Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1130032 original size:3 final size:3
Alignment explanation
Indices: 1130019--1130066 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
1130009 ATAAGAAATA
*
1130019 AAT AA- AAT AAT AAT AAG AAT AAT AAT AAAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
1130063 AAT A
1 AAT A
1130067 TTTTCAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1130036 original size:22 final size:21
Alignment explanation
Indices: 1129998--1130062 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
1129988 AAAACAAACA
*
1129998 AAAAATAAAAAATAAGAAATAA-
1 AAAAAT-AATAATAAG-AATAAT
1130020 ATAAAATAATAATAAGAATAAT
1 A-AAAATAATAATAAGAATAAT
*
1130042 AATAAATAATAATAATAATAA
1 AA-AAATAATAATAAGAATAA
1130063 AATATTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.16
22 27 0.71
23 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAAATAATAATAAGAATAAT
Found at i:1130244 original size:26 final size:26
Alignment explanation
Indices: 1130215--1130277 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
1130205 TTTCAAAATG
1130215 TTTTTAAAAAATATATAATATATAAA
1 TTTTTAAAAAATATATAATATATAAA
** *
1130241 TTTTTCAAAACTTATATATTATATAAA
1 TTTTT-AAAAAATATATAATATATAAA
*
1130268 TTTTCAAAAA
1 TTTTTAAAAA
1130278 TGTTTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTTTAAAAAATATATAATATATAAA
Found at i:1130250 original size:25 final size:25
Alignment explanation
Indices: 1130216--1130276 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
1130206 TTCAAAATGT
* *
1130216 TTTTAAAAAATATATAATATATAAA
1 TTTTCAAAACTATATAATATATAAA
*
1130241 TTTTTCAAAACTTATATATTATATAAA
1 -TTTTCAAAAC-TATATAATATATAAA
1130268 TTTTCAAAA
1 TTTTCAAAA
1130277 ATGTTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTCAAAACTATATAATATATAAA
Found at i:1130277 original size:27 final size:27
Alignment explanation
Indices: 1130226--1130276 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1130216 TTTTAAAAAA
1130226 TATATAATATATAAATTTTTCAAAACT
1 TATATAATATATAAATTTTTCAAAACT
*
1130253 TATATATTATATAAA-TTTTCAAAA
1 TATATAATATATAAATTTTTCAAAA
1130277 ATGTTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (27 bp):
TATATAATATATAAATTTTTCAAAACT
Found at i:1130333 original size:39 final size:36
Alignment explanation
Indices: 1130061--1130427 Score: 334
Period size: 37 Copynumber: 10.1 Consensus size: 36
1130051 TAATAATAAT
* * *
1130061 AAAATATTTTCAAAACATATA-ATATATA-AATTT-CT
1 AAAATGTTTTAAAAAC-TATATAT-TATATAATTTTCA
*
1130096 AAAATGTTTTTAAAAAATTATATATTATACGT-ATTTTCA
1 AAAATG-TTTT-AAAAACTATATATTATA--TAATTTTCA
* * *
1130135 AAAATGTTTTAAAAAATTATATAATATATATATTTTTA
1 AAAATGTTTT-AAAAACTATATATTATATA-ATTTTCA
1130173 AAAATGTTTTAAAAACTATATATTATATATATTTTC-
1 AAAATGTTTTAAAAACTATATATTATATA-ATTTTCA
1130209 AAAATGTTTTTAAAAA--ATATA-TA-AT-A---T-A
1 AAAATG-TTTTAAAAACTATATATTATATAATTTTCA
* *
1130237 TAAAT-TTTTCAAAACTTATATATTATATAAATTTTCA
1 AAAATGTTTTAAAAAC-TATATATTATAT-AATTTTCA
*
1130274 AAAATGTTTTCAAAACTATATATTATATAAGTTTTC-
1 AAAATGTTTTAAAAACTATATATTATATAA-TTTTCA
*
1130310 AAAATGATTTTAAAAACTATATATTATATATATTTTCT
1 AAAATG-TTTTAAAAACTATATATTATATA-ATTTTCA
*
1130348 AAAATGTTTTAAAAACTATATATTATATAGTTTTCAA
1 AAAATGTTTTAAAAACTATATATTATATAATTTTC-A
*
1130385 AAATATTTTTTTAAAAACTATATATTATATACATTTTCA
1 AAA-A-TGTTTTAAAAACTATATATTATATA-ATTTTCA
1130424 AAAA
1 AAAA
1130428 CCGTTTGCAA
Statistics
Matches: 284, Mismatches: 17, Indels: 59
0.79 0.05 0.16
Matches are distributed among these distances:
26 8 0.03
28 5 0.02
29 5 0.02
30 2 0.01
31 3 0.01
33 3 0.01
34 2 0.01
35 10 0.04
36 33 0.12
37 113 0.40
38 60 0.21
39 35 0.12
40 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAATTTTCA
Found at i:1130358 original size:175 final size:175
Alignment explanation
Indices: 1130044--1130426 Score: 473
Period size: 175 Copynumber: 2.2 Consensus size: 175
1130034 AGAATAATAA
* *
1130044 TAAATAATA-ATAATA-ATAAAATATTTTCAAAACATATAATATATAAATTTCTAAAATGTTTTT
1 TAAAAAATATATAATATAT-AAAT-TTTTCAAAACATATAATATATAAATTTCAAAAATGTTTTT
* *
1130107 AAAAAATTATATATTATACGTATTTTCAAAAATGTTTTAAAAAATTATATAATATATATATTTTT
64 AAAAAACTATATATTATAC-TATTTTCAAAAATGTTTTAAAAAACTATATAATATATATATTTTT
1130172 AAAAATGTTTTAAAAACTATATATTATATATATTTTC-AAA-ATGTTTT
128 AAAAATGTTTTAAAAACTATATATTATATA-ATTTTCAAAATATGTTTT
*
1130219 TAAAAAATATATAATATATAAATTTTTCAAAACTTATATATTATATAAATTTTCAAAAATG-TTT
1 TAAAAAATATATAATATATAAATTTTTCAAAAC--ATATAATATATAAA-TTTCAAAAATGTTTT
* *
1130283 T-CAAAACTATATATTATA-TAAGTTTTC-AAAATGATTTT-AAAAACTATATATTATATATATT
63 TAAAAAACTATATATTATACT-A-TTTTCAAAAATG-TTTTAAAAAACTATATAATATATATATT
* *
1130344 TTCT-AAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAAATATTTTTT
125 TT-TAAAAATGTTTTAAAAACTATATATTATATAATTTTC-AAAATATGTTTT
* * *
1130396 TAAAAACTATATATTATATACA-TTTTCAAAA
1 TAAAAAATATATAATATATAAATTTTTCAAAA
1130427 ACCGTTTGCA
Statistics
Matches: 184, Mismatches: 12, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
174 6 0.03
175 77 0.42
176 47 0.26
177 44 0.24
178 10 0.05
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (175 bp):
TAAAAAATATATAATATATAAATTTTTCAAAACATATAATATATAAATTTCAAAAATGTTTTTAA
AAAACTATATATTATACTATTTTCAAAAATGTTTTAAAAAACTATATAATATATATATTTTTAAA
AATGTTTTAAAAACTATATATTATATAATTTTCAAAATATGTTTT
Found at i:1130440 original size:76 final size:73
Alignment explanation
Indices: 1130240--1130452 Score: 259
Period size: 76 Copynumber: 2.8 Consensus size: 73
1130230 TAATATATAA
* *
1130240 ATTTTTCAAAACTTATATATTATATAAATTTTCAAAAATGTTTTCAAAACTATATATTATATAAG
1 ATTTTTAAAAAC-TATATATTATATAAATTTTCAAAAATGTTTAC-AAACTATATATTATAT-AG
1130305 TTTTCAAAATG
63 TTTTCAAAATG
* * *
1130316 A-TTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTT
1 ATTTTTAAAAACTATATATTATATAAATTTTCAAAAATG-TTTACAAACTATATATTATATAGTT
1130380 TTCAAAAAT-
65 TTC-AAAATG
* * * *
1130389 ATTTTTTTAAAAACTATATATTATATACATTTTCAAAAACCGTTTGCAAACTATATAATATATA
1 A--TTTTTAAAAACTATATATTATATAAATTTTCAAAAA-TGTTTACAAACTATATATTATATA
1130453 TATAAAAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
73 8 0.07
74 46 0.38
75 12 0.10
76 53 0.44
77 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (73 bp):
ATTTTTAAAAACTATATATTATATAAATTTTCAAAAATGTTTACAAACTATATATTATATAGTTT
TCAAAATG
Found at i:1131456 original size:48 final size:48
Alignment explanation
Indices: 1131158--1131456 Score: 348
Period size: 48 Copynumber: 6.2 Consensus size: 48
1131148 AATCCTAATC
* * * * * * * *
1131158 GACGAGGGTGGGCTGATTCCACAGGATCTCGCACCTGAAACGGCCA-T
1 GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
*
1131205 CGACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACC
1 -GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
* *
1131254 GACGAAGGTGGGTTGATTCCACAAGATAACGCACCAGGAGTGTCCACT
1 GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
** * * *
1131302 GTTGAAGGTGGGGTGATTCCGCAAGATATCGCACCAGGAGTGTCCACT
1 GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
* * * *
1131350 GATGAAGGCGGGGTGATTCCACAAGATATTGCACCAGGAATGTCCACT
1 GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
* * * * *
1131398 GAAGAAGGTGGATTGATTTCACAAGATATCACACCAGGAATGTCCACA
1 GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
*
1131446 GACGAGGGTGG
1 GACGAAGGTGG
1131457 TGGTGGTCCG
Statistics
Matches: 218, Mismatches: 32, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
48 218 1.00
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.19
Consensus pattern (48 bp):
GACGAAGGTGGGTTGATTCCACAAGATATCGCACCAGGAATGTCCACT
Found at i:1144778 original size:31 final size:31
Alignment explanation
Indices: 1144735--1144796 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1144725 TCTAGAAACA
* * *
1144735 AGAAGTATCTCTACGAGATGAGCATAACAAC
1 AGAAATATCTCTACAAGATGAACATAACAAC
*
1144766 AGAAATATCTCTACAAGATGAATATAACAAC
1 AGAAATATCTCTACAAGATGAACATAACAAC
1144797 CATTTCTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (31 bp):
AGAAATATCTCTACAAGATGAACATAACAAC
Found at i:1147212 original size:75 final size:75
Alignment explanation
Indices: 1147091--1147239 Score: 190
Period size: 75 Copynumber: 2.0 Consensus size: 75
1147081 AATAAATAAG
* * ** * **
1147091 CATGCTAAAAACCCCTTTCAATTAGAATCAGGAATGTTGACGCATTTTGAACGTTTGTATCAACA
1 CATGCTAAAAACCCATTTCAATCAGAATCAGGAATACTGACACATTTTGAACGTTCATATCAACA
1147156 AATGTTAGGA
66 AATGTTAGGA
* * * *
1147166 CATGCTGAAAGCCCATTTCAATCATAATCAGGAATACTGGCACATTTTGAACGTTCATATCAACA
1 CATGCTAAAAACCCATTTCAATCAGAATCAGGAATACTGACACATTTTGAACGTTCATATCAACA
*
1147231 ATTGTTAGG
66 AATGTTAGG
1147240 GCATATTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (75 bp):
CATGCTAAAAACCCATTTCAATCAGAATCAGGAATACTGACACATTTTGAACGTTCATATCAACA
AATGTTAGGA
Found at i:1148547 original size:22 final size:22
Alignment explanation
Indices: 1148517--1148574 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1148507 TACATCTACA
1148517 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
1148539 CTCTCCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
1148561 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
1148575 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:1149306 original size:45 final size:45
Alignment explanation
Indices: 1149240--1149642 Score: 612
Period size: 45 Copynumber: 9.0 Consensus size: 45
1149230 TATTTCCCAT
* *
1149240 ATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
1149285 ATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAACCTTTGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
1149330 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
1149375 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * * *
1149420 TTCTGTAAGCCCTTTAGTGCATGATG-TTTCAAAGCCTTCGGGTT
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
1149464 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
1149509 ATCTATAAGCCCTTCAGTGCATGATG-TTTCAAAGCCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
1149553 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * *
1149598 ATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGG
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1149643 AGCTTTTTGA
Statistics
Matches: 325, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
44 81 0.25
45 233 0.72
46 4 0.01
47 7 0.02
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (45 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
Found at i:1149504 original size:89 final size:89
Alignment explanation
Indices: 1149240--1149642 Score: 608
Period size: 89 Copynumber: 4.5 Consensus size: 89
1149230 TATTTCCCAT
* * * *
1149240 ATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCATTGC
1 ATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
1149305 ATGATGTTTTCAAAACCTTTGGGTC
65 ATGATGTTTTCAAAACCTTCGGGTC
*
1149330 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATCTGTAAGCCCTTCAGTGCATGATGTT-TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
1149395 ATGATGTTTTCAAAGCCTTCGGGTC
65 ATGATGTTTTCAAAACCTTCGGGTC
* * *
1149420 TTCTGTAAGCCCTTTAGTGCATGATGTTTCAAAGCCTTCGGGTTATCTGTAAGCCCTTCAGTGCA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1149485 TGATGTTATCAAAATCTTCGGGTC
66 TGATGTTTTCAAAACCTTCGGGTC
*
1149509 ATCTATAAGCCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1149574 TGATGTTTTCAAAACTTTCGGGTC
66 TGATGTTTTCAAAACCTTCGGGTC
* * *
1149598 ATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGG
1 ATCTGTAAGCCCTTCAGTGCATGATG-TTTC--AAAGCCTTCGGG
1149643 AGCTTTTTGA
Statistics
Matches: 286, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
89 162 0.57
90 112 0.39
92 12 0.04
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (89 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
TGATGTTTTCAAAACCTTCGGGTC
Found at i:1149520 original size:134 final size:135
Alignment explanation
Indices: 1149240--1149642 Score: 630
Period size: 134 Copynumber: 3.0 Consensus size: 135
1149230 TATTTCCCAT
* * * *
1149240 ATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCATTGC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
1149305 ATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTC
66 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTC
1149370 GGGTC
131 GGGTC
* *
1149375 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCTTCTGTAAGCCCTTTAGTGC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* * *
1149440 ATGATG-TTTCAAAGCCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAATCTTC
66 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTC
1149504 GGGTC
131 GGGTC
*
1149509 ATCTATAAGCCCTTCAGTGCATGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* * * * *
1149573 ATGATGTTTTCAAAACTTTCGGGTCATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCT
66 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATC-AAAA-CCT
1149638 TCGGG
129 TCGGG
1149643 AGCTTTTTGA
Statistics
Matches: 244, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
133 42 0.17
134 126 0.52
135 69 0.28
136 7 0.03
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (135 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTC
GGGTC
Found at i:1149907 original size:3 final size:3
Alignment explanation
Indices: 1149899--1149959 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
1149889 CAGTTTGCTT
1149899 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1149947 -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1149960 TAAATAAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1151158 original size:26 final size:24
Alignment explanation
Indices: 1151127--1151174 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
1151117 AATTCTTTAA
1151127 TTTTGATTATA-TTATAATATTATTGC
1 TTTTGA-TATAGTT-TAA-ATTATTGC
1151153 TTTTGATATAGTTTAAATTATT
1 TTTTGATATAGTTTAAATTATT
1151175 ATTTTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 7 0.33
26 8 0.38
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTTGATATAGTTTAAATTATTGC
Found at i:1154565 original size:36 final size:36
Alignment explanation
Indices: 1154518--1154621 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
1154508 ACATTAGAGT
* *
1154518 TTTACTTGGATTCAAACTCCTAAAAATATGATAAAG
1 TTTACTAGGATTCAAACTCCTAAAAATAGGATAAAG
*
1154554 TTTACTAGGATTCAAACTCCT-AAAATAGGATAGAG
1 TTTACTAGGATTCAAACTCCTAAAAATAGGATAAAG
*
1154589 TTCTACTATGATTCAAACTCCTAAAAATAGGAT
1 TT-TACTAGGATTCAAACTCCTAAAAATAGGAT
1154622 CCAGAAGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 14 0.23
36 38 0.61
37 10 0.16
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (36 bp):
TTTACTAGGATTCAAACTCCTAAAAATAGGATAAAG
Found at i:1155032 original size:8 final size:8
Alignment explanation
Indices: 1155019--1155070 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
1155009 CTTTTATGGA
1155019 TTTTATTT
1 TTTTATTT
1155027 TTTTATTT
1 TTTTATTT
*
1155035 ATTTATTT
1 TTTTATTT
*
1155043 TTTTCTTT
1 TTTTATTT
1155051 TCTTT-TCGTT
1 T-TTTAT--TT
1155061 TTTTATTT
1 TTTTATTT
1155069 TT
1 TT
1155071 ATTTAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 27 0.73
9 6 0.16
10 4 0.11
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:1158269 original size:13 final size:14
Alignment explanation
Indices: 1158239--1158288 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 14
1158229 AAAAAGAGAA
*
1158239 AAAGAGAAAAAAAC
1 AAAGAGAAAATAAC
1158253 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
1158266 AAAGAGAAAA-AAC
1 AAAGAGAAAATAAC
1158279 AAAG-GAAAAT
1 AAAGAGAAAAT
1158289 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 12 0.36
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:1158275 original size:26 final size:26
Alignment explanation
Indices: 1158237--1158288 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1158227 GCAAAAAGAG
1158237 AAAAAGAGAAAAAAACAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAG-GAAAAT
1158264 AAAAAGAG-AAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
1158289 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 11 0.44
27 8 0.32
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:1158482 original size:69 final size:69
Alignment explanation
Indices: 1158360--1158497 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
1158350 GATTCAAACT
* * * *
1158360 ATGAGTTTGATCAAGCACAATCATTTCCGAATCATTGAAACATTTCACGCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAAACACTCCACGCGAAGATCATAGAGCA
1158425 TCAA
66 TCAA
* * * *
1158429 ATGAGATTGATCAAGCACAATCATTTCTGAA-CTACTGAATCACTCCACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATC-ACTGAAACACTCCACGCGAAGATCATAGAGC
1158493 ATCAA
65 ATCAA
1158498 GAGAGAGACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAAACACTCCACGCGAAGATCATAGAGCA
TCAA
Found at i:1159474 original size:32 final size:32
Alignment explanation
Indices: 1159432--1159521 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
1159422 GCATCTTTGA
*
1159432 AGATTCAACATCAAATGTTGGTGCATTTTTTT
1 AGATTCAACATCAAATGTTGGGGCATTTTTTT
*
1159464 AGATTTAACATCAAATGTTGGGGCATTTTTTT
1 AGATTCAACATCAAATGTTGGGGCATTTTTTT
* * *
1159496 AGATTCAACATCGAATATTAGGGCAT
1 AGATTCAACATCAAATGTTGGGGCAT
1159522 CTTTGGGAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (32 bp):
AGATTCAACATCAAATGTTGGGGCATTTTTTT
Found at i:1160244 original size:106 final size:106
Alignment explanation
Indices: 1160117--1160357 Score: 383
Period size: 106 Copynumber: 2.3 Consensus size: 106
1160107 ATATCGTGCC
* * * *
1160117 ACTCGAGACAACACATGTTCAACTCCACAACGAAGGTACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1160182 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTGAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1160223 ACTTAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1160288 AATTTGGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTGAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1160329 ACTCGAGACAGCACAAGCTCAACTTCACA
1 ACTCAAGACAACACAAGTTCAACTTCACA
1160358 GCACAAGCTC
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 123 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTGAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1160360 original size:19 final size:19
Alignment explanation
Indices: 1160336--1160397 Score: 124
Period size: 19 Copynumber: 3.3 Consensus size: 19
1160326 TGGACTCGAG
1160336 ACAGCACAAGCTCAACTTC
1 ACAGCACAAGCTCAACTTC
1160355 ACAGCACAAGCTCAACTTC
1 ACAGCACAAGCTCAACTTC
1160374 ACAGCACAAGCTCAACTTC
1 ACAGCACAAGCTCAACTTC
1160393 ACAGC
1 ACAGC
1160398 GAAGGGGCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (19 bp):
ACAGCACAAGCTCAACTTC
Found at i:1160911 original size:37 final size:37
Alignment explanation
Indices: 1160836--1161024 Score: 134
Period size: 37 Copynumber: 5.4 Consensus size: 37
1160826 ATTGAAAACA
* * * * *
1160836 TTTCCCTTGAAA-AAAATTTTATCTCGCTTGGGGTAG
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* *
1160872 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* * *
1160909 TTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 TTTCTCTTGAAACA-AAATTTTGTCTCCCTTGAGATA-G
** *
1160938 TTTCAT-TTGAAA-TTAATTTTGTCTCTCTTGAGATAG
1 TTTC-TCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
1160974 TTTCTTTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1161011 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1161025 TAAACCTTGA
Statistics
Matches: 118, Mismatches: 19, Indels: 31
0.70 0.11 0.18
Matches are distributed among these distances:
27 2 0.02
28 2 0.02
29 15 0.13
30 1 0.01
35 1 0.01
36 26 0.22
37 68 0.58
38 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:1160923 original size:87 final size:88
Alignment explanation
Indices: 1160706--1160920 Score: 263
Period size: 87 Copynumber: 2.4 Consensus size: 88
1160696 TTTTGGAACT
**
1160706 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTCCCTTGAAATGAATTTTAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTG----A-AAACATTTCCCTTGAAAAAAATTTTAT
*
1160771 CTCGATTGAGATAGTTTTCCTTGAAACA
61 CTCGATTGAGATAGTTTCCCTTGAAACA
* * ** *
1160799 AAATTTTGTTTCCCTTGAAACA-TAAAC-ATTGAAAACATTTCCCTTGAAAAAAATTTTATCTCG
1 AAATTTTGTCTCCCTTGAGACAGT-TTCTCTTGAAAACATTTCCCTTGAAAAAAATTTTATCTCG
* * *
1160862 CTTGGGGTAGTTTCCCTTGAAACA
65 ATTGAGATAGTTTCCCTTGAAACA
1160886 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1160921 CATAAACATT
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
87 70 0.68
88 8 0.08
92 4 0.04
93 21 0.20
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (88 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAAAAAATTTTATCTCGA
TTGAGATAGTTTCCCTTGAAACA
Found at i:1160930 original size:102 final size:102
Alignment explanation
Indices: 1160806--1161051 Score: 366
Period size: 102 Copynumber: 2.4 Consensus size: 102
1160796 ACAAAATTTT
* * *
1160806 GTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTATCTCGCTTGGGGTA
1 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTATCTCGCTTGAGATA
1160871 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
66 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
** ** * *
1160908 GTTTCTCTTGAAACATAAACATTGAAAACATTTCATTTGAAATTAATTTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTATCTCGCTTGAGATA
** *
1160973 GTTTCTTTTGAAACAAAATTTTGTCTCCCTTGAGATA
66 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
* *
1161010 GTTTCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
1161052 CACAAAATAT
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 128 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (102 bp):
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTATCTCGCTTGAGATA
GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
Found at i:1161155 original size:35 final size:36
Alignment explanation
Indices: 1161089--1161181 Score: 145
Period size: 35 Copynumber: 2.6 Consensus size: 36
1161079 AAAACGAGTT
1161089 TTGAGACAGTTTCCCTTG-AACAAAATCTTGTCTCTC
1 TTGAGACAGTTT-CCTTGAAACAAAATCTTGTCTCTC
*
1161125 TTGAGACAGTTTCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCTTGAAACAAAATCTTGTCTCTC
1161160 TTGAGACAGTTTCTCTTGAAAC
1 TTGAGACAGTTTC-CTTGAAAC
1161182 GCCAATCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
35 31 0.57
36 23 0.43
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
TTGAGACAGTTTCCTTGAAACAAAATCTTGTCTCTC
Found at i:1161292 original size:260 final size:258
Alignment explanation
Indices: 1160836--1161318 Score: 553
Period size: 260 Copynumber: 1.8 Consensus size: 258
1160826 ATTGAAAACA
* * **
1160836 TTTCCCTTGAAAAAAATTTTATCTCGCTTGGGGTAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAAAAAATCTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* ** *
1160901 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCATTTGAAATTAATTTTGTCTCTCT
66 TGAGACAGTTTCTCTTGAAACACAAACATTGAAAACATTTCATTTGAAAAAAATTTTGCCTCTCT
* * *** * *
1160966 TGAGATAGTTTCTTTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACC
131 TGAGACAGTTTCTCTTGAAACAAAA---T-AAACCCTTGAAATAGTTTCTCTTGAAACAAAAACC
1161031 TTGAAAACGTTTCCCTTGAAACACAAAATATTTAAATCAGTTCCCCTTAAAACGAGTTTTGAGAC
192 TTGAAAACGTTTCCCTTGAAACACAAAATATTTAAATCAGTTCCCCTTAAAACGAGTTTTGAGAC
1161096 AG
257 AG
* * * *
1161098 TTTCCCTTGAACAAAATCTTGTCTCTCTTGAGACAGTTT-CCTTGAAAC-AAATTTTGTCTCTCT
1 TTTCCCTTGAAAAAAATCTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * * **
1161161 TGAGACAGTTTCTCTTGAAACGCCAATCTTTGAATATGTTTC-TCTTGAAACAAAATTTTGCCTC
66 TGAGACAGTTTCTCTTGAAAC-ACAAACATTGAAAACATTTCAT-TTGAAA-AAAATTTTGCCTC
* *
1161225 -CTTGAGACAGTTTCTCTTGAAACACAAA-AAACCTTTGAAATTGTTTCTCTTGAAACACAAAAA
128 TCTTGAGACAGTTTCTCTTGAAACA-AAATAAACCCTTGAAATAGTTTCTCTTG-AA-AC-AAAA
** * *
1161288 ACCTTGAAATTGTTTCTCTTTAAACACAAAA
189 ACCTTGAAAACGTTTCCCTTGAAACACAAAA
1161319 AAACCTTTGA
Statistics
Matches: 183, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
257 18 0.10
258 2 0.01
259 2 0.01
260 66 0.36
261 50 0.27
262 45 0.25
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (258 bp):
TTTCCCTTGAAAAAAATCTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACACAAACATTGAAAACATTTCATTTGAAAAAAATTTTGCCTCTCT
TGAGACAGTTTCTCTTGAAACAAAATAAACCCTTGAAATAGTTTCTCTTGAAACAAAAACCTTGA
AAACGTTTCCCTTGAAACACAAAATATTTAAATCAGTTCCCCTTAAAACGAGTTTTGAGACAG
Found at i:1161295 original size:32 final size:34
Alignment explanation
Indices: 1161234--1161383 Score: 234
Period size: 33 Copynumber: 4.4 Consensus size: 34
1161224 CCTTGAGACA
1161234 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
1161267 GTTTCTCTTGAAACAC-AAAAAACC-TTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
1161299 GTTTCTCTTTAAACACAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
1161333 GTTTCTCTTGAAACACAAAAAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACAC--AAAAAAA-CCTTTGAAATT
1161370 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
1161384 CCAATACCTT
Statistics
Matches: 109, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
32 23 0.21
33 32 0.29
34 23 0.21
36 7 0.06
37 24 0.22
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
Found at i:1162173 original size:36 final size:36
Alignment explanation
Indices: 1162131--1162236 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 36
1162121 AACATAACGT
1162131 TAGAGTTTTACTAGGATTCAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAACTCCTAAAAATAGGA
1162167 TAGAGTTTTACTAGGATTCAACTCCT-AAAATAGGA
1 TAGAGTTTTACTAGGATTCAACTCCTAAAAATAGGA
* * * *
1162202 TACAGTTCTATTATGATTCAAACTCCTAAAAATAG
1 TAGAGTTTTACTAGGATTC-AACTCCTAAAAATAG
1162237 ATCCAAAAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 24 0.38
36 33 0.52
37 7 0.11
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (36 bp):
TAGAGTTTTACTAGGATTCAACTCCTAAAAATAGGA
Found at i:1162556 original size:2 final size:2
Alignment explanation
Indices: 1162549--1162573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1162539 CTTATTAATT
1162549 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1162574 TTACTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162866 original size:16 final size:16
Alignment explanation
Indices: 1162832--1162880 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1162822 TTATTCGTTT
1162832 TATTTTATC--TTTTC
1 TATTTTATCAGTTTTC
*
1162846 CATTTTATCAGTTTTC
1 TATTTTATCAGTTTTC
* *
1162862 TATTTTGTTAGTTTT-
1 TATTTTATCAGTTTTC
1162877 TATT
1 TATT
1162881 ACCTTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
16 17 0.59
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.67
Consensus pattern (16 bp):
TATTTTATCAGTTTTC
Found at i:1167679 original size:179 final size:178
Alignment explanation
Indices: 1167350--1167706 Score: 673
Period size: 179 Copynumber: 2.0 Consensus size: 178
1167340 CCCTTCGGTA
1167350 TCTTCCTTATCAACGACTTCCTTTTGGCCTTTTTAATGCACCCACTAGTTTCTAGAAATGCATGG
1 TCTTCCTTATCAACGACTTCCTTTTGGCCTTTTTAATGCACCCACTAGTTTCTAGAAATGCATGG
1167415 TTAACGTTTTTCTAACTATTTCAAAAATGGAATTAAAGTCTTCATGGATGACTTTACAATATGGT
66 TTAACGTTTTTCTAACTATTTCAAAAATGGAATTAAAGTCTTCATGGATGACTTTACAATATGGT
1167480 AATCCCTTAATGAAGTCTTTTGAATTTAACTAATGTGCTTAAGCGATGC
131 AATCCCTTAATGAAGTCTTTTGAA-TTAACTAATGTGCTTAAGCGATGC
1167529 TCTTCCTTATCAACGACTTCCTTTTGGCCTTTTTAATGCACCCACTAGTTTCTAGAAATGCATGG
1 TCTTCCTTATCAACGACTTCCTTTTGGCCTTTTTAATGCACCCACTAGTTTCTAGAAATGCATGG
1167594 TTAACGTTTTTCTAACTATTTCAAAAATGGAATTAAAGTCTTCATGGATGAC-TTA-AATATGGT
66 TTAACGTTTTTCTAACTATTTCAAAAATGGAATTAAAGTCTTCATGGATGACTTTACAATATGGT
1167657 AATCCCTTTAATGAATGTCTTTTGAATTAACTAATGTGCTTAAGCGATGC
131 AATCCC-TTAATGAA-GTCTTTTGAATTAACTAATGTGCTTAAGCGATGC
1167707 CTTGAATTCA
Statistics
Matches: 176, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
177 14 0.08
178 35 0.20
179 127 0.72
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (178 bp):
TCTTCCTTATCAACGACTTCCTTTTGGCCTTTTTAATGCACCCACTAGTTTCTAGAAATGCATGG
TTAACGTTTTTCTAACTATTTCAAAAATGGAATTAAAGTCTTCATGGATGACTTTACAATATGGT
AATCCCTTAATGAAGTCTTTTGAATTAACTAATGTGCTTAAGCGATGC
Found at i:1168683 original size:25 final size:26
Alignment explanation
Indices: 1168636--1168687 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
1168626 GATAAGGTAA
1168636 TTTAGCAATGTGTTTCCAAAGCGAGG
1 TTTAGCAATGTGTTTCCAAAGCGAGG
1168662 TTTAGCAATGTG-TTCCAAAGCGAGG
1 TTTAGCAATGTGTTTCCAAAGCGAGG
1168687 T
1 T
1168688 AAACTCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (26 bp):
TTTAGCAATGTGTTTCCAAAGCGAGG
Found at i:1171684 original size:16 final size:16
Alignment explanation
Indices: 1171663--1171693 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1171653 TTGGCTTATA
1171663 ACTACTCAGGAAGAAG
1 ACTACTCAGGAAGAAG
1171679 ACTACTCAGGAAGAA
1 ACTACTCAGGAAGAA
1171694 ATGACTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (16 bp):
ACTACTCAGGAAGAAG
Found at i:1172571 original size:12 final size:12
Alignment explanation
Indices: 1172551--1172589 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1172541 ATCATGATCC
1172551 AAACAAAAA-AA
1 AAACAAAAAGAA
1172562 AAATCAAAAAGAA
1 AAA-CAAAAAGAA
*
1172575 AAACAAACAGAA
1 AAACAAAAAGAA
1172587 AAA
1 AAA
1172590 GAAAGGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 17 0.68
13 5 0.20
ACGTcount: A:0.82, C:0.10, G:0.05, T:0.03
Consensus pattern (12 bp):
AAACAAAAAGAA
Found at i:1173286 original size:26 final size:27
Alignment explanation
Indices: 1173222--1173286 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
1173212 CGTGTTAGAT
* *
1173222 AAAAAGGTAAGAAATAAATAAATTAAA
1 AAAAAGATAAGAAATAAACAAATTAAA
**
1173249 TTAAA-ATGAAGAAA-AAACAAATTAAA
1 AAAAAGAT-AAGAAATAAACAAATTAAA
1173275 AAAAAGATAAGA
1 AAAAAGATAAGA
1173287 TAAAGAAAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.17
Consensus pattern (27 bp):
AAAAAGATAAGAAATAAACAAATTAAA
Found at i:1173363 original size:24 final size:24
Alignment explanation
Indices: 1173336--1173407 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 24
1173326 ATATATATAG
*
1173336 AAAATATAAAAAAATAAAAAGGAA
1 AAAATATAAAAAAATAAAAAAGAA
* *
1173360 AAAATATAAATAAAACAAATAAATAA
1 AAAATATAAA-AAAATAAA-AAAGAA
*
1173386 AATAATAATAAAAAAGTAAAAA
1 AA-AAT-ATAAAAAAATAAAAA
1173408 TAATATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 10 0.26
25 7 0.18
26 8 0.21
27 9 0.23
28 5 0.13
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAATATAAAAAAATAAAAAAGAA
Found at i:1173399 original size:37 final size:35
Alignment explanation
Indices: 1173315--1173410 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 35
1173305 AATAGTAAGT
* *
1173315 AAAATAAAAATATATATATAGAAAATATAAAAAAATA
1 AAAATAAAAA-ATATAAATA-AAAAAATAAAAAAATA
*
1173352 AAAAGGAAAAAATATAAATAAAACAAATAAATAAAATA
1 AAAA-TAAAAAATATAAATAAAA-AAATAAA-AAAATA
* *
1173390 ATAATAAAAAAGTAAAAATAA
1 AAAATAAAAAA-TATAAATAA
1173411 TATATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
36 3 0.06
37 24 0.49
38 22 0.45
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (35 bp):
AAAATAAAAAATATAAATAAAAAAATAAAAAAATA
Found at i:1173435 original size:35 final size:35
Alignment explanation
Indices: 1173387--1173524 Score: 125
Period size: 37 Copynumber: 3.7 Consensus size: 35
1173377 AATAAATAAA
*
1173387 ATAATAATAAAAAAGTAAAAATAATATATATATAT
1 ATAATAATAAAAAAGTAAAAATAATAAATATATAT
*
1173422 ATAATAAATAAAAACA-TAAAAAATAGTAAATATATAT
1 ATAAT-AATAAAAA-AGT-AAAAATAATAAATATATAT
*
1173459 ATAAATTAATAAAAAAGATAATAAAAAATAACATATATAT
1 AT-AA-TAATAAAAAAG-TAA-AAATAATAA-ATATATAT
* *
1173499 ATATGTAATTTAAAAAAATAAAAATA
1 ATA-ATAA--TAAAAAAGTAAAAATA
1173525 TATACTAAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
35 5 0.06
36 9 0.11
37 21 0.25
38 12 0.14
39 17 0.20
40 13 0.15
41 7 0.08
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (35 bp):
ATAATAATAAAAAAGTAAAAATAATAAATATATAT
Found at i:1173453 original size:88 final size:88
Alignment explanation
Indices: 1173311--1173486 Score: 198
Period size: 88 Copynumber: 2.0 Consensus size: 88
1173301 ATAAAATAGT
*
1173311 AAGTAAAATAAAAATATATATATAGAAAATATAAAAAAATAAAAAGGAAAAAATATAAATA-AAA
1 AAGTAAAATAAAAATATATATATAGAAAATATAAAAAAATAAAAAAGAAAAAATATAAATATAAA
1173375 CAAATAAATAAA-ATAATAATAAAA
66 CAAATAAA-AAAGATAATAA-AAAA
* * * * ** *
1173399 AAGTAAAAATAATATATATATATATA-ATAA-ATAAAAACATAAAAAATAGTAAATATATATATA
1 AAGT-AAAATAA-AAATATATATATAGAAAATATAAAAAAATAAAAAAGAAAAAATATAAATATA
**
1173462 AATTAATAAAAAAGATAATAAAAAA
64 AACAAATAAAAAAGATAATAAAAAA
1173487 TAACATATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
88 36 0.49
89 26 0.35
90 12 0.16
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (88 bp):
AAGTAAAATAAAAATATATATATAGAAAATATAAAAAAATAAAAAAGAAAAAATATAAATATAAA
CAAATAAAAAAGATAATAAAAAA
Found at i:1173469 original size:42 final size:43
Alignment explanation
Indices: 1173322--1173501 Score: 134
Period size: 42 Copynumber: 4.3 Consensus size: 43
1173312 AGTAAAATAA
* *
1173322 AAATATATATATAGAAAAT-ATAAA-AAAATAA-AAAGGAA-A--
1 AAATATATATATA-AATATAATAAATAAAATAATAAA-AAATAGT
* * *
1173361 AAATATAAATA-AAACA-AATAAATAAAATAATAATAAAAAAGT
1 AAATATATATATAAATATAATAAATAAAATAATAA-AAAATAGT
*
1173403 AAAAATAATATATATATATATAATAAATAAAA-ACATAAAAAATAGT
1 --AAAT-ATATATATAAATATAATAAATAAAATA-ATAAAAAATAGT
1173449 AAATATATATATAAAT-TAATAAA-AAAGATAATAAAAAATA--
1 AAATATATATATAAATATAATAAATAAA-ATAATAAAAAATAGT
*
1173489 ACATATATATATA
1 AAATATATATATA
1173502 TGTAATTTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 29
0.75 0.06 0.19
Matches are distributed among these distances:
37 8 0.07
38 8 0.07
39 14 0.12
40 14 0.12
41 3 0.03
42 18 0.15
43 12 0.10
44 8 0.07
45 6 0.05
46 11 0.09
47 15 0.13
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (43 bp):
AAATATATATATAAATATAATAAATAAAATAATAAAAAATAGT
Found at i:1174109 original size:37 final size:37
Alignment explanation
Indices: 1174059--1174166 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
1174049 TTGTGGATCT
* * *
1174059 TATTTTAAGGAGTTTGAATCATAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
*
1174096 TATTTTTAGGAGTTTGAATCCTAATAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
1174133 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1174167 ACGTTATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
Found at i:1175483 original size:110 final size:110
Alignment explanation
Indices: 1175305--1175626 Score: 434
Period size: 110 Copynumber: 2.9 Consensus size: 110
1175295 ACTTCGAGTT
* * *
1175305 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTTACAAT
1 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGT
1175370 CAGTCACCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTC-AGGAC
66 CAGTCACCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGA-GAC
* * * *
1175415 CCATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTAAACTGAAAAGTTATTTGTTGACAGT
1 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGT
* * * * *
1175480 CAGTCA-CCTTTTCACTGTAAATTTGAGCTTGTGTTGTCTCGAGTC
66 CAGTCACCCCTTT-GCTGTGAAGTTGAGCTTGTGTTGTCTCGAGAC
* * *
1175525 CAATATCAC-TCACTGTGAAGTTGAAATTGACTCTGAATGAAAATGAAAAGTTGTTTGTTGATAG
1 CAATATC-CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAG
* * *
1175589 TCAGTCGCCCCTTCGCTGTGAAGTTGATCTTGTGTTGT
65 TCAGTCACCCCTTTGCTGTGAAGTTGAGCTTGTGTTGT
1175627 AAATTTCCTT
Statistics
Matches: 182, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
109 5 0.03
110 171 0.94
111 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (110 bp):
CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGT
CAGTCACCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGAC
Found at i:1177294 original size:12 final size:12
Alignment explanation
Indices: 1177238--1177299 Score: 63
Period size: 13 Copynumber: 4.9 Consensus size: 12
1177228 TTTTCCTTGA
*
1177238 TTTTTATTTCTC
1 TTTTTTTTTCTC
1177250 TTTTTTATTTTCTC
1 -TTTTT-TTTTCTC
*
1177264 TTTGTTTTTC-C
1 TTTTTTTTTCTC
1177275 TTTGTTTTTTCTC
1 TTT-TTTTTTCTC
1177288 TTTTTTTGTTCT
1 TTTTTTT-TTCT
1177300 TATTGGATCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.10
12 15 0.36
13 17 0.40
14 6 0.14
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:1180430 original size:2 final size:2
Alignment explanation
Indices: 1180423--1180453 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1180413 AGTAAAATAA
1180423 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 A
1180454 GAAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1180518 original size:38 final size:38
Alignment explanation
Indices: 1180476--1180599 Score: 115
Period size: 38 Copynumber: 3.1 Consensus size: 38
1180466 AAGAAAAAGG
* *
1180476 AAAAAATATAAATAAAACAAATAAATAAAATAATAATA
1 AAAAAATATAAATAATATAAATAAATAAAATAATAATA
* * * * *
1180514 AAAAAGTAAAAATAGTATATATATAAT-AAATAAAAACATA
1 AAAAAATATAAATAATATAAATA-AATAAAAT-AATA-ATA
*
1180554 AAAAAATAGTAAATATATATAAATTAATAAAATAGATAATA
1 AAAAAATA-TAAATA-ATATAAATAAATAAAATA-ATAATA
1180595 AAAAA
1 AAAAA
1180600 TAATATATAT
Statistics
Matches: 66, Mismatches: 13, Indels: 11
0.73 0.14 0.12
Matches are distributed among these distances:
38 21 0.32
39 6 0.09
40 10 0.15
41 17 0.26
42 12 0.18
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (38 bp):
AAAAAATATAAATAATATAAATAAATAAAATAATAATA
Found at i:1180546 original size:32 final size:33
Alignment explanation
Indices: 1180505--1180577 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
1180495 AATAAATAAA
*
1180505 ATAAT-AATAAAAA-AGT-AAAAATAGTATATAT
1 ATAATAAATAAAAACA-TAAAAAATAGTAAATAT
1180536 ATAATAAATAAAAACATAAAAAAATAGTAAATAT
1 ATAATAAATAAAAACAT-AAAAAATAGTAAATAT
1180570 AT-ATAAAT
1 ATAATAAAT
1180578 TAATAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 5 0.14
32 9 0.24
33 7 0.19
34 16 0.43
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (33 bp):
ATAATAAATAAAAACATAAAAAATAGTAAATAT
Found at i:1180559 original size:34 final size:37
Alignment explanation
Indices: 1180521--1180621 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 37
1180511 ATAAAAAAGT
1180521 AAAAATAGTATATATATAATAAATAAAA-ACAT-A-A
1 AAAAATAGTATATATATAATAAATAAAATACATAATA
* *
1180555 AAAAATAGTAAATATATATAAATTAATAAAATAGATAATA
1 AAAAATAGT--ATATATAT-AATAAATAAAATACATAATA
* *
1180595 AAAAATAATATATATATATATATATAA
1 AAAAATAGTATATATATA-ATAAATAA
1180622 TATATGTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
34 9 0.16
36 8 0.15
37 11 0.20
38 17 0.31
39 1 0.02
40 9 0.16
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (37 bp):
AAAAATAGTATATATATAATAAATAAAATACATAATA
Found at i:1180666 original size:80 final size:79
Alignment explanation
Indices: 1180476--1180666 Score: 189
Period size: 80 Copynumber: 2.4 Consensus size: 79
1180466 AAGAAAAAGG
1180476 AAAAAATATAAATA-AAAC-AAATAAATAAAATAATAATAAAAAAGTAAAAATAGTATATATATA
1 AAAAAATATAAATATAAACTAAATAAA-AAAATAATAATAAAAAAGTAAAAATAGTATATATATA
1180539 ATAAATAAAAACATA
65 ATAAATAAAAACATA
* *
1180554 AAAAAATAGTAAATATATA-TAAATTAATAAAATAGATAATAAAAAA-TAATATATATA-TATAT
1 AAAAAATA-TAAATATAAACTAAA-TAAAAAAATA-ATAATAAAAAAGTAA-A-A-ATAGTATAT
* ** *
1180616 ATATAATATATGTAATC-T-
60 ATATAATAAATAAAAACATA
* *
1180634 AAAAAATAAAAATATACACTAAAGTAAAAAAAT
1 AAAAAATATAAATATAAACTAAA-TAAAAAAAT
1180667 GCATAAAATG
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
78 8 0.09
79 14 0.15
80 34 0.36
81 16 0.17
82 19 0.20
83 3 0.03
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (79 bp):
AAAAAATATAAATATAAACTAAATAAAAAAATAATAATAAAAAAGTAAAAATAGTATATATATAA
TAAATAAAAACATA
Found at i:1181227 original size:37 final size:37
Alignment explanation
Indices: 1181177--1181284 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
1181167 TTGTGGATCC
*
1181177 TATTTTTAGGAGTTTGAATCATAGTAGAATTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCA
* *
1181214 TATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCA
* *
1181251 TATTTTTAGGAGTTTG-ATCCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAAT-CATAGTAGAACTCTA
1181285 ACGTTATGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 2 0.03
37 64 0.97
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCA
Found at i:1184271 original size:14 final size:14
Alignment explanation
Indices: 1184254--1184280 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1184244 ATATTAAATA
1184254 ATAAATATAATTAT
1 ATAAATATAATTAT
1184268 ATAAATATAATTA
1 ATAAATATAATTA
1184281 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:1191663 original size:178 final size:178
Alignment explanation
Indices: 1191364--1191715 Score: 650
Period size: 178 Copynumber: 2.0 Consensus size: 178
1191354 AGGCCTAGAA
*
1191364 AAATCATTCTGGCCAGAAGCAGTCAATACCACCTGTTATTTGGTGAATCGAGCTCCATCAACTGC
1 AAATCATTCTGGCCAGAAGCAGTCAATACCACCTGTTATTTGGTGAATCAAGCTCCATCAACTGC
*
1191429 AATAGAGCTGAAGACACCAATGGAGATGTGGACTGGTAAATCAGTTGATTATTCAAACCTCCATG
66 AATAGAGCTGAAGACACCAATGGAGATGTGGACTGGTAAACCAGTTGATTATTCAAACCTCCATG
1191494 TATTTGGAAGTATTGTGTACGTGATGTACAACTCCCAAGAAATTATTC
131 TATTTGGAAGTATTGTGTACGTGATGTACAACTCCCAAGAAATTATTC
* *
1191542 AAATCATTCTGGCCAGAAGCAGTCAATATCGCCTGTTATTTGGTGAATCAAGCTCCATCAACTGC
1 AAATCATTCTGGCCAGAAGCAGTCAATACCACCTGTTATTTGGTGAATCAAGCTCCATCAACTGC
*
1191607 AATAGAGCTGAAGACACCAATGGAGATGTGGACTGGTAAACCAGTTGATTATTCAAACCTCTATG
66 AATAGAGCTGAAGACACCAATGGAGATGTGGACTGGTAAACCAGTTGATTATTCAAACCTCCATG
*
1191672 TATTTGGAAGTATTGTGTACGTGATGTACAACTCCTAAGAAATT
131 TATTTGGAAGTATTGTGTACGTGATGTACAACTCCCAAGAAATT
1191716 TCAAAGATGG
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 168 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (178 bp):
AAATCATTCTGGCCAGAAGCAGTCAATACCACCTGTTATTTGGTGAATCAAGCTCCATCAACTGC
AATAGAGCTGAAGACACCAATGGAGATGTGGACTGGTAAACCAGTTGATTATTCAAACCTCCATG
TATTTGGAAGTATTGTGTACGTGATGTACAACTCCCAAGAAATTATTC
Found at i:1194282 original size:23 final size:23
Alignment explanation
Indices: 1194255--1194300 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1194245 ATCAATCGAC
1194255 CCAAACTCATCAACATTTTGGAA
1 CCAAACTCATCAACATTTTGGAA
1194278 CCAAACTCATCAACATTTTGGAA
1 CCAAACTCATCAACATTTTGGAA
1194301 GCCATTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (23 bp):
CCAAACTCATCAACATTTTGGAA
Found at i:1195789 original size:13 final size:13
Alignment explanation
Indices: 1195754--1195790 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1195744 AAATCCAATT
*
1195754 AAAAATACATAC-
1 AAAAATACAAACA
1195766 AAAAATA-AAACA
1 AAAAATACAAACA
1195778 AAAAATACAAACA
1 AAAAATACAAACA
1195791 TACATCAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 3 0.14
12 14 0.64
13 5 0.23
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAATACAAACA
Found at i:1196784 original size:109 final size:107
Alignment explanation
Indices: 1196668--1196917 Score: 281
Period size: 109 Copynumber: 2.3 Consensus size: 107
1196658 ACTAGAATGT
*
1196668 AAAAACACGCTCAACTATAGGGGTA-TAAAAAGCAAATAACCCAATAAATGTATAACACGCATAA
1 AAAAACACGCT-AACTATAGGGG-ACTAAAAAGCAAATAACCCAATAAATGTATAACACACATAA
* * * *
1196732 AAAAGGGTAAATAACAATTTTGGTCTTCACACGTGACCAAAGTGC
64 AAAAGGGTAAATAACAATCTT-GTCATCACACGTGACCAAAATAC
* * * * *
1196777 AAAAACACGCTAAAC-ATAGGGGGACTAAACAGAAAATAACTCAATAAATGTATAACACACCTGA
1 AAAAACACGCT-AACTATA-GGGGACTAAAAAGCAAATAACCCAATAAATGTATAACACACATAA
* * * * *
1196841 AATAGGGTAAATAGCAATCTTGTCATCTCAGGTGACTAAAATAC
64 AAAAGGGTAAATAACAATCTTGTCATCACACGTGACCAAAATAC
1196885 AAAAACACGACTAACT-TAGAGGGACTAAAAAGC
1 AAAAACACG-CTAACTATAG-GGGACTAAAAAGC
1196918 GATTAACCAC
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
107 1 0.01
108 46 0.39
109 71 0.60
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (107 bp):
AAAAACACGCTAACTATAGGGGACTAAAAAGCAAATAACCCAATAAATGTATAACACACATAAAA
AAGGGTAAATAACAATCTTGTCATCACACGTGACCAAAATAC
Found at i:1198322 original size:133 final size:131
Alignment explanation
Indices: 1198075--1198634 Score: 528
Period size: 133 Copynumber: 4.2 Consensus size: 131
1198065 TAGATCATCT
* * ** * ** *
1198075 GAAACGTTGATTCATTCCATTGCTCTTCATGGAATATTGAATCGAGATAGATTTGTTCCACTGTT
1 GAAATGTTGATTCATTCCACTATTCTTCA-GGAATATTAAATCGAGGCATATTTGTTCCAC-GTT
* * * *
1198140 CCTCAAGGAAGATCAAATATGGAAAAAGGGAATTTGATCCGCTGCTTCTTCAGAGTAAATCAGAT
64 CCTCAAGGAAGATCAAATATGGAAAAAGGGGATATGCTCCGCTACTTCTTCAGAGTAAATCAGAT
1198205 ATG
129 ATG
* * *
1198208 GAAATGTTTATTCATTCCACTATTCTTCAGTTAATATTAAATCGAGGCATATTTGTTCTATCGTT
1 GAAATGTTGATTCATTCCACTATTCTTCAG-GAATATTAAATCGAGGCATATTTGTTCCA-CGTT
* * * * *
1198273 CCTCATGGAAGATCAAATATGGAAAAAGGGGATTTGCTCTGCTACTTCTTTAGGGTAAATCAGAT
64 CCTCAAGGAAGATCAAATATGGAAAAAGGGGATATGCTCCGCTACTTCTTCAGAGTAAATCAGAT
* *
1198338 CTA
129 ATG
* * * * * * * *
1198341 GAAATGTTTATTCATTCCACTATTATTTAGGGAATAGTATATCGAGGCATATTTTTTCCAGAGCT
1 GAAATGTTGATTCATTCCACTATTCTTCA-GGAATATTAAATCGAGGCATATTTGTTCCA-CGTT
* * * * * *
1198406 CCTCAGGGAATATCAAATATGGAAAAAAGGGATATGCTCTGATACTTCTTCAGGGTAAATCAGAT
64 CCTCAAGGAAGATCAAATATGGAAAAAGGGGATATGCTCCGCTACTTCTTCAGAGTAAATCAGAT
1198471 ATG
129 ATG
* * * * * * *
1198474 GAAACGTTGATTCATTCCATTGTTCTTCAAGGAAGATTGAATCGCA-GTAGATTTGTTCCACTGT
1 GAAATGTTGATTCATTCCACTATTCTTC-AGGAATATTAAATCG-AGGCATATTTGTTCCAC-GT
* * * ** * * * *
1198538 TCCTCAAGGAATATCAAATCTAGAAAAAGGGGATATGCTCCATTTCTTTTTTTAGAGTAAATCAA
63 TCCTCAAGGAAGATCAAATATGGAAAAAGGGGATATGCTCCGCTAC-TTCTTCAGAGTAAATCAG
*
1198603 ATCTG
127 ATATG
* *
1198608 GAAATGTTGATTTATTCCATTATTCTT
1 GAAATGTTGATTCATTCCACTATTCTT
1198635 TAAGACAGAT
Statistics
Matches: 351, Mismatches: 69, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
132 1 0.00
133 304 0.87
134 46 0.13
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (131 bp):
GAAATGTTGATTCATTCCACTATTCTTCAGGAATATTAAATCGAGGCATATTTGTTCCACGTTCC
TCAAGGAAGATCAAATATGGAAAAAGGGGATATGCTCCGCTACTTCTTCAGAGTAAATCAGATAT
G
Found at i:1198566 original size:266 final size:267
Alignment explanation
Indices: 1198139--1198636 Score: 610
Period size: 266 Copynumber: 1.9 Consensus size: 267
1198129 GTTCCACTGT
* * *
1198139 TCCTCAAGGAAGATCAAATATGGAAAAAGGGAATTTGATCCGCTGCTTCTTCAGAGTAAATCAGA
1 TCCTCAAGGAAGATCAAATATGGAAAAAGGGAATATGATCCGATACTTCTTCAGAGTAAATCAGA
* * * * * *
1198204 TATGGAAATGTTTATTCATTCCACTATTCTTCAGTTAATATTAAATCGAGGCATATTTGTTCTAT
66 TATGGAAACGTTGATTCATTCCACTATTCTTCAGTGAAGATTAAATCGAGGCAGATTTGTTCCAT
* * * ** *
1198269 CGTTCCTCATGGAAGATCAAATATGGAAAAAGGGGATTTGCTCTGCTAC-TTCTTTAGGGTAAAT
131 CGTTCCTCAAGGAAGATCAAATATAGAAAAAGGGGATATGCTCCACTACTTTCTTTAGAGTAAAT
* *
1198333 CAGATCTAGAAATGTTTATTCATTCCACTATTATTTAGGGAATAGTATATCGAGGCATATTTTTT
196 CAAATCTAGAAATGTTGATTCATTCCACTATTATTTAGGGAATAGTATATCGAGGCATATTTTTT
1198398 CCAGAGC
261 CCAGAGC
* * * * *
1198405 TCCTCAGGGAATATCAAATATGGAAAAAAGGG-ATATGCTCTGATACTTCTTCAGGGTAAATCAG
1 TCCTCAAGGAAGATCAAATATGG-AAAAAGGGAATATGATCCGATACTTCTTCAGAGTAAATCAG
* * * *
1198469 ATATGGAAACGTTGATTCATTCCATTGTTCTTCAAG-GAAGATTGAATCGCA-GTAGATTTGTTC
65 ATATGGAAACGTTGATTCATTCCACTATTCTTC-AGTGAAGATTAAATCG-AGGCAGATTTGTTC
* * * * *
1198532 CA-CTGTTCCTCAAGGAATATCAAATCTAGAAAAAGGGGATATGCTCCATTTCTTTTTTTAGAGT
128 CATC-GTTCCTCAAGGAAGATCAAATATAGAAAAAGGGGATATGCTCCACTACTTTCTTTAGAGT
* * * *
1198596 AAATCAAATCTGGAAATGTTGATTTATTCCATTATTCTTTA
192 AAATCAAATCTAGAAATGTTGATTCATTCCACTATTATTTA
1198637 AGACAGATTG
Statistics
Matches: 192, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
265 1 0.01
266 136 0.71
267 55 0.29
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (267 bp):
TCCTCAAGGAAGATCAAATATGGAAAAAGGGAATATGATCCGATACTTCTTCAGAGTAAATCAGA
TATGGAAACGTTGATTCATTCCACTATTCTTCAGTGAAGATTAAATCGAGGCAGATTTGTTCCAT
CGTTCCTCAAGGAAGATCAAATATAGAAAAAGGGGATATGCTCCACTACTTTCTTTAGAGTAAAT
CAAATCTAGAAATGTTGATTCATTCCACTATTATTTAGGGAATAGTATATCGAGGCATATTTTTT
CCAGAGC
Found at i:1199490 original size:45 final size:45
Alignment explanation
Indices: 1199340--1199591 Score: 180
Period size: 43 Copynumber: 5.7 Consensus size: 45
1199330 GATACTACTA
* * * * *
1199340 AAAAG-TTGACTCC-CTTCCGCGAGAAATTCAAGAATAACACCATT
1 AAAAGATTGACTCCTCTT-CACGAGAAAGTCAAGAATGACAACACT
* ** * *
1199384 AAAAGGTTGACTATTCTTCGA-GAGGAAGTTAAGAATGA-AACACT
1 AAAAGATTGACTCCTCTTC-ACGAGAAAGTCAAGAATGACAACACT
* *
1199428 AAAAGATCT-TCTTCTCTTCACGAGAAAGTCAAGAATGACAACACT
1 AAAAGAT-TGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * * *
1199473 AAAAAATTGACTCCTCTTCA--AGAAAGTCAAGAATAACAATATT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * * * * * *
1199516 GAAATATTGACTTCTCTTCATGAGAAAGTTAAGAATG--AATATT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * *
1199559 GAAAGATTGTCTCCTCTTCACGAGAGAGTCAAG
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
1199592 TTGAAGCTTC
Statistics
Matches: 167, Mismatches: 32, Indels: 19
0.77 0.15 0.09
Matches are distributed among these distances:
43 71 0.43
44 38 0.23
45 55 0.33
46 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (45 bp):
AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
Found at i:1201080 original size:44 final size:45
Alignment explanation
Indices: 1201017--1201106 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1201007 CTTGTATTCT
*
1201017 TGGATGATATGGGCCTTC-AAGAATGCCCCAACATTTATCATTTC
1 TGGATGATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTC
* *
1201061 TGGATGATATGGGCCTTCAAAAAATGCCTCAACGTTTATCATTTC
1 TGGATGATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTC
1201106 T
1 T
1201107 TGCTACAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 18 0.43
45 24 0.57
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
TGGATGATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTC
Found at i:1208241 original size:10 final size:11
Alignment explanation
Indices: 1208216--1208240 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1208206 TTATCAACCC
1208216 AAAACAAAAAA
1 AAAACAAAAAA
1208227 AAAACAAAAAA
1 AAAACAAAAAA
1208238 AAA
1 AAA
1208241 CTCTCCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:1209073 original size:10 final size:10
Alignment explanation
Indices: 1209058--1209096 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
1209048 CATGCCACAG
1209058 AAATAAATAA
1 AAATAAATAA
1209068 AAATAAATAA
1 AAATAAATAA
1209078 AAATATAAGTAA
1 AAATA-AA-TAA
1209090 ATAATAA
1 A-AATAA
1209097 TAACAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 5 0.19
13 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1211890 original size:10 final size:10
Alignment explanation
Indices: 1211875--1211913 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
1211865 CGTGCCACAG
1211875 AAATAAATAA
1 AAATAAATAA
1211885 AAATAAATAA
1 AAATAAATAA
1211895 AAATATAAGTAA
1 AAATA-AA-TAA
1211907 ATAATAA
1 A-AATAA
1211914 TAACAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 5 0.19
13 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1211914 original size:3 final size:3
Alignment explanation
Indices: 1211906--1211948 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
1211896 AATATAAGTA
* * *
1211906 AAT AAT AAT AAC AAC AAC AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1211949 TCTACGGACG
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:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1212738 original size:19 final size:19
Alignment explanation
Indices: 1212714--1212924 Score: 144
Period size: 19 Copynumber: 10.8 Consensus size: 19
1212704 TCCAAGTTCG
*
1212714 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTGTCCAAATT
*
1212733 CGTTGCGATTTTCCAAA-T
1 CGTTGCGATTGTCCAAATT
*
1212751 --TTACG-TTAGTCCAAATT
1 CGTTGCGATT-GTCCAAATT
* * *
1212768 CGTTACGATAGTCCAAGTT
1 CGTTGCGATTGTCCAAATT
*
1212787 CACGTTGCGATAGT-CAAAGTT
1 --CGTTGCGATTGTCCAAA-TT
*
1212808 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTGTCCAAATT
* *
1212829 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTGTCCAAATT
*
1212848 CACGTTGCGATTTTCCAAATT
1 --CGTTGCGATTGTCCAAATT
* * *
1212869 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTGTCCAAATT
*
1212888 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTGTCCAAATT
* *
1212909 CATTGCGATAGTCCAA
1 CGTTGCGATTGTCCAA
1212925 GTTCACGTTC
Statistics
Matches: 153, Mismatches: 26, Indels: 26
0.75 0.13 0.13
Matches are distributed among these distances:
15 2 0.01
16 10 0.07
17 1 0.01
18 1 0.01
19 74 0.48
20 4 0.03
21 57 0.37
22 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (19 bp):
CGTTGCGATTGTCCAAATT
Found at i:1212783 original size:35 final size:35
Alignment explanation
Indices: 1212725--1212792 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1212715 GTTGCGATTT
* ** *
1212725 TCCAAATTCGTTGCGATTTTCCAAATTTACGTTAG
1 TCCAAATTCGTTACGATAGTCCAAATTCACGTTAG
*
1212760 TCCAAATTCGTTACGATAGTCCAAGTTCACGTT
1 TCCAAATTCGTTACGATAGTCCAAATTCACGTT
1212793 GCGATAGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (35 bp):
TCCAAATTCGTTACGATAGTCCAAATTCACGTTAG
Found at i:1212833 original size:40 final size:40
Alignment explanation
Indices: 1212789--1212933 Score: 245
Period size: 40 Copynumber: 3.6 Consensus size: 40
1212779 TCCAAGTTCA
* *
1212789 CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTCCAAATT
1212829 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTCCAAATT
* *
1212869 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTCCAAATT
*
1212909 CATTGCGATAGTCCAAGTTCACGTT
1 CGTTGCGATAGTCCAAGTTCACGTT
1212934 CGAAGTTCGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTCCAAATT
Found at i:1212960 original size:53 final size:53
Alignment explanation
Indices: 1212880--1212986 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
1212870 GTTGCGATAG
1212880 TCGAAGTTCGCGTTGCGATTTTCCAAATTCATTGCGATAGTCCAAGTTCACGT
1 TCGAAGTTCGCGTTGCGATTTTCCAAATTCATTGCGATAGTCCAAGTTCACGT
*
1212933 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
1 TCGAAGTTCGCGTTGCGATTTTCCAAATTCATTGCGATAGTCCAAGTTCACGT
1212986 T
1 T
1212987 GCGTTAGTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (53 bp):
TCGAAGTTCGCGTTGCGATTTTCCAAATTCATTGCGATAGTCCAAGTTCACGT
Found at i:1212988 original size:21 final size:20
Alignment explanation
Indices: 1212757--1213002 Score: 174
Period size: 21 Copynumber: 12.6 Consensus size: 20
1212747 AAATTTACGT
* *
1212757 TAGTCCAAATT-CGTTACGA
1 TAGTCCAAGTTCCGTTGCGA
1212776 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
*
1212797 TAGTCAAAGTTCGCGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** *
1212818 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
1212837 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** *
1212858 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
1212877 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** * *
1212898 TTTTCCAAATT-CATTGCGA
1 TAGTCCAAGTTCCGTTGCGA
1212917 TAGTCCAAGTTCACGTT-CGA
1 TAGTCCAAGTTC-CGTTGCGA
*
1212937 -AGTTC--G---CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
** *
1212951 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
1212970 TAGTCCAAGTTCACGTTGCGT
1 TAGTCCAAGTTC-CGTTGCGA
*
1212991 TAGTCGAAGTTC
1 TAGTCCAAGTTC
1213003 GCAACGACTG
Statistics
Matches: 174, Mismatches: 37, Indels: 30
0.72 0.15 0.12
Matches are distributed among these distances:
13 4 0.02
14 3 0.02
15 2 0.01
17 1 0.01
19 76 0.44
20 3 0.02
21 85 0.49
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TAGTCCAAGTTCCGTTGCGA
Found at i:1213099 original size:6 final size:6
Alignment explanation
Indices: 1213088--1213119 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1213078 GACACGTATT
1213088 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1213120 CGAGACGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1213440 original size:19 final size:20
Alignment explanation
Indices: 1213415--1213505 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 20
1213405 CTTATTTAGG
1213415 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
1213435 -TTTTTCACTATCGTAACAACAC
1 ATTTTTCACTATCG---CAACAC
* *
1213457 GTTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
* *
1213479 A-TTTTAACTATTGCAACAC
1 ATTTTTCACTATCGCAACAC
1213498 ATTTTTCA
1 ATTTTTCA
1213506 AAATCGCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 25 0.43
20 5 0.09
21 4 0.07
22 12 0.21
23 6 0.10
25 6 0.10
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:1215060 original size:369 final size:368
Alignment explanation
Indices: 1213960--1215063 Score: 1550
Period size: 368 Copynumber: 3.0 Consensus size: 368
1213950 TTGTTTAAGT
* *
1213960 TATGATTAGTGTCACATCAGACATGATTAACGATAATAACAGTGATTAAAACGAATTAAATGTGT
1 TATGATTAGTGTCACATCAGACATGATTAACGATAATAACAGTAATGAAAACGAATTAAATGTGT
* * * *
1214025 AGTGATTGTAATGTAAATTTCAAAAGTACGATGATCAAATGTAAGTGTTCTAAAAGTTTATGGAT
66 AGTGATTGTAATGTAAGTTTTAAAAGTACGATGATCAAATGTATGTGTCCTAAAAGTTTATGGAT
* * *
1214090 TATTAGTATACTTTAACCAAAAAAGTTAGTTGAGGGTAAACTACAAGGGTGACCATTTAGCTATA
131 TATTAGTATACTTTAACCAAAAAAGTTACTTAAGGGTAAACTACAAGAGTGACCATTTAGCTATA
* * * * * * *
1214155 GGCAGGTTCTAATCTGACTATTCATCTTTCAATTTTGTTAATCAGACCATTTAACTATTTAAATT
196 GGCAGATTCTAATTTGACTATTGATCTTTCAATTTTGTTAATCAAACCACTTAAATATTTAAATG
* * * *
1214220 AAGTCAATAAAGTCAATAGTCGTTAACATTTAACGAATAAGGTGGCGTGACAGTTAAAAAATTGG
261 ATGTCAATCAAGTCAATAGTCGTTAACATTTAACGAAGAAGGTGGCGTGACAGTT-AAAAATTTG
** *
1214285 TGTAACCGCACATTTGATCCCTGCTACATACATATTCTATCACA
325 TGTAACTACACATTTGATCCCTGCTACTTACATATTCTATCACA
* * * * * *
1214329 CATGATTAGTGTCACATCAGTCATGATTAATGATAATAACAGTAAAGAAAATGAATTAAATGTGG
1 TATGATTAGTGTCACATCAGACATGATTAACGATAATAACAGTAATGAAAACGAATTAAATGTGT
* * *
1214394 AGTGATTGTAATGTAAGTTTTAAAATTACGATGATCAAATGTATATGTCCTAAAAGTTTATAGAT
66 AGTGATTGTAATGTAAGTTTTAAAAGTACGATGATCAAATGTATGTGTCCTAAAAGTTTATGGAT
* *
1214459 TATTAGTATACTTTAACC-AAAAAGTTACATAAGGGTATACTACAAGAGTGACCATTTAGCTATA
131 TATTAGTATACTTTAACCAAAAAAGTTACTTAAGGGTAAACTACAAGAGTGACCATTTAGCTATA
* * *
1214523 GGCATATTCTAATTTGACTATTGATCTTTCAATTTTGTTAATTATACCACTTAAATATTTAAATG
196 GGCAGATTCTAATTTGACTATTGATCTTTCAATTTTGTTAATCAAACCACTTAAATATTTAAATG
* * *
1214588 ATGTCAATCAAGTCAATAGTCGTTAACATTTAACGAAGAAGGTAGCATGACAGTTAAAGAGTTTG
261 ATGTCAATCAAGTCAATAGTCGTTAACATTTAACGAAGAAGGTGGCGTGACAGTTAAA-AATTTG
* * * *
1214653 TATAACTACAAATTTGATCCCTTCTACTTACATATTCTATCAGA
325 TGTAACTACACATTTGATCCCTGCTACTTACATATTCTATCACA
* *
1214697 TATGATTAGTGTCACATCAGACATGATTAACGATAATAATAGTAATGAAAACGAGTTAAATGTGT
1 TATGATTAGTGTCACATCAGACATGATTAACGATAATAACAGTAATGAAAACGAATTAAATGTGT
* *
1214762 AGTGATTATAATGTAAGTTTTAACAGTACGATGATCAAATGTATGTGTCCTAAAAGTTTATGGAT
66 AGTGATTGTAATGTAAGTTTTAAAAGTACGATGATCAAATGTATGTGTCCTAAAAGTTTATGGAT
* * * *
1214827 TATT-GTTATACTTTAACCAAAAAAGTTACTTCAGGGTAAACTGCAAGAATGACCATATAGCTAT
131 TATTAG-TATACTTTAACCAAAAAAGTTACTTAAGGGTAAACTACAAGAGTGACCATTTAGCTAT
* * * *
1214891 AGGAAGATTCTAATTTGACTATTGATCTTTCAGTTTTGTTAATCAAACCACTTAAGTATTTAAGT
195 AGGCAGATTCTAATTTGACTATTGATCTTTCAATTTTGTTAATCAAACCACTTAAATATTTAAAT
* * * * * * *
1214956 GATGTCAATCACG-CGAATAGTCATCAACAATTAATGAAGCAA-GTGGCGTGATAGTTAAAATTT
260 GATGTCAATCAAGTC-AATAGTCGTTAACATTTAACGAAG-AAGGTGGCGTGACAGTTAAAA-AT
*
1215019 TTGTGTAACTACTCATTTGATCCCTGCTACTTACATATTCTATCA
322 TTGTGTAACTACACATTTGATCCCTGCTACTTACATATTCTATCA
1215064 ATTTGATCCT
Statistics
Matches: 647, Mismatches: 82, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
367 4 0.01
368 323 0.50
369 318 0.49
370 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (368 bp):
TATGATTAGTGTCACATCAGACATGATTAACGATAATAACAGTAATGAAAACGAATTAAATGTGT
AGTGATTGTAATGTAAGTTTTAAAAGTACGATGATCAAATGTATGTGTCCTAAAAGTTTATGGAT
TATTAGTATACTTTAACCAAAAAAGTTACTTAAGGGTAAACTACAAGAGTGACCATTTAGCTATA
GGCAGATTCTAATTTGACTATTGATCTTTCAATTTTGTTAATCAAACCACTTAAATATTTAAATG
ATGTCAATCAAGTCAATAGTCGTTAACATTTAACGAAGAAGGTGGCGTGACAGTTAAAAATTTGT
GTAACTACACATTTGATCCCTGCTACTTACATATTCTATCACA
Found at i:1215171 original size:25 final size:25
Alignment explanation
Indices: 1215134--1215191 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1215124 CAATATATAT
**
1215134 GTCATGTTTCCAGCCATCATGGACC
1 GTCATGTCGCCAGCCATCATGGACC
1215159 GTCATGTCGCCAGCCATCATGGACC
1 GTCATGTCGCCAGCCATCATGGACC
1215184 GTCATGTC
1 GTCATGTC
1215192 CTTACTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.26
Consensus pattern (25 bp):
GTCATGTCGCCAGCCATCATGGACC
Found at i:1216386 original size:161 final size:154
Alignment explanation
Indices: 1216035--1216432 Score: 518
Period size: 161 Copynumber: 2.5 Consensus size: 154
1216025 AAAAAAAGTA
* * * *
1216035 AGAATTG-AAGTTACATAGGTATTCTATTG-TGGTATATGAGCATGTGGTTCAAATTTGGTAAAA
1 AGAATTGAAAG-TACATATGTATTCTA-TGATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAA
* * *
1216098 ACAGACTTAAAAT-AACGATGTATTGAAGAAATAAGAAAATTATAAAAAAATTGAGGGACTAGAT
64 ACAGACTTAAAATAAATGATGGATTGAAGAAATAAGAAAATTATAAAAAAATTGAGGGACTAAAT
*
1216162 TGAAAAATTAAAAAATTATCAAAAAT
129 TGAAAAATTAAAAAATTATCAAAAAG
* * *
1216188 AGAATTGAAAGAACATATGTAGTCTATGATGGTTTAGGAGCATGTGGTTCAAAGTTGATAAAACA
1 AGAATTGAAAGTACATATGTATTCTATGATGGTTTAGGAGCATGTGGTTCAAATTTGAT-AAA-A
**
1216253 ACAGACTTAAAATAAAATGATGGATTGAAGAAATAATCAAATTATAAAAAAAATTGAGGGACTAA
64 ACAGACTTAAAAT-AAATGATGGATTGAAGAAATAAGAAAATTAT-AAAAAAATTGAGGGACTAA
*
1216318 ATTG-AAAA-TAGAAAATTTGTTATCAAAAAG
127 ATTGAAAAATTA-AAAA---ATTATCAAAAAG
*
1216348 AGAAATTGAAAGTACATATGCATTCTATGATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAAA
1 AG-AATTGAAAGTACATATGTATTCTATGATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAAA
*
1216413 CAAACTTAAAATAAATGATG
65 CAGACTTAAAATAAATGATG
1216433 AATTAAAGGA
Statistics
Matches: 214, Mismatches: 19, Indels: 19
0.85 0.08 0.08
Matches are distributed among these distances:
152 2 0.01
153 45 0.21
154 6 0.03
155 14 0.07
156 2 0.01
157 34 0.16
158 30 0.14
159 13 0.06
160 15 0.07
161 53 0.25
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (154 bp):
AGAATTGAAAGTACATATGTATTCTATGATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAAAC
AGACTTAAAATAAATGATGGATTGAAGAAATAAGAAAATTATAAAAAAATTGAGGGACTAAATTG
AAAAATTAAAAAATTATCAAAAAG
Found at i:1218978 original size:30 final size:30
Alignment explanation
Indices: 1218942--1219003 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1218932 TTTATGACTT
*
1218942 ATTGTATAAAATAAAATATCTATATTATAA
1 ATTGTATAAAATAAAATATCTATATTACAA
1218972 ATTGTATAAAATAAAATATCTATATTACAA
1 ATTGTATAAAATAAAATATCTATATTACAA
1219002 AT
1 AT
1219004 AATAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (30 bp):
ATTGTATAAAATAAAATATCTATATTACAA
Found at i:1219341 original size:13 final size:13
Alignment explanation
Indices: 1219323--1219349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1219313 AAAAATAAAT
1219323 AAAATTCAAAGAC
1 AAAATTCAAAGAC
1219336 AAAATTCAAAGAC
1 AAAATTCAAAGAC
1219349 A
1 A
1219350 TAAAAACCTG
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:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAATTCAAAGAC
Found at i:1220366 original size:12 final size:12
Alignment explanation
Indices: 1220349--1220399 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
1220339 TGTAATAATT
1220349 TAATAGTAATAA
1 TAATAGTAATAA
1220361 TAATAGTAATAA
1 TAATAGTAATAA
*
1220373 T-ATATTAAT-A
1 TAATAGTAATAA
1220383 T-ATA-TAATAAA
1 TAATAGTAAT-AA
1220394 TAATAG
1 TAATAG
1220400 AAACGACACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 9 0.26
12 16 0.47
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (12 bp):
TAATAGTAATAA
Found at i:1220626 original size:35 final size:35
Alignment explanation
Indices: 1220580--1220848 Score: 271
Period size: 35 Copynumber: 7.7 Consensus size: 35
1220570 CTGATCTTGT
*
1220580 TTCACTACTCTTCCGTGAAGGCT-AGATTGAATCAC
1 TTCACTACTCTTCCGTGAAGGCTGAGA-TGAATTAC
* * **
1220615 TTCACTACTCTTCTGTGAAGGTTGAGATTGCCTTAC
1 TTCACTACTCTTCCGTGAAGGCTGAGA-TGAATTAC
* ** * *
1220651 TTCACTACTCTTTCACGAA-GATCG-GATGATTTTAC
1 TTCACTACTCTTCCGTGAAGGCT-GAGATGA-ATTAC
*
1220686 TTCACTACTCTTCCGTGAAGGTTGAGATGAATTAC
1 TTCACTACTCTTCCGTGAAGGCTGAGATGAATTAC
** * *
1220721 TTCACTACTCTTTTGTGAAGGTTGAGATGCATTAC
1 TTCACTACTCTTCCGTGAAGGCTGAGATGAATTAC
1220756 TTCACTACTCTTCCGTGAAGGCTGA-AT-AATTTTAC
1 TTCACTACTCTTCCGTGAAGGCTGAGATGAA--TTAC
* *
1220791 TTCACTACTCTTCCGTAAAGGCTGA-ATGATTTAC
1 TTCACTACTCTTCCGTGAAGGCTGAGATGAATTAC
**
1220825 TTCACTACTCTTTTGTGAAGGCTG
1 TTCACTACTCTTCCGTGAAGGCTG
1220849 GATACGTTGC
Statistics
Matches: 197, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
33 1 0.01
34 29 0.15
35 134 0.68
36 33 0.17
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (35 bp):
TTCACTACTCTTCCGTGAAGGCTGAGATGAATTAC
Found at i:1220954 original size:20 final size:20
Alignment explanation
Indices: 1220919--1220995 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
1220909 TATTATCTAT
* *
1220919 CTCGAAAGACTTACAAAAGA
1 CTCGAAGGATTTACAAAAGA
* **
1220939 CTCTAAGGATTTACAAATTA
1 CTCGAAGGATTTACAAAAGA
* *
1220959 CTCGAAGGTTTTACAAATGA
1 CTCGAAGGATTTACAAAAGA
* * *
1220979 CCCGGAGGTTTTACAAA
1 CTCGAAGGATTTACAAA
1220996 TTACCTGAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (20 bp):
CTCGAAGGATTTACAAAAGA
Found at i:1220996 original size:20 final size:20
Alignment explanation
Indices: 1220948--1221071 Score: 176
Period size: 20 Copynumber: 6.2 Consensus size: 20
1220938 ACTCTAAGGA
* *
1220948 TTTACAAATTACTCGAAGGT
1 TTTACAAATTACCCGGAGGT
*
1220968 TTTACAAATGACCCGGAGGT
1 TTTACAAATTACCCGGAGGT
* *
1220988 TTTACAAATTACCTGAAGGT
1 TTTACAAATTACCCGGAGGT
*
1221008 TTTATAAATTACCCGGAGGT
1 TTTACAAATTACCCGGAGGT
1221028 TTTACAAATTACCCGGAGGT
1 TTTACAAATTACCCGGAGGT
* *
1221048 TTTACAAATTACCCTGAGGA
1 TTTACAAATTACCCGGAGGT
1221068 TTTA
1 TTTA
1221072 TTTTTCTTGA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (20 bp):
TTTACAAATTACCCGGAGGT
Found at i:1221072 original size:60 final size:60
Alignment explanation
Indices: 1220943--1221072 Score: 199
Period size: 60 Copynumber: 2.2 Consensus size: 60
1220933 AAAAGACTCT
* *
1220943 AAGGATTTACAAATTACTCGAAGGTTTTACAAATGACCCGGAGGTTTTACAAATTACCTG
1 AAGGATTTATAAATTACCCGAAGGTTTTACAAATGACCCGGAGGTTTTACAAATTACCTG
* * *
1221003 AAGGTTTTATAAATTACCCGGAGGTTTTACAAATTACCCGGAGGTTTTACAAATTACCCTG
1 AAGGATTTATAAATTACCCGAAGGTTTTACAAATGACCCGGAGGTTTTACAAATTA-CCTG
1221064 -AGGATTTAT
1 AAGGATTTAT
1221073 TTTTCTTGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 59 0.94
61 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (60 bp):
AAGGATTTATAAATTACCCGAAGGTTTTACAAATGACCCGGAGGTTTTACAAATTACCTG
Found at i:1222876 original size:16 final size:16
Alignment explanation
Indices: 1222855--1222907 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
1222845 ATCATCTTCC
*
1222855 TCTTGACTAGTTGCTT
1 TCTTGACTGGTTGCTT
1222871 TCTTGACTGGTTGCTT
1 TCTTGACTGGTTGCTT
*
1222887 TCTTGCCTGGTTGCTT
1 TCTTGACTGGTTGCTT
1222903 TCTTG
1 TCTTG
1222908 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.06, C:0.21, G:0.23, T:0.51
Consensus pattern (16 bp):
TCTTGACTGGTTGCTT
Found at i:1229800 original size:22 final size:23
Alignment explanation
Indices: 1229772--1229822 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1229762 CTGTTGGGTT
*
1229772 ATTGGGCTTGAACCA-GTT-TGTA
1 ATTGGGCCTGAACCAGGTTATG-A
1229794 ATTGGGCCTGAACCAGGTTATGA
1 ATTGGGCCTGAACCAGGTTATGA
1229817 ATTGGG
1 ATTGGG
1229823 TGTGGTTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.54
23 10 0.38
24 2 0.08
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (23 bp):
ATTGGGCCTGAACCAGGTTATGA
Found at i:1229909 original size:2 final size:2
Alignment explanation
Indices: 1229891--1229970 Score: 125
Period size: 2 Copynumber: 42.5 Consensus size: 2
1229881 TTAATTAATA
1229891 AT AT A- AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229970 A
1 A
1229971 ACGACACTCG
Statistics
Matches: 73, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
1 5 0.07
2 68 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1230176 original size:27 final size:25
Alignment explanation
Indices: 1230125--1230181 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
1230115 TGTCAATACA
1230125 TAAAAAAATCATTAAAAAATTTTAAT
1 TAAAAAAA-CATTAAAAAATTTTAAT
1230151 TAAAAAAA-ATTAAACAAATTACTTAAT
1 TAAAAAAACATTAAA-AAATT--TTAAT
1230178 TAAA
1 TAAA
1230182 CAAATTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.21
25 5 0.18
26 8 0.29
27 9 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAAAAAACATTAAAAAATTTTAAT
Found at i:1230833 original size:60 final size:60
Alignment explanation
Indices: 1230714--1230836 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
1230704 TCCTTAAGCC
* * ** * **
1230714 TTTAAATATTTTAATTTCATATTTAAACTATAACTTTTATTCTAAAGTAGTCCTTAAACT
1 TTTAAACAATTTAATTTCATACCTAAACTATAACTTTCATTCTAAAGTAGTCCCCAAACT
* * * *
1230774 TTTAAACAATTTAATTTCATCCCTAACCTATGACTTTCATTCTAAATTAGTCCCCAAACT
1 TTTAAACAATTTAATTTCATACCTAAACTATAACTTTCATTCTAAAGTAGTCCCCAAACT
1230834 TTT
1 TTT
1230837 TTTAGCAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (60 bp):
TTTAAACAATTTAATTTCATACCTAAACTATAACTTTCATTCTAAAGTAGTCCCCAAACT
Found at i:1231507 original size:8 final size:8
Alignment explanation
Indices: 1231472--1231521 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
1231462 TTATAAATTC
1231472 AAATTATA
1 AAATTATA
*
1231480 TAA-TATAA
1 AAATTAT-A
*
1231488 AAATTAAAA
1 AAATT-ATA
1231497 AAATTATA
1 AAATTATA
1231505 AAATTATA
1 AAATTATA
1231513 AAATTATA
1 AAATTATA
1231521 A
1 A
1231522 CTAAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 3 0.09
8 24 0.69
9 7 0.20
10 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATTATA
Found at i:1232022 original size:6 final size:6
Alignment explanation
Indices: 1232007--1232080 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
1231997 ATAATAAAAC
*
1232007 ATTA-T ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTAAT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * *
1232054 ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTATT ATTATT ATTATT ATTATT ATT
1232081 TTGCAGGCCC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 4 0.06
6 63 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTATT
Found at i:1234042 original size:20 final size:20
Alignment explanation
Indices: 1234017--1234064 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1234007 CGATTTTCTC
1234017 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCAAATTCGT
**
1234037 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCAAATTCGT
1234057 GTTGCGAT
1 GTTGCGAT
1234065 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGT
Found at i:1234070 original size:20 final size:20
Alignment explanation
Indices: 1234032--1234087 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1234022 GATAGTCAAA
**
1234032 TTCGTGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1234052 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
1234072 TTCGTTTTGCGATTTT
1 TTCGTGTTGCGATTTT
1234088 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1234094 original size:20 final size:20
Alignment explanation
Indices: 1234032--1234094 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
1234022 GATAGTCAAA
** * *
1234032 TTCGTGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTAAGT
* *
1234052 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTAAGT
*
1234072 TTCGTTTTGCGATTTTAAGT
1 TTCGTGTTGCGATTTTAAGT
1234092 TTC
1 TTC
1234095 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.52
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTAAGT
Found at i:1236031 original size:20 final size:20
Alignment explanation
Indices: 1236008--1236056 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1235998 GAAACTTAAA
1236008 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* **
1236028 ATCGCAGCGCGGAAATGACT
1 ATCGCAACGCAAAAATGACT
1236048 ATCGCAACG
1 ATCGCAACG
1236057 GGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:1236085 original size:33 final size:34
Alignment explanation
Indices: 1236048--1236123 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1236038 GGAAATGACT
*
1236048 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
1236081 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
1236115 ATCGCAACG
1 ATCGCAACG
1236124 CGAATTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:1236113 original size:20 final size:20
Alignment explanation
Indices: 1236090--1236127 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1236080 AATCGCAACG
*
1236090 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
1236110 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
1236128 TTTTGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:1236165 original size:19 final size:19
Alignment explanation
Indices: 1236123--1236166 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1236113 AAATCGCAAC
* * *
1236123 GCGAATTTTGTTTCGCGTT
1 GCGATTTTTATTTCGCATT
1236142 GCGATTTTTATTTCGCATT
1 GCGATTTTTATTTCGCATT
1236161 GCGATT
1 GCGATT
1236167 ATCTTGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTTATTTCGCATT
Found at i:1236233 original size:20 final size:20
Alignment explanation
Indices: 1236172--1236236 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1236162 CGATTATCTT
**
1236172 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
* * *
1236192 ATTGCGATTGTCATTTCCGC
1 GTTGCGATAGTCATTTTCGC
*
1236212 GTTGCGATAGTCATTTTTGC
1 GTTGCGATAGTCATTTTCGC
1236232 GTTGC
1 GTTGC
1236237 AATTTTAAGT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:1236255 original size:20 final size:20
Alignment explanation
Indices: 1236232--1236269 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1236222 TCATTTTTGC
1236232 GTTGCAATTTTAAGTTTCGT
1 GTTGCAATTTTAAGTTTCGT
*
1236252 GTTGCGATTTTAAGTTTC
1 GTTGCAATTTTAAGTTTC
1236270 AAAAACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCAATTTTAAGTTTCGT
Found at i:1236820 original size:42 final size:42
Alignment explanation
Indices: 1236756--1236867 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
1236746 CTTTCATCAT
* * * *
1236756 TCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTCCCACCATTCAAGAGGCCCCTATCATCCC
* **
1236798 TCAAGAGTCCCCTCCCACCATTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCATTCAAGAGGCCCCTATCATCCC
*
1236840 TGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCAAGA-GTCCCCTCCCACCATTCAAGAG
1236868 CTCGATTCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCACCATTCAAGAGGCCCCTATCATCCC
Found at i:1236830 original size:21 final size:21
Alignment explanation
Indices: 1236753--1236867 Score: 97
Period size: 21 Copynumber: 5.5 Consensus size: 21
1236743 CACCTTTCAT
* * *
1236753 CATTCAAGAGGCCTCTCCTAT
1 CATTCAAGAGGCCCCTCCCAC
**
1236774 CATTCAAGAGGCCCCTATCATC
1 CATTCAAGAGGCCCCTCCCA-C
* *
1236796 C-CTCAAGAGTCCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
** *
1236816 CATTCAAGAGGCCCCTGTCAT
1 CATTCAAGAGGCCCCTCCCAC
* * *
1236837 CGTTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
1236858 CATTCAAGAG
1 CATTCAAGAG
1236868 CTCGATTCAC
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 2 0.03
21 67 0.96
22 1 0.01
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (21 bp):
CATTCAAGAGGCCCCTCCCAC
Found at i:1238688 original size:15 final size:15
Alignment explanation
Indices: 1238668--1238697 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1238658 TTTTAATCAT
*
1238668 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1238683 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1238698 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1241866 original size:15 final size:15
Alignment explanation
Indices: 1241846--1241875 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1241836 TTTTAATCAT
*
1241846 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1241861 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1241876 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1245043 original size:15 final size:15
Alignment explanation
Indices: 1245023--1245052 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1245013 TTTTAATCAT
*
1245023 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1245038 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1245053 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1248156 original size:15 final size:15
Alignment explanation
Indices: 1248136--1248165 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1248126 TTTTAATCAT
*
1248136 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1248151 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1248166 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1251338 original size:15 final size:15
Alignment explanation
Indices: 1251318--1251347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1251308 TTTTAATCAT
*
1251318 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1251333 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1251348 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1254527 original size:15 final size:15
Alignment explanation
Indices: 1254507--1254536 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1254497 TTTTAATCAT
*
1254507 GTCCTAAAGATTCTC
1 GTCCTAAAGAATCTC
1254522 GTCCTAAAGAATCTC
1 GTCCTAAAGAATCTC
1254537 ATTTACAAGC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
GTCCTAAAGAATCTC
Found at i:1256935 original size:34 final size:35
Alignment explanation
Indices: 1256851--1256936 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 35
1256841 TAATTAAACT
*
1256851 TGTATCGTTTCTTTTC-CTATACTTACTCTTTTTTC
1 TGTATCG-TTCTTTTCACTATACTTACTCTTTTTCC
* *
1256886 TGTA-C-TAATCCTTTCACTATAC-TATTCTTTTTCC
1 TGTATCGT--TCTTTTCACTATACTTACTCTTTTTCC
1256920 TGTATCGTTCTTTTCAC
1 TGTATCGTTCTTTTCAC
1256937 CGTATTGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
32 1 0.02
34 29 0.69
35 11 0.26
36 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.55
Consensus pattern (35 bp):
TGTATCGTTCTTTTCACTATACTTACTCTTTTTCC
Found at i:1261740 original size:2 final size:2
Alignment explanation
Indices: 1261676--1261724 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1261666 CGTTGATAAT
1261676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1261718 TA TA TA T
1 TA TA TA T
1261725 TTTAATATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1261747 original size:20 final size:22
Alignment explanation
Indices: 1261683--1261748 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 22
1261673 AATTATATAT
* *
1261683 ATATATATATATATATATATATA
1 ATATAAATATATATATAT-TTTA
*
1261706 TATATATATATATATATATTTTA
1 -ATATAAATATATATATATTTTA
*
1261729 ATATAAATATAT-TATTTTTT
1 ATATAAATATATATATATTTT
1261749 TCATTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.18
22 11 0.28
23 3 0.08
24 18 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATAAATATATATATATTTTA
Found at i:1263300 original size:16 final size:16
Alignment explanation
Indices: 1263279--1263309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1263269 TATACTAAAC
*
1263279 ATATTTTTATTATCAT
1 ATATTTATATTATCAT
1263295 ATATTTATATTATCA
1 ATATTTATATTATCA
1263310 ATAATTATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTATATTATCAT
Found at i:1263531 original size:17 final size:17
Alignment explanation
Indices: 1263522--1263567 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1263512 TACCCATATG
1263522 ATCTGGGTACCCACAAA
1 ATCTGGGTACCCACAAA
1263539 ATCTGGGTACCCACAAA
1 ATCTGGGTACCCACAAA
*
1263556 ATCCGGGTACCC
1 ATCTGGGTACCC
1263568 GAAACATCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (17 bp):
ATCTGGGTACCCACAAA
Found at i:1267981 original size:2 final size:2
Alignment explanation
Indices: 1267974--1268041 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
1267964 ATGATACATG
* * *
1267974 TA TA TA TA TA TA TA TA TA GTA AA AA T- TA TA -A TA -A TGA TG TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA
*
1268015 TGA AA TA TA TA TA TA TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA
1268042 AATAAACAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
1 3 0.06
2 46 0.85
3 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1269612 original size:10 final size:10
Alignment explanation
Indices: 1269596--1269709 Score: 70
Period size: 10 Copynumber: 10.6 Consensus size: 10
1269586 TATTTTATTT
1269596 ATAATAAATA
1 ATAATAAATA
* *
1269606 TTAATAATTA
1 ATAATAAATA
1269616 ATAATAACAACTA
1 ATAAT-A-AA-TA
1269629 ATAATACTAATTA
1 ATAATA--AA-TA
1269642 ATAAT-AATA
1 ATAATAAATA
* *
1269651 ATAGTCAATA
1 ATAATAAATA
1269661 ATAAT-AATA
1 ATAATAAATA
**
1269670 ATAATATTTA
1 ATAATAAATA
1269680 ATAATAAAATTA
1 ATAAT-AAA-TA
1269692 ATAATGATAATA
1 ATAAT-A-AATA
1269704 ATAATA
1 ATAATA
1269710 TTAAGGGTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
9 15 0.18
10 29 0.35
11 3 0.04
12 17 0.21
13 18 0.22
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAATAAATA
Found at i:1269612 original size:13 final size:13
Alignment explanation
Indices: 1269596--1269709 Score: 85
Period size: 13 Copynumber: 9.0 Consensus size: 13
1269586 TATTTTATTT
*
1269596 ATAATAAATATTA
1 ATAATAAATAATA
*
1269609 ATAATTAATAATA
1 ATAATAAATAATA
*
1269622 ACAACT-AATAATA
1 ATAA-TAAATAATA
* *
1269635 CTAATTAATAATA
1 ATAATAAATAATA
*
1269648 ATAAT-AGTCAATA
1 ATAATAAAT-AATA
1269661 ATAAT-AATAATA
1 ATAATAAATAATA
* *
1269673 ATATTTAATAATA
1 ATAATAAATAATA
* *
1269686 A-AATTAATAATG
1 ATAATAAATAATA
1269698 ATAAT-AATAATA
1 ATAATAAATAATA
1269710 TTAAGGGTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
12 27 0.32
13 56 0.67
14 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:1269613 original size:3 final size:3
Alignment explanation
Indices: 1269596--1269709 Score: 104
Period size: 3 Copynumber: 36.0 Consensus size: 3
1269586 TATTTTATTT
* * *
1269596 ATA ATAA ATA TTA ATA ATTA ATA ATA ACA ACTA ATA ATA CTA ATTA ATA
1 ATA AT-A ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA
* *
1269645 ATA ATA ATA GTCA ATA ATA ATA ATA ATA ATA TTTA ATA ATA A-A ATTA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA
*
1269692 ATA ATG ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
1269710 TTAAGGGTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
2 2 0.02
3 72 0.79
4 17 0.19
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1269649 original size:19 final size:18
Alignment explanation
Indices: 1269596--1269709 Score: 104
Period size: 19 Copynumber: 6.0 Consensus size: 18
1269586 TATTTTATTT
*
1269596 ATAATAAATATTAATAATTA
1 ATAAT-AATAATAATAA-TA
*
1269616 ATAATAACAACTAATAATA
1 ATAATAATAA-TAATAATA
*
1269635 CTAATTAATAATAATAATA
1 ATAA-TAATAATAATAATA
*
1269654 GTCAATAATAATAATAATA
1 AT-AATAATAATAATAATA
*
1269673 ATATTTAATAATAA-AATTA
1 ATA-ATAATAATAATAA-TA
*
1269692 ATAATGATAATAATAATA
1 ATAATAATAATAATAATA
1269710 TTAAGGGTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.16
19 48 0.61
20 18 0.23
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAATAATAATAATAATA
Found at i:1271117 original size:35 final size:35
Alignment explanation
Indices: 1271061--1271129 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1271051 TTCATGTTCA
1271061 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* * *
1271096 AAATTCCAAAATACTTTAATTATATTCTAAACCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCC
1271130 TAAACTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:1271839 original size:8 final size:8
Alignment explanation
Indices: 1271826--1271861 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
1271816 CAGACTTATT
1271826 AAAAAATA
1 AAAAAATA
1271834 AAAAAATA
1 AAAAAATA
1271842 AAAAAATA
1 AAAAAATA
1271850 AAAAAATA
1 AAAAAATA
1271858 AAAA
1 AAAA
1271862 TGTAATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:1282462 original size:73 final size:73
Alignment explanation
Indices: 1282368--1282507 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 73
1282358 AAAGAAACAA
* * *
1282368 TAAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAGGATAAGATAAAA
1 TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
1282433 TAATATCC
66 TAATATCC
* * * *
1282441 TAAATCCTAATTAAAACACTTAAAGCTATTTAAACTAAACTACCTAAAACAAAGATAAAATATAA
1 TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
1282506 TA
66 TA
1282508 TTTAAAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.27
Consensus pattern (73 bp):
TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
TAATATCC
Done.