -GGATGCCACCAACTCATGTGGACTTTG-AAAAG-GT
*
2697800 GGTTGCCACCGACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTT-AACT-GG
1 -G-TGCCACCAACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTGAA-TGGG
*
2697863 GATGCCACCAACTCATATGGACTTTGAAAAGGTTAT
63 GATGCCACCAACTCATGTGGACTTTGAAAAGG---T
* * *
2697899 GTTGCCACCGACTTATGTGGACTTTGACTAGGGT
1 G-TGCCACCAACTTGTGTGGACTTTGAATAGGGT
2697933 TTAGTTGCCA
Statistics
Matches: 264, Mismatches: 41, Indels: 44
0.76 0.12 0.13
Matches are distributed among these distances:
92 28 0.11
93 20 0.08
94 2 0.01
95 49 0.19
96 23 0.09
97 7 0.03
98 76 0.29
99 5 0.02
101 1 0.00
102 3 0.01
103 44 0.17
104 6 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (95 bp):
GTGCCACCAACTTGTGTGGACTTTGAATAGGGTGCCACCAACTCGTGTGGACTTTGAATGGGGAT
GCCACCAACTCATGTGGACTTTGAAAAGGT
Found at i:2701202 original size:103 final size:102
Alignment explanation
Indices: 2701053--2701271 Score: 300
Period size: 103 Copynumber: 2.1 Consensus size: 102
2701043 TAAAAAAGGG
* *
2701053 GTTGGAGTATCCCCTTCGAAGATGGGGTTAGAGTATCCCCATGGATAACAAATAATTTTGACAAA
1 GTTGGAGTATCCCCTTCAAAGATGAGGTTAGAGTATCCCCATGGATAACAAATAATTTTGACAAA
* *
2701118 -AGAGGGGTTCAAATCTTGATAAATTTTGAAAAGC-GAA
66 GA-AGGAGTTCAAATCTAGATAAATTTTGAAAAGCAG-A
* * *
2701155 GTTGGAGTATCCCC-TCAAAAGGTCGAGGTTGGAGTATCCCTATGGATAACAAATAATTTTGACA
1 GTTGGAGTATCCCCTTC-AAAGAT-GAGGTTAGAGTATCCCCATGGATAACAAATAATTTTGACA
* *
2701219 AAGAAGGAGTTCAAATCTAGATAAATTTTGAAGAGCAGG
64 AAGAAGGAGTTCAAATCTAGATAAATTTTGAAAAGCAGA
2701258 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2701272 GCGAATAAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
101 2 0.02
102 18 0.17
103 82 0.79
104 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (102 bp):
GTTGGAGTATCCCCTTCAAAGATGAGGTTAGAGTATCCCCATGGATAACAAATAATTTTGACAAA
GAAGGAGTTCAAATCTAGATAAATTTTGAAAAGCAGA
Found at i:2703417 original size:40 final size:41
Alignment explanation
Indices: 2703332--2703423 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
2703322 ATGATGGAAA
2703332 TAGGGTGGCTGGTTTAAATGCTGAAATGATATACCAGCAAG
1 TAGGGTGGCTGGTTTAAATGCTGAAATGATATACCAGCAAG
* *
2703373 TAGGGTAGCTGGTTTAAATGCTGAAATGA-ATACCGGCAAG
1 TAGGGTGGCTGGTTTAAATGCTGAAATGATATACCAGCAAG
2703413 TAGGGTGGCTG
1 TAGGGTGGCTG
2703424 ATGGTGATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 20 0.42
41 28 0.58
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (41 bp):
TAGGGTGGCTGGTTTAAATGCTGAAATGATATACCAGCAAG
Found at i:2705321 original size:30 final size:31
Alignment explanation
Indices: 2705273--2705332 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
2705263 TGAGTTTATA
2705273 ATGAGATGATAGTGGATATGGGAT-CATGATG
1 ATGAGATGATAGTGGATATGGG-TGCATGATG
2705304 ATGA-ATGACTAGT-GATATGGGTGCATGAT
1 ATGAGATGA-TAGTGGATATGGGTGCATGAT
2705333 CAAGACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 1 0.04
30 18 0.67
31 8 0.30
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (31 bp):
ATGAGATGATAGTGGATATGGGTGCATGATG
Found at i:2710135 original size:28 final size:29
Alignment explanation
Indices: 2710066--2710136 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
2710056 TTCTTTATTC
*
2710066 TTCTTCATTGATTTCTTTTCCTTTGAAAT
1 TTCTTCATTGATTTCTTTTCCTTTCAAAT
*
2710095 TTCTTGC-TT-ATTT-TGTTTCCTTTCATAT
1 TTCTT-CATTGATTTCT-TTTCCTTTCAAAT
2710123 TTCTT-ATTGATTTC
1 TTCTTCATTGATTTC
2710137 ACTTCCTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
27 3 0.09
28 24 0.69
29 7 0.20
30 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (29 bp):
TTCTTCATTGATTTCTTTTCCTTTCAAAT
Found at i:2714840 original size:29 final size:29
Alignment explanation
Indices: 2714750--2714848 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
2714740 GAATAAAGCT
*
2714750 TGGAGCCCAATTCGTATGTCCAAGAAGAG
1 TGGAGCCCAATTCGCATGTCCAAGAAGAG
* * * * **
2714779 TGAAGCCCAATTTGCATGTATTCATG--GCT
1 TGGAGCCCAATTCGCATG--TCCAAGAAGAG
*
2714808 TGGAGCCCAATTCACATGTCCAAGAAGAG
1 TGGAGCCCAATTCGCATGTCCAAGAAGAG
*
2714837 TGGAGCCTAATT
1 TGGAGCCCAATT
2714849 TGCAAATATT
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
27 4 0.08
29 43 0.84
31 4 0.08
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (29 bp):
TGGAGCCCAATTCGCATGTCCAAGAAGAG
Found at i:2714926 original size:17 final size:17
Alignment explanation
Indices: 2714895--2714927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2714885 ATTATGATGT
2714895 ATTTATTATGAATAAGA
1 ATTTATTATGAATAAGA
2714912 ATTTGATTATG-ATAAG
1 ATTT-ATTATGAATAAG
2714928 GAGTAGGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
ATTTATTATGAATAAGA
Found at i:2717873 original size:24 final size:24
Alignment explanation
Indices: 2717845--2717912 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
2717835 CGCTTGCGGG
2717845 AGAGATAGGAGGGATGATAGGAGA
1 AGAGATAGGAGGGATGATAGGAGA
*
2717869 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGA
* *
2717893 AGAGATAGGAGAGATAATAG
1 AGAGATAGGAGGGATGATAG
2717913 AGCGAGGAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.44, T:0.13
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGAGA
Found at i:2717912 original size:12 final size:12
Alignment explanation
Indices: 2717844--2717912 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
2717834 TCGCTTGCGG
2717844 GAGA-GATAGGA
1 GAGATGATAGGA
*
2717855 GGGATGATAGGA
1 GAGATGATAGGA
2717867 GAAGA-GATAGGA
1 G-AGATGATAGGA
*
2717879 GGGATGATAGGA
1 GAGATGATAGGA
2717891 GGAGA-GATAGGA
1 -GAGATGATAGGA
*
2717903 GAGATAATAG
1 GAGATGATAG
2717913 AGCGAGGAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.19
12 34 0.71
13 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (12 bp):
GAGATGATAGGA
Found at i:2723508 original size:21 final size:22
Alignment explanation
Indices: 2723484--2723526 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2723474 AATTAAGCTC
*
2723484 TTAATTTATCTAATA-AATTAT
1 TTAATTCATCTAATATAATTAT
*
2723505 TTAATTCATCTTATATAATTAT
1 TTAATTCATCTAATATAATTAT
2723527 CTCATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATCTAATATAATTAT
Found at i:2725675 original size:21 final size:21
Alignment explanation
Indices: 2725612--2725675 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
2725602 TTATCTATAT
2725612 TTAATTCATATAAATATTTAAA
1 TTAATT-ATATAAATATTTAAA
** * *
2725634 CAAGATTATCTAGATATTTAAA
1 TTA-ATTATATAAATATTTAAA
*
2725656 TTAATTATATAAATAATTAA
1 TTAATTATATAAATATTTAA
2725676 TTTATCCATA
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 14 0.44
22 15 0.47
23 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
TTAATTATATAAATATTTAAA
Found at i:2725811 original size:18 final size:18
Alignment explanation
Indices: 2725774--2725813 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2725764 ATATTTACCG
*
2725774 AAATTATCTTATTACCAT
1 AAATTATCTTATTACAAT
2725792 AAATTATCTTATTTA-AAT
1 AAATTATCTTA-TTACAAT
2725810 AAAT
1 AAAT
2725814 AAATATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTATCTTATTACAAT
Found at i:2731025 original size:7 final size:6
Alignment explanation
Indices: 2731000--2731061 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
2730990 TTTCATTTTC
*
2731000 AAAAA- AAAAAG AAAAAG AAAACAG --AAAC AAAAA- AAAAAG AAAAA-
1 AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG
2731044 AAAGAAG AAAAAAG AAAA
1 AAA-AAG -AAAAAG AAAA
2731062 TAAATGATGT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
4 1 0.02
5 15 0.31
6 24 0.50
7 5 0.10
8 3 0.06
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2733762 original size:21 final size:21
Alignment explanation
Indices: 2733729--2733782 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2733719 ATACAAGTAA
* * *
2733729 AAATGTATCGATACATTATGT
1 AAATATATTGATACATTATAT
2733750 AAATATATTGATACATTATAT
1 AAATATATTGATACATTATAT
*
2733771 GAATATATTGAT
1 AAATATATTGAT
2733783 GCATCTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (21 bp):
AAATATATTGATACATTATAT
Found at i:2736336 original size:20 final size:20
Alignment explanation
Indices: 2736311--2736368 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2736301 GTTGGGCACA
*
2736311 ATGTATTGATACATTTCATC
1 ATGTATCGATACATTTCATC
*
2736331 ATGTATCGATACAATGTC-TC
1 ATGTATCGATAC-ATTTCATC
*
2736351 GTGTATCGATACATTTCA
1 ATGTATCGATACATTTCA
2736369 CTTAGGGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTCATC
Found at i:2736418 original size:20 final size:20
Alignment explanation
Indices: 2736393--2736504 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
2736383 TACTAGTTTC
2736393 ATGTATCGATACAATTGATT
1 ATGTATCGATACAATTGATT
* * **
2736413 ATGTATCAATACAA-GGAGC
1 ATGTATCGATACAATTGATT
2736432 ATGTATCGATACAATTGATT
1 ATGTATCGATACAATTGATT
*
2736452 ATGTATCGATACAATTGGTT
1 ATGTATCGATACAATTGATT
* * * **
2736472 ATTTATCAATACAA-GGAGC
1 ATGTATCGATACAATTGATT
2736491 ATGTATCGATACAA
1 ATGTATCGATACAA
2736505 AGCATAATGG
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
19 28 0.38
20 46 0.62
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGATT
Found at i:2736479 original size:59 final size:59
Alignment explanation
Indices: 2736393--2736504 Score: 206
Period size: 59 Copynumber: 1.9 Consensus size: 59
2736383 TACTAGTTTC
2736393 ATGTATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATTGATT
1 ATGTATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATTGATT
* *
2736452 ATGTATCGATACAATTGGTTATTTATCAATACAAGGAGCATGTATCGATACAA
1 ATGTATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAA
2736505 AGCATAATGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (59 bp):
ATGTATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATTGATT
Found at i:2736519 original size:59 final size:59
Alignment explanation
Indices: 2736397--2736523 Score: 193
Period size: 59 Copynumber: 2.2 Consensus size: 59
2736387 AGTTTCATGT
* * *
2736397 ATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATTGATTATGT
1 ATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATAGATAATGG
* *
2736456 ATCGATACAATTGGTTATTTATCAATACAAGGAGCATGTATCGATACAA-AGCATAATGG
1 ATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATAG-ATAATGG
2736515 ATCGATACA
1 ATCGATACA
2736524 TCTGGATGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (59 bp):
ATCGATACAATTGATTATGTATCAATACAAGGAGCATGTATCGATACAATAGATAATGG
Found at i:2743139 original size:15 final size:16
Alignment explanation
Indices: 2743115--2743162 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
2743105 CCTTTTCTAG
*
2743115 TTCAATAATTTTC-TT
1 TTCAAGAATTTTCATT
2743130 TTCAAGAA-TTTCATT
1 TTCAAGAATTTTCATT
*
2743145 TTCAAGAAATTTTGATT
1 TTCAAG-AATTTTCATT
2743162 T
1 T
2743163 ATTTTCTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 4 0.14
15 15 0.54
16 2 0.07
17 7 0.25
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (16 bp):
TTCAAGAATTTTCATT
Found at i:2745304 original size:19 final size:20
Alignment explanation
Indices: 2745259--2745311 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
2745249 CTACCAGTTT
**
2745259 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATAAAG
*
2745279 TATGTATCGATACAA-AAAG
1 CATGTATCGATACAATAAAG
*
2745298 CATGTATCAATACA
1 CATGTATCGATACA
2745312 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATAAAG
Found at i:2754205 original size:20 final size:21
Alignment explanation
Indices: 2754177--2754215 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2754167 GATACAAAGC
2754177 AAATAGTATCGATACATTTTG
1 AAATAGTATCGATACATTTTG
2754198 AAAT-GTATCGATACATTT
1 AAATAGTATCGATACATTT
2754216 ACTTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (21 bp):
AAATAGTATCGATACATTTTG
Found at i:2759360 original size:84 final size:84
Alignment explanation
Indices: 2759201--2759626 Score: 606
Period size: 84 Copynumber: 5.0 Consensus size: 84
2759191 AGATGGCCGG
*
2759201 AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAGAAAGAGGATAAACTGACAAATTAGTATCC
1 AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAG-AAGAGGACAAACTGACAAATTAGTATCC
* *
2759266 GAGATTCTCGTTGAATCAAA
65 AAGATTCTTGTTGAATCAAA
* * *
2759286 AAAGATGAGAGAAAATAGAAAGTAAATTTGGAACAGAAGAGGACAAACTGACAAGTTAGTATCCG
1 AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAGAAGAGGACAAACTGACAAATTAGTATCCA
*
2759351 AGATTCTCGTTGAATCAAA
66 AGATTCTTGTTGAATCAAA
* *
2759370 AAAGATGAGAGAAAATAGAAAGTAAATTTGGAACAGAAGAGGACAAACTGACAAGTTAGTATCCA
1 AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAGAAGAGGACAAACTGACAAATTAGTATCCA
2759435 AGATTCTTGTTGAATACAAA
66 AGATTCTTGTTGAAT-CAAA
* *
2759455 AAA-ATGAGAGAAAATAGAAAGTAAATTAGAAACAGAAGAGGACAAACTGACAAATTCGTATCCA
1 AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAGAAGAGGACAAACTGACAAATTAGTATCCA
2759519 AGATTCTTGTTGAATC-AA
66 AGATTCTTGTTGAATCAAA
* * * * * *
2759537 AAACATTA-ACTCCACAAAGTTGAAAGTAAATTAGAAACAGAAGAGGACAAACTGACAAATTCGT
1 AAAGATGAGA---GA-AAA-TAGAAAGTAAATTTGAAACAGAAGAGGACAAACTGACAAATTAGT
*
2759601 ATCCAAGATTCTTGCTGAATCAAA
61 ATCCAAGATTCTTGTTGAATCAAA
2759625 AA
1 AA
2759627 CATTAACTCC
Statistics
Matches: 320, Mismatches: 13, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
82 6 0.02
83 4 0.01
84 196 0.61
85 43 0.13
86 3 0.01
87 64 0.20
88 4 0.01
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (84 bp):
AAAGATGAGAGAAAATAGAAAGTAAATTTGAAACAGAAGAGGACAAACTGACAAATTAGTATCCA
AGATTCTTGTTGAATCAAA
Found at i:2760673 original size:6 final size:6
Alignment explanation
Indices: 2760664--2760742 Score: 133
Period size: 6 Copynumber: 13.3 Consensus size: 6
2760654 CACACACACA
*
2760664 AATAAT AATAAC AATAAC AA-AAC AATAAC AATAAC AATAAC AATAAC
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC
*
2760711 AATAAC AATAAC AATAAC AATAAT AATAAC AA
1 AATAAC AATAAC AATAAC AATAAC AATAAC AA
2760743 GGGGGGAGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
5 5 0.07
6 64 0.93
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAC
Found at i:2763146 original size:6 final size:6
Alignment explanation
Indices: 2763135--2763170 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2763125 TGTTAAACTA
2763135 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC
2763171 AATGTGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Found at i:2763237 original size:8 final size:8
Alignment explanation
Indices: 2763224--2763258 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
2763214 CACACAGCCA
2763224 AGGGAAAG
1 AGGGAAAG
2763232 AGGGAAAG
1 AGGGAAAG
*
2763240 AGGGAAAT
1 AGGGAAAG
2763248 AGGGAAAG
1 AGGGAAAG
2763256 AGG
1 AGG
2763259 AGGTGGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (8 bp):
AGGGAAAG
Found at i:2763465 original size:16 final size:15
Alignment explanation
Indices: 2763439--2763489 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
2763429 GGATCGAGGC
*
2763439 AAATTTTATTATTTA
1 AAATTTAATTATTTA
2763454 ATAATTTAATTATTTA
1 A-AATTTAATTATTTA
*
2763470 AGATTTAATTTAATTTA
1 AAATTTAA-TT-ATTTA
2763487 AAA
1 AAA
2763490 AAGTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AAATTTAATTATTTA
Found at i:2763557 original size:21 final size:22
Alignment explanation
Indices: 2763531--2763574 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2763521 TACTTAATAT
* *
2763531 TATTTATTTA-TTTATTATTAA
1 TATTTATATATTTTATAATTAA
2763552 TATTTATATATTTTATAATTAA
1 TATTTATATATTTTATAATTAA
2763574 T
1 T
2763575 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTATATATTTTATAATTAA
Found at i:2764264 original size:13 final size:13
Alignment explanation
Indices: 2764246--2764270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2764236 CAAGCTACTT
2764246 TGTATCGATACAA
1 TGTATCGATACAA
2764259 TGTATCGATACA
1 TGTATCGATACA
2764271 TGTTCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2764306 original size:21 final size:19
Alignment explanation
Indices: 2764255--2764312 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2764245 TTGTATCGAT
*
2764255 ACAATGTATCGATACATGT
1 ACAATGTATCGATACATGG
* *
2764274 TCAATATATCGATACATGG
1 ACAATGTATCGATACATGG
2764293 ACAAATTGTATCGATACATG
1 AC-AA-TGTATCGATACATG
2764313 AAATTGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
20 2 0.06
21 13 0.41
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:2764380 original size:13 final size:13
Alignment explanation
Indices: 2764362--2764387 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2764352 CATGGTTCAA
2764362 TGTATCGATACAT
1 TGTATCGATACAT
2764375 TGTATCGATACAT
1 TGTATCGATACAT
2764388 GAAGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2764383 original size:33 final size:33
Alignment explanation
Indices: 2764341--2764407 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2764331 CTATCACTAT
****
2764341 TTGTATCGATACATGGTTCAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
2764374 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
2764407 T
1 T
2764408 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGAAGAAATGTATCGATACA
Found at i:2765511 original size:17 final size:17
Alignment explanation
Indices: 2765489--2765527 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2765479 AAATTTTTGA
2765489 GTCATTTTTGAGTTAGG
1 GTCATTTTTGAGTTAGG
* *
2765506 GTCA-TTTTGGGTTCGG
1 GTCATTTTTGAGTTAGG
2765522 GTCATT
1 GTCATT
2765528 ATGGATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (17 bp):
GTCATTTTTGAGTTAGG
Found at i:2765576 original size:16 final size:16
Alignment explanation
Indices: 2765557--2765611 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2765547 GATTCAAGTT
*
2765557 ATTTCGAGTTCGGGTC
1 ATTTCGAGTTCTGGTC
* * *
2765573 ATTTTGAATTCTGATC
1 ATTTCGAGTTCTGGTC
* *
2765589 ATTTCGGGTTTTGGTC
1 ATTTCGAGTTCTGGTC
2765605 ATTTCGA
1 ATTTCGA
2765612 ATTTAGGTTG
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (16 bp):
ATTTCGAGTTCTGGTC
Found at i:2769038 original size:16 final size:16
Alignment explanation
Indices: 2769017--2769055 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2769007 TGAAGTTTAG
2769017 ATTTTTTATTTACTAT
1 ATTTTTTATTTACTAT
* * *
2769033 ATTTTTAATTTGCTTT
1 ATTTTTTATTTACTAT
2769049 ATTTTTT
1 ATTTTTT
2769056 TCATCTATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTTACTAT
Found at i:2770447 original size:18 final size:18
Alignment explanation
Indices: 2770424--2770464 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2770414 AGATAATGCC
*
2770424 TTAATTTT-TCTAAAAATT
1 TTAATTTTAT-TAAAAATA
2770442 TTAATTTTATTAAAAATA
1 TTAATTTTATTAAAAATA
2770460 TTAAT
1 TTAAT
2770465 AAAACATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTTTATTAAAAATA
Found at i:2771396 original size:21 final size:21
Alignment explanation
Indices: 2771343--2771401 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
2771333 TCGTTGGGCT
*
2771343 AATTGTATCGATACAATTCTGG
1 AATTGTATCGATAC-ATTTTGG
*
2771365 -A-TGTATTGATACATTTTGG
1 AATTGTATCGATACATTTTGG
2771384 AATTGTATCGATACATTT
1 AATTGTATCGATACATTT
2771402 GAAGGGTAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 11 0.34
21 15 0.47
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (21 bp):
AATTGTATCGATACATTTTGG
Found at i:2771487 original size:33 final size:33
Alignment explanation
Indices: 2771445--2771511 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2771435 ACTTTCTCAT
* * * *
2771445 AATGTATCGATATATTGCAATTTGTATTGATAC
1 AATGTATCGATACATTGAAACTTGTATCGATAC
2771478 AATGTATCGATACATTGAAACTTGTATCGATAC
1 AATGTATCGATACATTGAAACTTGTATCGATAC
2771511 A
1 A
2771512 TCTACATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACATTGAAACTTGTATCGATAC
Found at i:2772249 original size:15 final size:15
Alignment explanation
Indices: 2772207--2772257 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2772197 GAGCATTAAG
*
2772207 AACAGAATTTCATGAA
1 AACATAATTTCAT-AA
*
2772223 AACATAAATTCATAA
1 AACATAATTTCATAA
* *
2772238 ATCATAATTTCATAG
1 AACATAATTTCATAA
2772253 AACAT
1 AACAT
2772258 GAAAAAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (15 bp):
AACATAATTTCATAA
Found at i:2779508 original size:20 final size:20
Alignment explanation
Indices: 2779479--2779583 Score: 100
Period size: 20 Copynumber: 5.6 Consensus size: 20
2779469 TTTCTTATAA
2779479 TGTATCGATACATTGCAATT
1 TGTATCGATACATTGCAATT
*
2779499 TGTATAGAT--A---CAA--
1 TGTATCGATACATTGCAATT
*
2779512 TGTATCGTTACATTGCAATT
1 TGTATCGATACATTGCAATT
*
2779532 TGTATCGATACATTGCAACT
1 TGTATCGATACATTGCAATT
* *
2779552 TGTATCGATACATCTAC-ATG
1 TGTATCGATACAT-TGCAATT
2779572 TGTATCGATACA
1 TGTATCGATACA
2779584 AATAAGGGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.10
15 4 0.06
18 4 0.06
20 52 0.75
21 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGCAATT
Found at i:2779524 original size:33 final size:33
Alignment explanation
Indices: 2779477--2779543 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2779467 GCTTTCTTAT
2779477 AATGTATCGATACATTGCAATTTGTATAGATAC
1 AATGTATCGATACATTGCAATTTGTATAGATAC
* *
2779510 AATGTATCGTTACATTGCAATTTGTATCGATAC
1 AATGTATCGATACATTGCAATTTGTATAGATAC
2779543 A
1 A
2779544 TTGCAACTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACATTGCAATTTGTATAGATAC
Found at i:2782116 original size:13 final size:13
Alignment explanation
Indices: 2782098--2782123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2782088 GCAAAATGCA
2782098 TTCTAGTTGGGCC
1 TTCTAGTTGGGCC
2782111 TTCTAGTTGGGCC
1 TTCTAGTTGGGCC
2782124 ATTTCGGCCC
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:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (13 bp):
TTCTAGTTGGGCC
Found at i:2783228 original size:45 final size:45
Alignment explanation
Indices: 2783164--2783255 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
2783154 AAAATCCAGA
2783164 GATCATTTTATATTTCTATGTTCCCCATATCTCTGGAGCGCATAT
1 GATCATTTTATATTTCTATGTTCCCCATATCTCTGGAGCGCATAT
2783209 GATCATTTTATATTTCTATGTTCCCCATATCTCTGGAGCGCATAT
1 GATCATTTTATATTTCTATGTTCCCCATATCTCTGGAGCGCATAT
2783254 GA
1 GA
2783256 GATTAAAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (45 bp):
GATCATTTTATATTTCTATGTTCCCCATATCTCTGGAGCGCATAT
Found at i:2795327 original size:33 final size:33
Alignment explanation
Indices: 2795290--2795353 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
2795280 ACAAGCTATG
2795290 TATCGATACATT-T-CTTCATGTATCGATACAATA
1 TATCGATACATTGTAC--CATGTATCGATACAATA
2795323 TATCGATACATTGTACCATGTATCGATACAA
1 TATCGATACATTGTACCATGTATCGATACAA
2795354 ATAGTGATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (33 bp):
TATCGATACATTGTACCATGTATCGATACAATA
Found at i:2795999 original size:18 final size:19
Alignment explanation
Indices: 2795976--2796044 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
2795966 GTTTTCGTTT
2795976 TTCT-CCCCTTAAAAAATA
1 TTCTCCCCCTTAAAAAATA
*
2795994 TTCTCCCCCTTAAACAAT-
1 TTCTCCCCCTTAAAAAATA
* *
2796012 TATCT-CCTCTTAAAAAAAA
1 T-TCTCCCCCTTAAAAAATA
2796031 TTCTCCCCCTTAAA
1 TTCTCCCCCTTAAA
2796045 CGATTATCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 18 0.43
19 24 0.57
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.33
Consensus pattern (19 bp):
TTCTCCCCCTTAAAAAATA
Found at i:2796027 original size:37 final size:37
Alignment explanation
Indices: 2795977--2796053 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
2795967 TTTTCGTTTT
*
2795977 TCTCCCCTTAAAAAATATTCTCCCCCTTAAACAATTA
1 TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACAATTA
* *
2796014 TCTCCTCTTAAAAAAAATTCTCCCCCTTAAACGATTA
1 TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACAATTA
2796051 TCT
1 TCT
2796054 TTTCCCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (37 bp):
TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACAATTA
Found at i:2797187 original size:12 final size:12
Alignment explanation
Indices: 2797170--2797194 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2797160 TTTGGTCCAA
2797170 ATGTATCGATAC
1 ATGTATCGATAC
2797182 ATGTATCGATAC
1 ATGTATCGATAC
2797194 A
1 A
2797195 AGGTCCCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2797269 original size:33 final size:33
Alignment explanation
Indices: 2797232--2797298 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2797222 TTCAACGATC
2797232 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2797265 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2797298 T
1 T
2797299 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2797270 original size:13 final size:13
Alignment explanation
Indices: 2797252--2797276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2797242 CATAAAATGT
2797252 TGTATCGATACAA
1 TGTATCGATACAA
2797265 TGTATCGATACA
1 TGTATCGATACA
2797277 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2797360 original size:13 final size:13
Alignment explanation
Indices: 2797342--2797366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2797332 ATTACTCACA
2797342 TGTATCGATACAT
1 TGTATCGATACAT
2797355 TGTATCGATACA
1 TGTATCGATACA
2797367 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2797503 original size:52 final size:52
Alignment explanation
Indices: 2797375--2797495 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2797365 CACTGATCTT
*
2797375 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2797427 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2797479 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2797496 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2800194 original size:20 final size:20
Alignment explanation
Indices: 2800171--2800243 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2800161 ACAATTCAAA
2800171 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2800191 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2800212 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2800232 GTATCGATACAT
1 GTATCGATACAT
2800244 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2800215 original size:21 final size:21
Alignment explanation
Indices: 2800189--2800264 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2800179 ACATGTTGCA
2800189 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2800210 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2800230 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2800251 ATGTATCGATACAT
1 ATGTATCGATACAT
2800265 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2800222 original size:41 final size:41
Alignment explanation
Indices: 2800171--2800264 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2800161 ACAATTCAAA
*
2800171 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2800212 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2800253 GTATCGATACAT
1 GTATCGATACAT
2800265 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2800321 original size:13 final size:13
Alignment explanation
Indices: 2800303--2800328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2800293 TACAGCAAGT
2800303 ATGTATCGATACA
1 ATGTATCGATACA
2800316 ATGTATCGATACA
1 ATGTATCGATACA
2800329 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2804411 original size:15 final size:15
Alignment explanation
Indices: 2804391--2804421 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2804381 TAAAAATGTC
*
2804391 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2804406 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2804421 C
1 C
2804422 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2806519 original size:13 final size:13
Alignment explanation
Indices: 2806501--2806538 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2806491 CATTTTTATT
2806501 TGTATCGATACAA
1 TGTATCGATACAA
*
2806514 TGTATCGATACAC
1 TGTATCGATACAA
2806527 TGTATCGATACA
1 TGTATCGATACA
2806539 GGGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2809037 original size:20 final size:20
Alignment explanation
Indices: 2809014--2809086 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2809004 ACAATTCAAA
2809014 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2809034 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2809055 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2809075 GTATCGATACAT
1 GTATCGATACAT
2809087 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2809058 original size:21 final size:21
Alignment explanation
Indices: 2809032--2809107 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2809022 ACATGTTGCA
2809032 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2809053 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2809073 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2809094 ATGTATCGATACAT
1 ATGTATCGATACAT
2809108 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2809060 original size:41 final size:41
Alignment explanation
Indices: 2809014--2809107 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2809004 ACAATTCAAA
*
2809014 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2809055 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2809096 GTATCGATACAT
1 GTATCGATACAT
2809108 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2809164 original size:13 final size:13
Alignment explanation
Indices: 2809146--2809171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2809136 TACAGCAAGT
2809146 ATGTATCGATACA
1 ATGTATCGATACA
2809159 ATGTATCGATACA
1 ATGTATCGATACA
2809172 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2817765 original size:13 final size:13
Alignment explanation
Indices: 2817747--2817777 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2817737 ACATTTCTTC
2817747 ATGTATCGATACA
1 ATGTATCGATACA
2817760 ATGTATCGATACA
1 ATGTATCGATACA
*
2817773 TTGTA
1 ATGTA
2817778 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2817765 original size:33 final size:33
Alignment explanation
Indices: 2817727--2817793 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
2817717 GTTACAAGCT
2817727 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
2817760 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
2817793 A
1 A
2817794 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:2817881 original size:13 final size:13
Alignment explanation
Indices: 2817863--2817889 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2817853 TGCCTTGAAT
2817863 ATGTATCGATACA
1 ATGTATCGATACA
2817876 ATGTATCGATACA
1 ATGTATCGATACA
2817889 A
1 A
2817890 AGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2819242 original size:13 final size:13
Alignment explanation
Indices: 2819224--2819248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2819214 ATCACTTAAA
2819224 TGTATCGATACAT
1 TGTATCGATACAT
2819237 TGTATCGATACA
1 TGTATCGATACA
2819249 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2819313 original size:52 final size:52
Alignment explanation
Indices: 2819257--2819385 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2819247 CACTGATCTT
*
2819257 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
* **
2819309 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
2819361 TGTATCGATACATGCAGGCAATTTT
1 TGTATCGATACATGCAGGCAATTTT
2819386 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2827453 original size:51 final size:51
Alignment explanation
Indices: 2827398--2827513 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
2827388 AAATAGCGAG
* *
2827398 GTTGGAGTATCCCCGATTGTGAGAAA-TTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAATTTGGTATTTTAGAAATAAAATCGGA
* *
2827449 GTTGGAGTATCTCCGATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGA
2827500 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2827514 TTGAAAATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 3 0.05
51 56 0.95
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGA
Found at i:2827532 original size:28 final size:28
Alignment explanation
Indices: 2827496--2827577 Score: 121
Period size: 28 Copynumber: 2.9 Consensus size: 28
2827486 GAAATAAAAT
2827496 CGGGGTTGGAGTATCCCCTTGAAAATAA
1 CGGGGTTGGAGTATCCCCTTGAAAATAA
* *
2827524 CGGGATTGGAGTATCCCC-TCAGAAATAA
1 CGGGGTTGGAGTATCCCCTTGA-AAATAA
2827552 CGGGGTTGGAGTATCCCCGTTGAAAA
1 CGGGGTTGGAGTATCCCC-TTGAAAA
2827578 ATTGATGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.04
28 40 0.85
29 3 0.06
30 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTTGAAAATAA
Found at i:2827589 original size:104 final size:106
Alignment explanation
Indices: 2827449--2827644 Score: 297
Period size: 104 Copynumber: 1.9 Consensus size: 106
2827439 TAAAATCGGA
* * *
2827449 GTTGGAGTATCTCCGATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGA-TGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
** *
2827514 TTGAAAATAACGGGATTGGAGTATCCCCTCAGAAATAACGGG
65 TCAAAAATAACGGGATTGAAGTATCCCCTCAGAAATAACGGG
*
2827556 GTTGGAGTATCCCCG-T-TGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
1 GTTGGAGTATCCCCGATGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
*
2827619 CAAAAATAACGGGGTTGAAGTATCCC
66 CAAAAATAACGGGATTGAAGTATCCC
2827645 TGATGAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 66 0.81
105 1 0.01
107 14 0.17
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (106 bp):
GTTGGAGTATCCCCGATGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
CAAAAATAACGGGATTGAAGTATCCCCTCAGAAATAACGGG
Found at i:2827614 original size:76 final size:76
Alignment explanation
Indices: 2827524--2827693 Score: 286
Period size: 76 Copynumber: 2.2 Consensus size: 76
2827514 TTGAAAATAA
* * * *
2827524 CGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGTTGAAAAATTGATGTTTT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATGAAAAATTGATGTTTT
*
2827589 AGAAATAAAAT
66 AGAAATAAAAC
*
2827600 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCTGATGAAAAATTGATGTTTT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATGAAAAATTGATGTTTT
2827665 AGAAATAAAAC
66 AGAAATAAAAC
2827676 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
2827694 GAGATGAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 88 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (76 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATGAAAAATTGATGTTTT
AGAAATAAAAC
Found at i:2828579 original size:13 final size:13
Alignment explanation
Indices: 2828561--2828612 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
2828551 AGCTTCGTAG
2828561 CGATACATTGTAT
1 CGATACATTGTAT
2828574 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
2828593 CGATACATTGTAT
1 CGATACATTGTAT
2828606 CGATACA
1 CGATACA
2828613 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2828593 original size:19 final size:18
Alignment explanation
Indices: 2828569--2828631 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
2828559 AGCGATACAT
2828569 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2828588 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
2828601 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
2828620 TGTATCGATACA
1 TGTATCGATACA
2828632 TTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2828602 original size:32 final size:32
Alignment explanation
Indices: 2828561--2828633 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
2828551 AGCTTCGTAG
2828561 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
2828593 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
2828625 CGATACATT
1 CGATACATT
2828634 TACTGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Done.