Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold126
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: 2080828
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 191490 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:971859 original size:20 final size:21
Alignment explanation
Indices: 971821--971901 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 21
971811 TATCGATACA
* **
971821 ATGTATCGTTACAAAGAATTC
1 ATGTATCGATACATTGAATTC
971842 -TGTATCGATACATTGAATTTTCC
1 ATGTATCGATACATTGAA--TT-C
*
971865 AGATGTATCGATACATTGAA-AC
1 --ATGTATCGATACATTGAATTC
971887 ATGTATCGATACATT
1 ATGTATCGATACATT
971902 TTGGAAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 29 0.58
22 3 0.06
23 1 0.02
26 17 0.34
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACATTGAATTC
Found at i:978022 original size:13 final size:13
Alignment explanation
Indices: 978004--978028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
977994 CATTTTATGG
978004 TGTATCGATACAA
1 TGTATCGATACAA
978017 TGTATCGATACA
1 TGTATCGATACA
978029 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:979916 original size:29 final size:29
Alignment explanation
Indices: 979876--980918 Score: 1200
Period size: 28 Copynumber: 36.5 Consensus size: 29
979866 TGTTCATCCC
*
979876 TTTCAAAGCCCACGAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
979905 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
979933 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
979961 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
979990 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980019 TTTCAAAGCCCACAAATCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980047 TTTCAGAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980076 TTT-AAGGCCCACAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980104 TTTCAAAGCCCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
980133 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980161 TTTCAAAGCCCATAAGTCCGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980189 TTTC-AAGCCCACGAGTTAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980216 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980244 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
980275 TTTCAAAGCCCACACAAGTC-GATGGCAACT-T
1 TTTCAAAG-CC-CACAAGTCAG-TGGC-ACTCT
* * *
980306 ATTTCAAAGCCCATATGTCGGTGGCACTCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980336 TTTCAAAGCCCGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980364 TTTC-AAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980391 TTTC-AAGCCCACGAGTTAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980418 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
980446 TTTCAAAGCCCTCAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980474 TTTCAAAGCCCAAGCAAGTCAGTGGCACCCT
1 TTTCAAAGCCC-A-CAAGTCAGTGGCACTCT
*
980505 TTT-AAAGCCCATGCAAGTCAGTGGTAC-CT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* *
980534 TTTC-AAGCCCACGAGTCAGTGGCATTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980561 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980589 TTTCAAAGCCCATGCAAGTCAGTGGCACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
980620 TTT-AAAGCCCATGCAAGTTAGTGGCACTCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
980650 TTTCAAAGCCCACGCAAGTCAGTGGCACTCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* ** * *
980681 TTTCAAACCCCATGAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
980709 TTTCAAAGCCCATGAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980737 TTTC-AAGCCTACAAGTCAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
980764 TTT-TAAGCCCATAAGTTAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
980791 TTTCAAAGCCCACAAGTCAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980819 TTTC-AAGCCCACAAGTGAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980846 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
980875 TTTCAAAGCCCACAAG-CTAGTAGTAACTCT
1 TTTCAAAGCCCACAAGTC-AGT-GGCACTCT
980905 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
980919 CGTGTCGGTG
Statistics
Matches: 898, Mismatches: 78, Indels: 75
0.85 0.07 0.07
Matches are distributed among these distances:
27 164 0.18
28 324 0.36
29 205 0.23
30 121 0.13
31 73 0.08
32 11 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:980014 original size:114 final size:115
Alignment explanation
Indices: 979876--980918 Score: 1256
Period size: 114 Copynumber: 9.1 Consensus size: 115
979866 TGTTCATCCC
* * *
979876 TTTCAAAGCCCACGAGTCAGTGGCACTCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
979941 CCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCT
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
979990 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAGAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
980055 CCCACAAGTCAGTGGCACCCTTTT-AAGGCCCACAAGTCAGTGGCACTTT
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
980104 TTTCAAAGCCCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
980169 CCCATAAGTCCGTGGCAC-CTTTTC-AAGCCCACGAGTTAGTGGCACTC-
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
980216 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCA
* * *
980280 AAGCCCACACAAGTC-GATGGCAACT-TATTTCAAAGCCCATATGTCGGTGGCACTCT
63 AAG-CC-CACAAGTCAG-TGGC-ACTCT-TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
980336 TTTCAAAGCCCGCAAGTCAGTGGCAC-CCTTTC-AAGCCCACGAGTCAGTGGCACCCTTTC-AAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
980398 CCCACGAGTTAGTGGCAC-CTTTTCAAAGCCCACGAGTCAGTGGCACTC-
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
980446 TTTCAAAGCCCTCAAGTTAGTGGCA-TCCTTTCAAAGCCCAAGCAAGTCAGTGGCACCCTTTTAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCC-A-CAAGTCAGTGGCACCCTTTCAA
* * *
980510 AGCCCATGCAAGTCAGTGGTAC-CTTTTC-AAGCCCACGAGTCAGTGGCATTC-
64 AGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
*
980561 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCATGCAAGTCAGTGGCACCCTTTTAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAA
* *
980625 AGCCCATGCAAGTTAGTGGCACTCTTTTCAAAGCCCACGCAAGTCAGTGGCACTCC
64 AGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* ** * ** *
980681 TTTCAAACCCCATGAGTTAGTGGCAC-CCTTTCAAAGCCCATGAGTCAGTGGCACCTTTTC-AAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
980744 CCTACAAGTCAGTGGCACT-TTTT-TAAGCCCATAAGTTAGTGGCACT-T
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * **
980791 TTTCAAAGCCCACAAGTCAGTGGCACT-TTTTC-AAGCCCACAAGTGAGTGGCACTTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* **
980854 CCCACAAGTCAGTGACACTCTTTTCAAAGCCCACAAG-CTAGTAGTAACTCT
66 CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AGT-GGCACTCT
980905 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
980919 CGTGTCGGTG
Statistics
Matches: 813, Mismatches: 79, Indels: 74
0.84 0.08 0.08
Matches are distributed among these distances:
109 23 0.03
110 75 0.09
111 57 0.07
112 43 0.05
113 79 0.10
114 218 0.27
115 125 0.15
116 40 0.05
117 31 0.04
118 22 0.03
119 35 0.04
120 65 0.08
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (115 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:981540 original size:20 final size:20
Alignment explanation
Indices: 981512--981586 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
981502 TTTTACCCAG
981512 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
981532 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
981552 TTGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
981572 ATGTATCGATACATT
1 ATGTATCGATACATT
981587 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:981572 original size:40 final size:39
Alignment explanation
Indices: 981513--981589 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
981503 TTTACCCAGA
*
981513 TGTATCGATACATTTTTCAATATATCGATACATGTATGAT
1 TGTATCGATACATTCTTCAATATATCGATACAT-TATGAT
* *
981553 TGTATCGATATATTCTTCAATGTATCGATACATTATG
1 TGTATCGATACATTCTTCAATATATCGATACATTATG
981590 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (39 bp):
TGTATCGATACATTCTTCAATATATCGATACATTATGAT
Found at i:982533 original size:20 final size:20
Alignment explanation
Indices: 982497--982534 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
982487 AGCCTTTGAC
**
982497 CATGCATTTTTTTTATGTTT
1 CATGCATTTTTAATATGTTT
982517 CATGCATTTTTAATATGT
1 CATGCATTTTTAATATGT
982535 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
CATGCATTTTTAATATGTTT
Found at i:984337 original size:12 final size:13
Alignment explanation
Indices: 984320--984348 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
984310 GTAAAAATCA
984320 AAAATTAAAATT-
1 AAAATTAAAATTC
984332 AAAATTAAAATTC
1 AAAATTAAAATTC
984345 AAAA
1 AAAA
984349 AAATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:984544 original size:41 final size:41
Alignment explanation
Indices: 984499--984580 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
984489 GGTGGGAACT
*
984499 TACAACAATTGGCAGCATGGGAAAGGAAATAAAAAAATGCA
1 TACAACAATTGGCAACATGGGAAAGGAAATAAAAAAATGCA
984540 TACAACAATTGGCAACATGGGAAAGGAAATAAAAAAATGCA
1 TACAACAATTGGCAACATGGGAAAGGAAATAAAAAAATGCA
984581 ATGGGAGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (41 bp):
TACAACAATTGGCAACATGGGAAAGGAAATAAAAAAATGCA
Found at i:985861 original size:27 final size:28
Alignment explanation
Indices: 985827--985900 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 28
985817 GTTTTTCACA
985827 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
985854 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
985882 CGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
985901 GATTTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:985970 original size:51 final size:50
Alignment explanation
Indices: 985885--986003 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 50
985875 TTATTTCCGA
985885 GGGGATACTCCAA-CCCGATTTTATTTCAAAAATATCAATTTCACATAAT
1 GGGGATACTCCAACCCCGATTTTATTTCAAAAATATCAATTTCACATAAT
* * * *
985934 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAAT
1 -GGGGATACTCCAACCCCGATTTTATTTCAAAAATATCAATTTCACATAAT
985985 GAGGGATACTCCAACCCCG
1 G-GGGATACTCCAACCCCG
986004 TTGTTTCCGC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 14 0.22
51 49 0.78
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTTCAAAAATATCAATTTCACATAAT
Found at i:986033 original size:79 final size:79
Alignment explanation
Indices: 985934--986161 Score: 361
Period size: 79 Copynumber: 2.9 Consensus size: 79
985924 TTCACATAAT
985934 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAAT-GAGGGATACTCCA
1 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCG-GGGATACTCCA
*
985998 ACCCCGTTGTTTCCG
65 ACCCCGTTATTTCCG
* *
986013 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACT-TTAATTTTTCATAATCGGGGACACTCCA
1 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAA-TATTAATTTCTCATAATCGGGGATACTCCA
*
986077 ACCCCGTTATTTCTG
65 ACCCCGTTATTTCCG
* * *
986092 AGGGGATACTCCAACCTCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCTAA
1 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
986157 CCCCG
66 CCCCG
986162 ATTTTATTTC
Statistics
Matches: 137, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
78 1 0.01
79 134 0.98
80 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
CCCCGTTATTTCCG
Found at i:986147 original size:130 final size:130
Alignment explanation
Indices: 986013--986290 Score: 450
Period size: 130 Copynumber: 2.1 Consensus size: 130
986003 GTTGTTTCCG
* * *
986013 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTTAATTTTTCATAATCGGGGACACTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGACACTCCAA
* *
986078 CCCCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAA-TATTAATTTCTCATAA
66 CCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACT-TTAATTTCTCATAA
986142 T
130 T
* *
986143 CGGGGATACTCTAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGACACTCCAA
* * *
986208 CCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTTAATTTTTCATAAT
66 CCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTTAATTTCTCATAAT
986273 CGGGGATACTCCAACCCC
1 CGGGGATACTCCAACCCC
986291 ATTACCTCCG
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
130 135 0.99
131 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (130 bp):
CGGGGATACTCCAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGACACTCCAA
CCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTTAATTTCTCATAAT
Found at i:986167 original size:51 final size:51
Alignment explanation
Indices: 986093--986212 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 51
986083 TTATTTCTGA
* * *
986093 GGGGATACTCCAACCTCGGTTTTATTTCTAAAA-TATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACT-TCAATTTCTCATAATC
*
986144 GGGGATACTCTAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATC
986195 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
986213 TTGTTTCCGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 62 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATC
Found at i:986213 original size:209 final size:208
Alignment explanation
Indices: 985854--986370 Score: 813
Period size: 209 Copynumber: 2.5 Consensus size: 208
985844 CCCGTTAATC
985854 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCAAAAATA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCAAAAATA
* * * *
985919 TCAATTTCACATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAA
66 TTAATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTCTCATAA
985984 TGAGGGATACTCCAACCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACT
131 TGAGGGATACTCCAACCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACT
986049 TTAATTTTTCATA
196 TTAATTTTTCATA
* * * *
986062 ATCGGGGACACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC-CGATTTTATTTCAAAAAT
*
986127 ATTAATTTCTCATAATCGGGGATACTCTAACCCCGATTTTATTTCTAAAACT-TCAATTTCTCAT
65 ATTAATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAA-TATCAATTTCTCAT
986191 AATCG-GGGATACTCCAACCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAA
129 AAT-GAGGGATACTCCAACCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAA
986255 ACTTTAATTTTTCATA
193 ACTTTAATTTTTCATA
* ** * * * *
986271 ATCGGGGATACTCCAACCCCATTACCTCCGAAGGGATACTCCAACCCCGACTTTATTTCCAGAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGATTTTATTTCAAAAAT
* * *
986336 ATTGATTTCTCATAATTGGGGATATTCCAACCCCG
65 ATTAATTTCTCATAATCGGGGATACTCCAACCCCG
986371 TTATTTCCGA
Statistics
Matches: 282, Mismatches: 23, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
208 44 0.16
209 234 0.83
210 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (208 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCAAAAATA
TTAATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTCTCATAA
TGAGGGATACTCCAACCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACT
TTAATTTTTCATA
Found at i:986226 original size:79 final size:79
Alignment explanation
Indices: 986144--986507 Score: 401
Period size: 79 Copynumber: 4.6 Consensus size: 79
986134 TCTCATAATC
* *
986144 GGGGATACTCTAACCCCGATTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
* *
986209 CCCGTTGTTTCCGC
66 CCCGTTATTTCCGA
* * * *
986223 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTTAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
* **
986288 CCCATTACCTCCGA
66 CCCGTTATTTCCGA
* * * * *
986302 AGGGATACTCCAACCCCGACTTTATTTCCAGAATA-TT-GATTTCTCATAATTGGGGATATTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCCA-AA-ACTTCAATTTCTCATAATCGGGGATACTCCA
986365 ACCCCGTTATTTCCGA
64 ACCCCGTTATTTCCGA
* * * * * * * * *
986381 GGGGATACTCTAATCCCGATTTTATTTCCCAATCATCGATTTTTCACAACCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
* *
986446 CCCGTTATTTTCAA
66 CCCGTTATTTCCGA
* * *
986460 GGGGATACTCCAACCCCG-TTATTATCTCCAAAATATTAAATTTCTCAT
1 GGGGATACTCCAACCCCGATT-TTATTTCCAAAA-CTTCAATTTCTCAT
986508 CAGGACATAT
Statistics
Matches: 234, Mismatches: 45, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
78 5 0.02
79 216 0.92
80 12 0.05
81 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
CCCGTTATTTCCGA
Found at i:996886 original size:20 final size:20
Alignment explanation
Indices: 996860--996912 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
996850 ATTTGCCTGC
996860 ATGTATCGATACAAAGA-TCA
1 ATGTATCGATACAAAGAGT-A
* *
996880 TTGTATCGATACAATGAGTA
1 ATGTATCGATACAAAGAGTA
996900 ATGTATCGATACA
1 ATGTATCGATACA
996913 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAAAGAGTA
Found at i:996971 original size:19 final size:19
Alignment explanation
Indices: 996947--997011 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
996937 TATCGAGACA
996947 ATGTATCGATACAACACTT
1 ATGTATCGATACAACACTT
996966 ATGTATCGAT---ACA--T
1 ATGTATCGATACAACACTT
996980 -TGTATCGATACAACACTT
1 ATGTATCGATACAACACTT
996998 ATGTATCGATACAA
1 ATGTATCGATACAA
997012 ATCGTTGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 1 0.03
19 23 0.57
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAACACTT
Found at i:996973 original size:32 final size:32
Alignment explanation
Indices: 996933--997011 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
996923 AGTAGCTTAA
*
996933 TATGTATCGAGACAATGTATCGATACAACACT
1 TATGTATCGATACAATGTATCGATACAACACT
*
996965 TATGTATCGATACATTGTATCGATACAACACT
1 TATGTATCGATACAATGTATCGATACAACACT
996997 TATGTATCGATACAA
1 TATGTATCGATACAA
997012 ATCGTTGACA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
TATGTATCGATACAATGTATCGATACAACACT
Found at i:996985 original size:13 final size:13
Alignment explanation
Indices: 996967--996991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
996957 ACAACACTTA
996967 TGTATCGATACAT
1 TGTATCGATACAT
996980 TGTATCGATACA
1 TGTATCGATACA
996992 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:998075 original size:28 final size:28
Alignment explanation
Indices: 998017--998111 Score: 113
Period size: 28 Copynumber: 3.4 Consensus size: 28
998007 CACCAACATG
*
998017 TGTGGGCTTTTGAAAGGGTTG-CA-TCAACT
1 TGTGGGCTTTT-AAA-GGTTGCCACT-GACT
* *
998046 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
998074 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
998102 TGTGGACTTT
1 TGTGGGCTTT
998112 AAAAAGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 5 0.09
28 42 0.72
29 11 0.19
ACGTcount: A:0.17, C:0.16, G:0.29, T:0.38
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:998130 original size:34 final size:33
Alignment explanation
Indices: 998085--998245 Score: 156
Period size: 34 Copynumber: 5.0 Consensus size: 33
998075 GTGGGCTTTT
* *
998085 AAAGGTTGCCACTGACTTGTGGACTTTAAAAAGAA
1 AAAGG-TGCCACGGAGTTGTGGAC-TTAAAAAGAA
* *
998120 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGAA
* * *
998153 AAAGAGTGCCACGAAGTTGTGGGCTT-AAATGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAAGAA
*
998186 AAAGGAGCCACGGAGTTGTGGACTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGAA
*
998216 ---GGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
998246 GTGCCACGGA
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
27 18 0.17
28 2 0.02
29 5 0.05
32 22 0.20
33 21 0.19
34 35 0.32
35 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAAGAA
Found at i:998253 original size:29 final size:30
Alignment explanation
Indices: 998063--998412 Score: 266
Period size: 29 Copynumber: 11.7 Consensus size: 30
998053 TTTTGAAGGT
*
998063 TGCCACTGACTTGTGGGCTTT--TAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
*
998090 TTGCCACTGACTTGTGGACTTT-AAAAAGAAAAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAAG----A-G
* * * *
998125 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
1 TGCCACTGACTTGTGGGCTT----TGAAAAAGAG
*
998159 TGCCAC-GAAGTTGTGGGCTTAAATGAAAAAG-G
1 TGCCACTG-ACTTGTGGGCTT---TGAAAAAGAG
* * * * *
998191 AGCCACGGAGTTGTGGAC-TT--AAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
* *
998218 TGCCACGGAGTTGTGGGCTTT-AAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
* * * *
998247 TGCCACGGAGTTGTGGGCTTCGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
998277 TGCCACTGACTTGTGGGCTTTTG---AAG-G
1 TGCCACTGACTTGTGGGC-TTTGAAAAAGAG
998304 TTGCCACTGACTTGTGGGCTTTGAAAAAGA-
1 -TGCCACTGACTTGTGGGCTTTGAAAAAGAG
998334 TGCCACTGACTTGTGGGCTTTGAAAAAGA-
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
998363 TGCCACTGACTTGTGGGCTTTGAAAAAGA-
1 TGCCACTGACTTGTGGGCTTTGAAAAAGAG
*
998392 TGCCACTGATTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
998413 TGAAGGGTGA
Statistics
Matches: 279, Mismatches: 19, Indels: 47
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.02
27 22 0.08
28 44 0.16
29 108 0.39
30 26 0.09
31 4 0.01
32 15 0.05
33 11 0.04
34 36 0.13
35 2 0.01
39 6 0.02
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAGAG
Found at i:1003764 original size:13 final size:13
Alignment explanation
Indices: 1003746--1003770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1003736 CTCTTCTAAA
1003746 AAAAACAAAAAAC
1 AAAAACAAAAAAC
1003759 AAAAACAAAAAA
1 AAAAACAAAAAA
1003771 ATACAAAAAA
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:1003776 original size:23 final size:21
Alignment explanation
Indices: 1003743--1003784 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 21
1003733 CTTCTCTTCT
1003743 AAAAAAAACAAAAAACAAAAAC
1 AAAAAAAACAAAAAA-AAAAAC
1003765 AAAAAAATACAAAAAAAAAA
1 AAAAAAA-ACAAAAAAAAAA
1003785 TCAACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAAC
Found at i:1003794 original size:23 final size:23
Alignment explanation
Indices: 1003743--1003809 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
1003733 CTTCTCTTCT
1003743 AAAAAAAACAAAAAACAAAAACA
1 AAAAAAAACAAAAAACAAAAACA
* *
1003766 AAAAAATACAAAAAA-AAAATCA
1 AAAAAAAACAAAAAACAAAAACA
* *
1003788 ACTAAAAAAACAGAAAAGAAAA
1 A--AAAAAAACAAAAAACAAAA
1003810 GAATCTGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.19
23 14 0.38
24 12 0.32
25 4 0.11
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.04
Consensus pattern (23 bp):
AAAAAAAACAAAAAACAAAAACA
Found at i:1004876 original size:55 final size:55
Alignment explanation
Indices: 1004792--1004957 Score: 237
Period size: 55 Copynumber: 3.0 Consensus size: 55
1004782 AACGCCTTTT
**
1004792 CCTTTCAAAGCCCATGCAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACG
* *
1004847 CCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTT-AAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT-CTTCAAAGAGCAGGACG
* * *
1004902 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCTTCAAAGAGCAGGACG
1004957 C
1 C
1004958 TCTCTCCTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
54 6 0.06
55 90 0.91
56 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACG
Found at i:1005123 original size:154 final size:150
Alignment explanation
Indices: 1004821--1005108 Score: 420
Period size: 149 Copynumber: 1.9 Consensus size: 150
1004811 GTTGGTGGCA
* *
1004821 CCTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTC
*
1004886 CTTAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
66 CTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
*
1004951 AGGACGCTCTCTCCTTTCAC
131 AAGACGCTCTCTCCTTTCAC
* *
1004971 CCTTT-AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTC
*
1005034 CTCAAAGAGCAGGACGACTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-TTCAGTCCTC
66 CTCAAAGAGCAGGAC-A-----CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTC
*
1005098 AAAGAGTAAGA
124 AAAGAGCAAGA
1005109 TGCTTTCTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
148 21 0.17
149 48 0.39
150 5 0.04
153 1 0.01
154 48 0.39
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (150 bp):
CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
AAGACGCTCTCTCCTTTCAC
Found at i:1005130 original size:61 final size:61
Alignment explanation
Indices: 1004998--1005595 Score: 754
Period size: 61 Copynumber: 9.9 Consensus size: 61
1004988 GTAGGACACC
*
1004998 TTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGAC-TTCTCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG-CTTTCT-CT
* * * *
1005059 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAAGATGCTTTCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCT
* * * * *
1005119 TTTCAAGGCCCACACAAGTTGGTAGCAC-CTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT-CT
* * *
1005180 TTT-AAAGCCCACATAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT-T
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCT
* * * *
1005239 TTTGCAAATCCCACACTAGTTGGTGGCA-TCTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCT
1 TTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGGACGCTTTCT-CT
* *
1005302 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCT
* * *
1005362 TTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT-CT
* *
1005423 TTT-AAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT-T
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCT
* * *
1005482 TTTGCAAATCCCACACTAGTTGGTGGCA-TCTTCCAGTCCTCAAAGAGCAGGACGCCTTTC-CT
1 TTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGGACG-CTTTCTCT
* *
1005544 TTTCAAAGACCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
1005596 ACACTTCTTT
Statistics
Matches: 465, Mismatches: 52, Indels: 40
0.83 0.09 0.07
Matches are distributed among these distances:
59 8 0.02
60 130 0.28
61 312 0.67
62 11 0.02
63 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (61 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCT
Found at i:1005137 original size:121 final size:121
Alignment explanation
Indices: 1004998--1005594 Score: 980
Period size: 121 Copynumber: 4.9 Consensus size: 121
1004988 GTAGGACACC
*
1004998 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGACTTCTCCTTTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTA
* * *
1005063 AAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAAGATGCTTTCTTT
66 AAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
* * *
1005119 TTTCAAGGCCCACACAAGTTGGTAGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTA
*
1005184 AAGCCCACATAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
66 AAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
* * * * *
1005240 TTGCAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
*
1005305 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
65 AAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
*
1005362 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTA
1005427 AAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
66 AAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
* * * *
1005483 TTGCAAATCCCACACTAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
*
1005547 CAAAGACCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
65 -AAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
1005595 CACACTTCTT
Statistics
Matches: 442, Mismatches: 31, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
121 259 0.59
122 183 0.41
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (121 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTA
AAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTT
Found at i:1005456 original size:243 final size:243
Alignment explanation
Indices: 1005001--1005594 Score: 1048
Period size: 243 Copynumber: 2.4 Consensus size: 243
1004991 GGACACCTTT
* * * *
1005001 CAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGACTTCTCCTTTTAAA
1 CAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAA
* * *
1005065 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAAGATGCTTTCTTTTTTCAAGGCCC
66 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCAAAGCCC
1005130 ACACAAGTTGGTAGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACATA
131 ACACAAGTTGGTAGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACATA
*
1005195 AGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTG
196 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTG
*
1005243 CAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAA
1 CAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAA
1005308 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCAAAGCCC
66 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCAAAGCCC
*
1005373 ACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACATA
131 ACACAAGTTGGTAGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACATA
1005438 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTG
196 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTG
*
1005486 CAAATCCCACACTAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTCAA
1 CAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AA
* *
1005550 AGACCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
65 AGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
1005595 CACACTTCTT
Statistics
Matches: 336, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
242 29 0.09
243 307 0.91
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (243 bp):
CAAATCCCACACTAGTTGGTGGCATCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAA
GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCAAAGCCC
ACACAAGTTGGTAGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACATA
AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTG
Found at i:1006283 original size:12 final size:13
Alignment explanation
Indices: 1006266--1006294 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1006256 GTAAAAATCA
1006266 AAAATTAAAATT-
1 AAAATTAAAATTC
1006278 AAAATTAAAATTC
1 AAAATTAAAATTC
1006291 AAAA
1 AAAA
1006295 AAATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:1006488 original size:41 final size:41
Alignment explanation
Indices: 1006443--1006524 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1006433 GGTGGGAACT
* *
1006443 TACAACAATTGGTAGCATGGGAAAGGAAATAAAAAAATGCA
1 TACAACAATTGGCAGCATAGGAAAGGAAATAAAAAAATGCA
1006484 TACAACAATTGGCAGCATAGGAAAGGAAATAAAAAAATGCA
1 TACAACAATTGGCAGCATAGGAAAGGAAATAAAAAAATGCA
1006525 ATGGGAGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (41 bp):
TACAACAATTGGCAGCATAGGAAAGGAAATAAAAAAATGCA
Found at i:1007886 original size:79 final size:79
Alignment explanation
Indices: 1007795--1008131 Score: 523
Period size: 79 Copynumber: 4.3 Consensus size: 79
1007785 CCTATTAATC
1007795 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
1007860 ATCAATTTCTCATA
66 ATCAATTTCTCATA
* ** *
1007874 ATCGGGGATACTCCAATCCCGTTATTTTTGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
*
1007939 ATTAATTTCTCATA
66 ATCAATTTCTCATA
* * * *
1007953 ATCGGGGATACTCCAACCTCGTTGTTTTCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAA-
* *
1008018 T-TCAATTTTTCGTA
65 TATCAATTTCTCATA
* **
1008032 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCTTGGTTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
*
1008097 ATTAATTTCTCATA
66 ATCAATTTCTCATA
1008111 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1008132 GTTTTATTTT
Statistics
Matches: 232, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.00
79 230 0.99
80 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
ATCAATTTCTCATA
Found at i:1008126 original size:51 final size:51
Alignment explanation
Indices: 1008064--1008182 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
1008054 TATTTCCGAA
** *
1008064 GGGATACTCCAACCTTGGTTTTATTTCTAAAA-TATTAATTTCTCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACT-TCAATTTCTCATAATCG
*
1008115 GGGATACTCCAACCCCGGTTTTATTTTTAAAACTTCAATTTCTCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCG
*
1008166 AGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1008183 TTGTTTCCGC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 61 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCG
Found at i:1008136 original size:209 final size:209
Alignment explanation
Indices: 1007905--1008339 Score: 683
Period size: 209 Copynumber: 2.1 Consensus size: 209
1007895 TTATTTTTGA
* * *
1007905 GGGGATACTCCAACCTCGGTTTTATTTCTAAAA-TATTAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACT-TCAATTTCTCATAATCGAGGATACTCCAA
* * *
1007969 CCTCGTTGTTTTCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCGTAAT
65 CCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAAT
* * ** ** * *
1008034 CGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCTTGGTTTTATTTCTAAAATAT
130 CGGAGATACTCCAACCCCATTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
1008099 TAATTTCTCATAATC
195 TAATTTCTCATAATC
*
1008114 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACTTCAATTTCTCATAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGAGGATACTCCAAC
1008179 CCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAATC
66 CCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAATC
* *
1008244 GGAGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAGAATATT
131 GGAGATACTCCAACCCCATTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAATATT
* *
1008309 GATTTCTCATAATT
196 AATTTCTCATAATC
1008323 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1008340 ATTATTTCCG
Statistics
Matches: 206, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
209 205 1.00
210 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (209 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGAGGATACTCCAAC
CCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAATC
GGAGATACTCCAACCCCATTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAATATT
AATTTCTCATAATC
Found at i:1008138 original size:130 final size:130
Alignment explanation
Indices: 1007983--1008260 Score: 432
Period size: 130 Copynumber: 2.1 Consensus size: 130
1007973 GTTGTTTTCG
* * *
1007983 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCGTAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGAGGATACTCCAA
** *
1008048 CCCCGTTATTTCCGAAGGGATACTCCAACCTTGGTTTTATTTCTAAAA-TATTAATTTCTCATAA
66 CCCCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACT-TCAATTTCTCATAA
1008112 T
130 T
*
1008113 CGGGGATACTCCAACCCCGGTTTTATTTTTAAAACTTCAATTTCTCATAATCGAGGATACTCCAA
1 CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGAGGATACTCCAA
* ** *
1008178 CCCCGTTGTTTCCGCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAAT
66 CCCCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAAT
*
1008243 CGGAGATACTCCAACCCC
1 CGGGGATACTCCAACCCC
1008261 ATTACCTCCG
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 134 0.99
131 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (130 bp):
CGGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGAGGATACTCCAA
CCCCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAAT
Found at i:1008196 original size:79 final size:79
Alignment explanation
Indices: 1008114--1008446 Score: 384
Period size: 79 Copynumber: 4.2 Consensus size: 79
1008104 TCTCATAATC
* *
1008114 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACTTCAATTTCTCATAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
* * *
1008179 CCCGTTGTTTCCGC
66 CCCATTATTTCCGA
* *
1008193 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTTTCATAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
**
1008258 CCCATTACCTCCGA
66 CCCATTATTTCCGA
* * * *
1008272 GGGGATACTCCAACCCCGGCTTTATTTCCAGAATA-TT-GATTTCTCATAATTGGGGATACTCCA
1 GGGGATACTCCAACCCCGGTTTTATTTCTA-AA-ACTTCAATTTCTCATAATCGGGGATACTCCA
1008335 ACCCCATTATTTCCGA
64 ACCCCATTATTTCCGA
* * * * * * * * * * *
1008351 GGGGATACTCTAATCCCGATTTTATTTCTCAATCATCGATTTTTCACAACCGGGGTTACTCCAA-
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
* * *
1008415 CCCGTTATTTTCAA
66 CCCATTATTTCCGA
1008429 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1008447 TTATTATCTC
Statistics
Matches: 215, Mismatches: 35, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
78 30 0.14
79 180 0.84
80 4 0.02
81 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACTTCAATTTCTCATAATCGGGGATACTCCAAC
CCCATTATTTCCGA
Found at i:1013517 original size:52 final size:52
Alignment explanation
Indices: 1013432--1013577 Score: 206
Period size: 52 Copynumber: 2.8 Consensus size: 52
1013422 ATATGAAAAG
* *
1013432 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
1013484 TTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
1013536 TTGCCTGCATATATCGATACA--AAGATCAATGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTTA-AT-AATGTATCGATACAT
1013578 TAGAGTAATG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1013589 original size:21 final size:21
Alignment explanation
Indices: 1013547--1013599 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1013537 TGCCTGCATA
*
1013547 TATCGATACA-AAGATCAATG
1 TATCGATACATTAGATCAATG
1013567 TATCGATACATTAGAGT-AATG
1 TATCGATACATTAGA-TCAATG
1013588 TATCGATACATT
1 TATCGATACATT
1013600 TTTTGGCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.33
21 19 0.63
22 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (21 bp):
TATCGATACATTAGATCAATG
Found at i:1013658 original size:33 final size:33
Alignment explanation
Indices: 1013637--1013716 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
1013627 TACAAAAACA
1013637 TATGTATCGATACATTATATCGATACAACACTT
1 TATGTATCGATACATTATATCGATACAACACTT
*
1013670 TATGTATCGATACATTGTATCGATACAACACTT
1 TATGTATCGATACATTATATCGATACAACACTT
1013703 TATGTATCGATACA
1 TATGTATCGATACA
1013717 AATCATTGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
TATGTATCGATACATTATATCGATACAACACTT
Found at i:1013679 original size:20 final size:20
Alignment explanation
Indices: 1013654--1013717 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1013644 CGATACATTA
1013654 TATCGATACAACACTTTATG
1 TATCGATACAACACTTTATG
1013674 TATCGAT---ACA---T-TG
1 TATCGATACAACACTTTATG
1013687 TATCGATACAACACTTTATG
1 TATCGATACAACACTTTATG
1013707 TATCGATACAA
1 TATCGATACAA
1013718 ATCATTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 20 0.54
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (20 bp):
TATCGATACAACACTTTATG
Found at i:1013690 original size:13 final size:13
Alignment explanation
Indices: 1013672--1013696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1013662 CAACACTTTA
1013672 TGTATCGATACAT
1 TGTATCGATACAT
1013685 TGTATCGATACA
1 TGTATCGATACA
1013697 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1014087 original size:19 final size:20
Alignment explanation
Indices: 1014042--1014094 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1014032 CTGCCTATTT
* *
1014042 CATGTATCGATACAATTTAG
1 CATGTATCGATACAATTGAA
*
1014062 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1014081 CATGTATCGATACA
1 CATGTATCGATACA
1014095 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1014101 original size:13 final size:13
Alignment explanation
Indices: 1014083--1014107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1014073 ACAATGAACA
1014083 TGTATCGATACAT
1 TGTATCGATACAT
1014096 TGTATCGATACA
1 TGTATCGATACA
1014108 AAGCATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1014127 original size:33 final size:32
Alignment explanation
Indices: 1014064--1014128 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1014054 CAATTTAGTA
* *
1014064 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATATATCGATACAT
1014096 TGTATCGATACAAAGCATA-ATATATCGATACAT
1 TGTATCGATACAAAG-A-ACATATATCGATACAT
1014129 CTGGATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATATATCGATACAT
Found at i:1014395 original size:20 final size:20
Alignment explanation
Indices: 1014342--1014395 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1014332 GTTGGGCATA
* *
1014342 ATGTATCGATACAATTCTTC
1 ATGTATCGATACATTTCCTC
1014362 ATGTATCGATACATTGTCCT-
1 ATGTATCGATACATT-TCCTC
1014382 ATGTATCGATACAT
1 ATGTATCGATACAT
1014396 CTCACTTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTCCTC
Found at i:1014468 original size:19 final size:19
Alignment explanation
Indices: 1014423--1014478 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1014413 CTACCACTTT
*
1014423 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
1014443 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1014462 CATGTATTGATACAATG
1 CATGTATCGATACAATG
1014479 TATTGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1014481 original size:13 final size:13
Alignment explanation
Indices: 1014463--1014489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1014453 TACAATGAAC
1014463 ATGTATTGATACA
1 ATGTATTGATACA
1014476 ATGTATTGATACA
1 ATGTATTGATACA
1014489 A
1 A
1014490 AACATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:1014996 original size:33 final size:32
Alignment explanation
Indices: 1014932--1014997 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1014922 GTTTCATGTC
***
1014932 ATTTTATTTTTAAAAAAATATATATTTAAGTT
1 ATTTTATTTTTAAAAAAATATATAAAAAAGTT
*
1014964 ATTTTATTTTTAAATAAAATATTTAAAAAAGTT
1 ATTTTATTTTTAAA-AAAATATATAAAAAAGTT
1014997 A
1 A
1014998 GTCACACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
ATTTTATTTTTAAAAAAATATATAAAAAAGTT
Found at i:1015469 original size:18 final size:17
Alignment explanation
Indices: 1015446--1015479 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1015436 AAAATAAAAA
1015446 TTTATTTTATTAATTAAT
1 TTTATTTTATT-ATTAAT
1015464 TTTATTTTATTATTAA
1 TTTATTTTATTATTAA
1015480 ATGATGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTATTATTAAT
Found at i:1018369 original size:12 final size:12
Alignment explanation
Indices: 1018352--1018377 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1018342 ATACTAGGTT
1018352 ACTTGAATTTGG
1 ACTTGAATTTGG
1018364 ACTTGAATTTGG
1 ACTTGAATTTGG
1018376 AC
1 AC
1018378 GTAAGTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (12 bp):
ACTTGAATTTGG
Found at i:1018886 original size:13 final size:13
Alignment explanation
Indices: 1018870--1018894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1018860 TTTTTTAAAT
1018870 ATATTTATATTTG
1 ATATTTATATTTG
1018883 ATATTTATATTT
1 ATATTTATATTT
1018895 AATAAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:1018910 original size:8 final size:8
Alignment explanation
Indices: 1018896--1018946 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
1018886 TTTATATTTA
1018896 ATAAATAT
1 ATAAATAT
*
1018904 -TTAA-AT
1 ATAAATAT
1018910 ATAAATAT
1 ATAAATAT
1018918 ATAAATAT
1 ATAAATAT
* *
1018926 ATAATTTT
1 ATAAATAT
*
1018934 TTAAATAT
1 ATAAATAT
1018942 ATAAA
1 ATAAA
1018947 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
6 2 0.06
7 6 0.18
8 25 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATAAATAT
Found at i:1018915 original size:14 final size:14
Alignment explanation
Indices: 1018896--1018942 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
1018886 TTTATATTTA
1018896 ATAAATATTTAAAT
1 ATAAATATTTAAAT
*
1018910 ATAAATATATAAAT
1 ATAAATATTTAAAT
*
1018924 ATATAATTTTTTAAAT
1 ATA-AA-TATTTAAAT
1018940 ATA
1 ATA
1018943 TAAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 16 0.57
15 2 0.07
16 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAATATTTAAAT
Found at i:1019554 original size:19 final size:19
Alignment explanation
Indices: 1019530--1019579 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1019520 AAATTTAAAA
1019530 ATAATATTATAAATATAAC
1 ATAATATTATAAATATAAC
* * * *
1019549 ATAATATAATATATTTAAT
1 ATAATATTATAAATATAAC
1019568 ATACATATTATA
1 ATA-ATATTATA
1019580 TAATTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATATTATAAATATAAC
Found at i:1020995 original size:6 final size:6
Alignment explanation
Indices: 1020978--1021010 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1020968 CACCATTAAA
*
1020978 ACGACC ATGACC ACGACC ACGACC ACGACC ACG
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACG
1021011 TCCTCTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.45, G:0.18, T:0.03
Consensus pattern (6 bp):
ACGACC
Found at i:1021864 original size:18 final size:18
Alignment explanation
Indices: 1021821--1021864 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1021811 CAGCCTCTTT
1021821 CTCATCATCTGAAAACTC
1 CTCATCATCTGAAAACTC
** * *
1021839 GGCCTCATCTGACAACTC
1 CTCATCATCTGAAAACTC
1021857 CTCATCAT
1 CTCATCAT
1021865 TCTCACCAGA
Statistics
Matches: 19, Mismatches: 7, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (18 bp):
CTCATCATCTGAAAACTC
Found at i:1023492 original size:3 final size:3
Alignment explanation
Indices: 1023478--1023520 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1023468 TCTTCGTCTA
*
1023478 CCT CCT CTT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1023521 GTCATCATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CCT
Found at i:1023778 original size:93 final size:93
Alignment explanation
Indices: 1023666--1023941 Score: 428
Period size: 93 Copynumber: 3.0 Consensus size: 93
1023656 GTTGCCTTCT
* * ** *
1023666 GGTTTTGCCTCCTCTTCTTCCACCTTC-ACTGTACAGCCTGACTCACCTTCAACCAGCGCAGAAT
1 GGTTTTGACTCCTCTTCTTCCACCTTCAAC-GTAGAGCCTGACTCACCACCAAGCAGCGCAGAAT
*
1023730 CAGAAACAATTGGTTTGAACTCATCATCA
65 CACAAACAATTGGTTTGAACTCATCATCA
1023759 GGTTTTGACTCCTCTTCTTCCACCTTCAACGTAGAGCCTGACTCACCACCAAGCAGCGCAGAATC
1 GGTTTTGACTCCTCTTCTTCCACCTTCAACGTAGAGCCTGACTCACCACCAAGCAGCGCAGAATC
1023824 ACAAACAATTGGTTTGAACTCATCATCA
66 ACAAACAATTGGTTTGAACTCATCATCA
* * * *
1023852 GGTTTTGACTCCTCTTCTTCCACCTTCAACGTAGAGCGTGGCTCACCACCAAGCAGCGCGGAACC
1 GGTTTTGACTCCTCTTCTTCCACCTTCAACGTAGAGCCTGACTCACCACCAAGCAGCGCAGAATC
* *
1023917 ACAAACAATTGGCTTGAACCCATCA
66 ACAAACAATTGGTTTGAACTCATCA
1023942 AAATCCGTCT
Statistics
Matches: 170, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
93 168 0.99
94 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (93 bp):
GGTTTTGACTCCTCTTCTTCCACCTTCAACGTAGAGCCTGACTCACCACCAAGCAGCGCAGAATC
ACAAACAATTGGTTTGAACTCATCATCA
Found at i:1024285 original size:2 final size:2
Alignment explanation
Indices: 1024278--1024305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1024268 TAGGACACAA
1024278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1024306 GAGTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1026606 original size:21 final size:21
Alignment explanation
Indices: 1026582--1026634 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1026572 AGTTATATTT
1026582 TTTCATCCAAAAAATGCATTC-
1 TTTCATCCAAAAAATGCA-TCA
**
1026603 TTTCATCCAATCAATGCATCA
1 TTTCATCCAAAAAATGCATCA
1026624 TTTCATCCAAA
1 TTTCATCCAAA
1026635 TATATCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATCA
Found at i:1031654 original size:21 final size:21
Alignment explanation
Indices: 1031636--1031695 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1031626 TATTAAAAGT
*
1031636 TACATTTTTTCATCCAAAAAA
1 TACATTCTTTCATCCAAAAAA
* **
1031657 TATATTCTTTCATCCAACCAA
1 TACATTCTTTCATCCAAAAAA
*
1031678 TGCA-TCATTTCATCCAAA
1 TACATTC-TTTCATCCAAA
1031696 TATATCTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (21 bp):
TACATTCTTTCATCCAAAAAA
Found at i:1032542 original size:21 final size:21
Alignment explanation
Indices: 1032516--1032568 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1032506 TGGAGATGAT
1032516 GTATCGATACAATTACCCTAA
1 GTATCGATACAATTACCCTAA
*
1032537 GTATCGATACAATTATCCTAA
1 GTATCGATACAATTACCCTAA
*
1032558 GTATCAATACA
1 GTATCGATACA
1032569 TTTAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (21 bp):
GTATCGATACAATTACCCTAA
Found at i:1032669 original size:21 final size:19
Alignment explanation
Indices: 1032621--1032679 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1032611 ATAAGAAAAG
*
1032621 ATTGTATCGATATAATTCAT
1 ATTGTATCGATA-CATTCAT
*
1032641 AATGTATCGATACATTGCACT
1 ATTGTATCGATACATT-CA-T
*
1032662 ATTGTATCAATACATTCA
1 ATTGTATCGATACATTCA
1032680 AAGGTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 15 0.45
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
ATTGTATCGATACATTCAT
Found at i:1033567 original size:13 final size:13
Alignment explanation
Indices: 1033549--1033573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1033539 CATCTCATAT
1033549 ACCTAAAAATAAC
1 ACCTAAAAATAAC
1033562 ACCTAAAAATAA
1 ACCTAAAAATAA
1033574 AATAGGAGCA
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:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCTAAAAATAAC
Found at i:1034550 original size:20 final size:20
Alignment explanation
Indices: 1034525--1034573 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1034515 GTGAAGTCAT
*
1034525 AGCACCTGGACGCTAGATTA
1 AGCACCTAGACGCTAGATTA
1034545 AGCACCTAGACGCTAGATTA
1 AGCACCTAGACGCTAGATTA
*
1034565 AGCGCCTAG
1 AGCACCTAG
1034574 GCACTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (20 bp):
AGCACCTAGACGCTAGATTA
Found at i:1036334 original size:2 final size:2
Alignment explanation
Indices: 1036327--1036351 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1036317 TCCCCAAACC
1036327 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1036352 TTACAATCCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1041107 original size:2 final size:2
Alignment explanation
Indices: 1041100--1041129 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1041090 TGCCAAGAAT
1041100 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1041130 TAACACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1042860 original size:32 final size:32
Alignment explanation
Indices: 1042824--1042897 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
1042814 GCTTATAGTC
*
1042824 TAAAAAAAATTAAAA-TATATTTTAAATTTATA
1 TAAAAAAAATTAAAATTATA-TTAAAATTTATA
* * **
1042856 TAAAATAAGTTATTATTATATTAAAATTTATA
1 TAAAAAAAATTAAAATTATATTAAAATTTATA
*
1042888 TAAATAAAAT
1 TAAAAAAAAT
1042898 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
TAAAAAAAATTAAAATTATATTAAAATTTATA
Found at i:1042929 original size:21 final size:19
Alignment explanation
Indices: 1042905--1042950 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
1042895 AATATTTTAA
1042905 ATATAATTATTAATATAATAT
1 ATATAATTA-TAATATAA-AT
1042926 ATATAATTATAATATAAAT
1 ATATAATTATAATATAAAT
1042945 ATATAA
1 ATATAA
1042951 ATCATCGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.32
20 8 0.32
21 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATTATAATATAAAT
Found at i:1042938 original size:15 final size:15
Alignment explanation
Indices: 1042884--1042941 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 15
1042874 TATTAAAATT
*
1042884 TATATAAATAAAATA
1 TATATAAATATAATA
*
1042899 T-TTTAAATATAAT-
1 TATATAAATATAATA
1042912 TAT-T-AATATAATA
1 TATATAAATATAATA
*
1042925 TATATAATTATAATA
1 TATATAAATATAATA
1042940 TA
1 TA
1042942 AATATATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.22
13 5 0.14
14 12 0.33
15 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAAATATAATA
Found at i:1042945 original size:26 final size:25
Alignment explanation
Indices: 1042873--1042947 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
1042863 AGTTATTATT
* *
1042873 ATATTA-AAAT-TTATATAAATAAA
1 ATATTATAAATATAATATAAATATA
* *
1042896 ATATTTTAAATATAATTATTAATATA
1 ATATTATAAATATAA-TATAAATATA
*
1042922 ATATATATAATTATAATATAAATATA
1 ATAT-TATAAATATAATATAAATATA
1042948 TAAATCATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
23 5 0.12
24 4 0.10
25 2 0.05
26 21 0.51
27 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTATAAATATAATATAAATATA
Found at i:1043599 original size:14 final size:15
Alignment explanation
Indices: 1043573--1043601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1043563 AAGTATAAAA
1043573 ATTTTTATATTAATT
1 ATTTTTATATTAATT
1043588 ATTTTTAT-TTAATT
1 ATTTTTATATTAATT
1043602 TTTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATATTAATT
Found at i:1043830 original size:21 final size:21
Alignment explanation
Indices: 1043804--1043845 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1043794 CCAAAAAAAT
*
1043804 CTAAAATAAAAAGTTTTTATA
1 CTAAAATAAAAAGATTTTATA
1043825 CTAAAATAAAAAGATTTTATA
1 CTAAAATAAAAAGATTTTATA
1043846 AATGATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
CTAAAATAAAAAGATTTTATA
Found at i:1043868 original size:6 final size:6
Alignment explanation
Indices: 1043857--1043881 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1043847 ATGATTAATT
1043857 ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA A
1043882 ATAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:1045075 original size:21 final size:19
Alignment explanation
Indices: 1045046--1045094 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1045036 ATAATTAAAT
*
1045046 TTTAATAATTTTTAGTTATA
1 TTTAATAATTGTTAGTT-TA
1045066 TTTAATTAATTGTTAGTTTA
1 TTTAA-TAATTGTTAGTTTA
*
1045086 TTTTATAAT
1 TTTAATAAT
1045095 AGTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTAATAATTGTTAGTTTA
Found at i:1045459 original size:21 final size:20
Alignment explanation
Indices: 1045407--1045459 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1045397 ACTCAATCAT
*
1045407 TTAA-ATTAAATTTATTAAT
1 TTAATATTAAATTTATTAAG
1045426 TTAATATTCAAATTTAATTAAG
1 TTAATATT-AAATTT-ATTAAG
1045448 TTAGAT-TTAAAT
1 TTA-ATATTAAAT
1045460 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 10 0.34
22 10 0.34
23 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TTAATATTAAATTTATTAAG
Found at i:1053617 original size:20 final size:20
Alignment explanation
Indices: 1053590--1053687 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 20
1053580 TGCCAATTTT
1053590 ATGTATCGATACAATTATCC
1 ATGTATCGATACAATTATCC
* * *
1053610 ACGTATCGATACAATGA-AC
1 ATGTATCGATACAATTATCC
* *
1053629 ATGTATTGATACAATTGTCC
1 ATGTATCGATACAATTATCC
* * *
1053649 ATATATCGATACAATGA-AC
1 ATGTATCGATACAATTATCC
1053668 ATGTATCGATACAATGTATC
1 ATGTATCGATACAAT-TATC
1053688 GATACAAAAC
Statistics
Matches: 59, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
19 29 0.49
20 30 0.51
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTATCC
Found at i:1053639 original size:19 final size:19
Alignment explanation
Indices: 1053590--1053683 Score: 107
Period size: 19 Copynumber: 4.8 Consensus size: 19
1053580 TGCCAATTTT
* *
1053590 ATGTATCGATACAATTATCC
1 ATGTATCGATACAATGA-AC
*
1053610 ACGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
* **
1053629 ATGTATTGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
*
1053649 ATATATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
1053668 ATGTATCGATACAATG
1 ATGTATCGATACAATG
1053684 TATCGATACA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 31 0.51
20 30 0.49
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:1053644 original size:39 final size:39
Alignment explanation
Indices: 1053590--1053687 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
1053580 TGCCAATTTT
*
1053590 ATGTATCGATACAATTATCCACGTATCGATACAATGAAC
1 ATGTATCGATACAATTATCCACATATCGATACAATGAAC
* * *
1053629 ATGTATTGATACAATTGTCCATATATCGATACAATGAAC
1 ATGTATCGATACAATTATCCACATATCGATACAATGAAC
1053668 ATGTATCGATACAATGTATC
1 ATGTATCGATACAAT-TATC
1053688 GATACAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 49 0.94
40 3 0.06
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (39 bp):
ATGTATCGATACAATTATCCACATATCGATACAATGAAC
Found at i:1053686 original size:13 final size:13
Alignment explanation
Indices: 1053668--1053694 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1053658 TACAATGAAC
1053668 ATGTATCGATACA
1 ATGTATCGATACA
1053681 ATGTATCGATACA
1 ATGTATCGATACA
1053694 A
1 A
1053695 AACATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1054334 original size:21 final size:21
Alignment explanation
Indices: 1054295--1054334 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1054285 CATATTTCTT
**
1054295 CCCCTTTATCAAAGCATTTTC
1 CCCCTTTATCAAAAAATTTTC
1054316 CCCCTTTATCAAAAAATTT
1 CCCCTTTATCAAAAAATTT
1054335 ATTTTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (21 bp):
CCCCTTTATCAAAAAATTTTC
Found at i:1055696 original size:13 final size:13
Alignment explanation
Indices: 1055678--1055714 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1055668 ATAGTAACCC
*
1055678 ATGTATTGATACA
1 ATGTATCGATACA
1055691 ATGTATCGATACA
1 ATGTATCGATACA
1055704 ATGTATCGATA
1 ATGTATCGATA
1055715 TAAGGAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1061936 original size:20 final size:20
Alignment explanation
Indices: 1061911--1061965 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1061901 CCGCCAATTT
**
1061911 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1061931 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
1061950 CATATATCGATACAAT
1 CATGTATCGATACAAT
1061966 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1063564 original size:13 final size:13
Alignment explanation
Indices: 1063546--1063571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1063536 TACACAAAGT
1063546 ATGTATCGATACA
1 ATGTATCGATACA
1063559 ATGTATCGATACA
1 ATGTATCGATACA
1063572 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1063569 original size:32 final size:33
Alignment explanation
Indices: 1063528--1063591 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1063518 TAGCCAAACT
**
1063528 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1063560 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1063592 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1067667 original size:15 final size:15
Alignment explanation
Indices: 1067647--1067677 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1067637 TAAAAATGTC
*
1067647 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1067662 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1067677 C
1 C
1067678 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1069422 original size:60 final size:60
Alignment explanation
Indices: 1069261--1069407 Score: 276
Period size: 60 Copynumber: 2.5 Consensus size: 60
1069251 GGTATCAAAG
1069261 CACTTGACAAAAGTAGATTTTGCACCAACTTGCACCAACTTGCCAATATTTTCACTAAAC
1 CACTTGACAAAAGTAGATTTTGCACCAACTTGCACCAACTTGCCAATATTTTCACTAAAC
*
1069321 CACTTGACAAAAGTAGATTTTGCACCAACTTGCACCAACTTGCCGATATTTTCACTAAAC
1 CACTTGACAAAAGTAGATTTTGCACCAACTTGCACCAACTTGCCAATATTTTCACTAAAC
*
1069381 CACTTGATAAAAGTAGATTTTGCACCA
1 CACTTGACAAAAGTAGATTTTGCACCA
1069408 TTAGGAGAGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.29
Consensus pattern (60 bp):
CACTTGACAAAAGTAGATTTTGCACCAACTTGCACCAACTTGCCAATATTTTCACTAAAC
Found at i:1070023 original size:20 final size:20
Alignment explanation
Indices: 1069980--1070025 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1069970 AAATCTTTTG
1069980 CAAAATACTTTTTTTTCACTT
1 CAAAATACTTTTTTTTCAC-T
*
1070001 CAAATTACTTTGTTTTTCA-T
1 CAAAATACTTT-TTTTTCACT
1070021 CAAAA
1 CAAAA
1070026 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (20 bp):
CAAAATACTTTTTTTTCACT
Found at i:1072466 original size:32 final size:33
Alignment explanation
Indices: 1072425--1072488 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1072415 TAGCCAAACT
**
1072425 TGTATCGATACACAAAGTA-TATATCGATACAA
1 TGTATCGATACACAAAAAATTATATCGATACAA
1072457 TGTATCGATACACAAAAAATTATATCGATACA
1 TGTATCGATACACAAAAAATTATATCGATACA
1072489 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTATATCGATACAA
Found at i:1074539 original size:28 final size:28
Alignment explanation
Indices: 1074499--1074552 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1074489 ATTCAAGGAT
*
1074499 ACAATAATGCATGATGATCCTAAACATG
1 ACAATAACGCATGATGATCCTAAACATG
1074527 ACAATAACGCATGATGATCCTAAACA
1 ACAATAACGCATGATGATCCTAAACA
1074553 GGTCATGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (28 bp):
ACAATAACGCATGATGATCCTAAACATG
Found at i:1076397 original size:12 final size:11
Alignment explanation
Indices: 1076375--1076451 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 11
1076365 AGAGAAAGAA
*
1076375 GAGATAAGAGG
1 GAGATAGGAGG
1076386 GATGATAGGAGG
1 GA-GATAGGAGG
*
1076398 AAAGATAGGA--
1 -GAGATAGGAGG
*
1076408 GAGATAGTA--
1 GAGATAGGAGG
1076417 GAGATAGGAGG
1 GAGATAGGAGG
1076428 GATGATAGGAGG
1 GA-GATAGGAGG
*
1076440 AGAGATATGAGG
1 -GAGATAGGAGG
1076452 AGGAGAGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 32 0.59
13 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1076428 original size:42 final size:42
Alignment explanation
Indices: 1076365--1076446 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
1076355 TAACCCTCAA
1076365 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGAAAGATAGG
1 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGAAAGATAGG
* * * *
1076407 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATA
1 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGAAAGATA
1076447 TGAGGAGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.12
Consensus pattern (42 bp):
AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGAAAGATAGG
Found at i:1087301 original size:11 final size:11
Alignment explanation
Indices: 1087285--1087311 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1087275 TTTGGTTATA
1087285 TAAATTAACTC
1 TAAATTAACTC
1087296 TAAATTAACTC
1 TAAATTAACTC
1087307 TAAAT
1 TAAAT
1087312 AATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATTAACTC
Found at i:1087480 original size:16 final size:17
Alignment explanation
Indices: 1087459--1087494 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1087449 ATATAAATAT
*
1087459 TAATTTAAAT-TTTAAA
1 TAATTTAAATAATTAAA
1087475 TAATTTAAATAATTAAA
1 TAATTTAAATAATTAAA
1087492 TAA
1 TAA
1087495 AAATTTAAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTAAATAATTAAA
Found at i:1087492 original size:8 final size:9
Alignment explanation
Indices: 1087459--1087494 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1087449 ATATAAATAT
1087459 TAATTTAAA
1 TAATTTAAA
1087468 T--TTTAAA
1 TAATTTAAA
1087475 TAATTTAAA
1 TAATTTAAA
1087484 TAA-TTAAA
1 TAATTTAAA
1087492 TAA
1 TAA
1087495 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.28
8 8 0.32
9 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATTTAAA
Found at i:1089243 original size:24 final size:24
Alignment explanation
Indices: 1089216--1089263 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1089206 AATGATAATT
1089216 ATATTAATATAAATAATATTTTAA
1 ATATTAATATAAATAATATTTTAA
* *
1089240 ATATTGATATAATTAATATTTTAA
1 ATATTAATATAAATAATATTTTAA
1089264 TAATAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATATTAATATAAATAATATTTTAA
Found at i:1089465 original size:22 final size:23
Alignment explanation
Indices: 1089437--1089480 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1089427 TGGACATTTT
1089437 TTTATTTAAAAAATATT-CAAAA
1 TTTATTTAAAAAATATTACAAAA
* *
1089459 TTTATTTTATAAATATTACAAA
1 TTTATTTAAAAAATATTACAAA
1089481 TGGACGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATTTAAAAAATATTACAAAA
Found at i:1089935 original size:16 final size:16
Alignment explanation
Indices: 1089885--1089937 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1089875 CTTTAATCCC
*
1089885 AAAATGGCTTGAAATT
1 AAAATGACTTGAAATT
* * * **
1089901 GAAGTGCCTTGAACCT
1 AAAATGACTTGAAATT
1089917 AAAATGACTTGAAATT
1 AAAATGACTTGAAATT
1089933 AAAAT
1 AAAAT
1089938 AATCTAAATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (16 bp):
AAAATGACTTGAAATT
Found at i:1090217 original size:22 final size:22
Alignment explanation
Indices: 1090171--1090220 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1090161 TAGAATGATC
*
1090171 TAAATTTGATTAACTTAAGTAT
1 TAAACTTGATTAACTTAAGTAT
* * *
1090193 TAAACTTGATTAATTTGAGTGT
1 TAAACTTGATTAACTTAAGTAT
1090215 TAAACT
1 TAAACT
1090221 CAATTGACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (22 bp):
TAAACTTGATTAACTTAAGTAT
Found at i:1091185 original size:11 final size:11
Alignment explanation
Indices: 1091169--1091218 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
1091159 TTTCACCCTA
1091169 TTTCTTTCTTT
1 TTTCTTTCTTT
1091180 TTTCTTTCTTT
1 TTTCTTTCTTT
*
1091191 TCTTTTTCTCTTTT
1 T-TTCTT-TC-TTT
*
1091205 TTTCTCTCTTT
1 TTTCTTTCTTT
1091216 TTT
1 TTT
1091219 TCAGATGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 18 0.55
12 6 0.18
13 5 0.15
14 4 0.12
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:1091194 original size:16 final size:17
Alignment explanation
Indices: 1091169--1091209 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1091159 TTTCACCCTA
1091169 TTTC-TTTCTTTTT-TC
1 TTTCTTTTCTTTTTCTC
1091184 TTTCTTTTCTTTTTCTC
1 TTTCTTTTCTTTTTCTC
1091201 TTT-TTTTCT
1 TTTCTTTTCT
1091210 CTCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTCTTTTTCTC
Found at i:1091214 original size:12 final size:12
Alignment explanation
Indices: 1091177--1091220 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1091167 TATTTCTTTC
*
1091177 TTTTTTCTTTCT
1 TTTTTTCTCTCT
*
1091189 TTTCTTTTTCTCT
1 TTT-TTTCTCTCT
1091202 TTTTTTCTCTCT
1 TTTTTTCTCTCT
1091214 TTTTTTC
1 TTTTTTC
1091221 AGATGAACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTCTCTCT
Found at i:1092049 original size:166 final size:163
Alignment explanation
Indices: 1091842--1092275 Score: 545
Period size: 166 Copynumber: 2.6 Consensus size: 163
1091832 ATTTTTCAGG
* * *
1091842 AAAAGGGAAATTTCAAGAAAAAAA-TCAAAAACTCATGAAAATGAATAAATTTTTGAAAAATGAT
1 AAAAAGGAAATTTCAAGAAAAAAATTC-AAAACTCATGAAAATGAATGAATTTTTGAAAAATAAT
* * *
1091906 TTAATATGTAATAAAAAATAATATTTGATGAATTTTAAACACTAAAAATCAAGAAAAATCCCTTT
65 TTAATATG-AATAAAAAATAATATTTGATGAATTTTAAA-ACTAAAAACCAAGAAAAATCCCCTC
* ** * * *
1091971 GACAAAAATTTATGGAGTAGAAAACTCTGTATTTTGA
128 GA-AAAAATTAACAGAATAGAAAACTCTATATTTCGA
*
1092008 AAACAAGGAAATTTCAA-AAAAAAATTCAAAACTTATGAAAATGAATGAATTTTTGAAAAATAAT
1 AAA-AAGGAAATTTCAAGAAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAAATAAT
* * *
1092072 TTAATATAAAATAAATAATAATATTTGATGAATTTTAAAATTAAAAACCAAGAAAAATCCCCTCG
65 TTAATAT-GAATAAAAAATAATATTTGATGAATTTTAAAACTAAAAACCAAGAAAAATCCCCTCG
*
1092137 AAAAAATTAACAGAATAGAAAACTTTATATTTCGA
129 AAAAAATTAACAGAATAGAAAACTCTATATTTCGA
* * *
1092172 AAATAGAGAAATTTCAAGAAAAAAATTTAAAAACTCATAAAAATGAATGAATTTTT-AAAAACTA
1 AAAAAG-GAAATTTCAAGAAAAAAA-TTCAAAACTCATGAAAATGAATGAATTTTTGAAAAA-TA
* *
1092236 ATTTACTATGAAT--TAAATAATAATTTGATGAATTTTAAAA
63 ATTTAATATGAATAAAAAATAAT-ATTTGATGAATTTTAAAA
1092276 ATTTTAAACC
Statistics
Matches: 235, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
163 8 0.03
164 58 0.25
165 38 0.16
166 117 0.50
167 14 0.06
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (163 bp):
AAAAAGGAAATTTCAAGAAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAAATAATT
TAATATGAATAAAAAATAATATTTGATGAATTTTAAAACTAAAAACCAAGAAAAATCCCCTCGAA
AAAATTAACAGAATAGAAAACTCTATATTTCGA
Found at i:1093413 original size:155 final size:153
Alignment explanation
Indices: 1093194--1093644 Score: 424
Period size: 153 Copynumber: 2.9 Consensus size: 153
1093184 TAGAACCAAG
* * * * * *
1093194 TCCTAAGTCATCACTGGGTCGCTTTTATGCCAAAGGTATGCATTGAGGATAAGTTCATCTTTTTA
1 TCCTAGGTCATCAATGGGTCACTTTTATGCCAAAGGTATGCATTAAGGATAGGTT-A-CCTTTTA
*
1093259 CTTATCATTTTCGTGTCC-TTAAGGGTTACAGAGATACTTTCATGTCAAAAGGTATCCT-AAGGG
64 CTTATCATTTTCGTGTCCTTTAA-GGTTAC-GAGATACTTTCATGTCAAAAGGTATACTAAAGGG
1093322 CATTTT-G-ATAATTTCTCCAAAATCGAA
127 CATTTTAGTA-AATTT-TCCAAAATCGAA
* * * *
1093349 TCTTAGGTCATCAATGGGTCAATTTTATGTCAAAGGTGTGCATTAAGGATAGGTTTGACCTTTTA
1 TCCTAGGTCATCAATGGGTCACTTTTATGCCAAAGGTATGCATTAAGGATAGG-TT-ACCTTTTA
* * * * *
1093414 -TGATC-TTTT-GTATCCTTTAAAGTTACTGAGATACTTTTATGTC-GAAGGTATACTACAAGGG
64 CTTATCATTTTCGTGTCCTTTAAGGTTAC-GAGATACTTTCATGTCAAAAGGTATACTA-AAGGG
**
1093475 CATTTTAGTAAATTTTTTAAAATCGAA
127 CATTTTAGTAAATTTTCCAAAATCGAA
* * * *
1093502 TCCTAGGT-A-CTTATCGAGTCTCTTTTATGCCAAATGTATGCATTTAA-GATAGGTT-CCTTTT
1 TCCTAGGTCATC-AAT-GGGTCACTTTTATGCCAAAGGTATGCA-TTAAGGATAGGTTACCTTTT
* * * * * *
1093563 ACTTATCATTTTCGTGTCCTTTAAGGTTACTAGATACTGTCATATC-AAAGATATACTTTAAGGA
63 ACTTATCATTTTCGTGTCCTTTAAGGTTACGAGATACTTTCATGTCAAAAGGTATAC-TAAAGGG
*
1093627 CATTTTAGTAATTTTTCC
127 CATTTTAGTAAATTTTCC
1093645 TAGAACCGAG
Statistics
Matches: 241, Mismatches: 42, Indels: 29
0.77 0.13 0.09
Matches are distributed among these distances:
150 7 0.03
151 14 0.06
152 73 0.30
153 79 0.33
154 14 0.06
155 51 0.21
156 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (153 bp):
TCCTAGGTCATCAATGGGTCACTTTTATGCCAAAGGTATGCATTAAGGATAGGTTACCTTTTACT
TATCATTTTCGTGTCCTTTAAGGTTACGAGATACTTTCATGTCAAAAGGTATACTAAAGGGCATT
TTAGTAAATTTTCCAAAATCGAA
Found at i:1099713 original size:22 final size:22
Alignment explanation
Indices: 1099688--1099729 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1099678 TAAAAAAAAT
1099688 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1099710 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1099730 AATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1099746 original size:17 final size:18
Alignment explanation
Indices: 1099726--1099761 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1099716 TATAATTAAA
1099726 TTTAAATAAA-AATTATT
1 TTTAAATAAATAATTATT
*
1099743 TTTAATTAAATAATTATT
1 TTTAAATAAATAATTATT
1099761 T
1 T
1099762 AAGTCAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAAATAATTATT
Found at i:1100127 original size:16 final size:17
Alignment explanation
Indices: 1100106--1100161 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
1100096 AATAAATTAC
1100106 ATAAAAAAAT-TAAAAT
1 ATAAAAAAATATAAAAT
*
1100122 ATAAAATAATATAAAAAAT
1 ATAAAA-AA-ATATAAAAT
* *
1100141 ATATAAATATATAAAA-
1 ATAAAAAAATATAAAAT
1100157 ATAAA
1 ATAAA
1100162 CTTATCCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.31
17 9 0.28
18 3 0.09
19 10 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATATAAAAT
Found at i:1100139 original size:19 final size:19
Alignment explanation
Indices: 1100117--1100157 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1100107 TAAAAAAATT
1100117 AAAATATA-AAATAATATAA
1 AAAATATATAAAT-ATATAA
1100136 AAAATATATAAATATATAA
1 AAAATATATAAATATATAA
1100155 AAA
1 AAA
1100158 TAAACTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATATATAAATATATAA
Found at i:1100159 original size:10 final size:9
Alignment explanation
Indices: 1100117--1100157 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
1100107 TAAAAAAATT
1100117 AAAATATAA
1 AAAATATAA
1100126 AATAATATAA
1 AA-AATATAA
1100136 AAAATATATA
1 AAAATATA-A
*
1100146 AATATATAA
1 AAAATATAA
1100155 AAA
1 AAA
1100158 TAAACTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATATAA
Found at i:1100159 original size:27 final size:25
Alignment explanation
Indices: 1100109--1100159 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1100099 AAATTACATA
1100109 AAAAAATTAAAATATAAAATAATAT
1 AAAAAATTAAAATATAAAATAATAT
1100134 AAAAAATATATAAATATATAAA-AATA
1 AAAAAAT-TA-AAATATA-AAATAATA
1100160 AACTTATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
26 2 0.09
27 11 0.48
28 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAAATTAAAATATAAAATAATAT
Found at i:1102407 original size:33 final size:33
Alignment explanation
Indices: 1102340--1102408 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1102330 GATTATAAAA
*
1102340 ATAACATAAATATATGAATATATCAAAATTTAT
1 ATAACATAAATATATGAATATATCAAAATATAT
* * *
1102373 ATAACATAAAT-TATTAATATATTATATATATAT
1 ATAACATAAATATATGAATATATCA-AAATATAT
1102406 ATA
1 ATA
1102409 TATATAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
ATAACATAAATATATGAATATATCAAAATATAT
Found at i:1104585 original size:2 final size:2
Alignment explanation
Indices: 1104572--1104601 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1104562 ACATACATAC
*
1104572 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1104602 CATGTTACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1107113 original size:30 final size:32
Alignment explanation
Indices: 1107079--1107146 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1107069 GAATTAATCA
* *
1107079 AGTTCAG-ATTATTTTA-ATTT-ATTCATTTTG
1 AGTTCAGTATTATCTTATATTTGA-TCATTTAG
1107109 AGTTC-GTATTATCTTATATTTGATCATTTAG
1 AGTTCAGTATTATCTTATATTTGATCATTTAG
1107140 AGTTCAG
1 AGTTCAG
1107147 GTTCATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 1 0.03
30 13 0.41
31 16 0.50
32 2 0.06
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (32 bp):
AGTTCAGTATTATCTTATATTTGATCATTTAG
Found at i:1109057 original size:2 final size:2
Alignment explanation
Indices: 1109052--1109081 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1109042 ATATGAAAAA
*
1109052 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1109082 TGATTACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1109823 original size:26 final size:26
Alignment explanation
Indices: 1109794--1109844 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1109784 TCGAACTAAA
1109794 ACTTAAATA-CTTCACCAACCCTTTTT
1 ACTTAAATACCTT-ACCAACCCTTTTT
1109820 ACTTAAATACCTTACCAACCCTTTT
1 ACTTAAATACCTTACCAACCCTTTT
1109845 CTTGCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (26 bp):
ACTTAAATACCTTACCAACCCTTTTT
Found at i:1111073 original size:66 final size:65
Alignment explanation
Indices: 1110968--1111116 Score: 199
Period size: 66 Copynumber: 2.3 Consensus size: 65
1110958 TCTAGTGGCA
* * *
1110968 GGATTAATTGGTAGCCTACAACAAGTTATGATGCATTATAAAATGTAATAAGCGTTACCCTATGC
1 GGATTAATCGGTAGCTTACAACAAGTTATGATGCATTATAAAATGTAATAAGCATTACCCTATGC
* ** *
1111033 GGATTAATCGGCAGCTTACAAACAAGTTATGATGCATTATATGATGTAATGAGCATTACCCTATG
1 GGATTAATCGGTAGCTTAC-AACAAGTTATGATGCATTATAAAATGTAATAAGCATTACCCTATG
1111098 C
65 C
** *
1111099 AAATCAATCGGTAGCTTA
1 GGATTAATCGGTAGCTTA
1111117 ATCGAATCCC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 16 0.22
66 56 0.78
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (65 bp):
GGATTAATCGGTAGCTTACAACAAGTTATGATGCATTATAAAATGTAATAAGCATTACCCTATGC
Found at i:1117644 original size:39 final size:39
Alignment explanation
Indices: 1117532--1117645 Score: 115
Period size: 39 Copynumber: 2.9 Consensus size: 39
1117522 ATATCAAAAG
* * *
1117532 ATCACAAGATC-ATTCAAAATCATATAAATCCAAATATAA
1 ATCAAAAGATCAATT-AAATTCATATAAAACCAAATATAA
* * * ** **
1117571 AT-AAAAAAGCAATCAAATTCATATAAAAGTAAATATTT
1 ATCAAAAGATCAATTAAATTCATATAAAACCAAATATAA
1117609 ATCAAAAGATCAATTAAATTCATATAAAACCAAATAT
1 ATCAAAAGATCAATTAAATTCATATAAAACCAAATAT
1117646 GCATTAAAAG
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
38 25 0.43
39 33 0.57
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (39 bp):
ATCAAAAGATCAATTAAATTCATATAAAACCAAATATAA
Found at i:1121820 original size:3 final size:3
Alignment explanation
Indices: 1121812--1121842 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1121802 CCTTAACCTT
1121812 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1121843 CTTAGAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Done.