Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 182 of 198
Found at i:56744174 original size:108 final size:108
Alignment explanation
Indices: 56743979--56744411 Score: 674
Period size: 108 Copynumber: 4.0 Consensus size: 108
56743969 AAAAAAAAAG
56743979 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
56744044 GGTTTCGATTTCTCGTTTGACCAAATGACTTAATATCCTTTTCA
65 GGTTTCGATTTCTCGTTTGACCAAATGACTTAATATCCTTTTCA
*
56744088 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGTAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
56744153 GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
66 GTTTCGATTTCTCGTTTGACCAAATGACTTAATATCCTTTTCA
*
56744196 AAAATTTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
56744261 GTTTCGATTTCTCGTTTGACCAAAT-AGCTAAATATCCTTTTCAAAA
66 GTTTCGATTTCTCGTTTGACCAAATGA-CTTAATATCCTTTTC---A
* * * *
56744307 AAAACTTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAATGTGCCCTAAGGTGCT
1 AAAA-TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
* *
56744372 GGGTTTCGATTTCACGTTT-AGCCAAATTG-CTGAATATCCT
64 GGGTTTCGATTTCTCGTTTGA-CCAAA-TGACTTAATATCCT
56744412 CTTGAATTTT
Statistics
Matches: 302, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
107 1 0.00
108 202 0.67
109 5 0.02
111 5 0.02
112 6 0.02
113 82 0.27
114 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTTGACCAAATGACTTAATATCCTTTTCA
Found at i:56749193 original size:108 final size:108
Alignment explanation
Indices: 56748998--56749408 Score: 662
Period size: 108 Copynumber: 3.8 Consensus size: 108
56748988 AAAAAAAAAG
*
56748998 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTA
1 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
56749063 GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
65 GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
56749107 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
56749172 GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
66 GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
* *
56749215 AAAATTTTCAAAATAAGGCAATATTTTACGTTTAGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
* *
56749280 GTTTCGATTTCTCGTTTGACCAAAT-AGCTAAATATCCTTTTCAAAA
66 GTTTCGATTTCTCGTTCGACCAAATGA-CTTAATATCCTTTTC---A
* * * *
56749326 AAAACTTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAATGTGCCCTAAGGTGCT
1 AAAA-TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
*
56749391 GGGTTTCGATTTCACGTT
64 GGGTTTCGATTTCTCGTT
56749409 TAGCCAAATT
Statistics
Matches: 284, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
107 1 0.00
108 203 0.71
109 5 0.02
111 5 0.02
112 5 0.02
113 65 0.23
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
Found at i:56752332 original size:19 final size:21
Alignment explanation
Indices: 56752298--56752345 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
56752288 TACATAATTT
56752298 TTTTAAATTATTATCAATATG
1 TTTTAAATTATTATCAATATG
*
56752319 TTTTAAA-T-TTATCAATATTA
1 TTTTAAATTATTATCAATA-TG
56752339 TTTTAAA
1 TTTTAAA
56752346 AATATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAAATTATTATCAATATG
Found at i:56754132 original size:33 final size:33
Alignment explanation
Indices: 56754011--56754237 Score: 89
Period size: 33 Copynumber: 6.8 Consensus size: 33
56754001 TTACATTCGA
* * *
56754011 AGTGCCATAACCCAGTTATGGTCTTATC-ATCAG
1 AGTGCCATAACCCAGCTATGGTCTTA-CGTTCAT
* * * * *
56754044 AATGCCAT-AGCCAGCTATGGTCTTACATATAAAC
1 AGTGCCATAACCCAGCTATGGTCTTACGT-T-CAT
* *** * *
56754078 ACTGCCATGGTCCAACCATGGTCTTACGTTCAT
1 AGTGCCATAACCCAGCTATGGTCTTACGTTCAT
* ** *
56754111 AGTGCCATAACCCAGTTATGGTCTTACCATCAG
1 AGTGCCATAACCCAGCTATGGTCTTACGTTCAT
* * * * * *
56754144 AATGCCATAGCTCAGCTATGGTCTAACATATAAAT
1 AGTGCCATAACCCAGCTATGGTCTTACGT-T-CAT
* * *** * * *
56754179 ATTGCAATGGTCCAACCATTGTCTTACGTTCAT
1 AGTGCCATAACCCAGCTATGGTCTTACGTTCAT
* *
56754212 AGTGCCATAACCCGGTTATGGTCTTA
1 AGTGCCATAACCCAGCTATGGTCTTA
56754238 TCCATCAATT
Statistics
Matches: 134, Mismatches: 54, Indels: 12
0.67 0.27 0.06
Matches are distributed among these distances:
31 1 0.01
32 15 0.11
33 72 0.54
34 11 0.08
35 35 0.26
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (33 bp):
AGTGCCATAACCCAGCTATGGTCTTACGTTCAT
Found at i:56754207 original size:101 final size:100
Alignment explanation
Indices: 56754011--56754244 Score: 387
Period size: 101 Copynumber: 2.3 Consensus size: 100
56754001 TTACATTCGA
* *
56754011 AGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCAGCTATGGTCTTACATATAA
1 AGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGCCAGCTATGGTCTAACATATAA
*
56754076 ACACTGCCATGGTCCAACCATGGTCTTACGTTCAT
66 ACACTGCAATGGTCCAACCATGGTCTTACGTTCAT
56754111 AGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGCTCAGCTATGGTCTAACATATA
1 AGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGC-CAGCTATGGTCTAACATATA
* * *
56754176 AATATTGCAATGGTCCAACCATTGTCTTACGTTCAT
65 AACACTGCAATGGTCCAACCATGGTCTTACGTTCAT
*
56754212 AGTGCCATAACCCGGTTATGGTCTTATCCATCA
1 AGTGCCATAACCCAGTTATGGTCTTA-CCATCA
56754245 ATTCATCCTT
Statistics
Matches: 125, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
100 43 0.34
101 76 0.61
102 6 0.05
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (100 bp):
AGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGCCAGCTATGGTCTAACATATAA
ACACTGCAATGGTCCAACCATGGTCTTACGTTCAT
Found at i:56760203 original size:31 final size:29
Alignment explanation
Indices: 56760153--56760210 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
56760143 ATATATATAT
56760153 AAAATATTCATTAAAAATATAAATATAGA
1 AAAATATTCATTAAAAATATAAATATAGA
*
56760182 AAAATATTCGTTAGAAAAATATAAATATA
1 AAAATATTCATT--AAAAATATAAATATA
56760211 TATACAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
31 15 0.58
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAATATTCATTAAAAATATAAATATAGA
Found at i:56760233 original size:22 final size:20
Alignment explanation
Indices: 56760196--56760251 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
56760186 TATTCGTTAG
* * * *
56760196 AAAAATATAAATATATATAC
1 AAAAAAATAATTACATATAT
56760216 AAAAAAATAATTACATATAT
1 AAAAAAATAATTACATATAT
56760236 AAAAAAATAATTACAT
1 AAAAAAATAATTACAT
56760252 TATTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAAATAATTACATATAT
Found at i:56762111 original size:28 final size:28
Alignment explanation
Indices: 56762058--56762113 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
56762048 CGCATAAGTG
*
56762058 TATAGATTATAAAATTTTAAAGTTAAAA
1 TATAGATTATAAAATTATAAAGTTAAAA
* *
56762086 TATATATTATAATATTATAATA-TTAAAA
1 TATAGATTATAAAATTATAA-AGTTAAAA
56762114 CTTAAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
TATAGATTATAAAATTATAAAGTTAAAA
Found at i:56762218 original size:6 final size:6
Alignment explanation
Indices: 56762161--56762239 Score: 52
Period size: 6 Copynumber: 12.7 Consensus size: 6
56762151 AATAACAATC
* * * * * *
56762161 AAAGAAA AAAGAA ATAGAAA GAAAGAA ACAGAG AAAGCCA AACGAA ACAGAA
1 AAAG-AA AAAGAA AAAG-AA -AAAGAA AAAGAA AAAG-AA AAAGAA AAAGAA
*
56762213 AAAGAA AAAG-G AAAGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG
56762240 GAAGGAGAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
5 4 0.07
6 36 0.67
7 11 0.20
8 3 0.06
ACGTcount: A:0.72, C:0.06, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:56762251 original size:17 final size:17
Alignment explanation
Indices: 56762209--56762242 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56762199 CAAACGAAAC
56762209 AGAAAAAGAAAAAGGAA
1 AGAAAAAGAAAAAGGAA
56762226 AGAAAAAGAAAAAGGAA
1 AGAAAAAGAAAAAGGAA
56762243 GGAGAAAGAC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAAAAGGAA
Found at i:56766934 original size:3 final size:3
Alignment explanation
Indices: 56766926--56767024 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
56766916 CTAGCTTTGC
56766926 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56766974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56767022 ATT
1 ATT
56767025 TACCCATTTA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56767086 original size:24 final size:24
Alignment explanation
Indices: 56767054--56767100 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
56767044 TAGATTTTGT
56767054 TATATATATACATACTTACATATA
1 TATATATATACATACTTACATATA
56767078 TATATATATACATACTTACATAT
1 TATATATATACATACTTACATAT
56767101 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.43
Consensus pattern (24 bp):
TATATATATACATACTTACATATA
Found at i:56767528 original size:20 final size:20
Alignment explanation
Indices: 56767496--56767533 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56767486 TTTTTACTTA
56767496 CATTATCATAATTGTTATTC
1 CATTATCATAATTGTTATTC
*
56767516 CATTA-CATCAATTTTTAT
1 CATTATCAT-AATTGTTAT
56767534 CCAGATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.50
Consensus pattern (20 bp):
CATTATCATAATTGTTATTC
Found at i:56768349 original size:26 final size:25
Alignment explanation
Indices: 56768312--56768360 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
56768302 AGCCATCGTT
*
56768312 TTTACTTACATTTTTTTATTATTTTC
1 TTTACTTACATTTTATT-TTATTTTC
56768338 TTTATCTT-CATTTTATTTTATTT
1 TTTA-CTTACATTTTATTTTATTT
56768361 AAGCTAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 12 0.57
27 3 0.14
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTACTTACATTTTATTTTATTTTC
Found at i:56771339 original size:23 final size:23
Alignment explanation
Indices: 56771303--56771346 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
56771293 AAAAAATATT
56771303 AAATATATA-TTTTTTATTTTTA
1 AAATATATATTTTTTTATTTTTA
56771325 AAATATAATATTTTTTTATTTT
1 AAATAT-ATATTTTTTTATTTT
56771347 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
AAATATATATTTTTTTATTTTTA
Found at i:56771460 original size:9 final size:9
Alignment explanation
Indices: 56771446--56771473 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56771436 TTTTGTTACA
56771446 ACAATTAAT
1 ACAATTAAT
56771455 ACAATTAAT
1 ACAATTAAT
56771464 ACAATTAAT
1 ACAATTAAT
56771473 A
1 A
56771474 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:56771494 original size:68 final size:68
Alignment explanation
Indices: 56771416--56771616 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 68
56771406 TCAAGTTTGT
*
56771416 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
56771481 AAA
66 AAA
56771484 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
56771540 AAA
66 AAA
56771543 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
56771606 AAT
66 AAA
56771609 TTTACTAA
1 TTTACTAA
56771617 CAATTAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:56771626 original size:16 final size:16
Alignment explanation
Indices: 56771605--56771646 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
56771595 AATAATTTGA
*
56771605 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
56771621 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
56771637 TAGTTTTAAT
1 TAATTTTAAT
56771647 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:56771630 original size:22 final size:23
Alignment explanation
Indices: 56771620--56771675 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
56771610 TTACTAACAA
* * *
56771620 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
56771642 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
56771665 TTAATTTTAAT
1 TTAATTTTAAT
56771676 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:56783795 original size:24 final size:26
Alignment explanation
Indices: 56783765--56783860 Score: 107
Period size: 24 Copynumber: 3.9 Consensus size: 26
56783755 AAAGAGAGGG
56783765 AAAGAAAGAAA-AAGAAGGAAAG-AA
1 AAAGAAAGAAAGAAGAAGGAAAGAAA
*
56783789 AAGGAAAGGAGAAGAAGAA-G-AAGAAA
1 AAAGAAA-GA-AAGAAGAAGGAAAGAAA
*
56783815 AAAGAAAGAAAGGAGAA-G-AAGAAA
1 AAAGAAAGAAAGAAGAAGGAAAGAAA
56783839 AAAGAAAGAAAGAA-AAGGAAAG
1 AAAGAAAGAAAGAAGAAGGAAAG
56783861 GAGAAGAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.03
24 34 0.55
25 10 0.16
26 11 0.18
27 5 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (26 bp):
AAAGAAAGAAAGAAGAAGGAAAGAAA
Found at i:56783896 original size:34 final size:34
Alignment explanation
Indices: 56783766--56783878 Score: 137
Period size: 30 Copynumber: 3.4 Consensus size: 34
56783756 AAGAGAGGGA
56783766 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAG
1 AAGAAA-AAAAA-AA-GAAAGAAAAGGAAAGGAGAAG
* *
56783803 AAG-AAGAAGAAA-AAAG-AAA-GAAAGGAGAAG
1 AAGAAAAAAAAAAGAAAGAAAAGGAAAGGAGAAG
*
56783833 AAGAAAAAAGAAAGAAAGAAAAGGAAAGGAGAAG
1 AAGAAAAAAAAAAGAAAGAAAAGGAAAGGAGAAG
56783867 -AGAAAAAAAAAA
1 AAGAAAAAAAAAA
56783879 AGAAGAGGGG
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
30 14 0.21
31 11 0.16
32 8 0.12
33 14 0.21
34 13 0.19
35 3 0.04
36 2 0.03
37 3 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (34 bp):
AAGAAAAAAAAAAGAAAGAAAAGGAAAGGAGAAG
Found at i:56783969 original size:27 final size:28
Alignment explanation
Indices: 56783937--56783990 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
56783927 TTTTATTATG
* *
56783937 TTATTTAGCAT-ATAAATTTTATGAAAT
1 TTATTTAGCATGACAAAATTTATGAAAT
56783964 TTATTTAGCATGACAAAATTTATGAAA
1 TTATTTAGCATGACAAAATTTATGAAA
56783991 AAATTCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (28 bp):
TTATTTAGCATGACAAAATTTATGAAAT
Found at i:56784560 original size:287 final size:286
Alignment explanation
Indices: 56784232--56784839 Score: 1049
Period size: 287 Copynumber: 2.1 Consensus size: 286
56784222 AAAGTAAAAA
56784232 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGAAA-TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
56784297 GGCCAAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTAA
65 AGCCAAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAGAAATAATTAATACAAATATTTAA
56784362 AACAAAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTA
130 AACAAAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTA
56784427 ATAAAATTC-GAGAAAATAATACGAGCAAATGGC-AGGAATAAGGGTTTTTTTTACACTAAATTA
195 ATAAAATTCAG-GAAAATAATACGAGCAAATGGCGA-GAATAAGGGTTTTTTTTACACTAAATTA
*
56784490 ATTTAAAAAACACATTAAATTAATAAATT
258 ATTTAAAAAACACACTAAATTAATAAATT
56784519 TATAAAATTAGAAATTATGAAACTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGAAA-TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* * *
56784584 AGCCGAGGTAAGAGTGTTTTACAAAAATTTTTAAAACTTCAGAAATAATTAATACAAATATTTGA
65 AGCCAAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAGAAATAATTAATACAAATATTTAA
* * ** *
56784649 AACAAAATGTATTGAAATAATATAAAATAATAAAATACGTCAATAAAATTATTTTATTGAAAGTA
130 AACAAAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTA
56784714 ATAAAATTCAGGAAAATAATACGAGCAAATGGCGAGAATAAGGGTTTTTTTTACACTAAATTAAT
195 ATAAAATTCAGGAAAATAATACGAGCAAATGGCGAGAATAAGGGTTTTTTTTACACTAAATTAAT
56784779 TTAAAAAACACACTAAATTAATAAATT
260 TTAAAAAACACACTAAATTAATAAATT
* *
56784806 TATAAAATTAGAAATTATGATATTTTTAAGGTAA
1 TATAAAATTAGAAATTATGAAATTTTTAAAGTAA
56784840 GAGTGTTTTA
Statistics
Matches: 305, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
286 11 0.04
287 292 0.96
288 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (286 bp):
TATAAAATTAGAAATTATGAAATTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAATA
GCCAAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAGAAATAATTAATACAAATATTTAAA
ACAAAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTAA
TAAAATTCAGGAAAATAATACGAGCAAATGGCGAGAATAAGGGTTTTTTTTACACTAAATTAATT
TAAAAAACACACTAAATTAATAAATT
Found at i:56785159 original size:278 final size:279
Alignment explanation
Indices: 56784834--56785424 Score: 1015
Period size: 278 Copynumber: 2.1 Consensus size: 279
56784824 GATATTTTTA
56784834 AGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACAA
1 AGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACAA
* *
56784899 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAATAAA
66 AATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAAATTATTTTATTGAAAGTAATAAA
** *
56784964 ATTCCGGAAAATAATACGAGCAAATGGCGGGAATAAGGGTTTTTTTACACTAAATTAATTTAAAA
131 ATTCAAGAAAATAATACGAGCAAATGGCGGGAATAAGAGTTTTTTTACACTAAATTAATTTAAAA
56785029 AACACAC-TAAATTTATAAAATTAGAAATTATGAT-TTTTTTAAAAGTAATAAAATGCGGAGAAA
196 AACACACATAAATTTATAAAATTAGAAATTATGATATTTTTT-AAAGTAATAAAATGCGGAGAAA
56785092 AAAATACGAAGAAATGGCCG
260 AAAATACGAAGAAATGGCCG
56785112 AGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACAA
1 AGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACAA
56785177 AATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAAATTATTTTATTGAAAGTAATAAA
66 AATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAAATTATTTTATTGAAAGTAATAAA
56785242 ATTCAAGAAAATAATACGAGCAAATGGCGGGAATAAGAGTTTTTTTACACTAAATTAATTTAAAA
131 ATTCAAGAAAATAATACGAGCAAATGGCGGGAATAAGAGTTTTTTTACACTAAATTAATTTAAAA
*
56785307 AACACACTAAATTAATAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGTG
196 AACACAC-------ATAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCG
*
56785372 GAGAAAAAAATATGAAGAAATGGCCG
254 GAGAAAAAAATACGAAGAAATGGCCG
* *
56785398 AGGTAAGAGTGTTTTACTAACTTTTTT
1 AGGTAAGAGTGTTTTACAAAATTTTTT
56785425 TTCAACATGC
Statistics
Matches: 295, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
278 197 0.67
286 92 0.31
287 6 0.02
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (279 bp):
AGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACAA
AATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAAATTATTTTATTGAAAGTAATAAA
ATTCAAGAAAATAATACGAGCAAATGGCGGGAATAAGAGTTTTTTTACACTAAATTAATTTAAAA
AACACACATAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAA
AAATACGAAGAAATGGCCG
Found at i:56785357 original size:523 final size:525
Alignment explanation
Indices: 56784301--56785354 Score: 1830
Period size: 523 Copynumber: 2.0 Consensus size: 525
56784291 AGAAATGGCC
56784301 AAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTAAAACA
1 AAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTAAAACA
56784366 AAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTAATAA
66 AAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTAATAA
56784431 AATTCGAGAAAATAATACGAGCAAATGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAA
131 AATTCGAGAAAATAATACGAGCAAATGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAA
56784496 AAAACACATTAAATTAATAAATTTATAAAATTAGAAATTATGAAACTTTTTAAAGTAATAAAATG
196 AAAACAC-----A--AATAAATTTATAAAATTAGAAATTATGAAACTTTTTAAAGTAATAAAATG
*
56784561 CGGAGAAAAAAATACGAAGAAATAGCCGAGGTAAGAGTGTTTTACAAAAATTTTTAAAACTTCAG
254 CGGAGAAAAAAATACGAAGAAATAGCCGAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAG
* * ***
56784626 AAATAATTAATACAAATATTTGAAACAAAATGTATTGAAATAATATAAAATAATAAAATACGTCA
319 AAATAATTAATACAAATATTTGAAACAAAATGTACTAAAATAATATAAAATAATAAAATACAAAA
*
56784691 ATAAAATTATTTTATTGAAAGTAATAAAATTCAGGAAAATAATACGAGCAAATGGCGAGAATAAG
384 ATAAAATTATTTTATTGAAAGTAATAAAATTCAAGAAAATAATACGAGCAAATGGCGAGAATAAG
*
56784756 GGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAATTAATAAATTTATAAAATTAGAAAT
449 AGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAATTAATAAATTTATAAAATTAGAAAT
56784821 TATGATATTTTT
514 TATGATATTTTT
*
56784833 AAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAAACA
1 AAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTAAAACA
* *
56784898 AAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAATAA
66 AAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTAATAA
*
56784963 AATTCCG-GAAAATAATACGAGCAAATGGCGGGAATAAGGG-TTTTTTTACACTAAATTAATTTA
131 AATT-CGAGAAAATAATACGAGCAAATGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTA
* **
56785026 AAAAACAC-ACTAAATTTATAAAATTAGAAATTATG-ATTTTTTTAAAAGTAATAAAATGCGGAG
195 AAAAACACAAATAAATTTATAAAATTAGAAATTATGAAACTTTTT-AAAGTAATAAAATGCGGAG
* *
56785089 AAAAAAATACGAAGAAATGGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATA
259 AAAAAAATACGAAGAAATAGCCGAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAGAAATA
56785154 ATTAATACAAATATTTGAAACAAAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAA
324 ATTAATACAAATATTTGAAACAAAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAA
*
56785219 ATTATTTTATTGAAAGTAATAAAATTCAAGAAAATAATACGAGCAAATGGCGGGAATAAGAG-TT
389 ATTATTTTATTGAAAGTAATAAAATTCAAGAAAATAATACGAGCAAATGGCGAGAATAAGAGTTT
56785283 TTTTTACACTAAATTAATTTAAAAAACACACTAAATTAATAAATTTATAAAATTAGAAATTATGA
454 TTTTTACACTAAATTAATTTAAAAAACACACTAAATTAATAAATTTATAAAATTAGAAATTATGA
56785348 TATTTTT
519 TATTTTT
56785355 TAAAGTAATA
Statistics
Matches: 502, Mismatches: 18, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
522 80 0.16
523 226 0.45
531 31 0.06
532 163 0.32
533 2 0.00
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (525 bp):
AAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTAAAACA
AAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTAAAAGTAATAA
AATTCGAGAAAATAATACGAGCAAATGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAA
AAAACACAAATAAATTTATAAAATTAGAAATTATGAAACTTTTTAAAGTAATAAAATGCGGAGAA
AAAAATACGAAGAAATAGCCGAGGTAAGAGTGTTTTACAAAAATTTTTAAAAATTCAGAAATAAT
TAATACAAATATTTGAAACAAAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAAAAT
TATTTTATTGAAAGTAATAAAATTCAAGAAAATAATACGAGCAAATGGCGAGAATAAGAGTTTTT
TTTACACTAAATTAATTTAAAAAACACACTAAATTAATAAATTTATAAAATTAGAAATTATGATA
TTTTT
Found at i:56786659 original size:3 final size:3
Alignment explanation
Indices: 56786624--56786679 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
56786614 TTTAGGTTTT
* * *
56786624 TTA TTA TT- TTA ATA GTA TTA TCA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
56786669 TTA TTA TTA TT
1 TTA TTA TTA TT
56786680 TCTATACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:56786846 original size:28 final size:28
Alignment explanation
Indices: 56786815--56786871 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
56786805 ATGCGTATAC
*
56786815 ATTTTATA-ATACATATACATTTTTCTAT
1 ATTTTATATATACACATACA-TTTTCTAT
*
56786843 ATTTTATATATATACATACATTTTCTAT
1 ATTTTATATATACACATACATTTTCTAT
56786871 A
1 A
56786872 ATATATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTTATATATACACATACATTTTCTAT
Found at i:56786882 original size:26 final size:28
Alignment explanation
Indices: 56786829--56786883 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
56786819 TATAATACAT
*
56786829 ATACATTTTTCTATATTTTATATATATAC
1 ATACATTTTTCTATA-TATATATATATAC
*
56786858 ATACA-TTTTCTATA-ATATATGTATAC
1 ATACATTTTTCTATATATATATATATAC
56786884 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
28 9 0.38
29 5 0.21
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (28 bp):
ATACATTTTTCTATATATATATATATAC
Found at i:56787032 original size:13 final size:12
Alignment explanation
Indices: 56787014--56787053 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
56787004 ATTTTCATAG
56787014 TTTATTTATATA
1 TTTATTTATATA
*
56787026 TTATATTTATACA
1 TT-TATTTATATA
*
56787039 TTTTTTTATATA
1 TTTATTTATATA
56787051 TTT
1 TTT
56787054 TGTGAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATATA
Found at i:56789006 original size:88 final size:88
Alignment explanation
Indices: 56788857--56789022 Score: 260
Period size: 88 Copynumber: 1.9 Consensus size: 88
56788847 TGTTAGGATT
* * * *
56788857 ACGACTTTTGTAGTATGTAACATCATTCACAATAGTGTAATTTATAGCTAAACTAATGGGTAAAT
1 ACGACTTCTGTAATATGTAACATCATTCACAATAGTGAAATTCATAGCTAAACTAATGGGTAAAT
*
56788922 GATATCTTCTCATTTTACATTAC
66 GATATATTCTCATTTTACATTAC
* * *
56788945 ACGACTTCTGTAATATGTAGCATCATTCACAATAGTGAAATTCATAGTTAAATTAATGGGTAAAT
1 ACGACTTCTGTAATATGTAACATCATTCACAATAGTGAAATTCATAGCTAAACTAATGGGTAAAT
56789010 GATATATTCTCAT
66 GATATATTCTCAT
56789023 CGACATTACA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (88 bp):
ACGACTTCTGTAATATGTAACATCATTCACAATAGTGAAATTCATAGCTAAACTAATGGGTAAAT
GATATATTCTCATTTTACATTAC
Found at i:56790447 original size:16 final size:17
Alignment explanation
Indices: 56790426--56790461 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
56790416 AAAACATAAT
*
56790426 AATTAAGAAAT-AAATA
1 AATTAAAAAATAAAATA
56790442 AATTAAAAAATAAAATA
1 AATTAAAAAATAAAATA
56790459 AAT
1 AAT
56790462 CCATAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AATTAAAAAATAAAATA
Found at i:56793362 original size:2 final size:2
Alignment explanation
Indices: 56793355--56793396 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
56793345 TATGTAAGAG
*
56793355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56793397 CACATATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:56795175 original size:44 final size:43
Alignment explanation
Indices: 56795127--56795457 Score: 264
Period size: 44 Copynumber: 7.6 Consensus size: 43
56795117 ATTTTAATCC
* * *
56795127 GCTCCACTACAACTTCAGGGAGATAGGATTAGTAGATTTTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGT-GATTTTGTCT
* * *
56795171 GCTCCACTGCAACTTCAGGGAGATAAGACT-G-GA-TATGATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTGATTTTG-TCT
* * * * *
56795212 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTGATTTT-GTCT
* * * **
56795257 GCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGG-TGATTTTGTCT
* *
56795301 GCTCCACTGCAACTTCAGGGAGATAAGACT-G-GA-TGTGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTGATTTTG-TCT
* * * * * *
56795342 ACTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTTAGTCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTGATTTT-GTCT
* *
56795387 GCTCTACTGCAACTTCAGGGAGATAGGATTGGT--TTCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTGATT-TT--GTCT
*
56795431 GCTCCACTGCAACTTCAGTGAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
56795458 GCTTGATATG
Statistics
Matches: 231, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
40 5 0.02
41 59 0.26
42 4 0.02
43 6 0.03
44 92 0.40
45 64 0.28
46 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGGTGATTTTGTCT
Found at i:56795227 original size:41 final size:41
Alignment explanation
Indices: 56795168--56795499 Score: 268
Period size: 41 Copynumber: 7.8 Consensus size: 41
56795158 GTAGATTTTG
*
56795168 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATATGA
* * * * *
56795209 TTTGCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTTAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGA-C---TGGATATGA
* * * *
56795254 TCTGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTCA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGG-ATA-TGA
* *
56795297 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGA
1 -TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATATGA
* * * * *
56795339 TCTACTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTTA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGA-C-TG-GATATGA
* * * * * *
56795383 GTCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCA
1 -TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGG-AT-ATGA
* * * *
56795427 GTCTGCTCCACTGCAACTTCAGTGAGATAAGGCTTGATATGA
1 -TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATATGA
* * *
56795469 TCTGCTCTACTGTAACTTTAGAGAGATAAGA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGA
56795500 TCTGCAATGT
Statistics
Matches: 232, Mismatches: 46, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
41 85 0.37
42 9 0.04
43 9 0.04
44 68 0.29
45 61 0.26
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
TCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATATGA
Found at i:56795311 original size:130 final size:130
Alignment explanation
Indices: 56795037--56795502 Score: 628
Period size: 130 Copynumber: 3.6 Consensus size: 130
56795027 TTGTGATTTT
* * * * * ** * *
56795037 AGTCTACTTCACTGCAACTTTAGGGAAATAAGGCTGGATGCGATCTGCTCTACCGCAACTTCATA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATCTGCTCTACTGCAACTTCAGA
* * ** ** * * * ** *
56795102 GATATATGAT-TCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAGTAGATTT
66 GAGATAAGATCTTGTGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTC
* *
56795166 TGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATTTGCTCTACTGCAACTTCAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATCTGCTCTACTGCAACTTCAGA
*
56795231 GAGATAAGATCTTGTGGTTTTAATCTGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTC
66 GAGATAAGATCTTGTGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTC
* *
56795296 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTACTCTACTGCAACTTCAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATCTGCTCTACTGCAACTTCAGA
* *
56795361 GAGATAAGATCTTGTGGTTTTAGTCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTC
66 GAGATAAGATCTTGTGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTC
* * * * *
56795426 AGTCTGCTCCACTGCAACTTCAGTGAGATAAGGCTTGATATGATCTGCTCTACTGTAACTTTAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATCTGCTCTACTGCAACTTCAGA
56795491 GAGATAAGATCT
66 GAGATAAGATCT
56795503 GCAATGTATA
Statistics
Matches: 298, Mismatches: 38, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
129 62 0.21
130 236 0.79
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (130 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATATGATCTGCTCTACTGCAACTTCAGA
GAGATAAGATCTTGTGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTATTC
Found at i:56795691 original size:100 final size:99
Alignment explanation
Indices: 56795513--56796230 Score: 814
Period size: 100 Copynumber: 7.2 Consensus size: 99
56795503 GCAATGTATA
* * * * *
56795513 GCTTCAATCTTTTTAAACTGCAATGTCGGGGAAACAAAATTCACCGTTGTAGCTTCAACCTATTC
1 GCTTCAATC-TTTT-AATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTC
* * * * *
56795578 CGCTACACCGCCAGGGAAGTAAGATTCGCCATTGCG
64 CACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTG
* * * * * **
56795614 GCTTCAATCTTTTAAATTGCAATATCTGGTAAGCAAGATTCACCGTCGTAGCTTTAATCTACTCC
1 GCTTCAATCTTTT-AATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
** * * * *
56795679 ACTGCATTGCCAGAGAAGTAAGATTCGCCATTGCG
65 ACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTG
* * * * * * *
56795714 GCTTCAA--TATT--TTGCAATATCGGGGAAGTAAGATTCACCATCGTAGCTTTAATCTGCTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* * * *
56795775 CTGCACCGCTTGAGAAAGTAAGATTTGTCGTTGTG
66 CTGCACCGCCTG-GGAAGTAAGATTCGCCGTTGTG
* *
56795810 GCTTCAATCTTTCAATTGCAATGTCGGGGAAGCAAGATTCACCATTGTAGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
*
56795875 CTGCACCGCCTGGGAAAGTAAGATTCGCTGTTGTG
66 CTGCACCGCCTGGG-AAGTAAGATTCGCCGTTGTG
*
56795910 GCTTCAATCTTTCAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* ** *
56795975 TTGCAAAGCCTGGGAAAGTAAGATTTGCCGTTGTG
66 CTGCACCGCCTGGG-AAGTAAGATTCGCCGTTGTG
** * **
56796010 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTTACCGTCATAGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* *
56796075 CTGCATCGCCTGGGAAGGTAAGATTCTCCGTTGTG
66 CTGCACCGCCTGGGAA-GTAAGATTCGCCGTTGTG
* * * ** *
56796110 GCCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGCGGTTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* * *
56796175 CTGCACCGCTTGGAAGAGTAAGATTCGCTGTTGTG
66 CTGCACCGCCTGGGA-AGTAAGATTCGCCGTTGTG
56796210 GCTTCAATCTTTTAATTGCAA
1 GCTTCAATCTTTTAATTGCAA
56796231 ACTATGGTTT
Statistics
Matches: 534, Mismatches: 75, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
95 53 0.10
96 23 0.04
98 5 0.01
99 3 0.01
100 440 0.82
101 10 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (99 bp):
GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
CTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTG
Found at i:56795819 original size:51 final size:51
Alignment explanation
Indices: 56795739--56796219 Score: 332
Period size: 51 Copynumber: 9.6 Consensus size: 51
56795729 AATATCGGGG
* * * * * * * * *
56795739 AAGTAAGATTCACCATCGTAGCTTTAATCTGCTCCACTGCACCGCTTGAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* * * * * *
56795790 AAGTAAGATTTGTCGTTGTGGCTTCAATCT-TTCAATTGCAATG-TCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* * * * * * *
56795839 AAGCAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* * * * *
56795890 AAGTAAGATTCGCTGTTGTGGCTTCAATCT-TTCAATTGCAATG-TCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* * * * *
56795939 AAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCATTGCAAAGCCTGGGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* ** * * *
56795990 AAGTAAGATTTGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* ** ** * * * *
56796039 AAGTGAGATTTACCGTCATAGCTTCAATCTGTTCCACTGCATCGCCTGGGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
* * * ** * * *
56796090 AGGTAAGATTCTCCGTTGTGGCCTCAATCT-TTTAATTGCAATG-TCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
** * * * *
56796139 AAGCGAGATTCGCCGTTGCGGTTTCAATCTGTTCCACTGCACCGCTT-GGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
*
56796189 AGAGTAAGATTCGCTGTTGTGGCTTCAATCT
1 A-AGTAAGATTCGCCGTTGTGGCTTCAATCT
56796220 TTTAATTGCA
Statistics
Matches: 314, Mismatches: 107, Indels: 18
0.72 0.24 0.04
Matches are distributed among these distances:
49 110 0.35
50 74 0.24
51 130 0.41
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (51 bp):
AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCATTGCAACGCTTGGGA
Found at i:56797661 original size:12 final size:11
Alignment explanation
Indices: 56797641--56797680 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
56797631 TGGCTTCTCC
56797641 TTTTTTCTTTT
1 TTTTTTCTTTT
56797652 TTTCTTTCTTCTT
1 TTT-TTTCTT-TT
*
56797665 TTTTTTGTTTT
1 TTTTTTCTTTT
56797676 TTTTT
1 TTTTT
56797681 GAATTCGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.38
12 11 0.42
13 5 0.19
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:56797663 original size:15 final size:15
Alignment explanation
Indices: 56797640--56797669 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56797630 TTGGCTTCTC
*
56797640 CTTTTTTCTTTTTTT
1 CTTTCTTCTTTTTTT
56797655 CTTTCTTCTTTTTTT
1 CTTTCTTCTTTTTTT
56797670 TGTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTCTTCTTTTTTT
Found at i:56797665 original size:22 final size:23
Alignment explanation
Indices: 56797635--56797677 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
56797625 TCACCTTGGC
56797635 TTCTCCTTTTTTCT-TTTTTTCT
1 TTCTCCTTTTTTCTGTTTTTTCT
* *
56797657 TTCTTCTTTTTTTTGTTTTTT
1 TTCTCCTTTTTTCTGTTTTTT
56797678 TTTGAATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTCCTTTTTTCTGTTTTTTCT
Found at i:56807439 original size:44 final size:44
Alignment explanation
Indices: 56807326--56807766 Score: 389
Period size: 44 Copynumber: 10.0 Consensus size: 44
56807316 GTAAGACTTG
* * ***
56807326 TATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGC
* *
56807371 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG-
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
* * * * * * *
56807414 TATATTCGATCCACTTCGCTACCAATATAGGAAGACAGGACCTGC
1 TATCTTCGATCTACTTCAC-ACCAATACATGAAGACAAGATCTGC
*
56807459 TATCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
* * * *
56807503 TTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
* * * * *
56807547 TTTCTTCAATCTACTTCACGCCAATACATGAAGATAAGATTTGC
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
* * * *** * *
56807591 TCTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGT
1 TATCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGC
* * * * * *
56807636 TGTCTTTGATCTACTTCACGCCAGTACATAAAGATAAGATCTGC
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
* * * * *** *
56807680 TTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGC
* * * *
56807725 TATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCT
1 TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCT
56807767 TTTGTATTCA
Statistics
Matches: 323, Mismatches: 69, Indels: 9
0.81 0.17 0.02
Matches are distributed among these distances:
43 15 0.05
44 208 0.64
45 100 0.31
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
TATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGC
Found at i:56807653 original size:89 final size:89
Alignment explanation
Indices: 56807328--56807766 Score: 587
Period size: 89 Copynumber: 5.0 Consensus size: 89
56807318 AAGACTTGTA
56807328 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTT-TCTTCGATCTACTTCACGC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTCGATCTACTTCACGC
* * *
56807392 CAATACATGAAGACAAGATCTG-TA
65 CAGTACATGAAGATAAGATCTGCTT
* * * * * * * * *
56807416 TATTCGATCCACTTCGCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACACC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
*
56807481 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGATAAGATCTGCTT
* * *** * *
56807505 TCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
* * *
56807569 AATACATGAAGATAAGATTTGCTC
66 AGTACATGAAGATAAGATCTGCTT
* * *
56807593 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGTTGTCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
*
56807658 AGTACATAAAGATAAGATCTGCTT
66 AGTACATGAAGATAAGATCTGCTT
* *
56807682 TCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
56807747 AGTACATGAAGATAAGATCT
66 AGTACATGAAGATAAGATCT
56807767 TTTGTATTCA
Statistics
Matches: 302, Mismatches: 46, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
87 1 0.00
88 146 0.48
89 155 0.51
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
AGTACATGAAGATAAGATCTGCTT
Found at i:56809104 original size:48 final size:48
Alignment explanation
Indices: 56809027--56809124 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 48
56809017 CACCTTAGCC
* *
56809027 TCTCCATTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGG
1 TCTCCATTTTTTTTTACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGG
56809075 TCTCC-TTTTTTTTTGACTCAAAG-TGCCCTTTGTAGGCTTTCACCTTGG
1 TCTCCATTTTTTTTT-ACTCAAAGCT-CCCTTTGTAGGCTTTCACCTTGG
56809123 TC
1 TC
56809125 CCACCCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 10 0.22
48 36 0.78
ACGTcount: A:0.12, C:0.26, G:0.16, T:0.46
Consensus pattern (48 bp):
TCTCCATTTTTTTTTACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGG
Found at i:56809135 original size:48 final size:48
Alignment explanation
Indices: 56809035--56809136 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
56809025 CCTCTCCATT
* * * ***
56809035 TTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTCCTTT
1 TTTTTTGACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCCCCC
56809083 TTTTTTGACTCAAAG-TGCCCTTTGTAGGCTTTCACCTTGGTC-CCACCC
1 TTTTTTGACTCAAAGCT-CCCTTTGTAGGCTTTCACCTTGGTCTCC-CCC
56809131 TTTTTT
1 TTTTTT
56809137 AAGCAGAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 3 0.07
48 43 0.93
ACGTcount: A:0.12, C:0.26, G:0.16, T:0.46
Consensus pattern (48 bp):
TTTTTTGACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCCCCC
Found at i:56809936 original size:24 final size:24
Alignment explanation
Indices: 56809905--56809950 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
56809895 AGTTTGGCAG
56809905 AAAAAATC-CAAAGTAATGAAAGCA
1 AAAAAATCGCAAAG-AATGAAAGCA
*
56809929 AAAAAATCGTAAAGAATGAAAG
1 AAAAAATCGCAAAGAATGAAAG
56809951 AACATTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.63, C:0.09, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAAATCGCAAAGAATGAAAGCA
Found at i:56814133 original size:3 final size:3
Alignment explanation
Indices: 56814125--56814181 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
56814115 ATAGTAACAG
56814125 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56814173 TAA TAA TAA
1 TAA TAA TAA
56814182 CATAATTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:56817281 original size:24 final size:25
Alignment explanation
Indices: 56817253--56817303 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
56817243 ATCGTAATAA
*
56817253 GACAACATTT-TAAAAA-TAATATAT
1 GACAA-ATTTCTAAAAACAAATATAT
56817277 GACAAATTTCTAAAAACAAATATAT
1 GACAAATTTCTAAAAACAAATATAT
56817302 GA
1 GA
56817304 TAATAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (25 bp):
GACAAATTTCTAAAAACAAATATAT
Found at i:56817416 original size:4 final size:4
Alignment explanation
Indices: 56817401--56817448 Score: 87
Period size: 4 Copynumber: 11.8 Consensus size: 4
56817391 TAAAATCATA
56817401 AAAT ATAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
56817449 CAAACAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:56824055 original size:15 final size:15
Alignment explanation
Indices: 56824035--56824088 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
56824025 ATACTACAAA
56824035 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
56824050 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
56824067 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
56824084 ATATT
1 ATATT
56824089 AATATTGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:56826829 original size:23 final size:23
Alignment explanation
Indices: 56826803--56826850 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
56826793 AAAAAAAAGG
56826803 TTTAAGTGCCAACTTGCTTCCAA
1 TTTAAGTGCCAACTTGCTTCCAA
56826826 TTTAAGTGCCAACTTGCTTCCAA
1 TTTAAGTGCCAACTTGCTTCCAA
56826849 TT
1 TT
56826851 AAAAAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (23 bp):
TTTAAGTGCCAACTTGCTTCCAA
Found at i:56830056 original size:12 final size:12
Alignment explanation
Indices: 56830039--56830072 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56830029 CTTGTTGAAG
*
56830039 TCTACCTCTACC
1 TCTACCTCGACC
56830051 TCTACCTCGACC
1 TCTACCTCGACC
*
56830063 TCGACCTCGA
1 TCTACCTCGA
56830073 TCTCAAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.47, G:0.09, T:0.26
Consensus pattern (12 bp):
TCTACCTCGACC
Found at i:56839830 original size:2 final size:2
Alignment explanation
Indices: 56839825--56839849 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56839815 ATAACTTATC
56839825 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56839850 AAAGAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56842207 original size:29 final size:29
Alignment explanation
Indices: 56842138--56842211 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
56842128 ATATACATGT
*
56842138 AATAATTTTAATAATTTTATATTTCAAAA
1 AATAATTTTAATAATTATATATTTCAAAA
* *
56842167 AA-ATAGTATAATAATTATATATATT-AAAA
1 AATA-ATTTTAATAATTATATAT-TTCAAAA
56842196 AATAATTTTAATAATT
1 AATAATTTTAATAATT
56842212 TTAAAATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 33 0.89
30 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
AATAATTTTAATAATTATATATTTCAAAA
Found at i:56844383 original size:20 final size:21
Alignment explanation
Indices: 56844358--56844403 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
56844348 TATATTTTTT
*
56844358 AAAAATTATAAA-AAAATTTA
1 AAAAATTATAAAGAAAATATA
* *
56844378 AAAAATTCTAAAGAATATATA
1 AAAAATTATAAAGAAAATATA
56844399 AAAAA
1 AAAAA
56844404 AGTTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAATTATAAAGAAAATATA
Found at i:56844412 original size:29 final size:28
Alignment explanation
Indices: 56844357--56844419 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
56844347 ATATATTTTT
*
56844357 TAAAAATTATAAAAAAATTTAAAAAATTC
1 TAAAAATTATAAAAAAAGTT-AAAAATTC
*
56844386 TAAAGAATATATAAAAAAAGTT-AAAATTT
1 TAAA-AAT-TATAAAAAAAGTTAAAAATTC
56844415 TAAAA
1 TAAAA
56844420 TTTTTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.47
30 3 0.10
31 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAAAATTATAAAAAAAGTTAAAAATTC
Found at i:56847328 original size:5 final size:5
Alignment explanation
Indices: 56847318--56847353 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
56847308 AGTTATACAT
56847318 ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
56847354 CTTATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 25 0.86
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:56847338 original size:15 final size:13
Alignment explanation
Indices: 56847318--56847353 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
56847308 AGTTATACAT
56847318 ATATAATATAATATA
1 ATATAATAT-A-ATA
56847333 ATATAATATAATA
1 ATATAATATAATA
56847346 ATATAATA
1 ATATAATA
56847354 CTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 1 0.05
15 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:56851738 original size:105 final size:106
Alignment explanation
Indices: 56851544--56851770 Score: 316
Period size: 106 Copynumber: 2.2 Consensus size: 106
56851534 TAAAAACAAT
* * * *
56851544 CACT-AAATTTTTTTTATTTTTTTCGTATATTGATATCTGATTTTGACATGAAAAAAAAAAGAAG
1 CACTCAAATTTTTTTTATTTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAAG
* *
56851608 TTTTTTTAAATAGTATTGGGTGCCGGCCATTGACAGGCCAG
66 TTTTTTTAAATAGTACTGGGTGCCGGCCATTGACAGGCCAA
* *
56851649 CACTCAAATTTTTTTT-TATTTTTTCGTATACTGATATTTGACTCTGACACGAAAAAAAATA-AA
1 CACTCAAATTTTTTTTAT-TTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAA
* *
56851712 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAA
65 GTTTTTTTAAATAGTACTGGGTGCCGGCCATTGACAGGCCAA
*
56851754 CACGCAAAATTTTTTTT
1 CACTC-AAATTTTTTTT
56851771 CGTTTTTCTT
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
105 49 0.45
106 59 0.55
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (106 bp):
CACTCAAATTTTTTTTATTTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAAG
TTTTTTTAAATAGTACTGGGTGCCGGCCATTGACAGGCCAA
Found at i:56851778 original size:105 final size:106
Alignment explanation
Indices: 56851548--56851770 Score: 322
Period size: 105 Copynumber: 2.1 Consensus size: 106
56851538 AACAATCACT
* * * *
56851548 AAATTTTTTTTATTTTTTTCGTATATTGATATCTGATTTTGACATGAAAAAAAAAAGAAGTTTTT
1 AAATTTTTTTTA-TTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAAGTTTTT
* * *
56851613 TTAAATAGTATTGGGTGCCGGCCATTGACAGGCCAGCACTCA
65 TTAAATAGTACTGGGTGCCGGCCATTGACAGGCCAACACGCA
* * * *
56851655 AATTTTTTTTTATTTTTTCGTATACTGATATTTGACTCTGACACGAAAAAAAATA-AATTTTTTT
1 AAATTTTTTTTATTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAAGTTTTTT
*
56851719 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACGCA
66 TAAATAGTACTGGGTGCCGGCCATTGACAGGCCAACACGCA
56851760 AAATTTTTTTT
1 AAATTTTTTTT
56851771 CGTTTTTCTT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 55 0.53
106 37 0.36
107 11 0.11
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (106 bp):
AAATTTTTTTTATTTTTTCGTATACTGATATCTGACTCTGACACGAAAAAAAAAAGAAGTTTTTT
TAAATAGTACTGGGTGCCGGCCATTGACAGGCCAACACGCA
Found at i:56851784 original size:16 final size:16
Alignment explanation
Indices: 56851763--56851794 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56851753 ACACGCAAAA
56851763 TTTTTTTTCGTTTTTC
1 TTTTTTTTCGTTTTTC
*
56851779 TTTTTTTTCTTTTTTC
1 TTTTTTTTCGTTTTTC
56851795 ATATATCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCGTTTTTC
Found at i:56854388 original size:25 final size:24
Alignment explanation
Indices: 56854363--56854416 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
56854353 ATTATTGGTA
*
56854363 TTATTATCATATTATTTTATATG-
1 TTATTATCATATTAGTTTATATGT
56854386 -TATTATCATATTAGTTTATATGT
1 TTATTATCATATTAGTTTATATGT
56854409 TTACTTAT
1 TTA-TTAT
56854417 TTTCATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 21 0.78
24 2 0.07
25 4 0.15
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59
Consensus pattern (24 bp):
TTATTATCATATTAGTTTATATGT
Found at i:56854392 original size:22 final size:22
Alignment explanation
Indices: 56854364--56854408 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
56854354 TTATTGGTAT
*
56854364 TATTATCATATTATTTTATATG
1 TATTATCATATTAGTTTATATG
56854386 TATTATCATATTAGTTTATATG
1 TATTATCATATTAGTTTATATG
56854408 T
1 T
56854409 TTACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (22 bp):
TATTATCATATTAGTTTATATG
Found at i:56854428 original size:2 final size:2
Alignment explanation
Indices: 56854421--56854455 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56854411 ACTTATTTTC
56854421 AT 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 AT A
56854456 CACACTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56863902 original size:11 final size:11
Alignment explanation
Indices: 56863888--56863980 Score: 74
Period size: 11 Copynumber: 8.9 Consensus size: 11
56863878 AATATATTTA
56863888 TTTTAAAATAT
1 TTTTAAAATAT
56863899 TTTTAAAATACT
1 TTTTAAAATA-T
**
56863911 TTTTTCAAT-T
1 TTTTAAAATAT
*
56863921 TTTT--TA-AT
1 TTTTAAAATAT
56863929 TTTTAAAATAT
1 TTTTAAAATAT
56863940 TTTTAAAATACT
1 TTTTAAAATA-T
**
56863952 TTTTTCAAT-T
1 TTTTAAAATAT
56863962 TTTT-AAA-AT
1 TTTTAAAATAT
56863971 TTTTAAAATA
1 TTTTAAAATA
56863981 AAAATGGGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
8 6 0.09
9 7 0.11
10 14 0.21
11 23 0.35
12 16 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56863943 original size:41 final size:42
Alignment explanation
Indices: 56863888--56863980 Score: 170
Period size: 41 Copynumber: 2.2 Consensus size: 42
56863878 AATATATTTA
*
56863888 TTTTAAAATATTTTTAAAATACTTTTTTCAATTTTTT-TAAT
1 TTTTAAAATATTTTTAAAATACTTTTTTCAATTTTTTAAAAT
56863929 TTTTAAAATATTTTTAAAATACTTTTTTCAATTTTTTAAAAT
1 TTTTAAAATATTTTTAAAATACTTTTTTCAATTTTTTAAAAT
56863971 TTTTAAAATA
1 TTTTAAAATA
56863981 AAAATGGGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.74
42 13 0.26
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (42 bp):
TTTTAAAATATTTTTAAAATACTTTTTTCAATTTTTTAAAAT
Found at i:56864526 original size:32 final size:31
Alignment explanation
Indices: 56864456--56864536 Score: 76
Period size: 32 Copynumber: 2.5 Consensus size: 31
56864446 CTTTACCCTA
*
56864456 TTTT-AAATGAAAACATAAAAATTAAATAAAAC
1 TTTTAAAAT-AAAA-ATAAAAATTAAAAAAAAC
56864488 TCTTTAAAATAAAAATAAAAA-TAAAAAAAATC
1 T-TTTAAAATAAAAATAAAAATTAAAAAAAA-C
56864520 GTTTTAAATATATAAAA
1 -TTTTAAA-ATA-AAAA
56864537 AATTTCAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
31 8 0.19
32 15 0.36
33 11 0.26
34 8 0.19
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (31 bp):
TTTTAAAATAAAAATAAAAATTAAAAAAAAC
Found at i:56865222 original size:31 final size:32
Alignment explanation
Indices: 56865186--56865250 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
56865176 CTTATATAAT
56865186 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56865217 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56865249 TT
1 TT
56865251 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:56865557 original size:3 final size:3
Alignment explanation
Indices: 56865549--56865586 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56865539 ATCTATCCTT
56865549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56865587 TAACTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56867745 original size:3 final size:3
Alignment explanation
Indices: 56867739--56867803 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
56867729 TAATGTTACC
56867739 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
56867787 ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT AT
56867804 ATTTCCATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56868592 original size:112 final size:111
Alignment explanation
Indices: 56868306--56868618 Score: 495
Period size: 112 Copynumber: 2.8 Consensus size: 111
56868296 TTTCTAATTG
* *
56868306 AGGCAATATTTAGCGTTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
56868370 TCGTTCAACCAAGTAGCTAAATATCC-TTTCAAAAATTTTAAAATA
66 TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAATTTTAAAATA
*
56868415 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
56868480 TCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCGAAATA
66 TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAATTTT-AAAATA
*
56868527 AGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * * *
56868592 TCATTTAACCGAATAGCCAAATATCCT
66 TCGTTCAACCAAATAGCTAAATATCCT
56868619 CTTGAATTTC
Statistics
Matches: 187, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
109 16 0.09
110 69 0.37
111 12 0.06
112 90 0.48
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (111 bp):
AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAATTTTAAAATA
Found at i:56872477 original size:6 final size:6
Alignment explanation
Indices: 56872468--56872583 Score: 53
Period size: 6 Copynumber: 19.8 Consensus size: 6
56872458 AAGAAAAAGA
* * * *
56872468 AAAATC AAAATC AAAGTT AAAATG AAAATG AAAA-- AAAATC AAAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC -AAAATC
* * * ** * *
56872515 AAAATT AAAA-A AAAAAC AAAAAG AAGAA-- AGAATC AAAATC AAGATC
1 AAAATC AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC
* * *
56872561 AAAATG AAAATG AAAATG AAAAT
1 AAAATC AAAATC AAAATC AAAAT
56872584 GAGAAAAAGA
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
4 6 0.07
5 5 0.06
6 71 0.79
7 8 0.09
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:56872536 original size:34 final size:35
Alignment explanation
Indices: 56872467--56872553 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 35
56872457 GAAGAAAAAG
* * **
56872467 AAAAATC-AAAATCAAAGTTAAAATGAAAATGAAA
1 AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
56872501 AAAAATCAAAAATCAAAATTAAAA-AAAAAACAAA
1 AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
* *
56872535 AAGAA-GAAAGAATCAAAAT
1 AAAAATCAAA-AATCAAAAT
56872554 CAAGATCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 3 0.07
34 27 0.60
35 15 0.33
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (35 bp):
AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
Found at i:56872595 original size:20 final size:21
Alignment explanation
Indices: 56872566--56872616 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
56872556 AGATCAAAAT
*
56872566 GAAAATGAAAATGAA-AATGA
1 GAAAAAGAAAATGAAGAATGA
56872586 GAAAAAG-AAA-GAAGAATGA
1 GAAAAAGAAAATGAAGAATGA
56872605 -AAAAAGAGAAAT
1 GAAAAAGA-AAAT
56872617 CTAGATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.10
Consensus pattern (21 bp):
GAAAAAGAAAATGAAGAATGA
Found at i:56874545 original size:81 final size:83
Alignment explanation
Indices: 56874335--56874931 Score: 593
Period size: 81 Copynumber: 7.0 Consensus size: 83
56874325 AGATCAGTGA
* * * *
56874335 AGATCGAAAACAAAGTCTTGCCTCCATTGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATATTGC
1 AGATCG-AAA-AAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGA-A-CAGATCTTGC
*
56874400 CTTCCTGCGTTAACAGCTAAGC
62 CTTCCTGCGTTAACAGCGAAGC
* *
56874422 AGATCGAAAAAAAGCCTTGCCTTCATTGGGTGCAGTGGAGCTGGTTAAAGAA-AGATCTTACCTT
1 AGATCG-AAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAACAGATCTTGCCTT
56874486 CCTGCGTTAACAGCGAAGC
65 CCTGCGTTAACAGCGAAGC
* *
56874505 AGATCG-AAAAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAGAA-AGATCGTGCCTTC
1 AGATCGAAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAACAGATCTTGCCTTC
56874568 CTGCGTTAACAGCGAAGC
66 CTGCGTTAACAGCGAAGC
*
56874586 AGATC-AAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAAATCTTGCCTT
1 AGATCGAAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA-CAGATCTTGCCTT
*
56874650 CCTGCATTAACAGCGAAGC
65 CCTGCGTTAACAGCGAAGC
*
56874669 AGATCGAAAACAAGCCTTGCCTTCATTGGTTAG-AGTGGAGCTGGTTAAAGAAGCAGATCTTGTC
1 AGATCGAAAA-AAGCCTTGCCTTCATTGGTT-GCAGTGGAGCTGGTTAAAGAA-CAGATCTTGCC
* * * *
56874733 TTCCTGCATTGACACCTCAAGC
63 TTCCTGCGTTAACAGC-GAAGC
* * * * *
56874755 AGGTCGAAGACACAAACCTTG-CTTC-TCTCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATC
1 AGATCGAA-A-A-AAGCCTTGCCTTCAT-T-GGTTGCAG-TGGAGCTGGTT-AA-AGAACAGATC
** *
56874817 TTGCCTTCCTGTATTGACAGCGAAGC
58 TTGCCTTCCTGCGTTAACAGCGAAGC
* * * * * *
56874843 AGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATCT
1 AGATCGAA-A-A-AAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGTT-AA-AGAACAGATCT
* * * *
56874906 TGCCTTCTTGCATTGATAGCGAAGC
59 TGCCTTCCTGCGTTAACAGCGAAGC
56874931 A
1 A
56874932 AGTCGAAGAC
Statistics
Matches: 461, Mismatches: 33, Indels: 31
0.88 0.06 0.06
Matches are distributed among these distances:
81 119 0.26
83 67 0.15
84 4 0.01
85 64 0.14
86 50 0.11
87 18 0.04
88 106 0.23
89 27 0.06
90 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (83 bp):
AGATCGAAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAACAGATCTTGCCTTC
CTGCGTTAACAGCGAAGC
Found at i:56874565 original size:41 final size:40
Alignment explanation
Indices: 56874513--56874635 Score: 99
Period size: 40 Copynumber: 3.0 Consensus size: 40
56874503 GCAGATCGAA
*
56874513 AAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAG
1 AAAGCCGTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAG
* * * * * * *
56874553 AAAGATCGTGCCTTC-CTGCGTTAACAG-CGAAGCAGATCAAA-
1 AAAG-CCGTGCCTTCATTG-GTT-GCAGTAG-AGCTGGTTAAAG
* *
56874594 AAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAG
1 AAAGCCGTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAG
56874634 AA
1 AA
56874636 GCAAATCTTG
Statistics
Matches: 60, Mismatches: 16, Indels: 14
0.67 0.18 0.16
Matches are distributed among these distances:
39 11 0.18
40 20 0.33
41 18 0.30
42 11 0.18
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (40 bp):
AAAGCCGTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAG
Found at i:56874662 original size:164 final size:164
Alignment explanation
Indices: 56874335--56874931 Score: 582
Period size: 164 Copynumber: 3.5 Consensus size: 164
56874325 AGATCAGTGA
* * *
56874335 AGATCGAAAACAAAGTCTTGCCTCCATTGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATATTGC
1 AGATCG-AAA-AAAGCCTTGCCTTCATTGGTTG-AGTGGAGCTGGTTAAAGA-A-CAGATCTTGC
*
56874400 CTTCCTGCGTTAACAGCTAAGCAGATCGAAAAAAAGCCTTGCCTTCATTGGGTGCAGTGGAGCTG
61 CTTCCTGCGTTAACAGCGAAGCAGATC-AAAAAAAGCCTTGCCTTCATTGGGTGCAGTGGAGCTG
* *
56874465 GTTAAAGAAAGATCTTACCTTCCTGCGTTAACAGCGAAGC
125 GTTAAAGAAAAATCTTACCTTCCTGCATTAACAGCGAAGC
* *
56874505 AGATCG-AAAAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGGTTAAAGAA-AGATCGTGCCTTC
1 AGATCGAAAAAAGCCTTGCCTTCATTGGTTG-AGTGGAGCTGGTTAAAGAACAGATCTTGCCTTC
*
56874568 CTGCGTTAACAGCGAAGCAGATC-AAAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAA
65 CTGCGTTAACAGCGAAGCAGATCAAAAAAAGCCTTGCCTTCATTGGGTGCAGTGGAGCTGGTTAA
*
56874632 AGAAGCAAATCTTGCCTTCCTGCATTAACAGCGAAGC
130 AGAA--AAATCTTACCTTCCTGCATTAACAGCGAAGC
*
56874669 AGATCGAAAACAAGCCTTGCCTTCATTGGTTAGAGTGGAGCTGGTTAAAGAAGCAGATCTTGTCT
1 AGATCGAAAA-AAGCCTTGCCTTCATTGGTT-GAGTGGAGCTGGTTAAAGAA-CAGATCTTGCCT
* * * * *
56874734 TCCTGCATTGACACCTCAAGCAGGTCGAAGACACAAA-CCTTG-CTTC-TCTCGGTTGTG-A-TG
63 TCCTGCGTTAACAGC-GAAGCAGATC-AA-A-A-AAAGCCTTGCCTTCAT-T-GG--GTGCAGTG
* * * *
56874794 GAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGC
119 GAGCTGGTT-AA-AGAAAA-ATCTTACCTTCCTGCATTAACAGCGAAGC
* * * * * *
56874843 AGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
1 AGATCGAA-A-A-AAGCCTTGCCT-TCATTGGTTGAG-TGGAGCTGGTT-AA-AGAACAGATCTT
* * * *
56874907 GCCTTCTTGCATTGATAGCGAAGCA
59 GCCTTCCTGCGTTAACAGCGAAGCA
56874932 AGTCGAAGAC
Statistics
Matches: 367, Mismatches: 34, Indels: 46
0.82 0.08 0.10
Matches are distributed among these distances:
162 44 0.12
164 67 0.18
165 3 0.01
166 39 0.11
167 38 0.10
168 23 0.06
169 8 0.02
170 6 0.02
171 2 0.01
172 6 0.02
173 21 0.06
174 40 0.11
175 8 0.02
176 33 0.09
177 26 0.07
178 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (164 bp):
AGATCGAAAAAAGCCTTGCCTTCATTGGTTGAGTGGAGCTGGTTAAAGAACAGATCTTGCCTTCC
TGCGTTAACAGCGAAGCAGATCAAAAAAAGCCTTGCCTTCATTGGGTGCAGTGGAGCTGGTTAAA
GAAAAATCTTACCTTCCTGCATTAACAGCGAAGC
Found at i:56874843 original size:88 final size:87
Alignment explanation
Indices: 56874338--56874982 Score: 504
Period size: 88 Copynumber: 7.6 Consensus size: 87
56874328 TCAGTGAAGA
* * * ** *
56874338 TCGAA-AACAAAGTCTTGCCTC-CATTGGTTGT-AGTGGAGCTGGTTAAAGATAGCAGATATTGC
1 TCGAAGAACAAA-CCTTGCCTCTC-TCGGTTGTGAGTGGAGCTGGTTGAAGA-AAAAGATCTTGC
* * * *
56874400 CTTCCTGCGTTAACAGCTAAGCAGA
63 CTTCCTGCATTGACAGCGAAGCAGG
* * *
56874425 TCGAA-AA-AAAGCCTTGCCT-TCATTGG--GTGCAGTGGAGCTGGTT-AA-AGAAAGATCTTAC
1 TCGAAGAACAAA-CCTTGCCTCTC-TCGGTTGTG-AGTGGAGCTGGTTGAAGAAAAAGATCTTGC
* * *
56874483 CTTCCTGCGTTAACAGCGAAGCAGA
63 CTTCCTGCATTGACAGCGAAGCAGG
* * * * * *
56874508 TCG-A-AA-AAGCCTTGCCT-TCATTGGTTG-CAGTAGAGCTGGTT-AA-AGAAAGATCGTGCCT
1 TCGAAGAACAAACCTTGCCTCTC-TCGGTTGTGAGTGGAGCTGGTTGAAGAAAAAGATCTTGCCT
* * *
56874566 TCCTGCGTTAACAGCGAAGCAGA
65 TCCTGCATTGACAGCGAAGCAGG
* * * * *
56874589 TC-AA-AA-AAGCCTTGCCT-TCATTGGTTG-CAGTGGAGCTGGTTAAAGAAGCAA-ATCTTGCC
1 TCGAAGAACAAACCTTGCCTCTC-TCGGTTGTGAGTGGAGCTGGTTGAAGAA-AAAGATCTTGCC
* *
56874648 TTCCTGCATTAACAGCGAAGCAGA
64 TTCCTGCATTGACAGCGAAGCAGG
* * * * ** *
56874672 TCGAA-AACAAGCCTTGCCT-TCATTGGTT-AGAGTGGAGCTGGTTAAAGAAGCAGATCTTGTCT
1 TCGAAGAACAAACCTTGCCTCTC-TCGGTTGTGAGTGGAGCTGGTTGAAGAAAAAGATCTTGCCT
* *
56874734 TCCTGCATTGACACCTCAAGCAGG
65 TCCTGCATTGACAGC-GAAGCAGG
*
56874758 TCGAAGACACAAACCTTGCTTCTCTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCC
1 TCGAAGA-ACAAACCTTGCCTCTCTCGGTTGTGAGTGGAGCTGGTTGAAGA-AAAAGATCTTGCC
*
56874822 TTCCTGTATTGACAGCGAAGCAGG
64 TTCCTGCATTGACAGCGAAGCAGG
56874846 TCGAAGACACAAACCTTGCCTCTCTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCC
1 TCGAAGA-ACAAACCTTGCCTCTCTCGGTTGTGAGTGGAGCTGGTTGAAGA-AAAAGATCTTGCC
* * *
56874910 TTCTTGCATTGATAGCGAAGCAAG
64 TTCCTGCATTGACAGCGAAGCAGG
* * *
56874934 TCGAAG-ACGAACCTTACCTCTCTCGGTTGT-AGTGGAGCTGGCTGAAGAA
1 TCGAAGAACAAACCTTGCCTCTCTCGGTTGTGAGTGGAGCTGGTTGAAGAA
56874983 TTTCAGATCT
Statistics
Matches: 494, Mismatches: 44, Indels: 42
0.85 0.08 0.07
Matches are distributed among these distances:
81 104 0.21
82 7 0.01
83 68 0.14
84 10 0.02
85 64 0.13
86 78 0.16
87 8 0.02
88 127 0.26
89 28 0.06
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (87 bp):
TCGAAGAACAAACCTTGCCTCTCTCGGTTGTGAGTGGAGCTGGTTGAAGAAAAAGATCTTGCCTT
CCTGCATTGACAGCGAAGCAGG
Found at i:56874854 original size:45 final size:44
Alignment explanation
Indices: 56874803--56874941 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 44
56874793 GGAGCTGGTT
56874803 GAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTC
1 GAAGACAAAAGATCTTGCCTTCCTGTATTGA-AGCGAAGCAGGTC
* * * * * *
56874848 GAAGACACAA-ACCTTGCCTCTCTCGGT-TGTGATG-G-AGCTGGTT
1 GAAGACAAAAGATCTTGCCT-TC-CTGTAT-TGAAGCGAAGCAGGTC
* * *
56874891 GAAGACAAAAGATCTTGCCTTCTTGCATTGATAGCGAAGCAAGTC
1 GAAGACAAAAGATCTTGCCTTCCTGTATTGA-AGCGAAGCAGGTC
56874936 GAAGAC
1 GAAGAC
56874942 GAACCTTACC
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
42 4 0.06
43 19 0.27
44 18 0.25
45 24 0.34
46 6 0.08
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
GAAGACAAAAGATCTTGCCTTCCTGTATTGAAGCGAAGCAGGTC
Found at i:56874897 original size:43 final size:43
Alignment explanation
Indices: 56874760--56874897 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 43
56874750 CAAGCAGGTC
*
56874760 GAAGACACAAACCTTGCTTCTCTCGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
* * * * * *
56874803 GAAGACAAAAGATCTTGCCT-TC-CTGTAT-TGACAGCGAAGCAGGTC
1 GAAGACACAA-ACCTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTT
56874848 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
56874891 GAAGACA
1 GAAGACA
56874898 AAAGATCTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
42 6 0.08
43 26 0.35
44 17 0.23
45 19 0.26
46 6 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
Found at i:56874908 original size:44 final size:44
Alignment explanation
Indices: 56874772--56874910 Score: 151
Period size: 44 Copynumber: 3.2 Consensus size: 44
56874762 AGACACAAAC
*
56874772 CTTGCTTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * *
56874816 CTTGCCT-TC-CTGTAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
56874860 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
56874904 CTTGCCT
1 CTTGCCT
56874911 TCTTGCATTG
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
42 6 0.08
43 19 0.26
44 24 0.32
45 19 0.26
46 6 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:56874958 original size:174 final size:172
Alignment explanation
Indices: 56874335--56874982 Score: 511
Period size: 174 Copynumber: 3.8 Consensus size: 172
56874325 AGATCAGTGA
* * * ** *
56874335 AGATCGAAAACAAAGTCTTGCCTCCATTGGTT-GTAGTGGAGCTGGTTAAAGATAGCAGATATTG
1 AGATCGAAAACAAA-CCTTGCCTTCATCGGTTAG-AGTGGAGCTGGTTAAAGA-AAAAGATCTTG
* * * * * * *
56874399 CCTTCCTGCGTTAACAGCT-AAGC-AGATCGAA-AA-AAAGCCTTGCCT-TCATTGGGTGCAGTG
63 CCTTCCTGCATTGACACCTCAAGCAAG-TCGAAGAACAAA-CCTTACCTCTC-TCGGTTGTAGTG
* *
56874459 GAGCTGGTT--A-AAGAAAGATCTTACCTTCCTGCGTTAACAGCGAAGC
125 GAGCTGGTTGAAGAAGAAA-ATCTTGCCTTCCTGCATTAACAGCGAAGC
* * * *
56874505 AGATCG-AAA-AAGCCTTGCCTTCATTGGTT-GCAGTAGAGCTGGTTAAAG--AAAGATCGTGCC
1 AGATCGAAAACAAACCTTGCCTTCATCGGTTAG-AGTGGAGCTGGTTAAAGAAAAAGATCTTGCC
* * * * * * * *
56874565 TTCCTGCGTTAACAGC-GAAGC-AGATC-AA-AA-AAGCCTTGCCT-TCATTGGTTGCAGTGGAG
65 TTCCTGCATTGACACCTCAAGCAAG-TCGAAGAACAAACCTTACCTCTC-TCGGTTGTAGTGGAG
* *
56874624 CTGGTTAAAGAAGCAAATCTTGCCTTCCTGCATTAACAGCGAAGC
128 CTGGTTGAAGAAGAAAATCTTGCCTTCCTGCATTAACAGCGAAGC
* * ** *
56874669 AGATCGAAAACAAGCCTTGCCTTCATTGGTTAGAGTGGAGCTGGTTAAAGAAGCAGATCTTGTCT
1 AGATCGAAAACAAACCTTGCCTTCATCGGTTAGAGTGGAGCTGGTTAAAGAAAAAGATCTTGCCT
* * *
56874734 TCCTGCATTGACACCTCAAGCAGGTCGAAGACACAAACCTTGCTTCTCTCGGTTGT-GATGGAGC
66 TCCTGCATTGACACCTCAAGCAAGTCGAAGA-ACAAACCTTACCTCTCTCGGTTGTAG-TGGAGC
* *
56874798 TGGTTGAAGACA-AAAGATCTTGCCTTCCTGTATTGACAGCGAAGC
129 TGGTTGAAGA-AGAAA-ATCTTGCCTTCCTGCATTAACAGCGAAGC
* * *
56874843 AGGTCGAAGACACAAACCTTGCCTCTC-TCGGTT-GTGATGGAGCTGGTTGAAGACAAAAGATCT
1 AGATCGAA-A-ACAAACCTTGCCT-TCATCGGTTAGAG-TGGAGCTGGTTAAAGA-AAAAGATCT
* * * * *
56874906 TGCCTTCTTGCATTGATAGC-GAAGCAAGTCGAAG-ACGAACCTTACCTCTCTCGGTTGTAGTGG
61 TGCCTTCCTGCATTGACACCTCAAGCAAGTCGAAGAACAAACCTTACCTCTCTCGGTTGTAGTGG
*
56874969 AGCTGGCTGAAGAA
126 AGCTGGTTGAAGAA
56874983 TTTCAGATCT
Statistics
Matches: 404, Mismatches: 49, Indels: 47
0.81 0.10 0.09
Matches are distributed among these distances:
162 31 0.08
163 6 0.01
164 67 0.17
165 8 0.02
166 36 0.09
167 33 0.08
168 23 0.06
169 9 0.02
170 9 0.02
171 1 0.00
172 2 0.00
173 33 0.08
174 73 0.18
175 4 0.01
176 44 0.11
177 25 0.06
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (172 bp):
AGATCGAAAACAAACCTTGCCTTCATCGGTTAGAGTGGAGCTGGTTAAAGAAAAAGATCTTGCCT
TCCTGCATTGACACCTCAAGCAAGTCGAAGAACAAACCTTACCTCTCTCGGTTGTAGTGGAGCTG
GTTGAAGAAGAAAATCTTGCCTTCCTGCATTAACAGCGAAGC
Found at i:56881993 original size:31 final size:32
Alignment explanation
Indices: 56881955--56882019 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
56881945 CTTAGATAAT
*
56881955 TTTAAAGAG-TTTTGTTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56881986 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56882018 TT
1 TT
56882020 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:56882324 original size:3 final size:3
Alignment explanation
Indices: 56882316--56882355 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
56882306 AAATCTATCA
56882316 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
56882356 TAACTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:56882558 original size:16 final size:17
Alignment explanation
Indices: 56882527--56882607 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 17
56882517 TTAAAAAATA
56882527 ATATAAATCATT--TTAT
1 ATATAAAT-ATTAATTAT
*
56882543 ATCTAAAT-TTAATTAT
1 ATATAAATATTAATTAT
*
56882559 AATATTAATATTAATT-T
1 -ATATAAATATTAATTAT
56882576 ATATAAATATTAATT-T
1 ATATAAATATTAATTAT
56882592 ATAATCAAATATTAAT
1 AT-AT-AAATATTAAT
56882608 ATAAACTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.04
16 28 0.51
17 9 0.16
18 16 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAAATATTAATTAT
Found at i:56882610 original size:16 final size:15
Alignment explanation
Indices: 56882546--56882611 Score: 53
Period size: 18 Copynumber: 4.0 Consensus size: 15
56882536 ATTTTATATC
56882546 TAAAT-TTAATTATAA
1 TAAATATTAA-TATAA
*
56882561 TATTAATATTAATTTATA
1 TA--AATATTAATATA-A
56882579 TAAATATTAATTTATAA
1 TAAATATTAA--TATAA
56882596 TCAAATATTAATATAA
1 T-AAATATTAATATAA
56882612 ACTTTTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
16 13 0.31
17 8 0.19
18 19 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATTAATATAA
Found at i:56882867 original size:23 final size:23
Alignment explanation
Indices: 56882837--56882887 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
56882827 TACCCTAGCT
*
56882837 AATTTTATTGGTCGATATGGTCC
1 AATTTTATTGGTCGAAATGGTCC
*
56882860 AATTTTATTGGTCGAAATTGTCC
1 AATTTTATTGGTCGAAATGGTCC
56882883 AATTT
1 AATTT
56882888 AGACAGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (23 bp):
AATTTTATTGGTCGAAATGGTCC
Found at i:56906133 original size:26 final size:26
Alignment explanation
Indices: 56906097--56906149 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
56906087 GAACATTATT
56906097 GCACCATTGGCACATTTTAGGCATCA
1 GCACCATTGGCACATTTTAGGCATCA
56906123 GCACCATTGGCACATTTTAGGCATCA
1 GCACCATTGGCACATTTTAGGCATCA
56906149 G
1 G
56906150 TTAAGGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (26 bp):
GCACCATTGGCACATTTTAGGCATCA
Found at i:56908007 original size:28 final size:29
Alignment explanation
Indices: 56907941--56908040 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
56907931 ACCTTTTAAA
* *
56907941 TAAT-TAATATAA-ATTATTT-ATAAAAT
1 TAATATAATAAAATATTATTTAATAAATT
*
56907967 TGATGATATATAAAATATTA-TTAA-AAATT
1 TAAT-ATA-ATAAAATATTATTTAATAAATT
* *
56907996 TAAATATAAT-AAATAATATTTAATTAATT
1 T-AATATAATAAAATATTATTTAATAAATT
*
56908025 TAATATAATAATATAT
1 TAATATAATAAAATAT
56908041 AAAATATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
26 3 0.05
27 7 0.12
28 16 0.28
29 24 0.42
30 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TAATATAATAAAATATTATTTAATAAATT
Found at i:56910614 original size:28 final size:28
Alignment explanation
Indices: 56910561--56910616 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
56910551 AAAAAAGGGT
* * *
56910561 TAAATTCTACTGCTTTTTTTTTTTTAAC
1 TAAATTCTACTGCTTGTCTTTGTTTAAC
56910589 TAAATTCTACTG-TTAGTCTTTGTTTAAC
1 TAAATTCTACTGCTT-GTCTTTGTTTAAC
56910617 CTAATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.55
Consensus pattern (28 bp):
TAAATTCTACTGCTTGTCTTTGTTTAAC
Found at i:56912071 original size:31 final size:31
Alignment explanation
Indices: 56912036--56912103 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
56912026 AAAATAGCCT
56912036 AATGACTTAAATAAAAACTTTCGAATAGTTC
1 AATGACTTAAATAAAAACTTTCGAATAGTTC
* * * *
56912067 AATGACTTGAATTAAAATTTTTGAATAGTTC
1 AATGACTTAAATAAAAACTTTCGAATAGTTC
56912098 AATGAC
1 AATGAC
56912104 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAATAGTTC
Found at i:56926119 original size:149 final size:149
Alignment explanation
Indices: 56925849--56926154 Score: 594
Period size: 149 Copynumber: 2.1 Consensus size: 149
56925839 TTATATATTT
*
56925849 GACATTCATTCTTTAACCTTAAGAGCTGTAAATCAGGATATTTTCTTTTTATGGAAGCCATTTTC
1 GACATTCATTCTTTAACCTTAAGAGCTGTAAATCAGGATATTTTCTTTTTATAGAAGCCATTTTC
56925914 GGATCATTCTTTTCAATGAATAAGAACTAGTTCATTAGTTGATTCTGCATAAACCAGATTTATGG
66 GGATCATTCTTTTCAATGAATAAGAACTAGTTCATTAGTTGATTCTGCATAAACCAGATTTATGG
56925979 GAAATTTGAGGGTTTCAAA
131 GAAATTTGAGGGTTTCAAA
56925998 GACATTCATTCTTTAACCTTAAGAGCTGTAAATCAGGATATTTTCTTTTTATAGAAGCCATTTTC
1 GACATTCATTCTTTAACCTTAAGAGCTGTAAATCAGGATATTTTCTTTTTATAGAAGCCATTTTC
56926063 GGATCATTCTTTTCAATGAATAAGAACTAGTTCATTAGTTGATTCTGCATAAACCAGATTTATGG
66 GGATCATTCTTTTCAATGAATAAGAACTAGTTCATTAGTTGATTCTGCATAAACCAGATTTATGG
56926128 GAAATTTGAGGGTTTCAAA
131 GAAATTTGAGGGTTTCAAA
*
56926147 GAGATTCA
1 GACATTCA
56926155 AGCATTTATG
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (149 bp):
GACATTCATTCTTTAACCTTAAGAGCTGTAAATCAGGATATTTTCTTTTTATAGAAGCCATTTTC
GGATCATTCTTTTCAATGAATAAGAACTAGTTCATTAGTTGATTCTGCATAAACCAGATTTATGG
GAAATTTGAGGGTTTCAAA
Found at i:56926641 original size:3 final size:3
Alignment explanation
Indices: 56926633--56926660 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56926623 TTCATCTTCA
56926633 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
56926661 CAAGAGTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56934683 original size:31 final size:31
Alignment explanation
Indices: 56934648--56934708 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
56934638 TATTTCTTTA
* *
56934648 AATGTATACAACTGAATCAAAATTAAAGTTT
1 AATGTATACAACTGAACCAAAAATAAAGTTT
* **
56934679 AATGTGTACATTTGAACCAAAAATAAAGTT
1 AATGTATACAACTGAACCAAAAATAAAGTT
56934709 CCGAGTATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (31 bp):
AATGTATACAACTGAACCAAAAATAAAGTTT
Found at i:56937371 original size:18 final size:19
Alignment explanation
Indices: 56937335--56937372 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
56937325 TTTTAATTTC
*
56937335 TATTCCTGAATACTTTGTT
1 TATTCATGAATACTTTGTT
56937354 TATTCATGAATA-TTTGTT
1 TATTCATGAATACTTTGTT
56937372 T
1 T
56937373 CCTTGAGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (19 bp):
TATTCATGAATACTTTGTT
Found at i:56938701 original size:11 final size:11
Alignment explanation
Indices: 56938667--56938699 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
56938657 CGGCTTGCTC
56938667 ATATTAATTTTT
1 ATATT-ATTTTT
56938679 ATATTATTTTT
1 ATATTATTTTT
56938690 ATA-TATTTTT
1 ATATTATTTTT
56938700 TAACAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 9 0.43
12 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:56938817 original size:30 final size:30
Alignment explanation
Indices: 56938772--56938830 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
56938762 TTTAACAAGT
*
56938772 AAATGCCTCTAAAATAACAACAAAATTAAC
1 AAATACCTCTAAAATAACAACAAAATTAAC
* *
56938802 AAATACCTTTAAAATAATAACAAAATTAA
1 AAATACCTCTAAAATAACAACAAAATTAA
56938831 TAATAAAATA
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:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (30 bp):
AAATACCTCTAAAATAACAACAAAATTAAC
Found at i:56946783 original size:17 final size:17
Alignment explanation
Indices: 56946761--56946793 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56946751 TCGTTGGATT
56946761 TTAATATAATA-TAAATA
1 TTAATA-AATACTAAATA
56946778 TTAATAAATACTAAAT
1 TTAATAAATACTAAAT
56946794 GACAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATAAATACTAAATA
Found at i:56951123 original size:2 final size:2
Alignment explanation
Indices: 56951116--56951141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56951106 TATACTAAGA
56951116 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
56951142 TAAAAAATTA
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:56952766 original size:16 final size:16
Alignment explanation
Indices: 56952729--56952768 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
56952719 TTAATAAAAT
* *
56952729 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
56952745 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
56952761 TAAAATTA
1 TAAAATTA
56952769 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:56952768 original size:22 final size:22
Alignment explanation
Indices: 56952701--56952753 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
56952691 TAATTAAAAT
* * *
56952701 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
56952723 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
56952745 TAAAATTAA
1 TAAAATTAA
56952754 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:56952867 original size:77 final size:76
Alignment explanation
Indices: 56952774--56952937 Score: 294
Period size: 77 Copynumber: 2.2 Consensus size: 76
56952764 AATTATCAAA
56952774 TTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTAGTAAATTTATCA
1 TTATTAATTGTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTAGTAAATTTATCA
56952838 AATTATTAATT
66 AATTATTAATT
*
56952849 TTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTCATTAGTAAATTTATC
1 TTATTAATTGT-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTAGTAAATTTATC
56952914 AAATTATTAATT
65 AAATTATTAATT
*
56952926 GTATTAATTGTT
1 TTATTAATTGTT
56952938 GTAACAAAAT
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
75 10 0.12
76 1 0.01
77 74 0.87
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.50
Consensus pattern (76 bp):
TTATTAATTGTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTAGTAAATTTATCA
AATTATTAATT
Found at i:56952883 original size:9 final size:9
Alignment explanation
Indices: 56952841--56952877 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56952831 TTTATCAAAT
*
56952841 TATTAATTT
1 TATTAATTG
56952850 TATTAATTG
1 TATTAATTG
56952859 TATTAATTG
1 TATTAATTG
56952868 TATTAATTG
1 TATTAATTG
56952877 T
1 T
56952878 TGTAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (9 bp):
TATTAATTG
Found at i:56953062 original size:24 final size:22
Alignment explanation
Indices: 56953033--56953076 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 22
56953023 AAATAAACTT
56953033 AAAATAAAAAAATATTATATTTTA
1 AAAAT-AAAAAATA-TATATTTTA
56953057 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
56953077 AATTTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:56956274 original size:57 final size:59
Alignment explanation
Indices: 56956160--56956302 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 59
56956150 AATTGACAGT
*
56956160 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTAATATAGCCCTCCCGAAGAATATGCGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTAATATAACCCTCCCGAAGAATATGCG-G
* * *
56956223 AAAAAGATCTAGCCCGAACGGGTGAT-C-T-TGATATAACCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAACCCTCCCGAAGAATATGCGG
* *
56956279 AAAATGGATTTAGCCCGGACGGGT
1 AAAA-AGATCTAGCCCGGACGGGT
56956303 AATTCGAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 5 0.07
57 40 0.56
59 1 0.01
61 1 0.01
62 20 0.28
63 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.21
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAACCCTCCCGAAGAATATGCGG
Found at i:56957792 original size:26 final size:23
Alignment explanation
Indices: 56957762--56957842 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 23
56957752 GGACTCACCA
56957762 CAGCTCGTATGAGCTTACTGATATAT
1 CAGCTCGTATGAGCTTACTG-T-T-T
* *
56957788 CAGCTCTTATGAGCTTACCGTTT
1 CAGCTCGTATGAGCTTACTGTTT
56957811 CAGCTCG-ATAGAGCTTACTGTTCTT
1 CAGCTCGTAT-GAGCTTACTG-T-TT
56957836 CAGCTCG
1 CAGCTCG
56957843 AAATGAGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 2 0.04
23 16 0.33
24 2 0.04
25 10 0.21
26 18 0.38
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (23 bp):
CAGCTCGTATGAGCTTACTGTTT
Found at i:56957824 original size:23 final size:25
Alignment explanation
Indices: 56957798--56957843 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56957788 CAGCTCTTAT
56957798 GAGCTTACCG-T-TTCAGCTCGATA
1 GAGCTTACCGTTCTTCAGCTCGATA
*
56957821 GAGCTTACTGTTCTTCAGCTCGA
1 GAGCTTACCGTTCTTCAGCTCGA
56957844 AATGAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTACCGTTCTTCAGCTCGATA
Found at i:56957849 original size:49 final size:49
Alignment explanation
Indices: 56957762--56957855 Score: 111
Period size: 49 Copynumber: 1.9 Consensus size: 49
56957752 GGACTCACCA
**
56957762 CAGCTCGTATGAGCTTACTGATATATCAGCTCTTATGAGCTTACCGTTT
1 CAGCTCGTATGAGCTTACTGATATATCAGCTCAAATGAGCTTACCGTTT
* * *
56957811 CAGCTCG-ATAGAGCTTACTGTTCT-TCAGCTCGAAATGAGTTTACC
1 CAGCTCGTAT-GAGCTTACTGATATATCAGCTC-AAATGAGCTTACC
56957856 AATCATGGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 9 0.24
49 29 0.76
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (49 bp):
CAGCTCGTATGAGCTTACTGATATATCAGCTCAAATGAGCTTACCGTTT
Found at i:56962830 original size:2 final size:2
Alignment explanation
Indices: 56962823--56962849 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56962813 TGATCGGCCA
56962823 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 A
56962850 CTTTTATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56976575 original size:151 final size:150
Alignment explanation
Indices: 56976276--56976692 Score: 548
Period size: 151 Copynumber: 2.8 Consensus size: 150
56976266 TCAATCTCAA
* *
56976276 ATTTGAGT-AAAATATAGGGACCAAAACTGAAATTCAAACATAAAAAAATTAGAGGGATTA-AGA
1 ATTTGAGTGAAAA-ATAGGGATCAAAACTGAAATTTAAACAT--AAAAATTAGAGGGATTAGA-A
* * *
56976339 TTGAAATTTAGCCATTATCTTGTCA-TTT-AAAAG--AAAG-AGAAAACGTTAGACATGTGTCAT
62 TTGAAATTTAGCCATTATCTTATCATTTTAAAAAGAAAAAGAAGAAAACATTGGACATGTGTCAT
*
56976399 GTAGGGAAGGCCTTACGGCTATAG
127 GTAAGGAAGGCCTTACGGCTATAG
* * *
56976423 ATTTGAGTGAAAAATAGGGATCAAAATTGAAATTTGATCATAAAAATTAGAGGGATTAGAATTGA
1 ATTTGAGTGAAAAATAGGGATCAAAACTGAAATTTAAACATAAAAATTAGAGGGATTAGAATTGA
*
56976488 AATTTAGCCATTGTCTTATCATTTTAAAAAGAAAAGAGAAGAAAACATTGGACATGTGTCATGTA
66 AATTTAGCCATTATCTTATCATTTTAAAAAGAAAA-AGAAGAAAACATTGGACATGTGTCATGTA
*
56976553 AGGAAGGCCTTAGGGCTATAG
130 AGGAAGGCCTTACGGCTATAG
** *
56976574 ATTTGAGTGAAATGTAGGGATCAAAACTGAAATTTAACCATAAAAATTAGAGGGATTAGAATTGA
1 ATTTGAGTGAAAAATAGGGATCAAAACTGAAATTTAAACATAAAAATTAGAGGGATTAGAATTGA
* * *
56976639 AATTTAGCCATTATTCTTCTCATGTGAAAAA-AAAAA-AA-AAACACATTGGACATG
66 AATTTAGCCATTA-TCTTATCATTTTAAAAAGAAAAAGAAGAAA-ACATTGGACATG
56976693 GACATATGGT
Statistics
Matches: 240, Mismatches: 20, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
145 41 0.17
146 4 0.02
147 36 0.15
148 7 0.03
149 16 0.07
150 3 0.01
151 119 0.50
152 14 0.06
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.28
Consensus pattern (150 bp):
ATTTGAGTGAAAAATAGGGATCAAAACTGAAATTTAAACATAAAAATTAGAGGGATTAGAATTGA
AATTTAGCCATTATCTTATCATTTTAAAAAGAAAAAGAAGAAAACATTGGACATGTGTCATGTAA
GGAAGGCCTTACGGCTATAG
Found at i:56979511 original size:34 final size:34
Alignment explanation
Indices: 56979473--56979539 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
56979463 ACACATCAGT
*
56979473 TGCTATAATCATCAAATGGCTATGGATGTGAGGC
1 TGCTATAATCATCAAATGGCTATGGATCTGAGGC
56979507 TGCTATAATCATCAAATGGCTATGGATCTGAGG
1 TGCTATAATCATCAAATGGCTATGGATCTGAGG
56979540 GTTAGTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (34 bp):
TGCTATAATCATCAAATGGCTATGGATCTGAGGC
Found at i:56983949 original size:21 final size:21
Alignment explanation
Indices: 56983920--56983959 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56983910 AATATATATG
*
56983920 TCTATAAAA-ATATATAAATAA
1 TCTAAAAAACATATA-AAATAA
56983941 TCTAAAAAACATATAAAAT
1 TCTAAAAAACATATAAAAT
56983960 CTAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TCTAAAAAACATATAAAATAA
Found at i:56988418 original size:51 final size:51
Alignment explanation
Indices: 56988301--56988480 Score: 152
Period size: 51 Copynumber: 3.5 Consensus size: 51
56988291 GATGGTCGTG
* * * * * * * *
56988301 TGTGTAGTATTATGTGCAAGCTACTACGTGTACCGGA-A-TGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAAT-GATCACA
* * * *
56988351 TATGTAGTACTATGTGCAGGCTACTATGCGTGCC-GAATAGT-TTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAG-ATAGTAAT-GATCACA
* * * * *
56988402 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGATCACA
56988453 TGTGTAGTACTATGTGCAGGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
56988481 TGAACCGAAC
Statistics
Matches: 104, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
49 1 0.01
50 29 0.28
51 71 0.68
52 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGATCACA
Found at i:56988482 original size:26 final size:26
Alignment explanation
Indices: 56988402--56988482 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
56988392 TTCGATCACG
56988402 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
56988428 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
56988453 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
56988479 TGTG
1 TGTG
56988483 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:56988489 original size:102 final size:101
Alignment explanation
Indices: 56988300--56988489 Score: 265
Period size: 102 Copynumber: 1.9 Consensus size: 101
56988290 TGATGGTCGT
* * *
56988300 GTGTGTAGTATTATGTGCAAGCTACTACGTGTACCGGAATGATAGGTCGCATATGTAGTACTATG
1 GTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCACATATGTAGTACTATG
**
56988365 TGCAGGCTACTATGCGTGCCGAATAGTTTCGATCAC
66 TGCAGGCTACTATGCGAACCGAATAGTTTCGATCAC
* * * *
56988401 GTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGGTAATGGTCACATGTGTAGTACTA
1 GTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGAT-A-GGTCACATATGTAGTACTA
*
56988465 TGTGCAGGCTACTATGTGAACCGAA
64 TGTGCAGGCTACTATGCGAACCGAA
56988490 CATCATTGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
100 4 0.05
101 34 0.44
102 39 0.51
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCACATATGTAGTACTATG
TGCAGGCTACTATGCGAACCGAATAGTTTCGATCAC
Found at i:56991692 original size:3 final size:3
Alignment explanation
Indices: 56991686--56991747 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
56991676 ATAATAATAA
* * * *
56991686 TAT TAT TAT CAT TAT TAT TAT TAT TAC TAC TAC TAT TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
*
56991732 TAT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT T
56991748 CGTTACTACT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:56991894 original size:8 final size:8
Alignment explanation
Indices: 56991877--56991920 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
56991867 TACAAGCGTG
*
56991877 TATATATA
1 TATATTTA
56991885 TATATTTA
1 TATATTTA
56991893 TATATTTA
1 TATATTTA
56991901 TATATTCTA
1 TATATT-TA
*
56991910 TA-ATTTT
1 TATATTTA
56991917 TATA
1 TATA
56991921 CACATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 3 0.09
8 25 0.78
9 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:56998877 original size:11 final size:13
Alignment explanation
Indices: 56998851--56998875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56998841 AACTAGTTGT
56998851 TTATGTAAATATA
1 TTATGTAAATATA
56998864 TTATGTAAATAT
1 TTATGTAAATAT
56998876 TAAACATGAG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TTATGTAAATATA
Found at i:56999921 original size:33 final size:33
Alignment explanation
Indices: 56999884--56999948 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
56999874 CTAACTTAAA
56999884 CAAAAAAAAATTCAAACC-CTAATATAAAAACAG
1 CAAAAAAAAATTCAAACCTC-AATATAAAAACAG
*
56999917 CAAAATAAAATTCAAACCTCAATATAAAAACA
1 CAAAAAAAAATTCAAACCTCAATATAAAAACA
56999949 ATTGCAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.63, C:0.18, G:0.02, T:0.17
Consensus pattern (33 bp):
CAAAAAAAAATTCAAACCTCAATATAAAAACAG
Found at i:57007120 original size:15 final size:15
Alignment explanation
Indices: 57007100--57007142 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
57007090 ATGTTGAGTA
57007100 ATATATTATATTATT
1 ATATATTATATTATT
57007115 ATATA-TA-A-TA--
1 ATATATTATATTATT
57007125 ATATATTATATTATT
1 ATATATTATATTATT
57007140 ATA
1 ATA
57007143 ATAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 5 0.22
11 2 0.09
12 3 0.13
13 3 0.13
14 2 0.09
15 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTATATTATT
Found at i:57007127 original size:25 final size:24
Alignment explanation
Indices: 57007098--57007146 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
57007088 AAATGTTGAG
57007098 TAATATATTATATTATTATATATAA
1 TAATATATTATATTATTATA-ATAA
57007123 TAATATATTATATTATTATAATAA
1 TAATATATTATATTATTATAATAA
57007147 AACAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATATATTATATTATTATAATAA
Done.